In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function.

PubMed

Follin, Elna; Karlsson, Maria; Lundegaard, Claus; Nielsen, Morten; Wallin, Stefan; Paulsson, Kajsa; Westerdahl, Helena

2013-04-01

The major histocompatibility complex (MHC) genes are the most polymorphic genes found in the vertebrate genome, and they encode proteins that play an essential role in the adaptive immune response. Many songbirds (passerines) have been shown to have a large number of transcribed MHC class I genes compared to most mammals. To elucidate the reason for this large number of genes, we compared 14 MHC class I alleles (α1-α3 domains), from great reed warbler, house sparrow and tree sparrow, via phylogenetic analysis, homology modelling and in silico peptide-binding predictions to investigate their functional and genetic relationships. We found more pronounced clustering of the MHC class I allomorphs (allele specific proteins) in regards to their function (peptide-binding specificities) compared to their genetic relationships (amino acid sequences), indicating that the high number of alleles is of functional significance. The MHC class I allomorphs from house sparrow and tree sparrow, species that diverged 10 million years ago (MYA), had overlapping peptide-binding specificities, and these similarities across species were also confirmed in phylogenetic analyses based on amino acid sequences. Notably, there were also overlapping peptide-binding specificities in the allomorphs from house sparrow and great reed warbler, although these species diverged 30 MYA. This overlap was not found in a tree based on amino acid sequences. Our interpretation is that convergent evolution on the level of the protein function, possibly driven by selection from shared pathogens, has resulted in allomorphs with similar peptide-binding repertoires, although trans-species evolution in combination with gene conversion cannot be ruled out.

Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting.

PubMed

Naden, Levi N; Shirts, Michael R

2016-04-12

We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the computational cost to estimate thermodynamic properties from molecular simulations for over 130,000 tested parameter combinations from over 1000 CPU years to tens of CPU days. This speed increase is achieved primarily by computing the potential energy as a linear combination of basis functions, computed from either modified simulation code or as the difference of energy between two reference states, which can be done without any simulation code modification. The thermodynamic properties are then estimated with the Multistate Bennett Acceptance Ratio (MBAR) as a function of multiple model parameters without the need to define a priori how the states are connected by a pathway. Instead, we adaptively sample a set of points in parameter space to create mutual configuration space overlap. The existence of regions of poor configuration space overlap are detected by analyzing the eigenvalues of the sampled states' overlap matrix. The configuration space overlap to sampled states is monitored alongside the mean and maximum uncertainty to determine convergence, as neither the uncertainty or the configuration space overlap alone is a sufficient metric of convergence. This adaptive sampling scheme is demonstrated by estimating with high precision the solvation free energies of charged particles of Lennard-Jones plus Coulomb functional form with charges between -2 and +2 and generally physical values of σij and ϵij in TIP3P water. We also compute entropy, enthalpy, and radial distribution functions of arbitrary unsampled parameter combinations using only the data from these sampled states and use the estimates of free energies over the entire space to examine the deviation of atomistic simulations from the Born approximation to the solvation free energy.

Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method

PubMed Central

Ren, Jun; Zhou, Wei; Wang, Jianxin

2014-01-01

Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-module and “seed-expanding.” First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a λ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes. PMID:25143945

Functional genomics analysis of big data identifies novel PPARy target SNPs showing association with cardio metabolic outcomes

USDA-ARS?s Scientific Manuscript database

Background - Cardiovascular disease and type-2-diabetes represent overlapping diseases where a large portion of the variation attributable to genetics remains unexplained. An important player in their etiology is Peroxisome Proliferator-activated Receptor gamma (PPARy) that is involved in lipid and ...

Correspondence between large-scale ictal and interictal epileptic networks revealed by single photon emission computed tomography (SPECT) and electroencephalography (EEG)-functional magnetic resonance imaging (fMRI).

PubMed

Tousseyn, Simon; Dupont, Patrick; Goffin, Karolien; Sunaert, Stefan; Van Paesschen, Wim

2015-03-01

Epilepsy is increasingly recognized as a network disorder, but the spatial relationship between ictal and interictal networks is still largely unexplored. In this work, we compared hemodynamic changes related to seizures and interictal spikes on a whole brain scale. Twenty-eight patients with refractory focal epilepsy (14 temporal and 14 extratemporal lobe) underwent both subtraction ictal single photon emission computed tomography (SPECT) coregistered to magnetic resonance imaging (MRI) (SISCOM) and spike-related electroencephalography (EEG-functional MRI (fMRI). SISCOM visualized relative perfusion changes during seizures, whereas EEG-fMRI mapped blood oxygen level-dependent (BOLD) changes related to spikes. Similarity between statistical maps of both modalities was analyzed per patient using the following two measures: (1) correlation between unthresholded statistical maps (Pearson's correlation coefficient) and (2) overlap between thresholded images (Dice coefficient). Overlap was evaluated at a regional level, for hyperperfusions and activations and for hypoperfusions and deactivations separately, using different thresholds. Nonparametric permutation tests were applied to assess statistical significance (p ≤ 0.05). We found significant and positive correlations between hemodynamic changes related to seizures and spikes in 27 (96%) of 28 cases (median correlation coefficient 0.29 [range -0.12 to 0.62]). In 20 (71%) of 28 cases, spatial overlap between hyperperfusion on SISCOM and activation on EEG-fMRI was significantly larger than expected by chance. Congruent changes were not restricted to the territory of the presumed epileptogenic zone, but could be seen at distant sites (e.g., cerebellum and basal ganglia). Overlap between ictal hypoperfusion and interictal deactivation was statistically significant in 22 (79%) of 28 patients. Despite the high rate of congruence, discrepancies were observed for both modalities. We conclude that hemodynamic changes related to seizures and spikes varied spatially with the same sign and within a common network. Overlap was present in regions nearby and distant from discharge origin. Wiley Periodicals, Inc. © 2015 International League Against Epilepsy.

Hand2 loss-of-function in Hand1-expressing Cells Reveals Distinct Roles In Epicardial And Coronary Vessel Development

PubMed Central

Barnes, Ralston M.; Firulli, Beth A.; VanDusen, Nathan J.; Morikawa, Yuka; Conway, Simon J.; Cserjesi, Peter; Vincentz, Joshua W.; Firulli, Anthony B.

2011-01-01

Rationale The bHLH transcription factors Hand1 and Hand2 are essential for embryonic development. Given their requirement for cardiogenesis, it is imperative to determine their impact on cardiovascular function. Objective Deduce the role of Hand2 within the epicardium. Method & Results We engineered a Hand1 allele expressing Cre recombinase. Cardiac Hand1 expression is largely limited to cells of the primary heart field, overlapping little with Hand2 expression. Hand1 is expressed within the septum transversum (ST) and the Hand1-lineage marks the proepicardial organ and epicardium. To examine Hand factor functional overlap, we conditionally deleted Hand2 from Hand1-expressing cells. Hand2 mutants display defective epicardialization and fail to form coronary arteries, coincident with altered ECM deposition and Pdgfr expression. Conclusion These data demonstrate a hierarchal relationship whereby transient Hand1 ST expression defines epicardial precursors that are subsequently dependent upon Hand2 function. PMID:21350214

Recombining overlapping BACs into a single larger BAC.

PubMed

Kotzamanis, George; Huxley, Clare

2004-01-06

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. 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. 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.

High-Precision Registration of Point Clouds Based on Sphere Feature Constraints.

PubMed

Huang, Junhui; Wang, Zhao; Gao, Jianmin; Huang, Youping; Towers, David Peter

2016-12-30

Point cloud registration is a key process in multi-view 3D measurements. Its precision affects the measurement precision directly. However, in the case of the point clouds with non-overlapping areas or curvature invariant surface, it is difficult to achieve a high precision. A high precision registration method based on sphere feature constraint is presented to overcome the difficulty in the paper. Some known sphere features with constraints are used to construct virtual overlapping areas. The virtual overlapping areas provide more accurate corresponding point pairs and reduce the influence of noise. Then the transformation parameters between the registered point clouds are solved by an optimization method with weight function. In that case, the impact of large noise in point clouds can be reduced and a high precision registration is achieved. Simulation and experiments validate the proposed method.

High-Precision Registration of Point Clouds Based on Sphere Feature Constraints

PubMed Central

Huang, Junhui; Wang, Zhao; Gao, Jianmin; Huang, Youping; Towers, David Peter

2016-01-01

Point cloud registration is a key process in multi-view 3D measurements. Its precision affects the measurement precision directly. However, in the case of the point clouds with non-overlapping areas or curvature invariant surface, it is difficult to achieve a high precision. A high precision registration method based on sphere feature constraint is presented to overcome the difficulty in the paper. Some known sphere features with constraints are used to construct virtual overlapping areas. The virtual overlapping areas provide more accurate corresponding point pairs and reduce the influence of noise. Then the transformation parameters between the registered point clouds are solved by an optimization method with weight function. In that case, the impact of large noise in point clouds can be reduced and a high precision registration is achieved. Simulation and experiments validate the proposed method. PMID:28042846

Discovering herbal functional groups of traditional Chinese medicine.

PubMed

He, Ping; Deng, Ke; Liu, Zhihai; Liu, Delin; Liu, Jun S; Geng, Zhi

2012-03-30

For the traditional Chinese medicine (TCM), a prescription for a patient often contains several herbs. Some herbs are often used together in prescriptions, and these herbs can be considered as a functional group. In this paper, we propose an approach for discovering herbal functional groups from a large set of prescriptions recorded in TCM books. These functional groups are allowed to overlap with each other. Our approach is validated with a simulation study and applied to a data set containing thousands of TCM prescriptions. Copyright © 2011 John Wiley & Sons, Ltd.

The Importance of Role Definition in Combining School and Public Libraries.

ERIC Educational Resources Information Center

Amey, L. J.

Public and school libraries having begun as an outgrowth of each other and then separated, have some overlap in philosophy, function, and public served. Although studies have opposed the combined school and public library, communities continue to attempt mergers largely for promise of dollar savings. There is also a philosophical trend in…

Functional genomics analysis of big data identifies novel peroxisome proliferator–activated receptor gamma target single nucleotide polymorphisms showing association with cardiometabolic outcomes

USDA-ARS?s Scientific Manuscript database

Background Cardiovascular disease and type 2 diabetes mellitus represent overlapping diseases where a large portion of the variation attributable to genetics remains unexplained. An important player in their pathogenesis is peroxisome proliferator–activated receptor gamma (PPARgamma) that is involve...

The impact of atmospheric stability and wind shear on vertical cloud overlap over the Tibetan Plateau

NASA Astrophysics Data System (ADS)

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 account in the parameterization of decorrelation length scale L in order to further improve the calculation of the radiative budget and the prediction of climate change over the TP in the atmospheric models.

Markov models for fMRI correlation structure: Is brain functional connectivity small world, or decomposable into networks?

PubMed

Varoquaux, G; Gramfort, A; Poline, J B; Thirion, B

2012-01-01

Correlations in the signal observed via functional Magnetic Resonance Imaging (fMRI), are expected to reveal the interactions in the underlying neural populations through hemodynamic response. In particular, they highlight distributed set of mutually correlated regions that correspond to brain networks related to different cognitive functions. Yet graph-theoretical studies of neural connections give a different picture: that of a highly integrated system with small-world properties: local clustering but with short pathways across the complete structure. We examine the conditional independence properties of the fMRI signal, i.e. its Markov structure, to find realistic assumptions on the connectivity structure that are required to explain the observed functional connectivity. In particular we seek a decomposition of the Markov structure into segregated functional networks using decomposable graphs: a set of strongly-connected and partially overlapping cliques. We introduce a new method to efficiently extract such cliques on a large, strongly-connected graph. We compare methods learning different graph structures from functional connectivity by testing the goodness of fit of the model they learn on new data. We find that summarizing the structure as strongly-connected networks can give a good description only for very large and overlapping networks. These results highlight that Markov models are good tools to identify the structure of brain connectivity from fMRI signals, but for this purpose they must reflect the small-world properties of the underlying neural systems. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

2014-01-01

Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N 3) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix,more » based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.« less

Overlapping Networks Engaged during Spoken Language Production and Its Cognitive Control

PubMed Central

Wise, Richard J.S.; Mehta, Amrish; Leech, Robert

2014-01-01

Spoken language production is a complex brain function that relies on large-scale networks. These include domain-specific networks that mediate language-specific processes, as well as domain-general networks mediating top-down and bottom-up attentional control. Language control is thought to involve a left-lateralized fronto-temporal-parietal (FTP) system. However, these regions do not always activate for language tasks and similar regions have been implicated in nonlinguistic cognitive processes. These inconsistent findings suggest that either the left FTP is involved in multidomain cognitive control or that there are multiple spatially overlapping FTP systems. We present evidence from an fMRI study using multivariate analysis to identify spatiotemporal networks involved in spoken language production in humans. We compared spoken language production (Speech) with multiple baselines, counting (Count), nonverbal decision (Decision), and “rest,” to pull apart the multiple partially overlapping networks that are involved in speech production. A left-lateralized FTP network was activated during Speech and deactivated during Count and nonverbal Decision trials, implicating it in cognitive control specific to sentential spoken language production. A mirror right-lateralized FTP network was activated in the Count and Decision trials, but not Speech. Importantly, a second overlapping left FTP network showed relative deactivation in Speech. These three networks, with distinct time courses, overlapped in the left parietal lobe. Contrary to the standard model of the left FTP as being dominant for speech, we revealed a more complex pattern within the left FTP, including at least two left FTP networks with competing functional roles, only one of which was activated in speech production. PMID:24966373

Overlapping networks engaged during spoken language production and its cognitive control.

PubMed

Geranmayeh, Fatemeh; Wise, Richard J S; Mehta, Amrish; Leech, Robert

2014-06-25

Spoken language production is a complex brain function that relies on large-scale networks. These include domain-specific networks that mediate language-specific processes, as well as domain-general networks mediating top-down and bottom-up attentional control. Language control is thought to involve a left-lateralized fronto-temporal-parietal (FTP) system. However, these regions do not always activate for language tasks and similar regions have been implicated in nonlinguistic cognitive processes. These inconsistent findings suggest that either the left FTP is involved in multidomain cognitive control or that there are multiple spatially overlapping FTP systems. We present evidence from an fMRI study using multivariate analysis to identify spatiotemporal networks involved in spoken language production in humans. We compared spoken language production (Speech) with multiple baselines, counting (Count), nonverbal decision (Decision), and "rest," to pull apart the multiple partially overlapping networks that are involved in speech production. A left-lateralized FTP network was activated during Speech and deactivated during Count and nonverbal Decision trials, implicating it in cognitive control specific to sentential spoken language production. A mirror right-lateralized FTP network was activated in the Count and Decision trials, but not Speech. Importantly, a second overlapping left FTP network showed relative deactivation in Speech. These three networks, with distinct time courses, overlapped in the left parietal lobe. Contrary to the standard model of the left FTP as being dominant for speech, we revealed a more complex pattern within the left FTP, including at least two left FTP networks with competing functional roles, only one of which was activated in speech production. Copyright © 2014 Geranmayeh et al.

Improving Representation of Tropical Cloud Overlap in GCMs Based on Cloud-Resolving Model Data

NASA Astrophysics Data System (ADS)

Jing, Xianwen; Zhang, Hua; Satoh, Masaki; Zhao, Shuyun

2018-04-01

The decorrelation length ( L cf) has been widely used to describe the behavior of vertical overlap of clouds in general circulation models (GCMs); however, it has been a challenge to associate L cf with the large-scale meteorological conditions during cloud evolution. This study explored the relationship between L cf and the strength of atmospheric convection in the tropics based on output from a global cloud-resolving model. L cf tends to increase with vertical velocity in the mid-troposphere ( w 500) at locations of ascent, but shows little or no dependency on w 500 at locations of descent. A representation of L cf as a function of vertical velocity is obtained, with a linear regression in ascending regions and a constant value in descending regions. This simple and dynamic-related representation of L cf leads to a significant improvement in simulation of both cloud cover and radiation fields compared with traditional overlap treatments. This work presents a physically justifiable approach to depicting cloud overlap in the tropics in GCMs.

Relation of Cloud Occurrence Frequency, Overlap, and Effective Thickness Derived from CALIPSO and CloudSat Merged Cloud Vertical Profiles

NASA Technical Reports Server (NTRS)

Kato, Seiji; Sun-Mack, Sunny; Miller, Walter F.; Rose, Fred G.; Chen, Yan; Minnis, Patrick; Wielicki, Bruce A.

2009-01-01

A cloud frequency of occurrence matrix is generated using merged cloud vertical profile derived from Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) and Cloud Profiling Radar (CPR). The matrix contains vertical profiles of cloud occurrence frequency as a function of the uppermost cloud top. It is shown that the cloud fraction and uppermost cloud top vertical pro les can be related by a set of equations when the correlation distance of cloud occurrence, which is interpreted as an effective cloud thickness, is introduced. The underlying assumption in establishing the above relation is that cloud overlap approaches the random overlap with increasing distance separating cloud layers and that the probability of deviating from the random overlap decreases exponentially with distance. One month of CALIPSO and CloudSat data support these assumptions. However, the correlation distance sometimes becomes large, which might be an indication of precipitation. The cloud correlation distance is equivalent to the de-correlation distance introduced by Hogan and Illingworth [2000] when cloud fractions of both layers in a two-cloud layer system are the same.

Correspondence Between Aberrant Intrinsic Network Connectivity and Gray-Matter Volume in the Ventral Brain of Preterm Born Adults.

PubMed

Bäuml, Josef G; Daamen, Marcel; Meng, Chun; Neitzel, Julia; Scheef, Lukas; Jaekel, Julia; Busch, Barbara; Baumann, Nicole; Bartmann, Peter; Wolke, Dieter; Boecker, Henning; Wohlschläger, Afra M; Sorg, Christian

2015-11-01

Widespread brain changes are present in preterm born infants, adolescents, and even adults. While neurobiological models of prematurity facilitate powerful explanations for the adverse effects of preterm birth on the developing brain at microscale, convincing linking principles at large-scale level to explain the widespread nature of brain changes are still missing. We investigated effects of preterm birth on the brain's large-scale intrinsic networks and their relation to brain structure in preterm born adults. In 95 preterm and 83 full-term born adults, structural and functional magnetic resonance imaging at-rest was used to analyze both voxel-based morphometry and spatial patterns of functional connectivity in ongoing blood oxygenation level-dependent activity. Differences in intrinsic functional connectivity (iFC) were found in cortical and subcortical networks. Structural differences were located in subcortical, temporal, and cingulate areas. Critically, for preterm born adults, iFC-network differences were overlapping and correlating with aberrant regional gray-matter (GM) volume specifically in subcortical and temporal areas. Overlapping changes were predicted by prematurity and in particular by neonatal medical complications. These results provide evidence that preterm birth has long-lasting effects on functional connectivity of intrinsic networks, and these changes are specifically related to structural alterations in ventral brain GM. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Understanding the Control of Singlet-Triplet Splitting for Organic Exciton Manipulating: A Combined Theoretical and Experimental Approach

PubMed Central

Chen, Ting; Zheng, Lei; Yuan, Jie; An, Zhongfu; Chen, Runfeng; Tao, Ye; Li, Huanhuan; Xie, Xiaoji; Huang, Wei

2015-01-01

Developing organic optoelectronic materials with desired photophysical properties has always been at the forefront of organic electronics. The variation of singlet-triplet splitting (ΔEST) can provide useful means in modulating organic excitons for diversified photophysical phenomena, but controlling ΔEST in a desired manner within a large tuning scope remains a daunting challenge. Here, we demonstrate a convenient and quantitative approach to relate ΔEST to the frontier orbital overlap and separation distance via a set of newly developed parameters using natural transition orbital analysis to consider whole pictures of electron transitions for both the lowest singlet (S1) and triplet (T1) excited states. These critical parameters revealed that both separated S1 and T1 states leads to ultralow ΔEST; separated S1 and overlapped T1 states results in small ΔEST; and both overlapped S1 and T1 states induces large ΔEST. Importantly, we realized a widely-tuned ΔEST in a range from ultralow (0.0003 eV) to extra-large (1.47 eV) via a subtle symmetric control of triazine molecules, based on time-dependent density functional theory calculations combined with experimental explorations. These findings provide keen insights into ΔEST control for feasible excited state tuning, offering valuable guidelines for the construction of molecules with desired optoelectronic properties. PMID:26161684

Face Patch Resting State Networks Link Face Processing to Social Cognition

PubMed Central

Schwiedrzik, Caspar M.; Zarco, Wilbert; Everling, Stefan; Freiwald, Winrich A.

2015-01-01

Faces transmit a wealth of social information. How this information is exchanged between face-processing centers and brain areas supporting social cognition remains largely unclear. Here we identify these routes using resting state functional magnetic resonance imaging in macaque monkeys. We find that face areas functionally connect to specific regions within frontal, temporal, and parietal cortices, as well as subcortical structures supporting emotive, mnemonic, and cognitive functions. This establishes the existence of an extended face-recognition system in the macaque. Furthermore, the face patch resting state networks and the default mode network in monkeys show a pattern of overlap akin to that between the social brain and the default mode network in humans: this overlap specifically includes the posterior superior temporal sulcus, medial parietal, and dorsomedial prefrontal cortex, areas supporting high-level social cognition in humans. Together, these results reveal the embedding of face areas into larger brain networks and suggest that the resting state networks of the face patch system offer a new, easily accessible venue into the functional organization of the social brain and into the evolution of possibly uniquely human social skills. PMID:26348613

Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof-of-concept and roadmap for future studies

PubMed Central

Anttila, Verneri; Hibar, Derrek P; van Hulzen, Kimm J E; Arias-Vasquez, Alejandro; Smoller, Jordan W; Nichols, Thomas E; Neale, Michael C; McIntosh, Andrew M; Lee, Phil; McMahon, Francis J; Meyer-Lindenberg, Andreas; Mattheisen, Manuel; Andreassen, Ole A; Gruber, Oliver; Sachdev, Perminder S; Roiz-Santiañez, Roberto; Saykin, Andrew J; Ehrlich, Stefan; Mather, Karen A; Turner, Jessica A; Schwarz, Emanuel; Thalamuthu, Anbupalam; Shugart, Yin Yao; Ho, Yvonne YW; Martin, Nicholas G; Wright, Margaret J

2016-01-01

Schizophrenia is a devastating psychiatric illness with high heritability. Brain structure and function differ, on average, between schizophrenia cases and healthy individuals. As common genetic associations are emerging for both schizophrenia and brain imaging phenotypes, we can now use genome-wide data to investigate genetic overlap. Here we integrated results from common variant studies of schizophrenia (33,636 cases, 43,008 controls) and volumes of several (mainly subcortical) brain structures (11,840 subjects). We did not find evidence of genetic overlap between schizophrenia risk and subcortical volume measures either at the level of common variant genetic architecture or for single genetic markers. The current study provides proof-of-concept (albeit based on a limited set of structural brain measures), and defines a roadmap for future studies investigating the genetic covariance between structural/functional brain phenotypes and risk for psychiatric disorders. PMID:26854805

Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept.

PubMed

Franke, Barbara; Stein, Jason L; Ripke, Stephan; Anttila, Verneri; Hibar, Derrek P; van Hulzen, Kimm J E; Arias-Vasquez, Alejandro; Smoller, Jordan W; Nichols, Thomas E; Neale, Michael C; McIntosh, Andrew M; Lee, Phil; McMahon, Francis J; Meyer-Lindenberg, Andreas; Mattheisen, Manuel; Andreassen, Ole A; Gruber, Oliver; Sachdev, Perminder S; Roiz-Santiañez, Roberto; Saykin, Andrew J; Ehrlich, Stefan; Mather, Karen A; Turner, Jessica A; Schwarz, Emanuel; Thalamuthu, Anbupalam; Shugart, Yin Yao; Ho, Yvonne Yw; Martin, Nicholas G; Wright, Margaret J; O'Donovan, Michael C; Thompson, Paul M; Neale, Benjamin M; Medland, Sarah E; Sullivan, Patrick F

2016-03-01

Schizophrenia is a devastating psychiatric illness with high heritability. Brain structure and function differ, on average, between people with schizophrenia and healthy individuals. As common genetic associations are emerging for both schizophrenia and brain imaging phenotypes, we can now use genome-wide data to investigate genetic overlap. Here we integrated results from common variant studies of schizophrenia (33,636 cases, 43,008 controls) and volumes of several (mainly subcortical) brain structures (11,840 subjects). We did not find evidence of genetic overlap between schizophrenia risk and subcortical volume measures either at the level of common variant genetic architecture or for single genetic markers. These results provide a proof of concept (albeit based on a limited set of structural brain measures) and define a roadmap for future studies investigating the genetic covariance between structural or functional brain phenotypes and risk for psychiatric disorders.

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

PubMed

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.

Climate change alters stability and species potential interactions in a large marine ecosystem.

PubMed

Griffith, Gary P; Strutton, Peter G; Semmens, Jayson M

2018-01-01

We have little empirical evidence of how large-scale overlaps between large numbers of marine species may have altered in response to human impacts. Here, we synthesized all available distribution data (>1 million records) since 1992 for 61 species of the East Australian marine ecosystem, a global hot spot of ocean warming and continuing fisheries exploitation. Using a novel approach, we constructed networks of the annual changes in geographical overlaps between species. Using indices of changes in species overlap, we quantified changes in the ecosystem stability, species robustness, species sensitivity and structural keystone species. We then compared the species overlap indices with environmental and fisheries data to identify potential factors leading to the changes in distributional overlaps between species. We found that the structure of the ecosystem has changed with a decrease in asymmetrical geographical overlaps between species. This suggests that the ecosystem has become less stable and potentially more susceptible to environmental perturbations. Most species have shown a decrease in overlaps with other species. The greatest decrease in species overlap robustness and sensitivity to the loss of other species has occurred in the pelagic community. Some demersal species have become more robust and less sensitive. Pelagic structural keystone species, predominately the tunas and billfish, have been replaced by demersal fish species. The changes in species overlap were strongly correlated with regional oceanographic changes, in particular increasing ocean warming and the southward transport of warmer and saltier water with the East Australian Current, but less correlated with fisheries catch. Our study illustrates how large-scale multispecies distribution changes can help identify structural changes in marine ecosystems associated with climate change. © 2017 John Wiley & Sons Ltd.

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

PubMed

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.

Transcriptome and ultrastructural changes in dystrophic Epidermolysis bullosa resemble skin aging

PubMed Central

Trost, Andrea; Weber, Manuela; Klausegger, Alfred; Gruber, Christina; Bruckner, Daniela; Reitsamer, Herbert A.; Bauer, Johann W.; Breitenbach, Michael

2015-01-01

The aging process of skin has been investigated recently with respect to mitochondrial function and oxidative stress. We have here observed striking phenotypic and clinical similarity between skin aging and recessive dystrophic Epidermolysis bullosa (RDEB), which is caused by recessive mutations in the gene coding for collagen VII, COL7A1. Ultrastructural changes, defects in wound healing, and inflammation markers are in part shared with aged skin. We have here compared the skin transcriptomes of young adults suffering from RDEB with that of sex‐ and age‐matched healthy probands. In parallel we have compared the skin transcriptome of healthy young adults with that of elderly healthy donors. Quite surprisingly, there was a large overlap of the two gene lists that concerned a limited number of functional protein families. Most prominent among the proteins found are a number of proteins of the cornified envelope or proteins mechanistically involved in cornification and other skin proteins. Further, the overlap list contains a large number of genes with a known role in inflammation. We are documenting some of the most prominent ultrastructural and protein changes by immunofluorescence analysis of skin sections from patients, old individuals, and healthy controls. PMID:26143532

Transcriptome and ultrastructural changes in dystrophic Epidermolysis bullosa resemble skin aging.

PubMed

Breitenbach, Jenny S; Rinnerthaler, Mark; Trost, Andrea; Weber, Manuela; Klausegger, Alfred; Gruber, Christina; Bruckner, Daniela; Reitsamer, Herbert A; Bauer, Johann W; Breitenbach, Michael

2015-06-01

The aging process of skin has been investigated recently with respect to mitochondrial function and oxidative stress. We have here observed striking phenotypic and clinical similarity between skin aging and recessive dystrophic Epidermolysis bullosa (RDEB), which is caused by recessive mutations in the gene coding for collagen VII,COL7A1. Ultrastructural changes, defects in wound healing, and inflammation markers are in part shared with aged skin. We have here compared the skin transcriptomes of young adults suffering from RDEB with that of sex- and age-matched healthy probands. In parallel we have compared the skin transcriptome of healthy young adults with that of elderly healthy donors. Quite surprisingly, there was a large overlap of the two gene lists that concerned a limited number of functional protein families. Most prominent among the proteins found are a number of proteins of the cornified envelope or proteins mechanistically involved in cornification and other skin proteins. Further, the overlap list contains a large number of genes with a known role in inflammation. We are documenting some of the most prominent ultrastructural and protein changes by immunofluorescence analysis of skin sections from patients, old individuals, and healthy controls.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Influence of Blurred Ways on Pattern Recognition of a Scale-Free Hopfield Neural Network

NASA Astrophysics Data System (ADS)

Chang, Wen-Li

2010-01-01

We investigate the influence of blurred ways on pattern recognition of a Barabási-Albert scale-free Hopfield neural network (SFHN) with a small amount of errors. Pattern recognition is an important function of information processing in brain. Due to heterogeneous degree of scale-free network, different blurred ways have different influences on pattern recognition with same errors. Simulation shows that among partial recognition, the larger loading ratio (the number of patterns to average degree P/langlekrangle) is, the smaller the overlap of SFHN is. The influence of directed (large) way is largest and the directed (small) way is smallest while random way is intermediate between them. Under the ratio of the numbers of stored patterns to the size of the network P/N is less than 0. 1 conditions, there are three families curves of the overlap corresponding to directed (small), random and directed (large) blurred ways of patterns and these curves are not associated with the size of network and the number of patterns. This phenomenon only occurs in the SFHN. These conclusions are benefit for understanding the relation between neural network structure and brain function.

Modeling of chromosome intermingling by partially overlapping uniform random polygons.

PubMed

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.

Non-overlap subaperture interferometric testing for large optics

NASA Astrophysics Data System (ADS)

Wu, Xin; Yu, Yingjie; Zeng, Wenhan; Qi, Te; Chen, Mingyi; Jiang, Xiangqian

2017-08-01

It has been shown that the number of subapertures and the amount of overlap has a significant influence on the stitching accuracy. In this paper, a non-overlap subaperture interferometric testing method (NOSAI) is proposed to inspect large optical components. This method would greatly reduce the number of subapertures and the influence of environmental interference while maintaining the accuracy of reconstruction. A general subaperture distribution pattern of NOSAI is also proposed for the large rectangle surface. The square Zernike polynomial is employed to fit such wavefront. The effect of the minimum fitting terms on the accuracy of NOSAI and the sensitivities of NOSAI to subaperture's alignment error, power systematic error, and random noise are discussed. Experimental results validate the feasibility and accuracy of the proposed NOSAI in comparison with wavefront obtained by a large aperture interferometer and stitching surface by multi-aperture overlap-scanning technique (MAOST).

Age of language acquisition and cortical language organization in multilingual patients undergoing awake brain mapping.

PubMed

Fernández-Coello, Alejandro; Havas, Viktória; Juncadella, Montserrat; Sierpowska, Joanna; Rodríguez-Fornells, Antoni; Gabarrós, Andreu

2017-06-01

OBJECTIVE Most knowledge regarding the anatomical organization of multilingualism is based on aphasiology and functional imaging studies. However, the results have still to be validated by the gold standard approach, namely electrical stimulation mapping (ESM) during awake neurosurgical procedures. In this ESM study the authors describe language representation in a highly specific group of 13 multilingual individuals, focusing on how age of acquisition may influence the cortical organization of language. METHODS Thirteen patients who had a high degree of proficiency in multiple languages and were harboring lesions within the dominant, left hemisphere underwent ESM while being operated on under awake conditions. Demographic and language data were recorded in relation to age of language acquisition (for native languages and early- and late-acquired languages), neuropsychological pre- and postoperative language testing, the number and location of language sites, and overlapping distribution in terms of language acquisition time. Lesion growth patterns and histopathological characteristics, location, and size were also recorded. The distribution of language sites was analyzed with respect to age of acquisition and overlap. RESULTS The functional language-related sites were distributed in the frontal (55%), temporal (29%), and parietal lobes (16%). The total number of native language sites was 47. Early-acquired languages (including native languages) were represented in 97 sites (55 overlapped) and late-acquired languages in 70 sites (45 overlapped). The overlapping distribution was 20% for early-early, 71% for early-late, and 9% for late-late. The average lesion size (maximum diameter) was 3.3 cm. There were 5 fast-growing and 7 slow-growing lesions. CONCLUSIONS Cortical language distribution in multilingual patients is not homogeneous, and it is influenced by age of acquisition. Early-acquired languages have a greater cortical representation than languages acquired later. The prevalent native and early-acquired languages are largely represented within the perisylvian left hemisphere frontoparietotemporal areas, and the less prevalent late-acquired languages are mostly overlapped with them.

A Coordinate-Based Meta-Analysis of Overlaps in Regional Specialization and Functional Connectivity across Subjective Value and Default Mode Networks.

PubMed

Acikalin, M Yavuz; Gorgolewski, Krzysztof J; Poldrack, Russell A

2017-01-01

Previous research has provided qualitative evidence for overlap in a number of brain regions across the subjective value network (SVN) and the default mode network (DMN). In order to quantitatively assess this overlap, we conducted a series of coordinate-based meta-analyses (CBMA) of results from 466 functional magnetic resonance imaging experiments on task-negative or subjective value-related activations in the human brain. In these analyses, we first identified significant overlaps and dissociations across activation foci related to SVN and DMN. Second, we investigated whether these overlapping subregions also showed similar patterns of functional connectivity, suggesting a shared functional subnetwork. We find considerable overlap between SVN and DMN in subregions of central ventromedial prefrontal cortex (cVMPFC) and dorsal posterior cingulate cortex (dPCC). Further, our findings show that similar patterns of bidirectional functional connectivity between cVMPFC and dPCC are present in both networks. We discuss ways in which our understanding of how subjective value (SV) is computed and represented in the brain can be synthesized with what we know about the DMN, mind-wandering, and self-referential processing in light of our findings.

Radial sets: interactive visual analysis of large overlapping sets.

PubMed

Alsallakh, Bilal; Aigner, Wolfgang; Miksch, Silvia; Hauser, Helwig

2013-12-01

In many applications, data tables contain multi-valued attributes that often store the memberships of the table entities to multiple sets such as which languages a person masters, which skills an applicant documents, or which features a product comes with. With a growing number of entities, the resulting element-set membership matrix becomes very rich of information about how these sets overlap. Many analysis tasks targeted at set-typed data are concerned with these overlaps as salient features of such data. This paper presents Radial Sets, a novel visual technique to analyze set memberships for a large number of elements. Our technique uses frequency-based representations to enable quickly finding and analyzing different kinds of overlaps between the sets, and relating these overlaps to other attributes of the table entities. Furthermore, it enables various interactions to select elements of interest, find out if they are over-represented in specific sets or overlaps, and if they exhibit a different distribution for a specific attribute compared to the rest of the elements. These interactions allow formulating highly-expressive visual queries on the elements in terms of their set memberships and attribute values. As we demonstrate via two usage scenarios, Radial Sets enable revealing and analyzing a multitude of overlapping patterns between large sets, beyond the limits of state-of-the-art techniques.

Understanding COPD-overlap syndromes.

PubMed

Poh, Tuang Yeow; Mac Aogáin, Micheál; Chan, Adrian Kwok Wai; Yii, Anthony Chau Ang; Yong, Valerie Fei Lee; Tiew, Pei Yee; Koh, Mariko Siyue; Chotirmall, Sanjay Haresh

2017-04-01

Chronic obstructive pulmonary disease accounts for a large burden of lung disease. It can 'overlap' with other respiratory diseases including bronchiectasis, fibrosis and obstructive sleep apnea (OSA). While COPD alone confers morbidity and mortality, common features with contrasting clinical outcomes can occur in COPD 'overlap syndromes'. Areas covered: Given the large degree of heterogeneity in COPD, individual variation to treatment is adopted based on its observed phenotype, which in turn overlaps with features of other respiratory disease states such as asthma. This is coined asthma-COPD overlap syndrome ('ACOS'). Other examples of such overlapping clinical states include bronchiectasis-COPD ('BCOS'), fibrosis-COPD ('FCOS') and OSA-COPD ('OCOS'). The objective of this review is to highlight similarities and differences between the COPD-overlap syndromes in terms of risk factors, pathophysiology, diagnosis and potential treatment differences. Expert commentary: As a consequence of COPD overlap syndromes, a transition from the traditional 'one size fits all' treatment approach is necessary. Greater treatment stratification according to clinical phenotype using a precision medicine approach is now required. In this light, it is important to recognize and differentiate COPD overlap syndromes as distinct disease states compared to individual diseases such as asthma, COPD, fibrosis or bronchiectasis.

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

PubMed

Nagraj, V P; Magee, Neal E; Sheffield, Nathan C

2018-06-06

The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, new genomic data can be easily connected to annotations from external data sources. Here, we present an interactive interface for enrichment analysis of genomic locus overlaps using a web server called LOLAweb. LOLAweb accepts a set of genomic ranges from the user and tests it for enrichment against a database of region sets. LOLAweb renders results in an R Shiny application to provide interactive visualization features, enabling users to filter, sort, and explore enrichment results dynamically. LOLAweb is built and deployed in a Linux container, making it scalable to many concurrent users on our servers and also enabling users to download and run LOLAweb locally.

Identification of overlapping communities and their hierarchy by locally calculating community-changing resolution levels

NASA Astrophysics Data System (ADS)

Havemann, Frank; Heinz, Michael; Struck, Alexander; Gläser, Jochen

2011-01-01

We propose a new local, deterministic and parameter-free algorithm that detects fuzzy and crisp overlapping communities in a weighted network and simultaneously reveals their hierarchy. Using a local fitness function, the algorithm greedily expands natural communities of seeds until the whole graph is covered. The hierarchy of communities is obtained analytically by calculating resolution levels at which communities grow rather than numerically by testing different resolution levels. This analytic procedure is not only more exact than its numerical alternatives such as LFM and GCE but also much faster. Critical resolution levels can be identified by searching for intervals in which large changes of the resolution do not lead to growth of communities. We tested our algorithm on benchmark graphs and on a network of 492 papers in information science. Combined with a specific post-processing, the algorithm gives much more precise results on LFR benchmarks with high overlap compared to other algorithms and performs very similarly to GCE.

The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization.

PubMed

True, Jason D; Muldoon, Joseph J; Carver, Melissa N; Poorey, Kunal; Shetty, Savera J; Bekiranov, Stefan; Auble, David T

2016-07-15

Modifier of transcription 1 (Mot1) is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the facilitates chromatin transcription (FACT) histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. On a global scale, Spt16 was required for Mot1 promoter localization, and Mot1 also affected Spt16 localization to genes. Interestingly, we found that Mot1 has an unanticipated role in establishing or maintaining the occupancy and positioning of nucleosomes at the 5' ends of genes. Spt16 has a broad role in regulating chromatin organization in gene bodies, including those nucleosomes affected by Mot1. These results suggest that the large scale overlap in Mot1 and Spt16 function arises from a combination of both their unique and shared functions in transcription complex assembly and chromatin structure regulation. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Kinetic-energy matrix elements for atomic Hylleraas-CI wave functions.

PubMed

Harris, Frank E

2016-05-28

Hylleraas-CI is a superposition-of-configurations method in which each configuration is constructed from a Slater-type orbital (STO) product to which is appended (linearly) at most one interelectron distance rij. Computations of the kinetic energy for atoms by this method have been difficult due to the lack of formulas expressing these matrix elements for general angular momentum in terms of overlap and potential-energy integrals. It is shown here that a strategic application of angular-momentum theory, including the use of vector spherical harmonics, enables the reduction of all atomic kinetic-energy integrals to overlap and potential-energy matrix elements. The new formulas are validated by showing that they yield correct results for a large number of integrals published by other investigators.

Large Area Microcorrals and Cavity Formation on Cantilevers using a Focused Ion Beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saraf, Laxmikant V.; Britt, David W.

2011-09-14

We utilize focused ion beam (FIB) to explore various sputtering parameters to form large area microcorrals and cavities on cantilevers. Microcorrals were rapidly created by modifying ion beam blur and overlaps. Modification in FIB sputtering parameters affects the periodicity and shape of corral microstructure. Cantilever deflections show ion beam amorphization effects as a function of sputtered area and cantilever base cavities with or without side walls. The FIB sputtering parameters address a method for rapid creation of a cantilever tensiometer with integrated fluid storage and delivery.

50 CFR 229.32 - Atlantic large whale take reduction plan regulations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... South Channel Restricted Trap/Pot Area where it overlaps with Lobster Management Area (LMA) 2 and the... Trap/Pot Area overlaps with Lobster Management Area (LMA) 2 and the Outer Cape LMA (as defined in the... Offshore Management Area 3 (including the area known as the Area 2/3 Overlap and Area 3/5 Overlap as...

Cooperative interactions between hippocampal and striatal systems support flexible navigation

PubMed Central

Brown, Thackery I; Ross, Robert S; Tobyne, Sean M; Stern, Chantal E

2012-01-01

Research in animals and humans has demonstrated that the hippocampus is critical for retrieving distinct representations of overlapping sequences of information. There is recent evidence that the caudate nucleus and orbitofrontal cortex are also involved in disambiguation of overlapping spatial representations. The hippocampus and caudate are functionally distinct regions, but both have anatomical links with the orbitofrontal cortex. The present study used an fMRI-based functional connectivity analysis in humans to examine the functional relationship between the hippocampus, caudate, and orbitofrontal cortex when participants use contextual information to navigate well-learned spatial routes which share common elements. Participants were trained outside the scanner to navigate virtual mazes from a first-person perspective. Overlapping condition mazes began and ended at distinct locations, but converged in the middle to share some hallways with another maze. Non-overlapping condition mazes did not share any hallways with any other maze. Successful navigation through the overlapping hallways required contextual information identifying the current navigational route to guide the appropriate response for a given trial. Results revealed greater functional connectivity between the hippocampus, caudate, and orbitofrontal cortex for overlapping mazes compared to non-overlapping mazes. The current findings suggest that the hippocampus and caudate interact with prefrontal structures cooperatively for successful contextually-dependent navigation. PMID:22266411

Fast evaluation of solid harmonic Gaussian integrals for local resolution-of-the-identity methods and range-separated hybrid functionals.

PubMed

Golze, Dorothea; Benedikter, Niels; Iannuzzi, Marcella; Wilhelm, Jan; Hutter, Jürg

2017-01-21

An integral scheme for the efficient evaluation of two-center integrals over contracted solid harmonic Gaussian functions is presented. Integral expressions are derived for local operators that depend on the position vector of one of the two Gaussian centers. These expressions are then used to derive the formula for three-index overlap integrals where two of the three Gaussians are located at the same center. The efficient evaluation of the latter is essential for local resolution-of-the-identity techniques that employ an overlap metric. We compare the performance of our integral scheme to the widely used Cartesian Gaussian-based method of Obara and Saika (OS). Non-local interaction potentials such as standard Coulomb, modified Coulomb, and Gaussian-type operators, which occur in range-separated hybrid functionals, are also included in the performance tests. The speed-up with respect to the OS scheme is up to three orders of magnitude for both integrals and their derivatives. In particular, our method is increasingly efficient for large angular momenta and highly contracted basis sets.

Fast evaluation of solid harmonic Gaussian integrals for local resolution-of-the-identity methods and range-separated hybrid functionals

NASA Astrophysics Data System (ADS)

Golze, Dorothea; Benedikter, Niels; Iannuzzi, Marcella; Wilhelm, Jan; Hutter, Jürg

2017-01-01

An integral scheme for the efficient evaluation of two-center integrals over contracted solid harmonic Gaussian functions is presented. Integral expressions are derived for local operators that depend on the position vector of one of the two Gaussian centers. These expressions are then used to derive the formula for three-index overlap integrals where two of the three Gaussians are located at the same center. The efficient evaluation of the latter is essential for local resolution-of-the-identity techniques that employ an overlap metric. We compare the performance of our integral scheme to the widely used Cartesian Gaussian-based method of Obara and Saika (OS). Non-local interaction potentials such as standard Coulomb, modified Coulomb, and Gaussian-type operators, which occur in range-separated hybrid functionals, are also included in the performance tests. The speed-up with respect to the OS scheme is up to three orders of magnitude for both integrals and their derivatives. In particular, our method is increasingly efficient for large angular momenta and highly contracted basis sets.

Neurogenesis and pattern separation: time for a divorce.

PubMed

Becker, Suzanna

2017-05-01

The generation of new neurons in the adult mammalian brain has led to numerous theories as to their functional significance. One of the most widely held views is that adult neurogenesis promotes pattern separation, a process by which overlapping patterns of neural activation are mapped to less overlapping representations. While a large body of evidence supports a role for neurogenesis in high interference memory tasks, it does not support the proposed function of neurogenesis in mediating pattern separation. Instead, the adult-generated neurons seem to generate highly overlapping and yet distinct distributed representations for similar events. One way in which these immature, highly plastic, hyperactive neurons may contribute to novel memory formation while avoiding interference is by virtue of their extremely sparse connectivity with incoming perforant path fibers. Another intriguing proposal, awaiting empirical confirmation, is that the young neurons' recruitment into memory formation is gated by a novelty/mismatch mechanism mediated by CA3 or hilar back-projections. Ongoing research into the intriguing link between neurogenesis, stress-related mood disorders, and age-related neurodegeneration may lead to promising neurogenesis-based treatments for this wide range of clinical disorders. WIREs Cogn Sci 2017, 8:e1427. doi: 10.1002/wcs.1427 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Quark cluster model for deep-inelastic lepton-deuteron scattering

NASA Astrophysics Data System (ADS)

Yen, G.; Vary, J. P.; Harindranath, A.; Pirner, H. J.

1990-10-01

We evaluate the contribution of quasifree nucleon knockout and of inelastic lepton-nucleon scattering in inclusive electron-deuteron reactions at large momentum transfer. We examine the degree of quantitative agreement with deuteron wave functions from the Reid soft-core and Bonn realistic nucleon-nucleon interactions. For the range of data available there is strong sensitivity to the tensor correlations which are distinctively different in these two deuteron models. At this stage of the analyses the Reid soft-core wave function provides a reasonable description of the data while the Bonn wave function does not. We then include a six-quark cluster component whose relative contribution is based on an overlap criterion and obtain a good description of all the data with both interactions. The critical separation at which overlap occurs (formation of six-quark clusters) is taken to be 1.0 fm and the six-quark cluster probability is 4.7% for Reid and 5.4% for Bonn. As a consequence the quark cluster model with either Reid or Bonn wave function describe the SLAC inclusive electron-deuteron scattering data equally well. We then show how additional data would be decisive in resolving which model is ultimately more correct.

The familial co-aggregation of ASD and ADHD: a register-based cohort study.

PubMed

Ghirardi, L; Brikell, I; Kuja-Halkola, R; Freitag, C M; Franke, B; Asherson, P; Lichtenstein, P; Larsson, H

2018-02-01

Autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD) frequently co-occur. The presence of a genetic link between ASD and ADHD symptoms is supported by twin studies, but the genetic overlap between clinically ascertained ASD and ADHD remains largely unclear. We therefore investigated how ASD and ADHD co-aggregate in individuals and in families to test for the presence of a shared genetic liability and examined potential differences between low- and high-functioning ASD in the link with ADHD. We studied 1 899 654 individuals born in Sweden between 1987 and 2006. Logistic regression was used to estimate the association between clinically ascertained ASD and ADHD in individuals and in families. Stratified estimates were obtained for ASD with (low-functioning) and without (high-functioning) intellectual disability. Individuals with ASD were at higher risk of having ADHD compared with individuals who did not have ASD (odds ratio (OR)=22.33, 95% confidence interval (CI): 21.77-22.92). The association was stronger for high-functioning than for low-functioning ASD. Relatives of individuals with ASD were at higher risk of ADHD compared with relatives of individuals without ASD. The association was stronger in monozygotic twins (OR=17.77, 95% CI: 9.80-32.22) than in dizygotic twins (OR=4.33, 95% CI: 3.21-5.85) and full siblings (OR=4.59, 95% CI: 4.39-4.80). Individuals with ASD and their relatives are at increased risk of ADHD. The pattern of association across different types of relatives supports the existence of genetic overlap between clinically ascertained ASD and ADHD, suggesting that genomic studies might have underestimated this overlap.

Stimulus-response correspondence effect as a function of temporal overlap between relevant and irrelevant information processing.

PubMed

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.

Shared genetic risk between corticobasal degeneration, progressive supranuclear palsy, and frontotemporal dementia

PubMed Central

Yokoyama, Jennifer S.; Karch, Celeste M.; Fan, Chun C.; Bonham, Luke W.; Kouri, Naomi; Ross, Owen A.; Rademakers, Rosa; Kim, Jungsu; Wang, Yunpeng; Höglinger, Günter U.; Muller, Ulrich; Ferrari, Raffaele; Hardy, John; Momeni, Parastoo; Sugrue, Leo P.; Hess, Christopher P.; Barkovich, A. James; Boxer, Adam L.; Seeley, William W.; Rabinovici, Gil D.; Rosen, Howard J.; Miller, Bruce L.; Schmansky, Nicholas J.; Fischl, Bruce; Hyman, Bradley T.; Dickson, Dennis W.; Schellenberg, Gerard D.; Andreassen, Ole A.; Dale, Anders M.; Desikan, Rahul S.

2017-01-01

Corticobasal degeneration (CBD), progressive supranuclear palsy (PSP) and a subset of frontotemporal dementia (FTD) are neurodegenerative disorders characterized by tau inclusions in neurons and glia (tauopathies). Although clinical, pathological and genetic evidence suggests overlapping pathobiology between CBD, PSP, and FTD, the relationship between these disorders is still not well understood. Using summary statistics (odds ratios and p-values) from large genome-wide association studies (total n = 14,286 cases and controls) and recently established genetic methods, we investigated the genetic overlap between CBD and PSP and CBD and FTD. We found up to 800-fold enrichment of genetic risk in CBD across different levels of significance for PSP or FTD. In addition to NSF (tagging the MAPT H1 haplotype), we observed that SNPs in or near MOBP, CXCR4, EGFR, and GLDC showed significant genetic overlap between CBD and PSP, whereas only SNPs tagging the MAPT haplotype overlapped between CBD and FTD. The risk alleles of the shared SNPs were associated with expression changes in cis-genes. Evaluating transcriptome levels across adult human brains, we found a unique neuroanatomic gene expression signature for each of the five overlapping gene loci (omnibus ANOVA p < 2.0 × 10−16). Functionally, we found that these shared risk genes were associated with protein interaction and gene co-expression networks and showed enrichment for several neurodevelopmental pathways. Our findings suggest: i) novel genetic overlap between CBD and PSP beyond the MAPT locus; ii) strong ties between CBD and FTD through the MAPT clade, and; iii) unique combinations of overlapping genes that may, in part, influence selective regional or neuronal vulnerability observed in specific tauopathies. PMID:28271184

Locating overlapping dense subgraphs in gene (protein) association networks and predicting novel protein functional groups among these subgraphs

NASA Astrophysics Data System (ADS)

Palla, Gergely; Derenyi, Imre; Farkas, Illes J.; Vicsek, Tamas

2006-03-01

Most tasks in a cell are performed not by individual proteins, but by functional groups of proteins (either physically interacting with each other or associated in other ways). In gene (protein) association networks these groups show up as sets of densely connected nodes. In the yeast, Saccharomyces cerevisiae, known physically interacting groups of proteins (called protein complexes) strongly overlap: the total number of proteins contained by these complexes by far underestimates the sum of their sizes (2750 vs. 8932). Thus, most functional groups of proteins, both physically interacting and other, are likely to share many of their members with other groups. However, current algorithms searching for dense groups of nodes in networks usually exclude overlaps. With the aim to discover both novel functions of individual proteins and novel protein functional groups we combine in protein association networks (i) a search for overlapping dense subgraphs based on the Clique Percolation Method (CPM) (Palla, G., et.al. Nature 435, 814-818 (2005), http://angel.elte.hu/clustering), which explicitly allows for overlaps among the groups, and (ii) a verification and characterization of the identified groups of nodes (proteins) with the help of standard annotation databases listing known functions.

Patterns of resting state connectivity in human primary visual cortical areas: a 7T fMRI study.

PubMed

Raemaekers, Mathijs; Schellekens, Wouter; van Wezel, Richard J A; Petridou, Natalia; Kristo, Gert; Ramsey, Nick F

2014-01-01

The nature and origin of fMRI resting state fluctuations and connectivity are still not fully known. More detailed knowledge on the relationship between resting state patterns and brain function may help to elucidate this matter. We therefore performed an in depth study of how resting state fluctuations map to the well known architecture of the visual system. We investigated resting state connectivity at both a fine and large scale within and across visual areas V1, V2 and V3 in ten human subjects using a 7Tesla scanner. We found evidence for several coexisting and overlapping connectivity structures at different spatial scales. At the fine-scale level we found enhanced connectivity between the same topographic locations in the fieldmaps of V1, V2 and V3, enhanced connectivity to the contralateral functional homologue, and to a lesser extent enhanced connectivity between iso-eccentric locations within the same visual area. However, by far the largest proportion of the resting state fluctuations occurred within large-scale bilateral networks. These large-scale networks mapped to some extent onto the architecture of the visual system and could thereby obscure fine-scale connectivity. In fact, most of the fine-scale connectivity only became apparent after the large-scale network fluctuations were filtered from the timeseries. We conclude that fMRI resting state fluctuations in the visual cortex may in fact be a composite signal of different overlapping sources. Isolating the different sources could enhance correlations between BOLD and electrophysiological correlates of resting state activity. © 2013 Elsevier Inc. All rights reserved.

Functional and phylogenetic relatedness in temporary wetland invertebrates: current macroecological patterns and implications for future climatic change scenarios.

PubMed

Ruhí, Albert; Boix, Dani; Gascón, Stéphanie; Sala, Jordi; Batzer, Darold P

2013-01-01

In freshwater ecosystems, species compositions are known to be determined hierarchically by large to small‑scale environmental factors, based on the biological traits of the organisms. However, in ephemeral habitats this heuristic framework remains largely untested. Although temporary wetland faunas are constrained by a local filter (i.e., desiccation), we propose its magnitude may still depend on large-scale climate characteristics. If this is true, climate should be related to the degree of functional and taxonomic relatedness of invertebrate communities inhabiting seasonal wetlands. We tested this hypothesis in two ways. First, based on 52 biological traits for invertebrates, we conducted a case study to explore functional trends among temperate seasonal wetlands differing in the harshness (i.e., dryness) of their dry season. After finding evidence of trait filtering, we addressed whether it could be generalized across a broader climatic scale. To this end, a meta-analysis (225 seasonal wetlands spread across broad climatic categories: Arid, Temperate, and Cold) allowed us to identify whether an equivalent climate-dependent pattern of trait richness was consistent between the Nearctic and the Western Palearctic. Functional overlap of invertebrates increased from mild (i.e., Temperate) to harsher climates (i.e., Arid and Cold), and phylogenetic clustering (using taxonomy as a surrogate) was highest in Arid and lowest in Temperate wetlands. We show that, (i) as has been described in streams, higher relatedness than would be expected by chance is generally observed in seasonal wetland invertebrate communities; and (ii) this relatedness is not constant but climate-dependent, with the climate under which a given seasonal wetland is located determining the functional overlap and the phylogenetic clustering of the community. Finally, using a space-for-time substitution approach we suggest our results may anticipate how the invertebrate biodiversity embedded in these vulnerable and often overlooked ecosystems will be affected by long-term climate change.

Functional and Phylogenetic Relatedness in Temporary Wetland Invertebrates: Current Macroecological Patterns and Implications for Future Climatic Change Scenarios

PubMed Central

Ruhí, Albert; Boix, Dani; Gascón, Stéphanie; Sala, Jordi; Batzer, Darold P.

2013-01-01

In freshwater ecosystems, species compositions are known to be determined hierarchically by large to small‑scale environmental factors, based on the biological traits of the organisms. However, in ephemeral habitats this heuristic framework remains largely untested. Although temporary wetland faunas are constrained by a local filter (i.e., desiccation), we propose its magnitude may still depend on large-scale climate characteristics. If this is true, climate should be related to the degree of functional and taxonomic relatedness of invertebrate communities inhabiting seasonal wetlands. We tested this hypothesis in two ways. First, based on 52 biological traits for invertebrates, we conducted a case study to explore functional trends among temperate seasonal wetlands differing in the harshness (i.e., dryness) of their dry season. After finding evidence of trait filtering, we addressed whether it could be generalized across a broader climatic scale. To this end, a meta-analysis (225 seasonal wetlands spread across broad climatic categories: Arid, Temperate, and Cold) allowed us to identify whether an equivalent climate-dependent pattern of trait richness was consistent between the Nearctic and the Western Palearctic. Functional overlap of invertebrates increased from mild (i.e., Temperate) to harsher climates (i.e., Arid and Cold), and phylogenetic clustering (using taxonomy as a surrogate) was highest in Arid and lowest in Temperate wetlands. We show that, (i) as has been described in streams, higher relatedness than would be expected by chance is generally observed in seasonal wetland invertebrate communities; and (ii) this relatedness is not constant but climate-dependent, with the climate under which a given seasonal wetland is located determining the functional overlap and the phylogenetic clustering of the community. Finally, using a space-for-time substitution approach we suggest our results may anticipate how the invertebrate biodiversity embedded in these vulnerable and often overlooked ecosystems will be affected by long-term climate change. PMID:24312347

Cross-section fluctuations in chaotic scattering systems.

PubMed

Ericson, Torleif E O; Dietz, Barbara; Richter, Achim

2016-10-01

Exact analytical expressions for the cross-section correlation functions of chaotic scattering systems have hitherto been derived only under special conditions. The objective of the present article is to provide expressions that are applicable beyond these restrictions. The derivation is based on a statistical model of Breit-Wigner type for chaotic scattering amplitudes which has been shown to describe the exact analytical results for the scattering (S)-matrix correlation functions accurately. Our results are given in the energy and in the time representations and apply in the whole range from isolated to overlapping resonances. The S-matrix contributions to the cross-section correlations are obtained in terms of explicit irreducible and reducible correlation functions. Consequently, the model can be used for a detailed exploration of the key features of the cross-section correlations and the underlying physical mechanisms. In the region of isolated resonances, the cross-section correlations contain a dominant contribution from the self-correlation term. For narrow states the self-correlations originate predominantly from widely spaced states with exceptionally large partial width. In the asymptotic region of well-overlapping resonances, the cross-section autocorrelation functions are given in terms of the S-matrix autocorrelation functions. For inelastic correlations, in particular, the Ericson fluctuations rapidly dominate in that region. Agreement with known analytical and experimental results is excellent.

Kinetic-energy matrix elements for atomic Hylleraas-CI wave functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, Frank E., E-mail: harris@qtp.ufl.edu

Hylleraas-CI is a superposition-of-configurations method in which each configuration is constructed from a Slater-type orbital (STO) product to which is appended (linearly) at most one interelectron distance r{sub ij}. Computations of the kinetic energy for atoms by this method have been difficult due to the lack of formulas expressing these matrix elements for general angular momentum in terms of overlap and potential-energy integrals. It is shown here that a strategic application of angular-momentum theory, including the use of vector spherical harmonics, enables the reduction of all atomic kinetic-energy integrals to overlap and potential-energy matrix elements. The new formulas are validatedmore » by showing that they yield correct results for a large number of integrals published by other investigators.« less

Corrected Mean-Field Model for Random Sequential Adsorption on Random Geometric Graphs

NASA Astrophysics Data System (ADS)

Dhara, Souvik; van Leeuwaarden, Johan S. H.; Mukherjee, Debankur

2018-03-01

A notorious problem in mathematics and physics is to create a solvable model for random sequential adsorption of non-overlapping congruent spheres in the d-dimensional Euclidean space with d≥ 2 . Spheres arrive sequentially at uniformly chosen locations in space and are accepted only when there is no overlap with previously deposited spheres. Due to spatial correlations, characterizing the fraction of accepted spheres remains largely intractable. We study this fraction by taking a novel approach that compares random sequential adsorption in Euclidean space to the nearest-neighbor blocking on a sequence of clustered random graphs. This random network model can be thought of as a corrected mean-field model for the interaction graph between the attempted spheres. Using functional limit theorems, we characterize the fraction of accepted spheres and its fluctuations.

Wigner crystalline edges in ν<~1 quantum dots

NASA Astrophysics Data System (ADS)

Goldmann, Eyal; Renn, Scot R.

1999-12-01

We investigate the edge reconstruction phenomenon believed to occur in quantum dots in the quantum Hall regime when the filling fraction is ν<~1. Our approach involves the examination of large dots (<= 40 electrons) using a partial diagonalization technique in which the occupancies of the deep interior orbitals are frozen. To interpret the results of this calculation, we evaluate the overlap between the diagonalized ground state and a set of trial wave functions which we call projected necklace (PN) states. A PN state is simply the angular momentum projection of a maximum density droplet surrounded by a ring of localized electrons. Our calculations reveal that PN states have up to 99% overlap with the diagonalized ground states, and are lower in energy than the states identified in Chamon and Wen's study of the edge reconstruction.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

PubMed Central

Margulies, Elliott H.; Cooper, Gregory M.; Asimenos, George; Thomas, Daryl J.; Dewey, Colin N.; Siepel, Adam; Birney, Ewan; Keefe, Damian; Schwartz, Ariel S.; Hou, Minmei; Taylor, James; Nikolaev, Sergey; Montoya-Burgos, Juan I.; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Brown, James B.; Bickel, Peter; Holmes, Ian; Mullikin, James C.; Ureta-Vidal, Abel; Paten, Benedict; Stone, Eric A.; Rosenbloom, Kate R.; Kent, W. James; Bouffard, Gerard G.; Guan, Xiaobin; Hansen, Nancy F.; Idol, Jacquelyn R.; Maduro, Valerie V.B.; Maskeri, Baishali; McDowell, Jennifer C.; Park, Morgan; Thomas, Pamela J.; Young, Alice C.; Blakesley, Robert W.; Muzny, Donna M.; Sodergren, Erica; Wheeler, David A.; Worley, Kim C.; Jiang, Huaiyang; Weinstock, George M.; Gibbs, Richard A.; Graves, Tina; Fulton, Robert; Mardis, Elaine R.; Wilson, Richard K.; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B.; Chang, Jean L.; Lindblad-Toh, Kerstin; Lander, Eric S.; Hinrichs, Angie; Trumbower, Heather; Clawson, Hiram; Zweig, Ann; Kuhn, Robert M.; Barber, Galt; Harte, Rachel; Karolchik, Donna; Field, Matthew A.; Moore, Richard A.; Matthewson, Carrie A.; Schein, Jacqueline E.; Marra, Marco A.; Antonarakis, Stylianos E.; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross; Haussler, David; Miller, Webb; Pachter, Lior; Green, Eric D.; Sidow, Arend

2007-01-01

A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization. PMID:17567995

Identifying Risk: Concurrent Overlap of the Antarctic Krill Fishery with Krill-Dependent Predators in the Scotia Sea.

PubMed

Hinke, Jefferson T; Cossio, Anthony M; Goebel, Michael E; Reiss, Christian S; Trivelpiece, Wayne Z; Watters, George M

2017-01-01

Mitigating direct and indirect interactions between marine predators and fisheries is a motivating factor for ecosystem-based fisheries management (EBFM), especially where predators and fisheries compete for a shared resource. One difficulty in advancing EBFM is parameterizing clear functional responses of predators to indices of prey availability. Alternative characterizations of fishery-predator interactions may therefore benefit the implementation of EBFM. Telemetry data identify foraging areas used by predators and, therefore, represent critical information to mitigate potential competition between predators and fisheries. We analyzed six years (2009-2014) of telemetry data collected at Cape Shirreff, Livingston Island and Admiralty Bay, King George Island, Antarctica, on three species of Pygoscelid penguins and female Antarctic fur seals. In this region, all four species are primarily dependent on Antarctic krill. The tracking data demonstrate local movements near breeding colonies during the austral summer and dispersal from breeding colonies during the winter. We then assessed overlap between predators and the Antarctic krill fishery on a suite of spatiotemporal scales to examine how different data aggregations affect the extent and location of overlap. Concurrent overlap was observed on all spatiotemporal scales considered throughout the Antarctic Peninsula and South Orkney Islands region, including near tagging locations and in distant areas where recent fishing activity has concentrated. Overlap occurred at depths where mean krill densities were relatively high. Our results demonstrate that direct overlap of krill-dependent predators with the krill fishery on small spatiotemporal scales is relatively common throughout the Antarctic Peninsula region. As the krill fishery continues to develop and efforts to implement ecosystem-based management mature, indices of overlap may provide a useful metric for indicating where the risks of fishing are highest. A precautionary approach to allocating krill catches in space would be to avoid large increases in catch where overlap on small spatiotemporal scales is common.

Identifying Risk: Concurrent Overlap of the Antarctic Krill Fishery with Krill-Dependent Predators in the Scotia Sea

PubMed Central

Hinke, Jefferson T.

2017-01-01

Mitigating direct and indirect interactions between marine predators and fisheries is a motivating factor for ecosystem-based fisheries management (EBFM), especially where predators and fisheries compete for a shared resource. One difficulty in advancing EBFM is parameterizing clear functional responses of predators to indices of prey availability. Alternative characterizations of fishery-predator interactions may therefore benefit the implementation of EBFM. Telemetry data identify foraging areas used by predators and, therefore, represent critical information to mitigate potential competition between predators and fisheries. We analyzed six years (2009–2014) of telemetry data collected at Cape Shirreff, Livingston Island and Admiralty Bay, King George Island, Antarctica, on three species of Pygoscelid penguins and female Antarctic fur seals. In this region, all four species are primarily dependent on Antarctic krill. The tracking data demonstrate local movements near breeding colonies during the austral summer and dispersal from breeding colonies during the winter. We then assessed overlap between predators and the Antarctic krill fishery on a suite of spatiotemporal scales to examine how different data aggregations affect the extent and location of overlap. Concurrent overlap was observed on all spatiotemporal scales considered throughout the Antarctic Peninsula and South Orkney Islands region, including near tagging locations and in distant areas where recent fishing activity has concentrated. Overlap occurred at depths where mean krill densities were relatively high. Our results demonstrate that direct overlap of krill-dependent predators with the krill fishery on small spatiotemporal scales is relatively common throughout the Antarctic Peninsula region. As the krill fishery continues to develop and efforts to implement ecosystem-based management mature, indices of overlap may provide a useful metric for indicating where the risks of fishing are highest. A precautionary approach to allocating krill catches in space would be to avoid large increases in catch where overlap on small spatiotemporal scales is common. PMID:28085943

RNAi Experiments in D. melanogaster: Solutions to the Overlooked Problem of Off-Targets Shared by Independent dsRNAs

PubMed Central

Seinen, Erwin; Burgerhof, Johannes G. M.; Jansen, Ritsert C.; Sibon, Ody C. M.

2010-01-01

Background RNAi technology is widely used to downregulate specific gene products. Investigating the phenotype induced by downregulation of gene products provides essential information about the function of the specific gene of interest. When RNAi is applied in Drosophila melanogaster or Caenorhabditis elegans, often large dsRNAs are used. One of the drawbacks of RNAi technology is that unwanted gene products with sequence similarity to the gene of interest can be down regulated too. To verify the outcome of an RNAi experiment and to avoid these unwanted off-target effects, an additional non-overlapping dsRNA can be used to down-regulate the same gene. However it has never been tested whether this approach is sufficient to reduce the risk of off-targets. Methodology We created a novel tool to analyse the occurance of off-target effects in Drosophila and we analyzed 99 randomly chosen genes. Principal Findings Here we show that nearly all genes contain non-overlapping internal sequences that do show overlap in a common off-target gene. Conclusion Based on our in silico findings, off-target effects should not be ignored and our presented on-line tool enables the identification of two RNA interference constructs, free of overlapping off-targets, from any gene of interest. PMID:20957038

Relationships among cloud occurrence frequency, overlap, and effective thickness derived from CALIPSO and CloudSat merged cloud vertical profiles

NASA Astrophysics Data System (ADS)

Kato, Seiji; Sun-Mack, Sunny; Miller, Walter F.; Rose, Fred G.; Chen, Yan; Minnis, Patrick; Wielicki, Bruce A.

2010-01-01

A cloud frequency of occurrence matrix is generated using merged cloud vertical profiles derived from the satellite-borne Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) and cloud profiling radar. The matrix contains vertical profiles of cloud occurrence frequency as a function of the uppermost cloud top. It is shown that the cloud fraction and uppermost cloud top vertical profiles can be related by a cloud overlap matrix when the correlation length of cloud occurrence, which is interpreted as an effective cloud thickness, is introduced. The underlying assumption in establishing the above relation is that cloud overlap approaches random overlap with increasing distance separating cloud layers and that the probability of deviating from random overlap decreases exponentially with distance. One month of Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and CloudSat data (July 2006) support these assumptions, although the correlation length sometimes increases with separation distance when the cloud top height is large. The data also show that the correlation length depends on cloud top hight and the maximum occurs when the cloud top height is 8 to 10 km. The cloud correlation length is equivalent to the decorrelation distance introduced by Hogan and Illingworth (2000) when cloud fractions of both layers in a two-cloud layer system are the same. The simple relationships derived in this study can be used to estimate the top-of-atmosphere irradiance difference caused by cloud fraction, uppermost cloud top, and cloud thickness vertical profile differences.

Different left brain regions are essential for grasping a tool compared with its subsequent use.

PubMed

Randerath, Jennifer; Goldenberg, Georg; Spijkers, Will; Li, Yong; Hermsdörfer, Joachim

2010-10-15

Tool use engages a left hemispheric network including frontal, temporal and parietal regions. Patients with left brain lesions (LBD patients) exhibit deficits when demonstrating use of a single tool (apraxia). When attempting to use a tool, some apraxic patients show errors in the preceding grasping movement. Forty-two LBD patients and 18 healthy controls grasped individual tools and demonstrated their typical use. For patients with a tool use impairment (22), lesion analysis revealed a large area of overlap in the left hemisphere, mainly in the supramarginal gyrus (SMG). For patients with erroneous grasping (12), the lesion overlay showed overlaps in the left frontal and parietal cortices, especially in the inferior frontal gyrus (IFG) and the angular gyrus (ANG). However, contrasting lesions associated with impaired grasping versus tool use impairments reveal little overlap, limited to the inferior parietal cortex. Presumably the left IFG is involved in selection processes in the context of tool use, such as choosing a functional or non-functional grasping movement depending on the task and the online information about the tool's structure and orientation. The ANG might provide this grasp related information, which is relevant for the specific action. The contribution of the SMG to tool use involves more general principals, such as integrating online and learned tool use information into the action plan for the use movement. Copyright 2010 Elsevier Inc. All rights reserved.

Integrated defense system overlaps as a disease model: with examples for multiple chemical sensitivity.

PubMed Central

Rowat, S C

1998-01-01

The central nervous, immune, and endocrine systems communicate through multiple common messengers. Over evolutionary time, what may be termed integrated defense system(s) (IDS) have developed to coordinate these communications for specific contexts; these include the stress response, acute-phase response, nonspecific immune response, immune response to antigen, kindling, tolerance, time-dependent sensitization, neurogenic switching, and traumatic dissociation (TD). These IDSs are described and their overlap is examined. Three models of disease production are generated: damage, in which IDSs function incorrectly; inadequate/inappropriate, in which IDS response is outstripped by a changing context; and evolving/learning, in which the IDS learned response to a context is deemed pathologic. Mechanisms of multiple chemical sensitivity (MCS) are developed from several IDS disease models. Model 1A is pesticide damage to the central nervous system, overlapping with body chemical burdens, TD, and chronic zinc deficiency; model 1B is benzene disruption of interleukin-1, overlapping with childhood developmental windows and hapten-antigenic spreading; and model 1C is autoimmunity to immunoglobulin-G (IgG), overlapping with spreading to other IgG-inducers, sudden spreading of inciters, and food-contaminating chemicals. Model 2A is chemical and stress overload, including comparison with the susceptibility/sensitization/triggering/spreading model; model 2B is genetic mercury allergy, overlapping with: heavy metals/zinc displacement and childhood/gestational mercury exposures; and model 3 is MCS as evolution and learning. Remarks are offered on current MCS research. Problems with clinical measurement are suggested on the basis of IDS models. Large-sample patient self-report epidemiology is described as an alternative or addition to clinical biomarker and animal testing. Images Figure 1 Figure 2 Figure 3 Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:9539008

Graph theoretical analysis of functional network for comprehension of sign language.

PubMed

Liu, Lanfang; Yan, Xin; Liu, Jin; Xia, Mingrui; Lu, Chunming; Emmorey, Karen; Chu, Mingyuan; Ding, Guosheng

2017-09-15

Signed languages are natural human languages using the visual-motor modality. Previous neuroimaging studies based on univariate activation analysis show that a widely overlapped cortical network is recruited regardless whether the sign language is comprehended (for signers) or not (for non-signers). Here we move beyond previous studies by examining whether the functional connectivity profiles and the underlying organizational structure of the overlapped neural network may differ between signers and non-signers when watching sign language. Using graph theoretical analysis (GTA) and fMRI, we compared the large-scale functional network organization in hearing signers with non-signers during the observation of sentences in Chinese Sign Language. We found that signed sentences elicited highly similar cortical activations in the two groups of participants, with slightly larger responses within the left frontal and left temporal gyrus in signers than in non-signers. Crucially, further GTA revealed substantial group differences in the topologies of this activation network. Globally, the network engaged by signers showed higher local efficiency (t (24) =2.379, p=0.026), small-worldness (t (24) =2.604, p=0.016) and modularity (t (24) =3.513, p=0.002), and exhibited different modular structures, compared to the network engaged by non-signers. Locally, the left ventral pars opercularis served as a network hub in the signer group but not in the non-signer group. These findings suggest that, despite overlap in cortical activation, the neural substrates underlying sign language comprehension are distinguishable at the network level from those for the processing of gestural action. Copyright © 2017 Elsevier B.V. All rights reserved.

Radiative Impacts of Cloud Heterogeneity and Overlap in an Atmospheric General Circulation Model

NASA Technical Reports Server (NTRS)

Oreopoulos, L.; Lee, D.; Sud, Y. C.; Suarez, M. J.

2012-01-01

The radiative impacts of introducing horizontal heterogeneity of layer cloud condensate, and vertical overlap of condensate and cloud fraction are examined with the aid of a new radiation package operating in the GEOS-5 Atmospheric General Circulation Model. The impacts are examined in terms of diagnostic top-of-the-atmosphere shortwave (SW) and longwave (LW) cloud radiative effect (CRE) calculations for a range of assumptions and parameter specifications about the overlap. The investigation is conducted for two distinct cloud schemes, the one that comes with the standard GEOS-5 distribution, and another which has been recently used experimentally for its enhanced GEOS-5 distribution, and another which has been recently used experimentally for its enhanced cloud microphysical capabilities; both are coupled to a cloud generator allowing arbitrary cloud overlap specification. We find that cloud overlap radiative impacts are significantly stronger for the operational cloud scheme for which a change of cloud fraction overlap from maximum-random to generalized results to global changes of SW and LW CRE of approximately 4 Watts per square meter, and zonal changes of up to approximately 10 Watts per square meter. This is because of fewer occurrences compared to the other scheme of large layer cloud fractions and of multi-layer situations with large numbers of atmospheric being simultaneously cloudy, conditions that make overlap details more important. The impact on CRE of the details of condensate distribution overlap is much weaker. Once generalized overlap is adopted, both cloud schemes are only modestly sensitive to the exact values of the overlap parameters. We also find that if one of the CRE components is overestimated and the other underestimated, both cannot be driven towards observed values by adjustments to cloud condensate heterogeneity and overlap alone.

Conditional probability distribution function of "energy transfer rate" (PDF(ɛ|PVI)) as compared with its counterpart of temperature (PDF(T|PVI)) at the same condition of fluctuation

NASA Astrophysics Data System (ADS)

He, Jiansen; Wang, Yin; Pei, Zhongtian; Zhang, Lei; Tu, Chuanyi

2017-04-01

Energy transfer rate of turbulence is not uniform everywhere but suggested to follow a certain distribution, e.g., lognormal distribution (Kolmogorov 1962). The inhomogeneous transfer rate leads to emergence of intermittency, which may be identified with some parameter, e.g., normalized partial variance increments (PVI) (Greco et al., 2009). Large PVI of magnetic field fluctuations are found to have a temperature distribution with the median and mean values higher than that for small PVI level (Osman et al., 2012). However, there is a large proportion of overlap between temperature distributions associated with the smaller and larger PVIs. So it is recognized that only PVI cannot fully determine the temperature, since the one-to-one mapping relationship does not exist. One may be curious about the reason responsible for the considerable overlap of conditional temperature distribution for different levels of PVI. Usually the hotter plasma with higher temperature is speculated to be heated more with more dissipation of turbulence energy corresponding to more energy cascading rate, if the temperature fluctuation of the eigen wave mode is not taken into account. To explore the statistical relationship between turbulence cascading and plasma thermal state, we aim to study and reveal, for the first time, the conditional probability function of "energy transfer rate" under different levels of PVI condition (PDF(ɛ|PVI)), and compare it with the conditional probability function of temperature. The conditional probability distribution function, PDF(ɛ|PVI), is derived from PDF(PVI|ɛ)·PDF(ɛ)/PDF(PVI) according to the Bayesian theorem. PDF(PVI) can be obtained directly from the data. PDF(ɛ) is derived from the conjugate-gradient inversion of PDF(PVI) by assuming reasonably that PDF(δB|σ) is a Gaussian distribution, where PVI=|δB|/ σ and σ ( ɛι)1/3. PDF(ɛ) can also be acquired from fitting PDF(δB) with an integral function ∫PDF(δB|σ)PDF(σ)d σ. As a result, PDF(ɛ|PVI) is found to shift to higher median value of ɛ with increasing PVI but with a significant overlap of PDFs for different PVIs. Therefore, PDF(ɛ|PVI) is similar to PDF(T|PVI) in the sense of slow migration along with increasing PVI. The detailed comparison between these two conditional PDFs are also performed.

Meta-analysis: how does posterior parietal cortex contribute to reasoning?

PubMed Central

Wendelken, Carter

2015-01-01

Reasoning depends on the contribution of posterior parietal cortex (PPC). But PPC is involved in many basic operations—including spatial attention, mathematical cognition, working memory, long-term memory, and language—and the nature of its contribution to reasoning is unclear. Psychological theories of the processes underlying reasoning make divergent claims about the neural systems that are likely to be involved, and better understanding the specific contribution of PPC can help to inform these theories. We set out to address several competing hypotheses, concerning the role of PPC in reasoning: (1) reasoning involves application of formal logic and is dependent on language, with PPC activation for reasoning mainly reflective of linguistic processing; (2) reasoning involves probabilistic computation and is thus dependent on numerical processing mechanisms in PPC; and (3) reasoning is built upon the representation and processing of spatial relations, and PPC activation associated with reasoning reflects spatial processing. We conducted two separate meta-analyses. First, we pooled data from our own studies of reasoning in adults, and examined activation in PPC regions of interest (ROI). Second, we conducted an automated meta-analysis using Neurosynth, in which we examined overlap between activation maps associated with reasoning and maps associated with other key functions of PPC. In both analyses, we observed reasoning-related activation concentrated in the left Inferior Parietal Lobe (IPL). Reasoning maps demonstrated the greatest overlap with mathematical cognition. Maintenance, visuospatial, and phonological processing also demonstrated some overlap with reasoning, but a large portion of the reasoning map did not overlap with the map for any other function. This evidence suggests that the PPC’s contribution to reasoning may be most closely related to its role in mathematical cognition, but that a core component of this contribution may be specific to reasoning. PMID:25653604

Local structural change in zircon following radiation damage accumulation. Observation by 29Si nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Farnan, I.; Trachenko, K.

2003-04-01

29Si nuclear magnetic resonance (NMR) is a one of the most useful probes of the local structure of silicates. One of the results of recent studies of naturally radiation damaged zircons is that there is an evolution of the local structure in both crystalline and amorphous fractions of partially metamict zircon as a function of accumulated α-dose. We have examined the evolution of this local structure within the framework of several models of damage accumulation. The total number of displaced atoms produced per α-decay as function of accumulated dose, as measured by NMR, is not consistent with the idea of multiple overlap events being responsible for the evolution of the total damaged fraction. However, increased connectivity in the damaged region as the number of α-events increases is correlated to the degree of cascade overlap. The results of large scale atomistic (MD) simulations of heavy nuclei recoils at realistic energies (70keV) are consistent with the NMR quantification and also with TEM estimates of the diameters of damaged regions. The local heterogeneity (density and bonding) in the damaged area in the simulations is consistent with the existence of connected silicate tetrahedra. Detailed experiments on the annealing of damaged zircons at 500 and 600^oC have been performed. These show that a significant energetic barrier to the recrystallisation exists at these temperatures once a small fraction of damaged material has been recrystallised. This correlates well with the degree of cascade overlap. Indicating that the more connected SiO_4 tetrahedra present this barrier. A sample with very little cascade overlap can be annealed to ˜97% crystallinity at these temperatures.

Post-traumatic stress disorder vs traumatic brain injury

PubMed Central

Bryant, Richard

2011-01-01

Post-traumatic stress disorder (PTSD) and traumatic brain injury (TBI) often coexist because brain injuries are often sustained in traumatic experiences. This review outlines the significant overlap between PTSD and TBI by commencing with a critical outline of the overlapping symptoms and problems of differential diagnosis. The impact of TBI on PTSD is then described, with increasing evidence suggesting that mild TBI can increase risk for PTSD. Several explanations are offered for this enhanced risk. Recent evidence suggests that impairment secondary to mild TBI is largely attributable to stress reactions after TBI, which challenges the long-held belief that postconcussive symptoms are a function of neurological insult This recent evidence is pointing to new directions for treatment of postconcussive symptoms that acknowledge that treating stress factors following TBI may be the optimal means to manage the effects of many TBIs, PMID:22034252

Non-expanded dispersion and induction energies, and damping functions, for molecular interactions with application to HF-He

NASA Astrophysics Data System (ADS)

Knowles, Peter J.; Meath, William J.

The evaluation of second order non-expanded dispersion and induction energies, and the associated damping functions, for interactions involving molecules is discussed with emphasis placed on using the time-dependent coupled Hartree-Fock method. Results are given for the HF-He interaction for all individual partial wave non-expanded dispersion and induction energies varying asymptotically for large R through O(R-8) and O(R-10) respectively and for most of the individual dispersion energies varying as R-9 and R-10. They are used to illustrate various features of charge overlap effects and the damping functions for molecular interactions, which are considerably more complicated than for atom-atom interactions.

Mitochondrial and Chloroplast Stress Responses Are Modulated in Distinct Touch and Chemical Inhibition Phases1[OPEN

PubMed Central

Ivanova, Aneta; Millar, A. Harvey; Whelan, James

2016-01-01

Previous studies have identified a range of transcription factors that modulate retrograde regulation of mitochondrial and chloroplast functions in Arabidopsis (Arabidopsis thaliana). However, the relative importance of these regulators and whether they act downstream of separate or overlapping signaling cascades is still unclear. Here, we demonstrate that multiple stress-related signaling pathways, with distinct kinetic signatures, converge on overlapping gene sets involved in energy organelle function. The transcription factor ANAC017 is almost solely responsible for transcript induction of marker genes around 3 to 6 h after chemical inhibition of organelle function and is a key regulator of mitochondrial and specific types of chloroplast retrograde signaling. However, an independent and highly transient gene expression phase, initiated within 10 to 30 min after treatment, also targets energy organelle functions, and is related to touch and wounding responses. Metabolite analysis demonstrates that this early response is concurrent with rapid changes in tricarboxylic acid cycle intermediates and large changes in transcript abundance of genes encoding mitochondrial dicarboxylate carrier proteins. It was further demonstrated that transcription factors AtWRKY15 and AtWRKY40 have repressive regulatory roles in this touch-responsive gene expression. Together, our results show that several regulatory systems can independently affect energy organelle function in response to stress, providing different means to exert operational control. PMID:27208304

Maternal IL-6 during pregnancy can be estimated from newborn brain connectivity and predicts future working memory in offspring.

PubMed

Rudolph, Marc D; Graham, Alice M; Feczko, Eric; Miranda-Dominguez, Oscar; Rasmussen, Jerod M; Nardos, Rahel; Entringer, Sonja; Wadhwa, Pathik D; Buss, Claudia; Fair, Damien A

2018-05-01

Several lines of evidence support the link between maternal inflammation during pregnancy and increased likelihood of neurodevelopmental and psychiatric disorders in offspring. This longitudinal study seeks to advance understanding regarding implications of systemic maternal inflammation during pregnancy, indexed by plasma interleukin-6 (IL-6) concentrations, for large-scale brain system development and emerging executive function skills in offspring. We assessed maternal IL-6 during pregnancy, functional magnetic resonance imaging acquired in neonates, and working memory (an important component of executive function) at 2 years of age. Functional connectivity within and between multiple neonatal brain networks can be modeled to estimate maternal IL-6 concentrations during pregnancy. Brain regions heavily weighted in these models overlap substantially with those supporting working memory in a large meta-analysis. Maternal IL-6 also directly accounts for a portion of the variance of working memory at 2 years of age. Findings highlight the association of maternal inflammation during pregnancy with the developing functional architecture of the brain and emerging executive function.

Optical Lattice Bose-Einstein Condensates and the dd Fusion - Iwamura Connection

NASA Astrophysics Data System (ADS)

Chubb, Talbot

2003-03-01

My conjecture: LENR dd fusion occurs in PdDx when a subset of the interstitial deuterons occupy tetrahedral sites in a PdDx crystallite. The tetrahedral deuterons(d's), which occupy shallow potential wells, behave as a superfluid, similar to ultracold Na atoms in shallow-well optical traps, as modeled by Jaksch et al.(D. Jaksch, et al, Phys. Rev. Lett., 81, 3108 (1998).) The tetrahedral d's form a deuteron (d) subsystem, which is neutralized by an electron subsystem containing an equal number of electrons. In the superfluid all the properties of each quasiparticle d are partitioned among N_s_i_te equivalent sites. The partitioning of the d point charge reduces the Coulomb self-repulsion within each quasiparticle pair, which causes wave function overlap at large N_s_i_t_e, allowing d-d fusion. Similarly, partitioning of the point charge of each single quasiparticle d reduces the Coulomb repulsion between it and an obstructing impurity atom, which causes wave function overlap between quasiparticle and atom at large N_s_i_t_e, allowing transmutation of the impurity atom. The Iwamura reaction(Y. Iwamura, et al, Japan J. of Appl. Physics, 41A, 4642 (2002).) is 4 ^2D^+_B_l_o_ch + 4 e^-_B_l_o_ch + ^1^3^3Cs arrow ^1^4^1Pr, with the reaction energy incoherently transferred to the lattice.

Geographic structure of adelie penguin populations: overlap in colony-specific foraging areas

USGS Publications Warehouse

Ainley, D.G.; Ribic, C.A.; Ballard, G.; Heath, S.; Gaffney, I.; Karl, B.J.; Barton, K.J.; Wilson, P.R.; Webb, S.

2004-01-01

In an investigation of the factors leading to geographic structuring among Ade??lie Penguin (Pygoscelis adeliae) populations, we studied the size and overlap of colony-specific foraging areas within an isolated cluster of colonies. The study area, in the southwestern Ross Sea, included one large and three smaller colonies, ranging in size from 3900 to 135000 nesting pairs, clustered on Ross and Beaufort Islands. We used triangulation of radio signals from transmitters attached to breeding penguins to determine foraging locations and to define colony-specific foraging areas during the chick-provisioning period of four breeding seasons, 1997-2000. Colony populations (nesting pairs) were determined using aerial photography just after egg-laying; reproductive success was estimated by comparing ground counts of chicks fledged to the number of breeding pairs apparent in aerial photos. Foraging-trip duration, meal size, and adult body mass were estimated using RFID (radio frequency identification) tags and an automated reader and weighbridge. Chick growth was assessed by weekly weighing. We related the following variables to colony size: foraging distance, area, and duration; reproductive success; chick meal size and growth rate; and seasonal variation in adult body mass. We found that penguins foraged closest to their respective colonies, particularly at the smaller colonies. However, as the season progressed, foraging distance, duration, and area increased noticeably, especially at the largest colony. The foraging areas of the smaller colonies overlapped broadly, but very little foraging area overlap existed between the large colony and the smaller colonies, even though the foraging area of the large colony was well within range of the smaller colonies. Instead, the foraging areas of the smaller colonies shifted as that of the large colony grew. Colony size was not related to chick meal size, chick growth, or parental body mass. This differed from the year previous to the study, when foraging trips of the large colony were very long, parents lost mass, and chick meals were smaller. In light of existing data on prey abundance in neritic waters in Antarctica suggesting that krill are relatively evenly distributed and in high abundance in the Southern Ross Sea, we conclude that penguins depleted or changed the availability of their prey, that the degree of alteration was a function of colony size, and that the large colony affected the location (and perhaps ultimately the size) of foraging areas for the smaller colonies. It appears, therefore, that foraging dynamics play a role in the geographic structuring of colonies in this species. ?? 2004 by the Ecological Society of America.

Speech networks at rest and in action: interactions between functional brain networks controlling speech production.

PubMed

Simonyan, Kristina; Fuertinger, Stefan

2015-04-01

Speech production is one of the most complex human behaviors. Although brain activation during speaking has been well investigated, our understanding of interactions between the brain regions and neural networks remains scarce. We combined seed-based interregional correlation analysis with graph theoretical analysis of functional MRI data during the resting state and sentence production in healthy subjects to investigate the interface and topology of functional networks originating from the key brain regions controlling speech, i.e., the laryngeal/orofacial motor cortex, inferior frontal and superior temporal gyri, supplementary motor area, cingulate cortex, putamen, and thalamus. During both resting and speaking, the interactions between these networks were bilaterally distributed and centered on the sensorimotor brain regions. However, speech production preferentially recruited the inferior parietal lobule (IPL) and cerebellum into the large-scale network, suggesting the importance of these regions in facilitation of the transition from the resting state to speaking. Furthermore, the cerebellum (lobule VI) was the most prominent region showing functional influences on speech-network integration and segregation. Although networks were bilaterally distributed, interregional connectivity during speaking was stronger in the left vs. right hemisphere, which may have underlined a more homogeneous overlap between the examined networks in the left hemisphere. Among these, the laryngeal motor cortex (LMC) established a core network that fully overlapped with all other speech-related networks, determining the extent of network interactions. Our data demonstrate complex interactions of large-scale brain networks controlling speech production and point to the critical role of the LMC, IPL, and cerebellum in the formation of speech production network. Copyright © 2015 the American Physiological Society.

Functional mapping of the primate auditory system.

PubMed

Poremba, Amy; Saunders, Richard C; Crane, Alison M; Cook, Michelle; Sokoloff, Louis; Mishkin, Mortimer

2003-01-24

Cerebral auditory areas were delineated in the awake, passively listening, rhesus monkey by comparing the rates of glucose utilization in an intact hemisphere and in an acoustically isolated contralateral hemisphere of the same animal. The auditory system defined in this way occupied large portions of cerebral tissue, an extent probably second only to that of the visual system. Cortically, the activated areas included the entire superior temporal gyrus and large portions of the parietal, prefrontal, and limbic lobes. Several auditory areas overlapped with previously identified visual areas, suggesting that the auditory system, like the visual system, contains separate pathways for processing stimulus quality, location, and motion.

Functional Connectivity Parcellation of the Human Thalamus by Independent Component Analysis.

PubMed

Zhang, Sheng; Li, Chiang-Shan R

2017-11-01

As a key structure to relay and integrate information, the thalamus supports multiple cognitive and affective functions through the connectivity between its subnuclei and cortical and subcortical regions. Although extant studies have largely described thalamic regional functions in anatomical terms, evidence accumulates to suggest a more complex picture of subareal activities and connectivities of the thalamus. In this study, we aimed to parcellate the thalamus and examine whole-brain connectivity of its functional clusters. With resting state functional magnetic resonance imaging data from 96 adults, we used independent component analysis (ICA) to parcellate the thalamus into 10 components. On the basis of the independence assumption, ICA helps to identify how subclusters overlap spatially. Whole brain functional connectivity of each subdivision was computed for independent component's time course (ICtc), which is a unique time series to represent an IC. For comparison, we computed seed-region-based functional connectivity using the averaged time course across all voxels within a thalamic subdivision. The results showed that, at p < 10 -6 , corrected, 49% of voxels on average overlapped among subdivisions. Compared with seed-region analysis, ICtc analysis revealed patterns of connectivity that were more distinguished between thalamic clusters. ICtc analysis demonstrated thalamic connectivity to the primary motor cortex, which has eluded the analysis as well as previous studies based on averaged time series, and clarified thalamic connectivity to the hippocampus, caudate nucleus, and precuneus. The new findings elucidate functional organization of the thalamus and suggest that ICA clustering in combination with ICtc rather than seed-region analysis better distinguishes whole-brain connectivities among functional clusters of a brain region.

Brain activity during auditory and visual phonological, spatial and simple discrimination tasks.

PubMed

Salo, Emma; Rinne, Teemu; Salonen, Oili; Alho, Kimmo

2013-02-16

We used functional magnetic resonance imaging to measure human brain activity during tasks demanding selective attention to auditory or visual stimuli delivered in concurrent streams. Auditory stimuli were syllables spoken by different voices and occurring in central or peripheral space. Visual stimuli were centrally or more peripherally presented letters in darker or lighter fonts. The participants performed a phonological, spatial or "simple" (speaker-gender or font-shade) discrimination task in either modality. Within each modality, we expected a clear distinction between brain activations related to nonspatial and spatial processing, as reported in previous studies. However, within each modality, different tasks activated largely overlapping areas in modality-specific (auditory and visual) cortices, as well as in the parietal and frontal brain regions. These overlaps may be due to effects of attention common for all three tasks within each modality or interaction of processing task-relevant features and varying task-irrelevant features in the attended-modality stimuli. Nevertheless, brain activations caused by auditory and visual phonological tasks overlapped in the left mid-lateral prefrontal cortex, while those caused by the auditory and visual spatial tasks overlapped in the inferior parietal cortex. These overlapping activations reveal areas of multimodal phonological and spatial processing. There was also some evidence for intermodal attention-related interaction. Most importantly, activity in the superior temporal sulcus elicited by unattended speech sounds was attenuated during the visual phonological task in comparison with the other visual tasks. This effect might be related to suppression of processing irrelevant speech presumably distracting the phonological task involving the letters. Copyright © 2012 Elsevier B.V. All rights reserved.

Aspects and the Overlap Function.

ERIC Educational Resources Information Center

Levine, Marilyn M.; Levine, Leonard P.

1984-01-01

Presents system for automatic handling of ordered sets, states based on these sets, and differing points of view regarding Universe of Discourse. Aspects are represented by new logical "overlap" function with examples taken from Ranganathan's horse and carriage parable and several books involving four main concepts (history, geography,…

Modular biological function is most effectively captured by combining molecular interaction data types.

PubMed

Ames, Ryan M; Macpherson, Jamie I; Pinney, John W; Lovell, Simon C; Robertson, David L

2013-01-01

Large-scale molecular interaction data sets have the potential to provide a comprehensive, system-wide understanding of biological function. Although individual molecules can be promiscuous in terms of their contribution to function, molecular functions emerge from the specific interactions of molecules giving rise to modular organisation. As functions often derive from a range of mechanisms, we demonstrate that they are best studied using networks derived from different sources. Implementing a graph partitioning algorithm we identify subnetworks in yeast protein-protein interaction (PPI), genetic interaction and gene co-regulation networks. Among these subnetworks we identify cohesive subgraphs that we expect to represent functional modules in the different data types. We demonstrate significant overlap between the subgraphs generated from the different data types and show these overlaps can represent related functions as represented by the Gene Ontology (GO). Next, we investigate the correspondence between our subgraphs and the Gene Ontology. This revealed varying degrees of coverage of the biological process, molecular function and cellular component ontologies, dependent on the data type. For example, subgraphs from the PPI show enrichment for 84%, 58% and 93% of annotated GO terms, respectively. Integrating the interaction data into a combined network increases the coverage of GO. Furthermore, the different annotation types of GO are not predominantly associated with one of the interaction data types. Collectively our results demonstrate that successful capture of functional relationships by network data depends on both the specific biological function being characterised and the type of network data being used. We identify functions that require integrated information to be accurately represented, demonstrating the limitations of individual data types. Combining interaction subnetworks across data types is therefore essential for fully understanding the complex and emergent nature of biological function.

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

PubMed

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 < 0.05). The participants with FH had higher prevalence of anxiety and depression than those with NERD (92% vs. 75%, 88% vs. 65% respectively, P < 0.05). Fifty-two (47.3%) patients with 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 < 0.01). Epigastric pain syndrome (EPS), a subtype of FD, was slightly more likely to have overlapped NERD and FH symptoms than postprandial discomfort symdrome (PDS). But the difference was not significant (29. 1% vs. 18.2%, 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.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Granados, Carlos; Weiss, Christian

The nucleon's peripheral transverse charge and magnetization densities are computed in chiral effective field theory. The densities are represented in first-quantized form, as overlap integrals of chiral light-front wave functions describing the transition of the nucleon to soft pion-nucleon intermediate states. The orbital motion of the pion causes a large left-right asymmetry in a transversely polarized nucleon. As a result, the effect attests to the relativistic nature of chiral dynamics [pion momenta k = O(M π)] and could be observed in form factor measurements at low momentum transfer.

A Brain Centred View of Psychiatric Comorbidity in Tinnitus: From Otology to Hodology

PubMed Central

Minichino, Amedeo; Panico, Roberta; Testugini, Valeria; Altissimi, Giancarlo; Cianfrone, Giancarlo

2014-01-01

Introduction. Comorbid psychiatric disorders are frequent among patients affected by tinnitus. There are mutual clinical influences between tinnitus and psychiatric disorders, as well as neurobiological relations based on partially overlapping hodological and neuroplastic phenomena. The aim of the present paper is to review the evidence of alterations in brain networks underlying tinnitus physiopathology and to discuss them in light of the current knowledge of the neurobiology of psychiatric disorders. Methods. Relevant literature was identified through a search on Medline and PubMed; search terms included tinnitus, brain, plasticity, cortex, network, and pathways. Results. Tinnitus phenomenon results from systemic-neurootological triggers followed by neuronal remapping within several auditory and nonauditory pathways. Plastic reorganization and white matter alterations within limbic system, arcuate fasciculus, insula, salience network, dorsolateral prefrontal cortex, auditory pathways, ffrontocortical, and thalamocortical networks are discussed. Discussion. Several overlapping brain network alterations do exist between tinnitus and psychiatric disorders. Tinnitus, initially related to a clinicoanatomical approach based on a cortical localizationism, could be better explained by an holistic or associationist approach considering psychic functions and tinnitus as emergent properties of partially overlapping large-scale neural networks. PMID:25018882

Spatial relations between sympatric coyotes and red foxes in North Dakota

USGS Publications Warehouse

Sargeant, A.B.; Allen, S.H.; Hastings, J.O.

1987-01-01

Spatial relations between coyotes (Canis latrans) and red foxes (Vulpes vulpes) on a 360-km2 area in North Dakota were studied during 1977-78. Coyote families occupied large (mean = 61.2 km2), relatively exclusive territories that encompassed about one-half of the study area. Fox families occupied much smaller (mean = 11.9 km2), relatively exclusive, territories that overlapped perimeters of coyote territories and/or encompassed area unoccupied by coyotes. No fox family lived totally within a coyote territory, but 3 fox families lived within the 153.6-km2 home range of an unattached yearling male coyote. Both coyotes and foxes, from families with overlapping territories, tended to use their overlap areas less than was expected by amount of overlap. Encounters between radio-equipped coyotes and foxes from families with overlapping territories occurred less often than was expected by chance. Foxes living near coyotes exhibited considerable tenacity to their territories, and no monitored fox was killed by coyotes during 2,518 fox-days of radio surveillance. A hypothesis for coyote-induced fox population declines, based largely on fox avoidance mechanisms, is presented.

Systems analysis in Cellvibrio japonicus resolves predicted redundancy of β-glucosidases and determines essential physiological functions: Functional analysis of C. japonicus β-glucosidases

DOE PAGES

Nelson, Cassandra E.; Rogowski, Artur; Morland, Carl; ...

2017-02-28

Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes, many of which have been categorized as functionally redundant. Here we present data that suggests that carbohydrate active enzymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted β-glucosidases is required in amore » physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual β-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Finally, our approach for parsing related carbohydrate active enzymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.« less

Mechanism of water-stress induced cavitation in conifers: bordered pit structure and function support the hypothesis of seal capillary-seeding

PubMed Central

DELZON, SYLVAIN; DOUTHE, CYRIL; SALA, ANNA; COCHARD, HERVE

2010-01-01

Resistance to water-stress induced cavitation is an important indicator of drought tolerance in woody species and is known to be intimately linked to the anatomy of the xylem. However, the actual mechanical properties of the pit membrane are not well known and the exact mode of air-seeding by which cavitation occurs is still uncertain. We examined the relationship between cavitation resistance and bordered pit structure and function in 40 coniferous species. Xylem pressure inducing 50% loss of hydraulic conductance (P50, a proxy for cavitation resistance) varied widely among species, from −2.9 to −11.3 MPa. The valve effect of the pit membrane, measured as a function of margo flexibility and torus overlap, explained more variation in cavitation-resistance than simple anatomical traits such as pit membrane, pit aperture or torus size. Highly cavitation resistant species exhibited both a high flexibility of the margo and a large overlap between the torus and the pit aperture, allowing the torus to tightly seal the pit aperture. Our results support the hypothesis of seal capillary-seeding as the most likely mode of air-seeding, and suggest that the adhesion of the torus to the pit border may be the main determinant of cavitation resistance in conifers. PMID:20636490

Mechanism of water-stress induced cavitation in conifers: bordered pit structure and function support the hypothesis of seal capillary-seeding.

PubMed

Delzon, Sylvain; Douthe, Cyril; Sala, Anna; Cochard, Herve

2010-12-01

Resistance to water-stress induced cavitation is an important indicator of drought tolerance in woody species and is known to be intimately linked to the anatomy of the xylem. However, the actual mechanical properties of the pit membrane are not well known and the exact mode of air-seeding by which cavitation occurs is still uncertain. We examined the relationship between cavitation resistance and bordered pit structure and function in 40 coniferous species. Xylem pressure inducing 50% loss of hydraulic conductance (P(50), a proxy for cavitation resistance) varied widely among species, from -2.9 to -11.3 MPa. The valve effect of the pit membrane, measured as a function of margo flexibility and torus overlap, explained more variation in cavitation-resistance than simple anatomical traits such as pit membrane, pit aperture or torus size. Highly cavitation resistant species exhibited both a high flexibility of the margo and a large overlap between the torus and the pit aperture, allowing the torus to tightly seal the pit aperture. Our results support the hypothesis of seal capillary-seeding as the most likely mode of air-seeding, and suggest that the adhesion of the torus to the pit border may be the main determinant of cavitation resistance in conifers. © 2010 Blackwell Publishing Ltd.

Comparison of large-scale human brain functional and anatomical networks in schizophrenia.

PubMed

Nelson, Brent G; Bassett, Danielle S; Camchong, Jazmin; Bullmore, Edward T; Lim, Kelvin O

2017-01-01

Schizophrenia is a disease with disruptions in thought, emotion, and behavior. The dysconnectivity hypothesis suggests these disruptions are due to aberrant brain connectivity. Many studies have identified connectivity differences but few have been able to unify gray and white matter findings into one model. Here we develop an extension of the Network-Based Statistic (NBS) called NBSm (Multimodal Network-based statistic) to compare functional and anatomical networks in schizophrenia. Structural, resting functional, and diffusion magnetic resonance imaging data were collected from 29 chronic patients with schizophrenia and 29 healthy controls. Images were preprocessed, and average time courses were extracted for 90 regions of interest (ROI). Functional connectivity matrices were estimated by pairwise correlations between wavelet coefficients of ROI time series. Following diffusion tractography, anatomical connectivity matrices were estimated by white matter streamline counts between each pair of ROIs. Global and regional strength were calculated for each modality. NBSm was used to find significant overlap between functional and anatomical components that distinguished health from schizophrenia. Global strength was decreased in patients in both functional and anatomical networks. Regional strength was decreased in all regions in functional networks and only one region in anatomical networks. NBSm identified a distinguishing functional component consisting of 46 nodes with 113 links (p < 0.001), a distinguishing anatomical component with 47 nodes and 50 links (p = 0.002), and a distinguishing intermodal component with 26 nodes (p < 0.001). NBSm is a powerful technique for understanding network-based group differences present in both anatomical and functional data. In light of the dysconnectivity hypothesis, these results provide compelling evidence for the presence of significant overlapping anatomical and functional disruption in people with schizophrenia.

The Impacts of an Observationally-Based Cloud Fraction and Condensate Overlap Parameterization on a GCM's Cloud Radiative Effect

NASA Technical Reports Server (NTRS)

Oreopoulos, Lazaros; Lee, Dongmin; Norris, Peter; Yuan, Tianle

2011-01-01

It has been shown that the details of how cloud fraction overlap is treated in GCMs has substantial impact on shortwave and longwave fluxes. Because cloud condensate is also horizontally heterogeneous at GCM grid scales, another aspect of cloud overlap should in principle also be assessed, namely the vertical overlap of hydrometeor distributions. This type of overlap is usually examined in terms of rank correlations, i.e., linear correlations between hydrometeor amount ranks of the overlapping parts of cloud layers at specific separation distances. The cloud fraction overlap parameter and the rank correlation of hydrometeor amounts can be both expressed as inverse exponential functions of separation distance characterized by their respective decorrelation lengths (e-folding distances). Larger decorrelation lengths mean that hydrometeor fractions and probability distribution functions have high levels of vertical alignment. An analysis of CloudSat and CALIPSO data reveals that the two aspects of cloud overlap are related and their respective decorrelation lengths have a distinct dependence on latitude that can be parameterized and included in a GCM. In our presentation we will contrast the Cloud Radiative Effect (CRE) of the GEOS-5 atmospheric GCM (AGCM) when the observationally-based parameterization of decorrelation lengths is used to represent overlap versus the simpler cases of maximum-random overlap and globally constant decorrelation lengths. The effects of specific overlap representations will be examined for both diagnostic and interactive radiation runs in GEOS-5 and comparisons will be made with observed CREs from CERES and CloudSat (2B-FLXHR product). Since the radiative effects of overlap depend on the cloud property distributions of the AGCM, the availability of two different cloud schemes in GEOS-5 will give us the opportunity to assess a wide range of potential cloud overlap consequences on the model's climate.

Dependence of Excited State Potential Energy Surfaces on the Spatial Overlap of the Kohn-Sham Orbitals and the Amount of Nonlocal Hartree-Fock Exchange in Time-Dependent Density Functional Theory.

PubMed

Plötner, Jürgen; Tozer, David J; Dreuw, Andreas

2010-08-10

Time-dependent density functional theory (TDDFT) with standard GGA or hybrid exchange-correlation functionals is not capable of describing the potential energy surface of the S1 state of Pigment Yellow 101 correctly; an additional local minimum is observed at a twisted geometry with substantial charge transfer (CT) character. To investigate the influence of nonlocal exact orbital (Hartree-Fock) exchange on the shape of the potential energy surface of the S1 state in detail, it has been computed along the twisting coordinate employing the standard BP86, B3LYP, and BHLYP xc-functionals as well as the long-range separated (LRS) exchange-correlation (xc)-functionals LC-BOP, ωB97X, ωPBE, and CAM-B3LYP and compared to RI-CC2 benchmark results. Additionally, a recently suggested Λ-parameter has been employed that measures the amount of CT in an excited state by calculating the spatial overlap of the occupied and virtual molecular orbitals involved in the transition. Here, the error in the calculated S1 potential energy curves at BP86, B3LYP, and BHLYP can be clearly related to the Λ-parameter, i.e., to the extent of charge transfer. Additionally, it is demonstrated that the CT problem is largely alleviated when the BHLYP xc-functional is employed, although it still exhibits a weak tendency to underestimate the energy of CT states. The situation improves drastically when LRS-functionals are employed within TDDFT excited state calculations. All tested LRS-functionals give qualitatively the correct potential energy curves of the energetically lowest excited states of P. Y. 101 along the twisting coordinate. While LC-BOP and ωB97X overcorrect the CT problem and now tend to give too large excitation energies compared to other non-CT states, ωPBE and CAM-B3LYP are in excellent agreement with the RI-CC2 results, with respect to both the correct shape of the potential energy curve as well as the absolute values of the calculated excitation energies.

Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle

PubMed Central

Mesbah-Uddin, Md; Guldbrandtsen, Bernt; Iso-Touru, Terhi; Vilkki, Johanna; De Koning, Dirk-Jan; Boichard, Didier; Lund, Mogens Sandø; Sahana, Goutam

2018-01-01

Abstract Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp–773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 × 10−6). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 × 10−22, 2.06 × 10−22, 7.01 × 10−6, respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2-and 1.5-fold enrichment, Fisher’s P-value = 8.91 × 10−10 and 7.4 × 10−11, respectively). Finally, we identified and confirmed the breakpoint of a ∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle. PMID:28985340

Characterisation of protein families in spider digestive fluids and their role in extra-oral digestion.

PubMed

Walter, André; Bechsgaard, Jesper; Scavenius, Carsten; Dyrlund, Thomas S; Sanggaard, Kristian W; Enghild, Jan J; Bilde, Trine

2017-08-10

Spiders are predaceous arthropods that are capable of subduing and consuming relatively large prey items compared to their own body size. For this purpose, spiders have evolved potent venoms to immobilise prey and digestive fluids that break down nutrients inside the prey's body by means of extra-oral digestion (EOD). Both secretions contain an array of active proteins, and an overlap of some components has been anecdotally reported, but not quantified. We systematically investigated the extent of such protein overlap. As venom injection and EOD succeed each other, we further infer functional explanations, and, by comparing two spider species belonging to different clades, assess its adaptive significance for spider EOD in general. We describe the protein composition of the digestive fluids of the mygalomorph Acanthoscurria geniculata and the araneomorph Stegodyphus mimosarum, in comparison with previously published data on a third spider species. We found a number of similar hydrolases being highly abundant in all three species. Among them, members of the family of astacin-like metalloproteases were particularly abundant. While the importance of these proteases in spider venom and digestive fluid was previously noted, we now highlight their widespread use across different spider taxa. Finally, we found species specific differences in the protein overlap between venom and digestive fluid, with the difference being significantly greater in S. mimosarum compared to A. geniculata. The injection of venom precedes the injection with digestive fluid, and the overlap of proteins between venom and digestive fluid suggests an early involvement in EOD. Species specific differences in the overlap may reflect differences in ecology between our two study species. The protein composition of the digestive fluid of all the three species we compared is highly similar, suggesting that the cocktail of enzymes is highly conserved and adapted to spider EOD.

Representation of the speech effectors in the human motor cortex: somatotopy or overlap?

PubMed

Takai, Osamu; Brown, Steven; Liotti, Mario

2010-04-01

Somatotopy within the orofacial region of the human motor cortex has been a central concept in interpreting the results of neuroimaging and transcranial magnetic stimulation studies of normal and disordered speech. Yet, somatotopy has been challenged by studies showing overlap among the effectors within the homunculus. In order to address this dichotomy, we performed four voxel-based meta-analyses of 54 functional neuroimaging studies of non-speech tasks involving respiration, lip movement, tongue movement, and swallowing, respectively. While the centers of mass of the clusters supported the classic homuncular view of the motor cortex, there was significant variability in the locations of the activation-coordinates among studies, resulting in an overlapping arrangement. This "somatotopy with overlap" might reflect the intrinsic functional interconnectedness of the oral effectors for speech production.

Relationship between the transverse-field Ising model and the X Y model via the rotating-wave approximation

NASA Astrophysics Data System (ADS)

Kiely, Thomas G.; Freericks, J. K.

2018-02-01

In a large transverse field, there is an energy cost associated with flipping spins along the axis of the field. This penalty can be employed to relate the transverse-field Ising model in a large field to the X Y model in no field (when measurements are performed at the proper stroboscopic times). We describe the details for how this relationship works and, in particular, we also show under what circumstances it fails. We examine wave-function overlap between the two models and observables, such as spin-spin Green's functions. In general, the mapping is quite robust at short times, but will ultimately fail if the run time becomes too long. There is also a tradeoff between the length of time one can run a simulation out to and the time jitter of the stroboscopic measurements that must be balanced when planning to employ this mapping.

Grey Matter Alterations Co-Localize with Functional Abnormalities in Developmental Dyslexia: An ALE Meta-Analysis

PubMed Central

Linkersdörfer, Janosch; Lonnemann, Jan; Lindberg, Sven; Hasselhorn, Marcus; Fiebach, Christian J.

2012-01-01

The neural correlates of developmental dyslexia have been investigated intensively over the last two decades and reliable evidence for a dysfunction of left-hemispheric reading systems in dyslexic readers has been found in functional neuroimaging studies. In addition, structural imaging studies using voxel-based morphometry (VBM) demonstrated grey matter reductions in dyslexics in several brain regions. To objectively assess the consistency of these findings, we performed activation likelihood estimation (ALE) meta-analysis on nine published VBM studies reporting 62 foci of grey matter reduction in dyslexic readers. We found six significant clusters of convergence in bilateral temporo-parietal and left occipito-temporal cortical regions and in the cerebellum bilaterally. To identify possible overlaps between structural and functional deviations in dyslexic readers, we conducted additional ALE meta-analyses of imaging studies reporting functional underactivations (125 foci from 24 studies) or overactivations (95 foci from 11 studies ) in dyslexics. Subsequent conjunction analyses revealed overlaps between the results of the VBM meta-analysis and the meta-analysis of functional underactivations in the fusiform and supramarginal gyri of the left hemisphere. An overlap between VBM results and the meta-analysis of functional overactivations was found in the left cerebellum. The results of our study provide evidence for consistent grey matter variations bilaterally in the dyslexic brain and substantial overlap of these structural variations with functional abnormalities in left hemispheric regions. PMID:22916214

Discovering Link Communities in Complex Networks by an Integer Programming Model and a Genetic Algorithm

PubMed Central

Li, Zhenping; Zhang, Xiang-Sun; Wang, Rui-Sheng; Liu, Hongwei; Zhang, Shihua

2013-01-01

Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks. PMID:24386268

A game theoretic algorithm to detect overlapping community structure in networks

NASA Astrophysics Data System (ADS)

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.

Ultrasound window-modulated compounding Nakagami imaging: Resolution improvement and computational acceleration for liver characterization.

PubMed

Ma, Hsiang-Yang; Lin, Ying-Hsiu; Wang, Chiao-Yin; Chen, Chiung-Nien; Ho, Ming-Chih; Tsui, Po-Hsiang

2016-08-01

Ultrasound Nakagami imaging is an attractive method for visualizing changes in envelope statistics. Window-modulated compounding (WMC) Nakagami imaging was reported to improve image smoothness. The sliding window technique is typically used for constructing ultrasound parametric and Nakagami images. Using a large window overlap ratio may improve the WMC Nakagami image resolution but reduces computational efficiency. Therefore, the objectives of this study include: (i) exploring the effects of the window overlap ratio on the resolution and smoothness of WMC Nakagami images; (ii) proposing a fast algorithm that is based on the convolution operator (FACO) to accelerate WMC Nakagami imaging. Computer simulations and preliminary clinical tests on liver fibrosis samples (n=48) were performed to validate the FACO-based WMC Nakagami imaging. The results demonstrated that the width of the autocorrelation function and the parameter distribution of the WMC Nakagami image reduce with the increase in the window overlap ratio. One-pixel shifting (i.e., sliding the window on the image data in steps of one pixel for parametric imaging) as the maximum overlap ratio significantly improves the WMC Nakagami image quality. Concurrently, the proposed FACO method combined with a computational platform that optimizes the matrix computation can accelerate WMC Nakagami imaging, allowing the detection of liver fibrosis-induced changes in envelope statistics. FACO-accelerated WMC Nakagami imaging is a new-generation Nakagami imaging technique with an improved image quality and fast computation. Copyright © 2016 Elsevier B.V. All rights reserved.

Modification and identification of a vector for making a large phage antibody library.

PubMed

Zhang, Guo-min; Chen, Yü-ping; Guan, Yuan-zhi; Wang, Yan; An, Yun-qing

2007-11-20

The large phage antibody library is used to obtain high-affinity human antibody, and the Loxp/cre site-specific recombination system is a potential method for constructing a large phage antibody library. In the present study, a phage antibody library vector pDF was reconstructed to construct diabody more quickly and conveniently without injury to homologous recombination and the expression function of the vector and thus to integrate construction of the large phage antibody library with the preparation of diabodies. scFv was obtained by overlap polymerase chain reaction (PCR) amplification with the newly designed VL and VH extension primers. loxp511 was flanked by VL and VH and the endonuclease ACC III encoding sequences were introduced on both sides of loxp511. scFv was cloned into the vector pDF to obtain the vector pDscFv. The vector expression function was identified and the feasibility of diabody preparation was evaluated. A large phage antibody library was constructed in pDscFv. Several antigens were used to screen the antibody library and the quality of the antibody library was evaluated. The phage antibody library expression vector pDscFv was successfully constructed and confirmed to express functional scFv. The large phage antibody library constructed using this vector was of high diversity. Screening of the library on 6 antigens confirmed the generation of specific antibodies to these antigens. Two antibodies were subjected to enzymatic digestion and were prepared into diabody with functional expression. The reconstructed vector pDscFv retains its recombination capability and expression function and can be used to construct large phage antibody libraries. It can be used as a convenient and quick method for preparing diabodies after simple enzymatic digestion, which facilitates clinical trials and application of antibody therapy.

Overlap between age-at-onset and disease-progression determinants in Huntington disease.

PubMed

Aziz, N Ahmad; van der Burg, Jorien M M; Tabrizi, Sarah J; Landwehrmeyer, G Bernhard

2018-05-09

A fundamental but still unresolved issue regarding Huntington disease (HD) pathogenesis is whether the factors that determine age at onset are the same as those that govern disease progression. Because elucidation of this issue is crucial for the development as well as optimal timing of administration of novel disease-modifying therapies, we aimed to assess the extent of overlap between age-at-onset and disease-progression determinants in HD. Using observational data from Enroll-HD, the largest cohort of patients with HD worldwide, in this study we present, validate, and apply an intuitive method based on linear mixed-effect models to quantify the variability in the rate of disease progression in HD. A total of 3,411 patients with HD met inclusion criteria. We found that (1) about two-thirds of the rate of functional, motor, and cognitive progression in HD is determined by the same factors that also determine age at onset, with CAG repeat-dependent mechanisms having by far the largest effect; (2) although expanded HTT CAG repeat size had a large influence on average body weight, the rate of weight loss was largely independent of factors that determine age at onset in HD; and (3) about one-third of the factors that determine the rate of functional, motor, and cognitive progression are different from those that govern age at onset and need further elucidation. Our findings imply that targeting of CAG repeat-dependent mechanisms, for example through gene-silencing approaches, is likely to affect the rate of functional, motor, and cognitive impairment, but not weight loss, in manifest HD mutation carriers. Copyright © 2018 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

Concurrent Software Engineering Project

ERIC Educational Resources Information Center

Stankovic, Nenad; Tillo, Tammam

2009-01-01

Concurrent engineering or overlapping activities is a business strategy for schedule compression on large development projects. Design parameters and tasks from every aspect of a product's development process and their interdependencies are overlapped and worked on in parallel. Concurrent engineering suffers from negative effects such as excessive…

Charge Relaxation Dynamics of an Electrolytic Nanocapacitor

PubMed Central

2015-01-01

Understanding ion relaxation dynamics in overlapping electric double layers (EDLs) is critical for the development of efficient nanotechnology-based electrochemical energy storage, electrochemomechanical energy conversion, and bioelectrochemical sensing devices as well as the controlled synthesis of nanostructured materials. Here, a lattice Boltzmann (LB) method is employed to simulate an electrolytic nanocapacitor subjected to a step potential at t = 0 for various degrees of EDL overlap, solvent viscosities, ratios of cation-to-anion diffusivity, and electrode separations. The use of a novel continuously varying and Galilean-invariant molecular-speed-dependent relaxation time (MSDRT) with the LB equation recovers a correct microscopic description of the molecular-collision phenomena and enhances the stability of the LB algorithm. Results for large EDL overlaps indicated oscillatory behavior for the ionic current density, in contrast to monotonic relaxation to equilibrium for low EDL overlaps. Further, at low solvent viscosities and large EDL overlaps, anomalous plasmalike spatial oscillations of the electric field were observed that appeared to be purely an effect of nanoscale confinement. Employing MSDRT in our simulations enabled modeling of the fundamental physics of the transient charge relaxation dynamics in electrochemical systems operating away from equilibrium wherein Nernst–Einstein relation is known to be violated. PMID:25678941

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

PubMed

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. Secondly, correcting erroneous "overlapping concepts" may turn them into "non-overlapping concepts." We demonstrate that this may reduce the complexity of parts of the ontology, which in turn makes the ontology more comprehensible, simplifying maintenance and use of the ontology. Copyright © 2018. Published by Elsevier Inc.

Overlap Spectrum Fiber Bragg Grating Sensor Based on Light Power Demodulation

PubMed Central

Zhang, Hao; Jiang, Junzhen; Liu, Shuang; Chen, Huaixi; Zheng, Xiaoqian; Qiu, Yishen

2018-01-01

Demodulation is a bottleneck for applications involving fiber Bragg gratings (FBGs). An overlap spectrum FBG sensor based on a light power demodulation method is presented in this paper. The demodulation method uses two chirp FBGs (cFBGs) of which the reflection spectra partially overlap each other. The light power variation of the overlap spectrum can be linked to changes in the measurand, and the sensor function can be realized via this relationship. A temperature experiment showed that the relationship between the overlap power spectrum of the FBG sensor and temperature had good linearity and agreed with the theoretical analysis. PMID:29772793

Leveraging disjoint communities for detecting overlapping community structure

NASA Astrophysics Data System (ADS)

Chakraborty, Tanmoy

2015-05-01

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.

Shared genetic basis for migraine and ischemic stroke

PubMed Central

Malik, Rainer; Freilinger, Tobias; Winsvold, Bendik S.; Anttila, Verneri; Vander Heiden, Jason; Traylor, Matthew; de Vries, Boukje; Holliday, Elizabeth G.; Terwindt, Gisela M.; Sturm, Jonathan; Bis, Joshua C.; Hopewell, Jemma C.; Ferrari, Michel D.; Rannikmae, Kristiina; Wessman, Maija; Kallela, Mikko; Kubisch, Christian; Fornage, Myriam; Meschia, James F.; Lehtimäki, Terho; Sudlow, Cathie; Clarke, Robert; Chasman, Daniel I.; Mitchell, Braxton D.; Maguire, Jane; Kaprio, Jaakko; Farrall, Martin; Raitakari, Olli T.; Kurth, Tobias; Ikram, M. Arfan; Reiner, Alex P.; Longstreth, W.T.; Rothwell, Peter M.; Strachan, David P.; Sharma, Pankaj; Seshadri, Sudha; Quaye, Lydia; Cherkas, Lynn; Schürks, Markus; Rosand, Jonathan; Ligthart, Lannie; Boncoraglio, Giorgio B.; Davey Smith, George; van Duijn, Cornelia M.; Stefansson, Kari; Worrall, Bradford B.; Nyholt, Dale R.; Markus, Hugh S.; van den Maagdenberg, Arn M.J.M.; Cotsapas, Chris; Zwart, John A.; Palotie, Aarno

2015-01-01

Objective: To quantify genetic overlap between migraine and ischemic stroke (IS) with respect to common genetic variation. Methods: We applied 4 different approaches to large-scale meta-analyses of genome-wide data on migraine (23,285 cases and 95,425 controls) and IS (12,389 cases and 62,004 controls). First, we queried known genome-wide significant loci for both disorders, looking for potential overlap of signals. We then analyzed the overall shared genetic load using polygenic scores and estimated the genetic correlation between disease subtypes using data derived from these models. We further interrogated genomic regions of shared risk using analysis of covariance patterns between the 2 phenotypes using cross-phenotype spatial mapping. Results: We found substantial genetic overlap between migraine and IS using all 4 approaches. Migraine without aura (MO) showed much stronger overlap with IS and its subtypes than migraine with aura (MA). The strongest overlap existed between MO and large artery stroke (LAS; p = 6.4 × 10−28 for the LAS polygenic score in MO) and between MO and cardioembolic stroke (CE; p = 2.7 × 10−20 for the CE score in MO). Conclusions: Our findings indicate shared genetic susceptibility to migraine and IS, with a particularly strong overlap between MO and both LAS and CE pointing towards shared mechanisms. Our observations on MA are consistent with a limited role of common genetic variants in this subtype. PMID:25934857

Orthogonality catastrophe and fractional exclusion statistics

NASA Astrophysics Data System (ADS)

Ares, Filiberto; Gupta, Kumar S.; de Queiroz, Amilcar R.

2018-02-01

We show that the N -particle Sutherland model with inverse-square and harmonic interactions exhibits orthogonality catastrophe. For a fixed value of the harmonic coupling, the overlap of the N -body ground state wave functions with two different values of the inverse-square interaction term goes to zero in the thermodynamic limit. When the two values of the inverse-square coupling differ by an infinitesimal amount, the wave function overlap shows an exponential suppression. This is qualitatively different from the usual power law suppression observed in the Anderson's orthogonality catastrophe. We also obtain an analytic expression for the wave function overlaps for an arbitrary set of couplings, whose properties are analyzed numerically. The quasiparticles constituting the ground state wave functions of the Sutherland model are known to obey fractional exclusion statistics. Our analysis indicates that the orthogonality catastrophe may be valid in systems with more general kinds of statistics than just the fermionic type.

Orthogonality catastrophe and fractional exclusion statistics.

PubMed

Ares, Filiberto; Gupta, Kumar S; de Queiroz, Amilcar R

2018-02-01

We show that the N-particle Sutherland model with inverse-square and harmonic interactions exhibits orthogonality catastrophe. For a fixed value of the harmonic coupling, the overlap of the N-body ground state wave functions with two different values of the inverse-square interaction term goes to zero in the thermodynamic limit. When the two values of the inverse-square coupling differ by an infinitesimal amount, the wave function overlap shows an exponential suppression. This is qualitatively different from the usual power law suppression observed in the Anderson's orthogonality catastrophe. We also obtain an analytic expression for the wave function overlaps for an arbitrary set of couplings, whose properties are analyzed numerically. The quasiparticles constituting the ground state wave functions of the Sutherland model are known to obey fractional exclusion statistics. Our analysis indicates that the orthogonality catastrophe may be valid in systems with more general kinds of statistics than just the fermionic type.

Compression of Flow Can Reveal Overlapping-Module Organization in Networks

NASA Astrophysics Data System (ADS)

Viamontes Esquivel, Alcides; Rosvall, Martin

2011-10-01

To better understand the organization of overlapping modules in large networks with respect to flow, we introduce the map equation for overlapping modules. In this information-theoretic framework, we use the correspondence between compression and regularity detection. The generalized map equation measures how well we can compress a description of flow in the network when we partition it into modules with possible overlaps. When we minimize the generalized map equation over overlapping network partitions, we detect modules that capture flow and determine which nodes at the boundaries between modules should be classified in multiple modules and to what degree. With a novel greedy-search algorithm, we find that some networks, for example, the neural network of the nematode Caenorhabditis elegans, are best described by modules dominated by hard boundaries, but that others, for example, the sparse European-roads network, have an organization of highly overlapping modules.

Impact of coexisting irritable bowel syndrome and non-erosive reflux disease on postprandial abdominal fullness and sleep disorders in functional dyspepsia.

PubMed

Futagami, Seiji; Yamawaki, Hiroshi; Shimpuku, Mayumi; Izumi, Nikki; Wakabayashi, Taiga; Kodaka, Yasuhiro; Nagoya, Hiroyuki; Shindo, Tomotaka; Kawagoe, Tetsuro; Sakamoto, Choitsu

2013-01-01

The association between clinical symptoms and sleep disorders in functional dyspepsia (FD)-overlap syndrome has not been studied in detail. The subjects were 139 patients with FD, 14 with irritable bowel syndrome (IBS), 12 with nonerosive reflux disease (NERD), and 41 healthy volunteers. Gastric motility was evaluated with the (13)C-acetate breath test. We used Rome III criteria to evaluate upper abdominal symptoms, and Self-Rating Questionnaire for Depression (SRQ-D) scores to determine depression status. Sleep disorders were evaluated with Pittsburgh Sleep Quality Index (PSQI) scores. There were no significant differences in age, body-mass index, alcohol intake, and smoking rate between patients with FD alone and those with FD-overlap syndrome. The postprandial abdominal fullness score in patients with FD-NERD-IBS was significantly greater than that in patients with FD-NERD overlap syndrome (p<0.001) or FD alone (p<0.001). The score for the feeling of hunger in patients with FD-NERD-IBS was significantly greater than that in patients with FD alone (p=0.0025), FD-NERD overlap syndrome (p=0.0088), or FD-IBS overlap syndrome (p=0.0057). The heartburn score in subjects with FD-NERD-IBS overlap syndrome was significantly greater than that in subjects with FD alone (p=0.0035) or FD-IBS overlap syndrome (p=0.0026). The Tmax in patients with FD-overlap syndrome or FD alone was significantly higher than that in healthy volunteers. The Pittsburgh Sleep Quality Index score in subjects with FD-NERD-IBS overlap syndrome was significantly greater than that in subjects with FD alone. Symptom scores, such as those for postprandial abdominal fullness, heartburn, and the feeling of hunger, in patients with FD-overlap syndromes are significantly greater than those in patients with FD alone. Further studies are necessary to clarify whether various symptoms are related to sleep disorders in patients with FD-NERD-IBS overlap syndrome.

Automated registration of large deformations for adaptive radiation therapy of prostate cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Godley, Andrew; Ahunbay, Ergun; Peng Cheng

2009-04-15

Available deformable registration methods are often inaccurate over large organ variation encountered, for example, in the rectum and bladder. The authors developed a novel approach to accurately and effectively register large deformations in the prostate region for adaptive radiation therapy. A software tool combining a fast symmetric demons algorithm and the use of masks was developed in C++ based on ITK libraries to register CT images acquired at planning and before treatment fractions. The deformation field determined was subsequently used to deform the delivered dose to match the anatomy of the planning CT. The large deformations involved required that themore » bladder and rectum volume be masked with uniform intensities of -1000 and 1000 HU, respectively, in both the planning and treatment CTs. The tool was tested for five prostate IGRT patients. The average rectum planning to treatment contour overlap improved from 67% to 93%, the lowest initial overlap is 43%. The average bladder overlap improved from 83% to 98%, with a lowest initial overlap of 60%. Registration regions were set to include a volume receiving 4% of the maximum dose. The average region was 320x210x63, taking approximately 9 min to register on a dual 2.8 GHz Linux system. The prostate and seminal vesicles were correctly placed even though they are not masked. The accumulated doses for multiple fractions with large deformation were computed and verified. The tool developed can effectively supply the previously delivered dose for adaptive planning to correct for interfractional changes.« less

The putative drug efflux systems of the Bacillus cereus group

PubMed Central

Elbourne, Liam D. H.; Vörös, Aniko; Kroeger, Jasmin K.; Simm, Roger; Tourasse, Nicolas J.; Finke, Sarah; Henderson, Peter J. F.; Økstad, Ole Andreas; Paulsen, Ian T.; Kolstø, Anne-Brit

2017-01-01

The Bacillus cereus group of bacteria includes seven closely related species, three of which, B. anthracis, B. cereus and B. thuringiensis, are pathogens of humans, animals and/or insects. Preliminary investigations into the transport capabilities of different bacterial lineages suggested that genes encoding putative efflux systems were unusually abundant in the B. cereus group compared to other bacteria. To explore the drug efflux potential of the B. cereus group all putative efflux systems were identified in the genomes of prototypical strains of B. cereus, B. anthracis and B. thuringiensis using our Transporter Automated Annotation Pipeline. More than 90 putative drug efflux systems were found within each of these strains, accounting for up to 2.7% of their protein coding potential. Comparative analyses demonstrated that the efflux systems are highly conserved between these species; 70–80% of the putative efflux pumps were shared between all three strains studied. Furthermore, 82% of the putative efflux system proteins encoded by the prototypical B. cereus strain ATCC 14579 (type strain) were found to be conserved in at least 80% of 169 B. cereus group strains that have high quality genome sequences available. However, only a handful of these efflux pumps have been functionally characterized. Deletion of individual efflux pump genes from B. cereus typically had little impact to drug resistance phenotypes or the general fitness of the strains, possibly because of the large numbers of alternative efflux systems that may have overlapping substrate specificities. Therefore, to gain insight into the possible transport functions of efflux systems in B. cereus, we undertook large-scale qRT-PCR analyses of efflux pump gene expression following drug shocks and other stress treatments. Clustering of gene expression changes identified several groups of similarly regulated systems that may have overlapping drug resistance functions. In this article we review current knowledge of the small molecule efflux pumps encoded by the B. cereus group and suggest the likely functions of numerous uncharacterised pumps. PMID:28472044

A common network of functional areas for attention and eye movements

NASA Technical Reports Server (NTRS)

Corbetta, M.; Akbudak, E.; Conturo, T. E.; Snyder, A. Z.; Ollinger, J. M.; Drury, H. A.; Linenweber, M. R.; Petersen, S. E.; Raichle, M. E.; Van Essen, D. C.;

Influence of gate overlap engineering on ambipolar and high frequency characteristics of tunnel-CNTFET

NASA Astrophysics Data System (ADS)

Shaker, Ahmed; Ossaimee, Mahmoud; Zekry, A.; Abouelatta, Mohamed

2015-10-01

In this paper, we have investigated the effect of gate overlapping-on-drain on the ambipolar behavior and high frequency performance of tunnel CNTFET (T-CNTFET). It is found that gate overlapping-on-drain suppresses the ambipolar behavior and improves OFF-state current. The simulation results show that there is an optimum choice for the overlapped length. On the other hand, this overlap deteriorates the high frequency performance. The high frequency figure of merit is analyzed in terms of the unit-gain cutoff frequency (fT). Further, we propose two different approaches to improve the high frequency performance of the overlapped T-CNTFET. The first one is based on inserting a high-dielectric constant material below the overlapped part of the gate and the second is based on depositing a different work function gate metal for the overlapped region. The two solutions show very good improvement in the high frequency performance with maintaining the suppression of the ambipolar characteristics.

Mof-Tree: A Spatial Access Method To Manipulate Multiple Overlapping Features.

ERIC Educational Resources Information Center

Manolopoulos, Yannis; Nardelli, Enrico; Papadopoulos, Apostolos; Proietti, Guido

1997-01-01

Investigates the manipulation of large sets of two-dimensional data representing multiple overlapping features, and presents a new access method, the MOF-tree. Analyzes storage requirements and time with respect to window query operations involving multiple features. Examines both the pointer-based and pointerless MOF-tree representations.…

Reconstitution of infectious laryngotracheitis from a collection of overlapping cosmid clones

USDA-ARS?s Scientific Manuscript database

We have generated overlapping cosmids that span the complete genome of infectious laryngotracheitis virus (ILTV) and have used these clones in transfection experiments to reconstitute the virus. This is the first example of the use of large deoxyribose nucleic acid fragment(s) (cosmid, fosmid, bact...

Ultrafast frequency-selective optical switching based on thin self-assembled organic chromophoric films with a large second-order nonlinear response

NASA Astrophysics Data System (ADS)

Wang, Gang; Zhu, Peiwang; Marks, Tobin J.; Ketterson, J. B.

2002-09-01

Thin films consisting of self-assembled chromophoric superlattices exhibit very large second-order nonlinear responses [chi](2). Using such films, a "static" diffraction grating is created by the interference of two coherent infrared beams from a pulsed yttritium-aluminum-garnet laser. This grating is used to switch the second-harmonic and third-harmonic "signal" beams (generated from the fundamental "pump" beam or mixed within the chromophoric superlattice) into different channels (directions). Ultrafast switching response as a function of the time overlap of the pumping beams is demonstrated. It is suggested that such devices can be used to spatially and temporally separate signal trains consisting of pulses having different frequencies and arrival times.

Detecting community structure via the maximal sub-graphs and belonging degrees in complex networks

NASA Astrophysics Data System (ADS)

Cui, Yaozu; Wang, Xingyuan; Eustace, Justine

2014-12-01

Community structure is a common phenomenon in complex networks, and it has been shown that some communities in complex networks often overlap each other. So in this paper we propose a new algorithm to detect overlapping community structure in complex networks. To identify the overlapping community structure, our algorithm firstly extracts fully connected sub-graphs which are maximal sub-graphs from original networks. Then two maximal sub-graphs having the key pair-vertices can be merged into a new larger sub-graph using some belonging degree functions. Furthermore we extend the modularity function to evaluate the proposed algorithm. In addition, overlapping nodes between communities are founded successfully. Finally we report the comparison between the modularity and the computational complexity of the proposed algorithm with some other existing algorithms. The experimental results show that the proposed algorithm gives satisfactory results.

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

PubMed

Eyrich, V A; Standley, D M; Friesner, R A

1999-05-14

We report the tertiary structure predictions for 95 proteins ranging in size from 17 to 160 residues starting from known secondary structure. Predictions are obtained from global minimization of an empirical potential function followed by the application of a refined atomic overlap potential. The minimization strategy employed represents a variant of the Monte Carlo plus minimization scheme of Li and Scheraga applied to a reduced model of the protein chain. For all of the cases except beta-proteins larger than 75 residues, a native-like structure, usually 4-6 A root-mean-square deviation from the native, is located. For beta-proteins larger than 75 residues, the energy gap between native-like structures and the lowest energy structures produced in the simulation is large, so that low RMSD structures are not generated starting from an unfolded state. This is attributed to the lack of an explicit hydrogen bond term in the potential function, which we hypothesize is necessary to stabilize large assemblies of beta-strands. Copyright 1999 Academic Press.

Compressive Detection of Highly Overlapped Spectra Using Walsh-Hadamard-Based Filter Functions.

PubMed

Corcoran, Timothy C

2018-03-01

In the chemometric context in which spectral loadings of the analytes are already known, spectral filter functions may be constructed which allow the scores of mixtures of analytes to be determined in on-the-fly fashion directly, by applying a compressive detection strategy. Rather than collecting the entire spectrum over the relevant region for the mixture, a filter function may be applied within the spectrometer itself so that only the scores are recorded. Consequently, compressive detection shrinks data sets tremendously. The Walsh functions, the binary basis used in Walsh-Hadamard transform spectroscopy, form a complete orthonormal set well suited to compressive detection. A method for constructing filter functions using binary fourfold linear combinations of Walsh functions is detailed using mathematics borrowed from genetic algorithm work, as a means of optimizing said functions for a specific set of analytes. These filter functions can be constructed to automatically strip the baseline from analysis. Monte Carlo simulations were performed with a mixture of four highly overlapped Raman loadings and with ten excitation-emission matrix loadings; both sets showed a very high degree of spectral overlap. Reasonable estimates of the true scores were obtained in both simulations using noisy data sets, proving the linearity of the method.

Vertical overlap of probability density functions of cloud and precipitation hydrometeors: CLOUD AND PRECIPITATION PDF OVERLAP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ovchinnikov, Mikhail; Lim, Kyo-Sun Sunny; Larson, Vincent E.

Coarse-resolution climate models increasingly rely on probability density functions (PDFs) to represent subgrid-scale variability of prognostic variables. While PDFs characterize the horizontal variability, a separate treatment is needed to account for the vertical structure of clouds and precipitation. When sub-columns are drawn from these PDFs for microphysics or radiation parameterizations, appropriate vertical correlations must be enforced via PDF overlap specifications. This study evaluates the representation of PDF overlap in the Subgrid Importance Latin Hypercube Sampler (SILHS) employed in the assumed PDF turbulence and cloud scheme called the Cloud Layers Unified By Binormals (CLUBB). PDF overlap in CLUBB-SILHS simulations of continentalmore » and tropical oceanic deep convection is compared with overlap of PDF of various microphysics variables in cloud-resolving model (CRM) simulations of the same cases that explicitly predict the 3D structure of cloud and precipitation fields. CRM results show that PDF overlap varies significantly between different hydrometeor types, as well as between PDFs of mass and number mixing ratios for each species, - a distinction that the current SILHS implementation does not make. In CRM simulations that explicitly resolve cloud and precipitation structures, faster falling species, such as rain and graupel, exhibit significantly higher coherence in their vertical distributions than slow falling cloud liquid and ice. These results suggest that to improve the overlap treatment in the sub-column generator, the PDF correlations need to depend on hydrometeor properties, such as fall speeds, in addition to the currently implemented dependency on the turbulent convective length scale.« less

Which DSM-IV-TR criteria best differentiate high-functioning autism spectrum disorder from ADHD and anxiety disorders in older children?

PubMed Central

HARTLEY, SIGAN L.; SIKORA, DARRYN M.

2010-01-01

Diagnosis of autism spectrum disorder (ASD) is often delayed in high-functioning children with milder and more varied forms of ASD. The substantial overlap between ASD and other psychiatric disorders is thought to contribute to this delay. This study examined the endorsement of DSM-IV-TR diagnostic criteria for ASD based on semi-structured parent interviews across three groups of older children referred to an ASD clinic: 55 children diagnosed with high-functioning ASD, 27 children diagnosed with attention-deficit/hyperactivity disorder (ADHD), and 23 children diagnosed with anxiety disorder. Results indicate that the criteria within the domains of communication and social relatedness were largely able to discriminate the high-functioning ASD group from the ADHD and anxiety disorder groups, but criteria within the domain of restricted/repetitive/stereotyped patterns were not. PMID:19759063

Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes.

PubMed

Aref-Eshghi, Erfan; Rodenhiser, David I; Schenkel, Laila C; Lin, Hanxin; Skinner, Cindy; Ainsworth, Peter; Paré, Guillaume; Hood, Rebecca L; Bulman, Dennis E; Kernohan, Kristin D; Boycott, Kym M; Campeau, Philippe M; Schwartz, Charles; Sadikovic, Bekim

2018-01-04

Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Language and Traits of Autism Spectrum Conditions: Evidence of Limited Phenotypic and Etiological Overlap

PubMed Central

Taylor, Mark J.; Charman, Tony; Robinson, Elise B.; Hayiou-Thomas, Marianna E.; Happé, Francesca; Dale, Philip S.; Ronald, Angelica

2015-01-01

Language difficulties have historically been viewed as integral to autism spectrum conditions (ASC), leading molecular genetic studies to consider whether ASC and language difficulties have overlapping genetic bases. The extent of genetic, and also environmental, overlap between ASC and language is, however, unclear. We hence conducted a twin study of the concurrent association between autistic traits and receptive language abilities. Internet-based language tests were completed by ~3,000 pairs of twins, while autistic traits were assessed via parent ratings. Twin model fitting explored the association between these measures in the full sample, while DeFries-Fulker analysis tested these associations at the extremes of the sample. Phenotypic associations between language ability and autistic traits were modest and negative. The degree of genetic overlap was also negative, indicating that genetic influences on autistic traits lowered language scores in the full sample (mean genetic correlation = −0.13). Genetic overlap was also low at the extremes of the sample (mean genetic correlation = 0.14), indicating that genetic influences on quantitatively defined language difficulties were largely distinct from those on extreme autistic traits. Variation in language ability and autistic traits were also associated with largely different nonshared environmental influences. Language and autistic traits are influenced by largely distinct etiological factors. This has implications for molecular genetic studies of ASC and understanding the etiology of ASC. Additionally, these findings lend support to forthcoming DSM-5 changes to ASC diagnostic criteria that will see language difficulties separated from the core ASC communication symptoms, and instead listed as a clinical specifier. PMID:25088445

Language and traits of autism spectrum conditions: evidence of limited phenotypic and etiological overlap.

PubMed

Taylor, Mark J; Charman, Tony; Robinson, Elise B; Hayiou-Thomas, Marianna E; Happé, Francesca; Dale, Philip S; Ronald, Angelica

2014-10-01

Language difficulties have historically been viewed as integral to autism spectrum conditions (ASC), leading molecular genetic studies to consider whether ASC and language difficulties have overlapping genetic bases. The extent of genetic, and also environmental, overlap between ASC and language is, however, unclear. We hence conducted a twin study of the concurrent association between autistic traits and receptive language abilities. Internet-based language tests were completed by ~3,000 pairs of twins, while autistic traits were assessed via parent ratings. Twin model fitting explored the association between these measures in the full sample, while DeFries-Fulker analysis tested these associations at the extremes of the sample. Phenotypic associations between language ability and autistic traits were modest and negative. The degree of genetic overlap was also negative, indicating that genetic influences on autistic traits lowered language scores in the full sample (mean genetic correlation = -0.13). Genetic overlap was also low at the extremes of the sample (mean genetic correlation = 0.14), indicating that genetic influences on quantitatively defined language difficulties were largely distinct from those on extreme autistic traits. Variation in language ability and autistic traits were also associated with largely different nonshared environmental influences. Language and autistic traits are influenced by largely distinct etiological factors. This has implications for molecular genetic studies of ASC and understanding the etiology of ASC. Additionally, these findings lend support to forthcoming DSM-5 changes to ASC diagnostic criteria that will see language difficulties separated from the core ASC communication symptoms, and instead listed as a clinical specifier. © 2014 Wiley Periodicals, Inc.

The structure of a three-dimensional turbulent boundary layer

NASA Technical Reports Server (NTRS)

Degani, A. T.; Smith, F. T.; Walker, J. D. A.

1993-01-01

The three-dimensional turbulent boundary layer is shown to have a self-consistent two-layer asymptotic structure in the limit of large Reynolds number. In a streamline coordinate system, the streamwise velocity distribution is similar to that in two-dimensional flows, having a defect-function form in the outer layer which is adjusted to zero at the wall through an inner wall layer. An asymptotic expansion accurate to two orders is required for the cross-stream velocity which is shown to exhibit a logarithmic form in the overlap region. The inner wall-layer flow is collateral to leading order but the influence of the pressure gradient, at large but finite Reynolds numbers, is not negligible and can cause substantial skewing of the velocity profile near the wall. Conditions under which the boundary layer achieves self-similarity and the governing set of ordinary differential equations for the outer layer are derived. The calculated solution of these equations is matched asymptotically to an inner wall-layer solution and the composite profiles so formed describe the flow throughout the entire boundary layer. The effects of Reynolds number and cross-stream pressure gradient on the crossstream velocity profile are discussed and it is shown that the location of the maximum cross-stream velocity is within the overlap region.

Shared genetic basis for migraine and ischemic stroke: A genome-wide analysis of common variants.

PubMed

Malik, Rainer; Freilinger, Tobias; Winsvold, Bendik S; Anttila, Verneri; Vander Heiden, Jason; Traylor, Matthew; de Vries, Boukje; Holliday, Elizabeth G; Terwindt, Gisela M; Sturm, Jonathan; Bis, Joshua C; Hopewell, Jemma C; Ferrari, Michel D; Rannikmae, Kristiina; Wessman, Maija; Kallela, Mikko; Kubisch, Christian; Fornage, Myriam; Meschia, James F; Lehtimäki, Terho; Sudlow, Cathie; Clarke, Robert; Chasman, Daniel I; Mitchell, Braxton D; Maguire, Jane; Kaprio, Jaakko; Farrall, Martin; Raitakari, Olli T; Kurth, Tobias; Ikram, M Arfan; Reiner, Alex P; Longstreth, W T; Rothwell, Peter M; Strachan, David P; Sharma, Pankaj; Seshadri, Sudha; Quaye, Lydia; Cherkas, Lynn; Schürks, Markus; Rosand, Jonathan; Ligthart, Lannie; Boncoraglio, Giorgio B; Davey Smith, George; van Duijn, Cornelia M; Stefansson, Kari; Worrall, Bradford B; Nyholt, Dale R; Markus, Hugh S; van den Maagdenberg, Arn M J M; Cotsapas, Chris; Zwart, John A; Palotie, Aarno; Dichgans, Martin

2015-05-26

To quantify genetic overlap between migraine and ischemic stroke (IS) with respect to common genetic variation. We applied 4 different approaches to large-scale meta-analyses of genome-wide data on migraine (23,285 cases and 95,425 controls) and IS (12,389 cases and 62,004 controls). First, we queried known genome-wide significant loci for both disorders, looking for potential overlap of signals. We then analyzed the overall shared genetic load using polygenic scores and estimated the genetic correlation between disease subtypes using data derived from these models. We further interrogated genomic regions of shared risk using analysis of covariance patterns between the 2 phenotypes using cross-phenotype spatial mapping. We found substantial genetic overlap between migraine and IS using all 4 approaches. Migraine without aura (MO) showed much stronger overlap with IS and its subtypes than migraine with aura (MA). The strongest overlap existed between MO and large artery stroke (LAS; p = 6.4 × 10(-28) for the LAS polygenic score in MO) and between MO and cardioembolic stroke (CE; p = 2.7 × 10(-20) for the CE score in MO). Our findings indicate shared genetic susceptibility to migraine and IS, with a particularly strong overlap between MO and both LAS and CE pointing towards shared mechanisms. Our observations on MA are consistent with a limited role of common genetic variants in this subtype. © 2015 American Academy of Neurology.

A Resonance Overlap Criterion for the Onset of Chaos in Systems of Two Eccentric Planets

NASA Astrophysics Data System (ADS)

Hadden, Sam; Lithwick, Yoram

2018-04-01

I will desrcribe a new analytic criterion to predict the onset of chaos in systems consisting of two massive, eccentric planets. Given a planet pair's spacing and masses, the criterion predicts the eccentricities at which the onset of large-scale chaos occurs. The onset of chaos is predicted based on overlap of mean motion resonances as in Wisdom (1980)'s pioneering work. Whereas Wisdom's work was limited to the overlap of first-order resonance and therefore to nearly circular planets, we account for resonances of all orders. This allows us to consider resonance overlap for planets with arbitrary eccentricities (up to orbit-crossing). Our results show excellent agreement with numerical simulations.

Merge measuring mesh for complex surface parts

NASA Astrophysics Data System (ADS)

Ye, Jianhua; Gao, Chenghui; Zeng, Shoujin; Xu, Mingsan

2018-04-01

Due to most parts self-occlude and limitation of scanner range, it is difficult to scan the entire part by one time. For modeling of part, multi measuring meshes need to be merged. In this paper, a new merge method is presented. At first, using the grid voxelization method to eliminate the most of non-overlap regions, and retrieval overlap triangles method by the topology of mesh is proposed due to its ability to improve the efficiency. Then, to remove the large deviation of overlap triangles, deleting by overlap distance is discussion. After that, this paper puts forward a new method of merger meshes by registration and combination mesh boundary point. Through experimental analysis, the suggested methods are effective.

Peripheral functional organisation of vagally evoked gastric motor responses in the ferret.

PubMed Central

Andrews, P L; Lawes, I N; Bower, A J

1980-01-01

The aims of the present study were to determine the relative amplitudes of intragastric motor responses evoked by different vagal branches and to establish whether the effects of acute or chronic vagotomy could be predicted from these data. Intragastric pressure responses to electrical stimulation of the vagus were measured in urethane-anaesthetised ferrets and acute or chronic vagotomies were performed. The results show that the left and right cervical vagi were equipotential and fully overlaped each other. Their contributions to the dorsal trunk were equipotential and fully overlapping and so were their contributions to the ventral trunk. The dorsal trunk was more effective than the ventral trunk and there was total functional overlap between these two trunks. Vagal evoked gastric motor responses of the ferret are apparently organised in a different way from vagally induced acid secretion or hormone release in the cat. Acute removal of a trunk led to a reduction in evoked responses that was not linear function of the effect of stimulation of that trunk. In contrast, chronic removal caused a relative increase in evoked responses that ws inversely related to the decrease caused by acute removal. The implications of total functional overlap and neuromuscular reorganisation after chronic vagotomy are discussed. PMID:7439800

Overlap of functional heartburn and gastroesophageal reflux disease with irritable bowel syndrome

PubMed Central

de Bortoli, Nicola; Martinucci, Irene; Bellini, Massimo; Savarino, Edoardo; Savarino, Vincenzo; Blandizzi, Corrado; Marchi, Santino

2013-01-01

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. PMID:24124323

Overlap of functional heartburn and gastroesophageal reflux disease with irritable bowel syndrome.

PubMed

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.

The LPM effect in sequential bremsstrahlung 2: factorization

DOE PAGES

Arnold, Peter; Chang, Han-Chih; Iqbal, Shahin

2016-09-13

The splitting processes of bremsstrahlung and pair production in a medium are coherent over large distances in the very high energy limit, which leads to a suppression known as the Landau-Pomeranchuk-Migdal (LPM) effect. In this paper, we continue analysis of the case when the coherence lengths of two consecutive splitting processes overlap (which is important for understanding corrections to standard treatments of the LPM effect in QCD), avoiding soft-gluon approximations. In particular, this paper analyzes the subtle problem of how to precisely separate overlapping double splitting (e.g. overlapping double bremsstrahlung) from the case of consecutive, independent bremsstrahlung (which is themore » case that would be implemented in a Monte Carlo simulation based solely on single splitting rates). As an example of the method, we consider the rate of real double gluon bremsstrahlung from an initial gluon with various simplifying assumptions (thick media; q approximation; large N c; and neglect for the moment of processes involving 4-gluon ver-tices) and explicitly compute the correction Δ dΓ/dx dy due to overlapping formation times.« less

Phylogenetic relatedness and leaf functional traits, not introduced status, influence community assembly.

PubMed

Lemoine, Nathan P; Shue, Jessica; Verrico, Brittany; Erickson, David; Kress, W John; Parker, John D

2015-10-01

Considerable debate focuses on whether invasive species establish and become abundant by being functionally and phylogenetically distinct from native species, leading to a host of invasion-specific hypotheses of community assembly. Few studies, however, have quantitatively assessed whether similar patterns of phylogenetic and functional similarity explain local abundance of both native and introduced species, which would suggest similar assembly mechanisms regardless of origin. Using a chronosequence of invaded temperate forest stands, we tested whether the occurrence and abundance of both introduced and native species were predicted by phylogenetic relatedness, functional overlap, and key environmental characteristics including forest age. Environmental filtering against functionally and phylogenetically distinct species strongly dictated the occurrence and abundance of both introduced and native species, with slight modifications of these patterns according to forest age. Thus, once functional and evolutionary novelty were quantified, introduced status provided little information about species' presence or abundance, indicating largely similar sorting mechanisms for both native and introduced species.

The statistical overlap theory of chromatography using power law (fractal) statistics.

PubMed

Schure, Mark R; Davis, Joe M

2011-12-30

The chromatographic dimensionality was recently proposed as a measure of retention time spacing based on a power law (fractal) distribution. Using this model, a statistical overlap theory (SOT) for chromatographic peaks is developed that estimates the number of peak maxima as a function of the chromatographic dimension, saturation and scale. Power law models exhibit a threshold region whereby below a critical saturation value no loss of peak maxima due to peak fusion occurs as saturation increases. At moderate saturation, behavior is similar to the random (Poisson) peak model. At still higher saturation, the power law model shows loss of peaks nearly independent of the scale and dimension of the model. The physicochemical meaning of the power law scale parameter is discussed and shown to be equal to the Boltzmann-weighted free energy of transfer over the scale limits. The scale is discussed. Small scale range (small β) is shown to generate more uniform chromatograms. Large scale range chromatograms (large β) are shown to give occasional large excursions of retention times; this is a property of power laws where "wild" behavior is noted to occasionally occur. Both cases are shown to be useful depending on the chromatographic saturation. A scale-invariant model of the SOT shows very simple relationships between the fraction of peak maxima and the saturation, peak width and number of theoretical plates. These equations provide much insight into separations which follow power law statistics. Copyright © 2011 Elsevier B.V. All rights reserved.

Assessing the Response of Nematode Communities to Climate Change-Driven Warming: A Microcosm Experiment.

PubMed

Gingold, Ruth; Moens, Tom; Rocha-Olivares, Axayácatl

2013-01-01

Biodiversity has diminished over the past decades with climate change being among the main responsible factors. One consequence of climate change is the increase in sea surface temperature, which, together with long exposure periods in intertidal areas, may exceed the tolerance level of benthic organisms. Benthic communities may suffer structural changes due to the loss of species or functional groups, putting ecological services at risk. In sandy beaches, free-living marine nematodes usually are the most abundant and diverse group of intertidal meiofauna, playing an important role in the benthic food web. While apparently many functionally similar nematode species co-exist temporally and spatially, experimental results on selected bacterivore species suggest no functional overlap, but rather an idiosyncratic contribution to ecosystem functioning. However, we hypothesize that functional redundancy is more likely to observe when taking into account the entire diversity of natural assemblages. We conducted a microcosm experiment with two natural communities to assess their stress response to elevated temperature. The two communities differed in diversity (high [HD] vs. low [LD]) and environmental origin (harsh vs. moderate conditions). We assessed their stress resistance to the experimental treatment in terms of species and diversity changes, and their function in terms of abundance, biomass, and trophic diversity. According to the Insurance Hypothesis, we hypothesized that the HD community would cope better with the stressful treatment due to species functional overlap, whereas the LD community functioning would benefit from species better adapted to harsh conditions. Our results indicate no evidence of functional redundancy in the studied nematofaunal communities. The species loss was more prominent and size specific in the HD; large predators and omnivores were lost, which may have important consequences for the benthic food web. Yet, we found evidence for alternative diversity-ecosystem functioning relationships, such as the Rivets and the Idiosyncrasy Model.

Hints of hybridizing Majorana fermions in a nanowire coupled to superconducting leads

NASA Astrophysics Data System (ADS)

Finck, A. D. K.; van Harlingen, D. J.; Mohseni, P. K.; Jung, K.; Li, X.

2013-03-01

It has been proposed that a nanowire with strong spin-orbit coupling that is contacted with a conventional superconductor and subjected to a large magnetic field can be driven through a topological phase transition. In this regime, the two ends of the nanowire together host a pair of quasi-particles known as Majorana fermions (MFs). A key feature of MFs is that they are pinned to zero energy when the topological nanowire is long enough such that the wave functions of the two MFs do not overlap significantly, resulting in a zero bias anomaly (ZBA). It has been recently predicted that changes in external parameters can vary the wave function overlap and cause the MFs to hybridize in an oscillatory fashion. This would lead to a non-monotonic splitting or broadening of the ZBA and help distinguish MF transport signatures from a Kondo effect. Here, we present transport studies of an InAs nanowire contacted with niobium nitride leads in high magnetic fields. We observe a number of robust ZBAs that can persist for a wide range of back gate bias and magnetic field strength. Under certain conditions, we find that the height and width of the ZBA can oscillate with back gate bias or magnetic field. This work was supported by Microsoft Project Q.

From painkiller to empathy killer: acetaminophen (paracetamol) reduces empathy for pain

PubMed Central

Crocker, Jennifer; Way, Baldwin M.

2016-01-01

Simulation theories of empathy hypothesize that empathizing with others’ pain shares some common psychological computations with the processing of one’s own pain. Support for this perspective has largely relied on functional neuroimaging evidence of an overlap between activations during the experience of physical pain and empathy for other people’s pain. Here, we extend the functional overlap perspective to the neurochemical level and test whether a common physical painkiller, acetaminophen (paracetamol), can reduce empathy for another’s pain. In two double-blind placebo-controlled experiments, participants rated perceived pain, personal distress and empathic concern in response to reading scenarios about another's physical or social pain, witnessing ostracism in the lab, or visualizing another study participant receiving painful noise blasts. As hypothesized, acetaminophen reduced empathy in response to others’ pain. Acetaminophen also reduced the unpleasantness of noise blasts delivered to the participant, which mediated acetaminophen's effects on empathy. Together, these findings suggest that the physical painkiller acetaminophen reduces empathy for pain and provide a new perspective on the neurochemical bases of empathy. Because empathy regulates prosocial and antisocial behavior, these drug-induced reductions in empathy raise concerns about the broader social side effects of acetaminophen, which is taken by almost a quarter of adults in the United States each week. PMID:27217114

Neural correlates of somatoform disorders from a meta-analytic perspective on neuroimaging studies.

PubMed

Boeckle, Markus; Schrimpf, Marlene; Liegl, Gregor; Pieh, Christoph

2016-01-01

Somatoform disorders (SD) are common medical disorders with prevalence rates between 3.5% and 18.4%, depending on country and medical setting. SD as outlined in the ICD-10 exhibits various biological, social, and psychological pathogenic factors. Little is known about the neural correlates of SD. The aims of this meta-analysis are to identify neuronal areas that are involved in SD and consistently differ between patients and healthy controls. We conducted a systematic literature research on neuroimaging studies of SD. Ten out of 686 studies fulfilled the inclusion criteria and were analyzed using activation likelihood estimation. Five neuronal areas differ between patients with SD and healthy controls namely the premotor and supplementary motor cortexes, the middle frontal gyrus, the anterior cingulate cortex, the insula, and the posterior cingulate cortex. These areas seem to have a particular importance for the occurrence of SD. Out of the ten studies two did not contribute to any of the clusters. Our results seem to largely overlap with the circuit network model of somatosensory amplification for SD. It is conceivable that functional disorders, independent of the clinical impression, show similar neurobiological processes. While overlaps do occur it is necessary to understand single functional somatic syndromes and their aetiology for future research, terminology, and treatment guidelines.

From music making to speaking: Engaging the mirror neuron system in autism

PubMed Central

Wan, Catherine Y.; Demaine, Krystal; Zipse, Lauryn; Norton, Andrea; Schlaug, Gottfried

2010-01-01

Individuals with autism show impairments in emotional tuning, social interactions and communication. These are functions that have been attributed to the putative human mirror neuron system (MNS), which contains neurons that respond to the actions of self and others. It has been proposed that a dysfunction of that system underlies some of the characteristics of autism. Here, we review behavioral and imaging studies that implicate the MNS (or a brain network with similar functions) in sensory-motor integration and speech representation, and review data supporting the hypothesis that MNS activity could be abnormal in autism. In addition, we propose that an intervention designed to engage brain regions that overlap with the MNS may have significant clinical potential. We argue that this engagement could be achieved through forms of music making. Music making with others (e.g., playing instruments or singing) is a multi-modal activity that has been shown to engage brain regions that largely overlap with the human MNS. Furthermore, many children with autism thoroughly enjoy participating in musical activities. Such activities may enhance their ability to focus and interact with others, thereby fostering the development of communication and social skills. Thus, interventions incorporating methods of music making may offer a promising approach for facilitating expressive language in otherwise nonverbal children with autism. PMID:20433906

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Cassandra E.; Rogowski, Artur; Morland, Carl

Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes, many of which have been categorized as functionally redundant. Here we present data that suggests that carbohydrate active enzymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted β-glucosidases is required in amore » physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual β-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Finally, our approach for parsing related carbohydrate active enzymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.« less

Visual Short-Term Memory Activity in Parietal Lobe Reflects Cognitive Processes beyond Attentional Selection.

PubMed

Sheremata, Summer L; Somers, David C; Shomstein, Sarah

2018-02-07

Visual short-term memory (VSTM) and attention are distinct yet interrelated processes. While both require selection of information across the visual field, memory additionally requires the maintenance of information across time and distraction. VSTM recruits areas within human (male and female) dorsal and ventral parietal cortex that are also implicated in spatial selection; therefore, it is important to determine whether overlapping activation might reflect shared attentional demands. Here, identical stimuli and controlled sustained attention across both tasks were used to ask whether fMRI signal amplitude, functional connectivity, and contralateral visual field bias reflect memory-specific task demands. While attention and VSTM activated similar cortical areas, BOLD amplitude and functional connectivity in parietal cortex differentiated the two tasks. Relative to attention, VSTM increased BOLD amplitude in dorsal parietal cortex and decreased BOLD amplitude in the angular gyrus. Additionally, the tasks differentially modulated parietal functional connectivity. Contrasting VSTM and attention, intraparietal sulcus (IPS) 1-2 were more strongly connected with anterior frontoparietal areas and more weakly connected with posterior regions. This divergence between tasks demonstrates that parietal activation reflects memory-specific functions and consequently modulates functional connectivity across the cortex. In contrast, both tasks demonstrated hemispheric asymmetries for spatial processing, exhibiting a stronger contralateral visual field bias in the left versus the right hemisphere across tasks, suggesting that asymmetries are characteristic of a shared selection process in IPS. These results demonstrate that parietal activity and patterns of functional connectivity distinguish VSTM from more general attention processes, establishing a central role of the parietal cortex in maintaining visual information. SIGNIFICANCE STATEMENT Visual short-term memory (VSTM) and attention are distinct yet interrelated processes. Cognitive mechanisms and neural activity underlying these tasks show a large degree of overlap. To examine whether activity within the posterior parietal cortex (PPC) reflects object maintenance across distraction or sustained attention per se, it is necessary to control for attentional demands inherent in VSTM tasks. We demonstrate that activity in PPC reflects VSTM demands even after controlling for attention; remembering items across distraction modulates relationships between parietal and other areas differently than during periods of sustained attention. Our study fills a gap in the literature by directly comparing and controlling for overlap between visual attention and VSTM tasks. Copyright © 2018 the authors 0270-6474/18/381511-09$15.00/0.

Short superstrings and the structure of overlapping strings.

PubMed

Armen, C; Stein, C

1995-01-01

Given a collection of strings S = [s1,...,sn] over an alphabet sigma, a superstring alpha of S is a string containing each si as a substring, that is, for each i, 1 < or = i < or = n, alpha contains a block of magnitude of si consecutive characters that match si exactly. The shortest superstring problem is the problem of finding a superstring alpha of minimum length. The shortest superstring problem has applications in both computational biology and data compression. The shortest superstring problem is NP-hard (Gallant et al., 1980); in fact, it was recently shown to be MAX SNP-hard (Blum et al., 1994). Given the importance of the applications, several heuristics and approximation algorithms have been proposed. Constant factor approximation algorithms have been given in Blum et al. (1994) (factor of 3), Teng and Yao (1993) (factor of 2 8/9), Czumaj et al. (1994) (factor of 2 5/6), and Kosaraju et al. (1994) (factor of 2 50/63). Informally, the key to any algorithm for the shortest superstring problem is to identify sets of strings with large amounts of similarity, or overlap. Although the previous algorithms and their analyses have grown increasingly sophisticated, they reveal remarkably little about the structure of strings with large amounts of overlap. In this sense, they are solving a more general problem than the one at hand. In this paper, we study the structure of strings with large amounts of overlap and use our understanding to give an algorithm that finds a superstring whose length is no more than 2 3/4 times that of the optimal superstring. Our algorithm runs in O(magnitude of S + n3) time, which matches that of previous algorithms. We prove several interesting properties about short periodic strings, allowing us to answer questions of the following form: Given a string with some periodic structure, characterize all the possible periodic strings that can have a large amount of overlap with the first string.

Possible roles for fronto-striatal circuits in reading disorder

PubMed Central

Hancock, Roeland; Richlan, Fabio; Hoeft, Fumiko

2016-01-01

Several studies have reported hyperactivation in frontal and striatal regions in individuals with reading disorder (RD) during reading-related tasks. Hyperactivation in these regions is typically interpreted as a form of neural compensation and related to articulatory processing. Fronto-striatal hyperactivation in RD can however, also arise from fundamental impairment in reading related processes, such as phonological processing and implicit sequence learning relevant to early language acquisition. We review current evidence for the compensation hypothesis in RD and apply large-scale reverse inference to investigate anatomical overlap between hyperactivation regions and neural systems for articulation, phonological processing, implicit sequence learning. We found anatomical convergence between hyperactivation regions and regions supporting articulation, consistent with the proposed compensatory role of these regions, and low convergence with phonological and implicit sequence learning regions. Although the application of large-scale reverse inference to decode function in a clinical population should be interpreted cautiously, our findings suggest future lines of research that may clarify the functional significance of hyperactivation in RD. PMID:27826071

Ovarian follicle maturation and ovulation: An integrated perspective

USGS Publications Warehouse

Patino, R.; Thomas, P.; Yoshizaki, G.

2003-01-01

Numerous studies with teleosts have addressed the regulation and mechanisms of oocyte maturation, but largely at the exclusion of ovulation. A smaller but still considerable number of studies have focused on ovulation, and ignored maturation. Consequently, little is known about the mechanistic linkages between these two events. New information is presented here indicating that luteinizing hormone regulates the acquisition not only of oocyte maturational competence, but also ovulatory competence. The thesis is presented that maturation and ovulation are closely integrated and overlapping events that are best viewed conceptually and experimentally as parts of a functional whole. ?? 2004 Kluwer Academic Publishers.

EPR spectra of Cu(2+) in KH(2)PO(4) single crystals.

PubMed

Biyik, Recep; Tapramaz, Recep

2008-01-01

Cu(2+) doped single crystals of KH(2)PO(4) were investigated using EPR technique at room temperature. The spectra of the complex contains large number of overlapping lines. Five sites are resolved and four of them are compatible with the tetragonal symmetry, and the fifth one belongs to an interstitial site. The results are discussed and compared with previous studies. Detailed investigation of the EPR spectra indicate that Cu(2+) substitute with K(+) ions. The principal values of the g and hyperfine tensors and the ground state wave function of Cu(2+) ions are obtained.

Specific surface area of overlapping spheres in the presence of obstructions

NASA Astrophysics Data System (ADS)

Jenkins, D. R.

2013-02-01

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.

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

PubMed

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.

Coexistence of Fish Species in a Large Lowland River: Food Niche Partitioning between Small-Sized Percids, Cyprinids and Sticklebacks in Submersed Macrophytes

PubMed Central

Dukowska, Małgorzata; Grzybkowska, Maria

2014-01-01

In the spring and summer of each year, large patches of submersed aquatic macrophytes overgrow the bottom of the alluvial Warta River downstream of a large dam reservoir owing to water management practices. Environmental variables, macroinvertebrates (zoobenthos and epiphytic fauna, zooplankton) and fish abundance and biomass were assessed at this biologically productive habitat to learn intraseasonal dynamics of food types, and their occurrence in the gut contents of small-sized roach, dace, perch, ruffe and three-spined stickleback. Gut fullness coefficient, niche breadth and niche overlap indicated how the fishes coexist in the macrophytes. Chironomidae dominated in the diet of the percids. However, ruffe consumed mostly benthic chironomids, while perch epiphytic chironomids and zooplankton. The diet of dace resembled that in fast flowing water although this rheophilic species occurred at unusual density there. The generalist roach displayed the lowest gut fullness coefficient values and widest niche breadth; consequently, intraspecific rather than interspecific competition decided the fate of roach. Three-spined stickleback differed from the other fishes by consuming epiphytic simuliids and fish eggs. The diet overlap between fishes reaching higher gut fullness coefficient values was rather low when the food associated with the submersed aquatic macrophytes was most abundant; this is congruent with the niche overlap hypothesis that maximal tolerable niche overlap can be higher in less intensely competitive conditions. PMID:25365420

The Use of Large Valve Overlap in Scavenging a Supercharged Spark-ignition Engine Using Fuel Injection

NASA Technical Reports Server (NTRS)

Schey, Oscar W; Young, Alfred W

1932-01-01

This investigation was conducted to determine the effect of more complete scavenging on the full throttle power and the fuel consumption of a four-stroke-cycle engine. The NACA single-cylinder universal test engine equipped with both a fuel-injection system and a carburetor was used. The engine was scavenged by using a large valve overlap and maintaining a pressure in the inlet manifold of 2 inches of mercury above atmospheric. The maximum valve overlap used was 112 degrees. Tests were conducted for a range of compression ratios from 5.5 to 8.5. Except for variable speed tests, all tests were conducted at an engine speed of 1,500 r.p.m. The results of the tests show that the clearance volume of an engine can be scavenged by using a large valve overlap and about 2 to 5 inches of mercury pressure difference between the inlet and exhaust valve. With a fuel-injection system when the clearance volume was scavenged, a b.m.e.p. of over 185 pounds per square inch and a fuel consumption of 9.45 pound per brake horsepower per hour were obtained with a 6.5 compression ratio. An increase of approximately 10 pounds per square inch b.m.e.p. was obtained with a fuel-injection system over that with a carburetor.

Large-scale Cortical Network Properties Predict Future Sound-to-Word Learning Success

PubMed Central

Sheppard, John Patrick; Wang, Ji-Ping; Wong, Patrick C. M.

2013-01-01

The human brain possesses a remarkable capacity to interpret and recall novel sounds as spoken language. These linguistic abilities arise from complex processing spanning a widely distributed cortical network and are characterized by marked individual variation. Recently, graph theoretical analysis has facilitated the exploration of how such aspects of large-scale brain functional organization may underlie cognitive performance. Brain functional networks are known to possess small-world topologies characterized by efficient global and local information transfer, but whether these properties relate to language learning abilities remains unknown. Here we applied graph theory to construct large-scale cortical functional networks from cerebral hemodynamic (fMRI) responses acquired during an auditory pitch discrimination task and found that such network properties were associated with participants’ future success in learning words of an artificial spoken language. Successful learners possessed networks with reduced local efficiency but increased global efficiency relative to less successful learners and had a more cost-efficient network organization. Regionally, successful and less successful learners exhibited differences in these network properties spanning bilateral prefrontal, parietal, and right temporal cortex, overlapping a core network of auditory language areas. These results suggest that efficient cortical network organization is associated with sound-to-word learning abilities among healthy, younger adults. PMID:22360625

Visualising inter-subject variability in fMRI using threshold-weighted overlap maps

NASA Astrophysics Data System (ADS)

Seghier, Mohamed L.; Price, Cathy J.

2016-02-01

Functional neuroimaging studies are revealing the neural systems sustaining many sensory, motor and cognitive abilities. A proper understanding of these systems requires an appreciation of the degree to which they vary across subjects. Some sources of inter-subject variability might be easy to measure (demographics, behavioural scores, or experimental factors), while others are more difficult (cognitive strategies, learning effects, and other hidden sources). Here, we introduce a simple way of visualising whole-brain consistency and variability in brain responses across subjects using threshold-weighted voxel-based overlap maps. The output quantifies the proportion of subjects activating a particular voxel or region over a wide range of statistical thresholds. The sensitivity of our approach was assessed in 30 healthy adults performing a matching task with their dominant hand. We show how overlap maps revealed many effects that were only present in a subsample of our group; we discuss how overlap maps can provide information that may be missed or misrepresented by standard group analysis, and how this information can help users to understand their data. In particular, we emphasize that functional overlap maps can be particularly useful when it comes to explaining typical (or atypical) compensatory mechanisms used by patients following brain damage.

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

PubMed Central

Imanian, Behzad; Keeling, Patrick J

2007-01-01

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. PMID:17892581

On the ground state of Yang-Mills theory

NASA Astrophysics Data System (ADS)

Bakry, Ahmed S.; Leinweber, Derek B.; Williams, Anthony G.

2011-08-01

We investigate the overlap of the ground state meson potential with sets of mesonic-trial wave functions corresponding to different gluonic distributions. We probe the transverse structure of the flux tube through the creation of non-uniform smearing profiles for the string of glue connecting two color sources in Wilson loop operator. The non-uniformly UV-regulated flux-tube operators are found to optimize the overlap with the ground state and display interesting features in the ground state overlap.

Bipolar disorder, schizoaffective disorder, and schizophrenia overlap: a new comorbidity index.

PubMed

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.

An improved game-theoretic approach to uncover overlapping communities

NASA Astrophysics Data System (ADS)

Sun, Hong-Liang; Ch'Ng, Eugene; Yong, Xi; Garibaldi, Jonathan M.; See, Simon; Chen, Duan-Bing

How can we uncover overlapping communities from complex networks to understand the inherent structures and functions? Chen et al. firstly proposed a community game (Game) to study this problem, and the overlapping communities have been discovered when the game is convergent. It is based on the assumption that each vertex of the underlying network is a rational game player to maximize its utility. In this paper, we investigate how similar vertices affect the formation of community game. The Adamic-Adar Index (AA Index) has been employed to define the new utility function. This novel method has been evaluated on both synthetic and real-world networks. Experimental study shows that it has significant improvement of accuracy (from 4.8% to 37.6%) compared with the Game on 10 real networks. It is more efficient on Facebook networks (FN) and Amazon co-purchasing networks than on other networks. This result implicates that “friend circles of friends” of Facebook are valuable to understand the overlapping community division.

Functional Specialization and Flexibility in Human Association Cortex

PubMed Central

Yeo, B. T. Thomas; Krienen, Fenna M.; Eickhoff, Simon B.; Yaakub, Siti N.; Fox, Peter T.; Buckner, Randy L.; Asplund, Christopher L.; Chee, Michael W.L.

2015-01-01

The association cortex supports cognitive functions enabling flexible behavior. Here, we explored the organization of human association cortex by mathematically formalizing the notion that a behavioral task engages multiple cognitive components, which are in turn supported by multiple overlapping brain regions. Application of the model to a large data set of neuroimaging experiments (N = 10 449) identified complex zones of frontal and parietal regions that ranged from being highly specialized to highly flexible. The network organization of the specialized and flexible regions was explored with an independent resting-state fMRI data set (N = 1000). Cortical regions specialized for the same components were strongly coupled, suggesting that components function as partially isolated networks. Functionally flexible regions participated in multiple components to different degrees. This heterogeneous selectivity was predicted by the connectivity between flexible and specialized regions. Functionally flexible regions might support binding or integrating specialized brain networks that, in turn, contribute to the ability to execute multiple and varied tasks. PMID:25249407

Avoiding and tolerating latency in large-scale next-generation shared-memory multiprocessors

NASA Technical Reports Server (NTRS)

Probst, David K.

1993-01-01

A scalable solution to the memory-latency problem is necessary to prevent the large latencies of synchronization and memory operations inherent in large-scale shared-memory multiprocessors from reducing high performance. We distinguish latency avoidance and latency tolerance. Latency is avoided when data is brought to nearby locales for future reference. Latency is tolerated when references are overlapped with other computation. Latency-avoiding locales include: processor registers, data caches used temporally, and nearby memory modules. Tolerating communication latency requires parallelism, allowing the overlap of communication and computation. Latency-tolerating techniques include: vector pipelining, data caches used spatially, prefetching in various forms, and multithreading in various forms. Relaxing the consistency model permits increased use of avoidance and tolerance techniques. Each model is a mapping from the program text to sets of partial orders on program operations; it is a convention about which temporal precedences among program operations are necessary. Information about temporal locality and parallelism constrains the use of avoidance and tolerance techniques. Suitable architectural primitives and compiler technology are required to exploit the increased freedom to reorder and overlap operations in relaxed models.

Gene network interconnectedness and the generalized topological overlap measure

PubMed Central

Yip, Andy M; Horvath, Steve

2007-01-01

Background Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency) between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz et al. [1] can be interpreted as a measure of agreement between the m = 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness. Results We generalize the topological overlap measure from m = 1 step neighborhoods to m ≥ 2 step neighborhoods. This allows us to define the m-th order generalized topological overlap measure (GTOM) by (i) counting the number of m-step neighbors that a pair of nodes share and (ii) normalizing it to take a value between 0 and 1. Using theoretical arguments, a yeast co-expression network application, and a fly protein network application, we illustrate the usefulness of the proposed measure for module detection and gene neighborhood analysis. Conclusion Topological overlap can serve as an important filter to counter the effects of spurious or missing connections between network nodes. The m-th order topological overlap measure allows one to trade-off sensitivity versus specificity when it comes to defining pairwise interconnectedness and network modules. PMID:17250769

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crowder, Jeff; Cornish, Neil J.; Reddinger, J. Lucas

This work presents the first application of the method of genetic algorithms (GAs) to data analysis for the Laser Interferometer Space Antenna (LISA). In the low frequency regime of the LISA band there are expected to be tens of thousands of galactic binary systems that will be emitting gravitational waves detectable by LISA. The challenge of parameter extraction of such a large number of sources in the LISA data stream requires a search method that can efficiently explore the large parameter spaces involved. As signals of many of these sources will overlap, a global search method is desired. GAs representmore » such a global search method for parameter extraction of multiple overlapping sources in the LISA data stream. We find that GAs are able to correctly extract source parameters for overlapping sources. Several optimizations of a basic GA are presented with results derived from applications of the GA searches to simulated LISA data.« less

Genome-wide methylation and gene expression changes in newborn rats following maternal protein restriction and reversal by folic acid.

PubMed

Altobelli, Gioia; Bogdarina, Irina G; Stupka, Elia; Clark, Adrian J L; Langley-Evans, Simon

2013-01-01

A large body of evidence from human and animal studies demonstrates that the maternal diet during pregnancy can programme physiological and metabolic functions in the developing fetus, effectively determining susceptibility to later disease. The mechanistic basis of such programming is unclear but may involve resetting of epigenetic marks and fetal gene expression. The aim of this study was to evaluate genome-wide DNA methylation and gene expression in the livers of newborn rats exposed to maternal protein restriction. On day one postnatally, there were 618 differentially expressed genes and 1183 differentially methylated regions (FDR 5%). The functional analysis of differentially expressed genes indicated a significant effect on DNA repair/cycle/maintenance functions and of lipid, amino acid metabolism and circadian functions. Enrichment for known biological functions was found to be associated with differentially methylated regions. Moreover, these epigenetically altered regions overlapped genetic loci associated with metabolic and cardiovascular diseases. Both expression changes and DNA methylation changes were largely reversed by supplementing the protein restricted diet with folic acid. Although the epigenetic and gene expression signatures appeared to underpin largely different biological processes, the gene expression profile of DNA methyl transferases was altered, providing a potential link between the two molecular signatures. The data showed that maternal protein restriction is associated with widespread differential gene expression and DNA methylation across the genome, and that folic acid is able to reset both molecular signatures.

Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis

PubMed Central

Khushi, Matloob; Liddle, Christopher; Clarke, Christine L.; Graham, J. Dinny

2014-01-01

Genome-wide mapping of transcription factor binding and histone modification reveals complex patterns of interactions. Identifying overlaps in binding patterns by different factors is a major objective of genomic studies, but existing methods to archive large numbers of datasets in a personalised database lack sophistication and utility. Therefore we have developed transcription factor DNA binding site analyser software (BiSA), for archiving of binding regions and easy identification of overlap with or proximity to other regions of interest. Analysis results can be restricted by chromosome or base pair overlap between regions or maximum distance between binding peaks. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby; regions that are not overlapping; and average region sizes. BiSA can identify genes located near binding regions of interest, genomic features near a gene or locus of interest and statistical significance of overlapping regions can also be reported. Overlapping results can be visualized as Venn diagrams. A major strength of BiSA is that it is supported by a comprehensive database of publicly available transcription factor binding sites and histone modifications, which can be directly compared to user data. The documentation and source code are available on http://bisa.sourceforge.net PMID:24533055

Sentinel-1 TOPS interferometry for along-track displacement measurement

NASA Astrophysics Data System (ADS)

Jiang, H. J.; Pei, Y. Y.; Li, J.

2017-02-01

The European Space Agency’s Sentinel-1 mission, a constellation of two C-band synthetic aperture radar (SAR) satellites, utilizes terrain observation by progressive scan (TOPS) antenna beam steering as its default operation mode to achieve wide-swath coverage and short revisit time. The beam steering during the TOPS acquisition provides a means to measure azimuth motion by using the phase difference between forward and backward looking interferograms within regions of burst overlap. Hence, there are two spectral diversity techniques for along-track displacement measurement, including multi-aperture interferometry (MAI) and “burst overlap interferometry”. This paper analyses the measurement accuracies of MAI and burst overlap interferometry. Due to large spectral separation in the overlap region, burst overlap interferometry is a more sensitive measurement. We present a TOPS interferometry approach for along-track displacement measurement. The phase bias caused by azimuth miscoregistration is first estimated by burst overlap interferometry over stationary regions. After correcting the coregistration error, the MAI phase and the interferometric phase difference between burst overlaps are recalculated to obtain along-track displacements. We test the approach with Sentinel-1 TOPS interferometric data over the 2015 Mw 7.8 Nepal earthquake fault. The results prove the feasibility of our approach and show the potential of joint estimation of along-track displacement with burst overlap interferometry and MAI.

Coseismic Displacement Analysis of the 12 November 2017 MW 7.3 Sarpol-E Zahab (iran) Earthquake from SAR Interferometry, Burst Overlap Interferometry and Offset Tracking

NASA Astrophysics Data System (ADS)

Vajedian, Sanaz; Motagh, Mahdi

2018-04-01

Interferometric wide-swath mode of Sentinel-1, which is implemented by Terrain Observation by Progressive Scan (TOPS) technique, is the main mode of SAR data acquisition in this mission. It aims at global monitoring of large areas with enhanced revisit frequency of 6 days at the expense of reduced azimuth resolution, compared to classical ScanSAR mode. TOPS technique is equipped by steering the beam from backward to forward along the heading direction for each burst, in addition to the steering along the range direction, which is the only sweeping direction in standard ScanSAR mode. This leads to difficulty in measuring along-track displacement by applying the conventional method of multi-aperture interferometry (MAI), which exploits a double difference interferometry to estimate azimuth offset. There is a possibility to solve this issue by a technique called "Burst Overlap Interferometry" which focuses on the region of burst overlap. Taking advantage of large squint angle diversity of 1° in burst overlapped area leads to improve the accuracy of ground motion measurement especially in along-track direction. We investigate the advantage of SAR Interferometry (InSAR), burst overlap interferometry and offset tracking to investigate coseismic deformation and coseismic-induced landslide related to 12 November 2017 Mw 7.3 Sarpol-e Zahab earthquake in Iran.

Development of Novel p16INK4a Mimetics as Anticancer Therapy

DTIC Science & Technology

2015-10-01

peptide (or substituted peptide) or the crystal structure of the relevant sequence from p16INK4 ( PDB 1BI7) was used as the starting structure . Model...small peptides that interact with CDK4/6. The specific aims are as follows. (1) Determine structure -function relationships of overlapping peptides...Determine structure -function relationships of overlapping peptides derived from p16 INK4a that inhibit the activity of CDK4/6 and identify stabilized

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.

PubMed

Palmer, Lance E; Dejori, Mathaeus; Bolanos, Randall; Fasulo, Daniel

2010-01-15

With the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and apply it to de novo sequencing of new organisms. As an example, this paper demonstrates how such extra information can be used to improve de novo assemblies by augmenting the overlapping step. Finding all pairs of overlapping reads is a key task in many genome assemblers, and to this end, highly efficient algorithms have been developed to find alignments in large collections of sequences. It is well known that due to repeated sequences, many aligned pairs of reads nevertheless do not overlap. But no overlapping algorithm to date takes a rigorous approach to separating aligned but non-overlapping read pairs from true overlaps. We present an approach that extends the Minimus assembler by a data driven step to classify overlaps as true or false prior to contig construction. We trained several different classification models within the Weka framework using various statistics derived from overlaps of reads available from prior sequencing projects. These statistics included percent mismatch and k-mer frequencies within the overlaps as well as a comparative genomics score derived from mapping reads to multiple reference genomes. We show that in real whole-genome sequencing data from the E. coli and S. aureus genomes, by providing a curated set of overlaps to the contigging phase of the assembler, we nearly doubled the median contig length (N50) without sacrificing coverage of the genome or increasing the number of mis-assemblies. Machine learning methods that use comparative and non-comparative features to classify overlaps as true or false can be used to improve the quality of a sequence assembly.

Lesion localization of global aphasia without hemiparesis by overlapping of the brain magnetic resonance images

PubMed Central

Kim, Woo Jin; Paik, Nam-Jong

2014-01-01

Global aphasia without hemiparesis is a striking stroke syndrome involving language impairment without the typically manifested contralateral hemiparesis, which is usually seen in patients with global aphasia following large left perisylvian lesions. The objective of this study is to elucidate the specific areas for lesion localization of global aphasia without hemiparesis by retrospectively studying the brain magnetic resonance images of six patients with global aphasia without hemiparesis to define global aphasia without hemiparesis-related stroke lesions before overlapping the images to visualize the most overlapped area. Talairach coordinates for the most overlapped areas were converted to corresponding anatomical regions. Lesions where the images of more than three patients overlapped were considered significant. The overlapped global aphasia without hemiparesis related stroke lesions of six patients revealed that the significantly involved anatomical lesions were as follows: frontal lobe, sub-gyral, sub-lobar, extra-nuclear, corpus callosum, and inferior frontal gyrus, while caudate, claustrum, middle frontal gyrus, limbic lobe, temporal lobe, superior temporal gyrus, uncus, anterior cingulate, parahippocampal, amygdala, and subcallosal gyrus were seen less significantly involved. This study is the first to demonstrate the heterogeneous anatomical involvement in global aphasia without hemiparesis by overlapping of the brain magnetic resonance images. PMID:25657725

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

NASA Technical Reports Server (NTRS)

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.

Default network activation during episodic and semantic memory retrieval: A selective meta-analytic comparison.

PubMed

Kim, Hongkeun

2016-01-08

It remains unclear whether and to what extent the default network subregions involved in episodic memory (EM) and semantic memory (SM) processes overlap or are separated from one another. This study addresses this issue through a controlled meta-analysis of functional neuroimaging studies involving healthy participants. Various EM and SM task paradigms differ widely in the extent of default network involvement. Therefore, the issue at hand cannot be properly addressed without some control for this factor. In this regard, this study employs a two-stage analysis: a preliminary meta-analysis to select EM and SM task paradigms that recruit relatively extensive default network regions and a main analysis to compare the selected task paradigms. Based on a within-EM comparison, the default network contributed more to recollection/familiarity effects than to old/new effects, and based on a within-SM comparison, it contributed more to word/pseudoword effects than to semantic/phonological effects. According to a direct comparison of recollection/familiarity and word/pseudoword effects, each involving a range of default network regions, there were more overlaps than separations in default network subregions involved in these two effects. More specifically, overlaps included the bilateral posterior cingulate/retrosplenial cortex, left inferior parietal lobule, and left anteromedial prefrontal regions, whereas separations included only the hippocampal formation and the parahippocampal cortex region, which was unique to recollection/familiarity effects. These results indicate that EM and SM retrieval processes involving strong memory signals recruit extensive and largely overlapping default network regions and differ mainly in distinct contributions of hippocampus and parahippocampal regions to EM retrieval. Copyright © 2015 Elsevier Ltd. All rights reserved.

Randomly picked cosmid clones overlap the pyrB and oriC gap in the physical map of the E. coli chromosome.

PubMed Central

Knott, V; Rees, D J; Cheng, Z; Brownlee, G G

1988-01-01

Sets of overlapping cosmid clones generated by random sampling and fingerprinting methods complement data at pyrB (96.5') and oriC (84') in the published physical map of E. coli. A new cloning strategy using sheared DNA, and a low copy, inducible cosmid vector were used in order to reduce bias in libraries, in conjunction with micro-methods for preparing cosmid DNA from a large number of clones. Our results are relevant to the design of the best approach to the physical mapping of large genomes. PMID:2834694

The Landscape of long non-coding RNA classification

PubMed Central

St Laurent, Georges; Wahlestedt, Claes; Kapranov, Philipp

2015-01-01

Advances in the depth and quality of transcriptome sequencing have revealed many new classes of long non-coding RNAs (lncRNAs). lncRNA classification has mushroomed to accommodate these new findings, even though the real dimensions and complexity of the non-coding transcriptome remain unknown. Although evidence of functionality of specific lncRNAs continues to accumulate, conflicting, confusing, and overlapping terminology has fostered ambiguity and lack of clarity in the field in general. The lack of fundamental conceptual un-ambiguous classification framework results in a number of challenges in the annotation and interpretation of non-coding transcriptome data. It also might undermine integration of the new genomic methods and datasets in an effort to unravel function of lncRNA. Here, we review existing lncRNA classifications, nomenclature, and terminology. Then we describe the conceptual guidelines that have emerged for their classification and functional annotation based on expanding and more comprehensive use of large systems biology-based datasets. PMID:25869999

A subtype specific function for the extracellular domain of neuroligin 1 in hippocampal LTP

PubMed Central

Shipman, Seth L.; Nicoll, Roger A.

2014-01-01

Summary At neuronal excitatory synapses, two major subtypes of the synaptic adhesion molecule neuroligin are present. These subtypes, neuroligin 1 and neuroligin 3, have roles in synaptogenesis and synaptic maintenance that appear largely overlapping. In this study we combine electrophysiology with molecular deletion and replacement of these proteins to identify similarities and differences between these subtypes. In doing so, we identify a subtype specific role in LTP for neuroligin 1 in young CA1, which persists into adulthood in the dentate gyrus. As neuroligin 3 showed no requirement for LTP, we constructed chimeric proteins of the two excitatory neuroligin subtypes to identify the molecular determinants particular to the unique function of neuroligin 1. Using in vivo molecular replacement experiments, we find that these unique functions depend on a region in its extracellular domain containing the B site splice insertion previously shown to determine specificity of neurexin binding. PMID:23083734

Artifacts and power corrections: Reexamining Z{sub {psi}}(p{sup 2}) and Z{sub V} in the momentum-subtraction scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boucaud, Ph.; Leroy, J. P.; Le Yaouanc, A.

2006-08-01

The next-to-leading-order (NLO) term in the operator product expansion (OPE) of the quark propagator vector part Z{sub {psi}} and the vertex function g{sub 1} of the vector current in the Landau gauge should be dominated by the same condensate as in the gluon propagator. On the other hand, the perturbative part has been calculated to a very high precision thanks to Chetyrkin and collaborators. We test this on the lattice, with both clover and overlap fermion actions at {beta}=6.0, 6.4, 6.6, 6.8. Elucidation of discretization artifacts appears to be absolutely crucial. First hypercubic artifacts are eliminated by amore » powerful method, which gives results notably different from the standard democratic method. Then, the presence of unexpected, very large, nonperturbative, O(4) symmetric discretization artifacts, increasing towards small momenta, is demonstrated by considering Z{sub V}{sup MOM}, which should be constant in the absence of such artifacts. They impede in general the analysis of OPE. However, in two special cases with overlap action--(1) for Z{sub {psi}}; (2) for g{sub 1}, but only at large p{sup 2}--we are able to identify the condensate; it agrees with the one resulting from gluonic Green functions. We conclude that the OPE analysis of quark and gluon Green function has reached a quite consistent status, and that the power corrections have been correctly identified. A practical consequence of the whole analysis is that the renormalization constant Z{sub {psi}} (=Z{sub 2}{sup -1} of the momentum-subtraction (MOM) scheme) may differ sizably from the one given by democratic selection methods. More generally, the values of the renormalization constants may be seriously affected by the differences in the treatment of the various types of artifacts, and by the subtraction of power corrections.« less

Prenatal drug exposure and selective attention in preschoolers.

PubMed

Noland, Julia S; Singer, Lynn T; Short, Elizabeth J; Minnes, Sonia; Arendt, Robert E; Kirchner, H Lester; Bearer, Cynthia

2005-01-01

Deficits in sustained attention and impulsivity have previously been demonstrated in preschoolers prenatally exposed to cocaine. We assessed an additional component of attention, selective attention, in a large, poly-substance cocaine-exposed cohort of 4 year olds and their at-risk comparison group. Employing postpartum maternal report and biological assay, we assigned children to overlapping exposed and complementary control groups for maternal use of cocaine, alcohol, marijuana, and cigarettes. Maternal pregnancy use of cocaine and use of cigarettes were both associated with increased commission errors, indicative of inferior selective attention. Severity of maternal use of marijuana during pregnancy was positively correlated with omission errors, suggesting impaired sustained attention. Substance exposure effects were independent of maternal postpartum psychological distress, birth mother cognitive functioning, current caregiver functioning, other substance exposures and child concurrent verbal IQ.

Fibromyalgia: a stress disorder? Piecing the biopsychosocial puzzle together.

PubMed

Van Houdenhove, Boudewijn; Egle, Ulrich T

2004-01-01

Fibromyalgia (FM) is a controversial syndrome, characterised by persistent widespread pain, abnormal pain sensitivity and additional symptoms such as fatigue and sleep disturbance. The syndrome largely overlaps with other functional somatic disorders, particularly chronic fatigue syndrome (CFS). Although the exact aetiology and pathogenesis of FM are still unknown, it has been suggested that stress may play a key role in the syndrome. This article first reviews the function of the stress response system, placing special emphasis on the relationships between adverse life experiences, stress regulation and pain-processing mechanisms, and summarising the evidence for a possible aetiopathogenetic role of stress in FM. Finally, an integrative biopsychosocial model that conceptualizes FM as a stress disorder is proposed, and the clinical and research implications of the model are discussed.

Dreaming as mind wandering: evidence from functional neuroimaging and first-person content reports.

PubMed

Fox, Kieran C R; Nijeboer, Savannah; Solomonova, Elizaveta; Domhoff, G William; Christoff, Kalina

2013-01-01

Isolated reports have long suggested a similarity in content and thought processes across mind wandering (MW) during waking, and dream mentation during sleep. This overlap has encouraged speculation that both "daydreaming" and dreaming may engage similar brain mechanisms. To explore this possibility, we systematically examined published first-person experiential reports of MW and dreaming and found many similarities: in both states, content is largely audiovisual and emotional, follows loose narratives tinged with fantasy, is strongly related to current concerns, draws on long-term memory, and simulates social interactions. Both states are also characterized by a relative lack of meta-awareness. To relate first-person reports to neural evidence, we compared meta-analytic data from numerous functional neuroimaging (PET, fMRI) studies of the default mode network (DMN, with high chances of MW) and rapid eye movement (REM) sleep (with high chances of dreaming). Our findings show large overlaps in activation patterns of cortical regions: similar to MW/DMN activity, dreaming and REM sleep activate regions implicated in self-referential thought and memory, including medial prefrontal cortex (PFC), medial temporal lobe structures, and posterior cingulate. Conversely, in REM sleep numerous PFC executive regions are deactivated, even beyond levels seen during waking MW. We argue that dreaming can be understood as an "intensified" version of waking MW: though the two share many similarities, dreams tend to be longer, more visual and immersive, and to more strongly recruit numerous key hubs of the DMN. Further, whereas MW recruits fewer PFC regions than goal-directed thought, dreaming appears to be characterized by an even deeper quiescence of PFC regions involved in cognitive control and metacognition, with a corresponding lack of insight and meta-awareness. We suggest, then, that dreaming amplifies the same features that distinguish MW from goal-directed waking thought.

Light-front representation of chiral dynamics with Δ isobar and large-N c relations

DOE PAGES

Granados, C.; Weiss, C.

2016-06-13

Transverse densities describe the spatial distribution of electromagnetic current in the nucleon at fixed light-front time. At peripheral distances b = O(M π –1) the densities are governed by chiral dynamics and can be calculated model-independently using chiral effective field theory (EFT). Recent work has shown that the EFT results can be represented in first-quantized form, as overlap integrals of chiral light-front wave functions describing the transition of the nucleon to soft-pion-nucleon intermediate states, resulting in a quantum-mechanical picture of the peripheral transverse densities. We now extend this representation to include intermediate states with Δ isobars and implement relations basedmore » on the large-N c limit of QCD. We derive the wave function overlap formulas for the Δ contributions to the peripheral transverse densities by way of a three-dimensional reduction of relativistic chiral EFT expressions. Our procedure effectively maintains rotational invariance and avoids the ambiguities with higher-spin particles in the light-front time-ordered approach. We study the interplay of πN and πΔ intermediate states in the quantum-mechanical picture of the densities in a transversely polarized nucleon. We show that the correct N c-scaling of the charge and magnetization densities emerges as the result of the particular combination of currents generated by intermediate states with degenerate N and Δ. The off-shell behavior of the chiral EFT is summarized in contact terms and can be studied easily. As a result, the methods developed here can be applied to other peripheral densities and to moments of the nucleon's generalized parton distributions.« less

An Efficient Method to Detect Mutual Overlap of a Large Set of Unordered Images for Structure-From

NASA Astrophysics Data System (ADS)

Wang, X.; Zhan, Z. Q.; Heipke, C.

2017-05-01

Recently, low-cost 3D reconstruction based on images has become a popular focus of photogrammetry and computer vision research. Methods which can handle an arbitrary geometric setup of a large number of unordered and convergent images are of particular interest. However, determining the mutual overlap poses a considerable challenge. We propose a new method which was inspired by and improves upon methods employing random k-d forests for this task. Specifically, we first derive features from the images and then a random k-d forest is used to find the nearest neighbours in feature space. Subsequently, the degree of similarity between individual images, the image overlaps and thus images belonging to a common block are calculated as input to a structure-from-motion (sfm) pipeline. In our experiments we show the general applicability of the new method and compare it with other methods by analyzing the time efficiency. Orientations and 3D reconstructions were successfully conducted with our overlap graphs by sfm. The results show a speed-up of a factor of 80 compared to conventional pairwise matching, and of 8 and 2 compared to the VocMatch approach using 1 and 4 CPU, respectively.

Real-world injury patterns associated with Hybrid III sternal deflections in frontal crash tests.

PubMed

Brumbelow, Matthew L; Farmer, Charles M

2013-01-01

This study investigated the relationship between the peak sternal deflection measurements recorded by the Hybrid III 50th percentile male anthropometric test device (ATD) in frontal crash tests and injury and fatality outcomes for drivers in field crashes. ATD sternal deflection data were obtained from the Insurance Institute for Highway Safety's 64 km/h, 40 percent overlap crashworthiness evaluation tests for vehicles with seat belt crash tensioners, load limiters, and good-rated structure. The National Automotive Sampling System Crashworthiness Data System (NASS-CDS) was queried for frontal crashes of these vehicles in which the driver was restrained by a seat belt and air bag. Injury probability curves were calculated by frontal crash type using the injuries coded in NASS-CDS and peak ATD sternal deflection data. Fatality Analysis Reporting System (FARS) front-to-front crashes with exactly one driver death were also studied to determine whether the difference in measured sternal deflections for the 2 vehicles was related to the odds of fatality. For center impacts, moderate overlaps, and large overlaps in NASS-CDS, the probability of the driver sustaining an Abbreviated Injury Scale (AIS) score ≥ 3 thoracic injury, or any nonextremity AIS ≥ 3 injury, increased with increasing ATD sternal deflection measured in crash tests. For small overlaps, however, these probabilities decreased with increasing deflection. For FARS crashes, the fatally injured driver more often was in the vehicle with the lower measured deflection in crash tests (55 vs. 45%). After controlling for other factors, a 5-mm difference in measured sternal deflections between the 2 vehicles was associated with a fatality odds ratio of 0.762 for the driver in the vehicle with the greater deflection (95% confidence interval = 0.373, 1.449). Restraint systems that reduce peak Hybrid III sternal deflection in a moderate overlap crash test are beneficial in real-world crashes with similar or greater overlap but likely have a disbenefit in crashes with small overlap. This may occur because belt-force limiters employed to control deflections allow excursion that could produce contact with interior vehicle components in small overlaps, given the more oblique occupant motion and potential inboard movement of the air bag. Although based on a limited number of cases, this interpretation is supported by differences in skeletal fracture locations among drivers in crashes with different overlaps. Current restraint systems could be improved by designs that reduce sternal deflection in moderate and large overlap crashes without increasing occupant excursion in small overlap crashes.

An ant colony based algorithm for overlapping community detection in complex networks

NASA Astrophysics Data System (ADS)

Zhou, Xu; Liu, Yanheng; Zhang, Jindong; Liu, Tuming; Zhang, Di

2015-06-01

Community detection is of great importance to understand the structures and functions of networks. Overlap is a significant feature of networks and overlapping community detection has attracted an increasing attention. Many algorithms have been presented to detect overlapping communities. In this paper, we present an ant colony based overlapping community detection algorithm which mainly includes ants' location initialization, ants' movement and post processing phases. An ants' location initialization strategy is designed to identify initial location of ants and initialize label list stored in each node. During the ants' movement phase, the entire ants move according to the transition probability matrix, and a new heuristic information computation approach is redefined to measure similarity between two nodes. Every node keeps a label list through the cooperation made by ants until a termination criterion is reached. A post processing phase is executed on the label list to get final overlapping community structure naturally. We illustrate the capability of our algorithm by making experiments on both synthetic networks and real world networks. The results demonstrate that our algorithm will have better performance in finding overlapping communities and overlapping nodes in synthetic datasets and real world datasets comparing with state-of-the-art algorithms.

Individual differences and time-varying features of modular brain architecture.

PubMed

Liao, Xuhong; Cao, Miao; Xia, Mingrui; He, Yong

2017-05-15

Recent studies have suggested that human brain functional networks are topologically organized into functionally specialized but inter-connected modules to facilitate efficient information processing and highly flexible cognitive function. However, these studies have mainly focused on group-level network modularity analyses using "static" functional connectivity approaches. How these extraordinary modular brain structures vary across individuals and spontaneously reconfigure over time remain largely unknown. Here, we employed multiband resting-state functional MRI data (N=105) from the Human Connectome Project and a graph-based modularity analysis to systematically investigate individual variability and dynamic properties in modular brain networks. We showed that the modular structures of brain networks dramatically vary across individuals, with higher modular variability primarily in the association cortex (e.g., fronto-parietal and attention systems) and lower variability in the primary systems. Moreover, brain regions spontaneously changed their module affiliations on a temporal scale of seconds, which cannot be simply attributable to head motion and sampling error. Interestingly, the spatial pattern of intra-subject dynamic modular variability largely overlapped with that of inter-subject modular variability, both of which were highly reproducible across repeated scanning sessions. Finally, the regions with remarkable individual/temporal modular variability were closely associated with network connectors and the number of cognitive components, suggesting a potential contribution to information integration and flexible cognitive function. Collectively, our findings highlight individual modular variability and the notable dynamic characteristics in large-scale brain networks, which enhance our understanding of the neural substrates underlying individual differences in a variety of cognition and behaviors. Copyright © 2017 Elsevier Inc. All rights reserved.

FUNCTIONAL OVERLAP OF ROOT SYSTEMS IN AN OLD-GROWTH FOREST INFERRED FROM TRACER 15N UPTAKE

EPA Science Inventory

Belowground competition for nutrients and water is considered a key factor affecting spatial organization and productivity of individual stems within forest stands, yet there are few data describing the lateral extent and overlap of competing root systems. We quantified the func...

Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture

PubMed Central

2010-01-01

Background The biological dimensions of genes are manifold. These include genomic properties, (e.g., X/autosomal linkage, recombination) and functional properties (e.g., expression level, tissue specificity). Multiple properties, each generally of subtle influence individually, may affect the evolution of genes or merely be (auto-)correlates. Results of multidimensional analyses may reveal the relative importance of these properties on the evolution of genes, and therefore help evaluate whether these properties should be considered during analyses. While numerous properties are now considered during studies, most work still assumes the stereotypical solitary gene as commonly depicted in textbooks. Here, we investigate the Drosophila melanogaster genome to determine whether deviations from the stereotypical gene architecture correlate with other properties of genes. Results Deviations from the stereotypical gene architecture were classified as the following gene constellations: Overlapping genes were defined as those that overlap in the 5-prime, exonic, or intronic regions. Chromatin co-clustering genes were defined as genes that co-clustered within 20 kb of transcriptional territories. If this scheme is applied the stereotypical gene emerges as a rare occurrence (7.5%), slightly varied schemes yielded between ~1%-50%. Moreover, when following our scheme, paired-overlapping genes and chromatin co-clustering genes accounted for 50.1 and 42.4% of the genes analyzed, respectively. Gene constellation was a correlate of a number of functional and evolutionary properties of genes, but its statistical effect was ~1-2 orders of magnitude lower than the effects of recombination, chromosome linkage and protein function. Analysis of datasets on male reproductive proteins showed these were biased in their representation of gene constellations and evolutionary rate Ka/Ks estimates, but these biases did not overwhelm the biologically meaningful observation of high evolutionary rates of male reproductive genes. Conclusion Given the rarity of the solitary stereotypical gene, and the abundance of gene constellations that deviate from it, the presence of gene constellations, while once thought to be exceptional in large Eukaryote genomes, might have broader relevance to the understanding and study of the genome. However, according to our definition, while gene constellations can be significant correlates of functional properties of genes, they generally are weak correlates of the evolution of genes. Thus, the need for their consideration would depend on the context of studies. PMID:20497561

Functional (Psychogenic) Cognitive Disorders: A Perspective from the Neurology Clinic.

PubMed

Stone, Jon; Pal, Suvankar; Blackburn, Daniel; Reuber, Markus; Thekkumpurath, Parvez; Carson, Alan

2015-09-24

Cognitive symptoms such as poor memory and concentration represent a common cause of morbidity among patients presenting to general practitioners and may result in referral for a neurological opinion. In many cases, these symptoms do not relate to an underlying neurological disease or dementia. In this article we present a personal perspective on the differential diagnosis of cognitive symptoms in the neurology clinic, especially as this applies to patients who seek advice about memory problems but have no neurological disease process. These overlapping categories include the following 'functional' categories: 1) cognitive symptoms as part of anxiety or depression; 2) "normal" cognitive symptoms that become the focus of attention; 3) isolated functional cognitive disorder in which symptoms are outwith 'normal' but not explained by anxiety; 4) health anxiety about dementia; 5) cognitive symptoms as part of another functional disorder; and 6) retrograde dissociative (psychogenic) amnesia. Other 'non-dementia' diagnoses to consider in addition are 1) cognitive symptoms secondary to prescribed medication or substance misuse; 2) diseases other than dementia causing cognitive disorders; 3) patients who appear to have functional cognitive symptoms but then go on to develop dementia/another neurological disease; and finally 4) exaggeration/malingering. We discuss previous attempts to classify the problem of functional cognitive symptoms, the importance of making a positive diagnosis for the patient, and the need for large cohort studies to better define and manage this large group of patients.

Simulation requirements for the Large Deployable Reflector (LDR)

NASA Technical Reports Server (NTRS)

Soosaar, K.

1984-01-01

Simulation tools for the large deployable reflector (LDR) are discussed. These tools are often the transfer function variety equations. However, transfer functions are inadequate to represent time-varying systems for multiple control systems with overlapping bandwidths characterized by multi-input, multi-output features. Frequency domain approaches are the useful design tools, but a full-up simulation is needed. Because of the need for a dedicated computer for high frequency multi degree of freedom components encountered, non-real time smulation is preferred. Large numerical analysis software programs are useful only to receive inputs and provide output to the next block, and should be kept out of the direct loop of simulation. The following blocks make up the simulation. The thermal model block is a classical heat transfer program. It is a non-steady state program. The quasistatic block deals with problems associated with rigid body control of reflector segments. The steady state block assembles data into equations of motion and dynamics. A differential raytrace is obtained to establish a change in wave aberrations. The observation scene is described. The focal plane module converts the photon intensity impinging on it into electron streams or into permanent film records.

Functional Heterogeneity and Convergence in the Right Temporoparietal Junction

PubMed Central

Lee, Su Mei; McCarthy, Gregory

2016-01-01

The right temporoparietal junction (rTPJ) is engaged by tasks that manipulate biological motion processing, Theory of Mind attributions, and attention reorienting. The proximity of activations elicited by these tasks raises the question of whether these tasks share common cognitive component processes that are subserved by common neural substrates. Here, we used high-resolution whole-brain functional magnetic resonance imaging in a within-subjects design to determine whether these tasks activate common regions of the rTPJ. Each participant was presented with the 3 tasks in the same imaging session. In a whole-brain analysis, we found that only the right and left TPJs were activated by all 3 tasks. Multivoxel pattern analysis revealed that the regions of overlap could still discriminate the 3 tasks. Notably, we found significant cross-task classification in the right TPJ, which suggests a shared neural process between the 3 tasks. Taken together, these results support prior studies that have indicated functional heterogeneity within the rTPJ but also suggest a convergence of function within a region of overlap. These results also call for further investigation into the nature of the function subserved in this overlap region. PMID:25477367

Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hansen, Simon; Stüber, Jakob C.; Ernst, Patrick

Green fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here in this paper we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that “wrap around” GFP, have very high affinities of about 10–30 pM, and extremely slow off-rates. Theymore » can be natively produced in E. coli in very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a “clamp” from two different high-affinity repeat proteins, even if their epitopes overlap.« less

Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity

DOE PAGES

Hansen, Simon; Stüber, Jakob C.; Ernst, Patrick; ...

2017-11-24

Green fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here in this paper we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that “wrap around” GFP, have very high affinities of about 10–30 pM, and extremely slow off-rates. Theymore » can be natively produced in E. coli in very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a “clamp” from two different high-affinity repeat proteins, even if their epitopes overlap.« less

TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations.

PubMed

O'Rawe, Jason A; Wu, Yiyang; Dörfel, Max J; Rope, Alan F; Au, P Y Billie; Parboosingh, Jillian S; Moon, Sungjin; Kousi, Maria; Kosma, Konstantina; Smith, Christopher S; Tzetis, Maria; Schuette, Jane L; Hufnagel, Robert B; Prada, Carlos E; Martinez, Francisco; Orellana, Carmen; Crain, Jonathan; Caro-Llopis, Alfonso; Oltra, Silvestre; Monfort, Sandra; Jiménez-Barrón, Laura T; Swensen, Jeffrey; Ellingwood, Sara; Smith, Rosemarie; Fang, Han; Ospina, Sandra; Stegmann, Sander; Den Hollander, Nicolette; Mittelman, David; Highnam, Gareth; Robison, Reid; Yang, Edward; Faivre, Laurence; Roubertie, Agathe; Rivière, Jean-Baptiste; Monaghan, Kristin G; Wang, Kai; Davis, Erica E; Katsanis, Nicholas; Kalscheuer, Vera M; Wang, Edith H; Metcalfe, Kay; Kleefstra, Tjitske; Innes, A Micheil; Kitsiou-Tzeli, Sophia; Rosello, Monica; Keegan, Catherine E; Lyon, Gholson J

2015-12-03

We describe an X-linked genetic syndrome associated with mutations in TAF1 and manifesting with global developmental delay, intellectual disability (ID), characteristic facial dysmorphology, generalized hypotonia, and variable neurologic features, all in male individuals. Simultaneous studies using diverse strategies led to the identification of nine families with overlapping clinical presentations and affected by de novo or maternally inherited single-nucleotide changes. Two additional families harboring large duplications involving TAF1 were also found to share phenotypic overlap with the probands harboring single-nucleotide changes, but they also demonstrated a severe neurodegeneration phenotype. Functional analysis with RNA-seq for one of the families suggested that the phenotype is associated with downregulation of a set of genes notably enriched with genes regulated by E-box proteins. In addition, knockdown and mutant studies of this gene in zebrafish have shown a quantifiable, albeit small, effect on a neuronal phenotype. Our results suggest that mutations in TAF1 play a critical role in the development of this X-linked ID syndrome. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Overlapping contributions of Msh1p and putative recombination proteins Cce1p, Din7p, and Mhr1p in large-scale recombination and genome sorting events in the mitochondrial genome of Saccharomyces cerevisiae.

PubMed

Mookerjee, Shona A; Sia, Elaine A

2006-03-20

The mechanisms that govern mutation avoidance in the mitochondrial genome, though believed to be numerous, are poorly understood. The identification of individual genes has implicated mismatch repair and several recombination pathways in maintaining the fidelity and structural stability of mitochondrial DNA. However, the majority of genes in these pathways have not been identified and the interactions between different pathways have not been extensively studied. Additionally, the multicopy presence of the mitochondrial genome affects the occurrence and persistence of mutant phenotypes, making mitochondrial DNA transmission and sorting important factors affecting mutation accumulation. We present new evidence that the putative recombination genes CCE1, DIN7, and MHR1 have overlapping function with the mismatch repair homolog MSH1 in point mutation avoidance and suppression of aberrant recombination events. In addition, we demonstrate a novel role for Msh1p in mtDNA transmission, a role not predicted by studies of its nuclear homologs.

Thermally induced texture flip in semiconducting polymer stabilized by epitaxial relationship

NASA Astrophysics Data System (ADS)

O'Hara, Kathryn A.; Pokuri, Balaji S. S.; Takacs, Christopher J.; Beaujuge, Pierre M.; Ganapathysubramanian, Baskar; Chabinyc, Michael L.

The morphology of semiconducting polymer films has a large effect on the charge transport properties. Charges can move easily along the conjugated backbone and in the pi-pi stacking direction. However, transport through the film is determined by the connectivity between domains, which is not well understood. We previously observed quadrites in the polymer, PSBTBT, and proposed that the preferential overlap between lamellae may improve connectivity and provide an additional conduction pathway. Now, the presence of quadrites is revealed in another successful donor polymer, PBDTTPD, using high resolution transmission electron microscopy (HRTEM). A study of how side-chain substitution affects the epitaxial crossing is conducted by examining several PBDTTPD derivatives. The stability of the film texture with annealing is also examined as a function of quadrite formation. It has been shown that heating some semicrystalline polymers above the melting temperature and slow cooling can flip the lamellar texture from face-on to edge-on. We hypothesize that the orientation of lamellar crystallites in PBDTTPD films is stabilized by the epitaxial overlap between adjacent crystalline domains. This may have important implications for the electronic transport properties.

Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution.

PubMed

Marlétaz, Ferdinand; Maeso, Ignacio; Faas, Laura; Isaacs, Harry V; Holland, Peter W H

2015-08-01

The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate. We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication. Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates.

Prediction of CpG-island function: CpG clustering vs. sliding-window methods

PubMed Central

2010-01-01

Background Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence. Results We compare sliding-window to clustering (i.e. CpGcluster) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size vs. statistical significance (p-value), CpGcluster shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with Alu retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster. Many of these islets seem to be functional, as they are unmethylated, highly conserved and/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter CpGcluster islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains. Conclusions The main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by CpGcluster. This suggests that CpGcluster may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands. PMID:20500903

Genetics, Cognition, and Neurobiology of Schizotypal Personality: A Review of the Overlap with Schizophrenia

PubMed Central

Ettinger, Ulrich; Meyhöfer, Inga; Steffens, Maria; Wagner, Michael; Koutsouleris, Nikolaos

2013-01-01

Schizotypy refers to a set of temporally stable traits that are observed in the general population and that resemble the signs and symptoms of schizophrenia. Here, we review evidence from studies on genetics, cognition, perception, motor and oculomotor control, brain structure, brain function, and psychopharmacology in schizotypy. We specifically focused on identifying areas of overlap between schizotypy and schizophrenia. Evidence was corroborated that significant overlap exists between the two, covering the behavioral brain structural and functional as well molecular levels. In particular, several studies showed that individuals with high levels of schizotypal traits exhibit alterations in neurocognitive task performance and underlying brain function similar to the deficits seen in patients with schizophrenia. Studies of brain structure have shown both volume reductions and increase in schizotypy, pointing to schizophrenia-like deficits as well as possible protective or compensatory mechanisms. Experimental pharmacological studies have shown that high levels of schizotypy are associated with (i) enhanced dopaminergic response in striatum following administration of amphetamine and (ii) improvement of cognitive performance following administration of antipsychotic compounds. Together, this body of work suggests that schizotypy shows overlap with schizophrenia across multiple behavioral and neurobiological domains, suggesting that the study of schizotypal traits may be useful in improving our understanding of the etiology of schizophrenia. PMID:24600411

Functional redundancy and complementarities of seed dispersal by the last neotropical megafrugivores.

PubMed

Bueno, Rafael S; Guevara, Roger; Ribeiro, Milton C; Culot, Laurence; Bufalo, Felipe S; Galetti, Mauro

2013-01-01

Functional redundancy has been debated largely in ecology and conservation, yet we lack detailed empirical studies on the roles of functionally similar species in ecosystem function. Large bodied frugivores may disperse similar plant species and have strong impact on plant recruitment in tropical forests. The two largest frugivores in the neotropics, tapirs (Tapirus terrestris) and muriquis (Brachyteles arachnoides) are potential candidates for functional redundancy on seed dispersal effectiveness. Here we provide a comparison of the quantitative, qualitative and spatial effects on seed dispersal by these megafrugivores in a continuous Brazilian Atlantic forest. We found a low overlap of plant species dispersed by both muriquis and tapirs. A group of 35 muriquis occupied an area of 850 ha and dispersed 5 times more plant species, and 13 times more seeds than 22 tapirs living in the same area. Muriquis dispersed 2.4 times more seeds in any random position than tapirs. This can be explained mainly because seed deposition by muriquis leaves less empty space than tapirs. However, tapirs are able to disperse larger seeds than muriquis and move them into sites not reached by primates, such as large forest gaps, open areas and fragments nearby. Based on published information we found 302 plant species that are dispersed by at least one of these megafrugivores in the Brazilian Atlantic forest. Our study showed that both megafrugivores play complementary rather than redundant roles as seed dispersers. Although tapirs disperse fewer seeds and species than muriquis, they disperse larger-seeded species and in places not used by primates. The selective extinction of these megafrugivores will change the spatial seed rain they generate and may have negative effects on the recruitment of several plant species, particularly those with large seeds that have muriquis and tapirs as the last living seed dispersers.

Functional comparison of microarray data across multiple platforms using the method of percentage of overlapping functions.

PubMed

Li, Zhiguang; Kwekel, Joshua C; Chen, Tao

2012-01-01

Functional comparison across microarray platforms is used to assess the comparability or similarity of the biological relevance associated with the gene expression data generated by multiple microarray platforms. Comparisons at the functional level are very important considering that the ultimate purpose of microarray technology is to determine the biological meaning behind the gene expression changes under a specific condition, not just to generate a list of genes. Herein, we present a method named percentage of overlapping functions (POF) and illustrate how it is used to perform the functional comparison of microarray data generated across multiple platforms. This method facilitates the determination of functional differences or similarities in microarray data generated from multiple array platforms across all the functions that are presented on these platforms. This method can also be used to compare the functional differences or similarities between experiments, projects, or laboratories.

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

NASA Astrophysics Data System (ADS)

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.

Interleaved neuromuscular electrical stimulation: Motor unit recruitment overlap.

PubMed

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.

Estimates of projection overlap and zones of convergence within frontal-striatal circuits.

PubMed

Averbeck, Bruno B; Lehman, Julia; Jacobson, Moriah; Haber, Suzanne N

2014-07-16

Frontal-striatal circuits underlie important decision processes, and pathology in these circuits is implicated in many psychiatric disorders. Studies have shown a topographic organization of cortical projections into the striatum. However, work has also shown that there is considerable overlap in the striatal projection zones of nearby cortical regions. To characterize this in detail, we quantified the complete striatal projection zones from 34 cortical injection locations in rhesus monkeys. We first fit a statistical model that showed that the projection zone of a cortical injection site could be predicted with considerable accuracy using a cross-validated model estimated on only the other injection sites. We then examined the fraction of overlap in striatal projection zones as a function of distance between cortical injection sites, and found that there was a highly regular relationship. Specifically, nearby cortical locations had as much as 80% overlap, and the amount of overlap decayed exponentially as a function of distance between the cortical injection sites. Finally, we found that some portions of the striatum received inputs from all the prefrontal regions, making these striatal zones candidates as information-processing hubs. Thus, the striatum is a site of convergence that allows integration of information spread across diverse prefrontal cortical areas. Copyright © 2014 the authors 0270-6474/14/339497-09$15.00/0.

Recessive and dominant mutations in COL12A1 cause a novel EDS/myopathy overlap syndrome in humans and mice

PubMed Central

Zou, Yaqun; Zwolanek, Daniela; Izu, Yayoi; Gandhy, Shreya; Schreiber, Gudrun; Brockmann, Knut; Devoto, Marcella; Tian, Zuozhen; Hu, Ying; Veit, Guido; Meier, Markus; Stetefeld, Jörg; Hicks, Debbie; Straub, Volker; Voermans, Nicol C.; Birk, David E.; Barton, Elisabeth R.; Koch, Manuel; Bönnemann, Carsten G.

2014-01-01

Collagen VI-related myopathies are disorders of connective tissue presenting with an overlap phenotype combining clinical involvement from the muscle and from the connective tissue. Not all patients displaying related overlap phenotypes between muscle and connective tissue have mutations in collagen VI. Here, we report a homozygous recessive loss of function mutation and a de novo dominant mutation in collagen XII (COL12A1) as underlying a novel overlap syndrome involving muscle and connective tissue. Two siblings homozygous for a loss of function mutation showed widespread joint hyperlaxity combined with weakness precluding independent ambulation, while the patient with the de novo missense mutation was more mildly affected, showing improvement including the acquisition of walking. A mouse model with inactivation of the Col12a1 gene showed decreased grip strength, a delay in fiber-type transition and a deficiency in passive force generation while the muscle seems more resistant to eccentric contraction induced force drop, indicating a role for a matrix-based passive force-transducing elastic element in the generation of the weakness. This new muscle connective tissue overlap syndrome expands on the emerging importance of the muscle extracellular matrix in the pathogenesis of muscle disease. PMID:24334604

Category inference as a function of correlational structure, category discriminability, and number of available cues.

PubMed

Lancaster, Matthew E; Shelhamer, Ryan; Homa, Donald

2013-04-01

Two experiments investigated category inference when categories were composed of correlated or uncorrelated dimensions and the categories overlapped minimally or moderately. When the categories minimally overlapped, the dimensions were strongly correlated with the category label. Following a classification learning phase, subsequent transfer required the selection of either a category label or a feature when one, two, or three features were missing. Experiments 1 and 2 differed primarily in the number of learning blocks prior to transfer. In each experiment, the inference of the category label or category feature was influenced by both dimensional and category correlations, as well as their interaction. The number of cues available at test impacted performance more when the dimensional correlations were zero and category overlap was high. However, a minimal number of cues were sufficient to produce high levels of inference when the dimensions were highly correlated; additional cues had a positive but reduced impact, even when overlap was high. Subjects were generally more accurate in inferring the category label than a category feature regardless of dimensional correlation, category overlap, or number of cues available at test. Whether the category label functioned as a special feature or not was critically dependent upon these embedded correlations, with feature inference driven more strongly by dimensional correlations.

Does standard deviation matter? Using "standard deviation" to quantify security of multistage testing.

PubMed

Wang, Chun; Zheng, Yi; Chang, Hua-Hua

2014-01-01

With the advent of web-based technology, online testing is becoming a mainstream mode in large-scale educational assessments. Most online tests are administered continuously in a testing window, which may post test security problems because examinees who take the test earlier may share information with those who take the test later. Researchers have proposed various statistical indices to assess the test security, and one most often used index is the average test-overlap rate, which was further generalized to the item pooling index (Chang & Zhang, 2002, 2003). These indices, however, are all defined as the means (that is, the expected proportion of common items among examinees) and they were originally proposed for computerized adaptive testing (CAT). Recently, multistage testing (MST) has become a popular alternative to CAT. The unique features of MST make it important to report not only the mean, but also the standard deviation (SD) of test overlap rate, as we advocate in this paper. The standard deviation of test overlap rate adds important information to the test security profile, because for the same mean, a large SD reflects that certain groups of examinees share more common items than other groups. In this study, we analytically derived the lower bounds of the SD under MST, with the results under CAT as a benchmark. It is shown that when the mean overlap rate is the same between MST and CAT, the SD of test overlap tends to be larger in MST. A simulation study was conducted to provide empirical evidence. We also compared the security of MST under the single-pool versus the multiple-pool designs; both analytical and simulation studies show that the non-overlapping multiple-pool design will slightly increase the security risk.

Overlap of gastroesophageal reflux disease and functional bowel disorders in the general Chinese rural population.

PubMed

Cai, Shun Tian; Wang, Li Ying; Sun, Gang; Peng, Li Hua; Guo, Xu; Wang, Wei Feng; Yang, Yun Sheng

2015-07-01

This study aimed to investigate the prevalence of the overlap between gastroesophageal reflux disease (GERD) and functional bowel disorders (FBD) in the general population in rural areas in China. A population-based cross-sectional study was conducted in six villages in Nanmazhuang area in Lankao County (Henan Province, China) from December 2010 to October 2011. The GERD questionnaire (GerdQ) and Rome III criteria were used for the diagnosis of GERD and FBD and to determine the prevalence of GERD-FBD overlap. The response rate to the questionnaires of the patients was 91.5%. In all, 2950 of 3700 residents with a mean age of 42.4 ± 16.8 years were included. Among them, 4.8% were diagnosed with GERD and 4.6% with FBD. The proportion of respondents with FBD was significantly higher in the GERD group than that in the non-GERD group (25.53% vs 3.60%, P < 0.05). The prevalence of GERD in the FBD group was significantly higher than that in the non-FBD group (26.28% vs 3.73%, P < 0.05). The prevalence of GERD-FBD overlap in the general rural population was 1.22%. Logistic regression analysis indicated that anxiety was an independent predictor for the GERD-FBD overlap in GERD and FBD (odds ratio [OR] 1.05, 95% confidence interval [CI] 1.02-1.09 and OR 1.06, 95% CI 1.02-1.10, respectively). GERD-FBD overlap is more common than expected by chance in the general rural population, and anxiety is significantly related to the overlap. © 2015 Chinese Medical Association Shanghai Branch, Chinese Society of Gastroenterology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine and Wiley Publishing Asia Pty Ltd.

Equivalent peak resolution: characterization of the extent of separation for two components based on their relative peak overlap.

PubMed

Dvořák, Martin; Svobodová, Jana; Dubský, Pavel; Riesová, Martina; Vigh, Gyula; Gaš, Bohuslav

2015-03-01

Although the classical formula of peak resolution was derived to characterize the extent of separation only for Gaussian peaks of equal areas, it is often used even when the peaks follow non-Gaussian distributions and/or have unequal areas. This practice can result in misleading information about the extent of separation in terms of the severity of peak overlap. We propose here the use of the equivalent peak resolution value, a term based on relative peak overlap, to characterize the extent of separation that had been achieved. The definition of equivalent peak resolution is not constrained either by the form(s) of the concentration distribution function(s) of the peaks (Gaussian or non-Gaussian) or the relative area of the peaks. The equivalent peak resolution value and the classically defined peak resolution value are numerically identical when the separated peaks are Gaussian and have identical areas and SDs. Using our new freeware program, Resolution Analyzer, one can calculate both the classically defined and the equivalent peak resolution values. With the help of this tool, we demonstrate here that the classical peak resolution values mischaracterize the extent of peak overlap even when the peaks are Gaussian but have different areas. We show that under ideal conditions of the separation process, the relative peak overlap value is easily accessible by fitting the overall peak profile as the sum of two Gaussian functions. The applicability of the new approach is demonstrated on real separations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Embedded function methods for supersonic turbulent boundary layers

NASA Technical Reports Server (NTRS)

He, J.; Kazakia, J. Y.; Walker, J. D. A.

1990-01-01

The development of embedded functions to represent the mean velocity and total enthalpy distributions in the wall layer of a supersonic turbulent boundary layer is considered. The asymptotic scaling laws (in the limit of large Reynolds number) for high speed compressible flows are obtained to facilitate eventual implementation of the embedded functions in a general prediction method. A self-consistent asymptotic structure is derived, as well as a compressible law of the wall in which the velocity and total enthalpy are logarithmic within the overlap zone, but in the Howarth-Dorodnitsyn variable. Simple outer region turbulence models are proposed (some of which are modifications of existing incompressible models) to reflect the effects of compressibility. As a test of the methodology and the new turbulence models, a set of self-similar outer region profiles is obtained for constant pressure flow; these are then coupled with embedded functions in the wall layer. The composite profiles thus obtained are compared directly with experimental data and good agreement is obtained for flows with Mach numbers up to 10.

Evaluation of crystallographic strain, rotation and defects in functional oxides by the moiré effect in scanning transmission electron microscopy.

PubMed

Naden, A B; O'Shea, K J; MacLaren, D A

2018-04-20

Moiré patterns in scanning transmission electron microscopy (STEM) images of epitaxial perovskite oxides are used to assess strain and defect densities over fields of view extending over several hundred nanometers. The patterns arise from the geometric overlap of the rastered STEM electron beam and the samples' crystal periodicities and we explore the emergence and application of these moiré fringes for rapid strain analysis. Using the epitaxial functional oxide perovskites BiFeO 3 and Pr 1-x Ca x MnO 3 , we discuss the impact of large degrees of strain on the quantification of STEM moiré patterns, identify defects in the fringe patterns and quantify strain and lattice rotation. Such a wide-area analysis of crystallographic strain and defects is crucial for developing structure-function relations of functional oxides and we find the STEM moiré technique to be an attractive means of structural assessment that can be readily applied to low dose studies of damage sensitive crystalline materials.

Evaluation of crystallographic strain, rotation and defects in functional oxides by the moiré effect in scanning transmission electron microscopy

NASA Astrophysics Data System (ADS)

Naden, A. B.; O'Shea, K. J.; MacLaren, D. A.

2018-04-01

Moiré patterns in scanning transmission electron microscopy (STEM) images of epitaxial perovskite oxides are used to assess strain and defect densities over fields of view extending over several hundred nanometers. The patterns arise from the geometric overlap of the rastered STEM electron beam and the samples’ crystal periodicities and we explore the emergence and application of these moiré fringes for rapid strain analysis. Using the epitaxial functional oxide perovskites BiFeO3 and Pr1-x Ca x MnO3, we discuss the impact of large degrees of strain on the quantification of STEM moiré patterns, identify defects in the fringe patterns and quantify strain and lattice rotation. Such a wide-area analysis of crystallographic strain and defects is crucial for developing structure-function relations of functional oxides and we find the STEM moiré technique to be an attractive means of structural assessment that can be readily applied to low dose studies of damage sensitive crystalline materials.

The miR-29 family: genomics, cell biology, and relevance to renal and cardiovascular injury.

PubMed

Kriegel, Alison J; Liu, Yong; Fang, Yi; Ding, Xiaoqiang; Liang, Mingyu

2012-02-27

The human miR-29 family of microRNAs has three mature members, miR-29a, miR-29b, and miR-29c. miR-29s are encoded by two gene clusters. Binding sites for several transcriptional factors have been identified in the promoter regions of miR-29 genes. The miR-29 family members share a common seed region sequence and are predicted to target largely overlapping sets of genes. However, the miR-29 family members exhibit differential regulation in several cases and different subcellular distribution, suggesting their functional relevance may not be identical. miR-29s directly target at least 16 extracellular matrix genes, providing a dramatic example of a single microRNA targeting a large group of functionally related genes. Strong antifibrotic effects of miR-29s have been demonstrated in heart, kidney, and other organs. miR-29s have also been shown to be proapoptotic and involved in the regulation of cell differentiation. It remains to be explored how various cellular effects of miR-29s determine functional relevance of miR-29s to specific diseases and how the miR-29 family members may function cooperatively or separately.

Parcellating an Individual Subject's Cortical and Subcortical Brain Structures Using Snowball Sampling of Resting-State Correlations

PubMed Central

Wig, Gagan S.; Laumann, Timothy O.; Cohen, Alexander L.; Power, Jonathan D.; Nelson, Steven M.; Glasser, Matthew F.; Miezin, Francis M.; Snyder, Abraham Z.; Schlaggar, Bradley L.; Petersen, Steven E.

2014-01-01

We describe methods for parcellating an individual subject's cortical and subcortical brain structures using resting-state functional correlations (RSFCs). Inspired by approaches from social network analysis, we first describe the application of snowball sampling on RSFC data (RSFC-Snowballing) to identify the centers of cortical areas, subdivisions of subcortical nuclei, and the cerebellum. RSFC-Snowballing parcellation is then compared with parcellation derived from identifying locations where RSFC maps exhibit abrupt transitions (RSFC-Boundary Mapping). RSFC-Snowballing and RSFC-Boundary Mapping largely complement one another, but also provide unique parcellation information; together, the methods identify independent entities with distinct functional correlations across many cortical and subcortical locations in the brain. RSFC parcellation is relatively reliable within a subject scanned across multiple days, and while the locations of many area centers and boundaries appear to exhibit considerable overlap across subjects, there is also cross-subject variability—reinforcing the motivation to parcellate brains at the level of individuals. Finally, examination of a large meta-analysis of task-evoked functional magnetic resonance imaging data reveals that area centers defined by task-evoked activity exhibit correspondence with area centers defined by RSFC-Snowballing. This observation provides important evidence for the ability of RSFC to parcellate broad expanses of an individual's brain into functionally meaningful units. PMID:23476025

Not one extrastriate body area: Using anatomical landmarks, hMT+, and visual field maps to parcellate limb-selective activations in human lateral occipitotemporal cortex

PubMed Central

Weiner, Kevin S.; Grill-Spector, Kalanit

2011-01-01

The prevailing view of human lateral occipitotemporal cortex (LOTC) organization suggests a single area selective for images of the human body (extrastriate body area, EBA) that highly overlaps with the human motion-selective complex (hMT+). Using functional magnetic resonance imaging with higher resolution (1.5mm voxels) than past studies (3–4mm voxels), we examined the fine-scale spatial organization of these activations relative to each other, as well as to visual field maps in LOTC. Rather than one contiguous EBA highly overlapping hMT+, results indicate three limb-selective activations organized in a crescent surrounding hMT+: (1) an activation posterior to hMT+ on the lateral occipital sulcus/middle occipital gyrus (LOS/MOG) overlapping the lower vertical meridian shared between visual field maps LO-2 and TO-1, (2) an activation anterior to hMT+ on the middle temporal gyrus (MTG) consistently overlapping the lower vertical meridian of TO-2 and extending outside presently defined visual field maps, and (3) an activation inferior to hMT+ on the inferotemporal gyrus (ITG) overlapping the parafoveal representation of the TO cluster. This crescent organization of limb-selective activations surrounding hMT+ is reproducible over a span of three years and is consistent across different image types used for localization. Further, these regions exhibit differential position properties: preference for contralateral image presentation decreases and preference for foveal presentation increases from the limb-selective LOS to the MTG. Finally, the relationship between limb-selective activations and visual field maps extends to the dorsal stream where a posterior IPS activation overlaps V7. Overall, our measurements demonstrate a series of LOTC limb-selective activations that 1) have separate anatomical and functional boundaries, 2) overlap distinct visual field maps, and 3) illustrate differential position properties. These findings indicate that category selectivity alone is an insufficient organization principle for defining brain areas. Instead, multiple properties are necessary in order to parcellate and understand the functional organization of high-level visual cortex. PMID:21439386

Concurrent credit portfolio losses

PubMed Central

Sicking, Joachim; Schäfer, Rudi

2018-01-01

We consider the problem of concurrent portfolio losses in two non-overlapping credit portfolios. In order to explore the full statistical dependence structure of such portfolio losses, we estimate their empirical pairwise copulas. Instead of a Gaussian dependence, we typically find a strong asymmetry in the copulas. Concurrent large portfolio losses are much more likely than small ones. Studying the dependences of these losses as a function of portfolio size, we moreover reveal that not only large portfolios of thousands of contracts, but also medium-sized and small ones with only a few dozens of contracts exhibit notable portfolio loss correlations. Anticipated idiosyncratic effects turn out to be negligible. These are troublesome insights not only for investors in structured fixed-income products, but particularly for the stability of the financial sector. JEL codes: C32, F34, G21, G32, H81. PMID:29425246

Imaging of the outer valence orbitals of CO by electron momentum spectroscopy — Comparison with high level MRSD-CI and DFT calculations

NASA Astrophysics Data System (ADS)

Fan, X. W.; Chen, X. J.; Zhou, S. J.; Zheng, Y.; Brion, C. E.; Frey, R.; Davidson, E. R.

1997-09-01

A newly constructed energy dispersive multichannel electron momentum spectrometer has been used to image the electron density of the outer valence orbitals of CO with high precision. Binding energy spectra are obtained at a coincidence energy resolution of 1.2 eV fwhm. The measured electron density profiles in momentum space for the outer valence orbitals of CO are compared with cross sections calculated using SCF wavefunctions with basis sets of varying complexity up to near-Hartree-Fock limit in quality. The effects of correlation and electronic relaxation on the calculated momentum profiles are investigated using large MRSD-CI calculations of the full ion-neutral overlap distributions, as well as large basis set DFT calculations with local and non-local (gradient corrected) functionals.

Concurrent credit portfolio losses.

PubMed

Sicking, Joachim; Guhr, Thomas; Schäfer, Rudi

2018-01-01

We consider the problem of concurrent portfolio losses in two non-overlapping credit portfolios. In order to explore the full statistical dependence structure of such portfolio losses, we estimate their empirical pairwise copulas. Instead of a Gaussian dependence, we typically find a strong asymmetry in the copulas. Concurrent large portfolio losses are much more likely than small ones. Studying the dependences of these losses as a function of portfolio size, we moreover reveal that not only large portfolios of thousands of contracts, but also medium-sized and small ones with only a few dozens of contracts exhibit notable portfolio loss correlations. Anticipated idiosyncratic effects turn out to be negligible. These are troublesome insights not only for investors in structured fixed-income products, but particularly for the stability of the financial sector. JEL codes: C32, F34, G21, G32, H81.

Characteristics and self-rated health of overlap syndrome.

PubMed

Chung, Jung Wha; Kong, Kyoung Ae; Lee, Jin Hwa; Lee, Seok Jeong; Ryu, Yon Ju; Chang, Jung Hyun

2014-01-01

Overlap syndrome shares features of both asthma and chronic obstructive pulmonary disease (COPD). The aim of this study was to investigate characteristics of overlap syndrome and their effect on self-rated health (SRH). We analyzed data from the Fourth Korea National Health and Nutrition Examination Survey of 2007-2009. Subjects with acceptable spirometry and available wheezing history were included. Subjects were classified into four groups based on forced expiratory volume in one second (FEV1)/forced vital capacity (FVC) results and the presence or absence of self-reported wheezing for the previous 12 months: 1) COPD group, defined as having FEV1/FVC <0.7 without self-reported wheezing history; 2) asthma group, defined as having self-reported wheezing history without FEV1/FVC <0.7; 3) overlap syndrome group, having both FEV1/FVC <0.7 and wheezing history; and 4) non-obstructive disease (NOD) group, having neither FEV1/FVC <0.7 nor self-reported wheezing. SRH was categorized as better or lower based on responses to a questionnaire. From a total 9,104 subjects, 700 were assigned to the COPD group, 560 to the asthma group, 210 to the overlap syndrome group, and 7,634 to the NOD group. Compared to the other groups, subjects in the overlap syndrome group were more likely to have low lung function, a high proportion of smokers, low socioeconomic status, short education duration, lower SRH, and past diagnosis of pulmonary tuberculosis or bronchiectasis. Multiple logistic regression analysis revealed that both overlap syndrome and asthma groups were independently associated with lower SRH after adjustment for age, sex, socioeconomic status, education level, smoking status, comorbidities, and lung function. Female, old age, low education level, low economic status, smoker and other comorbidities were also associated with lower SRH. Overlap syndrome was accompanied by high morbidity and was associated with lower SRH, which needs more appropriate care.

Genetic overlap between type 2 diabetes and major depressive disorder identified by bioinformatics analysis.

PubMed

Ji, Hong-Fang; Zhuang, Qi-Shuai; Shen, Liang

2016-04-05

Our study investigated the shared genetic etiology underlying type 2 diabetes (T2D) and major depressive disorder (MDD) by analyzing large-scale genome wide association studies statistics. A total of 496 shared SNPs associated with both T2D and MDD were identified at p-value ≤ 1.0E-07. Functional enrichment analysis showed that the enriched pathways pertained to immune responses (Fc gamma R-mediated phagocytosis, T cell and B cell receptors signaling), cell signaling (MAPK, Wnt signaling), lipid metabolism, and cancer associated pathways. The findings will have potential implications for future interventional studies of the two diseases.

Functional ultrasound imaging of intrinsic connectivity in the living rat brain with high spatiotemporal resolution

PubMed Central

Osmanski, Bruno-Félix; Pezet, Sophie; Ricobaraza, Ana; Lenkei, Zsolt; Tanter, Mickael

2014-01-01

Long-range coherences in spontaneous brain activity reflect functional connectivity. Here we propose a novel, highly resolved connectivity mapping approach, using ultrafast functional ultrasound (fUS), which enables imaging of cerebral microvascular haemodynamics deep in the anaesthetized rodent brain, through a large thinned-skull cranial window, with pixel dimensions of 100 μm × 100 μm in-plane. The millisecond-range temporal resolution allows unambiguous cancellation of low-frequency cardio-respiratory noise. Both seed-based and singular value decomposition analysis of spatial coherences in the low-frequency (<0.1 Hz) spontaneous fUS signal fluctuations reproducibly report, at different coronal planes, overlapping high-contrast, intrinsic functional connectivity patterns. These patterns are similar to major functional networks described in humans by resting-state fMRI, such as the lateral task-dependent network putatively anticorrelated with the midline default-mode network. These results introduce fUS as a powerful novel neuroimaging method, which could be extended to portable systems for three-dimensional functional connectivity imaging in awake and freely moving rodents. PMID:25277668

The Energy of Substituted Ethanes. Asymmetry Orbitals

PubMed Central

Salem, Lionel; Hoffmann, Roald; Otto, Peter

1973-01-01

The leading terms in the energy of a general substituted ethane are derived in explicit form as a function of the torsional angle θ, the substituent electronegativities, and their mutual overlaps. The energy is found to be the sum of all four overlaps between pairs of asymmetry orbitals, and satisfies the requisite symmetry properties. PMID:16592060

Autism and Schizophrenia in High Functioning Adults: Behavioral Differences and Overlap

ERIC Educational Resources Information Center

Spek, Annelies A.; Wouters, Saskia G. M.

2010-01-01

Several recent studies have demonstrated a genetical overlap between autism and schizophrenia. However, at a behavioral level it remains unclear which features can validly distinguish adults with autism from an adult schizophrenia group. To this end, the present study compared 21 individuals with the autistic disorder and 21 individuals with…

Saccadic Eye Movements in Adults with High-Functioning Autism Spectrum Disorder

ERIC Educational Resources Information Center

Zalla, Tiziana; Seassau, Magali; Cazalis, Fabienne; Gras, Doriane; Leboyer, Marion

2018-01-01

In this study, we examined the accuracy and dynamics of visually guided saccades in 20 adults with autism spectrum disorder, as compared to 20 typically developed adults using the Step/Overlap/Gap paradigms. Performances in participants with autistic spectrum disorder were characterized by preserved Gap/Overlap effect, but reduced gain and peak…

Mechanisms of signal transduction by ethylene: overlapping and non-overlapping signalling roles in a receptor family

PubMed Central

Shakeel, Samina N.; Wang, Xiaomin; Binder, Brad M.; Schaller, G. Eric

2013-01-01

The plant hormone ethylene regulates growth and development as well as responses to biotic and abiotic stresses. Over the last few decades, key elements involved in ethylene signal transduction have been identified through genetic approaches, these elements defining a pathway that extends from initial ethylene perception at the endoplasmic reticulum to changes in transcriptional regulation within the nucleus. Here, we present our current understanding of ethylene signal transduction, focusing on recent developments that support a model with overlapping and non-overlapping roles for members of the ethylene receptor family. We consider the evidence supporting this model for sub-functionalization within the receptor family, and then discuss mechanisms by which such a sub-functionalization may occur. To this end, we consider the importance of receptor interactions in modulating their signal output and how such interactions vary in the receptor family. In addition, we consider evidence indicating that ethylene signal output by the receptors involves both phosphorylation-dependent and phosphorylation-independent mechanisms. We conclude with a current model for signalling by the ethylene receptors placed within the overall context of ethylene signal transduction. PMID:23543258

Functional genomics of the evolution of increased resistance to parasitism in Drosophila.

PubMed

Wertheim, Bregje; Kraaijeveld, Alex R; Hopkins, Meirion G; Walther Boer, Mark; Godfray, H Charles J

2011-03-01

Individual hosts normally respond to parasite attack by launching an acute immune response (a phenotypic plastic response), while host populations can respond in the longer term by evolving higher level of defence against parasites. Little is known about the genetics of the evolved response: the identity and number of genes involved and whether it involves a pre-activation of the regulatory systems governing the plastic response. We explored these questions by surveying transcriptional changes in a Drosophila melanogaster strain artificially selected for resistance against the hymenopteran endoparasitoid Asobara tabida. Using micro-arrays, we profiled gene expression at seven time points during development (from the egg to the second instar larva) and found a large number of genes (almost 900) with altered expression levels. Bioinformatic analysis showed that some were involved in immunity or defence-associated functions but many were not. Previously, we had defined a set of genes whose level of expression changed after parasitoid attack and a comparison with the present set showed a significant though comparatively small overlap. This suggests that the evolutionary response to parasitism is not a simple pre-activation of the plastic, acute response. We also found overlap in the genes involved in the evolutionary response to parasitism and to other biotic and abiotic stressors, perhaps suggesting a 'module' of genes involved in a generalized stress response as has been found in other organisms. © 2010 Blackwell Publishing Ltd.

From music making to speaking: engaging the mirror neuron system in autism.

PubMed

Wan, Catherine Y; Demaine, Krystal; Zipse, Lauryn; Norton, Andrea; Schlaug, Gottfried

2010-05-31

Individuals with autism show impairments in emotional tuning, social interactions and communication. These are functions that have been attributed to the putative human mirror neuron system (MNS), which contains neurons that respond to the actions of self and others. It has been proposed that a dysfunction of that system underlies some of the characteristics of autism. Here, we review behavioral and imaging studies that implicate the MNS (or a brain network with similar functions) in sensory-motor integration and speech representation, and review data supporting the hypothesis that MNS activity could be abnormal in autism. In addition, we propose that an intervention designed to engage brain regions that overlap with the MNS may have significant clinical potential. We argue that this engagement could be achieved through forms of music making. Music making with others (e.g., playing instruments or singing) is a multi-modal activity that has been shown to engage brain regions that largely overlap with the human MNS. Furthermore, many children with autism thoroughly enjoy participating in musical activities. Such activities may enhance their ability to focus and interact with others, thereby fostering the development of communication and social skills. Thus, interventions incorporating methods of music making may offer a promising approach for facilitating expressive language in otherwise nonverbal children with autism. Copyright (c) 2010 Elsevier Inc. All rights reserved.

From painkiller to empathy killer: acetaminophen (paracetamol) reduces empathy for pain.

PubMed

Mischkowski, Dominik; Crocker, Jennifer; Way, Baldwin M

2016-09-01

Simulation theories of empathy hypothesize that empathizing with others' pain shares some common psychological computations with the processing of one's own pain. Support for this perspective has largely relied on functional neuroimaging evidence of an overlap between activations during the experience of physical pain and empathy for other people's pain. Here, we extend the functional overlap perspective to the neurochemical level and test whether a common physical painkiller, acetaminophen (paracetamol), can reduce empathy for another's pain. In two double-blind placebo-controlled experiments, participants rated perceived pain, personal distress and empathic concern in response to reading scenarios about another's physical or social pain, witnessing ostracism in the lab, or visualizing another study participant receiving painful noise blasts. As hypothesized, acetaminophen reduced empathy in response to others' pain. Acetaminophen also reduced the unpleasantness of noise blasts delivered to the participant, which mediated acetaminophen's effects on empathy. Together, these findings suggest that the physical painkiller acetaminophen reduces empathy for pain and provide a new perspective on the neurochemical bases of empathy. Because empathy regulates prosocial and antisocial behavior, these drug-induced reductions in empathy raise concerns about the broader social side effects of acetaminophen, which is taken by almost a quarter of adults in the United States each week. © The Author (2016). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

How many atoms are required to characterize accurately trajectory fluctuations of a protein?

NASA Astrophysics Data System (ADS)

Cukier, Robert I.

2010-06-01

Large molecules, whose thermal fluctuations sample a complex energy landscape, exhibit motions on an extended range of space and time scales. Principal component analysis (PCA) is often used to extract dominant motions that in proteins are typically domain motions. These motions are captured in the large eigenvalue (leading) principal components. There is also information in the small eigenvalues, arising from approximate linear dependencies among the coordinates. These linear dependencies suggest that instead of using all the atom coordinates to represent a trajectory, it should be possible to use a reduced set of coordinates with little loss in the information captured by the large eigenvalue principal components. In this work, methods that can monitor the correlation (overlap) between a reduced set of atoms and any number of retained principal components are introduced. For application to trajectory data generated by simulations, where the overall translational and rotational motion needs to be eliminated before PCA is carried out, some difficulties with the overlap measures arise and methods are developed to overcome them. The overlap measures are evaluated for a trajectory generated by molecular dynamics for the protein adenylate kinase, which consists of a stable, core domain, and two more mobile domains, referred to as the LID domain and the AMP-binding domain. The use of reduced sets corresponding, for the smallest set, to one-eighth of the alpha carbon (CA) atoms relative to using all the CA atoms is shown to predict the dominant motions of adenylate kinase. The overlap between using all the CA atoms and all the backbone atoms is essentially unity for a sum over PCA modes that effectively capture the exact trajectory. A reduction to a few atoms (three in the LID and three in the AMP-binding domain) shows that at least the first principal component, characterizing a large part of the LID-binding and AMP-binding motion, is well described. Based on these results, the overlap criterion should be applicable as a guide to postulating and validating coarse-grained descriptions of generic biomolecular assemblies.

Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach

PubMed Central

Ruderfer, Douglas M; Charney, Alexander W; Readhead, Ben; Kidd, Brian A; Kähler, Anna K; Kenny, Paul J; Keiser, Michael J; Moran, Jennifer L; Hultman, Christina M; Scott, Stuart A; Sullivan, Patrick F; Purcell, Shaun M; Dudley, Joel T; Sklar, Pamela

2016-01-01

Summary Background Therapeutic treatments for schizophrenia do not alleviate symptoms for all patients and efficacy is limited by common, often severe, side-effects. Genetic studies of disease can identify novel drug targets, and drugs for which the mechanism has direct genetic support have increased likelihood of clinical success. Large-scale genetic studies of schizophrenia have increased the number of genes and gene sets associated with risk. We aimed to examine the overlap between schizophrenia risk loci and gene targets of a comprehensive set of medications to potentially inform and improve treatment of schizophrenia. Methods We defined schizophrenia risk loci as genomic regions reaching genome-wide significance in the latest Psychiatric Genomics Consortium schizophrenia genome-wide association study (GWAS) of 36 989 cases and 113 075 controls and loss of function variants observed only once among 5079 individuals in an exome-sequencing study of 2536 schizophrenia cases and 2543 controls (Swedish Schizophrenia Study). Using two large and orthogonally created databases, we collated drug targets into 167 gene sets targeted by pharmacologically similar drugs and examined enrichment of schizophrenia risk loci in these sets. We further linked the exome-sequenced data with a national drug registry (the Swedish Prescribed Drug Register) to assess the contribution of rare variants to treatment response, using clozapine prescription as a proxy for treatment resistance. Findings We combined results from testing rare and common variation and, after correction for multiple testing, two gene sets were associated with schizophrenia risk: agents against amoebiasis and other protozoal diseases (106 genes, p=0·00046, pcorrected =0·024) and antipsychotics (347 genes, p=0·00078, pcorrected=0·046). Further analysis pointed to antipsychotics as having independent enrichment after removing genes that overlapped these two target sets. We noted significant enrichment both in known targets of antipsychotics (70 genes, p=0·0078) and novel predicted targets (277 genes, p=0·019). Patients with treatment-resistant schizophrenia had an excess of rare disruptive variants in gene targets of antipsychotics (347 genes, p=0·0067) and in genes with evidence for a role in antipsychotic efficacy (91 genes, p=0·0029). Interpretation Our results support genetic overlap between schizophrenia pathogenesis and antipsychotic mechanism of action. This finding is consistent with treatment efficacy being polygenic and suggests that single-target therapeutics might be insufficient. We provide evidence of a role for rare functional variants in antipsychotic treatment response, pointing to a subset of patients where their genetic information could inform treatment. Finally, we present a novel framework for identifying treatments from genetic data and improving our understanding of therapeutic mechanism. PMID:26915512

Dark-field microscopic image stitching method for surface defects evaluation of large fine optics.

PubMed

Liu, Dong; Wang, Shitong; Cao, Pin; Li, Lu; Cheng, Zhongtao; Gao, Xin; Yang, Yongying

2013-03-11

One of the challenges in surface defects evaluation of large fine optics is to detect defects of microns on surfaces of tens or hundreds of millimeters. Sub-aperture scanning and stitching is considered to be a practical and efficient method. But since there are usually few defects on the large aperture fine optics, resulting in no defects or only one run-through line feature in many sub-aperture images, traditional stitching methods encounter with mismatch problem. In this paper, a feature-based multi-cycle image stitching algorithm is proposed to solve the problem. The overlapping areas of sub-apertures are categorized based on the features they contain. Different types of overlapping areas are then stitched in different cycles with different methods. The stitching trace is changed to follow the one that determined by the features. The whole stitching procedure is a region-growing like process. Sub-aperture blocks grow bigger after each cycle and finally the full aperture image is obtained. Comparison experiment shows that the proposed method is very suitable to stitch sub-apertures that very few feature information exists in the overlapping areas and can stitch the dark-field microscopic sub-aperture images very well.

Percolation in multiplex networks with overlap.

PubMed

Cellai, Davide; López, Eduardo; Zhou, Jie; Gleeson, James P; Bianconi, Ginestra

2013-11-01

From transportation networks to complex infrastructures, and to social and communication networks, a large variety of systems can be described in terms of multiplexes formed by a set of nodes interacting through different networks (layers). Multiplexes may display an increased fragility with respect to the single layers that constitute them. However, so far the overlap of the links in different layers has been mostly neglected, despite the fact that it is an ubiquitous phenomenon in most multiplexes. Here, we show that the overlap among layers can improve the robustness of interdependent multiplex systems and change the critical behavior of the percolation phase transition in a complex way.

Covariant extension of the GPD overlap representation at low Fock states

DOE PAGES

Chouika, N.; Mezrag, C.; Moutarde, H.; ...

2017-12-26

Here, we present a novel approach to compute generalized parton distributions within the lightfront wave function overlap framework. We show how to systematically extend generalized parton distributions computed within the DGLAP region to the ERBL one, fulfilling at the same time both the polynomiality and positivity conditions. We exemplify our method using pion lightfront wave functions inspired by recent results of non-perturbative continuum techniques and algebraic nucleon lightfront wave functions. We also test the robustness of our algorithm on reggeized phenomenological parameterizations. This approach paves the way to a better understanding of the nucleon structure from non-perturbative techniques and tomore » a unification of generalized parton distributions and transverse momentum dependent parton distribution functions phenomenology through lightfront wave functions.« less

An Overlap Syndrome of Pigment Dispersion and Pigmentary Glaucoma accompanied by Marfan Syndrome: Case Report with Literature Review.

PubMed

Chakravarti, Tutul; Spaeth, George

2013-01-01

'Overlap syndrome' describes the situation in which two or more 'independent' conditions are present, either one of which could cause a particular finding. This current presentation reports a case with bilateral pigment dispersion syndrome (PDS), advanced pigmentary glaucoma (PG), and the Marfan syndrome, with bilateral subluxation of the lenses, and large short-term and long-term fluctuations of intraocular pressure. It is interesting to consider whether the associated advanced glaucomatous nerve damage could be a manifestation of just the PDS, just the Marfan syndrome, or rather a combination of these two overlapping independent conditions. How to cite this article: Chakravarti T, George S. An Overlap Syndrome of Pigment Dispersion and Pigmentary Glaucoma accompanied by Marfan Syndrome: Case Report with Literature Review. J Current Glau Prac 2013;7(2):91-95.

Overlapping Leaves Covering Flowers in the Alpine Species Eriophyton wallichii (Lamiaceae): Key Driving Factors and Their Potential Impact on Pollination.

PubMed

Peng, De-Li; Song, Bo; Yang, Yang; Niu, Yang; Sun, Hang

2016-01-01

Extrafloral structures are supposed to have evolved to protect flowers from harsh physical environments but might have effects on pollination. Overlapping leaves cover flowers in Eriophyton wallichii, an alpine perennial endemic to the Himalaya-Hengduan Mountains. In previous study, it has showed that these extrafloral leaves can protect interior flowers from temperature fluctuations caused by drastic solar radiation fluctuations, but these leaves may also protect interior flowers from rain wash and UVB damage, and we do not know which one is the main function. In this study, we investigated whether rain and UVB protection are the main functions of overlapping leaves covering flowers and their potential impact on pollination. We first measured the intensities of UVB radiation in open air, beneath leaves and corollas, and then examined pollen susceptibility to different intensities of UVB and rain in the laboratory to estimate whether corollas per se protect interior pollen from UVB and rain damage. We also carried out pollination treatments and observed pollinator visitation of flowers with and without leaves in the field to assess whether the overlapping leaves covering flowers impair pollinator attraction. Our results showed that (1) water and strong UVB significantly decreased pollen germinability, but corollas per se could protect pollen from UVB and rain damage; (2) no autonomous self-pollination and apomixis occurred, and pollinators were essential for the reproduction of E. wallichii; however, flower coverage by overlapping leaves did not limit pollination. We suggested that rain and UVB protection was not the main function of overlapping leaves covered flowers, given that this protection can be provided by corollas per se. Alternatively, this extrafloral structure in E. wallichii may have evolved in response to extreme high temperatures associated with the strong solar radiation fluctuations. This indicates that, even in alpine plants, extreme high temperature may affect the evolution of plant extrafloral structures.

Overlapping Leaves Covering Flowers in the Alpine Species Eriophyton wallichii (Lamiaceae): Key Driving Factors and Their Potential Impact on Pollination

PubMed Central

Peng, De-Li; Song, Bo; Yang, Yang; Niu, Yang; Sun, Hang

2016-01-01

Extrafloral structures are supposed to have evolved to protect flowers from harsh physical environments but might have effects on pollination. Overlapping leaves cover flowers in Eriophyton wallichii, an alpine perennial endemic to the Himalaya-Hengduan Mountains. In previous study, it has showed that these extrafloral leaves can protect interior flowers from temperature fluctuations caused by drastic solar radiation fluctuations, but these leaves may also protect interior flowers from rain wash and UVB damage, and we do not know which one is the main function. In this study, we investigated whether rain and UVB protection are the main functions of overlapping leaves covering flowers and their potential impact on pollination. We first measured the intensities of UVB radiation in open air, beneath leaves and corollas, and then examined pollen susceptibility to different intensities of UVB and rain in the laboratory to estimate whether corollas per se protect interior pollen from UVB and rain damage. We also carried out pollination treatments and observed pollinator visitation of flowers with and without leaves in the field to assess whether the overlapping leaves covering flowers impair pollinator attraction. Our results showed that (1) water and strong UVB significantly decreased pollen germinability, but corollas per se could protect pollen from UVB and rain damage; (2) no autonomous self-pollination and apomixis occurred, and pollinators were essential for the reproduction of E. wallichii; however, flower coverage by overlapping leaves did not limit pollination. We suggested that rain and UVB protection was not the main function of overlapping leaves covered flowers, given that this protection can be provided by corollas per se. Alternatively, this extrafloral structure in E. wallichii may have evolved in response to extreme high temperatures associated with the strong solar radiation fluctuations. This indicates that, even in alpine plants, extreme high temperature may affect the evolution of plant extrafloral structures. PMID:27716786

Separation of overlapping vibrational peaks in terahertz spectra using two-dimensional correlation spectroscopy

NASA Astrophysics Data System (ADS)

Hoshina, Hiromichi; Ishii, Shinya; Otani, Chiko

2014-07-01

In this study, the terahertz (THz) absorption spectra of poly(3-hydroxybutyrate) (PHB) were measured during isothermal crystallization at 90-120 °C. The temporal changes in the absorption spectra were analyzed using two-dimensional correlation spectroscopy (2DCOS). In the asynchronous plot, cross peaks were observed around 2.4 THz, suggesting that two vibrational modes overlap in the raw spectrum. By comparing this to the peak at 2.9 THz corresponding to the stretching mode of the helical structure of PHB and the assignment obtained using polarization spectroscopy, we concluded that the high-frequency band could be attributed to the vibration of the helical structure and the low-frequency band to the vibration between the helical structures. The exact frequencies of the overlapping vibrational bands and their assignments provide a new means to inspect the thermal behavior of the intermolecular vibrational modes. The large red-shift of the interhelix vibrational mode suggests a large anharmonicity in the vibrational potential.

Do Large Carnivores and Mesocarnivores Have Redundant Impacts on Intertidal Prey?

PubMed Central

Clinchy, Michael; Zanette, Liana Y.

2017-01-01

The presence of large carnivores can affect lower trophic levels by suppressing mesocarnivores and reducing their impacts on prey. The mesopredator release hypothesis therefore predicts prey abundance will be higher where large carnivores are present, but this prediction assumes limited dietary overlap between large and mesocarnivores. Where dietary overlap is high, e.g., among omnivorous carnivore species, or where prey are relatively easily accessible, the potential exists for large and mesocarnivores to have redundant impacts on prey, though this possibility has not been explored. The intertidal community represents a potentially important but poorly studied resource for coastal carnivore populations, and one for which dietary overlap between carnivores may be high. To evaluate usage of the intertidal community by coastal carnivores and the potential for redundancy between large and mesocarnivores, we surveyed (i) intertidal prey abundance (crabs and fish) and (ii) the abundance and activity of large carnivores (predominantly black bears) and mesocarnivores (raccoons and mink) in an area with an intact carnivore community in coastal British Columbia, Canada. Overall carnivore activity was strongly related to intertidal prey availability. Notably, this relationship was not contingent on carnivore species identity, suggestive of redundancy–high intertidal prey availability was associated with either greater large carnivore activity or greater mesocarnivore activity. We then compared intertidal prey abundances in this intact system, in which bears dominate, with those in a nearby system where bears and other large carnivores have been extirpated, and raccoons are the primary intertidal predator. We found significant similarities in intertidal species abundances, providing additional evidence for redundancy between large (bear) and mesocarnivore (raccoon) impacts on intertidal prey. Taken together, our results indicate that intertidal prey shape habitat use and competition among coastal carnivores, and raise the interesting possibility of redundancy between mesocarnivores and large carnivores in their role as intertidal top predators. PMID:28085962

Distribution and Functionality of Copy Number Variation across European Cattle Populations.

PubMed

Upadhyay, Maulik; da Silva, Vinicus H; Megens, Hendrik-Jan; Visker, Marleen H P W; Ajmone-Marsan, Paolo; Bâlteanu, Valentin A; Dunner, Susana; Garcia, Jose F; Ginja, Catarina; Kantanen, Juha; Groenen, Martien A M; Crooijmans, Richard P M A

2017-01-01

Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.

Distribution and Functionality of Copy Number Variation across European Cattle Populations

PubMed Central

Upadhyay, Maulik; da Silva, Vinicus H.; Megens, Hendrik-Jan; Visker, Marleen H. P. W.; Ajmone-Marsan, Paolo; Bâlteanu, Valentin A.; Dunner, Susana; Garcia, Jose F.; Ginja, Catarina; Kantanen, Juha; Groenen, Martien A. M.; Crooijmans, Richard P. M. A.

2017-01-01

Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations. PMID:28878807

THE CHANDRA SURVEY OF THE COSMOS FIELD. II. SOURCE DETECTION AND PHOTOMETRY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puccetti, S.; Vignali, C.; Cappelluti, N.

2009-12-01

The Chandra COSMOS Survey (C-COSMOS) is a large, 1.8 Ms, Chandra program that covers the central contiguous {approx}0.92 deg{sup 2} of the COSMOS field. C-COSMOS is the result of a complex tiling, with every position being observed in up to six overlapping pointings (four overlapping pointings in most of the central {approx}0.45 deg{sup 2} area with the best exposure, and two overlapping pointings in most of the surrounding area, covering an additional {approx}0.47 deg{sup 2}). Therefore, the full exploitation of the C-COSMOS data requires a dedicated and accurate analysis focused on three main issues: (1) maximizing the sensitivity when themore » point-spread function (PSF) changes strongly among different observations of the same source (from {approx}1 arcsec up to {approx}10 arcsec half-power radius); (2) resolving close pairs; and (3) obtaining the best source localization and count rate. We present here our treatment of four key analysis items: source detection, localization, photometry, and survey sensitivity. Our final procedure consists of a two step procedure: (1) a wavelet detection algorithm to find source candidates and (2) a maximum likelihood PSF fitting algorithm to evaluate the source count rates and the probability that each source candidate is a fluctuation of the background. We discuss the main characteristics of this procedure, which was the result of detailed comparisons between different detection algorithms and photometry tools, calibrated with extensive and dedicated simulations.« less

Informational structure of genetic sequences and nature of gene splicing

NASA Astrophysics Data System (ADS)

Trifonov, E. N.

1991-10-01

Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

Brain aromatase (Cyp19A2) and estrogen receptors, in larvae and adult pejerrey fish Odontesthes bonariensis: Neuroanatomical and functional relations

USGS Publications Warehouse

Strobl-Mazzulla, P. H.; Lethimonier, C.; Gueguen, M.M.; Karube, M.; Fernandino, J.I.; Yoshizaki, G.; Patino, R.; Strussmann, C.A.; Kah, O.; Somoza, G.M.

2008-01-01

Although estrogens exert many functions on vertebrate brains, there is little information on the relationship between brain aromatase and estrogen receptors. Here, we report the cloning and characterization of two estrogen receptors, ?? and ??, in pejerrey. Both receptors' mRNAs largely overlap and were predominantly expressed in the brain, pituitary, liver, and gonads. Also brain aromatase and estrogen receptors were up-regulated in the brain of estradiol-treated males. In situ hybridization was performed to study in more detail, the distribution of the two receptors in comparison with brain aromatase mRNA in the brain of adult pejerrey. The estrogen receptors' mRNAs exhibited distinct but partially overlapping patterns of expression in the preoptic area and the mediobasal hypothalamus, as well as in the pituitary gland. Moreover, the estrogen receptor ??, but not ??, were found to be expressed in cells lining the preoptic recess, similarly as observed for brain aromatase. Finally, it was shown that the onset expression of brain aromatase and both estrogen receptors in the head of larvae preceded the morphological differentiation of the gonads. Because pejerrey sex differentiation is strongly influenced by temperature, brain aromatase expression was measured during the temperature-sensitive window and was found to be significantly higher at male-promoting temperature. Taken together these results suggest close neuroanatomical and functional relationships between brain aromatase and estrogen receptors, probably involved in the sexual differentiation of the brain and raising interesting questions on the origin (central or peripheral) of the brain aromatase substrate. ?? 2008 Elsevier Inc.

Some Aspects of Self-Field Effects in Large Vanadium-Based Josephson Junctions

NASA Astrophysics Data System (ADS)

Cristiano, R.; Russo, M.; Di Chiara, A.; Huang, Hesheng; Peluso, G.

1984-03-01

Experiments concerning large V-VxOy-Pb Josephson junctions have been performed. Structures having an overlap-type geometry have been considered. Preliminary experimental results are justified in the framework of the linearized current-phase model.

Diameter Effect Curve and Detonation Front Curvature Measurements for ANFO

NASA Astrophysics Data System (ADS)

Catanach, R. A.; Hill, L. G.

2002-07-01

Diameter effect and front curvature measurements are reported for rate stick experiments on commercially available prilled ANFO (ammonium-nitrate/fuel-oil) at ambient temperature. The shots were fired in paper tubes so as to provide minimal confinement. Diameters ranged from 77 mm (approximately failure diameter) to 205 mm, with the tube length being ten diameters in all cases. Each detonation wave shape was fit with an analytic form, from which the local normal velocity Dn, and local total curvature kappa, were generated as a function of radius R, then plotted parametrically to generate a Dn(kappa) function. The observed behavior deviates substantially from that of previous explosives, for which curves for different diameters overlay well for small kappa but diverge for large kappa, and for which kappa increases monotonically with R. For ANFO, we find that Dn(kappa) curves for individual sticks 1) show little or no overlap--with smaller sticks lying to the right of larger ones, 2) exhibit a large velocity deficit with little kappa variation, and 3) reach a peak kappa at an intermediate R.

Neuroanatomic overlap between intelligence and cognitive factors: morphometry methods provide support for the key role of the frontal lobes.

PubMed

Colom, Roberto; Burgaleta, Miguel; Román, Francisco J; Karama, Sherif; Alvarez-Linera, Juan; Abad, Francisco J; Martínez, Kenia; Quiroga, Ma Ángeles; Haier, Richard J

2013-05-15

Evidence from neuroimaging studies suggests that intelligence differences may be supported by a parieto-frontal network. Research shows that this network is also relevant for cognitive functions such as working memory and attention. However, previous studies have not explicitly analyzed the commonality of brain areas between a broad array of intelligence factors and cognitive functions tested in the same sample. Here fluid, crystallized, and spatial intelligence, along with working memory, executive updating, attention, and processing speed were each measured by three diverse tests or tasks. These twenty-one measures were completed by a group of one hundred and four healthy young adults. Three cortical measures (cortical gray matter volume, cortical surface area, and cortical thickness) were regressed against psychological latent scores obtained from a confirmatory factor analysis for removing test and task specific variance. For cortical gray matter volume and cortical surface area, the main overlapping clusters were observed in the middle frontal gyrus and involved fluid intelligence and working memory. Crystallized intelligence showed an overlapping cluster with fluid intelligence and working memory in the middle frontal gyrus. The inferior frontal gyrus showed overlap for crystallized intelligence, spatial intelligence, attention, and processing speed. The fusiform gyrus in temporal cortex showed overlap for spatial intelligence and attention. Parietal and occipital areas did not show any overlap across intelligence and cognitive factors. Taken together, these findings underscore that structural features of gray matter in the frontal lobes support those aspects of intelligence related to basic cognitive processes. Copyright © 2013 Elsevier Inc. All rights reserved.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

PubMed

Lu, Jonathan; Trnka, Michael J; Roh, Soung-Hun; Robinson, Philip J J; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L; Guan, Shenheng

2015-12-01

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.

Film excerpts shown to specifically elicit various affects lead to overlapping activation foci in a large set of symmetrical brain regions in males.

PubMed

Karama, Sherif; Armony, Jorge; Beauregard, Mario

2011-01-01

While the limbic system theory continues to be part of common scientific parlance, its validity has been questioned on multiple grounds. Nonetheless, the issue of whether or not there exists a set of brain areas preferentially dedicated to emotional processing remains central within affective neuroscience. Recently, a widespread neural reference space for emotion which includes limbic as well as other regions was characterized in a large meta-analysis. As methodologically heterogeneous studies go into such meta-analyses, showing in an individual study in which all parameters are kept constant, the involvement of overlapping areas for various emotion conditions in keeping with the neural reference space for emotion, would serve as valuable confirmatory evidence. Here, using fMRI, 20 young adult men were scanned while viewing validated neutral and effective emotion-eliciting short film excerpts shown to quickly and specifically elicit disgust, amusement, or sexual arousal. Each emotion-specific run included, in random order, multiple neutral and emotion condition blocks. A stringent conjunction analysis revealed a large overlap across emotion conditions that fit remarkably well with the neural reference space for emotion. This overlap included symmetrical bilateral activation of the medial prefrontal cortex, the anterior cingulate, the temporo-occipital junction, the basal ganglia, the brainstem, the amygdala, the hippocampus, the thalamus, the subthalamic nucleus, the posterior hypothalamus, the cerebellum, as well as the frontal operculum extending towards the anterior insula. This study clearly confirms for the visual modality, that processing emotional stimuli leads to widespread increases in activation that cluster within relatively confined areas, regardless of valence.

Detecting independent and recurrent copy number aberrations using interval graphs.

PubMed

Wu, Hsin-Ta; Hajirasouliha, Iman; Raphael, Benjamin J

2014-06-15

Somatic copy number aberrations SCNAS: are frequent in cancer genomes, but many of these are random, passenger events. A common strategy to distinguish functional aberrations from passengers is to identify those aberrations that are recurrent across multiple samples. However, the extensive variability in the length and position of SCNA: s makes the problem of identifying recurrent aberrations notoriously difficult. We introduce a combinatorial approach to the problem of identifying independent and recurrent SCNA: s, focusing on the key challenging of separating the overlaps in aberrations across individuals into independent events. We derive independent and recurrent SCNA: s as maximal cliques in an interval graph constructed from overlaps between aberrations. We efficiently enumerate all such cliques, and derive a dynamic programming algorithm to find an optimal selection of non-overlapping cliques, resulting in a very fast algorithm, which we call RAIG (Recurrent Aberrations from Interval Graphs). We show that RAIG outperforms other methods on simulated data and also performs well on data from three cancer types from The Cancer Genome Atlas (TCGA). In contrast to existing approaches that employ various heuristics to select independent aberrations, RAIG optimizes a well-defined objective function. We show that this allows RAIG to identify rare aberrations that are likely functional, but are obscured by overlaps with larger passenger aberrations. http://compbio.cs.brown.edu/software. © The Author 2014. Published by Oxford University Press.

Habitat preferences of baleen whales in a mid-latitude habitat

NASA Astrophysics Data System (ADS)

Prieto, Rui; Tobeña, Marta; Silva, Mónica A.

2017-07-01

Understanding the dynamics of baleen whale distribution is essential to predict how environmental changes can affect their ecology and, in turn, ecosystem functioning. Recent work showed that mid-latitude habitats along migratory routes may play an important role on the feeding ecology of baleen whales. This study aimed to investigate the function of a mid-latitude habitat for blue (Balaenoptera musculus), fin (Balaenoptera physalus) and sei (Balaenoptera borealis) whales occurring in sympatry during spring and summer months and to what extent their environmental niches overlap. We addressed those questions by developing environmental niche models (ENM) for each species and then making pairwise comparisons of niche overlap and relative habitat patch importance among the three species. ENMs were created using sightings from the Azorean Fisheries Observer Program from May to November, between 2004 and 2009, and a set of 18 predictor environmental variables. We then assessed monthly (April-July) overlap among ENMs using a modified Hellinger's distance metric (I). Results show that the habitat niches of blue and fin whales are strongly influenced by primary productivity and sea surface temperature and are highly dynamic both spatially and temporally due to the oceanography of the region. Niche overlap analyses show that blue and fin whale environmental niches are similar and that the suitable habitats for the two species have high degree of spatial coincidence. These results in combination suggest that this habitat may function as a mid-latitude feeding ground to both species while conditions are adequate. The sei whale model, on the other hand, did not include variables considered to be proxies for prey distribution and little environmental niche overlap was found between this species and the other two. We argue that these results suggest that the region holds little importance as a foraging habitat for the sei whale.

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacArthur, Stewart; Li, Xiao-Yong; Li, Jingyi

2009-05-15

BACKGROUND: We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional. RESULTS: Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of functionmore » and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors. CONCLUSIONS: It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.« less

Role of the hippocampus and orbitofrontal cortex during the disambiguation of social cues in working memory

PubMed Central

Ross, Robert S.; LoPresti, Matthew L.; Schon, Karin; Stern, Chantal E.

2013-01-01

Human social interactions are complex behaviors requiring the concerted effort of multiple neural systems to track and monitor the individuals around us. Cognitively, adjusting our behavior based on changing social cues such as facial expressions relies on working memory and the ability to disambiguate, or separate, representations of overlapping stimuli resulting from viewing the same individual with different facial expressions. We conducted an fMRI experiment examining brain regions contributing to the encoding, maintenance and retrieval of overlapping identity information during working memory using a delayed match-to-sample (DMS) task. In the overlapping condition, two faces from the same individual with different facial expressions were presented at sample. In the non-overlapping condition, the two sample faces were from two different individuals with different expressions. fMRI activity was assessed by contrasting the overlapping and non-overlapping condition at sample, delay, and test. The lateral orbitofrontal cortex showed increased fMRI signal in the overlapping condition in all three phases of the DMS task and increased functional connectivity with the hippocampus when encoding overlapping stimuli. The hippocampus showed increased fMRI signal at test. These data suggest lateral orbitofrontal cortex helps encode and maintain representations of overlapping stimuli in working memory while the orbitofrontal cortex and hippocampus contribute to the successful retrieval of overlapping stimuli. We suggest the lateral orbitofrontal cortex and hippocampus play a role in encoding, maintaining, and retrieving social cues, especially when multiple interactions with an individual need to be disambiguated in a rapidly changing social context in order to make appropriate social responses. PMID:23640112

Semantic integration to identify overlapping functional modules in protein interaction networks

PubMed Central

Cho, Young-Rae; Hwang, Woochang; Ramanathan, Murali; Zhang, Aidong

2007-01-01

Background The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms. Results We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO) annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches. Conclusion The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification. PMID:17650343

Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states.

PubMed

Li, Wei Vivian; Razaee, Zahra S; Li, Jingyi Jessica

2016-01-11

The dynamics of epigenomic marks in their relevant chromatin states regulate distinct gene expression patterns, biological functions and phenotypic variations in biological processes. The availability of high-throughput epigenomic data generated by next-generation sequencing technologies allows a data-driven approach to evaluate the similarities and differences of diverse tissue and cell types in terms of epigenomic features. While ChromImpute has allowed for the imputation of large-scale epigenomic information to yield more robust data to capture meaningful relationships between biological samples, widely used methods such as hierarchical clustering and correlation analysis cannot adequately utilize epigenomic data to accurately reveal the distinction and grouping of different tissue and cell types. We utilize a three-step testing procedure-ANOVA, t test and overlap test to identify tissue/cell-type- associated enhancers and promoters and to calculate a newly defined Epigenomic Overlap Measure (EPOM). EPOM results in a clear correspondence map of biological samples from different tissue and cell types through comparison of epigenomic marks evaluated in their relevant chromatin states. Correspondence maps by EPOM show strong capability in distinguishing and grouping different tissue and cell types and reveal biologically meaningful similarities between Heart and Muscle, Blood & T-cell and HSC & B-cell, Brain and Neurosphere, etc. The gene ontology enrichment analysis both supports and explains the discoveries made by EPOM and suggests that the associated enhancers and promoters demonstrate distinguishable functions across tissue and cell types. Moreover, the tissue/cell-type-associated enhancers and promoters show enrichment in the disease-related SNPs that are also associated with the corresponding tissue or cell types. This agreement suggests the potential of identifying causal genetic variants relevant to cell-type-specific diseases from our identified associated enhancers and promoters. The proposed EPOM measure demonstrates superior capability in grouping and finding a clear correspondence map of biological samples from different tissue and cell types. The identified associated enhancers and promoters provide a comprehensive catalog to study distinct biological processes and disease variants in different tissue and cell types. Our results also find that the associated promoters exhibit more cell-type-specific functions than the associated enhancers do, suggesting that the non-associated promoters have more housekeeping functions than the non-associated enhancers.

Focal overlap gating in velocity map imaging to achieve high signal-to-noise ratio in photo-ion pump-probe experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shivaram, Niranjan; Champenois, Elio G.; Cryan, James P.

We demonstrate a technique in velocity map imaging (VMI) that allows spatial gating of the laser focal overlap region in time resolved pump-probe experiments. This significantly enhances signal-to-noise ratio by eliminating background signal arising outside the region of spatial overlap of pump and probe beams. This enhancement is achieved by tilting the laser beams with respect to the surface of the VMI electrodes which creates a gradient in flight time for particles born at different points along the beam. By suitably pulsing our microchannel plate detector, we can select particles born only where the laser beams overlap. Furthermore, this spatialmore » gating in velocity map imaging can benefit nearly all photo-ion pump-probe VMI experiments especially when extreme-ultraviolet light or X-rays are involved which produce large background signals on their own.« less

Effect of high repetition laser shock peening on biocompatibility and corrosion resistance of magnesium

NASA Astrophysics Data System (ADS)

Caralapatti, Vinodh Krishna; Narayanswamy, Sivakumar

2017-02-01

Magnesium, as a biomaterial has the potential to replace conventional implant materials owing to its numerous advantages. However, high corrosion rate is a major obstacle that has to be addressed for its implementation as implants. This study aims to evaluate the feasibility and effects of High Repetition Laser Shock Peening (HRLSP) on biocompatibility and corrosion resistance of Mg samples and as well as to analyze the effect of operational parameters such as peening with overlap on corrosion rate. From the results obtained using hydrogen evolution and mass loss methods, it was found that corrosion rates of both 0% overlap and 66% overlap peened samples reduced by more than 50% compared to that of unpeened sample and sample peened with 66% overlap exhibited least corrosion. The biocompatibility of peened Mg samples was also enhanced as there was neither rapid pH variation nor large hydrogen bubble formation around samples.

Overlapping community detection in weighted networks via a Bayesian approach

NASA Astrophysics Data System (ADS)

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.

Underwater Laser Micromilling of Commercially-Pure Titanium Using Different Scan Overlaps

NASA Astrophysics Data System (ADS)

Charee, Wisan; Tangwarodomnukun, Viboon

2018-01-01

Underwater laser milling process is a technique for minimizing the thermal damage and gaining a higher material removal rate than processing in air. This paper presents the effect of laser scan overlap on cavity width, depth and surface roughness in the laser milling of commercially-pure titanium in water. The effects of laser pulse energy and pulse repetition rate were also examined, in which a nanosecond pulse laser emitting a 1064-nm wavelength was used in this study. The experimental results indicated that a wide and deep cavity was achievable under high laser energy and large scan overlap. According to the surface roughness, the use of high pulse repetition rate together with low laser energy can promote a smooth laser-milled surface particularly at 50% scan overlap. These findings can further suggest a suitable laser micromilling condition for titanium in roughing and finishing operations.

Focal overlap gating in velocity map imaging to achieve high signal-to-noise ratio in photo-ion pump-probe experiments

DOE PAGES

Shivaram, Niranjan; Champenois, Elio G.; Cryan, James P.; ...

2016-12-19

We demonstrate a technique in velocity map imaging (VMI) that allows spatial gating of the laser focal overlap region in time resolved pump-probe experiments. This significantly enhances signal-to-noise ratio by eliminating background signal arising outside the region of spatial overlap of pump and probe beams. This enhancement is achieved by tilting the laser beams with respect to the surface of the VMI electrodes which creates a gradient in flight time for particles born at different points along the beam. By suitably pulsing our microchannel plate detector, we can select particles born only where the laser beams overlap. Furthermore, this spatialmore » gating in velocity map imaging can benefit nearly all photo-ion pump-probe VMI experiments especially when extreme-ultraviolet light or X-rays are involved which produce large background signals on their own.« less

[A functional orthodontic magnetic appliance (FOMA) after Vardimon. 1. A three-dimensional analysis of the force system of the attractive magnets].

PubMed

Bourauel, C; Vardimon, A D; Drescher, D; Schmuth, G P

1995-09-01

The functional magnetic system (FMS) is a removable functional appliance which induces mandibular advance by means of mandibular and maxillary magnets in an attracting configuration. The maxillary and mandibular plates are each equipped with 2 cylindrically shaped cobalt-samarium magnets, 4 mm in diameter and 3 mm in height, which are welded into stainless steel housings. The force system of this magnetic configuration was analyzed using the orthodontic measurement and simulation system (OMSS). OMSS simulated the mandibular jaw movements by separating the installed magnets vertically, corresponding to a mouth opening of X = -10 mm, transversally (right excursion, +/left excursion, -) at Y = +/- 10 mm and sagittally (anterior displacement, +/posterior displacement, -) at Z = +/- 10 mm. The resulting 2D and 3D force/displacement diagrams elucidate the outstanding centripetal-spatial orientation characteristics of the functional magnetic appliance in reference to the full overlap brought about by the attraction of the mandibular magnet by the maxillary magnet. The maximum centripetal forces reached a value of approximately FY, max = 0.65 N for the vertical attracting force at full overlap of the mandibular and maxillary magnets (X = 0.55 mm, Y = Z = 0 mm), a value of FY, max = 0.65 N for the medial shearing force at a partial transversal overlap Z = 0, Y = +/- 2 mm and Y = +/- 6 mm), and for the sagittal shearing force a value of FZ, max = 1.2 N at a partial sagittal overlap of the magnets (Y = 0 mm, Z = +/- 2 mm).(ABSTRACT TRUNCATED AT 250 WORDS)

What can the occult do for you?

NASA Astrophysics Data System (ADS)

Holwerda, B. W.; Keel, W. C.

2017-03-01

Interstellar dust is still a dominant uncertainty in Astronomy, limiting precision in e.g., cosmological distance estimates and models of how light is re-processed within a galaxy. When a foreground galaxy serendipitously overlaps a more distant one, the latter backlights the dusty structures in the nearer foreground galaxy. Such an overlapping or occulting galaxy pair can be used to measure the distribution of dust in the closest galaxy with great accuracy. The STARSMOG program uses Hubble to map the distribution of dust in foreground galaxies in fine (<100 pc) detail. Integral Field Unit (IFU) observations will map the effective extinction curve, disentangling the role of fine-scale geometry and grain composition on the path of light through a galaxy. The overlapping galaxy technique promises to deliver a clear understanding of the dust in galaxies: geometry, a probability function of dimming as a function of galaxy mass and radius, and its dependence on wavelength.

Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response

PubMed Central

Lamacchia, Marina; Dyrka, Witold; Breton, Annick; Saupe, Sven J.; Paoletti, Mathieu

2016-01-01

Recognition and response to non self is essential to development and survival of all organisms. It can occur between individuals of the same species or between different organisms. Fungi are established models for conspecific non self recognition in the form of vegetative incompatibility (VI), a genetically controlled process initiating a programmed cell death (PCD) leading to the rejection of a fusion cell between genetically different isolates of the same species. In Podospora anserina VI is controlled by members of the hnwd gene family encoding for proteins analogous to NOD Like Receptors (NLR) immune receptors in eukaryotes. It was hypothesized that the hnwd controlled VI reaction was derived from the fungal innate immune response. Here we analyze the P. anserina transcriptional responses to two bacterial species, Serratia fonticola to which P. anserina survives and S. marcescens to which P. anserina succumbs, and compare these to the transcriptional response induced under VI conditions. Transcriptional responses to both bacteria largely overlap, however the number of genes regulated and magnitude of regulation is more important when P. anserina survives. Transcriptional responses to bacteria also overlap with the VI reaction for both up or down regulated gene sets. Genes up regulated tend to be clustered in the genome, and display limited phylogenetic distribution. In all three responses we observed genes related to autophagy to be up-regulated. Autophagy contributes to the fungal survival in all three conditions. Genes encoding for secondary metabolites and histidine kinase signaling are also up regulated in all three conditions. Transcriptional responses also display differences. Genes involved in response to oxidative stress, or encoding small secreted proteins are essentially expressed in response to bacteria, while genes encoding NLR proteins are expressed during VI. Most functions encoded in response to bacteria favor survival of the fungus while most functions up regulated during VI would lead to cell death. These differences are discussed in the frame of a multilayered response to non self in fungi. PMID:27148175

Recombination in liquid-filled ionization chambers beyond the Boag limit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brualla-González, L.; Roselló, J.

Purpose: The high mass density and low mobilities of charge carriers can cause important recombination in liquid-filled ionization chambers (LICs). Saturation correction methods have been proposed for LICs. Correction methods for pulsed irradiation are based on Boag equation. However, Boag equation assumes that the charge ionized by one pulse is fully collected before the arrival of the next pulse. This condition does not hold in many clinical beams where the pulse repetition period may be shorter than the charge collection time, causing overlapping between charge carriers ionized by different pulses, and Boag equation is not applicable there. In this work,more » the authors present an experimental and numerical characterization of collection efficiencies in LICs beyond the Boag limit, with overlapping between charge carriers ionized by different pulses. Methods: The authors have studied recombination in a LIC array for different dose-per-pulse, pulse repetition frequency, and polarization voltage values. Measurements were performed in a Truebeam Linac using FF and FFF modalities. Dose-per-pulse and pulse repetition frequency have been obtained by monitoring the target current with an oscilloscope. Experimental collection efficiencies have been obtained by using a combination of the two-dose-rate method and ratios to the readout of a reference chamber (CC13, IBA). The authors have also used numerical simulation to complement the experimental data. Results: The authors have found that overlap significantly increases recombination in LICs, as expected. However, the functional dependence of collection efficiencies on the dose-per-pulse does not change (a linear dependence has been observed in the near-saturation region for different degrees of overlapping, the same dependence observed in the nonoverlapping scenario). On the other hand, the dependence of collection efficiencies on the polarization voltage changes in the overlapping scenario and does not follow that of Boag equation, the reason being that changing the polarization voltage also affects the charge collection time, thus changing the amount of overlapping. Conclusions: These results have important consequences for saturation correction methods for LICs. On one hand, the two-dose-rate method, which relies on the functional dependence of the collection efficiencies on dose-per-pulse, can also be used in the overlapping situation, provided that the two measurements needed to feed the method are performed at the same pulse repetition frequency (monitor unit rate). This result opens the door to computing collection efficiencies in LICs in many clinical setups where charge overlap in the LIC exists. On the other hand, correction methods based on the voltage-dependence of Boag equation like the three-voltage method or the modified two-voltage method will not work in the overlapping scenario due to the different functional dependence of collection efficiencies on the polarization voltage.« less

Alignment of large image series using cubic B-splines tessellation: application to transmission electron microscopy data.

PubMed

Dauguet, Julien; Bock, Davi; Reid, R Clay; Warfield, Simon K

2007-01-01

3D reconstruction from serial 2D microscopy images depends on non-linear alignment of serial sections. For some structures, such as the neuronal circuitry of the brain, very large images at very high resolution are necessary to permit reconstruction. These very large images prevent the direct use of classical registration methods. We propose in this work a method to deal with the non-linear alignment of arbitrarily large 2D images using the finite support properties of cubic B-splines. After initial affine alignment, each large image is split into a grid of smaller overlapping sub-images, which are individually registered using cubic B-splines transformations. Inside the overlapping regions between neighboring sub-images, the coefficients of the knots controlling the B-splines deformations are blended, to create a virtual large grid of knots for the whole image. The sub-images are resampled individually, using the new coefficients, and assembled together into a final large aligned image. We evaluated the method on a series of large transmission electron microscopy images and our results indicate significant improvements compared to both manual and affine alignment.

Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis.

PubMed

Hobbs, Brian D; de Jong, Kim; Lamontagne, Maxime; Bossé, Yohan; Shrine, Nick; Artigas, María Soler; Wain, Louise V; Hall, Ian P; Jackson, Victoria E; Wyss, Annah B; London, Stephanie J; North, Kari E; Franceschini, Nora; Strachan, David P; Beaty, Terri H; Hokanson, John E; Crapo, James D; Castaldi, Peter J; Chase, Robert P; Bartz, Traci M; Heckbert, Susan R; Psaty, Bruce M; Gharib, Sina A; Zanen, Pieter; Lammers, Jan W; Oudkerk, Matthijs; Groen, H J; Locantore, Nicholas; Tal-Singer, Ruth; Rennard, Stephen I; Vestbo, Jørgen; Timens, Wim; Paré, Peter D; Latourelle, Jeanne C; Dupuis, Josée; O'Connor, George T; Wilk, Jemma B; Kim, Woo Jin; Lee, Mi Kyeong; Oh, Yeon-Mok; Vonk, Judith M; de Koning, Harry J; Leng, Shuguang; Belinsky, Steven A; Tesfaigzi, Yohannes; Manichaikul, Ani; Wang, Xin-Qun; Rich, Stephen S; Barr, R Graham; Sparrow, David; Litonjua, Augusto A; Bakke, Per; Gulsvik, Amund; Lahousse, Lies; Brusselle, Guy G; Stricker, Bruno H; Uitterlinden, André G; Ampleford, Elizabeth J; Bleecker, Eugene R; Woodruff, Prescott G; Meyers, Deborah A; Qiao, Dandi; Lomas, David A; Yim, Jae-Joon; Kim, Deog Kyeom; Hawrylkiewicz, Iwona; Sliwinski, Pawel; Hardin, Megan; Fingerlin, Tasha E; Schwartz, David A; Postma, Dirkje S; MacNee, William; Tobin, Martin D; Silverman, Edwin K; Boezen, H Marike; Cho, Michael H

2017-03-01

Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. We performed a genetic association study in 15,256 cases and 47,936 controls, with replication of select top results (P < 5 × 10 -6 ) in 9,498 cases and 9,748 controls. In the combined meta-analysis, we identified 22 loci associated at genome-wide significance, including 13 new associations with COPD. Nine of these 13 loci have been associated with lung function in general population samples, while 4 (EEFSEC, DSP, MTCL1, and SFTPD) are new. We noted two loci shared with pulmonary fibrosis (FAM13A and DSP) but that had opposite risk alleles for COPD. None of our loci overlapped with genome-wide associations for asthma, although one locus has been implicated in joint susceptibility to asthma and obesity. We also identified genetic correlation between COPD and asthma. Our findings highlight new loci associated with COPD, demonstrate the importance of specific loci associated with lung function to COPD, and identify potential regions of genetic overlap between COPD and other respiratory diseases.

Arabidopsis SEPALLATA proteins differ in cooperative DNA-binding during the formation of floral quartet-like complexes

PubMed Central

Jetha, Khushboo; Theißen, Günter; Melzer, Rainer

2014-01-01

The SEPALLATA (SEP) genes of Arabidopsis thaliana encode MADS-domain transcription factors that specify the identity of all floral organs. The four Arabidopsis SEP genes function in a largely yet not completely redundant manner. Here, we analysed interactions of the SEP proteins with DNA. All of the proteins were capable of forming tetrameric quartet-like complexes on DNA fragments carrying two sequence elements termed CArG-boxes. Distances between the CArG-boxes for strong cooperative DNA-binding were in the range of 4–6 helical turns. However, SEP1 also bound strongly to CArG-box pairs separated by smaller or larger distances, whereas SEP2 preferred large and SEP4 preferred small inter-site distances for binding. Cooperative binding of SEP3 was comparatively weak for most of the inter-site distances tested. All SEP proteins constituted floral quartet-like complexes together with the floral homeotic proteins APETALA3 (AP3) and PISTILLATA (PI) on the target genes AP3 and SEP3. Our results suggest an important part of an explanation for why the different SEP proteins have largely, but not completely redundant functions in determining floral organ identity: they may bind to largely overlapping, but not identical sets of target genes that differ in the arrangement and spacing of the CArG-boxes in their cis-regulatory regions. PMID:25183521

Visual attention capacity: a review of TVA-based patient studies.

PubMed

Habekost, Thomas; Starrfelt, Randi

2009-02-01

Psychophysical studies have identified two distinct limitations of visual attention capacity: processing speed and apprehension span. Using a simple test, these cognitive factors can be analyzed by Bundesen's Theory of Visual Attention (TVA). The method has strong specificity and sensitivity, and measurements are highly reliable. As the method is theoretically founded, it also has high validity. TVA-based assessment has recently been used to investigate a broad range of neuropsychological and neurological conditions. We present the method, including the experimental paradigm and practical guidelines to patient testing, and review existing TVA-based patient studies organized by lesion anatomy. Lesions in three anatomical regions affect visual capacity: The parietal lobes, frontal cortex and basal ganglia, and extrastriate cortex. Visual capacity thus depends on large, bilaterally distributed anatomical networks that include several regions outside the visual system. The two visual capacity parameters are functionally separable, but seem to rely on largely overlapping brain areas.

Many-body design of highly strained GaInNAs electroabsorption modulators on GaInAs ternary substrates

NASA Astrophysics Data System (ADS)

Fujisawa, Takeshi; Arai, Masakazu; Kano, Fumiyoshi

2010-05-01

Electroabsorption in highly strained GaInAs and GaInNAs quantum wells (QWs) grown on GaInAs or quasi-GaInAs substrates is investigated by using microscopic many-body theory. The effects of various parameters, such as strain, barrier height, substrate composition, and temperature are thoroughly examined. It is shown that the value of the absorption coefficient strongly depends on the depth of the QWs under large bias electric field due to the small overlap integral of wave functions between the conduction and valence bands. The use of GaInNAs QWs makes the strain in the well layer very small. Further, the effective quantum-well depth is increased in GaInNAs QWs due to the anticrossing interaction between the conduction and N-resonant bands, making it possible to obtain larger absorption coefficient under large bias electric fields without using wide-band gap materials for barriers.

Eye-Hand Coordination in Children with High Functioning Autism and Asperger's Disorder Using a Gap-Overlap Paradigm

ERIC Educational Resources Information Center

Crippa, Alessandro; Forti, Sara; Perego, Paolo; Molteni, Massimo

2013-01-01

We investigated eye-hand coordination in children with autism spectrum disorders (ASD) in comparison with age-matched normally developing peers. The eye-hand correlation was measured by putting fixation latencies in relation with pointing and key pressing responses in visual detection tasks where a gap-overlap paradigm was used and compared to…

Chromatogram simulation by area reproduction.

PubMed

Boe, Bjarne

2007-01-12

A modified Poisson function has been developed for the simulation of chromatographic peaks. The proposed model is shown to have the property of exactly recreating the experimentally determined peak area. Model parameters are obtained directly from the experimental peak, and overlapping peaks are deconvoluted such that the area sum of overlapping peaks is kept unchanged. The method was applied to real, complex chromatograms.

A finite element method with overlapping meshes for free-boundary axisymmetric plasma equilibria in realistic geometries

NASA Astrophysics Data System (ADS)

Heumann, Holger; Rapetti, Francesca

2017-04-01

Existing finite element implementations for the computation of free-boundary axisymmetric plasma equilibria approximate the unknown poloidal flux function by standard lowest order continuous finite elements with discontinuous gradients. As a consequence, the location of critical points of the poloidal flux, that are of paramount importance in tokamak engineering, is constrained to nodes of the mesh leading to undesired jumps in transient problems. Moreover, recent numerical results for the self-consistent coupling of equilibrium with resistive diffusion and transport suggest the necessity of higher regularity when approximating the flux map. In this work we propose a mortar element method that employs two overlapping meshes. One mesh with Cartesian quadrilaterals covers the vacuum chamber domain accessible by the plasma and one mesh with triangles discretizes the region outside. The two meshes overlap in a narrow region. This approach gives the flexibility to achieve easily and at low cost higher order regularity for the approximation of the flux function in the domain covered by the plasma, while preserving accurate meshing of the geometric details outside this region. The continuity of the numerical solution in the region of overlap is weakly enforced by a mortar-like mapping.

One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections

PubMed Central

Mingo, Janire; Erramuzpe, Asier; Luna, Sandra; Aurtenetxe, Olaia; Amo, Laura; Diez, Ibai; Schepens, Jan T. G.; Hendriks, Wiljan J. A. J.; Cortés, Jesús M.; Pulido, Rafael

2016-01-01

Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis. PMID:27548698

Pollination syndromes in African Marantaceae.

PubMed

Ley, Alexandra C; Classen-Bockhoff, Regine

2009-07-01

The Marantaceae (550 spp.) is the most derived family in the order Zingiberales and exhibits a complex explosive pollination mechanism. To understand the evolutionary significance of this unique process of pollen transfer, comparative morphological and ecological studies were conducted in Gabon. During a total stay of 11 months, 31 species of Marantaceae were investigated at different sites in Gabon. The study included analyses of floral diversity, observations on the pollinator spectrum as well as ecological measurements (e.g. nectar sugar concentration and volume). Analyses reveal five flower types based on flower size and pigmentation, spatial arrangement of the floral tube and presence/absence of nectar guides and conspicuous outer staminodes. Each type is associated with a specific functional pollinator group leading to the description of distinct pollination syndromes. The 'small (horizontal)' flowers are predominantly pollinated by small bees (Thrinchostoma spp., Allodapula ornaticeps), the 'large (horizontal)' and 'medium-sized (horizontal)' flowers by medium-sized bees (Amegilla vivida, Thrinchostoma bicometes), the 'locked (horizontal)' flowers by large bees (Xylocopa nigrita, X. varipes) and the '(large) vertical' flowers by sunbirds. The longevity of Marantaceae individuals and the omnipresence of their pollinators allowed the specialization to a given functional pollinator group. Intermediate ecological values, however, make occasional pollinator overlaps possible, indicating potential pathways of pollinator shifts. Similar radiation tendencies observed on other continents hint at similar selective pressures and evolutionary constraints.

Hearing voices in the resting brain: A review of intrinsic functional connectivity research on auditory verbal hallucinations

PubMed Central

Alderson-Day, Ben; McCarthy-Jones, Simon; Fernyhough, Charles

2018-01-01

Resting state networks (RSNs) are thought to reflect the intrinsic functional connectivity of brain regions. Alterations to RSNs have been proposed to underpin various kinds of psychopathology, including the occurrence of auditory verbal hallucinations (AVH). This review outlines the main hypotheses linking AVH and the resting state, and assesses the evidence for alterations to intrinsic connectivity provided by studies of resting fMRI in AVH. The influence of hallucinations during data acquisition, medication confounds, and movement are also considered. Despite a large variety of analytic methods and designs being deployed, it is possible to conclude that resting connectivity in the left temporal lobe in general and left superior temporal gyrus in particular are disrupted in AVH. There is also preliminary evidence of atypical connectivity in the default mode network and its interaction with other RSNs. Recommendations for future research include the adoption of a common analysis protocol to allow for more overlapping datasets and replication of intrinsic functional connectivity alterations. PMID:25956256

CDK regulation of transcription by RNAP II: Not over 'til it's over?

PubMed

Fisher, Robert P

2017-03-15

Transcription by RNA polymerase (RNAP) II is regulated at multiple steps by phosphorylation, catalyzed mainly by members of the cyclin-dependent kinase (CDK) family. The CDKs involved in transcription have overlapping substrate specificities, but play largely non-redundant roles in coordinating gene expression. Novel functions and targets of CDKs have recently emerged at the end of the transcription cycle, when the primary transcript is cleaved, and in most cases polyadenylated, and transcription is terminated by the action of the "torpedo" exonuclease Xrn2, which is a CDK substrate. Collectively, various functions have been ascribed to CDKs or CDK-mediated phosphorylation: recruiting cleavage and polyadenylation factors, preventing premature termination within gene bodies while promoting efficient termination of full-length transcripts, and preventing extensive readthrough transcription into intergenic regions or neighboring genes. The assignment of precise functions to specific CDKs is still in progress, but recent advances suggest ways in which the CDK network and RNAP II machinery might cooperate to ensure timely exit from the transcription cycle.

CDK regulation of transcription by RNAP II: Not over ‘til it's over?

PubMed Central

Fisher, Robert P.

2017-01-01

ABSTRACT Transcription by RNA polymerase (RNAP) II is regulated at multiple steps by phosphorylation, catalyzed mainly by members of the cyclin-dependent kinase (CDK) family. The CDKs involved in transcription have overlapping substrate specificities, but play largely non-redundant roles in coordinating gene expression. Novel functions and targets of CDKs have recently emerged at the end of the transcription cycle, when the primary transcript is cleaved, and in most cases polyadenylated, and transcription is terminated by the action of the “torpedo” exonuclease Xrn2, which is a CDK substrate. Collectively, various functions have been ascribed to CDKs or CDK-mediated phosphorylation: recruiting cleavage and polyadenylation factors, preventing premature termination within gene bodies while promoting efficient termination of full-length transcripts, and preventing extensive readthrough transcription into intergenic regions or neighboring genes. The assignment of precise functions to specific CDKs is still in progress, but recent advances suggest ways in which the CDK network and RNAP II machinery might cooperate to ensure timely exit from the transcription cycle. PMID:28005463

Processing of Intentional and Automatic Number Magnitudes in Children Born Prematurely: Evidence From fMRI

PubMed Central

Klein, Elise; Moeller, Korbinian; Kiechl-Kohlendorfer, Ursula; Kremser, Christian; Starke, Marc; Cohen Kadosh, Roi; Pupp-Peglow, Ulrike; Schocke, Michael; Kaufmann, Liane

2014-01-01

This study examined the neural correlates of intentional and automatic number processing (indexed by number comparison and physical Stroop task, respectively) in 6- and 7-year-old children born prematurely. Behavioral results revealed significant numerical distance and size congruity effects. Imaging results disclosed (1) largely overlapping fronto-parietal activation for intentional and automatic number processing, (2) a frontal to parietal shift of activation upon considering the risk factors gestational age and birth weight, and (3) a task-specific link between math proficiency and functional magnetic resonance imaging (fMRI) signal within distinct regions of the parietal lobes—indicating commonalities but also specificities of intentional and automatic number processing. PMID:25090014

Learning deep features with adaptive triplet loss for person reidentification

NASA Astrophysics Data System (ADS)

Li, Zhiqiang; Sang, Nong; Chen, Kezhou; Gao, Changxin; Wang, Ruolin

2018-03-01

Person reidentification (re-id) aims to match a specified person across non-overlapping cameras, which remains a very challenging problem. While previous methods mostly focus on feature extraction or metric learning, this paper makes the attempt in jointly learning both the global full-body and local body-parts features of the input persons with a multichannel convolutional neural network (CNN) model, which is trained by an adaptive triplet loss function that serves to minimize the distance between the same person and maximize the distance between different persons. The experimental results show that our approach achieves very promising results on the large-scale Market-1501 and DukeMTMC-reID datasets.

Context Switching with Multiple Register Windows: A RISC Performance Study

NASA Technical Reports Server (NTRS)

Konsek, Marion B.; Reed, Daniel A.; Watcharawittayakul, Wittaya

1987-01-01

Although previous studies have shown that a large file of overlapping register windows can greatly reduce procedure call/return overhead, the effects of register windows in a multiprogramming environment are poorly understood. This paper investigates the performance of multiprogrammed, reduced instruction set computers (RISCs) as a function of window management strategy. Using an analytic model that reflects context switch and procedure call overheads, we analyze the performance of simple, linearly self-recursive programs. For more complex programs, we present the results of a simulation study. These studies show that a simple strategy that saves all windows prior to a context switch, but restores only a single window following a context switch, performs near optimally.

Understanding emotion with brain networks.

PubMed

Pessoa, Luiz

2018-02-01

Emotional processing appears to be interlocked with perception, cognition, motivation, and action. These interactions are supported by the brain's large-scale non-modular anatomical and functional architectures. An important component of this organization involves characterizing the brain in terms of networks. Two aspects of brain networks are discussed: brain networks should be considered as inherently overlapping (not disjoint) and dynamic (not static). Recent work on multivariate pattern analysis shows that affective dimensions can be detected in the activity of distributed neural systems that span cortical and subcortical regions. More broadly, the paper considers how we should think of causation in complex systems like the brain, so as to inform the relationship between emotion and other mental aspects, such as cognition.

A High-Resolution Study of Hippocampal and Medial Temporal Lobe Correlates of Spatial Context and Prospective Overlapping Route Memory

PubMed Central

Brown, Thackery I.; Hasselmo, Michael E.; Stern, Chantal E.

2015-01-01

When navigating our world we often first plan or retrieve an ideal route to our goal, avoiding alternative paths that lead to other destinations. The medial temporal lobe (MTL) has been implicated in processing contextual information, sequence memory, and uniquely retrieving routes that overlap or “cross paths.” However, the identity of subregions of the hippocampus and neighboring cortex that support these functions in humans remains unclear. The present study used high-resolution functional magnetic resonance imaging (hr-fMRI) in humans to test whether the CA3/DG hippocampal subfield and para-hippocampal cortex are important for processing spatial context and route retrieval, and whether the CA1 subfield facilitates prospective planning of mazes that must be distinguished from alternative overlapping routes. During hr-fMRI scanning, participants navigated virtual mazes that were well-learned from prior training while also learning new mazes. Some routes learned during scanning shared hallways with those learned during pre-scan training, requiring participants to select between alternative paths. Critically, each maze began with a distinct spatial contextual Cue period. Our analysis targeted activity from the Cue period, during which participants identified the current navigational episode, facilitating retrieval of upcoming route components and distinguishing mazes that overlap. Results demonstrated that multiple MTL regions were predominantly active for the contextual Cue period of the task, with specific regions of CA3/DG, parahippocampal cortex, and perirhinal cortex being consistently recruited across trials for Cue periods of both novel and familiar mazes. During early trials of the task, both CA3/DG and CA1 were more active for overlapping than non-overlapping Cue periods. Trial-by-trial Cue period responses in CA1 tracked subsequent overlapping maze performance across runs. Together, our findings provide novel insight into the contributions of MTL subfields to processing spatial context and route retrieval, and support a prominent role for CA1 in distinguishing overlapping episodes during navigational “look-ahead” periods. PMID:24659134

Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues.

PubMed

Anafi, Ron C; Pellegrino, Renata; Shockley, Keith R; Romer, Micah; Tufik, Sergio; Pack, Allan I

2013-05-30

Many have assumed that the primary function of sleep is for the brain. We evaluated the molecular consequences of sleep and sleep deprivation outside the brain, in heart and lung. Using microarrays we compared gene expression in tissue from sleeping and sleep deprived mice euthanized at the same diurnal times. In each tissue, nearly two thousand genes demonstrated statistically significant differential expression as a function of sleep/wake behavioral state. To mitigate the influence of an artificial deprivation protocol, we identified a subset of these transcripts as specifically sleep-enhanced or sleep-repressed by requiring that their expression also change over the course of unperturbed sleep. 3% and 6% of the assayed transcripts showed "sleep specific" changes in the lung and heart respectively. Sleep specific transcripts in these tissues demonstrated highly significant overlap and shared temporal dynamics. Markers of cellular stress and the unfolded protein response were reduced during sleep in both tissues. These results mirror previous findings in brain. Sleep-enhanced pathways reflected the unique metabolic functions of each tissue. Transcripts related to carbohydrate and sulfur metabolic processes were enhanced by sleep in the lung, and collectively favor buffering from oxidative stress. DNA repair and protein metabolism annotations were significantly enriched among the sleep-enhanced transcripts in the heart. Our results also suggest that sleep may provide a Zeitgeber, or synchronizing cue, in the lung as a large cluster of transcripts demonstrated systematic changes in inter-animal variability as a function of both sleep duration and circadian time. Our data support the notion that the molecular consequences of sleep/wake behavioral state extend beyond the brain to include peripheral tissues. Sleep state induces a highly overlapping response in both heart and lung. We conclude that sleep enhances organ specific molecular functions and that it has a ubiquitous role in reducing cellular metabolic stress in both brain and peripheral tissues. Finally, our data suggest a novel role for sleep in synchronizing transcription in peripheral tissues.

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

PubMed Central

2010-01-01

Background Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. Results We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes. Conclusions ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as GenomicFeatures and BSgenome, provides flexibility. Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database. PMID:20459804

Analysis of a Novel Diffractive Scanning Wire Beam Position Monitor (BPM) for Discriminative Profiling of Electron Vs. X Ray Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tatchyn, Roman; /SLAC

2011-09-01

Recent numerical studies of Free Electron Lasers (FELs) operating in the Self Amplified Spontaneous Emission (SASE) regime indicate a large sensitivity of the gain to the degree of transverse overlap (and associated phase coherence) between the electron and photon beams traveling down the insertion device. Simulations of actual systems imply that accurate detection and correction for this relative loss of overlap, rather than correction for the absolute departure of the electron beam from a fixed axis, is the preferred function of an FEL amplifier's Beam Position Monitor (BPM) and corrector systems. In this note we propose a novel diffractive BPMmore » with the capability of simultaneously detecting and resolving the absolute (and relative) transverse positions and profiles of electron and x-ray beams co-propagating through an undulator. We derive the equations governing the performance of the BPM and examine its predicted performance for the SLAC Linac Coherent Light Source (LCLS), viz., for profiling multi-GeV electron bunches co-propagating with one-to-several-hundred keV x-ray beams. Selected research and development (r&d) tasks for fabricating and testing the proposed BPM are discussed.« less

Spatio-temporal interactions facilitate large carnivore sympatry across a resource gradient

PubMed Central

Karanth, K. Ullas; Srivathsa, Arjun; Puri, Mahi; Parameshwaran, Ravishankar; Kumar, N. Samba

2017-01-01

Species within a guild vary their use of time, space and resources, thereby enabling sympatry. As intra-guild competition intensifies, such behavioural adaptations may become prominent. We assessed mechanisms of facilitating sympatry among dhole (Cuon alpinus), leopard (Panthera pardus) and tiger (Panthera tigris) in tropical forests of India using camera-trap surveys. We examined population-level temporal, spatial and spatio-temporal segregation among them across four reserves representing a gradient of carnivore and prey densities. Temporal and spatial overlaps were higher at lower prey densities. Combined spatio-temporal overlap was minimal, possibly due to chance. We found fine-scale avoidance behaviours at one high-density reserve. Our results suggest that: (i) patterns of spatial, temporal and spatio-temporal segregation in sympatric carnivores do not necessarily mirror each other; (ii) carnivores are likely to adopt temporal, spatial, and spatio-temporal segregation as alternative mechanisms to facilitate sympatry; and (iii) carnivores show adaptability across a gradient of resource availability, a driver of inter-species competition. We discuss behavioural mechanisms that permit carnivores to co-occupy rather than dominate functional niches, and adaptations to varying intensities of competition that are likely to shape structure and dynamics of carnivore guilds. PMID:28179511

StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images.

PubMed

De Backer, A; van den Bos, K H W; Van den Broek, W; Sijbers, J; Van Aert, S

2016-12-01

An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. Copyright © 2016 Elsevier B.V. All rights reserved.

Spatio-temporal interactions facilitate large carnivore sympatry across a resource gradient.

PubMed

Karanth, K Ullas; Srivathsa, Arjun; Vasudev, Divya; Puri, Mahi; Parameshwaran, Ravishankar; Kumar, N Samba

2017-02-08

Species within a guild vary their use of time, space and resources, thereby enabling sympatry. As intra-guild competition intensifies, such behavioural adaptations may become prominent. We assessed mechanisms of facilitating sympatry among dhole ( Cuon alpinus ), leopard ( Panthera pardus ) and tiger ( Panthera tigris ) in tropical forests of India using camera-trap surveys. We examined population-level temporal, spatial and spatio-temporal segregation among them across four reserves representing a gradient of carnivore and prey densities. Temporal and spatial overlaps were higher at lower prey densities. Combined spatio-temporal overlap was minimal, possibly due to chance. We found fine-scale avoidance behaviours at one high-density reserve. Our results suggest that: (i) patterns of spatial, temporal and spatio-temporal segregation in sympatric carnivores do not necessarily mirror each other; (ii) carnivores are likely to adopt temporal, spatial, and spatio-temporal segregation as alternative mechanisms to facilitate sympatry; and (iii) carnivores show adaptability across a gradient of resource availability, a driver of inter-species competition. We discuss behavioural mechanisms that permit carnivores to co-occupy rather than dominate functional niches, and adaptations to varying intensities of competition that are likely to shape structure and dynamics of carnivore guilds. © 2017 The Author(s).

Parcellating an individual subject's cortical and subcortical brain structures using snowball sampling of resting-state correlations.

PubMed

Wig, Gagan S; Laumann, Timothy O; Cohen, Alexander L; Power, Jonathan D; Nelson, Steven M; Glasser, Matthew F; Miezin, Francis M; Snyder, Abraham Z; Schlaggar, Bradley L; Petersen, Steven E

2014-08-01

We describe methods for parcellating an individual subject's cortical and subcortical brain structures using resting-state functional correlations (RSFCs). Inspired by approaches from social network analysis, we first describe the application of snowball sampling on RSFC data (RSFC-Snowballing) to identify the centers of cortical areas, subdivisions of subcortical nuclei, and the cerebellum. RSFC-Snowballing parcellation is then compared with parcellation derived from identifying locations where RSFC maps exhibit abrupt transitions (RSFC-Boundary Mapping). RSFC-Snowballing and RSFC-Boundary Mapping largely complement one another, but also provide unique parcellation information; together, the methods identify independent entities with distinct functional correlations across many cortical and subcortical locations in the brain. RSFC parcellation is relatively reliable within a subject scanned across multiple days, and while the locations of many area centers and boundaries appear to exhibit considerable overlap across subjects, there is also cross-subject variability-reinforcing the motivation to parcellate brains at the level of individuals. Finally, examination of a large meta-analysis of task-evoked functional magnetic resonance imaging data reveals that area centers defined by task-evoked activity exhibit correspondence with area centers defined by RSFC-Snowballing. This observation provides important evidence for the ability of RSFC to parcellate broad expanses of an individual's brain into functionally meaningful units. © The Author 2013. Published by Oxford University Press.

Ultracold Polar Molecules

DTIC Science & Technology

2016-04-01

large positive scattering lengths make clouds difficult to overlap (but 85RbCs looked promising), but 85RbCs is difficult because 85Rb is hard to...produce at high densities. We revealed broad Feshbach resonances that we hope will allow production of higher-density 85Rb clouds . We are now...and this makes clouds of 87Rb and Cs hard to overlap. We therefore investi- gated 85RbCs, using the potentials we had developed for 85RbCs, and showed

Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.

PubMed

Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji

2015-12-01

Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

Decoding 2D-PAGE complex maps: relevance to proteomics.

PubMed

Pietrogrande, Maria Chiara; Marchetti, Nicola; Dondi, Francesco; Righetti, Pier Giorgio

2006-03-20

This review describes two mathematical approaches useful for decoding the complex signal of 2D-PAGE maps of protein mixtures. These methods are helpful for interpreting the large amount of data of each 2D-PAGE map by extracting all the analytical information hidden therein by spot overlapping. Here the basic theory and application to 2D-PAGE maps are reviewed: the means for extracting information from the experimental data and their relevance to proteomics are discussed. One method is based on the quantitative theory of statistical model of peak overlapping (SMO) using the spot experimental data (intensity and spatial coordinates). The second method is based on the study of the 2D-autocovariance function (2D-ACVF) computed on the experimental digitised map. They are two independent methods that are able to extract equal and complementary information from the 2D-PAGE map. Both methods permit to obtain fundamental information on the sample complexity and the separation performance and to single out ordered patterns present in spot positions: the availability of two independent procedures to compute the same separation parameters is a powerful tool to estimate the reliability of the obtained results. The SMO procedure is an unique tool to quantitatively estimate the degree of spot overlapping present in the map, while the 2D-ACVF method is particularly powerful in simply singling out the presence of order in the spot position from the complexity of the whole 2D map, i.e., spot trains. The procedures were validated by extensive numerical computation on computer-generated maps describing experimental 2D-PAGE gels of protein mixtures. Their applicability to real samples was tested on reference maps obtained from literature sources. The review describes the most relevant information for proteomics: sample complexity, separation performance, overlapping extent, identification of spot trains related to post-translational modifications (PTMs).

Overlapping communities from dense disjoint and high total degree clusters

NASA Astrophysics Data System (ADS)

Zhang, Hongli; Gao, Yang; Zhang, Yue

2018-04-01

Community plays an important role in the field of sociology, biology and especially in domains of computer science, where systems are often represented as networks. And community detection is of great importance in the domains. A community is a dense subgraph of the whole graph with more links between its members than between its members to the outside nodes, and nodes in the same community probably share common properties or play similar roles in the graph. Communities overlap when nodes in a graph belong to multiple communities. A vast variety of overlapping community detection methods have been proposed in the literature, and the local expansion method is one of the most successful techniques dealing with large networks. The paper presents a density-based seeding method, in which dense disjoint local clusters are searched and selected as seeds. The proposed method selects a seed by the total degree and density of local clusters utilizing merely local structures of the network. Furthermore, this paper proposes a novel community refining phase via minimizing the conductance of each community, through which the quality of identified communities is largely improved in linear time. Experimental results in synthetic networks show that the proposed seeding method outperforms other seeding methods in the state of the art and the proposed refining method largely enhances the quality of the identified communities. Experimental results in real graphs with ground-truth communities show that the proposed approach outperforms other state of the art overlapping community detection algorithms, in particular, it is more than two orders of magnitude faster than the existing global algorithms with higher quality, and it obtains much more accurate community structure than the current local algorithms without any priori information.

Film Excerpts Shown to Specifically Elicit Various Affects Lead to Overlapping Activation Foci in a Large Set of Symmetrical Brain Regions in Males

PubMed Central

Karama, Sherif; Armony, Jorge; Beauregard, Mario

2011-01-01

While the limbic system theory continues to be part of common scientific parlance, its validity has been questioned on multiple grounds. Nonetheless, the issue of whether or not there exists a set of brain areas preferentially dedicated to emotional processing remains central within affective neuroscience. Recently, a widespread neural reference space for emotion which includes limbic as well as other regions was characterized in a large meta-analysis. As methodologically heterogeneous studies go into such meta-analyses, showing in an individual study in which all parameters are kept constant, the involvement of overlapping areas for various emotion conditions in keeping with the neural reference space for emotion, would serve as valuable confirmatory evidence. Here, using fMRI, 20 young adult men were scanned while viewing validated neutral and effective emotion-eliciting short film excerpts shown to quickly and specifically elicit disgust, amusement, or sexual arousal. Each emotion-specific run included, in random order, multiple neutral and emotion condition blocks. A stringent conjunction analysis revealed a large overlap across emotion conditions that fit remarkably well with the neural reference space for emotion. This overlap included symmetrical bilateral activation of the medial prefrontal cortex, the anterior cingulate, the temporo-occipital junction, the basal ganglia, the brainstem, the amygdala, the hippocampus, the thalamus, the subthalamic nucleus, the posterior hypothalamus, the cerebellum, as well as the frontal operculum extending towards the anterior insula. This study clearly confirms for the visual modality, that processing emotional stimuli leads to widespread increases in activation that cluster within relatively confined areas, regardless of valence. PMID:21818311

Improving Discoverability of Geophysical Data using Location Based Services

NASA Astrophysics Data System (ADS)

Morrison, D.; Barnes, R. J.; Potter, M.; Nylund, S. R.; Patrone, D.; Weiss, M.; Talaat, E. R.; Sarris, T. E.; Smith, D.

2014-12-01

The great promise of Virtual Observatories is the ability to perform complex search operations across the metadata of a large variety of different data sets. This allows the researcher to isolate and select the relevant measurements for their topic of study. The Virtual ITM Observatory (VITMO) has many diverse geophysical datasets that cover a large temporal and spatial range that present a unique search problem. VITMO provides many methods by which the user can search for and select data of interest including restricting selections based on geophysical conditions (solar wind speed, Kp, etc) as well as finding those datasets that overlap in time. One of the key challenges in improving discoverability is the ability to identify portions of datasets that overlap in time and in location. The difficulty is that location data is not contained in the metadata for datasets produced by satellites and would be extremely large in volume if it were available, making searching for overlapping data very time consuming. To solve this problem we have developed a series of light-weight web services that can provide a new data search capability for VITMO and others. The services consist of a database of spacecraft ephemerides and instrument fields of view; an overlap calculator to find times when the fields of view of different instruments intersect; and a magnetic field line tracing service that maps in situ and ground based measurements to the equatorial plane in magnetic coordinates for a number of field models and geophysical conditions. These services run in real-time when the user queries for data. They will allow the non-specialist user to select data that they were previously unable to locate, opening up analysis opportunities beyond the instrument teams and specialists, making it easier for future students who come into the field.

Uncovering the Legionella genus effector repertoire - strength in diversity and numbers

PubMed Central

Burstein, David; Amaro, Francisco; Zusman, Tal; Lifshitz, Ziv; Cohen, Ofir; Gilbert, Jack A; Pupko, Tal; Shuman, Howard A; Segal, Gil

2016-01-01

Infection by the human pathogen Legionella pneumophila relies on the translocation of ~300 virulence proteins, termed effectors, which manipulate host-cell processes. However, almost no information exists regarding effectors in other Legionella pathogens. Here we sequenced, assembled and characterized the genomes of 38 Legionella species, and predicted their effector repertoire using a previously validated machine-learning approach. This analysis revealed a treasure trove of 5,885 predicted effectors. The effector repertoire of different Legionella species was found to be largely non-overlapping, and only seven core-effectors were shared among all species studied. Species-specific effectors had atypically low GC content, suggesting exogenous acquisition, possibly from their natural protozoan hosts. Furthermore, we detected numerous novel conserved effector domains, and discovered new domain combinations, which allowed inferring yet undescribed effector functions. The effector collection and network of domain architectures described here can serve as a roadmap for future studies of effector function and evolution. PMID:26752266

Layout optimization with algebraic multigrid methods

NASA Technical Reports Server (NTRS)

Regler, Hans; Ruede, Ulrich

1993-01-01

Finding the optimal position for the individual cells (also called functional modules) on the chip surface is an important and difficult step in the design of integrated circuits. This paper deals with the problem of relative placement, that is the minimization of a quadratic functional with a large, sparse, positive definite system matrix. The basic optimization problem must be augmented by constraints to inhibit solutions where cells overlap. Besides classical iterative methods, based on conjugate gradients (CG), we show that algebraic multigrid methods (AMG) provide an interesting alternative. For moderately sized examples with about 10000 cells, AMG is already competitive with CG and is expected to be superior for larger problems. Besides the classical 'multiplicative' AMG algorithm where the levels are visited sequentially, we propose an 'additive' variant of AMG where levels may be treated in parallel and that is suitable as a preconditioner in the CG algorithm.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brewer, Brendon J.; Foreman-Mackey, Daniel; Hogg, David W., E-mail: bj.brewer@auckland.ac.nz

We present and implement a probabilistic (Bayesian) method for producing catalogs from images of stellar fields. The method is capable of inferring the number of sources N in the image and can also handle the challenges introduced by noise, overlapping sources, and an unknown point-spread function. The luminosity function of the stars can also be inferred, even when the precise luminosity of each star is uncertain, via the use of a hierarchical Bayesian model. The computational feasibility of the method is demonstrated on two simulated images with different numbers of stars. We find that our method successfully recovers the inputmore » parameter values along with principled uncertainties even when the field is crowded. We also compare our results with those obtained from the SExtractor software. While the two approaches largely agree about the fluxes of the bright stars, the Bayesian approach provides more accurate inferences about the faint stars and the number of stars, particularly in the crowded case.« less

A second generation 50 Mbps VLSI level zero processing system prototype

NASA Technical Reports Server (NTRS)

Harris, Jonathan C.; Shi, Jeff; Speciale, Nick; Bennett, Toby

1994-01-01

Level Zero Processing (LZP) generally refers to telemetry data processing functions performed at ground facilities to remove all communication artifacts from instrument data. These functions typically include frame synchronization, error detection and correction, packet reassembly and sorting, playback reversal, merging, time-ordering, overlap deletion, and production of annotated data sets. The Data Systems Technologies Division (DSTD) at Goddard Space Flight Center (GSFC) has been developing high-performance Very Large Scale Integration Level Zero Processing Systems (VLSI LZPS) since 1989. The first VLSI LZPS prototype demonstrated 20 Megabits per second (Mbp's) capability in 1992. With a new generation of high-density Application-specific Integrated Circuits (ASIC) and a Mass Storage System (MSS) based on the High-performance Parallel Peripheral Interface (HiPPI), a second prototype has been built that achieves full 50 Mbp's performance. This paper describes the second generation LZPS prototype based upon VLSI technologies.

Aspect in Past Tenses in English and French.

ERIC Educational Resources Information Center

Andrews, Barry

1992-01-01

Aspectual functions performed by the various past tense forms do not overlap in French and English. Difficulties compounded by inaccurate and oversimplified explanations are noted, and different functions are discussed. (LB)

Functional overlap of top-down emotion regulation and generation: an fMRI study identifying common neural substrates between cognitive reappraisal and cognitively generated emotions.

PubMed

Otto, Benjamin; Misra, Supriya; Prasad, Aditya; McRae, Kateri

2014-09-01

One factor that influences the success of emotion regulation is the manner in which the regulated emotion was generated. Recent research has suggested that reappraisal, a top-down emotion regulation strategy, is more effective in decreasing self-reported negative affect when emotions were generated from the top-down, versus the bottom-up. On the basis of a process overlap framework, we hypothesized that the neural regions active during reappraisal would overlap more with emotions that were generated from the top-down, rather than from the bottom-up. In addition, we hypothesized that increased neural overlap between reappraisal and the history effects of top-down emotion generation would be associated with increased reappraisal success. The results of several analyses suggested that reappraisal and emotions that were generated from the top-down share a core network of prefrontal, temporal, and cingulate regions. This overlap is specific; no such overlap was observed between reappraisal and emotions that were generated in a bottom-up fashion. This network consists of regions previously implicated in linguistic processing, cognitive control, and self-relevant appraisals, which are processes thought to be crucial to both reappraisal and top-down emotion generation. Furthermore, individuals with high reappraisal success demonstrated greater neural overlap between reappraisal and the history of top-down emotion generation than did those with low reappraisal success. The overlap of these key regions, reflecting overlapping processes, provides an initial insight into the mechanism by which generation history may facilitate emotion regulation.

VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery.

PubMed

Nim, Hieu T; Furtado, Milena B; Costa, Mauro W; Rosenthal, Nadia A; Kitano, Hiroaki; Boyd, Sarah E

2015-05-01

Existing de novo software platforms have largely overlooked a valuable resource, the expertise of the intended biologist users. Typical data representations such as long gene lists, or highly dense and overlapping transcription factor networks often hinder biologists from relating these results to their expertise. VISIONET, a streamlined visualisation tool built from experimental needs, enables biologists to transform large and dense overlapping transcription factor networks into sparse human-readable graphs via numerically filtering. The VISIONET interface allows users without a computing background to interactively explore and filter their data, and empowers them to apply their specialist knowledge on far more complex and substantial data sets than is currently possible. Applying VISIONET to the Tbx20-Gata4 transcription factor network led to the discovery and validation of Aldh1a2, an essential developmental gene associated with various important cardiac disorders, as a healthy adult cardiac fibroblast gene co-regulated by cardiogenic transcription factors Gata4 and Tbx20. We demonstrate with experimental validations the utility of VISIONET for expertise-driven gene discovery that opens new experimental directions that would not otherwise have been identified.

ψ-Epistemic Models are Exponentially Bad at Explaining the Distinguishability of Quantum States

NASA Astrophysics Data System (ADS)

Leifer, M. S.

2014-04-01

The status of the quantum state is perhaps the most controversial issue in the foundations of quantum theory. Is it an epistemic state (state of knowledge) or an ontic state (state of reality)? In realist models of quantum theory, the epistemic view asserts that nonorthogonal quantum states correspond to overlapping probability measures over the true ontic states. This naturally accounts for a large number of otherwise puzzling quantum phenomena. For example, the indistinguishability of nonorthogonal states is explained by the fact that the ontic state sometimes lies in the overlap region, in which case there is nothing in reality that could distinguish the two states. For this to work, the amount of overlap of the probability measures should be comparable to the indistinguishability of the quantum states. In this Letter, I exhibit a family of states for which the ratio of these two quantities must be ≤2de-cd in Hilbert spaces of dimension d that are divisible by 4. This implies that, for large Hilbert space dimension, the epistemic explanation of indistinguishability becomes implausible at an exponential rate as the Hilbert space dimension increases.

Mood stabilizing drugs regulate transcription of immune, neuronal and metabolic pathway genes in Drosophila.

PubMed

Herteleer, L; Zwarts, L; Hens, K; Forero, D; Del-Favero, J; Callaerts, P

2016-05-01

Lithium and valproate (VPA) are drugs used in the management of bipolar disorder. Even though they reportedly act on various pathways, the transcriptional targets relevant for disease mechanism and therapeutic effect remain unclear. Furthermore, multiple studies used lymphoblasts of bipolar patients as a cellular proxy, but it remains unclear whether peripheral cells provide a good readout for the effects of these drugs in the brain. We used Drosophila culture cells and adult flies to analyze the transcriptional effects of lithium and VPA and define mechanistic pathways. Transcriptional profiles were determined for Drosophila S2-cells and adult fly heads following lithium or VPA treatment. Gene ontology categories were identified using the DAVID functional annotation tool with a cut-off of p < 0.05. Significantly enriched GO terms were clustered using REVIGO and DAVID functional annotation clustering. Significance of overlap between transcript lists was determined with a Fisher's exact hypergeometric test. Treatment of cultured cells and adult flies with lithium and VPA induces transcriptional responses in genes with similar ontology, with as most prominent immune response, neuronal development, neuronal function, and metabolism. (i) Transcriptional effects of lithium and VPA in Drosophila S2 cells and heads show significant overlap. (ii) The overlap between transcriptional alterations in peripheral versus neuronal cells at the single gene level is negligible, but at the gene ontology and pathway level considerable overlap can be found. (iii) Lithium and VPA act on evolutionarily conserved pathways in Drosophila and mammalian models.

Overlapping neurobehavioral circuits in ADHD, obesity, and binge eating: Evidence from Neuroimaging Research

PubMed Central

Seymour, Karen E.; Reinblatt, Shauna P.; Benson, Leora; Carnell, Susan

2015-01-01

Attention-deficit/hyperactivity disorder (ADHD) and conditions involving excessive eating (e.g. obesity, binge / loss of control eating) are increasingly prevalent within pediatric populations, and correlational and some longitudinal studies have suggested inter-relationships between these disorders. In addition, a number of common neural correlates are emerging across conditions, e.g. functional abnormalities within circuits subserving reward processing and executive functioning. To explore this potential cross-condition overlap in neurobehavioral underpinnings, we selectively review relevant functional neuroimaging literature, specifically focusing on studies probing i) reward processing, ii) response inhibition, and iii) emotional processing and regulation, and outline three specific shared neurobehavioral circuits. Based on our review, we also identify gaps within the literature that would benefit from further research. PMID:26098969

Single-particle strength from nucleon transfer in oxygen isotopes: Sensitivity to model parameters

NASA Astrophysics Data System (ADS)

Flavigny, F.; Keeley, N.; Gillibert, A.; Obertelli, A.

2018-03-01

In the analysis of transfer reaction data to extract nuclear structure information the choice of input parameters to the reaction model such as distorting potentials and overlap functions has a significant impact. In this paper we consider a set of data for the (d ,t ) and (d ,3He ) reactions on 14,16,18O as a well-delimited subject for a study of the sensitivity of such analyses to different choices of distorting potentials and overlap functions with particular reference to a previous investigation of the variation of valence nucleon correlations as a function of the difference in nucleon separation energy Δ S =| Sp-Sn| [Phys. Rev. Lett. 110, 122503 (2013), 10.1103/PhysRevLett.110.122503].

SVM2Motif—Reconstructing Overlapping DNA Sequence Motifs by Mimicking an SVM Predictor

PubMed Central

Vidovic, Marina M. -C.; Görnitz, Nico; Müller, Klaus-Robert; Rätsch, Gunnar; Kloft, Marius

2015-01-01

Identifying discriminative motifs underlying the functionality and evolution of organisms is a major challenge in computational biology. Machine learning approaches such as support vector machines (SVMs) achieve state-of-the-art performances in genomic discrimination tasks, but—due to its black-box character—motifs underlying its decision function are largely unknown. As a remedy, positional oligomer importance matrices (POIMs) allow us to visualize the significance of position-specific subsequences. Although being a major step towards the explanation of trained SVM models, they suffer from the fact that their size grows exponentially in the length of the motif, which renders their manual inspection feasible only for comparably small motif sizes, typically k ≤ 5. In this work, we extend the work on positional oligomer importance matrices, by presenting a new machine-learning methodology, entitled motifPOIM, to extract the truly relevant motifs—regardless of their length and complexity—underlying the predictions of a trained SVM model. Our framework thereby considers the motifs as free parameters in a probabilistic model, a task which can be phrased as a non-convex optimization problem. The exponential dependence of the POIM size on the oligomer length poses a major numerical challenge, which we address by an efficient optimization framework that allows us to find possibly overlapping motifs consisting of up to hundreds of nucleotides. We demonstrate the efficacy of our approach on a synthetic data set as well as a real-world human splice site data set. PMID:26690911

Overlaps with arbitrary two-site states in the XXZ spin chain

NASA Astrophysics Data System (ADS)

Pozsgay, B.

2018-05-01

We present a conjectured exact formula for overlaps between the Bethe states of the spin-1/2 XXZ chain and generic two-site states. The result takes the same form as in the previously known cases: it involves the same ratio of two Gaudin-like determinants, and a product of single-particle overlap functions, which can be fixed using a combination of the quench action and quantum transfer matrix methods. Our conjecture is confirmed by numerical data from exact diagonalization. For one-site states, the formula is found to be correct even in chains with odd length. It is also pointed out that the ratio of the Gaudin-like determinants plays a crucial role in the overlap sum rule: it guarantees that in the thermodynamic limit there remains no term in the quench action.

Two-stage decompositions for the analysis of functional connectivity for fMRI with application to Alzheimer’s disease risk

PubMed Central

Caffo, Brian S.; Crainiceanu, Ciprian M.; Verduzco, Guillermo; Joel, Suresh; Mostofsky, Stewart H.; Bassett, Susan Spear; Pekar, James J.

2010-01-01

Functional connectivity is the study of correlations in measured neurophysiological signals. Altered functional connectivity has been shown to be associated with a variety of cognitive and memory impairments and dysfunction, including Alzheimer’s disease. In this manuscript we use a two-stage application of the singular value decomposition to obtain data driven population-level measures of functional connectivity in functional magnetic resonance imaging (fMRI). The method is computationally simple and amenable to high dimensional fMRI data with large numbers of subjects. Simulation studies suggest the ability of the decomposition methods to recover population brain networks and their associated loadings. We further demonstrate the utility of these decompositions in a functional logistic regression model. The method is applied to a novel fMRI study of Alzheimer’s disease risk under a verbal paired associates task. We found a indication of alternative connectivity in clinically asymptomatic at-risk subjects when compared to controls, that was not significant in the light of multiple comparisons adjustment. The relevant brain network loads primarily on the temporal lobe and overlaps significantly with the olfactory areas and temporal poles. PMID:20227508

Two-stage decompositions for the analysis of functional connectivity for fMRI with application to Alzheimer's disease risk.

PubMed

Caffo, Brian S; Crainiceanu, Ciprian M; Verduzco, Guillermo; Joel, Suresh; Mostofsky, Stewart H; Bassett, Susan Spear; Pekar, James J

2010-07-01

Functional connectivity is the study of correlations in measured neurophysiological signals. Altered functional connectivity has been shown to be associated with a variety of cognitive and memory impairments and dysfunction, including Alzheimer's disease. In this manuscript we use a two-stage application of the singular value decomposition to obtain data driven population-level measures of functional connectivity in functional magnetic resonance imaging (fMRI). The method is computationally simple and amenable to high dimensional fMRI data with large numbers of subjects. Simulation studies suggest the ability of the decomposition methods to recover population brain networks and their associated loadings. We further demonstrate the utility of these decompositions in a functional logistic regression model. The method is applied to a novel fMRI study of Alzheimer's disease risk under a verbal paired associates task. We found an indication of alternative connectivity in clinically asymptomatic at-risk subjects when compared to controls, which was not significant in the light of multiple comparisons adjustment. The relevant brain network loads primarily on the temporal lobe and overlaps significantly with the olfactory areas and temporal poles. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Neural systems for speech and song in autism

PubMed Central

Pantazatos, Spiro P.; Schneider, Harry

2012-01-01

Despite language disabilities in autism, music abilities are frequently preserved. Paradoxically, brain regions associated with these functions typically overlap, enabling investigation of neural organization supporting speech and song in autism. Neural systems sensitive to speech and song were compared in low-functioning autistic and age-matched control children using passive auditory stimulation during functional magnetic resonance and diffusion tensor imaging. Activation in left inferior frontal gyrus was reduced in autistic children relative to controls during speech stimulation, but was greater than controls during song stimulation. Functional connectivity for song relative to speech was also increased between left inferior frontal gyrus and superior temporal gyrus in autism, and large-scale connectivity showed increased frontal–posterior connections. Although fractional anisotropy of the left arcuate fasciculus was decreased in autistic children relative to controls, structural terminations of the arcuate fasciculus in inferior frontal gyrus were indistinguishable between autistic and control groups. Fractional anisotropy correlated with activity in left inferior frontal gyrus for both speech and song conditions. Together, these findings indicate that in autism, functional systems that process speech and song were more effectively engaged for song than for speech and projections of structural pathways associated with these functions were not distinguishable from controls. PMID:22298195

Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes

PubMed Central

Fernández-Sanlés, Alba; Ríos-Marco, Pablo; Romero-López, Cristina; Berzal-Herranz, Alfredo

2017-01-01

The genus Flavivirus comprises a large number of small, positive-sense single-stranded, RNA viruses able to replicate in the cytoplasm of certain arthropod and/or vertebrate host cells. The genus, which has some 70 member species, includes a number of emerging and re-emerging pathogens responsible for outbreaks of human disease around the world, such as the West Nile, dengue, Zika, yellow fever, Japanese encephalitis, St. Louis encephalitis, and tick-borne encephalitis viruses. Like other RNA viruses, flaviviruses have a compact RNA genome that efficiently stores all the information required for the completion of the infectious cycle. The efficiency of this storage system is attributable to supracoding elements, i.e., discrete, structural units with essential functions. This information storage system overlaps and complements the protein coding sequence and is highly conserved across the genus. It therefore offers interesting potential targets for novel therapeutic strategies. This review summarizes our knowledge of the features of flavivirus genome functional RNA domains. It also provides a brief overview of the main achievements reported in the design of antiviral nucleic acid-based drugs targeting functional genomic RNA elements. PMID:28421048

Generation of signaling specificity in Arabidopsis by spatially restricted buffering of ligand-receptor interactions.

PubMed

Abrash, Emily B; Davies, Kelli A; Bergmann, Dominique C

2011-08-01

Core signaling pathways function in multiple programs during multicellular development. The mechanisms that compartmentalize pathway function or confer process specificity, however, remain largely unknown. In Arabidopsis thaliana, ERECTA (ER) family receptors have major roles in many growth and cell fate decisions. The ER family acts with receptor TOO MANY MOUTHS (TMM) and several ligands of the EPIDERMAL PATTERNING FACTOR LIKE (EPFL) family, which play distinct yet overlapping roles in patterning of epidermal stomata. Here, our examination of EPFL genes EPFL6/CHALLAH (CHAL), EPFL5/CHALLAH-LIKE1, and EPFL4/CHALLAH-LIKE2 (CLL2) reveals that this family may mediate additional ER-dependent processes. chal cll2 mutants display growth phenotypes characteristic of er mutants, and genetic interactions are consistent with CHAL family molecules acting as ER family ligands. We propose that different classes of EPFL genes regulate different aspects of ER family function and introduce a TMM-based discriminatory mechanism that permits simultaneous, yet compartmentalized and distinct, function of the ER family receptors in growth and epidermal patterning.

Generalization and capacity of extensively large two-layered perceptrons.

PubMed

Rosen-Zvi, Michal; Engel, Andreas; Kanter, Ido

2002-09-01

The generalization ability and storage capacity of a treelike two-layered neural network with a number of hidden units scaling as the input dimension is examined. The mapping from the input to the hidden layer is via Boolean functions; the mapping from the hidden layer to the output is done by a perceptron. The analysis is within the replica framework where an order parameter characterizing the overlap between two networks in the combined space of Boolean functions and hidden-to-output couplings is introduced. The maximal capacity of such networks is found to scale linearly with the logarithm of the number of Boolean functions per hidden unit. The generalization process exhibits a first-order phase transition from poor to perfect learning for the case of discrete hidden-to-output couplings. The critical number of examples per input dimension, alpha(c), at which the transition occurs, again scales linearly with the logarithm of the number of Boolean functions. In the case of continuous hidden-to-output couplings, the generalization error decreases according to the same power law as for the perceptron, with the prefactor being different.

Strong Unitary and Overlap Uncertainty Relations: Theory and Experiment

NASA Astrophysics Data System (ADS)

Bong, Kok-Wei; Tischler, Nora; Patel, Raj B.; Wollmann, Sabine; Pryde, Geoff J.; Hall, Michael J. W.

2018-06-01

We derive and experimentally investigate a strong uncertainty relation valid for any n unitary operators, which implies the standard uncertainty relation and others as special cases, and which can be written in terms of geometric phases. It is saturated by every pure state of any n -dimensional quantum system, generates a tight overlap uncertainty relation for the transition probabilities of any n +1 pure states, and gives an upper bound for the out-of-time-order correlation function. We test these uncertainty relations experimentally for photonic polarization qubits, including the minimum uncertainty states of the overlap uncertainty relation, via interferometric measurements of generalized geometric phases.

Epigenomics and the concept of degeneracy in biological systems

PubMed Central

Mason, Paul H.; Barron, Andrew B.

2014-01-01

Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy—referring to the multiple pathways that a system recruits to achieve functional plasticity—is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability. PMID:24335757

An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse

PubMed Central

Keller, Daniel; Babai, Norbert; Kochubey, Olexiy; Han, Yunyun; Markram, Henry; Schürmann, Felix; Schneggenburger, Ralf

2015-01-01

The spatial arrangement of Ca2+ channels and vesicles remains unknown for most CNS synapses, despite of the crucial importance of this geometrical parameter for the Ca2+ control of transmitter release. At a large model synapse, the calyx of Held, transmitter release is controlled by several Ca2+ channels in a "domain overlap" mode, at least in young animals. To study the geometrical constraints of Ca2+ channel placement in domain overlap control of release, we used stochastic MCell modelling, at active zones for which the position of docked vesicles was derived from electron microscopy (EM). We found that random placement of Ca2+ channels was unable to produce high slope values between release and presynaptic Ca2+ entry, a hallmark of domain overlap, and yielded excessively large release probabilities. The simple assumption that Ca2+ channels can be located anywhere at active zones, except below a critical distance of ~ 30 nm away from docked vesicles ("exclusion zone"), rescued high slope values and low release probabilities. Alternatively, high slope values can also be obtained by placing all Ca2+ channels into a single supercluster, which however results in significantly higher heterogeneity of release probabilities. We also show experimentally that high slope values, and the sensitivity to the slow Ca2+ chelator EGTA-AM, are maintained with developmental maturation of the calyx synapse. Taken together, domain overlap control of release represents a highly organized active zone architecture in which Ca2+ channels must obey a certain distance to docked vesicles. Furthermore, domain overlap can be employed by near-mature, fast-releasing synapses. PMID:25951120

An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads

PubMed Central

2013-01-01

Background Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates. The advent of next generation sequencing has led to the development of numerous computational tools to analyze and assemble the millions to billions of short sequencing reads produced by these technologies. While these tools filled an important gap, current approaches for storing, processing, and analyzing short read datasets generally have remained simple and lack the complexity needed to efficiently model the produced reads and assemble them correctly. Results Previously, we presented an overlap graph coarsening scheme for modeling read overlap relationships on multiple levels. Most current read assembly and analysis approaches use a single graph or set of clusters to represent the relationships among a read dataset. Instead, we use a series of graphs to represent the reads and their overlap relationships across a spectrum of information granularity. At each information level our algorithm is capable of generating clusters of reads from the reduced graph, forming an integrated graph modeling and clustering approach for read analysis and assembly. Previously we applied our algorithm to simulated and real 454 datasets to assess its ability to efficiently model and cluster next generation sequencing data. In this paper we extend our algorithm to large simulated and real Illumina datasets to demonstrate that our algorithm is practical for both sequencing technologies. Conclusions Our overlap graph theoretic algorithm is able to model next generation sequencing reads at various levels of granularity through the process of graph coarsening. Additionally, our model allows for efficient representation of the read overlap relationships, is scalable for large datasets, and is practical for both Illumina and 454 sequencing technologies. PMID:24564333

Epidemiology, clinical characteristics, and associations for symptom-based Rome IV functional dyspepsia in adults in the USA, Canada, and the UK: a cross-sectional population-based study.

PubMed

Aziz, Imran; Palsson, Olafur S; Törnblom, Hans; Sperber, Ami D; Whitehead, William E; Simrén, Magnus

2018-04-01

The population prevalence, clinical characteristics, and associations for Rome IV functional dyspepsia are not known. Following the publication of the Rome IV criteria for functional gastrointestinal disorders, we aimed to assess the prevalence, characteristics, and associations for symptom-based Rome IV functional dyspepsia in adults across the USA, Canada, and the UK. We sent an internet-based cross-sectional health survey to adults in the general population of three English-speaking countries: the USA, Canada, and the UK. We used quota-based sampling to generate demographically balanced and population-representative samples. Individuals were invited to complete an online questionnaire on general health, without mention that the purpose of this survey was to examine gastrointestinal symptoms. We excluded participants who failed two attention-test questions or were excessively inconsistent on the three gastrointestinal questions that were presented twice in the survey for this particular purpose. The survey enquired about demographics, health-care visits, medications, somatisation, quality of life, and symptom-based criteria for Rome IV functional dyspepsia as well as for irritable bowel syndrome (IBS) and functional heartburn. We made subsequent comparisons between participants with Rome IV functional dyspepsia and controls without dyspepsia. The primary objective was to identify participants who fulfilled symptom-based criteria for Rome IV functional dyspepsia and categorise them into postprandial distress syndrome, epigastric pain syndrome, or overlapping subtypes. 6300 general population adults completed the health survey; 2100 each from the USA, Canada, and the UK. 369 responses were deemed inconsistent, leaving data for 5931 adults. Rome IV functional dyspepsia was significantly more prevalent in the USA (232 [12%] of 1949) than in Canada (167 [8%] of 1988) and the UK (152 [8%] of 1994; p<0·0001). The subtype distribution was 61% postprandial distress syndrome, 18% epigastric pain syndrome, and 21% overlapping variant with both syndromes; this pattern was similar across the countries. Participants with functional dyspepsia had significantly greater health impairment and health-care usage than those without dyspepsia. Participants with the overlapping variant showed greater somatisation and poorer quality-of-life scores than did individuals with either postprandial distress syndrome or epigastric pain syndrome alone. In multivariate analysis, independent factors associated with all functional dyspepsia subtypes included worsening quality of life and the presence of symptoms compatible with functional heartburn and IBS, with functional heartburn and IBS having the strongest association with overlapping postprandial distress syndrome and epigastric pain syndrome. Notably, somatisation showed a positive association with postprandial distress syndrome and the overlapping variant, and use of antidepressants showed a negative association with postprandial distress syndrome. Approximately 10% of the adult population fulfils symptom-based criteria for Rome IV functional dyspepsia and incurs considerable associated health impairment. The functional dyspepsia subtypes show differing associations, suggesting differences in pathophysiological processes or influences. The Rome Foundation, the US National Institute of Diabetes and Digestive and Kidney Diseases, the Swedish Medical Research Council, AFA Insurance, Ferring Pharmaceuticals, and the Faculty of Medicine, University of Gothenburg, Gothenburg, Sweden. Copyright © 2018 Elsevier Ltd. All rights reserved.

An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

PubMed Central

Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

2012-01-01

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

Exploring biorthonormal transformations of pair-correlation functions in atomic structure variational calculations

NASA Astrophysics Data System (ADS)

Verdebout, S.; Jönsson, P.; Gaigalas, G.; Godefroid, M.; Froese Fischer, C.

2010-04-01

Multiconfiguration expansions frequently target valence correlation and correlation between valence electrons and the outermost core electrons. Correlation within the core is often neglected. A large orbital basis is needed to saturate both the valence and core-valence correlation effects. This in turn leads to huge numbers of configuration state functions (CSFs), many of which are unimportant. To avoid the problems inherent to the use of a single common orthonormal orbital basis for all correlation effects in the multiconfiguration Hartree-Fock (MCHF) method, we propose to optimize independent MCHF pair-correlation functions (PCFs), bringing their own orthonormal one-electron basis. Each PCF is generated by allowing single- and double-excitations from a multireference (MR) function. This computational scheme has the advantage of using targeted and optimally localized orbital sets for each PCF. These pair-correlation functions are coupled together and with each component of the MR space through a low dimension generalized eigenvalue problem. Nonorthogonal orbital sets being involved, the interaction and overlap matrices are built using biorthonormal transformation of the coupled basis sets followed by a counter-transformation of the PCF expansions. Applied to the ground state of beryllium, the new method gives total energies that are lower than the ones from traditional complete active space (CAS)-MCHF calculations using large orbital active sets. It is fair to say that we now have the possibility to account for, in a balanced way, correlation deep down in the atomic core in variational calculations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, G. Barratt, E-mail: barratt@mit.edu

Franck-Condon vibrational overlap integrals for the A{sup ~1}A{sub u}—X{sup ~1}Σ{sup +}{sub g} transition in acetylene have been calculated in full dimension in the harmonic normal mode basis. The calculation uses the method of generating functions first developed for polyatomic Franck-Condon factors by Sharp and Rosenstock [J. Chem. Phys. 41(11), 3453–3463 (1964)], and previously applied to acetylene by Watson [J. Mol. Spectrosc. 207(2), 276–284 (2001)] in a reduced-dimension calculation. Because the transition involves a large change in the equilibrium geometry of the electronic states, two different types of corrections to the coordinate transformation are considered to first order: corrections for axis-switchingmore » between the Cartesian molecular frames and corrections for the curvilinear nature of the normal modes at large amplitude. The angular factor in the wave function for the out-of-plane component of the trans bending mode, ν{sub 4}{sup ″}, is treated as a rotation, which results in an Eckart constraint on the polar coordinates of the bending modes. To simplify the calculation, the other degenerate bending mode, ν{sub 5}{sup ″}, is integrated in the Cartesian basis and later transformed to the constrained polar coordinate basis, restoring the conventional v and l quantum numbers. An updated A{sup ~}-state harmonic force field obtained recently in the R. W. Field research group is evaluated. The results for transitions involving the gerade vibrational modes are in qualitative agreement with experiment. Calculated results for transitions involving ungerade modes are presented in Paper II of this series [G. B. Park, J. H. Baraban, and R. W. Field, “Full dimensional Franck–Condon factors for the acetylene A{sup ~1}A{sub u}—X{sup ~1}Σ{sup +}{sub g} transition. II. Vibrational overlap factors for levels involving excitation in ungerade modes,” J. Chem. Phys. 141, 134305 (2014)].« less

Dreaming as mind wandering: evidence from functional neuroimaging and first-person content reports

PubMed Central

Fox, Kieran C. R.; Nijeboer, Savannah; Solomonova, Elizaveta; Domhoff, G. William; Christoff, Kalina

2013-01-01

Isolated reports have long suggested a similarity in content and thought processes across mind wandering (MW) during waking, and dream mentation during sleep. This overlap has encouraged speculation that both “daydreaming” and dreaming may engage similar brain mechanisms. To explore this possibility, we systematically examined published first-person experiential reports of MW and dreaming and found many similarities: in both states, content is largely audiovisual and emotional, follows loose narratives tinged with fantasy, is strongly related to current concerns, draws on long-term memory, and simulates social interactions. Both states are also characterized by a relative lack of meta-awareness. To relate first-person reports to neural evidence, we compared meta-analytic data from numerous functional neuroimaging (PET, fMRI) studies of the default mode network (DMN, with high chances of MW) and rapid eye movement (REM) sleep (with high chances of dreaming). Our findings show large overlaps in activation patterns of cortical regions: similar to MW/DMN activity, dreaming and REM sleep activate regions implicated in self-referential thought and memory, including medial prefrontal cortex (PFC), medial temporal lobe structures, and posterior cingulate. Conversely, in REM sleep numerous PFC executive regions are deactivated, even beyond levels seen during waking MW. We argue that dreaming can be understood as an “intensified” version of waking MW: though the two share many similarities, dreams tend to be longer, more visual and immersive, and to more strongly recruit numerous key hubs of the DMN. Further, whereas MW recruits fewer PFC regions than goal-directed thought, dreaming appears to be characterized by an even deeper quiescence of PFC regions involved in cognitive control and metacognition, with a corresponding lack of insight and meta-awareness. We suggest, then, that dreaming amplifies the same features that distinguish MW from goal-directed waking thought. PMID:23908622

Obstructive sleep apnoea/hypopnoea syndrome in adults with Down syndrome.

PubMed

Hill, Elizabeth A

2016-12-01

Adults with Down syndrome are predisposed to obstructive sleep apnoea/hypopnoea syndrome (OSAHS) due to overlap between the Down syndrome phenotype and OSAHS risk factors.The prevalence of OSAHS in adults with Down syndrome is estimated at 35-42%. This is up to ten-times higher than in the general adult population.Symptoms of OSAHS, including behavioural and emotional disturbances as well as standard symptoms such as sleepiness, should be monitored as part of regular health surveillance in adults with Down syndrome.There is evidence that the use of continuous positive airway pressure (CPAP) therapy in adults with Down syndrome and comorbid OSAHS can lead to significant improvements in subjective sleepiness, behaviour and cognitive function, though further large-scale trials are required. To discuss the relationship between the phenotypic features of Down syndrome and the risk factors for obstructive sleep apnoea/hypopnoea syndrome (OSAHS).To examine the prevalence of OSAHS in adults with Down syndrome.To review recent research into the effectiveness of treatment of OSAHS in adults with Down syndrome using continuous positive airway pressure (CPAP) therapy. Obstructive sleep apnoea/hypopnoea syndrome (OSAHS) is characterised by repeated cycles of upper airway obstruction during sleep, leading to diurnal symptoms. Individuals with Down syndrome are predisposed to OSAHS due to overlap between the Down syndrome phenotype and OSAHS risk factors. Recent large studies using subjective and objective measures estimate that OSAHS affects around 40% of adults with Down syndrome, in contrast to 2-4% of the general adult population. The "double-hit" of comorbid Down syndrome and OSAHS may accelerate cognitive decline in adults with Down syndrome. However, with the appropriate care and support, OSAHS can be treated effectively in this group using continuous positive airway pressure (CPAP) therapy, improving daytime function and behaviour. Symptoms of OSAHS should be routinely monitored in this population, with testing and treatment available to all adults with Down syndrome; however, this is not currently commonplace, and health inequalities are evident.

Functional Redundancy and Complementarities of Seed Dispersal by the Last Neotropical Megafrugivores

PubMed Central

Bueno, Rafael S.; Guevara, Roger; Ribeiro, Milton C.; Culot, Laurence; Bufalo, Felipe S.; Galetti, Mauro

2013-01-01

Background Functional redundancy has been debated largely in ecology and conservation, yet we lack detailed empirical studies on the roles of functionally similar species in ecosystem function. Large bodied frugivores may disperse similar plant species and have strong impact on plant recruitment in tropical forests. The two largest frugivores in the neotropics, tapirs (Tapirus terrestris) and muriquis (Brachyteles arachnoides) are potential candidates for functional redundancy on seed dispersal effectiveness. Here we provide a comparison of the quantitative, qualitative and spatial effects on seed dispersal by these megafrugivores in a continuous Brazilian Atlantic forest. Methodology/Principal Findings We found a low overlap of plant species dispersed by both muriquis and tapirs. A group of 35 muriquis occupied an area of 850 ha and dispersed 5 times more plant species, and 13 times more seeds than 22 tapirs living in the same area. Muriquis dispersed 2.4 times more seeds in any random position than tapirs. This can be explained mainly because seed deposition by muriquis leaves less empty space than tapirs. However, tapirs are able to disperse larger seeds than muriquis and move them into sites not reached by primates, such as large forest gaps, open areas and fragments nearby. Based on published information we found 302 plant species that are dispersed by at least one of these megafrugivores in the Brazilian Atlantic forest. Conclusions/Significance Our study showed that both megafrugivores play complementary rather than redundant roles as seed dispersers. Although tapirs disperse fewer seeds and species than muriquis, they disperse larger-seeded species and in places not used by primates. The selective extinction of these megafrugivores will change the spatial seed rain they generate and may have negative effects on the recruitment of several plant species, particularly those with large seeds that have muriquis and tapirs as the last living seed dispersers. PMID:23409161

Two mechanisms of resonance overlapping in excitation of azimuthal surface waves by rotating relativistic electron beams

NASA Astrophysics Data System (ADS)

Girka, Igor O.; Pavlenko, Ivan V.; Thumm, Manfred

2018-05-01

Azimuthal surface waves are electromagnetic eigenwaves of cylindrical plasma-filled metallic waveguides with a stationary axial magnetic field. These waves with extraordinary polarization can effectively interact with relativistic electron beams rotating along large Larmor orbits in the gap, which separates the plasma column from the waveguide wall. Both widening the layer and increasing the beam particle density are demonstrated to cause resonance overlapping seen from the perspective of the growth rate dependence on the effective wave number.

β-Amyloid Deposition Is Associated with Decreased Right Prefrontal Activation during Task Switching among Cognitively Normal Elderly

PubMed Central

Steffener, Jason; Razlighi, Qolamreza R.; Habeck, Christian; Stern, Yaakov

2016-01-01

The accumulation of β-amyloid (Aβ) peptides, a pathological hallmark of Alzheimer's disease (AD), has been associated with functional alterations, often in an episodic memory system with a particular emphasis on medial temporal lobe function. The topography of Aβ deposition, however, largely overlaps with frontoparietal control (FPC) regions implicated in cognitive control that has been shown to be impaired in early mild AD. To understand the neural mechanism underlying early changes in cognitive control with AD, we examined the impact of Aβ deposition on task-evoked FPC activation using functional magnetic resonance imaging (fMRI) in humans. Forty-three young and 62 cognitively normal older adults underwent an fMRI session during an executive contextual task in which task difficulty varied: single (either letter case or vowel/consonant judgment task) vs dual (switching between letter case and vowel/consonant decisions) task. Older subjects additionally completed 18F-florbetaben positron emission tomography scans and were classified as either amyloid positive (Aβ+) or negative (Aβ−). Consistent with previous reports, age-related increases in brain activity were found in FPC regions commonly identified across groups. For both task conditions, Aβ-related increases in brain activity were found compared with baseline activity. For higher cognitive control load, however, Aβ+ elderly showed reduced task-switching activation in the right inferior frontal cortex. Our findings suggest that with Aβ deposition, brain activation in the cognitive control region reaches a maximum with lower control demand and decreases with higher control demand, which may underlie early impairment in cognitive control with AD progression. SIGNIFICANCE STATEMENT The accumulation of β-amyloid (Aβ) peptides, a pathological hallmark of Alzheimer's disease, spatially overlaps with frontoparietal control (FPC) regions implicated in cognitive control, but the impact of Aβ deposition on FPC regions is largely unknown. Using functional magnetic resonance imaging with a task-switching task, we found Aβ-related increases in FPC regions compared with baseline activity. For higher cognitive control load, however, Aβ-related hypoactivity was found in the right inferior frontal cortex, a region highly implicated in cognitive control. The findings suggest that with Aβ deposition, task-related brain activity may reach a plateau early and undergo downstream pathways of neural dysfunction, which may relate to the early impairment of cognitive control seen in the progression of Aβ pathology. PMID:26865619

Hypochondriasis and somatization: two distinct aspects of somatoform disorders?

PubMed

Leibbrand, R; Hiller, W; Fichter, M M

2000-01-01

We investigated boundaries and overlap between somatization and hypochondriasis on different levels of psychopathology: (1) comorbidity between hypochondriasis and somatization on the level of diagnoses in the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV; American Psychiatric Association, 1994): (2) comorbidity with other mental disorders; (3) differences in clinical characteristics: and (4) overlap on the level of psychometric measures. The sample consisted of 120 psycho somatic inpatients. Somatoform, hypochondriacal, and depressive symptomatology, cognitions about body and health, and further aspects of general symptomatology were investigated. Diagnoses of Axis I and II were based on DSM-IV Our results suggest a large overlap on the level of DSM-IV-diagnoses: only 3 of 31 hypochondriacal patients had no multiple somatoform symptoms, while 58 of 86 patients with multiple somatoform symptoms had no hypochondriasis. However, the overlap between hypochondriacal and somatization symptomatology on the level of psychometric measurement is only moderate, indicating that hypochondriasis is a markedly distinct aspect of somatoform disorders.

Overlapped Partitioning for Ensemble Classifiers of P300-Based Brain-Computer Interfaces

PubMed Central

Onishi, Akinari; Natsume, Kiyohisa

2014-01-01

A P300-based brain-computer interface (BCI) enables a wide range of people to control devices that improve their quality of life. Ensemble classifiers with naive partitioning were recently applied to the P300-based BCI and these classification performances were assessed. However, they were usually trained on a large amount of training data (e.g., 15300). In this study, we evaluated ensemble linear discriminant analysis (LDA) classifiers with a newly proposed overlapped partitioning method using 900 training data. In addition, the classification performances of the ensemble classifier with naive partitioning and a single LDA classifier were compared. One of three conditions for dimension reduction was applied: the stepwise method, principal component analysis (PCA), or none. The results show that an ensemble stepwise LDA (SWLDA) classifier with overlapped partitioning achieved a better performance than the commonly used single SWLDA classifier and an ensemble SWLDA classifier with naive partitioning. This result implies that the performance of the SWLDA is improved by overlapped partitioning and the ensemble classifier with overlapped partitioning requires less training data than that with naive partitioning. This study contributes towards reducing the required amount of training data and achieving better classification performance. PMID:24695550

Overlapped partitioning for ensemble classifiers of P300-based brain-computer interfaces.

PubMed

Onishi, Akinari; Natsume, Kiyohisa

2014-01-01

A P300-based brain-computer interface (BCI) enables a wide range of people to control devices that improve their quality of life. Ensemble classifiers with naive partitioning were recently applied to the P300-based BCI and these classification performances were assessed. However, they were usually trained on a large amount of training data (e.g., 15300). In this study, we evaluated ensemble linear discriminant analysis (LDA) classifiers with a newly proposed overlapped partitioning method using 900 training data. In addition, the classification performances of the ensemble classifier with naive partitioning and a single LDA classifier were compared. One of three conditions for dimension reduction was applied: the stepwise method, principal component analysis (PCA), or none. The results show that an ensemble stepwise LDA (SWLDA) classifier with overlapped partitioning achieved a better performance than the commonly used single SWLDA classifier and an ensemble SWLDA classifier with naive partitioning. This result implies that the performance of the SWLDA is improved by overlapped partitioning and the ensemble classifier with overlapped partitioning requires less training data than that with naive partitioning. This study contributes towards reducing the required amount of training data and achieving better classification performance.

Evaluating spatial overlap and relatedness of white-tailed deer in a chronic wasting disease management zone

USGS Publications Warehouse

Samuel, Michael D.; Magle, Seth B.; Van Deelen, Timothy R.; Robinson, Stacie J.; Mathews, Nancy E.

2013-01-01

Wildlife disease transmission, at a local scale, can occur from interactions between infected and susceptible conspecifics or from a contaminated environment. Thus, the degree of spatial overlap and rate of contact among deer is likely to impact both direct and indirect transmission of infectious diseases such chronic wasting disease (CWD) or bovine tuberculosis. We identified a strong relationship between degree of spatial overlap (volume of intersection) and genetic relatedness for female white-tailed deer in Wisconsin’s area of highest CWD prevalence. We used volume of intersection as a surrogate for contact rates between deer and concluded that related deer are more likely to have contact, which may drive disease transmission dynamics. In addition, we found that age of deer influences overlap, with fawns exhibiting the highest degree of overlap with other deer. Our results further support the finding that female social groups have higher contact among related deer which can result in transmission of infectious diseases. We suggest that control of large social groups comprised of closely related deer may be an effective strategy in slowing the transmission of infectious pathogens, and CWD in particular.

Shifting Interests: Changes in the Lexical Semantics of ED-MEDIA

ERIC Educational Resources Information Center

Wild, Fridolin; Valentine, Chris; Scott, Peter

2010-01-01

Large research networks naturally form complex communities with overlapping but not identical expertise. To map the distribution of professional competence in field of "technology-enhanced learning", the lexical semantics expressed in research articles published in a representative, large-scale conference (ED-MEDIA) can be investigated and changes…

Cognitive Prediction of Reading, Math, and Attention: Shared and Unique Influences.

PubMed

Peterson, Robin L; Boada, Richard; McGrath, Lauren M; Willcutt, Erik G; Olson, Richard K; Pennington, Bruce F

The current study tested a multiple-cognitive predictor model of word reading, math ability, and attention in a community-based sample of twins ages 8 to 16 years ( N = 636). The objective was to identify cognitive predictors unique to each skill domain as well as cognitive predictors shared among skills that could help explain their overlap and thus help illuminate the basis for comorbidity of related disorders (reading disability, math disability, and attention deficit hyperactivity disorder). Results indicated that processing speed contributes to the overlap between reading and attention as well as math and attention, whereas verbal comprehension contributes to the overlap between reading and math. There was no evidence that executive functioning skills help account for covariation among these skill domains. Instead, specific executive functions differentially related to certain outcomes (i.e., working memory to math and inhibition to attention). We explored whether the model varied in younger versus older children and found only minor differences. Results are interpreted within the context of the multiple deficit framework for neurodevelopmental disorders.

Why does the sign problem occur in evaluating the overlap of HFB wave functions?

NASA Astrophysics Data System (ADS)

Mizusaki, Takahiro; Oi, Makito; Shimizu, Noritaka

2018-04-01

For the overlap matrix element between Hartree-Fock-Bogoliubov states, there are two analytically different formulae: one with the square root of the determinant (the Onishi formula) and the other with the Pfaffian (Robledo's Pfaffian formula). The former formula is two-valued as a complex function, hence it leaves the sign of the norm overlap undetermined (i.e., the so-called sign problem of the Onishi formula). On the other hand, the latter formula does not suffer from the sign problem. The derivations for these two formulae are so different that the reasons are obscured why the resultant formulae possess different analytical properties. In this paper, we discuss the reason why the difference occurs by means of the consistent framework, which is based on the linked cluster theorem and the product-sum identity for the Pfaffian. Through this discussion, we elucidate the source of the sign problem in the Onishi formula. We also point out that different summation methods of series expansions may result in analytically different formulae.

Characteristics associated with mortality in patients with chronic obstructive pulmonary disease (COPD)-heart failure coexistence.

PubMed

Plachi, Franciele; Balzan, Fernanda M; Sanseverino, Renata A; Palombini, Dora V; Marques, Renata D; Clausell, Nadine O; Knorst, Marli M; Neder, J Alberto; Berton, Danilo C

2018-02-21

Aim To investigate if cardiac/pulmonary functional tests and variables obtained from clinical practice (body mass index, dyspnea, functional class, clinical judgment of disability to perform an exercise test and previous hospitalization rate) are related to mortality in patients with overlap chronic obstructive pulmonary disease (COPD) and chronic heart failure (CHF). Although the coexistence of COPD and CHF has been growingly reported, description of survival predictors considering the presence of both conditions is still scarce. Using a cohort design, outpatients with the previous diagnosis of COPD and/or CHF that performed both spirometry and echocardiography in the same year were followed-up during a mean of 20.9±8.5 months. Findings Of the 550 patients initially evaluated, 301 had both spirometry and echocardiography: 160 (53%) with COPD on isolation; 100 (33%) with CHF on isolation; and 41 (14%) with overlap. All groups presented similar mortality: COPD 17/160 (11%); CHF 12/100 (12%); and overlap 7/41 (17%) (P=0.73). In the overlap group (n=41), inability to exercise and hospitalization rate were the unique parameters associated with higher mortality (seven events) in univariate analyses. In conclusion, inability to exercise and hospitalization rate emerged as the unique parameters associated with mortality in our sample.

Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing.

PubMed

Conway, Tyrrell; Creecy, James P; Maddox, Scott M; Grissom, Joe E; Conkle, Trevor L; Shadid, Tyler M; Teramoto, Jun; San Miguel, Phillip; Shimada, Tomohiro; Ishihama, Akira; Mori, Hirotada; Wanner, Barry L

2014-07-08

We analyzed the transcriptome of Escherichia coli K-12 by strand-specific RNA sequencing at single-nucleotide resolution during steady-state (logarithmic-phase) growth and upon entry into stationary phase in glucose minimal medium. To generate high-resolution transcriptome maps, we developed an organizational schema which showed that in practice only three features are required to define operon architecture: the promoter, terminator, and deep RNA sequence read coverage. We precisely annotated 2,122 promoters and 1,774 terminators, defining 1,510 operons with an average of 1.98 genes per operon. Our analyses revealed an unprecedented view of E. coli operon architecture. A large proportion (36%) of operons are complex with internal promoters or terminators that generate multiple transcription units. For 43% of operons, we observed differential expression of polycistronic genes, despite being in the same operons, indicating that E. coli operon architecture allows fine-tuning of gene expression. We found that 276 of 370 convergent operons terminate inefficiently, generating complementary 3' transcript ends which overlap on average by 286 nucleotides, and 136 of 388 divergent operons have promoters arranged such that their 5' ends overlap on average by 168 nucleotides. We found 89 antisense transcripts of 397-nucleotide average length, 7 unannotated transcripts within intergenic regions, and 18 sense transcripts that completely overlap operons on the opposite strand. Of 519 overlapping transcripts, 75% correspond to sequences that are highly conserved in E. coli (>50 genomes). Our data extend recent studies showing unexpected transcriptome complexity in several bacteria and suggest that antisense RNA regulation is widespread. Importance: We precisely mapped the 5' and 3' ends of RNA transcripts across the E. coli K-12 genome by using a single-nucleotide analytical approach. Our resulting high-resolution transcriptome maps show that ca. one-third of E. coli operons are complex, with internal promoters and terminators generating multiple transcription units and allowing differential gene expression within these operons. We discovered extensive antisense transcription that results from more than 500 operons, which fully overlap or extensively overlap adjacent divergent or convergent operons. The genomic regions corresponding to these antisense transcripts are highly conserved in E. coli (including Shigella species), although it remains to be proven whether or not they are functional. Our observations of features unearthed by single-nucleotide transcriptome mapping suggest that deeper layers of transcriptional regulation in bacteria are likely to be revealed in the future. Copyright © 2014 Conway et al.

Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology.

PubMed

Verheijen, Lieneke M; Aerts, Rien; Bönisch, Gerhard; Kattge, Jens; Van Bodegom, Peter M

2016-01-01

Plant functional types (PFTs) aggregate the variety of plant species into a small number of functionally different classes. We examined to what extent plant traits, which reflect species' functional adaptations, can capture functional differences between predefined PFTs and which traits optimally describe these differences. We applied Gaussian kernel density estimation to determine probability density functions for individual PFTs in an n-dimensional trait space and compared predicted PFTs with observed PFTs. All possible combinations of 1-6 traits from a database with 18 different traits (total of 18 287 species) were tested. A variety of trait sets had approximately similar performance, and 4-5 traits were sufficient to classify up to 85% of the species into PFTs correctly, whereas this was 80% for a bioclimatically defined tree PFT classification. Well-performing trait sets included combinations of correlated traits that are considered functionally redundant within a single plant strategy. This analysis quantitatively demonstrates how structural differences between PFTs are reflected in functional differences described by particular traits. Differentiation between PFTs is possible despite large overlap in plant strategies and traits, showing that PFTs are differently positioned in multidimensional trait space. This study therefore provides the foundation for important applications for predictive ecology. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Improving Reading Outcomes for Children with Learning Disabilities: Using Brief Experimental Analysis to Develop Parent-tutoring Interventions

PubMed Central

Gortmaker, Valerie J; Daly, Edward J; McCurdy, Merilee; Persampieri, Michael J; Hergenrader, Melanie

2007-01-01

The present study assessed the effects of summer parent tutoring on 3 children with learning disabilities using empirically derived reading interventions. Brief experimental analyses were used to identify customized reading fluency interventions. Parents were trained to use the intervention strategies with their children. Parents implemented the procedures during parent-tutoring sessions at home and results were measured continuously in high-word-overlap and low-word-overlap passages to determine whether generalization occurred. Parent and child satisfaction with the procedures was assessed. Results demonstrated generalized increases in reading fluency in both high-word-overlap and low-word-overlap passages as a function of parent tutoring. Also, acceptability ratings by children and their parents indicated that they viewed the interventions as acceptable and effective. Results are discussed in terms of structuring reading fluency interventions that promote generalization and maintenance of treatment effects. PMID:17624063

Automated lung sound analysis for detecting pulmonary abnormalities.

PubMed

Datta, Shreyasi; Dutta Choudhury, Anirban; Deshpande, Parijat; Bhattacharya, Sakyajit; Pal, Arpan

2017-07-01

Identification of pulmonary diseases comprises of accurate auscultation as well as elaborate and expensive pulmonary function tests. Prior arts have shown that pulmonary diseases lead to abnormal lung sounds such as wheezes and crackles. This paper introduces novel spectral and spectrogram features, which are further refined by Maximal Information Coefficient, leading to the classification of healthy and abnormal lung sounds. A balanced lung sound dataset, consisting of publicly available data and data collected with a low-cost in-house digital stethoscope are used. The performance of the classifier is validated over several randomly selected non-overlapping training and validation samples and tested on separate subjects for two separate test cases: (a) overlapping and (b) non-overlapping data sources in training and testing. The results reveal that the proposed method sustains an accuracy of 80% even for non-overlapping data sources in training and testing.

Disrupted Topological Patterns of Large-Scale Network in Conduct Disorder

PubMed Central

Jiang, Yali; Liu, Weixiang; Ming, Qingsen; Gao, Yidian; Ma, Ren; Zhang, Xiaocui; Situ, Weijun; Wang, Xiang; Yao, Shuqiao; Huang, Bingsheng

2016-01-01

Regional abnormalities in brain structure and function, as well as disrupted connectivity, have been found repeatedly in adolescents with conduct disorder (CD). Yet, the large-scale brain topology associated with CD is not well characterized, and little is known about the systematic neural mechanisms of CD. We employed graphic theory to investigate systematically the structural connectivity derived from cortical thickness correlation in a group of patients with CD (N = 43) and healthy controls (HCs, N = 73). Nonparametric permutation tests were applied for between-group comparisons of graphical metrics. Compared with HCs, network measures including global/local efficiency and modularity all pointed to hypo-functioning in CD, despite of preserved small-world organization in both groups. The hubs distribution is only partially overlapped with each other. These results indicate that CD is accompanied by both impaired integration and segregation patterns of brain networks, and the distribution of highly connected neural network ‘hubs’ is also distinct between groups. Such misconfiguration extends our understanding regarding how structural neural network disruptions may underlie behavioral disturbances in adolescents with CD, and potentially, implicates an aberrant cytoarchitectonic profiles in the brain of CD patients. PMID:27841320

Impossible spaces: maximizing natural walking in virtual environments with self-overlapping architecture.

PubMed

Suma, Evan A; Lipps, Zachary; Finkelstein, Samantha; Krum, David M; Bolas, Mark

2012-04-01

Walking is only possible within immersive virtual environments that fit inside the boundaries of the user's physical workspace. To reduce the severity of the restrictions imposed by limited physical area, we introduce "impossible spaces," a new design mechanic for virtual environments that wish to maximize the size of the virtual environment that can be explored with natural locomotion. Such environments make use of self-overlapping architectural layouts, effectively compressing comparatively large interior environments into smaller physical areas. We conducted two formal user studies to explore the perception and experience of impossible spaces. In the first experiment, we showed that reasonably small virtual rooms may overlap by as much as 56% before users begin to detect that they are in an impossible space, and that the larger virtual rooms that expanded to maximally fill our available 9.14 m x 9.14 m workspace may overlap by up to 31%. Our results also demonstrate that users perceive distances to objects in adjacent overlapping rooms as if the overall space was uncompressed, even at overlap levels that were overtly noticeable. In our second experiment, we combined several well-known redirection techniques to string together a chain of impossible spaces in an expansive outdoor scene. We then conducted an exploratory analysis of users' verbal feedback during exploration, which indicated that impossible spaces provide an even more powerful illusion when users are naive to the manipulation.

Large herbivores that strive mightily but eat and drink as friends.

PubMed

de Boer, W F; Prins, H H T

1990-02-01

Grazing in patches of Cynodon dactylon and of Sporobolus spicatus by four large herbivores, and the interaction between these sedentary herbivores was studied in Lake Manyara National Park, northern Tanzania. The herbivores were the African buffalo, Syncerus caffer; the African elephan, Loxodonta africana; the Burchell's zebra, Equus burchelli; and the wildebeest, Connochaetus taurinus. Four different hypotheses of the interactions between the herbivores were tested, viz., increased predator detection/protection through association of species, facilitation of the food intake through the influence of other species, use by other species of the food manipulation strategy of buffalo, and interspecific competition for food. On the level of a single day, zebra and wildebeest were symbiotic, which could have been caused by an increased chance of predator detection. A similar association between buffalo and wildebeest or zebra was also detected on C. dactylon grasslands. There was no indication of facilitation between any of the herbivores. Buffalo had a despotic relationship with elephant, that is the elephant's consumption was lowered when buffalo had visited a patch prior to their arrival. When elephant and buffalo arrived at the same time there appeared to be scramble competition between them.Habitat overlap was calculated for four pairs of species. In conjunction with the analyses of the patch visits, it was concluded that a small overlap was associated with interspecific competition and a large habitat overlap was associated with symbiosis.

A 3D Kinematic Measurement of Knee Prosthesis Using X-ray Projection Images

NASA Astrophysics Data System (ADS)

Hirokawa, Shunji; Ariyoshi, Shogo; Hossain, Mohammad Abrar

We have developed a technique for estimating 3D motion of knee prosthesis from its 2D perspective projections. As Fourier descriptors were used for compact representation of library templates and contours extracted from the prosthetic X-ray images, the entire silhouette contour of each prosthetic component was required. This caused such a problem as our algorithm did not function when the silhouettes of tibio and femoral components overlapped with each other. Here we planned a novel method to overcome it; which was processed in two steps. First, the missing part of silhouette contour due to overlap was interpolated using a free-formed curvature such as Bezier. Then the first step position/orientation estimation was performed. In the next step, a clipping window was set in the projective coordinate so as to separate the overlapped silhouette drawn using the first step estimates. After that the localized library whose templates were clipped in shape was prepared and the second step estimation was performed. Computer model simulation demonstrated sufficient accuracies of position/orientation estimation even for overlapped silhouettes; equivalent to those without overlap.

Lupus erythematosus/lichen planus overlap syndrome: successful treatment with acitretin.

PubMed

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.

Comparison of the NCI open database with seven large chemical structural databases.

PubMed

Voigt, J H; Bienfait, B; Wang, S; Nicklaus, M C

2001-01-01

Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.

Fast and Accurate Simulation Technique for Large Irregular Arrays

NASA Astrophysics Data System (ADS)

Bui-Van, Ha; Abraham, Jens; Arts, Michel; Gueuning, Quentin; Raucy, Christopher; Gonzalez-Ovejero, David; de Lera Acedo, Eloy; Craeye, Christophe

2018-04-01

A fast full-wave simulation technique is presented for the analysis of large irregular planar arrays of identical 3-D metallic antennas. The solution method relies on the Macro Basis Functions (MBF) approach and an interpolatory technique to compute the interactions between MBFs. The Harmonic-polynomial (HARP) model is established for the near-field interactions in a modified system of coordinates. For extremely large arrays made of complex antennas, two approaches assuming a limited radius of influence for mutual coupling are considered: one is based on a sparse-matrix LU decomposition and the other one on a tessellation of the array in the form of overlapping sub-arrays. The computation of all embedded element patterns is sped up with the help of the non-uniform FFT algorithm. Extensive validations are shown for arrays of log-periodic antennas envisaged for the low-frequency SKA (Square Kilometer Array) radio-telescope. The analysis of SKA stations with such a large number of elements has not been treated yet in the literature. Validations include comparison with results obtained with commercial software and with experiments. The proposed method is particularly well suited to array synthesis, in which several orders of magnitude can be saved in terms of computation time.

Culture and behaviour in the English National Health Service: overview of lessons from a large multimethod study

PubMed Central

Dixon-Woods, Mary; Baker, Richard; Charles, Kathryn; Dawson, Jeremy; Jerzembek, Gabi; Martin, Graham; McCarthy, Imelda; McKee, Lorna; Minion, Joel; Ozieranski, Piotr; Willars, Janet; Wilkie, Patricia; West, Michael

2014-01-01

Background Problems of quality and safety persist in health systems worldwide. We conducted a large research programme to examine culture and behaviour in the English National Health Service (NHS). Methods Mixed-methods study involving collection and triangulation of data from multiple sources, including interviews, surveys, ethnographic case studies, board minutes and publicly available datasets. We narratively synthesised data across the studies to produce a holistic picture and in this paper present a high-level summary. Results We found an almost universal desire to provide the best quality of care. We identified many ‘bright spots’ of excellent caring and practice and high-quality innovation across the NHS, but also considerable inconsistency. Consistent achievement of high-quality care was challenged by unclear goals, overlapping priorities that distracted attention, and compliance-oriented bureaucratised management. The institutional and regulatory environment was populated by multiple external bodies serving different but overlapping functions. Some organisations found it difficult to obtain valid insights into the quality of the care they provided. Poor organisational and information systems sometimes left staff struggling to deliver care effectively and disempowered them from initiating improvement. Good staff support and management were also highly variable, though they were fundamental to culture and were directly related to patient experience, safety and quality of care. Conclusions Our results highlight the importance of clear, challenging goals for high-quality care. Organisations need to put the patient at the centre of all they do, get smart intelligence, focus on improving organisational systems, and nurture caring cultures by ensuring that staff feel valued, respected, engaged and supported. PMID:24019507

Classification of pediatric functional gastrointestinal disorders related to abdominal pain using Rome III vs. Rome IV criterions.

PubMed

Edwards, Trent; Friesen, Craig; Schurman, Jennifer V

2018-03-17

The primary purpose of this study was to compare Rome III and IV evaluation criteria for irritable bowel syndrome (IBS), functional dyspepsia (FD), and an overlap syndrome consisting of both IBS and FD by assessing the frequency of each diagnosis in a population of children with chronic abdominal pain. Frequencies of Rome IV FD subtypes of postprandial distress syndrome (PDS) and epigastric pain syndrome (EPS) were determined and FD/IBS overlap symptom associations were also assessed. We conducted a cross-sectional retrospective chart review of 106 pediatric patients who had completed standardized medical histories as part of their evaluation for chronic abdominal pain. The patients ranged from eight to 17 years of age and reported having abdominal pain at least weekly for 8 weeks. Patients whose evaluation revealed gastrointestinal disease were excluded. The patients' diagnoses were determined by a single pediatric gastroenterologist utilizing the specific criteria for Rome III and IV, respectively. Patients were significantly more likely to be diagnosed with FD (84.9% vs. 52.8%), IBS (69.8% vs. 34%), and FD/IBS overlap (58.5% vs. 17.9%) by Rome IV criteria, as compared to Rome III criteria. With regard to Rome IV FD subtypes, 81.1% fulfilled criteria for PDS, 11.1% fulfilled criteria for EPS, 6.7% fulfilled criteria for both, and 1.1% did not fulfill criteria for either. Finally, we found an increased frequency of diarrhea and pain with eating in the overlap group compared to the non-overlap group of Rome III, while only an increased frequency of diarrhea was found in the overlap group compared to the non-overlap group of Rome IV. Our data demonstrate that utilizing Rome IV criteria, as compared to Rome III, results in an increase in the diagnosis of FD, a two-fold increase in the diagnosis of IBS, and a three-fold increase in the diagnosis of FD/IBS overlap. Rome IV criteria appears to result in greater heterogeneity within diagnostic categories. It is important to determine whether Rome IV diagnoses are predictive of treatment response, and if so, whether assessing symptom variability within a diagnosis will enhance the ability to select patients for a particular treatment.

Structure of edge-state inner products in the fractional quantum Hall effect

NASA Astrophysics Data System (ADS)

Fern, R.; Bondesan, R.; Simon, S. H.

2018-04-01

We analyze the inner products of edge state wave functions in the fractional quantum Hall effect, specifically for the Laughlin and Moore-Read states. We use an effective description for these inner products given by a large-N expansion ansatz proposed in a recent work by J. Dubail, N. Read, and E. Rezayi [Phys. Rev. B 86, 245310 (2012), 10.1103/PhysRevB.86.245310]. As noted by these authors, the terms in this ansatz can be constrained using symmetry, a procedure we perform to high orders. We then check this conjecture by calculating the overlaps exactly for small system sizes and compare the numerics with our high-order expansion. We find the effective description to be very accurate.

Pairwise-additive hydrophobic effect for alkanes in water

PubMed Central

Wu, Jianzhong; Prausnitz, John M.

2008-01-01

Pairwise additivity of the hydrophobic effect is indicated by reliable experimental Henry's constants for a large number of linear and branched low-molecular-weight alkanes in water. Pairwise additivity suggests that the hydrophobic effect is primarily a local phenomenon and that the hydrophobic interaction may be represented by a semiempirical force field. By representing the hydrophobic potential between two methane molecules as a linear function of the overlap volume of the hydration layers, we find that the contact value of the hydrophobic potential (−0.72 kcal/mol) is smaller than that from quantum mechanics simulations (−2.8 kcal/mol) but is close to that from classical molecular dynamics (−0.5∼−0.9 kcal/mol). PMID:18599448

Anemia in children: prevalence, causes, diagnostic work-up, and long-term consequences.

PubMed

Allali, Slimane; Brousse, Valentine; Sacri, Anne-Sylvia; Chalumeau, Martin; de Montalembert, Mariane

2017-11-01

Anemia in children is a major public health problem throughout the world. It is often multifactorial, iron deficiency being the most frequent etiology. Consequences are diverse and largely under evaluated. Areas covered: This paper briefly reviews the main causes and focus on the potential consequences of acute and chronic anemia in children. Expert commentary: Anemia in children should never be trivialized. Even if iron deficiency is frequently involved, other potentially life-threatening causes are possible and should be looked for. The exact contribution of anemia to child mortality and morbidity is difficult to assess because of overlapping comorbidities. Chronic anemia may impair growth, cardiac function and cognitive development in infants but other consequences are rather poorly described and should be explored more thoroughly.

Middle atmosphere project: A radiative heating and cooling algorithm for a numerical model of the large scale stratospheric circulation

NASA Technical Reports Server (NTRS)

Wehrbein, W. M.; Leovy, C. B.

1981-01-01

A Curtis matrix is used to compute cooling by the 15 micron and 10 micron bands of carbon dioxide. Escape of radiation to space and exchange the lower boundary are used for the 9.6 micron band of ozone. Voigt line shape, vibrational relaxation, line overlap, and the temperature dependence of line strength distributions and transmission functions are incorporated into the Curtis matrices. The distributions of the atmospheric constituents included in the algorithm, and the method used to compute the Curtis matrices are discussed as well as cooling or heating by the 9.6 micron band of ozone. The FORTRAN programs and subroutines that were developed are described and listed.

Overlap and specificity of genetic and environmental influences on mathematics and reading disability in 10-year-old twins

PubMed Central

Kovas, Y.; Haworth, C.M.A.; Harlaar, N.; Petrill, S.A.; Dale, P.S.; Plomin, R.

2009-01-01

Background To what extent do genetic and environmental influences on reading disability overlap with those on mathematics disability? Multivariate genetic research on the normal range of variation in unselected samples has led to a Generalist Genes Hypothesis which posits that the same genes largely affect individual differences in these abilities in the normal range. However, little is known about the etiology of co-morbidity for the disability extremes of reading and mathematics. Method From 2596 pairs of 10-year-old monozygotic and dizygotic twins assessed on a web-based battery of reading and mathematics tests, we selected the lowest 15% on reading and on mathematics. We conducted bivariate DeFries–Fulker (DF) extremes analyses to assess overlap and specificity of genetic and environmental influences on reading and mathematics disability defined by a 15% cut-off. Results Both reading and mathematics disability are moderately heritable (47% and 43%, respectively) and show only modest shared environmental influence (16% and 20%). There is substantial phenotypic co-morbidity between reading and mathematics disability. Bivariate DF extremes analyses yielded a genetic correlation of .67 between reading disability and mathematics disability, suggesting that they are affected largely by the same genetic factors. The shared environmental correlation is .96 and the non-shared environmental correlation is .08. Conclusions In line with the Generalist Genes Hypothesis, the same set of generalist genes largely affects mathematical and reading disabilities. The dissociation between the disabilities occurs largely due to independent non-shared environmental influences. PMID:17714376

a Metadata Based Approach for Analyzing Uav Datasets for Photogrammetric Applications

NASA Astrophysics Data System (ADS)

Dhanda, A.; Remondino, F.; Santana Quintero, M.

2018-05-01

This paper proposes a methodology for pre-processing and analysing Unmanned Aerial Vehicle (UAV) datasets before photogrammetric processing. In cases where images are gathered without a detailed flight plan and at regular acquisition intervals the datasets can be quite large and be time consuming to process. This paper proposes a method to calculate the image overlap and filter out images to reduce large block sizes and speed up photogrammetric processing. The python-based algorithm that implements this methodology leverages the metadata in each image to determine the end and side overlap of grid-based UAV flights. Utilizing user input, the algorithm filters out images that are unneeded for photogrammetric processing. The result is an algorithm that can speed up photogrammetric processing and provide valuable information to the user about the flight path.

Combined node and link partitions method for finding overlapping communities in complex networks

PubMed Central

Jin, Di; Gabrys, Bogdan; Dang, Jianwu

2015-01-01

Community detection in complex networks is a fundamental data analysis task in various domains, and how to effectively find overlapping communities in real applications is still a challenge. In this work, we propose a new unified model and method for finding the best overlapping communities on the basis of the associated node and link partitions derived from the same framework. Specifically, we first describe a unified model that accommodates node and link communities (partitions) together, and then present a nonnegative matrix factorization method to learn the parameters of the model. Thereafter, we infer the overlapping communities based on the derived node and link communities, i.e., determine each overlapped community between the corresponding node and link community with a greedy optimization of a local community function conductance. Finally, we introduce a model selection method based on consensus clustering to determine the number of communities. We have evaluated our method on both synthetic and real-world networks with ground-truths, and compared it with seven state-of-the-art methods. The experimental results demonstrate the superior performance of our method over the competing ones in detecting overlapping communities for all analysed data sets. Improved performance is particularly pronounced in cases of more complicated networked community structures. PMID:25715829

Contributions of Medial Temporal Lobe and Striatal Memory Systems to Learning and Retrieving Overlapping Spatial Memories

PubMed Central

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

Anatomo-clinical overlapping maps (AnaCOM): a new method to create anatomo-functional maps from neuropsychological tests and structural MRI scan of subjects with brain lesions

NASA Astrophysics Data System (ADS)

Kinkingnehun, Serge R. J.; du Boisgueheneuc, Foucaud; Golmard, Jean-Louis; Zhang, Sandy X.; Levy, Richard; Dubois, Bruno

2004-04-01

We have developed a new technique to analyze correlations between brain anatomy and its neurological functions. The technique is based on the anatomic MRI of patients with brain lesions who are administered neuropsychological tests. Brain lesions of the MRI scans are first manually segmented. The MRI volumes are then normalized to a reference map, using the segmented area as a mask. After normalization, the brain lesions of the MRI are segmented again in order to redefine the border of the lesions in the context of the normalized brain. Once the MRI is segmented, the patient's score on the neuropsychological test is assigned to each voxel in the lesioned area, while the rest of the voxels of the image are set to 0. Subsequently, the individual patient's MRI images are superimposed, and each voxel is reassigned the average score of the patients who have a lesion at that voxel. A threshold is applied to remove regions having less than three overlaps. This process leads to an anatomo-functional map that links brain areas to functional loss. Other maps can be created to aid in analyzing the functional maps, such as one that indicates the 95% confidence interval of the averaged scores for each area. This anatomo-clinical overlapping map (AnaCOM) method was used to obtain functional maps from patients with lesions in the superior frontal gyrus. By finding particular subregions more responsible for a particular deficit, this method can generate new hypotheses to be tested by conventional group methods.

Exosomes and Homeostatic Synaptic Plasticity Are Linked to Each other and to Huntington's, Parkinson's, and Other Neurodegenerative Diseases by Database-Enabled Analyses of Comprehensively Curated Datasets

PubMed Central

Wang, James K. T.; Langfelder, Peter; Horvath, Steve; Palazzolo, Michael J.

2017-01-01

Huntington's disease (HD) is a progressive and autosomal dominant neurodegeneration caused by CAG expansion in the huntingtin gene (HTT), but the pathophysiological mechanism of mutant HTT (mHTT) remains unclear. To study HD using systems biological methodologies on all published data, we undertook the first comprehensive curation of two key PubMed HD datasets: perturbation genes that impact mHTT-driven endpoints and therefore are putatively linked causally to pathogenic mechanisms, and the protein interactome of HTT that reflects its biology. We perused PubMed articles containing co-citation of gene IDs and MeSH terms of interest to generate mechanistic gene sets for iterative enrichment analyses and rank ordering. The HD Perturbation database of 1,218 genes highly overlaps the HTT Interactome of 1,619 genes, suggesting links between normal HTT biology and mHTT pathology. These two HD datasets are enriched for protein networks of key genes underlying two mechanisms not previously implicated in HD nor in each other: exosome synaptic functions and homeostatic synaptic plasticity. Moreover, proteins, possibly including HTT, and miRNA detected in exosomes from a wide variety of sources also highly overlap the HD datasets, suggesting both mechanistic and biomarker links. Finally, the HTT Interactome highly intersects protein networks of pathogenic genes underlying Parkinson's, Alzheimer's and eight non-HD polyglutamine diseases, ALS, and spinal muscular atrophy. These protein networks in turn highly overlap the exosome and homeostatic synaptic plasticity gene sets. Thus, we hypothesize that HTT and other neurodegeneration pathogenic genes form a large interlocking protein network involved in exosome and homeostatic synaptic functions, particularly where the two mechanisms intersect. Mutant pathogenic proteins cause dysfunctions at distinct points in this network, each altering the two mechanisms in specific fashion that contributes to distinct disease pathologies, depending on the gene mutation and the cellular and biological context. This protein network is rich with drug targets, and exosomes may provide disease biomarkers, thus enabling drug discovery. All the curated datasets are made available for other investigators. Elucidating the roles of pathogenic neurodegeneration genes in exosome and homeostatic synaptic functions may provide a unifying framework for the age-dependent, progressive and tissue selective nature of multiple neurodegenerative diseases. PMID:28611571

Exosomes and Homeostatic Synaptic Plasticity Are Linked to Each other and to Huntington's, Parkinson's, and Other Neurodegenerative Diseases by Database-Enabled Analyses of Comprehensively Curated Datasets.

PubMed

Wang, James K T; Langfelder, Peter; Horvath, Steve; Palazzolo, Michael J

2017-01-01

Huntington's disease (HD) is a progressive and autosomal dominant neurodegeneration caused by CAG expansion in the huntingtin gene ( HTT ), but the pathophysiological mechanism of mutant HTT (mHTT) remains unclear. To study HD using systems biological methodologies on all published data, we undertook the first comprehensive curation of two key PubMed HD datasets: perturbation genes that impact mHTT-driven endpoints and therefore are putatively linked causally to pathogenic mechanisms, and the protein interactome of HTT that reflects its biology. We perused PubMed articles containing co-citation of gene IDs and MeSH terms of interest to generate mechanistic gene sets for iterative enrichment analyses and rank ordering. The HD Perturbation database of 1,218 genes highly overlaps the HTT Interactome of 1,619 genes, suggesting links between normal HTT biology and mHTT pathology. These two HD datasets are enriched for protein networks of key genes underlying two mechanisms not previously implicated in HD nor in each other: exosome synaptic functions and homeostatic synaptic plasticity. Moreover, proteins, possibly including HTT, and miRNA detected in exosomes from a wide variety of sources also highly overlap the HD datasets, suggesting both mechanistic and biomarker links. Finally, the HTT Interactome highly intersects protein networks of pathogenic genes underlying Parkinson's, Alzheimer's and eight non-HD polyglutamine diseases, ALS, and spinal muscular atrophy. These protein networks in turn highly overlap the exosome and homeostatic synaptic plasticity gene sets. Thus, we hypothesize that HTT and other neurodegeneration pathogenic genes form a large interlocking protein network involved in exosome and homeostatic synaptic functions, particularly where the two mechanisms intersect. Mutant pathogenic proteins cause dysfunctions at distinct points in this network, each altering the two mechanisms in specific fashion that contributes to distinct disease pathologies, depending on the gene mutation and the cellular and biological context. This protein network is rich with drug targets, and exosomes may provide disease biomarkers, thus enabling drug discovery. All the curated datasets are made available for other investigators. Elucidating the roles of pathogenic neurodegeneration genes in exosome and homeostatic synaptic functions may provide a unifying framework for the age-dependent, progressive and tissue selective nature of multiple neurodegenerative diseases.

Inversion of chalcogen defect levels in silicon - An MNDO study. [modified neglect of diatomic overlap

NASA Technical Reports Server (NTRS)

Singh, R. K.; Sahu, S. N.; Singh, V. A.; Corbett, J. W.

1985-01-01

MNDO (modified neglect of diatomic overlap) calculations have been carried out for substitutional oxygen and sulfur impurities in silicon. The calculations of the gap levels reveal a reversal of trend with atomic ionization energies in agreement with self-consistent Green function results, and analysis of the MNDO charge distribution supports the view that the electronegativity difference between oxygen and sulfur gives rise to this shallower energy level.

On the genealogy of branching random walks and of directed polymers

NASA Astrophysics Data System (ADS)

Derrida, Bernard; Mottishaw, Peter

2016-08-01

It is well known that the mean-field theory of directed polymers in a random medium exhibits replica symmetry breaking with a distribution of overlaps which consists of two delta functions. Here we show that the leading finite-size correction to this distribution of overlaps has a universal character which can be computed explicitly. Our results can also be interpreted as genealogical properties of branching Brownian motion or of branching random walks.

Overlap Properties of Clouds Generated by a Cloud Resolving Model

NASA Technical Reports Server (NTRS)

Oreopoulos, L.; Khairoutdinov, M.

2002-01-01

In order for General Circulation Models (GCMs), one of our most important tools to predict future climate, to correctly describe the propagation of solar and thermal radiation through the cloudy atmosphere a realistic description of the vertical distribution of cloud amount is needed. Actually, one needs not only the cloud amounts at different levels of the atmosphere, but also how these cloud amounts are related, in other words, how they overlap. Currently GCMs make some idealized assumptions about cloud overlap, for example that contiguous cloud layers overlap maximally and non-contiguous cloud layers overlap in a random fashion. Since there are difficulties in obtaining the vertical profile of cloud amount from observations, the realism of the overlap assumptions made in GCMs has not been yet rigorously investigated. Recently however, cloud observations from a relatively new type of ground radar have been used to examine the vertical distribution of cloudiness. These observations suggest that the GCM overlap assumptions are dubious. Our study uses cloud fields from sophisticated models dedicated to simulate cloud formation, maintenance, and dissipation called Cloud Resolving Models . These models are generally considered capable of producing realistic three-dimensional representation of cloudiness. Using numerous cloud fields produced by such a CRM we show that the degree of overlap between cloud layers is a function of their separation distance, and is in general described by a combination of the maximum and random overlap assumption, with random overlap dominating as separation distances increase. We show that it is possible to parameterize this behavior in a way that can eventually be incorporated in GCMs. Our results seem to have a significant resemblance to the results from the radar observations despite the completely different nature of the datasets. This consistency is encouraging and will promote development of new radiative transfer codes that will estimate the radiation effects of multi-layer cloud fields more accurately.

Overcoming the heterologous bias: An in vivo functional analysis of multidrug efflux transporter, CgCdr1p in matched pair clinical isolates of Candida glabrata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puri, Nidhi; Manoharlal, Raman; Sharma, Monika

2011-01-07

Research highlights: {yields} First report to demonstrate an in vivo expression system of an ABC multidrug transporter CgCdr1p of C. glabrata. {yields} First report on the structure and functional characterization of CgCdr1p. {yields} Functional conservation of divergent but typical residues of CgCdr1p. {yields} CgCdr1p elicits promiscuity towards substrates and has a large drug binding pocket with overlapping specificities. -- Abstract: We have taken advantage of the natural milieu of matched pair of azole sensitive (AS) and azole resistant (AR) clinical isolates of Candida glabrata for expressing its major ABC multidrug transporter, CgCdr1p for structure and functional analysis. This was accomplishedmore » by tagging a green fluorescent protein (GFP) downstream of ORF of CgCDR1 and integrating the resultant fusion protein at its native chromosomal locus in AS and AR backgrounds. The characterization confirmed that in comparison to AS isolate, CgCdr1p-GFP was over-expressed in AR isolates due to its hyperactive native promoter and the GFP tag did not affect its functionality in either construct. We observed that in addition to Rhodamine 6 G (R6G) and Fluconazole (FLC), a recently identified fluorescent substrate of multidrug transporters Nile Red (NR) could also be expelled by CgCdr1p. Competition assays with these substrates revealed the presence of overlapping multiple drug binding sites in CgCdr1p. Point mutations employing site directed mutagenesis confirmed that the role played by unique amino acid residues critical to ATP catalysis and localization of ABC drug transporter proteins are well conserved in C. glabrata as in other yeasts. This study demonstrates a first in vivo novel system where over-expression of GFP tagged MDR transporter protein can be driven by its own hyperactive promoter of AR isolates. Taken together, this in vivo system can be exploited for the structure and functional analysis of CgCdr1p and similar proteins wherein the arte-factual concerns encountered in using heterologous systems are totally excluded.« less

An ALMA Archival Study of the Clump Mass Function in the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Brunetti, Nathan

2017-11-01

This thesis presents 1.3 mm and 3.1 mm continuum maps of seven star forming regions within the Large Magellanic Cloud (LMC) as observed with the Atacama Large Millimeter/Submillimeter Array (ALMA). The data were taken as part of six projects retrieved from the ALMA public archive plus one project observed specifically for this work. We developed a technique to combine Band 3 and Band 6 maps to estimate dust-only emission corrected for free-free emission contamination. We also present an automated clean masking script, with a listing of the code, which we adapted and used for all of the imaging in this thesis. From these observations we identify 32 molecular clumps in the LMC and estimate their total mass from their dust emission. We derive a cumulative clump mass function (N(≥M) ≈ M(α+1)) and fit it with a double power law to find α_low = -1.76+0.07-0.1, α_high = -3.3+0.3-0.6, and a break mass of 2500+700-300 M⊙. Comparing to the clump mass function derived by Indebetouw et al. (2013) from carbon monoxide spectral line emission for 30 Doradus-10 shows a consistent mass range of clumps between 205 M⊙ and 5740 M⊙ as well as consistency between their single power law fit and our low mass power law index. Also comparing to core and clump mass functions from several star forming regions in the Milky Way we find consistency between most of their high mass indices and our low mass index, which is where the clump mass ranges overlap.

Comparative Initial and Sustained Engagement in Web-based Training by Behavioral Healthcare Providers in New York State.

PubMed

Talley, Rachel; Chiang, I-Chin; Covell, Nancy H; Dixon, Lisa

2018-06-01

Improved dissemination is critical to implementation of evidence-based practice in community behavioral healthcare settings. Web-based training modalities are a promising strategy for dissemination of evidence-based practice in community behavioral health settings. Initial and sustained engagement of these modalities in large, multidisciplinary community provider samples is not well understood. This study evaluates comparative engagement and user preferences by provider type in a web-based training platform in a large, multidisciplinary community sample of behavioral health staff in New York State. Workforce make-up among platform registrants was compared to the general NYS behavioral health workforce. Training completion by functional job type was compared to characterize user engagement and preferences. Frequently completed modules were classified by credit and requirement incentives. High initial training engagement across professional role was demonstrated, with significant differences in initial and sustained engagement by professional role. The most frequently completed modules across functional job types contained credit or requirement incentives. The analysis demonstrated that high engagement of a web-based training in a multidisciplinary provider audience can be achieved without tailoring content to specific professional roles. Overlap between frequently completed modules and incentives suggests a role for incentives in promoting engagement of web-based training. These findings further the understanding of strategies to promote large-scale dissemination of evidence-based practice in community behavioral health settings.

Ptychographic overlap constraint errors and the limits of their numerical recovery using conjugate gradient descent methods.

PubMed

Tripathi, Ashish; McNulty, Ian; Shpyrko, Oleg G

2014-01-27

Ptychographic coherent x-ray diffractive imaging is a form of scanning microscopy that does not require optics to image a sample. A series of scanned coherent diffraction patterns recorded from multiple overlapping illuminated regions on the sample are inverted numerically to retrieve its image. The technique recovers the phase lost by detecting the diffraction patterns by using experimentally known constraints, in this case the measured diffraction intensities and the assumed scan positions on the sample. The spatial resolution of the recovered image of the sample is limited by the angular extent over which the diffraction patterns are recorded and how well these constraints are known. Here, we explore how reconstruction quality degrades with uncertainties in the scan positions. We show experimentally that large errors in the assumed scan positions on the sample can be numerically determined and corrected using conjugate gradient descent methods. We also explore in simulations the limits, based on the signal to noise of the diffraction patterns and amount of overlap between adjacent scan positions, of just how large these errors can be and still be rendered tractable by this method.

How Long Do Satellites Need to Overlap? Evaluation of Climate Data Stability from Overlapping Satellite Records

NASA Technical Reports Server (NTRS)

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;

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

NASA Astrophysics Data System (ADS)

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 applicable to satellite Earth observations. Approaches for Earth observations offer additional challenges due to the complexity of the observations, but Earth observations may also benefit from ancillary observations taken from ground-based and in situ sources. Difficult choices need to be made when monitoring approaches are considered; we outline some attempts at optimizing networks based on economic principles. The careful evaluation of monitoring overlap is important to the appropriate application of observational resources and to the usefulness of current and future observations.

A Modified Gibson Assembly Method for Cloning Large DNA Fragments with High GC Contents.

PubMed

Li, Lei; Jiang, Weihong; Lu, Yinhua

2018-01-01

Gibson one-step, isothermal assembly method (Gibson assembly) can be used to efficiently assemble large DNA molecules by in vitro recombination involving a 5'-exonuclease, a DNA polymerase and a DNA ligase. In the past few years, this robust DNA assembly method has been widely applied to seamlessly construct genes, genetic pathways and even entire genomes. Here, we expand this method to clone large DNA fragments with high GC contents, such as antibiotic biosynthetic gene clusters from Streptomyces . Due to the low isothermal condition (50 °C) in the Gibson reaction system, the complementary overlaps with high GC contents are proposed to easily form mismatched linker pairings, which leads to low assembly efficiencies mainly due to vector self-ligation. So, we modified this classic method by the following two steps. First, a pair of universal terminal single-stranded DNA overhangs with high AT contents are added to the ends of the BAC vector. Second, two restriction enzyme sites are introduced into the respective sides of the designed overlaps to achieve the hierarchical assembly of large DNA molecules. The optimized Gibson assembly method facilitates fast acquisition of large DNA fragments with high GC contents from Streptomyces.

Evaluation of right ventricular remodeling using cardiac magnetic resonance imaging in co-existent chronic obstructive pulmonary disease and obstructive sleep apnea.

PubMed

Sharma, Bhavneesh; Neilan, Tomas G; Kwong, Raymond Y; Mandry, Damien; Owens, Robert L; McSharry, David; Bakker, Jessie P; Malhotra, Atul

2013-02-01

Untreated chronic obstructive pulmonary disease (COPD) co-existing with obstructive sleep apnea (OSA), also known as overlap syndrome, has higher cardiovascular mortality than COPD alone but its underlying mechanism remains unclear. We hypothesize that the presence of overlap syndrome is associated with more extensive right ventricular (RV) remodeling compared to patients with COPD alone. Adult COPD patients (GOLD stage 2 or higher) with at least 10 pack-years of smoking history were included. Overnight laboratory-based polysomnography was performed to test for OSA. Subjects with an apnea-hypopnea index (AHI) >10/h were classified as having overlap syndrome (n = 7), else classified as having COPD-only (n = 11). A cardiac MRI was performed to assess right and left cardiac chambers sizes, ventricular masses, and cine function. RV mass index (RVMI) was markedly higher in the overlap group than the COPD-only group (19 ± 6 versus 11 ± 6; p = 0.02). Overlap syndrome subjects had a reduced RV remodeling index (defined as the ratio between RVMI and RV end-diastolic volume index) compared to the COPD-only group (0.27 ± 0.06 versus 0.18 ± 0.08; p = 0.02). In the overlap syndrome subjects, the extent of RV remodeling was associated with severity of oxygen desaturation (R(2) = 0.65, p = 0.03). Our pilot results suggest that untreated overlap syndrome may cause more extensive RV remodeling than COPD alone.

Song matching, overlapping, and switching in the banded wren: the sender’s perspective

PubMed Central

Vehrencamp, Sandra L.; Hall, Michelle L.; Bohman, Erin R.; Depeine, Catherine D.; Dalziell, Anastasia H.

2008-01-01

Interpreting receiver responses to on-territory playback of aggressive signals is problematic. One solution is to combine such receiver-perspective experiments with a sender-perspective experiment that allows subjects to demonstrate how their choice of singing strategies is associated with their approach behavior. Here we report the results of a sender-perspective study on the banded wren (Thryothorus pleurostictus), and combine information on context and results of previous receiver-perspective experiments to clarify function. Territorial males were presented with a 5-min playback consisting of song types present in their repertoire. We assessed the degree to which the subjects’ song matching rate, overlapping rate, and song-type versatility were correlated with their approach latency, closeness of approach, latency to first retreat, and time spent close to the speaker. Male age, breeding stage, and features of the playback stimuli were also considered. Song matching was associated with rapid and close approach, consistent with the receiver-perspective interpretation of type matching as a conventional signal of aggressive motivation. Overlapping was associated with earlier retreat, and together with the aversive receiver response to our previous overlapping playback experiment suggests that overlapping is a defensive withdrawal signal. High versatility was associated with slower first retreat from the speaker and high levels of reciprocal matching between subject and playback. Males with fledglings sang with particularly low versatility and approached the speaker aggressively, whereas males with nestlings overlapped more and retreated quickly. Finally, older males matched more but overlapped less. PMID:18392112

Photonic reagents for concentration measurement of flu-orescent proteins with overlapping spectra

NASA Astrophysics Data System (ADS)

Goun, Alexei; Bondar, Denys I.; Er, Ali O.; Quine, Zachary; Rabitz, Herschel A.

2016-05-01

By exploiting photonic reagents (i.e., coherent control by shaped laser pulses), we employ Optimal Dynamic Discrimination (ODD) as a novel means for quantitatively characterizing mixtures of fluorescent proteins with a large spectral overlap. To illustrate ODD, we simultaneously measured concentrations of in vitro mixtures of Enhanced Blue Fluorescent Protein (EBFP) and Enhanced Cyan Fluorescent Protein (ECFP). Building on this foundational study, the ultimate goal is to exploit the capabilities of ODD for parallel monitoring of genetic and protein circuits by suppressing the spectral cross-talk among multiple fluorescent reporters.

Network localization of neurological symptoms from focal brain lesions

PubMed Central

Prasad, Sashank; Liu, Hesheng; Liu, Qi; Pascual-Leone, Alvaro; Caviness, Verne S.; Fox, Michael D.

2015-01-01

A traditional and widely used approach for linking neurological symptoms to specific brain regions involves identifying overlap in lesion location across patients with similar symptoms, termed lesion mapping. This approach is powerful and broadly applicable, but has limitations when symptoms do not localize to a single region or stem from dysfunction in regions connected to the lesion site rather than the site itself. A newer approach sensitive to such network effects involves functional neuroimaging of patients, but this requires specialized brain scans beyond routine clinical data, making it less versatile and difficult to apply when symptoms are rare or transient. In this article we show that the traditional approach to lesion mapping can be expanded to incorporate network effects into symptom localization without the need for specialized neuroimaging of patients. Our approach involves three steps: (i) transferring the three-dimensional volume of a brain lesion onto a reference brain; (ii) assessing the intrinsic functional connectivity of the lesion volume with the rest of the brain using normative connectome data; and (iii) overlapping lesion-associated networks to identify regions common to a clinical syndrome. We first tested our approach in peduncular hallucinosis, a syndrome of visual hallucinations following subcortical lesions long hypothesized to be due to network effects on extrastriate visual cortex. While the lesions themselves were heterogeneously distributed with little overlap in lesion location, 22 of 23 lesions were negatively correlated with extrastriate visual cortex. This network overlap was specific compared to other subcortical lesions (P < 10−5) and relative to other cortical regions (P < 0.01). Next, we tested for generalizability of our technique by applying it to three additional lesion syndromes: central post-stroke pain, auditory hallucinosis, and subcortical aphasia. In each syndrome, heterogeneous lesions that themselves had little overlap showed significant network overlap in cortical areas previously implicated in symptom expression (P < 10−4). These results suggest that (i) heterogeneous lesions producing similar symptoms share functional connectivity to specific brain regions involved in symptom expression; and (ii) publically available human connectome data can be used to incorporate these network effects into traditional lesion mapping approaches. Because the current technique requires no specialized imaging of patients it may prove a versatile and broadly applicable approach for localizing neurological symptoms in the setting of brain lesions. PMID:26264514

Atomistic Tight-Binding Theory Applied to Structural and Optical Properties of Silicon Nanodisks

NASA Astrophysics Data System (ADS)

Sukkabot, Worasak

2018-05-01

The use of ultrathin crystalline silicon (c-Si) wafers in solar cells necessitates a highly effective light absorber to compensate for poor light absorption. One route to overcoming this problem is to use a periodic array of Si nanodisks on ultrathin c-Si. In the present manuscript, we numerically investigate the effects of the geometrical parameters of the Si nanodisks, including disk diameter (D) and length (L), on the structural and optical properties, using atomistic tight-binding theory. These computations confirm that the electronic structure and optical properties are sensitive to the structural parameters. As the disk diameter and length increase, the single-electron energies decrease, and the single-hole energies increase. These calculations also reveal that, because of the quantum confinement effect, the optical band gaps gradually decrease independently of the increasing disk diameter and length. The optical spectra can be tuned across the visible region by varying the disk diameter and length, which is a useful feature for optimizing light absorption in solar cell applications. As the disk diameter and length increased, the optical intensities also increased; however, the atomistic electron-hole interactions and ground electron-hole wave function overlap progressively decreased. The ground electron-hole wave function overlap, Stokes shift, and fine structure splitting decreased as the disk diameter and length were increased. Thus, Si nanodisks with a large diameter and length might be a suitable candidate source of entangled photons. The Si nanodisks in this study also show promise for applications to solar cells based on ultrathin c-Si wafers.

Comparison of molecular dynamics and superfamily spaces of protein domain deformation.

PubMed

Velázquez-Muriel, Javier A; Rueda, Manuel; Cuesta, Isabel; Pascual-Montano, Alberto; Orozco, Modesto; Carazo, José-María

2009-02-17

It is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. In this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (MD-space), and ii) the study of the structural changes within superfamily (SF-space). Our analysis indicates that the MD-space and the SF-space display a significant overlap, but are still different enough to be considered as complementary. The SF-space space is wider but less complex than the MD-space, irrespective of the number of members in the superfamily. Also, the SF-space does not sample all possibilities offered by the MD-space, but often introduces very large changes along just a few deformation modes, whose number tend to a plateau as the number of related folds in the superfamily increases. Theoretically, we obtained two conclusions. First, that function restricts the access to some flexibility patterns to evolution, as we observe that when a superfamily member changes to become another, the path does not completely overlap with the physical deformability. Second, that conformational changes from variation in a superfamily are larger and much simpler than those allowed by physical deformability. Methodologically, the conclusion is that both spaces studied are complementary, and have different size and complexity. We expect this fact to have application in fields as 3D-EM/X-ray hybrid models or ab initio protein folding.

Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA.

PubMed

Kotaka, Masayo; Johnson, Christopher; Lamb, Heather K; Hawkins, Alastair R; Ren, Jingshan; Stammers, David K

2008-08-29

Amongst the most common protein motifs in eukaryotes are zinc fingers (ZFs), which, although largely known as DNA binding modules, also can have additional important regulatory roles in forming protein:protein interactions. AreA is a transcriptional activator central to nitrogen metabolism in Aspergillus nidulans. AreA contains a GATA-type ZF that has a competing dual recognition function, binding either DNA or the negative regulator NmrA. We report the crystal structures of three AreA ZF-NmrA complexes including two with bound NAD(+) or NADP(+). The molecular recognition of AreA ZF-NmrA involves binding of the ZF to NmrA via hydrophobic and hydrogen bonding interactions through helices alpha1, alpha6 and alpha11. Comparison with an earlier NMR solution structure of AreA ZF-DNA complex by overlap of the AreA ZFs shows that parts of helices alpha6 and alpha11 of NmrA are positioned close to the GATA motif of the DNA, mimicking the major groove of DNA. The extensive overlap of DNA with NmrA explains their mutually exclusive binding to the AreA ZF. The presence of bound NAD(+)/NADP(+) in the NmrA-AreaA ZF complex, however, causes minimal structural changes. Thus, any regulatory effects on AreA function mediated by the binding of oxidised nicotinamide dinucleotides to NmrA in the NmrA-AreA ZF complex appear not to be modulated via protein conformational rearrangements.

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

PubMed Central

Velázquez-Muriel, Javier A; Rueda, Manuel; Cuesta, Isabel; Pascual-Montano, Alberto; Orozco, Modesto; Carazo, José-María

2009-01-01

Background It is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. In this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (MD-space), and ii) the study of the structural changes within superfamily (SF-space). Results Our analysis indicates that the MD-space and the SF-space display a significant overlap, but are still different enough to be considered as complementary. The SF-space space is wider but less complex than the MD-space, irrespective of the number of members in the superfamily. Also, the SF-space does not sample all possibilities offered by the MD-space, but often introduces very large changes along just a few deformation modes, whose number tend to a plateau as the number of related folds in the superfamily increases. Conclusion Theoretically, we obtained two conclusions. First, that function restricts the access to some flexibility patterns to evolution, as we observe that when a superfamily member changes to become another, the path does not completely overlap with the physical deformability. Second, that conformational changes from variation in a superfamily are larger and much simpler than those allowed by physical deformability. Methodologically, the conclusion is that both spaces studied are complementary, and have different size and complexity. We expect this fact to have application in fields as 3D-EM/X-ray hybrid models or ab initio protein folding. PMID:19220918

Resilient protein co-expression network in male orbitofrontal cortex layer 2/3 during human aging.

PubMed

Pabba, Mohan; Scifo, Enzo; Kapadia, Fenika; Nikolova, Yuliya S; Ma, Tianzhou; Mechawar, Naguib; Tseng, George C; Sibille, Etienne

2017-10-01

The orbitofrontal cortex (OFC) is vulnerable to normal and pathologic aging. Currently, layer resolution large-scale proteomic studies describing "normal" age-related alterations at OFC are not available. Here, we performed a large-scale exploratory high-throughput mass spectrometry-based protein analysis on OFC layer 2/3 from 15 "young" (15-43 years) and 18 "old" (62-88 years) human male subjects. We detected 4193 proteins and identified 127 differentially expressed (DE) proteins (p-value ≤0.05; effect size >20%), including 65 up- and 62 downregulated proteins (e.g., GFAP, CALB1). Using a previously described categorization of biological aging based on somatic tissues, that is, peripheral "hallmarks of aging," and considering overlap in protein function, we show the highest representation of altered cell-cell communication (54%), deregulated nutrient sensing (39%), and loss of proteostasis (35%) in the set of OFC layer 2/3 DE proteins. DE proteins also showed a significant association with several neurologic disorders; for example, Alzheimer's disease and schizophrenia. Notably, despite age-related changes in individual protein levels, protein co-expression modules were remarkably conserved across age groups, suggesting robust functional homeostasis. Collectively, these results provide biological insight into aging and associated homeostatic mechanisms that maintain normal brain function with advancing age. Copyright © 2017 Elsevier Inc. All rights reserved.

Learning to reach by reinforcement learning using a receptive field based function approximation approach with continuous actions.

PubMed

Tamosiunaite, Minija; Asfour, Tamim; Wörgötter, Florentin

2009-03-01

Reinforcement learning methods can be used in robotics applications especially for specific target-oriented problems, for example the reward-based recalibration of goal directed actions. To this end still relatively large and continuous state-action spaces need to be efficiently handled. The goal of this paper is, thus, to develop a novel, rather simple method which uses reinforcement learning with function approximation in conjunction with different reward-strategies for solving such problems. For the testing of our method, we use a four degree-of-freedom reaching problem in 3D-space simulated by a two-joint robot arm system with two DOF each. Function approximation is based on 4D, overlapping kernels (receptive fields) and the state-action space contains about 10,000 of these. Different types of reward structures are being compared, for example, reward-on- touching-only against reward-on-approach. Furthermore, forbidden joint configurations are punished. A continuous action space is used. In spite of a rather large number of states and the continuous action space these reward/punishment strategies allow the system to find a good solution usually within about 20 trials. The efficiency of our method demonstrated in this test scenario suggests that it might be possible to use it on a real robot for problems where mixed rewards can be defined in situations where other types of learning might be difficult.

Wave Function Engineering in CdSe/PbS Core/Shell Quantum Dots.

PubMed

Wieliczka, Brian M; Kaledin, Alexey L; Buhro, William E; Loomis, Richard A

2018-05-25

The synthesis of epitaxial CdSe/PbS core/shell quantum dots (QDs) is reported. The PbS shell grows in a rock salt structure on the zinc blende CdSe core, thereby creating a crystal structure mismatch through additive growth. Absorption and photoluminescence (PL) band edge features shift to lower energies with increasing shell thickness, but remain above the CdSe bulk band gap. Nevertheless, the profiles of the absorption spectra vary with shell growth, indicating that the overlap of the electron and hole wave functions is changing significantly. This leads to over an order of magnitude reduction of absorption near the band gap and a large, tunable energy shift, of up to 550 meV, between the onset of strong absorption and the band edge PL. While the bulk valence and conduction bands adopt an inverse type-I alignment, the observed spectroscopic behavior is consistent with a transition between quasi-type-I and quasi-type-II behavior depending on shell thickness. Three effective mass approximation models support this hypothesis and suggest that the large difference in effective masses between the core and shell results in hole localization in the CdSe core and a delocalization of the electron across the entire QD. These results show the tuning of wave functions and transition energies in CdSe/PbS nanoheterostructures with prospects for use in optoelectronic devices for luminescent solar concentration or multiexciton generation.

Scaling of echolocation call parameters in bats.

PubMed

Jones, G

1999-12-01

I investigated the scaling of echolocation call parameters (frequency, duration and repetition rate) in bats in a functional context. Low-duty-cycle bats operate with search phase cycles of usually less than 20 %. They process echoes in the time domain and are therefore intolerant of pulse-echo overlap. High-duty-cycle (>30 %) species use Doppler shift compensation, and they separate pulse and echo in the frequency domain. Call frequency scales negatively with body mass in at least five bat families. Pulse duration scales positively with mass in low-duty-cycle quasi-constant-frequency (QCF) species because the large aerial-hawking species that emit these signals fly fast in open habitats. They therefore detect distant targets and experience pulse-echo overlap later than do smaller bats. Pulse duration also scales positively with mass in the Hipposideridae, which show at least partial Doppler shift compensation. Pulse repetition rate corresponds closely with wingbeat frequency in QCF bat species that fly relatively slowly. Larger, fast-flying species often skip pulses when detecting distant targets. There is probably a trade-off between call intensity and repetition rate because 'whispering' bats (and hipposiderids) produce several calls per predicted wingbeat and because batches of calls are emitted per wingbeat during terminal buzzes. Severe atmospheric attenuation at high frequencies limits the range of high-frequency calls. Low-duty-cycle bats that call at high frequencies must therefore use short pulses to avoid pulse-echo overlap. Rhinolophids escape this constraint by Doppler shift compensation and, importantly, can exploit advantages associated with the emission of both high-frequency and long-duration calls. Low frequencies are unsuited for the detection of small prey, and low repetition rates may limit prey detection rates. Echolocation parameters may therefore constrain maximum body size in aerial-hawking bats.

Sensitivity to biomechanical limitations during postural decision-making depends on the integrity of posterior superior parietal cortex.

PubMed

Wood, Daniel K; Chouinard, Philippe A; Major, Alex J; Goodale, Melvyn A

2017-12-01

Most object-directed limb movements can be carried out with a comfortable grasp posture. However, the orientation of an object relative to our bodies can sometimes lead us to select an uncomfortable or awkward grasp posture due to limitations imposed by the biomechanics of the arm. In a series of experiments, we identified a network of cortical areas that are engaged during the selection of movement strategies. Neurologically intact participants and two brain-damaged patients with overlapping lesions in the right posterior superior parietal lobule (pSPL) performed a grasp posture selection task in which biomechanical constraints were the primary consideration for selecting an action. The task induced states of bistable actions whereby the same stimulus gave rise to categorically different grasp postures. In a behavioral experiment, the two patients displayed a large range of manual bistability with the contralesional hand, resulting in a higher incidence of awkward grasping postures. In neurologically intact participants, a separate functional magnetic resonance imaging (fMRI) experiment revealed activation of a parieto-frontal network, which included the posterior intraparietal sulcus (pIPS) along the banks of the pSPL that was parametrically modulated by the degree of bistability in grasp posture selection. Superimposing this activation over the patients' structural MRIs revealed that the pIPS/pSPL activation in the neurologically intact participants overlapped with lesioned cortical tissue in both patients; all other areas of activation overlapped with intact cortical tissue in the patients. These results provide converging evidence that the posterior parietal cortex plays a critical role in selecting biomechanically appropriate postures during reach-to-grasp behaviors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effect of Temperature and Hydration Level on Purple Membrane Dynamics Studied Using Broadband Dielectric Spectroscopy from Sub-GHz to THz Regions.

PubMed

Yamamoto, Naoki; Ito, Shota; Nakanishi, Masahiro; Chatani, Eri; Inoue, Keiichi; Kandori, Hideki; Tominaga, Keisuke

2018-02-01

To investigate the effects of temperature and hydration on the dynamics of purple membrane (PM), we measured the broadband complex dielectric spectra from 0.5 GHz to 2.3 THz using a vector network analyzer and terahertz time-domain spectroscopy from 233 to 293 K. In the lower temperature region down to 83 K, the complex dielectric spectra in the THz region were also obtained. The complex dielectric spectra were analyzed through curve fitting using several model functions. We found that the hydrated states of one relaxational mode, which was assigned as the coupled motion of water molecules with the PM surface, began to overlap with the THz region at approximately 230 K. On the other hand, the relaxational mode was not observed for the dehydrated state. On the basis of this result, we conclude that the protein-dynamical-transition-like behavior in the THz region is due to the onset of the overlap of the relaxational mode with the THz region. Temperature hysteresis was observed in the dielectric spectrum at 263 K when the hydration level was high. It is suggested that the hydration water behaves similarly to supercooled liquid at that temperature. The third hydration layer may be partly formed to observe such a phenomenon. We also found that the relaxation time is slower than that of a globular protein, lysozyme, and the microscopic environment in the vicinity of the PM surface is suggested to be more heterogeneous than lysozyme. It is proposed that the spectral overlap of the relaxational mode and the low-frequency vibrational mode is necessary for the large conformational change of protein.

CHIMERA: Top-down model for hierarchical, overlapping and directed cluster structures in directed and weighted complex networks

NASA Astrophysics Data System (ADS)

Franke, R.

2016-11-01

In many networks discovered in biology, medicine, neuroscience and other disciplines special properties like a certain degree distribution and hierarchical cluster structure (also called communities) can be observed as general organizing principles. Detecting the cluster structure of an unknown network promises to identify functional subdivisions, hierarchy and interactions on a mesoscale. It is not trivial choosing an appropriate detection algorithm because there are multiple network, cluster and algorithmic properties to be considered. Edges can be weighted and/or directed, clusters overlap or build a hierarchy in several ways. Algorithms differ not only in runtime, memory requirements but also in allowed network and cluster properties. They are based on a specific definition of what a cluster is, too. On the one hand, a comprehensive network creation model is needed to build a large variety of benchmark networks with different reasonable structures to compare algorithms. On the other hand, if a cluster structure is already known, it is desirable to separate effects of this structure from other network properties. This can be done with null model networks that mimic an observed cluster structure to improve statistics on other network features. A third important application is the general study of properties in networks with different cluster structures, possibly evolving over time. Currently there are good benchmark and creation models available. But what is left is a precise sandbox model to build hierarchical, overlapping and directed clusters for undirected or directed, binary or weighted complex random networks on basis of a sophisticated blueprint. This gap shall be closed by the model CHIMERA (Cluster Hierarchy Interconnection Model for Evaluation, Research and Analysis) which will be introduced and described here for the first time.

MR-guided noninvasive thermal coagulation of in-vivo liver tissue using ultrasonic phased array

NASA Astrophysics Data System (ADS)

Daum, Douglas R.; Smith, Nadine; McDannold, Nathan; Hynynen, Kullervo H.

1999-05-01

Magnetic resonance (MR) imaging was used to guide and monitor the thermal tissue coagulation of in vivo porcine tissue using a 256 element ultrasonic phased array. The array could coagulate tissue volumes greater than 2 cm3 in liver and 0.5 cm3 in kidney using a single 20 second sonication. This sonication used multiple focus fields which were temporally cycled to heat large tissue volumes simultaneously. Estimates of the coagulated tissue using a thermal dose threshold compare well with T2-weighted images of post sonication lesions. The overlapping large focal volumes could aid in the treatment of large tumor volumes which require multiple overlapping sonications. The ability of MR to detect the presence and undesirable thermal increases at acoustic obstacle such as cartilaginous and bony ribs is demonstrated. This could have a significant impact on the ability to monitor thermal treatments of the liver and other organs which are acoustically blocked.

Iterative and function-continuation Fourier deconvolution methods for enhancing mass spectrometer resolution

NASA Technical Reports Server (NTRS)

Ioup, J. W.; Ioup, G. E.; Rayborn, G. H., Jr.; Wood, G. M., Jr.; Upchurch, B. T.

1984-01-01

Mass spectrometer data in the form of ion current versus mass-to-charge ratio often include overlapping mass peaks, especially in low- and medium-resolution instruments. Numerical deconvolution of such data effectively enhances the resolution by decreasing the overlap of mass peaks. In this paper two approaches to deconvolution are presented: a function-domain iterative technique and a Fourier transform method which uses transform-domain function-continuation. Both techniques include data smoothing to reduce the sensitivity of the deconvolution to noise. The efficacy of these methods is demonstrated through application to representative mass spectrometer data and the deconvolved results are discussed and compared to data obtained from a spectrometer with sufficient resolution to achieve separation of the mass peaks studied. A case for which the deconvolution is seriously affected by Gibbs oscillations is analyzed.

Foot Disorders, Foot Posture, and Foot Function: The Framingham Foot Study

PubMed Central

Hagedorn, Thomas J.; Dufour, Alyssa B.; Riskowski, Jody L.; Hillstrom, Howard J.; Menz, Hylton B.; Casey, Virginia A.; Hannan, Marian T.

2013-01-01

Introduction Foot disorders are common among older adults and may lead to outcomes such as falls and functional limitation. However, the associations of foot posture and foot function to specific foot disorders at the population level remain poorly understood. The purpose of this study was to assess the relation between specific foot disorders, foot posture, and foot function. Methods Participants were from the population-based Framingham Foot Study. Quintiles of the modified arch index and center of pressure excursion index from plantar pressure scans were used to create foot posture and function subgroups. Adjusted odds ratios of having each specific disorder were calculated for foot posture and function subgroups relative to a referent 3 quintiles. Results Pes planus foot posture was associated with increased odds of hammer toes and overlapping toes. Cavus foot posture was not associated with the foot disorders evaluated. Odds of having hallux valgus and overlapping toes were significantly increased in those with pronated foot function, while odds of hallux valgus and hallux rigidus were significantly decreased in those with supinated function. Conclusions Foot posture and foot function were associated with the presence of specific foot disorders. PMID:24040231

Association between structural and functional brain alterations in drug-free patients with schizophrenia: a multimodal meta-analysis

PubMed

Gao, Xin; Zhang, Wenjing; Yao, Li; Xiao, Yuan; Liu, Lu; Liu, Jieke; Li, Siyi; Tao, Bo; Shah, Chandan; Gong, Qiyong; Sweeney, John; Lui, Su

2017-12-05

Neuroimaging studies have shown both structural and functional abnormalities in patients with schizophrenia. Recently, studies have begun to explore the association between structural and functional grey matter abnormalities. By conducting a meta­-analysis on morphometric and functional imaging studies of grey matter alterations in drug-free patients, the present study aims to examine the degree of overlap between brain regions with anatomic and functional changes in patients with schizophrenia. We performed a systematic search of PubMed, Embase, Web of Science and the Cochrane Library to identify relevant publications. A multimodal analysis was then conducted using Seed-based d Mapping software. Exploratory analyses included jackknife, subgroup and meta-regression analyses. We included 15 structural MRI studies comprising 486 drug-free patients and 485 healthy controls, and 16 functional MRI studies comprising 403 drug-free patients and 428 controls in our meta-analysis. Drug-free patients were examined to reduce pharmacological effects on the imaging data. Multimodal analysis showed considerable overlap between anatomic and functional changes, mainly in frontotemporal regions, bilateral medial posterior cingulate/paracingulate gyrus, bilateral insula, basal ganglia and left cerebellum. There were also brain regions showing only anatomic changes in the right superior frontal gyrus, left supramarginal gyrus, right lingual gyrus and functional alternations involving the right angular ­gyrus. The methodological aspects, patient characteristics and clinical variables of the included studies were heterogeneous, and we cannot exclude medication effects. The present study showed overlapping anatomic and functional brain abnormalities mainly in the default mode (DMN) and auditory networks (AN) in drug-free patients with schizophrenia. However, the pattern of changes differed in these networks. Decreased grey matter was associated with decreased activation within the DMN, whereas it was associated with increased activation within the AN. These discrete patterns suggest different pathophysiological changes impacting structural and functional associations within different neural networks in patients with schizophrenia. 2017 Joule Inc., or its licensors

Association between structural and functional brain alterations in drug-free patients with schizophrenia: a multimodal meta-analysis.

PubMed

Gao, Xin; Zhang, Wenjing; Yao, Li; Xiao, Yuan; Liu, Lu; Liu, Jieke; Li, Siyi; Tao, Bo; Shah, Chandan; Gong, Qiyong; Sweeney, John A; Lui, Su

2018-03-01

Neuroimaging studies have shown both structural and functional abnormalities in patients with schizophrenia. Recently, studies have begun to explore the association between structural and functional grey matter abnormalities. By conducting a meta-analysis on morphometric and functional imaging studies of grey matter alterations in drug-free patients, the present study aims to examine the degree of overlap between brain regions with anatomic and functional changes in patients with schizophrenia. We performed a systematic search of PubMed, Embase, Web of Science and the Cochrane Library to identify relevant publications. A multimodal analysis was then conducted using Seed-based d Mapping software. Exploratory analyses included jackknife, subgroup and meta-regression analyses. We included 15 structural MRI studies comprising 486 drug-free patients and 485 healthy controls, and 16 functional MRI studies comprising 403 drug-free patients and 428 controls in our meta-analysis. Drug-free patients were examined to reduce pharmacological effects on the imaging data. Multimodal analysis showed considerable overlap between anatomic and functional changes, mainly in frontotemporal regions, bilateral medial posterior cingulate/paracingulate gyrus, bilateral insula, basal ganglia and left cerebellum. There were also brain regions showing only anatomic changes in the right superior frontal gyrus, left supramarginal gyrus, right lingual gyrus and functional alternations involving the right angular gyrus. The methodological aspects, patient characteristics and clinical variables of the included studies were heterogeneous, and we cannot exclude medication effects. The present study showed overlapping anatomic and functional brain abnormalities mainly in the default mode (DMN) and auditory networks (AN) in drug-free patients with schizophrenia. However, the pattern of changes differed in these networks. Decreased grey matter was associated with decreased activation within the DMN, whereas it was associated with increased activation within the AN. These discrete patterns suggest different pathophysiological changes impacting structural and functional associations within different neural networks in patients with schizophrenia.

Association between structural and functional brain alterations in drug-free patients with schizophrenia: a multimodal meta-analysis.

PubMed

Gao, Xin; Zhang, Wenjing; Yao, Li; Xiao, Yuan; Liu, Lu; Liu, Jieke; Li, Siyi; Tao, Bo; Shah, Chandan; Gong, Qiyong; Sweeney, John A; Lui, Su

2017-12-15

Neuroimaging studies have shown both structural and functional abnormalities in patients with schizophrenia. Recently, studies have begun to explore the association between structural and functional grey matter abnormalities. By conducting a meta-analysis on morphometric and functional imaging studies of grey matter alterations in drug-free patients, the present study aims to examine the degree of overlap between brain regions with anatomic and functional changes in patients with schizophrenia. We performed a systematic search of PubMed, Embase, Web of Science and the Cochrane Library to identify relevant publications. A multimodal analysis was then conducted using Seed-based d Mapping software. Exploratory analyses included jackknife, subgroup and meta-regression analyses. We included 15 structural MRI studies comprising 486 drug-free patients and 485 healthy controls, and 16 functional MRI studies comprising 403 drug-free patients and 428 controls in our meta-analysis. Drug-free patients were examined to reduce pharmacological effects on the imaging data. Multimodal analysis showed considerable overlap between anatomic and functional changes, mainly in frontotemporal regions, bilateral medial posterior cingulate/paracingulate gyrus, bilateral insula, basal ganglia and left cerebellum. There were also brain regions showing only anatomic changes in the right superior frontal gyrus, left supramarginal gyrus, right lingual gyrus and functional alternations involving the right angular gyrus. The methodological aspects, patient characteristics and clinical variables of the included studies were heterogeneous, and we cannot exclude medication effects. The present study showed overlapping anatomic and functional brain abnormalities mainly in the default mode (DMN) and auditory networks (AN) in drug-free patients with schizophrenia. However, the pattern of changes differed in these networks. Decreased grey matter was associated with decreased activation within the DMN, whereas it was associated with increased activation within the AN. These discrete patterns suggest different pathophysiological changes impacting structural and functional associations within different neural networks in patients with schizophrenia.

Reverse engineering development: Crosstalk opportunities between developmental biology and tissue engineering.

PubMed

Marcucio, Ralph S; Qin, Ling; Alsberg, Eben; Boerckel, Joel D

2017-11-01

The fields of developmental biology and tissue engineering have been revolutionized in recent years by technological advancements, expanded understanding, and biomaterials design, leading to the emerging paradigm of "developmental" or "biomimetic" tissue engineering. While developmental biology and tissue engineering have long overlapping histories, the fields have largely diverged in recent years at the same time that crosstalk opportunities for mutual benefit are more salient than ever. In this perspective article, we will use musculoskeletal development and tissue engineering as a platform on which to discuss these emerging crosstalk opportunities and will present our opinions on the bright future of these overlapping spheres of influence. The multicellular programs that control musculoskeletal development are rapidly becoming clarified, represented by shifting paradigms in our understanding of cellular function, identity, and lineage specification during development. Simultaneously, advancements in bioartificial matrices that replicate the biochemical, microstructural, and mechanical properties of developing tissues present new tools and approaches for recapitulating development in tissue engineering. Here, we introduce concepts and experimental approaches in musculoskeletal developmental biology and biomaterials design and discuss applications in tissue engineering as well as opportunities for tissue engineering approaches to inform our understanding of fundamental biology. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2356-2368, 2017. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Electrical properties, phase transitions and conduction mechanisms of the [(C2H5)NH3]2CdCl4 compound

NASA Astrophysics Data System (ADS)

Mohamed, C. Ben; Karoui, K.; Saidi, S.; Guidara, K.; Rhaiem, A. Ben

2014-10-01

The [(C2H5)NH3]2CdCl4 hybrid material was prepared and its calorimetric study and electric properties were investigated at low temperature. The X-ray powder diffractogram has shown that the compound is crystallized in the orthorhombic system with Abma space group, and the refined unit cell parameters are a=7.546 Å, b=7.443 Å, and c=21.831 Å. The calorimetric study has revealed two endothermic peaks at 216 K and 357 K, which are confirmed by the variation of fp and σdc as a function of temperature. The equivalent circuit based on the Z-View-software was proposed and the conduction mechanisms were determined. The obtained results have been discussed in terms of the correlated barrier hopping model (CBH) in phase I (low temperature (OLT)), non-overlapping small polaron tunneling model (NSPT) in phase II (room temperature (ORT)) and the overlapping large polaron tunneling model in phase III (high temperature (OHT)). The density of localized states NF(E) at the Fermi level and the binding energy Wm were calculated. The variation of the dielectric loss log(εʺ) with log(ω) was found to follow the empirical law, ε″=B ωm(T).

Role of Naphthenic Acids in Controlling Self-Aggregation of a Polyaromatic Compound in Toluene.

PubMed

Teklebrhan, Robel B; Jian, Cuiying; Choi, Phillip; Xu, Zhenghe; Sjöblom, Johan

2016-04-14

In this work, a series of molecular dynamics simulations were performed to investigate the effect of naphthenic acids (NAs) in early stage self-assembly of polyaromatic (PA) molecules in toluene. By exploiting NA molecules of the same polar functional group but different aliphatic/cycloaliphatic nonpolar tails, it was found that irrespective of the presence of the NA molecules in the system, the dominant mode of π-π stacking is a twisted, offset parallel stacking of a slightly larger overlapping area. Unlike large NA molecules, the presence of small NA molecules enhanced the number of π-π stacked PA molecules by suppressing the hydrogen bonding interactions among the PA molecules. Smaller NA molecules were found to have a higher tendency to associate with PA molecules than larger NA molecules. Moreover, the size and distribution of π-π stacking structures were affected to different degrees by changing the size and structural features of the NA molecules in the system. It was further revealed that the association between NA and PA molecules, mainly through hydrogen bonding, creates a favorable local environment for the overlap of PA cores (i.e., π-π stacking growth) by depressing the hydrogen bonding between PA molecules, which results in the removal of some toluene molecules from the vicinity of the PA molecules.

Automated lung tumor segmentation for whole body PET volume based on novel downhill region growing

NASA Astrophysics Data System (ADS)

Ballangan, Cherry; Wang, Xiuying; Eberl, Stefan; Fulham, Michael; Feng, Dagan

2010-03-01

We propose an automated lung tumor segmentation method for whole body PET images based on a novel downhill region growing (DRG) technique, which regards homogeneous tumor hotspots as 3D monotonically decreasing functions. The method has three major steps: thoracic slice extraction with K-means clustering of the slice features; hotspot segmentation with DRG; and decision tree analysis based hotspot classification. To overcome the common problem of leakage into adjacent hotspots in automated lung tumor segmentation, DRG employs the tumors' SUV monotonicity features. DRG also uses gradient magnitude of tumors' SUV to improve tumor boundary definition. We used 14 PET volumes from patients with primary NSCLC for validation. The thoracic region extraction step achieved good and consistent results for all patients despite marked differences in size and shape of the lungs and the presence of large tumors. The DRG technique was able to avoid the problem of leakage into adjacent hotspots and produced a volumetric overlap fraction of 0.61 +/- 0.13 which outperformed four other methods where the overlap fraction varied from 0.40 +/- 0.24 to 0.59 +/- 0.14. Of the 18 tumors in 14 NSCLC studies, 15 lesions were classified correctly, 2 were false negative and 15 were false positive.

Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers

NASA Astrophysics Data System (ADS)

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Cho, Kwang-Jin; Dolino, Drew M.; Chen, Wei; Li, Hongyang; Grant, Barry J.; Hancock, John F.; Gorfe, Alemayehu A.

2017-01-01

Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers. For validation we used mutagenesis, electron microscopy and biochemical assays under non-denaturing conditions. We show that partial disruption of a predicted interface through charge reversal mutation of apposed residues reduces oligomerization while introduction of cysteines at these positions enhanced dimerization likely through the formation of an intermolecular disulfide bond. Free energy calculations indicated that K-Ras dimerization involves direct but weak protein-protein interactions in solution, consistent with the notion that dimerization is facilitated by membrane binding. Taken together, our atomically detailed analyses provide unique mechanistic insights into K-Ras dimer formation and membrane organization as well as the conformational fluctuations and equilibrium thermodynamics underlying these processes.

Approaches to Measuring the Effects of Wake-Promoting Drugs: A Focus on Cognitive Function

PubMed Central

Edgar, Christopher J.; Pace-Schott, Edward F.; Wesnes, Keith A.

2009-01-01

Objectives In clinical drug development, wakefulness and wake-promotion maybe assessed by a large number of scales and questionnaires. Objective assessment of wakefulness is most commonly made using sleep latency/maintenance of wakefulness tests, polysomnography and/or behavioral measures. The purpose of the present review is to highlight the degree of overlap in the assessment of wakefulness and cognition, with consideration of assessment techniques and the underlying neurobiology of both concepts. Design Reviews of four key areas were conducted: commonly used techniques in the assessment of wakefulness; neurobiology of sleep/wake and cognition; targets of wake promoting and/or cognition enhancing drugs; and ongoing clinical trials investigating wake promoting effects. Results There is clear overlap between the assessment of wakefulness and cognition. There are common techniques which may be used to assess both concepts; aspects of the neurobiology of both concepts may be closely related; and wake promoting drugs may have nootropic properties (and vice-versa). Clinical trials of wake promoting drugs often, though not routinely, assess aspects of cognition. Conclusions Routine and broad assessment of cognition in the development of wake promoting drugs may reveal important nootropic effects, which are not secondary to alertness/wakefulness, whilst existing cognitive enhancers may have under explored or unknown wake promoting properties. PMID:19565524

Local–global overlap in diversity informs mechanisms of bacterial biogeography

PubMed Central

Livermore, Joshua A; Jones, Stuart E

2015-01-01

Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local–global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among ‘patches', global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity. PMID:25848869

Revised Criteria for Mild Cognitive Impairment May Compromise the Diagnosis of Alzheimer Disease Dementia

PubMed Central

Morris, John C.

2012-01-01

Objective To evaluate the potential impact of revised criteria for mild cognitive impairment (MCI), developed by a Workgroup sponsored by the National Institute on Aging and the Alzheimer’s Association, on the diagnosis of very mild and mild Alzheimer disease (AD) dementia. Design Retrospective review of ratings of functional impairment across diagnostic categories. Participants: The functional ratings of individuals (N = 17,535) with normal cognition, MCI, or AD dementia who were evaluated at Alzheimer’s Disease Centers and submitted to the National Alzheimer’s Coordinating Center were assessed in accordance with the definition of “functional independence” allowed by the revised criteria. Methods Pairwise demographic differences between the 3 diagnostic groups were tested using t-tests for continuous variables and chi-square for categorical variables. Results Almost all (99.8%) of individuals currently diagnosed with very mild AD dementia and the large majority (92.7%) of those diagnosed with mild AD dementia could be reclassified as MCI with the revised criteria, based on their level of impairment in the Clinical Dementia Rating domains for performance of instrumental activities of daily living in the community and at home. Large percentages of these AD dementia individuals also meet the revised “functional independence” criterion for MCI as measured by the Functional Assessment Questionnaire. Conclusions The categorical distinction between MCI and milder stages of Alzheimer dementia has been compromised by the revised criteria. The resulting diagnostic overlap supports the premise that “MCI due to AD” represents the earliest symptomatic stage of AD. PMID:22312163

Revised criteria for mild cognitive impairment may compromise the diagnosis of Alzheimer disease dementia.

PubMed

Morris, John C

2012-06-01

To evaluate the potential impact of revised criteria for mild cognitive impairment (MCI), developed by a work group sponsored by the National Institute on Aging and the Alzheimer's Association, on the diagnosis of very mild and mild Alzheimer disease (AD)dementia. Retrospective review of ratings of functional impairment across diagnostic categories. Alzheimer's Disease Centers and the National Alzheimer's Coordinating Center. Individuals (N=17 535) with normal cognition,MCI, or AD dementia. The functional ratings of individuals with normal cognition, MCI, or AD dementia who were evaluated at Alzheimer's Disease Centers and submitted to the National Alzheimer's Coordinating Center were assessed in accordance with the definition of "functional independence" allowed by the revised criteria. Pairwise demographic differences between the 3 diagnostic groups were tested using t tests for continuous variables and 2 for categorical variables. Almost all (99.8%) individuals currently diagnosed with very mild AD dementia and the large majority(92.7%) of those diagnosed with mild AD dementia could be reclassified as having MCI with the revised criteria,based on their level of impairment in the Clinical Dementia Rating domains for performance of instrumental activities of daily living in the community and at home.Large percentages of these individuals with AD dementia also meet the revised "functional independence" criterion for MCI as measured by the Functional Assessment Questionnaire. The categorical distinction between MCI and milder stages of AD dementia has been compromised by the revised criteria. The resulting diagnostic overlap supports the premise that "MCI due to AD" represents the earliest symptomatic stage of AD.

Cross section and transverse single-spin asymmetry of η mesons in p↑+p collisions at √s =200 GeV at forward rapidity

NASA Astrophysics Data System (ADS)

Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Al-Bataineh, H.; Alexander, J.; Alfred, M.; Angerami, A.; Aoki, K.; Apadula, N.; Aramaki, Y.; Asano, H.; Atomssa, E. T.; Averbeck, R.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Baksay, G.; Baksay, L.; Bandara, N. S.; Bannier, B.; Barish, K. N.; Bassalleck, B.; Basye, A. T.; Bathe, S.; Baublis, V.; Baumann, C.; Bazilevsky, A.; Beaumier, M.; Beckman, S.; Belikov, S.; Belmont, R.; Bennett, R.; Berdnikov, A.; Berdnikov, Y.; Bhom, J. H.; Black, D.; Blau, D. S.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Bryslawskyj, J.; Buesching, H.; Bumazhnov, V.; Bunce, G.; Butsyk, S.; Campbell, S.; Caringi, A.; Chen, C.-H.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Choudhury, R. K.; Christiansen, P.; Chujo, T.; Chung, P.; Chvala, O.; Cianciolo, V.; Citron, Z.; Cole, B. A.; Conesa Del Valle, Z.; Connors, M.; Csanád, M.; Csörgő, T.; Dahms, T.; Dairaku, S.; Danchev, I.; Das, K.; Datta, A.; Daugherity, M. S.; David, G.; Dayananda, M. K.; Deblasio, K.; Dehmelt, K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Dharmawardane, K. V.; Dietzsch, O.; Ding, L.; Dion, A.; Do, J. H.; Donadelli, M.; Drapier, O.; Drees, A.; Drees, K. A.; Durham, J. M.; Durum, A.; Dutta, D.; D'Orazio, L.; Edwards, S.; Efremenko, Y. V.; Ellinghaus, F.; Engelmore, T.; Enokizono, A.; En'yo, H.; Esumi, S.; Eyser, K. O.; Fadem, B.; Feege, N.; Fields, D. E.; Finger, M.; Finger, M.; Fleuret, F.; Fokin, S. L.; Fraenkel, Z.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fujiwara, K.; Fukao, Y.; Fusayasu, T.; Gal, C.; Gallus, P.; Garg, P.; Garishvili, I.; Ge, H.; Giordano, F.; Glenn, A.; Gong, H.; Gonin, M.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grim, G.; Grosse Perdekamp, M.; Gu, Y.; Gunji, T.; Guragain, H.; Gustafsson, H.-Å.; Hachiya, T.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamblen, J.; Han, R.; Han, S. Y.; Hanks, J.; Hasegawa, S.; Haslum, E.; Hayano, R.; He, X.; Heffner, M.; Hemmick, T. K.; Hester, T.; Hill, J. C.; Hohlmann, M.; Hollis, R. S.; Holzmann, W.; Homma, K.; Hong, B.; Horaguchi, T.; Hornback, D.; Hoshino, T.; Huang, S.; Ichihara, T.; Ichimiya, R.; Ikeda, Y.; Imai, K.; Imazu, Y.; Inaba, M.; Iordanova, A.; Isenhower, D.; Ishihara, M.; Issah, M.; Ivanischev, D.; Ivanishchev, D.; Iwanaga, Y.; Jacak, B. V.; Jeon, S. J.; Jezghani, M.; Jia, J.; Jiang, X.; Jin, J.; Johnson, B. M.; Jones, T.; Joo, E.; Joo, K. S.; Jouan, D.; Jumper, D. S.; Kajihara, F.; Kamin, J.; Kang, J. H.; Kang, J. S.; Kapustinsky, J.; Karatsu, K.; Kasai, M.; Kawall, D.; Kawashima, M.; Kazantsev, A. V.; Kempel, T.; Key, J. A.; Khachatryan, V.; Khanzadeev, A.; Kihara, K.; Kijima, K. M.; Kikuchi, J.; Kim, A.; Kim, B. I.; Kim, C.; Kim, D. H.; Kim, D. J.; Kim, E.-J.; Kim, H.-J.; Kim, M.; Kim, Y.-J.; Kim, Y. K.; Kinney, E.; Kiss, Á.; Kistenev, E.; Klatsky, J.; Kleinjan, D.; Kline, P.; Koblesky, T.; Kochenda, L.; Kofarago, M.; Komkov, B.; Konno, M.; Koster, J.; Kotov, D.; Král, A.; Kravitz, A.; Kunde, G. J.; Kurita, K.; Kurosawa, M.; Kwon, Y.; Kyle, G. S.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Lebedev, A.; Lee, D. M.; Lee, J.; Lee, K. B.; Lee, K. S.; Lee, S. H.; Leitch, M. J.; Leite, M. A. L.; Leitgab, M.; Li, X.; Lichtenwalner, P.; Liebing, P.; Lim, S. H.; Linden Levy, L. A.; Liška, T.; Liu, H.; Liu, M. X.; Love, B.; Lynch, D.; Maguire, C. F.; Makdisi, Y. I.; Makek, M.; Malik, M. D.; Manion, A.; Manko, V. I.; Mannel, E.; Mao, Y.; Masui, H.; Matathias, F.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Means, N.; Meles, A.; Mendoza, M.; Meredith, B.; Miake, Y.; Mibe, T.; Mignerey, A. C.; Miki, K.; Miller, A. J.; Milov, A.; Mishra, D. K.; Mitchell, J. T.; Miyasaka, S.; Mizuno, S.; Mohanty, A. K.; Montuenga, P.; Moon, H. J.; Moon, T.; Morino, Y.; Morreale, A.; Morrison, D. P.; Moukhanova, T. V.; Murakami, T.; Murata, J.; Mwai, A.; Nagamiya, S.; Nagle, J. L.; Naglis, M.; Nagy, M. I.; Nakagawa, I.; Nakagomi, H.; Nakamiya, Y.; Nakamura, K. R.; Nakamura, T.; Nakano, K.; Nam, S.; Nattrass, C.; Netrakanti, P. K.; Newby, J.; Nguyen, M.; Nihashi, M.; Niida, T.; Nouicer, R.; Novitzky, N.; Nyanin, A. S.; Oakley, C.; O'Brien, E.; Oda, S. X.; Ogilvie, C. A.; Oka, M.; Okada, K.; Onuki, Y.; Orjuela Koop, J. D.; Oskarsson, A.; Ouchida, M.; Ozaki, H.; Ozawa, K.; Pak, R.; Pantuev, V.; Papavassiliou, V.; Park, I. H.; Park, S.; Park, S. K.; Park, W. J.; Pate, S. F.; Patel, L.; Patel, M.; Pei, H.; Peng, J.-C.; Pereira, H.; Perepelitsa, D. V.; Perera, G. D. N.; Peressounko, D. Yu.; Perry, J.; Petti, R.; Pinkenburg, C.; Pinson, R.; Pisani, R. P.; Proissl, M.; Purschke, M. L.; Qu, H.; Rak, J.; Ravinovich, I.; Read, K. F.; Rembeczki, S.; Reygers, K.; Reynolds, D.; Riabov, V.; Riabov, Y.; Richardson, E.; Riveli, N.; Roach, D.; Roche, G.; Rolnick, S. D.; Rosati, M.; Rosen, C. A.; Rosendahl, S. S. E.; Rowan, Z.; Rubin, J. G.; Ružička, P.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Sakashita, K.; Sako, H.; Samsonov, V.; Sano, S.; Sarsour, M.; Sato, S.; Sato, T.; Sawada, S.; Schaefer, B.; Schmoll, B. K.; Sedgwick, K.; Seele, J.; Seidl, R.; Sen, A.; Seto, R.; Sett, P.; Sexton, A.; Sharma, D.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shimomura, M.; Shoji, K.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Silvestre, C.; Sim, K. S.; Singh, B. K.; Singh, C. P.; Singh, V.; Slunečka, M.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Stenlund, E.; Stepanov, M.; Stoll, S. P.; Sugitate, T.; Sukhanov, A.; Sumita, T.; Sun, J.; Sziklai, J.; Takagui, E. M.; Takahara, A.; Taketani, A.; Tanabe, R.; Tanaka, Y.; Taneja, S.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Themann, H.; Thomas, D.; Thomas, T. L.; Timilsina, A.; Todoroki, T.; Togawa, M.; Toia, A.; Tomášek, L.; Tomášek, M.; Torii, H.; Towell, M.; Towell, R.; Towell, R. S.; Tserruya, I.; Tsuchimoto, Y.; Vale, C.; Valle, H.; van Hecke, H. W.; Vargyas, M.; Vazquez-Zambrano, E.; Veicht, A.; Velkovska, J.; Vértesi, R.; Virius, M.; Vrba, V.; Vznuzdaev, E.; Wang, X. R.; Watanabe, D.; Watanabe, K.; Watanabe, Y.; Watanabe, Y. S.; Wei, F.; Wei, R.; Wessels, J.; Whitaker, S.; White, S. N.; Winter, D.; Wolin, S.; Woody, C. L.; Wright, R. M.; Wysocki, M.; Xia, B.; Xue, L.; Yalcin, S.; Yamaguchi, Y. L.; Yamaura, K.; Yang, R.; Yanovich, A.; Ying, J.; Yokkaichi, S.; Yoon, I.; You, Z.; Young, G. R.; Younus, I.; Yushmanov, I. E.; Zajc, W. A.; Zelenski, A.; Zhou, S.; Phenix Collaboration

2014-10-01

We present a measurement of the cross section and transverse single-spin asymmetry (AN) for η mesons at large pseudorapidity from √s =200 GeV p↑+p collisions. The measured cross section for 0.5

An Update on ToxCast™ | Science Inventory | US EPA

EPA Pesticide Factsheets

In its first phase, ToxCast™ is profiling over 300 well-characterized chemicals (primarily pesticides) in over 400 HTS endpoints. These endpoints include biochemical assays of protein function, cell-based transcriptional reporter assays, multi-cell interaction assays, transcriptomics on primary cell cultures, and developmental assays in zebrafish embryos. Almost all of the compounds being examined in Phase 1 of ToxCast™ have been tested in traditional toxicology tests, including developmental toxicity, multi-generation studies, and sub-chronic and chronic rodent bioassays Lessons learned to date for ToxCast: Large amounts of quality HTS data can be economically obtained. Large scale data sets will be required to understand potential for biological activity. Value in having multiple assays with overlapping coverage of biological pathways and a variety of methodologies Concentration-response will be important for ultimate interpretation Data transparency will be important for acceptance. Metabolic capabilities and coverage of developmental toxicity pathways will need additional attention. Need to define the gold standard Partnerships are needed to bring critical mass and expertise.

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

PubMed Central

Ramirez, Kelly S.; Leff, Jonathan W.; Barberán, Albert; Bates, Scott Thomas; Betley, Jason; Crowther, Thomas W.; Kelly, Eugene F.; Oldfield, Emily E.; Shaw, E. Ashley; Steenbock, Christopher; Bradford, Mark A.; Wall, Diana H.; Fierer, Noah

2014-01-01

Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of above-ground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity. Despite high variability across the Park, below-ground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographic patterns. Further, Central Park soils harboured nearly as many distinct soil microbial phylotypes and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents. PMID:25274366

Contrastive thermoelectric properties of strained SnSe crystals from the first-principles calculations

NASA Astrophysics Data System (ADS)

Tang, Yu; Cheng, Feng; Li, Decong; Deng, Shuping; Chen, Zhong; Sun, Luqi; Liu, Wenting; Shen, Lanxian; Deng, Shukang

2018-06-01

SnSe is a promising thermoelectric material with a record high dimensionless figure of merit ZT at high temperature ∼923 K. However, the ZT values for low-Temperature Pnma phase SnSe are just 0.1-0.9. Here, we use First-principle combine with Boltzmann transport theory methods to study the effect of tensile and compressible strain on the thermoelectric transport properties. The power factor of SnSe with -4% strain have a large boost along b and c directions of 7.7 and 3.9 μW cm-1 K-2, respectively, which are 2.5 and 2 times as large as those pristine SnSe. The charge density distributions reveal that the overlap of wave function has significant change due to the changed bond lengths and bond angles under different strain, which lead to the change of band gap and band dispersion. Our work provides a new effective strategy to enhance the thermoelectric properties of materials.

Carpentry and Masonry Career Ladders, AFSCs 552X0/552X1/55273.

DTIC Science & Technology

1985-01-01

he follows numerous safety practices in operating machines and Using tools and equipment. Some of the protective devices the wood craftsman uses may...performance. Overlap was found only in -he tool repair independent job type. AFR 39-1 Specialty Description. The AFR 39-1 Specialty Descriptions for...between Carpentry and Masonry Personnel, with the exception of Shop Personnel, and here overlap was found as a function of those tasks common to tool

Strong Genetic Overlap Between Executive Functions and Intelligence

PubMed Central

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

2016-01-01

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 7-15 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. PMID:27359131

The species-area relationship, self-similarity, and the true meaning of the z-value.

PubMed

Tjørve, Even; Tjørve, Kathleen M Calf

2008-12-01

The power model, S= cA(z) (where S is number of species, A is area, and c and z are fitted constants), is the model most commonly fitted to species-area data assessing species diversity. We use the self-similarity properties of this model to reveal patterns implicated by the z parameter. We present the basic arithmetic leading both to the fraction of new species added when two areas are combined and to species overlap between two areas of the same size, given a continuous sampling scheme. The fraction of new species resulting from expansion of an area can be expressed as alpha(z)-1, where alpha is the expansion factor. Consequently, z-values can be converted to a scale-invariant species overlap between two equally sized areas, since the proportion of species in common between the two areas is 2-2(z). Calculating overlap when adding areas of the same size reveals the intrinsic effect of distance assumed by the bisectional scheme. We use overlap area relationships from empirical data sets to illustrate how answers to the single large or several small reserves (SLOSS) question vary between data sets and with scale. We conclude that species overlap and the effect of distance between sample areas or isolates should be addressed when discussing species area relationships, and lack of fit to the power model can be caused by its assumption of a scale-invariant overlap relationship.

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.

PubMed

Aguilera-Mendoza, Longendri; Marrero-Ponce, Yovani; Tellez-Ibarra, Roberto; Llorente-Quesada, Monica T; Salgado, Jesús; Barigye, Stephen J; Liu, Jun

2015-08-01

The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Solving radiative transfer with line overlaps using Gauss-Seidel algorithms

NASA Astrophysics Data System (ADS)

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.

Ear nose throat manifestations in hypoidrotic ectodermal dysplasia.

PubMed

Callea, Michele; Teggi, Roberto; Yavuz, Izzet; Tadini, Gianluca; Priolo, Manuela; Crovella, Sergio; Clarich, Gabriella; Grasso, Domenico Leonardo

2013-11-01

The ectodermal dysplasias (EDs) are a large and complex group of inherited disorders. In various combinations, they all share anomalies in ectodermal derived structures: hair, teeth, nails and sweat gland function. Clinical overlap is present among EDs. Few causative genes have been identified, to date. Altered gene expression is not limited to the ectoderm but a concomitant effect on developing mesenchymal structures, with modification of ectodermal-mesenchymal signaling, takes place. The two major categories of ED include the hidrotic and hypohidrotic form, the latter more frequent; they differentiate each other for the presence or absence of sweat glands. We report Ear Nose Throat manifestations of ED, linked to the reduction of mucous glands in the nasal fossae with reduced ciliar function, and decrease salivary glands function. Often patients report an increased rate of infections of the upper respiratory tract and of the ear. Nasal obstruction due to the presence of nasal crusting, hearing loss and throat hoarseness are the most represented symptoms. Environmental measures, including a correct air temperature and humidification, is mandatory above all in subjects affected by hypohidrotic form. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Increased risk of exacerbation and hospitalization in subjects with an overlap phenotype: COPD-asthma.

PubMed

Menezes, Ana Maria B; Montes de Oca, Maria; Pérez-Padilla, Rogelio; Nadeau, Gilbert; Wehrmeister, Fernando César; Lopez-Varela, Maria Victorina; Muiño, Adriana; Jardim, José Roberto B; Valdivia, Gonzalo; Tálamo, Carlos

2014-02-01

Several COPD phenotypes have been described; the COPD-asthma overlap is one of the most recognized. The aim of this study was to evaluate the prevalence of three subgroups (asthma, COPD, and COPD-asthma overlap) in the Latin American Project for the Investigation of Obstructive Lung Disease (PLATINO) study population, to describe their main characteristics, and to determine the association of the COPD-asthma overlap group with exacerbations, hospitalizations, limitations due to physical health, and perception of general health status (GHS). The PLATINO study is a multicenter population-based survey carried out in five Latin American cities. Outcomes were self-reported exacerbations (defined by deterioration of breathing symptoms that affected usual daily activities or caused missed work), hospitalizations due to exacerbations, physical health limitations, and patients' perception of their GHS obtained by questionnaire. Subjects were classified in three specific groups: COPD--a postbronchodilator (post-BD) FEV₁/FVC ratio of < 0.70; asthma--presence of wheezing in the last year and a minimum post-BD increase in FEV₁ or FVC of 12% and 200 mL; and overlap COPD-asthma--the combination of the two. Out of 5,044 subjects, 767 were classified as having COPD (12%), asthma (1.7%), and COPD-asthma overlap (1.8%). Subjects with COPD-asthma overlap had more respiratory symptoms, had worse lung function, used more respiratory medication, had more hospitalization and exacerbations, and had worse GHS. After adjusting for confounders, the COPD-asthma overlap was associated with higher risks for exacerbations (prevalence ratio [PR], 2.11; 95% CI, 1.08-4.12), hospitalizations (PR, 4.11; 95% CI, 1.45-11.67), and worse GHS (PR, 1.47; 95% CI, 1.18-1.85) compared with those with COPD. The coexisting COPD-asthma phenotype is possibly associated with increased disease severity.

The functional unit of Japanese word naming: evidence from masked priming.

PubMed

Verdonschot, Rinus G; Kiyama, Sachiko; Tamaoka, Katsuo; Kinoshita, Sachiko; Heij, Wido La; Schiller, Niels O

2011-11-01

Theories of language production generally describe the segment as the basic unit in phonological encoding (e.g., Dell, 1988; Levelt, Roelofs, & Meyer, 1999). However, there is also evidence that such a unit might be language specific. Chen, Chen, and Dell (2002), for instance, found no effect of single segments when using a preparation paradigm. To shed more light on the functional unit of phonological encoding in Japanese, a language often described as being mora based, we report the results of 4 experiments using word reading tasks and masked priming. Experiment 1 demonstrated using Japanese kana script that primes, which overlapped in the whole mora with target words, sped up word reading latencies but not when just the onset overlapped. Experiments 2 and 3 investigated a possible role of script by using combinations of romaji (Romanized Japanese) and hiragana; again, facilitation effects were found only when the whole mora and not the onset segment overlapped. Experiment 4 distinguished mora priming from syllable priming and revealed that the mora priming effects obtained in the first 3 experiments are also obtained when a mora is part of a syllable. Again, no priming effect was found for single segments. Our findings suggest that the mora and not the segment (phoneme) is the basic functional phonological unit in Japanese language production planning.

Variable δ(15)N diet-tissue discrimination factors among sharks: implications for trophic position, diet and food web models.

PubMed

Olin, Jill A; Hussey, Nigel E; Grgicak-Mannion, Alice; Fritts, Mark W; Wintner, Sabine P; Fisk, Aaron T

2013-01-01

The application of stable isotopes to characterize the complexities of a species foraging behavior and trophic relationships is dependent on assumptions of δ(15)N diet-tissue discrimination factors (∆(15)N). As ∆(15)N values have been experimentally shown to vary amongst consumers, tissues and diet composition, resolving appropriate species-specific ∆(15)N values can be complex. Given the logistical and ethical challenges of controlled feeding experiments for determining ∆(15)N values for large and/or endangered species, our objective was to conduct an assessment of a range of reported ∆(15)N values that can hypothetically serve as surrogates for describing the predator-prey relationships of four shark species that feed on prey from different trophic levels (i.e., different mean δ(15)N dietary values). Overall, the most suitable species-specific ∆(15)N values decreased with increasing dietary-δ(15)N values based on stable isotope Bayesian ellipse overlap estimates of shark and the principal prey functional groups contributing to the diet determined from stomach content analyses. Thus, a single ∆(15)N value was not supported for this speciose group of marine predatory fishes. For example, the ∆(15)N value of 3.7‰ provided the highest percent overlap between prey and predator isotope ellipses for the bonnethead shark (mean diet δ(15)N = 9‰) whereas a ∆(15)N value < 2.3‰ provided the highest percent overlap between prey and predator isotope ellipses for the white shark (mean diet δ(15)N = 15‰). These data corroborate the previously reported inverse ∆(15)N-dietary δ(15)N relationship when both isotope ellipses of principal prey functional groups and the broader identified diet of each species were considered supporting the adoption of different ∆(15)N values that reflect the predators' δ(15)N-dietary value. These findings are critical for refining the application of stable isotope modeling approaches as inferences regarding a species' ecological role in their community will be influenced with consequences for conservation and management actions.

Variable δ15N Diet-Tissue Discrimination Factors among Sharks: Implications for Trophic Position, Diet and Food Web Models

PubMed Central

Olin, Jill A.; Hussey, Nigel E.; Grgicak-Mannion, Alice; Fritts, Mark W.; Wintner, Sabine P.; Fisk, Aaron T.

2013-01-01

The application of stable isotopes to characterize the complexities of a species foraging behavior and trophic relationships is dependent on assumptions of δ15N diet-tissue discrimination factors (∆15N). As ∆15N values have been experimentally shown to vary amongst consumers, tissues and diet composition, resolving appropriate species-specific ∆15N values can be complex. Given the logistical and ethical challenges of controlled feeding experiments for determining ∆15N values for large and/or endangered species, our objective was to conduct an assessment of a range of reported ∆15N values that can hypothetically serve as surrogates for describing the predator-prey relationships of four shark species that feed on prey from different trophic levels (i.e., different mean δ15N dietary values). Overall, the most suitable species-specific ∆15N values decreased with increasing dietary-δ15N values based on stable isotope Bayesian ellipse overlap estimates of shark and the principal prey functional groups contributing to the diet determined from stomach content analyses. Thus, a single ∆15N value was not supported for this speciose group of marine predatory fishes. For example, the ∆15N value of 3.7‰ provided the highest percent overlap between prey and predator isotope ellipses for the bonnethead shark (mean diet δ15N = 9‰) whereas a ∆15N value < 2.3‰ provided the highest percent overlap between prey and predator isotope ellipses for the white shark (mean diet δ15N = 15‰). These data corroborate the previously reported inverse ∆15N-dietary δ15N relationship when both isotope ellipses of principal prey functional groups and the broader identified diet of each species were considered supporting the adoption of different ∆15N values that reflect the predators’ δ15N-dietary value. These findings are critical for refining the application of stable isotope modeling approaches as inferences regarding a species’ ecological role in their community will be influenced with consequences for conservation and management actions. PMID:24147026

Auditing Complex Concepts in Overlapping Subsets of SNOMED

PubMed Central

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

Auditing complex concepts in overlapping subsets of SNOMED.

PubMed

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

2008-11-06

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.

Measuring droplet size distributions from overlapping interferometric particle images.

PubMed

Bocanegra Evans, Humberto; Dam, Nico; van der Voort, Dennis; Bertens, Guus; van de Water, Willem

2015-02-01

Interferometric particle imaging provides a simple way to measure the probability density function (PDF) of droplet sizes from out-focus images. The optical setup is straightforward, but the interpretation of the data is a problem when particle images overlap. We propose a new way to analyze the images. The emphasis is not on a precise identification of droplets, but on obtaining a good estimate of the PDF of droplet sizes in the case of overlapping particle images. The algorithm is tested using synthetic and experimental data. We next use these methods to measure the PDF of droplet sizes produced by spinning disk aerosol generators. The mean primary droplet diameter agrees with predictions from the literature, but we find a broad distribution of satellite droplet sizes.

MOLECULAR DYNAMICS OF CASCADES OVERLAP IN TUNGSTEN WITH 20-KEV PRIMARY KNOCK-ON ATOMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.

2015-04-16

Molecular dynamics simulations are performed to investigate the mutual influence of two subsequent cascades in tungsten. The influence is studied using 20-keV primary knock-on atoms, to induce one cascade after another separated by 15 ps, in a lattice temperature of 1025 K (i.e. 0.25 of the melting temperature of the interatomic potential). The center of mass of the vacancies at the peak damage during the cascade is taken as the location of the cascade. The distance between this location to that of the next cascade is taken as the overlap parameter. Empirical fits describing the number of surviving vacancies andmore » interstitial atoms as a function of overlap are presented.« less

High-Level Location Based Search Services That Improve Discoverability of Geophysical Data in the Virtual ITM Observatory

NASA Astrophysics Data System (ADS)

Schaefer, R. K.; Morrison, D.; Potter, M.; Barnes, R. J.; Nylund, S. R.; Patrone, D.; Aiello, J.; Talaat, E. R.; Sarris, T.

2015-12-01

The great promise of Virtual Observatories is the ability to perform complex search operations across the metadata of a large variety of different data sets. This allows the researcher to isolate and select the relevant measurements for their topic of study. The Virtual ITM Observatory (VITMO) has many diverse geophysical datasets that cover a large temporal and spatial range that present a unique search problem. VITMO provides many methods by which the user can search for and select data of interest including restricting selections based on geophysical conditions (solar wind speed, Kp, etc) as well as finding those datasets that overlap in time. One of the key challenges in improving discoverability is the ability to identify portions of datasets that overlap in time and in location. The difficulty is that location data is not contained in the metadata for datasets produced by satellites and would be extremely large in volume if it were available, making searching for overlapping data very time consuming. To solve this problem we have developed a series of light-weight web services that can provide a new data search capability for VITMO and others. The services consist of a database of spacecraft ephemerides and instrument fields of view; an overlap calculator to find times when the fields of view of different instruments intersect; and a magnetic field line tracing service that maps in situ and ground based measurements to the equatorial plane in magnetic coordinates for a number of field models and geophysical conditions. These services run in real-time when the user queries for data. These services will allow the non-specialist user to select data that they were previously unable to locate, opening up analysis opportunities beyond the instrument teams and specialists, making it easier for future students who come into the field.

Large-scale dark diversity estimates: new perspectives with combined methods.

PubMed

Ronk, Argo; de Bello, Francesco; Fibich, Pavel; Pärtel, Meelis

2016-09-01

Large-scale biodiversity studies can be more informative if observed diversity in a study site is accompanied by dark diversity, the set of absent although ecologically suitable species. Dark diversity methodology is still being developed and a comparison of different approaches is needed. We used plant data at two different scales (European and seven large regions) and compared dark diversity estimates from two mathematical methods: species co-occurrence (SCO) and species distribution modeling (SDM). We used plant distribution data from the Atlas Florae Europaeae (50 × 50 km grid cells) and seven different European regions (10 × 10 km grid cells). Dark diversity was estimated by SCO and SDM for both datasets. We examined the relationship between the dark diversity sizes (type II regression) and the overlap in species composition (overlap coefficient). We tested the overlap probability according to the hypergeometric distribution. We combined the estimates of the two methods to determine consensus dark diversity and composite dark diversity. We tested whether dark diversity and completeness of site diversity (log ratio of observed and dark diversity) are related to various natural and anthropogenic factors differently than simple observed diversity. Both methods provided similar dark diversity sizes and distribution patterns; dark diversity is greater in southern Europe. The regression line, however, deviated from a 1:1 relationship. The species composition overlap of two methods was about 75%, which is much greater than expected by chance. Both consensus and composite dark diversity estimates showed similar distribution patterns. Both dark diversity and completeness measures exhibit relationships to natural and anthropogenic factors different than those exhibited by observed richness. In summary, dark diversity revealed new biodiversity patterns which were not evident when only observed diversity was examined. A new perspective in dark diversity studies can incorporate a combination of methods.

Securely Measuring the Overlap between Private Datasets with Cryptosets

PubMed Central

Swamidass, S. Joshua; Matlock, Matthew; Rozenblit, Leon

2015-01-01

Many scientific questions are best approached by sharing data—collected by different groups or across large collaborative networks—into a combined analysis. Unfortunately, some of the most interesting and powerful datasets—like health records, genetic data, and drug discovery data—cannot be freely shared because they contain sensitive information. In many situations, knowing if private datasets overlap determines if it is worthwhile to navigate the institutional, ethical, and legal barriers that govern access to sensitive, private data. We report the first method of publicly measuring the overlap between private datasets that is secure under a malicious model without relying on private protocols or message passing. This method uses a publicly shareable summary of a dataset’s contents, its cryptoset, to estimate its overlap with other datasets. Cryptosets approach “information-theoretic” security, the strongest type of security possible in cryptography, which is not even crackable with infinite computing power. We empirically and theoretically assess both the accuracy of these estimates and the security of the approach, demonstrating that cryptosets are informative, with a stable accuracy, and secure. PMID:25714898

Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation

PubMed Central

Kozhuharova, Ana; Sharma, Harshita; Ohyama, Takako; Fasolo, Francesca; Yamazaki, Toshio; Cotella, Diego; Santoro, Claudio; Zucchelli, Silvia; Gustincich, Stefano; Carninci, Piero

2018-01-01

SINEUPs are antisense long noncoding RNAs, in which an embedded SINE B2 element UP-regulates translation of partially overlapping target sense mRNAs. SINEUPs contain two functional domains. First, the binding domain (BD) is located in the region antisense to the target, providing specific targeting to the overlapping mRNA. Second, the inverted SINE B2 represents the effector domain (ED) and enhances translation. To adapt SINEUP technology to a broader number of targets, we took advantage of a high-throughput, semi-automated imaging system to optimize synthetic SINEUP BD and ED design in HEK293T cell lines. Using SINEUP-GFP as a model SINEUP, we extensively screened variants of the BD to map features needed for optimal design. We found that most active SINEUPs overlap an AUG-Kozak sequence. Moreover, we report our screening of the inverted SINE B2 sequence to identify active sub-domains and map the length of the minimal active ED. Our synthetic SINEUP-GFP screening of both BDs and EDs constitutes a broad test with flexible applications to any target gene of interest. PMID:29414979

Visual attention shift to printed words during spoken word recognition in Chinese: The role of phonological information.

PubMed

Shen, Wei; Qu, Qingqing; Tong, Xiuhong

2018-05-01

The aim of this study was to investigate the extent to which phonological information mediates the visual attention shift to printed Chinese words in spoken word recognition by using an eye-movement technique with a printed-word paradigm. In this paradigm, participants are visually presented with four printed words on a computer screen, which include a target word, a phonological competitor, and two distractors. Participants are then required to select the target word using a computer mouse, and the eye movements are recorded. In Experiment 1, phonological information was manipulated at the full-phonological overlap; in Experiment 2, phonological information at the partial-phonological overlap was manipulated; and in Experiment 3, the phonological competitors were manipulated to share either fulloverlap or partial-overlap with targets directly. Results of the three experiments showed that the phonological competitor effects were observed at both the full-phonological overlap and partial-phonological overlap conditions. That is, phonological competitors attracted more fixations than distractors, which suggested that phonological information mediates the visual attention shift during spoken word recognition. More importantly, we found that the mediating role of phonological information varies as a function of the phonological similarity between target words and phonological competitors.

Chemometric Data Analysis for Deconvolution of Overlapped Ion Mobility Profiles

NASA Astrophysics Data System (ADS)

Zekavat, Behrooz; Solouki, Touradj

2012-11-01

We present the details of a data analysis approach for deconvolution of the ion mobility (IM) overlapped or unresolved species. This approach takes advantage of the ion fragmentation variations as a function of the IM arrival time. The data analysis involves the use of an in-house developed data preprocessing platform for the conversion of the original post-IM/collision-induced dissociation mass spectrometry (post-IM/CID MS) data to a Matlab compatible format for chemometric analysis. We show that principle component analysis (PCA) can be used to examine the post-IM/CID MS profiles for the presence of mobility-overlapped species. Subsequently, using an interactive self-modeling mixture analysis technique, we show how to calculate the total IM spectrum (TIMS) and CID mass spectrum for each component of the IM overlapped mixtures. Moreover, we show that PCA and IM deconvolution techniques provide complementary results to evaluate the validity of the calculated TIMS profiles. We use two binary mixtures with overlapping IM profiles, including (1) a mixture of two non-isobaric peptides (neurotensin (RRPYIL) and a hexapeptide (WHWLQL)), and (2) an isobaric sugar isomer mixture of raffinose and maltotriose, to demonstrate the applicability of the IM deconvolution.

Trophic overlap between expanding and contracting fish predators in a range margin undergoing change.

PubMed

Westerbom, Mats; Lappalainen, Antti; Mustonen, Olli; Norkko, Alf

2018-05-21

Climate change is predicted to cause a freshening of the Baltic Sea, facilitating range expansions of freshwater species and contractions of marine. Resident marine flounders (Platichthys flesus) and expansive freshwater roach (Rutilus rutilus) are dominant consumers in the Baltic Sea sublittoral where they occur in partial sympatry. By comparing patterns of resource use by flounders and roach along a declining resource gradient of blue mussels (Mytilus trossulus) our aim was to explore predator functional responses and the degree of trophic overlap. Understanding the nature of density-dependent prey acquisition has important implications for predicting population dynamics of both predators and their shared prey. Results showed a highly specialized diet for both species, high reliance on blue mussels throughout the range, similar prey size preference and high trophic overlap. Highest overlap occurred where blue mussels were abundant but overlap was also high where they were scarce. Our results highlight the importance of a single food item - the blue mussel - for both species, likely promoting high population size and range expansion of roach. Findings also suggest that range expansion of roach may have a top-down structuring force on mussels that differ in severity and location from that originating from resident flounders.

Networks and landscapes: a framework for setting goals and evaluating performance at the large landscape scale

Treesearch

R Patrick Bixler; Shawn Johnson; Kirk Emerson; Tina Nabatchi; Melly Reuling; Charles Curtin; Michele Romolini; Morgan Grove

2016-01-01

The objective of large landscape conser vation is to mitigate complex ecological problems through interventions at multiple and overlapping scales. Implementation requires coordination among a diverse network of individuals and organizations to integrate local-scale conservation activities with broad-scale goals. This requires an understanding of the governance options...

Patterns and controls on historical channel change in the Willamette River, Oregon, USA

Treesearch

Jennifer Rose Wallick; Gordon E. Grant; Stephen T. Lancaster; John P. Bolte; Roger P. Denlinger

2007-01-01

Distinguishing human impacts on channel morphology from the natural behaviour of fluvial systems is problematic for large river basins. Large river basins, by virtue of their size, typically encompass wide ranges of geology and landforms resulting in diverse controls on channel form. They also inevitably incorporate long and complex histories of overlapping human and...

USING CLASSIFICATION CONSISTENCY IN INTER-SCENE OVERLAP AREAS TO MODEL SPATIAL VARIATIONS IN LAND-COVER ACCURACY OVER LARGE GEOGRAPHIC REGIONS

EPA Science Inventory

During the last decade, a number of initiatives have been undertaken to create systematic national and global data sets of processed satellite imagery. An important application of these data is the derivation of large area (i.e. multi-scene) land cover products. Such products, ho...

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

PubMed

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 culturally distinct populations, suggests that they relate to the underlying architecture of the saccade system.

Post-deployment Multi-symptom Disorder rehabilitation: An integrated approach to rehabilitation.

PubMed

Bosco, Michelle A; Murphy, Jennifer; Peters, Walter E; Clark, Michael E

2015-01-01

Veterans and active duty service members returning from Operation New Dawn and those having returned from Operations Iraqi and Enduring Freedom frequently report the presence of overlapping, co-morbid symptom clusters consisting of chronic pain, mild cognitive complaints, and posttraumatic stress symptoms/disorder or mood disturbance. This presentation has been called Post-deployment Multi-symptom Disorder (PMD) and its implications not only impact various functional domains, but have also influenced a system/continuum of care to rise to meet the challenges of treating PMD. This continuum is based on innovation informed by evidence-based therapies, systemic limitations, and a focus on functional improvement rather than diagnostic classification. The purpose of this paper is to describe the symptomatic, functional and systemic challenges inherent to PMD conceptualization and treatment. The constituent clusters of PMD are defined and exemplified, its functional impact is illustrated, and a continuum of care at a large southeastern Veterans Affairs (VA) hospital offering an interdisciplinary approach to integrated rehabilitation is described. Three case examples are provided that that underscore the importance of vocation for improved behavioral health and quality of life. The case examples demonstrate how vocational rehabilitation services are an integral component of PMD treatment.}

Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis.

PubMed

Alabadí, David; Yanovsky, Marcelo J; Más, Paloma; Harmer, Stacey L; Kay, Steve A

2002-04-30

Circadian clocks are autoregulatory, endogenous mechanisms that allow organisms, from bacteria to humans, to advantageously time a wide range of activities within 24-hr environmental cycles. CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) are thought to be important components of the circadian clock in the model plant Arabidopsis. The similar circadian phenotypes of lines overexpressing either CCA1 or LHY have suggested that the functions of these two transcription factors are largely overlapping. cca1-1 plants, which lack CCA1 protein, show a short-period phenotype for the expression of several genes when assayed under constant light conditions. This suggests that LHY function is able to only partially compensate for the lack of CCA1 protein, resulting in a clock with a faster pace in cca1-1 plants. We have obtained plants lacking CCA1 and with LHY function strongly reduced, cca1-1 lhy-R, and show that these plants are unable to maintain sustained oscillations in both constant light and constant darkness. However, these plants exhibit some circadian function in light/dark cycles, showing that the Arabidopsis circadian clock is not entirely dependent on CCA1 and LHY activities.

Role of Bassoon and Piccolo in Assembly and Molecular Organization of the Active Zone

PubMed Central

Gundelfinger, Eckart D.; Reissner, Carsten; Garner, Craig C.

2016-01-01

Bassoon and Piccolo are two very large scaffolding proteins of the cytomatrix assembled at the active zone (CAZ) where neurotransmitter is released. They share regions of high sequence similarity distributed along their entire length and seem to share both overlapping and distinct functions in organizing the CAZ. Here, we survey our present knowledge on protein-protein interactions and recent progress in understanding of molecular functions of these two giant proteins. These include roles in the assembly of active zones (AZ), the localization of voltage-gated Ca2+ channels (VGCCs) in the vicinity of release sites, synaptic vesicle (SV) priming and in the case of Piccolo, a role in the dynamic assembly of the actin cytoskeleton. Piccolo and Bassoon are also important for the maintenance of presynaptic structure and function, as well as for the assembly of CAZ specializations such as synaptic ribbons. Recent findings suggest that they are also involved in the regulation activity-dependent communication between presynaptic boutons and the neuronal nucleus. Together these observations suggest that Bassoon and Piccolo use their modular structure to organize super-molecular complexes essential for various aspects of presynaptic function. PMID:26793095

Function and regulation of AUTS2, a gene implicated in autism and human evolution.

PubMed

Oksenberg, Nir; Stevison, Laurie; Wall, Jeffrey D; Ahituv, Nadav

2013-01-01

Nucleotide changes in the AUTS2 locus, some of which affect only noncoding regions, are associated with autism and other neurological disorders, including attention deficit hyperactivity disorder, epilepsy, dyslexia, motor delay, language delay, visual impairment, microcephaly, and alcohol consumption. In addition, AUTS2 contains the most significantly accelerated genomic region differentiating humans from Neanderthals, which is primarily composed of noncoding variants. However, the function and regulation of this gene remain largely unknown. To characterize auts2 function, we knocked it down in zebrafish, leading to a smaller head size, neuronal reduction, and decreased mobility. To characterize AUTS2 regulatory elements, we tested sequences for enhancer activity in zebrafish and mice. We identified 23 functional zebrafish enhancers, 10 of which were active in the brain. Our mouse enhancer assays characterized three mouse brain enhancers that overlap an ASD-associated deletion and four mouse enhancers that reside in regions implicated in human evolution, two of which are active in the brain. Combined, our results show that AUTS2 is important for neurodevelopment and expose candidate enhancer sequences in which nucleotide variation could lead to neurological disease and human-specific traits.

Theoretical insights into the origin of magnetic exchange and magnetic anisotropy in {Re(IV)-M(II)} (M = Mn, Fe, Co, Ni and Cu) single chain magnets.

PubMed

Singh, Saurabh Kumar; Vignesh, Kuduva R; Archana, Velloth; Rajaraman, Gopalan

2016-05-10

Density functional calculations have been performed on a series of {Re(IV)-M(II)} (M = Mn(), Fe(), Co(), Ni(), Cu()) complexes to compute the magnetic exchange interaction between the Re(IV) and M(II) ions, and understand the mechanism of magnetic coupling in this series. DFT calculations yield J values of -5.54 cm(-1), +0.44 cm(-1), +10.5 cm(-1), +4.54 cm(-1) and +19 cm(-1) for complexes respectively, and these estimates are in general agreement with the experimental reports. Using molecular orbital (MO) and overlap integral analysis, we have established a mechanism of coupling for a {3d-5d} pair and the proposed mechanism rationalises both the sign and the magnitude of J values observed in this series. Our proposed mechanism of coupling has five contributing factors: (i) (Re)dyz-dyz(3d) overlap, (ii) (Re)dxz-dxz(3d) overlap, (iii) (Re)dxy-dxy(3d) overlap, (iv) (Re)eg-t2g(3d) overlaps and (v) (Re)eg-eg(3d) overlaps. Here, the first two terms are found to contribute to the antiferromagnetic part of the exchange, while the other three contribute to the ferromagnetic part. The last two terms correspond to the cross-interactions and also contribute to the ferromagnetic part of the exchange. A record high ferromagnetic J value observed for the {Re(IV)-Cu(II)} pair in complex is found to be due to a significant cross interaction between the dz(2) orbital of the Re(IV) ion and the dx(2)-y(2) orbital of the Cu(ii) ion. Magneto-structural correlations are developed for Re-C and M-N bond lengths and Re-C-N and M-N-C bond angles. Among the developed correlations, the M-N-C bond angle is found to be the most sensitive parameter which influences the sign and strength of J values in this series. The J values are found to be more positive (or less negative) as the angle increases, indicating stronger ferromagnetic coupling at linear M-N-C angles. Apart from the magnetic exchange interaction, we have also estimated the magnetic anisotropy of [ReCl4(CN)2](2-) and [(DMF)4(CN)M(II)(CN)] (M(II)-Fe(II), Co(II) and Ni(II)) units using the state-of-the-art ab initio CASSCF/PT2/RASSI-SO/SINGLE_ANISO approach. The calculated D and E values for these building units are found to be in agreement with the available experimental results. Particularly a large positive D computed for the [ReCl4(CN)2](2-) unit was found to arise from dxz/dyz → dxy excitations corresponding to the low-lying doublet states. Similarly, a very large positive D value computed for Fe(II) and Co(II) units are also rationalised based on the corresponding ground state electronic configurations computed. The non-collinearity of the Re(IV) ion and the M(II) ion axial anisotropy (DZZ) axis are found to diminish the anisotropy of the building unit, leading to the observation of moderate relaxation barriers for these molecules.

Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes.

PubMed

Taylor, Louis J; Strebel, Klaus

2017-01-07

Gene knockouts are a common tool used to study gene function in various organisms. However, designing gene knockouts is complicated in viruses, which frequently contain sequences that code for multiple overlapping genes. Designing mutants that can be traced by the creation of new or elimination of existing restriction sites further compounds the difficulty in experimental design of knockouts of overlapping genes. While software is available to rapidly identify restriction sites in a given nucleotide sequence, no existing software addresses experimental design of mutations involving multiple overlapping amino acid sequences in generating gene knockouts. Pyviko performed well on a test set of over 240,000 gene pairs collected from viral genomes deposited in the National Center for Biotechnology Information Nucleotide database, identifying a point mutation which added a premature stop codon within the first 20 codons of the target gene in 93.2% of all tested gene-overprinted gene pairs. This shows that Pyviko can be used successfully in a wide variety of contexts to facilitate the molecular cloning and study of viral overprinted genes. Pyviko is an extensible and intuitive Python tool for designing knockouts of overlapping genes. Freely available as both a Python package and a web-based interface ( http://louiejtaylor.github.io/pyViKO/ ), Pyviko simplifies the experimental design of gene knockouts in complex viruses with overlapping genes.

Auditing complex concepts of SNOMED using a refined hierarchical abstraction network.

PubMed

Wang, Yue; Halper, Michael; Wei, Duo; Gu, Huanying; Perl, Yehoshua; Xu, Junchuan; Elhanan, Gai; Chen, Yan; Spackman, Kent A; Case, James T; Hripcsak, George

2012-02-01

Auditors of a large terminology, such as SNOMED CT, face a daunting challenge. To aid them in their efforts, it is essential to devise techniques that can automatically identify concepts warranting special attention. "Complex" concepts, which by their very nature are more difficult to model, fall neatly into this category. A special kind of grouping, called a partial-area, is utilized in the characterization of complex concepts. In particular, the complex concepts that are the focus of this work are those appearing in intersections of multiple partial-areas and are thus referred to as overlapping concepts. In a companion paper, an automatic methodology for identifying and partitioning the entire collection of overlapping concepts into disjoint, singly-rooted groups, that are more manageable to work with and comprehend, has been presented. The partitioning methodology formed the foundation for the development of an abstraction network for the overlapping concepts called a disjoint partial-area taxonomy. This new disjoint partial-area taxonomy offers a collection of semantically uniform partial-areas and is exploited herein as the basis for a novel auditing methodology. The review of the overlapping concepts is done in a top-down order within semantically uniform groups. These groups are themselves reviewed in a top-down order, which proceeds from the less complex to the more complex overlapping concepts. The results of applying the methodology to SNOMED's Specimen hierarchy are presented. Hypotheses regarding error ratios for overlapping concepts and between different kinds of overlapping concepts are formulated. Two phases of auditing the Specimen hierarchy for two releases of SNOMED are reported on. With the use of the double bootstrap and Fisher's exact test (two-tailed), the auditing of concepts and especially roots of overlapping partial-areas is shown to yield a statistically significant higher proportion of errors. Copyright © 2011 Elsevier Inc. All rights reserved.

Auditing Complex Concepts of SNOMED using a Refined Hierarchical Abstraction Network

PubMed Central

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

2012-01-01

Auditors of a large terminology, such as SNOMED CT, face a daunting challenge. To aid them in their efforts, it is essential to devise techniques that can automatically identify concepts warranting special attention. “Complex” concepts, which by their very nature are more difficult to model, fall neatly into this category. A special kind of grouping, called a partial-area, is utilized in the characterization of complex concepts. In particular, the complex concepts that are the focus of this work are those appearing in intersections of multiple partial-areas and are thus referred to as overlapping concepts. In a companion paper, an automatic methodology for identifying and partitioning the entire collection of overlapping concepts into disjoint, singly-rooted groups, that are more manageable to work with and comprehend, has been presented. The partitioning methodology formed the foundation for the development of an abstraction network for the overlapping concepts called a disjoint partial-area taxonomy. This new disjoint partial-area taxonomy offers a collection of semantically uniform partial-areas and is exploited herein as the basis for a novel auditing methodology. The review of the overlapping concepts is done in a top-down order within semantically uniform groups. These groups are themselves reviewed in a top-down order, which proceeds from the less complex to the more complex overlapping concepts. The results of applying the methodology to SNOMED’s Specimen hierarchy are presented. Hypotheses regarding error ratios for overlapping concepts and between different kinds of overlapping concepts are formulated. Two phases of auditing the Specimen hierarchy for two releases of SNOMED are reported on. With the use of the double bootstrap and Fisher’s exact test (two-tailed), the auditing of concepts and especially roots of overlapping partial-areas is shown to yield a statistically significant higher proportion of errors. PMID:21907827

Multimorbidity Patterns in the Elderly: A New Approach of Disease Clustering Identifies Complex Interrelations between Chronic Conditions

PubMed Central

Schäfer, Ingmar; von Leitner, Eike-Christin; Schön, Gerhard; Koller, Daniela; Hansen, Heike; Kolonko, Tina; Kaduszkiewicz, Hanna; Wegscheider, Karl; Glaeske, Gerd; van den Bussche, Hendrik

2010-01-01

Objective Multimorbidity is a common problem in the elderly that is significantly associated with higher mortality, increased disability and functional decline. Information about interactions of chronic diseases can help to facilitate diagnosis, amend prevention and enhance the patients' quality of life. The aim of this study was to increase the knowledge of specific processes of multimorbidity in an unselected elderly population by identifying patterns of statistically significantly associated comorbidity. Methods Multimorbidity patterns were identified by exploratory tetrachoric factor analysis based on claims data of 63,104 males and 86,176 females in the age group 65+. Analyses were based on 46 diagnosis groups incorporating all ICD-10 diagnoses of chronic diseases with a prevalence ≥ 1%. Both genders were analyzed separately. Persons were assigned to multimorbidity patterns if they had at least three diagnosis groups with a factor loading of 0.25 on the corresponding pattern. Results Three multimorbidity patterns were found: 1) cardiovascular/metabolic disorders [prevalence female: 30%; male: 39%], 2) anxiety/depression/somatoform disorders and pain [34%; 22%], and 3) neuropsychiatric disorders [6%; 0.8%]. The sampling adequacy was meritorious (Kaiser-Meyer-Olkin measure: 0.85 and 0.84, respectively) and the factors explained a large part of the variance (cumulative percent: 78% and 75%, respectively). The patterns were largely age-dependent and overlapped in a sizeable part of the population. Altogether 50% of female and 48% of male persons were assigned to at least one of the three multimorbidity patterns. Conclusion This study shows that statistically significant co-occurrence of chronic diseases can be subsumed in three prevalent multimorbidity patterns if accounting for the fact that different multimorbidity patterns share some diagnosis groups, influence each other and overlap in a large part of the population. In recognizing the full complexity of multimorbidity we might improve our ability to predict needs and achieve possible benefits for elderly patients who suffer from multimorbidity. PMID:21209965

Measurements of the pairwise kinematic Sunyaev-Zel'dovich effect with the Atacama Cosmology Telescope and future surveys

NASA Astrophysics Data System (ADS)

Vavagiakis, Eve Marie; De Bernardis, Francesco; Aiola, Simone; Battaglia, Nicholas; Niemack, Michael D.; ACTPol Collaboration

2017-06-01

We have made improved measurements of the kinematic Sunyaev-Zel’dovich (kSZ) effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). We used a map of the Cosmic Microwave Background (CMB) from two seasons of observations each by ACT and the Atacama Cosmology Telescope Polarimeter (ACTPol) receiver. We evaluated the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog via 600 square degrees of overlapping sky area. The measurement of the kSZ signal arising from the large-scale motions of clusters was made by fitting data to an analytical model. The free parameter of the fit determined the optical depth to microwave photon scattering for the cluster sample. We estimated the covariance matrix of the mean pairwise momentum as a function of galaxy separation using CMB simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based uncertainties gave signal-to-noise estimates between 3.6 and 4.1 for various luminosity cuts. Additionally, we explored a novel approach to estimating cluster optical depths from the average thermal Sunyaev-Zel’dovich (tSZ) signal at the BOSS DR11 catalog positions. Our results were broadly consistent with those obtained from the kSZ signal. In the future, the tSZ signal may provide a valuable probe of cluster optical depths, enabling the extraction of velocities from the kSZ sourced mean pairwise momenta. New CMB maps from three seasons of ACTPol observations with multi-frequency coverage overlap with nearly four times as many DR11 sources and promise to improve statistics and systematics for SZ measurements. With these and other upcoming data, the pairwise kSZ signal is poised to become a powerful new cosmological tool, able to probe large physical scales to inform neutrino physics and test models of modified gravity and dark energy.

H2AX foci in late S/G2- and M-phase cells after hydroxyurea- and aphidicolin-induced DNA replication stress in Vicia.

PubMed

Rybaczek, Dorota; Bodys, Aleksandra; Maszewski, Janusz

2007-09-01

Immunocytochemistry using alpha-phospho-H2AX antibodies shows that hydroxyurea (HU), an inhibitor of ribonucleotide reductase, and aphidicolin (APH), an inhibitor of DNA-polymerases alpha and delta, may promote formation of phospho-H2AX foci in late S/G2-phase cells in root meristems of Vicia faba. Although fluorescent foci spread throughout the whole area of nucleoplasm, large phospho-H2AX aggregates in HU-treated cells allocate mainly in perinucleolar regions. A strong tendency of ATR/ATM-dependent phospho-Chk1S317 kinase to focus in analogous compartments, as opposed to phospho-Chk2T68 and to both effector kinases in APH-treated cells, may suggest that selected elements of the intra-S-phase cell cycle checkpoints share overlapping locations with DNA repair factors known to concentrate in phospho-H2AX aggregates. APH-induced phosphorylation of H2AX exhibits little or no overlap with the areas positioned close to nucleoli. Following G2-M transition of the HU- and APH-pretreated cells, altered chromatin structures are still discernible as large phospho-H2AX foci in the vicinity of chromosomes. Both in HU- and APH-treated roots, immunofluorescence analysis revealed a dominant fraction of small foci and a less frequent population of large phospho-H2AX aggregates, similar to those observed in animal cells exposed to ionizing radiation. The extent of H2AX phosphorylation has been found considerably reduced in root meristem cells treated with HU and caffeine. The frequencies of phospho-H2AX foci observed during mitosis and caffeine-mediated premature chromosome condensation (PCC) suggest that there may be functional links between the checkpoint mechanisms that control genome integrity and those activities which operate throughout the unperturbed mitosis in plants.

Structure of p73 DNA-binding domain tetramer modulates p73 transactivation

PubMed Central

Ethayathulla, Abdul S.; Tse, Pui-Wah; Monti, Paola; Nguyen, Sonha; Inga, Alberto; Fronza, Gilberto; Viadiu, Hector

2012-01-01

The transcription factor p73 triggers developmental pathways and overlaps stress-induced p53 transcriptional pathways. How p53-family response elements determine and regulate transcriptional specificity remains an unsolved problem. In this work, we have determined the first crystal structures of p73 DNA-binding domain tetramer bound to response elements with spacers of different length. The structure and function of the adaptable tetramer are determined by the distance between two half-sites. The structures with zero and one base-pair spacers show compact p73 DNA-binding domain tetramers with large tetramerization interfaces; a two base-pair spacer results in DNA unwinding and a smaller tetramerization interface, whereas a four base-pair spacer hinders tetramerization. Functionally, p73 is more sensitive to spacer length than p53, with one base-pair spacer reducing 90% of transactivation activity and longer spacers reducing transactivation to basal levels. Our results establish the quaternary structure of the p73 DNA-binding domain required as a scaffold to promote transactivation. PMID:22474346

Designing ECG-based physical unclonable function for security of wearable devices.

PubMed

Shihui Yin; Chisung Bae; Sang Joon Kim; Jae-Sun Seo

2017-07-01

As a plethora of wearable devices are being introduced, significant concerns exist on the privacy and security of personal data stored on these devices. Expanding on recent works of using electrocardiogram (ECG) as a modality for biometric authentication, in this work, we investigate the possibility of using personal ECG signals as the individually unique source for physical unclonable function (PUF), which eventually can be used as the key for encryption and decryption engines. We present new signal processing and machine learning algorithms that learn and extract maximally different ECG features for different individuals and minimally different ECG features for the same individual over time. Experimental results with a large 741-subject in-house ECG database show that the distributions of the intra-subject (same person) Hamming distance of extracted ECG features and the inter-subject Hamming distance have minimal overlap. 256-b random numbers generated from the ECG features of 648 (out of 741) subjects pass the NIST randomness tests.

Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster

PubMed Central

Dobson, Adam J.; Chaston, John M.; Newell, Peter D.; Donahue, Leanne; Hermann, Sara L.; Sannino, David R.; Westmiller, Stephanie; Wong, Adam C.-N.; Clark, Andrew G.; Lazzaro, Brian P.; Douglas, Angela E.

2015-01-01

Animals bear communities of gut microorganisms with substantial effects on animal nutrition, but the host genetic basis of these effects is unknown. Here, we use Drosophila to demonstrate substantial among-genotype variation in the effects of eliminating the gut microbiota on five host nutritional indices (weight, and protein, lipid, glucose and glycogen contents); this includes variation in both the magnitude and direction of microbiota-dependent effects. Genome-wide associations to identify the genetic basis of the microbiota-dependent variation reveal polymorphisms in largely non-overlapping sets of genes associated with variation in the nutritional traits, including strong representation of conserved genes functioning in signaling. Key genes identified by the GWA study are validated by loss-of-function mutations that altered microbiota-dependent nutritional effects. We conclude that the microbiota interacts with the animal at multiple points in the signaling and regulatory networks that determine animal nutrition. These interactions with the microbiota are likely conserved across animals, including humans. PMID:25692519

Similar microbial communities found on two distant seafloor basalts

NASA Astrophysics Data System (ADS)

Singer, E.; Chong, L. S.; Heidelberg, J. F.; Edwards, K. J.

2016-12-01

The oceanic crust forms two thirds of the Earth's surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present a comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō'ihi Seamount, Hawai'i, and the East Pacific Rise (EPR) (9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō'ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy.

To peep into Pif1 helicase: multifaceted all the way from genome stability to repair-associated DNA synthesis.

PubMed

Chung, Woo-Hyun

2014-02-01

Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.

Plasma membrane transporters for arginine.

PubMed

Closs, Ellen I; Simon, Alexandra; Vékony, Nicole; Rotmann, Alexander

2004-10-01

The supply of arginine may become rate limiting for enzymatic reactions that use this semiessential amino acid as a substrate (e.g., nitric oxide, agmatine, creatine, and urea synthesis), particularly under conditions of high demand such as growth, sepsis, or wound healing. In addition, arginine acts as a signaling molecule that regulates essential cellular functions such as protein synthesis, apoptosis, and growth. In the past decade, a number of carrier proteins for amino acids have been identified on the molecular level. They belong to different gene families, exhibit overlapping but distinctive substrate specificities, and can further be distinguished by their requirement for the cotransport or countertransport of inorganic ions. A number of these transporters function as exchangers rather than uniporters. Uptake of amino acids by these transporters therefore depends largely on the intracellular substrate composition. Hence, there is a complex crosstalk between transporters for cationic and neutral amino acids as well as for peptides. This article briefly reviews current knowledge regarding mammalian plasma membrane transporters that accept arginine as a substrate.

Chemokine Function in Periodontal Disease and Oral Cavity Cancer

PubMed Central

Sahingur, Sinem Esra; Yeudall, W. Andrew

2015-01-01

The chemotactic cytokines, or chemokines, comprise a superfamily of polypeptides with a wide range of activities that include recruitment of immune cells to sites of infection and inflammation, as well as stimulation of cell proliferation. As such, they function as antimicrobial molecules and play a central role in host defenses against pathogen challenge. However, their ability to recruit leukocytes and potentiate or prolong the inflammatory response may have profound implications for the progression of oral diseases such as chronic periodontitis, where tissue destruction may be widespread. Moreover, it is increasingly recognized that chronic inflammation is a key component of tumor progression. Interaction between cancer cells and their microenvironment is mediated in large part by secreted factors such as chemokines, and serves to enhance the malignant phenotype in oral and other cancers. In this article, we will outline the biological and biochemical mechanisms of chemokine action in host–microbiome interactions in periodontal disease and in oral cancer, and how these may overlap and contribute to pathogenesis. PMID:25999952

Predicting overlapping protein complexes from weighted protein interaction graphs by gradually expanding dense neighborhoods.

PubMed

Dimitrakopoulos, Christos; Theofilatos, Konstantinos; Pegkas, Andreas; Likothanassis, Spiros; Mavroudi, Seferina

2016-07-01

Proteins are vital biological molecules driving many fundamental cellular processes. They rarely act alone, but form interacting groups called protein complexes. The study of protein complexes is a key goal in systems biology. Recently, large protein-protein interaction (PPI) datasets have been published and a plethora of computational methods that provide new ideas for the prediction of protein complexes have been implemented. However, most of the methods suffer from two major limitations: First, they do not account for proteins participating in multiple functions and second, they are unable to handle weighted PPI graphs. Moreover, the problem remains open as existing algorithms and tools are insufficient in terms of predictive metrics. In the present paper, we propose gradually expanding neighborhoods with adjustment (GENA), a new algorithm that gradually expands neighborhoods in a graph starting from highly informative "seed" nodes. GENA considers proteins as multifunctional molecules allowing them to participate in more than one protein complex. In addition, GENA accepts weighted PPI graphs by using a weighted evaluation function for each cluster. In experiments with datasets from Saccharomyces cerevisiae and human, GENA outperformed Markov clustering, restricted neighborhood search and clustering with overlapping neighborhood expansion, three state-of-the-art methods for computationally predicting protein complexes. Seven PPI networks and seven evaluation datasets were used in total. GENA outperformed existing methods in 16 out of 18 experiments achieving an average improvement of 5.5% when the maximum matching ratio metric was used. Our method was able to discover functionally homogeneous protein clusters and uncover important network modules in a Parkinson expression dataset. When used on the human networks, around 47% of the detected clusters were enriched in gene ontology (GO) terms with depth higher than five in the GO hierarchy. In the present manuscript, we introduce a new method for the computational prediction of protein complexes by making the realistic assumption that proteins participate in multiple protein complexes and cellular functions. Our method can detect accurate and functionally homogeneous clusters. Copyright © 2016 Elsevier B.V. All rights reserved.

Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues

PubMed Central

2013-01-01

Background Many have assumed that the primary function of sleep is for the brain. We evaluated the molecular consequences of sleep and sleep deprivation outside the brain, in heart and lung. Using microarrays we compared gene expression in tissue from sleeping and sleep deprived mice euthanized at the same diurnal times. Results In each tissue, nearly two thousand genes demonstrated statistically significant differential expression as a function of sleep/wake behavioral state. To mitigate the influence of an artificial deprivation protocol, we identified a subset of these transcripts as specifically sleep-enhanced or sleep-repressed by requiring that their expression also change over the course of unperturbed sleep. 3% and 6% of the assayed transcripts showed “sleep specific” changes in the lung and heart respectively. Sleep specific transcripts in these tissues demonstrated highly significant overlap and shared temporal dynamics. Markers of cellular stress and the unfolded protein response were reduced during sleep in both tissues. These results mirror previous findings in brain. Sleep-enhanced pathways reflected the unique metabolic functions of each tissue. Transcripts related to carbohydrate and sulfur metabolic processes were enhanced by sleep in the lung, and collectively favor buffering from oxidative stress. DNA repair and protein metabolism annotations were significantly enriched among the sleep-enhanced transcripts in the heart. Our results also suggest that sleep may provide a Zeitgeber, or synchronizing cue, in the lung as a large cluster of transcripts demonstrated systematic changes in inter-animal variability as a function of both sleep duration and circadian time. Conclusion Our data support the notion that the molecular consequences of sleep/wake behavioral state extend beyond the brain to include peripheral tissues. Sleep state induces a highly overlapping response in both heart and lung. We conclude that sleep enhances organ specific molecular functions and that it has a ubiquitous role in reducing cellular metabolic stress in both brain and peripheral tissues. Finally, our data suggest a novel role for sleep in synchronizing transcription in peripheral tissues. PMID:23721503

Action and Perception Are Temporally Coupled by a Common Mechanism That Leads to a Timing Misperception

PubMed Central

Astefanoaei, Corina; Daye, Pierre M.; FitzGibbon, Edmond J.; Creanga, Dorina-Emilia; Rufa, Alessandra; Optican, Lance M.

2015-01-01

We move our eyes to explore the world, but visual areas determining where to look next (action) are different from those determining what we are seeing (perception). Whether, or how, action and perception are temporally coordinated is not known. The preparation time course of an action (e.g., a saccade) has been widely studied with the gap/overlap paradigm with temporal asynchronies (TA) between peripheral target onset and fixation point offset (gap, synchronous, or overlap). However, whether the subjects perceive the gap or overlap, and when they perceive it, has not been studied. We adapted the gap/overlap paradigm to study the temporal coupling of action and perception. Human subjects made saccades to targets with different TAs with respect to fixation point offset and reported whether they perceived the stimuli as separated by a gap or overlapped in time. Both saccadic and perceptual report reaction times changed in the same way as a function of TA. The TA dependencies of the time change for action and perception were very similar, suggesting a common neural substrate. Unexpectedly, in the perceptual task, subjects misperceived lights overlapping by less than ∼100 ms as separated in time (overlap seen as gap). We present an attention-perception model with a map of prominence in the superior colliculus that modulates the stimulus signal's effectiveness in the action and perception pathways. This common source of modulation determines how competition between stimuli is resolved, causes the TA dependence of action and perception to be the same, and causes the misperception. PMID:25632126

Dynamic trajectory-based couch motion for improvement of radiation therapy trajectories in cranial SRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacDonald, R. Lee; Thomas, Christopher G., E-mail: Chris.Thomas@cdha.nshealth.ca; Department of Medical Physics, Nova Scotia Cancer Centre, Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia B3H 1V7

2015-05-15

Purpose: To investigate potential improvement in external beam stereotactic radiation therapy plan quality for cranial cases using an optimized dynamic gantry and patient support couch motion trajectory, which could minimize exposure to sensitive healthy tissue. Methods: Anonymized patient anatomy and treatment plans of cranial cancer patients were used to quantify the geometric overlap between planning target volumes and organs-at-risk (OARs) based on their two-dimensional projection from source to a plane at isocenter as a function of gantry and couch angle. Published dose constraints were then used as weighting factors for the OARs to generate a map of couch-gantry coordinate space,more » indicating degree of overlap at each point in space. A couch-gantry collision space was generated by direct measurement on a linear accelerator and couch using an anthropomorphic solid-water phantom. A dynamic, fully customizable algorithm was written to generate a navigable ideal trajectory for the patient specific couch-gantry space. The advanced algorithm can be used to balance the implementation of absolute minimum values of overlap with the clinical practicality of large-scale couch motion and delivery time. Optimized cranial cancer treatment trajectories were compared to conventional treatment trajectories. Results: Comparison of optimized treatment trajectories with conventional treatment trajectories indicated an average decrease in mean dose to the OARs of 19% and an average decrease in maximum dose to the OARs of 12%. Degradation was seen for homogeneity index (6.14% ± 0.67%–5.48% ± 0.76%) and conformation number (0.82 ± 0.02–0.79 ± 0.02), but neither was statistically significant. Removal of OAR constraints from volumetric modulated arc therapy optimization reveals that reduction in dose to OARs is almost exclusively due to the optimized trajectory and not the OAR constraints. Conclusions: The authors’ study indicated that simultaneous couch and gantry motion during radiation therapy to minimize the geometrical overlap in the beams-eye-view of target volumes and the organs-at-risk can have an appreciable dose reduction to organs-at-risk.« less

Biological sex affects the neurobiology of autism

PubMed Central

Lombardo, Michael V.; Suckling, John; Ruigrok, Amber N. V.; Chakrabarti, Bhismadev; Ecker, Christine; Deoni, Sean C. L.; Craig, Michael C.; Murphy, Declan G. M.; Bullmore, Edward T.; Baron-Cohen, Simon

2013-01-01

In autism, heterogeneity is the rule rather than the exception. One obvious source of heterogeneity is biological sex. Since autism was first recognized, males with autism have disproportionately skewed research. Females with autism have thus been relatively overlooked, and have generally been assumed to have the same underlying neurobiology as males with autism. Growing evidence, however, suggests that this is an oversimplification that risks obscuring the biological base of autism. This study seeks to answer two questions about how autism is modulated by biological sex at the level of the brain: (i) is the neuroanatomy of autism different in males and females? and (ii) does the neuroanatomy of autism fit predictions from the ‘extreme male brain’ theory of autism, in males and/or in females? Neuroanatomical features derived from voxel-based morphometry were compared in a sample of equal-sized high-functioning male and female adults with and without autism (n = 120, n = 30/group). The first question was investigated using a 2 × 2 factorial design, and by spatial overlap analyses of the neuroanatomy of autism in males and females. The second question was tested through spatial overlap analyses of specific patterns predicted by the extreme male brain theory. We found that the neuroanatomy of autism differed between adult males and females, evidenced by minimal spatial overlap (not different from that occurred under random condition) in both grey and white matter, and substantially large white matter regions showing significant sex × diagnosis interactions in the 2 × 2 factorial design. These suggest that autism manifests differently by biological sex. Furthermore, atypical brain areas in females with autism substantially and non-randomly (P < 0.001) overlapped with areas that were sexually dimorphic in neurotypical controls, in both grey and white matter, suggesting neural ‘masculinization’. This was not seen in males with autism. How differences in neuroanatomy relate to the similarities in cognition between males and females with autism remains to be understood. Future research should stratify by biological sex to reduce heterogeneity and to provide greater insight into the neurobiology of autism. PMID:23935125

Biological sex affects the neurobiology of autism.

PubMed

Lai, Meng-Chuan; Lombardo, Michael V; Suckling, John; Ruigrok, Amber N V; Chakrabarti, Bhismadev; Ecker, Christine; Deoni, Sean C L; Craig, Michael C; Murphy, Declan G M; Bullmore, Edward T; Baron-Cohen, Simon

2013-09-01

In autism, heterogeneity is the rule rather than the exception. One obvious source of heterogeneity is biological sex. Since autism was first recognized, males with autism have disproportionately skewed research. Females with autism have thus been relatively overlooked, and have generally been assumed to have the same underlying neurobiology as males with autism. Growing evidence, however, suggests that this is an oversimplification that risks obscuring the biological base of autism. This study seeks to answer two questions about how autism is modulated by biological sex at the level of the brain: (i) is the neuroanatomy of autism different in males and females? and (ii) does the neuroanatomy of autism fit predictions from the 'extreme male brain' theory of autism, in males and/or in females? Neuroanatomical features derived from voxel-based morphometry were compared in a sample of equal-sized high-functioning male and female adults with and without autism (n = 120, n = 30/group). The first question was investigated using a 2 × 2 factorial design, and by spatial overlap analyses of the neuroanatomy of autism in males and females. The second question was tested through spatial overlap analyses of specific patterns predicted by the extreme male brain theory. We found that the neuroanatomy of autism differed between adult males and females, evidenced by minimal spatial overlap (not different from that occurred under random condition) in both grey and white matter, and substantially large white matter regions showing significant sex × diagnosis interactions in the 2 × 2 factorial design. These suggest that autism manifests differently by biological sex. Furthermore, atypical brain areas in females with autism substantially and non-randomly (P < 0.001) overlapped with areas that were sexually dimorphic in neurotypical controls, in both grey and white matter, suggesting neural 'masculinization'. This was not seen in males with autism. How differences in neuroanatomy relate to the similarities in cognition between males and females with autism remains to be understood. Future research should stratify by biological sex to reduce heterogeneity and to provide greater insight into the neurobiology of autism.

Genetic risk for neurodegenerative disorders, and its overlap with cognitive ability and physical function.

PubMed

Hagenaars, Saskia P; Radaković, Ratko; Crockford, Christopher; Fawns-Ritchie, Chloe; Harris, Sarah E; Gale, Catharine R; Deary, Ian J

2018-01-01

Neurodegenerative disorders are associated with impaired cognitive function and worse physical health outcomes. This study aims to test whether polygenic risk for Alzheimer's disease, Amyotrophic Lateral Sclerosis (ALS), or frontotemporal dementia (FTD) is associated with cognitive function and physical health in the UK Biobank, a cohort of healthy individuals. Group-based analyses were then performed to compare the top and bottom 10% for the three neurodegenerative polygenic risk scores; these groups were compared on the cognitive and physical health variables. Higher polygenic risk for AD, ALS, and FTD was associated with lower cognitive performance. Higher polygenic risk for FTD was also associated with increased forced expiratory volume in 1s and peak expiratory flow. A significant group difference was observed on the symbol digit substitution task between individuals with high polygenic risk for FTD and high polygenic risk for ALS. The results suggest some overlap between polygenic risk for neurodegenerative disorders, cognitive function and physical health.

Rome III functional dyspepsia subdivision in PDS and EPS: recognizing postprandial symptoms reduces overlap.

PubMed

Carbone, F; Holvoet, L; Tack, J

2015-08-01

The Rome III consensus proposed to subdivide functional dyspepsia (FD) into two groups: meal-related dyspepsia or postprandial distress syndrome (PDS), and meal-unrelated dyspepsia or epigastric pain syndrome (EPS). However, in clinical practice, overlap between both has been reported to be as high as 50%, thereby hampering clinical applicability. Although EPS is referred to as meal-unrelated dyspepsia, relationship of symptoms to meal ingestion in this category is not formally addressed in the Rome III criteria. The aim of our study was to investigate whether taking into account the relationship of epigastric pain and nausea to meal ingestion may help to improve separation between EPS and PDS. Consecutive ambulatory tertiary-care patients with epigastric symptoms filled out Rome III gastro-duodenal questionnaires with supplementary questions. Those fulfilling Rome III FD criteria and a negative endoscopy were identified and subdivided into 'pure' PDS patients (i.e., meeting criteria for PDS without EPS symptoms), 'pure' EPS (i.e., meeting criteria for EPS without PDS symptoms), and overlapping PDS-EPS (i.e., symptoms of both PDS and EPS). Out of 1029 patients coming to endoscopy, 199 patients (73% females, 45.9 ± 1.0 years, BMI: 23.7 ± 0.35) fulfilled Rome III FD diagnostic criteria, and could be subdivided into pure PDS (69% females, 49 ± 2 years, BMI: 24.2 ± 0.61), pure EPS (59% females, 47.4 ± 2 years, BMI: 23.2 ± 0.97) and overlapping PDS-EPS (64% females, age 43 ± 5 years, BMI: 26 ± 0.46). Compared with pure EPS patients, the overlap PDS-EPS patients were characterized by a higher occurrence of postprandial epigastric pain (70% vs 31%, p < 0.0001), while the occurrence of epigastric pain in between meals was borderline (48% vs 38%, p = 0.05). In addition, the overlap PDS-EPS patients reported a higher occurrence of postprandial nausea (23% vs 0%, p < 0.0001), and bloating (79% vs 28%, p = 0.0001). When postprandial epigastric pain and postprandial nausea were considered as PDS symptoms, the 'adapted' subdivision identified 48% pure PDS, 16% pure EPS, and 36% overlapping PDS-EPS patients. EPS and PDS symptoms frequently coexist in FD patients, with postprandial symptoms substantially contributing to the overlap. A more rigorous linking of postprandially occurring symptoms to PDS, regardless of their qualitative nature, may improve the separation between PDS and EPS. © 2015 John Wiley & Sons Ltd.

Nonperturbative renormalization of the axial current in Nf=3 lattice QCD with Wilson fermions and a tree-level improved gauge action

NASA Astrophysics Data System (ADS)

Bulava, John; Della Morte, Michele; Heitger, Jochen; Wittemeier, Christian

2016-06-01

We nonperturbatively determine the renormalization factor of the axial vector current in lattice QCD with Nf=3 flavors of Wilson-clover fermions and the tree-level Symanzik-improved gauge action. The (by now standard) renormalization condition is derived from the massive axial Ward identity, and it is imposed among Schrödinger functional states with large overlap on the lowest lying hadronic state in the pseudoscalar channel, in order to reduce kinematically enhanced cutoff effects. We explore a range of couplings relevant for simulations at lattice spacings of ≈0.09 fm and below. An interpolation formula for ZA(g02) , smoothly connecting the nonperturbative values to the 1-loop expression, is provided together with our final results.

HIF1α and HIF2α: sibling rivalry in hypoxic tumour growth and progression.

PubMed

Keith, Brian; Johnson, Randall S; Simon, M Celeste

2011-12-15

Hypoxia-inducible factors (HIFs) are broadly expressed in human cancers, and HIF1α and HIF2α were previously suspected to promote tumour progression through largely overlapping functions. However, this relatively simple model has now been challenged in light of recent data from various approaches that reveal unique and sometimes opposing activities of these HIFα isoforms in both normal physiology and disease. These effects are mediated in part through the regulation of unique target genes, as well as through direct and indirect interactions with important oncoproteins and tumour suppressors, including MYC and p53. As HIF inhibitors are currently undergoing clinical evaluation as cancer therapeutics, a more thorough understanding of the unique roles performed by HIF1α and HIF2α in human neoplasia is warranted.

Lexical decision as an endophenotype for reading comprehension: An exploration of an association

PubMed Central

NAPLES, ADAM; KATZ, LEN; GRIGORENKO, ELENA L.

2012-01-01

Based on numerous suggestions in the literature, we evaluated lexical decision (LD) as a putative endophenotype for reading comprehension by investigating heritability estimates and segregation analyses parameter estimates for both of these phenotypes. Specifically, in a segregation analysis of a large sample of families, we established that there is little to no overlap between genes contributing to LD and reading comprehension and that the genetic mechanism behind LD derived from this analysis appears to be more complex than that for reading comprehension. We conclude that in our sample, LD is not a good candidate as an endophenotype for reading comprehension, despite previous suggestions from the literature. Based on this conclusion, we discuss the role and benefit of the endophenotype approach in studies of complex human cognitive functions. PMID:23062302

Cognitive Contributions of the Ventral Parietal Cortex: An Integrative Theoretical Account

PubMed Central

Cabeza, Roberto; Ciaramelli, Elisa; Moscovitch, Morris

2012-01-01

Although ventral parietal cortex (VPC) activations can be found in a variety of cognitive domains, these activations have been typically attributed to cognitive operations specific to each domain. In this article, we propose a hypothesis that can account for VPC activations across all the cognitive domains reviewed. We first review VPC activations in the domains of perceptual and motor reorienting, episodic memory retrieval, language and number processing, theory of mind, and episodic memory encoding. Then, we consider the localization of VPC activations across domains, and conclude that they are largely overlapping with some differences around the edges. Finally, we assess how well four different hypotheses of VPC function can explain findings in various domains, and conclude that a bottom-up attention hypothesis provides the most complete and parsimonious account. PMID:22609315

Non-overlapping Neural Networks in Hydra vulgaris.

PubMed

Dupre, Christophe; Yuste, Rafael

2017-04-24

To understand the emergent properties of neural circuits, it would be ideal to record the activity of every neuron in a behaving animal and decode how it relates to behavior. We have achieved this with the cnidarian Hydra vulgaris, using calcium imaging of genetically engineered animals to measure the activity of essentially all of its neurons. Although the nervous system of Hydra is traditionally described as a simple nerve net, we surprisingly find instead a series of functional networks that are anatomically non-overlapping and are associated with specific behaviors. Three major functional networks extend through the entire animal and are activated selectively during longitudinal contractions, elongations in response to light, and radial contractions, whereas an additional network is located near the hypostome and is active during nodding. These results demonstrate the functional sophistication of apparently simple nerve nets, and the potential of Hydra and other basal metazoans as a model system for neural circuit studies. Published by Elsevier Ltd.

Executive control, ERP and pro-inflammatory activity in emotionally exhausted middle-aged employees. Comparison between subclinical burnout and mild to moderate depression.

PubMed

Gajewski, Patrick D; Boden, Sylvia; Freude, Gabriele; Potter, Guy G; Claus, Maren; Bröde, Peter; Watzl, Carsten; Getzmann, Stephan; Falkenstein, Michael

2017-12-01

Burnout is a syndrome occurring mainly in individuals with long-term stressful work. The main complaints are emotional exhaustion and reduced performance. Burnout also largely overlaps with depression. Both are characterized by increased incidence of infections due to dysregulation of the immune system, overexpression of pro-inflammatory cytokines and cognitive deficits, particularly related to executive functions. To distinguish between burnout and depression already at the pre-clinical stage, the present double-blinded study compared immunological and cognitive parameters in seventy-six employees from emotionally demanding occupations who were post-hoc subdivided into two groups scoring low (EE-) and high (EE+) in emotional exhaustion and low (DE-) and high (DE+) in depression. Immunological parameters were measured from blood samples. Executive functions were studied by analyzing event-related brain potentials (ERPs) and performance during a task switching paradigm. Psychosocial job parameters were measured with standardized questionnaires. Burnout and mild to moderate depression largely overlapped. However, several subjects showed burnout without depressive symptoms. Higher levels of the pro-inflammatory cytokines IL-6 and IL-12 were correlated with burnout severity and depressive symptoms in male individuals. In the switch task a trend for lower performance in the EE+ vs. EE- group and no difference between DE+ and DE- groups were found. In the ERPs, however, differences were observed which distinguished between subclinical burnout and depression: the terminal contingent negative variation (CNV), indicating preparatory activity and the P3b, related to allocation of cognitive resources were generally reduced in EE+ vs. EE-, whereas no differences were found in the DE+ vs. DE- groups. The frontal P3a was selectively reduced in switch trials in the EE+ vs. EE- group and showed only a trend in DE+ vs. DE-, indicating impairment of executive control in subclinical burnout. Taken together, the results unveil specific immunological changes and declines in brain functions in employees with subclinical burnout that are not apparent in persons with moderate depression. Hence, the combination of immunological, behavioral and ERP methods renders a promising method for distinguishing both syndromes and for improving an early diagnosis of burnout before a clinical stage is reached. Copyright © 2017 Elsevier Ltd. All rights reserved.

Patterns of temporal and enemy niche use by a community of leaf cone moths (Caloptilia) coexisting on maples (Acer) as revealed by metabarcoding.

PubMed

Nakadai, Ryosuke; Kawakita, Atsushi

2017-06-01

The diversity of herbivorous insects is often considered a function of host plant diversity. However, recent research has uncovered many examples of closely related herbivores using the same host plant(s), suggesting that partitioning of host plants is not the only mechanism generating diversity. Herbivores sharing hosts may utilize different parts of the same plant, but such resource partitioning is often not apparent; hence, the factors that allow closely related herbivores to coexist are still largely undetermined. We examined whether partitioning of phenology or natural enemies may explain the coexistence of leaf cone moths (Caloptilia; Gracillariidae) associated with maples (Acer; Sapindaceae). Larval activity of 10 sympatric Caloptilia species found on nine maple species was monitored every 2-3 weeks for a total of 13 sampling events, and an exhaustive search for internal parasitoid wasps was conducted using high-throughput sequencing. Blocking primers were used to facilitate the detection of wasp larvae inside moth tissue. We found considerable phenological overlap among Caloptilia species, with two clear peaks in July and September-October. Coexisting Caloptilia species also had largely overlapping parasitoid communities; a total of 13 chalcid and ichneumon wasp species attacked Caloptilia in a nonspecific fashion at an overall parasitism rate of 46.4%. Although coexistence may be facilitated by factors not accounted for in this study, it appears that niche partitioning is not necessary for closely related herbivores to stably coexist on shared hosts. Co-occurrence without resource partitioning may provide an additional axis along which herbivorous insects attain increased species richness. © 2017 John Wiley & Sons Ltd.

Recruitment Variability in North Atlantic Cod and Match-Mismatch Dynamics

PubMed Central

Kristiansen, Trond; Drinkwater, Kenneth F.; Lough, R. Gregory; Sundby, Svein

2011-01-01

Background Fisheries exploitation, habitat destruction, and climate are important drivers of variability in recruitment success. Understanding variability in recruitment can reveal mechanisms behind widespread decline in the abundance of key species in marine and terrestrial ecosystems. For fish populations, the match-mismatch theory hypothesizes that successful recruitment is a function of the timing and duration of larval fish abundance and prey availability. However, the underlying mechanisms of match-mismatch dynamics and the factors driving spatial differences between high and low recruitment remain poorly understood. Methodology/Principal Findings We used empirical observations of larval fish abundance, a mechanistic individual-based model, and a reanalysis of ocean temperature data from 1960 to 2002 to estimate the survival of larval cod (Gadus morhua). From the model, we quantified how survival rates changed during the warmest and coldest years at four important cod spawning sites in the North Atlantic. The modeled difference in survival probability was not large for any given month between cold or warm years. However, the cumulative effect of higher growth rates and survival through the entire spawning season in warm years was substantial with 308%, 385%, 154%, and 175% increases in survival for Georges Bank, Iceland, North Sea, and Lofoten cod stocks, respectively. We also found that the importance of match-mismatch dynamics generally increased with latitude. Conclusions/Significance Our analyses indicate that a key factor for enhancing survival is the duration of the overlap between larval and prey abundance and not the actual timing of the peak abundance. During warm years, the duration of the overlap between larval fish and their prey is prolonged due to an early onset of the spring bloom. This prolonged season enhances cumulative growth and survival, leading to a greater number of large individuals with enhanced potential for survival to recruitment. PMID:21408215

Photonic reagents for concentration measurement of flu-orescent proteins with overlapping spectra

PubMed Central

Goun, Alexei; Bondar, Denys I.; Er, Ali O.; Quine, Zachary; Rabitz, Herschel A.

2016-01-01

By exploiting photonic reagents (i.e., coherent control by shaped laser pulses), we employ Optimal Dynamic Discrimination (ODD) as a novel means for quantitatively characterizing mixtures of fluorescent proteins with a large spectral overlap. To illustrate ODD, we simultaneously measured concentrations of in vitro mixtures of Enhanced Blue Fluorescent Protein (EBFP) and Enhanced Cyan Fluorescent Protein (ECFP). Building on this foundational study, the ultimate goal is to exploit the capabilities of ODD for parallel monitoring of genetic and protein circuits by suppressing the spectral cross-talk among multiple fluorescent reporters. PMID:27181496

Genetic overlap between Alzheimer’s disease and Parkinson’s disease at the MAPT locus

PubMed Central

Desikan, Rahul S.; Schork, Andrew J.; Wang, Yunpeng; Witoelar, Aree; Sharma, Manu; McEvoy, Linda K.; Holland, Dominic; Brewer, James B.; Chen, Chi-Hua; Thompson, Wesley K.; Harold, Denise; Williams, Julie; Owen, Michael J.; O’Donovan, Michael C.; Pericak-Vance, Margaret A.; Mayeux, Richard; Haines, Jonathan L.; Farrer, Lindsay A.; Schellenberg, Gerard D.; Heutink, Peter; Singleton, Andrew B.; Brice, Alexis; Wood, Nicolas W.; Hardy, John; Martinez, Maria; Choi, Seung Hoi; DeStefano, Anita; Ikram, M. Arfan; Bis, Joshua C.; Smith, Albert; Fitzpatrick, Annette L.; Launer, Lenore; van Duijn, Cornelia; Seshadri, Sudha; Ulstein, Ingun Dina; Aarsland, Dag; Fladby, Tormod; Djurovic, Srdjan; Hyman, Bradley T.; Snaedal, Jon; Stefansson, Hreinn; Stefansson, Kari; Gasser, Thomas; Andreassen, Ole A.; Dale, Anders M.

2015-01-01

We investigated genetic overlap between Alzheimer’s disease (AD) and Parkinson’s disease (PD). Using summary statistics (p-values) from large recent genomewide association studies (GWAS) (total n = 89,904 individuals), we sought to identify single nucleotide polymorphisms (SNPs) associating with both AD and PD. We found and replicated association of both AD and PD with the A allele of rs393152 within the extended MAPT region on chromosome 17 (meta analysis p-value across 5 independent AD cohorts = 1.65 × 10−7). In independent datasets, we found a dose-dependent effect of the A allele of rs393152 on intra-cerebral MAPT transcript levels and volume loss within the entorhinal cortex and hippocampus. Our findings identify the tau-associated MAPT locus as a site of genetic overlap between AD and PD and extending prior work, we show that the MAPT region increases risk of Alzheimer’s neurodegeneration. PMID:25687773

Palisaded Neutrophilic and Granulomatous Dermatitis/Interstitial Granulomatous Dermatitis Overlap: A Striking Clinical and Histologic Presentation With "Burning Rope Sign" and Subsequent Mirror-Image Contralateral Recurrence.

PubMed

Kern, Malan; Shiver, Mallory B; Addis, Kristen M; Gardner, Jerad M

2017-09-01

Palisaded neutrophilic and granulomatous dermatitis and interstitial granulomatous dermatitis are uncommon granulomatous dermatoses that often arise in association with rheumatoid arthritis. These 2 entities have overlapping features and may exist on a spectrum. We report an intriguing case of a 53-year-old man with advanced rheumatoid arthritis who presented with a large indurated painful truncal plaque with a palpable cord in addition to a papulonodular eruption on his dorsal hands. Furthermore, our patient had a recurrence in a near-identical mirror-image pattern on the contralateral trunk. The constellation of clinical and histopathological findings in our patient further suggests that palisaded neutrophilic and granulomatous dermatitis and interstitial granulomatous dermatitis exist as overlapping disease entities on a continuum. In addition, we propose that recurrence of skin findings may be indicative of the severity of the underlying systemic disease process.

Implantation of a cone-shaped double-fixed patch increases abdominal space and prevents recurrence of large defects in congenital diaphragmatic hernia.

PubMed

Loff, Steffan; Wirth, Hartmut; Jester, Iwgo; Hosie, Stuart; Wollmann, Carmen; Schaible, Thomas; Ataman, Ozge; Waag, Karl-Ludwig

2005-11-01

Large defects in patients with congenital diaphragmatic hernia (CDH) are frequently closed with a polytetrafluoroethylene patch (PTFE). Intraoperative problems include lack of abdominal domain for the reduction of organs and closure of the abdominal wall. Main surgical postoperative complication is the recurrence of the hernia. We suggest a new and easy method of patch implantation, improving these problems, and report first follow-up results. In our clinic, 103 children with CDH were treated, and 87 children underwent reconstruction of the diaphragm in the 5 years between 1998 and 2002. In 52 patients, a patch implantation had to be performed. We have been optimizing our complete pediatric and surgical procedure and present a new standardized technique of preparation and implantation of a PTFE patch. The flat patch is folded to a 90 degrees cone. The cone is fixed in its form with few single stitches. It is implanted with an overlapping border of 1 cm circumferentially. The border is separately fixed with absorbable single stitches to keep from rolling up. The rough side of the patch points toward the rim of the diaphragm to enable ingrowth of the connective tissue. In a 1-year follow-up study, the recurrences in the 3 following groups of PTFE patches were studied: conventional implantation (simple patch without overlapping border), patch with separately fixed overlapping border, and cone-shaped patch with overlapping separately fixed border. Thirty-three patients were included in the study. After conventional PTFE-patch implantation, 6 (46%) of 13 patients developed reherniation. After PTFE-patch implantation with separately fixed overlapping border, 1 (11%) of 9 patients had a recurrent hernia. In the group with the PTFE-cone implantation, 1 (9%) of 11 patients developed a recurrence. Meanwhile, another 20 CDH patients received implantation of a cone-shaped patch, and no further recurrence occurred up to now. With the additional space (20 mL) provided by the cone-shaped patch, the closure of the abdomen was easier, and the fundus had intraoperatively a physiological position. This optimized patch implantation technique in large diaphragmatic defects offers considerable advantages especially regarding recurrence of the hernia and closure of the abdomen, which are currently the most challenging surgical problems. 1. The cone-shaped 3-dimensional patch increases abdominal capacity. 2. Redundant chest capacity is reduced, and the reconstructed diaphragm shows a physiological shape. 3. The dome of the patch allows a physiological position of the gastric fundus and a normal Hiss angle, thus preventing gastroesophageal reflux. 4. Additional safety of the implantation is achieved by separate fixation of the overlapping border of the cone, preventing recurrence.

Spreadsheet-based program for alignment of overlapping DNA sequences.

PubMed

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.

Overlapping Phenotypes in Autism Spectrum Disorder and Developmental Coordination Disorder: A Cross-Syndrome Comparison of Motor and Social Skills.

PubMed

Sumner, Emma; Leonard, Hayley C; Hill, Elisabeth L

2016-08-01

Motor and social difficulties are often found in children with an autism spectrum disorder (ASD) and with developmental coordination disorder (DCD), to varying degrees. This study investigated the extent of overlap of these problems in children aged 7-10 years who had a diagnosis of either ASD or DCD, compared to typically-developing controls. Children completed motor and face processing assessments. Parents completed questionnaires concerning their child's early motor and current motor and social skills. There was considerable overlap between the ASD and DCD groups on the motor and social assessments, with both groups more impaired than controls. Furthermore, motor skill predicted social functioning for both groups. Future research should consider the relationships between core symptoms and their consequences in other domains.

CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription

PubMed Central

Carlson, Jonathan; Yan, Jiyu; Akinsiku, Olusimidele T.; Schaefer, Malinda; Sabbaj, Steffanie; Bet, Anne; Levy, David N.; Heath, Sonya; Tang, Jianming; Kaslow, Richard A.; Walker, Bruce D.; Ndung’u, Thumbi; Goulder, Philip J.; Heckerman, David; Hunter, Eric; Goepfert, Paul A.

2010-01-01

Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). To examine the extent of active immune response to virally encoded CEs, we analyzed human leukocyte antigen class I–associated polymorphisms in HIV-1 gag, pol, and nef genes from a large cohort of South Africans with chronic infection. In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts. In further evaluation of CD8 T cell responses to a subset of the predicted CEs in patients with primary or chronic infection, both sense- and antisense-encoded CEs were immunogenic at both stages of infection. In addition, CEs often mutated during the first year of infection, which was consistent with immune selection for escape variants. These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity. PMID:20065064

GPU-Accelerated Large-Scale Electronic Structure Theory on Titan with a First-Principles All-Electron Code

NASA Astrophysics Data System (ADS)

Huhn, William Paul; Lange, Björn; Yu, Victor; Blum, Volker; Lee, Seyong; Yoon, Mina

Density-functional theory has been well established as the dominant quantum-mechanical computational method in the materials community. Large accurate simulations become very challenging on small to mid-scale computers and require high-performance compute platforms to succeed. GPU acceleration is one promising approach. In this talk, we present a first implementation of all-electron density-functional theory in the FHI-aims code for massively parallel GPU-based platforms. Special attention is paid to the update of the density and to the integration of the Hamiltonian and overlap matrices, realized in a domain decomposition scheme on non-uniform grids. The initial implementation scales well across nodes on ORNL's Titan Cray XK7 supercomputer (8 to 64 nodes, 16 MPI ranks/node) and shows an overall speed up in runtime due to utilization of the K20X Tesla GPUs on each Titan node of 1.4x, with the charge density update showing a speed up of 2x. Further acceleration opportunities will be discussed. Work supported by the LDRD Program of ORNL managed by UT-Battle, LLC, for the U.S. DOE and by the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725.

Simulations of the Formation and Evolution of X-ray Clusters

NASA Astrophysics Data System (ADS)

Bryan, G. L.; Klypin, A.; Norman, M. L.

1994-05-01

We describe results from a set of Omega = 1 Cold plus Hot Dark Matter (CHDM) and Cold Dark Matter (CDM) simulations. We examine the formation and evolution of X-ray clusters in a cosmological setting with sufficient numbers to perform statistical analysis. We find that CDM, normalized to COBE, seems to produce too many large clusters, both in terms of the luminosity (dn/dL) and temperature (dn/dT) functions. The CHDM simulation produces fewer clusters and the temperature distribution (our numerically most secure result) matches observations where they overlap. The computed cluster luminosity function drops below observations, but we are almost surely underestimating the X-ray luminosity. Because of the lower fluctuations in CHDM, there are only a small number of bright clusters in our simulation volume; however we can use the simulated clusters to fix the relation between temperature and velocity dispersion, allowing us to use collisionless N-body codes to probe larger length scales with correspondingly brighter clusters. The hydrodynamic simulations have been performed with a hybrid particle-mesh scheme for the dark matter and a high resolution grid-based piecewise parabolic method for the adiabatic gas dynamics. This combination has been implemented for massively parallel computers, allowing us to achive grids as large as 512(3) .

On the classification of normally distributed neurons: an application to human dentate nucleus.

PubMed

Ristanović, Dušan; Milošević, Nebojša T; Marić, Dušica L

2011-03-01

One of the major goals in cellular neurobiology is the meaningful cell classification. However, in cell classification there are many unresolved issues that need to be addressed. Neuronal classification usually starts with grouping cells into classes according to their main morphological features. If one tries to test quantitatively such a qualitative classification, a considerable overlap in cell types often appears. There is little published information on it. In order to remove the above-mentioned shortcoming, we undertook the present study with the aim to offer a novel method for solving the class overlapping problem. To illustrate our method, we analyzed a sample of 124 neurons from adult human dentate nucleus. Among them we qualitatively selected 55 neurons with small dendritic fields (the small neurons), and 69 asymmetrical neurons with large dendritic fields (the large neurons). We showed that these two samples are normally and independently distributed. By measuring the neuronal soma areas of both samples, we observed that the corresponding normal curves cut each other. We proved that the abscissa of the point of intersection of the curves could represent the boundary between the two adjacent overlapping neuronal classes, since the error done by such division is minimal. Statistical evaluation of the division was also performed.

DALMATIAN: An Algorithm for Automatic Cell Detection and Counting in 3D.

PubMed

Shuvaev, Sergey A; Lazutkin, Alexander A; Kedrov, Alexander V; Anokhin, Konstantin V; Enikolopov, Grigori N; Koulakov, Alexei A

2017-01-01

Current 3D imaging methods, including optical projection tomography, light-sheet microscopy, block-face imaging, and serial two photon tomography enable visualization of large samples of biological tissue. Large volumes of data obtained at high resolution require development of automatic image processing techniques, such as algorithms for automatic cell detection or, more generally, point-like object detection. Current approaches to automated cell detection suffer from difficulties originating from detection of particular cell types, cell populations of different brightness, non-uniformly stained, and overlapping cells. In this study, we present a set of algorithms for robust automatic cell detection in 3D. Our algorithms are suitable for, but not limited to, whole brain regions and individual brain sections. We used watershed procedure to split regional maxima representing overlapping cells. We developed a bootstrap Gaussian fit procedure to evaluate the statistical significance of detected cells. We compared cell detection quality of our algorithm and other software using 42 samples, representing 6 staining and imaging techniques. The results provided by our algorithm matched manual expert quantification with signal-to-noise dependent confidence, including samples with cells of different brightness, non-uniformly stained, and overlapping cells for whole brain regions and individual tissue sections. Our algorithm provided the best cell detection quality among tested free and commercial software.

Polygenic risk for psychiatric disorders correlates with executive function in typical development.

PubMed

Schork, A J; Brown, T T; Hagler, D J; Thompson, W K; Chen, C-H; Dale, A M; Jernigan, T L; Akshoomoff, N

2018-04-16

Executive functions are a diverse and critical suite of cognitive abilities that are often disrupted in individuals with psychiatric disorders. Despite their moderate to high heritability, little is known about the molecular genetic factors that contribute to variability in executive functions and how these factors may be related to those that predispose to psychiatric disorders. We examined the relationship between polygenic risk scores built from large genome-wide association studies of psychiatric disorders and executive functioning in typically developing children. In our discovery sample (N = 417), consistent with previous reports on general cognitive abilities, polygenic risk for autism spectrum disorder was associated with better performance on the Dimensional Change Card Sort test from the NIH Cognition Toolbox, with the largest effect in the youngest children. Polygenic risk for major depressive disorder was associated with poorer performance on the Flanker test in the same sample. This second association replicated for performance on the Penn Conditional Exclusion Test in an independent cohort (N = 3681). Our results suggest that the molecular genetic factors contributing to variability in executive function during typical development are at least partially overlapping with those associated with psychiatric disorders, although larger studies and further replication are needed. © 2018 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Förster-Induced Energy Transfer in Functionalized Graphene

PubMed Central

2014-01-01

Carbon nanostructures are ideal substrates for functionalization with molecules since they consist of a single atomic layer giving rise to an extraordinary sensitivity to changes in their surrounding. The functionalization opens a new research field of hybrid nanostructures with tailored properties. Here, we present a microscopic view on the substrate–molecule interaction in the exemplary hybrid material consisting of graphene functionalized with perylene molecules. First experiments on similar systems have been recently realized illustrating an extremely efficient transfer of excitation energy from adsorbed molecules to the carbon substrate, a process with a large application potential for high-efficiency photovoltaic devices and biomedical imaging and sensing. So far, there has been no microscopically founded explanation for the observed energy transfer. Based on first-principle calculations, we have explicitly investigated the different transfer mechanisms revealing the crucial importance of Förster coupling. Due to the efficient Coulomb interaction in graphene, we obtain strong Förster rates in the range of 1/fs. We investigate its dependence on the substrate–molecule distance R and describe the impact of the momentum transfer q for an efficient energy transfer. Furthermore, we find that the Dexter transfer mechanism is negligibly small due to the vanishing overlap between the involved strongly localized orbital functions. The gained insights are applicable to a variety of carbon-based hybrid nanostructures. PMID:24808936

Measuring content overlap during handoff communication using distributional semantics: An exploratory study.

PubMed

Abraham, Joanna; Kannampallil, Thomas G; Srinivasan, Vignesh; Galanter, William L; Tagney, Gail; Cohen, Trevor

2017-01-01

We develop and evaluate a methodological approach to measure the degree and nature of overlap in handoff communication content within and across clinical professions. This extensible, exploratory approach relies on combining techniques from conversational analysis and distributional semantics. We audio-recorded handoff communication of residents and nurses on the General Medicine floor of a large academic hospital (n=120 resident and n=120 nurse handoffs). We measured semantic similarity, a proxy for content overlap, between resident-resident and nurse-nurse communication using multiple steps: a qualitative conversational content analysis; an automated semantic similarity analysis using Reflective Random Indexing (RRI); and comparing semantic similarity generated by RRI analysis with human ratings of semantic similarity. There was significant association between the semantic similarity as computed by the RRI method and human rating (ρ=0.88). Based on the semantic similarity scores, content overlap was relatively higher for content related to patient active problems, assessment of active problems, patient-identifying information, past medical history, and medications/treatments. In contrast, content overlap was limited on content related to allergies, family-related information, code status, and anticipatory guidance. Our approach using RRI analysis provides new opportunities for characterizing the nature and degree of overlap in handoff communication. Although exploratory, this method provides a basis for identifying content that can be used for determining shared understanding across clinical professions. Additionally, this approach can inform the development of flexibly standardized handoff tools that reflect clinical content that are most appropriate for fostering shared understanding during transitions of care. Copyright © 2016 Elsevier Inc. All rights reserved.

Neural Systems for Speech and Song in Autism

ERIC Educational Resources Information Center

Lai, Grace; Pantazatos, Spiro P.; Schneider, Harry; Hirsch, Joy

2012-01-01

Despite language disabilities in autism, music abilities are frequently preserved. Paradoxically, brain regions associated with these functions typically overlap, enabling investigation of neural organization supporting speech and song in autism. Neural systems sensitive to speech and song were compared in low-functioning autistic and age-matched…

Computational Study of Axial Fatigue for Peripheral Nitinol Stents

NASA Astrophysics Data System (ADS)

Meoli, Alessio; Dordoni, Elena; Petrini, Lorenza; Migliavacca, Francesco; Dubini, Gabriele; Pennati, Giancarlo

2014-07-01

Despite their success as primary treatment for vascular diseases, Nitinol peripheral stents are still affected by complications related to fatigue failure. Hip and knee movements during daily activities produce large and cyclic deformations of the superficial femoral artery, that concomitant to the effects of pulsatile blood pressure, may cause fatigue failure in the stent. Fatigue failure typically occurs in cases of very extended lesions, which often require the use of two or more overlapping stents. In this study, finite element models were used to study the fatigue behavior of Nitinol stents when subjected to cyclic axial compression in different conditions. A specific commercial Nitinol stent was chosen for the analysis and subjected to cyclic axial compression typical of the femoral vascular region. Three different configurations were investigated: stent alone, stent deployed in a tube, and two overlapping stents deployed in a tube. Results confirm that stent oversizing has an influence in determining both the mean and amplitude strains induced in the stent and plays an important role in determining the fatigue response of Nitinol stents. In case of overlapping stents, numerical results suggest higher amplitude strains concentrate in the region close to the overlapping portion where the abrupt change in stiffness causes higher cyclic compression. These findings help to explain the high incidence of stent fractures observed in various clinical trials located close to the overlapping portion.

Investigating the relationship among transformational leadership, interpersonal interaction and mentoring functions.

PubMed

Huang, Ching-Yuan; Weng, Rhay-Hung; Chen, Yi-Ting

2016-08-01

This study aims to ascertain the relationship between transformational leadership, interpersonal interaction and mentoring functions among new staff nurses. Mentoring functions could improve the job performance of new nurses, provide them with support and thus reduce their turnover rate. A cross-sectional study was employed. A questionnaire survey was carried out to collect data among a sample of new nurses from three hospitals in Taiwan. After gathering a total of 306 valid surveys, multiple regression analysis was applied to test the hypothesis. Inspirational motivation, idealised influence and individualised consideration had positive correlations with the overall mentoring function, but intellectual stimulation showed a positive association only with career development function. Perceived similarity and interaction frequency also had positive correlations with mentoring functions. When the shift overlap rate exceeded 80%, mentoring function showed a negative result. The transformational leadership of mentors would improve the mentoring functions among new staff nurses. Perceived similarity and interaction frequency between mentees and mentors also had positive correlations with mentoring functions. It is crucial for hospitals to redesign their leadership training and motivation programmes to enhance the transformational leadership of mentors. Furthermore, nursing managers should promote interaction between new staff nurses and their mentors; however, the shift overlap rate should not be too high. © 2016 John Wiley & Sons Ltd.

Strong genetic overlap between executive functions and intelligence.

PubMed

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).

Replication stress induces accumulation of FANCD2 at central region of large fragile genes

PubMed Central

Okamoto, Yusuke; Iwasaki, Watal M; Kugou, Kazuto; Takahashi, Kazuki K; Oda, Arisa; Sato, Koichi; Kobayashi, Wataru; Kawai, Hidehiko; Sakasai, Ryo; Takaori-Kondo, Akifumi; Yamamoto, Takashi; Kanemaki, Masato T; Taoka, Masato; Isobe, Toshiaki; Kurumizaka, Hitoshi; Innan, Hideki; Ohta, Kunihiro; Ishiai, Masamichi; Takata, Minoru

2018-01-01

Abstract During mild replication stress provoked by low dose aphidicolin (APH) treatment, the key Fanconi anemia protein FANCD2 accumulates on common fragile sites, observed as sister foci, and protects genome stability. To gain further insights into FANCD2 function and its regulatory mechanisms, we examined the genome-wide chromatin localization of FANCD2 in this setting by ChIP-seq analysis. We found that FANCD2 mostly accumulates in the central regions of a set of large transcribed genes that were extensively overlapped with known CFS. Consistent with previous studies, we found that this FANCD2 retention is R-loop-dependent. However, FANCD2 monoubiquitination and RPA foci formation were still induced in cells depleted of R-loops. Interestingly, we detected increased Proximal Ligation Assay dots between FANCD2 and R-loops following APH treatment, which was suppressed by transcriptional inhibition. Collectively, our data suggested that R-loops are required to retain FANCD2 in chromatin at the middle intronic region of large genes, while the replication stress-induced upstream events leading to the FA pathway activation are not triggered by R-loops. PMID:29394375

GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage▿ †

PubMed Central

Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Van Nostrand, Joy D.; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou

2011-01-01

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems. PMID:21097602

Pollination syndromes in African Marantaceae

PubMed Central

Ley, Alexandra C.; Claßen-Bockhoff, Regine

2009-01-01

Background and Aims The Marantaceae (550 spp.) is the most derived family in the order Zingiberales and exhibits a complex explosive pollination mechanism. To understand the evolutionary significance of this unique process of pollen transfer, comparative morphological and ecological studies were conducted in Gabon. Methods During a total stay of 11 months, 31 species of Marantaceae were investigated at different sites in Gabon. The study included analyses of floral diversity, observations on the pollinator spectrum as well as ecological measurements (e.g. nectar sugar concentration and volume). Key Results Analyses reveal five flower types based on flower size and pigmentation, spatial arrangement of the floral tube and presence/absence of nectar guides and conspicuous outer staminodes. Each type is associated with a specific functional pollinator group leading to the description of distinct pollination syndromes. The ‘small (horizontal)’ flowers are predominantly pollinated by small bees (Thrinchostoma spp., Allodapula ornaticeps), the ‘large (horizontal)’ and ‘medium-sized (horizontal)’ flowers by medium-sized bees (Amegilla vivida, Thrinchostoma bicometes), the ‘locked (horizontal)’ flowers by large bees (Xylocopa nigrita, X. varipes) and the ‘(large) vertical’ flowers by sunbirds. Conclusions The longevity of Marantaceae individuals and the omnipresence of their pollinators allowed the specialization to a given functional pollinator group. Intermediate ecological values, however, make occasional pollinator overlaps possible, indicating potential pathways of pollinator shifts. Similar radiation tendencies observed on other continents hint at similar selective pressures and evolutionary constraints. PMID:19443460

Nonhost Resistance of Barley to Different Fungal Pathogens Is Associated with Largely Distinct, Quantitative Transcriptional Responses1[W][OA

PubMed Central

Zellerhoff, Nina; Himmelbach, Axel; Dong, Wubei; Bieri, Stephane; Schaffrath, Ulrich; Schweizer, Patrick

2010-01-01

Nonhost resistance protects plants against attack by the vast majority of potential pathogens, including phytopathogenic fungi. Despite its high biological importance, the molecular architecture of nonhost resistance has remained largely unexplored. Here, we describe the transcriptional responses of one particular genotype of barley (Hordeum vulgare subsp. vulgare ‘Ingrid’) to three different pairs of adapted (host) and nonadapted (nonhost) isolates of fungal pathogens, which belong to the genera Blumeria (powdery mildew), Puccinia (rust), and Magnaporthe (blast). Nonhost resistance against each of these pathogens was associated with changes in transcript abundance of distinct sets of nonhost-specific genes, although general (not nonhost-associated) transcriptional responses to the different pathogens overlapped considerably. The powdery mildew- and blast-induced differences in transcript abundance between host and nonhost interactions were significantly correlated with differences between a near-isogenic pair of barley lines that carry either the Mlo wild-type allele or the mutated mlo5 allele, which mediates basal resistance to powdery mildew. Moreover, during the interactions of barley with the different host or nonhost pathogens, similar patterns of overrepresented and underrepresented functional categories of genes were found. The results suggest that nonhost resistance and basal host defense of barley are functionally related and that nonhost resistance to different fungal pathogens is associated with more robust regulation of complex but largely nonoverlapping sets of pathogen-responsive genes involved in similar metabolic or signaling pathways. PMID:20172964