WorldWideScience

Sample records for partially overlapping expression

  1. Overlaps of partial Néel states and Bethe states

    International Nuclear Information System (INIS)

    Foda, O; Zarembo, K

    2016-01-01

    Partial Néel states are generalizations of the ordinary Néel (classical anti-ferromagnet) state that can have arbitrary integer spin. We study overlaps of these states with Bethe states. We first identify this overlap with a partial version of reflecting-boundary domain-wall partition function, and then derive various determinant representations for off-shell and on-shell Bethe states. (paper: quantum statistical physics, condensed matter, integrable systems)

  2. Partial Stator Overlap in a Linear Generator for Wave Power: An Experimental Study

    Directory of Open Access Journals (Sweden)

    Anna E. Frost

    2017-11-01

    Full Text Available This paper presents a study on how the power absorption and damping in a linear generator for wave energy conversion are affected by partial overlap between stator and translator. The theoretical study shows that the electrical power as well as the damping coefficient change quadratically with partial stator overlap, if inductance, friction and iron losses are assumed independent of partial stator overlap or can be neglected. Results from onshore experiments on a linear generator for wave energy conversion cannot reject the quadratic relationship. Measurements were done on the inductance of the linear generator and no dependence on partial stator overlap could be found. Simulations of the wave energy converter’s operation in high waves show that entirely neglecting partial stator overlap will overestimate the energy yield and underestimate the peak forces in the line between the buoy and the generator. The difference between assuming a linear relationship instead of a quadratic relationship is visible but small in the energy yield in the simulation. Since the theoretical deduction suggests a quadratic relationship, this is advisable to use during modeling. However, a linear assumption could be seen as an acceptable simplification when modeling since other relationships can be computationally costly.

  3. Modeling of chromosome intermingling by partially overlapping uniform random polygons.

    Science.gov (United States)

    Blackstone, T; Scharein, R; Borgo, B; Varela, R; Diao, Y; Arsuaga, J

    2011-03-01

    During the early phase of the cell cycle the eukaryotic genome is organized into chromosome territories. The geometry of the interface between any two chromosomes remains a matter of debate and may have important functional consequences. The Interchromosomal Network model (introduced by Branco and Pombo) proposes that territories intermingle along their periphery. In order to partially quantify this concept we here investigate the probability that two chromosomes form an unsplittable link. We use the uniform random polygon as a crude model for chromosome territories and we model the interchromosomal network as the common spatial region of two overlapping uniform random polygons. This simple model allows us to derive some rigorous mathematical results as well as to perform computer simulations easily. We find that the probability that one uniform random polygon of length n that partially overlaps a fixed polygon is bounded below by 1 − O(1/√n). We use numerical simulations to estimate the dependence of the linking probability of two uniform random polygons (of lengths n and m, respectively) on the amount of overlapping. The degree of overlapping is parametrized by a parameter [Formula: see text] such that [Formula: see text] indicates no overlapping and [Formula: see text] indicates total overlapping. We propose that this dependence relation may be modeled as f (ε, m, n) = [Formula: see text]. Numerical evidence shows that this model works well when [Formula: see text] is relatively large (ε ≥ 0.5). We then use these results to model the data published by Branco and Pombo and observe that for the amount of overlapping observed experimentally the URPs have a non-zero probability of forming an unsplittable link.

  4. Interference management with partial uplink/downlink spectrum overlap

    KAUST Repository

    Randrianantenaina, Itsikiantsoa

    2016-07-26

    Simultaneous reuse of spectral resources by uplink and downlink, denoted as in-band full duplex (FD) communication, is promoted to double the spectral efficiency when compared to its half-duplex (HD) counterpart. Interference management, however, remains challenging in FD cellular networks, especially when high disparity between uplink and downlink transmission powers exists. The uplink performance can be particularly deteriorated when operating on channels that are simultaneously occupied with downlink transmission. This paper considers a cellular wireless system with partial spectrum overlap between the downlink and uplink. The performance of the system becomes, therefore, a function of the overlap fraction, as well as the power levels of both the uplink and downlink transmissions. The paper considers the problem of maximizing an overall network utility to find the uplink/downlink transmission powers and the spectrum overlap fraction between the uplink and downlink spectrum in each cell, and proposes solving the problem using interior point method. Simulations results confirm the vulnerability of the uplink performance to the FD operation, and show the superiority of the proposed scheme over the FD and HD schemes. The results further show that explicit uplink and downlink performance should be considered for efficient design of cellular networks with overlapping uplink/downlink resources. © 2016 IEEE.

  5. Segmentation, Inference and Classification of Partially Overlapping Nanoparticles

    KAUST Repository

    Chiwoo Park,

    2013-03-01

    This paper presents a method that enables automated morphology analysis of partially overlapping nanoparticles in electron micrographs. In the undertaking of morphology analysis, three tasks appear necessary: separate individual particles from an agglomerate of overlapping nano-objects; infer the particle\\'s missing contours; and ultimately, classify the particles by shape based on their complete contours. Our specific method adopts a two-stage approach: the first stage executes the task of particle separation, and the second stage conducts simultaneously the tasks of contour inference and shape classification. For the first stage, a modified ultimate erosion process is developed for decomposing a mixture of particles into markers, and then, an edge-to-marker association method is proposed to identify the set of evidences that eventually delineate individual objects. We also provided theoretical justification regarding the separation capability of the first stage. In the second stage, the set of evidences become inputs to a Gaussian mixture model on B-splines, the solution of which leads to the joint learning of the missing contour and the particle shape. Using twelve real electron micrographs of overlapping nanoparticles, we compare the proposed method with seven state-of-the-art methods. The results show the superiority of the proposed method in terms of particle recognition rate.

  6. Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap.

    Science.gov (United States)

    Lawhorn, Chelsea M; Schomaker, Rachel; Rowell, Jonathan T; Rueppell, Olav

    2018-04-16

    Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression. Neglecting this variability could therefore lead to inflated estimates of significant overlap between DEG lists. With computer simulations, we demonstrate that such biases arise from variation in the control of gene expression. Significant overlap commonly arises between two lists of DEGs that are randomly generated, assuming that the control of gene expression is variable among genes but consistent between corresponding experiments. More overlap is observed when transcription factors are specific to their binding sites and when the number of genes is considerably higher than the number of different transcription factors. In contrast, overlap between two DEG lists is always lower than expected when the genetic architecture of expression is independent between the two experiments. Thus, the current methods for determining significant overlap between DEGs are potentially confounding biologically meaningful overlap with overlap that arises due to variability in control of expression among genes, and more sophisticated approaches are needed.

  7. Sense and antisense transcripts of the developmentally regulated murine hsp70.2 gene are expressed in distinct and only partially overlapping areas in the adult brain

    Science.gov (United States)

    Murashov, A. K.; Wolgemuth, D. J.

    1996-01-01

    We have examined the spatial pattern of expression of a member of the hsp70 gene family, hsp70.2, in the mouse central nervous system. Surprisingly, RNA blot analysis and in situ hybridization revealed abundant expression of an 'antisense' hsp70.2 transcript in several areas of adult mouse brain. Two different transcripts recognized by sense and antisense riboprobes for the hsp70.2 gene were expressed in distinct and only partially overlapping neuronal populations. RNA blot analysis revealed low levels of the 2.7 kb transcript of hsp70.2 in several areas of the brain, with highest signal in the hippocampus. Abundant expression of a slightly larger (approximately 2.8 kb) 'antisense' transcript was detected in several brain regions, notably in the brainstem, cerebellum, mesencephalic tectum, thalamus, cortex, and hippocampus. In situ hybridization revealed that the sense and antisense transcripts were both predominantly neuronal and localized to the same cell types in the granular layer of the cerebellum, trapezoid nucleus of the superior olivary complex, locus coeruleus and hippocampus. The hsp70.2 antisense transcripts were particularly abundant in the frontal cortex, dentate gyrus, subthalamic nucleus, zona incerta, superior and inferior colliculi, central gray, brainstem, and cerebellar Purkinje cells. Our findings have revealed a distinct cellular and spatial localization of both sense and antisense transcripts, demonstrating a new level of complexity in the function of the heat shock genes.

  8. Partially Overlapping Ownership and Contagion in Financial Networks

    Directory of Open Access Journals (Sweden)

    Micah Pollak

    2017-01-01

    Full Text Available Using historical banking data for the United States from the years 2000 to 2015 we characterize the probability and extent of a financial contagion using a calibrated network model of heterogeneous interbank exposures. Both the probability and the average extent of a contagion begin to rise in 2007 prior to the US financial crisis. Including a common asset in the model increases both the probability and extent of contagion, especially during the years of the financial crisis. Based on rising institutional ownership in the banking industry, we introduce a partially overlapping ownership asset that devalues endogenously. The addition of this asset increases the extent of a financial contagion. Our results show that trends in capital buffers and the distribution and type of assets have a significant effect on the predictions of financial network contagion models and that the rising trend in ownership of banks by banks amplifies shocks to the financial system.

  9. Epidemics in partially overlapped multiplex networks.

    Directory of Open Access Journals (Sweden)

    Camila Buono

    Full Text Available Many real networks exhibit a layered structure in which links in each layer reflect the function of nodes on different environments. These multiple types of links are usually represented by a multiplex network in which each layer has a different topology. In real-world networks, however, not all nodes are present on every layer. To generate a more realistic scenario, we use a generalized multiplex network and assume that only a fraction [Formula: see text] of the nodes are shared by the layers. We develop a theoretical framework for a branching process to describe the spread of an epidemic on these partially overlapped multiplex networks. This allows us to obtain the fraction of infected individuals as a function of the effective probability that the disease will be transmitted [Formula: see text]. We also theoretically determine the dependence of the epidemic threshold on the fraction [Formula: see text] of shared nodes in a system composed of two layers. We find that in the limit of [Formula: see text] the threshold is dominated by the layer with the smaller isolated threshold. Although a system of two completely isolated networks is nearly indistinguishable from a system of two networks that share just a few nodes, we find that the presence of these few shared nodes causes the epidemic threshold of the isolated network with the lower propagating capacity to change discontinuously and to acquire the threshold of the other network.

  10. Interference Management in Full-Duplex Cellular Networks with Partial Spectrum Overlap

    KAUST Repository

    Randrianantenaina, Itsikiantsoa

    2017-03-31

    Full-duplex (FD) communication is promoted to double the spectral efficiency when compared to the halfduplex (HD) counterpart. In the context of cellular networks, however, FD communication exacerbates the aggregate uplink and downlink interference, which diminishes the foreseen FD gains. This paper considers a flexible duplex system, denoted by -duplex (-D) system, wherein a fine-grained bandwidth control for each uplink/downlink channel pair in each base station (BS) is allowed, which also leads to partial spectrum overlap between the uplink and downlink channels. The paper addresses the resulting interference management problem by maximizing a network-wide rate-based utility function subject to uplink/downlink power constraints, so as to determine userto- BS association, user-to-channel scheduling, the UL and DL transmit powers, and the fraction of spectrum overlap between UL and DL for every user, under the assumption that the number of available channels and users are equal. The paper solves such a non-convex mixed-integer optimization problem in an iterative way by decoupling the problem into several subproblems. Particularly, the user-to-BS association problem is solved using a matching algorithm that is a generalization of the stable marriage problem. The scheduling problem is solved by iterative Hungarian algorithm. The power and spectrum overlap problem is solved by successive convex approximation. The proposed iterative strategy guarantees an efficient one-toone user to BS and channel assignment. It further provides optimized flexible duplexing and power allocation schemes for all transceivers. Simulations results show appreciable gains when comparing the proposed solution to different schemes from the literature.

  11. Interference Management in Full-Duplex Cellular Networks with Partial Spectrum Overlap

    KAUST Repository

    Randrianantenaina, Itsikiantsoa; Dahrouj, Hayssam; Elsawy, Hesham; Alouini, Mohamed-Slim

    2017-01-01

    Full-duplex (FD) communication is promoted to double the spectral efficiency when compared to the halfduplex (HD) counterpart. In the context of cellular networks, however, FD communication exacerbates the aggregate uplink and downlink interference, which diminishes the foreseen FD gains. This paper considers a flexible duplex system, denoted by -duplex (-D) system, wherein a fine-grained bandwidth control for each uplink/downlink channel pair in each base station (BS) is allowed, which also leads to partial spectrum overlap between the uplink and downlink channels. The paper addresses the resulting interference management problem by maximizing a network-wide rate-based utility function subject to uplink/downlink power constraints, so as to determine userto- BS association, user-to-channel scheduling, the UL and DL transmit powers, and the fraction of spectrum overlap between UL and DL for every user, under the assumption that the number of available channels and users are equal. The paper solves such a non-convex mixed-integer optimization problem in an iterative way by decoupling the problem into several subproblems. Particularly, the user-to-BS association problem is solved using a matching algorithm that is a generalization of the stable marriage problem. The scheduling problem is solved by iterative Hungarian algorithm. The power and spectrum overlap problem is solved by successive convex approximation. The proposed iterative strategy guarantees an efficient one-toone user to BS and channel assignment. It further provides optimized flexible duplexing and power allocation schemes for all transceivers. Simulations results show appreciable gains when comparing the proposed solution to different schemes from the literature.

  12. In-Band Full-Duplex Communications for Cellular Networks with Partial Uplink/Downlink Overlap

    KAUST Repository

    Alammouri, Ahmad; Elsawy, Hesham; Amin, Osama; Alouini, Mohamed-Slim

    2015-01-01

    In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization in cellular networks. However, the explicit impact of spatial interference, imposed by FD communications, on uplink and downlink transmissions has been overlooked in the literature. This paper presents an extensive study of the explicit effect of FD communications on the uplink and downlink performances. For the sake of rigorous analysis, we develop a tractable framework based on stochastic geometry toolset. The developed model accounts for uplink truncated channel inversion power control in FD cellular networks. The study shows that FD communications improve the downlink throughput at the expense of significant degradation in the uplink throughput. Therefore, we propose a novel fine-grained duplexing scheme, denoted as α-duplex scheme, which allows a partial overlap between uplink and downlink frequency bands. To this end, we show that the amount of the overlap can be optimized via adjusting α to achieve a certain design objective.

  13. In-Band Full-Duplex Communications for Cellular Networks with Partial Uplink/Downlink Overlap

    KAUST Repository

    AlAmmouri, Ahmad

    2015-12-06

    In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization in cellular networks. However, the explicit impact of spatial interference, imposed by FD communications, on uplink and downlink transmissions has been overlooked in the literature. This paper presents an extensive study of the explicit effect of FD communications on the uplink and downlink performances. For the sake of rigorous analysis, we develop a tractable framework based on stochastic geometry toolset. The developed model accounts for uplink truncated channel inversion power control in FD cellular networks. The study shows that FD communications improve the downlink throughput at the expense of significant degradation in the uplink throughput. Therefore, we propose a novel fine-grained duplexing scheme, denoted as α-duplex scheme, which allows a partial overlap between uplink and downlink frequency bands. To this end, we show that the amount of the overlap can be optimized via adjusting α to achieve a certain design objective.

  14. CRISPR Detection From Short Reads Using Partial Overlap Graphs.

    Science.gov (United States)

    Ben-Bassat, Ilan; Chor, Benny

    2016-06-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are structured regions in bacterial and archaeal genomes, which are part of an adaptive immune system against phages. CRISPRs are important for many microbial studies and are playing an essential role in current gene editing techniques. As such, they attract substantial research interest. The exponential growth in the amount of bacterial sequence data in recent years enables the exploration of CRISPR loci in more and more species. Most of the automated tools that detect CRISPR loci rely on fully assembled genomes. However, many assemblers do not handle repetitive regions successfully. The first tool to work directly on raw sequence data is Crass, which requires reads that are long enough to contain two copies of the same repeat. We present a method to identify CRISPR repeats from raw sequence data of short reads. The algorithm is based on an observation differentiating CRISPR repeats from other types of repeats, and it involves a series of partial constructions of the overlap graph. This enables us to avoid many of the difficulties that assemblers face, as we merely aim to identify the repeats that belong to CRISPR loci. A preliminary implementation of the algorithm shows good results and detects CRISPR repeats in cases where other existing tools fail to do so.

  15. Partially overlapping sensorimotor networks underlie speech praxis and verbal short-term memory: evidence from apraxia of speech following acute stroke.

    Science.gov (United States)

    Hickok, Gregory; Rogalsky, Corianne; Chen, Rong; Herskovits, Edward H; Townsley, Sarah; Hillis, Argye E

    2014-01-01

    We tested the hypothesis that motor planning and programming of speech articulation and verbal short-term memory (vSTM) depend on partially overlapping networks of neural regions. We evaluated this proposal by testing 76 individuals with acute ischemic stroke for impairment in motor planning of speech articulation (apraxia of speech, AOS) and vSTM in the first day of stroke, before the opportunity for recovery or reorganization of structure-function relationships. We also evaluated areas of both infarct and low blood flow that might have contributed to AOS or impaired vSTM in each person. We found that AOS was associated with tissue dysfunction in motor-related areas (posterior primary motor cortex, pars opercularis; premotor cortex, insula) and sensory-related areas (primary somatosensory cortex, secondary somatosensory cortex, parietal operculum/auditory cortex); while impaired vSTM was associated with primarily motor-related areas (pars opercularis and pars triangularis, premotor cortex, and primary motor cortex). These results are consistent with the hypothesis, also supported by functional imaging data, that both speech praxis and vSTM rely on partially overlapping networks of brain regions.

  16. Segmentation, Inference and Classification of Partially Overlapping Nanoparticles

    KAUST Repository

    Chiwoo Park,; Huang, J. Z.; Ji, J. X.; Yu Ding,

    2013-01-01

    an agglomerate of overlapping nano-objects; infer the particle's missing contours; and ultimately, classify the particles by shape based on their complete contours. Our specific method adopts a two-stage approach: the first stage executes the task of particle

  17. Partially Overlapping Sensorimotor Networks Underlie Speech Praxis and Verbal Short-Term Memory: Evidence from Apraxia of Speech Following Acute Stroke

    Directory of Open Access Journals (Sweden)

    Gregory eHickok

    2014-08-01

    Full Text Available We tested the hypothesis that motor planning and programming of speech articulation and verbal short-term memory (vSTM depend on partially overlapping networks of neural regions. We evaluated this proposal by testing 76 individuals with acute ischemic stroke for impairment in motor planning of speech articulation (apraxia of speech; AOS and vSTM in the first day of stroke, before the opportunity for recovery or reorganization of structure-function relationships. We also evaluate areas of both infarct and low blood flow that might have contributed to AOS or impaired vSTM in each person. We found that AOS was associated with tissue dysfunction in motor-related areas (posterior primary motor cortex, pars opercularis; premotor cortex, insula and sensory-related areas (primary somatosensory cortex, secondary somatosensory cortex, parietal operculum/auditory cortex; while impaired vSTM was associated with primarily motor-related areas (pars opercularis and pars triangularis, premotor cortex, and primary motor cortex. These results are consistent with the hypothesis, also supported by functional imaging data, that both speech praxis and vSTM rely on partially overlapping networks of brain regions.

  18. Facial expression recognition under partial occlusion based on fusion of global and local features

    Science.gov (United States)

    Wang, Xiaohua; Xia, Chen; Hu, Min; Ren, Fuji

    2018-04-01

    Facial expression recognition under partial occlusion is a challenging research. This paper proposes a novel framework for facial expression recognition under occlusion by fusing the global and local features. In global aspect, first, information entropy are employed to locate the occluded region. Second, principal Component Analysis (PCA) method is adopted to reconstruct the occlusion region of image. After that, a replace strategy is applied to reconstruct image by replacing the occluded region with the corresponding region of the best matched image in training set, Pyramid Weber Local Descriptor (PWLD) feature is then extracted. At last, the outputs of SVM are fitted to the probabilities of the target class by using sigmoid function. For the local aspect, an overlapping block-based method is adopted to extract WLD features, and each block is weighted adaptively by information entropy, Chi-square distance and similar block summation methods are then applied to obtain the probabilities which emotion belongs to. Finally, fusion at the decision level is employed for the data fusion of the global and local features based on Dempster-Shafer theory of evidence. Experimental results on the Cohn-Kanade and JAFFE databases demonstrate the effectiveness and fault tolerance of this method.

  19. Norm overlap between many-body states: Uncorrelated overlap between arbitrary Bogoliubov product states

    Science.gov (United States)

    Bally, B.; Duguet, T.

    2018-02-01

    -form expression allowing its computation without any phase ambiguity. The formula is physically intuitive, accurate, and versatile. It equally applies to norm overlaps between Bogoliubov states of even or odd number parity. Numerical applications illustrate these features and provide a transparent representation of the content of the norm overlaps. Conclusions: The complex norm overlap between arbitrary Bogoliubov states is computed, without any phase ambiguity, via elementary linear algebra operations. The method can be used in any configuration mixing of orthogonal and non-orthogonal product states. Furthermore, the closed-form expression extends naturally to correlated overlaps at play in PNR-BCC and PNR-BMBPT. As such, the straight overlap between Bogoliubov states is the zero-order reduction of more involved norm kernels to be studied in a forthcoming paper.

  20. Metallothionein expression during liver regeneration after partial hepatectomy in cadmium-pretreated rats

    Energy Technology Data Exchange (ETDEWEB)

    Margeli, A.P. (Dept. of Forensic Medicine and Toxicology, School of Medicine, Univ. of Athens (Greece)); Theocharis, S.E. (Dept. of Forensic Medicine and Toxicology, School of Medicine, Univ. of Athens (Greece)); Yannacou, N.N. (Dept. of Forensic Medicine and Toxicology, School of Medicine, Univ. of Athens (Greece)); Spiliopoulou, C. (Dept. of Forensic Medicine and Toxicology, School of Medicine, Univ. of Athens (Greece)); Koutselinis, A. (Dept. of Forensic Medicine and Toxicology, School of Medicine, Univ. of Athens (Greece))

    1994-10-01

    Metallothionein is a low molecular mass protein inducible mainly by heavy metals, having high affinity for binding cadmium, zinc and copper. In the present study we investigated the expression of metallothionein in regenerating liver, at different time intervals, in cadmium pretreated partially hepatectomized rats. Liver metallothionein is highly expressed during regeneration induced by partial hepatectomy in rats, providing zinc within the rapidly growing tissue. Cadmium pretreatment caused inhibition of the first peak of liver regeneration, while metallothionein expression was markedly more prominent in the liver residues of cadmium-pretreated rats. These results demonstrate that although metallothionein able to bind temporarily metal ions as zinc and cadmium has been highly expressed, the liver regenerative process was inhibited possibly due to the effects of cadmium on other pivotal events necessary to the DNA replication. (orig.)

  1. Pattern overlap implies runaway growth in hierarchical tile systems

    Directory of Open Access Journals (Sweden)

    David Doty

    2015-11-01

    Full Text Available We show that in the hierarchical tile assembly model, if there is a producible assembly that overlaps a nontrivial translation of itself consistently (i.e., the pattern of tile types in the overlap region is identical in both translations, then arbitrarily large assemblies are producible. The significance of this result is that tile systems intended to controllably produce finite structures must avoid pattern repetition in their producible assemblies that would lead to such overlap.This answers an open question of Chen and Doty (SODA 2012, who showed that so-called "partial-order" systems producing a unique finite assembly and avoiding such overlaps must require time linear in the assembly diameter. An application of our main result is that any system producing a unique finite assembly is automatically guaranteed to avoid such overlaps, simplifying the hypothesis of Chen and Doty's main theorem.

  2. Diagnosis of partial body radiation exposure in mice using peripheral blood gene expression profiles.

    Directory of Open Access Journals (Sweden)

    Sarah K Meadows

    2010-07-01

    Full Text Available In the event of a terrorist-mediated attack in the United States using radiological or improvised nuclear weapons, it is expected that hundreds of thousands of people could be exposed to life-threatening levels of ionizing radiation. We have recently shown that genome-wide expression analysis of the peripheral blood (PB can generate gene expression profiles that can predict radiation exposure and distinguish the dose level of exposure following total body irradiation (TBI. However, in the event a radiation-mass casualty scenario, many victims will have heterogeneous exposure due to partial shielding and it is unknown whether PB gene expression profiles would be useful in predicting the status of partially irradiated individuals. Here, we identified gene expression profiles in the PB that were characteristic of anterior hemibody-, posterior hemibody- and single limb-irradiation at 0.5 Gy, 2 Gy and 10 Gy in C57Bl6 mice. These PB signatures predicted the radiation status of partially irradiated mice with a high level of accuracy (range 79-100% compared to non-irradiated mice. Interestingly, PB signatures of partial body irradiation were poorly predictive of radiation status by site of injury (range 16-43%, suggesting that the PB molecular response to partial body irradiation was anatomic site specific. Importantly, PB gene signatures generated from TBI-treated mice failed completely to predict the radiation status of partially irradiated animals or non-irradiated controls. These data demonstrate that partial body irradiation, even to a single limb, generates a characteristic PB signature of radiation injury and thus may necessitate the use of multiple signatures, both partial body and total body, to accurately assess the status of an individual exposed to radiation.

  3. Calsyntenins Are Expressed in a Dynamic and Partially Overlapping Manner during Neural Development

    Directory of Open Access Journals (Sweden)

    Gemma de Ramon Francàs

    2017-08-01

    Full Text Available Calsyntenins form a family of linker proteins between distinct populations of vesicles and kinesin motors for axonal transport. They were implicated in synapse formation and synaptic plasticity by findings in worms, mice and humans. These findings were in accordance with the postsynaptic localization of the Calsyntenins in the adult brain. However, they also affect the formation of neural circuits, as loss of Calsyntenin-1 (Clstn1 was shown to interfere with axonal branching and axon guidance. Despite the fact that Calsyntenins were discovered originally in embryonic chicken motoneurons, their distribution in the developing nervous system has not been analyzed in detail so far. Here, we summarize our analysis of the temporal and spatial expression patterns of the cargo-docking proteins Clstn1, Clstn2 and Clstn3 during neural development by comparing the dynamic distribution of their mRNAs by in situ hybridization in the spinal cord, the cerebellum, the retina and the tectum, as well as in the dorsal root ganglia (DRG.

  4. Efficient methods for overlapping group lasso.

    Science.gov (United States)

    Yuan, Lei; Liu, Jun; Ye, Jieping

    2013-09-01

    The group Lasso is an extension of the Lasso for feature selection on (predefined) nonoverlapping groups of features. The nonoverlapping group structure limits its applicability in practice. There have been several recent attempts to study a more general formulation where groups of features are given, potentially with overlaps between the groups. The resulting optimization is, however, much more challenging to solve due to the group overlaps. In this paper, we consider the efficient optimization of the overlapping group Lasso penalized problem. We reveal several key properties of the proximal operator associated with the overlapping group Lasso, and compute the proximal operator by solving the smooth and convex dual problem, which allows the use of the gradient descent type of algorithms for the optimization. Our methods and theoretical results are then generalized to tackle the general overlapping group Lasso formulation based on the l(q) norm. We further extend our algorithm to solve a nonconvex overlapping group Lasso formulation based on the capped norm regularization, which reduces the estimation bias introduced by the convex penalty. We have performed empirical evaluations using both a synthetic and the breast cancer gene expression dataset, which consists of 8,141 genes organized into (overlapping) gene sets. Experimental results show that the proposed algorithm is more efficient than existing state-of-the-art algorithms. Results also demonstrate the effectiveness of the nonconvex formulation for overlapping group Lasso.

  5. Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED

    Science.gov (United States)

    Wang, Yue; Halper, Michael; Wei, Duo; Perl, Yehoshua; Geller, James

    2012-01-01

    An algorithmically-derived abstraction network, called the partial-area taxonomy, for a SNOMED hierarchy has led to the identification of concepts considered complex. The designation “complex” is arrived at automatically on the basis of structural analyses of overlap among the constituent concept groups of the partial-area taxonomy. Such complex concepts, called overlapping concepts, constitute a tangled portion of a hierarchy and can be obstacles to users trying to gain an understanding of the hierarchy’s content. A new methodology for partitioning the entire collection of overlapping concepts into singly-rooted groups, that are more manageable to work with and comprehend, is presented. Different kinds of overlapping concepts with varying degrees of complexity are identified. This leads to an abstract model of the overlapping concepts called the disjoint partial-area taxonomy, which serves as a vehicle for enhanced, high-level display. The methodology is demonstrated with an application to SNOMED’s Specimen hierarchy. Overall, the resulting disjoint partial-area taxonomy offers a refined view of the hierarchy’s structural organization and conceptual content that can aid users, such as maintenance personnel, working with SNOMED. The utility of the disjoint partial-area taxonomy as the basis for a SNOMED auditing regimen is presented in a companion paper. PMID:21878396

  6. Quality Assurance in the Determination of Overlapping Peak Areas

    DEFF Research Database (Denmark)

    Christensen, L.H.; Heydorn, K.

    1987-01-01

    The ability of different computer programs to yield accurate peak areas in statistical control in the case of partially overlapping photopeaks has been tested by the Analysis of Precision. A modified Covell method, two commercially available peak-fitting programs from Nuclear Data and Ortec, and ...

  7. Chironomidae larvae (Diptera) of Neotropical floodplain: overlap niche in different habitats.

    Science.gov (United States)

    Butakka, C M M; Ragonha, F H; Takeda, A M

    2014-05-01

    The niche overlap between trophic groups of Chironomidae larvae in different habitats was observed between trophic groups and between different environments in Neotropical floodplain. For the evaluation we used the index of niche overlap (CXY) and analysis of trophic networks, both from the types and amount of food items identified in the larval alimentary canal. In all environments, the larvae fed on mainly organic matter such as plants fragments and algae, but there were many omnivore larvae. Species that have high values of food items occurred in diverse environments as generalists with great overlap niche and those with a low amount of food items with less overlap niche were classified as specialists. The largest number of trophic niche overlap was observed among collector-gatherers in connected floodplain lakes. The lower values of index niche overlap were predators. The similarity in the diet of different taxa in the same niche does not necessarily imply competition between them, but coexistence when the food resource is not scarce in the environment even in partially overlapping niches.

  8. Blind separation of overlapping partials in harmonic musical notes using amplitude and phase reconstruction

    Science.gov (United States)

    de León, Jesús Ponce; Beltrán, José Ramón

    2012-12-01

    In this study, a new method of blind audio source separation (BASS) of monaural musical harmonic notes is presented. The input (mixed notes) signal is processed using a flexible analysis and synthesis algorithm (complex wavelet additive synthesis, CWAS), which is based on the complex continuous wavelet transform. When the harmonics from two or more sources overlap in a certain frequency band (or group of bands), a new technique based on amplitude similarity criteria is used to obtain an approximation to the original partial information. The aim is to show that the CWAS algorithm can be a powerful tool in BASS. Compared with other existing techniques, the main advantages of the proposed algorithm are its accuracy in the instantaneous phase estimation, its synthesis capability and that the only input information needed is the mixed signal itself. A set of synthetically mixed monaural isolated notes have been analyzed using this method, in eight different experiments: the same instrument playing two notes within the same octave and two harmonically related notes (5th and 12th intervals), two different musical instruments playing 5th and 12th intervals, two different instruments playing non-harmonic notes, major and minor chords played by the same musical instrument, three different instruments playing non-harmonically related notes and finally the mixture of a inharmonic instrument (piano) and one harmonic instrument. The results obtained show the strength of the technique.

  9. Skn-1a/Oct-11 and ΔNp63α exert antagonizing effects on human keratin expression

    International Nuclear Information System (INIS)

    Lena, Anna Maria; Cipollone, Rita; Amelio, Ivano; Catani, Maria Valeria; Ramadan, Safaa; Browne, Gareth; Melino, Gerry; Candi, Eleonora

    2010-01-01

    Research highlights: → Skn-1a markedly downregulates ΔNp63-driven K14 expression. → ΔNp63 inhibits Skn-1a-mediated K10 expression. → ΔNp63, mutated in SAM domain, is less effecting in K10 downregulation. → Immunolocalization in human skin of the two transcription factors is partially overlapping. → The antagonistic effects of Skn-1a and p63 is through competition for overlapping responsive elements or through an indirect interaction. -- Abstract: The formation of a stratified epidermis requires a carefully controlled balance between keratinocyte proliferation and differentiation. Here, we report the reciprocal effect on keratin expression of ΔNp63, pivotal in normal epidermal morphogenesis and maintenance, and Skn-1a/Oct-11, a POU transcription factor that triggers and regulates the differentiation of keratinocytes. The expression of Skn-1a markedly downregulated ΔNp63-driven K14 expression in luciferase reporter assays. The extent of downregulation was comparable to the inhibition of Skn-1a-mediated K10 expression upon expression of ΔNp63. ΔNp63, mutated in the protein-protein interaction domain (SAM domain; mutated in human ectodermal dysplasia syndrome), was significantly less effecting in downregulating K10, raising the possibility of a direct interaction among Skn-1a and ΔNp63. Immunolocalization in human skin biopsies revealed that the expression of the two transcription factors is partially overlapping. Co-immunoprecipitation experiments did not, however, demonstrate a direct interaction between ΔNp63 and Skn-1a, suggesting that the antagonistic effects of Skn-1a and p63 on keratin promoter transactivation is probably through competition for overlapping binding sites on target gene promoter or through an indirect interaction.

  10. Skn-1a/Oct-11 and {Delta}Np63{alpha} exert antagonizing effects on human keratin expression

    Energy Technology Data Exchange (ETDEWEB)

    Lena, Anna Maria; Cipollone, Rita; Amelio, Ivano; Catani, Maria Valeria; Ramadan, Safaa [Biochemistry IDI-IRCCS Laboratory and Department of Experimental Medicine and Biochemical Sciences, University of Rome ' Tor Vergata' , 00133, Rome (Italy); Browne, Gareth [MRC Toxicology Unit, Leicester University, Leicester LE1 9HN (United Kingdom); Melino, Gerry [Biochemistry IDI-IRCCS Laboratory and Department of Experimental Medicine and Biochemical Sciences, University of Rome ' Tor Vergata' , 00133, Rome (Italy); MRC Toxicology Unit, Leicester University, Leicester LE1 9HN (United Kingdom); Candi, Eleonora, E-mail: candi@uniroma2.it [Biochemistry IDI-IRCCS Laboratory and Department of Experimental Medicine and Biochemical Sciences, University of Rome ' Tor Vergata' , 00133, Rome (Italy)

    2010-10-29

    Research highlights: {yields} Skn-1a markedly downregulates {Delta}Np63-driven K14 expression. {yields} {Delta}Np63 inhibits Skn-1a-mediated K10 expression. {yields} {Delta}Np63, mutated in SAM domain, is less effecting in K10 downregulation. {yields} Immunolocalization in human skin of the two transcription factors is partially overlapping. {yields} The antagonistic effects of Skn-1a and p63 is through competition for overlapping responsive elements or through an indirect interaction. -- Abstract: The formation of a stratified epidermis requires a carefully controlled balance between keratinocyte proliferation and differentiation. Here, we report the reciprocal effect on keratin expression of {Delta}Np63, pivotal in normal epidermal morphogenesis and maintenance, and Skn-1a/Oct-11, a POU transcription factor that triggers and regulates the differentiation of keratinocytes. The expression of Skn-1a markedly downregulated {Delta}Np63-driven K14 expression in luciferase reporter assays. The extent of downregulation was comparable to the inhibition of Skn-1a-mediated K10 expression upon expression of {Delta}Np63. {Delta}Np63, mutated in the protein-protein interaction domain (SAM domain; mutated in human ectodermal dysplasia syndrome), was significantly less effecting in downregulating K10, raising the possibility of a direct interaction among Skn-1a and {Delta}Np63. Immunolocalization in human skin biopsies revealed that the expression of the two transcription factors is partially overlapping. Co-immunoprecipitation experiments did not, however, demonstrate a direct interaction between {Delta}Np63 and Skn-1a, suggesting that the antagonistic effects of Skn-1a and p63 on keratin promoter transactivation is probably through competition for overlapping binding sites on target gene promoter or through an indirect interaction.

  11. Comparison of Non-overlapping and Overlapping Local/Global Iteration Schemes for Whole-Core Deterministic Transport Calculation

    International Nuclear Information System (INIS)

    Yuk, Seung Su; Cho, Bumhee; Cho, Nam Zin

    2013-01-01

    In the case of deterministic transport model, fixed-k problem formulation is necessary and the overlapping local domain is chosen. However, as mentioned in, the partial current-based Coarse Mesh Finite Difference (p-CMFD) procedure enables also non-overlapping local/global (NLG) iteration. In this paper, NLG iteration is combined with p-CMFD and with CMFD (augmented with a concept of p-CMFD), respectively, and compared to OLG iteration on a 2-D test problem. Non-overlapping local/global iteration with p-CMFD and CMFD global calculation is introduced and tested on a 2-D deterministic transport problem. The modified C5G7 problem is analyzed with both NLG and OLG methods and the solutions converge to the reference solution except for some cases of NLG with CMFD. NLG with CMFD gives the best performance if the solution converges. But if fission-source iteration in local calculation is not enough, it is prone to diverge. The p-CMFD global solver gives unconditional convergence (for both OLG and NLG). A study of switching scheme is in progress, where NLG/p-CMFD is used as 'starter' and then switched to NLG/CMFD to render the whole-core transport calculation more efficient and robust. Parallel computation is another obvious future work

  12. Track with overlapping links for dry coal extrusion pumps

    Science.gov (United States)

    Saunders, Timothy; Brady, John D

    2014-01-21

    A chain for a particulate material extrusion pump includes a plurality of links, each of the plurality of links having a link body and a link ledge, wherein each link ledge of the plurality of links at least partially overlaps the link body of an adjacent one of the plurality of links.

  13. Partially Overlapping Brain Networks for Singing and Cello Playing

    Directory of Open Access Journals (Sweden)

    Melanie Segado

    2018-05-01

    Full Text Available This research uses an MR-Compatible cello to compare functional brain activation during singing and cello playing within the same individuals to determine the extent to which arbitrary auditory-motor associations, like those required to play the cello, co-opt functional brain networks that evolved for singing. Musical instrument playing and singing both require highly specific associations between sounds and movements. Because these are both used to produce musical sounds, it is often assumed in the literature that their neural underpinnings are highly similar. However, singing is an evolutionarily old human trait, and the auditory-motor associations used for singing are also used for speech and non-speech vocalizations. This sets it apart from the arbitrary auditory-motor associations required to play musical instruments. The pitch range of the cello is similar to that of the human voice, but cello playing is completely independent of the vocal apparatus, and can therefore be used to dissociate the auditory-vocal network from that of the auditory-motor network. While in the MR-Scanner, 11 expert cellists listened to and subsequently produced individual tones either by singing or cello playing. All participants were able to sing and play the target tones in tune (<50C deviation from target. We found that brain activity during cello playing directly overlaps with brain activity during singing in many areas within the auditory-vocal network. These include primary motor, dorsal pre-motor, and supplementary motor cortices (M1, dPMC, SMA,the primary and periprimary auditory cortices within the superior temporal gyrus (STG including Heschl's gyrus, anterior insula (aINS, anterior cingulate cortex (ACC, and intraparietal sulcus (IPS, and Cerebellum but, notably, exclude the periaqueductal gray (PAG and basal ganglia (Putamen. Second, we found that activity within the overlapping areas is positively correlated with, and therefore likely contributing to

  14. Functional Associations by Response Overlap (FARO, a functional genomics approach matching gene expression phenotypes.

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    Henrik Bjørn Nielsen

    2007-08-01

    Full Text Available The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between experimental factors affecting a biological system. Unfortunately, direct comparisons of gene expression profiles obtained in independent, publicly available microarray experiments are typically compromised by substantial, experiment-specific biases. Here we suggest a novel yet conceptually simple approach for deriving 'Functional Association(s by Response Overlap' (FARO between microarray gene expression studies. The transcriptional response is defined by the set of differentially expressed genes independent from the magnitude or direction of the change. This approach overcomes the limited comparability between studies that is typical for methods that rely on correlation in gene expression. We apply FARO to a compendium of 242 diverse Arabidopsis microarray experimental factors, including phyto-hormones, stresses and pathogens, growth conditions/stages, tissue types and mutants. We also use FARO to confirm and further delineate the functions of Arabidopsis MAP kinase 4 in disease and stress responses. Furthermore, we find that a large, well-defined set of genes responds in opposing directions to different stress conditions and predict the effects of different stress combinations. This demonstrates the usefulness of our approach for exploiting public microarray data to derive biologically meaningful associations between experimental factors. Finally, our

  15. Predicting 3D pose in partially overlapped X-ray images of knee prostheses using model-based Roentgen stereophotogrammetric analysis (RSA).

    Science.gov (United States)

    Hsu, Chi-Pin; Lin, Shang-Chih; Shih, Kao-Shang; Huang, Chang-Hung; Lee, Chian-Her

    2014-12-01

    After total knee replacement, the model-based Roentgen stereophotogrammetric analysis (RSA) technique has been used to monitor the status of prosthetic wear, misalignment, and even failure. However, the overlap of the prosthetic outlines inevitably increases errors in the estimation of prosthetic poses due to the limited amount of available outlines. In the literature, quite a few studies have investigated the problems induced by the overlapped outlines, and manual adjustment is still the mainstream. This study proposes two methods to automate the image processing of overlapped outlines prior to the pose registration of prosthetic models. The outline-separated method defines the intersected points and segments the overlapped outlines. The feature-recognized method uses the point and line features of the remaining outlines to initiate registration. Overlap percentage is defined as the ratio of overlapped to non-overlapped outlines. The simulated images with five overlapping percentages are used to evaluate the robustness and accuracy of the proposed methods. Compared with non-overlapped images, overlapped images reduce the number of outlines available for model-based RSA calculation. The maximum and root mean square errors for a prosthetic outline are 0.35 and 0.04 mm, respectively. The mean translation and rotation errors are 0.11 mm and 0.18°, respectively. The errors of the model-based RSA results are increased when the overlap percentage is beyond about 9%. In conclusion, both outline-separated and feature-recognized methods can be seamlessly integrated to automate the calculation of rough registration. This can significantly increase the clinical practicability of the model-based RSA technique.

  16. Prediction of peak overlap in NMR spectra

    International Nuclear Information System (INIS)

    Hefke, Frederik; Schmucki, Roland; Güntert, Peter

    2013-01-01

    Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.

  17. Multiple scattering in closely packed systems of arbitrary non-overlapping shapes

    International Nuclear Information System (INIS)

    Keister, B.D.

    1982-11-01

    It has long been known that the multiple scattering of waves from a system of obstacles of finite extent can be described completely with a knowledge of the on-shell amplitudes of the individual scatterers, provided that the minimally enclosing spheres concentric with the scattering centers do not overlap. In this paper, it is shown that on-shell amplitudes alone suffice for a wider class of scattering configurations, in which the individual scatterers do not overlap, but their geometries do not satisfy the above condition. These extended geometries require a careful treatment of certain partial wave sums. An example is also discussed in which a pair of non-overlapping scatterers requires more than the on-shell amplitudes for a solution

  18. Can subtle changes in gene expression be consistently detected with different microarray platforms?

    Directory of Open Access Journals (Sweden)

    Kuiper Rowan

    2008-03-01

    Full Text Available Abstract Background The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Results Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms. Conclusion The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to

  19. Linear inequalities and overlap bounds: a novel use of an operator inequality

    International Nuclear Information System (INIS)

    Cohen, M.; Leopold, J.G.

    1976-01-01

    Bounds to overlap integrals are obtained by an operator inequality technique. The formulation involves a set of linear inequalities with several overlap integrals as unknowns. The 'solution' of this set of inequalities leads to bound expressions which complement those of other workers. (author)

  20. Some new results on the central overlap problem in astrometry

    Science.gov (United States)

    Rapaport, M.

    1998-07-01

    The central overlap problem in astrometry has been revisited in the recent last years by Eichhorn (1988) who explicitly inverted the matrix of a constrained least squares problem. In this paper, the general explicit solution of the unconstrained central overlap problem is given. We also give the explicit solution for an other set of constraints; this result is a confirmation of a conjecture expressed by Eichhorn (1988). We also consider the use of iterative methods to solve the central overlap problem. A surprising result is obtained when the classical Gauss Seidel method is used; the iterations converge immediately to the general solution of the equations; we explain this property writing the central overlap problem in a new set of variables.

  1. Gender variation, partial male sterility and labile sex expression in gynodioecious Plantago coronopus

    NARCIS (Netherlands)

    Koelewijn, HP; VanDamme, JMM

    Gynodioecy is a breeding system consisting of male steriles (MS, females) and hermaphrodites (H). There is however within such sq stems a third, often neglected, class of partially male sterile plants (PMS), i.e. plants with an intermediate sex expression. In natural populations of Plantago

  2. Gender variation, partial male sterility and labile sex expression in gynodioecious Plantago coronopus

    NARCIS (Netherlands)

    Koelewijn, H.P.; Van Damme, J.M.M.

    1996-01-01

    Gynodioecy is a breeding system consisting of male steriles (MS, females) and hermaphrodites (H). There is however within such sq stems a third, often neglected, class of partially male sterile plants (PMS), i.e. plants with an intermediate sex expression. In natural populations of Plantago

  3. PARTIAL TRISOMY 4p AND PARTIAL MONOSOMY 13q: CASE REPORT AND A LITERATURE REVIEW.

    Science.gov (United States)

    Puvabanditsin, S; Herrera-Garcia, G; Gengel, N; Hussein, K; February, M; Mayne, J; Mehta, R

    2016-01-01

    We report on a term first born dichorionic-diamniotic twin with deletion of the distal long arm of chromosome 13, partial trisomy of the short arm of chromosome 4, intrauterine growth retardation, and multiple anomalies including microcephaly, colpocephaly, absent corpus callosum, bulbous tip of the nose, large and low set ears, macroglossia, thin upper lip, double outlet right ventricle, atria/ventricular septal defect, cleft mitral valve, pulmonary stenosis, single umbilical artery, multicystic dysplastic left kidney, sacral dimple, anterior displacement of anus, simian creases, abnormal thumb (congenital clasped thumb), overlapping toes, and congenital hypothyroidism. This is the first report of a patient with partial trisomy 4p and partial monosomy 13q.

  4. Structure and expression of two nuclear receptor genes in marsupials: insights into the evolution of the antisense overlap between the α-thyroid hormone receptor and Rev-erbα

    Directory of Open Access Journals (Sweden)

    Brown M Scott

    2010-12-01

    Full Text Available Abstract Background Alternative processing of α-thyroid hormone receptor (TRα, NR1A1 mRNAs gives rise to two functionally antagonistic nuclear receptors: TRα1, the α-type receptor, and TRα2, a non-hormone binding variant that is found only in mammals. TRα2 shares an unusual antisense coding overlap with mRNA for Rev-erbα (NR1D1, another nuclear receptor protein. In this study we examine the structure and expression of these genes in the gray short-tailed opossum, Monodelphis domestica, in comparison with that of eutherian mammals and three other marsupial species, Didelphis virginiana, Potorous tridactylus and Macropus eugenii, in order to understand the evolution and regulatory role of this antisense overlap. Results The sequence, expression and genomic organization of mRNAs encoding TRα1 and Rev-erbα are very similar in the opossum and eutherian mammals. However, the sequence corresponding to the TRα2 coding region appears truncated by almost 100 amino acids. While expression of TRα1 and Rev-erbα was readily detected in all tissues of M. domestica ages 0 days to 18 weeks, TRα2 mRNA was not detected in any tissue or stage examined. These results contrast with the widespread and abundant expression of TRα2 in rodents and other eutherian mammals. To examine requirements for alternative splicing of TRα mRNAs, a series of chimeric minigenes was constructed. Results show that the opossum TRα2-specific 5' splice site sequence is fully competent for splicing but the sequence homologous to the TRα2 3' splice site is not, even though the marsupial sequences are remarkably similar to core splice site elements in rat. Conclusions Our results strongly suggest that the variant nuclear receptor isoform, TRα2, is not expressed in marsupials and that the antisense overlap between TRα and Rev-erbα thus is unique to eutherian mammals. Further investigation of the TRα and Rev-erbα genes in marsupial and eutherian species promises to yield

  5. Structure and expression of two nuclear receptor genes in marsupials: insights into the evolution of the antisense overlap between the α-thyroid hormone receptor and Rev-erbα

    Science.gov (United States)

    2010-01-01

    Background Alternative processing of α-thyroid hormone receptor (TRα, NR1A1) mRNAs gives rise to two functionally antagonistic nuclear receptors: TRα1, the α-type receptor, and TRα2, a non-hormone binding variant that is found only in mammals. TRα2 shares an unusual antisense coding overlap with mRNA for Rev-erbα (NR1D1), another nuclear receptor protein. In this study we examine the structure and expression of these genes in the gray short-tailed opossum, Monodelphis domestica, in comparison with that of eutherian mammals and three other marsupial species, Didelphis virginiana, Potorous tridactylus and Macropus eugenii, in order to understand the evolution and regulatory role of this antisense overlap. Results The sequence, expression and genomic organization of mRNAs encoding TRα1 and Rev-erbα are very similar in the opossum and eutherian mammals. However, the sequence corresponding to the TRα2 coding region appears truncated by almost 100 amino acids. While expression of TRα1 and Rev-erbα was readily detected in all tissues of M. domestica ages 0 days to 18 weeks, TRα2 mRNA was not detected in any tissue or stage examined. These results contrast with the widespread and abundant expression of TRα2 in rodents and other eutherian mammals. To examine requirements for alternative splicing of TRα mRNAs, a series of chimeric minigenes was constructed. Results show that the opossum TRα2-specific 5' splice site sequence is fully competent for splicing but the sequence homologous to the TRα2 3' splice site is not, even though the marsupial sequences are remarkably similar to core splice site elements in rat. Conclusions Our results strongly suggest that the variant nuclear receptor isoform, TRα2, is not expressed in marsupials and that the antisense overlap between TRα and Rev-erbα thus is unique to eutherian mammals. Further investigation of the TRα and Rev-erbα genes in marsupial and eutherian species promises to yield additional insight into the

  6. Spatially generalizable representations of facial expressions: Decoding across partial face samples.

    Science.gov (United States)

    Greening, Steven G; Mitchell, Derek G V; Smith, Fraser W

    2018-04-01

    A network of cortical and sub-cortical regions is known to be important in the processing of facial expression. However, to date no study has investigated whether representations of facial expressions present in this network permit generalization across independent samples of face information (e.g., eye region vs mouth region). We presented participants with partial face samples of five expression categories in a rapid event-related fMRI experiment. We reveal a network of face-sensitive regions that contain information about facial expression categories regardless of which part of the face is presented. We further reveal that the neural information present in a subset of these regions: dorsal prefrontal cortex (dPFC), superior temporal sulcus (STS), lateral occipital and ventral temporal cortex, and even early visual cortex, enables reliable generalization across independent visual inputs (faces depicting the 'eyes only' vs 'eyes removed'). Furthermore, classification performance was correlated to behavioral performance in STS and dPFC. Our results demonstrate that both higher (e.g., STS, dPFC) and lower level cortical regions contain information useful for facial expression decoding that go beyond the visual information presented, and implicate a key role for contextual mechanisms such as cortical feedback in facial expression perception under challenging conditions of visual occlusion. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. High expression of Rac1 is correlated with partial reversed cell polarity and poor prognosis in invasive ductal carcinoma of the breast.

    Science.gov (United States)

    Liu, Bingbing; Xiong, Jianhua; Liu, Guiqiu; Wu, Jing; Wen, Likun; Zhang, Qin; Zhang, Chuanshan

    2017-07-01

    The change of cell polarity is usually associated with invasion and metastasis. Partial reverse cell polarity in IDC-NOS may play a role in lymphatic tumor spread. Rac1 is a kind of polarity related protein. It plays an important role in invasion and metastasis in tumors. We here investigated the expression of Rac1 and partial reverse cell polarity status in breast cancer and evaluated their value for prognosis in breast cancer. The association of the expression of Rac1 and MUC-1 with clinicopathological parameters and prognostic significance was evaluated in 162 cases of IDC-NOS paraffin-embedded tissues by immunohistochemical method. The Rac1 messenger RNA expression was measured by real-time polymerase chain reaction in 30 breast cancer patients, which was divided into two groups of partial reverse cell polarity and no partial reverse cell polarity. We found that lymph node metastasis of partial reverse cell polarity patients was higher than no partial reverse cell polarity patients (Z = -4.030, p = 0.000). Rac1 was upregulated in partial reverse cell polarity group than no partial reverse cell polarity group (Z = -3.164, p = 0.002), and there was correlationship between the expression of Rac1 and partial reverse cell polarity status (r s  = 0.249, p = 0.001). The level of Rac1 messenger RNA expression in partial reverse cell polarity group was significantly higher compared to no partial reverse cell polarity group (t = -2.527, p = 0.017). Overexpression of Rac1 and partial reverse cell polarity correlates with poor prognosis of IDC-NOS patients (p = 0.011). Partial reverse cell polarity and lymph node metastasis remained as independent predictors for poor disease-free survival of IDC-NOS (p = 0.023, p = 0.046). Our study suggests that partial reverse cell polarity may lead to poor prognosis of breast cancer. Overexpression of Rac1 may lead to polarity change in IDC-NOS of the breast. Therefore, Rac1 could be a

  8. Impaired expression of mitochondrial and adipogenic genes in adipose tissue from a patient with acquired partial lipodystrophy (Barraquer-Simons syndrome: a case report

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    Guallar Jordi P

    2008-08-01

    Full Text Available Abstract Introduction Acquired partial lipodystrophy or Barraquer-Simons syndrome is a rare form of progressive lipodystrophy. The etiopathogenesis of adipose tissue atrophy in these patients is unknown. Case presentation This is a case report of a 44-year-old woman with acquired partial lipodystrophy. To obtain insight into the molecular basis of lipoatrophy in acquired partial lipodystrophy, we examined gene expression in adipose tissue from this patient newly diagnosed with acquired partial lipodystrophy. A biopsy of subcutaneous adipose tissue was obtained from the patient, and DNA and RNA were extracted in order to evaluate mitochondrial DNA abundance and mRNA expression levels. Conclusion The expression of marker genes of adipogenesis and adipocyte metabolism, including the master regulator PPARγ, was down-regulated in subcutaneous adipose tissue from this patient. Adiponectin mRNA expression was also reduced but leptin mRNA levels were unaltered. Markers of local inflammatory status were unaltered. Expression of genes related to mitochondrial function was reduced despite unaltered levels of mitochondrial DNA. It is concluded that adipogenic and mitochondrial gene expression is impaired in adipose tissue in this patient with acquired partial lipodystrophy.

  9. Sleep overlap syndrome

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    Fariba Rezaeetalab

    2016-12-01

    Full Text Available Overlap syndrome, which is known as the coexistence of chronic obstructive pulmonary disease (COPD and obstructive sleep apnea (OSA, was first defined by Flenley. Although it can refer to concomitant occurrence of any of the pulmonary diseases and OSA, overlap syndrome is commonly considered as the coexistence of OSA and COPD. This disease has unique adverse health consequences distinct from either condition alone. Given the high prevalence of each solitary disease, overlap syndrome is also likely to be common and clinically relevant. Despite the fact that overlap syndrome has been described in the literature for nearly 30 years, paucity of evaluations and studies limited the discussion on diagnosis, prevalence, pathophysiology, treatment, and outcomes of this disease. This review article addresses these issues by reviewing several recent studies conducted in Iran or other countries. This review suggests that overlap syndrome has worse outcomes than either disease alone. Our findings accentuated the urgent need for further studies on overlap syndrome and all overlaps between OSA and chronic pulmonary disease to provide a deeper insight into diagnosis and non-invasive treatments of this disease.

  10. Epidemic spreading on complex networks with overlapping and non-overlapping community structure

    Science.gov (United States)

    Shang, Jiaxing; Liu, Lianchen; Li, Xin; Xie, Feng; Wu, Cheng

    2015-02-01

    Many real-world networks exhibit community structure where vertices belong to one or more communities. Recent studies show that community structure plays an import role in epidemic spreading. In this paper, we investigate how the extent of overlap among communities affects epidemics. In order to experiment on the characteristic of overlapping communities, we propose a rewiring algorithm that can change the community structure from overlapping to non-overlapping while maintaining the degree distribution of the network. We simulate the Susceptible-Infected-Susceptible (SIS) epidemic process on synthetic scale-free networks and real-world networks by applying our rewiring algorithm. Experiments show that epidemics spread faster on networks with higher level of overlapping communities. Furthermore, overlapping communities' effect interacts with the average degree's effect. Our work further illustrates the important role of overlapping communities in the process of epidemic spreading.

  11. Multicolor fluorescent in situ hybridization to define abutting and overlapping gene expression in the embryonic zebrafish brain

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    Hauptmann Giselbert

    2011-04-01

    Full Text Available Abstract Background In recent years, mapping of overlapping and abutting regulatory gene expression domains by chromogenic two-color in situ hybridization has helped define molecular subdivisions of the developing vertebrate brain and shed light on its basic organization. Despite the benefits of this technique, visualization of overlapping transcript distributions by differently colored precipitates remains difficult because of masking of lighter signals by darker color precipitates and lack of three-dimensional visualization properties. Fluorescent detection of transcript distributions may be able to solve these issues. However, despite the use of signal amplification systems for increasing sensitivity, fluorescent detection in whole-mounts suffers from rapid quenching of peroxidase (POD activity compared to alkaline phosphatase chromogenic reactions. Thus, less strongly expressed genes cannot be efficiently detected. Results We developed an optimized procedure for fluorescent detection of transcript distribution in whole-mount zebrafish embryos using tyramide signal amplification (TSA. Conditions for hybridization and POD-TSA reaction were optimized by the application of the viscosity-increasing polymer dextran sulfate and the use of the substituted phenol compounds 4-iodophenol and vanillin as enhancers of POD activity. In combination with highly effective bench-made tyramide substrates, these improvements resulted in dramatically increased signal-to-noise ratios. The strongly enhanced signal intensities permitted fluorescent visualization of less abundant transcripts of tissue-specific regulatory genes. When performing multicolor fluorescent in situ hybridization (FISH experiments, the highly sensitive POD reaction conditions required effective POD inactivation after each detection cycle by glycine-hydrochloric acid treatment. This optimized FISH procedure permitted the simultaneous fluorescent visualization of up to three unique transcripts

  12. Over-expression of Eph and ephrin genes in advanced ovarian cancer: ephrin gene expression correlates with shortened survival

    Directory of Open Access Journals (Sweden)

    Lincoln Douglas

    2006-06-01

    Full Text Available Abstract Background Increased expression of Eph receptor tyrosine kinases and their ephrin ligands has been implicated in tumor progression in a number of malignancies. This report describes aberrant expression of these genes in ovarian cancer, the commonest cause of death amongst gynaecological malignancies. Methods Eph and ephrin expression was determined using quantitative real time RT-PCR. Correlation of gene expression was measured using Spearman's rho statistic. Survival was analysed using log-rank analysis and (was visualised by Kaplan-Meier survival curves. Results Greater than 10 fold over-expression of EphA1 and a more modest over-expression of EphA2 were observed in partially overlapping subsets of tumors. Over-expression of EphA1 strongly correlated (r = 0.801; p Conclusion These data imply that increased levels of ephrins A1 and A5 in the presence of high expression of Ephs A1 and A2 lead to a more aggressive tumor phenotype. The known functions of Eph/ephrin signalling in cell de-adhesion and movement may explain the observed correlation of ephrin expression with poor prognosis.

  13. Heterologous expression of a deuterated membrane-integrated receptor and partial deuteration in methylotrophic yeasts

    International Nuclear Information System (INIS)

    Massou, S.; Puech, V.; Talmont, F.; Demange, P.; Lindley, N.D.; Tropis, M.; Milon, A.

    1999-01-01

    Methylotrophic yeast has previously been shown to be an excellent system for the cost-effective production of perdeuterated biomass and for the heterologous expression of membrane receptors. A protocol for the expression of 85% deuterated, functional human μ-opiate receptor was established. For partially deuterated biomass, deuteration level and distribution were determined for fatty acids, amino acids and carbohydrates. It was shown that prior to biosynthesis of lipids and amino acids (and of carbohydrates, to a lower extent), exchange occurs between water and methanol hydrogen atoms, so that 80%-90% randomly deuterated biomass and over-expressed proteins may be obtained using only deuterated water

  14. Instrument Identification in Polyphonic Music: Feature Weighting to Minimize Influence of Sound Overlaps

    Directory of Open Access Journals (Sweden)

    Goto Masataka

    2007-01-01

    Full Text Available We provide a new solution to the problem of feature variations caused by the overlapping of sounds in instrument identification in polyphonic music. When multiple instruments simultaneously play, partials (harmonic components of their sounds overlap and interfere, which makes the acoustic features different from those of monophonic sounds. To cope with this, we weight features based on how much they are affected by overlapping. First, we quantitatively evaluate the influence of overlapping on each feature as the ratio of the within-class variance to the between-class variance in the distribution of training data obtained from polyphonic sounds. Then, we generate feature axes using a weighted mixture that minimizes the influence via linear discriminant analysis. In addition, we improve instrument identification using musical context. Experimental results showed that the recognition rates using both feature weighting and musical context were 84.1 for duo, 77.6 for trio, and 72.3 for quartet; those without using either were 53.4, 49.6, and 46.5 , respectively.

  15. Direct and indirect effects in the regulation of overlapping promoters

    DEFF Research Database (Denmark)

    Bendtsen, Kristian Moss; Erdossy, Janos; Csiszovski, Zsolt

    2011-01-01

    promoter database we found that ~14% of the identified 'forward' promoters overlap with a promoter oriented in the opposite direction. In this article we combine a mathematical model with experimental analysis of synthetic regulatory regions to investigate interference of overlapping promoters. We find...... that promoter interference depends on the characteristics of overlapping promoters. The model predicts that promoter strength and interference can be regulated separately, which provides unique opportunities for regulation. Our experimental data suggest that in principle any DNA binding protein can be used......Optimal response to environmental stimuli often requires activation of certain genes and repression of others. Dual function regulatory proteins play a key role in the differential regulation of gene expression. While repression can be achieved by any DNA binding protein through steric occlusion...

  16. Overlap functions

    Czech Academy of Sciences Publication Activity Database

    Bustince, H.; Fernández, J.; Mesiar, Radko; Montero, J.; Orduna, R.

    2010-01-01

    Roč. 72, 3-4 (2010), s. 1488-1499 ISSN 0362-546X R&D Projects: GA ČR GA402/08/0618 Institutional research plan: CEZ:AV0Z10750506 Keywords : t-norm * Migrative property * Homogeneity property * Overlap function Subject RIV: BA - General Mathematics Impact factor: 1.279, year: 2010 http://library.utia.cas.cz/separaty/2009/E/mesiar-overlap functions.pdf

  17. Changes in Gene Expression of Arabidopsis Thaliana Cell Cultures Upon Exposure to Real and Simulated Partial- g Forces

    Science.gov (United States)

    Fengler, Svenja; Spirer, Ina; Neef, Maren; Ecke, Margret; Hauslage, Jens; Hampp, Rüdiger

    2016-06-01

    Cell cultures of the plant model organism Arabidopsis thaliana were exposed to partial- g forces during parabolic flight and clinostat experiments (0.16 g, 0.38 g and 0.5 g were tested). In order to investigate gravity-dependent alterations in gene expression, samples were metabolically quenched by the fixative RNA later Ⓡ to stabilize nucleic acids and used for whole-genome microarray analysis. An attempt to identify the potential threshold acceleration for the gravity-dependent response showed that the smaller the experienced g-force, the greater was the susceptibility of the cell cultures. Compared to short-term μ g during a parabolic flight, the number of differentially expressed genes under partial- g was lower. In addition, the effect on the alteration of amounts of transcripts decreased during partial- g parabolic flight due to the sequence of the different parabolas (0.38 g, 0.16 g and μ g). A time-dependent analysis under simulated 0.5 g indicates that adaptation occurs within minutes. Differentially expressed genes (at least 2-fold up- or down-regulated in expression) under real flight conditions were to some extent identical with those affected by clinorotation. The highest number of homologuous genes was detected within seconds of exposure to 0.38 g (both flight and clinorotation). To a considerable part, these genes deal with cell wall properties. Additionally, responses specific for clinorotation were observed.

  18. Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2009-03-01

    Full Text Available Abstract The plant-infecting members of the genus Fijivirus (family Reoviridae have linear dsRNA genomes divided into 10 segments, two of which contain two substantial and non-overlapping ORFs, while the remaining eight are apparently monocistronic. However, one of these – namely segment 5 – contains a second long ORF (~200+ codons that overlaps the 3' end of the major ORF (~920–940 codons in the +1 reading frame. In this report, we use bioinformatic techniques to analyze the pattern of base variations across an alignment of fijivirus segment 5 sequences, and show that this 3' ORF has a strong coding signature. Possible translation mechanisms for this unusually positioned ORF are discussed.

  19. Living as an LGBTQ Adolescent and a Parent's Child: Overlapping or Separate Experiences.

    Science.gov (United States)

    Mehus, Christopher J; Watson, Ryan J; Eisenberg, Marla E; Corliss, Heather L; Porta, Carolyn M

    2017-05-01

    It is well known that parental and community-based support are each related to healthy development in lesbian, gay, bisexual, transgender, queer, and questioning (LGBTQ) youth, but little research has explored the ways these contexts interact and overlap. Through go-along interviews (a method in which participants guide the interviewer around the community) with 66 youth in British Columbia, Massachusetts, and Minnesota, adolescents (aged 14-19 years) reported varying extent of overlap between their LGBTQ experiences and their parent-youth experiences; parents and youth each contributed to the extent of overlap. Youth who reported high overlap reported little need for resources outside their families but found resources easy to access if wanted. Youth who reported little overlap found it difficult to access resources. Findings suggest that in both research and practice, considering the extent to which youth feel they can express their authentic identity in multiple contexts may be more useful than simply evaluating parental acceptance or access to resources.

  20. THE AVAILABILITY VERSUS THE USE OF PARTIAL INFORMATION - MULTIPLE LEVELS OF SELECTIVE PROCESSING BETWEEN PERCEPTION AND ACTION

    NARCIS (Netherlands)

    SMID, HGOM; MULDER, G

    Temporal overlap of cognitive processes occurs when partial information about a stimulus activates associated responses before the stimulus has been fully identified. Recent evidence obtained with psychophysiological measures suggests that such overlap sometimes does, and sometimes does not occur.

  1. OVERLAPPING VIRTUAL CADASTRAL DOCUMENTATION

    Directory of Open Access Journals (Sweden)

    Madalina - Cristina Marian

    2013-12-01

    Full Text Available Two cadastrale plans of buildings, can overlap virtual. Overlap is highlighted when digital reception. According to Law no. 7/1996 as amended and supplemented, to solve these problems is by updating the database graphs, the repositioning. This paper addresses the issue of overlapping virtual cadastre in the history of the period 1999-2012.

  2. Ancestral amphibian v2rs are expressed in the main olfactory epithelium

    Science.gov (United States)

    Syed, Adnan S.; Sansone, Alfredo; Nadler, Walter; Manzini, Ivan; Korsching, Sigrun I.

    2013-01-01

    Mammalian olfactory receptor families are segregated into different olfactory organs, with type 2 vomeronasal receptor (v2r) genes expressed in a basal layer of the vomeronasal epithelium. In contrast, teleost fish v2r genes are intermingled with all other olfactory receptor genes in a single sensory surface. We report here that, strikingly different from both lineages, the v2r gene family of the amphibian Xenopus laevis is expressed in the main olfactory as well as the vomeronasal epithelium. Interestingly, late diverging v2r genes are expressed exclusively in the vomeronasal epithelium, whereas “ancestral” v2r genes, including the single member of v2r family C, are restricted to the main olfactory epithelium. Moreover, within the main olfactory epithelium, v2r genes are expressed in a basal zone, partially overlapping, but clearly distinct from an apical zone of olfactory marker protein and odorant receptor-expressing cells. These zones are also apparent in the spatial distribution of odor responses, enabling a tentative assignment of odor responses to olfactory receptor gene families. Responses to alcohols, aldehydes, and ketones show an apical localization, consistent with being mediated by odorant receptors, whereas amino acid responses overlap extensively with the basal v2r-expressing zone. The unique bimodal v2r expression pattern in main and accessory olfactory system of amphibians presents an excellent opportunity to study the transition of v2r gene expression during evolution of higher vertebrates. PMID:23613591

  3. Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps.

    Science.gov (United States)

    Sood, Mariam R; Sereno, Martin I

    2016-08-01

    Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor-preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface-based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory-motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory-motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M-I. Hum Brain Mapp 37:2784-2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

  4. Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

    Directory of Open Access Journals (Sweden)

    Harrington Eoghan D

    2008-07-01

    Full Text Available Abstract Background Across the fully sequenced microbial genomes there are thousands of examples of overlapping genes. Many of these are only a few nucleotides long and are thought to function by permitting the coordinated regulation of gene expression. However, there should also be selective pressure against long overlaps, as the existence of overlapping reading frames increases the risk of deleterious mutations. Here we examine the longest overlaps and assess whether they are the product of special functional constraints or of erroneous annotation. Results We analysed the genes that overlap by 60 bps or more among 338 fully-sequenced prokaryotic genomes. The likely functional significance of an overlap was determined by comparing each of the genes to its respective orthologs. If a gene showed a significantly different length from its orthologs it was considered unlikely to be functional and therefore the result of an error either in sequencing or gene prediction. Focusing on 715 co-directional overlaps longer than 60 bps, we classified the erroneous ones into five categories: i 5'-end extension of the downstream gene due to either a mispredicted start codon or a frameshift at 5'-end of the gene (409 overlaps, ii fragmentation of a gene caused by a frameshift (163, iii 3'-end extension of the upstream gene due to either a frameshift at 3'-end of a gene or point mutation at the stop codon (68, iv Redundant gene predictions (4, v 5' & 3'-end extension which is a combination of i and iii (71. We also studied 75 divergent overlaps that could be classified as misannotations of group i. Nevertheless we found some convergent long overlaps (54 that might be true overlaps, although an important part of convergent overlaps could be classified as group iii (124. Conclusion Among the 968 overlaps larger than 60 bps which we analysed, we did not find a single real one among the co-directional and divergent orientations and concluded that there had been an

  5. Living as an LGBTQ adolescent and a parent’s child: Overlapping or separate experiences

    Science.gov (United States)

    Watson, Ryan J.; Eisenberg, Marla E.; Corliss, Heather L.; Porta, Carolyn M.

    2017-01-01

    It is well known that parental and community-based support are each related to healthy development in LGBTQ youth, but little research has explored the ways these contexts interact and overlap. Through go-along interviews (a method in which participants guide the interviewer around the community) with 66 youth in British Columbia, Massachusetts, and Minnesota, adolescents (aged 14–19 years) reported varying extent of overlap between their LGBTQ experiences and their parent-youth experiences; parents and youth each contributed to the extent of overlap. Youth who reported high overlap reported little need for resources outside their families but found resources easy to access if wanted. Youth who reported little overlap found it difficult to access resources. Findings suggest that in both research and practice, considering the extent to which youth feel they can express their authentic identity in multiple contexts may be more useful than simply evaluating parental acceptance or access to resources. PMID:28795897

  6. Overlapping clusters for distributed computation.

    Energy Technology Data Exchange (ETDEWEB)

    Mirrokni, Vahab (Google Research, New York, NY); Andersen, Reid (Microsoft Corporation, Redmond, WA); Gleich, David F.

    2010-11-01

    Scalable, distributed algorithms must address communication problems. We investigate overlapping clusters, or vertex partitions that intersect, for graph computations. This setup stores more of the graph than required but then affords the ease of implementation of vertex partitioned algorithms. Our hope is that this technique allows us to reduce communication in a computation on a distributed graph. The motivation above draws on recent work in communication avoiding algorithms. Mohiyuddin et al. (SC09) design a matrix-powers kernel that gives rise to an overlapping partition. Fritzsche et al. (CSC2009) develop an overlapping clustering for a Schwarz method. Both techniques extend an initial partitioning with overlap. Our procedure generates overlap directly. Indeed, Schwarz methods are commonly used to capitalize on overlap. Elsewhere, overlapping communities (Ahn et al, Nature 2009; Mishra et al. WAW2007) are now a popular model of structure in social networks. These have long been studied in statistics (Cole and Wishart, CompJ 1970). We present two types of results: (i) an estimated swapping probability {rho}{infinity}; and (ii) the communication volume of a parallel PageRank solution (link-following {alpha} = 0.85) using an additive Schwarz method. The volume ratio is the amount of extra storage for the overlap (2 means we store the graph twice). Below, as the ratio increases, the swapping probability and PageRank communication volume decreases.

  7. Frontal cortical asymmetry may partially mediate the influence of social power on anger expression

    Directory of Open Access Journals (Sweden)

    Dongdong eLi

    2016-02-01

    Full Text Available When irritated by other people, powerful people usually tend to express their anger explicitly and directly, whereas people in less powerful positions are more likely not to show their feelings freely. The neural mechanism behind power and its influence on expression tendency has been scarcely explored. This study recorded frontal EEG activity at rest and frontal EEG activation while participants were engaged in a writing task describing an anger-eliciting event, in which they were irritated by people with higher or lower social power. Participants’ anger levels and expression inclination levels were self-reported on nine-point visual analog Likert scales, and also rated by independent raters based on the essays they had written. The results showed that high social power was indeed associated with greater anger expression tendency and greater left frontal activation than low social power. This is in line with the approach-inhibition theory of power. The mid-frontal asymmetric activation served as a partial mediator between social power and expression inclination. This effect may relate to the functions of the prefrontal cortex, which is in charge of information integration and evaluation and the control of motivation direction, as reported by previous studies.

  8. Striking similarity in the gene expression levels of individual Myc module members among ESCs, EpiSCs, and partial iPSCs.

    Directory of Open Access Journals (Sweden)

    Masataka Hirasaki

    Full Text Available Predominant transcriptional subnetworks called Core, Myc, and PRC modules have been shown to participate in preservation of the pluripotency and self-renewality of embryonic stem cells (ESCs. Epiblast stem cells (EpiSCs are another cell type that possesses pluripotency and self-renewality. However, the roles of these modules in EpiSCs have not been systematically examined to date. Here, we compared the average expression levels of Core, Myc, and PRC module genes between ESCs and EpiSCs. EpiSCs showed substantially higher and lower expression levels of PRC and Core module genes, respectively, compared with those in ESCs, while Myc module members showed almost equivalent levels of average gene expression. Subsequent analyses revealed that the similarity in gene expression levels of the Myc module between these two cell types was not just overall, but striking similarities were evident even when comparing the expression of individual genes. We also observed equivalent levels of similarity in the expression of individual Myc module genes between induced pluripotent stem cells (iPSCs and partial iPSCs that are an unwanted byproduct generated during iPSC induction. Moreover, our data demonstrate that partial iPSCs depend on a high level of c-Myc expression for their self-renewal properties.

  9. On the Evaluation Overlap Integrals with the Same and Different Screening Parameters Over Slater Type Orbitals via the Fourier-Transform Method

    International Nuclear Information System (INIS)

    Yavuz, M.; Yuekcue, N.; Oeztekin, E.; Yilmaz, H.; Doenduer, S.

    2005-01-01

    In this paper, derivation of analytical expressions for overlap integrals with the same and different screening parameters of Slater type orbitals (STOs) via the Fourier-transform method is presented. Consequently, it is relatively easy to express the Fourier integral representations of the overlap integrals with same and different screening parameters mentioned as finite sums of Gegenbauer, Gaunt, binomial coefficients, and STOs.

  10. Genetic overlap between impulsivity and alcohol dependence: a large-scale national twin study.

    Science.gov (United States)

    Khemiri, L; Kuja-Halkola, R; Larsson, H; Jayaram-Lindström, N

    2016-04-01

    Alcohol dependence is associated with increased levels of impulsivity, but the genetic and environmental underpinnings of this overlap remain unclear. The purpose of the current study was to investigate the degree to which genetic and environmental factors contribute to the overlap between alcohol dependence and impulsivity. Univariate and bivariate twin model fitting was conducted for alcohol dependence and impulsivity in a national sample of 16 819 twins born in Sweden from 1959 to 1985. The heritability estimate for alcohol dependence was 44% [95% confidence interval (CI) 31-57%] for males and 62% (95% CI 52-72%) for females. For impulsivity, the heritability was 33% (95% CI 30-36%) in males and females. The bivariate twin analysis indicated a statistically significant genetic correlation between alcohol dependence and impulsivity of 0.40 (95% CI 0.23-0.58) in males and 0.20 (95% CI 0.07-0.33) in females. The phenotypic correlation between alcohol dependence and impulsivity was 0.20 and 0.17 for males and females, respectively, and the bivariate heritability was 80% (95% CI 47-117%) for males and 53% (95% CI 19-86%) for females. The remaining variance in all models was accounted for by non-shared environmental factors. The association between alcohol dependence and impulsivity can be partially accounted for by shared genetic factors. The genetic correlation was greater in men compared with women, which may indicate different pathways to the development of alcohol dependence between sexes. The observed genetic overlap has clinical implications regarding treatment and prevention, and partially explains the substantial co-morbidity between alcohol dependence and psychiatric disorders characterized by impulsive behaviour.

  11. Partially Overlapping Brain Networks for Singing and Cello Playing.

    Science.gov (United States)

    Segado, Melanie; Hollinger, Avrum; Thibodeau, Joseph; Penhune, Virginia; Zatorre, Robert J

    2018-01-01

    This research uses an MR-Compatible cello to compare functional brain activation during singing and cello playing within the same individuals to determine the extent to which arbitrary auditory-motor associations, like those required to play the cello, co-opt functional brain networks that evolved for singing. Musical instrument playing and singing both require highly specific associations between sounds and movements. Because these are both used to produce musical sounds, it is often assumed in the literature that their neural underpinnings are highly similar. However, singing is an evolutionarily old human trait, and the auditory-motor associations used for singing are also used for speech and non-speech vocalizations. This sets it apart from the arbitrary auditory-motor associations required to play musical instruments. The pitch range of the cello is similar to that of the human voice, but cello playing is completely independent of the vocal apparatus, and can therefore be used to dissociate the auditory-vocal network from that of the auditory-motor network. While in the MR-Scanner, 11 expert cellists listened to and subsequently produced individual tones either by singing or cello playing. All participants were able to sing and play the target tones in tune (singing in many areas within the auditory-vocal network. These include primary motor, dorsal pre-motor, and supplementary motor cortices (M1, dPMC, SMA),the primary and periprimary auditory cortices within the superior temporal gyrus (STG) including Heschl's gyrus, anterior insula (aINS), anterior cingulate cortex (ACC), and intraparietal sulcus (IPS), and Cerebellum but, notably, exclude the periaqueductal gray (PAG) and basal ganglia (Putamen). Second, we found that activity within the overlapping areas is positively correlated with, and therefore likely contributing to, both singing and playing in tune determined with performance measures. Third, we found that activity in auditory areas is functionally

  12. Illusion induced overlapped optics.

    Science.gov (United States)

    Zang, XiaoFei; Shi, Cheng; Li, Zhou; Chen, Lin; Cai, Bin; Zhu, YiMing; Zhu, HaiBin

    2014-01-13

    The traditional transformation-based cloak seems like it can only hide objects by bending the incident electromagnetic waves around the hidden region. In this paper, we prove that invisible cloaks can be applied to realize the overlapped optics. No matter how many in-phase point sources are located in the hidden region, all of them can overlap each other (this can be considered as illusion effect), leading to the perfect optical interference effect. In addition, a singular parameter-independent cloak is also designed to obtain quasi-overlapped optics. Even more amazing of overlapped optics is that if N identical separated in-phase point sources covered with the illusion media, the total power outside the transformation region is N2I0 (not NI0) (I0 is the power of just one point source, and N is the number point sources), which seems violating the law of conservation of energy. A theoretical model based on interference effect is proposed to interpret the total power of these two kinds of overlapped optics effects. Our investigation may have wide applications in high power coherent laser beams, and multiple laser diodes, and so on.

  13. Influence of Growth Stage and Leaf Age on Expression of the Components of Partial Resistance of Faba Bean to Botrytis fabae Sard.

    Directory of Open Access Journals (Sweden)

    A. Bouhassan

    2004-12-01

    Full Text Available In detached leaf tests on faba bean (Vicia faba L., genotypes partially resistant and susceptible to Botrytis fabae were examined. Expression of four components of partial resistance to a virulent isolate of B. fabae differed depending on the plant age and the leaf age of the genotypes. The incubation period of resistant genotypes at the podding stage was longer than that of susceptible genotypes at the same stage. The area under disease progress curve (AUDPC of the lesion size increased from the seedling to the flowering stage but declined at the podding stage in all genotypes. Differences between resistant and susceptible genotypes for lesion size were significant except on old leaves from plants at the podding stage. The latent period decreased, and spore production increased with increasing growth and leaf age but there was significant interaction with the genotype. These last two components of partial resistance were more clearly expressed at all growth stages on FRY167 (highly resistant but were expressed only at the seedling and podding stages on FRY7 (resistant. The resistant line BPL710 was not significantly different from the susceptible genotypes for the latent period at any growth stage, and for spore production at the seedling and flowering stages. Leaf age affected all genotypes, but with a significant interaction between leaf age and growth stage. Components of partial resistance were more strongly expressed on young leaves from plants at the seedling or flowering stage.

  14. Partial least squares based gene expression analysis in estrogen receptor positive and negative breast tumors.

    Science.gov (United States)

    Ma, W; Zhang, T-F; Lu, P; Lu, S H

    2014-01-01

    Breast cancer is categorized into two broad groups: estrogen receptor positive (ER+) and ER negative (ER-) groups. Previous study proposed that under trastuzumab-based neoadjuvant chemotherapy, tumor initiating cell (TIC) featured ER- tumors response better than ER+ tumors. Exploration of the molecular difference of these two groups may help developing new therapeutic strategies, especially for ER- patients. With gene expression profile from the Gene Expression Omnibus (GEO) database, we performed partial least squares (PLS) based analysis, which is more sensitive than common variance/regression analysis. We acquired 512 differentially expressed genes. Four pathways were found to be enriched with differentially expressed genes, involving immune system, metabolism and genetic information processing process. Network analysis identified five hub genes with degrees higher than 10, including APP, ESR1, SMAD3, HDAC2, and PRKAA1. Our findings provide new understanding for the molecular difference between TIC featured ER- and ER+ breast tumors with the hope offer supports for therapeutic studies.

  15. Probability distribution of wave packet delay time for strong overlapping of resonance levels

    International Nuclear Information System (INIS)

    Lyuboshits, V.L.

    1983-01-01

    Time behaviour of nuclear reactions in the case of high level densities is investigated basing on the theory of overlapping resonances. In the framework of a model of n equivalent channels an analytical expression is obtained for the probability distribution function for wave packet delay time at the compound nucleus production. It is shown that at strong overlapping of the resonance levels the relative fluctuation of the delay time is small at the stage of compound nucleus production. A possible increase in the duration of nuclear reactions with the excitation energy rise is discussed

  16. On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies

    Science.gov (United States)

    Degiacomi, Matteo T.

    2018-05-01

    Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers. [Figure not available: see fulltext.

  17. A comparative study of numerical methods for the overlap Dirac operator--a status report

    International Nuclear Information System (INIS)

    Eshof, J. van den; Frommer, A.; Lippert, Th.; Schilling, K.; Vorst, H. van der

    2002-01-01

    Improvements of various methods to compute the sign function of the hermitian Wilson-Dirac matrix within the overlap operator are presented. An optimal partial fraction expansion (PFE) based on a theorem of Zolotarev is given. Benchmarks show that this PFE together with removal of converged systems within a multi-shift CG appears to approximate the sign function times a vector most efficiently. A posteriori error bounds are given

  18. Diversity and overlap of Parvalbumin and Somatostatin expressing interneurons in mouse presubiculum

    Directory of Open Access Journals (Sweden)

    Mérie eNassar

    2015-05-01

    Full Text Available The presubiculum, located between hippocampus and entorhinal cortex, plays a fundamental role in representing spatial information, notably head direction. Little is known about GABAergic interneurons of this region. Here, we used three transgenic mouse lines, Pvalb-Cre, Sst-Cre and X98, to examine distinct interneurons labeled with tdTomato or green fluorescent protein. The distribution of interneurons in presubicular lamina for each animal line was compared to that in the GAD67-GFP knock-in animal line. Labelling was specific in the Pvalb-Cre line with 87% of labeled interneurons immunopositive for (PV. Immunostaining for somatostatin (SOM revealed good specificity in the X98 line with 89% of fluorescent cells, but a lesser specificity in Sst-Cre animals where only 71% of labeled cells were immunopositive. A minority of ~ 6% of interneurons co-expressed PV and SOM in the presubiculum of Sst-Cre animals. The electrophysiological and morphological properties of fluorescent interneurons from Pvalb-Cre, Sst-Cre and X98 mice differed. Distinct physiological groups of presubicular interneurons were resolved by unsupervised cluster analysis of parameters describing passive properties, firing patterns and AP shapes. One group consisted of SOM-positive, Martinotti type neurons with a low firing threshold (cluster 1. Fast spiking basket cells, mainly from the Pvalb-Cre line, formed a distinct group (cluster 3. Another group (cluster 2 contained interneurons of intermediate electrical properties and basket-cell like morphologies. These labeled neurons were recorded from both Sst-Cre and Pvalb-Cre animals. Thus, our results reveal a wide variation in anatomical and physiological properties for these interneurons, a real overlap of interneurons immuno-positive for both PV and SOM as well as an off-target recombination in the Sst-Cre line, possibly linked to maternal cre inheritance.

  19. Overlapping structures in sensory-motor mappings.

    Directory of Open Access Journals (Sweden)

    Kevin Earland

    Full Text Available This paper examines a biologically-inspired representation technique designed for the support of sensory-motor learning in developmental robotics. An interesting feature of the many topographic neural sheets in the brain is that closely packed receptive fields must overlap in order to fully cover a spatial region. This raises interesting scientific questions with engineering implications: e.g. is overlap detrimental? does it have any benefits? This paper examines the effects and properties of overlap between elements arranged in arrays or maps. In particular we investigate how overlap affects the representation and transmission of spatial location information on and between topographic maps. Through a series of experiments we determine the conditions under which overlap offers advantages and identify useful ranges of overlap for building mappings in cognitive robotic systems. Our motivation is to understand the phenomena of overlap in order to provide guidance for application in sensory-motor learning robots.

  20. An Exercise on Calibration: DRIFTS Study of Binary Mixtures of Calcite and Dolomite with Partially Overlapping Spectral Features

    Science.gov (United States)

    De Lorenzi Pezzolo, Alessandra

    2013-01-01

    Unlike most spectroscopic calibrations that are based on the study of well-separated features ascribable to the different components, this laboratory experience is especially designed to exploit spectral features that are nearly overlapping. The investigated system consists of a binary mixture of two commonly occurring minerals, calcite and…

  1. Microbial expression of proteins containing long repetitive Arg-Gly-Asp cell adhesive motifs created by overlap elongation PCR

    International Nuclear Information System (INIS)

    Kurihara, Hiroyuki; Shinkai, Masashige; Nagamune, Teruyuki

    2004-01-01

    We developed a novel method for creating repetitive DNA libraries using overlap elongation PCR, and prepared a DNA library encoding repetitive Arg-Gly-Asp (RGD) cell adhesive motifs. We obtained various length DNAs encoding repetitive RGD from a short monomer DNA (18 bp) after a thermal cyclic reaction without a DNA template for amplification, and isolated DNAs encoding 2, 21, and 43 repeats of the RGD motif. We cloned these DNAs into a protein expression vector and overexpressed them as thioredoxin fusion proteins: RGD2, RGD21, and RGD43, respectively. The solubility of RGD43 in water was low and it formed a fibrous precipitate in water. Scanning electron microscopy revealed that RGD43 formed a branched 3D-network structure in the solid state. To evaluate the function of the cell adhesive motifs in RGD43, mouse fibroblast cells were cultivated on the RGD43 scaffold. The fibroblast cells adhered to the RGD43 scaffold and extended long filopodia

  2. Inferring microRNA regulation of mRNA with partially ordered samples of paired expression data and exogenous prediction algorithms.

    Directory of Open Access Journals (Sweden)

    Brian Godsey

    Full Text Available MicroRNAs (miRs are known to play an important role in mRNA regulation, often by binding to complementary sequences in "target" mRNAs. Recently, several methods have been developed by which existing sequence-based target predictions can be combined with miR and mRNA expression data to infer true miR-mRNA targeting relationships. It has been shown that the combination of these two approaches gives more reliable results than either by itself. While a few such algorithms give excellent results, none fully addresses expression data sets with a natural ordering of the samples. If the samples in an experiment can be ordered or partially ordered by their expected similarity to one another, such as for time-series or studies of development processes, stages, or types, (e.g. cell type, disease, growth, aging, there are unique opportunities to infer miR-mRNA interactions that may be specific to the underlying processes, and existing methods do not exploit this. We propose an algorithm which specifically addresses [partially] ordered expression data and takes advantage of sample similarities based on the ordering structure. This is done within a Bayesian framework which specifies posterior distributions and therefore statistical significance for each model parameter and latent variable. We apply our model to a previously published expression data set of paired miR and mRNA arrays in five partially ordered conditions, with biological replicates, related to multiple myeloma, and we show how considering potential orderings can improve the inference of miR-mRNA interactions, as measured by existing knowledge about the involved transcripts.

  3. Consistency of the directionality of partially coherent beams in turbulence expressed in terms of the angular spread and the far-field average intensity

    International Nuclear Information System (INIS)

    Xiao-Wen, Chen; Xiao-Ling, Ji

    2010-01-01

    Under the quadratic approximation of the Rytov's phase structure function, this paper derives the general closed-form expressions for the mean-squared width and the angular spread of partially coherent beams in turbulence. It finds that under a certain condition different types of partially coherent beams may have the same directionality as a fully coherent Gaussian beam in free space and also in atmospheric turbulence if the angular spread is chosen as the characteristic parameter of beam directionality. On the other hand, it shows that generally, the directionality of partially coherent beams expressed in terms of the angular spread is not consistent with that in terms of the normalized far-field average intensity distribution in free space, but the consistency can be achieved due to turbulence. (classical areas of phenomenology)

  4. Partial Least Squares Based Gene Expression Analysis in EBV- Positive and EBV-Negative Posttransplant Lymphoproliferative Disorders.

    Science.gov (United States)

    Wu, Sa; Zhang, Xin; Li, Zhi-Ming; Shi, Yan-Xia; Huang, Jia-Jia; Xia, Yi; Yang, Hang; Jiang, Wen-Qi

    2013-01-01

    Post-transplant lymphoproliferative disorder (PTLD) is a common complication of therapeutic immunosuppression after organ transplantation. Gene expression profile facilitates the identification of biological difference between Epstein-Barr virus (EBV) positive and negative PTLDs. Previous studies mainly implemented variance/regression analysis without considering unaccounted array specific factors. The aim of this study is to investigate the gene expression difference between EBV positive and negative PTLDs through partial least squares (PLS) based analysis. With a microarray data set from the Gene Expression Omnibus database, we performed PLS based analysis. We acquired 1188 differentially expressed genes. Pathway and Gene Ontology enrichment analysis identified significantly over-representation of dysregulated genes in immune response and cancer related biological processes. Network analysis identified three hub genes with degrees higher than 15, including CREBBP, ATXN1, and PML. Proteins encoded by CREBBP and PML have been reported to be interact with EBV before. Our findings shed light on expression distinction of EBV positive and negative PTLDs with the hope to offer theoretical support for future therapeutic study.

  5. Influence of gap and overlap paradigms on saccade latencies and vergence eye movements in seven-year-old children.

    Science.gov (United States)

    Bucci, Maria Pia; Pouvreau, Nathalie; Yang, Qing; Kapoula, Zoï

    2005-07-01

    The latency of eye movements is influenced by the fixation task; when the fixation stimulus is switched off before the target presentation (gap paradigm) the latency becomes short and express movements occur. In contrast, when the fixation stimulus remains on when the target appears (overlap paradigm), eye movement latency is longer. Several previous studies have shown increased rates of express saccades in children; however the presence of an express type of latency for vergence and combined movements in children has never been explored. The present study examines the effects of the gap and the overlap paradigms on horizontal saccades at far (150 cm) and at close (20 cm) viewing distances, on vergence along the median plane, and on saccades combined with convergence or divergence in 15 normal seven-year-old children. The results show that the gap paradigm produced shorter latency for all eye movements than the overlap paradigm, but the difference was only significant for saccades at close viewing distances, for divergence (pure and combined), and for saccades combined with vergence. The gap paradigm produced significantly higher rates of express latencies for saccades at close viewing distances, for divergence, and for saccades combined with divergence; in contrast, the frequencies of express latencies for saccades at far viewing distances and for convergence (pure or combined) were similar in the gap and the overlap paradigms. Interestingly, the rate of anticipatory latencies (gap paradigm. Our collective findings suggest that the initiation of saccades at close viewing distances and of divergence is more reflexive, particularly in the gap paradigm. The finding of frequent anticipatory divergence that occurs at similar rates for seven-year-old children (this study) and for adults (Coubard et al., 2004, Exp Brain Res 154:368-381) indicates that predictive initiation of divergence is dominant.

  6. Oxygen partial pressure modulates 67-kDa laminin receptor expression, leading to altered activity of the green tea polyphenol, EGCG.

    Science.gov (United States)

    Tsukamoto, Shuntaro; Yamashita, Shuya; Kim, Yoon Hee; Kumazoe, Motofumi; Huang, Yuhui; Yamada, Koji; Tachibana, Hirofumi

    2012-09-21

    (-)-Epigallocatechin-3-O-gallate (EGCG) exhibits anti-tumor activity mediated via the 67-kDa laminin receptor (67LR). In this study, we found that 67LR protein levels are reduced by exposure to low O(2) levels (5%), without affecting the expression of HIF-1α. We also found that EGCG-induced anti-cancer activity is abrogated under low O(2) levels (5%) in various cancer cells. Notably, treatment with the proteasome inhibitor, prevented down-regulation of 67LR and restored sensitivity to EGCG under 5% O(2). In summary, 67LR expression is highly sensitive to O(2) partial pressure, and the activity of EGCG can be regulated in cancer cells by O(2) partial pressure. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  7. How long do satellites need to overlap? Evaluation of climate data stability from overlapping satellite records

    Science.gov (United States)

    Weatherhead, Elizabeth C.; Harder, Jerald; Araujo-Pradere, Eduardo A.; Bodeker, Greg; English, Jason M.; Flynn, Lawrence E.; Frith, Stacey M.; Lazo, Jeffrey K.; Pilewskie, Peter; Weber, Mark; Woods, Thomas N.

    2017-12-01

    Sensors on satellites provide unprecedented understanding of the Earth's climate system by measuring incoming solar radiation, as well as both passive and active observations of the entire Earth with outstanding spatial and temporal coverage. A common challenge with satellite observations is to quantify their ability to provide well-calibrated, long-term, stable records of the parameters they measure. Ground-based intercomparisons offer some insight, while reference observations and internal calibrations give further assistance for understanding long-term stability. A valuable tool for evaluating and developing long-term records from satellites is the examination of data from overlapping satellite missions. This paper addresses how the length of overlap affects the ability to identify an offset or a drift in the overlap of data between two sensors. Ozone and temperature data sets are used as examples showing that overlap data can differ by latitude and can change over time. New results are presented for the general case of sensor overlap by using Solar Radiation and Climate Experiment (SORCE) Spectral Irradiance Monitor (SIM) and Solar Stellar Irradiance Comparison Experiment (SOLSTICE) solar irradiance data as an example. To achieve a 1 % uncertainty in estimating the offset for these two instruments' measurement of the Mg II core (280 nm) requires approximately 5 months of overlap. For relative drift to be identified within 0.1 % yr-1 uncertainty (0.00008 W m-2 nm-1 yr-1), the overlap for these two satellites would need to be 2.5 years. Additional overlap of satellite measurements is needed if, as is the case for solar monitoring, unexpected jumps occur adding uncertainty to both offsets and drifts; the additional length of time needed to account for a single jump in the overlap data may be as large as 50 % of the original overlap period in order to achieve the same desired confidence in the stability of the merged data set. Results presented here are directly

  8. Expression analysis on 14-3-3 proteins in regenerative liver following partial hepatectomy

    Directory of Open Access Journals (Sweden)

    Deming Xue

    2017-11-01

    Full Text Available Abstract 14-3-3 proteins play a vital part in the regulation of cell cycle and apoptosis as signaling integration points. During liver regeneration, the quiescent hepatocytes go through hypertrophy and proliferation to restore liver weight. Therefore, we speculated that 14-3-3 proteins regulate the progression of liver regeneration. In this study, we analyzed the expression patterns of 14-3-3 proteins during liver regeneration of rat to provide an insight into the regenerative mechanism using western blotting. Only four isoforms (γ, ε, σ and τ/θ of the 14-3-3 proteins were expressed in regenerative liver after partial hepatectomy (PH. The dual effects, the significant down-regulation of 14-3-3ε and the significant up-regulation of 14-3-3τ/θ at 2 h after PH, might play particularly important roles in S-phase entry. The significant peaks of 14-3-3σ at 30 h and of ε and τ/θ at 24 h might be closely related not only to the G2/M transition but also to the size of hepatocytes. Possibly, the peak of 14-3-3ε expression seen at 168 h plays critical roles in the termination of liver regeneration by inhibiting cellular proliferation.

  9. Birth and death of gene overlaps in vertebrates

    Directory of Open Access Journals (Sweden)

    Makałowska Izabela

    2007-10-01

    Full Text Available Abstract Background Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several mechanisms have been proposed to explain gene overlap origination the evolutionary basis of these phenomenon are still not well understood. Here, we present results of the comparative analysis of several vertebrate genomes. The purpose of this study was to examine overlapping genes in the context of their evolution and mechanisms leading to their origin. Results Based on the presence and arrangement of human overlapping genes orthologs in rodent and fish genomes we developed 15 theoretical scenarios of overlapping genes evolution. Analysis of these theoretical scenarios and close examination of genomic sequences revealed new mechanisms leading to the overlaps evolution and confirmed that many of the vertebrate gene overlaps are not conserved. This study also demonstrates that repetitive elements contribute to the overlapping genes origination and, for the first time, that evolutionary events could lead to the loss of an ancient overlap. Conclusion Birth as well as most probably death of gene overlaps occurred over the entire time of vertebrate evolution and there wasn't any rapid origin or 'big bang' in the course of overlapping genes evolution. The major forces in the gene overlaps origination are transposition and exaptation. Our results also imply that origin of overlapping genes is not an issue of saving space and contracting genomes size.

  10. A 5' UTR-Overlapping LncRNA Activates the Male-Determining Gene doublesex1 in the Crustacean Daphnia magna.

    Science.gov (United States)

    Kato, Yasuhiko; Perez, Christelle Alexa G; Mohamad Ishak, Nur Syafiqah; Nong, Quang D; Sudo, Yuumi; Matsuura, Tomoaki; Wada, Tadashi; Watanabe, Hajime

    2018-06-04

    Long noncoding RNAs (lncRNAs) are pervasively transcribed in the eukaryotic genome [1] and are important for the control of master regulatory genes that are involved in cell differentiation and development [2, 3]. Here, we show that a 5' UTR-overlapping lncRNA regulates the male-specific expression of the DM-domain gene doublesex1 (dsx1) in the crustacean Daphnia magna, which produces males in response to environmental stimuli. This lncRNA, named doublesex1 alpha promoter-associated long RNA (DAPALR), is transcribed upstream the transcription start site (TSS) in a sense orientation and subjected to 5' end capping and 3' end processing at a stem-loop structure before the dsx1 coding exon. Similar to dsx1, its expression is only activated in males by the juvenile hormone (JH) and basic-leucine zipper (bZIP) transcription factor Vrille (Vri) and is maintained during embryogenesis. Knockdown of DAPALR in males silenced dsx1 and led to feminization, including egg production, whereas ectopic expression of DAPALR in dsx1-silenced females resulted in the de-repression of dsx1. We further demonstrate that the DAPALR transcript overlaps the dsx1 5'-UTR, and this overlapping region is required for dsx1 activation. Our results suggest that DAPALR can transactivate and possibly maintain dsx1 expression. This might be important for converting transient environmental signals into stable male development, controlled by the continuous expression of dsx1. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. A convergent overlapping domain decomposition method for total variation minimization

    KAUST Repository

    Fornasier, Massimo

    2010-06-22

    In this paper we are concerned with the analysis of convergent sequential and parallel overlapping domain decomposition methods for the minimization of functionals formed by a discrepancy term with respect to the data and a total variation constraint. To our knowledge, this is the first successful attempt of addressing such a strategy for the nonlinear, nonadditive, and nonsmooth problem of total variation minimization. We provide several numerical experiments, showing the successful application of the algorithm for the restoration of 1D signals and 2D images in interpolation/inpainting problems, respectively, and in a compressed sensing problem, for recovering piecewise constant medical-type images from partial Fourier ensembles. © 2010 Springer-Verlag.

  12. An extension to artifact-free projection overlaps

    International Nuclear Information System (INIS)

    Lin, Jianyu

    2015-01-01

    Purpose: In multipinhole single photon emission computed tomography, the overlapping of projections has been used to increase sensitivity. Avoiding artifacts in the reconstructed image associated with projection overlaps (multiplexing) is a critical issue. In our previous report, two types of artifact-free projection overlaps, i.e., projection overlaps that do not lead to artifacts in the reconstructed image, were formally defined and proved, and were validated via simulations. In this work, a new proposition is introduced to extend the previously defined type-II artifact-free projection overlaps so that a broader range of artifact-free overlaps is accommodated. One practical purpose of the new extension is to design a baffle window multipinhole system with artifact-free projection overlaps. Methods: First, the extended type-II artifact-free overlap was theoretically defined and proved. The new proposition accommodates the situation where the extended type-II artifact-free projection overlaps can be produced with incorrectly reconstructed portions in the reconstructed image. Next, to validate the theory, the extended-type-II artifact-free overlaps were employed in designing the multiplexing multipinhole spiral orbit imaging systems with a baffle window. Numerical validations were performed via simulations, where the corresponding 1-pinhole nonmultiplexing reconstruction results were used as the benchmark for artifact-free reconstructions. The mean square error (MSE) was the metric used for comparisons of noise-free reconstructed images. Noisy reconstructions were also performed as part of the validations. Results: Simulation results show that for noise-free reconstructions, the MSEs of the reconstructed images of the artifact-free multiplexing systems are very similar to those of the corresponding 1-pinhole systems. No artifacts were observed in the reconstructed images. Therefore, the testing results for artifact-free multiplexing systems designed using the

  13. Leveraging disjoint communities for detecting overlapping community structure

    International Nuclear Information System (INIS)

    Chakraborty, Tanmoy

    2015-01-01

    Network communities represent mesoscopic structure for understanding the organization of real-world networks, where nodes often belong to multiple communities and form overlapping community structure in the network. Due to non-triviality in finding the exact boundary of such overlapping communities, this problem has become challenging, and therefore huge effort has been devoted to detect overlapping communities from the network.In this paper, we present PVOC (Permanence based Vertex-replication algorithm for Overlapping Community detection), a two-stage framework to detect overlapping community structure. We build on a novel observation that non-overlapping community structure detected by a standard disjoint community detection algorithm from a network has high resemblance with its actual overlapping community structure, except the overlapping part. Based on this observation, we posit that there is perhaps no need of building yet another overlapping community finding algorithm; but one can efficiently manipulate the output of any existing disjoint community finding algorithm to obtain the required overlapping structure. We propose a new post-processing technique that by combining with any existing disjoint community detection algorithm, can suitably process each vertex using a new vertex-based metric, called permanence, and thereby finds out overlapping candidates with their community memberships. Experimental results on both synthetic and large real-world networks show that PVOC significantly outperforms six state-of-the-art overlapping community detection algorithms in terms of high similarity of the output with the ground-truth structure. Thus our framework not only finds meaningful overlapping communities from the network, but also allows us to put an end to the constant effort of building yet another overlapping community detection algorithm. (paper)

  14. NF-kappaB mediates FGF signal regulation of msx-1 expression.

    Science.gov (United States)

    Bushdid, P B; Chen, C L; Brantley, D M; Yull, F; Raghow, R; Kerr, L D; Barnett, J V

    2001-09-01

    The nuclear factor-kappaB (NF-kappaB) family of transcription factors is involved in proliferation, differentiation, and apoptosis in a stage- and cell-dependent manner. Recent evidence has shown that NF-kappaB activity is necessary for both chicken and mouse limb development. We report here that the NF-kappaB family member c-rel and the homeodomain gene msx-1 have partially overlapping expression patterns in the developing chick limb. In addition, inhibition of NF-kappaB activity resulted in a decrease in msx-1 mRNA expression. Sequence analysis of the msx-1 promoter revealed three potential kappaB-binding sites similar to the interferon-gamma (IFN-gamma) kappaB-binding site. These sites bound to c-Rel, as shown by electrophoretic mobility shift assay (EMSA). Furthermore, inhibition of NF-kappaB activity significantly reduced transactivation of the msx-1 promoter in response to FGF-2/-4, known stimulators of msx-1 expression. These results suggest that NF-kappaB mediates the FGF-2/-4 signal regulation of msx-1 gene expression. Copyright 2001 Academic Press.

  15. The role of self-math overlap in understanding math anxiety and the relation between math anxiety and performance.

    Science.gov (United States)

    Necka, Elizabeth A; Sokolowski, H Moriah; Lyons, Ian M

    2015-01-01

    Recent work has demonstrated that math anxiety is more than just the product of poor math skills. Psychosocial factors may play a key role in understanding what it means to be math anxious, and hence may aid in attempts to sever the link between math anxiety and poor math performance. One such factor may be the extent to which individuals integrate math into their sense of self. We adapted a well-established measure of this degree of integration (i.e., self-other overlap) to assess individuals' self-math overlap. This non-verbal single-item measure showed that identifying oneself with math (having higher self-math overlap) was strongly associated with lower math anxiety (r = -0.610). We also expected that having higher self-math overlap would leave one especially susceptible to the threat of poor math performance to the self. We identified two competing hypotheses regarding how this plays out in terms of math anxiety. Those higher in self-math overlap might be more likely to worry about poor math performance, exacerbating the negative relation between math anxiety and math ability. Alternatively, those higher in self-math overlap might exhibit self-serving biases regarding their math ability, which would instead predict a decoupling of the relation between their perceived and actual math ability, and in turn the relation between their math ability and math anxiety. Results clearly favored the latter hypothesis: those higher in self-math overlap exhibited almost no relation between math anxiety and math ability, whereas those lower in self-math overlap showed a strong negative relation between math anxiety and math ability. This was partially explained by greater self-serving biases among those higher in self-math overlap. In sum, these results reveal that the degree to which one integrates math into one's self - self-math overlap - may provide insight into how the pernicious negative relation between math anxiety and math ability may be ameliorated.

  16. The role of self-math overlap in understanding math anxiety and the relation between math anxiety and performance

    Science.gov (United States)

    Necka, Elizabeth A.; Sokolowski, H. Moriah; Lyons, Ian M.

    2015-01-01

    Recent work has demonstrated that math anxiety is more than just the product of poor math skills. Psychosocial factors may play a key role in understanding what it means to be math anxious, and hence may aid in attempts to sever the link between math anxiety and poor math performance. One such factor may be the extent to which individuals integrate math into their sense of self. We adapted a well-established measure of this degree of integration (i.e., self-other overlap) to assess individuals’ self-math overlap. This non-verbal single-item measure showed that identifying oneself with math (having higher self-math overlap) was strongly associated with lower math anxiety (r = -0.610). We also expected that having higher self-math overlap would leave one especially susceptible to the threat of poor math performance to the self. We identified two competing hypotheses regarding how this plays out in terms of math anxiety. Those higher in self-math overlap might be more likely to worry about poor math performance, exacerbating the negative relation between math anxiety and math ability. Alternatively, those higher in self-math overlap might exhibit self-serving biases regarding their math ability, which would instead predict a decoupling of the relation between their perceived and actual math ability, and in turn the relation between their math ability and math anxiety. Results clearly favored the latter hypothesis: those higher in self-math overlap exhibited almost no relation between math anxiety and math ability, whereas those lower in self-math overlap showed a strong negative relation between math anxiety and math ability. This was partially explained by greater self-serving biases among those higher in self-math overlap. In sum, these results reveal that the degree to which one integrates math into one’s self – self-math overlap – may provide insight into how the pernicious negative relation between math anxiety and math ability may be ameliorated. PMID

  17. The role of self-math overlap in understanding math anxiety and the relation between math anxiety and performance

    Directory of Open Access Journals (Sweden)

    Elizabeth A Necka

    2015-10-01

    Full Text Available Recent work has demonstrated that math anxiety is more than just the product of poor math skills. Psychosocial factors may play a key role in understanding what it means to be math anxious, and hence may aid in attempts to sever the link between math anxiety and poor math performance. One such factor may be the extent to which individuals integrate math into their sense of self. We adapted a well-established measure of this degree of integration (i.e., self-other overlap to assess individuals’ self-math overlap. This nonverbal single-item measure showed that identifying oneself with math (having higher self-math overlap was strongly associated with lower math anxiety (r=-.610. We also expected that having higher self-math overlap would leave one especially susceptible to the threat of poor math performance to the self. We identified two competing hypotheses regarding how this plays out in terms of math anxiety. Those higher in self-math overlap might be more likely to worry about poor math performance, exacerbating the negative relation between math anxiety and math ability. Alternatively, those higher in self-math overlap might exhibit self-serving biases regarding their math ability, which would instead predict a decoupling of the relation between their perceived and actual math ability, and in turn the relation between their math ability and math anxiety. Results clearly favored the latter hypothesis: those higher in self-math overlap exhibited almost no relation between math anxiety and math ability, whereas those lower in self-math overlap showed a strong negative relation between math anxiety and math ability. This was partially explained by greater self-serving biases among those higher in self-math overlap. In sum, these results reveal that the degree to which one integrates math into one’s self – self-math overlap – may provide insight into how the pernicious negative relation between math anxiety and math ability may be

  18. The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111.

    Directory of Open Access Journals (Sweden)

    Nadine Schmid

    Full Text Available Quorum sensing in Burkholderia cenocepacia H111 involves two signalling systems that depend on different signal molecules, namely N-acyl homoserine lactones (AHLs and the diffusible signal factor cis-2-dodecenoic acid (BDSF. Previous studies have shown that AHLs and BDSF control similar phenotypic traits, including biofilm formation, proteolytic activity and pathogenicity. In this study we mapped the BDSF stimulon by RNA-Seq and shotgun proteomics analysis. We demonstrate that a set of the identified BDSF-regulated genes or proteins are also controlled by AHLs, suggesting that the two regulons partially overlap. The detailed analysis of two mutually regulated operons, one encoding three lectins and the other one encoding the large surface protein BapA and its type I secretion machinery, revealed that both AHLs and BDSF are required for full expression, suggesting that the two signalling systems operate in parallel. In accordance with this, we show that both AHLs and BDSF are required for biofilm formation and protease production.

  19. A comparative analysis of biclustering algorithms for gene expression data

    Science.gov (United States)

    Eren, Kemal; Deveci, Mehmet; Küçüktunç, Onur; Çatalyürek, Ümit V.

    2013-01-01

    The need to analyze high-dimension biological data is driving the development of new data mining methods. Biclustering algorithms have been successfully applied to gene expression data to discover local patterns, in which a subset of genes exhibit similar expression levels over a subset of conditions. However, it is not clear which algorithms are best suited for this task. Many algorithms have been published in the past decade, most of which have been compared only to a small number of algorithms. Surveys and comparisons exist in the literature, but because of the large number and variety of biclustering algorithms, they are quickly outdated. In this article we partially address this problem of evaluating the strengths and weaknesses of existing biclustering methods. We used the BiBench package to compare 12 algorithms, many of which were recently published or have not been extensively studied. The algorithms were tested on a suite of synthetic data sets to measure their performance on data with varying conditions, such as different bicluster models, varying noise, varying numbers of biclusters and overlapping biclusters. The algorithms were also tested on eight large gene expression data sets obtained from the Gene Expression Omnibus. Gene Ontology enrichment analysis was performed on the resulting biclusters, and the best enrichment terms are reported. Our analyses show that the biclustering method and its parameters should be selected based on the desired model, whether that model allows overlapping biclusters, and its robustness to noise. In addition, we observe that the biclustering algorithms capable of finding more than one model are more successful at capturing biologically relevant clusters. PMID:22772837

  20. Optimization of control bank overlap for SMART

    International Nuclear Information System (INIS)

    Song, Jae Seung; Cho, Byung Oh; Zee, Sung Quun

    1998-07-01

    In the pressurized water reactor, control banks are operated by 40% effective core height overlap to avoid decrease of differential rod worth. This overlap does not effect on the core depletion history because the pressurized water reactor core operated at all rod out condition for the most of the operation time. For the boron free reactor SMART, however, one or more control banks are always inserted in the core to maintain critical condition, and the control bank overlap effects on the core depletion history. Since the cycle length of SMART is limited by three-dimensional core peaking factor at EOC, at which the control bank located at the core center is withdrawn, the cycle length of SMART is affected by the control bank overlap. In this report, the effect of control bank overlap on the core depletion history was evaluated. It is concluded that 60 cm control bank overlap corresponding to 30% effective core height was selected not to increase maximum peaking factor at EOC so that the control bank overlap does not affect the cycle length of the core. (author). 8 refs., 2 tabs., 19 figs

  1. Topological susceptibility from the overlap

    International Nuclear Information System (INIS)

    Del Debbio, Luigi; Pica, Claudio

    2004-01-01

    The chiral symmetry at finite lattice spacing of Ginsparg-Wilson fermionic actions constrains the renormalization of the lattice operators; in particular, the topological susceptibility does not require any renormalization, when using a fermionic estimator to define the topological charge. Therefore, the overlap formalism appears as an appealing candidate to study the continuum limit of the topological susceptibility while keeping the systematic errors under theoretical control. We present results for the SU(3) pure gauge theory using the index of the overlap Dirac operator to study the topology of the gauge configurations. The topological charge is obtained from the zero modes of the overlap and using a new algorithm for the spectral flow analysis. A detailed comparison with cooling techniques is presented. Particular care is taken in assessing the systematic errors. Relatively high statistics (500 to 1000 independent configurations) yield an extrapolated continuum limit with errors that are comparable with other methods. Our current value from the overlap is χ 1/4 = 188±12±5MeV (author)

  2. An Empirical Study of Overlapping Rotor Interference for a Small Unmanned Aircraft Propulsion System

    Directory of Open Access Journals (Sweden)

    Mantas Brazinskas

    2016-10-01

    Full Text Available The majority of research into full-sized helicopter overlapping propulsion systems involves co-axial setups (fully overlapped. Partially overlapping rotor setups (tandem, multirotor have received less attention, and empirical data produced over the years is limited. The increase in demand for compact small unmanned aircraft has exposed the need for empirical investigations of overlapping propulsion systems at a small scale (Reynolds Number < 250,000. Rotor-to-rotor interference at the static state in various overlapping propulsion system configurations was empirically measured using off the shelf T-Motor 16 inch × 5.4 inch rotors. A purpose-built test rig was manufactured allowing various overlapping rotor configurations to be tested. First, single rotor data was gathered, then performance measurements were taken at different thrust and tip speeds on a range of overlap configurations. The studies were conducted in a system torque balance mode. Overlapping rotor performance was compared to an isolated dual rotor propulsion system revealing interference factors which were compared to the momentum theory. Tests revealed that in the co-axial torque-balanced propulsion system the upper rotor outperforms the lower rotor at axial separation ratios between 0.05 and 0.85. Additionally, in the same region, thrust sharing between the two rotors changed by 21%; the upper rotor produced more thrust than the lower rotor at all times. Peak performance was recorded as a 22% efficiency loss when the axial separation ratio was greater than 0.25. The performance of a co-axial torque-balanced system reached a 27% efficiency loss when the axial separation ratio was equal to 0.05. The co-axial system swirl recovery effect was recorded to have a 4% efficiency gain in the axial separation ratio region between 0.05 and 0.85. The smallest efficiency loss (3% was recorded when the rotor separation ratio was between 0.95 and 1 (axial separation ratio was kept at 0

  3. Recursion relations for the overlap of a Morse continuum state with a Lanczos basis state

    International Nuclear Information System (INIS)

    Lutrus, C.K.; Suck Salk, S.H.

    1988-01-01

    In the resonant reactive scattering theory of Mundel, Berman, and Domcke [Phys. Rev. A 32, 181 (1985)], the overlap of a Morse continuum state and a Lanczos basis state appears in the expression of transition amplitude. In their study, recursion relations for Green's functions in the Lanczos basis were used for computational efficiency. In this paper we derive new recursion relations specifically for the evaluation of overlap between the Morse continuum wave and Lanczos basis state that appears in the transition amplitude of resonant scattering. They are found to be simple to use with great accuracy

  4. Phenotypic overlap between MMP-13 and the plasminogen activation system during wound healing in mice

    DEFF Research Database (Denmark)

    Juncker-Jensen, Anna; Lund, Leif R

    2011-01-01

    combined completely prevent wound healing. Both urokinase-type plasminogen activator and several matrix metallo proteinases (MMPs), such as MMP-3, -9 and -13, are expressed in the leading-edge keratinocytes of skin wounds, which may account for this phenotypic overlap between these classes of proteases....

  5. Exergy of partially coherent thermal radiation

    International Nuclear Information System (INIS)

    Wijewardane, S.; Goswami, Yogi

    2012-01-01

    Exergy of electromagnetic radiation has been studied by a number of researchers for well over four decades in order to estimate the maximum conversion efficiencies of thermal radiation. As these researchers primarily dealt with solar and blackbody radiation, which have a low degree of coherence, they did not consider the partial coherence properties of thermal radiation. With the recent development of surface structures, which can emit radiation with high degree of coherence, the importance of considering the partial coherent properties in exergy calculation has become a necessity as the coherence properties directly influence the entropy of the wave field. Here in this paper we derive an expression for the exergy of quasi-monochromatic radiation using statistical thermodynamics and show that it is identical with the expressions derived using classical thermodynamics. We also present a method to calculate the entropy, thereby the exergy of partially coherent radiation using statistical thermodynamics and a method called matrix treatment of wave field. -- Highlights: ► Considered partial coherence of radiation for the first time to calculate exergy. ► The importance of this method is emphasized with energy conversion examples. ► Derived an expression for the exergy of radiation using statistical thermodynamics. ► Adopted a method to calculate intensity of statistically independent principle wave.

  6. Symmetrized partial-wave method for density-functional cluster calculations

    International Nuclear Information System (INIS)

    Averill, F.W.; Painter, G.S.

    1994-01-01

    The computational advantage and accuracy of the Harris method is linked to the simplicity and adequacy of the reference-density model. In an earlier paper, we investigated one way the Harris functional could be extended to systems outside the limits of weakly interacting atoms by making the charge density of the interacting atoms self-consistent within the constraints of overlapping spherical atomic densities. In the present study, a method is presented for augmenting the interacting atom charge densities with symmetrized partial-wave expansions on each atomic site. The added variational freedom of the partial waves leads to a scheme capable of giving exact results within a given exchange-correlation approximation while maintaining many of the desirable convergence and stability properties of the original Harris method. Incorporation of the symmetry of the cluster in the partial-wave construction further reduces the level of computational effort. This partial-wave cluster method is illustrated by its application to the dimer C 2 , the hypothetical atomic cluster Fe 6 Al 8 , and the benzene molecule

  7. Influences of overlap index on Fourier ptychography imaging

    Science.gov (United States)

    Wang, Honghong; Rong, Lu; Wang, Dayong; Zhang, Xu; Zhai, Changchao; Panezai, Spozmai; Wang, Yunxin; Zhao, Jie

    2018-01-01

    Fourier ptychography is a new type of synthetic aperture imaging technique based on phase retrieval method which can improve microscopeic imaging performance beyond the diffraction limit of the employed optical components by illuminating the object with oblique waves of different incident angles where the field of view remains unchanged. illumination angle and the overlap rate of spectrum will have a certain impact on the quality of reconstruction. In this paper, we study the effects of illumination angle and spectral overlap rate on the image quality of Fourier ptychography. The simulation results show that increasing the illumination angle and spectral overlap can improve the resolution, but there is a threshold for the key parameters of spectral overlap rate. The convergence rate decreases when the overlap rate exceeds 70%, and the reconstruction process is more time-consuming due to the high overlap rate. However the results of proposed study shows that an overlap of 60% is the optimal choice to acquire a high-quality recovery with high speed.

  8. Impacts of cloud overlap assumptions on radiative budgets and heating fields in convective regions

    Science.gov (United States)

    Wang, XiaoCong; Liu, YiMin; Bao, Qing

    2016-01-01

    Impacts of cloud overlap assumptions on radiative budgets and heating fields are explored with the aid of a cloud-resolving model (CRM), which provided cloud geometry as well as cloud micro and macro properties. Large-scale forcing data to drive the CRM are from TRMM Kwajalein Experiment and the Global Atmospheric Research Program's Atlantic Tropical Experiment field campaigns during which abundant convective systems were observed. The investigated overlap assumptions include those that were traditional and widely used in the past and the one that was recently addressed by Hogan and Illingworth (2000), in which the vertically projected cloud fraction is expressed by a linear combination of maximum and random overlap, with the weighting coefficient depending on the so-called decorrelation length Lcf. Results show that both shortwave and longwave cloud radiative forcings (SWCF/LWCF) are significantly underestimated under maximum (MO) and maximum-random (MRO) overlap assumptions, whereas remarkably overestimated under the random overlap (RO) assumption in comparison with that using CRM inherent cloud geometry. These biases can reach as high as 100 Wm- 2 for SWCF and 60 Wm- 2 for LWCF. By its very nature, the general overlap (GenO) assumption exhibits an encouraging performance on both SWCF and LWCF simulations, with the biases almost reduced by 3-fold compared with traditional overlap assumptions. The superiority of GenO assumption is also manifested in the simulation of shortwave and longwave radiative heating fields, which are either significantly overestimated or underestimated under traditional overlap assumptions. The study also pointed out the deficiency of constant assumption on Lcf in GenO assumption. Further examinations indicate that the CRM diagnostic Lcf varies among different cloud types and tends to be stratified in the vertical. The new parameterization that takes into account variation of Lcf in the vertical well reproduces such a relationship and

  9. Neural overlap in processing music and speech

    Science.gov (United States)

    Peretz, Isabelle; Vuvan, Dominique; Lagrois, Marie-Élaine; Armony, Jorge L.

    2015-01-01

    Neural overlap in processing music and speech, as measured by the co-activation of brain regions in neuroimaging studies, may suggest that parts of the neural circuitries established for language may have been recycled during evolution for musicality, or vice versa that musicality served as a springboard for language emergence. Such a perspective has important implications for several topics of general interest besides evolutionary origins. For instance, neural overlap is an important premise for the possibility of music training to influence language acquisition and literacy. However, neural overlap in processing music and speech does not entail sharing neural circuitries. Neural separability between music and speech may occur in overlapping brain regions. In this paper, we review the evidence and outline the issues faced in interpreting such neural data, and argue that converging evidence from several methodologies is needed before neural overlap is taken as evidence of sharing. PMID:25646513

  10. Alteration of a recombinant protein N-glycan structure in silkworms by partial suppression of N-acetylglucosaminidase gene expression.

    Science.gov (United States)

    Kato, Tatsuya; Kikuta, Kotaro; Kanematsu, Ayumi; Kondo, Sachiko; Yagi, Hirokazu; Kato, Koichi; Park, Enoch Y

    2017-09-01

    To synthesize complex type N-glycans in silkworms, shRNAs against the fused lobe from Bombyx mori (BmFDL), which codes N-acetylglucosaminidase (GlcNAcase) in the Golgi, was expressed by recombinant B. mori nucleopolyhedrovirus (BmNPV) in silkworm larvae. Expression was under the control of the actin promoter of B. mori or the U6-2 and i.e.-2 promoters from Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV). The reduction of specific GlcNAcase activity was observed in Bm5 cells and silkworm larvae using the U6-2 promoter. In silkworm larvae, the partial suppression of BmFDL gene expression was observed. When shRNA against BmFDL was expressed under the control of U6-2 promoter, the Man 3 GlcNAc(Fuc)GlcNAc structure appeared in a main N-glycans of recombinant human IgG. These results suggested that the control of BmFDL expression by its shRNA in silkworms caused the modification of its N-glycan synthetic pathway, which may lead to the alteration of N-glycans in the expressed recombinant proteins. Suppression of BmFDL gene expression by shRNA is not sufficient to synthesize complex N-glycans in silkworm larvae but can modify the N-glycan synthetic pathway.

  11. Visual search for emotional expressions: Effect of stimulus set on anger and happiness superiority.

    Science.gov (United States)

    Savage, Ruth A; Becker, Stefanie I; Lipp, Ottmar V

    2016-01-01

    Prior reports of preferential detection of emotional expressions in visual search have yielded inconsistent results, even for face stimuli that avoid obvious expression-related perceptual confounds. The current study investigated inconsistent reports of anger and happiness superiority effects using face stimuli drawn from the same database. Experiment 1 excluded procedural differences as a potential factor, replicating a happiness superiority effect in a procedure that previously yielded an anger superiority effect. Experiments 2a and 2b confirmed that image colour or poser gender did not account for prior inconsistent findings. Experiments 3a and 3b identified stimulus set as the critical variable, revealing happiness or anger superiority effects for two partially overlapping sets of face stimuli. The current results highlight the critical role of stimulus selection for the observation of happiness or anger superiority effects in visual search even for face stimuli that avoid obvious expression related perceptual confounds and are drawn from a single database.

  12. Comparison of various HFB overlap formulae

    International Nuclear Information System (INIS)

    Oi, M.

    2015-01-01

    The nuclear many-body approach beyond the mean-field approximation demands overlap calculations of different many-body states. Norm overlaps between two different Hartree-Fock-Bogoliubov states can be calculated by means of the Onishi formula. However, the formula leaves the sign of the norm overlap undetermined. Several approaches have been proposed by Hara-Hayashi-Ring, Neergård-Wüst, and Robledo. In the present paper, the Neergård-Wüst formula is examined whether it is applicable to practical numerical calculations, although the formula was dismissed by many nuclear theoreticians so far for unknown reasons

  13. SAGE: String-overlap Assembly of GEnomes.

    Science.gov (United States)

    Ilie, Lucian; Haider, Bahlul; Molnar, Michael; Solis-Oba, Roberto

    2014-09-15

    De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in this area, better solutions are still very much needed. We present a new program, SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers. SAGE benefits from innovations in almost every aspect of the assembly process: error correction of input reads, string-overlap graph construction, read copy counts estimation, overlap graph analysis and reduction, contig extraction, and scaffolding. We hope that these new ideas will help advance the current state-of-the-art in an essential area of research in genomics.

  14. Neural overlap in processing music and speech.

    Science.gov (United States)

    Peretz, Isabelle; Vuvan, Dominique; Lagrois, Marie-Élaine; Armony, Jorge L

    2015-03-19

    Neural overlap in processing music and speech, as measured by the co-activation of brain regions in neuroimaging studies, may suggest that parts of the neural circuitries established for language may have been recycled during evolution for musicality, or vice versa that musicality served as a springboard for language emergence. Such a perspective has important implications for several topics of general interest besides evolutionary origins. For instance, neural overlap is an important premise for the possibility of music training to influence language acquisition and literacy. However, neural overlap in processing music and speech does not entail sharing neural circuitries. Neural separability between music and speech may occur in overlapping brain regions. In this paper, we review the evidence and outline the issues faced in interpreting such neural data, and argue that converging evidence from several methodologies is needed before neural overlap is taken as evidence of sharing. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  15. On the acoustics of overlapping laughter in conversational speech

    NARCIS (Netherlands)

    Truong, Khiet Phuong; Trouvain, Jürgen

    The social nature of laughter invites people to laugh together. This joint vocal action often results in overlapping laughter. In this paper, we show that the acoustics of overlapping laughs are different from non-overlapping laughs. We found that overlapping laughs are stronger prosodically marked

  16. Overlapping hotspots in CDRs are critical sites for V region diversification.

    Science.gov (United States)

    Wei, Lirong; Chahwan, Richard; Wang, Shanzhi; Wang, Xiaohua; Pham, Phuong T; Goodman, Myron F; Bergman, Aviv; Scharff, Matthew D; MacCarthy, Thomas

    2015-02-17

    Activation-induced deaminase (AID) mediates the somatic hypermutation (SHM) of Ig variable (V) regions that is required for the affinity maturation of the antibody response. An intensive analysis of a published database of somatic hypermutations that arose in the IGHV3-23*01 human V region expressed in vivo by human memory B cells revealed that the focus of mutations in complementary determining region (CDR)1 and CDR2 coincided with a combination of overlapping AGCT hotspots, the absence of AID cold spots, and an abundance of polymerase eta hotspots. If the overlapping hotspots in the CDR1 or CDR2 did not undergo mutation, the frequency of mutations throughout the V region was reduced. To model this result, we examined the mutation of the human IGHV3-23*01 biochemically and in the endogenous heavy chain locus of Ramos B cells. Deep sequencing revealed that IGHV3-23*01 in Ramos cells accumulates AID-induced mutations primarily in the AGCT in CDR2, which was also the most frequent site of mutation in vivo. Replacing the overlapping hotspots in CDR1 and CDR2 with neutral or cold motifs resulted in a reduction in mutations within the modified motifs and, to some degree, throughout the V region. In addition, some of the overlapping hotspots in the CDRs were at sites in which replacement mutations could change the structure of the CDR loops. Our analysis suggests that the local sequence environment of the V region, and especially of the CDR1 and CDR2, is highly evolved to recruit mutations to key residues in the CDRs of the IgV region.

  17. Cloning, expression and purification of recombinant streptokinase: partial characterization of the protein expressed in Escherichia coli

    Directory of Open Access Journals (Sweden)

    L. Avilán

    1997-12-01

    Full Text Available We cloned the streptokinase (STK gene of Streptococcus equisimilis in an expression vector of Escherichia coli to overexpress the profibrinolytic protein under the control of a tac promoter. Almost all the recombinant STK was exported to the periplasmic space and recovered after gentle lysozyme digestion of induced cells. The periplasmic fraction was chromatographed on DEAE Sepharose followed by chromatography on phenyl-agarose. Active proteins eluted between 4.5 and 0% ammonium sulfate, when a linear gradient was applied. Three major STK derivatives of 47.5 kDa, 45 kDa and 32 kDa were detected by Western blot analysis with a polyclonal antibody. The 32-kDa protein formed a complex with human plasminogen but did not exhibit Glu-plasminogen activator activity, as revealed by a zymographic assay, whereas the 45-kDa protein showed a Km = 0.70 µM and kcat = 0.82 s-1, when assayed with a chromogen-coupled substrate. These results suggest that these proteins are putative fragments of STK, possibly derived from partial degradation during the export pathway or the purification steps. The 47.5-kDa band corresponded to the native STK, as revealed by peptide sequencing

  18. Influence of slice overlap on positron emission tomography image quality

    International Nuclear Information System (INIS)

    McKeown, Clare; Gillen, Gerry; Dempsey, Mary Frances; Findlay, Caroline

    2016-01-01

    PET scans use overlapping acquisition beds to correct for reduced sensitivity at bed edges. The optimum overlap size for the General Electric (GE) Discovery 690 has not been established. This study assesses how image quality is affected by slice overlap. Efficacy of 23% overlaps (recommended by GE) and 49% overlaps (maximum possible overlap) were specifically assessed. European Association of Nuclear Medicine (EANM) guidelines for calculating minimum injected activities based on overlap size were also reviewed. A uniform flood phantom was used to assess noise (coefficient of variation, (COV)) and voxel accuracy (activity concentrations, Bq ml −1 ). A NEMA (National Electrical Manufacturers Association) body phantom with hot/cold spheres in a background activity was used to assess contrast recovery coefficients (CRCs) and signal to noise ratios (SNR). Different overlap sizes and sphere-to-background ratios were assessed. COVs for 49% and 23% overlaps were 9% and 13% respectively. This increased noise was difficult to visualise on the 23% overlap images. Mean voxel activity concentrations were not affected by overlap size. No clinically significant differences in CRCs were observed. However, visibility and SNR of small, low contrast spheres (⩽13 mm diameter, 2:1 sphere to background ratio) may be affected by overlap size in low count studies if they are located in the overlap area. There was minimal detectable influence on image quality in terms of noise, mean activity concentrations or mean CRCs when comparing 23% overlap with 49% overlap. Detectability of small, low contrast lesions may be affected in low count studies—however, this is a worst-case scenario. The marginal benefits of increasing overlap from 23% to 49% are likely to be offset by increased patient scan times. A 23% overlap is therefore appropriate for clinical use. An amendment to EANM guidelines for calculating injected activities is also proposed which better reflects the effect overlap size

  19. Link overlap, viability, and mutual percolation in multiplex networks

    International Nuclear Information System (INIS)

    Min, Byungjoon; Lee, Sangchul; Lee, Kyu-Min; Goh, K.-I.

    2015-01-01

    Many real-world complex systems are best modeled by multiplex networks. The multiplexity has proved to have broad impact on the system’s structure and function. Most theoretical studies on multiplex networks to date, however, have largely ignored the effect of the link overlap across layers despite strong empirical evidences for its significance. In this article, we investigate the effect of the link overlap in the viability of multiplex networks, both analytically and numerically. After a short recap of the original multiplex viability study, the distinctive role of overlapping links in viability and mutual connectivity is emphasized and exploited for setting up a proper analytic framework. A rich phase diagram for viability is obtained and greatly diversified patterns of hysteretic behavior in viability are observed in the presence of link overlap. Mutual percolation with link overlap is revisited as a limit of multiplex viability problem, and the controversy between existing results is clarified. The distinctive role of overlapping links is further demonstrated by the different responses of networks under random removals of overlapping and non-overlapping links, respectively, as well as under several link-removal strategies. Our results show that the link overlap facilitates the viability and mutual percolation; at the same time, the presence of link overlap poses a challenge in analytical approaches to the problem

  20. Iterative Overlap FDE for Multicode DS-CDMA

    Science.gov (United States)

    Takeda, Kazuaki; Tomeba, Hiromichi; Adachi, Fumiyuki

    Recently, a new frequency-domain equalization (FDE) technique, called overlap FDE, that requires no GI insertion was proposed. However, the residual inter/intra-block interference (IBI) cannot completely be removed. In addition to this, for multicode direct sequence code division multiple access (DS-CDMA), the presence of residual interchip interference (ICI) after FDE distorts orthogonality among the spreading codes. In this paper, we propose an iterative overlap FDE for multicode DS-CDMA to suppress both the residual IBI and the residual ICI. In the iterative overlap FDE, joint minimum mean square error (MMSE)-FDE and ICI cancellation is repeated a sufficient number of times. The bit error rate (BER) performance with the iterative overlap FDE is evaluated by computer simulation.

  1. FLIC-overlap fermions and topology

    International Nuclear Information System (INIS)

    Kamleh, W.; Kusterer, D.J.; Leinweber, D.B.; Williams, A.G.

    2003-01-01

    APE smearing the links in the irrelevant operators of clover fermions (Fat-Link Irrelevant Clover (FLIC) fermions) provides significant improvement in the condition number of the Hermitian-Dirac operator and gives rise to a factor of two savings in computing the overlap operator. This report investigates the effects of using a highly-improved definition of the lattice field-strength tensor F μν in the fermion action, made possible through the use of APE-smeared fat links in the construction of the irrelevant operators. Spurious double-zero crossings in the spectral flow of the Hermitian-Wilson Dirac operator associated with lattice artifacts at the scale of the lattice spacing are removed with FLIC fermions composed with an O(α 4 )-improved lattice field strength tensor. Hence, FLIC-Overlap fermions provide an additional benefit to the overlap formalism: a correct realization of topology in the fermion sector on the lattice

  2. Piles, tabs and overlaps in navigation among documents

    DEFF Research Database (Denmark)

    Jakobsen, Mikkel Rønne; Hornbæk, Kasper

    2010-01-01

    Navigation among documents is a frequent, but ill supported activity. Overlapping or tabbed documents are widespread, but they offer limited visibility of their content. We explore variations on navigation support: arranging documents with tabs, as overlapping windows, and in piles. In an experim......Navigation among documents is a frequent, but ill supported activity. Overlapping or tabbed documents are widespread, but they offer limited visibility of their content. We explore variations on navigation support: arranging documents with tabs, as overlapping windows, and in piles....... In an experiment we compared 11 participants’ navigation with these variations and found strong task effects. Overall, overlapping windows were preferred and their structured layout worked well with some tasks. Surprisingly, tabbed documents were efficient in tasks requiring simply finding a document. Piled...... on document navigation and its support by piling....

  3. TRPA1 expression levels and excitability brake by KV channels influence cold sensitivity of TRPA1-expressing neurons.

    Science.gov (United States)

    Memon, Tosifa; Chase, Kevin; Leavitt, Lee S; Olivera, Baldomero M; Teichert, Russell W

    2017-06-14

    The molecular sensor of innocuous (painless) cold sensation is well-established to be transient receptor potential cation channel, subfamily M, member 8 (TRPM8). However, the role of transient receptor potential cation channel, subfamily A, member 1 (TRPA1) in noxious (painful) cold sensation has been controversial. We find that TRPA1 channels contribute to the noxious cold sensitivity of mouse somatosensory neurons, independent of TRPM8 channels, and that TRPA1-expressing neurons are largely non-overlapping with TRPM8-expressing neurons in mouse dorsal-root ganglia (DRG). However, relatively few TRPA1-expressing neurons (e.g., responsive to allyl isothiocyanate or AITC, a selective TRPA1 agonist) respond overtly to cold temperature in vitro, unlike TRPM8-expressing neurons, which almost all respond to cold. Using somatosensory neurons from TRPM8-/- mice and subtype-selective blockers of TRPM8 and TRPA1 channels, we demonstrate that responses to cold temperatures from TRPA1-expressing neurons are mediated by TRPA1 channels. We also identify two factors that affect the cold-sensitivity of TRPA1-expressing neurons: (1) cold-sensitive AITC-sensitive neurons express relatively more TRPA1 transcripts than cold-insensitive AITC-sensitive neurons and (2) voltage-gated potassium (K V ) channels attenuate the cold-sensitivity of some TRPA1-expressing neurons. The combination of these two factors, combined with the relatively weak agonist-like activity of cold temperature on TRPA1 channels, partially explains why few TRPA1-expressing neurons respond to cold. Blocking K V channels also reveals another subclass of noxious cold-sensitive DRG neurons that do not express TRPM8 or TRPA1 channels. Altogether, the results of this study provide novel insights into the cold-sensitivity of different subclasses of somatosensory neurons. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

  4. Topological susceptibility from the overlap

    DEFF Research Database (Denmark)

    Del Debbio, Luigi; Pica, Claudio

    2003-01-01

    The chiral symmetry at finite lattice spacing of Ginsparg-Wilson fermionic actions constrains the renormalization of the lattice operators; in particular, the topological susceptibility does not require any renormalization, when using a fermionic estimator to define the topological charge....... Therefore, the overlap formalism appears as an appealing candidate to study the continuum limit of the topological susceptibility while keeping the systematic errors under theoretical control. We present results for the SU(3) pure gauge theory using the index of the overlap Dirac operator to study...

  5. A computational formalization for partial evaluation

    DEFF Research Database (Denmark)

    Hatcliff, John; Danvy, Olivier

    1996-01-01

    We formalize a partial evaluator for Eugenio Moggi's computational metalanguage. This formalization gives an evaluation-order independent view of binding-time analysis and program specialization, including a proper treatment of call unfolding. It also enables us to express the essence of `control......-based binding-time improvements' for let expressions. Specically, we prove that the binding-time improvements given by `continuation-based specialization' can be expressed in the metalanguage via monadic laws....

  6. Memoization in Type-Directed Partial Evaluation

    DEFF Research Database (Denmark)

    Balat, Vincent; Danvy, Olivier

    2002-01-01

    We use a code generator—type-directed partial evaluation— to verify conversions between isomorphic types, or more precisely to verify that a composite function is the identity function at some complicated type. A typed functional language such as ML provides a natural support to express the funct......We use a code generator—type-directed partial evaluation— to verify conversions between isomorphic types, or more precisely to verify that a composite function is the identity function at some complicated type. A typed functional language such as ML provides a natural support to express...... originate in the handling of sums, which uses delimited continuations. We successfully eliminate these redundancies by extending type-directed partial evaluation with memoization capabilities. The result only works for pure functional programs, but it provides an unexpected use of code generation...... and it yields orders-of-magnitude improvements both in time and in space for type isomorphisms. Basic Research in Computer Science (www. brics. dk), funded by the Danish National Research Foundation....

  7. Finding overlapping communities in multilayer networks.

    Science.gov (United States)

    Liu, Weiyi; Suzumura, Toyotaro; Ji, Hongyu; Hu, Guangmin

    2018-01-01

    Finding communities in multilayer networks is a vital step in understanding the structure and dynamics of these layers, where each layer represents a particular type of relationship between nodes in the natural world. However, most community discovery methods for multilayer networks may ignore the interplay between layers or the unique topological structure in a layer. Moreover, most of them can only detect non-overlapping communities. In this paper, we propose a new community discovery method for multilayer networks, which leverages the interplay between layers and the unique topology in a layer to reveal overlapping communities. Through a comprehensive analysis of edge behaviors within and across layers, we first calculate the similarities for edges from the same layer and the cross layers. Then, by leveraging these similarities, we can construct a dendrogram for the multilayer networks that takes both the unique topological structure and the important interplay into consideration. Finally, by introducing a new community density metric for multilayer networks, we can cut the dendrogram to get the overlapping communities for these layers. By applying our method on both synthetic and real-world datasets, we demonstrate that our method has an accurate performance in discovering overlapping communities in multilayer networks.

  8. Novel absorptivity centering method utilizing normalized and factorized spectra for analysis of mixtures with overlapping spectra in different matrices using built-in spectrophotometer software.

    Science.gov (United States)

    Lotfy, Hayam Mahmoud; Omran, Yasmin Rostom

    2018-07-05

    A novel, simple, rapid, accurate, and economical spectrophotometric method, namely absorptivity centering (a-Centering) has been developed and validated for the simultaneous determination of mixtures with partially and completely overlapping spectra in different matrices using either normalized or factorized spectrum using built-in spectrophotometer software without a need of special purchased program. Mixture I (Mix I) composed of Simvastatin (SM) and Ezetimibe (EZ) is the one with partial overlapping spectra formulated as tablets, while mixture II (Mix II) formed by Chloramphenicol (CPL) and Prednisolone acetate (PA) is that with complete overlapping spectra formulated as eye drops. These procedures do not require any separation steps. Resolution of spectrally overlapping binary mixtures has been achieved getting recovered zero-order (D 0 ) spectrum of each drug, then absorbance was recorded at their maxima 238, 233.5, 273 and 242.5 nm for SM, EZ, CPL and PA, respectively. Calibration graphs were established with good correlation coefficients. The method shows significant advantages as simplicity, minimal data manipulation besides maximum reproducibility and robustness. Moreover, it was validated according to ICH guidelines. Selectivity was tested using laboratory-prepared mixtures. Accuracy, precision and repeatability were found to be within the acceptable limits. The proposed method is good enough to be applied to an assay of drugs in their combined formulations without any interference from excipients. The obtained results were statistically compared with those of the reported and official methods by applying t-test and F-test at 95% confidence level concluding that there is no significant difference with regard to accuracy and precision. Generally, this method could be used successfully for the routine quality control testing. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Serial or overlapping processing in multitasking as individual preference: Effects of stimulus preview on task switching and concurrent dual-task performance.

    Science.gov (United States)

    Reissland, Jessika; Manzey, Dietrich

    2016-07-01

    Understanding the mechanisms and performance consequences of multitasking has long been in focus of scientific interest, but has been investigated by three research lines more or less isolated from each other. Studies in the fields of the psychological refractory period, task switching, and interruptions have scored with a high experimental control, but usually do not give participants many degrees of freedom to self-organize the processing of two concurrent tasks. Individual strategies as well as their impact on efficiency have mainly been neglected. Self-organized multitasking has been investigated in the field of human factors, but primarily with respect to overall performance without detailed investigation of how the tasks are processed. The current work attempts to link aspects of these research lines. All of them, explicitly or implicitly, provide hints about an individually preferred type of task organization, either more cautious trying to work strictly serially on only one task at a time or more daring with a focus on task interleaving and, if possible, also partially overlapping (parallel) processing. In two experiments we investigated different strategies of task organization and their impact on efficiency using a new measure of overall multitasking efficiency. Experiment 1 was based on a classical task switching paradigm with two classification tasks, but provided one group of participants with a stimulus preview of the task to switch to next, enabling at least partial overlapping processing. Indeed, this preview led to a reduction of switch costs and to an increase of dual-task efficiency, but only for a subgroup of participants. They obviously exploited the possibility of overlapping processing, while the others worked mainly serially. While task-sequence was externally guided in the first experiment, Experiment 2 extended the approach by giving the participants full freedom of task organization in concurrent performance of the same tasks. Fine

  10. Interleaved neuromuscular electrical stimulation: Motor unit recruitment overlap.

    Science.gov (United States)

    Wiest, Matheus J; Bergquist, Austin J; Schimidt, Helen L; Jones, Kelvin E; Collins, David F

    2017-04-01

    In this study, we quantified the "overlap" between motor units recruited by single pulses of neuromuscular electrical stimulation (NMES) delivered over the tibialis anterior muscle (mNMES) and the common peroneal nerve (nNMES). We then quantified the torque produced when pulses were alternated between the mNMES and nNMES sites at 40 Hz ("interleaved" NMES; iNMES). Overlap was assessed by comparing torque produced by twitches evoked by mNMES, nNMES, and both delivered together, over a range of stimulus intensities. Trains of iNMES were delivered at the intensity that produced the lowest overlap. Overlap was lowest (5%) when twitches evoked by both mNMES and nNMES produced 10% peak twitch torque. iNMES delivered at this intensity generated 25% of maximal voluntary dorsiflexion torque (11 Nm). Low intensity iNMES leads to low overlap and produces torque that is functionally relevant to evoke dorsiflexion during walking. Muscle Nerve 55: 490-499, 2017. © 2016 Wiley Periodicals, Inc.

  11. Overlap valence quarks on a twisted mass sea. A case study for mixed action lattice QCD

    International Nuclear Information System (INIS)

    Cichy, Krzysztof; Herdoiza, Gregorio; UAM/CSIC Univ. Autonoma de Madrid

    2012-11-01

    We discuss a Lattice QCD mixed action investigation employing Wilson maximally twisted mass sea and overlap valence fermions. Using four values of the lattice spacing, we demonstrate that the overlap Dirac operator assumes a point-like locality in the continuum limit. We also show that by adopting suitable matching conditions for the sea and valence theories a consistent continuum limit for the pion decay constant and light baryon masses can be obtained. Finally, we confront results for sea-valence mixed meson masses and the valence scalar correlator with corresponding expressions of chiral perturbation theory. This allows us to extract low energy constants of mixed action chiral perturbation which characterize the strength of unitarity violations in our mixed action setup.

  12. Overlap valence quarks on a twisted mass sea. A case study for mixed action lattice QCD

    Energy Technology Data Exchange (ETDEWEB)

    Cichy, Krzysztof [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Poznan Univ. (Poland). Faculty of Physics; Drach, Vincent; Jansen, Karl [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Garcia-Ramos, Elena [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Humboldt-Universitaet, Berlin (Germany); Herdoiza, Gregorio [UAM/CSIC Univ. Autonoma de Madrid (Spain). Dept. de Fisica Teorica; UAM/CSIC Univ. Autonoma de Madrid (Spain). Inst. de Fisica Teorica; Collaboration: European Twisted Mass Collaboration

    2012-11-15

    We discuss a Lattice QCD mixed action investigation employing Wilson maximally twisted mass sea and overlap valence fermions. Using four values of the lattice spacing, we demonstrate that the overlap Dirac operator assumes a point-like locality in the continuum limit. We also show that by adopting suitable matching conditions for the sea and valence theories a consistent continuum limit for the pion decay constant and light baryon masses can be obtained. Finally, we confront results for sea-valence mixed meson masses and the valence scalar correlator with corresponding expressions of chiral perturbation theory. This allows us to extract low energy constants of mixed action chiral perturbation which characterize the strength of unitarity violations in our mixed action setup.

  13. Partial IGF-1 deficiency is sufficient to reduce heart contractibility, angiotensin II sensibility, and alter gene expression of structural and functional cardiac proteins.

    Science.gov (United States)

    González-Guerra, José Luis; Castilla-Cortazar, Inma; Aguirre, Gabriel A; Muñoz, Úrsula; Martín-Estal, Irene; Ávila-Gallego, Elena; Granado, Miriam; Puche, Juan E; García-Villalón, Ángel Luis

    2017-01-01

    Circulating levels of IGF-1 may decrease under several circumstances like ageing, metabolic syndrome, and advanced cirrhosis. This reduction is associated with insulin resistance, dyslipidemia, progression to type 2 diabetes, and increased risk for cardiovascular diseases. However, underlying mechanisms between IGF-1 deficiency and cardiovascular disease remain elusive. The specific aim of the present work was to study whether the partial IGF-1 deficiency influences heart and/or coronary circulation, comparing vasoactive factors before and after of ischemia-reperfusion (I/R). In addition, histology of the heart was performed together with cardiac gene expression for proteins involved in structure and function (extracellular matrix, contractile proteins, active peptides); carried out using microarrays, followed by RT-qPCR confirmation of the three experimental groups. IGF-1 partial deficiency is associated to a reduction in contractility and angiotensin II sensitivity, interstitial fibrosis as well as altered expression pattern of genes involved in extracellular matrix proteins, calcium dynamics, and cardiac structure and function. Although this work is descriptive, it provides a clear insight of the impact that partial IGF-1 deficiency on the heart and establishes this experimental model as suitable for studying cardiac disease mechanisms and exploring therapeutic options for patients under IGF-1 deficiency conditions.

  14. Partial IGF-1 deficiency is sufficient to reduce heart contractibility, angiotensin II sensibility, and alter gene expression of structural and functional cardiac proteins.

    Directory of Open Access Journals (Sweden)

    José Luis González-Guerra

    Full Text Available Circulating levels of IGF-1 may decrease under several circumstances like ageing, metabolic syndrome, and advanced cirrhosis. This reduction is associated with insulin resistance, dyslipidemia, progression to type 2 diabetes, and increased risk for cardiovascular diseases. However, underlying mechanisms between IGF-1 deficiency and cardiovascular disease remain elusive. The specific aim of the present work was to study whether the partial IGF-1 deficiency influences heart and/or coronary circulation, comparing vasoactive factors before and after of ischemia-reperfusion (I/R. In addition, histology of the heart was performed together with cardiac gene expression for proteins involved in structure and function (extracellular matrix, contractile proteins, active peptides; carried out using microarrays, followed by RT-qPCR confirmation of the three experimental groups. IGF-1 partial deficiency is associated to a reduction in contractility and angiotensin II sensitivity, interstitial fibrosis as well as altered expression pattern of genes involved in extracellular matrix proteins, calcium dynamics, and cardiac structure and function. Although this work is descriptive, it provides a clear insight of the impact that partial IGF-1 deficiency on the heart and establishes this experimental model as suitable for studying cardiac disease mechanisms and exploring therapeutic options for patients under IGF-1 deficiency conditions.

  15. Transiting topological sectors with the overlap

    International Nuclear Information System (INIS)

    Creutz, Michael

    2003-01-01

    The overlap operator provides an elegant definition for the winding number of lattice gauge field configurations. Only for a set of configurations of measure zero is this procedure undefined. Without restrictions on the lattice fields, however, the space of gauge fields is simply connected. I present a simple low dimensional illustration of how the eigenvalues of a truncated overlap operator flow as one travels between different topological sectors

  16. Brucella melitensis and Mycobacterium tuberculosis depict overlapping gene expression patterns induced in infected THP-1 macrophages.

    Science.gov (United States)

    Masoudian, M; Derakhshandeh, A; Ghahramani Seno, M M

    2015-01-01

    Pathogens infecting mammalian cells have developed various strategies to suppress and evade their hosts' defensive mechanisms. In this line, the intracellular bacteria that are able to survive and propagate within their host cells must have developed strategies to avert their host's killing attitude. Studying the interface of host-pathogen confrontation can provide valuable information for defining therapeutic approaches. Brucellosis, caused by the Brucella strains, is a zoonotic bacterial disease that affects thousands of humans and animals around the world inflicting discomfort and huge economic losses. Similar to many other intracellular dwelling bacteria, infections caused by Brucella are difficult to treat, and hence any attempt at identifying new and common therapeutic targets would prove beneficial for the purpose of curing infections caused by the intracellular bacteria. In THP-1 macrophage infected with Brucella melitensis we studied the expression levels of four host's genes, i.e. EMP2, ST8SIA4, HCP5 and FRMD5 known to be involved in pathogenesis of Mycobacterium tuberculosis. Our data showed that at this molecular level, except for FRMD5 that was downregulated, the other three genes were upregulated by B. melitensis. Brucella melitensis and M. tuberculosis go through similar intracellular processes and interestingly two of the investigated genes, i.e. EMP2 and ST4SIA8 were upregulated in THP-1 cell infected with B. melitensis similar to that reported for THP-1 cells infected with M. tuberculosis. At the host-pathogen interaction interface, this study depicts overlapping changes for different bacteria with common survival strategies; a fact that implies designing therapeutic approaches based on common targets may be possible.

  17. Design optimization of continuous partially prestressed concrete beams

    Science.gov (United States)

    Al-Gahtani, A. S.; Al-Saadoun, S. S.; Abul-Feilat, E. A.

    1995-04-01

    An effective formulation for optimum design of two-span continuous partially prestressed concrete beams is described in this paper. Variable prestressing forces along the tendon profile, which may be jacked from one end or both ends with flexibility in the overlapping range and location, and the induced secondary effects are considered. The imposed constraints are on flexural stresses, ultimate flexural strength, cracking moment, ultimate shear strength, reinforcement limits cross-section dimensions, and cable profile geometries. These constraints are formulated in accordance with ACI (American Concrete Institute) code provisions. The capabilities of the program to solve several engineering problems are presented.

  18. Electron thermal confinement in a partially stochastic magnetic structure

    Science.gov (United States)

    Morton, L. A.; Young, W. C.; Hegna, C. C.; Parke, E.; Reusch, J. A.; Den Hartog, D. J.

    2018-04-01

    Using a high-repetition-rate Thomson scattering diagnostic, we observe a peak in electron temperature Te coinciding with the location of a large magnetic island in the Madison Symmetric Torus. Magnetohydrodynamic modeling of this quasi-single helicity plasma indicates that smaller adjacent islands overlap with and destroy the large island flux surfaces. The estimated stochastic electron thermal conductivity ( ≈30 m 2/s ) is consistent with the conductivity inferred from the observed Te gradient and ohmic heating power. Island-shaped Te peaks can result from partially stochastic magnetic islands.

  19. Numerical properties of staggered overlap fermions

    CERN Document Server

    de Forcrand, Philippe; Panero, Marco

    2010-01-01

    We report the results of a numerical study of staggered overlap fermions, following the construction of Adams which reduces the number of tastes from 4 to 2 without fine-tuning. We study the sensitivity of the operator to the topology of the gauge field, its locality and its robustness to fluctuations of the gauge field. We make a first estimate of the computing cost of a quark propagator calculation, and compare with Neuberger's overlap.

  20. Mirroring Facial Expressions and Emotions in Dyadic Conversations

    DEFF Research Database (Denmark)

    Navarretta, Costanza

    2016-01-01

    This paper presents an investigation of mirroring facial expressions and the emotions which they convey in dyadic naturally occurring first encounters. Mirroring facial expressions are a common phenomenon in face-to-face interactions, and they are due to the mirror neuron system which has been...... and overlapping facial expressions are very frequent. In this study, we want to determine whether the overlapping facial expressions are mirrored or are otherwise correlated in the encounters, and to what extent mirroring facial expressions convey the same emotion. The results of our study show that the majority...... of smiles and laughs, and one fifth of the occurrences of raised eyebrows are mirrored in the data. Moreover some facial traits in co-occurring expressions co-occur more often than it would be expected by chance. Finally, amusement, and to a lesser extent friendliness, are often emotions shared by both...

  1. Overexpression, purification, and partial characterization of ADP-ribosyltransferases modA and modB of bacteriophage T4.

    Science.gov (United States)

    Tiemann, B; Depping, R; Rüger, W

    1999-01-01

    There is increasing experimental evidence that ADP-ribosylation of host proteins is an important means to regulate gene expression of bacteriophage T4. Surprisingly, this phage codes for three different ADP-ribosyltransferases, gene products Alt, ModA, and ModB, modifying partially overlapping sets of host proteins. While gene product Alt already has been isolated as a recombinant protein and its action on host RNA polymerases and transcription regulation have been studied, the nucleotide sequences of the two mod genes was published only recently. Their mode of action in the course of the infection cycle and the consequences of the ADP-ribosylations catalyzed by these enzymes remain to be investigated. Here we describe the cloning of the genes, the overexpression, purification, and partial characterization of ADP-ribosyltransferases ModA and ModB. Both proteins seem to act independently, and the ADP-ribosyl moieties are transferred to different sets of host proteins. While gene product ModA, similarly to the Alt protein, acts also on the alpha-subunit of host RNA polymerase, the ModB activity serves another set of proteins, one of which was identified as the S1 protein associated with the 30S subunit of the E. coli ribosomes.

  2. Phenotypic expression of partial AZFc deletions is independent of the variations in DAZL and BOULE in a Han population.

    Science.gov (United States)

    Chen, Pu; Ma, Mingyi; Li, Lei; Zhang, Sizhong; Su, Dan; Ma, Yongxin; Liu, Yunqiang; Tao, Dachang; Lin, Li; Yang, Yuan

    2010-01-01

    DAZ on the Y chromosome and 2 autosomal ancestral genes DAZL and BOULE are suggested to represent functional conservation in spermatogenesis. The partial AZFc deletion, a common mutation of the Y chromosome, always involves 2 DAZ copies and represents a different spermatogenic phenotype in the populations studied. To investigate whether the variations in DAZL and BOULE influence partial AZFc deletion phenotype, the genotyping of 15 loci variations, including 4 known mutations and 11 single-nucleotide polymorphisms (SNPs), was carried out in 157 azoo-/oligzoospermic men and 57 normozoospermic men, both groups with partial AZFc deletions. The frequencies of the alleles, genotypes, and haplotypes of the variations were compared between the 2 groups. As a result, for 9 exonic variations in DAZL and BOULE, only T12A was observed in both groups with similar frequency, and I71V was identified in an azoospermic man with b2/b3 deletion, whereas the rest were absent in the population. The distribution of DAZL haplotypes from 4 variations, including T12A, and of BOULE haplotypes from 2 SNPs was similar between men with normozoospermia and spermatogenic failure. Our findings indicate that the contribution of DAZL and BOULE variations to spermatogenic impairment in men with the DAZ defect is greatly limited, suggesting that expression of spermatogenic phenotypes of partial AZFc deletions is independent of the variations in DAZL and BOULE in the Han population.

  3. Holographic measurement of distortion during laser melting: Additive distortion from overlapping pulses

    Science.gov (United States)

    Haglund, Peter; Frostevarg, Jan; Powell, John; Eriksson, Ingemar; Kaplan, Alexander F. H.

    2018-03-01

    Laser - material interactions such as welding, heat treatment and thermal bending generate thermal gradients which give rise to thermal stresses and strains which often result in a permanent distortion of the heated object. This paper investigates the thermal distortion response which results from pulsed laser surface melting of a stainless steel sheet. Pulsed holography has been used to accurately monitor, in real time, the out-of-plane distortion of stainless steel samples melted on one face by with both single and multiple laser pulses. It has been shown that surface melting by additional laser pulses increases the out of plane distortion of the sample without significantly increasing the melt depth. The distortion differences between the primary pulse and subsequent pulses has also been analysed for fully and partially overlapping laser pulses.

  4. Overlapping Requirements for Tet2 and Tet3 in Normal Development and Hematopoietic Stem Cell Emergence

    Directory of Open Access Journals (Sweden)

    Cheng Li

    2015-08-01

    Full Text Available The Tet family of methylcytosine dioxygenases (Tet1, Tet2, and Tet3 convert 5-methylcytosine to 5-hydroxymethylcytosine. To date, functional overlap among Tet family members has not been examined systematically in the context of embryonic development. To clarify the potential for overlap among Tet enzymes during development, we mutated the zebrafish orthologs of Tet1, Tet2, and Tet3 and examined single-, double-, and triple-mutant genotypes. Here, we identify Tet2 and Tet3 as the major 5-methylcytosine dioxygenases in the zebrafish embryo and uncover a combined requirement for Tet2 and Tet3 in hematopoietic stem cell (HSC emergence. We demonstrate that Notch signaling in the hemogenic endothelium is regulated by Tet2/3 prior to HSC emergence and show that restoring expression of the downstream gata2b/scl/runx1 transcriptional network can rescue HSCs in tet2/3 double mutant larvae. Our results reveal essential, overlapping functions for tet genes during embryonic development and uncover a requirement for 5hmC in regulating HSC production.

  5. Inactivation of Bmp4 from the Tbx1 Expression Domain Causes Abnormal Pharyngeal Arch Artery and Cardiac Outflow Tract Remodeling

    Science.gov (United States)

    Nie, Xuguang; Brown, Christopher B.; Wang, Qin; Jiao, Kai

    2011-01-01

    Maldevelopment of outflow tract and aortic arch arteries is among the most common forms of human congenital heart diseases. Both Bmp4 and Tbx1 are known to play critical roles during cardiovascular development. Expression of these two genes partially overlaps in pharyngeal arch areas in mouse embryos. In this study, we applied a conditional gene inactivation approach to test the hypothesis that Bmp4 expressed from the Tbx1 expression domain plays a critical role for normal development of outflow tract and pharyngeal arch arteries. We showed that inactivation of Bmp4 from Tbx1-expressing cells leads to the spectrum of deformities resembling the cardiovascular defects observed in human DiGeorge syndrome patients. Inactivation of Bmp4 from the Tbx1 expression domain did not cause patterning defects, but affected remodeling of outflow tract and pharyngeal arch arteries. Our further examination revealed that Bmp4 is required for normal recruitment/differentiation of smooth muscle cells surrounding the PAA4 and survival of outflow tract cushion mesenchymal cells. PMID:21123999

  6. New tools to analyze overlapping coding regions.

    Science.gov (United States)

    Bayegan, Amir H; Garcia-Martin, Juan Antonio; Clote, Peter

    2016-12-13

    Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We

  7. FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data

    DEFF Research Database (Denmark)

    Manijak, Mieszko P.; Nielsen, Henrik Bjørn

    2011-01-01

    circumvented by instead matching gene expression signatures to signatures of other experiments. FINDINGS: To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700...... Arabidopsis microarray experiments. CONCLUSIONS: Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at http://www.cbs.dtu.dk/services/faro/....

  8. Functional dyspepsia (FD) and non-erosive reflux disease (NERD): overlapping or discrete entities?

    LENUS (Irish Health Repository)

    Quigley, Eamonn M M

    2012-02-03

    As the incidence of both gastric cancer and peptic ulcer disease have declined, that of gastro-oesophageal reflux disease (GORD) and non-ulcer, or functional dyspepsia (FD) have reached virtually epidemic proportions. As we come to appreciate the expression of these disorders in the community, the real spectrum of each disease has become evident. FD and non-erosive reflux disease (NERD), the most prevalent manifestation of GORD, frequently overlap. Where then does GORD end and FD begin? Is it realistic, or even clinically relevant, to attempt a clear separation between these entities? These are more than issues of mere semantics; therapeutic options may be dictated by the classification of the patient as one or the other. Recent work indicates clearly that NERD is a heterogeneous disorder incorporating some patients who may well harbour subtle manifestations of oesophagitis and others who have entirely normal 24-hour pH studies. These differences may be crucial to the concept of NERD\\/FD overlap. While evidence in support of this concept is far from complete, it would appear that this overlap is most relevant to those NERD patients who do not exhibit abnormal esophageal acid exposure. These patients truly belong in the spectrum of functional gastrointestinal disorders rather than in GORD; attempts to shoe-horn these individuals into the spectrum of GORD will result in therapeutic disappointment and surgical disaster.

  9. Separation of the overlapping effects in spectra for WDXRF using the Rietveld method

    International Nuclear Information System (INIS)

    Salvador, Vera Lucia Ribeiro

    2005-01-01

    This work presents a new methodology for the overlapping spectra separation obtained by the technique of wavelength dispersion X-ray fluorescence (WDXRF). This methodology allows to improve the conventional analytic results and to facilitate the determination of chemical species of a same element without chemical separation, by means of the separation of coming spectra of electronic transitions of valence electrons or chemical effects in internal electrons. With the software 'GSAS-EXPGUI' and the method of Rietveld overcomes the problem of overlapping lines of the present species in the sample and it facilitates the determination of the same ones simultaneously, without the need of samples patterns and calibration curves, what means an expressive gain in relation to other techniques. The preparation of the surface of the sample for the collection of the spectrum represents a critical stage for the acting of the analysis whose effects can be minimized being used the refinement of Rietveld, that allows the determination of the relationships of the intensities of the lines put upon by means of mathematical models, what establishes the basic conditions for obtaining of more precise results in the quantitative analysis. In the case of the determination of chemical species it can separate, for example Cr (III), Cr (VI) and Fe (II), Fe(III) that present overlapping of almost 100%. (author)

  10. Vascular ATP-sensitive potassium channels are over-expressed and partially regulated by nitric oxide in experimental septic shock.

    Science.gov (United States)

    Collin, Solène; Sennoun, Nacira; Dron, Anne-Gaëlle; de la Bourdonnaye, Mathilde; Montemont, Chantal; Asfar, Pierre; Lacolley, Patrick; Meziani, Ferhat; Levy, Bruno

    2011-05-01

    To study the activation and expression of vascular (aorta and small mesenteric arteries) potassium channels during septic shock with or without modulation of the NO pathway. Septic shock was induced in rats by peritonitis. Selective inhibitors of vascular K(ATP) (PNU-37883A) or BK(Ca) [iberiotoxin (IbTX)] channels were used to demonstrate their involvement in vascular hyporeactivity. Vascular response to phenylephrine was measured on aorta and small mesenteric arteries mounted on a wire myograph. Vascular expression of potassium channels was studied by PCR and Western blot, in the presence or absence of 1400W, an inducible NO synthase (iNOS) inhibitor. Aortic activation of the transcriptional factor nuclear factor-kappaB (NF-κB) was assessed by electrophoretic mobility shift assay. Arterial pressure as well as in vivo and ex vivo vascular reactivity were reduced by sepsis and improved by PNU-37883A but not by IbTX. Sepsis was associated with an up-regulation of mRNA and protein expression of vascular K(ATP) channels, while expression of vascular BK(Ca) channels remained unchanged. Selective iNOS inhibition blunted the sepsis-induced increase in aortic NO, decreased NF-κB activation, and down-regulated vascular K(ATP) channel expression. Vascular K(ATP) but not BK(Ca) channels are activated, over-expressed, and partially regulated by NO via NF-κB activation during septic shock. Their selective inhibition restores arterial pressure and vascular reactivity and decreases lactate concentration. The present data suggest that selective vascular K(ATP) channel inhibitors offer potential therapeutic perspectives for septic shock.

  11. Criterion for testing multiparticle negative-partial-transpose entanglement

    International Nuclear Information System (INIS)

    Zeng, B.; Zhou, D.L.; Zhang, P.; Xu, Z.; You, L.

    2003-01-01

    We revisit the criterion of multiparticle entanglement based on the overlaps of a given quantum state ρ with maximally entangled states. For a system of m particles, each with N distinct states, we prove that ρ is m-particle negative partial transpose entangled, if there exists a maximally entangled state vertical bar MES>, such that >1/N. While this sufficiency condition is weaker than the Peres-Horodecki criterion in all cases, it applies to multi-particle systems, and becomes especially useful when the number of particles (m) is large. We also consider the converse of this criterion and illustrate its invalidity with counter examples

  12. 'Stent in a stent'--an alternative technique for removing partially covered stents following sleeve gastrectomy complications.

    Science.gov (United States)

    Vasilikostas, Georgios; Sanmugalingam, Nimalan; Khan, Omar; Reddy, Marcus; Groves, Chris; Wan, Andrew

    2014-03-01

    Endoscopic stenting is a relatively new technique for the treatment of post sleeve gastrectomy complications. Partially covered stents are used in this method to minimise the risk of migration but they are associated with difficulties with removal. Patients requiring emergency stenting following sleeve gastrectomy underwent insertion of a partially covered metallic stent. One month later, if the stent was not easily removable, a fully covered overlapping stent was inserted and the patient was readmitted 2 weeks later for removal of both stents. Four patients required stenting following sleeve gastrectomy leaks, and one patient required stenting for a stricture. In these cases, a 'stent in a stent' technique was used for removal. This technique allows the safe removal of partially covered stents inserted following sleeve gastrectomy complications.

  13. Detecting highly overlapping community structure by greedy clique expansion

    OpenAIRE

    Lee, Conrad; Reid, Fergal; McDaid, Aaron; Hurley, Neil

    2010-01-01

    In complex networks it is common for each node to belong to several communities, implying a highly overlapping community structure. Recent advances in benchmarking indicate that existing community assignment algorithms that are capable of detecting overlapping communities perform well only when the extent of community overlap is kept to modest levels. To overcome this limitation, we introduce a new community assignment algorithm called Greedy Clique Expansion (GCE). The algorithm identifies d...

  14. Generation of non-overlapping fiber architecture

    DEFF Research Database (Denmark)

    Chapelle, Lucie; Lévesque, M.; Brøndsted, Povl

    2015-01-01

    and polymer networks. The model takes into account the complex geometry of the fiber arrangement in which a fiber can be modeled with a certain degree of bending while keeping a main fiber orientation. The model is built in two steps. First, fibers are generated as a chain of overlapping spheres or as a chain......: a repulsion force to suppress the overlap between two fibers and a bending and stretching force to ensure that the fiber structure is kept unchanged. The model can be used as the geometrical basis for further finite-element modelling....

  15. [Asthma-COPD overlap syndrome].

    Science.gov (United States)

    Odler, Balázs; Müller, Veronika

    2016-08-01

    Obstructive lung diseases represent a major health problem worldwide due to their high prevalence associated with elevated socioeconomic costs. Bronchial asthma and chronic obstructive pulmonary disease are chronic obstructive ventilatory disorders with airway inflammation, however they are separate nosological entities based on thedifferent development, diagnostic and therapeutic approaches, and prognostic features. However, these diseases may coexist and can be defined as the coexistence of increased variability of airflow in a patient with incompletely reversible airway obstruction. This phenotype is called asthma - chronic obstructive pulmonary disease overlap syndrome. The syndrome is a clinical and scientific challenge as the majority of these patients have been excluded from the clinical and pharmacological trials, thus well-defined clinical characteristics and therapeutic approaches are lacking. The aim of this review is to summarize the currently available literature focusing on pathophysiological and clinical features, and discuss possible therapeutic approaches of patients with asthma - chronic obstructive pulmonary disease overlap syndrome. Orv. Hetil., 2016, 157(33), 1304-1313.

  16. Different Temporal Effects of Ebola Virus VP35 and VP24 Proteins on Global Gene Expression in Human Dendritic Cells.

    Science.gov (United States)

    Ilinykh, Philipp A; Lubaki, Ndongala M; Widen, Steven G; Renn, Lynnsey A; Theisen, Terence C; Rabin, Ronald L; Wood, Thomas G; Bukreyev, Alexander

    2015-08-01

    Ebola virus (EBOV) causes a severe hemorrhagic fever with a deficient immune response, lymphopenia, and lymphocyte apoptosis. Dendritic cells (DC), which trigger the adaptive response, do not mature despite EBOV infection. We recently demonstrated that DC maturation is unblocked by disabling the innate response antagonizing domains (IRADs) in EBOV VP35 and VP24 by the mutations R312A and K142A, respectively. Here we analyzed the effects of VP35 and VP24 with the IRADs disabled on global gene expression in human DC. Human monocyte-derived DC were infected by wild-type (wt) EBOV or EBOVs carrying the mutation in VP35 (EBOV/VP35m), VP24 (EBOV/VP24m), or both (EBOV/VP35m/VP24m). Global gene expression at 8 and 24 h was analyzed by deep sequencing, and the expression of interferon (IFN) subtypes up to 5 days postinfection was analyzed by quantitative reverse transcription-PCR (qRT-PCR). wt EBOV induced a weak global gene expression response, including markers of DC maturation, cytokines, chemokines, chemokine receptors, and multiple IFNs. The VP35 mutation unblocked the expression, resulting in a dramatic increase in expression of these transcripts at 8 and 24 h. Surprisingly, DC infected with EBOV/VP24m expressed lower levels of many of these transcripts at 8 h after infection, compared to wt EBOV. In contrast, at 24 h, expression of the transcripts increased in DC infected with any of the three mutants, compared to wt EBOV. Moreover, sets of genes affected by the two mutations only partially overlapped. Pathway analysis demonstrated that the VP35 mutation unblocked pathways involved in antigen processing and presentation and IFN signaling. These data suggest that EBOV IRADs have profound effects on the host adaptive immune response through massive transcriptional downregulation of DC. This study shows that infection of DC with EBOV, but not its mutant forms with the VP35 IRAD and/or VP24 IRAD disabled, causes a global block in expression of host genes. The temporal

  17. Mutations in the FHA-domain of ectopically expressed NBS1 lead to radiosensitization and to no increase in somatic mutation rates via a partial suppression of homologous recombination

    International Nuclear Information System (INIS)

    Ohara, Maki; Funyu, Yumi; Ebara, Shunsuke

    2014-01-01

    Ionizing radiation induces DNA double-strand breaks (DSBs). Mammalian cells repair DSBs through multiple pathways, and the repair pathway that is utilized may affect cellular radiation sensitivity. In this study, we examined effects on cellular radiosensitivity resulting from functional alterations in homologous recombination (HR). HR was inhibited by overexpression of the forkhead-associated (FHA) domain-mutated NBS1 (G27D/R28D: FHA-2D) protein in HeLa cells or in hamster cells carrying a human X-chromosome. Cells expressing FHA-2D presented partially (but significantly) HR-deficient phenotypes, which were assayed by the reduction of gene conversion frequencies measured with a reporter assay, a decrease in radiation-induced Mre11 foci formation, and hypersensitivity to camptothecin treatments. Interestingly, ectopic expression of FHA-2D did not increase the frequency of radiation-induced somatic mutations at the HPRT locus, suggesting that a partial reduction of HR efficiency has only a slight effect on genomic stability. The expression of FHA-2D rendered the exponentially growing cell population slightly (but significantly) more sensitive to ionizing radiation. This radiosensitization effect due to the expression of FHA-2D was enhanced when the cells were irradiated with split doses delivered at 24-h intervals. Furthermore, enhancement of radiation sensitivity by split dose irradiation was not seen in contact-inhibited G0/G1 populations, even though the cells expressed FHA-2D. These results suggest that the FHA domain of NBS1 might be an effective molecular target that can be used to induce radiosensitization using low molecular weight chemicals, and that partial inhibition of HR might improve the effectiveness of cancer radiotherapy. (author)

  18. Partial Correlation Matrix Estimation using Ridge Penalty Followed by Thresholding and Reestimation

    Science.gov (United States)

    2014-01-01

    Summary Motivated by the problem of construction gene co-expression network, we propose a statistical framework for estimating high-dimensional partial correlation matrix by a three-step approach. We first obtain a penalized estimate of a partial correlation matrix using ridge penalty. Next we select the non-zero entries of the partial correlation matrix by hypothesis testing. Finally we reestimate the partial correlation coefficients at these non-zero entries. In the second step, the null distribution of the test statistics derived from penalized partial correlation estimates has not been established. We address this challenge by estimating the null distribution from the empirical distribution of the test statistics of all the penalized partial correlation estimates. Extensive simulation studies demonstrate the good performance of our method. Application on a yeast cell cycle gene expression data shows that our method delivers better predictions of the protein-protein interactions than the Graphic Lasso. PMID:24845967

  19. Fluctuations of nuclear cross sections in the region of strong overlapping resonances and at large number of open channels

    International Nuclear Information System (INIS)

    Kun, S.Yu.

    1985-01-01

    On the basis of the symmetrized Simonius representation of the S matrix statistical properties of its fluctuating component in the presence of direct reactions are investigated. The case is considered where the resonance levels are strongly overlapping and there is a lot of open channels, assuming that compound-nucleus cross sections which couple different channels are equal. It is shown that using the averaged unitarity condition on the real energy axis one can eliminate both resonance-resonance and channel-channel correlations from partial r transition amplitudes. As a result, we derive the basic points of the Epicson fluctuation theory of nuclear cross sections, independently of the relation between the resonance overlapping and the number of open channels, and the validity of the Hauser-Feshbach model is established. If the number of open channels is large, the time of uniform population of compound-nucleus configurations, for an open excited nuclear system, is much smaller than the Poincare time. The life time of compound nucleus is discussed

  20. Local esperience on frequency and significance of immunological overlap in the field of primary biliary cirrhosis (PBC

    Directory of Open Access Journals (Sweden)

    Caterina Defendenti

    2008-06-01

    Full Text Available The aim of this study was to investigate the frequency and quality of immunological overlap in serum AMA M2 positives. During the period January 2004 - December 2006, out of 3000 sera evaluated, 40 were AMA M2 positive. Six of these (15% were without immunological overlap; they had clinical, histological and biochemical features of classical PBC with a normal length of life and ursodeoxycholic acid responding. In other 16 patients (40%, there was an association with antibody against antigens as SLA/LP, gp210 and Sp100, that causes the overlap syndrome AIH/PBC with various level of seriousness.The association with anti SLA/LP or with high level of autoantibody anti-Sp100 (index ELISA>10 waspresent in the patients investigated, as AIH type I°. Patients positive for anti gp210 with low anti-Sp100 index had instead a weak overlap AIH/PBC with slow evolving aspects. Nobody was positive for anti-LKM1, anti-LC, PML, or LBR.The remaining 45% of sera were positive for ANA, ENA,ANCA, with different clinical features. The antibody anti-SSARo52 and anti-centromere were frequent (17% and modified the liver disease evolution.The most serious clinical case was a double overlap anti-centromere/SSARo52 with biochemical and histological AIH symptoms. Other ENA patterns did worsen the prognosis of PBC but showed or were associated with systemic diseases, often after a long asymptomatic period.The ANA IFI positive with a speckled pattern ENA negative, in other 7 patients (17% worsened the long term prognosis because they expressed an overlap AIH/PBC with slowly evolving aspects.The most serious and intense clinical picture, with transplant perspective, was the association of the AMA M2 with anti Sp100 (index > 10 and pANNA. Four case were male (10% but females were prevalent.

  1. Identification of small secreted peptides (SSPs) in maize and expression analysis of partial SSP genes in reproductive tissues.

    Science.gov (United States)

    Li, Ye Long; Dai, Xin Ren; Yue, Xun; Gao, Xin-Qi; Zhang, Xian Sheng

    2014-10-01

    Maize 1,491 small secreted peptides were identified, which were classified according to the character of peptide sequences. Partial SSP gene expressions in reproductive tissues were determined by qRT-PCR. Small secreted peptides (SSPs) are important cell-cell communication messengers in plants. Most information on plant SSPs come from Arabidopsis thaliana and Oryza sativa, while little is known about the SSPs of other grass species such as maize (Zea mays). In this study, we identified 1,491 SSP genes from maize genomic sequences. These putative SSP genes were distributed throughout the ten maize chromosomes. Among them, 611 SSPs were classified into 198 superfamilies according to their conserved domains, and 725 SSPs with four or more cysteines at their C-termini shared similar cysteine arrangements with their counterparts in other plant species. Moreover, the SSPs requiring post-translational modification, as well as defensin-like (DEFL) proteins, were identified. Further, the expression levels of 110 SSP genes were analyzed in reproductive tissues, including male flower, pollen, silk, and ovary. Most of the genes encoding basal-layer antifungal peptide-like, small coat proteins-like, thioredoxin-like proteins, γ-thionins-like, and DEFL proteins showed high expression levels in the ovary and male flower compared with their levels in silk and mature pollen. The rapid alkalinization factor-like genes were highly expressed only in the mature ovary and mature pollen, and pollen Ole e 1-like genes showed low expression in silk. The results of this study provide basic information for further analysis of SSP functions in the reproductive process of maize.

  2. Network module detection: Affinity search technique with the multi-node topological overlap measure.

    Science.gov (United States)

    Li, Ai; Horvath, Steve

    2009-07-20

    Many clustering procedures only allow the user to input a pairwise dissimilarity or distance measure between objects. We propose a clustering method that can input a multi-point dissimilarity measure d(i1, i2, ..., iP) where the number of points P can be larger than 2. The work is motivated by gene network analysis where clusters correspond to modules of highly interconnected nodes. Here, we define modules as clusters of network nodes with high multi-node topological overlap. The topological overlap measure is a robust measure of interconnectedness which is based on shared network neighbors. In previous work, we have shown that the multi-node topological overlap measure yields biologically meaningful results when used as input of network neighborhood analysis. We adapt network neighborhood analysis for the use of module detection. We propose the Module Affinity Search Technique (MAST), which is a generalized version of the Cluster Affinity Search Technique (CAST). MAST can accommodate a multi-node dissimilarity measure. Clusters grow around user-defined or automatically chosen seeds (e.g. hub nodes). We propose both local and global cluster growth stopping rules. We use several simulations and a gene co-expression network application to argue that the MAST approach leads to biologically meaningful results. We compare MAST with hierarchical clustering and partitioning around medoid clustering. Our flexible module detection method is implemented in the MTOM software which can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/MTOM/

  3. An accurate clone-based haplotyping method by overlapping pool sequencing.

    Science.gov (United States)

    Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao

    2016-07-08

    Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. The overlapping of sound and the narrative structure of the audiovisual message / La anticipación del sonido y su relación con la estructura narrativa del mensaje audiovisual

    OpenAIRE

    Ddo. Luis Fernando Morales Morante -

    2008-01-01

    Abstract: The delete in sound with respect to the image (overlapping) is an expressive resource of the audiovisual editing that is frequently used by directors to introduce a new or relevant action into the story being told. Nevertheless, there are no empirical studies that state this effect as a consequence of the overlapping. In this article, we carry out a qualitative study of 235 overlappings from sequences of films, news and TV commercials, retrieved in the Internet. As a result, we note...

  5. Higher-Order Rewriting and Partial Evaluation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Rose, Kristoffer H.

    1997-01-01

    transformations as meta-reductions, i.e., reductions in the internal “substitution calculus.” For partial-evaluation problems, this means that instead of having to prove on a case-by-case basis that one's “two-level functions” operate properly, one can concisely formalize them as a combinatory reduction system...... and obtain as a corollary that static reduction does not go wrong and yields a well-formed residual program. We have found that the CRS substitution calculus provides an adequate expressive power to formalize partial evaluation: it provides sufficient termination strength while avoiding the need...

  6. Overlap syndrome of COPD and OSA in Koreans.

    Science.gov (United States)

    Choi, Kyung-Mee; Thomas, Robert J; Kim, Jinkwan; Lee, Seung Ku; Yoon, Dae Wui; Shin, Chol

    2017-07-01

    Overlap syndrome of chronic obstructive pulmonary disease (COPD) and obstructive sleep apnea (OSA) leads to increased morbidity and mortality. There have been no reports available on the overlap syndrome for Koreans. Our primary aim was to identify prevalence and predictors of the overlap syndrome in Koreans.This is a cross-sectional study with a community-based sample of 1298 participants (mean age, 59.7 ± 6.7) from the cohort of Korean Genomic and Epidemiologic Study during 2013 to 2014. OSA and COPD were assessed by apnea-hypopnea index (AHI) and the ratio of forced expiratory volume in 1 s to forced vital capacity (FEV1/FVC syndrome. The prevalence of COPD remained the same as 10.8% regardless of the presence of OSA. The mean ratio of FEV1/FVC for those with COPD was 0.77, regardless of OSA. The OR increased for age (OR, 1.1; 95% CI, 1.0-1.1) and smokers (OR, 3.6; 95% CI, 2.0-6.4), but decreased for body mass index (BMI) (OR, 0.84; 95% CI, 0.8-0.9) and overweight state (OR, 0.4; 95% CI, 0.2-0.7). Risk factors of the overlap syndrome differed by OSA severity, that is, BMI in those with moderate-to-severe OSA, whereas sex (OR, 4.7; 95% CI, 2.1-10.6) and age (OR, 1.1; 95% CI, 1.0-1.1) in those with mild OSA.In a population study from Korea, 10.8% of OSA patients had an overlap syndrome with COPD. Although BMI is a well-known risk factor of OSA, it is likely that being overweight may be protective for moderate-to-severe OSA patients from the risk of COPD (i.e., overlap syndrome).

  7. [Elderly people and removable partial dentures

    NARCIS (Netherlands)

    Baat, C. de

    2009-01-01

    The most frequently reported disadvantages of removable partial dentures are the more demanding daily oral hygiene self-care, especially for people who already experience difficulties in self-care, and the possible harmful influence on the remaining dentition. These disadvantages can be expressed in

  8. A computational formalization for partial evaluation

    DEFF Research Database (Denmark)

    Hatcliff, John; Danvy, Olivier

    1997-01-01

    We formalize a partial evaluator for Eugenio Moggi's computational metalanguage. This formalization gives an evaluation-order independent view of binding-time analysis and program specialization, including a proper treatment of call unfolding. It also enables us to express the essence of `control...

  9. Perceived Non-Overlap of Objects in an Audiovisual Stream/Bounce Display

    Directory of Open Access Journals (Sweden)

    Yousuke Kawachi

    2011-10-01

    Full Text Available In a stream/bounce display in which two identical visual objects move toward each other, coincide (completely overlap, and then move apart, the objects can be perceived as either streaming through or bouncing off each other. Despite the perceptual ambiguity in this display, the streaming percept is dominant. However, a sound burst presented at the time that the objects coincide facilitates the bouncing percept. Herein, we report a perceptual phenomenon in which the overlap between objects is illusorily perceived as a non-overlap in the stream/bounce display accompanied with sound. In the experiment, the amount of overlap between two objects was systematically manipulated in the presence/absence of a sound. Observers were asked to judge whether the two objects overlapped with each other and then asked whether the objects appeared to stream through or bounce off each other. The results were consistent with those of previous studies showing that sound promoted the bouncing percept. Most importantly, the sound presentation facilitated the perception of a non-overlap between the objects instead of a physical overlap, suggesting that the momentary overlap was inadequately perceived. We discuss the possibility that an abrupt sound temporally interrupts visual processing such as the formation of dynamic object representations.

  10. Research on Some Bus Transport Networks with Random Overlapping Clique Structure

    International Nuclear Information System (INIS)

    Yang Xuhua; Sun Youxian; Wang Bo; Wang Wanliang

    2008-01-01

    On the basis of investigating the statistical data of bus transport networks of three big cities in China, we propose that each bus route is a clique (maximal complete subgraph) and a bus transport network (BTN) consists of a lot of cliques, which intensively connect and overlap with each other. We study the network properties, which include the degree distribution, multiple edges' overlapping time distribution, distribution of the overlap size between any two overlapping cliques, distribution of the number of cliques that a node belongs to. Naturally, the cliques also constitute a network, with the overlapping nodes being their multiple links. We also research its network properties such as degree distribution, clustering, average path length, and so on. We propose that a BTN has the properties of random clique increment and random overlapping clique, at the same time, a BTN is a small-world network with highly clique-clustered and highly clique-overlapped. Finally, we introduce a BTN evolution model, whose simulation results agree well with the statistical laws that emerge in real BTNs

  11. Iterative methods for overlap and twisted mass fermions

    International Nuclear Information System (INIS)

    Chiarappa, T.; Jansen, K.; Shindler, A.; Wetzorke, I.; Scorzato, L.; Urbach, C.; Wenger, U.

    2006-09-01

    We present a comparison of a number of iterative solvers of linear systems of equations for obtaining the fermion propagator in lattice QCD. In particular, we consider chirally invariant overlap and chirally improved Wilson (maximally) twisted mass fermions. The comparison of both formulations of lattice QCD is performed at four fixed values of the pion mass between 230 MeV and 720 MeV. For overlap fermions we address adaptive precision and low mode preconditioning while for twisted mass fermions we discuss even/odd preconditioning. Taking the best available algorithms in each case we find that calculations with the overlap operator are by a factor of 30-120 more expensive than with the twisted mass operator. (orig.)

  12. Iterative methods for overlap and twisted mass fermions

    Energy Technology Data Exchange (ETDEWEB)

    Chiarappa, T. [Univ. di Milano Bicocca (Italy); Jansen, K.; Shindler, A.; Wetzorke, I. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Nagai, K.I. [Wuppertal Univ. (Gesamthochschule) (Germany). Fachbereich Physik; Papinutto, M. [INFN Sezione di Roma Tre, Rome (Italy); Scorzato, L. [European Centre for Theoretical Studies in Nuclear Physics and Related Areas (ECT), Villazzano (Italy); Urbach, C. [Liverpool Univ. (United Kingdom). Dept. of Mathematical Sciences; Wenger, U. [ETH Zuerich (Switzerland). Inst. fuer Theoretische Physik

    2006-09-15

    We present a comparison of a number of iterative solvers of linear systems of equations for obtaining the fermion propagator in lattice QCD. In particular, we consider chirally invariant overlap and chirally improved Wilson (maximally) twisted mass fermions. The comparison of both formulations of lattice QCD is performed at four fixed values of the pion mass between 230 MeV and 720 MeV. For overlap fermions we address adaptive precision and low mode preconditioning while for twisted mass fermions we discuss even/odd preconditioning. Taking the best available algorithms in each case we find that calculations with the overlap operator are by a factor of 30-120 more expensive than with the twisted mass operator. (orig.)

  13. A Comparison of Item Selection Techniques and Exposure Control Mechanisms in CATs Using the Generalized Partial Credit Model.

    Science.gov (United States)

    Pastor, Dena A.; Dodd, Barbara G.; Chang, Hua-Hua

    2002-01-01

    Studied the impact of using five different exposure control algorithms in two sizes of item pool calibrated using the generalized partial credit model. Simulation results show that the a-stratified design, in comparison to a no-exposure control condition, could be used to reduce item exposure and overlap and increase pool use, while degrading…

  14. Interference-free acquisition of overlapping sequences in explicit spatial memory.

    Science.gov (United States)

    Eggert, Thomas; Drever, Johannes; Straube, Andreas

    2014-04-01

    Some types of human sequential memory, e.g. the acquisition of a new composition by a trained musician, seem to be very efficient in extending the length of a memorized sequence and in flexible reuse of known subsequences in a newly acquired sequential context. This implies that interference between known and newly acquired subsequences can be avoided even when learning a sequence which is a partial mutation of a known sequence. It is known that established motor sequences do not have such flexibility. Using learning of deferred imitation, the current study investigates the flexibility of explicit spatial memory by quantifying the interferences between successively acquired, partially overlapping sequences. After learning a spatial sequence on day 1, this sequence was progressively modified on day 2. On day 3, a retention test was performed with both the initial and the modified sequence. The results show that subjects performed very well on day 1 and day 2. No spatial interference between changed and unchanged targets was observed during the stepwise progressive modification of the reproduced sequence. Surprisingly, subjects performed well on both sequences on day 3. Comparison with a control experiment without intermediate mutation training showed that the initial training on day 1 did not proactively interfere with the retention of the modified sequence on day 3. Vice versa, the mutation training on day 2 did not interfere retroactively with the retention of the original sequence as tested on day 3. The results underline the flexibility in acquiring explicit spatial memory. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Prune belly syndrome with overlapping presentation of partial urorectal septum malformation sequence in a female newborn with absent perineal openings.

    Science.gov (United States)

    Farooqui, Azhar; AlAqeel, Alaa; Habib, Zakaria

    2014-01-01

    Prune belly syndrome (PBS) is a rare congenital anomaly characterized in males by a triad of anomalous genitourinary tract, deficient development of abdominal wall muscles, and bilateral cryptorchidism. Although similar anomalies have been reported in females, by definition they do not full fill the classical triad. Urorectal septum malformation sequence (URSM) is a lethal condition characterized by presence of ambiguous genitalia, absent perineal openings (urogenital and anal), and lumbosacral abnormalities. In this original case report, the authors discuss the presentation and management of what would be analogous to a Woodhouse category 1 PBS in a female newborn associated with an overlapping presentation of URSM.

  16. Prune Belly Syndrome with Overlapping Presentation of Partial Urorectal Septum Malformation Sequence in a Female Newborn with Absent Perineal Openings

    Directory of Open Access Journals (Sweden)

    Azhar Farooqui

    2014-01-01

    Full Text Available Prune belly syndrome (PBS is a rare congenital anomaly characterized in males by a triad of anomalous genitourinary tract, deficient development of abdominal wall muscles, and bilateral cryptorchidism. Although similar anomalies have been reported in females, by definition they do not full fill the classical triad. Urorectal septum malformation sequence (URSM is a lethal condition characterized by presence of ambiguous genitalia, absent perineal openings (urogenital and anal, and lumbosacral abnormalities. In this original case report, the authors discuss the presentation and management of what would be analogous to a Woodhouse category 1 PBS in a female newborn associated with an overlapping presentation of URSM.

  17. Presentation of dynamically overlapping auditory messages in user interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Papp, III, Albert Louis [Univ. of California, Davis, CA (United States)

    1997-09-01

    This dissertation describes a methodology and example implementation for the dynamic regulation of temporally overlapping auditory messages in computer-user interfaces. The regulation mechanism exists to schedule numerous overlapping auditory messages in such a way that each individual message remains perceptually distinct from all others. The method is based on the research conducted in the area of auditory scene analysis. While numerous applications have been engineered to present the user with temporally overlapped auditory output, they have generally been designed without any structured method of controlling the perceptual aspects of the sound. The method of scheduling temporally overlapping sounds has been extended to function in an environment where numerous applications can present sound independently of each other. The Centralized Audio Presentation System is a global regulation mechanism that controls all audio output requests made from all currently running applications. The notion of multimodal objects is explored in this system as well. Each audio request that represents a particular message can include numerous auditory representations, such as musical motives and voice. The Presentation System scheduling algorithm selects the best representation according to the current global auditory system state, and presents it to the user within the request constraints of priority and maximum acceptable latency. The perceptual conflicts between temporally overlapping audio messages are examined in depth through the Computational Auditory Scene Synthesizer. At the heart of this system is a heuristic-based auditory scene synthesis scheduling method. Different schedules of overlapped sounds are evaluated and assigned penalty scores. High scores represent presentations that include perceptual conflicts between over-lapping sounds. Low scores indicate fewer and less serious conflicts. A user study was conducted to validate that the perceptual difficulties predicted by

  18. Express saccades in distinct populations: east, west, and in-between.

    Science.gov (United States)

    Knox, Paul C; Wolohan, Felicity D A; Helmy, Mai S

    2017-12-01

    Express saccades are low latency (80-130 ms), visually guided saccades. While their occurrence is encouraged by the use of gap tasks (the fixation target is extinguished 200 ms prior to the saccade target appearing) and suppressed by the use of overlap tasks (the fixation target remains present when the saccade target appears), there are some healthy, adult participants, "express saccade makers" (ESMs), who persist in generating high proportions (> 30%) of express saccades in overlap conditions. These participants are encountered much more frequently in Chinese participant groups than amongst the Caucasian participants tested to date. What is not known is whether this high number of ESMs is only a feature of Chinese participant groups. More broadly, there are few comparative studies of saccade behaviour across large participant groups drawn from different populations. We, therefore, tested an independent group of 70 healthy adult Egyptian participants, using the same equipment and procedures as employed in the previous studies. Each participant was exposed to two blocks of 200 gap, and two blocks of 200 overlap trials, with block order counterbalanced. Results from the Schwartz Value Survey were used to confirm that this group of participants was culturally distinct from the Chinese and Caucasian (white British) groups tested previously. Fourteen percent (10/70) of this new group were ESMs, and the pattern of latency distribution in these ESMs was identical to that identified in the other participant groups, with a prominent peak in the express latency range in overlap conditions. Overall, we identified three modes in the distribution of saccade latency in overlap conditions, the timing of which (express peak at 110 ms, subsequent peaks at 160 and 210 ms) were strikingly consistent with our previous observations. That these behavioural patterns of saccade latency are observed consistently in large participant groups, drawn from geographically, ethnically, and

  19. [The effect of altered oxygen partial pressure on the resisitance to hypoxia and expression of oxygen-sensitive genes in Drosophila melanogaster].

    Science.gov (United States)

    Berezovs'kyĭ, V Ia; Chaka, O H; Litovka, I H; Levashov, M I; Ianko, R V

    2014-01-01

    As a result of resistance test to hypoxia of Drosophilas melanogaster of Oregon strain, we identified a high resistance (Group II) and low resistance (Group III) subpopulations of flies. Flies from groups II and III were incubated in a constant normobaric hypoxia (Po2=62-64 mm Hg) for 10 generations. A highly resistant group (Group IV) were exposed to a shortterm anoxia (Po,=1,5 mm Hg, 5 min) every generation. Larvae from Groups II, III, and IV demonstrated significantly elevated levels of Sir and CG 14740 expression. Larvae from Group II had a significantly higher expression of CG 14740 compared to group III. The restitution time after exposure to anoxia was significantly reduced in Group II (on 31% of the control values) Our results suggest that long-term adaptation to low oxygen partial pressure of highly resistant Drosophila significantly reduces the time of restitution and increases the expression of Sir2 and CG14740 genes.

  20. T-cell memory responses elicited by yellow fever vaccine are targeted to overlapping epitopes containing multiple HLA-I and -II binding motifs.

    Directory of Open Access Journals (Sweden)

    Andréa Barbosa de Melo

    Full Text Available The yellow fever vaccines (YF-17D-204 and 17DD are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection, although other immune effector mechanisms are known to be involved. T-cell responses are known to play an important role modulating antibody production and the killing of infected cells. However, little is known about the repertoire of T-cell responses elicited by the YF-17DD vaccine in humans. In this report, a library of 653 partially overlapping 15-mer peptides covering the envelope (Env and nonstructural (NS proteins 1 to 5 of the vaccine was utilized to perform a comprehensive analysis of the virus-specific CD4(+ and CD8(+ T-cell responses. The T-cell responses were screened ex-vivo by IFN-γ ELISPOT assays using blood samples from 220 YF-17DD vaccinees collected two months to four years after immunization. Each peptide was tested in 75 to 208 separate individuals of the cohort. The screening identified sixteen immunodominant antigens that elicited activation of circulating memory T-cells in 10% to 33% of the individuals. Biochemical in-vitro binding assays and immunogenetic and immunogenicity studies indicated that each of the sixteen immunogenic 15-mer peptides contained two or more partially overlapping epitopes that could bind with high affinity to molecules of different HLAs. The prevalence of the immunogenicity of a peptide in the cohort was correlated with the diversity of HLA-II alleles that they could bind. These findings suggest that overlapping of HLA binding motifs within a peptide enhances its T-cell immunogenicity and the prevalence of the response in the population. In summary, the results suggests that in addition to factors of the innate immunity, "promiscuous" T-cell antigens might contribute to the high efficacy of the yellow fever vaccines.

  1. Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation

    Directory of Open Access Journals (Sweden)

    Wright Anthony PH

    2010-01-01

    Full Text Available Abstract Background Histone acetyltransferase enzymes (HATs are implicated in regulation of transcription. HATs from different families may overlap in target and substrate specificity. Results We isolated the elp3+ gene encoding the histone acetyltransferase subunit of the Elongator complex in fission yeast and characterized the phenotype of an Δelp3 mutant. We examined genetic interactions between Δelp3 and two other HAT mutants, Δmst2 and Δgcn5 and used whole genome microarray analysis to analyze their effects on gene expression. Conclusions Comparison of phenotypes and expression profiles in single, double and triple mutants indicate that these HAT enzymes have overlapping functions. Consistent with this, overlapping specificity in histone H3 acetylation is observed. However, there is no evidence for overlap with another HAT enzyme, encoded by the essential mst1+ gene.

  2. Diversification of the celiac disease α-gliadin complex in wheat: a 33-mer peptide with six overlapping epitopes, evolved following polyploidization.

    Science.gov (United States)

    Ozuna, Carmen V; Iehisa, Julio C M; Giménez, María J; Alvarez, Juan B; Sousa, Carolina; Barro, Francisco

    2015-06-01

    The gluten proteins from wheat, barley and rye are responsible both for celiac disease (CD) and for non-celiac gluten sensitivity, two pathologies affecting up to 6-8% of the human population worldwide. The wheat α-gliadin proteins contain three major CD immunogenic peptides: p31-43, which induces the innate immune response; the 33-mer, formed by six overlapping copies of three highly stimulatory epitopes; and an additional DQ2.5-glia-α3 epitope which partially overlaps with the 33-mer. Next-generation sequencing (NGS) and Sanger sequencing of α-gliadin genes from diploid and polyploid wheat provided six types of α-gliadins (named 1-6) with strong differences in their frequencies in diploid and polyploid wheat, and in the presence and abundance of these CD immunogenic peptides. Immunogenic variants of the p31-43 peptide were found in most of the α-gliadins. Variants of the DQ2.5-glia-α3 epitope were associated with specific types of α-gliadins. Remarkably, only type 1 α-gliadins contained 33-mer epitopes. Moreover, the full immunodominant 33-mer fragment was only present in hexaploid wheat at low abundance, probably as the result of allohexaploidization events from subtype 1.2 α-gliadins found only in Aegilops tauschii, the D-genome donor of hexaploid wheat. Type 3 α-gliadins seem to be the ancestral type as they are found in most of the α-gliadin-expressing Triticeae species. These findings are important for reducing the incidence of CD by the breeding/selection of wheat varieties with low stimulatory capacity of T cells. Moreover, advanced genome-editing techniques (TALENs, CRISPR) will be easier to implement on the small group of α-gliadins containing only immunogenic peptides. © 2015 Society for Experimental Biology and John Wiley & Sons Ltd.

  3. Cloning and analysis of the mouse Fanconi anemia group A cDNA and an overlapping penta zinc finger cDNA.

    Science.gov (United States)

    Wong, J C; Alon, N; Norga, K; Kruyt, F A; Youssoufian, H; Buchwald, M

    2000-08-01

    Despite the cloning of four disease-associated genes for Fanconi anemia (FA), the molecular pathogenesis of FA remains largely unknown. To study FA complementation group A using the mouse as a model system, we cloned and characterized the mouse homolog of the human FANCA cDNA. The mouse cDNA (Fanca) encodes a 161-kDa protein that shares 65% amino acid sequence identity with human FANCA. Fanca is located at the distal region of mouse chromosome 8 and has a ubiquitous pattern of expression in embryonic and adult tissues. Expression of the mouse cDNA in human FA-A cells restores the cellular drug sensitivity to normal levels. Thus, the expression pattern, protein structure, chromosomal location, and function of FANCA are conserved in the mouse. We also isolated a novel zinc finger protein, Zfp276, which has five C(2)H(2) domains. Interestingly, Zfp276 is situated in the Fanca locus, and the 3'UTR of its cDNA overlaps with the last four exons of Fanca in a tail-to-tail manner. Zfp276 is expressed in the same tissues as Fanca, but does not complement the mitomycin C (MMC)-sensitive phenotype of FA-A cells. The overlapping genomic organization between Zfp276 and Fanca may have relevance to the disease phenotype of FA. Copyright 2000 Academic Press.

  4. Markers of Psychological Differences and Social and Health Inequalities: Possible Genetic and Phenotypic Overlaps.

    Science.gov (United States)

    Mõttus, René; Marioni, Riccardo; Deary, Ian J

    2017-02-01

    Associations between markers of ostensible psychological characteristics and social and health inequalities are pervasive but difficult to explain. In some cases, there may be causal influence flowing from social and health inequalities to psychological differences, whereas sometimes it may be the other way around. Here, we focus on the possibility that some markers that we often consider as indexing different domains of individual differences may in fact reflect at least partially overlapping genetic and/or phenotypic bases. For example, individual differences in cognitive abilities and educational attainment appear to reflect largely overlapping genetic influences, whereas cognitive abilities and health literacy may be almost identical phenomena at the phenotypic, never mind genetic, level. We make the case for employing molecular genetic data and quantitative genetic techniques to better understand the associations of psychological individual differences with social and health inequalities. We illustrate these arguments by using published findings from the Lothian Birth Cohort and the Generation Scotland studies. We also present novel findings pertaining to longitudinal stability and change in older age personality traits and some correlates of the change, molecular genetic data-based heritability estimates of Neuroticism and Extraversion, and the genetic correlations of these personality traits with markers of social and health inequalities. © 2015 The Authors. Journal of Personality published by Wiley Periodicals, Inc.

  5. Memorization in Type-Directed Partial Evaluation

    DEFF Research Database (Denmark)

    Balat, Vincent; Danvy, Olivier

    2002-01-01

    We use a code generator—type-directed partial evaluation— to verify conversions between isomorphic types, or more precisely to verify that a composite function is the identity function at some complicated type. A typed functional language such as ML provides a natural support to express the funct...

  6. Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation.

    Science.gov (United States)

    Ha, Min Jin; Sun, Wei

    2014-09-01

    Motivated by the problem of construction of gene co-expression network, we propose a statistical framework for estimating high-dimensional partial correlation matrix by a three-step approach. We first obtain a penalized estimate of a partial correlation matrix using ridge penalty. Next we select the non-zero entries of the partial correlation matrix by hypothesis testing. Finally we re-estimate the partial correlation coefficients at these non-zero entries. In the second step, the null distribution of the test statistics derived from penalized partial correlation estimates has not been established. We address this challenge by estimating the null distribution from the empirical distribution of the test statistics of all the penalized partial correlation estimates. Extensive simulation studies demonstrate the good performance of our method. Application on a yeast cell cycle gene expression data shows that our method delivers better predictions of the protein-protein interactions than the Graphic Lasso. © 2014, The International Biometric Society.

  7. A dynamic model for managing overlapped iterative product development

    NARCIS (Netherlands)

    Lin, J.; Chai, K.H.; Wong, Y.S.; Brombacher, A.C.

    2008-01-01

    Intense competition in many industries impels firms to develop more products in less time. Overlapping of development activities is regarded as one of the most promising strategies to reduce project cycle time. However, the gain from overlapping must be weighed against the additional resource and

  8. Optimization of overlap uniformness for ptychography.

    Science.gov (United States)

    Huang, Xiaojing; Yan, Hanfei; Harder, Ross; Hwu, Yeukuang; Robinson, Ian K; Chu, Yong S

    2014-05-19

    We demonstrate the advantages of imaging with ptychography scans that follow a Fermat spiral trajectory. This scan pattern provides a more uniform coverage and a higher overlap ratio with the same number of scan points over the same area than the presently used mesh and concentric [13] patterns. Under realistically imperfect measurement conditions, numerical simulations show that the quality of the reconstructed image is improved significantly with a Fermat spiral compared with a concentric scan pattern. The result is confirmed by the performance enhancement with experimental data, especially under low-overlap conditions. These results suggest that the Fermat spiral pattern increases the quality of the reconstructed image and tolerance to data with imperfections.

  9. Communication Avoiding and Overlapping for Numerical Linear Algebra

    Science.gov (United States)

    2012-05-08

    future exascale systems, communication cost must be avoided or overlapped. Communication-avoiding 2.5D algorithms improve scalability by reducing...linear algebra problems to future exascale systems, communication cost must be avoided or overlapped. Communication-avoiding 2.5D algorithms improve...will continue to grow relative to the cost of computation. With exascale computing as the long-term goal, the community needs to develop techniques

  10. PairWise Neighbours database: overlaps and spacers among prokaryote genomes

    Directory of Open Access Journals (Sweden)

    Garcia-Vallvé Santiago

    2009-06-01

    Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

  11. Parentage of overlapping offspring of an arboreal-breeding frog with no nest defense: implications for nest site selection and reproductive strategy.

    Science.gov (United States)

    Tung, Wan-Ping; Chen, Yi-Huey; Cheng, Wei-Chun; Chuang, Ming-Feng; Hsu, Wan-Tso; Kam, Yeong-Choy; Lehtinen, Richard M

    2015-01-01

    Overlapping offspring occurs when eggs are laid in a nest containing offspring from earlier reproduction. Earlier studies showed that the parentage is not always obvious due to difficulties in field observation and/or alternative breeding tactics. To unveil the parentage between overlapping offspring and parents is critical in understanding oviposition site selection and the reproductive strategies of parents. Amplectant pairs of an arboreal-breeding frog, Kurixalus eiffingeri, lay eggs in tadpole-occupied nests where offspring of different life stages (embryos and tadpoles) coexist. We used five microsatellite DNA markers to assess the parentage between parents and overlapping offspring. We also tested the hypothesis that the male or female frog would breed in the same breeding site because of the scarcity of nest sites. Results showed varied parentage patterns, which may differ from the phenomenon of overlapping egg clutches reported earlier. Parentage analyses showed that only 58 and 25% of the tadpole-occupied stumps were reused by the same male and female respectively, partially confirming our prediction. Re-nesting by the same individual was more common in males than females, which is most likely related to the cost of tadpole feeding and/or feeding schemes of females. On the other hand, results of parentage analyses showed that about 42 and 75% of male and female respectively bred in tadpole-occupied stumps where tadpoles were genetically unrelated. Results of a nest-choice experiment revealed that 40% of frogs chose tadpole-occupied bamboo cups when we presented identical stumps, without or with tadpoles, suggesting that the habitat saturation hypothesis does not fully explain why frogs used the tadpole-occupied stumps. Several possible benefits of overlapping offspring with different life stages were proposed. Our study highlights the importance of integrating molecular data with field observations to better understand the reproductive biology and nest

  12. Privacy-Preserving Detection of Inter-Domain SDN Rules Overlaps

    KAUST Repository

    Dethise, Arnaud

    2017-08-24

    SDN approaches to inter-domain routing promise better traffic engineering, enhanced security, and higher automation. Yet, naïve deployment of SDN on the Internet is dangerous as the control-plane expressiveness of BGP is significantly more limited than the data-plane expressiveness of SDN, which allows fine-grained rules to deflect traffic from BGP\\'s default routes. This mismatch may lead to incorrect forwarding behaviors such as forwarding loops and blackholes, ultimately hindering SDN deployment at the inter-domain level. In this work, we make a first step towards verifying the correctness of inter-domain forwarding state with a focus on loop freedom while keeping private the SDN rules, as they comprise confidential routing information. To this end, we design a simple yet powerful primitive that allows two networks to verify whether their SDN rules overlap, i.e., the set of packets matched by these rules is non-empty, without leaking any information about the SDN rules. We propose an efficient implementation of this primitive by using recent advancements in Secure Multi-Party Computation and we then leverage it as the main building block for designing a system that detects Internet-wide forwarding loops among any set of SDN-enabled Internet eXchange Points.

  13. The overlap Dirac operator as a continued fraction

    International Nuclear Information System (INIS)

    Wenger, U.; Deutsches Elektronen-Synchrotron

    2004-03-01

    We use a continued fraction expansion of the sign-function in order to obtain a five dimensional formulation of the overlap lattice Dirac operator. Within this formulation the inverse of the overlap operator can be calculated by a single Krylov space method and nested conjugate gradient procedures are avoided. We point out that the five dimensional linear system can be made well conditioned using equivalence transformations on the continued fractions. (orig.)

  14. Dissection of two soybean QTL conferring partial resistance to Phytophthora sojae through sequence and gene expression analysis

    Directory of Open Access Journals (Sweden)

    Wang Hehe

    2012-08-01

    Full Text Available Abstract Background Phytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide there are populations that have adapted to the most commonly deployed resistance to P. sojae ( Rps genes. Hence, this system has received increased attention towards identifying mechanisms and molecular markers associated with partial resistance to this pathogen. Several quantitative trait loci (QTL have been identified in the soybean cultivar ‘Conrad’ that contributes to the expression of partial resistance to multiple P. sojae isolates. Results In this study, two of the Conrad QTL on chromosome 19 were dissected through sequence and expression analysis of genes in both resistant (Conrad and susceptible (‘Sloan’ genotypes. There were 1025 single nucleotide polymorphisms (SNPs in 87 of 153 genes sequenced from Conrad and Sloan. There were 304 SNPs in 54 genes sequenced from Conrad compared to those from both Sloan and Williams 82, of which 11 genes had SNPs unique to Conrad. Eleven of 19 genes in these regions analyzed with qRT-PCR had significant differences in fold change of transcript abundance in response to infection with P. sojae in lines with QTL haplotype from the resistant parent compared to those with the susceptible parent haplotype. From these, 8 of the 11 genes had SNPs in the upstream, untranslated region, exon, intron, and/or downstream region. These 11 candidate genes encode proteins potentially involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance. Conclusions These findings may indicate a complex defense network with multiple mechanisms underlying these two soybean QTL conferring resistance to P. sojae. SNP markers derived from these candidate genes can contribute to fine mapping of QTL and marker assisted breeding for

  15. Detection and Evaluation of Pre-Preg Gaps and Overlaps in Glare Laminates

    Science.gov (United States)

    Nardi, Davide; Abouhamzeh, Morteza; Leonard, Rob; Sinke, Jos

    2018-03-01

    Gaps and overlaps between pre-preg plies represent common flaws in composite materials that can be introduced easily in an automated fibre placement manufacturing process and are potentially detrimental for the mechanical performances of the final laminates. Whereas gaps and overlaps have been addressed for full composite material, the topic has not been extended to a hybrid composite material such as Glare, a member of the family of Fibre Metal Laminates (FMLs). In this paper/research, the manufacturing, the detection, and the optical evaluation of intraply gaps and overlaps in Glare laminates are investigated. As part of an initial assessment study on the effect of gaps and overlaps on Glare, only the most critical lay-up has been considered. The experimental investigation started with the manufacturing of specimens having gaps and overlaps with different widths, followed by a non-destructive ultrasonic-inspection. An optical evaluation of the gaps and overlaps was performed by means of microscope image analysis of the cross sections of the specimens. The results from the non-destructive evaluations show the effectiveness of the ultrasonic detection of gaps and overlaps both in position, shape, width, and severity. The optical inspections confirm the accuracy of the non-destructive evaluation also adding useful insights about the geometrical features due to the presence of gaps and overlaps in the final Glare laminates. All the results justify the need for a further investigation on the effect of gaps and overlaps on the mechanical properties.

  16. Comparison of Patient Outcomes and Cost of Overlapping Versus Nonoverlapping Spine Surgery.

    Science.gov (United States)

    Zygourakis, Corinna C; Sizdahkhani, Saman; Keefe, Malla; Lee, Janelle; Chou, Dean; Mummaneni, Praveen V; Ames, Christopher P

    2017-04-01

    Overlapping surgery recently has gained significant media attention, but there are limited data on its safety and efficacy. To date, there has been no analysis of overlapping surgery in the field of spine. Our goal was to compare overlapping versus nonoverlapping spine surgery patient outcomes and cost. A retrospective review was undertaken of 2319 spine surgeries (n = 848 overlapping; 1471 nonoverlapping) performed by 3 neurosurgery attendings from 2012 to 2015 at the University of California San Francisco. Collected variables included patient age, sex, insurance, American Society of Anesthesiology score, severity of illness, risk of mortality, procedure type, surgeon, day of surgery, source of transfer, admission type, overlapping versus nonoverlapping surgery (≥1 minute of overlapping procedure time), Medicare-Severity Diagnosis-Related Group, osteotomy, and presence of another attending/fellow/resident. Univariate, then multivariate mixed-effect models were used to evaluate the effect of the collected variables on the following outcomes: procedure time, estimated blood loss, length of stay, discharge status, 30-day mortality, 30-day unplanned readmission, unplanned return to OR, and total hospital cost. Urgent spine cases were more likely to be done in an overlapping fashion (all P return to the operating room, estimated blood loss, length of stay, and total hospital cost (all P = ns). Overlapping spine surgery may be performed safely at our institution, although continued monitoring of patient outcomes is necessary. Overlapping surgery does not lead to greater hospital costs. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Structural studies of formic acid using partial form-factor analysis

    International Nuclear Information System (INIS)

    Swan, G.; Dore, J.C.; Bellissent-Funel, M.C.

    1993-01-01

    Neutron diffraction measurements have been made of liquid formic acid using H/D isotopic substitution. Data are recorded for samples of DCOOD, HCOOD and a (H/D)COOD mixture (α D =0.36). A first-order difference method is used to determine the intra-molecular contribution through the introduction of a partial form-factor analysis technique incorporating a hydrogen-bond term. The method improves the sensitivity of the parameters defining the molecular geometry and avoids some of the ambiguities arising from terms involving spatial overlap of inter- and intra-molecular features. The possible application to other systems is briefly reviewed. (authors). 8 figs., 2 tabs., 8 refs

  18. Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect.

    Directory of Open Access Journals (Sweden)

    Guido Veit

    2016-05-01

    Full Text Available The most common cystic fibrosis (CF causing mutation, deletion of phenylalanine 508 (ΔF508 or Phe508del, results in functional expression defect of the CF transmembrane conductance regulator (CFTR at the apical plasma membrane (PM of secretory epithelia, which is attributed to the degradation of the misfolded channel at the endoplasmic reticulum (ER. Deletion of phenylalanine 670 (ΔF670 in the yeast oligomycin resistance 1 gene (YOR1, an ABC transporter of Saccharomyces cerevisiae phenocopies the ΔF508-CFTR folding and trafficking defects. Genome-wide phenotypic (phenomic analysis of the Yor1-ΔF670 biogenesis identified several modifier genes of mRNA processing and translation, which conferred oligomycin resistance to yeast. Silencing of orthologues of these candidate genes enhanced the ΔF508-CFTR functional expression at the apical PM in human CF bronchial epithelia. Although knockdown of RPL12, a component of the ribosomal stalk, attenuated the translational elongation rate, it increased the folding efficiency as well as the conformational stability of the ΔF508-CFTR, manifesting in 3-fold augmented PM density and function of the mutant. Combination of RPL12 knockdown with the corrector drug, VX-809 (lumacaftor restored the mutant function to ~50% of the wild-type channel in primary CFTRΔF508/ΔF508 human bronchial epithelia. These results and the observation that silencing of other ribosomal stalk proteins partially rescue the loss-of-function phenotype of ΔF508-CFTR suggest that the ribosomal stalk modulates the folding efficiency of the mutant and is a potential therapeutic target for correction of the ΔF508-CFTR folding defect.

  19. Location of frame overlap choppers on pulsed source instruments

    International Nuclear Information System (INIS)

    Narehood, D.G.; Pearce, J.V.; Sokol, P.E.

    2002-01-01

    A detailed study has been performed to investigate the effect of frame overlap in a cold neutron chopper spectrometer. The basic spectrometer is defined by two high-speed choppers, one near the moderator to shape the pulse from the moderator, and one near the sample to define energy resolution. Using ray-tracing timing diagrams, we have observed that there are regions along the guide where the trajectories of neutrons with different velocities converge temporally at characteristic points along the spectrometer. At these points of convergence, a frame overlap chopper would be totally ineffective, allowing neutrons of all velocities to pass through. Conversely, at points where trajectories of different velocity neutrons are divergent, a frame overlap chopper is most effective. An analytical model to describe this behaviour has been developed, and leads us to the counterintuitive conclusion that the optimum position for a frame overlap chopper is as close to the initial chopper as possible. We further demonstrate that detailed Monte Carlo simulations produce results which are consistent with this model

  20. Segmenting overlapping nano-objects in atomic force microscopy image

    Science.gov (United States)

    Wang, Qian; Han, Yuexing; Li, Qing; Wang, Bing; Konagaya, Akihiko

    2018-01-01

    Recently, techniques for nanoparticles have rapidly been developed for various fields, such as material science, medical, and biology. In particular, methods of image processing have widely been used to automatically analyze nanoparticles. A technique to automatically segment overlapping nanoparticles with image processing and machine learning is proposed. Here, two tasks are necessary: elimination of image noises and action of the overlapping shapes. For the first task, mean square error and the seed fill algorithm are adopted to remove noises and improve the quality of the original image. For the second task, four steps are needed to segment the overlapping nanoparticles. First, possibility split lines are obtained by connecting the high curvature pixels on the contours. Second, the candidate split lines are classified with a machine learning algorithm. Third, the overlapping regions are detected with the method of density-based spatial clustering of applications with noise (DBSCAN). Finally, the best split lines are selected with a constrained minimum value. We give some experimental examples and compare our technique with two other methods. The results can show the effectiveness of the proposed technique.

  1. Of overlapping Cantor sets and earthquakes: analysis of the discrete Chakrabarti-Stinchcombe model

    Science.gov (United States)

    Bhattacharyya, Pratip

    2005-03-01

    We report an exact analysis of a discrete form of the Chakrabarti-Stinchcombe model for earthquakes (Physica A 270 (1999) 27), which considers a pair of dynamically overlapping finite generations of the Cantor set as a prototype of geological faults. In this model the nth generation of the Cantor set shifts on its replica in discrete steps of the length of a line segment in that generation and periodic boundary conditions are assumed. We determine the general form of time sequences for the constant magnitude overlaps and, hence, obtain the complete time-series of overlaps by the superposition of these sequences for all overlap magnitudes. From the time-series we derive the exact frequency distribution of the overlap magnitudes. The corresponding probability distribution of the logarithm of overlap magnitudes for the nth generation is found to assume the form of the binomial distribution for n Bernoulli trials with probability {1}/{3} for the success of each trial. For an arbitrary pair of consecutive overlaps in the time-series where the magnitude of the earlier overlap is known, we find that the magnitude of the later overlap can be determined with a definite probability; the conditional probability for each possible magnitude of the later overlap follows the binomial distribution for k Bernoulli trials with probability {1}/{2} for the success of each trial and the number k is determined by the magnitude of the earlier overlap. Although this model does not produce the Gutenberg-Richter law for earthquakes, our results indicate that the fractal structure of faults admits a probabilistic prediction of earthquake magnitudes.

  2. Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses

    International Nuclear Information System (INIS)

    Firth, Andrew E.; Blitvich, Bradley J.; Wills, Norma M.; Miller, Cathy L.; Atkins, John F.

    2010-01-01

    Flaviviruses have a positive-sense, single-stranded RNA genome of ∼11 kb, encoding a large polyprotein that is cleaved to produce ∼10 mature proteins. Cell fusing agent virus, Kamiti River virus, Culex flavivirus and several recently discovered flaviviruses have no known vertebrate host and apparently infect only insects. We present compelling bioinformatic evidence for a 253-295 codon overlapping gene (designated fifo) conserved throughout these insect-specific flaviviruses and immunofluorescent detection of its product. Fifo overlaps the NS2A/NS2B coding sequence in the - 1/+ 2 reading frame and is most likely expressed as a trans-frame fusion protein via ribosomal frameshifting at a conserved GGAUUUY slippery heptanucleotide with 3'-adjacent RNA secondary structure (which stimulates efficient frameshifting in vitro). The discovery bears striking parallels to the recently discovered ribosomal frameshifting site in the NS2A coding sequence of the Japanese encephalitis serogroup of flaviviruses and suggests that programmed ribosomal frameshifting may be more widespread in flaviviruses than currently realized.

  3. Overlapping communities detection based on spectral analysis of line graphs

    Science.gov (United States)

    Gui, Chun; Zhang, Ruisheng; Hu, Rongjing; Huang, Guoming; Wei, Jiaxuan

    2018-05-01

    Community in networks are often overlapping where one vertex belongs to several clusters. Meanwhile, many networks show hierarchical structure such that community is recursively grouped into hierarchical organization. In order to obtain overlapping communities from a global hierarchy of vertices, a new algorithm (named SAoLG) is proposed to build the hierarchical organization along with detecting the overlap of community structure. SAoLG applies the spectral analysis into line graphs to unify the overlap and hierarchical structure of the communities. In order to avoid the limitation of absolute distance such as Euclidean distance, SAoLG employs Angular distance to compute the similarity between vertices. Furthermore, we make a micro-improvement partition density to evaluate the quality of community structure and use it to obtain the more reasonable and sensible community numbers. The proposed SAoLG algorithm achieves a balance between overlap and hierarchy by applying spectral analysis to edge community detection. The experimental results on one standard network and six real-world networks show that the SAoLG algorithm achieves higher modularity and reasonable community number values than those generated by Ahn's algorithm, the classical CPM and GN ones.

  4. On the interpretation of wave function overlaps in quantum dots

    DEFF Research Database (Denmark)

    Stobbe, Søren; Hvam, Jørn Märcher; Lodahl, Peter

    2011-01-01

    The spontaneous emission rate of excitons strongly confined in quantum dots (QDs) is proportional to the overlap integral of electron and hole envelope wave functions. A common and intuitive interpretation of this result is that the spontaneous emission rate is proportional to the probability...... that the electron and the hole are located at the same point or region in space, i.e., they must coincide spatially to recombine. Here, we show that this interpretation is not correct even loosely speaking. By general mathematical considerations we compare the envelope wave function overlap, the exchange overlap...... integral, and the probability of electrons and holes coinciding, and find that the frequency dependence of the envelope wave function overlap integral is very different from that expected from the common interpretation. We show that these theoretical considerations lead to predictions for measurements. We...

  5. Same-strand overlapping genes in bacteria: compositional determinants of phase bias

    Directory of Open Access Journals (Sweden)

    Landan Giddy

    2008-08-01

    Full Text Available Abstract Background Same-strand overlapping genes may occur in frameshifts of one (phase 1 or two nucleotides (phase 2. In previous studies of bacterial genomes, long phase-1 overlaps were found to be more numerous than long phase-2 overlaps. This bias was explained by either genomic location or an unspecified selection advantage. Models that focused on the ability of the two genes to evolve independently did not predict this phase bias. Here, we propose that a purely compositional model explains the phase bias in a more parsimonious manner. Same-strand overlapping genes may arise through either a mutation at the termination codon of the upstream gene or a mutation at the initiation codon of the downstream gene. We hypothesized that given these two scenarios, the frequencies of initiation and termination codons in the two phases may determine the number for overlapping genes. Results We examined the frequencies of initiation- and termination-codons in the two phases, and found that termination codons do not significantly differ between the two phases, whereas initiation codons are more abundant in phase 1. We found that the primary factors explaining the phase inequality are the frequencies of amino acids whose codons may combine to form start codons in the two phases. We show that the frequencies of start codons in each of the two phases, and, hence, the potential for the creation of overlapping genes, are determined by a universal amino-acid frequency and species-specific codon usage, leading to a correlation between long phase-1 overlaps and genomic GC content. Conclusion Our model explains the phase bias in same-strand overlapping genes by compositional factors without invoking selection. Therefore, it can be used as a null model of neutral evolution to test selection hypotheses concerning the evolution of overlapping genes. Reviewers This article was reviewed by Bill Martin, Itai Yanai, and Mikhail Gelfand.

  6. Overlapping bio-absorbable scaffolds: Aim for D2D technique?

    Science.gov (United States)

    Khan, Asaad A; Dangas, George D

    2018-06-01

    The results of overlapping metallic stents have been concerning but this practice is often unavoidable in the setting of long or tortuous lesions, diameter discrepancy of proximal and distal vessel, and for residual dissections. Theoretically, bio-absorbable scaffolds may carry an advantage over metallic stents due to the progressive resorption of the scaffold theoretically rendering the overlap a non-issue; this has not been clinically evident. Since stent/scaffold overlap cannot be entirely avoided, improved stent delivery/deployment and scaffold design modification may reduce complications in this complex patient subset. © 2018 Wiley Periodicals, Inc.

  7. Guided Classification System for Conceptual Overlapping Classes in OpenStreetMap

    Directory of Open Access Journals (Sweden)

    Ahmed Loai Ali

    2016-06-01

    Full Text Available The increased development of Volunteered Geographic Information (VGI and its potential role in GIScience studies raises questions about the resulting data quality. Several studies address VGI quality from various perspectives like completeness, positional accuracy, consistency, etc. They mostly have consensus on the heterogeneity of data quality. The problem may be due to the lack of standard procedures for data collection and absence of quality control feedback for voluntary participants. In our research, we are concerned with data quality from the classification perspective. Particularly in VGI-mapping projects, the limited expertise of participants and the non-strict definition of geographic features lead to conceptual overlapping classes, where an entity could plausibly belong to multiple classes, e.g., lake or pond, park or garden, marsh or swamp, etc. Usually, quantitative and/or qualitative characteristics exist that distinguish between classes. Nevertheless, these characteristics might not be recognizable for non-expert participants. In previous work, we developed the rule-guided classification approach that guides participants to the most appropriate classes. As exemplification, we tackle the conceptual overlapping of some grass-related classes. For a given data set, our approach presents the most highly recommended classes for each entity. In this paper, we present the validation of our approach. We implement a web-based application called Grass&Green that presents recommendations for crowdsourcing validation. The findings show the applicability of the proposed approach. In four months, the application attracted 212 participants from more than 35 countries who checked 2,865 entities. The results indicate that 89% of the contributions fully/partially agree with our recommendations. We then carried out a detailed analysis that demonstrates the potential of this enhanced data classification. This research encourages the development of

  8. Specific surface area of overlapping spheres in the presence of obstructions.

    Science.gov (United States)

    Jenkins, D R

    2013-02-21

    This study considers the random placement of uniform sized spheres, which may overlap, in the presence of another set of randomly placed (hard) spheres, which do not overlap. The overlapping spheres do not intersect the hard spheres. It is shown that the specific surface area of the collection of overlapping spheres is affected by the hard spheres, such that there is a minimum in the specific surface area as a function of the relative size of the two sets of spheres. The occurrence of the minimum is explained in terms of the break-up of pore connectivity. The configuration can be considered to be a simple model of the structure of a porous composite material. In particular, the overlapping particles represent voids while the hard particles represent fillers. Example materials are pervious concrete, metallurgical coke, ice cream, and polymer composites. We also show how the material properties of such composites are affected by the void structure.

  9. The overlap between cyberbullying and traditional bullying.

    Science.gov (United States)

    Waasdorp, Tracy E; Bradshaw, Catherine P

    2015-05-01

    Cyberbullying appears to be on the rise among adolescents due in part to increased access to electronic devices and less online supervision. Less is known about how cyberbullying differs from traditional bullying which occurs in person and the extent to which these two forms overlap. Our first aim was to examine the overlap of traditional bullying (relational, verbal, and physical) with cyberbullying. The second aim examined student- and school-level correlates of cyber victimization as compared to traditional victims. The final aim explored details of the cyberbullying experience (e.g., who sent the message, how was the message sent, and what was the message about). Data came from 28,104 adolescents (grades, 9-12) attending 58 high schools. Approximately 23% of the youth reported being victims of any form of bullying (cyber, relational, physical, and verbal) within the last month, with 25.6% of those victims reporting being cyberbullied. The largest proportion (50.3%) of victims reported they were victimized by all four forms, whereas only 4.6% reported being only cyberbullied. Multilevel analyses indicated that as compared to those who were only traditionally bullied, those who were cyberbullied were more likely to have externalizing (odds ratio = 1.44) and internalizing symptoms (odds ratio = 1.25). Additional analyses examined detailed characteristics of the cyberbullying experiences, indicating a relatively high level of overlap between cyber and traditional bullying. Implications for preventive interventions targeting youth involved with cyberbullying and its overlap with other forms of bullying are discussed. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

  10. Overlapping community detection using weighted consensus ...

    Indian Academy of Sciences (India)

    2016-09-21

    Sep 21, 2016 ... Complex networks; overlapping community; consensus clustering. PACS Nos 89.75 ... networks, a person may be in several social groups like family, friends ..... the social interactions between individuals in a karate club in an.

  11. Overlapping ETF: Pair trading between two gold stocks

    OpenAIRE

    Bell, Peter N; Lui, Brian; Brekke, Alex

    2012-01-01

    The purpose of this paper is to propose a trading strategy for overlapping ETF and calculate the profitability using real price data. For two overlapping ETF that are designed to provide the same intraday percentage change, the difference in percentage changes is a measure of mispricing. This mispricing is the central focus of the paper. The premise of the paper is that mispricing can take large positive or negative values, but it will always come back to zero. This assumption reflects ou...

  12. Optimal overlapping of waveform relaxation method for linear differential equations

    International Nuclear Information System (INIS)

    Yamada, Susumu; Ozawa, Kazufumi

    2000-01-01

    Waveform relaxation (WR) method is extremely suitable for solving large systems of ordinary differential equations (ODEs) on parallel computers, but the convergence of the method is generally slow. In order to accelerate the convergence, the methods which decouple the system into many subsystems with overlaps some of the components between the adjacent subsystems have been proposed. The methods, in general, converge much faster than the ones without overlapping, but the computational cost per iteration becomes larger due to the increase of the dimension of each subsystem. In this research, the convergence of the WR method for solving constant coefficients linear ODEs is investigated and the strategy to determine the number of overlapped components which minimizes the cost of the parallel computations is proposed. Numerical experiments on an SR2201 parallel computer show that the estimated number of the overlapped components by the proposed strategy is reasonable. (author)

  13. Resolution enhancement of holographic printer using a hogel overlapping method.

    Science.gov (United States)

    Hong, Keehoon; Park, Soon-gi; Yeom, Jiwoon; Kim, Jonghyun; Chen, Ni; Pyun, Kyungsuk; Choi, Chilsung; Kim, Sunil; An, Jungkwuen; Lee, Hong-Seok; Chung, U-in; Lee, Byoungho

    2013-06-17

    We propose a hogel overlapping method for the holographic printer to enhance the lateral resolution of holographic stereograms. The hogel size is directly related to the lateral resolution of the holographic stereogram. Our analysis by computer simulation shows that there is a limit to decreasing the hogel size while printing holographic stereograms. Instead of reducing the size of hogel, the lateral resolution of holographic stereograms can be enhanced by printing overlapped hogels, which makes it possible to take advantage of multiplexing property of the volume hologram. We built a holographic printer, and recorded two holographic stereograms using the conventional and proposed overlapping methods. The images and movies of the holographic stereograms experimentally captured were compared between the conventional and proposed methods. The experimental results confirm that the proposed hogel overlapping method improves the lateral resolution of holographic stereograms compared to the conventional holographic printing method.

  14. The overlapping community structure of structural brain network in young healthy individuals.

    Directory of Open Access Journals (Sweden)

    Kai Wu

    2011-05-01

    Full Text Available Community structure is a universal and significant feature of many complex networks in biology, society, and economics. Community structure has also been revealed in human brain structural and functional networks in previous studies. However, communities overlap and share many edges and nodes. Uncovering the overlapping community structure of complex networks remains largely unknown in human brain networks. Here, using regional gray matter volume, we investigated the structural brain network among 90 brain regions (according to a predefined anatomical atlas in 462 young, healthy individuals. Overlapped nodes between communities were defined by assuming that nodes (brain regions can belong to more than one community. We demonstrated that 90 brain regions were organized into 5 overlapping communities associated with several well-known brain systems, such as the auditory/language, visuospatial, emotion, decision-making, social, control of action, memory/learning, and visual systems. The overlapped nodes were mostly involved in an inferior-posterior pattern and were primarily related to auditory and visual perception. The overlapped nodes were mainly attributed to brain regions with higher node degrees and nodal efficiency and played a pivotal role in the flow of information through the structural brain network. Our results revealed fuzzy boundaries between communities by identifying overlapped nodes and provided new insights into the understanding of the relationship between the structure and function of the human brain. This study provides the first report of the overlapping community structure of the structural network of the human brain.

  15. The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2007-09-01

    Full Text Available Abtract Background The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully integrated with the host cell cycle and is so altered in structure as to be difficult to recognize it as a diatom, and yet it retains a number of features normally lost in tertiary and secondary endosymbionts, most notably mitochondria. The dinoflagellate host is also reported to retain mitochondrion-like structures, making these cells unique in retaining two evolutionarily distinct mitochondria. This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them. Results We show that both host and endosymbiont mitochondrial genomes encode genes for electron transport proteins. We have characterized cytochrome c oxidase 1 (cox1, cytochrome oxidase 2 (cox2, cytochrome oxidase 3 (cox3, cytochrome b (cob, and large subunit of ribosomal RNA (LSUrRNA of endosymbiont mitochondrial ancestry, and cox1 and cob of host mitochondrial ancestry. We show that all genes are transcribed and that those ascribed to the host mitochondrial genome are extensively edited at the RNA level, as expected for a dinoflagellate mitochondrion-encoded gene. We also found evidence for extensive recombination in the host mitochondrial genes and that recombination products are also transcribed, as expected for a dinoflagellate. Conclusion Durinskia baltica and K. foliaceum retain two mitochondria from evolutionarily distinct lineages, and the functions of these organelles are at least partially overlapping, since both express genes for proteins in electron transport.

  16. Overlapped flowers yield detection using computer-based interface

    Directory of Open Access Journals (Sweden)

    Anuradha Sharma

    2016-09-01

    Full Text Available Precision agriculture has always dealt with the accuracy and timely information about agricultural products. With the help of computer hardware and software technology designing a decision support system that could generate flower yield information and serve as base for management and planning of flower marketing is made so easy. Despite such technologies, some problem still arise, for example, a colour homogeneity of a specimen which cannot be obtained similar to actual colour of image and overlapping of image. In this paper implementing a new ‘counting algorithm’ for overlapped flower is being discussed. For implementing this algorithm, some techniques and operations such as colour image segmentation technique, image segmentation, using HSV colour space and morphological operations have been used. In this paper used two most popular colour space; those are RGB and HSV. HSV colour space decouples brightness from a chromatic component in the image, by which it provides better result in case for occlusion and overlapping.

  17. An Economical Analytical Equation for the Integrated Vertical Overlap of Cumulus and Stratus

    Science.gov (United States)

    Park, Sungsu

    2018-03-01

    By extending the previously proposed heuristic parameterization, the author derived an analytical equation computing the overlap areas between the precipitation (or radiation) areas and the cloud areas in a cloud system consisting of cumulus and stratus. The new analytical equation is accurate and much more efficient than the previous heuristic equation, which suffers from the truncation error in association with the digitalization of the overlap areas. Global test simulations with the new analytical formula in an offline mode showed that the maximum cumulus overlap simulates more surface precipitation flux than the random cumulus overlap. On the other hand, the maximum stratus overlap simulates less surface precipitation flux than random stratus overlap, which is due to the increase in the evaporation rate of convective precipitation from the random to maximum stratus overlap. The independent precipitation approximation (IPA) marginally decreases the surface precipitation flux, implying that IPA works well with other parameterizations. In contrast to the net production rate of precipitation and surface precipitation flux that increase when the cumulus and stratus are maximally and randomly overlapped, respectively, the global mean net radiative cooling and longwave cloud radiative forcing (LWCF) increase when the cumulus and stratus are randomly overlapped. On the global average, the vertical cloud overlap exerts larger impacts on the precipitation flux than on the radiation flux. The radiation scheme taking the subgrid variability of water vapor between the cloud and clear portions into account substantially increases the global mean LWCF in tropical deep convection and midlatitude storm track regions.

  18. Overlapping sphincteroplasty and posterior repair.

    Science.gov (United States)

    Crane, Andrea K; Myers, Erinn M; Lippmann, Quinn K; Matthews, Catherine A

    2014-12-01

    Knowledge of how to anatomically reconstruct extensive posterior-compartment defects is variable among gynecologists. The objective of this video is to demonstrate an effective technique of overlapping sphincteroplasty and posterior repair. In this video, a scripted storyboard was constructed that outlines the key surgical steps of a comprehensive posterior compartment repair: (1) surgical incision that permits access to posterior compartment and perineal body, (2) dissection of the rectovaginal space up to the level of the cervix, (3) plication of the rectovaginal muscularis, (4) repair of internal and external anal sphincters, and (5) reconstruction of the perineal body. Using a combination of graphic illustrations and live video footage, tips on repair are highlighted. The goals at the end of repair are to: (1) have improved vaginal caliber, (2) increase rectal tone along the entire posterior vaginal wall, (3) have the posterior vaginal wall at a perpendicular plane to the perineal body, (4) reform the hymenal ring, and (5) not have an overly elongated perineal body. This video provides a step-by-step guide on how to perform an overlapping sphincteroplasty and posterior repair.

  19. Evidence for a novel coding sequence overlapping the 5'-terminal ~90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2009-12-01

    Full Text Available Abstract The genus Okavirus (order Nidovirales includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of ~26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.

  20. Optimizing Bandwidth Limited Problems Using One-SidedCommunication and Overlap

    Energy Technology Data Exchange (ETDEWEB)

    Bell, Christian; Bonachea, Dan; Nishtala, Rajesh; Yelick, Katherine

    2005-10-14

    Partitioned Global Address Space languages like Unified Parallel C (UPC) are typically valued for their expressiveness, especially for computations with fine-grained random accesses. In this paper we show that the one-sided communication model used in these languages also has a significant performance advantage for bandwidth-limited applications. We demonstrate this benefit through communication microbenchmarks and a case-study that compares UPC and MPI implementations of the NAS Fourier Transform (FT) benchmark. Our optimizations rely on aggressively overlapping communication with computation but spreading communication events throughout the course of the local computation. This alleviates the potential communication bottleneck that occurs when the communication is packed into a single phase (e.g., the large all-to-all in a multidimensional FFT). Even though the new algorithms require more messages for the same total volume of data, the resulting overlap leads to speedups of over 1.75x and 1.9x for the two-sided and one-sided implementations, respectively, when compared to the default NAS Fortran/MPI release. Our best one-sided implementations show an average improvement of 15 percent over our best two-sided implementations. We attribute this difference to the lower software overhead of one-sided communication, which is partly fundamental to the semantic difference between one-sided and two-sided communication. Our UPC results use the Berkeley UPC compiler with the GASNet communication system, and demonstrate the portability and scalability of that language and implementation, with performance approaching 0.5TFlop/s on the FT benchmark running on 512 processors.

  1. Therapeutic approaches to asthma-chronic obstructive pulmonary disease overlap syndromes.

    Science.gov (United States)

    Barnes, Peter J

    2015-09-01

    The recognition that there are some patients with features of asthma and chronic obstructive pulmonary disease (COPD) has highlighted the need to develop more specific treatments for these clinical phenotypes. Some patients with COPD have predominantly eosinophilic inflammation and might respond to high doses of inhaled corticosteroids and newly developed specific antieosinophil therapies, including blocking antibodies against IL-5, IL-13, IL-33, and thymic stromal lymphopoietin, as well as oral chemoattractant receptor-homologous molecule expressed on TH2 cells antagonists. Other patients have severe asthma or are asthmatic patients who smoke with features of COPD-induced inflammation and might benefit from treatments targeting neutrophils, including macrolides, CXCR2 antagonists, phosphodiesterase 4 inhibitors, p38 mitogen-activating protein kinase inhibitors, and antibodies against IL-1 and IL-17. Other patients appear to have largely fixed obstruction with little inflammation and might respond to long-acting bronchodilators, including long-acting muscarinic antagonists, to reduce hyperinflation. Highly selected patients with severe asthma might benefit from bronchial thermoplasty. Some patients with overlap syndromes can be conveniently treated with triple fixed-dose combination inhaler therapy with an inhaled corticosteroid, long-acting β2-agonist, and long-acting muscarinic antagonist, several of which are now in development. Corticosteroid resistance is a feature of asthma-COPD overlap syndrome, and understanding the various molecular mechanisms of this resistance has identified novel therapeutic targets and presented the prospect of therapies that can restore corticosteroid responsiveness. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  2. Overlapping Chronic Pain Conditions: Implications for Diagnosis and Classification.

    Science.gov (United States)

    Maixner, William; Fillingim, Roger B; Williams, David A; Smith, Shad B; Slade, Gary D

    2016-09-01

    There is increasing recognition that many if not most common chronic pain conditions are heterogeneous with a high degree of overlap or coprevalence of other common pain conditions along with influences from biopsychosocial factors. At present, very little attention is given to the high degree of overlap of many common pain conditions when recruiting for clinical trials. As such, many if not most patients enrolled into clinical studies are not representative of most chronic pain patients. The failure to account for the heterogeneous and overlapping nature of most common pain conditions may result in treatment responses of small effect size when these treatments are administered to patients with chronic overlapping pain conditions (COPCs) represented in the general population. In this brief review we describe the concept of COPCs and the putative mechanisms underlying COPCs. Finally, we present a series of recommendations that will advance our understanding of COPCs. This brief review describes the concept of COPCs. A mechanism-based heuristic model is presented and current knowledge and evidence for COPCs are presented. Finally, a set of recommendations is provided to advance our understanding of COPCs. Copyright © 2016 American Pain Society. Published by Elsevier Inc. All rights reserved.

  3. Derivation of a macroscale formulation for a class of nonlinear partial differential equations

    International Nuclear Information System (INIS)

    Pantelis, G.

    1995-05-01

    A macroscale formulation is constructed from a system of partial differential equations which govern the microscale dependent variables. The construction is based upon the requirement that the solutions of the macroscale partial differential equations satisfy, in some approximate sense, the system of partial differential equations associated with the microscale. These results are restricted to the class of nonlinear partial differential equations which can be expressed as polynomials of the dependent variables and their partial derivatives up to second order. A linear approximation of transformations of second order contact manifolds is employed. 6 refs

  4. Angular overlap model in actinides

    International Nuclear Information System (INIS)

    Gajek, Z.; Mulak, J.

    1991-01-01

    Quantitative foundations of the Angular Overlap Model in actinides based on ab initio calculations of the crystal field effect in the uranium (III) (IV) and (V) ions in various crystals are presented. The calculations justify some common simplifications of the model and fix up the relations between the AOM parameters. Traps and limitations of the AOM phenomenology are discussed

  5. Angular overlap model in actinides

    Energy Technology Data Exchange (ETDEWEB)

    Gajek, Z.; Mulak, J. (Polska Akademia Nauk, Wroclaw (PL). Inst. Niskich Temperatur i Badan Strukturalnych)

    1991-01-01

    Quantitative foundations of the Angular Overlap Model in actinides based on ab initio calculations of the crystal field effect in the uranium (III) (IV) and (V) ions in various crystals are presented. The calculations justify some common simplifications of the model and fix up the relations between the AOM parameters. Traps and limitations of the AOM phenomenology are discussed.

  6. Partial correction of a severe molecular defect in hemophilia A, because of errors during expression of the factor VIII gene

    Energy Technology Data Exchange (ETDEWEB)

    Young, M.; Antonarakis, S.E. [Univ. of Geneva (Switzerland); Inaba, Hiroshi [Tokyo Medical College (Japan)] [and others

    1997-03-01

    Although the molecular defect in patients in a Japanese family with mild to moderately severe hemophilia A was a deletion of a single nucleotide T within an A{sub 8}TA{sub 2} sequence of exon 14 of the factor VIII gene, the severity of the clinical phenotype did not correspond to that expected of a frameshift mutation. A small amount of functional factor VIII protein was detected in the patient`s plasma. Analysis of DNA and RNA molecules from normal and affected individuals and in vitro transcription/translation suggested a partial correction of the molecular defect, because of the following: (i) DNA replication/RNA transcription errors resulting in restoration of the reading frame and/or (ii) {open_quotes}ribosomal frameshifting{close_quotes} resulting in the production of normal factor VIII polypeptide and, thus, in a milder than expected hemophilia A. All of these mechanisms probably were promoted by the longer run of adenines, A{sub 10} instead of A{sub 8}TA{sub 2}, after the delT. Errors in the complex steps of gene expression therefore may partially correct a severe frameshift defect and ameliorate an expected severe phenotype. 36 refs., 6 figs.

  7. Symmetry and symmetry restoration of lattice chiral fermions in the overlap formalism

    International Nuclear Information System (INIS)

    Kikukawa, Y.

    1999-01-01

    Three aspects of the symmetry structure of lattice chiral fermions in the overlap formalism are discussed. By the weak coupling expansion of the overlap Dirac operator, the axial anomaly associated to the chiral transformation proposed by Luescher is evaluated and is shown to have the correct form of the topological charge density for perturbative backgrounds. Next we discuss the exponential suppression of the self-energy correction of the lightest mode in the domain-wall fermion/truncated overlap. Finally, we consider a supersymmetric extension of the overlap formula in the case of the chiral multiplet and examine the symmetry structure of the action

  8. Improving Phrap-based assembly of the rat using "reliable" overlaps.

    Directory of Open Access Journals (Sweden)

    Michael Roberts

    2008-03-01

    Full Text Available The assembly methods used for whole-genome shotgun (WGS data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of "reliable" overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our "reliable-overlap" algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.

  9. Segmentation of Overlapping Shapes using Test Ray Intersections

    DEFF Research Database (Denmark)

    Rasmusson, Allan

    As the use of digital images have become standard in everyday bioimaging, people are naturally trying to utilize computer algorithms for automating laborious and repetetive image analysis tasks. A preliminary task is the segmentation of structures of interest from digital images. This may in itself....... This may, however, quickly lead to the implementation of complex descriptions of any possible configuration the overlapping shapes may appear in. Presented here is a new approach to segment overlapping shapes which utilizes information gained from probing the image with test rays. Test rays intersections...

  10. Improving Inversions of the Overlap Operator

    International Nuclear Information System (INIS)

    Krieg, S.; Cundy, N.; Eshof, J. van den; Frommer, A.; Lippert, Th.; Schaefer, K.

    2005-01-01

    We present relaxation and preconditioning techniques which accelerate the inversion of the overlap operator by a factor of four on small lattices, with larger gains as the lattice size increases. These improvements can be used in both propagator calculations and dynamical simulations

  11. Low Self-Control and the Victim-Offender Overlap: A Gendered Analysis.

    Science.gov (United States)

    Flexon, Jamie L; Meldrum, Ryan C; Piquero, Alex R

    2016-07-01

    The overlap between victimization and offending is well documented. Yet, there have been fewer investigations of the reasons underlying this relationship. One possible, but understudied, explanation lies with Gottfredson and Hirschi's arguments regarding self-control. The current study adds to this line of inquiry by assessing whether low self-control accounts for the victim-offender overlap in a sample of young adults and whether self-control accounts for the observed overlap similarly across gender. Results from a series of bivariate probit regression models indicate that low self-control is positively related to both victimization and offending. However, only among males does low self-control account for a substantive portion of the victim-offender overlap. Limitations of the study and implications and directions for future research are discussed. © The Author(s) 2015.

  12. Mechanisms of ceramide-induced COX-2-dependent apoptosis in human ovarian cancer OVCAR-3 cells partially overlapped with resveratrol

    DEFF Research Database (Denmark)

    Lin, Hung-Yun; Delmas, Dominique; Vang, Ole

    2013-01-01

    -2 appears at the apex of the p38 kinase-mediated signaling cascade induced by ceramide. Induction of apoptosis by ceramide or resveratrol was inhibited by the endocytosis inhibitor, cytochalasin D (CytD); however, cells exposed to resveratrol showed greater sensitivity than ceramide-treated cells....... Ceramide-treated cells underwent a dose-dependent reduction in trans-membrane potential. Although both ceramide and resveratrol induced the expressions of caspase-3 and -7, the effect of inducible COX-2 was different in caspase-7 expression induced by ceramide compared to resveratrol. In summary......, resveratrol and ceramide converge on an endocytosis-requiring, ERK1/2-dependent signal transduction pathway and induction of COX-expression as an essential molecular antecedent for subsequent p53-dependent apoptosis. In addition, expressions of caspase-3 and -7 are observed. However, a p38 kinase...

  13. Speech overlap detection in a two-pass speaker diarization system

    NARCIS (Netherlands)

    Huijbregts, M.A.H.; Leeuwen, D.A. van; Jong, F. M. G de

    2009-01-01

    In this paper we present the two-pass speaker diarization system that we developed for the NIST RT09s evaluation. In the first pass of our system a model for speech overlap detection is gen- erated automatically. This model is used in two ways to reduce the diarization errors due to overlapping

  14. Speech overlap detection in a two-pass speaker diarization system

    NARCIS (Netherlands)

    Huijbregts, M.; Leeuwen, D.A. van; Jong, F.M.G. de

    2009-01-01

    In this paper we present the two-pass speaker diarization system that we developed for the NIST RT09s evaluation. In the first pass of our system a model for speech overlap detection is generated automatically. This model is used in two ways to reduce the diarization errors due to overlapping

  15. Comparisons of Satellite-Deduced Overlapping Cloud Properties and CALIPSO CloudSat Data

    Science.gov (United States)

    Chang, Fu-Lung; Minnis, Patrick; Lin, Bing; Sun-Mack, Sunny

    2010-01-01

    Introduction to the overlapped cloud properties derived from polar-orbiting (MODIS) and geostationary (GOES-12, -13, Meteosat-8, -9, etc.) meteorological satellites, which are produced at the NASA Langley Research Center (LaRC) cloud research & development team (NASA lead scientist: Dr. Patrick Minnis). Comparison of the LaRC CERES MODIS Edition-3 overlapped cloud properties to the CALIPSO and the CloudSat active sensing data. High clouds and overlapped clouds occur frequently as deduced by CALIPSO (44 & 25%), CloudSat (25 & 4%), and MODIS (37 & 6%). Large fractions of optically-thin cirrus and overlapped clouds are deduced from CALIPSO, but much smaller fractions are from CloudSat and MODIS. For overlapped clouds, the averaged upper-layer CTHs are about 12.8 (CALIPSO), 10.9 (CloudSat) and 10 km (MODIS), and the averaged lower-layer CTHs are about 3.6 (CALIPSO), 3.2 (CloudSat) and 3.9 km (MODIS). Based on comparisons of upper and lower-layer cloud properties as deduced from the MODIS, CALIPSO and CloudSat data, more enhanced passive satellite methods for retrieving thin cirrus and overlapped cloud properties are needed and are under development.

  16. Partial dependency parsing for Irish

    OpenAIRE

    Uí Dhonnchadha, Elaine; van Genabith, Josef

    2010-01-01

    In this paper we present a partial dependency parser for Irish, in which Constraint Grammar (CG) rules are used to annotate dependency relations and grammatical functions in unrestricted Irish text. Chunking is performed using a regular-expression grammar which operates on the dependency tagged sentences. As this is the first implementation of a parser for unrestricted Irish text (to our knowledge), there were no guidelines or precedents available. Therefore deciding what constitutes a syntac...

  17. [Symptom overlaps between functional heartburn, functional dyspepsia, and irritable bowel syndrome].

    Science.gov (United States)

    2014-05-01

    To determine symptom overlaps between functional heartburn (FH), functional dyspepsia (FD), and irritable bowel syndrome (IBS). One hundred and ten patients with frequent heartburn but no mucosa breakage under endoscopy were enrolled consecutively. They were required to fill out a questionnaire. The overlapped symptoms of FD and IBS symptoms were screened using Rome ill criteria. The participants were also examined using Hamilton anxiety scale/Hamilton depression scale. All of the participants were followed with 24 h esophageal multichannel intra-luminal impedance monitoring with pH sensor (MII-pH) monitoring and proton pump inhibitor (PPI) trials. The participants were divided into non-erosive reflux disease (NERD) and FH groups. The prevalence of symptom overlaps FD and IBS, between NERD and FH groups was analyzed. Women were more likely to present with FH than with NERD (P heartburn symptom had FD symptoms; 31 (28.2%) had IBS symptoms, and 10 (9.09%) had both FD and IBS symptoms. Patients with FH were more likely to have symptom overlaps of FD and IBS than those with NERD (62% vs. 35%, 48% vs. 11.7%, respectively; P 0.05). IBS-diarrhea was also slightly more likely to have overlapped NERD and FH symptoms than IBS-constipation. Again, the difference was not significant (16.4% vs. 11.8%, P > 0.05). Female, higher prevalence of anxiety and depression, overlapped FD and IBS symptoms are more likely to appear in FH patients than in NERD patients.

  18. Partial Portal Vein Arterialization Attenuates Acute Bile Duct Injury Induced by Hepatic Dearterialization in a Rat Model.

    Science.gov (United States)

    Jiang, Jun; Wei, Jishu; Wu, Junli; Gao, Wentao; Li, Qiang; Jiang, Kuirong; Miao, Yi

    2016-01-01

    Hepatic infarcts or abscesses occur after hepatic artery interruption. We explored the mechanisms of hepatic deprivation-induced acute liver injury and determine whether partial portal vein arterialization attenuated this injury in rats. Male Sprague-Dawley rats underwent either complete hepatic arterial deprivation or partial portal vein arterialization, or both. Hepatic ischemia was evaluated using biochemical analysis, light microscopy, and transmission electron microscopy. Hepatic ATP levels, the expression of hypoxia- and inflammation-associated genes and proteins, and the expression of bile transporter genes were assessed. Complete dearterialization of the liver induced acute liver injury, as evidenced by the histological changes, significantly increased serum biochemical markers, decreased ATP content, increased expression of hypoxia- and inflammation-associated genes and proteins, and decreased expression of bile transporter genes. These detrimental changes were extenuated but not fully reversed by partial portal vein arterialization, which also attenuated ductular reaction and fibrosis in completely dearterialized rat livers. Collectively, complete hepatic deprivation causes severe liver injury, including bile infarcts and biloma formation. Partial portal vein arterialization seems to protect against acute ischemia-hypoxia-induced liver injury.

  19. Partial Portal Vein Arterialization Attenuates Acute Bile Duct Injury Induced by Hepatic Dearterialization in a Rat Model

    Directory of Open Access Journals (Sweden)

    Jun Jiang

    2016-01-01

    Full Text Available Hepatic infarcts or abscesses occur after hepatic artery interruption. We explored the mechanisms of hepatic deprivation-induced acute liver injury and determine whether partial portal vein arterialization attenuated this injury in rats. Male Sprague-Dawley rats underwent either complete hepatic arterial deprivation or partial portal vein arterialization, or both. Hepatic ischemia was evaluated using biochemical analysis, light microscopy, and transmission electron microscopy. Hepatic ATP levels, the expression of hypoxia- and inflammation-associated genes and proteins, and the expression of bile transporter genes were assessed. Complete dearterialization of the liver induced acute liver injury, as evidenced by the histological changes, significantly increased serum biochemical markers, decreased ATP content, increased expression of hypoxia- and inflammation-associated genes and proteins, and decreased expression of bile transporter genes. These detrimental changes were extenuated but not fully reversed by partial portal vein arterialization, which also attenuated ductular reaction and fibrosis in completely dearterialized rat livers. Collectively, complete hepatic deprivation causes severe liver injury, including bile infarcts and biloma formation. Partial portal vein arterialization seems to protect against acute ischemia-hypoxia-induced liver injury.

  20. Listeria monocytogenes differential transcriptome analysis reveals temperature-dependent Agr regulation and suggests overlaps with other regulons.

    Science.gov (United States)

    Garmyn, Dominique; Augagneur, Yoann; Gal, Laurent; Vivant, Anne-Laure; Piveteau, Pascal

    2012-01-01

    Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its ΔagrA mutant at the saprophytic temperature of 25°C and in vivo temperature of 37°C. Variations of transcriptome were higher at 37°C than at 25°C. Results suggested that AgrA may be involved in the regulation of nitrogen transport, amino acids, purine and pyrimidine biosynthetic pathways and phage-related functions. Deregulations resulted in a growth advantage at 37°C, but affected salt tolerance. Finally, our results suggest overlaps with PrfA, σB, σH and CodY regulons. These overlaps may suggest that through AgrA, Listeria monocytogenes integrates information on its biotic environment.

  1. Generalized morphea/eosinophilic fasciitis overlap after epoxy exposure

    Directory of Open Access Journals (Sweden)

    Warren H. Chan, MS

    2018-03-01

    Full Text Available Generalized morphea is associated with epoxy resin vapors and is characterized by the development of lesions shortly after exposure. Morphea presenting along with eosinophilic fasciitis (EF, or morphea/EF overlap, is rare and an indicator of poor prognosis and resistance to treatment. Here we present a case of generalized morphea/EF overlap linked to epoxy exposure. Our patient received multiple therapies—ultraviolet A1 phototherapy, prednisone, methotrexate, azathioprine, mycophenolate mofetil, cyclophosphamide, cyclosporine, and rituximab—none of which led to a significant response. The refractory nature of this disease warrants vigilance in its association with epoxy exposure.

  2. Walkable self-overlapping virtual reality maze and map visualization demo

    DEFF Research Database (Denmark)

    Serubugo, Sule; Skantarova, Denisa; Evers, Nicolaj

    2017-01-01

    This paper describes our demonstration of a walkable self-overlapping maze and its corresponding map to facilitate asymmetric collaboration for room-scale virtual reality setups in public places.......This paper describes our demonstration of a walkable self-overlapping maze and its corresponding map to facilitate asymmetric collaboration for room-scale virtual reality setups in public places....

  3. [The automatic iris map overlap technology in computer-aided iridiagnosis].

    Science.gov (United States)

    He, Jia-feng; Ye, Hu-nian; Ye, Miao-yuan

    2002-11-01

    In the paper, iridology and computer-aided iridiagnosis technologies are briefly introduced and the extraction method of the collarette contour is then investigated. The iris map can be overlapped on the original iris image based on collarette contour extraction. The research on collarette contour extraction and iris map overlap is of great importance to computer-aided iridiagnosis technologies.

  4. An empirical analysis of overlap publication in Chinese language and English research manuscripts.

    Directory of Open Access Journals (Sweden)

    Joseph D Tucker

    Full Text Available BACKGROUND: There are a number of sound justifications for publishing nearly identical information in Chinese and English medical journals, assuming several conditions are met. Although overlap publication is perceived as undesirable and ethically questionable in Europe and North America, it may serve an important function in some regions where English is not the native tongue. There is no empirical data on the nature and degree of overlap publication in English and Chinese language journals. METHODS/PRINCIPAL FINDINGS: A random sample of 100 English manuscripts from Chinese institutions was selected from PubMed. Key words and institutions were searched in the China National Knowledge Infrastructure, a comprehensive Chinese language research database. Unacknowledged overlap was a priori defined according to International Committee of Medical Journal Editor (ICMJE guidelines following examination by two individuals. 19% (95% CI 11-27 of English manuscripts from Chinese institutions were found to have substantial overlap with Chinese published work based on full text examination. None of the manuscripts met all of the criteria established by the ICMJE for an acknowledged overlap publication. Individual-level, journal-level, and institutional factors seem to influence overlap publication. Manuscripts associated with an institution outside of China and with more than one institution were significantly less likely to have substantial overlap (p<0.05. CONCLUSIONS/SIGNIFICANCE: Overlap publication was common in this context, but instances of standard ICMJE notations to acknowledge this practice were rare. This research did not cite the identified overlap manuscripts with the hope that these empirical data will inform journal policy changes and structural initiatives to promote clearer policies and manuscripts.

  5. Continuum-limit scaling of overlap fermions as valence quarks

    International Nuclear Information System (INIS)

    Cichy, Krzysztof; Herdoiza, Gregorio; Jansen, Karl

    2009-10-01

    We present the results of a mixed action approach, employing dynamical twisted mass fermions in the sea sector and overlap valence fermions, with the aim of testing the continuum limit scaling behaviour of physical quantities, taking the pion decay constant as an example. To render the computations practical, we impose for this purpose a fixed finite volume with lattice size L∼1.3 fm. We also briefly review the techniques we have used to deal with overlap fermions. (orig.)

  6. Solving radiative transfer with line overlaps using Gauss-Seidel algorithms

    Science.gov (United States)

    Daniel, F.; Cernicharo, J.

    2008-09-01

    Context: The improvement in observational facilities requires refining the modelling of the geometrical structures of astrophysical objects. Nevertheless, for complex problems such as line overlap in molecules showing hyperfine structure, a detailed analysis still requires a large amount of computing time and thus, misinterpretation cannot be dismissed due to an undersampling of the whole space of parameters. Aims: We extend the discussion of the implementation of the Gauss-Seidel algorithm in spherical geometry and include the case of hyperfine line overlap. Methods: We first review the basics of the short characteristics method that is used to solve the radiative transfer equations. Details are given on the determination of the Lambda operator in spherical geometry. The Gauss-Seidel algorithm is then described and, by analogy to the plan-parallel case, we see how to introduce it in spherical geometry. Doing so requires some approximations in order to keep the algorithm competitive. Finally, line overlap effects are included. Results: The convergence speed of the algorithm is compared to the usual Jacobi iterative schemes. The gain in the number of iterations is typically factors of 2 and 4 for the two implementations made of the Gauss-Seidel algorithm. This is obtained despite the introduction of approximations in the algorithm. A comparison of results obtained with and without line overlaps for N2H^+, HCN, and HNC shows that the J=3-2 line intensities are significantly underestimated in models where line overlap is neglected.

  7. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms.

    Science.gov (United States)

    Taillon-Miller, P; Gu, Z; Li, Q; Hillier, L; Kwok, P Y

    1998-07-01

    An efficient strategy to develop a dense set of single-nucleotide polymorphism (SNP) markers is to take advantage of the human genome sequencing effort currently under way. Our approach is based on the fact that bacterial artificial chromosomes (BACs) and P1-based artificial chromosomes (PACs) used in long-range sequencing projects come from diploid libraries. If the overlapping clones sequenced are from different lineages, one is comparing the sequences from 2 homologous chromosomes in the overlapping region. We have analyzed in detail every SNP identified while sequencing three sets of overlapping clones found on chromosome 5p15.2, 7q21-7q22, and 13q12-13q13. In the 200.6 kb of DNA sequence analyzed in these overlaps, 153 SNPs were identified. Computer analysis for repetitive elements and suitability for STS development yielded 44 STSs containing 68 SNPs for further study. All 68 SNPs were confirmed to be present in at least one of the three (Caucasian, African-American, Hispanic) populations studied. Furthermore, 42 of the SNPs tested (62%) were informative in at least one population, 32 (47%) were informative in two or more populations, and 23 (34%) were informative in all three populations. These results clearly indicate that developing SNP markers from overlapping genomic sequence is highly efficient and cost effective, requiring only the two simple steps of developing STSs around the known SNPs and characterizing them in the appropriate populations.

  8. Immunohistochemical analyses of cell cycle progression and gene expression of biliary epithelial cells during liver regeneration after partial hepatectomy of the mouse.

    Science.gov (United States)

    Fukuda, Tatsuya; Fukuchi, Tomokazu; Yagi, Shinomi; Shiojiri, Nobuyoshi

    2016-05-20

    The liver has a remarkable regeneration capacity, and, after surgical removal of its mass, the remaining tissue undergoes rapid regeneration through compensatory growth of its constituent cells. Although hepatocytes synchronously proliferate under the control of various signaling molecules from neighboring cells, there have been few detailed analyses on how biliary cells regenerate for their cell population after liver resection. The present study was undertaken to clarify how biliary cells regenerate after partial hepatectomy of mice through extensive analyses of their cell cycle progression and gene expression using immunohistochemical and RT-PCR techniques. When expression of PCNA, Ki67 antigen, topoisomerase IIα and phosphorylated histone H3, which are cell cycle markers, was immunohistochemically examined during liver regeneration, hepatocytes had a peak of the S phase and M phase at 48-72 h after resection. By contrast, biliary epithelial cells had much lower proliferative activity than that of hepatocytes, and their peak of the S phase was delayed. Mitotic figures were rarely detectable in biliary cells. RT-PCR analyses of gene expression of biliary markers such as Spp1 (osteopontin), Epcam and Hnf1b demonstrated that they were upregulated during liver regeneration. Periportal hepatocytes expressed some of biliary markers, including Spp1 mRNA and protein. Some periportal hepatocytes had downregulated expression of HNF4α and HNF1α. Gene expression of Notch signaling molecules responsible for cell fate decision of hepatoblasts to biliary cells during development was upregulated during liver regeneration. Notch signaling may be involved in biliary regeneration.

  9. Measuring the extent of overlaps in protected area designations.

    Science.gov (United States)

    Deguignet, Marine; Arnell, Andy; Juffe-Bignoli, Diego; Shi, Yichuan; Bingham, Heather; MacSharry, Brian; Kingston, Naomi

    2017-01-01

    Over the past decades, a number of national policies and international conventions have been implemented to promote the expansion of the world's protected area network, leading to a diversification of protected area strategies, types and designations. As a result, many areas are protected by more than one convention, legal instrument, or other effective means which may result in a lack of clarity around the governance and management regimes of particular locations. We assess the degree to which different designations overlap at global, regional and national levels to understand the extent of this phenomenon at different scales. We then compare the distribution and coverage of these multi-designated areas in the terrestrial and marine realms at the global level and among different regions, and we present the percentage of each county's protected area extent that is under more than one designation. Our findings show that almost a quarter of the world's protected area network is protected through more than one designation. In fact, we have documented up to eight overlapping designations. These overlaps in protected area designations occur in every region of the world, both in the terrestrial and marine realms, but are more common in the terrestrial realm and in some regions, notably Europe. In the terrestrial realm, the most common overlap is between one national and one international designation. In the marine realm, the most common overlap is between any two national designations. Multi-designations are therefore a widespread phenomenon but its implications are not well understood. This analysis identifies, for the first time, multi-designated areas across all designation types. This is a key step to understand how these areas are managed and governed to then move towards integrated and collaborative approaches that consider the different management and conservation objectives of each designation.

  10. Coordinated Expression of Phosphoinositide Metabolic Genes during Development and Aging of Human Dorsolateral Prefrontal Cortex.

    Directory of Open Access Journals (Sweden)

    Stanley I Rapoport

    Full Text Available Phosphoinositides, lipid-signaling molecules, participate in diverse brain processes within a wide metabolic cascade.Gene transcriptional networks coordinately regulate the phosphoinositide cascade during human brain Development and Aging.We used the public BrainCloud database for human dorsolateral prefrontal cortex to examine age-related expression levels of 49 phosphoinositide metabolic genes during Development (0 to 20+ years and Aging (21+ years.We identified three groups of partially overlapping genes in each of the two intervals, with similar intergroup correlations despite marked phenotypic differences between Aging and Development. In each interval, ITPKB, PLCD1, PIK3R3, ISYNA1, IMPA2, INPPL1, PI4KB, and AKT1 are in Group 1, PIK3CB, PTEN, PIK3CA, and IMPA1 in Group 2, and SACM1L, PI3KR4, INPP5A, SYNJ1, and PLCB1 in Group 3. Ten of the genes change expression nonlinearly during Development, suggesting involvement in rapidly changing neuronal, glial and myelination events. Correlated transcription for some gene pairs likely is facilitated by colocalization on the same chromosome band.Stable coordinated gene transcriptional networks regulate brain phosphoinositide metabolic pathways during human Development and Aging.

  11. The probability distribution of the delay time of a wave packet in strong overlap of resonance levels

    International Nuclear Information System (INIS)

    Lyuboshitz, V.L.

    1982-01-01

    The time development of nuclear reactions at a large density of levels is investigated using the theory of overlapping resonances. The analytical expression for the function describing the time delay probability distribution of a wave packet is obtained in the framework of the model of n equi - valent channels. It is shown that a relative fluctuation of the time delay at the stage of the compound nucleus is snall. The possibility is discussed of increasing the duration of nuclear raactions with rising excitation energy

  12. A Heuristic Parameterization for the Integrated Vertical Overlap of Cumulus and Stratus

    Science.gov (United States)

    Park, Sungsu

    2017-10-01

    The author developed a heuristic parameterization to handle the contrasting vertical overlap structures of cumulus and stratus in an integrated way. The parameterization assumes that cumulus is maximum-randomly overlapped with adjacent cumulus; stratus is maximum-randomly overlapped with adjacent stratus; and radiation and precipitation areas at each model interface are grouped into four categories, that is, convective, stratiform, mixed, and clear areas. For simplicity, thermodynamic scalars within individual portions of cloud, radiation, and precipitation areas are assumed to be internally homogeneous. The parameterization was implemented into the Seoul National University Atmosphere Model version 0 (SAM0) in an offline mode and tested over the globe. The offline control simulation reasonably reproduces the online surface precipitation flux and longwave cloud radiative forcing (LWCF). Although the cumulus fraction is much smaller than the stratus fraction, cumulus dominantly contributes to precipitation production in the tropics. For radiation, however, stratus is dominant. Compared with the maximum overlap, the random overlap of stratus produces stronger LWCF and, surprisingly, more precipitation flux due to less evaporation of convective precipitation. Compared with the maximum overlap, the random overlap of cumulus simulates stronger LWCF and weaker precipitation flux. Compared with the control simulation with separate cumulus and stratus, the simulation with a single-merged cloud substantially enhances the LWCF in the tropical deep convection and midlatitude storm track regions. The process-splitting treatment of convective and stratiform precipitation with an independent precipitation approximation (IPA) simulates weaker surface precipitation flux than the control simulation in the tropical region.

  13. Overlap between functional abdominal pain disorders and organic diseases in children.

    Science.gov (United States)

    Langshaw, A H; Rosen, J M; Pensabene, L; Borrelli, O; Salvatore, S; Thapar, N; Concolino, D; Saps, M

    2018-04-02

    Functional abdominal pain disorders are highly prevalent in children. These disorders can be present in isolation or combined with organic diseases, such as celiac disease and inflammatory bowel diseases. Intestinal inflammation (infectious and non-infectious) predisposes children to the development of visceral hypersensitivity that can manifest as functional abdominal pain disorders, including irritable bowel syndrome. The new onset of irritable bowel syndrome symptoms in a patient with an underlying organic disease, such as inflammatory bowel disease, is clinically challenging, given that the same symptomatology may represent a flare-up of the inflammatory bowel disease or an overlapping functional abdominal pain disorder. Similarly, irritable bowel syndrome symptoms in a child previously diagnosed with celiac disease may occur due to poorly controlled celiac disease or the overlap with a functional abdominal pain disorder. There is little research on the overlap of functional abdominal disorders with organic diseases in children. Studies suggest that the overlap between functional abdominal pain disorders and inflammatory bowel disease is more common in adults than in children. The causes for these differences in prevalence are unknown. Only a handful of studies have been published on the overlap between celiac disease and functional abdominal pain disorders in children. The present article provides a review of the literature on the overlap between celiac disease, inflammatory bowel disease, and functional abdominal pain disorders in children and establish comparisons with studies conducted on adults. Copyright © 2018 Asociación Mexicana de Gastroenterología. Publicado por Masson Doyma México S.A. All rights reserved.

  14. Investigation of generalized overlap amplitudes via (e,2e) spectroscopy

    International Nuclear Information System (INIS)

    Williams, G.R.J.; McCarthy, I.E.; Weigold, E.

    1976-11-01

    The (e,2e) reaction has previously been shown to be an extremely direct and accurate measure of the overlap of the wave function of a target molecule with that of different resolved electronic states of the positive ion resulting from electron knockout. The present paper discusses the reaction in relation to the direct computation of the structure overlaps for different ion states as the generalized overlap amplitudes appearing in the spectral resolution of the one-particle Green's function. The case of water is used to illustrate the effectiveness of the Green's function technique for calculating (e,2e) cross sections of the principal ion states and the use of the reaction as a very sensitive measure of the long-range charge density. (Author)

  15. Communication: Unambiguous comparison of many-electron wavefunctions through their overlaps

    Energy Technology Data Exchange (ETDEWEB)

    Plasser, Felix, E-mail: felix.plasser@univie.ac.at; González, Leticia, E-mail: leticia.gonzalez@univie.ac.at [Institute for Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna (Austria)

    2016-07-14

    A simple and powerful method for comparing many-electron wavefunctions constructed at different levels of theory is presented. By using wavefunction overlaps, it is possible to analyze the effects of varying wavefunction models, molecular orbitals, and one-electron basis sets. The computation of wavefunction overlaps eliminates the inherent ambiguity connected to more rudimentary wavefunction analysis protocols, such as visualization of orbitals or comparing selected physical observables. Instead, wavefunction overlaps allow processing the many-electron wavefunctions in their full inherent complexity. The presented method is particularly effective for excited state calculations as it allows for automatic monitoring of changes in the ordering of the excited states. A numerical demonstration based on multireference computations of two test systems, the selenoacrolein molecule and an iridium complex, is presented.

  16. A new approach to study of seabird-fishery overlap: Connecting chick feeding with parental foraging and overlap with fishing vessels

    Directory of Open Access Journals (Sweden)

    Junichi Sugishita

    2015-07-01

    Full Text Available Incidental fisheries bycatch is recognised as a major threat to albatross populations worldwide. However, fishery discards and offal produced in large quantities might benefit some scavenging seabirds. Here, we demonstrate an integrated approach to better understand the ecological ramifications of fine-scale overlap between seabirds and fisheries. As a case study, we examined whether foraging in association with a fishing vessel is advantageous for chick provisioning in terms of quantity of food delivered to chicks, in northern royal albatross (Diomedea sanfordi at Taiaroa Head, New Zealand. Fine-scale overlap between albatrosses and vessels was quantified by integrating GPS tracking and Vessel Monitoring Systems (VMS. Meal size delivered to chicks was measured using custom-designed nest balances, and monitoring of attendance of adults fitted with radio transmitters was used in conjunction with time-lapse photography at the nest allowed us to allocate each feeding event to a specific parent. The combination of these techniques enabled comparison of meal sizes delivered to chicks with parental foraging trip durations with or without fishing vessels association. A total of 45 foraging trips and associated chick feeding events were monitored during the chick-rearing period in 2012. Differences in the meal size and foraging trip duration relative to foraging overlap with fisheries were examined using a linear mixed-effect model, adjusted for chick age. Our results, based on three birds, suggest that foraging in association with vessels does not confer an advantage for chick feeding for this population that demonstrated low rates of overlap while foraging. The integrated research design presented can be applied to other seabird species that are susceptible to bycatch, and offers a valuable approach to evaluate habitat quality by linking habitat use and foraging success in terms of total amount of food delivered to offspring.

  17. Reconsidering harmonic and anharmonic coherent states: Partial differential equations approach

    Energy Technology Data Exchange (ETDEWEB)

    Toutounji, Mohamad, E-mail: Mtoutounji@uaeu.ac.ae

    2015-02-15

    This article presents a new approach to dealing with time dependent quantities such as autocorrelation function of harmonic and anharmonic systems using coherent states and partial differential equations. The approach that is normally used to evaluate dynamical quantities involves formidable operator algebra. That operator algebra becomes insurmountable when employing Morse oscillator coherent states. This problem becomes even more complicated in case of Morse oscillator as it tends to exhibit divergent dynamics. This approach employs linear partial differential equations, some of which may be solved exactly and analytically, thereby avoiding the cumbersome noncommutative algebra required to manipulate coherent states of Morse oscillator. Additionally, the arising integrals while using the herein presented method feature stability and high numerical efficiency. The correctness, applicability, and utility of the above approach are tested by reproducing the partition and optical autocorrelation function of the harmonic oscillator. A closed-form expression for the equilibrium canonical partition function of the Morse oscillator is derived using its coherent states and partial differential equations. Also, a nonequilibrium autocorrelation function expression for weak electron–phonon coupling in condensed systems is derived for displaced Morse oscillator in electronic state. Finally, the utility of the method is demonstrated through further simplifying the Morse oscillator partition function or autocorrelation function expressions reported by other researchers in unevaluated form of second-order derivative exponential. Comparison with exact dynamics shows identical results.

  18. Architecture and dynamics of overlapped RNA regulatory networks.

    Science.gov (United States)

    Lapointe, Christopher P; Preston, Melanie A; Wilinski, Daniel; Saunders, Harriet A J; Campbell, Zachary T; Wickens, Marvin

    2017-11-01

    A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is known about the architecture or dynamics of overlapped networks. We focused on three proteins with similar structures and related RNA-binding specificities-Puf3p, Puf4p, and Puf5p of S. cerevisiae Using RNA Tagging, we identified a "super-network" comprised of four subnetworks: Puf3p, Puf4p, and Puf5p subnetworks, and one controlled by both Puf4p and Puf5p. The architecture of individual subnetworks, and thus the super-network, is determined by competition among particular PUF proteins to bind mRNAs, their affinities for binding elements, and the abundances of the proteins. The super-network responds dramatically: The remaining network can either expand or contract. These strikingly opposite outcomes are determined by an interplay between the relative abundance of the RNAs and proteins, and their affinities for one another. The diverse interplay between overlapping RNA-protein networks provides versatile opportunities for regulation and evolution. © 2017 Lapointe et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  19. On the propagation of errors without using partial derivates

    International Nuclear Information System (INIS)

    Giordano, J.L.

    1990-01-01

    The expression Δz = (z + - z - )/2 for the error of an indirect is not only a simple and didactical fashion but is also an alternative method for those cases in which partial derivates are null or non existent. (Author) [es

  20. Overlapping community detection in networks with positive and negative links

    International Nuclear Information System (INIS)

    Chen, Y; Wang, X L; Yuan, B; Tang, B Z

    2014-01-01

    Complex networks considering both positive and negative links have gained considerable attention during the past several years. Community detection is one of the main challenges for complex network analysis. Most of the existing algorithms for community detection in a signed network aim at providing a hard-partition of the network where any node should belong to a community or not. However, they cannot detect overlapping communities where a node is allowed to belong to multiple communities. The overlapping communities widely exist in many real-world networks. In this paper, we propose a signed probabilistic mixture (SPM) model for overlapping community detection in signed networks. Compared with the existing models, the advantages of our methodology are (i) providing soft-partition solutions for signed networks; (ii) providing soft memberships of nodes. Experiments on a number of signed networks show that our SPM model: (i) can identify assortative structures or disassortative structures as the same as other state-of-the-art models; (ii) can detect overlapping communities; (iii) outperforms other state-of-the-art models at shedding light on the community detection in synthetic signed networks. (paper)

  1. Expression

    Directory of Open Access Journals (Sweden)

    Wang-Xia Wang

    2014-02-01

    Full Text Available The miR-15/107 family comprises a group of 10 paralogous microRNAs (miRNAs, sharing a 5′ AGCAGC sequence. These miRNAs have overlapping targets. In order to characterize the expression of miR-15/107 family miRNAs, we employed customized TaqMan Low-Density micro-fluid PCR-array to investigate the expression of miR-15/107 family members, and other selected miRNAs, in 11 human tissues obtained at autopsy including the cerebral cortex, frontal cortex, primary visual cortex, thalamus, heart, lung, liver, kidney, spleen, stomach and skeletal muscle. miR-103, miR-195 and miR-497 were expressed at similar levels across various tissues, whereas miR-107 is enriched in brain samples. We also examined the expression patterns of evolutionarily conserved miR-15/107 miRNAs in three distinct primary rat brain cell preparations (enriched for cortical neurons, astrocytes and microglia, respectively. In primary cultures of rat brain cells, several members of the miR-15/107 family are enriched in neurons compared to other cell types in the central nervous system (CNS. In addition to mature miRNAs, we also examined the expression of precursors (pri-miRNAs. Our data suggested a generally poor correlation between the expression of mature miRNAs and their precursors. In summary, we provide a detailed study of the tissue and cell type-specific expression profile of this highly expressed and phylogenetically conserved family of miRNA genes.

  2. First-order partial differential equations

    CERN Document Server

    Rhee, Hyun-Ku; Amundson, Neal R

    2001-01-01

    This first volume of a highly regarded two-volume text is fully usable on its own. After going over some of the preliminaries, the authors discuss mathematical models that yield first-order partial differential equations; motivations, classifications, and some methods of solution; linear and semilinear equations; chromatographic equations with finite rate expressions; homogeneous and nonhomogeneous quasilinear equations; formation and propagation of shocks; conservation equations, weak solutions, and shock layers; nonlinear equations; and variational problems. Exercises appear at the end of mo

  3. Efficient and Flexible Computation of Many-Electron Wave Function Overlaps.

    Science.gov (United States)

    Plasser, Felix; Ruckenbauer, Matthias; Mai, Sebastian; Oppel, Markus; Marquetand, Philipp; González, Leticia

    2016-03-08

    A new algorithm for the computation of the overlap between many-electron wave functions is described. This algorithm allows for the extensive use of recurring intermediates and thus provides high computational efficiency. Because of the general formalism employed, overlaps can be computed for varying wave function types, molecular orbitals, basis sets, and molecular geometries. This paves the way for efficiently computing nonadiabatic interaction terms for dynamics simulations. In addition, other application areas can be envisaged, such as the comparison of wave functions constructed at different levels of theory. Aside from explaining the algorithm and evaluating the performance, a detailed analysis of the numerical stability of wave function overlaps is carried out, and strategies for overcoming potential severe pitfalls due to displaced atoms and truncated wave functions are presented.

  4. 9 CFR 121.6 - Exemptions for overlap select agents and toxins.

    Science.gov (United States)

    2010-01-01

    .... (a) Clinical or diagnostic laboratories and other entities that possess, use, or transfer an overlap... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Exemptions for overlap select agents and toxins. 121.6 Section 121.6 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE...

  5. Extracting attosecond delays from spectrally overlapping interferograms

    Science.gov (United States)

    Jordan, Inga; Wörner, Hans Jakob

    2018-02-01

    Attosecond interferometry is becoming an increasingly popular technique for measuring the dynamics of photoionization in real time. Whereas early measurements focused on atomic systems with very simple photoelectron spectra, the technique is now being applied to more complex systems including isolated molecules and solids. The increase in complexity translates into an augmented spectral congestion, unavoidably resulting in spectral overlap in attosecond interferograms. Here, we discuss currently used methods for phase retrieval and introduce two new approaches for determining attosecond photoemission delays from spectrally overlapping photoelectron spectra. We show that the previously used technique, consisting in the spectral integration of the areas of interest, does in general not provide reliable results. Our methods resolve this problem, thereby opening the technique of attosecond interferometry to complex systems and fully exploiting its specific advantages in terms of spectral resolution compared to attosecond streaking.

  6. On the improvement of speaker diarization by detecting overlapped speech

    OpenAIRE

    Hernando Pericás, Francisco Javier; Hernando Pericás, Francisco Javier

    2010-01-01

    Simultaneous speech in meeting environment is responsible for a certain amount of errors caused by standard speaker diarization systems. We are presenting an overlap detection system for far-field data based on spectral and spatial features, where the spatial features obtained on different microphone pairs are fused by means of principal component analysis. Detected overlap segments are applied for speaker diarization in order to increase the purity of speaker clusters an...

  7. Overlapping Neural Correlates of Reading Emotionally Positive and Negative Adjectives

    OpenAIRE

    Demirakca, Traute; Herbert, Cornelia; Kissler, Johanna; Ruf, Matthias; Wokrina, Tim; Ende, Gabriele

    2009-01-01

    Comparison of positive and negative naturally read adjectives to neutral adjectives yielded an overlapping higher BOLD response in the occipital and the orbitofrontal cortex (gyrus rectus). Superior medial frontal gyrus and posterior cingulate gyrus showed higher BOLD response to negative adjectives and inferior frontal gyrus to positive adjectives. The overlap of activated regions and lack of pronounced distinct regions supports the assumption that the processing of negative and positive wor...

  8. Expression Pattern of Myogenic Regulatory Transcription Factor mRNAs in the Embryo and Adult Labeo rohita (Hamilton, 1822

    Directory of Open Access Journals (Sweden)

    Archya Sengupta

    2014-01-01

    Full Text Available Understanding the regulation of skeletal muscle development is important to meet the increasing demand of Indian major carp Labeo rohita. Myogenic regulatory factors (MRFs along with myocyte specific enhancer factor 2 (MEF2 play the pivotal role in the determination and differentiation of skeletal muscle. The majority of skeletal muscle genes require both MRFs and MEF2 family members to activate their transcription. In this study, the expression pattern of MyoD, myf-5, myogenin, and MEF2A was observed from 6 h after fertilization to 12 months of age using semiquantitative RT-PCR as well as real-time PCR method. MyoD and myf-5 mRNAs were expressed at high level at the early embryonic stages. Myogenin and MEF2A were expressed after MyoD and myf-5 and remained active up to adult stage. Expression of MyoD was lower than that of Myf-5 after the 5th month. Partial sequencing of MyoD, myf-5, and MEF2A was done to draw phylogeny. In phylogenetic study, Labeo MyoD, MEF2A and myf-5 were found to be closely related to those of common carp. The present investigation suggests that the four transcription factors play pivotal role in the regulation of muscle growth of Labeo rohita in an overlapping and interconnected way.

  9. The Influence of Sex and Season on Conspecific Spatial Overlap in a Large, Actively-Foraging Colubrid Snake.

    Directory of Open Access Journals (Sweden)

    Javan M Bauder

    Full Text Available Understanding the factors influencing the degree of spatial overlap among conspecifics is important for understanding multiple ecological processes. Compared to terrestrial carnivores, relatively little is known about the factors influencing conspecific spatial overlap in snakes, although across snake taxa there appears to be substantial variation in conspecific spatial overlap. In this study, we described conspecific spatial overlap of eastern indigo snakes (Drymarchon couperi in peninsular Florida and examined how conspecific spatial overlap varied by sex and season (breeding season vs. non-breeding season. We calculated multiple indices of spatial overlap using 6- and 3-month utilization distributions (UD of dyads of simultaneously adjacent telemetered snakes. We also measured conspecific UD density values at each telemetry fix and modeled the distribution of those values as a function of overlap type, sex, and season using generalized Pareto distributions. Home range overlap between males and females was significantly greater than overlap between individuals of the same sex and male home ranges often completely contained female home ranges. Male home ranges overlapped little during both seasons, whereas females had higher levels of overlap during the non-breeding season. The spatial patterns observed in our study are consistent with those seen in many mammalian carnivores, in which low male-male overlap and high inter-sexual overlap provides males with greater access to females. We encourage additional research on the influence of prey availability on conspecific spatial overlap in snakes as well as the behavioral mechanisms responsible for maintaining the low levels of overlap we observed.

  10. Regional and temporal differences in gene expression of LH(BETA)T(AG) retinoblastoma tumors.

    Science.gov (United States)

    Houston, Samuel K; Pina, Yolanda; Clarke, Jennifer; Koru-Sengul, Tulay; Scott, William K; Nathanson, Lubov; Schefler, Amy C; Murray, Timothy G

    2011-07-23

    The purpose of this study was to evaluate by microarray the hypothesis that LH(BETA)T(AG) retinoblastoma tumors exhibit regional and temporal variations in gene expression. LH(BETA)T(AG) mice aged 12, 16, and 20 weeks were euthanatized (n = 9). Specimens were taken from five tumor areas (apex, anterior lateral, center, base, and posterior lateral). Samples were hybridized to gene microarrays. The data were preprocessed and analyzed, and genes with a P 2.5 were considered to be differentially expressed. Differentially expressed genes were analyzed for overlap with known networks by using pathway analysis tools. There were significant temporal (P regional differences in gene expression for LH(BETA)T(AG) retinoblastoma tumors. At P 2.5, there were significant changes in gene expression of 190 genes apically, 84 genes anterolaterally, 126 genes posteriorly, 56 genes centrally, and 134 genes at the base. Differentially expressed genes overlapped with known networks, with significant involvement in regulation of cellular proliferation and growth, response to oxygen levels and hypoxia, regulation of cellular processes, cellular signaling cascades, and angiogenesis. There are significant temporal and regional variations in the LH(BETA)T(AG) retinoblastoma model. Differentially expressed genes overlap with key pathways that may play pivotal roles in murine retinoblastoma development. These findings suggest the mechanisms involved in tumor growth and progression in murine retinoblastoma tumors and identify pathways for analysis at a functional level, to determine significance in human retinoblastoma. Microarray analysis of LH(BETA)T(AG) retinal tumors showed significant regional and temporal variations in gene expression, including dysregulation of genes involved in hypoxic responses and angiogenesis.

  11. Overlap valence quarks on an twisted mass sea

    Energy Technology Data Exchange (ETDEWEB)

    Cichy, K. [Adam Mickiewicz Univ., Poznan (Poland). Faculty of Physics; Drach, V.; Garcia-Ramos, E.; Herdoiza, G.; Jansen, K. [DESY, Zeuthen (Germany). John von Neumann-Institut fuer Computing NIC

    2010-12-15

    We present the results of an investigation of a mixed action approach of overlap valence and maximally twisted mass sea quarks. Employing a particular matching condition on the pion mass, we analyze the continuum limit scaling of the pion decay constant and the role of chiral zero modes of the overlap operator in this process. We employ gauge field configurations generated by the European Twisted Mass Collaboration with linear lattice size L ranging from 1.3 to 1.9 fm. The continuum limit is taken at a fixed value of L=1.3 fm, employing three values of the lattice spacing and two values of the pion mass constructed from sea quarks only. (orig.)

  12. A parametric level-set method for partially discrete tomography

    NARCIS (Netherlands)

    A. Kadu (Ajinkya); T. van Leeuwen (Tristan); K.J. Batenburg (Joost)

    2017-01-01

    textabstractThis paper introduces a parametric level-set method for tomographic reconstruction of partially discrete images. Such images consist of a continuously varying background and an anomaly with a constant (known) grey-value. We express the geometry of the anomaly using a level-set function,

  13. Fingerprint image reconstruction for swipe sensor using Predictive Overlap Method

    Directory of Open Access Journals (Sweden)

    Mardiansyah Ahmad Zafrullah

    2018-01-01

    Full Text Available Swipe sensor is one of many biometric authentication sensor types that widely applied to embedded devices. The sensor produces an overlap on every pixel block of the image, so the picture requires a reconstruction process before heading to the feature extraction process. Conventional reconstruction methods require extensive computation, causing difficult to apply to embedded devices that have limited computing process. In this paper, image reconstruction is proposed using predictive overlap method, which determines the image block shift from the previous set of change data. The experiments were performed using 36 images generated by a swipe sensor with 128 x 8 pixels size of the area, where each image has an overlap in each block. The results reveal computation can increase up to 86.44% compared with conventional methods, with accuracy decreasing to 0.008% in average.

  14. Femtosecond resolved diagnostics for electron beam and XUV seed temporal overlap at sFLASH

    International Nuclear Information System (INIS)

    Tarkeshian, Roxana

    2012-02-01

    sFLASH is a seeded experiment at the Free-Electron Laser FLASH in Hamburg. It uses a 38 nm High-Harmonic-Generation (HHG) scheme to seed the FEL-process in a 10m long variable-gap undulator. The temporal overlap between the electron and HHG pulses is critical to the seeding process. The use of a 3 rd harmonic accelerating module provides a high current electron beam with ∝ (400 fs) FWHM bunch duration. The duration of the HHG laser pulse is ≤ (30 fs) FWHM . The desired overlap is achieved in two steps. Firstly, the HHG drive laser is brought to temporal overlap with the incoherent spontaneous radiation from an upstream undulator with picosecond resolution. The temporal overlap is periodically monitored using a streak camera installed in the linear accelerator tunnel. Next, the coherent radiation from an undulator is used to determine the exact overlap of the electron beam in a modulator-radiator set-up with sub-picosecond resolution. The physical and technical principles of the setup providing the temporal overlap are described. Results of the system are analyzed. An analytical approach and simulation results for the performance of the seeding experiment are presented. First attempts at demonstration of seeding are discussed. Strategies for optimizing overlap conditions are presented. (orig.)

  15. Femtosecond resolved diagnostics for electron beam and XUV seed temporal overlap at sFLASH

    Energy Technology Data Exchange (ETDEWEB)

    Tarkeshian, Roxana

    2012-02-15

    sFLASH is a seeded experiment at the Free-Electron Laser FLASH in Hamburg. It uses a 38 nm High-Harmonic-Generation (HHG) scheme to seed the FEL-process in a 10m long variable-gap undulator. The temporal overlap between the electron and HHG pulses is critical to the seeding process. The use of a 3{sup rd} harmonic accelerating module provides a high current electron beam with {proportional_to} (400 fs){sub FWHM} bunch duration. The duration of the HHG laser pulse is {<=} (30 fs){sub FWHM}. The desired overlap is achieved in two steps. Firstly, the HHG drive laser is brought to temporal overlap with the incoherent spontaneous radiation from an upstream undulator with picosecond resolution. The temporal overlap is periodically monitored using a streak camera installed in the linear accelerator tunnel. Next, the coherent radiation from an undulator is used to determine the exact overlap of the electron beam in a modulator-radiator set-up with sub-picosecond resolution. The physical and technical principles of the setup providing the temporal overlap are described. Results of the system are analyzed. An analytical approach and simulation results for the performance of the seeding experiment are presented. First attempts at demonstration of seeding are discussed. Strategies for optimizing overlap conditions are presented. (orig.)

  16. Expression of isgylation related genes in regenerating rat liver

    Directory of Open Access Journals (Sweden)

    Kuklin A. V.

    2015-10-01

    Full Text Available Our recent studies have revealed the early up-regulated expression of interferon alpha (IFNα in the liver, induced by partial hepatectomy. The role of this cytokine of innate immune response in liver regeneration is still controversial. Aim. To analyze expression of canonical interferon-stimulated genes Ube1l, Ube2l6, Trim25, Usp18 and Isg15 during the liver transition from quiescence to proliferation induced by partial hepatectomy, and acute phase response induced by laparotomy. These genes are responsible for posttranslational modification of proteins by ISGylation. The expression of genes encoding TATA binding protein (TBP and 18S rRNA served as indirect general markers of transcriptional and translational activities. Methods. The abundance of investigated RNAs was assessed in total liver RNA by real time RT–qPCR. Results. Partial hepatecomy induced steady upregulation of the Tbp and 18S rRNA genes expression during 12 hours post-surgery and downregulation or no change in expression of ISGylation-related genes during the first 3 hours followed by slight upregulation at 12 hours. The level of Isg15 transcripts was permanently below that of the control during the prereplicative period. Laparotomy induced a continuous downregulation of Tbp and 18S rRNA expression and early (1–3h upregulation of ISGylation–related transcripts followed by a sharp drop at 6 hours and slight increase/decrease at 12 hours. The changes in the abundance of Ifnα and ISGylation-related mRNAs were oppositely directed at each stage of the response to partial hepatectomy and laparotomy. Conclusion. We suggest that the expression of ISGylation-related genes does not depend on the expression of Ifnα gene after both surgeries. The indirect indices of transcription and translation as well as the expression of ISGylation-relaled genes are principally different in response to partial hepatectomy and laparotomy and argue for the high specificity of innate immune response.

  17. Tyrosine kinase chromosomal translocations mediate distinct and overlapping gene regulation events

    International Nuclear Information System (INIS)

    Kim, Hani; Gillis, Lisa C; Jarvis, Jordan D; Yang, Stuart; Huang, Kai; Der, Sandy; Barber, Dwayne L

    2011-01-01

    Leukemia is a heterogeneous disease commonly associated with recurrent chromosomal translocations that involve tyrosine kinases including BCR-ABL, TEL-PDGFRB and TEL-JAK2. Most studies on the activated tyrosine kinases have focused on proximal signaling events, but little is known about gene transcription regulated by these fusions. Oligonucleotide microarray was performed to compare mRNA changes attributable to BCR-ABL, TEL-PDGFRB and TEL-JAK2 after 1 week of activation of each fusion in Ba/F3 cell lines. Imatinib was used to control the activation of BCR-ABL and TEL-PDGFRB, and TEL-JAK2-mediated gene expression was examined 1 week after Ba/F3-TEL-JAK2 cells were switched to factor-independent conditions. Microarray analysis revealed between 800 to 2000 genes induced or suppressed by two-fold or greater by each tyrosine kinase, with a subset of these genes commonly induced or suppressed among the three fusions. Validation by Quantitative PCR confirmed that eight genes (Dok2, Mrvi1, Isg20, Id1, gp49b, Cxcl10, Scinderin, and collagen Vα1(Col5a1)) displayed an overlapping regulation among the three tested fusion proteins. Stat1 and Gbp1 were induced uniquely by TEL-PDGFRB. Our results suggest that BCR-ABL, TEL-PDGFRB and TEL-JAK2 regulate distinct and overlapping gene transcription profiles. Many of the genes identified are known to be involved in processes associated with leukemogenesis, including cell migration, proliferation and differentiation. This study offers the basis for further work that could lead to an understanding of the specificity of diseases caused by these three chromosomal translocations

  18. The overlapped radial basis function-finite difference (RBF-FD) method: A generalization of RBF-FD

    Science.gov (United States)

    Shankar, Varun

    2017-08-01

    We present a generalization of the RBF-FD method that computes RBF-FD weights in finite-sized neighborhoods around the centers of RBF-FD stencils by introducing an overlap parameter δ ∈ (0 , 1 ] such that δ = 1 recovers the standard RBF-FD method and δ = 0 results in a full decoupling of stencils. We provide experimental evidence to support this generalization, and develop an automatic stabilization procedure based on local Lebesgue functions for the stable selection of stencil weights over a wide range of δ values. We provide an a priori estimate for the speedup of our method over RBF-FD that serves as a good predictor for the true speedup. We apply our method to parabolic partial differential equations with time-dependent inhomogeneous boundary conditions - Neumann in 2D, and Dirichlet in 3D. Our results show that our method can achieve as high as a 60× speedup in 3D over existing RBF-FD methods in the task of forming differentiation matrices.

  19. Safety of Running Two Rooms: A Systematic Review and Meta-Analysis of Overlapping Neurosurgical Procedures.

    Science.gov (United States)

    Self, D Mitchell; Ilyas, Adeel; Stetler, William R

    2018-04-27

    Overlapping surgery, a long-standing practice within academic neurosurgery centers nationwide, has recently come under scrutiny from the government and media as potentially harmful to patients. Therefore, the objective of this systematic review and meta-analysis is to determine the safety of overlapping neurosurgical procedures. The authors performed a systematic review and meta-analysis in accordance with PRISMA guidelines. A review of PubMed and Medline databases was undertaken with the search phrase "overlapping surgery AND neurosurgery AND outcomes." Data regarding patient demographics, type of neurosurgical procedure, and outcomes and complications were extracted from each study. The principle summary measure was odds ratio (OR) of the association of overlapping versus non-overlapping surgery with outcomes. The literature search yielded a total of 36 studies, of which 5 studies met inclusion criteria and were included in this study. These studies included a total of 25,764 patients undergoing neurosurgical procedures. Overlapping surgery was associated with an increased likelihood of being discharged home (OR = 1.32; 95% CI 1.20 to 1.44; P < 0.001) and a reduced 30-day unexpected return to the operating room (OR = 0.79; 95% CI 0.72 to 0.87; P < 0.001). Overlapping surgery did not significantly affect OR of length of surgery, 30-day mortality, or 30-day readmission. Overlapping neurosurgical procedures were not associated with worse patient outcomes. Additional, prospective studies are needed to further assess the safety overlapping procedures. Copyright © 2018. Published by Elsevier Inc.

  20. On-the-fly Overlapping of Sparse Generations

    DEFF Research Database (Denmark)

    Sørensen, Chres Wiant; Roetter, Daniel Enrique Lucani; Fitzek, Frank

    2014-01-01

    Traditionally, the idea of overlapping generations in network coding research has focused on reducing the complexity of decoding large data files while maintaining the delay performance expected of a system that combines all data packets. However, the effort for encoding and decoding individual g...

  1. Overlapping community detection in weighted networks via a Bayesian approach

    Science.gov (United States)

    Chen, Yi; Wang, Xiaolong; Xiang, Xin; Tang, Buzhou; Chen, Qingcai; Fan, Shixi; Bu, Junzhao

    2017-02-01

    Complex networks as a powerful way to represent complex systems have been widely studied during the past several years. One of the most important tasks of complex network analysis is to detect communities embedded in networks. In the real world, weighted networks are very common and may contain overlapping communities where a node is allowed to belong to multiple communities. In this paper, we propose a novel Bayesian approach, called the Bayesian mixture network (BMN) model, to detect overlapping communities in weighted networks. The advantages of our method are (i) providing soft-partition solutions in weighted networks; (ii) providing soft memberships, which quantify 'how strongly' a node belongs to a community. Experiments on a large number of real and synthetic networks show that our model has the ability in detecting overlapping communities in weighted networks and is competitive with other state-of-the-art models at shedding light on community partition.

  2. Overlapping Genomic Sequences: A Treasure Trove of Single-Nucleotide Polymorphisms

    Science.gov (United States)

    Taillon-Miller, Patricia; Gu, Zhijie; Li, Qun; Hillier, LaDeana; Kwok, Pui-Yan

    1998-01-01

    An efficient strategy to develop a dense set of single-nucleotide polymorphism (SNP) markers is to take advantage of the human genome sequencing effort currently under way. Our approach is based on the fact that bacterial artificial chromosomes (BACs) and P1-based artificial chromosomes (PACs) used in long-range sequencing projects come from diploid libraries. If the overlapping clones sequenced are from different lineages, one is comparing the sequences from 2 homologous chromosomes in the overlapping region. We have analyzed in detail every SNP identified while sequencing three sets of overlapping clones found on chromosome 5p15.2, 7q21–7q22, and 13q12–13q13. In the 200.6 kb of DNA sequence analyzed in these overlaps, 153 SNPs were identified. Computer analysis for repetitive elements and suitability for STS development yielded 44 STSs containing 68 SNPs for further study. All 68 SNPs were confirmed to be present in at least one of the three (Caucasian, African-American, Hispanic) populations studied. Furthermore, 42 of the SNPs tested (62%) were informative in at least one population, 32 (47%) were informative in two or more populations, and 23 (34%) were informative in all three populations. These results clearly indicate that developing SNP markers from overlapping genomic sequence is highly efficient and cost effective, requiring only the two simple steps of developing STSs around the known SNPs and characterizing them in the appropriate populations. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AC003015 (for GS113423), AC002380 (GS330J10), AC000066 (RG293F11), AC003086 (RG104F04), AC002525 (257C22A), and U73331 (96A18A).] PMID:9685323

  3. Partial least square method for modelling ergonomic risks factors on express bus accidents in the east coast of peninsular west Malaysia

    International Nuclear Information System (INIS)

    Hashim, Yusof bin; Taha, Zahari bin

    2015-01-01

    Public, stake holders and authorities in Malaysian government show great concern towards high numbers of passenger’s injuries and passengers fatalities in express bus accident. This paper studies the underlying factors involved in determining ergonomics risk factors towards human error as the reasons in express bus accidents in order to develop an integrated analytical framework. Reliable information about drivers towards bus accident should lead to the design of strategies intended to make the public feel safe in public transport services. In addition there is an analysis of ergonomics risk factors to determine highly ergonomic risk factors which led to accidents. The research was performed in east coast of peninsular Malaysia using variance-based structural equation modeling namely the Partial Least Squares (PLS) regression techniques. A questionnaire survey was carried out at random among 65 express bus drivers operating from the city of Kuantan in Pahang and among 49 express bus drivers operating from the city of Kuala Terengganu in Terengganu to all towns in the east coast of peninsular west Malaysia. The ergonomic risks factors questionnaire is based on demographic information, occupational information, organizational safety climate, ergonomic workplace, physiological factors, stress at workplace, physical fatigue and near miss accidents. The correlation and significant values between latent constructs (near miss accident) were analyzed using SEM SmartPLS, 3M. The finding shows that the correlated ergonomic risks factors (occupational information, t=2.04, stress at workplace, t = 2.81, physiological factor, t=2.08) are significant to physical fatigue and as the mediator to near miss accident at t = 2.14 at p<0.05and T-statistics, t>1.96. The results shows that the effects of physical fatigue due to ergonomic risks factors influence the human error as the reasons in express bus accidents

  4. Partial least square method for modelling ergonomic risks factors on express bus accidents in the east coast of peninsular west Malaysia

    Energy Technology Data Exchange (ETDEWEB)

    Hashim, Yusof bin [Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang 26300 Kuantan, Pahang (Malaysia); Taha, Zahari bin [Faculty of Manufacturing Engineering, Malaysia Pahang, 26600 Pekan, Pahang (Malaysia)

    2015-02-03

    Public, stake holders and authorities in Malaysian government show great concern towards high numbers of passenger’s injuries and passengers fatalities in express bus accident. This paper studies the underlying factors involved in determining ergonomics risk factors towards human error as the reasons in express bus accidents in order to develop an integrated analytical framework. Reliable information about drivers towards bus accident should lead to the design of strategies intended to make the public feel safe in public transport services. In addition there is an analysis of ergonomics risk factors to determine highly ergonomic risk factors which led to accidents. The research was performed in east coast of peninsular Malaysia using variance-based structural equation modeling namely the Partial Least Squares (PLS) regression techniques. A questionnaire survey was carried out at random among 65 express bus drivers operating from the city of Kuantan in Pahang and among 49 express bus drivers operating from the city of Kuala Terengganu in Terengganu to all towns in the east coast of peninsular west Malaysia. The ergonomic risks factors questionnaire is based on demographic information, occupational information, organizational safety climate, ergonomic workplace, physiological factors, stress at workplace, physical fatigue and near miss accidents. The correlation and significant values between latent constructs (near miss accident) were analyzed using SEM SmartPLS, 3M. The finding shows that the correlated ergonomic risks factors (occupational information, t=2.04, stress at workplace, t = 2.81, physiological factor, t=2.08) are significant to physical fatigue and as the mediator to near miss accident at t = 2.14 at p<0.05and T-statistics, t>1.96. The results shows that the effects of physical fatigue due to ergonomic risks factors influence the human error as the reasons in express bus accidents.

  5. Partial least square method for modelling ergonomic risks factors on express bus accidents in the east coast of peninsular west Malaysia

    Science.gov (United States)

    Hashim, Yusof bin; Taha, Zahari bin

    2015-02-01

    Public, stake holders and authorities in Malaysian government show great concern towards high numbers of passenger's injuries and passengers fatalities in express bus accident. This paper studies the underlying factors involved in determining ergonomics risk factors towards human error as the reasons in express bus accidents in order to develop an integrated analytical framework. Reliable information about drivers towards bus accident should lead to the design of strategies intended to make the public feel safe in public transport services. In addition there is an analysis of ergonomics risk factors to determine highly ergonomic risk factors which led to accidents. The research was performed in east coast of peninsular Malaysia using variance-based structural equation modeling namely the Partial Least Squares (PLS) regression techniques. A questionnaire survey was carried out at random among 65 express bus drivers operating from the city of Kuantan in Pahang and among 49 express bus drivers operating from the city of Kuala Terengganu in Terengganu to all towns in the east coast of peninsular west Malaysia. The ergonomic risks factors questionnaire is based on demographic information, occupational information, organizational safety climate, ergonomic workplace, physiological factors, stress at workplace, physical fatigue and near miss accidents. The correlation and significant values between latent constructs (near miss accident) were analyzed using SEM SmartPLS, 3M. The finding shows that the correlated ergonomic risks factors (occupational information, t=2.04, stress at workplace, t = 2.81, physiological factor, t=2.08) are significant to physical fatigue and as the mediator to near miss accident at t = 2.14 at p1.96. The results shows that the effects of physical fatigue due to ergonomic risks factors influence the human error as the reasons in express bus accidents.

  6. An asymptotic expression for the eigenvalues of the normalization kernel of the resonating group method

    International Nuclear Information System (INIS)

    Lomnitz-Adler, J.; Brink, D.M.

    1976-01-01

    A generating function for the eigenvalues of the RGM Normalization Kernel is expressed in terms of the diagonal matrix elements of thw GCM Overlap Kernel. An asymptotic expression for the eigenvalues is obtained by using the Method of Steepest Descent. (Auth.)

  7. Online calibration of high-frequency partial discharge signals in three-phase belted power cables

    NARCIS (Netherlands)

    Wouters, P.A.A.F.

    2005-01-01

    Partial discharge (PD) magnitudes from classical detection techniques are expressed in terms of apparent charges. Signals from HF/VHF/UHF techniques on substation components are often hard to express in this quantity because of complex signal excitation and propagation channels. A method to

  8. Interference management with partial uplink/downlink spectrum overlap

    KAUST Repository

    Randrianantenaina, Itsikiantsoa; Elsawy, Hesham; Dahrouj, Hayssam; Alouini, Mohamed-Slim

    2016-01-01

    Simultaneous reuse of spectral resources by uplink and downlink, denoted as in-band full duplex (FD) communication, is promoted to double the spectral efficiency when compared to its half-duplex (HD) counterpart. Interference management, however

  9. New class of uncertainty relations for partially coherent light

    NARCIS (Netherlands)

    Bastiaans, M.J.

    1984-01-01

    A class of uncertainty relations for partially coherent light is derived; the uncertainty relations in this class express the fact that the product of the effective widths of the space-domain intensity and the spatial-frequency-domain intensity of the light has a lower bound and that this lower

  10. Ovarian cancer stem cells are enriched in side population and aldehyde dehydrogenase bright overlapping population.

    Directory of Open Access Journals (Sweden)

    Kazuyo Yasuda

    Full Text Available Cancer stem-like cells (CSCs/cancer-initiaiting cells (CICs are defined as a small population of cancer cells that have self-renewal capacity, differentiation potential and high tumor-initiating ability. CSCs/CICs of ovarian cancer have been isolated by side population (SP analysis, ALDEFLUOR assay and using cell surface markers. However, these approaches are not definitive markers for CSCs/CICs, and it is necessary to refine recent methods for identifying more highly purified CSCs/CICs. In this study, we analyzed SP cells and aldehyde dehydrogenese bright (ALDH(Br cells from ovarian cancer cells. Both SP cells and ALDH(Br cells exhibited higher tumor-initiating ability and higher expression level of a stem cell marker, sex determining region Y-box 2 (SOX2, than those of main population (MP cells and ALDH(Low cells, respectively. We analyzed an SP and ALDH(Br overlapping population (SP/ALDH(Br, and the SP/ALDH(Br population exhibited higher tumor-initiating ability than that of SP cells or ALDH(Br cells, enabling initiation of tumor with as few as 10(2 cells. Furthermore, SP/ADLH(Br population showed higher sphere-forming ability, cisplatin resistance, adipocyte differentiation ability and expression of SOX2 than those of SP/ALDH(Low, MP/ALDH(Br and MP/ALDH(Low cells. Gene knockdown of SOX2 suppressed the tumor-initiation of ovarian cancer cells. An SP/ALDH(Br population was detected in several gynecological cancer cells with ratios of 0.1% for HEC-1 endometrioid adenocarcinoma cells to 1% for MCAS ovary mucinous adenocarcinoma cells. Taken together, use of the SP and ALDH(Br overlapping population is a promising approach to isolate highly purified CSCs/CICs and SOX2 might be a novel functional marker for ovarian CSCs/CICs.

  11. Retinal genes are differentially expressed in areas of primary versus secondary degeneration following partial optic nerve injury.

    Directory of Open Access Journals (Sweden)

    Wissam Chiha

    Full Text Available Partial transection (PT of the optic nerve is an established experimental model of secondary degeneration in the central nervous system. After a dorsal transection, retinal ganglion cells (RGCs with axons in ventral optic nerve are intact but vulnerable to secondary degeneration, whereas RGCs in dorsal retina with dorsal axons are affected by primary and secondary injuries. Using microarray, we quantified gene expression changes in dorsal and ventral retina at 1 and 7 days post PT, to characterize pathogenic pathways linked to primary and secondary degeneration.In comparison to uninjured retina Cryba1, Cryba2 and Crygs, were significantly downregulated in injured dorsal retina at days 1 and 7. While Ecel1, Timp1, Mt2A and CD74, which are associated with reducing excitotoxicity, oxidative stress and inflammation, were significantly upregulated. Genes associated with oxygen binding pathways, immune responses, cytokine receptor activity and apoptosis were enriched in dorsal retina at day 1 after PT. Oxygen binding and apoptosis remained enriched at day 7, as were pathways involved in extracellular matrix modification. Fewer changes were observed in ventral retina at day 1 after PT, most associated with the regulation of protein homodimerization activity. By day 7, apoptosis, matrix organization and signal transduction pathways were enriched. Discriminant analysis was also performed for specific functional gene groups to compare expression intensities at each time point. Altered expression of selected genes (ATF3, GFAP, Ecel1, TIMP1, Tp53 and proteins (GFAP, ECEL1 and ATF3 were semi-quantitatively assessed by qRT-PCR and immunohistochemistry respectively.There was an acute and complex primary injury response in dorsal retina indicative of a dynamic interaction between neuroprotective and neurodegenerative events; ventral retina vulnerable to secondary degeneration showed a delayed injury response. Both primary and secondary injury resulted in the

  12. ADHD and autism: differential diagnosis or overlapping traits? A selective review.

    Science.gov (United States)

    Taurines, Regina; Schwenck, Christina; Westerwald, Eva; Sachse, Michael; Siniatchkin, Michael; Freitag, Christine

    2012-09-01

    According to DSM-IV TR and ICD-10, a diagnosis of autism or Asperger Syndrome precludes a diagnosis of attention-deficit/hyperactivity disorder (ADHD). However, despite the different conceptualization, population-based twin studies reported symptom overlap, and a recent epidemiologically based study reported a high rate of ADHD in autism and autism spectrum disorders (ASD). In the planned revision of the DSM-IV TR, dsm5 (www.dsm5.org), the diagnoses of autistic disorder and ADHD will not be mutually exclusive any longer. This provides the basis of more differentiated studies on overlap and distinction between both disorders. This review presents data on comorbidity rates and symptom overlap and discusses common and disorder-specific risk factors, including recent proteomic studies. Neuropsychological findings in the areas of attention, reward processing, and social cognition are then compared between both disorders, as these cognitive abilities show overlapping as well as specific impairment for one of both disorders. In addition, selective brain imaging findings are reported. Therapeutic options are summarized, and new approaches are discussed. The review concludes with a prospectus on open questions for research and clinical practice.

  13. Evaluation of partial beta-adrenoceptor agonist activity.

    Science.gov (United States)

    Lipworth, B J; Grove, A

    1997-01-01

    A partial beta-adrenoceptor (beta-AR) agonist will exhibit opposite agonist and antagonist activity depending on the prevailing degree of adrenergic tone or the presence of a beta-AR agonist with higher intrinsic activity. In vivo partial beta-AR agonist activity will be evident at rest with low endogenous adrenergic tone, as for example with chronotropicity (beta 1/beta 2), inotropicity (beta 1) or peripheral vasodilatation and finger tremor (beta 2). beta-AR blocking drugs which have partial agonist activity may exhibit a better therapeutic profile when used for hypertension because of maintained cardiac output without increased systemic vascular resistance, along with an improved lipid profile. In the presence of raised endogenous adrenergic tone such as exercise or an exogenous full agonist, beta-AR subtype antagonist activity will become evident in terms of effects on exercise induced heart rate (beta 1) and potassium (beta 2) responses. Reduction of exercise heart rate will occur to a lesser degree in the case of a beta-adrenoceptor blocker with partial beta 1-AR agonist activity compared with a beta-adrenoceptor blocker devoid of partial agonist activity. This may result in reduced therapeutic efficacy in the treatment of angina on effort when using beta-AR blocking drugs with partial beta 1-AR agonist activity. Effects on exercise hyperkalaemia are determined by the balance between beta 2-AR partial agonist activity and endogenous adrenergic activity. For predominantly beta 2-AR agonist such as salmeterol and salbutamol, potentiation of exercise hyperkalaemia occurs. For predominantly beta 2-AR antagonists such as carteolol, either potentiation or attenuation of exercise hyperkalaemia occurs at low and high doses respectively. beta 2-AR partial agonist activity may also be expressed as antagonism in the presence of an exogenous full agonist, as for example attenuation of fenoterol induced responses by salmeterol. Studies are required to investigate whether

  14. Anxiety Partially Mediates Cybersickness Symptoms in Immersive Virtual Reality Environments.

    Science.gov (United States)

    Pot-Kolder, Roos; Veling, Wim; Counotte, Jacqueline; van der Gaag, Mark

    2018-03-01

    The use of virtual reality (VR) in psychological treatment is expected to increase. Cybersickness (CS) is a negative side effect of VR exposure and is associated with treatment dropout. This study aimed to investigate the following: (a) if gender differences in CS can be replicated, (b) if differences in anxiety and CS symptoms between patients and controls can be replicated, and (c) whether the relationship between exposure to VR and CS symptoms is mediated by anxiety. A sample (N = 170) of participants with different levels of psychosis liability was exposed to VR environments. CS and anxiety were assessed with self-report measures before and after the VR experiment. This study replicated gender differences in CS symptoms, most of which were present before exposure to VR. It also replicated findings that a significant correlation between anxiety and CS can be found in healthy individuals, but not in patients. In a VR environment, anxiety partially mediated CS symptoms, specifically nausea and disorientation. A partial explanation for the differences found between patients and controls may lie in a ceiling effect for the symptoms of CS. A second explanation may be the partial overlap between CS symptoms and physiological anxiety responses. CS symptoms reported at baseline cannot be explained by exposure to VR, but are related to anxiety. Caution is required when interpreting studies on both CS and anxiety, until the specificity in measurements has been improved. Since anxiety mediated the CS symptoms, CS is expected to decline during treatment together with the reduction of anxiety.

  15. Temporal overlap estimation based on interference spectrum in CARS microscopy

    Science.gov (United States)

    Zhang, Yongning; Jiang, Junfeng; Liu, Kun; Huang, Can; Wang, Shuang; Zhang, Xuezhi; Liu, Tiegen

    2018-01-01

    Coherent Anti-Stokes Raman Scattering (CARS) microscopy has attracted lots of attention because of the advantages, such as noninvasive, label-free, chemical specificity, intrinsic three-dimension spatial resolution and so on. However, the temporal overlap of pump and Stokes has not been solved owing to the ultrafast optical pulse used in CARS microscopy. We combine interference spectrum of residual pump in Stokes path and nonlinear Schrodinger equation (NLSE) to realize the temporal overlap of pump pulse and Stokes pulse. At first, based on the interference spectrum of pump pulse and residual pump in Stokes path, the optical delay is defined when optical path difference between pump path and Stokes path is zero. Then the relative optical delay between Stokes pulse and residual pump in PCF can be calculated by NLSE. According to the spectrum interference and NLSE, temporal overlap of pump pulse and Stokes pulse will be realized easily and the imaging speed will be improved in CARS microscopy.

  16. On formation of a partially coherent beam in a stable-resonator laser

    International Nuclear Information System (INIS)

    Suvorov, A A

    2010-01-01

    A new method involving the expansion of the field coherence function in partially coherent modes - the eigensolutions of the problem for the second-order coherence function in a stable resonator - is proposed for the theoretical description of the process of multimode laser beam formation. The method for solving the problem for arbitrary partially coherent modes is formulated and the expressions for these modes are derived in the general form. The characteristics of the fundamental partially coherent mode, which coincides with the coherence function of a Gaussian partially coherent beam, are analysed in detail. The partially coherent modes are shown to possess two spatial scales - the effective radius and the coherence radius, which makes them a convenient tool for solving the problem of generation of a partially coherent beam. It is found that the unambiguous relation between the characteristics of partially coherent modes and the stable-resonator parameters is achieved by involving into consideration not only the process of the beam formation by the resonator mirrors but also the process of interaction of radiation with the active laser medium. (laser beams and resonators)

  17. Information-optimal genome assembly via sparse read-overlap graphs.

    Science.gov (United States)

    Shomorony, Ilan; Kim, Samuel H; Courtade, Thomas A; Tse, David N C

    2016-09-01

    In the context of third-generation long-read sequencing technologies, read-overlap-based approaches are expected to play a central role in the assembly step. A fundamental challenge in assembling from a read-overlap graph is that the true sequence corresponds to a Hamiltonian path on the graph, and, under most formulations, the assembly problem becomes NP-hard, restricting practical approaches to heuristics. In this work, we avoid this seemingly fundamental barrier by first setting the computational complexity issue aside, and seeking an algorithm that targets information limits In particular, we consider a basic feasibility question: when does the set of reads contain enough information to allow unambiguous reconstruction of the true sequence? Based on insights from this information feasibility question, we present an algorithm-the Not-So-Greedy algorithm-to construct a sparse read-overlap graph. Unlike most other assembly algorithms, Not-So-Greedy comes with a performance guarantee: whenever information feasibility conditions are satisfied, the algorithm reduces the assembly problem to an Eulerian path problem on the resulting graph, and can thus be solved in linear time. In practice, this theoretical guarantee translates into assemblies of higher quality. Evaluations on both simulated reads from real genomes and a PacBio Escherichia coli K12 dataset demonstrate that Not-So-Greedy compares favorably with standard string graph approaches in terms of accuracy of the resulting read-overlap graph and contig N50. Available at github.com/samhykim/nsg courtade@eecs.berkeley.edu or dntse@stanford.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Equation of state of partially-ionized dense plasmas

    International Nuclear Information System (INIS)

    Rogers, F.J.

    1989-01-01

    This paper describes methods for calculating the equation of state of partially-ionized dense plasmas. The term dense plasma is used rather than strongly coupled plasma, since it is possible that at plasma conditions such that only a few levels can be observed spectroscopically the plasma coupling parameters are not large. Due mainly to their importance in theoretical astrophysics, the properties of partially ionized plasmas have been of interest for a long while. More recently, this interest has intensified due to the development of methods for producing partially ionized plasmas in the laboratory. This has opened up large programs of experimental investigation and of practical application. In this paper we consider detailed statistical mechanical methods that explicitly treat the distribution over ionic species and their energy level structure. These detailed approaches are generally characterized as being in the ''chemical picture'' when a free energy expression is minimized or in the ''physical picture'' when the starting point is the grand canonical ensemble. 52 refs., 2 tabs

  19. Intensity-modulated radiation therapy: overlapping co-axial modulated fields

    International Nuclear Information System (INIS)

    Metcalfe, P; Tangboonduangjit, P; White, P

    2004-01-01

    The Varian multi-leaf collimator has a 14.5 cm leaf extension limit from each carriage. This means the target volumes in the head and neck region are sometimes too wide for standard width-modulated fields to provide adequate dose coverage. A solution is to set up asymmetric co-axial overlapping fields. This protects the MLC carriage while in return the MLC provides modulated dose blending in the field overlap region. Planar dose maps for coincident fields from the Pinnacle radiotherapy treatment planning system are compared with planar dose maps reconstructed from radiographic film and electronic portal images. The film and portal images show small leaf-jaw matchlines at each field overlap border. Linear profiles taken across each image show that the observed leaf-jaw matchlines from the accelerator images are not accounted for by the treatment planning system. Dose difference between film reconstructed electronic portal images and planning system are about 2.5 cGy in a modulated field at d max . While the magnitude of the dose differences are small improved round end leaf modelling combined with a finer dose calculation grid may minimize the discrepancy between calculated and delivered dose

  20. Enhanced angular overlap model for nonmetallic f -electron systems

    Science.gov (United States)

    Gajek, Z.

    2005-07-01

    An efficient method of interpretation of the crystal field effect in nonmetallic f -electron systems, the enhanced angular overlap model (EAOM), is presented. The method is established on the ground of perturbation expansion of the effective Hamiltonian for localized electrons and first-principles calculations related to available experimental data. The series of actinide compounds AO2 , oxychalcogenides AOX , and dichalcogenides UX2 where X=S ,Se,Te and A=U ,Np serve as probes of the effectiveness of the proposed method. An idea is to enhance the usual angular overlap model with ab initio calculations of those contributions to the crystal field potential, which cannot be represented by the usual angular overlap model (AOM). The enhancement leads to an improved fitting and makes the approach intrinsically coherent. In addition, the ab initio calculations of the main, AOM-consistent part of the crystal field potential allows one to fix the material-specific relations for the EAOM parameters in the effective Hamiltonian. Consequently, the electronic structure interpretation based on EAOM can be extended to systems of the lowest point symmetries or/and deficient experimental data. Several examples illustrating the promising capabilities of EAOM are given.

  1. Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment

    DEFF Research Database (Denmark)

    Le Hellard, Stéphanie; Wang, Yunpeng; Witoelar, Aree

    2017-01-01

    . Here we investigated the shared genetic architecture between SCZ and educational attainment, which is regarded as a "proxy phenotype" for cognitive abilities, but may also reflect other traits. We applied a conditional false discovery rate (condFDR) method to GWAS of SCZ (n = 82 315), college...... completion ("College," n = 95 427), and years of education ("EduYears," n = 101 069). Variants associated with College or EduYears showed enrichment of association with SCZ, demonstrating polygenic overlap. This was confirmed by an increased replication rate in SCZ. By applying a condFDR threshold ... of these loci had effects in opposite directions. Our results provide evidence for polygenic overlap between SCZ and educational attainment, and identify novel pleiotropic loci. Other studies have reported genetic overlap between SCZ and cognition, or SCZ and educational attainment, with negative correlation...

  2. MR imaging of the Achilles tendon: overlap of findings in symptomatic and asymptomatic individuals

    International Nuclear Information System (INIS)

    Haims, A.H.; Schweitzer, M.E.; Patel, R.S.

    2000-01-01

    significant overlap of MR findings in symptomatic and asymptomatic Achilles tendons. Furthermore, there is apparently a spectrum of disease in symptomatic tendons ranging from subtle intratendinous and peritendinous signal to partial and complete tendon tear. (orig.)

  3. Barley peroxidase isozymes. Expression and post-translational modification in mature seeds as identified by two-dimensional gel electrophoresis and mass spectrometry

    DEFF Research Database (Denmark)

    Laugesen, Sabrina; Bak-Jensen, Kristian Sass; Hägglund, Per

    2007-01-01

    spectrometric analysis. Distinct peroxidase spot patterns divided the 16 cultivars tested into two groups. The distribution of the three isozymes in different seed tissues (endosperm, embryo, and aleurone layer) suggested the peroxidases to play individual albeit partially overlapping roles during germination...

  4. Distinct and overlapping functions of ptpn11 genes in Zebrafish development.

    Directory of Open Access Journals (Sweden)

    Monica Bonetti

    Full Text Available The PTPN11 (protein-tyrosine phosphatase, non-receptor type 11 gene encodes SHP2, a cytoplasmic PTP that is essential for vertebrate development. Mutations in PTPN11 are associated with Noonan and LEOPARD syndrome. Human patients with these autosomal dominant disorders display various symptoms, including short stature, craniofacial defects and heart abnormalities. We have used the zebrafish as a model to investigate the role of Shp2 in embryonic development. The zebrafish genome encodes two ptpn11 genes, ptpn11a and ptpn11b. Here, we report that ptpn11a is expressed constitutively and ptpn11b expression is strongly upregulated during development. In addition, the products of both ptpn11 genes, Shp2a and Shp2b, are functional. Target-selected inactivation of ptpn11a and ptpn11b revealed that double homozygous mutants are embryonic lethal at 5-6 days post fertilization (dpf. Ptpn11a-/-ptpn11b-/- embryos showed pleiotropic defects from 4 dpf onwards, including reduced body axis extension and craniofacial defects, which was accompanied by low levels of phosphorylated Erk at 5 dpf. Interestingly, defects in homozygous ptpn11a-/- mutants overlapped with defects in the double mutants albeit they were milder, whereas ptpn11b-/- single mutants did not show detectable developmental defects and were viable and fertile. Ptpn11a-/-ptpn11b-/- mutants were rescued by expression of exogenous ptpn11a and ptpn11b alike, indicating functional redundance of Shp2a and Shp2b. The ptpn11 mutants provide a good basis for further unravelling of the function of Shp2 in vertebrate development.

  5. Asynchronous partial contact motion due to internal resonance in multiple degree-of-freedom rotordynamics.

    Science.gov (United States)

    Shaw, A D; Champneys, A R; Friswell, M I

    2016-08-01

    Sudden onset of violent chattering or whirling rotor-stator contact motion in rotational machines can cause significant damage in many industrial applications. It is shown that internal resonance can lead to the onset of bouncing-type partial contact motion away from primary resonances. These partial contact limit cycles can involve any two modes of an arbitrarily high degree-of-freedom system, and can be seen as an extension of a synchronization condition previously reported for a single disc system. The synchronization formula predicts multiple drivespeeds, corresponding to different forms of mode-locked bouncing orbits. These results are backed up by a brute-force bifurcation analysis which reveals numerical existence of the corresponding family of bouncing orbits at supercritical drivespeeds, provided the damping is sufficiently low. The numerics reveal many overlapping families of solutions, which leads to significant multi-stability of the response at given drive speeds. Further, secondary bifurcations can also occur within each family, altering the nature of the response and ultimately leading to chaos. It is illustrated how stiffness and damping of the stator have a large effect on the number and nature of the partial contact solutions, illustrating the extreme sensitivity that would be observed in practice.

  6. Non-fusion and fusion expression of beta-galactosidase from Lactobacillus bulgaricus in Lactococcus lactis.

    Science.gov (United States)

    Wang, Chuan; Zhang, Chao-Wu; Liu, Heng-Chuan; Yu, Qian; Pei, Xiao-Fang

    2008-10-01

    To construct four recombinant Lactococcus lactis strains exhibiting high beta-galactosidase activity in fusion or non-fusion ways, and to study the influence factors for their protein expression and secretion. The gene fragments encoding beta-galactosidase from two strains of Lactobacillus bulgaricus, wch9901 isolated from yogurt and 1.1480 purchased from the Chinese Academy of Sciences, were amplified and inserted into lactococcal expression vector pMG36e. For fusion expression, the open reading frame of the beta-galactosidase gene was amplified, while for non-fusion expression, the open reading frame of the beta-galactosidase gene was amplified with its native Shine-Dalgarno sequence upstream. The start codon of the beta-galactosidase gene partially overlapped with the stop codon of vector origin open reading frame. Then, the recombinant plasmids were transformed into Escherichia coli DH5 alpha and Lactococcus lactis subsp. lactis MG1363 and confirmed by determining beta-galactosidase activities. The non-fusion expression plasmids showed a significantly higher beta-galactosidase activity in transformed strains than the fusion expression plasmids. The highest enzyme activity was observed in Lactococcus lactis transformed with the non-fusion expression plasmids which were inserted into the beta-galactosidase gene from Lactobacillus bulgaricus wch9901. The beta-galactosidase activity was 2.75 times as high as that of the native counterpart. In addition, beta-galactosidase expressed by recombinant plasmids in Lactococcus lactis could be secreted into the culture medium. The highest secretion rate (27.1%) was observed when the culture medium contained 20 g/L of lactose. Different properties of the native bacteria may have some effects on the protein expression of recombinant plasmids. Non-fusion expression shows a higher enzyme activity in host bacteria. There may be a host-related weak secretion signal peptide gene within the structure gene of Lb. bulgaricus beta

  7. Overlapping positive and negative regulatory domains of the human β-interferon gene

    International Nuclear Information System (INIS)

    Goodbourn, S.; Maniatis, T.

    1988-01-01

    Virus of poly(I) x poly(C) induction of human β-interferon gene expression requires a 40-base-pair DNA sequence designated the interferon gene regulatory element (IRE). Previous studies have shown that the IRE contains both positive and negative regulatory DNA sequences. To localize these sequences and study their interactions, the authors have examined the effects of a large number of single-base mutations within the IRE on β-interferon gene regulation. They find that the IRE consists of two genetically separable positive regulatory domains and an overlapping negative control sequence. They propose that the β-interferon gene is switched off in uninduced cells by a repressor that blocks the interaction between one of the two positive regulatory sequences and a specific transcription factor. Induction would then lead to inactivation or displacement of the repressor and binding of transcription factors to both positive regulatory domains

  8. Depression, anxiety and somatization in primary care: syndrome overlap and functional impairment.

    Science.gov (United States)

    Löwe, Bernd; Spitzer, Robert L; Williams, Janet B W; Mussell, Monika; Schellberg, Dieter; Kroenke, Kurt

    2008-01-01

    To determine diagnostic overlap of depression, anxiety and somatization as well as their unique and overlapping contribution to functional impairment. Two thousand ninety-one consecutive primary care clinic patients participated in a multicenter cross-sectional survey in 15 primary care clinics in the United States (participation rate, 92%). Depression, anxiety, somatization and functional impairment were assessed using validated scales from the Patient Health Questionnaire (PHQ) (PHQ-8, eight-item depression module; GAD-7, seven-item Generalized Anxiety Disorder Scale; and PHQ-15, 15-item somatic symptom scale) and the Short-Form General Health Survey (SF-20). Multiple linear regression analyses were used to investigate unique and overlapping associations of depression, anxiety and somatization with functional impairment. In over 50% of cases, comorbidities existed between depression, anxiety and somatization. The contribution of the commonalities of depression, anxiety and somatization to functional impairment substantially exceeded the contribution of their independent parts. Nevertheless, depression, anxiety and somatization did have important and individual effects (i.e., separate from their overlap effect) on certain areas of functional impairment. Given the large syndrome overlap, a potential consideration for future diagnostic classification would be to describe basic diagnostic criteria for a single overarching disorder and to optionally code additional diagnostic features that allow a more detailed classification into specific depressive, anxiety and somatoform subtypes.

  9. Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events1[OPEN

    Science.gov (United States)

    Haberer, Georg; Panda, Arup; Das Laha, Shayani; Ghosh, Tapas Chandra; Schäffner, Anton R.

    2016-01-01

    The identification of functionally equivalent, orthologous genes (functional orthologs) across genomes is necessary for accurate transfer of experimental knowledge from well-characterized organisms to others. This frequently relies on automated, coding sequence-based approaches such as OrthoMCL, Inparanoid, and KOG, which usually work well for one-to-one homologous states. However, this strategy does not reliably work for plants due to the occurrence of extensive gene/genome duplication. Frequently, for one query gene, multiple orthologous genes are predicted in the other genome, and it is not clear a priori from sequence comparison and similarity which one preserves the ancestral function. We have studied 11 organ-dependent and stress-induced gene expression patterns of 286 Arabidopsis lyrata duplicated gene groups and compared them with the respective Arabidopsis (Arabidopsis thaliana) genes to predict putative expressologs and nonexpressologs based on gene expression similarity. Promoter sequence divergence as an additional tool to substantiate functional orthology only partially overlapped with expressolog classification. By cloning eight A. lyrata homologs and complementing them in the respective four Arabidopsis loss-of-function mutants, we experimentally proved that predicted expressologs are indeed functional orthologs, while nonexpressologs or nonfunctionalized orthologs are not. Our study demonstrates that even a small set of gene expression data in addition to sequence homologies are instrumental in the assignment of functional orthologs in the presence of multiple orthologs. PMID:27303025

  10. Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2010-01-01

    Full Text Available Abstract Background Overlapping genes are common in RNA viruses where they serve as a mechanism to optimize the coding potential of compact genomes. However, annotation of overlapping genes can be difficult using conventional gene-finding software. Recently we have been using a number of complementary approaches to systematically identify previously undetected overlapping genes in RNA virus genomes. In this article we gather together a number of promising candidate new overlapping genes that may be of interest to the community. Results Overlapping gene predictions are presented for the astroviruses, seadornaviruses, cytorhabdoviruses and coronaviruses (families Astroviridae, Reoviridae, Rhabdoviridae and Coronaviridae, respectively.

  11. [The Overlap Syndrome: association of COPD and Obstructive Sleep Apnoea].

    Science.gov (United States)

    Weitzenblum, E; Chaouat, A; Kessler, R; Canuet, M; Hirschi, S

    2010-04-01

    Chronic obstructive pulmonary disease (COPD) and the obstructive sleep apnoea-hypopnoea syndrome (OSAHS) are both common diseases affecting respectively 10 and 5% of the adult population over 40 years of age. Their coexistence, which is denominated "Overlap Syndrome", can be expected to occur in about 0.5% of this population. Two recent epidemiologic studies have shown that the prevalence of OSAHS is not higher in COPD than in the general population, and that the coexistence of the two conditions is due to chance and not through a pathophysiological linkage. Patients with "overlap" have a higher risk of sleep-related O(2) desaturation than do patients with COPD alone and the same degree of bronchial obstruction. They have an increased risk of developing hypercapnic respiratory failure and pulmonary hypertension when compared with patients with OSAHS alone and with patients with "usual" COPD. In patients with overlap, hypoxaemia, hypercapnia, and pulmonary hypertension can be observed in the presence of mild to moderate bronchial obstruction, which is different from "usual" COPD. Treatment of the overlap syndrome consists of nasal continuous positive airway pressure or nocturnal non-invasive ventilation (NIV), with or without nocturnal O(2). Patients who are markedly hypoxaemic during the daytime (PaO(2)<55-60 mmHg) should be given conventional long-term O(2) therapy in addition to nocturnal ventilation. Copyright 2010 SPLF. Published by Elsevier Masson SAS. All rights reserved.

  12. Genetic architecture of sporadic frontotemporal dementia and overlap with Alzheimer's and Parkinson's diseases

    DEFF Research Database (Denmark)

    Ferrari, Raffaele; Wang, Yunpeng; Vandrovcova, Jana

    2017-01-01

    BACKGROUND: Clinical, pathological and genetic overlap between sporadic frontotemporal dementia (FTD), Alzheimer's disease (AD) and Parkinson's disease (PD) has been suggested; however, the relationship between these disorders is still not well understood. Here we evaluated genetic overlap between...

  13. Hybridized Kibble-Zurek scaling in the driven critical dynamics across an overlapping critical region

    Science.gov (United States)

    Zhai, Liang-Jun; Wang, Huai-Yu; Yin, Shuai

    2018-04-01

    The conventional Kibble-Zurek scaling describes the scaling behavior in the driven dynamics across a single critical region. In this paper, we study the driven dynamics across an overlapping critical region, in which a critical region (Region A) is overlaid by another critical region (Region B). We develop a hybridized Kibble-Zurek scaling (HKZS) to characterize the scaling behavior in the driven process. According to the HKZS, the driven dynamics in the overlapping region can be described by the critical theories for both Region A and Region B simultaneously. This results in a constraint on the scaling function in the overlapping critical region. We take the quantum Ising chain in an imaginary longitudinal field as an example. In this model, the critical region of the Yang-Lee edge singularity and the critical region of the ferromagnetic-paramagnetic phase transition overlap with each other. We numerically confirm the HKZS by simulating the driven dynamics in this overlapping critical region. The HKZSs in other models are also discussed.

  14. Cast Partial Denture versus Acrylic Partial Denture for Replacement of Missing Teeth in Partially Edentulous Patients

    Directory of Open Access Journals (Sweden)

    Pramita Suwal

    2017-03-01

    Full Text Available Aim: To compare the effects of cast partial denture with conventional all acrylic denture in respect to retention, stability, masticatory efficiency, comfort and periodontal health of abutments. Methods: 50 adult partially edentulous patient seeking for replacement of missing teeth having Kennedy class I and II arches with or without modification areas were selected for the study. Group-A was treated with cast partial denture and Group-B with acrylic partial denture. Data collected during follow-up visit of 3 months, 6 months, and 1 year by evaluating retention, stability, masticatory efficiency, comfort, periodontal health of abutment. Results: Chi-square test was applied to find out differences between the groups at 95% confidence interval where p = 0.05. One year comparison shows that cast partial denture maintained retention and stability better than acrylic partial denture (p< 0.05. The masticatory efficiency was significantly compromising from 3rd month to 1 year in all acrylic partial denture groups (p< 0.05. The comfort of patient with cast partial denture was maintained better during the observation period (p< 0.05. Periodontal health of abutment was gradually deteriorated in all acrylic denture group (p

  15. Latin Square Thue-Morse Sequences are Overlap-Free

    Directory of Open Access Journals (Sweden)

    Christopher Robinson Tompkins

    2007-01-01

    Full Text Available We define a morphism based upon a Latin square that generalizes the Thue-Morse morphism. We prove that fixed points of this morphism are overlap-free sequences, generalizing results of Allouche - Shallit and Frid.

  16. DNA Measurement of Overlapping Cell Nuclei in Thick Tissue Sections

    Directory of Open Access Journals (Sweden)

    Liang Ji

    1997-01-01

    Full Text Available The paper describes an improved image analysis procedure for measuring the DNA content of cell nuclei in thick sections of liver tissue by absorption densitometry. Whereas previous methods only permitted the analysis of isolated nuclei, the new technique enables both isolated and overlapping nuclei to be measured. A 3D segmentation procedure determines whether each object is an isolated nucleus or a pair of overlapping nuclei; in the latter case the combined optical density is redistributed to the individual nuclei. A selection procedure ensures that only complete nuclei are measured.

  17. Device for overlapping of a column of pump compressor pipes

    Energy Technology Data Exchange (ETDEWEB)

    Sharafutdinov, I.G.; Akhmerov, M.N.; Asadullin, Kh.F.; Prokopov, O.I.

    1980-02-16

    A device is proposed for automatic overlapping of pump compressor pipes of gushing petroleum and gas wells when losses occur near the well. The objective of the invention is to increase efficiency of the overlapping of the pipe column by recharging the device directly at the hole without disassembling the head equipment. This objective is achieved as follows. The device is equipped with elastic spacers located in the channels of a ring. They are mounted with the possibility of interaction with ball catches. A drawing and description of the device are given.

  18. Reversible effects of oxygen partial pressure on genes associated with placental angiogenesis and differentiation in primary-term cytotrophoblast cell culture.

    Science.gov (United States)

    Debiève, F; Depoix, C; Gruson, D; Hubinont, C

    2013-09-01

    Timely regulated changes in oxygen partial pressure are important for placental formation. Disturbances could be responsible for pregnancy-related diseases like preeclampsia and intrauterine growth restriction. We aimed to (i) determine the effect of oxygen partial pressure on cytotrophoblast differentiation; (ii) measure mRNA expression and protein secretion from genes associated with placental angiogenesis; and (iii) determine the reversibility of these effects at different oxygen partial pressures. Term cytotrophoblasts were incubated at 21% and 2.5% O2 for 96 hr, or were switched between the two oxygen concentrations after 48 hr. Real-time PCR and enzyme-linked immunosorbent assays (ELISAs) were used to evaluate cell fusion and differentiation, measuring transcript levels for those genes involved in cell fusion and placental angiogenesis, including VEGF, PlGF, VEGFR1, sVEGFR1, sENG, INHA, and GCM1. Cytotrophoblasts underwent fusion and differentiation in 2.5% O2 . PlGF expression was inhibited while sVEGFR1 expression increased. VEGF and sENG mRNA expressions increased in 2.5% compared to 21% O2 , but no protein was detected in the cell supernatants. Finally, GCM1 mRNA expression increased during trophoblast differentiation at 21% O2 , but was inhibited at 2.5% O2 . These mRNA expression effects were reversed by returning the cells to 21% O2 . Thus, low-oxygen partial pressure does not inhibit term-cytotrophoblast cell fusion and differentiation in vitro. Lowering the oxygen partial pressure from 21% to 2.5% caused normal-term trophoblasts to reversibly modify their expression of genes associated with placental angiogenesis. This suggests that modifications observed in pregnancy diseases such as preeclampsia or growth retardation are probably due to an extrinsic effect on trophoblasts. Copyright © 2013 Wiley Periodicals, Inc.

  19. Strong genetic overlap between executive functions and intelligence.

    Science.gov (United States)

    Engelhardt, Laura E; Mann, Frank D; Briley, Daniel A; Church, Jessica A; Harden, K Paige; Tucker-Drob, Elliot M

    2016-09-01

    Executive functions (EFs) are cognitive processes that control, monitor, and coordinate more basic cognitive processes. EFs play instrumental roles in models of complex reasoning, learning, and decision making, and individual differences in EFs have been consistently linked with individual differences in intelligence. By middle childhood, genetic factors account for a moderate proportion of the variance in intelligence, and these effects increase in magnitude through adolescence. Genetic influences on EFs are very high, even in middle childhood, but the extent to which these genetic influences overlap with those on intelligence is unclear. We examined genetic and environmental overlap between EFs and intelligence in a racially and socioeconomically diverse sample of 811 twins ages 7 to 15 years (M = 10.91, SD = 1.74) from the Texas Twin Project. A general EF factor representing variance common to inhibition, switching, working memory, and updating domains accounted for substantial proportions of variance in intelligence, primarily via a genetic pathway. General EF continued to have a strong, genetically mediated association with intelligence even after controlling for processing speed. Residual variation in general intelligence was influenced only by shared and nonshared environmental factors, and there remained no genetic variance in general intelligence that was unique of EF. Genetic variance independent of EF did remain, however, in a more specific perceptual reasoning ability. These results provide evidence that genetic influences on general intelligence are highly overlapping with those on EF. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  20. Individual foraging strategies reveal niche overlap between endangered galapagos pinnipeds.

    Directory of Open Access Journals (Sweden)

    Stella Villegas-Amtmann

    Full Text Available Most competition studies between species are conducted from a population-level approach. Few studies have examined inter-specific competition in conjunction with intra-specific competition, with an individual-based approach. To our knowledge, none has been conducted on marine top predators. Sympatric Galapagos fur seals (Arctocephalus galapagoensis and sea lions (Zalophus wollebaeki share similar geographic habitats and potentially compete. We studied their foraging niche overlap at Cabo Douglas, Fernandina Island from simultaneously collected dive and movement data to examine spatial and temporal inter- and intra-specific competition. Sea lions exhibited 3 foraging strategies (shallow, intermediate and deep indicating intra-specific competition. Fur seals exhibited one foraging strategy, diving predominantly at night, between 0-80 m depth and mostly at 19-22 h. Most sea lion dives also occurred at night (63%, between 0-40 m, within fur seals' diving depth range. 34% of sea lions night dives occurred at 19-22 h, when fur seals dived the most, but most of them occurred at dawn and dusk, when fur seals exhibited the least amount of dives. Fur seals and sea lions foraging behavior overlapped at 19 and 21 h between 0-30 m depths. Sea lions from the deep diving strategy exhibited the greatest foraging overlap with fur seals, in time (19 h, depth during overlapping time (21-24 m, and foraging range (37.7%. Fur seals foraging range was larger. Cabo Douglas northwest coastal area, region of highest diving density, is a foraging "hot spot" for both species. Fur seals and sea lions foraging niche overlap occurred, but segregation also occurred; fur seals primarily dived at night, while sea lions exhibited night and day diving. Both species exploited depths and areas exclusive to their species. Niche breadth generally increases with environmental uncertainty and decreased productivity. Potential competition between these species could be greater during

  1. Transgenic Expression of the piRNA-Resistant Masculinizer Gene Induces Female-Specific Lethality and Partial Female-to-Male Sex Reversal in the Silkworm, Bombyx mori.

    Science.gov (United States)

    Sakai, Hiroki; Sumitani, Megumi; Chikami, Yasuhiko; Yahata, Kensuke; Uchino, Keiro; Kiuchi, Takashi; Katsuma, Susumu; Aoki, Fugaku; Sezutsu, Hideki; Suzuki, Masataka G

    2016-08-01

    In Bombyx mori (B. mori), Fem piRNA originates from the W chromosome and is responsible for femaleness. The Fem piRNA-PIWI complex targets and cleaves mRNAs transcribed from the Masc gene. Masc encodes a novel CCCH type zinc-finger protein and is required for male-specific splicing of B. mori doublesex (Bmdsx) transcripts. In the present study, several silkworm strains carrying a transgene, which encodes a Fem piRNA-resistant Masc mRNA (Masc-R), were generated. Forced expression of the Masc-R transgene caused female-specific lethality during the larval stages. One of the Masc-R strains weakly expressed Masc-R in various tissues. Females heterozygous for the transgene expressed male-specific isoform of the Bombyx homolog of insulin-like growth factor II mRNA-binding protein (ImpM) and Bmdsx. All examined females showed a lower inducibility of vitellogenin synthesis and exhibited abnormalities in the ovaries. Testis-like tissues were observed in abnormal ovaries and, notably, the tissues contained considerable numbers of sperm bundles. Homozygous expression of the transgene resulted in formation of the male-specific abdominal segment in adult females and caused partial male differentiation in female genitalia. These results strongly suggest that Masc is an important regulatory gene of maleness in B. mori.

  2. Retrospective analysis of autoimmune hepatitis-primary biliary cirrhosis overlap syndrome in Korea: characteristics, treatments, and outcomes

    Directory of Open Access Journals (Sweden)

    Yoonsang Park

    2015-06-01

    Full Text Available Background/AimsOverlap syndrome of autoimmune hepatitis (AIH and primary biliary cirrhosis (PBC (AIH-PBC overlap syndrome is a rare disease that has not been clearly characterized in Korean patients. This study investigated the clinical features of AIH-PBC overlap syndrome compared with those of AIH and PBC alone.MethodsThis retrospective cohort study included 158 consecutive patients who were diagnosed as AIH (n=61, PBC (n=81, or AIH-PBC overlap syndrome (n=9 based on the Paris and the International Autoimmune Hepatitis Group (IAIHG criteria from 2001 to 2011 in Korea. We compared the clinical features of these three groups retrospectively, including their biochemical characteristics, treatments, responses, and clinical outcomes.ResultsThe AIH-PBC overlap syndrome patients exhibited biochemical characteristics of both AIH and PBC, and showed a similar response to ursodeoxycholic acid (UDCA monotherapy as for the PBC patients. However, the response of AIH-PBC overlap syndrome patients to UDCA and steroid combination therapy was worse than the response of AIH patients to steroid-based therapy (P=0.024. Liver cirrhosis developed more rapidly in AIH-PBC overlap syndrome patients than in AIH patients group (P=0.013, but there was no difference between AIH-PBC overlap syndrome patients and PBC patients. The rates of developing hepatic decompensation did not differ significantly between the groups.ConclusionsThe AIH-PBC overlap syndrome patients exhibited a worse response to UDCA and steroid combination therapy and a faster cirrhotic progression compared with AIH patients.

  3. General formalism for partial spatial coherence in reflection Mueller matrix polarimetry.

    Science.gov (United States)

    Ossikovski, Razvigor; Hingerl, Kurt

    2016-09-01

    Starting from the first principles, we derive the expressions governing partially coherent Mueller matrix reflection polarimetry on spatially inhomogeneous samples. These are reported both in their general form and in the practically important specific form for two juxtaposed media.

  4. Auditing Complex Concepts in Overlapping Subsets of SNOMED

    Science.gov (United States)

    Wang, Yue; Wei, Duo; Xu, Junchuan; Elhanan, Gai; Perl, Yehoshua; Halper, Michael; Chen, Yan; Spackman, Kent A.; Hripcsak, George

    2008-01-01

    Limited resources and the sheer volume of concepts make auditing a large terminology, such as SNOMED CT, a daunting task. It is essential to devise techniques that can aid an auditor by automatically identifying concepts that deserve attention. A methodology for this purpose based on a previously introduced abstraction network (called the p-area taxonomy) for a SNOMED CT hierarchy is presented. The methodology algorithmically gathers concepts appearing in certain overlapping subsets, defined exclusively with respect to the p-area taxonomy, for review. The results of applying the methodology to SNOMED’s Specimen hierarchy are presented. These results are compared against a control sample composed of concepts residing in subsets without the overlaps. With the use of the double bootstrap, the concept group produced by our methodology is shown to yield a statistically significant higher proportion of error discoveries. PMID:18998838

  5. Phenotype of asthma-chronic obstructive pulmonary disease overlap syndrome.

    Science.gov (United States)

    Rhee, Chin Kook

    2015-07-01

    Many patients with asthma or chronic obstructive pulmonary disease (COPD) have overlapping characteristics of both diseases. By spirometric definition, patients with both fixed airflow obstruction (AO) and bronchodilator reversibility or fixed AO and bronchial hyperresponsiveness can be considered to have asthma-COPD overlap syndrome (ACOS). However, patients regarded to have ACOS by spirometric criteria alone are heterogeneous and can be classified by phenotype. Eosinophilic inflammation, a history of allergic disease, and smoke exposure are important components in the classification of ACOS. Each phenotype has a different underlying pathophysiology, set of characteristics, and prognosis. Medical treatment for ACOS should be tailored according to phenotype. A narrower definition of ACOS that includes both spirometric and clinical criteria is needed.

  6. ORIGINAL ARTICLE Farber disease overlapping with stiff skin ...

    African Journals Online (AJOL)

    salah

    Aim of the Study: Diagnosis and clarification of overlapping in the clinical presentation of the ... and heart are particularly affected with ... painful swelling of the joints, especially the ankle, wrist ... exons and encoding a 395 amino acid precursor ...

  7. Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Mundy, J.; Willenbrock, Hanni

    2007-01-01

    The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental facto...

  8. Autism and ADHD: Overlapping and Discriminating Symptoms

    Science.gov (United States)

    Mayes, Susan Dickerson; Calhoun, Susan L.; Mayes, Rebecca D.; Molitoris, Sarah

    2012-01-01

    Children with ADHD and autism have some similar features, complicating a differential diagnosis. The purpose of our study was to determine the degree to which core ADHD and autistic symptoms overlap in and discriminate between children 2-16 years of age with autism and ADHD. Our study demonstrated that 847 children with autism were easily…

  9. Magnetic breakdown in an array of overlapping Fermi surfaces

    International Nuclear Information System (INIS)

    Kadigrobov, A.M.; Radić, D.; Bjeliš, A.

    2015-01-01

    We develop a theoretical framework for a magnetic breakdown in an array of circular two-dimensional bands with a finite overlap of neighboring Fermi surfaces due to the presence of a presumably weak periodic potential, and apply the obtained results to the electron bands in carbon honeycomb structures of doped graphene and intercalated graphite compounds. In contrast to the standard treatment, inaugurated more than fifty years ago by Slutskin and Kadigrobov, with electron semiclassical trajectories encircling significantly overlapping Fermi surfaces, we examine a configuration in which bands are related in a way that the Fermi surfaces only slightly overlap, forming internal band pockets with areas of the size comparable to the area of the quantum magnetic flux for a given external magnetic field. Such band configuration has to be treated quantum mechanically. The calculation leads to the results for magnetic breakdown coefficients comprising an additional large factor with respect to the standard results, proportional to the ratio of the Fermi energy and the cyclotron energy. Also, these coefficients show oscillating dependence on energy, as well as on the wave number of periodic potential. Both mentioned elements enable the adjustment of the preferred wave vector of possible magnetic breakdown induced density wave instability at the highest possible critical temperature

  10. Heterojunction fully depleted SOI-TFET with oxide/source overlap

    Science.gov (United States)

    Chander, Sweta; Bhowmick, B.; Baishya, S.

    2015-10-01

    In this work, a hetero-junction fully depleted (FD) Silicon-on-Insulator (SOI) Tunnel Field Effect Transistor (TFET) nanostructure with oxide overlap on the Germanium-source region is proposed. Investigations using Synopsys Technology Computer Aided Design (TCAD) simulation tools reveal that the simple oxide overlap on the Germanium-source region increases the tunneling area as well as the tunneling current without degrading the band-to-band tunneling (BTBT) and improves the device performance. More importantly, the improvement is independent of gate overlap. Simulation study shows improvement in ON current, subthreshold swing (SS), OFF current, ION/IOFF ration, threshold voltage and transconductance. The proposed device with hafnium oxide (HfO2)/Aluminium Nitride (AlN) stack dielectric material offers an average subthreshold swing of 22 mV/decade and high ION/IOFF ratio (∼1010) at VDS = 0.4 V. Compared to conventional TFET, the Miller capacitance of the device shows the enhanced performance. The impact of the drain voltage variation on different parameters such as threshold voltage, subthreshold swing, transconductance, and ION/IOFF ration are also found to be satisfactory. From fabrication point of view also it is easy to utilize the existing CMOS process flows to fabricate the proposed device.

  11. Statistically validated network of portfolio overlaps and systemic risk.

    Science.gov (United States)

    Gualdi, Stanislao; Cimini, Giulio; Primicerio, Kevin; Di Clemente, Riccardo; Challet, Damien

    2016-12-21

    Common asset holding by financial institutions (portfolio overlap) is nowadays regarded as an important channel for financial contagion with the potential to trigger fire sales and severe losses at the systemic level. We propose a method to assess the statistical significance of the overlap between heterogeneously diversified portfolios, which we use to build a validated network of financial institutions where links indicate potential contagion channels. The method is implemented on a historical database of institutional holdings ranging from 1999 to the end of 2013, but can be applied to any bipartite network. We find that the proportion of validated links (i.e. of significant overlaps) increased steadily before the 2007-2008 financial crisis and reached a maximum when the crisis occurred. We argue that the nature of this measure implies that systemic risk from fire sales liquidation was maximal at that time. After a sharp drop in 2008, systemic risk resumed its growth in 2009, with a notable acceleration in 2013. We finally show that market trends tend to be amplified in the portfolios identified by the algorithm, such that it is possible to have an informative signal about institutions that are about to suffer (enjoy) the most significant losses (gains).

  12. Overlapping community detection based on link graph using distance dynamics

    Science.gov (United States)

    Chen, Lei; Zhang, Jing; Cai, Li-Jun

    2018-01-01

    The distance dynamics model was recently proposed to detect the disjoint community of a complex network. To identify the overlapping structure of a network using the distance dynamics model, an overlapping community detection algorithm, called L-Attractor, is proposed in this paper. The process of L-Attractor mainly consists of three phases. In the first phase, L-Attractor transforms the original graph to a link graph (a new edge graph) to assure that one node has multiple distances. In the second phase, using the improved distance dynamics model, a dynamic interaction process is introduced to simulate the distance dynamics (shrink or stretch). Through the dynamic interaction process, all distances converge, and the disjoint community structure of the link graph naturally manifests itself. In the third phase, a recovery method is designed to convert the disjoint community structure of the link graph to the overlapping community structure of the original graph. Extensive experiments are conducted on the LFR benchmark networks as well as real-world networks. Based on the results, our algorithm demonstrates higher accuracy and quality than other state-of-the-art algorithms.

  13. Network neighborhood analysis with the multi-node topological overlap measure.

    Science.gov (United States)

    Li, Ai; Horvath, Steve

    2007-01-15

    The goal of neighborhood analysis is to find a set of genes (the neighborhood) that is similar to an initial 'seed' set of genes. Neighborhood analysis methods for network data are important in systems biology. If individual network connections are susceptible to noise, it can be advantageous to define neighborhoods on the basis of a robust interconnectedness measure, e.g. the topological overlap measure. Since the use of multiple nodes in the seed set may lead to more informative neighborhoods, it can be advantageous to define multi-node similarity measures. The pairwise topological overlap measure is generalized to multiple network nodes and subsequently used in a recursive neighborhood construction method. A local permutation scheme is used to determine the neighborhood size. Using four network applications and a simulated example, we provide empirical evidence that the resulting neighborhoods are biologically meaningful, e.g. we use neighborhood analysis to identify brain cancer related genes. An executable Windows program and tutorial for multi-node topological overlap measure (MTOM) based analysis can be downloaded from the webpage (http://www.genetics.ucla.edu/labs/horvath/MTOM/).

  14. Specificity and overlap of attention and memory biases in depression.

    Science.gov (United States)

    Marchetti, Igor; Everaert, Jonas; Dainer-Best, Justin; Loeys, Tom; Beevers, Christopher G; Koster, Ernst H W

    2018-01-01

    Attentional and memory biases are viewed as crucial cognitive processes underlying symptoms of depression. However, it is still unclear whether these two biases are uniquely related to depression or whether they show substantial overlap. We investigated the degree of specificity and overlap of attentional and memory biases for depressotypic stimuli in relation to depression and anxiety by means of meta-analytic commonality analysis. By including four published studies, we considered a pool of 463 healthy and subclinically depressed individuals, different experimental paradigms, and different psychological measures. Memory bias is reliably and strongly related to depression and, specifically, to symptoms of negative mood, worthlessness, feelings of failure, and pessimism. Memory bias for negative information was minimally related to anxiety. Moreover, neither attentional bias nor the overlap between attentional and memory biases were significantly related to depression. Limitations include cross-sectional nature of the study. Our study showed that, across different paradigms and psychological measures, memory bias (and not attentional bias) represents a primary mechanism in depression. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Epidemiological study of overlapping of involved organs in functional gastrointestinal disorders in the Chinese naval servicemen

    Directory of Open Access Journals (Sweden)

    Zi-kai WANG

    2013-07-01

    Full Text Available Objective To study the overlapping of involved organs in functional gastrointestinal disorders (FGIDs occurring in the Chinese naval servicemen, and to provide a sound basis for its diagnosis and treatment. Methods From November 2006 to April 2007, a questionnaire survey was conducted in 8600 officers and soldiers of Chinese naval force in three regions using randomized, stratified, multistage sampling method. All respondents completed the Rome Ⅲ Modular Questionnaire. The collected data were double input by EpiData3.02 software and analyzed by SPSS 13.0 software. Results 7454 valid questionnaires were retrieved. The incidence of overlapping was 46.7% involving two to five sites. In two-site overlap of FGIDs, the incidence of overlap functional gastroduodenal disorder (FGD and functional bowel disorder (FBD was shown to be highest (51.2%, 339/662, followed by the overlap of functional esophageal disorder (FED and FBD (15.4%, 102/662. In three-site overlap of FGIDs, the overlapping rate of FED, FGD and FBD was the highest (44.4%, 151/340, followed by that of FGD, FBD and functional abdominal pain syndrome (FAPS (20.3%, 69/340. The commonest four-site overlap of FGIDs included FED, FGD, FBD and FAPS (57.7%, 94/163. The five-site overlap of FGIDs was the combination of FED, FGD, FBD, FAPS and functional anorectal disorder (FAD. The incidence of FGIDs in southern military region was 49.8% (987/1983, which was higher than that of northern (31.8%, 1064/3351 and eastern (23.8%, 533/2240 regions. The incidence of FGIDs of single organ was 44.9% in southern military region, which was lower than 59.0% in eastern and 58.4% in northern region. The incidence of the illness involving two to five sites were higher in southern military region as compared with that of eastern and northern regions. Conclusions The rate of overlapping of FGIDs at different sites is common in the Chinese naval servicemen. There is a difference in rate of overlapping

  16. Low Load Limit Extension for Gasoline Compression Ignition Using Negative Valve Overlap Strategy

    KAUST Repository

    Vallinayagam, R.

    2018-04-03

    Gasoline compression ignition (GCI) is widely studied for the benefits of simultaneous reduction in nitrogen oxide (NO) and soot emissions without compromising the engine efficiency. Despite this advantage, the operational range for GCI is not widely expanded, as the auto-ignition of fuel at low load condition is difficult. The present study aims to extend the low load operational limit for GCI using negative valve overlap (NVO) strategy. The engine used for the current experimentation is a single cylinder diesel engine that runs at an idle speed of 800 rpm with a compression ratio of 17.3. The engine is operated at homogeneous charge compression ignition (HCCI) and partially premixed combustion (PPC) combustion modes with the corresponding start of injection (SOI) at 180 CAD (aTDC) and 30 CAD (aTDC), respectively. In the presented work, intake air temperature is used as control parameter to maintain combustion stability at idle and low load condition, while the intake air pressure is maintained at 1 bar (ambient). The engine is equipped with variable valve cam phasers that can phase both inlet and exhaust valves from the original timing. For the maximum cam phasing range (56 CAD) at a valve lift of 0.3 mm, the maximum allowable positive valve overlap was 20 CAD. In the present study, the exhaust cam is phased to 26 CAD and 6 CAD and the corresponding NVO is noted to be 10 CAD and 30 CAD, respectively. With exhaust cam phasing adjustment, the exhaust valve is closed early to retain hot residual gases inside the cylinder. As such, the in-cylinder temperature is increased and a reduction in the required intake air temperature to control combustion phasing is possible. For a constant combustion phasing of 3 CAD (aTDC), a minimum load of indicated mean effective pressure (IMEP) = 1 bar is attained for gasoline (RON = 91) at HCCI and PPC modes. The coefficient of variance was observed to below 5% at these idle and low load conditions. At the minimum load point, the

  17. Comparison of co-expression measures: mutual information, correlation, and model based indices.

    Science.gov (United States)

    Song, Lin; Langfelder, Peter; Horvath, Steve

    2012-12-09

    Co-expression measures are often used to define networks among genes. Mutual information (MI) is often used as a generalized correlation measure. It is not clear how much MI adds beyond standard (robust) correlation measures or regression model based association measures. Further, it is important to assess what transformations of these and other co-expression measures lead to biologically meaningful modules (clusters of genes). We provide a comprehensive comparison between mutual information and several correlation measures in 8 empirical data sets and in simulations. We also study different approaches for transforming an adjacency matrix, e.g. using the topological overlap measure. Overall, we confirm close relationships between MI and correlation in all data sets which reflects the fact that most gene pairs satisfy linear or monotonic relationships. We discuss rare situations when the two measures disagree. We also compare correlation and MI based approaches when it comes to defining co-expression network modules. We show that a robust measure of correlation (the biweight midcorrelation transformed via the topological overlap transformation) leads to modules that are superior to MI based modules and maximal information coefficient (MIC) based modules in terms of gene ontology enrichment. We present a function that relates correlation to mutual information which can be used to approximate the mutual information from the corresponding correlation coefficient. We propose the use of polynomial or spline regression models as an alternative to MI for capturing non-linear relationships between quantitative variables. The biweight midcorrelation outperforms MI in terms of elucidating gene pairwise relationships. Coupled with the topological overlap matrix transformation, it often leads to more significantly enriched co-expression modules. Spline and polynomial networks form attractive alternatives to MI in case of non-linear relationships. Our results indicate that MI

  18. Ripple artifact reduction using slice overlap in slice encoding for metal artifact correction.

    Science.gov (United States)

    den Harder, J Chiel; van Yperen, Gert H; Blume, Ulrike A; Bos, Clemens

    2015-01-01

    Multispectral imaging (MSI) significantly reduces metal artifacts. Yet, especially in techniques that use gradient selection, such as slice encoding for metal artifact correction (SEMAC), a residual ripple artifact may be prominent. Here, an analysis is presented of the ripple artifact and of slice overlap as an approach to reduce the artifact. The ripple artifact was analyzed theoretically to clarify its cause. Slice overlap, conceptually similar to spectral bin overlap in multi-acquisition with variable resonances image combination (MAVRIC), was achieved by reducing the selection gradient and, thus, increasing the slice profile width. Time domain simulations and phantom experiments were performed to validate the analyses and proposed solution. Discontinuities between slices are aggravated by signal displacement in the frequency encoding direction in areas with deviating B0. Specifically, it was demonstrated that ripple artifacts appear only where B0 varies both in-plane and through-plane. Simulations and phantom studies of metal implants confirmed the efficacy of slice overlap to reduce the artifact. The ripple artifact is an important limitation of gradient selection based MSI techniques, and can be understood using the presented simulations. At a scan-time penalty, slice overlap effectively addressed the artifact, thereby improving image quality near metal implants. © 2014 Wiley Periodicals, Inc.

  19. Multidimensional flamelet-generated manifolds for partially premixed combustion

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Phuc-Danh; Vervisch, Luc; Subramanian, Vallinayagam; Domingo, Pascale [CORIA - CNRS and INSA de Rouen, Technopole du Madrillet, BP 8, 76801 Saint-Etienne-du-Rouvray (France)

    2010-01-15

    Flamelet-generated manifolds have been restricted so far to premixed or diffusion flame archetypes, even though the resulting tables have been applied to nonpremixed and partially premixed flame simulations. By using a projection of the full set of mass conservation species balance equations into a restricted subset of the composition space, unsteady multidimensional flamelet governing equations are derived from first principles, under given hypotheses. During the projection, as in usual one-dimensional flamelets, the tangential strain rate of scalar isosurfaces is expressed in the form of the scalar dissipation rates of the control parameters of the multidimensional flamelet-generated manifold (MFM), which is tested in its five-dimensional form for partially premixed combustion, with two composition space directions and three scalar dissipation rates. It is shown that strain-rate-induced effects can hardly be fully neglected in chemistry tabulation of partially premixed combustion, because of fluxes across iso-equivalence-ratio and iso-progress-of-reaction surfaces. This is illustrated by comparing the 5D flamelet-generated manifold with one-dimensional premixed flame and unsteady strained diffusion flame composition space trajectories. The formal links between the asymptotic behavior of MFM and stratified flame, weakly varying partially premixed front, triple-flame, premixed and nonpremixed edge flames are also evidenced. (author)

  20. Probing the topological structure of the QCD vacuum with overlap fermions

    International Nuclear Information System (INIS)

    Ilgenfritz, E.M.; Schierholz, G.; Deutsches Elektronen-Synchrotron; Streuer, T.; Weinberg, V.; Freie Univ. Berlin

    2005-12-01

    Overlap fermions implement exact chiral symmetry on the lattice and are thus an appropriate tool for investigating the chiral and topological structure of the QCD vacuum. We study various chiral and topological aspects on Luescher-Weisz-type quenched gauge field configurations using overlap fermions as a probe. Particular emphasis is placed upon the analysis of the spectral density and the localisation properties of the eigenmodes as well as on the local structure of topological charge fluctuations. (orig.)

  1. Analysis of stacking overlap in nucleic acid structures: algorithm and application.

    Science.gov (United States)

    Pingali, Pavan Kumar; Halder, Sukanya; Mukherjee, Debasish; Basu, Sankar; Banerjee, Rahul; Choudhury, Devapriya; Bhattacharyya, Dhananjay

    2014-08-01

    RNA contains different secondary structural motifs like pseudo-helices, hairpin loops, internal loops, etc. in addition to anti-parallel double helices and random coils. The secondary structures are mainly stabilized by base-pairing and stacking interactions between the planar aromatic bases. The hydrogen bonding strength and geometries of base pairs are characterized by six intra-base pair parameters. Similarly, stacking can be represented by six local doublet parameters. These dinucleotide step parameters can describe the quality of stacking between Watson-Crick base pairs very effectively. However, it is quite difficult to understand the stacking pattern for dinucleotides consisting of non canonical base pairs from these parameters. Stacking interaction is a manifestation of the interaction between two aromatic bases or base pairs and thus can be estimated best by the overlap area between the planar aromatic moieties. We have calculated base pair overlap between two consecutive base pairs as the buried van der Waals surface between them. In general, overlap values show normal distribution for the Watson-Crick base pairs in most double helices within a range from 45 to 50 Å(2) irrespective of base sequence. The dinucleotide steps with non-canonical base pairs also are seen to have high overlap value, although their twist and few other parameters are rather unusual. We have analyzed hairpin loops of different length, bulges within double helical structures and pseudo-continuous helices using our algorithm. The overlap area analyses indicate good stacking between few looped out bases especially in GNRA tetraloop, which was difficult to quantitatively characterise from analysis of the base pair or dinucleotide step parameters. This parameter is also seen to be capable to distinguish pseudo-continuous helices from kinked helix junctions.

  2. Impact of optical hard limiter on the performance of an optical overlapped-code division multiple access system

    Science.gov (United States)

    Inaty, Elie; Raad, Robert; Tablieh, Nicole

    2011-08-01

    Throughout this paper, a closed form expression of the multiple access interference (MAI) limited bit error rate (BER) is provided for the multiwavelength optical code-division multiple-access system when the system is working above the nominal transmission rate limit imposed by the passive encoding-decoding operation. This system is known in literature as the optical overlapped code division multiple access (OV-CDMA) system. A unified analytical framework is presented emphasizing the impact of optical hard limiter (OHL) on the BER performance of such a system. Results show that the performance of the OV-CDMA system may be highly improved when using OHL preprocessing at the receiver side.

  3. Overlapping illusions by transformation optics without any negative refraction material

    Science.gov (United States)

    Sun, Fei; He, Sailing

    2016-01-01

    A novel method to achieve an overlapping illusion without any negative refraction index material is introduced with the help of the optic-null medium (ONM) designed by an extremely stretching spatial transformation. Unlike the previous methods to achieve such an optical illusion by transformation optics (TO), our method can achieve a power combination and reshape the radiation pattern at the same time. Unlike the overlapping illusion with some negative refraction index material, our method is not sensitive to the loss of the materials. Other advantages over existing methods are discussed. Numerical simulations are given to verify the performance of the proposed devices.

  4. Characterization of stochastic spatially and spectrally partially coherent electromagnetic pulsed beams

    International Nuclear Information System (INIS)

    Ding Chaoliang; Lue Baida; Pan Liuzhan

    2009-01-01

    The unified theory of coherence and polarization proposed by Wolf is extended from stochastic stationary electromagnetic beams to stochastic spatially and spectrally partially coherent electromagnetic pulsed beams. Taking the stochastic electromagnetic Gaussian Schell-model pulsed (GSMP) beam as a typical example of stochastic spatially and spectrally partially coherent electromagnetic pulsed beams, the expressions for the spectral density, spectral degree of polarization and spectral degree of coherence of stochastic electromagnetic GSMP beams propagating in free space are derived. Some special cases are analyzed. The illustrative examples are given and the results are interpreted physically.

  5. Identifying Overlapping Language Communities: The Case of Chiriquí and Panamanian Signed Languages

    Science.gov (United States)

    Parks, Elizabeth S.

    2016-01-01

    In this paper, I use a holographic metaphor to explain the identification of overlapping sign language communities in Panama. By visualizing Panama's complex signing communities as emitting community "hotspots" through social drama on multiple stages, I employ ethnographic methods to explore overlapping contours of Panama's sign language…

  6. Partial relay selection based on shadowing side information over generalized composite fading channels

    KAUST Repository

    Yilmaz, Ferkan

    2011-11-01

    In this paper, in contrast to the relay selection protocols available in the literature, we propose a partial relay selection protocol utilizing only the shadowing side information of the relays instead of their full channel side information in order to select a relay in a dual-hop relaying system through the available limited feedback channels and power budget. We then presented an exact unified performance expression combining the average bit error probability, ergodic capacity, and moments-generating function of the proposed partial relay selection over generalized fading channels. Referring to the unified performance expression introduced in [1], we explicitly offer a generic unified performance expression that can be easily calculated and that is applicable to a wide variety of fading scenarios. Finally, as an illustration of the mathematical formalism, some numerical and simulation results are generated for an extended generalized-K fading environment, and these numerical and simulation results are shown to be in perfect agreement. © 2011 IEEE.

  7. Overlapping coalition formation games in wireless communication networks

    CERN Document Server

    Wang, Tianyu; Saad, Walid; Han, Zhu

    2017-01-01

    This brief introduces overlapping coalition formation games (OCF games), a novel mathematical framework from cooperative game theory that can be used to model, design and analyze cooperative scenarios in future wireless communication networks. The concepts of OCF games are explained, and several algorithmic aspects are studied. In addition, several major application scenarios are discussed. These applications are drawn from a variety of fields that include radio resource allocation in dense wireless networks, cooperative spectrum sensing for cognitive radio networks, and resource management for crowd sourcing. For each application, the use of OCF games is discussed in detail in order to show how this framework can be used to solve relevant wireless networking problems. Overlapping Coalition Formation Games in Wireless Communication Networks provides researchers, students and practitioners with a concise overview of existing works in this emerging area, exploring the relevant fundamental theories, key techniqu...

  8. Phase Grouping Line Extraction Algorithm Using Overlapped Partition

    Directory of Open Access Journals (Sweden)

    WANG Jingxue

    2015-07-01

    Full Text Available Aiming at solving the problem of fracture at the discontinuities area and the challenges of line fitting in each partition, an innovative line extraction algorithm is proposed based on phase grouping using overlapped partition. The proposed algorithm adopted dual partition steps, which will generate overlapped eight partitions. Between the two steps, the middle axis in the first step coincides with the border lines in the other step. Firstly, the connected edge points that share the same phase gradients are merged into the line candidates, and fitted into line segments. Then to remedy the break lines at the border areas, the break segments in the second partition steps are refitted. The proposed algorithm is robust and does not need any parameter tuning. Experiments with various datasets have confirmed that the method is not only capable of handling the linear features, but also powerful enough in handling the curve features.

  9. Omalizumab Treatment Response in a Population With Severe Allergic Asthma and Overlapping COPD.

    Science.gov (United States)

    Maltby, Steven; Gibson, Peter G; Powell, Heather; McDonald, Vanessa M

    2017-01-01

    Asthma and COPD are common airway diseases. Individuals with overlapping asthma and COPD experience increased health impairment and severe disease exacerbations. Efficacious treatment options are required for this population. Omalizumab (anti-IgE) therapy is effective in patients with severe persistent asthma, but limited data are available on efficacy in populations with overlapping asthma and COPD. Data from the Australian Xolair Registry were used to compare treatment responses in individuals with asthma-COPD overlap with responses in patients with severe asthma alone. Participants were assessed at baseline and after 6 months of omalizumab treatment. We used several different definitions of asthma-COPD overlap. First, we compared participants with a previous physician diagnosis of COPD to participants with no COPD diagnosis. We then made comparisons based on baseline lung function, comparing participants with an FEV 1 80% predicted after bronchodilator use. In the population with an FEV 1 Omalizumab treatment markedly improved asthma control and health-related quality of life in all populations assessed based on the Asthma Control Questionnaire and Asthma Quality of Life Questionnaire scores. Omalizumab treatment did not improve lung function (FEV 1 , FVC, or FEV 1 /FVC ratio) in populations that were enriched for asthma-COPD overlap (diagnosis of COPD or FEV 1  omalizumab improves asthma control and health-related quality of life in individuals with severe allergic asthma and overlapping COPD. These findings provide real-world efficacy data for this patient population and suggest that omalizumab is useful in the management of severe asthma with COPD overlap. Copyright © 2016 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

  10. Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies.

    Science.gov (United States)

    Zheng, Ling; Chen, Yan; Elhanan, Gai; Perl, Yehoshua; Geller, James; Ochs, Christopher

    2018-05-28

    In previous research, we have demonstrated for a number of ontologies that structurally complex concepts (for different definitions of "complex") in an ontology are more likely to exhibit errors than other concepts. Thus, such complex concepts often become fertile ground for quality assurance (QA) in ontologies. They should be audited first. One example of complex concepts is given by "overlapping concepts" (to be defined below.) Historically, a different auditing methodology had to be developed for every single ontology. For better scalability and efficiency, it is desirable to identify family-wide QA methodologies. Each such methodology would be applicable to a whole family of similar ontologies. In past research, we had divided the 685 ontologies of BioPortal into families of structurally similar ontologies. We showed for four ontologies of the same large family in BioPortal that "overlapping concepts" are indeed statistically significantly more likely to exhibit errors. In order to make an authoritative statement concerning the success of "overlapping concepts" as a methodology for a whole family of similar ontologies (or of large subhierarchies of ontologies), it is necessary to show that "overlapping concepts" have a higher likelihood of errors for six out of six ontologies of the family. In this paper, we are demonstrating for two more ontologies that "overlapping concepts" can successfully predict groups of concepts with a higher error rate than concepts from a control group. The fifth ontology is the Neoplasm subhierarchy of the National Cancer Institute thesaurus (NCIt). The sixth ontology is the Infectious Disease subhierarchy of SNOMED CT. We demonstrate quality assurance results for both of them. Furthermore, in this paper we observe two novel, important, and useful phenomena during quality assurance of "overlapping concepts." First, an erroneous "overlapping concept" can help with discovering other erroneous "non-overlapping concepts" in its vicinity

  11. 42 CFR 73.4 - Overlap select agents and toxins.

    Science.gov (United States)

    2010-10-01

    ... genetically modified. (d) Overlap select agents or toxins that meet any of the following criteria are excluded... Equine Encephalitis virus (c) Genetic Elements, Recombinant Nucleic Acids, and Recombinant Organisms: (1...

  12. Overlap Syndrome in Respiratory Medicine: Asthma and Chronic Obstructive Pulmonary Disease

    Directory of Open Access Journals (Sweden)

    Alexandru Corlateanu

    2014-02-01

    Full Text Available Asthma and chronic obstructive pulmonary disease (COPD are highly prevalent chronic diseases in the general population. Both are characterized by similar mechanisms: airway inflammation, airway obstruction, and airway hyperresponsiveness. However, the distinction between the two obstructive diseases is not always clear. Multiple epidemiological studies demonstrate that in elderly people with obstructive airway disease, as many as half or more may have overlapping diagnoses of asthma and COPD. A COPD-Asthma overlap syndrome is defined as an airflow obstruction that is not completely reversible, accompanied by symptoms and signs of increased obstruction reversibility. For the clinical identification of overlap syndrome COPD-Asthma Spanish guidelines proposed six diagnostic criteria. The major criteria include very positive bronchodilator test [increase in forced expiratory volume in one second (FEV1 ≥15% and ≥400 ml], eosinophilia in sputum, and personal history of asthma. The minor criteria include high total IgE, personal history of atopy and positive bronchodilator test (increase in FEV1 ≥12% and ≥200 ml on two or more occasions. The overlap syndrome COPD-Asthma is associated with enhanced response to inhaled corticosteroids due to the predominance of eosinophilic bronchial inflammation.The future clinical studies and multicenter clinical trials should lead to the investigation of disease mechanisms and simultaneous development of the novel treatment.

  13. Rework Impacts Evaluation Through System Dynamics Approach in Overlapped Product Development Schedule

    Directory of Open Access Journals (Sweden)

    Lino Guimarães Marujo

    2009-07-01

    Full Text Available This work aims to explore a novel framework to analyze the planning concepts in product development projects employing techniques to reduce the lead-time of activities, such as overlapping of a pair of each. With the System Dynamics methodology a model to evaluate the rework fraction needed to accommodate the deviations proportional to the overlapping grade of the activities. A numerical example is provided to demonstrate the validity of the model. Although problems encountered during the project management are dynamic, they have been treated on a static basis, what has as result, chronic schedules delays, overruns and cost overspent persist in follow the managers’ (reactions. In this work, we have addressed this known problem by introducing and reviewing some characteristics of the concept of rework in overlapped schedules. This consists in observe and capture the relations feedbacks among the original planned project schedule, the overlapping strategy and the inherent uncertainty in a work being done with poor information. To realize this concept, we have faced with many behaviors patterns (e.g. rework, new duration, non-conformity, and analyze the output behavior pattern, produced by the proposed model.

  14. Function of chemoreceptor organs in spatial orientation of the lobster, Homarus americanus: differences and overlap

    Energy Technology Data Exchange (ETDEWEB)

    Devine, D.V.; Atema, J.

    1982-08-01

    Three of the lobster's main chemoreceptor organs, the lateral and medial antennules (representing smell) and the dactylus-propodus segments of the walking legs (representing taste), are physiologically quite similar. The authors examined their role in spatial orientation in a food-odor stimulus field. Control animals almost always oriented correctly and immediately to an odor plume. Lobsters with unilateral ablations of lateral antennules lost this ability, but did not show preferential turning toward the intact side. Unilateral medial antennule ablation did not affect orientation. Removal of all aesthetasc hairs from one lateral antennule caused loss of orientation ability less severe than unilateral ablation of the entire lateral antennule. Lobsters with unilaterally ablated lateral antennules and blocked walking leg receptors turned preferentially toward the side of the intact antennule. Thus, it appears that intact lobsters orient in odor space by tropotaxis principally using aesthetasc receptor input. Since loss of appendages is relatively common in lobsters, this partial overlap of organ function may serve the animal well in nature.

  15. Decoding Overlapping Memories in the Medial Temporal Lobes Using High-Resolution fMRI

    Science.gov (United States)

    Chadwick, Martin J.; Hassabis, Demis; Maguire, Eleanor A.

    2011-01-01

    The hippocampus is proposed to process overlapping episodes as discrete memory traces, although direct evidence for this in human episodic memory is scarce. Using green-screen technology we created four highly overlapping movies of everyday events. Participants were scanned using high-resolution fMRI while recalling the movies. Multivariate…

  16. Equitoxic doses of 5-azacytidine and 5-aza-2'deoxycytidine induce diverse immediate and overlapping heritable changes in the transcriptome.

    Directory of Open Access Journals (Sweden)

    Xiangning Qiu

    2010-09-01

    Full Text Available The hypomethylating agent 5-Azacytidine (5-Aza-CR is the first drug to prolong overall survival in patients with myelodysplastic syndrome (MDS. Surprisingly, the deoxyribonucleoside analog 5-Aza-2'deoxycytidine (5-Aza-CdR did not have a similar effect on survival in a large clinical trial. Both drugs are thought to exert their effects after incorporation into DNA by covalent binding of DNA methyltransferase (DNMT. While 5-Aza-CdR is incorporated into only DNA, 5-Aza-CR is also incorporated into RNA. Here, we have analyzed whether this difference in nucleic acid incorporation may influence the capacities of these drugs to regulate the expression of mRNA and microRNAs (miRNA, which may potentially affect the activities of the drugs in patients.A hematopoietic (HL-60; acute myeloid leukemia and a solid (T24; transitional cell carcinoma cancer cell line were treated with equitoxic doses of 5-Aza-CR and 5-Aza-CdR for 24 hrs, and the immediate (day 2 and lasting (day 8 effects on RNA expression examined. There was considerable overlap between the RNAs heritably upregulated by both drugs on day 8 but more RNAs were stably induced by the deoxy analog. Both drugs strongly induced expression of cancer testis antigens. On day 2 more RNAs were downregulated by 5-Aza-CR, particularly at higher doses. A remarkable downregulation of miRNAs and a significant upregulation of tRNA synthetases and other genes involved in amino acid metabolism was observed in T24 cells.Overall, this suggests that significant differences exist in the immediate action of the two drugs, however the dominant pattern of the lasting, and possible heritable changes, is overlapping.

  17. Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa

    DEFF Research Database (Denmark)

    Gómez Lozano, María; Marvig, Rasmus Lykke; Tulstrup, Monica Vera-Lise

    2014-01-01

    Background: RNA sequencing technologies reveal that bacteria express RNA molecules other than mRNA, rRNA or tRNA. During the last years genome-wide bacterial transcriptomes have been shown to comprise intergenic RNA, antisense RNA, and untranslated regions, all capable of performing diverse...... that the extent of overlap between the studies is very limited. Conclusions: RNA-seq experiments are revealing hundreds of novel transcripts in all bacterial genomes investigated. The comparison between independent studies that used RNA-seq to detect novel asRNAs in P. aeruginosa shows that the overlap between...

  18. Pre-asymptotic behavior of single-particle overlap integrals of non-Borromean two-neutron halos

    International Nuclear Information System (INIS)

    Timofeyuk, N.K.; Tostevin, J.A.; Blokhintsev, L.D.

    2003-01-01

    For non-Borromean two-neutron halo nuclei, modifications to the behavior of single-particle overlap integrals will arise due to the correlations of the two interacting nucleons in the halo. An additional contribution to the overlap integral can be obtained using the Feynman diagram approach. This additional term is modeled using a simple local potential model. We show that these modifications may play a role in detailed interpretations of experimental results from single-nucleon knockout, transfer, and other reactions that probe the single-nucleon overlap functions

  19. Effect of overlapping on location of peaks in qualitative X-ray fluorescent analysis

    International Nuclear Information System (INIS)

    Jordanov, J.; Stefanov, R.; Tsanov, T.; Jordanov, N.

    1982-01-01

    To determine the location of the maxima in spectra without resorting to the comparatively complex Fourier-analysis apparatus it is proposed to take into account the overlapping of two adjacent peaks. A formula for the correction of the locations of overlapping maxima with an infinitely small step has been obtained and it is recommended when using X-ray apparatus with great resolution. With flat crystal-analyser apparata, which has a comparatively small resolution, a considerable number of maxima are obtained from the overlapping of at least two adjacent peaks. For that case another formula for the estimation of the shift of the maxima's location from their tabular values is proposed. (authors)

  20. Optimum source/drain overlap design for 16 nm high-k/metal gate MOSFETs

    International Nuclear Information System (INIS)

    Jang, Junyong; Lim, Towoo; Kim, Youngmin

    2009-01-01

    We explore a source/drain (S/D) design for a 16 nm MOSFET utilizing a replacement process for a high-k gate dielectric and metal gate electrode integration. Using TCAD simulation, a trade-off study between series resistance and overlap capacitance is carried out for a high-k dielectric surrounding gate structure, which results from the replacement process. An optimum S/D overlap to gate for the high-k surrounding gate structure is found to be different from the conventional gate structure, i.e. 0∼1 nm underlap is preferred for the surround high-k gate structure while 1∼2 nm overlap for the conventional gate one

  1. A game theoretic algorithm to detect overlapping community structure in networks

    Science.gov (United States)

    Zhou, Xu; Zhao, Xiaohui; Liu, Yanheng; Sun, Geng

    2018-04-01

    Community detection can be used as an important technique for product and personalized service recommendation. A game theory based approach to detect overlapping community structure is introduced in this paper. The process of the community formation is converted into a game, when all agents (nodes) cannot improve their own utility, the game process will be terminated. The utility function is composed of a gain and a loss function and we present a new gain function in this paper. In addition, different from choosing action randomly among join, quit and switch for each agent to get new label, two new strategies for each agent to update its label are designed during the game, and the strategies are also evaluated and compared for each agent in order to find its best result. The overlapping community structure is naturally presented when the stop criterion is satisfied. The experimental results demonstrate that the proposed algorithm outperforms other similar algorithms for detecting overlapping communities in networks.

  2. An Overlapping Communities Detection Algorithm via Maxing Modularity in Opportunistic Networks

    Directory of Open Access Journals (Sweden)

    Gao Zhi-Peng

    2016-01-01

    Full Text Available Community detection in opportunistic networks has been a significant and hot issue, which is used to understand characteristics of networks through analyzing structure of it. Community is used to represent a group of nodes in a network where nodes inside the community have more internal connections than external connections. However, most of the existing community detection algorithms focus on binary networks or disjoint community detection. In this paper, we propose a novel algorithm via maxing modularity of communities (MMCto find overlapping community structure in opportunistic networks. It utilizes contact history of nodes to calculate the relation intensity between nodes. It finds nodes with high relation intensity as the initial community and extend the community with nodes of higher belong degree. The algorithm achieves a rapid and efficient overlapping community detection method by maxing the modularity of community continuously. The experiments prove that MMC is effective for uncovering overlapping communities and it achieves better performance than COPRA and Conductance.

  3. Activation of words with phonological overlap

    Directory of Open Access Journals (Sweden)

    Claudia K. Friedrich

    2013-08-01

    Full Text Available Multiple lexical representations overlapping with the input (cohort neighbors are temporarily activated in the listener’s mental lexicon when speech unfolds in time. Activation for cohort neighbors appears to rapidly decline as soon as there is mismatch with the input. However, it is a matter of debate whether or not they are completely excluded from further processing. We recorded behavioral data and event-related brain potentials (ERPs in auditory-visual word onset priming during a lexical decision task. As primes we used the first two syllables of spoken German words. In a carrier word condition, the primes were extracted from spoken versions of the target words (ano-ANORAK 'anorak'. In a cohort neighbor condition, the primes were taken from words that overlap with the target word up to the second nucleus (ana- taken from ANANAS 'pineapple'. Relative to a control condition, where primes and targets were unrelated, lexical decision responses for cohort neighbors were delayed. This reveals that cohort neighbors are disfavored by the decision processes at the behavioral front end. In contrast, left-anterior ERPs reflected long-lasting facilitated processing of cohort neighbors. We interpret these results as evidence for extended parallel processing of cohort neighbors. That is, in parallel to the preparation and elicitation of delayed lexical decision responses to cohort neighbors, aspects of the processing system appear to keep track of those less efficient candidates.

  4. Capacities and overlap indexes with an application in fuzzy rule-based classification systems

    Czech Academy of Sciences Publication Activity Database

    Paternain, D.; Bustince, H.; Pagola, M.; Sussner, P.; Kolesárová, A.; Mesiar, Radko

    2016-01-01

    Roč. 305, č. 1 (2016), s. 70-94 ISSN 0165-0114 Institutional support: RVO:67985556 Keywords : Capacity * Overlap index * Overlap function * Choquet integral * Fuzzy rule-based classification systems Subject RIV: BA - General Mathematics Impact factor: 2.718, year: 2016 http://library.utia.cas.cz/separaty/2016/E/mesiar-0465739.pdf

  5. Emotional face expression modulates occipital-frontal effective connectivity during memory formation in a bottom-up fashion

    Directory of Open Access Journals (Sweden)

    Daiming eXiu

    2015-04-01

    Full Text Available This study investigated the role of bottom-up and top-down neural mechanisms in the processing of emotional face expression during memory formation. Functional brain imaging data was acquired during incidental learning of positive (‘happy’, neutral and negative (‘angry’ or ‘fearful’ faces. Dynamic Causal Modeling (DCM was applied on the fMRI data to characterize effective connectivity within a brain network involving face perception (inferior occipital gyrus and fusiform gyrus and successful memory formation related areas (hippocampus, superior parietal lobule, amygdala and orbitofrontal cortex. The bottom-up models assumed processing of emotional face expression along feed forward pathways to the orbitofrontal cortex. The top-down models assumed that the orbitofrontal cortex processed emotional valence and mediated connections to the hippocampus. A subsequent recognition memory test showed an effect of negative emotion on the response bias, but not on memory performance. Our DCM findings showed that the bottom-up model family of effective connectivity best explained the data across all subjects and specified that emotion affected most bottom-up connections to the orbitofrontal cortex, especially from the occipital visual cortex and superior parietal lobule. Of those pathways to the orbitofrontal cortex the connection from the inferior occipital gyrus correlated with memory performance independently of valence. We suggest that bottom-up neural mechanisms support effects of emotional face expression and memory formation in a parallel and partially overlapping fashion.

  6. Expression of cytokine signaling genes in morbidly obese patients with non-alcoholic steatohepatitis and hepatic fibrosis.

    Science.gov (United States)

    Estep, J Michael; Baranova, Ancha; Hossain, Noreen; Elariny, Hazem; Ankrah, Kathy; Afendy, Arian; Chandhoke, Vikas; Younossi, Zobair M

    2009-05-01

    White adipose tissue (WAT) from visceral adiposity plays an important role in the pathogenesis of non-alcoholic steatohepatitis (NASH). Development of NASH and its progression to fibrosis is partially due to cytokines and adipokines produced by WAT. The aim of this study was to assess the association of hepatic fibrosis and NASH by evaluating the intrinsic differences in the inflammatory cytokine signaling in the visceral adipose tissue obtained from morbidly obese patients. We used targeted microarrays representing human genes involved in the inflammatory and fibrogenic reactions to profile visceral adipose samples of 15 well-matched NASH patients with and without fibrosis. Additionally, visceral adipose samples were subjected to real-time polymerase chain reaction profiling of 84 inflammations related genes. Eight genes (CCL2, CCL4, CCL18, CCR1, IL10RB, IL15RA, and LTB) were differentially expressed in NASH with fibrosis. Additionally, an overlapping but distinct list of the differentially expressed genes were found in NASH with type II diabetes (DM; IL8, BLR1, IL2RA, CD40LG, IL1RN, IL15RA, and CCL4) as compared to NASH without DM. Inflammatory cytokines are differentially expressed in the adipose tissue of NASH with fibrosis, as well in NASH with DM. These findings point at the interaction of adipose inflammatory cytokines, DM, hepatic fibrosis in NASH, and its progression to cirrhosis and end-stage liver disease.

  7. Dissociating maternal responses to sad and happy facial expressions of their own child: An fMRI study.

    Science.gov (United States)

    Kluczniok, Dorothea; Hindi Attar, Catherine; Stein, Jenny; Poppinga, Sina; Fydrich, Thomas; Jaite, Charlotte; Kappel, Viola; Brunner, Romuald; Herpertz, Sabine C; Boedeker, Katja; Bermpohl, Felix

    2017-01-01

    Maternal sensitive behavior depends on recognizing one's own child's affective states. The present study investigated distinct and overlapping neural responses of mothers to sad and happy facial expressions of their own child (in comparison to facial expressions of an unfamiliar child). We used functional MRI to measure dissociable and overlapping activation patterns in 27 healthy mothers in response to happy, neutral and sad facial expressions of their own school-aged child and a gender- and age-matched unfamiliar child. To investigate differential activation to sad compared to happy faces of one's own child, we used interaction contrasts. During the scan, mothers had to indicate the affect of the presented face. After scanning, they were asked to rate the perceived emotional arousal and valence levels for each face using a 7-point Likert-scale (adapted SAM version). While viewing their own child's sad faces, mothers showed activation in the amygdala and anterior cingulate cortex whereas happy facial expressions of the own child elicited activation in the hippocampus. Conjoint activation in response to one's own child happy and sad expressions was found in the insula and the superior temporal gyrus. Maternal brain activations differed depending on the child's affective state. Sad faces of the own child activated areas commonly associated with a threat detection network, whereas happy faces activated reward related brain areas. Overlapping activation was found in empathy related networks. These distinct neural activation patterns might facilitate sensitive maternal behavior.

  8. Metabolome Profiling of Partial and Fully Reprogrammed Induced Pluripotent Stem Cells.

    Science.gov (United States)

    Park, Soon-Jung; Lee, Sang A; Prasain, Nutan; Bae, Daekyeong; Kang, Hyunsu; Ha, Taewon; Kim, Jong Soo; Hong, Ki-Sung; Mantel, Charlie; Moon, Sung-Hwan; Broxmeyer, Hal E; Lee, Man Ryul

    2017-05-15

    Acquisition of proper metabolomic fate is required to convert somatic cells toward fully reprogrammed pluripotent stem cells. The majority of induced pluripotent stem cells (iPSCs) are partially reprogrammed and have a transcriptome different from that of the pluripotent stem cells. The metabolomic profile and mitochondrial metabolic functions required to achieve full reprogramming of somatic cells to iPSC status have not yet been elucidated. Clarification of the metabolites underlying reprogramming mechanisms should enable further optimization to enhance the efficiency of obtaining fully reprogrammed iPSCs. In this study, we characterized the metabolites of human fully reprogrammed iPSCs, partially reprogrammed iPSCs, and embryonic stem cells (ESCs). Using capillary electrophoresis time-of-flight mass spectrometry-based metabolomics, we found that 89% of analyzed metabolites were similarly expressed in fully reprogrammed iPSCs and human ESCs (hESCs), whereas partially reprogrammed iPSCs shared only 74% similarly expressed metabolites with hESCs. Metabolomic profiling analysis suggested that converting mitochondrial respiration to glycolytic flux is critical for reprogramming of somatic cells into fully reprogrammed iPSCs. This characterization of metabolic reprogramming in iPSCs may enable the development of new reprogramming parameters for enhancing the generation of fully reprogrammed human iPSCs.

  9. Deformation analysis of a film-overlapped micro-pump membrane structure

    International Nuclear Information System (INIS)

    Lee, Fu-Shin; Wang, Pi-Wen; Chen, Chih-Hsiung

    2008-01-01

    A novel approach is developed to study a film-overlapped membrane structure. Meanwhile, the established model is employed to design the micro-pump membrane structure and to evaluate its pumping efficiency. Two-dimensional coupling effects between the overlapping actuator films and the deformable membrane are thoroughly investigated, including the influences on the membrane from the overlapping films' elongation effects, Poisson's ratio effects and shear strain effects. Overall deformations and interactions for the three-layer membrane structures are accurately calculated through exercising the developed model, in contrast to what difficulties are usually encountered in carrying out FEM methods with very thin elements meshed for the actuator films. Furthermore, this study demonstrates that the high stiffness of the actuating metal films needs to be reflected in the equivalent stiffness of the membrane structures, especially when the sizes of the actuator films become compatible with the sizes of the membranes. Hence, the optimal micro-pumping efficiency of a membrane structure is acquired upon exercising the developed model, and larger sizes of the actuating films do not definitely obtain larger pumping efficiencies for the electromagnetically actuated micro-pumps

  10. The putative imprinted locus D15S9 within the common deletion region for the Prader-Willi and Angelman syndromes encodes two overlapping mRNAs transcribed from opposite strands

    Energy Technology Data Exchange (ETDEWEB)

    Glenn, C.C.; Driscoll, D.J. [Univ. of Florida, Gainesville, FL (United States); Saitoh, S. [Case Western Reserve Univ., Cleveland, OH (United States)] [and others

    1994-09-01

    Prader-Willi syndrome is typically caused by a deletion of paternal 15q11-q13, or maternal uniparental disomy (UPD) of chromosome 15, while Angelman syndrome is caused by a maternal deletion or paternal UPD of the same region. Therefore, these two clinically distinct neurobehavioral syndromes result from differential expression of imprinted genes within 15q11-q13. A 3.1 kb cDNA, DN34, from the D15S9 locus within 15q11-q13 was isolated from a human fetal brain library. We showed previously that DN34 probe detects a DNA methylation imprint and therefore may represent a candidate imprinted gene. Isolation of genomic clones and DNA sequencing demonstrated that the gene segment encoding the partial cDNA DN34 was split by a 2 kb intron, but did not encode a substantial open reading frame (ORF). Preliminary analysis of expression by RT-PCR suggests that this gene is expressed in fetal but not in tested tissue types from the adult, and thus its imprinting status has not been possible to assess at present. Surprisingly, we found an ORF on the antisense strand of the DN34 cDNA. This ORF encodes a putative polypeptide of 505 amino acid residues containing a RING C{sub 3}HC{sub 4} zinc-finger motif and other features of nuclear proteins. Subsequent characterization of this gene, ZNF127, and a mouse homolog, demonstrated expression of 3.2 kb transcript from all tested fetal and adult tissues. Transcripts initiate from within a CpG-island, shown to be differentially methylated on parental alleles in the human. Interestingly, functional imprinting of the mouse homolog was subsequently demonstrated in an F{sub 1} cross by analyzing a VNTR polymorphism in the mRNA. The ZNF127 gene is intronless, has significant overlap with the DN34 gene on the antisense strand, and a 1 kb 3{prime} end within the 2 kb DN34 intron.

  11. The importance of predator–prey overlap: predicting North Sea cod recovery with a multispecies assessment model

    DEFF Research Database (Denmark)

    Kempf, Alexander; Dingsør, Gjert Endre; Huse, Geir

    2010-01-01

    The overlap between predator and prey is known as a sensitive parameter in multispecies assessment models for fish, and its parameterization is notoriously difficult. Overlap indices were derived from trawl surveys and used to parametrize the North Sea stochastic multispecies model. The effect...... of time-invariant and year- and quarter-specific overlap estimates on the historical (1991–2007) and predicted trophic interactions, as well as the development of predator and prey stocks, was investigated. The focus was set on a general comparison between single-species and multispecies forecasts...... and the sensitivity of the predicted development of North Sea cod for the two types of overlap implementation. The spatial–temporal overlap between cod and its predators increased with increasing temperature, indicating that foodweb processes might reduce the recovery potential of cod during warm periods...

  12. List length and overlap effects in forced-choice associative recognition.

    Science.gov (United States)

    Clark, S E; Hori, A

    1995-07-01

    Two experiments examined forced-choice associative recognition for OLAP and NOLAP test conditions. OLAP test trials consist of pairs with overlapping items (e.g., AB vs. AD), whereas NOLAP test trials contain no overlapping items (e.g., AB vs. CF). Previous results show better performance for NOLAP than for OLAP tests, contrary to the predictions of global memory models. The present experiments varied list length to examine the hypothesis that the NOLAP advantage is produced by recall-like retrieval processes. The use of longer lists either eliminated (Experiment 1) or greatly reduced (Experiment 2) the NOLAP advantage. However, a reliable OLAP advantage was not obtained. Implications for models are discussed.

  13. Symptom overlap in anxiety and multiple sclerosis.

    LENUS (Irish Health Repository)

    O Donnchadha, Seán

    2013-02-14

    BACKGROUND: The validity of self-rated anxiety inventories in people with multiple sclerosis (pwMS) is unclear. However, the appropriateness of self-reported depression scales has been widely examined. Given somatic symptom overlap between depression and MS, research emphasises caution when using such scales. OBJECTIVE: This study evaluates symptom overlap between anxiety and MS in a group of 33 individuals with MS, using the Beck Anxiety Inventory (BAI). METHODS: Participants underwent a neurological examination and completed the BAI. RESULTS: A novel procedure using hierarchical cluster analysis revealed three distinct symptom clusters. Cluster one (\\'wobbliness\\' and \\'unsteady\\') grouped separately from all other BAI items. These symptoms are well-recognised MS-related symptoms and we question whether their endorsement in pwMS can be considered to reflect anxiety. A modified 19-item BAI (mBAI) was created which excludes cluster one items. This removal reduced the number of MS participants considered \\'anxious\\' by 21.21% (low threshold) and altered the level of anxiety severity for a further 27.27%. CONCLUSION: Based on these data, it is suggested that, as with depression measures, researchers and clinicians should exercise caution when using brief screening measures for anxiety in pwMS.

  14. Effect of radiotherapy on experimental liver regenerative capacities following partial hepatectomy in rats

    International Nuclear Information System (INIS)

    Du Shisuo; Zeng Zhaochong; Tang Zhaoyou; Zhang Zhenyu; Wu Zheng; Shi Liusheng

    2008-01-01

    Objective: To investigate the regenerative capacities and proliferation related cytokines expression of normal and irradiated livers following 70% partial hepatectomy in rats. Methods: 90 male Sprague-Dawley rats were divided into 3 groups. The control group was only received 70% partial hepatectomy. The two irradiated groups were performed a single dose of 4 Gy and 8 Gy photon irradiation respectively followed 70% partial hepatectomy. The remanent liver were excised at 0.5,1.0,2.0,3.0,7.0 and 10.0 d after hepatectomy, and liver regeneration capacities in normal and irradiated rats were evaluated through remanent liver weigh, BrdU incorporation, PCNA labeling, and mitotic indices. The proliferation related cytokines expression were also compared. Results: After radiotherapy and hepatectomy 1 rats died of infection in control group, and two rats in 8 Gy group died of radiation induced enteritis. The original liver weigh is regained within 12 days in control and 4 Gy group, and proliferative speed was lower in 4 Gy group than control group. The weigh of remanent liver in 8 Gy group was significantly lower than the two groups all time points from 2d. The apex of PCNA labeling index was 80.2 ± 7.6%, 71.2 ± 6.5% and 55.3 ± 4.7% in control, 4 Gy and 8 Gy groups respectively at 2d, and 44.2 ± 5.4%, 35.3 ± 5.72% and 5.3 ± 6.9% with BrdU incorporation index. HGF mRNA expression peak of 4 Gy group was significantly lower than in control at 1 d, but no apparent peak value in 8 Gy group. TGF-β1 and TGF-β RII level of radiation groups was apparently higher than the control group at different time points. Meanwhile the p53 protein tend to increase at 1 d then decline with high expression in irradiated groups. Conclusion: Whole radiation can significantly inhibit the regenerative capacities following partial hepatectomy in rats with dose dependent. (authors)

  15. Sensitivity analysis overlaps of friction elements in cartridge seals

    Directory of Open Access Journals (Sweden)

    Žmindák Milan

    2018-01-01

    Full Text Available Cartridge seals are self-contained units consisting of a shaft sleeve, seals, and gland plate. The applications of mechanical seals are numerous. The most common example of application is in bearing production for automobile industry. This paper deals with the sensitivity analysis of overlaps friction elements in cartridge seal and their influence on the friction torque sealing and compressive force. Furthermore, it describes materials for the manufacture of sealings, approaches usually used to solution of hyperelastic materials by FEM and short introduction into the topic wheel bearings. The practical part contains one of the approach for measurement friction torque, which results were used to specifying the methodology and precision of FEM calculation realized by software ANSYS WORKBENCH. This part also contains the sensitivity analysis of overlaps friction elements.

  16. Spreadsheet-based program for alignment of overlapping DNA sequences.

    Science.gov (United States)

    Anbazhagan, R; Gabrielson, E

    1999-06-01

    Molecular biology laboratories frequently face the challenge of aligning small overlapping DNA sequences derived from a long DNA segment. Here, we present a short program that can be used to adapt Excel spreadsheets as a tool for aligning DNA sequences, regardless of their orientation. The program runs on any Windows or Macintosh operating system computer with Excel 97 or Excel 98. The program is available for use as an Excel file, which can be downloaded from the BioTechniques Web site. Upon execution, the program opens a specially designed customized workbook and is capable of identifying overlapping regions between two sequence fragments and displaying the sequence alignment. It also performs a number of specialized functions such as recognition of restriction enzyme cutting sites and CpG island mapping without costly specialized software.

  17. Exploring overlapping functional units with various structure in protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Xiao-Fei Zhang

    Full Text Available Revealing functional units in protein-protein interaction (PPI networks are important for understanding cellular functional organization. Current algorithms for identifying functional units mainly focus on cohesive protein complexes which have more internal interactions than external interactions. Most of these approaches do not handle overlaps among complexes since they usually allow a protein to belong to only one complex. Moreover, recent studies have shown that other non-cohesive structural functional units beyond complexes also exist in PPI networks. Thus previous algorithms that just focus on non-overlapping cohesive complexes are not able to present the biological reality fully. Here, we develop a new regularized sparse random graph model (RSRGM to explore overlapping and various structural functional units in PPI networks. RSRGM is principally dominated by two model parameters. One is used to define the functional units as groups of proteins that have similar patterns of connections to others, which allows RSRGM to detect non-cohesive structural functional units. The other one is used to represent the degree of proteins belonging to the units, which supports a protein belonging to more than one revealed unit. We also propose a regularizer to control the smoothness between the estimators of these two parameters. Experimental results on four S. cerevisiae PPI networks show that the performance of RSRGM on detecting cohesive complexes and overlapping complexes is superior to that of previous competing algorithms. Moreover, RSRGM has the ability to discover biological significant functional units besides complexes.

  18. On the overlap formulation of chiral gauge theory

    International Nuclear Information System (INIS)

    Randjbar Daemi, S.; Strathdee, J.

    1994-12-01

    The overlap formula proposed by Narayanan and Neuberger in chiral gauge theories is examined. The free chiral and Dirac Green's functions are constructed in this formalism. Four dimensional anomalies are calculated and the usual anomaly cancellation for one standard family of quarks and leptons is verified. (author). 4 refs

  19. Detailed analysis of the δ-crystallin mRNA-expressing region in early development of the chick pituitary gland.

    Science.gov (United States)

    Inoue, Makiko; Shiina, Tomoya; Aizawa, Sayaka; Sakata, Ichiro; Takagi, Hiroyasu; Sakai, Takafumi

    2012-06-01

    Although δ-crystallin (δ-crys), also known as lens protein, is transiently expressed in Rathke's pouch (RP) of the chick embryo, detailed temporal and spatial expression patterns have been obscure. In this study, to understand the relationship between the δ-crys mRNA-expressing region and RP formation, we examined the embryonic expression pattern of δ-crys mRNA in the primordium of the adenohypophysis. δ-crys mRNA expression was initially found at stage 15 anterior to the foregut and posterior to the invaginated oral ectoderm. After RP formation, the δ-crys mRNA was expressed in the post-ventral region of RP and the anterior region of RP. δ-crys mRNA expression was then restricted to the cephalic lobe of the pituitary gland. From stage 20, the δ-crys and alpha-glycoprotein subunit (αGSU) mRNA-expressing regions were almost completely overlapping. The αGSU mRNA-expressing region is thought to be the primordium of the pars tuberalis, and these regions were overlapped with the Lhx3 mRNA-expressing region. The intensity of δ-crys mRNA expression gradually decreased with development and completely disappeared by stage 34. These results suggest that the embryonic chick pituitary gland consists of two different regions labeled with δ-crys and Lhx3.

  20. Frequency and predictive factors for overlap syndrome between autoimmune hepatitis and primary cholestatic liver disease.

    Science.gov (United States)

    Gheorghe, Liana; Iacob, Speranta; Gheorghe, Cristian; Iacob, Razvan; Simionov, Iulia; Vadan, Roxana; Becheanu, Gabriel; Parvulescu, Iuliana; Toader, Cristina

    2004-06-01

    To evaluate the frequency of cholestatic pattern in patients with autoimmune hepatitis (AIH) and to identify predictive factors associated with the development of the overlap syndrome. Eighty-two consecutive patients diagnosed with AIH at the referral centre between January 1998 and June 2002 were included in the study. The new scoring system modified by the International Autoimmune Hepatitis Group was used to classify patients as definite/probable. Overlap syndrome was considered when the patient had clinical, serological and histological characteristics of two conditions: AIH and primary biliary cirrhosis (PBC) or AIH and primary sclerosing cholangitis (PSC). From the 82 AIH patients (76 female and six male), 84.1% presented definite AIH (> 15 points) and 15.9% probable AIH (10 - 15 points). The frequency of the overlap syndrome was 20%: 13% with PBC and 7% with PSC. In the univariate analysis the overlap syndrome was associated with male gender (P = 0.01), age < 35 years (P < 0.0001), histopathological aspect of cholestasis (P < 0.0001), suboptimal response to treatment (P < 0.0001) and probable AIH (P < 0.0001). Age < 35 years, probable AIH and the absence of anti-nuclear antibody (ANA) have been identified as independent indicators of the overlap diagnosis by the logistic regression analysis. Patients with overlap syndrome between AIH and primary cholestatic liver disease are frequently diagnosed in clinical practice, representing 20% of AIH cases in our study. The independent predictive factors associated with the diagnosis of overlap syndrome are young age, ANA(-) profile, and probable diagnosis according with the scoring system for AIH.

  1. Recurrent Partial Words

    Directory of Open Access Journals (Sweden)

    Francine Blanchet-Sadri

    2011-08-01

    Full Text Available Partial words are sequences over a finite alphabet that may contain wildcard symbols, called holes, which match or are compatible with all letters; partial words without holes are said to be full words (or simply words. Given an infinite partial word w, the number of distinct full words over the alphabet that are compatible with factors of w of length n, called subwords of w, refers to a measure of complexity of infinite partial words so-called subword complexity. This measure is of particular interest because we can construct partial words with subword complexities not achievable by full words. In this paper, we consider the notion of recurrence over infinite partial words, that is, we study whether all of the finite subwords of a given infinite partial word appear infinitely often, and we establish connections between subword complexity and recurrence in this more general framework.

  2. Facial Expression Aftereffect Revealed by Adaption to Emotion-Invisible Dynamic Bubbled Faces

    Science.gov (United States)

    Luo, Chengwen; Wang, Qingyun; Schyns, Philippe G.; Kingdom, Frederick A. A.; Xu, Hong

    2015-01-01

    Visual adaptation is a powerful tool to probe the short-term plasticity of the visual system. Adapting to local features such as the oriented lines can distort our judgment of subsequently presented lines, the tilt aftereffect. The tilt aftereffect is believed to be processed at the low-level of the visual cortex, such as V1. Adaptation to faces, on the other hand, can produce significant aftereffects in high-level traits such as identity, expression, and ethnicity. However, whether face adaptation necessitate awareness of face features is debatable. In the current study, we investigated whether facial expression aftereffects (FEAE) can be generated by partially visible faces. We first generated partially visible faces using the bubbles technique, in which the face was seen through randomly positioned circular apertures, and selected the bubbled faces for which the subjects were unable to identify happy or sad expressions. When the subjects adapted to static displays of these partial faces, no significant FEAE was found. However, when the subjects adapted to a dynamic video display of a series of different partial faces, a significant FEAE was observed. In both conditions, subjects could not identify facial expression in the individual adapting faces. These results suggest that our visual system is able to integrate unrecognizable partial faces over a short period of time and that the integrated percept affects our judgment on subsequently presented faces. We conclude that FEAE can be generated by partial face with little facial expression cues, implying that our cognitive system fills-in the missing parts during adaptation, or the subcortical structures are activated by the bubbled faces without conscious recognition of emotion during adaptation. PMID:26717572

  3. The Expression of the Zonula Adhaerens Protein PLEKHA7 Is Strongly Decreased in High Grade Ductal and Lobular Breast Carcinomas.

    Directory of Open Access Journals (Sweden)

    Jean-Christophe Tille

    Full Text Available PLEKHA7 is a junctional protein, which participates in a complex that stabilizes E-cadherin at the zonula adhaerens. Since E-cadherin is involved in epithelial morphogenesis, signaling, and tumor progression, we explored PLEKHA7 expression in cancer. PLEKHA7 expression was assessed in invasive ductal and lobular carcinomas of the breast by immunohistochemistry, immunofluorescence and quantitative RT-PCR. PLEKHA7 was detected at epithelial junctions of normal mammary ducts and lobules, and of tubular and micropapillary structures within G1 and G2 ductal carcinomas. At these junctions, the localization of PLEKHA7 was along the circumferential belt (zonula adhaerens, and only partially overlapping with that of E-cadherin, p120ctn and ZO-1, as shown previously in rodent tissues. PLEKHA7 immunolabeling was strongly decreased in G3 ductal carcinomas and undetectable in lobular carcinomas. PLEKHA7 mRNA was detected in both ductal and lobular carcinomas, with no observed correlation between mRNA levels and tumor type or grade. In summary, PLEKHA7 is a junctional marker of epithelial cells within tubular structures both in normal breast tissue and ductal carcinomas, and since PLEKHA7 protein but not mRNA expression is strongly decreased or lost in high grade ductal carcinomas and in lobular carcinomas, loss of PLEKHA7 is a newly characterized feature of these carcinomas.

  4. A DNA vaccine co-expressing Trichinella spiralis MIF and MCD-1 with murine ubiquitin induces partial protective immunity in mice.

    Science.gov (United States)

    Tang, F; Xu, L; Yan, R; Song, X; Li, X

    2013-03-01

    Co-expression of Trichinella spiralis macrophage migration inhibitory factor (TsMIF) with T. spiralis cystatin-like domain protein (TsMCD-1) in a DNA vaccine induces a Th1 immune response and partial protection against T. spiralis infection. The present study evaluated whether co-expression of mouse ubiquitin (Ub) with TsMIF and TsMCD-1 might improve the immune response against T. spiralis infection. Groups of BALB/c mice were immunized twice at 2-week intervals with 100 μg of plasmid DNA encoding either a TsMIF-TsMCD-1 fusion protein (pVAX1-Tsmif-Tsmcd-1) or an Ub-co-expressing triple fusion protein Ub-TsMIF-TsMCD-1 (pVAX1-Ub-Tsmif-Tsmcd-1). Control animals were immunized with pVAX1-Ub or blank vector plasmid. Specific antibody levels (IgG, IgG1, IgG2a, IgG2b, IgM, IgA, IgE) against the recombinant protein TsMIF-TsMCD-1, serum cytokines (interferon (IFN)-γ, interleukin (IL)-4, IL-5, transforming growth factor (TGF)-β1 and IL-17), CD4+/CD8+ T cells and cytotoxic T lymphocyte (CTL) responses were monitored. Challenge infection was performed 2 weeks after the second immunization and worm burden was assayed at 35 days post-challenge. Antibody responses induced by pVAX1-Ub-Tsmif-Tsmcd-1 were significantly lower than for TsMIF-TsMCD-1, but the vaccine induced increased levels of Th1 cytokine (IFN-γ) and increased T-cell cytotoxicity. The reduction of worm burden (37.95%) following immunization with pVAX1-Ub-Tsmif-Tsmcd-1 was significantly greater than that induced by the pVAX1-Tsmif-Tsmcd-1 vaccine (23.17%; P< 0.05).

  5. Limited dietary overlap amongst resident Arctic herbivores in winter: complementary insights from complementary methods.

    Science.gov (United States)

    Schmidt, Niels M; Mosbacher, Jesper B; Vesterinen, Eero J; Roslin, Tomas; Michelsen, Anders

    2018-04-26

    Snow may prevent Arctic herbivores from accessing their forage in winter, forcing them to aggregate in the few patches with limited snow. In High Arctic Greenland, Arctic hare and rock ptarmigan often forage in muskox feeding craters. We therefore hypothesized that due to limited availability of forage, the dietary niches of these resident herbivores overlap considerably, and that the overlap increases as winter progresses. To test this, we analyzed fecal samples collected in early and late winter. We used molecular analysis to identify the plant taxa consumed, and stable isotope ratios of carbon and nitrogen to quantify the dietary niche breadth and dietary overlap. The plant taxa found indicated only limited dietary differentiation between the herbivores. As expected, dietary niches exhibited a strong contraction from early to late winter, especially for rock ptarmigan. This may indicate increasing reliance on particular plant resources as winter progresses. In early winter, the diet of rock ptarmigan overlapped slightly with that of muskox and Arctic hare. Contrary to our expectations, no inter-specific dietary niche overlap was observed in late winter. This overall pattern was specifically revealed by combined analysis of molecular data and stable isotope contents. Hence, despite foraging in the same areas and generally feeding on the same plant taxa, the quantitative dietary overlap between the three herbivores was limited. This may be attributable to species-specific consumption rates of plant taxa. Yet, Arctic hare and rock ptarmigan may benefit from muskox opening up the snow pack, thereby allowing them to access the plants.

  6. Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo

    International Nuclear Information System (INIS)

    Johnson, Jennifer A.; Bragg, Jennifer N.; Lawrence, Diane M.; Jackson, Andrew O.

    2003-01-01

    Barley stripe mosaic virus (BSMV) contains three positive-sense, single-stranded genomic RNAs, designated α, β, and γ, that encode seven major proteins and one minor translational readthrough protein. Three proteins (αa, βa, and γa) are translated directly from the genomic RNAs and the remaining proteins encoded on RNAβ and RNAγ are expressed via three subgenomic messenger RNAs (sgRNAs). sgRNAβ1 directs synthesis of the triple gene block 1 (TGB1) protein. The TGB2 protein, the TGB2' minor translational readthrough protein, and the TGB3 protein are expressed from sgRNAβ2, which is present in considerably lower abundance than sgRNAβ1. A third sgRNA, sgRNAγ, is required for expression of the γb protein. We have used deletion analyses and site-specific mutations to define the boundaries of promoter regions that are critical for expression of the BSMV sgRNAs in infected protoplasts. The results reveal that the sgRNAβ1 promoter encompasses positions -29 to -2 relative to its transcription start site and is adjacent to a cis-acting element required for RNAβ replication that maps from -107 to -74 relative to the sgRNAβ1 start site. The core sgRNAβ2 promoter includes residues -32 to -17 relative to the sgRNAβ2 transcriptional start site, although maximal activity requires an upstream hexanucleotide sequence residing from positions -64 to -59. The sgRNAγ promoter maps from -21 to +2 relative to its transcription start site and therefore partially overlaps the γa gene. The sgRNAβ1, β2, and γ promoters also differ substantially in sequence, but have similarities to the putative homologous promoters of other Hordeiviruses. These differences are postulated to affect competition for the viral polymerase, coordination of the temporal expression and abundance of the TGB proteins, and constitutive expression of the γb protein

  7. A novel method for detecting and counting overlapping tracks in SSNTD by image processing techniques

    International Nuclear Information System (INIS)

    Ab Azar, N.; Babakhani, A.; Broumandnia, A.; Sepanloo, K.

    2016-01-01

    Overlapping object detection and counting is a challenge in image processing. A new method for detecting and counting overlapping circles is presented in this paper. This method is based on pattern recognition and feature extraction using “neighborhood values“ in an object image by implementation of image processing techniques. The junction points are detected by assignment of a value for each pixel in an image. As is shown, the neighborhood values for junction points are larger than the values for other points. This distinction of neighborhood values is the main feature which can be utilized to identify the junction points and to count the overlapping tracks. This method can be used for recognizing and counting charged particle tracks, blood cells and also cancer cells. The method is called “Track Counting based on Neighborhood Values” and is symbolized by “TCNV”. - Highlights: • A new method is introduced to recognize nuclear tracks by image processing. • The method is used to specify neighborhood pixels in junction points in overlapping tracks. • Enhanced method of counting overlapping tracks. • New counting system has linear behavior in counting tracks with density less than 300,000 tracks per cm"2. • In the new method, the overlap tracks can be recognized even to 10× tracks and more.

  8. Overlap and distinction between measures of insight and self-stigma.

    Science.gov (United States)

    Hasson-Ohayon, Ilanit

    2018-05-24

    Multiple studies on insight into one's illness and self-stigma among patients with serious mental illness and their relatives have shown that these constructs are related to one another and that they affect outcome. However, a critical exploration of the items used to assess both constructs raises questions with regard to the possible overlapping and centrality of items. The current study used five different samples to explore the possible overlap and distinction between insight and self-stigma, and to identify central items, via network analyses and principal component factor analysis. Findings from the network analyses showed overlap between insight and self-stigma exist with a relatively clearer observational distinction between the constructs among the two parent samples in comparison to the patient samples. Principal component factor analysis constrained to two factors showed that a relatively high percentage of items were not loaded on either factor, and in a few datasets, several insight items were loaded on the self-stigma scale and vice versa. The author discusses implications for research and calls for rethinking the way insight is assessed. Clinical implications are also discussed in reference to central items of social isolation, future worries and stereotype endorsement among the different study groups. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Nonuniform Overlapping Method in Designing Microstrip Patch Antennas Using Genetic Algorithm Optimization

    Directory of Open Access Journals (Sweden)

    J. M. Jeevani W. Jayasinghe

    2015-01-01

    Full Text Available Genetic algorithm (GA has been a popular optimization technique used for performance improvement of microstrip patch antennas (MPAs. When using GA, the patch geometry is optimized by dividing the patch area into small rectangular cells. This has an inherent problem of adjacent cells being connected to each other with infinitesimal connections, which may not be achievable in practice due to fabrication tolerances in chemical etching. As a solution, this paper presents a novel method of dividing the patch area into cells with nonuniform overlaps. The optimized design, which is obtained by using fixed overlap sizes, shows a quad-band performance covering GSM1800, GSM1900, LTE2300, and Bluetooth bands. In contrast, use of nonuniform overlap sizes leads to obtaining a pentaband design covering GSM1800, GSM1900, UMTS, LTE2300, and Bluetooth bandswith fractional bands with of 38% due to the extra design flexibility.

  10. Decaying states as physically nonisolable partial systems

    International Nuclear Information System (INIS)

    Szasz, G.I.

    1976-01-01

    Presently the investigations of decaying quantum mechanical systems lack a well-founded concept, which is reflected by several formal difficulties of the corresponding mathematical treatment. In order to clarify in some respect the situation, it is investigated, within the framework of nonrelativistic quantum mechanics, the resonant scattering of an initially well localized partial wave packet. If the potential decreases sufficiently fast for r→infinite, the wave packet can be expressed at sufficiently long time after the scattering has taken place, as the sum of a term describing the direct scattering and a function of the resonant solution with complex 'momentum'. From such a heuristic relation one can deduce not only the probability for the creation of unstable particles but also obtain some hints to a connection between decaying states and physically nonisolable partial systems. On the other hand, this connection can perhaps display the inadequacy of attempts which suggest to solve the problem of decaying states within the usual Hilbert space methods. (author)

  11. Overlapping constraint for variational surface reconstruction

    DEFF Research Database (Denmark)

    Aanæs, Henrik; Solem, J.E.

    2005-01-01

    In this paper a counter example, illustrating a shortcoming in most variational formulations for 3D surface estimation, is presented. The nature of this shortcoming is a lack of an overlapping constraint. A remedy for this shortcoming is presented in the form of a penalty function with an analysi...... of the effects of this function on surface motion. For practical purposes, this will only have minor influence on current methods. However, the insight provided in the analysis is likely to influence future developments in the field of variational surface reconstruction....

  12. A comparison of brain gene expression levels in domesticated and wild animals.

    Directory of Open Access Journals (Sweden)

    Frank W Albert

    2012-09-01

    Full Text Available Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits. We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30-75 genes (less than 1% of expressed genes were differentially expressed, while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.

  13. Recombining overlapping BACs into a single larger BAC

    Directory of Open Access Journals (Sweden)

    Huxley Clare

    2004-01-01

    Full Text Available Abstract Background BAC clones containing entire mammalian genes including all the transcribed region and long range controlling elements are very useful for functional analysis. Sequenced BACs are available for most of the human and mouse genomes and in many cases these contain intact genes. However, large genes often span more than one BAC, and single BACs covering the entire region of interest are not available. Here we describe a system for linking two or more overlapping BACs into a single clone by homologous recombination. Results The method was used to link a 61-kb insert carrying the final 5 exons of the human CFTR gene onto a 160-kb BAC carrying the first 22 exons. Two rounds of homologous recombination were carried out in the EL350 strain of bacteria which can be induced for the Red genes. In the first round, the inserts of the two overlapping BACs were subcloned into modified BAC vectors using homologous recombination. In the second round, the BAC to be added was linearised with the very rare-cutting enzyme I-PpoI and electroporated into recombination efficient EL350 bacteria carrying the other BAC. Recombined BACs were identified by antibiotic selection and PCR screening and 10% of clones contained the correctly recombined 220-kb BAC. Conclusion The system can be used to link the inserts from any overlapping BAC or PAC clones. The original orientation of the inserts is not important and desired regions of the inserts can be selected. The size limit for the fragments recombined may be larger than the 61 kb used here and multiple BACs in a contig could be combined by alternating use of the two pBACLink vectors. This system should be of use to many investigators wishing to carry out functional analysis on large mammalian genes which are not available in single BAC clones.

  14. A Markov random walk under constraint for discovering overlapping communities in complex networks

    International Nuclear Information System (INIS)

    Jin, Di; Yang, Bo; Liu, Dayou; He, Dongxiao; Liu, Jie; Baquero, Carlos

    2011-01-01

    The detection of overlapping communities in complex networks has motivated recent research in relevant fields. Aiming to address this problem, we propose a Markov-dynamics-based algorithm, called UEOC, which means 'unfold and extract overlapping communities'. In UEOC, when identifying each natural community that overlaps, a Markov random walk method combined with a constraint strategy, which is based on the corresponding annealed network (degree conserving random network), is performed to unfold the community. Then, a cutoff criterion with the aid of a local community function, called conductance, which can be thought of as the ratio between the number of edges inside the community and those leaving it, is presented to extract this emerged community from the entire network. The UEOC algorithm depends on only one parameter whose value can be easily set, and it requires no prior knowledge of the hidden community structures. The proposed UEOC has been evaluated both on synthetic benchmarks and on some real-world networks, and has been compared with a set of competing algorithms. The experimental result has shown that UEOC is highly effective and efficient for discovering overlapping communities

  15. Analysis of transcript and protein overlap in a human osteosarcoma cell line

    Directory of Open Access Journals (Sweden)

    Emanuelsson Olof

    2010-12-01

    Full Text Available Abstract Background An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC and immunofluorescence microscopy (IF. Results A large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2% were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies. Conclusion This suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.

  16. Overlap syndrome: obstructive sleep apnea in patients with chronic obstructive pulmonary disease.

    Science.gov (United States)

    Weitzenblum, Emmanuel; Chaouat, Ari; Kessler, Romain; Canuet, Matthieu

    2008-02-15

    Chronic obstructive pulmonary disease (COPD) and sleep apnea-hypopnea syndrome (SAHS) are both common diseases affecting respectively 10 and 5% of the adult population over 40 years of age, and their coexistence, which is denominated overlap syndrome, can be expected to occur in about 0.5% of this population. A recent epidemiologic study has shown that the prevalence of SAHS is not higher in COPD than in the general population, and that the coexistence of the two conditions is due to chance and not through a pathophysiologic linkage between these two diseases. Patients with overlap have a more important sleep-related O(2) desaturation than do patients with COPD with the same degree of bronchial obstruction. They have an increased risk of developing hypercapnic respiratory insufficiency and pulmonary hypertension when compared with patients with SAHS alone and with patients with "usual" COPD. In patients with overlap, hypoxemia, hypercapnia, and pulmonary hypertension can be observed in the presence of mild to moderate bronchial obstruction, which is different from "usual" COPD. Therapy of the overlap syndrome consists of nasal continuous positive airway pressure or nocturnal noninvasive ventilation (NIV), with or without associated nocturnal O(2). Patients who are markedly hypoxemic during daytime (Pa(O(2)) < 55-60 mm Hg) should be given conventional long-term O(2) therapy in addition to nocturnal ventilation.

  17. ROBUST PERSON TRACKING WITH MULTIPLE NON-OVERLAPPING CAMERAS IN AN OUTDOOR ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    S. Hellwig

    2012-07-01

    Full Text Available The aim of our work is to combine multiple cameras for a robust tracking of persons in an outdoor environment. Although surveillance is a well established field, many algorithms apply various constraints like overlapping fields of view or precise calibration of the cameras to improve results. An application of these developed systems in a realistic outdoor environment is often difficult. Our aim is to be widely independent from the camera setup and the observed scene, in order to use existing cameras. Thereby our algorithm needs to be capable to work with both overlapping and non-overlapping fields of views. We propose an algorithm that allows flexible combination of different static cameras with varying properties. Another requirement of a practical application is that the algorithm is able to work online. Our system is able to process the data during runtime and to provide results immediately. In addition to seeking flexibility in the camera setup, we present a specific approach that combines state of the art algorithms in order to be robust to environment influences. We present results that indicate a good performance of our introduced algorithm in different scenarios. We show its robustness to different types of image artifacts. In addition we demonstrate that our algorithm is able to match persons between cameras in a non-overlapping scenario.

  18. New model reduction technique for a class of parabolic partial differential equations

    NARCIS (Netherlands)

    Vajta, Miklos

    1991-01-01

    A model reduction (or lumping) technique for a class of parabolic-type partial differential equations is given, and its application is discussed. The frequency response of the temperature distribution in any multilayer solid is developed and given by a matrix expression. The distributed transfer

  19. Hypochondriasis and panic disorder. Boundary and overlap.

    Science.gov (United States)

    Barsky, A J; Barnett, M C; Cleary, P D

    1994-11-01

    To determine the nosological and phenomenological overlap and boundaries between panic disorder and hypochondriasis, we compared the symptoms, disability, comorbidity, and medical care of primary care patients with each diagnosis. Patients with DSM-III-R panic disorder were recruited by screening consecutive primary care clinic attenders and then administering a structured diagnostic interview for panic disorder. Patients also completed self-report questionnaires, and their primary care physicians completed questionnaires about them. They were then compared with patients with DSM-III-R hypochondriasis from the same setting who had been studied previously. One thousand six hundred thirty-four patients were screened; 135 (71.0% of the 190 eligible patients) completed the research battery; 100 met lifetime panic disorder criteria. Twenty-five of these had comorbid hypochondriasis. Those without comorbid hypochondriasis (n = 75) were then compared with patients with hypochondriasis without comorbid panic disorder (n = 51). Patients with panic disorder were less hypochondriacal (P somatized less (P somatization disorder symptoms (P hypochondriasis. While hypochondriasis and panic disorder co-occur to some extent in a primary care population, the overlap is by no means complete. These patients are phenomenologically and functionally differentiable and distinct and are viewed differently by their primary care physicians.

  20. Vector parametrization, partial angular momenta and unusual commutation relations in physics

    International Nuclear Information System (INIS)

    Gatti, Fabien; Nauts, Andre

    2003-01-01

    When studying an N-particle system by means of N-1 vectors i.e., by means of a vector parametrization, one unavoidably comes across several angular momenta: not only the total angular momentum of the system but also the various partial angular momenta corresponding to the motion of the various vectors. All these momenta can, in addition, be referred to a variety of reference frames. The use of vector parametrizations and partial angular momenta in physics greatly simplifies the classical as well as quantum expressions of the kinetic energy. The present paper is devoted to a detailed and rigorous study of the partial angular momenta and the various commutation relations they satisfy, in particular the unusual commutation relations whose origin is traced back to the very structure of the coordinate changes used to define the Body-Fixed (BF) frames. The direct quantization of the classical expressions of the kinetic energy obtained in the context of various vector parametrizations is also given in detail. It turns out to be an efficient extension of well-known quantization procedures to the case where supernumerary quasi-momenta are used. As an illustration, the case of a four-particle system is treated in detail for a particular choice of the BF frames. Finally, the analogies between the classical and quantum approaches are emphasized

  1. Direct Calculation of the Scattering Amplitude Without Partial Wave Analysis

    Science.gov (United States)

    Shertzer, J.; Temkin, A.; Fisher, Richard R. (Technical Monitor)

    2001-01-01

    Two new developments in scattering theory are reported. We show, in a practical way, how one can calculate the full scattering amplitude without invoking a partial wave expansion. First, the integral expression for the scattering amplitude f(theta) is simplified by an analytic integration over the azimuthal angle. Second, the full scattering wavefunction which appears in the integral expression for f(theta) is obtained by solving the Schrodinger equation with the finite element method (FEM). As an example, we calculate electron scattering from the Hartree potential. With minimal computational effort, we obtain accurate and stable results for the scattering amplitude.

  2. Lizard assemblage from a sand dune habitat from southeastern Brazil: a niche overlap analysis.

    Science.gov (United States)

    Winck, Gisele R; Hatano, Fabio; Vrcibradic, Davor; VAN Sluys, Monique; Rocha, Carlos F D

    2016-01-01

    Communities are structured by interactions of historical and ecological factors, which influence the use of different resources in time and space. We acquired data on time of activity, microhabitat use and diet of a lizard assemblage from a sand dune habitat in a coastal area, southeastern Brazil (Restinga de Jurubatiba). We analyzed the data of niche overlap among species in these three axes (temporal, spatial and trophic) using null models. We found a significant overlap within the trophic niche, whereas the overlap for the other axes did not differ from the expected. Based on this result, we discuss the factors acting on the structure of the local lizard community.

  3. Maximal overlap with a fully separable state and translational invariance for multipartite entangled states

    International Nuclear Information System (INIS)

    Cui, H. T.; Yuan Di; Tian, J. L.

    2010-01-01

    The maximal overlap with the fully separable state for the multipartite entangled pure state with translational invariance is studied explicitly by some exact and numerical evaluations, focusing on the one-dimensional qubit system and some representative types of translational invariance. The results show that the translational invariance of the multipartite state could have an intrinsic effect on the determination of the maximal overlap and the nearest fully separable state for multipartite entangled states. Furthermore, a hierarchy of the basic entangled states with translational invariance is found, from which one could readily find the maximal overlap and a related fully separable state for the multipartite state composed of different translational invariance structures.

  4. Xenopus msx-1 regulates dorso-ventral axis formation by suppressing the expression of organizer genes.

    Science.gov (United States)

    Takeda, M; Saito, Y; Sekine, R; Onitsuka, I; Maeda, R; Maéno, M

    2000-06-01

    We demonstrated previously that Xmsx-1 is involved in mesoderm patterning along the dorso-ventral axis, under the regulation of BMP-4 signaling. When Xmsx-1 RNA was injected into the dorsal blastomeres, a mass of muscle tissue formed instead of notochord. This activity was similar to that of Xwnt-8 reported previously. In this study, we investigated whether the activity of Xmsx-1 is related to the ventralizing signal and myogenesis promoting factor, Xwnt-8. Whole-mount in situ hybridization showed that Xmsx-1, Xwnt-8, and XmyoD were expressed in overlapping areas, including the ventro-lateral marginal zone at mid-gastrula stage. The expression of XmyoD was induced by the ectopic expression of either Xmsx-1 or Xwnt-8 in dorsal blastomeres, and Xwnt-8 was induced by the ectopic expression of Xmsx-1. On the other hand, the expression of Xmsx-1 was not affected by the loading of pCSKA-Xwnt-8 or dominant-negative Xwnt-8 (DN-Xwnt-8) RNA. In addition, Xmsx-1 RNA did not abrogate the formation of notochord if coinjected with DN-Xwnt-8 RNA. These results suggest that Xmsx-1 functions upstream of the Xwnt-8 signal. Furthermore, the antagonistic function of Xmsx-1 to the expression of organizer genes, such as Xlim-1 and goosecoid, was shown by in situ hybridization analysis and luciferase reporter assay using the goosecoid promoter construct. Finally if Xmsx-1/VP-16 fusion RNA, which was expected to function as a dominant-negative Xmsx-1, was injected into ventral blastomeres, a partial secondary axis formed in a significant number of embryos. In such embryos, the activity of luciferase, under the control of goosecoid promoter sequence, was significantly elevated at gastrula stage. These results led us to conclude that Xmsx-1 plays a central role in establishing dorso-ventral axis in gastrulating embryo, by suppressing the expression of organizer genes.

  5. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.

    Science.gov (United States)

    Mathelier, Anthony; Lefebvre, Calvin; Zhang, Allen W; Arenillas, David J; Ding, Jiarui; Wasserman, Wyeth W; Shah, Sohrab P

    2015-04-23

    With the rapid increase of whole-genome sequencing of human cancers, an important opportunity to analyze and characterize somatic mutations lying within cis-regulatory regions has emerged. A focus on protein-coding regions to identify nonsense or missense mutations disruptive to protein structure and/or function has led to important insights; however, the impact on gene expression of mutations lying within cis-regulatory regions remains under-explored. We analyzed somatic mutations from 84 matched tumor-normal whole genomes from B-cell lymphomas with accompanying gene expression measurements to elucidate the extent to which these cancers are disrupted by cis-regulatory mutations. We characterize mutations overlapping a high quality set of well-annotated transcription factor binding sites (TFBSs), covering a similar portion of the genome as protein-coding exons. Our results indicate that cis-regulatory mutations overlapping predicted TFBSs are enriched in promoter regions of genes involved in apoptosis or growth/proliferation. By integrating gene expression data with mutation data, our computational approach culminates with identification of cis-regulatory mutations most likely to participate in dysregulation of the gene expression program. The impact can be measured along with protein-coding mutations to highlight key mutations disrupting gene expression and pathways in cancer. Our study yields specific genes with disrupted expression triggered by genomic mutations in either the coding or the regulatory space. It implies that mutated regulatory components of the genome contribute substantially to cancer pathways. Our analyses demonstrate that identifying genomically altered cis-regulatory elements coupled with analysis of gene expression data will augment biological interpretation of mutational landscapes of cancers.

  6. Partial mortality in massive reef corals as an indicator of sediment stress on coral reefs

    International Nuclear Information System (INIS)

    Nugues, Maggy M.; Roberts, Callum M.

    2003-01-01

    Partial mortality and fission on colonies of four common massive coral species were examined at sites differing in their exposure to river sediments in St. Lucia, West Indies. Rates of partial mortality were higher close to the river mouths, where more sediments were deposited, than away from the rivers in two coral species. Frequency of fission showed no significant trend. The percent change in coral cover on reefs from 1995 to 1998 was negatively related to the rate of partial mortality estimated in 1998 in all species. This suggests that partial mortality rates could reflect longer-term temporal changes in coral communities. Similar conclusions could also be reached using a less precise measure and simply recording partial mortality on colonies as <50% and ≥50% dead tissue. We conclude that partial mortality in some species of massive reef corals, expressed as the amount of dead tissue per colony, could provide a rapid and effective means of detecting sediment stress on coral reefs

  7. Partial mortality in massive reef corals as an indicator of sediment stress on coral reefs

    Energy Technology Data Exchange (ETDEWEB)

    Nugues, Maggy M.; Roberts, Callum M

    2003-03-01

    Partial mortality and fission on colonies of four common massive coral species were examined at sites differing in their exposure to river sediments in St. Lucia, West Indies. Rates of partial mortality were higher close to the river mouths, where more sediments were deposited, than away from the rivers in two coral species. Frequency of fission showed no significant trend. The percent change in coral cover on reefs from 1995 to 1998 was negatively related to the rate of partial mortality estimated in 1998 in all species. This suggests that partial mortality rates could reflect longer-term temporal changes in coral communities. Similar conclusions could also be reached using a less precise measure and simply recording partial mortality on colonies as <50% and {>=}50% dead tissue. We conclude that partial mortality in some species of massive reef corals, expressed as the amount of dead tissue per colony, could provide a rapid and effective means of detecting sediment stress on coral reefs.

  8. Overlapping consensus versus discourse in climate change policy: The case of Norway's Sovereign Wealth Fund

    International Nuclear Information System (INIS)

    Nilsen, Heidi Rapp

    2010-01-01

    This paper is motivated by the mismatch between emission of greenhouse gases and effective mitigation policies. Science now calls for every tool to be considered in order for radical changes to mitigate the situation more effectively. This paper considers Norway's huge Sovereign Wealth Fund which, although withdrawing investment from firms causing severe environmental damage, does not categorize climate change as 'severe environmental damage'. The main reason is a basis of overlapping consensus, which also hinders argumentation for this practice. Overlapping consensus is part of the broader theory 'Justice as Fairness' as conceived by John Rawls. The consensus is with regard to having a socially just system. The word 'overlapping' refers to people having different reasons for supporting the system. However using overlapping consensus for investment-strategies represents an extension beyond its original intention, and moreover, removes mitigating climate change from the agenda. Removing the basis of overlapping consensus opens up scope for value-based discourse conceived by Habermas' communicative action and discourse ethics. The immense severity of climate change demands value-based and substantial arguments from powerful sovereign wealth funds, to consider the acceptability of their practice.

  9. 9 CFR 121.4 - Overlap select agents and toxins.

    Science.gov (United States)

    2010-01-01

    ... in paragraph (b) of this section that have been genetically modified. (d) Overlap select agents or... OF AGRICULTURE VIRUSES, SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS POSSESSION, USE... elements, recombinant nucleic acids, and recombinant organisms: (1) Nucleic acids that can produce...

  10. Study of the structure of the QCD vacuum by means of overlap fermions; Untersuchung der Struktur des QCD-Vakuums mit Hilfe von Overlap-Fermionen

    Energy Technology Data Exchange (ETDEWEB)

    Weinberg, Volker

    2008-12-15

    In this thesis the structure of the QCD vacuum and the nature of the chiral phase transition were studied by means of overlap fermions. The main topic of the theiss lies in the study of the infrared long-range aspects shown by the low-lying eigenmodes of the overlap operator. For the characterization of the structure and dimension of an arbitray density embedded in the four-dimensional space-time diverse analysis tools were developed. These are applied both at low temperature (T=0) in the valence-quark approximation of QCD and in the environment of the high-temperature phase transition of the full QCD for the description of the structure of the modes and the topological density, as well as for the analysis of the local self-duality of the basing gauge fields.

  11. Lupus erythematosus/lichen planus overlap syndrome: successful treatment with acitretin.

    Science.gov (United States)

    Lospinoso, D J; Fernelius, C; Edhegard, K D; Finger, D R; Arora, N S

    2013-07-01

    Lupus erythematosus/lichen planus overlap syndrome is a rare disorder combining the clinical, histological and immunopathological features of both lupus erythematosus (LE) and lichen planus (LP). Cutaneous lesions mostly affect the distal arms, legs, face and trunk. Palmoplantar involvement is felt to be characteristic of this condition. Plaques are often painful, centrally atrophic, bluish-red to hypopigmented in color, large, and scaly. On biopsy of clinically ambiguous lesions, histopathological features of one or both processes can be found, obscuring the diagnosis and complicating prognosis and treatment. Thus, direct immunofluorescence has become an essential tool in helping to diagnose this condition. In this report we describe the unique clinical and immunohistopathological manifestations of lupus erythematosus/lichen planus overlap syndrome along with a successful response to treatment with acitretin.

  12. Expression and molecular evolution of two DREB1 genes in black poplar (Populus nigra.

    Directory of Open Access Journals (Sweden)

    Yanguang Chu

    Full Text Available Environmental stresses such as low temperature, drought, and high salinity significantly affect plant growth and yield. As selective forces, these adverse factors play essential roles in shaping phenotypic variation in plant populations. Black poplar (Populus nigra is an economically and ecologically important forest tree species with widely distributed populations and is thus suitable for experiments detecting evolutionary footprints left by stress. Here, we performed expression and evolutionary analysis of two duplicated DREB A1-subgroup (DREB1 genes, PnDREB68 and PnDREB69, encoding transcription factors that are involved in stress responses. The two genes showed partially overlapping but distinct expression patterns in response to stresses. These genes were strongly and rapidly induced by cold stress in leaves, stems, and roots. In leaf tissue, dehydration stress induced the expression of PnDREB68 but not PnDREB69. PnDREB69 displayed more rapid responses and longer expression durations than PnDREB68 under salt and ABA stress, respectively. Based on single nucleotide polymorphism (SNP analysis, we found significant population genetic differentiation, with a greater FST value (0.09189 for PnDREB69 than for PnDREB68 (0.07743. Nucleotide diversity analysis revealed a two-fold higher πT for PnDREB68 than for PnDREB69 (0.00563 vs. 0.00243, reflecting strong purifying selection acting on the former. The results suggest that positive selection acted on PnDREB69, as evidenced by neutral testing using Tajima's D statistic. The distinct selective forces to which each of the genes was subjected may be associated with expression divergence. Linkage disequilibrium (LD was low for the sequenced region, with a higher level for PnDREB68 than for PnDREB69. Additionally, analysis of the relationship among carbon isotope ratios, SNP classes and gene expression, together with motif and domain analysis, suggested that 14 polymorphisms within the two genes may be

  13. Anti-scar Treatment for Deep Partial-thickness Burn Wounds

    Science.gov (United States)

    2017-10-01

    applied topically to deep partial-thickness burn wounds reduced α-SMA protein expression ( ELISA ). Mouse burn wounds were treated with PFD twice...immediately and at 48 hrs post- burn. α-SMA in wound skin homogenates was assayed by ELISA . α-SMA protein was significantly lower in mice treated with...Inflammatory cytokines in wound skin homogenates were assayed by ELISA . This early treatment during the inflammatory stage of healing significantly reduced

  14. Overlap and Nonoverlap Between the ICF Core Sets for Hearing Loss and Otology and Audiology Intake Documentation.

    Science.gov (United States)

    van Leeuwen, Lisette M; Merkus, Paul; Pronk, Marieke; van der Torn, Marein; Maré, Marcel; Goverts, S Theo; Kramer, Sophia E

    The International Classification of Functioning Disability and Health (ICF) Core Sets for Hearing Loss (HL) were developed to serve as a standard for the assessment and reporting of the functioning and health of patients with HL. The aim of the present study was to compare the content of the intake documentation currently used in secondary and tertiary hearing care settings in the Netherlands with the content of the ICF Core Sets for HL. Research questions were (1) to what extent are the ICF Core Sets for HL represented in the Dutch Otology and Audiology intake documentation? (2) are there any extra ICF categories expressed in the intake documentation that are currently not part of the ICF Core Sets for HL, or constructs expressed that are not part of the ICF? Multicenter patient record study including 176 adult patients from two secondary, and two tertiary hearing care settings. The intake documentation was selected from anonymized patient records. The content was linked to the appropriate ICF category from the whole ICF classification using established linking rules. The extent to which the ICF Core Sets for HL were represented in the intake documentation was determined by assessing the overlap between the ICF categories in the Core Sets and the list of unique ICF categories extracted from the intake documentation. Any extra constructs that were expressed in the intake documentation but are not part of the Core Sets were described as well, differentiating between ICF categories that are not part of the Core Sets and constructs that are not part of the ICF classification. In total, otology and audiology intake documentation represented 24 of the 27 Brief ICF Core Set categories (i.e., 89%), and 60 of the 117 Comprehensive ICF Core Set categories (i.e., 51%). Various ICF Core Sets categories were not represented, including higher mental functions (Body Functions), civic life aspects (Activities and Participation), and support and attitudes of family (Environmental

  15. On the practical modeling of conceptual overlap among multiple facets in ontology domain concepts (Mini-thesis)

    OpenAIRE

    Rodriguez-Castro, Benedicto; Glaser, Hugh; Carr, Leslie

    2007-01-01

    This report presents a study on the practical modelling of the conceptual overlap that might exist among the multiple facets that define a particular ontology domain concept. The notions of conceptual overlap and facet are defined, together with their relation to scenarios of multiple inheritance in ontology models. Starting from the notion of a value partition, a terminology of ontology modelling constructs is introduced that allows the characterization of two types of conceptual overlap wit...

  16. Arsenic exposure from drinking water is associated with decreased gene expression and increased DNA methylation in peripheral blood

    Energy Technology Data Exchange (ETDEWEB)

    Ameer, Syeda Shegufta [Department of Laboratory Medicine, Division of Occupational and Environmental Medicine, Lund University, Lund (Sweden); Engström, Karin [Department of Laboratory Medicine, Division of Occupational and Environmental Medicine, Lund University, Lund (Sweden); Institute of Environmental Medicine, Unit of Metals & Health, Karolinska Institutet, Stockholm (Sweden); Hossain, Mohammad Bakhtiar [Department of Laboratory Medicine, Division of Occupational and Environmental Medicine, Lund University, Lund (Sweden); Concha, Gabriela [Science Department, Risk Benefit Assessment Unit, National Food Agency, Uppsala (Sweden); Vahter, Marie [Institute of Environmental Medicine, Unit of Metals & Health, Karolinska Institutet, Stockholm (Sweden); Broberg, Karin, E-mail: Karin.broberg@ki.se [Institute of Environmental Medicine, Unit of Metals & Health, Karolinska Institutet, Stockholm (Sweden)

    2017-04-15

    Background: Exposure to inorganic arsenic increases the risk of cancer and non-malignant diseases. Inefficient arsenic metabolism is a marker for susceptibility to arsenic toxicity. Arsenic may alter gene expression, possibly by altering DNA methylation. Objectives: To elucidate the associations between arsenic exposure, gene expression, and DNA methylation in peripheral blood, and the modifying effects of arsenic metabolism. Methods: The study participants, women from the Andes, Argentina, were exposed to arsenic via drinking water. Arsenic exposure was assessed as the sum of arsenic metabolites in urine (U-As), using high performance liquid-chromatography hydride-generation inductively-coupled-plasma-mass-spectrometry, and arsenic metabolism efficiency was assessed by the urinary fractions (%) of the individual metabolites. Genome-wide gene expression (N = 80 women) and DNA methylation (N = 93; 80 overlapping with gene expression) in peripheral blood were measured using Illumina DirectHyb HumanHT-12 v4.0 and Infinium Human-Methylation 450K BeadChip, respectively. Results: U-As concentrations, ranging 10–1251 μg/L, was associated with decreased gene expression: 64% of the top 1000 differentially expressed genes were down-regulated with increasing U-As. U-As was also associated with hypermethylation: 87% of the top 1000 CpGs were hypermethylated with increasing U-As. The expression of six genes and six individual CpG sites were significantly associated with increased U-As concentration. Pathway analyses revealed enrichment of genes related to cell death and cancer. The pathways differed somewhat depending on arsenic metabolism efficiency. We found no overlap between arsenic-related gene expression and DNA methylation for individual genes. Conclusions: Increased arsenic exposure was associated with lower gene expression and hypermethylation in peripheral blood, but with no evident overlap. - Highlights: • Women exposed to inorganic arsenic were studied for

  17. Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions.

    Science.gov (United States)

    Raleigh, David R; Marchiando, Amanda M; Zhang, Yong; Shen, Le; Sasaki, Hiroyuki; Wang, Yingmin; Long, Manyuan; Turner, Jerrold R

    2010-04-01

    In vitro studies have demonstrated that occludin and tricellulin are important for tight junction barrier function, but in vivo data suggest that loss of these proteins can be overcome. The presence of a heretofore unknown, yet related, protein could explain these observations. Here, we report marvelD3, a novel tight junction protein that, like occludin and tricellulin, contains a conserved four-transmembrane MARVEL (MAL and related proteins for vesicle trafficking and membrane link) domain. Phylogenetic tree reconstruction; analysis of RNA and protein tissue distribution; immunofluorescent and electron microscopic examination of subcellular localization; characterization of intracellular trafficking, protein interactions, dynamic behavior, and siRNA knockdown effects; and description of remodeling after in vivo immune activation show that marvelD3, occludin, and tricellulin have distinct but overlapping functions at the tight junction. Although marvelD3 is able to partially compensate for occludin or tricellulin loss, it cannot fully restore function. We conclude that marvelD3, occludin, and tricellulin define the tight junction-associated MARVEL protein family. The data further suggest that these proteins are best considered as a group with both redundant and unique contributions to epithelial function and tight junction regulation.

  18. Iterative methods used in overlap astrometric reduction techniques do not always converge

    Science.gov (United States)

    Rapaport, M.; Ducourant, C.; Colin, J.; Le Campion, J. F.

    1993-04-01

    In this paper we prove that the classical Gauss-Seidel type iterative methods used for the solution of the reduced normal equations occurring in overlapping reduction methods of astrometry do not always converge. We exhibit examples of divergence. We then analyze an alternative algorithm proposed by Wang (1985). We prove the consistency of this algorithm and verify that it can be convergent while the Gauss-Seidel method is divergent. We conjecture the convergence of Wang method for the solution of astrometric problems using overlap techniques.

  19. Partial tooth gear bearings

    Science.gov (United States)

    Vranish, John M. (Inventor)

    2010-01-01

    A partial gear bearing including an upper half, comprising peak partial teeth, and a lower, or bottom, half, comprising valley partial teeth. The upper half also has an integrated roller section between each of the peak partial teeth with a radius equal to the gear pitch radius of the radially outwardly extending peak partial teeth. Conversely, the lower half has an integrated roller section between each of the valley half teeth with a radius also equal to the gear pitch radius of the peak partial teeth. The valley partial teeth extend radially inwardly from its roller section. The peak and valley partial teeth are exactly out of phase with each other, as are the roller sections of the upper and lower halves. Essentially, the end roller bearing of the typical gear bearing has been integrated into the normal gear tooth pattern.

  20. Handover Incentives for Self-Interested WLANs with Overlapping Coverage

    DEFF Research Database (Denmark)

    Fafoutis, Xenofon; Siris, Vasilios A.

    2012-01-01

    We consider an environment where self-interested IEEE 802.11 Wireless Local Area Networks (WLANs) have overlapping coverage, and investigate the incentives that can trigger handovers between the WLANs. Our focus is on the incentives for supporting handovers due solely to the improved performance...

  1. A Bayesian Approach to the Overlap Analysis of Epidemiologically Linked Traits.

    Science.gov (United States)

    Asimit, Jennifer L; Panoutsopoulou, Kalliope; Wheeler, Eleanor; Berndt, Sonja I; Cordell, Heather J; Morris, Andrew P; Zeggini, Eleftheria; Barroso, Inês

    2015-12-01

    Diseases often cooccur in individuals more often than expected by chance, and may be explained by shared underlying genetic etiology. A common approach to genetic overlap analyses is to use summary genome-wide association study data to identify single-nucleotide polymorphisms (SNPs) that are associated with multiple traits at a selected P-value threshold. However, P-values do not account for differences in power, whereas Bayes' factors (BFs) do, and may be approximated using summary statistics. We use simulation studies to compare the power of frequentist and Bayesian approaches with overlap analyses, and to decide on appropriate thresholds for comparison between the two methods. It is empirically illustrated that BFs have the advantage over P-values of a decreasing type I error rate as study size increases for single-disease associations. Consequently, the overlap analysis of traits from different-sized studies encounters issues in fair P-value threshold selection, whereas BFs are adjusted automatically. Extensive simulations show that Bayesian overlap analyses tend to have higher power than those that assess association strength with P-values, particularly in low-power scenarios. Calibration tables between BFs and P-values are provided for a range of sample sizes, as well as an approximation approach for sample sizes that are not in the calibration table. Although P-values are sometimes thought more intuitive, these tables assist in removing the opaqueness of Bayesian thresholds and may also be used in the selection of a BF threshold to meet a certain type I error rate. An application of our methods is used to identify variants associated with both obesity and osteoarthritis. © 2015 The Authors. *Genetic Epidemiology published by Wiley Periodicals, Inc.

  2. Targeted Memory Reactivation during Sleep Adaptively Promotes the Strengthening or Weakening of Overlapping Memories.

    Science.gov (United States)

    Oyarzún, Javiera P; Morís, Joaquín; Luque, David; de Diego-Balaguer, Ruth; Fuentemilla, Lluís

    2017-08-09

    System memory consolidation is conceptualized as an active process whereby newly encoded memory representations are strengthened through selective memory reactivation during sleep. However, our learning experience is highly overlapping in content (i.e., shares common elements), and memories of these events are organized in an intricate network of overlapping associated events. It remains to be explored whether and how selective memory reactivation during sleep has an impact on these overlapping memories acquired during awake time. Here, we test in a group of adult women and men the prediction that selective memory reactivation during sleep entails the reactivation of associated events and that this may lead the brain to adaptively regulate whether these associated memories are strengthened or pruned from memory networks on the basis of their relative associative strength with the shared element. Our findings demonstrate the existence of efficient regulatory neural mechanisms governing how complex memory networks are shaped during sleep as a function of their associative memory strength. SIGNIFICANCE STATEMENT Numerous studies have demonstrated that system memory consolidation is an active, selective, and sleep-dependent process in which only subsets of new memories become stabilized through their reactivation. However, the learning experience is highly overlapping in content and thus events are encoded in an intricate network of related memories. It remains to be explored whether and how memory reactivation has an impact on overlapping memories acquired during awake time. Here, we show that sleep memory reactivation promotes strengthening and weakening of overlapping memories based on their associative memory strength. These results suggest the existence of an efficient regulatory neural mechanism that avoids the formation of cluttered memory representation of multiple events and promotes stabilization of complex memory networks. Copyright © 2017 the authors 0270-6474/17/377748-11$15.00/0.

  3. Galaxy Zoo: A Catalog of Overlapping Galaxy Pairs for Dust Studies

    Science.gov (United States)

    Keel, William C.; Manning, Anna M.; Holwerda, Benne W.; Mezzoprete, Massimo; Lintott, Chris J.; Schawinski, Kevin; Gay, Pamela; Masters, Karen L.

    2013-01-01

    Analysis of galaxies with overlapping images offers a direct way to probe the distribution of dust extinction and its effects on the background light. We present a catalog of 1990 such galaxy pairs selected from the Sloan Digital Sky Survey (SDSS) by volunteers of the Galaxy Zoo project. We highlight subsamples which are particularly useful for retrieving such properties of the dust distribution as UV extinction, the extent perpendicular to the disk plane, and extinction in the inner parts of disks. The sample spans wide ranges of morphology and surface brightness, opening up the possibility of using this technique to address systematic changes in dust extinction or distribution with galaxy type. This sample will form the basis for forthcoming work on the ranges of dust distributions in local disk galaxies, both for their astrophysical implications and as the low-redshift part of a study of the evolution of dust properties. Separate lists and figures show deep overlaps, where the inner regions of the foreground galaxy are backlit, and the relatively small number of previously-known overlapping pairs outside the SDSS DR7 sky coverage.

  4. Extracting scattering phase shifts in higher partial waves from lattice QCD calculations

    Energy Technology Data Exchange (ETDEWEB)

    Luu, Thomas; Savage, Martin J.

    2011-06-01

    Lüscher’s method is routinely used to determine meson-meson, meson-baryon, and baryon-baryon s-wave scattering amplitudes below inelastic thresholds from lattice QCD calculations—presently at unphysical light-quark masses. In this work we review the formalism and develop the requisite expressions to extract phase shifts describing meson-meson scattering in partial waves with angular momentum l≤6 and l=9. The implications of the underlying cubic symmetry, and strategies for extracting the phase shifts from lattice QCD calculations, are presented, along with a discussion of the signal-to-noise problem that afflicts the higher partial waves.

  5. Lizard assemblage from a sand dune habitat from southeastern Brazil: a niche overlap analysis

    Directory of Open Access Journals (Sweden)

    GISELE R. WINCK

    2016-01-01

    Full Text Available ABSTRACT Communities are structured by interactions of historical and ecological factors, which influence the use of different resources in time and space. We acquired data on time of activity, microhabitat use and diet of a lizard assemblage from a sand dune habitat in a coastal area, southeastern Brazil (Restinga de Jurubatiba. We analyzed the data of niche overlap among species in these three axes (temporal, spatial and trophic using null models. We found a significant overlap within the trophic niche, whereas the overlap for the other axes did not differ from the expected. Based on this result, we discuss the factors acting on the structure of the local lizard community.

  6. Domestic Violence and the Victim/Offender Overlap Across the Life Course.

    Science.gov (United States)

    Iratzoqui, Amaia

    2018-07-01

    The current article examined the overlap of domestic violence across the life course, connecting childhood abuse and adolescent dating victimization to adult intimate partner victimization, and the connection between these behaviors and adult domestic violence perpetration against partners and children. Using three waves of Add Health data, the study found that childhood and adolescent domestic victimization were directly and indirectly linked to adult intimate partner victimization and that domestic violence perpetration also played a role. These findings indicate that offending must be accounted for in tracking patterns of victimization over the life course and that the overlap must more directly be reconciled in current criminal justice policy.

  7. Technology initiatives with government/business overlap

    Science.gov (United States)

    Knapp, Robert H., Jr.

    2015-03-01

    Three important present-day technology development settings involve significant overlap between government and private sectors. The Advanced Research Project Agency for Energy (ARPA-E) supports a wide range of "high risk, high return" projects carried out in academic, non-profit or private business settings. The Materials Genome Initiative (MGI), based in the White House, aims at radical acceleration of the development process for advanced materials. California public utilities such as Pacific Gas & Electric operate under a structure of financial returns and political program mandates that make them arms of public policy as much as independent businesses.

  8. Vacuum structure as seen by overlap fermions

    International Nuclear Information System (INIS)

    Ilgenfritz, E.M.

    2006-11-01

    Three complementary views on the QCD vacuum structure, all based on eigenmodes of the overlap operator, are reported in their interrelation: (i) spectral density, localization and chiral properties of the modes, (ii) the possibility of filtering the field strength with the aim to detect selfdual and antiselfdual domains and (iii) the various faces of the topological charge density, with and without a cutoff λ cut = O(Λ QCD ). The techniques are tested on quenched SU(3) configurations. (orig.)

  9. Overlap of functional heartburn and gastroesophageal reflux disease with irritable bowel syndrome.

    Science.gov (United States)

    de Bortoli, Nicola; Martinucci, Irene; Bellini, Massimo; Savarino, Edoardo; Savarino, Vincenzo; Blandizzi, Corrado; Marchi, Santino

    2013-09-21

    Several studies indicate a significant degree of overlap between irritable bowel syndrome (IBS) and gastroesophageal reflux disease (GERD). Likewise, both functional heartburn (FH) and IBS are functional digestive disorders that may occur in the same patients. However, data establishing a solid link between FH and IBS are lacking, mainly because the clinical definition of FH has undergone substantial changes over the years. The available literature on the overlap between GERD or FH and IBS highlights considerable heterogeneity in terms of the criteria and diagnostic procedures used to assess heartburn and IBS. In particular, several epidemiological studies included patients with concomitant IBS and GERD without any attempt to distinguish FH (as defined by the Rome III criteria) from GERD via pathophysiological investigations. Independent of these critical issues, there is preliminary evidence supporting a significant degree of FH-IBS overlap. This underscores the need for studies based on updated diagnostic criteria and accurate pathophysiological classifications, particularly to distinguish FH from GERD. This distinction would represent an essential starting point to achieving a better understanding of pathophysiology in the subclasses of patients with GERD and FH and properly assessing the different degrees of overlap between IBS and the subcategories of heartburn.The present review article intends to appraise and critically discuss current evidence supporting a possible concomitance of GERD or FH with IBS in the same patients and to highlight the pathophysiological relationships between these disorders.

  10. Partial widths of boson resonances in the quark-gluon model of strong interactions

    International Nuclear Information System (INIS)

    Kaidalov, A.B.; Volkovitsky, P.E.

    1981-01-01

    The quark-gluon model of strong interactions based on the topological expansion and the string model ib used for the calculation of the partial widths of boson resonances in the channels with two pseudoscalar mesons. The partial widths of mesons with arbitrary spins lying on the vector and tensor Regge trajectories are expressed in terms of the only rho-meson width. The violation of SU(3) symmetry increases with the growth of the spin of the resonance. The theoretical predictions are in a good agreement with experimental data [ru

  11. Room acoustic transition time based on reflection overlap

    DEFF Research Database (Denmark)

    Jeong, Cheol-Ho; Brunskog, Jonas; Jacobsen, Finn

    2010-01-01

    A transition time is defined based on the temporal overlap of reflected pulses in room impulse responses. Assuming specular reflections only, the temporal distance between adjacent reflections, which is proportional to the volume of a room, is compared with the characteristic width of a pulse at ...... in a room with nonuniform absorption and furniture than in a room that satisfies the underlying assumptions....

  12. Room acoustic transition time based on reflection overlap

    DEFF Research Database (Denmark)

    Jeong, Cheol-Ho; Brunskog, Jonas; Jacobsen, Finn

    2013-01-01

    A transition time is defined based on the temporal overlap of reflected pulses in room impulse responses. Assuming specular reflections only, the temporal distance between adjacent reflections, which is proportional to the volume of a room, is compared with the characteristic width of a pulse at ...... in a room with nonuniform absorption and furniture than in a room that satisfies the underlying assumptions....

  13. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Directory of Open Access Journals (Sweden)

    Jiang-Ke Yang

    Full Text Available In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp and Aspergillus niger phytase gene phyA (1404 bp. Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  14. Study on hybrid heat source overlap welding of magnesium alloy AZ31B

    International Nuclear Information System (INIS)

    Liang, G.L.; Zhou, G.; Yuan, S.Q.

    2009-01-01

    The magnesium alloy AZ31B was overlap welded by hybrid welding (laser-tungsten inert gas arc). According to the hybrid welding interaction principle, a new heat source model, hybrid welding heat source model, was developed with finite element analysis. At the same time, using a high-temperature metallographical microscope, the macro-appearance and microstructure characteristics of the joint after hybrid overlap welding were studied. The results indicate that the hybrid welding was superior to the single tungsten inert gas welding or laser welding on the aspects of improving the utilized efficiency of the arc and enhancing the absorptivity of materials to laser energy. Due to the energy characteristics of hybrid overlap welding the macro-appearance of the joint was cup-shaped, the top weld showed the hybrid welding microstructure, while, the lower weld showed the typical laser welding microstructure

  15. Study on hybrid heat source overlap welding of magnesium alloy AZ31B

    Energy Technology Data Exchange (ETDEWEB)

    Liang, G.L. [Department of Electromechanical Engineering, Tangshan College, Tangshan 063000 (China)], E-mail: guoliliang@sohu.com; Zhou, G. [School of Material Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Yuan, S.Q. [Department of Electromechanical Engineering, Tangshan College, Tangshan 063000 (China)

    2009-01-15

    The magnesium alloy AZ31B was overlap welded by hybrid welding (laser-tungsten inert gas arc). According to the hybrid welding interaction principle, a new heat source model, hybrid welding heat source model, was developed with finite element analysis. At the same time, using a high-temperature metallographical microscope, the macro-appearance and microstructure characteristics of the joint after hybrid overlap welding were studied. The results indicate that the hybrid welding was superior to the single tungsten inert gas welding or laser welding on the aspects of improving the utilized efficiency of the arc and enhancing the absorptivity of materials to laser energy. Due to the energy characteristics of hybrid overlap welding the macro-appearance of the joint was cup-shaped, the top weld showed the hybrid welding microstructure, while, the lower weld showed the typical laser welding microstructure.

  16. Overlapping reliable control for a cable-stayed bridge benchmark

    Czech Academy of Sciences Publication Activity Database

    Bakule, Lubomír; Paulet-Crainiceanu, F.; Rodellar, J.; Rossell, J. M.

    2005-01-01

    Roč. 13, č. 4 (2005), s. 663-669 ISSN 1063-6536 R&D Projects: GA AV ČR IAA2075304 Institutional research plan: CEZ:AV0Z10750506 Keywords : decentralized control * reliable control * overlapping Subject RIV: BC - Control Systems Theory Impact factor: 1.027, year: 2005

  17. Joint Multi-person Detection and Tracking from Overlapping Cameras

    NARCIS (Netherlands)

    Liem, M.C.; Gavrila, D.M.

    2014-01-01

    We present a system to track the positions of multiple persons in a scene from overlapping cameras. The distinguishing aspect of our method is a novel, two-step approach that jointly estimates person position and track assignment. The proposed approach keeps solving the assignment problem tractable,

  18. Multiclass Prediction with Partial Least Square Regression for Gene Expression Data: Applications in Breast Cancer Intrinsic Taxonomy

    Directory of Open Access Journals (Sweden)

    Chi-Cheng Huang

    2013-01-01

    Full Text Available Multiclass prediction remains an obstacle for high-throughput data analysis such as microarray gene expression profiles. Despite recent advancements in machine learning and bioinformatics, most classification tools were limited to the applications of binary responses. Our aim was to apply partial least square (PLS regression for breast cancer intrinsic taxonomy, of which five distinct molecular subtypes were identified. The PAM50 signature genes were used as predictive variables in PLS analysis, and the latent gene component scores were used in binary logistic regression for each molecular subtype. The 139 prototypical arrays for PAM50 development were used as training dataset, and three independent microarray studies with Han Chinese origin were used for independent validation (n=535. The agreement between PAM50 centroid-based single sample prediction (SSP and PLS-regression was excellent (weighted Kappa: 0.988 within the training samples, but deteriorated substantially in independent samples, which could attribute to much more unclassified samples by PLS-regression. If these unclassified samples were removed, the agreement between PAM50 SSP and PLS-regression improved enormously (weighted Kappa: 0.829 as opposed to 0.541 when unclassified samples were analyzed. Our study ascertained the feasibility of PLS-regression in multi-class prediction, and distinct clinical presentations and prognostic discrepancies were observed across breast cancer molecular subtypes.

  19. Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLalphas/ALEX Relay.

    Directory of Open Access Journals (Sweden)

    2005-08-01

    Full Text Available XLalphas and ALEX are structurally unrelated mammalian proteins translated from alternative overlapping reading frames of a single transcript. Not only are they encoded by the same locus, but a specific XLalphas/ALEX interaction is essential for G-protein signaling in neuroendocrine cells. A disruption of this interaction leads to abnormal human phenotypes, including mental retardation and growth deficiency. The region of overlap between the two reading frames evolves at a remarkable speed: the divergence between human and mouse ALEX polypeptides makes them virtually unalignable. To trace the evolution of this puzzling locus, we sequenced it in apes, Old World monkeys, and a New World monkey. We show that the overlap between the two reading frames and the physical interaction between the two proteins force the locus to evolve in an unprecedented way. Namely, to maintain two overlapping protein-coding regions the locus is forced to have high GC content, which significantly elevates its intrinsic evolutionary rate. However, the two encoded proteins cannot afford to change too quickly relative to each other as this may impair their interaction and lead to severe physiological consequences. As a result XLalphas and ALEX evolve in an oscillating fashion constantly balancing the rates of amino acid replacements. This is the first example of a rapidly evolving locus encoding interacting proteins via overlapping reading frames, with a possible link to the origin of species-specific neurological differences.

  20. Features of systemic sclerosis-rheumatoid arthritis overlap syndrome (SS-RA overlap syndrome

    Directory of Open Access Journals (Sweden)

    O. V. Desinova

    2007-01-01

    Full Text Available Objective. To reveal clinico-laboratory, immunologic and immunogenetic features of systemic sclerosis-rheumatoid arthritis overlap syndrome (SS-RA.Material and methods. 32 pts with SS-RA (1 male, 31 female aged 22 to 74 years with disease onset at 18 to 69 years and disease duration from 1 to 35 years were included. Complex laboratory and instrumental examination was performed including nailfold capillaroscopy. A part of pts was also evaluated with magnetic resonance imaging of hands. Serum level of rheumatoid factor, antinuclear factor, circulating immune complexes, C-reactive protein, antibodies to cyclic citrullinated peptide (ACCP was evaluated. Genotyping of DRB1 alleles was performed.Results. Characteristic features of SS-RA were prevalence of limited skin damage, less prominent peripheral and visceral symptoms of SS, presence of anti-topoisomerase antibodies and erosive arthritis, high laboratory and immunological activity, more frequent association with DRB1*01.Conclusion. SS-RA possesses its own clinical features and can be considered as a distinct subtype of SS.

  1. Diagnosis and Management of the Overlap Syndromes of Autoimmune Hepatitis

    Directory of Open Access Journals (Sweden)

    Albert J Czaja

    2013-01-01

    Full Text Available BACKGROUND: Autoimmune hepatitis may have cholestatic features that are outside the classical phenotype and that resemble findings in other immune-mediated liver diseases. These cholestatic phenotypes have been designated ‘overlap syndromes’.

  2. Cloud Overlapping Detection Algorithm Using Solar and IR Wavelengths With GOSE Data Over ARM/SGP Site

    Science.gov (United States)

    Kawamoto, Kazuaki; Minnis, Patrick; Smith, William L., Jr.

    2001-01-01

    One of the most perplexing problems in satellite cloud remote sensing is the overlapping of cloud layers. Although most techniques assume a 1-layer cloud system in a given retrieval of cloud properties, many observations are affected by radiation from more than one cloud layer. As such, cloud overlap can cause errors in the retrieval of many properties including cloud height, optical depth, phase, and particle size. A variety of methods have been developed to identify overlapped clouds in a given satellite imager pixel. Baum el al. (1995) used CO2 slicing and a spatial coherence method to demonstrate a possible analysis method for nighttime detection of multilayered clouds. Jin and Rossow (1997) also used a multispectral CO2 slicing technique for a global analysis of overlapped cloud amount. Lin et al. (1999) used a combination infrared, visible, and microwave data to detect overlapped clouds over water. Recently, Baum and Spinhirne (2000) proposed 1.6 and 11 microns. bispectral threshold method. While all of these methods have made progress in solving this stubborn problem, none have yet proven satisfactory for continuous and consistent monitoring of multilayer cloud systems. It is clear that detection of overlapping clouds from passive instruments such as satellite radiometers is in an immature stage of development and requires additional research. Overlapped cloud systems also affect the retrievals of cloud properties over the ARM domains (e.g., Minnis et al 1998) and hence should identified as accurately as possible. To reach this goal, it is necessary to determine which information can be exploited for detecting multilayered clouds from operational meteorological satellite data used by ARM. This paper examines the potential information available in spectral data available on the Geostationary Operational Environmental Satellite (GOES) imager and the NOAA Advanced Very High Resolution Radiometer (AVHRR) used over the ARM SGP and NSA sites to study the

  3. The antagonistic regulation of abscisic acid-inhibited root growth by brassinosteroids is partially mediated via direct suppression of ABSCISIC ACID INSENSITIVE 5 expression by BRASSINAZOLE RESISTANT 1.

    Science.gov (United States)

    Yang, Xiaorui; Bai, Yang; Shang, Jianxiu; Xin, Ruijiao; Tang, Wenqiang

    2016-09-01

    Brassinosteroids (BRs) and abscisic acid (ABA) are plant hormones that antagonistically regulate many aspects of plant growth and development; however, the mechanisms that regulate the crosstalk of these two hormones are still not well understood. BRs regulate plant growth and development by activating BRASSINAZOLE RESISTANT 1 (BZR1) family transcription factors. Here we show that the crosstalk between BRs and ABA signalling is partially mediated by BZR1 regulated gene expression. bzr1-1D is a dominant mutant with enhanced BR signalling; our results showed that bzr1-1D mutant is less sensitive to ABA-inhibited primary root growth. By RNA sequencing, a subset of BZR1 regulated ABA-responsive root genes were identified. Of these genes, the expression of a major ABA signalling component ABA INSENSITIVE 5 (ABI5) was found to be suppressed by BR and by BZR1. Additional evidences showed that BZR1 could bind strongly with several G-box cis-elements in the promoter of ABI5, suppress the expression of ABI5 and make plants less sensitive to ABA. Our study demonstrated that ABI5 is a direct target gene of BZR1, and modulating the expression of ABI5 by BZR1 plays important roles in regulating the crosstalk between the BR and ABA signalling pathways. © 2016 John Wiley & Sons Ltd.

  4. Binomial distribution of Poisson statistics and tracks overlapping probability to estimate total tracks count with low uncertainty

    International Nuclear Information System (INIS)

    Khayat, Omid; Afarideh, Hossein; Mohammadnia, Meisam

    2015-01-01

    In the solid state nuclear track detectors of chemically etched type, nuclear tracks with center-to-center neighborhood of distance shorter than two times the radius of tracks will emerge as overlapping tracks. Track overlapping in this type of detectors causes tracks count losses and it becomes rather severe in high track densities. Therefore, tracks counting in this condition should include a correction factor for count losses of different tracks overlapping orders since a number of overlapping tracks may be counted as one track. Another aspect of the problem is the cases where imaging the whole area of the detector and counting all tracks are not possible. In these conditions a statistical generalization method is desired to be applicable in counting a segmented area of the detector and the results can be generalized to the whole surface of the detector. Also there is a challenge in counting the tracks in densely overlapped tracks because not sufficient geometrical or contextual information are available. It this paper we present a statistical counting method which gives the user a relation between the tracks overlapping probabilities on a segmented area of the detector surface and the total number of tracks. To apply the proposed method one can estimate the total number of tracks on a solid state detector of arbitrary shape and dimensions by approximating the tracks averaged area, whole detector surface area and some orders of tracks overlapping probabilities. It will be shown that this method is applicable in high and ultra high density tracks images and the count loss error can be enervated using a statistical generalization approach. - Highlights: • A correction factor for count losses of different tracks overlapping orders. • For the cases imaging the whole area of the detector is not possible. • Presenting a statistical generalization method for segmented areas. • Giving a relation between the tracks overlapping probabilities and the total tracks

  5. Experimental characterization of Raman overlaps between mode-groups

    DEFF Research Database (Denmark)

    Christensen, Erik Nicolai; Koefoed, Jacob Gade; Friis, Søren Michael Mørk

    2016-01-01

    Mode-division multiplexing has the potential to further increase data transmission capacity through optical fibers. In addition, distributed Raman amplification is a promising candidate for multi-mode signal amplification due to its desirable noise properties and the possibility of mode-equalized......Mode-division multiplexing has the potential to further increase data transmission capacity through optical fibers. In addition, distributed Raman amplification is a promising candidate for multi-mode signal amplification due to its desirable noise properties and the possibility of mode......-equalized gain. In this paper, we present an experimental characterization of the intermodal Raman intensity overlaps of a few-mode fiber using backward-pumped Raman amplification. By varying the input pump power and the degree of higher order mode-excitation for the pump and the signal in a 10km long two......-mode fiber, we are able to characterize all intermodal Raman intensity overlaps. Using these results, we perform a Raman amplification measurement and demonstrate a mode-differential gain of only 0.25dB per 10dB overall gain. This is, to the best of our knowledge, the lowest mode differential gain achieved...

  6. Responses of the crab Heterozius rotundifrons to heterospecific chemical alarm cues: phylogeny vs. ecological overlap.

    Science.gov (United States)

    Hazlett, Brian A; McLay, Colin

    2005-03-01

    The big-handed brachyuran crab Heterozius rotundifrons extends the time spent in its anti-predator posture, limb extended posture, if exposed to chemical cues from crushed conspecifics. In this study, we tested whether crabs also respond to chemical cues from crushed heterospecific crabs, and if so, whether phylogenetic relations or ecological overlap is more important in influencing the duration of the anti-predator posture. Chemical cues from two other brachyuran crabs (Cyclograpsus lavauxi and Hemigrapsus sexdentatus), which do not overlap directly in ecological distribution with H. rotundifrons, elicited a duration of the anti-predator posture that was indistinguishable from that produced by conspecific chemical cues. In contrast, chemical cues from two anomuran crabs (Petrolisthes elongatus and Pagurus novizealandiae) that overlap in ecological distribution with H. rotundifrons, elicited durations of the antipredator posture that were significantly shorter than those of either conspecifics or more closely related crab species. Thus, phylogenetic relationship seems to be more important than ecological overlap in influencing anti-predator behavior in H. rotundifrons.

  7. Bipolar disorder, schizoaffective disorder, and schizophrenia overlap: a new comorbidity index.

    Science.gov (United States)

    Laursen, Thomas Munk; Agerbo, Esben; Pedersen, Carsten Bøcker

    2009-10-01

    Growing evidence of an etiologic overlap between schizophrenia, schizoaffective disorder, and bipolar disorder has become increasingly difficult to disregard. We investigated the magnitude of the overlap between the clinical diagnoses of bipolar affective disorder, schizoaffective disorder, and schizophrenia over a 35-year period based on the entire Danish population. We established a register-based prospective cohort study of more than 2.5 million persons born in Denmark after 1954. Risks for the 3 psychiatric disorders were estimated by survival analysis using the Aalen-Johansen method. Cohort members were followed from 1970 to 2006. We introduced a new comorbidity index measuring the magnitude of the overlap between the 3 disorders. Overall, 12,734 patients were admitted with schizophrenia, 4,205 with bipolar disorder, and 1,881 with schizoaffective disorder. A female bipolar patient's risk of also being admitted with a schizoaffective disorder by the age of 45 years was approximately 103 times higher than that of a woman at the same age in the general population. Thus, we defined the comorbidity index between schizoaffective disorder and bipolar disorder at age 45 years to be 103. At age 45 years, the index between schizophrenia and schizoaffective disorder was 80 and between schizophrenia and bipolar disorder was 20. Similar large comorbidity indexes were found for men. A large comorbidity index between schizophrenia and schizoaffective disorder was found, as well as a large index between bipolar disorder and schizoaffective disorder. But, more surprisingly, it was clear that a substantial comorbidity index between bipolar disorder and schizophrenia was present. This study supports the existence of an overlap between bipolar disorder and schizophrenia and thus challenges the strict categorical approach used in both DSM-IV and ICD-10 classification systems. Copyright 2009 Physicians Postgraduate Press, Inc.

  8. TAF10 and TAF10b partially redundant roles during Drosophila melanogaster morphogenesis.

    Science.gov (United States)

    Pahi, Z; Borsos, B N; Vedelek, B; Shidlovskii, Y V; Georgieva, S G; Boros, I M; Pankotai, T

    2017-01-01

    Transcription of eukaryotic genes requires the cooperative action of the RNA polymerase complex, the general transcription factors (TFIIB, TFIID, TFIIE, TFIIF and TFIIH) and chromatin modifiers. The TFIID complex contributes to transcriptional activation by several mechanisms and has a subunit with associated histone acetyltransferase (HAT) activity. The histone modifier SAGA complex has both HAT and deubiquitylase (DUB) activities. TFIID and SAGA share several TBP-associated factors (TAFs), but not their HAT subunit. Recently, several duplicated TAF proteins have been identified in higher eukaryotes, but their functional diversity has been so far poorly characterized. Here, we report the functional similarities and differences of TAF10 and TAF10b, the two TAF10 orthologs of Drosophila melanogaster. Results from in silico modeling suggest that dTAF10 and dTAF10b have similar secondary structures characterized by the presence of a histone-fold domain. Additionally, dTAF10 and dTAF10b share interaction partners and show similar expression patterns in neuronal tissues. Nonetheless, dTAF10 and dTAF10b seem to have partly distinct functions. To investigate their roles, we generated dTaf10-dTaf10b double-mutants and rescued the mutant flies with transgenes, which allowed the translation of either dTAF10 or dTAF10b protein. We found that the loss of dTAF10b resulted in pupal lethality, while animals lacking dTAF10 were able to form puparium. dTaf10 mutant adults showed distorted eye morphology. During DNA repair, dTAF10 and dTAF10b act redundantly, suggesting that these proteins have distinct but partially overlapping functions.

  9. EU-Type Carbon Emissions Trade and the Distributional Impact of Overlapping Emissions Taxes

    OpenAIRE

    Thomas Eichner; Rüdiger Pethig

    2009-01-01

    The European Union fulfills its emissions reductions commitments by means of an emissions trading scheme covering some part of each member state’s economy and by national emissions control in the rest of their economies. The member states also levy energy/emissions taxes overlapping with the trading scheme. Restricting our focus on cost-effective policies, this paper investigates the distributive consequences of increasing the overlapping emissions tax that is uniform across countries. For ...

  10. A convergent overlapping domain decomposition method for total variation minimization

    KAUST Repository

    Fornasier, Massimo; Langer, Andreas; Schö nlieb, Carola-Bibiane

    2010-01-01

    In this paper we are concerned with the analysis of convergent sequential and parallel overlapping domain decomposition methods for the minimization of functionals formed by a discrepancy term with respect to the data and a total variation

  11. Comparison of partial and full nitrification processes applied for treating high-strength nitrogen wastewaters: microbial ecology through nitrous oxide production.

    Science.gov (United States)

    Ahn, Joon Ho; Kwan, Tiffany; Chandran, Kartik

    2011-04-01

    The goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N2O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. Based on sequencing of 16S rRNA and ammonia monooxygenase subunit A (amoA) genes, ammonia oxidizing bacteria (AOB) populations during full- and partial-nitrification modes were distinct from one another. The concentrations of AOB (XAOB) and their respiration rates during full- and partial-nitrification modes were statistically similar, whereas the concentrations of nitrite oxidizing bacteria (XNOB) and their respiration rates declined significantly after the switch from full- to partial-nitrification. The transition from full-nitrification to partial nitrification resulted in a protracted transient spike of nitrous oxide (N2O) and nitric oxide (NO) emissions, which later stabilized. The trends in N2O and NO emissions correlated well with trends in the expression of nirK and norB genes that code for the production of these gases in AOB. Both the transient and stabilized N2O and NO emissions during partial nitrification were statistically higher than those during steady-state full-nitrification. Based on these results, partial nitrification strategies for biological nitrogen removal, although attractive for their reduced operating costs and energy demand, may need to be optimized against the higher carbon foot-print attributed to their N2O emissions.

  12. Continuum limit of overlap valence quarks on a twisted mass sea

    International Nuclear Information System (INIS)

    Cichy, Krzysztof; Herdoiza, Gregorio; Univ. Autonoma de Madrid; Jansen, Karl

    2010-12-01

    We study a lattice QCD mixed action with overlap valence quarks on two flavours of Wilson maximally twisted mass sea quarks. Employing three different matching conditions to relate both actions to each other, we investigate the continuum limit by using three values of the lattice spacing ranging from a∼0.05 fm to 0.08 fm. A particular emphasis is put on the effect on physical observables of the topological zero modes appearing in the valence overlap operator. We estimate the region of parameter space where the contribution from these zero modes is sufficiently small such that their effects can be safely controlled and a restoration of unitarity of the mixed action in the continuum limit is reached. (orig.)

  13. Discursive Overlap and Conflictive Fragmentation of Risk and Security in the Geopolitics of Energy

    Directory of Open Access Journals (Sweden)

    Julio E. Rubio

    2013-03-01

    Full Text Available As it touches all aspects of human activity and society in general, energy has become an object of discourse. Two main discourses have formed on the use of energy: risk discourse and security discourse. While environmental changes and oil depletion continue, a new application for the term security has appeared: energy security. This concept can be interpreted within the terms of risk discourse, which is oriented towards rational consensus and decision making, or as an exercise of power, sovereignty and hegemony. The boundaries between interpretations are often unclear. Thus, in an institutional framework that has fragmented principles, norms and rules, opposing discourses will overlap. Political agents and institutions deploy strategies based on these discourses. With this overlapping of discourses, the performative powers of different institutions clash, thus creating conflictive fragmentation in a governance architecture. The purpose of this investigation is to analyze the use of, replication of, and ambiguities surrounding the concept of energy security, so as to understand how and why these discourses overlap and the profound consequences that this overlap may have for present and future energy use, environmental negotiations, and political climate.

  14. Eigenspaces of networks reveal the overlapping and hierarchical community structure more precisely

    International Nuclear Information System (INIS)

    Ma, Xiaoke; Gao, Lin; Yong, Xuerong

    2010-01-01

    Identifying community structure is fundamental for revealing the structure–functionality relationship in complex networks, and spectral algorithms have been shown to be powerful for this purpose. In a traditional spectral algorithm, each vertex of a network is embedded into a spectral space by making use of the eigenvectors of the adjacency matrix or Laplacian matrix of the graph. In this paper, a novel spectral approach for revealing the overlapping and hierarchical community structure of complex networks is proposed by not only using the eigenvalues and eigenvectors but also the properties of eigenspaces of the networks involved. This gives us a better characterization of community. We first show that the communicability between a pair of vertices can be rewritten in term of eigenspaces of a network. An agglomerative clustering algorithm is then presented to discover the hierarchical communities using the communicability matrix. Finally, these overlapping vertices are discovered with the corresponding eigenspaces, based on the fact that the vertices more densely connected amongst one another are more likely to be linked through short cycles. Compared with the traditional spectral algorithms, our algorithm can identify both the overlapping and hierarchical community without increasing the time complexity O(n 3 ), where n is the size of the network. Furthermore, our algorithm can also distinguish the overlapping vertices from bridges. The method is tested by applying it to some computer-generated and real-world networks. The experimental results indicate that our algorithm can reveal community structure more precisely than the traditional spectral approaches

  15. Pointillist, Cyclical, and Overlapping: Multidimensional Facets of Time in Online Learning

    Directory of Open Access Journals (Sweden)

    Pekka Ihanainen

    2011-11-01

    Full Text Available A linear, sequential time conception based on in-person meetings and pedagogical activities is not enough for those who practice and hope to enhance contemporary education, particularly where online interactions are concerned. In this article, we propose a new model for understanding time in pedagogical contexts. Conceptual parts of the model will be employed as a “cultural technology” to help us relate to evolving phenomena, both physical and virtual. We label these constructs as pointillist, cyclical, and overlapping times.Pointillist time and learning takes place in “dots” of actions that consist of small, discrete moments (e.g., tweeting. Producing, receiving, and sharing ideas in this context are separate points in each actor’s timeline. Cyclical time and learning emerges from intensive periods, which are highly visible in online forums. This construct reveals itself through interactions that often exist in multiple online environments. Overlapping time and learning involves various configurations of linear, pointillist, and cyclical layers, which are mainly evident through the simultaneous uses of social communication technologies.Pointillist, cyclical, and overlapping time constructs enable new orientations for conceptualizing time in pedagogy. In this article we also introduce de-, re-, and en- modes of these pedagogies that connect with approaches to meet the needs of learners for individualization, personalization, and cyborgization.

  16. Mixing phases of unstable two-level systems

    International Nuclear Information System (INIS)

    Sokolov, V.V.; Brentano, P. von.

    1993-01-01

    An unstable two-level system decaying into an arbitrary number of channels is considered. It is shown that the mixing phases of the two overlapping resonances can be expressed in the terms of their partial widths and one additional universal mixing parameter. Some applications to a doublet of 2 + resonances in 8 Be and to the ρ-ω systems are considered. 18 refs

  17. Application of the Chimera overlapped grid scheme to simulation of Space Shuttle ascent flows

    Science.gov (United States)

    Buning, Pieter G.; Parks, Steven J.; Chan, William M.; Renze, Kevin J.

    1992-01-01

    Several issues relating to the application of Chimera overlapped grids to complex geometries and flowfields are discussed. These include the addition of geometric components with different grid topologies, gridding for intersecting pieces of geometry, and turbulence modeling in grid overlap regions. Sample results are presented for transonic flow about the Space Shuttle launch vehicle. Comparisons with wind tunnel and flight measured pressures are shown.

  18. Experts' understanding of partial derivatives using the Partial Derivative Machine

    OpenAIRE

    Roundy, David; Dorko, Allison; Dray, Tevian; Manogue, Corinne A.; Weber, Eric

    2014-01-01

    Partial derivatives are used in a variety of different ways within physics. Most notably, thermodynamics uses partial derivatives in ways that students often find confusing. As part of a collaboration with mathematics faculty, we are at the beginning of a study of the teaching of partial derivatives, a goal of better aligning the teaching of multivariable calculus with the needs of students in STEM disciplines. As a part of this project, we have performed a pilot study of expert understanding...

  19. The effect of pattern overlap on the accuracy of high resolution electron backscatter diffraction measurements

    Energy Technology Data Exchange (ETDEWEB)

    Tong, Vivian, E-mail: v.tong13@imperial.ac.uk [Department of Materials, Imperial College London, Prince Consort Road, London SW7 2AZ (United Kingdom); Jiang, Jun [Department of Materials, Imperial College London, Prince Consort Road, London SW7 2AZ (United Kingdom); Wilkinson, Angus J. [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Britton, T. Ben [Department of Materials, Imperial College London, Prince Consort Road, London SW7 2AZ (United Kingdom)

    2015-08-15

    High resolution, cross-correlation-based, electron backscatter diffraction (EBSD) measures the variation of elastic strains and lattice rotations from a reference state. Regions near grain boundaries are often of interest but overlap of patterns from the two grains could reduce accuracy of the cross-correlation analysis. To explore this concern, patterns from the interior of two grains have been mixed to simulate the interaction volume crossing a grain boundary so that the effect on the accuracy of the cross correlation results can be tested. It was found that the accuracy of HR-EBSD strain measurements performed in a FEG-SEM on zirconium remains good until the incident beam is less than 18 nm from a grain boundary. A simulated microstructure was used to measure how often pattern overlap occurs at any given EBSD step size, and a simple relation was found linking the probability of overlap with step size. - Highlights: • Pattern overlap occurs at grain boundaries and reduces HR-EBSD accuracy. • A test is devised to measure the accuracy of HR-EBSD in the presence of overlap. • High pass filters can sometimes, but not generally, improve HR-EBSD measurements. • Accuracy of HR-EBSD remains high until the reference pattern intensity is <72%. • 9% of points near a grain boundary will have significant error for 200nm step size in Zircaloy-4.

  20. Idiopathic Inflammatory Myopathies; Association with Overlap Myositis and Syndromes: Classification, Clinical Characteristics, and Associated Autoantibodies

    Directory of Open Access Journals (Sweden)

    Pari Basharat

    2016-07-01

    Full Text Available Idiopathic inflammatory myopathies (IIM are traditionally identified as a group of disorders that target skeletal muscle due to autoimmune dysfunction. The IIM can be divided into subtypes based on certain clinical characteristics, and several classification schemes have been proposed. The predominant diagnostic criteria for IIM is the Bohan and Peter criteria, which subdivides IIM into primary polymyositis (PM, primary dermatomyositis (DM, myositis with another connective tissue disease, and myositis associated with cancer. However, this measure has been criticised for several reasons including lack of specific criteria to help distinguish between muscle biopsy findings of PM, DM, and immune-mediated necrotising myopathy, as well as the lack of identification of cases of overlap myositis (OM. Because of this issue, other classification criteria for IIM have been proposed, which include utilising myositis-associated antibodies and myositis-specific antibodies, as well as overlap features such as Raynaud’s phenomenon, polyarthritis, oesophageal abnormalities, interstitial lung disease, small bowel abnormalities such as hypomotility and malabsorption, and renal crises, amongst others. Indeed, the identification of autoantibodies associated with certain clinical phenotypes of myositis, in particular connective tissue disease-myositis overlap, has further helped divide IIM into distinct clinical subsets, which include OM and overlap syndromes (OS. This paper reviews the concepts of OM and OS as they pertain to IIM, including definitions in the literature, clinical characteristics, and overlap autoantibodies.

  1. Overlapping double potential wells in a single optical microtube cavity with vernier-scale-like tuning effect

    International Nuclear Information System (INIS)

    Madani, A.; Schmidt, O. G.; Bolaños Quiñones, V. A.; Ma, L. B.; Jorgensen, M. R.; Miao, S. D.

    2016-01-01

    Spatially and temporally overlapping double potential wells are realized in a hybrid optical microtube cavity due to the coexistence of an aggregate of luminescent quantum dots embedded in the tube wall and the cone-shaped tube's geometry. The double potential wells produce two independent sets of optical modes with different sets of mode numbers, indicating phase velocity separation for the modes overlapping at the same frequency. The overlapping mode position can be tuned by modifying the tube cavity, where these mode sets shift with different magnitudes, allowing for a vernier-scale-like tuning effect.

  2. [Primary biliary cirrhosis-autoimmune hepatitis overlap syndrome. Contribution of two new cases].

    Science.gov (United States)

    Fernández Fernández, F J; de la Fuente Aguado, J; Pérez Fernández, S; Sopeña Pérez-Argüelles, B; Nodar Germiñas, A; Butrón Vila, M

    2005-03-01

    The autoimmune hepatitis (AIH)-primary biliary cirrhosis (PBC) overlap syndrome is characterized for clinical, biochemical, immunological, and histological features overlapping those of AIH and PBC, whose pathogenesis and more appropriate treatment are unknown at present. We describe two new patients of this entity, which made debut with cholestasic acute hepatitis accompanied of hypergammaglobulinemia. In the first patient was demonstrated the presence of AMA, ASMA, and anti-LKM1 autoantibodies; and ANA in the second one. The histological findings showed changes suggestive of AIH and PBC. After the start of immunosuppressive treatment, associated to ursodeoxycholic acid in one patient, a successful outcome was observed.

  3. Ras proteins have multiple functions in vegetative cells of Dictyostelium.

    Science.gov (United States)

    Bolourani, Parvin; Spiegelman, George; Weeks, Gerald

    2010-11-01

    During the aggregation of Dictyostelium cells, signaling through RasG is more important in regulating cyclic AMP (cAMP) chemotaxis, whereas signaling through RasC is more important in regulating the cAMP relay. However, RasC is capable of substituting for RasG for chemotaxis, since rasG⁻ cells are only partially deficient in chemotaxis, whereas rasC⁻/rasG⁻ cells are totally incapable of chemotaxis. In this study we have examined the possible functional overlap between RasG and RasC in vegetative cells by comparing the vegetative cell properties of rasG⁻, rasC⁻, and rasC⁻/rasG⁻ cells. In addition, since RasD, a protein not normally found in vegetative cells, is expressed in vegetative rasG⁻ and rasC⁻/rasG⁻ cells and appears to partially compensate for the absence of RasG, we have also examined the possible functional overlap between RasG and RasD by comparing the properties of rasG⁻ and rasC⁻/rasG⁻ cells with those of the mutant cells expressing higher levels of RasD. The results of these two lines of investigation show that RasD is capable of totally substituting for RasG for cytokinesis and growth in suspension, whereas RasC is without effect. In contrast, for chemotaxis to folate, RasC is capable of partially substituting for RasG, but RasD is totally without effect. Finally, neither RasC nor RasD is able to substitute for the role that RasG plays in regulating actin distribution and random motility. These specificity studies therefore delineate three distinct and none-overlapping functions for RasG in vegetative cells.

  4. Linking self and group: cognitive routes to self-group overlap as driving forces of group phenomena

    NARCIS (Netherlands)

    van Veelen, Ruth; Otten, Sabine

    2014-01-01

    Group affiliation implies that there is overlap in the mental representations of seld and group. Combining research on social cognition and group processes, this symposium brings together various perspectives on self-group overlap and its consequences for intra- and intergroup phenomena.

  5. Partial molar volumes of L-alanine, DL-serine, DL-threonine, L-histidine, glycine, and glycylglycine in water, NaCl, and DMSO aqueous solutions at T 298.15 K

    International Nuclear Information System (INIS)

    Yuan Quan; Li Zhifen; Wang Baohuai

    2006-01-01

    The apparent molar volumes of L-alanine, DL-serine, DL-threonine, L-histidine, glycine, and glycylglycine in water and in the aqueous solutions of NaCl and DMSO with various concentrations at T = 298.15 K have been measured by the precise vibrating-tube digital densimeter. The calculated partial molar volumes at infinite dilution have been used to obtain corresponding transfer volumes from water to various solutions. The experimental results show that the standard partial molar volumes of the above amino acids and peptide at the dilute DMSO aqueous solutions are very close to those in water. However, the volumes show several types of variations with the increase of the concentrations of DMSO due to different types of side chain of amino acids, which should be discussed specifically. The NaCl changes considerably the infinite dilution standard partial molar volumes of the above amino acids and peptide in the aqueous solutions. The infinite dilution standard partial molar volumes of the each amino acids and peptide increase with the concentrations of NaCl. The experimental results have been rationalized by a cosphere overlap model

  6. Evidence for an Overlapping Role of CLOCK and NPAS2 Transcription Factors in Liver Circadian Oscillators▿

    Science.gov (United States)

    Bertolucci, Cristiano; Cavallari, Nicola; Colognesi, Ilaria; Aguzzi, Jacopo; Chen, Zheng; Caruso, Pierpaolo; Foá, Augusto; Tosini, Gianluca; Bernardi, Francesco; Pinotti, Mirko

    2008-01-01

    The mechanisms underlying the circadian control of gene expression in peripheral tissues and influencing many biological pathways are poorly defined. Factor VII (FVII), the protease triggering blood coagulation, represents a valuable model to address this issue in liver since its plasma levels oscillate in a circadian manner and its promoter contains E-boxes, which are putative DNA-binding sites for CLOCK-BMAL1 and NPAS2-BMAL1 heterodimers and hallmarks of circadian regulation. The peaks of FVII mRNA levels in livers of wild-type mice preceded those in plasma, indicating a transcriptional regulation, and were abolished in Clock−/−; Npas2−/− mice, thus demonstrating a role for CLOCK and NPAS2 circadian transcription factors. The investigation of Npas2−/− and ClockΔ19/Δ19 mice, which express functionally defective heterodimers, revealed robust rhythms of FVII expression in both animal models, suggesting a redundant role for NPAS2 and CLOCK. The molecular bases of these observations were established through reporter gene assays. FVII transactivation activities of the NPAS2-BMAL1 and CLOCK-BMAL1 heterodimers were (i) comparable (a fourfold increase), (ii) dampened by the negative circadian regulators PER2 and CRY1, and (iii) abolished upon E-box mutagenesis. Our data provide the first evidence in peripheral oscillators for an overlapping role of CLOCK and NPAS2 in the regulation of circadianly controlled genes. PMID:18316400

  7. Expression of background potassium channels in rat DRG is cell-specific and down-regulated in a neuropathic pain model.

    Science.gov (United States)

    Pollema-Mays, Sarah L; Centeno, Maria Virginia; Ashford, Crystle J; Apkarian, A Vania; Martina, Marco

    2013-11-01

    Neuropathic pain is associated with hyperexcitability of DRG neurons. Despite the importance of leakage potassium channels for neuronal excitability, little is known about their cell-specific expression in DRGs and possible modulation in neuropathic pain. Multiple leakage channels are expressed in DRG neurons, including TASK1, TASK3, TRESK, TRAAK, TWIK1, TREK1 and TREK2 but little is known about their distribution among different cell types. Our immunohistochemical studies show robust TWIK1 expression in large and medium size neurons, without overlap with TRPV1 or IB4 staining. TASK1 and TASK3, on the contrary, are selectively expressed in small cells; TASK1 expression closely overlaps TRPV1-positive cells, while TASK3 is expressed in TRPV1- and IB4-negative cells. We also studied mRNA expression of these channels in L4-L5 DRGs in control conditions and up to 4 weeks after spared nerve injury lesion. We found that TWIK1 expression is much higher than TASK1 and TASK3 and is strongly decreased 1, 2 and 4 weeks after neuropathic injury. TASK3 expression, on the other hand, decreases 1 week after surgery but reverts to baseline by 2weeks; TASK1 shows no significant change at any time point. These data suggest an involvement of TWIK1 in the maintenance of the pain condition. © 2013.

  8. The impact of atmospheric stability and wind shear on vertical cloud overlap over the Tibetan Plateau

    Directory of Open Access Journals (Sweden)

    J. Li

    2018-05-01

    Full Text Available Studies have shown that changes in cloud cover are responsible for the rapid climate warming over the Tibetan Plateau (TP in the past 3 decades. To simulate the total cloud cover, atmospheric models have to reasonably represent the characteristics of vertical overlap between cloud layers. Until now, however, this subject has received little attention due to the limited availability of observations, especially over the TP. Based on the above information, the main aim of this study is to examine the properties of cloud overlaps over the TP region and to build an empirical relationship between cloud overlap properties and large-scale atmospheric dynamics using 4 years (2007–2010 of data from the CloudSat cloud product and collocated ERA-Interim reanalysis data. To do this, the cloud overlap parameter α, which is an inverse exponential function of the cloud layer separation D and decorrelation length scale L, is calculated using CloudSat and is discussed. The parameters α and L are both widely used to characterize the transition from the maximum to random overlap assumption with increasing layer separations. For those non-adjacent layers without clear sky between them (that is, contiguous cloud layers, it is found that the overlap parameter α is sensitive to the unique thermodynamic and dynamic environment over the TP, i.e., the unstable atmospheric stratification and corresponding weak wind shear, which leads to maximum overlap (that is, greater α values. This finding agrees well with the previous studies. Finally, we parameterize the decorrelation length scale L as a function of the wind shear and atmospheric stability based on a multiple linear regression. Compared with previous parameterizations, this new scheme can improve the simulation of total cloud cover over the TP when the separations between cloud layers are greater than 1 km. This study thus suggests that the effects of both wind shear and atmospheric stability on cloud overlap

  9. The impact of atmospheric stability and wind shear on vertical cloud overlap over the Tibetan Plateau

    Science.gov (United States)

    Li, Jiming; Lv, Qiaoyi; Jian, Bida; Zhang, Min; Zhao, Chuanfeng; Fu, Qiang; Kawamoto, Kazuaki; Zhang, Hua

    2018-05-01

    Studies have shown that changes in cloud cover are responsible for the rapid climate warming over the Tibetan Plateau (TP) in the past 3 decades. To simulate the total cloud cover, atmospheric models have to reasonably represent the characteristics of vertical overlap between cloud layers. Until now, however, this subject has received little attention due to the limited availability of observations, especially over the TP. Based on the above information, the main aim of this study is to examine the properties of cloud overlaps over the TP region and to build an empirical relationship between cloud overlap properties and large-scale atmospheric dynamics using 4 years (2007-2010) of data from the CloudSat cloud product and collocated ERA-Interim reanalysis data. To do this, the cloud overlap parameter α, which is an inverse exponential function of the cloud layer separation D and decorrelation length scale L, is calculated using CloudSat and is discussed. The parameters α and L are both widely used to characterize the transition from the maximum to random overlap assumption with increasing layer separations. For those non-adjacent layers without clear sky between them (that is, contiguous cloud layers), it is found that the overlap parameter α is sensitive to the unique thermodynamic and dynamic environment over the TP, i.e., the unstable atmospheric stratification and corresponding weak wind shear, which leads to maximum overlap (that is, greater α values). This finding agrees well with the previous studies. Finally, we parameterize the decorrelation length scale L as a function of the wind shear and atmospheric stability based on a multiple linear regression. Compared with previous parameterizations, this new scheme can improve the simulation of total cloud cover over the TP when the separations between cloud layers are greater than 1 km. This study thus suggests that the effects of both wind shear and atmospheric stability on cloud overlap should be taken into

  10. The broad-band overlap problem in atmospheric trace gases

    International Nuclear Information System (INIS)

    Subasilar, B.

    1991-01-01

    In relation to a better understanding of climate change and the related greenhouse problem, one way of projecting for the next decades is through general circulation models (GCMs). The only input as a driving force in the changing atmospheric and oceanic circulation patterns is the amount of heat perturbation either due to natural or man-caused activities. Among these, CO 2 concentrations resulting from the latter has been observed to be accelerating at alarmingly high rates especially after the advent of the industrialization which just began in the last century. In addition to that, collective effects of other greenhouse gases (freons, SO 2 , H 2 O, CH 4 , etc.) are as important as CO 2 . Hence, it is evident from the above considerations that, in the predictions of climate models, the heat input which triggers changes in the atmospheric patterns, should be formulated accurately. In order to realize this objective, in this research, beginning with the available line parameter data, the problems of absorption have been investigated and attacked in the frame known as the broad band modeling since that is the only best and fastest manageable representation for GCMs. The first step was the construction of a full broad band (intra band overlap) model that was also flexible enough to accommodate the individual peculiarities of the bands. Before, the well known and very useful Ramanathan model had a limited applicability in the concentration scale, and it was also not systematically or successfully incorporated into an inter band overlap picture. Then, the established ideas that served as bases up to present, have been employed but found to have a limited practical applicability when it came to predict the inter band overlaps

  11. Overlap knock-out effects in the CERN intersecting storage rings (ISR)

    CERN Document Server

    Gourber, J P; Myers, S

    1977-01-01

    Overlap knock-out arises from an overlap between frequencies present in a bunched beam and the betatron frequencies in a stack. The 'single ring' effect in the interaction of a bunched beam with a stack in the same ring. Here the coupling forces are fairly linear and are transmitted by machine elements. The 'two-ring' effect is the interaction of a bunched beam with a stack in the other ring. Here the coupling forces are nonlinear since they are produced by the beam-beam interaction. A brief outline of the general theory of these effects is given. The single ring and two-ring dipole effects have been observed and shown to cause a large increase in the transverse size of the stacked beam. (4 refs).

  12. Continuum limit of overlap valence quarks on a twisted mass sea

    Energy Technology Data Exchange (ETDEWEB)

    Cichy, Krzysztof [Adam Mickiewicz Univ., Poznan (Poland). Faculty of Physics; Herdoiza, Gregorio [DESY, Zeuthen (Germany). John von Neumann-Institut fuer Computing NIC; Univ. Autonoma de Madrid (Spain). Dept. de Fisica Teorica; Jansen, Karl [DESY, Zeuthen (Germany). John von Neumann-Institut fuer Computing NIC

    2010-12-15

    We study a lattice QCD mixed action with overlap valence quarks on two flavours of Wilson maximally twisted mass sea quarks. Employing three different matching conditions to relate both actions to each other, we investigate the continuum limit by using three values of the lattice spacing ranging from a{approx}0.05 fm to 0.08 fm. A particular emphasis is put on the effect on physical observables of the topological zero modes appearing in the valence overlap operator. We estimate the region of parameter space where the contribution from these zero modes is sufficiently small such that their effects can be safely controlled and a restoration of unitarity of the mixed action in the continuum limit is reached. (orig.)

  13. The effects of reverberant self- and overlap-masking on speech recognition in cochlear implant listeners.

    Science.gov (United States)

    Desmond, Jill M; Collins, Leslie M; Throckmorton, Chandra S

    2014-06-01

    Many cochlear implant (CI) listeners experience decreased speech recognition in reverberant environments [Kokkinakis et al., J. Acoust. Soc. Am. 129(5), 3221-3232 (2011)], which may be caused by a combination of self- and overlap-masking [Bolt and MacDonald, J. Acoust. Soc. Am. 21(6), 577-580 (1949)]. Determining the extent to which these effects decrease speech recognition for CI listeners may influence reverberation mitigation algorithms. This study compared speech recognition with ideal self-masking mitigation, with ideal overlap-masking mitigation, and with no mitigation. Under these conditions, mitigating either self- or overlap-masking resulted in significant improvements in speech recognition for both normal hearing subjects utilizing an acoustic model and for CI listeners using their own devices.

  14. Developmental expression of "germline"- and "sex determination"-related genes in the ctenophore Mnemiopsis leidyi.

    Science.gov (United States)

    Reitzel, Adam M; Pang, Kevin; Martindale, Mark Q

    2016-01-01

    An essential developmental pathway in sexually reproducing animals is the specification of germ cells and the differentiation of mature gametes, sperm and oocytes. The "germline" genes vasa, nanos and piwi are commonly identified in primordial germ cells, suggesting a molecular signature for the germline throughout animals. However, these genes are also expressed in a diverse set of somatic stem cells throughout the animal kingdom leaving open significant questions for whether they are required for germline specification. Similarly, members of the Dmrt gene family are essential components regulating sex determination and differentiation in bilaterian animals, but the functions of these transcription factors, including potential roles in sex determination, in early diverging animals remain unknown. The phylogenetic position of ctenophores and the genome sequence of the lobate Mnemiopsis leidyi motivated us to determine the compliment of these gene families in this species and determine expression patterns during development. Our phylogenetic analyses of the vasa, piwi and nanos gene families show that Mnemiopsis has multiple genes in each family with multiple lineage-specific paralogs. Expression domains of Mnemiopsis nanos, vasa and piwi, during embryogenesis from fertilization to the cydippid stage, were diverse, with little overlapping expression and no or little expression in what we think are the germ cells or gametogenic regions. piwi paralogs in Mnemiopsis had distinct expression domains in the ectoderm during development. We observed overlapping expression domains in the apical organ and tentacle apparatus of the cydippid for a subset of "germline genes," which are areas of high cell proliferation, suggesting that these genes are involved with "stem cell" specification and maintenance. Similarly, the five Dmrt genes show diverse non-overlapping expression domains, with no clear evidence for expression in future gametogenic regions of the adult. We also

  15. Contrasting seasonal overlaps between primary and secondary growth are linked to wood anatomy in Mediterranean sub-shrubs.

    Science.gov (United States)

    Camarero, J J; Palacio, S; Montserrat-Martí, G

    2013-09-01

    Whole-plant approaches allow quantification of the temporal overlap between primary and secondary growth. If the amount of time available to grow is short, there may be a high temporal overlap between shoot growth and wood formation. We hypothesise that such overlap depends on the duration of the growing season and relates to wood anatomy. We evaluated wood anatomy, shoot longitudinal and radial growth rates, fine root production and the concentrations of non-structural carbohydrates (NSC) in the wood of six sub-shrub species growing in sites with contrasting climatic conditions (Lepidium subulatum, Linum suffruticosum, Salvia lavandulifolia, Satureja montana, Ononis fruticosa, Echinospartum horridum). Sub-shrub species living in sites with a short growing season displayed a high overlap between aboveground primary and secondary growth and formed wide vessels, whereas species from the warmest and driest sites presented the reverse characteristics. The highest overlap was linked to a rapid shoot extension and thickening through the enhanced hydraulic conductivity provided by wide vessels. The reductions in NSC concentrations when growth peaked were low or moderate, indicating that sub-shrubs accumulate NSC in excess, as do trees. The temporal overlap among primary and secondary growth in woody plants may be connected to the duration and rates of shoot and wood growth, which in turn depend on the vessel lumen area. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  16. A model for evolution of overlapping community networks

    Science.gov (United States)

    Karan, Rituraj; Biswal, Bibhu

    2017-05-01

    A model is proposed for the evolution of network topology in social networks with overlapping community structure. Starting from an initial community structure that is defined in terms of group affiliations, the model postulates that the subsequent growth and loss of connections is similar to the Hebbian learning and unlearning in the brain and is governed by two dominant factors: the strength and frequency of interaction between the members, and the degree of overlap between different communities. The temporal evolution from an initial community structure to the current network topology can be described based on these two parameters. It is possible to quantify the growth occurred so far and predict the final stationary state to which the network is likely to evolve. Applications in epidemiology or the spread of email virus in a computer network as well as finding specific target nodes to control it are envisaged. While facing the challenge of collecting and analyzing large-scale time-resolved data on social groups and communities one faces the most basic questions: how do communities evolve in time? This work aims to address this issue by developing a mathematical model for the evolution of community networks and studying it through computer simulation.

  17. Decoupling of a tight-fit transceiver phased array for human brain imaging at 9.4T: Loop overlapping rediscovered.

    Science.gov (United States)

    Avdievich, Nikolai I; Giapitzakis, Ioannis-Angelos; Pfrommer, Andreas; Henning, Anke

    2018-02-01

    To improve the decoupling of a transceiver human head phased array at ultra-high fields (UHF, ≥ 7T) and to optimize its transmit (Tx) and receive (Rx) performance, a single-row eight-element (1 × 8) tight-fit transceiver overlapped loop array was developed and constructed. Overlapping the loops increases the RF field penetration depth but can compromise decoupling by generating substantial mutual resistance. Based on analytical modeling, we optimized the loop geometry and relative positioning to simultaneously minimize the resistive and inductive coupling and constructed a 9.4T eight-loop transceiver head phased array decoupled entirely by overlapping loops. We demonstrated that both the magnetic and electric coupling between adjacent loops is compensated at the same time by overlapping and nearly perfect decoupling (below -30 dB) can be obtained without additional decoupling strategies. Tx-efficiency and SNR of the overlapped array outperformed that of a common UHF gapped array of similar dimensions. Parallel Rx-performance was also not compromised due to overlapping the loops. As a proof of concept we developed and constructed a 9.4T (400 MHz) overlapped transceiver head array based on results of the analytical modeling. We demonstrated that at UHF overlapping loops not only provides excellent decoupling but also improves both Tx- and Rx-performance. Magn Reson Med 79:1200-1211, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  18. Partial androgen deficiency, depression and testosterone treatment in aging men.

    Science.gov (United States)

    Amore, Mario; Scarlatti, Fabiano; Quarta, Antonio Lucio; Tagariello, Pietro

    2009-02-01

    This study provides a critical review of the literature on depressive symptoms of partial androgen deficiency (PADAM) and their treatment with Testosterone (T). PADAM in aging males is responsible for a variety of behavioral symptoms, such as weakness, decreased libido and erectile dysfunction, lower psychological vitality, depressive mood, anxiety, insomnia, difficulty in concentrating, and memory impairment. The psychological and behavioural aspects of PADAM may overlap with signs and symptoms of major depression. Evidence of the relationship between androgen deficiency and male depression comes from studies that have assessed depression in hypogonadal subjects, the association between low T level and male depressive illness, and the antidepressant action of androgen replacement. The etiology of depressive symptoms of PADAM is multifactorial, and results from the interaction of the biological and psychosocial changes that take place during the mid-life transition. Although data derived from androgen treatment trials and androgen replacement do not support T treatment or replacement as more efficacious than placebo for major depressive disorder (MDD), the clinical impression is that, in some sub-threshold depressive syndromes, T may lead to antidepressant benefits.

  19. Metastatic canine mammary carcinomas can be identified by a gene expression profile that partly overlaps with human breast cancer profiles

    International Nuclear Information System (INIS)

    Klopfleisch, Robert; Lenze, Dido; Hummel, Michael; Gruber, Achim D

    2010-01-01

    Similar to human breast cancer mammary tumors of the female dog are commonly associated with a fatal outcome due to the development of distant metastases. However, the molecular defects leading to metastasis are largely unknown and the value of canine mammary carcinoma as a model for human breast cancer is unclear. In this study, we analyzed the gene expression signatures associated with mammary tumor metastasis and asked for parallels with the human equivalent. Messenger RNA expression profiles of twenty-seven lymph node metastasis positive or negative canine mammary carcinomas were established by microarray analysis. Differentially expressed genes were functionally characterized and associated with molecular pathways. The findings were also correlated with published data on human breast cancer. Metastatic canine mammary carcinomas had 1,011 significantly differentially expressed genes when compared to non-metastatic carcinomas. Metastatic carcinomas had a significant up-regulation of genes associated with cell cycle regulation, matrix modulation, protein folding and proteasomal degradation whereas cell differentiation genes, growth factor pathway genes and regulators of actin organization were significantly down-regulated. Interestingly, 265 of the 1,011 differentially expressed canine genes are also related to human breast cancer and, vice versa, parts of a human prognostic gene signature were identified in the expression profiles of the metastatic canine tumors. Metastatic canine mammary carcinomas can be discriminated from non-metastatic carcinomas by their gene expression profiles. More than one third of the differentially expressed genes are also described of relevance for human breast cancer. Many of the differentially expressed genes are linked to functions and pathways which appear to be relevant for the induction and maintenance of metastatic progression and may represent new therapeutic targets. Furthermore, dogs are in some aspects suitable as a

  20. Overlapping double potential wells in a single optical microtube cavity with vernier-scale-like tuning effect

    Energy Technology Data Exchange (ETDEWEB)

    Madani, A.; Schmidt, O. G. [Institute for Integrative Nanosciences, IFW Dresden, Helmholtzstr. 20, 01069 Dresden (Germany); Material Systems for Nanoelectronics, Chemnitz University of Technology, Reichenhainer Str. 70, 09107 Chemnitz (Germany); Bolaños Quiñones, V. A.; Ma, L. B., E-mail: l.ma@ifw-dresden.de; Jorgensen, M. R. [Institute for Integrative Nanosciences, IFW Dresden, Helmholtzstr. 20, 01069 Dresden (Germany); Miao, S. D. [Anhui Key Lab of Controllable Chemical Reaction and Material Chemical Engineering, School of Chemical Engineering, Hefei University of Technology, Tunxi Road. 193, Hefei, Anhui 230009 (China)

    2016-04-25

    Spatially and temporally overlapping double potential wells are realized in a hybrid optical microtube cavity due to the coexistence of an aggregate of luminescent quantum dots embedded in the tube wall and the cone-shaped tube's geometry. The double potential wells produce two independent sets of optical modes with different sets of mode numbers, indicating phase velocity separation for the modes overlapping at the same frequency. The overlapping mode position can be tuned by modifying the tube cavity, where these mode sets shift with different magnitudes, allowing for a vernier-scale-like tuning effect.

  1. Contributions of Medial Temporal Lobe and Striatal Memory Systems to Learning and Retrieving Overlapping Spatial Memories

    Science.gov (United States)

    Brown, Thackery I.; Stern, Chantal E.

    2014-01-01

    Many life experiences share information with other memories. In order to make decisions based on overlapping memories, we need to distinguish between experiences to determine the appropriate behavior for the current situation. Previous work suggests that the medial temporal lobe (MTL) and medial caudate interact to support the retrieval of overlapping navigational memories in different contexts. The present study used functional magnetic resonance imaging (fMRI) in humans to test the prediction that the MTL and medial caudate play complementary roles in learning novel mazes that cross paths with, and must be distinguished from, previously learned routes. During fMRI scanning, participants navigated virtual routes that were well learned from prior training while also learning new mazes. Critically, some routes learned during scanning shared hallways with those learned during pre-scan training. Overlap between mazes required participants to use contextual cues to select between alternative behaviors. Results demonstrated parahippocampal cortex activity specific for novel spatial cues that distinguish between overlapping routes. The hippocampus and medial caudate were active for learning overlapping spatial memories, and increased their activity for previously learned routes when they became context dependent. Our findings provide novel evidence that the MTL and medial caudate play complementary roles in the learning, updating, and execution of context-dependent navigational behaviors. PMID:23448868

  2. Decomposition and correction overlapping peaks of LIBS using an error compensation method combined with curve fitting.

    Science.gov (United States)

    Tan, Bing; Huang, Min; Zhu, Qibing; Guo, Ya; Qin, Jianwei

    2017-09-01

    The laser induced breakdown spectroscopy (LIBS) technique is an effective method to detect material composition by obtaining the plasma emission spectrum. The overlapping peaks in the spectrum are a fundamental problem in the qualitative and quantitative analysis of LIBS. Based on a curve fitting method, this paper studies an error compensation method to achieve the decomposition and correction of overlapping peaks. The vital step is that the fitting residual is fed back to the overlapping peaks and performs multiple curve fitting processes to obtain a lower residual result. For the quantitative experiments of Cu, the Cu-Fe overlapping peaks in the range of 321-327 nm obtained from the LIBS spectrum of five different concentrations of CuSO 4 ·5H 2 O solution were decomposed and corrected using curve fitting and error compensation methods. Compared with the curve fitting method, the error compensation reduced the fitting residual about 18.12-32.64% and improved the correlation about 0.86-1.82%. Then, the calibration curve between the intensity and concentration of the Cu was established. It can be seen that the error compensation method exhibits a higher linear correlation between the intensity and concentration of Cu, which can be applied to the decomposition and correction of overlapping peaks in the LIBS spectrum.

  3. Trophodynamics and diet overlap of small pelagic fish species in the Bay of Biscay

    KAUST Repository

    Bachiller, E

    2015-08-27

    Small pelagic fish are the link between planktonic production and higher trophic levels. Competition for resources may play a role in the population dynamics of species, some of them probably standing out from the others due to greater feeding success. It is therefore important to understand the trophic niche of species overlapping both spatially and temporally. In this study, we have investigated the diet, prey preference, trophic niche breadth and diet overlap of the 8 major small pelagic species (anchovy, sardine, sprat, Atlantic and Mediterranean horse mackerel, bogue, Atlantic mackerel and Atlantic chub mackerel) inhabiting the Bay of Biscay. Results indicate that all fish feed mainly on calanoid copepods, incorporating larger prey like euphausiids and decapods to complete their diet. Differences in ingested prey diversity seem to be more limited by the available zooplankton at sea than by a specific diet preference by fish species, resulting in an overall high diet overlap, especially within clupeids but also between clupeids and other (larger) predator species. Consumption estimations for different prey groups could therefore determine whether such a large diet overlap between small pelagic fish, together with spatial co-occurrence, results in competition or enhances the effects of intraguild predation, which is important in terms of an ecosystem approach to fisheries management.

  4. Trophodynamics and diet overlap of small pelagic fish species in the Bay of Biscay

    KAUST Repository

    Bachiller, E; Irigoien, Xabier

    2015-01-01

    Small pelagic fish are the link between planktonic production and higher trophic levels. Competition for resources may play a role in the population dynamics of species, some of them probably standing out from the others due to greater feeding success. It is therefore important to understand the trophic niche of species overlapping both spatially and temporally. In this study, we have investigated the diet, prey preference, trophic niche breadth and diet overlap of the 8 major small pelagic species (anchovy, sardine, sprat, Atlantic and Mediterranean horse mackerel, bogue, Atlantic mackerel and Atlantic chub mackerel) inhabiting the Bay of Biscay. Results indicate that all fish feed mainly on calanoid copepods, incorporating larger prey like euphausiids and decapods to complete their diet. Differences in ingested prey diversity seem to be more limited by the available zooplankton at sea than by a specific diet preference by fish species, resulting in an overall high diet overlap, especially within clupeids but also between clupeids and other (larger) predator species. Consumption estimations for different prey groups could therefore determine whether such a large diet overlap between small pelagic fish, together with spatial co-occurrence, results in competition or enhances the effects of intraguild predation, which is important in terms of an ecosystem approach to fisheries management.

  5. Simplicity of state and overlap structure in finite-volume realistic spin glasses

    International Nuclear Information System (INIS)

    Newman, C.M.; Stein, D.L.

    1998-01-01

    We present a combination of heuristic and rigorous arguments indicating that both the pure state structure and the overlap structure of realistic spin glasses should be relatively simple: in a large finite volume with coupling-independent boundary conditions, such as periodic, at most a pair of flip-related (or the appropriate number of symmetry-related in the non-Ising case) states appear, and the Parisi overlap distribution correspondingly exhibits at most a pair of δ functions at ±q EA . This rules out the nonstandard mean-field picture introduced by us earlier, and when combined with our previous elimination of more standard versions of the mean-field picture, argues against the possibility of even limited versions of mean-field ordering in realistic spin glasses. If broken spin-flip symmetry should occur, this leaves open two main possibilities for ordering in the spin glass phase: the droplet-scaling two-state picture, and the chaotic pairs many-state picture introduced by us earlier. We present scaling arguments which provide a possible physical basis for the latter picture, and discuss possible reasons behind numerical observations of more complicated overlap structures in finite volumes. copyright 1998 The American Physical Society

  6. Methylphenidate and Atomoxetine-Responsive Prefrontal Cortical Genetic Overlaps in "Impulsive" SHR/NCrl and Wistar Rats.

    Science.gov (United States)

    Dela Peña, Ike; Dela Peña, Irene Joy; de la Peña, June Bryan; Kim, Hee Jin; Shin, Chan Young; Han, Doug Hyun; Kim, Bung-Nyun; Ryu, Jong Hoon; Cheong, Jae Hoon

    2017-09-01

    Impulsivity, the predisposition to act prematurely without foresight, is associated with a number of neuropsychiatric disorders, including attention-deficit/hyperactivity disorder (ADHD). Identifying genetic underpinnings of impulsive behavior may help decipher the complex etiology and neurobiological factors of disorders marked by impulsivity. To identify potential genetic factors of impulsivity, we examined common differentially expressed genes (DEGs) in the prefrontal cortex (PFC) of adolescent SHR/NCrl and Wistar rats, which showed marked decrease in preference for the large but delayed reward, compared with WKY/NCrl rats, in the delay discounting task. Of these DEGs, we examined drug-responsive transcripts whose mRNA levels were altered following treatment (in SHR/NCrl and Wistar rats) with drugs that alleviate impulsivity, namely, the ADHD medications methylphenidate and atomoxetine. Prefrontal cortical genetic overlaps between SHR/NCrl and Wistar rats in comparison with WKY/NCrl included genes associated with transcription (e.g., Btg2, Fos, Nr4a2), synaptic plasticity (e.g., Arc, Homer2), and neuron apoptosis (Grik2, Nmnat1). Treatment with methylphenidate and/or atomoxetine increased choice of the large, delayed reward in SHR/NCrl and Wistar rats and changed, in varying degrees, mRNA levels of Nr4a2, Btg2, and Homer2, genes with previously described roles in neuropsychiatric disorders characterized by impulsivity. While further studies are required, we dissected potential genetic factors that may influence impulsivity by identifying genetic overlaps in the PFC of "impulsive" SHR/NCrl and Wistar rats. Notably, these are also drug-responsive transcripts which may be studied further as biomarkers to predict response to ADHD drugs, and as potential targets for the development of treatments to improve impulsivity.

  7. Computational assessment of the influence of the overlap ratio on the power characteristics of a Classical Savonius wind turbine

    Directory of Open Access Journals (Sweden)

    Kacprzak Konrad

    2015-09-01

    Full Text Available An influence of the overlap on the performance of the Classical Savonius wind turbine was investigated. Unsteady two-dimensional numerical simulations were carried out for a wide range of overlap ratios. For selected configurations computation quality was verified by comparison with three-dimensional simulations and the wind tunnel experimental data available in literature. A satisfactory agreement was achieved. Power characteristics were determined for all the investigated overlap ratios for selected tip speed ratios. Obtained results indicate that the maximum device performance is achieved for the buckets overlap ratio close to 0.

  8. Partially blind instantly decodable network codes for lossy feedback environment

    KAUST Repository

    Sorour, Sameh

    2014-09-01

    In this paper, we study the multicast completion and decoding delay minimization problems for instantly decodable network coding (IDNC) in the case of lossy feedback. When feedback loss events occur, the sender falls into uncertainties about packet reception at the different receivers, which forces it to perform partially blind selections of packet combinations in subsequent transmissions. To determine efficient selection policies that reduce the completion and decoding delays of IDNC in such an environment, we first extend the perfect feedback formulation in our previous works to the lossy feedback environment, by incorporating the uncertainties resulting from unheard feedback events in these formulations. For the completion delay problem, we use this formulation to identify the maximum likelihood state of the network in events of unheard feedback and employ it to design a partially blind graph update extension to the multicast IDNC algorithm in our earlier work. For the decoding delay problem, we derive an expression for the expected decoding delay increment for any arbitrary transmission. This expression is then used to find the optimal policy that reduces the decoding delay in such lossy feedback environment. Results show that our proposed solutions both outperform previously proposed approaches and achieve tolerable degradation even at relatively high feedback loss rates.

  9. Effects of partial slip boundary condition and radiation on the heat and mass transfer of MHD-nanofluid flow

    Science.gov (United States)

    Abd Elazem, Nader Y.; Ebaid, Abdelhalim

    2017-12-01

    In this paper, the effect of partial slip boundary condition on the heat and mass transfer of the Cu-water and Ag-water nanofluids over a stretching sheet in the presence of magnetic field and radiation. Such partial slip boundary condition has attracted much attention due to its wide applications in industry and chemical engineering. The flow is basically governing by a system of partial differential equations which are reduced to a system of ordinary differential equations. This system has been exactly solved, where exact analytical expression has been obtained for the fluid velocity in terms of exponential function, while the temperature distribution, and the nanoparticles concentration are expressed in terms of the generalized incomplete gamma function. In addition, explicit formulae are also derived from the rates of heat transfer and mass transfer. The effects of the permanent parameters on the skin friction, heat transfer coefficient, rate of mass transfer, velocity, the temperature profile, and concentration profile have been discussed through tables and graphs.

  10. Type-Directed Partial Evaluation

    DEFF Research Database (Denmark)

    Danvy, Olivier

    1998-01-01

    Type-directed partial evaluation uses a normalization function to achieve partial evaluation. These lecture notes review its background, foundations, practice, and applications. Of specific interest is the modular technique of offline and online type-directed partial evaluation in Standard ML...

  11. Type-Directed Partial Evaluation

    DEFF Research Database (Denmark)

    Danvy, Olivier

    1998-01-01

    Type-directed partial evaluation uses a normalization function to achieve partial evaluation. These lecture notes review its background, foundations, practice, and applications. Of specific interest is the modular technique of offline and online type-directed partial evaluation in Standard ML of ...

  12. Osteogenesis imperfecta type III/Ehlers-Danlos overlap syndrome in a Chinese man.

    Science.gov (United States)

    Lu, Yanqin; Wang, Yanzhou; Rauch, Frank; Li, Hu; Zhang, Yao; Zhai, Naixiang; Zhang, Jian; Ren, Xiuzhi; Han, Jinxiang

    2018-02-01

    Osteogenesis imperfecta (OI) and Ehlers-Danlos syndrome (EDS) are rare genetic disorders that are typically inherited in an autosomal dominant manner. Few cases of OI/EDS overlap syndrome have been documented. Described here is a 30-year-old Chinese male with OI type III and EDS. Sequencing of genomic DNA revealed a heterozygous COL1A1 mutation (c.671G>A, p.Gly224Asp) that affected the N-anchor domain of the alpha 1 chain of collagen type I. Ultrastructural analysis of a skin biopsy specimen revealed thin collagen fibers with irregular alignment of collagen fibers. These findings have expanded the genotypic spectrum of the OI/EDS overlap syndrome.

  13. Locating overlap information in quantum systems

    International Nuclear Information System (INIS)

    Albrecht, A.

    1994-01-01

    When discussing the black hole information problem the term ''information flow'' is frequently used in a rather loose fashion. In this paper I attempt to make this notion more concrete. I consider a Hilbert space which is constructed as a tensor product of two subspaces (representing, for example, inside and outside the black hole). I discuss how the system has the capacity to contain information which is in neither of the subspaces. I attempt to quantify the amount of information located in each of the two subspaces, and elsewere, and analyze the exent to which unitary evolution can correspond to ''information flow.'' I define the notion of ''overlap information'' which appears to be well suited to the problem

  14. Burnout and depression: Label-related stigma, help-seeking, and syndrome overlap.

    Science.gov (United States)

    Bianchi, Renzo; Verkuilen, Jay; Brisson, Romain; Schonfeld, Irvin Sam; Laurent, Eric

    2016-11-30

    We investigated whether burnout and depression differed in terms of public stigma and help-seeking attitudes and behaviors. Secondarily, we examined the overlap of burnout and depressive symptoms. A total of 1046 French schoolteachers responded to an Internet survey in November-December 2015. The survey included measures of public stigma, help-seeking attitudes and behaviors, burnout and depressive symptoms, self-rated health, neuroticism, extraversion, history of anxiety or depressive disorder, social desirability, and socio-demographic variables. The burnout label appeared to be less stigmatizing than the depression label. In either case, however, fewer than 1% of the participants exhibited stigma scores signaling agreement with the proposed stigmatizing statements. Help-seeking attitudes and behaviors did not differ between burnout and depression. Participants considered burnout and depression similarly worth-treating. A huge overlap was observed between the self-report, time-standardized measures of burnout and depressive symptoms (disattenuated correlation: .91). The overlap was further evidenced in a confirmatory factor analysis. Thus, while burnout and depression as syndromes are unlikely to be distinct, how burnout and depression are socially represented may differ. To our knowledge, this study is the first to compare burnout- and depression-related stigma and help-seeking in the French context. Cross-national, multi-occupational studies examining different facets of stigma are needed. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  15. Cross-species comparison of biological themes and underlying genes on a global gene expression scale in a mouse model of colorectal liver metastasis and in clinical specimens

    Directory of Open Access Journals (Sweden)

    Schirmacher Peter

    2008-09-01

    Full Text Available Abstract Background Invasion-related genes over-expressed by tumor cells as well as by reacting host cells represent promising drug targets for anti-cancer therapy. Such candidate genes need to be validated in appropriate animal models. Results This study examined the suitability of a murine model (CT26/Balb/C of colorectal liver metastasis to represent clinical liver metastasis specimens using a global gene expression approach. Cross-species similarity was examined between pure liver, liver invasion, tumor invasion and pure tumor compartments through overlap of up-regulated genes and gene ontology (GO-based biological themes on the level of single GO-terms and of condensed GO-term families. Three out of four GO-term families were conserved in a compartment-specific way between the species: secondary metabolism (liver, invasion (invasion front, and immune response (invasion front and liver. Among the individual GO-terms over-represented in the invasion compartments in both species were "extracellular matrix", "cell motility", "cell adhesion" and "antigen presentation" indicating that typical invasion related processes are operating in both species. This was reflected on the single gene level as well, as cross-species overlap of potential target genes over-expressed in the combined invasion front compartments reached up to 36.5%. Generally, histopathology and gene expression correlated well as the highest single gene overlap was found to be 44% in syn-compartmental comparisons (liver versus liver whereas cross-compartmental overlaps were much lower (e.g. liver versus tumor: 9.7%. However, single gene overlap was surprisingly high in some cross-compartmental comparisons (e.g. human liver invasion compartment and murine tumor invasion compartment: 9.0% despite little histolopathologic similarity indicating that invasion relevant genes are not necessarily confined to histologically defined compartments. Conclusion In summary, cross

  16. Multi-person tracking with overlapping cameras in complex, dynamic environments

    NARCIS (Netherlands)

    Liem, M.; Gavrila, D.M.

    2009-01-01

    This paper presents a multi-camera system to track multiple persons in complex, dynamic environments. Position measurements are obtained by carving out the space defined by foreground regions in the overlapping camera views and projecting these onto blobs on the ground plane. Person appearance is

  17. A new mathematical formulation of the line-by-line method in case of weak line overlapping

    Science.gov (United States)

    Ishov, Alexander G.; Krymova, Natalie V.

    1994-01-01

    A rigorous mathematical proof is presented for multiline representation on the equivalent width of a molecular band which consists in the general case of n overlapping spectral lines. The multiline representation includes a principal term and terms of minor significance. The principal term is the equivalent width of the molecular band consisting of the same n nonoverlapping spectral lines. The terms of minor significance take into consideration the overlapping of two, three and more spectral lines. They are small in case of the weak overlapping of spectral lines in the molecular band. The multiline representation can be easily generalized for optically inhomogeneous gas media and holds true for combinations of molecular bands. If the band lines overlap weakly the standard formulation of line-by-line method becomes too labor-consuming. In this case the multiline representation permits line-by-line calculations to be performed more effectively. Other useful properties of the multiline representation are pointed out.

  18. Stimulus-response correspondence effect as a function of temporal overlap between relevant and irrelevant information processing.

    Science.gov (United States)

    Wang, Dong-Yuan Debbie; Richard, F Dan; Ray, Brittany

    2016-01-01

    The stimulus-response correspondence (SRC) effect refers to advantages in performance when stimulus and response correspond in dimensions or features, even if the common features are irrelevant to the task. Previous research indicated that the SRC effect depends on the temporal course of stimulus information processing. The current study investigated how the temporal overlap between relevant and irrelevant stimulus processing influences the SRC effect. In this experiment, the irrelevant stimulus (a previously associated tone) preceded the relevant stimulus (a coloured rectangle). The irrelevant and relevant stimuli onset asynchrony was varied to manipulate the temporal overlap between the irrelevant and relevant stimuli processing. Results indicated that the SRC effect size varied as a quadratic function of the temporal overlap between the relevant stimulus and irrelevant stimulus. This finding extends previous experimental observations that the SRC effect size varies in an increasing or decreasing function with reaction time. The current study demonstrated a quadratic function between effect size and the temporal overlap.

  19. Flight performance and feather quality: paying the price of overlapping moult and breeding in a tropical highland bird.

    Directory of Open Access Journals (Sweden)

    Maria Angela Echeverry-Galvis

    Full Text Available A temporal separation of energetically costly life history events like reproduction and maintenance of the integumentary system is thought to be promoted by selection to avoid trade-offs and maximize fitness. It has therefore remained somewhat of a paradox that certain vertebrate species can undergo both events simultaneously. Identifying potential costs of overlapping two demanding life history stages will further our understanding of the selection pressures that shape the temporal regulation of life history events in vertebrates. We studied free-living tropical Slaty brush-finches (Atlapetes schistaceus, in which individuals spontaneously overlap reproduction and moult or undergo both events in separation. To assess possible costs of such an overlap we quantified feather quality and flight performance of individuals in different states. We determined individual's life history state by measuring gonad size and scoring moult stage, and collected a newly grown 7(th primary wing feather for later analysis of feather quality. Finally, we quantified flight performance for each individual in the wild. Overlapping individuals produced lighter and shorter wing feathers than individuals just moulting, with females decreasing feather quality more strongly during the overlap than males. Moreover, overlapping individuals had a reduced flight speed during escape flights, while their foraging flight speed was unaffected. Despite overlappers being larger and having a smaller wing area, their lower body mass resulted in a similar wing load as in breeders or moulters. Individuals measured repeatedly in different states also showed significant decreases in feather quality and escape flight speed during the overlap. Reduced escape flight speed may represent a major consequence of the overlap by increasing predation risk. Our data document costs to undergoing two life history stages simultaneously, which likely arise from energetic trade-offs. Impairments in

  20. The Ixodes scapularis Salivary Protein, Salp15, Prevents the Association of HIV-1 gp120 and CD4

    OpenAIRE

    Juncadella, Ignacio J.; Garg, Renu; Bates, Tonya C.; Olivera, Elias R.; Anguita, Juan

    2007-01-01

    Ixodes scapularis salivary protein, Salp15, inhibits CD4+ T cell activation by binding to the most-extracellular domains of the CD4 molecule, potentially overlapping with the gp120-binding region. We now show that Salp15 inhibits the interaction of gp120 and CD4. Furthermore, Salp15 prevents syncytia formation between HL2/3 (a stable HeLa cell line expressing the envelope protein) and CD4-expressing cells. Salp15 prevented gp120-CD4 interaction at least partially through its direct interactio...