fMRI activation patterns in an analytic reasoning task: consistency with EEG source localization

NASA Astrophysics Data System (ADS)

Li, Bian; Vasanta, Kalyana C.; O'Boyle, Michael; Baker, Mary C.; Nutter, Brian; Mitra, Sunanda

2010-03-01

Functional magnetic resonance imaging (fMRI) is used to model brain activation patterns associated with various perceptual and cognitive processes as reflected by the hemodynamic (BOLD) response. While many sensory and motor tasks are associated with relatively simple activation patterns in localized regions, higher-order cognitive tasks may produce activity in many different brain areas involving complex neural circuitry. We applied a recently proposed probabilistic independent component analysis technique (PICA) to determine the true dimensionality of the fMRI data and used EEG localization to identify the common activated patterns (mapped as Brodmann areas) associated with a complex cognitive task like analytic reasoning. Our preliminary study suggests that a hybrid GLM/PICA analysis may reveal additional regions of activation (beyond simple GLM) that are consistent with electroencephalography (EEG) source localization patterns.

Entropic Movement Complexity Reflects Subjective Creativity Rankings of Visualized Hand Motion Trajectories

PubMed Central

Peng, Zhen; Braun, Daniel A.

2015-01-01

In a previous study we have shown that human motion trajectories can be characterized by translating continuous trajectories into symbol sequences with well-defined complexity measures. Here we test the hypothesis that the motion complexity individuals generate in their movements might be correlated to the degree of creativity assigned by a human observer to the visualized motion trajectories. We asked participants to generate 55 novel hand movement patterns in virtual reality, where each pattern had to be repeated 10 times in a row to ensure reproducibility. This allowed us to estimate a probability distribution over trajectories for each pattern. We assessed motion complexity not only by the previously proposed complexity measures on symbolic sequences, but we also propose two novel complexity measures that can be directly applied to the distributions over trajectories based on the frameworks of Gaussian Processes and Probabilistic Movement Primitives. In contrast to previous studies, these new methods allow computing complexities of individual motion patterns from very few sample trajectories. We compared the different complexity measures to how a group of independent jurors rank ordered the recorded motion trajectories according to their personal creativity judgment. We found three entropic complexity measures that correlate significantly with human creativity judgment and discuss differences between the measures. We also test whether these complexity measures correlate with individual creativity in divergent thinking tasks, but do not find any consistent correlation. Our results suggest that entropic complexity measures of hand motion may reveal domain-specific individual differences in kinesthetic creativity. PMID:26733896

A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.

PubMed

Romero, José R; Carballido, Jessica A; Garbus, Ingrid; Echenique, Viviana C; Ponzoni, Ignacio

2016-01-01

The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size. The methodology used in this study, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa , revealed that it is possible to identify putative nested TEs by detecting these three types of patterns. The results were validated through BLAST alignments, which revealed the efficacy and usefulness of the new method, which is called Mamushka.

Audio-based, unsupervised machine learning reveals cyclic changes in earthquake mechanisms in the Geysers geothermal field, California

NASA Astrophysics Data System (ADS)

Holtzman, B. K.; Paté, A.; Paisley, J.; Waldhauser, F.; Repetto, D.; Boschi, L.

2017-12-01

The earthquake process reflects complex interactions of stress, fracture and frictional properties. New machine learning methods reveal patterns in time-dependent spectral properties of seismic signals and enable identification of changes in faulting processes. Our methods are based closely on those developed for music information retrieval and voice recognition, using the spectrogram instead of the waveform directly. Unsupervised learning involves identification of patterns based on differences among signals without any additional information provided to the algorithm. Clustering of 46,000 earthquakes of $0.3

Differential Roles of the Fan-Shaped Body and the Ellipsoid Body in "Drosophila" Visual Pattern Memory

ERIC Educational Resources Information Center

Pan, Yufeng; Zhou, Yanqiong; Guo, Chao; Gong, Haiyun; Gong, Zhefeng; Liu, Li

2009-01-01

The central complex is a prominent structure in the "Drosophila" brain. Visual learning experiments in the flight simulator, with flies with genetically altered brains, revealed that two groups of horizontal neurons in one of its substructures, the fan-shaped body, were required for "Drosophila" visual pattern memory. However,…

A framework for the comparative study of language.

PubMed

Uriagereka, Juan; Reggia, James A; Wilkinson, Gerald S

2013-07-18

Comparative studies of language are difficult because few language precursors are recognized. In this paper we propose a framework for designing experiments that test for structural and semantic patterns indicative of simple or complex grammars as originally described by Chomsky. We argue that a key issue is whether animals can recognize full recursion, which is the hallmark of context-free grammar. We discuss limitations of recent experiments that have attempted to address this issue, and point out that experiments aimed at detecting patterns that follow a Fibonacci series have advantages over other artificial context-free grammars. We also argue that experiments using complex sequences of behaviors could, in principle, provide evidence for fully recursive thought. Some of these ideas could also be approached using artificial life simulations, which have the potential to reveal the types of evolutionary transitions that could occur over time. Because the framework we propose has specific memory and computational requirements, future experiments could target candidate genes with the goal of revealing the genetic underpinnings of complex cognition.

Cell-type- and tissue-specific transcriptomes of the white spruce (Picea glauca) bark unmask fine-scale spatial patterns of constitutive and induced conifer defense.

PubMed

Celedon, Jose M; Yuen, Macaire M S; Chiang, Angela; Henderson, Hannah; Reid, Karen E; Bohlmann, Jörg

2017-11-01

Plant defenses often involve specialized cells and tissues. In conifers, specialized cells of the bark are important for defense against insects and pathogens. Using laser microdissection, we characterized the transcriptomes of cortical resin duct cells, phenolic cells and phloem of white spruce (Picea glauca) bark under constitutive and methyl jasmonate (MeJa)-induced conditions, and we compared these transcriptomes with the transcriptome of the bark tissue complex. Overall, ~3700 bark transcripts were differentially expressed in response to MeJa. Approximately 25% of transcripts were expressed in only one cell type, revealing cell specialization at the transcriptome level. MeJa caused cell-type-specific transcriptome responses and changed the overall patterns of cell-type-specific transcript accumulation. Comparison of transcriptomes of the conifer bark tissue complex and specialized cells resolved a masking effect inherent to transcriptome analysis of complex tissues, and showed the actual cell-type-specific transcriptome signatures. Characterization of cell-type-specific transcriptomes is critical to reveal the dynamic patterns of spatial and temporal display of constitutive and induced defense systems in a complex plant tissue or organ. This was demonstrated with the improved resolution of spatially restricted expression of sets of genes of secondary metabolism in the specialized cell types. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

A Design Principle for an Autonomous Post-translational Pattern Formation.

PubMed

Sugai, Shuhei S; Ode, Koji L; Ueda, Hiroki R

2017-04-25

Previous autonomous pattern-formation models often assumed complex molecular and cellular networks. This theoretical study, however, shows that a system composed of one substrate with multisite phosphorylation and a pair of kinase and phosphatase can generate autonomous spatial information, including complex stripe patterns. All (de-)phosphorylation reactions are described with a generic Michaelis-Menten scheme, and all species freely diffuse without pre-existing gradients. Computational simulation upon >23,000,000 randomly generated parameter sets revealed the design motifs of cyclic reaction and enzyme sequestration by slow-diffusing substrates. These motifs constitute short-range positive and long-range negative feedback loops to induce Turing instability. The width and height of spatial patterns can be controlled independently by distinct reaction-diffusion processes. Therefore, multisite reversible post-translational modification can be a ubiquitous source for various patterns without requiring other complex regulations such as autocatalytic regulation of enzymes and is applicable to molecular mechanisms for inducing subcellular localization of proteins driven by post-translational modifications. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

The benefits of flexible team interaction during crises.

PubMed

Stachowski, Alicia A; Kaplan, Seth A; Waller, Mary J

2009-11-01

Organizations increasingly rely on teams to respond to crises. While research on team effectiveness during nonroutine events is growing, naturalistic studies examining team behaviors during crises are relatively scarce. Furthermore, the relevant literature offers competing theoretical rationales concerning effective team response to crises. In this article, the authors investigate whether high- versus average-performing teams can be distinguished on the basis of the number and complexity of their interaction patterns. Using behavioral observation methodology, the authors coded the discrete verbal and nonverbal behaviors of 14 nuclear power plant control room crews as they responded to a simulated crisis. Pattern detection software revealed systematic differences among crews in their patterns of interaction. Mean comparisons and discriminant function analysis indicated that higher performing crews exhibited fewer, shorter, and less complex interaction patterns. These results illustrate the limitations of standardized response patterns and highlight the importance of team adaptability. Implications for future research and for team training are included.

Regimes of Flow over Complex Structures of Endothelial Glycocalyx: A Molecular Dynamics Simulation Study.

PubMed

Jiang, Xi Zhuo; Feng, Muye; Ventikos, Yiannis; Luo, Kai H

2018-04-10

Flow patterns on surfaces grafted with complex structures play a pivotal role in many engineering and biomedical applications. In this research, large-scale molecular dynamics (MD) simulations are conducted to study the flow over complex surface structures of an endothelial glycocalyx layer. A detailed structure of glycocalyx has been adopted and the flow/glycocalyx system comprises about 5,800,000 atoms. Four cases involving varying external forces and modified glycocalyx configurations are constructed to reveal intricate fluid behaviour. Flow profiles including temporal evolutions and spatial distributions of velocity are illustrated. Moreover, streamline length and vorticity distributions under the four scenarios are compared and discussed to elucidate the effects of external forces and glycocalyx configurations on flow patterns. Results show that sugar chain configurations affect streamline length distributions but their impact on vorticity distributions is statistically insignificant, whilst the influence of the external forces on both streamline length and vorticity distributions are trivial. Finally, a regime diagram for flow over complex surface structures is proposed to categorise flow patterns.

Small peptides patterned after the N-terminus domain of SNAP25 inhibit SNARE complex assembly and regulated exocytosis.

PubMed

Blanes-Mira, Clara; Merino, Jaime M; Valera, Elvira; Fernández-Ballester, Gregorio; Gutiérrez, Luis M; Viniegra, Salvador; Pérez-Payá, Enrique; Ferrer-Montiel, Antonio

2004-01-01

Synthetic peptides patterned after the C-terminus of synaptosomal associated protein of 25 kDa (SNAP25) efficiently abrogate regulated exocytosis. In contrast, the use of SNAP25 N-terminal-derived peptides to modulate SNAP receptors (SNARE) complex assembly and neurosecretion has not been explored. Here, we show that the N-terminus of SNAP25, specially the segment that encompasses 22Ala-44Ile, is essential for the formation of the SNARE complex. Peptides patterned after this protein domain are potent inhibitors of SNARE complex formation. The inhibitory activity correlated with their propensity to adopt an alpha-helical secondary structure. These peptides abrogated SNARE complex formation only when added previous to the onset of aggregate assembly. Analysis of the mechanism of action revealed that these peptides disrupted the binary complex formed by SNAP25 and syntaxin. The identified peptides inhibited Ca2+-dependent exocytosis from detergent-permeabilized excitable cells. Noteworthy, these amino acid sequences markedly protected intact hippocampal neurones against hypoglycaemia-induced, glutamate-mediated excitotoxicity with a potency that rivalled that displayed by botulinum neurotoxins. Our findings indicate that peptides patterned after the N-terminus of SNAP25 are potent inhibitors of SNARE complex formation and neuronal exocytosis. Because of their activity in intact neurones, these cell permeable peptides may be hits for antispasmodic and analgesic drug development.

Candidate gene screen in the red flour beetle Tribolium reveals six3 as ancient regulator of anterior median head and central complex development.

PubMed

Posnien, Nico; Koniszewski, Nikolaus Dieter Bernhard; Hein, Hendrikje Jeannette; Bucher, Gregor

2011-12-01

Several highly conserved genes play a role in anterior neural plate patterning of vertebrates and in head and brain patterning of insects. However, head involution in Drosophila has impeded a systematic identification of genes required for insect head formation. Therefore, we use the red flour beetle Tribolium castaneum in order to comprehensively test the function of orthologs of vertebrate neural plate patterning genes for a function in insect head development. RNAi analysis reveals that most of these genes are indeed required for insect head capsule patterning, and we also identified several genes that had not been implicated in this process before. Furthermore, we show that Tc-six3/optix acts upstream of Tc-wingless, Tc-orthodenticle1, and Tc-eyeless to control anterior median development. Finally, we demonstrate that Tc-six3/optix is the first gene known to be required for the embryonic formation of the central complex, a midline-spanning brain part connected to the neuroendocrine pars intercerebralis. These functions are very likely conserved among bilaterians since vertebrate six3 is required for neuroendocrine and median brain development with certain mutations leading to holoprosencephaly.

Candidate Gene Screen in the Red Flour Beetle Tribolium Reveals Six3 as Ancient Regulator of Anterior Median Head and Central Complex Development

PubMed Central

Hein, Hendrikje Jeannette; Bucher, Gregor

2011-01-01

Several highly conserved genes play a role in anterior neural plate patterning of vertebrates and in head and brain patterning of insects. However, head involution in Drosophila has impeded a systematic identification of genes required for insect head formation. Therefore, we use the red flour beetle Tribolium castaneum in order to comprehensively test the function of orthologs of vertebrate neural plate patterning genes for a function in insect head development. RNAi analysis reveals that most of these genes are indeed required for insect head capsule patterning, and we also identified several genes that had not been implicated in this process before. Furthermore, we show that Tc-six3/optix acts upstream of Tc-wingless, Tc-orthodenticle1, and Tc-eyeless to control anterior median development. Finally, we demonstrate that Tc-six3/optix is the first gene known to be required for the embryonic formation of the central complex, a midline-spanning brain part connected to the neuroendocrine pars intercerebralis. These functions are very likely conserved among bilaterians since vertebrate six3 is required for neuroendocrine and median brain development with certain mutations leading to holoprosencephaly. PMID:22216011

Unraveling dynamics of human physical activity patterns in chronic pain conditions

NASA Astrophysics Data System (ADS)

Paraschiv-Ionescu, Anisoara; Buchser, Eric; Aminian, Kamiar

2013-06-01

Chronic pain is a complex disabling experience that negatively affects the cognitive, affective and physical functions as well as behavior. Although the interaction between chronic pain and physical functioning is a well-accepted paradigm in clinical research, the understanding of how pain affects individuals' daily life behavior remains a challenging task. Here we develop a methodological framework allowing to objectively document disruptive pain related interferences on real-life physical activity. The results reveal that meaningful information is contained in the temporal dynamics of activity patterns and an analytical model based on the theory of bivariate point processes can be used to describe physical activity behavior. The model parameters capture the dynamic interdependence between periods and events and determine a `signature' of activity pattern. The study is likely to contribute to the clinical understanding of complex pain/disease-related behaviors and establish a unified mathematical framework to quantify the complex dynamics of various human activities.

Complex Ordered Patterns in Mechanical Instability Induced Geometrically Frustrated Triangular Cellular Structures

NASA Astrophysics Data System (ADS)

Kang, Sung Hoon; Shan, Sicong; Košmrlj, Andrej; Noorduin, Wim L.; Shian, Samuel; Weaver, James C.; Clarke, David R.; Bertoldi, Katia

2014-03-01

Geometrical frustration arises when a local order cannot propagate throughout the space because of geometrical constraints. This phenomenon plays a major role in many systems leading to disordered ground-state configurations. Here, we report a theoretical and experimental study on the behavior of buckling-induced geometrically frustrated triangular cellular structures. To our surprise, we find that buckling induces complex ordered patterns which can be tuned by controlling the porosity of the structures. Our analysis reveals that the connected geometry of the cellular structure plays a crucial role in the generation of ordered states in this frustrated system.

Night and day variations of sleep in patients with disorders of consciousness.

PubMed

Wislowska, Malgorzata; Del Giudice, Renata; Lechinger, Julia; Wielek, Tomasz; Heib, Dominik P J; Pitiot, Alain; Pichler, Gerald; Michitsch, Gabriele; Donis, Johann; Schabus, Manuel

2017-03-21

Brain injuries substantially change the entire landscape of oscillatory dynamics and render detection of typical sleep patterns difficult. Yet, sleep is characterized not only by specific EEG waveforms, but also by its circadian organization. In the present study we investigated whether brain dynamics of patients with disorders of consciousness systematically change between day and night. We recorded ~24 h EEG at the bedside of 18 patients diagnosed to be vigilant but unaware (Unresponsive Wakefulness Syndrome) and 17 patients revealing signs of fluctuating consciousness (Minimally Conscious State). The day-to-night changes in (i) spectral power, (ii) sleep-specific oscillatory patterns and (iii) signal complexity were analyzed and compared to 26 healthy control subjects. Surprisingly, the prevalence of sleep spindles and slow waves did not systematically vary between day and night in patients, whereas day-night changes in EEG power spectra and signal complexity were revealed in minimally conscious but not unaware patients.

Conceptual recurrence plots: revealing patterns in human discourse.

PubMed

Angus, Daniel; Smith, Andrew; Wiles, Janet

2012-06-01

Human discourse contains a rich mixture of conceptual information. Visualization of the global and local patterns within this data stream is a complex and challenging problem. Recurrence plots are an information visualization technique that can reveal trends and features in complex time series data. The recurrence plot technique works by measuring the similarity of points in a time series to all other points in the same time series and plotting the results in two dimensions. Previous studies have applied recurrence plotting techniques to textual data; however, these approaches plot recurrence using term-based similarity rather than conceptual similarity of the text. We introduce conceptual recurrence plots, which use a model of language to measure similarity between pairs of text utterances, and the similarity of all utterances is measured and displayed. In this paper, we explore how the descriptive power of the recurrence plotting technique can be used to discover patterns of interaction across a series of conversation transcripts. The results suggest that the conceptual recurrence plotting technique is a useful tool for exploring the structure of human discourse.

A model of the transverse modes of stable and unstable porro-prism resonators using symmetry considerations

NASA Astrophysics Data System (ADS)

Burger, Liesl; Forbes, Andrew

2007-09-01

A simple model of a Porro prism laser resonator has been found to correctly predict the formation of the "petal" mode patterns typical of these resonators. A geometrical analysis of the petals suggests that these petals are the lowest-order modes of this type of resonator. Further use of the model reveals the formation of more complex beam patterns, and the nature of these patterns is investigated. Also, the output of stable and unstable resonator modes is presented.

Task-phase-specific dynamics of basal forebrain neuronal ensembles

PubMed Central

Tingley, David; Alexander, Andrew S.; Kolbu, Sean; de Sa, Virginia R.; Chiba, Andrea A.; Nitz, Douglas A.

2014-01-01

Cortically projecting basal forebrain neurons play a critical role in learning and attention, and their degeneration accompanies age-related impairments in cognition. Despite the impressive anatomical and cell-type complexity of this system, currently available data suggest that basal forebrain neurons lack complexity in their response fields, with activity primarily reflecting only macro-level brain states such as sleep and wake, onset of relevant stimuli and/or reward obtainment. The current study examined the spiking activity of basal forebrain neuron populations across multiple phases of a selective attention task, addressing, in particular, the issue of complexity in ensemble firing patterns across time. Clustering techniques applied to the full population revealed a large number of distinct categories of task-phase-specific activity patterns. Unique population firing-rate vectors defined each task phase and most categories of task-phase-specific firing had counterparts with opposing firing patterns. An analogous set of task-phase-specific firing patterns was also observed in a population of posterior parietal cortex neurons. Thus, consistent with the known anatomical complexity, basal forebrain population dynamics are capable of differentially modulating their cortical targets according to the unique sets of environmental stimuli, motor requirements, and cognitive processes associated with different task phases. PMID:25309352

An evaluation of space time cube representation of spatiotemporal patterns.

PubMed

Kristensson, Per Ola; Dahlbäck, Nils; Anundi, Daniel; Björnstad, Marius; Gillberg, Hanna; Haraldsson, Jonas; Mårtensson, Ingrid; Nordvall, Mathias; Ståhl, Josefine

2009-01-01

Space time cube representation is an information visualization technique where spatiotemporal data points are mapped into a cube. Information visualization researchers have previously argued that space time cube representation is beneficial in revealing complex spatiotemporal patterns in a data set to users. The argument is based on the fact that both time and spatial information are displayed simultaneously to users, an effect difficult to achieve in other representations. However, to our knowledge the actual usefulness of space time cube representation in conveying complex spatiotemporal patterns to users has not been empirically validated. To fill this gap, we report on a between-subjects experiment comparing novice users' error rates and response times when answering a set of questions using either space time cube or a baseline 2D representation. For some simple questions, the error rates were lower when using the baseline representation. For complex questions where the participants needed an overall understanding of the spatiotemporal structure of the data set, the space time cube representation resulted in on average twice as fast response times with no difference in error rates compared to the baseline. These results provide an empirical foundation for the hypothesis that space time cube representation benefits users analyzing complex spatiotemporal patterns.

Biological pattern formation: from basic mechanisms to complex structures

NASA Astrophysics Data System (ADS)

Koch, A. J.; Meinhardt, H.

1994-10-01

The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns? Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of Drosophila and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

Stability in Real Food Webs: Weak Links in Long Loops

NASA Astrophysics Data System (ADS)

Neutel, Anje-Margriet; Heesterbeek, Johan A. P.; de Ruiter, Peter C.

2002-05-01

Increasing evidence that the strengths of interactions among populations in biological communities form patterns that are crucial for system stability requires clarification of the precise form of these patterns, how they come about, and why they influence stability. We show that in real food webs, interaction strengths are organized in trophic loops in such a way that long loops contain relatively many weak links. We show and explain mathematically that this patterning enhances stability, because it reduces maximum ``loop weight'' and thus reduces the amount of intraspecific interaction needed for matrix stability. The patterns are brought about by biomass pyramids, a feature common to most ecosystems. Incorporation of biomass pyramids in 104 food-web descriptions reveals that the low weight of the long loops stabilizes complex food webs. Loop-weight analysis could be a useful tool for exploring the structure and organization of complex communities.

Complex Patterns of Local Adaptation in Teosinte

PubMed Central

Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

2013-01-01

Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network.

PubMed

Sikkink, Kristin L; Reynolds, Rose M; Cresko, William A; Phillips, Patrick C

2015-05-01

Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks. © 2015 The Author(s).

ENVIRONMENTALLY INDUCED CHANGES IN CORRELATED RESPONSES TO SELECTION REVEAL VARIABLE PLEIOTROPY ACROSS A COMPLEX GENETIC NETWORK

PubMed Central

Sikkink, Kristin L.; Reynolds, Rose M.; Cresko, William A.; Phillips, Patrick C.

2017-01-01

Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks. PMID:25809411

Machine learning reveals cyclic changes in seismic source spectra in Geysers geothermal field.

PubMed

Holtzman, Benjamin K; Paté, Arthur; Paisley, John; Waldhauser, Felix; Repetto, Douglas

2018-05-01

The earthquake rupture process comprises complex interactions of stress, fracture, and frictional properties. New machine learning methods demonstrate great potential to reveal patterns in time-dependent spectral properties of seismic signals and enable identification of changes in faulting processes. Clustering of 46,000 earthquakes of 0.3 < M L < 1.5 from the Geysers geothermal field (CA) yields groupings that have no reservoir-scale spatial patterns but clear temporal patterns. Events with similar spectral properties repeat on annual cycles within each cluster and track changes in the water injection rates into the Geysers reservoir, indicating that changes in acoustic properties and faulting processes accompany changes in thermomechanical state. The methods open new means to identify and characterize subtle changes in seismic source properties, with applications to tectonic and geothermal seismicity.

A case of brugada syndrome presenting with ventricular fibrillation storm and prominent early repolarization.

PubMed

Iizuka, Chifumi; Sato, Masahito; Kitazawa, Hitoshi; Ikeda, Yoshio; Okabe, Masaaki; Kugiyama, Kiyotaka; Aizawa, Yoshifusa

2016-01-01

A 21-year-old man developed ventricular fibrillation (VF) while drinking alcohol and was admitted to our hospital. An electrocardiogram (ECG) on admission revealed remarkably prominent slurs on the terminal part of QRS complexes in the left precordial leads and a coved type ST elevation at higher intercostal spaces. After hypothermia therapy, he underwent implantation of an implantable cardioverter-defibrillator (ICD). Standard twelve-lead follow-up ECGs revealed early repolarization pattern and an intermittent coved type ST elevation. When the coved type ST elevation appeared, the early repolarization pattern in the inferior and left precordial leads was attenuated. Prominent early repolarization pattern was the most likely trigger of the VF storm in this Brugada patient. Copyright © 2016 Elsevier Inc. All rights reserved.

Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative.

PubMed

Hertach, Thomas; Puissant, Stéphane; Gogala, Matija; Trilar, Tomi; Hagmann, Reto; Baur, Hannes; Kunz, Gernot; Wade, Elizabeth J; Loader, Simon P; Simon, Chris; Nagel, Peter

2016-01-01

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a "complex within the complex": the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive introgression and mitochondrial capture.

Single-cell analysis of peptide expression and electrophysiology of right parietal neurons involved in male copulation behavior of a simultaneous hermaphrodite.

PubMed

El Filali, Z; de Boer, P A C M; Pieneman, A W; de Lange, R P J; Jansen, R F; Ter Maat, A; van der Schors, R C; Li, K W; van Straalen, N M; Koene, J M

2015-12-01

Male copulation is a complex behavior that requires coordinated communication between the nervous system and the peripheral reproductive organs involved in mating. In hermaphroditic animals, such as the freshwater snail Lymnaea stagnalis, this complexity increases since the animal can behave both as male and female. The performance of the sexual role as a male is coordinated via a neuronal communication regulated by many peptidergic neurons, clustered in the cerebral and pedal ganglia and dispersed in the pleural and parietal ganglia. By combining single-cell matrix-assisted laser mass spectrometry with retrograde staining and electrophysiology, we analyzed neuropeptide expression of single neurons of the right parietal ganglion and their axonal projections into the penial nerve. Based on the neuropeptide profile of these neurons, we were able to reconstruct a chemical map of the right parietal ganglion revealing a striking correlation with the earlier electrophysiological and neuroanatomical studies. Neurons can be divided into two main groups: (i) neurons that express heptapeptides and (ii) neurons that do not. The neuronal projection of the different neurons into the penial nerve reveals a pattern where (spontaneous) activity is related to branching pattern. This heterogeneity in both neurochemical anatomy and branching pattern of the parietal neurons reflects the complexity of the peptidergic neurotransmission involved in the regulation of male mating behavior in this simultaneous hermaphrodite.

Temporal Structure and Complexity Affect Audio-Visual Correspondence Detection

PubMed Central

Denison, Rachel N.; Driver, Jon; Ruff, Christian C.

2013-01-01

Synchrony between events in different senses has long been considered the critical temporal cue for multisensory integration. Here, using rapid streams of auditory and visual events, we demonstrate how humans can use temporal structure (rather than mere temporal coincidence) to detect multisensory relatedness. We find psychophysically that participants can detect matching auditory and visual streams via shared temporal structure for crossmodal lags of up to 200 ms. Performance on this task reproduced features of past findings based on explicit timing judgments but did not show any special advantage for perfectly synchronous streams. Importantly, the complexity of temporal patterns influences sensitivity to correspondence. Stochastic, irregular streams – with richer temporal pattern information – led to higher audio-visual matching sensitivity than predictable, rhythmic streams. Our results reveal that temporal structure and its complexity are key determinants for human detection of audio-visual correspondence. The distinctive emphasis of our new paradigms on temporal patterning could be useful for studying special populations with suspected abnormalities in audio-visual temporal perception and multisensory integration. PMID:23346067

Community Detection in Complex Networks via Clique Conductance.

PubMed

Lu, Zhenqi; Wahlström, Johan; Nehorai, Arye

2018-04-13

Network science plays a central role in understanding and modeling complex systems in many areas including physics, sociology, biology, computer science, economics, politics, and neuroscience. One of the most important features of networks is community structure, i.e., clustering of nodes that are locally densely interconnected. Communities reveal the hierarchical organization of nodes, and detecting communities is of great importance in the study of complex systems. Most existing community-detection methods consider low-order connection patterns at the level of individual links. But high-order connection patterns, at the level of small subnetworks, are generally not considered. In this paper, we develop a novel community-detection method based on cliques, i.e., local complete subnetworks. The proposed method overcomes the deficiencies of previous similar community-detection methods by considering the mathematical properties of cliques. We apply the proposed method to computer-generated graphs and real-world network datasets. When applied to networks with known community structure, the proposed method detects the structure with high fidelity and sensitivity. When applied to networks with no a priori information regarding community structure, the proposed method yields insightful results revealing the organization of these complex networks. We also show that the proposed method is guaranteed to detect near-optimal clusters in the bipartition case.

Robust hierarchical state-space models reveal diel variation in travel rates of migrating leatherback turtles.

PubMed

Jonsen, Ian D; Myers, Ransom A; James, Michael C

2006-09-01

1. Biological and statistical complexity are features common to most ecological data that hinder our ability to extract meaningful patterns using conventional tools. Recent work on implementing modern statistical methods for analysis of such ecological data has focused primarily on population dynamics but other types of data, such as animal movement pathways obtained from satellite telemetry, can also benefit from the application of modern statistical tools. 2. We develop a robust hierarchical state-space approach for analysis of multiple satellite telemetry pathways obtained via the Argos system. State-space models are time-series methods that allow unobserved states and biological parameters to be estimated from data observed with error. We show that the approach can reveal important patterns in complex, noisy data where conventional methods cannot. 3. Using the largest Atlantic satellite telemetry data set for critically endangered leatherback turtles, we show that the diel pattern in travel rates of these turtles changes over different phases of their migratory cycle. While foraging in northern waters the turtles show similar travel rates during day and night, but on their southward migration to tropical waters travel rates are markedly faster during the day. These patterns are generally consistent with diving data, and may be related to changes in foraging behaviour. Interestingly, individuals that migrate southward to breed generally show higher daytime travel rates than individuals that migrate southward in a non-breeding year. 4. Our approach is extremely flexible and can be applied to many ecological analyses that use complex, sequential data.

Human area MT+ shows load-dependent activation during working memory maintenance with continuously morphing stimulation.

PubMed

Galashan, Daniela; Fehr, Thorsten; Kreiter, Andreas K; Herrmann, Manfred

2014-07-11

Initially, human area MT+ was considered a visual area solely processing motion information but further research has shown that it is also involved in various different cognitive operations, such as working memory tasks requiring motion-related information to be maintained or cognitive tasks with implied or expected motion.In the present fMRI study in humans, we focused on MT+ modulation during working memory maintenance using a dynamic shape-tracking working memory task with no motion-related working memory content. Working memory load was systematically varied using complex and simple stimulus material and parametrically increasing retention periods. Activation patterns for the difference between retention of complex and simple memorized stimuli were examined in order to preclude that the reported effects are caused by differences in retrieval. Conjunction analysis over all delay durations for the maintenance of complex versus simple stimuli demonstrated a wide-spread activation pattern. Percent signal change (PSC) in area MT+ revealed a pattern with higher values for the maintenance of complex shapes compared to the retention of a simple circle and with higher values for increasing delay durations. The present data extend previous knowledge by demonstrating that visual area MT+ presents a brain activity pattern usually found in brain regions that are actively involved in working memory maintenance.

Profile of High School Students’ Propositional Network Representation when Interpreting Convention Diagrams

NASA Astrophysics Data System (ADS)

Fatiha, M.; Rahmat, A.; Solihat, R.

2017-09-01

The delivery of concepts in studying Biology often represented through a diagram to easily makes student understand about Biology material. One way to knowing the students’ understanding about diagram can be seen from causal relationship that is constructed by student in the propositional network representation form. This research reveal the trend of students’ propositional network representation patterns when confronted with convention diagram. This descriptive research involved 32 students at one of senior high school in Bandung. The research data was acquired by worksheet that was filled by diagram and it was developed according on information processing standards. The result of this research revealed three propositional network representation patterns are linear relationship, simple reciprocal relationship, and complex reciprocal relationship. The dominating pattern is linear form that is simply connect some information components in diagram by 59,4% students, the reciprocal relationship form with medium level by 28,1% students while the complex reciprocal relationship by only 3,1% and the rest was students who failed to connect information components by 9,4%. Based on results, most of student only able to connect information components on the picture in linear form and a few student constructing reciprocal relationship between information components on convention diagram.

Network based approaches reveal clustering in protein point patterns

NASA Astrophysics Data System (ADS)

Parker, Joshua; Barr, Valarie; Aldridge, Joshua; Samelson, Lawrence E.; Losert, Wolfgang

2014-03-01

Recent advances in super-resolution imaging have allowed for the sub-diffraction measurement of the spatial location of proteins on the surfaces of T-cells. The challenge is to connect these complex point patterns to the internal processes and interactions, both protein-protein and protein-membrane. We begin analyzing these patterns by forming a geometric network amongst the proteins and looking at network measures, such the degree distribution. This allows us to compare experimentally observed patterns to models. Specifically, we find that the experimental patterns differ from heterogeneous Poisson processes, highlighting an internal clustering structure. Further work will be to compare our results to simulated protein-protein interactions to determine clustering mechanisms.

Machine learning reveals cyclic changes in seismic source spectra in Geysers geothermal field

PubMed Central

Paisley, John

2018-01-01

The earthquake rupture process comprises complex interactions of stress, fracture, and frictional properties. New machine learning methods demonstrate great potential to reveal patterns in time-dependent spectral properties of seismic signals and enable identification of changes in faulting processes. Clustering of 46,000 earthquakes of 0.3 < ML < 1.5 from the Geysers geothermal field (CA) yields groupings that have no reservoir-scale spatial patterns but clear temporal patterns. Events with similar spectral properties repeat on annual cycles within each cluster and track changes in the water injection rates into the Geysers reservoir, indicating that changes in acoustic properties and faulting processes accompany changes in thermomechanical state. The methods open new means to identify and characterize subtle changes in seismic source properties, with applications to tectonic and geothermal seismicity. PMID:29806015

Characteristics, location and origin of flare activity in a complex active region

NASA Technical Reports Server (NTRS)

Machado, M. E.; Gary, G. A.; Hagyard, M. J.; Hernandez, A. M.; Rovira, M. G.

1986-01-01

The observational characteristics of series of multiple-loop flares from a complex active region are summarized. The location of the highest observed photospheric magnetic shear is found to be the commonly observed site of flare onset, but not, in many cases, the magnetic region where the largest time-integrated energy release is observed. The observations thus reveal a consistent pattern of energy-release processes related to the magnetic-field topology.

Application of Remote-Sensing Observations for Detecting Patterns of Localization of PGM Mineralization of Western Bushveld

NASA Astrophysics Data System (ADS)

Milovsky, G. A.; Ishmukhametova, V. T.; Orlyankin, V. N.; Shemyakina, E. M.

2017-12-01

The differentiated Bushveld complex is studied by remote-space and gravimagnetic methods. The syncline of Western Bushveld is recognized in the southwestern part of the complex, which is characterized by a radial and ring structure of the higher order. The structures, which control the localization of Pt mineralization, are revealed and the possible use of the Landsat 7 ETM+ multizonal space survey is shown for recognizing the rocks of the Basal, Critical, Main, and Upper zones of the norite complex of Western Bushveld.

Complex Pattern Formation from Current-Driven Dynamics of Single-Layer Epitaxial Islands on Crystalline Conducting Substrates

NASA Astrophysics Data System (ADS)

Kumar, Ashish; Dasgupta, Dwaipayan; Maroudas, Dimitrios

We report a systematic study of complex pattern formation resulting from the driven dynamics of single-layer homoepitaxial islands on face-centered cubic (FCC) crystalline conducting substrate surfaces under the action of an externally applied electric field. The analysis is based on an experimentally validated nonlinear model of mass transport via island edge atomic diffusion, which also accounts for edge diffusional anisotropy. We analyze the morphological stability and simulate the field-driven evolution of rounded islands for an electric field oriented along the fast diffusion direction. For larger than critical island sizes on {110} and {100} FCC substrates, we show that multiple necking instabilities generate complex island patterns, including void-containing islands, mediated by sequences of breakup and coalescence events and distributed symmetrically with respect to the electric field direction. We analyze the dependence of the formed patterns on the original island size and on the duration of application of the external field. Starting from a single large rounded island, we characterize the evolution of the number of daughter islands and their average size and uniformity. The analysis reveals that the pattern formation kinetics follows a universal scaling relation. Division of Materials Sciences & Engineering, Office of Basic Energy Sciences, U.S. Department of Energy (Award No.: DE-FG02-07ER46407).

Binary Gene Expression Patterning of the Molt Cycle: The Case of Chitin Metabolism

PubMed Central

Abehsera, Shai; Glazer, Lilah; Tynyakov, Jenny; Plaschkes, Inbar; Chalifa-Caspi, Vered; Khalaila, Isam; Aflalo, Eliahu D.; Sagi, Amir

2015-01-01

In crustaceans, like all arthropods, growth is accompanied by a molting cycle. This cycle comprises major physiological events in which mineralized chitinous structures are built and degraded. These events are in turn governed by genes whose patterns of expression are presumably linked to the molting cycle. To study these genes we performed next generation sequencing and constructed a molt-related transcriptomic library from two exoskeletal-forming tissues of the crayfish Cherax quadricarinatus, namely the gastrolith and the mandible cuticle-forming epithelium. To simplify the study of such a complex process as molting, a novel approach, binary patterning of gene expression, was employed. This approach revealed that key genes involved in the synthesis and breakdown of chitin exhibit a molt-related pattern in the gastrolith-forming epithelium. On the other hand, the same genes in the mandible cuticle-forming epithelium showed a molt-independent pattern of expression. Genes related to the metabolism of glucosamine-6-phosphate, a chitin precursor synthesized from simple sugars, showed a molt-related pattern of expression in both tissues. The binary patterning approach unfolds typical patterns of gene expression during the molt cycle of a crustacean. The use of such a simplifying integrative tool for assessing gene patterning seems appropriate for the study of complex biological processes. PMID:25919476

Decoding complex flow-field patterns in visual working memory.

PubMed

Christophel, Thomas B; Haynes, John-Dylan

2014-05-01

There has been a long history of research on visual working memory. Whereas early studies have focused on the role of lateral prefrontal cortex in the storage of sensory information, this has been challenged by research in humans that has directly assessed the encoding of perceptual contents, pointing towards a role of visual and parietal regions during storage. In a previous study we used pattern classification to investigate the storage of complex visual color patterns across delay periods. This revealed coding of such contents in early visual and parietal brain regions. Here we aim to investigate whether the involvement of visual and parietal cortex is also observable for other types of complex, visuo-spatial pattern stimuli. Specifically, we used a combination of fMRI and multivariate classification to investigate the retention of complex flow-field stimuli defined by the spatial patterning of motion trajectories of random dots. Subjects were trained to memorize the precise spatial layout of these stimuli and to retain this information during an extended delay. We used a multivariate decoding approach to identify brain regions where spatial patterns of activity encoded the memorized stimuli. Content-specific memory signals were observable in motion sensitive visual area MT+ and in posterior parietal cortex that might encode spatial information in a modality independent manner. Interestingly, we also found information about the memorized visual stimulus in somatosensory cortex, suggesting a potential crossmodal contribution to memory. Our findings thus indicate that working memory storage of visual percepts might be distributed across unimodal, multimodal and even crossmodal brain regions. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural and functional impacts of copy number variations on the cattle genome

USDA-ARS?s Scientific Manuscript database

Although there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs), similar realizations for larger, more complex forms of genetic variation have just emerged. Several recent publications reveal that copy number variations (CNVs) are common an...

Population Genetics of Two Key Mosquito Vectors of Rift Valley Fever Virus Reveals New Insights into the Changing Disease Outbreak Patterns in Kenya

PubMed Central

Tchouassi, David P.; Bastos, Armanda D. S.; Sole, Catherine L.; Diallo, Mawlouth; Lutomiah, Joel; Mutisya, James; Mulwa, Francis; Borgemeister, Christian; Sang, Rosemary; Torto, Baldwyn

2014-01-01

Rift Valley fever (RVF) outbreaks in Kenya have increased in frequency and range to include northeastern Kenya where viruses are increasingly being isolated from known (Aedes mcintoshi) and newly-associated (Ae. ochraceus) vectors. The factors contributing to these changing outbreak patterns are unclear and the population genetic structure of key vectors and/or specific virus-vector associations, in particular, are under-studied. By conducting mitochondrial and nuclear DNA analyses on >220 Kenyan specimens of Ae. mcintoshi and Ae. ochraceus, we uncovered high levels of vector complexity which may partly explain the disease outbreak pattern. Results indicate that Ae. mcintoshi consists of a species complex with one of the member species being unique to the newly-established RVF outbreak-prone northeastern region of Kenya, whereas Ae. ochraceus is a homogeneous population that appears to be undergoing expansion. Characterization of specimens from a RVF-prone site in Senegal, where Ae. ochraceus is a primary vector, revealed direct genetic links between the two Ae. ochraceus populations from both countries. Our data strongly suggest that unlike Ae. mcintoshi, Ae. ochraceus appears to be a relatively recent, single 'introduction' into Kenya. These results, together with increasing isolations from this vector, indicate that Ae. ochraceus will likely be of greater epidemiological importance in future RVF outbreaks in Kenya. Furthermore, the overall vector complexity calls into question the feasibility of mosquito population control approaches reliant on genetic modification. PMID:25474018

Plain faces are more expressive: comparative study of facial colour, mobility and musculature in primates

PubMed Central

Santana, Sharlene E.; Dobson, Seth D.; Diogo, Rui

2014-01-01

Facial colour patterns and facial expressions are among the most important phenotypic traits that primates use during social interactions. While colour patterns provide information about the sender's identity, expressions can communicate its behavioural intentions. Extrinsic factors, including social group size, have shaped the evolution of facial coloration and mobility, but intrinsic relationships and trade-offs likely operate in their evolution as well. We hypothesize that complex facial colour patterning could reduce how salient facial expressions appear to a receiver, and thus species with highly expressive faces would have evolved uniformly coloured faces. We test this hypothesis through a phylogenetic comparative study, and explore the underlying morphological factors of facial mobility. Supporting our hypothesis, we find that species with highly expressive faces have plain facial colour patterns. The number of facial muscles does not predict facial mobility; instead, species that are larger and have a larger facial nucleus have more expressive faces. This highlights a potential trade-off between facial mobility and colour patterning in primates and reveals complex relationships between facial features during primate evolution. PMID:24850898

Asynchronous oscillations of rigid rods drive viscous fluid to swirl

NASA Astrophysics Data System (ADS)

Hayashi, Rintaro; Takagi, Daisuke

2017-12-01

We present a minimal system for generating flow at low Reynolds number by oscillating a pair of rigid rods in silicone oil. Experiments show that oscillating them in phase produces no net flow, but a phase difference alone can generate rich flow fields. Tracer particles follow complex trajectory patterns consisting of small orbital movements every cycle and then drifting or swirling in larger regions after many cycles. Observations are consistent with simulations performed using the method of regularized Stokeslets, which reveal complex three-dimensional flow structures emerging from simple oscillatory actuation. Our findings reveal the basic underlying flow structure around oscillatory protrusions such as hairs and legs as commonly featured on living and nonliving bodies.

Ecological factors affecting gene flow in the Brachionus plicatilis complex (Rotifera).

PubMed

Gómez, Africa; Carmona, María José; Serra, Manuel

1997-07-01

We investigated how adaptation to salinity and temperature acts as reproductive barriers in three sympatric species from the Brachionus plicatilis species complex. These species co-occur in a salt marsh in Spain, and a previous electrophoretic study of variation revealed no hybrids between them. A factorial experiment was designed to test for differences in population growth rates and patterns of bisexual reproduction. The design combined representative strains from each species in different salinity and temperature conditions, representing the range over which these rotifers are found in their natural environment. We found differences in the growth response of the three species to both factors and in the pattern of bisexual reproduction. These differences help to explain patterns of succession observed in the field. We conclude that these ecological factors, together with mate recognition systems, account for the absence of gene flow in these sympatric species.

Universal principles governing multiple random searchers on complex networks: The logarithmic growth pattern and the harmonic law

NASA Astrophysics Data System (ADS)

Weng, Tongfeng; Zhang, Jie; Small, Michael; Harandizadeh, Bahareh; Hui, Pan

2018-03-01

We propose a unified framework to evaluate and quantify the search time of multiple random searchers traversing independently and concurrently on complex networks. We find that the intriguing behaviors of multiple random searchers are governed by two basic principles—the logarithmic growth pattern and the harmonic law. Specifically, the logarithmic growth pattern characterizes how the search time increases with the number of targets, while the harmonic law explores how the search time of multiple random searchers varies relative to that needed by individual searchers. Numerical and theoretical results demonstrate these two universal principles established across a broad range of random search processes, including generic random walks, maximal entropy random walks, intermittent strategies, and persistent random walks. Our results reveal two fundamental principles governing the search time of multiple random searchers, which are expected to facilitate investigation of diverse dynamical processes like synchronization and spreading.

Generalised power graph compression reveals dominant relationship patterns in complex networks

PubMed Central

Ahnert, Sebastian E.

2014-01-01

We introduce a framework for the discovery of dominant relationship patterns in complex networks, by compressing the networks into power graphs with overlapping power nodes. When paired with enrichment analysis of node classification terms, the most compressible sets of edges provide a highly informative sketch of the dominant relationship patterns that define the network. In addition, this procedure also gives rise to a novel, link-based definition of overlapping node communities in which nodes are defined by their relationships with sets of other nodes, rather than through connections within the community. We show that this completely general approach can be applied to undirected, directed, and bipartite networks, yielding valuable insights into the large-scale structure of real-world networks, including social networks and food webs. Our approach therefore provides a novel way in which network architecture can be studied, defined and classified. PMID:24663099

Roles for SH2 and SH3 domains in Lyn kinase association with activated FcepsilonRI in RBL mast cells revealed by patterned surface analysis.

PubMed

Hammond, Stephanie; Wagenknecht-Wiesner, Alice; Veatch, Sarah L; Holowka, David; Baird, Barbara

2009-10-01

In mast cells, antigen-mediated cross-linking of IgE bound to its high-affinity surface receptor, FcepsilonRI, initiates a signaling cascade that culminates in degranulation and release of allergic mediators. Antigen-patterned surfaces, in which the antigen is deposited in micron-sized features on a silicon substrate, were used to examine the spatial relationship between clustered IgE-FcepsilonRI complexes and Lyn, the signal-initiating tyrosine kinase. RBL mast cells expressing wild-type Lyn-EGFP showed co-redistribution of this protein with clustered IgE receptors on antigen-patterned surfaces, whereas Lyn-EGFP containing an inhibitory point mutation in its SH2 domain did not significantly accumulate with the patterned antigen, and Lyn-EGFP with an inhibitory point mutation in its SH3 domain exhibited reduced interactions. Our results using antigen-patterned surfaces and quantitative cross-correlation image analysis reveal that both the SH2 and SH3 domains contribute to interactions between Lyn kinase and cross-linked IgE receptors in stimulated mast cells.

Interhemispheric Transmission Time in Persons with Down Syndrome

ERIC Educational Resources Information Center

Heath, M.; Grierson, L.; Binsted, G.; Elliott, D.

2007-01-01

Background: The study of cerebral specialization in persons with Down syndrome (DS) has revealed an anomalous pattern of organization. Specifically, persons with DS elicit a right cerebral hemisphere lateralization for receptive language and a left cerebral hemisphere lateralization for the production of simple and complex movements: a pattern…

Psychophysiology of Aggression, Psychopathy, and Conduct Problems: A Meta-Analysis

ERIC Educational Resources Information Center

Lorber, Michael F.

2004-01-01

A meta-analysis of 95 studies was conducted to investigate the relations of heart rate (HR) and electrodermal activity (EDA) with aggression, psychopathy, and conduct problems. Analyses revealed a complex constellation of interactive effects, with a failure in some cases of autonomic patterns to generalize across antisocial spectrum behavior…

Brain histamine depletion enhances the behavioural sequences complexity of mice tested in the open-field: Partial reversal effect of the dopamine D2/D3 antagonist sulpiride.

PubMed

Santangelo, Andrea; Provensi, Gustavo; Costa, Alessia; Blandina, Patrizio; Ricca, Valdo; Crescimanno, Giuseppe; Casarrubea, Maurizio; Passani, M Beatrice

2017-02-01

Markers of histaminergic dysregulation were found in several neuropsychiatric disorders characterized by repetitive behaviours, thoughts and stereotypies. We analysed the effect of acute histamine depletion by means of i. c.v. injections of alpha-fluoromethylhistidine, a blocker of histidine decarboxylase, on the temporal organization of motor sequences of CD1 mice behaviour in the open-field test. An ethogram encompassing 9 behavioural components was employed. Durations and frequencies were only slightly affected by treatments. However, as revealed by multivariate t-pattern analysis, histamine depletion was associated with a striking increase in the number of behavioural patterns. We found 42 patterns of different composition occurring, on average, 520.90 ± 50.23 times per mouse in the histamine depleted (HD) group, whereas controls showed 12 different patterns occurring on average 223.30 ± 20.64 times. Exploratory and grooming behaviours clustered separately, and the increased pattern complexity involved exclusively exploratory patterns. To test the hypothesis of a histamine-dopamine interplay on behavioural pattern phenotype, non-sedative doses of the D2/D3 antagonist sulpiride (12.5-25-50 mg/kg) were additionally administered to different groups of HD mice. Sulpiride counterbalanced the enhancement of exploratory patterns of different composition, but it did not affect the mean number of patterns at none of the doses used. Our results provide new insights on the role of histamine on repetitive behavioural sequences of freely moving mice. Histamine deficiency is correlated with a general enhancement of pattern complexity. This study supports a putative involvement of histamine in the pathophysiology of tics and related disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative

PubMed Central

Hertach, Thomas; Puissant, Stéphane; Gogala, Matija; Trilar, Tomi; Hagmann, Reto; Baur, Hannes; Kunz, Gernot; Wade, Elizabeth J.; Loader, Simon P.; Simon, Chris; Nagel, Peter

2016-01-01

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a “complex within the complex”: the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive introgression and mitochondrial capture. PMID:27851754

Groundwater flow pattern and related environmental phenomena in complex geologic setting based on integrated model construction

NASA Astrophysics Data System (ADS)

Tóth, Ádám; Havril, Tímea; Simon, Szilvia; Galsa, Attila; Monteiro Santos, Fernando A.; Müller, Imre; Mádl-Szőnyi, Judit

2016-08-01

Groundwater flow, driven, controlled and determined by topography, geology and climate, is responsible for several natural surface manifestations and affected by anthropogenic processes. Therefore, flowing groundwater can be regarded as an environmental agent. Numerical simulation of groundwater flow could reveal the flow pattern and explain the observed features. In complex geologic framework, where the geologic-hydrogeologic knowledge is limited, the groundwater flow model could not be constructed based solely on borehole data, but geophysical information could aid the model building. The integrated model construction was presented via the case study of the Tihany Peninsula, Hungary, with the aims of understanding the background and occurrence of groundwater-related environmental phenomena, such as wetlands, surface water-groundwater interaction, slope instability, and revealing the potential effect of anthropogenic activity and climate change. The hydrogeologic model was prepared on the basis of the compiled archive geophysical database and the results of recently performed geophysical measurements complemented with geologic-hydrogeologic data. Derivation of different electrostratigraphic units, revealing fracturing and detecting tectonic elements was achieved by systematically combined electromagnetic geophysical methods. The deduced information can be used as model input for groundwater flow simulation concerning hydrostratigraphy, geometry and boundary conditions. The results of numerical modelling were interpreted on the basis of gravity-driven regional groundwater flow concept and validated by field mapping of groundwater-related phenomena. The 3D model clarified the hydraulic behaviour of the formations, revealed the subsurface hydraulic connection between groundwater and wetlands and displayed the groundwater discharge pattern, as well. The position of wetlands, their vegetation type, discharge features and induced landslides were explained as environmental imprints of groundwater. The highly vulnerable wetlands and groundwater-dependent ecosystems have to be in the focus of water management and natural conservation policy.

Plasmodium vivax Isolates from Cambodia and Thailand Show High Genetic Complexity and Distinct Patterns of P. vivax Multidrug Resistance Gene 1 (pvmdr1) Polymorphisms

PubMed Central

Lin, Jessica T.; Patel, Jaymin C.; Kharabora, Oksana; Sattabongkot, Jetsumon; Muth, Sinuon; Ubalee, Ratawan; Schuster, Anthony L.; Rogers, William O.; Wongsrichanalai, Chansuda; Juliano, Jonathan J.

2013-01-01

Plasmodium vivax accounts for an increasing fraction of malaria infections in Thailand and Cambodia. We compared P. vivax genetic complexity and antimalarial resistance patterns in the two countries. Use of a heteroduplex tracking assay targeting the merozoite surface protein 1 gene revealed that vivax infections in both countries are frequently polyclonal (84%), with parasites that are highly diverse (HE = 0.86) but closely related (GST = 0.18). Following a history of different drug policies in Thailand and Cambodia, distinct patterns of antimalarial resistance have emerged: most Cambodian isolates harbor the P. vivax multidrug resistance gene 1 (pvmdr1) 976F mutation associated with chloroquine resistance (89% versus 8%, P < 0.001), whereas Thai isolates more often display increased pvmdr1 copy number (39% versus 4%, P < 0.001). Finally, genotyping of paired isolates from individuals suspected of suffering relapse supports a complex scheme of relapse whereby recurrence of multiple identical variants is sometimes accompanied by the appearance of novel variants. PMID:23509126

Characterizing heterogeneous cellular responses to perturbations.

PubMed

Slack, Michael D; Martinez, Elisabeth D; Wu, Lani F; Altschuler, Steven J

2008-12-09

Cellular populations have been widely observed to respond heterogeneously to perturbation. However, interpreting the observed heterogeneity is an extremely challenging problem because of the complexity of possible cellular phenotypes, the large dimension of potential perturbations, and the lack of methods for separating meaningful biological information from noise. Here, we develop an image-based approach to characterize cellular phenotypes based on patterns of signaling marker colocalization. Heterogeneous cellular populations are characterized as mixtures of phenotypically distinct subpopulations, and responses to perturbations are summarized succinctly as probabilistic redistributions of these mixtures. We apply our method to characterize the heterogeneous responses of cancer cells to a panel of drugs. We find that cells treated with drugs of (dis-)similar mechanism exhibit (dis-)similar patterns of heterogeneity. Despite the observed phenotypic diversity of cells observed within our data, low-complexity models of heterogeneity were sufficient to distinguish most classes of drug mechanism. Our approach offers a computational framework for assessing the complexity of cellular heterogeneity, investigating the degree to which perturbations induce redistributions of a limited, but nontrivial, repertoire of underlying states and revealing functional significance contained within distinct patterns of heterogeneous responses.

Classroom learning and achievement: how the complexity of classroom interaction impacts students' learning

NASA Astrophysics Data System (ADS)

Podschuweit, Sören; Bernholt, Sascha; Brückmann, Maja

2016-05-01

Background: Complexity models have provided a suitable framework in various domains to assess students' educational achievement. Complexity is often used as the analytical focus when regarding learning outcomes, i.e. when analyzing written tests or problem-centered interviews. Numerous studies reveal negative correlations between the complexity of a task and the probability of a student solving it. Purpose: Thus far, few detailed investigations explore the importance of complexity in actual classroom lessons. Moreover, the few efforts made so far revealed inconsistencies. Hence, the present study sheds light on the influence the complexity of students' and teachers' class contributions have on students' learning outcomes. Sample: Videos of 10 German 8th grade physics courses covering three consecutive lessons on two topics each (electricity, mechanics) have been analyzed. The sample includes 10 teachers and 290 students. Design and methods: Students' and teachers' verbal contributions were coded manual-based according to the level of complexity. Additionally, pre-post testing of knowledge in electricity and mechanics was applied to assess the students' learning gain. ANOVA analysis was used to characterize the influence of the complexity on the learning gain. Results: Results indicate that the mean level of complexity in classroom contributions explains a large portion of variance in post-test results on class level. Despite this overarching trend, taking classroom activities into account as well reveals even more fine-grained patterns, leading to more specific relations between the complexity in the classroom and students' achievement. Conclusions: In conclusion, we argue for more reflected teaching approaches intended to gradually increase class complexity to foster students' level of competency.

Identification of the altered pyrrole in the isomeric sulfmyoglobins: hyperfine shift patterns as indicators of ring saturation in ferric chlorins.

PubMed

Chatfield, M J; La Mar, G N; Smith, K M; Leung, H K; Pandey, R K

1988-03-08

Analysis of the 1H NMR hyperfine shift patterns of isomeric sulfmyoglobins is carried out in the met-aquo and met-cyano states to determine the site of saturation in each protein. The utility of the patterns for structure elucidation is established by specific deuterium labeling of the heme methyls of the terminal base product. On the basis of the known saturation of ring B in this isomer [Chatfield, M.J., La Mar, G.N., Lecomte, J.T.J., Balch, A.L., Smith, K.M., & Langry, K.C. (1986) J. Am. Chem. Soc. 108, 7108-7110], the methyl resonance of the saturated ring is found to have strongly attenuated contact shift. Thus, the heme methyl contact shift pattern is diagnostic for the saturated pyrrole in the high-spin state. This rationale is then applied to analyze the assigned NMR spectra of the initial and terminal acid sulfmyoglobin products, revealing that the same ring B is saturated in each isomer. In contrast, the heme methyl contact shift pattern in low-spin ferric complexes reveals that the methyls both on the affected pyrrole and on the trans pyrrole are influenced similarly on sulfmyoglobin formation, precluding the use of this methyl shift pattern as a unique indicator of the site of saturation. Identification of exchangeable proximal histidine resonances for met-aquo sulfmyoglobin complexes with shifts similar to that in native myoglobin dictates inconsequential axial alterations in the sulfmyoglobins, while location of downfield meso proton resonances analogous to those of the native protein demonstrates the retention of the coordinate water in the active site of met-sulfmyoglobin.

Effect of pattern complexity on the visual span for Chinese and alphabet characters

PubMed Central

Wang, Hui; He, Xuanzi; Legge, Gordon E.

2014-01-01

The visual span for reading is the number of letters that can be recognized without moving the eyes and is hypothesized to impose a sensory limitation on reading speed. Factors affecting the size of the visual span have been studied using alphabet letters. There may be common constraints applying to recognition of other scripts. The aim of this study was to extend the concept of the visual span to Chinese characters and to examine the effect of the greater complexity of these characters. We measured visual spans for Chinese characters and alphabet letters in the central vision of bilingual subjects. Perimetric complexity was used as a metric to quantify the pattern complexity of binary character images. The visual span tests were conducted with four sets of stimuli differing in complexity—lowercase alphabet letters and three groups of Chinese characters. We found that the size of visual spans decreased with increasing complexity, ranging from 10.5 characters for alphabet letters to 4.5 characters for the most complex Chinese characters studied. A decomposition analysis revealed that crowding was the dominant factor limiting the size of the visual span, and the amount of crowding increased with complexity. Errors in the spatial arrangement of characters (mislocations) had a secondary effect. We conclude that pattern complexity has a major effect on the size of the visual span, mediated in large part by crowding. Measuring the visual span for Chinese characters is likely to have high relevance to understanding visual constraints on Chinese reading performance. PMID:24993020

Isolation of Ion-Driven Conformations in Diphenylacetylene Molecular Switches Using Cryogenic Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Wolk, Arron B.; Garand, Etienne; Jones, Ian M.; Kamrath, Michael Z.; Hamilton, Rew; Johnson, Mark A.

2012-06-01

We report the infrared predissociation spectra of a family of ionic diphenylacetylene molecular switch complexes. The electrosprayed complexes were trapped and cooled in a cryogenic (10K) quadrupole ion trap and tagged with molecular deuterium. The infrared spectra of the vibrationally cold species reveal sharp transitions over a wide energy range (800 - 3800 cm-1), facilitating comparison to harmonic spectra. The evolution of the band pattern upon derivatization of the complexes exposes the signatures of the amide, urea, and carbonyl functionalities, enabling unambiguous identification of the non-covalent interactions that control the secondary structure of the molecule. Complexation with the tetramethylammonium cation reveals a conformation analogous to that of the neutral molecule, while halide ion attachment induces a conformational change similar to that observed earlier in solution. In several cases, both the donor and acceptor groups involved in the multidentate H-bonds are observed, providing a microscopic mechanical picture of the interactions at play. I. Jones, and A. Hamilton, Angew. Chem. Intl. Edit. 50, 4597 (2011).

Resiliency of small rural communities in the interior Columbia Basin.

Treesearch

Sally Duncan

1998-01-01

As part of the Interior Columbia Basin Ecosystem Management Project, 198 small communities were assessed for their ability to deal with change and the characteristics that contribute to this ability. Scientists conducted on-the-ground studies and had communities assess themselves.The data revealed complex differences, patterns, and underlying relationships....

Transcriptome and secretome analyses of Phanerochaete chrysosporium reveal complex patterns of gene expression

Treesearch

Amber J. Vanden Wymelenberg; Jill A. Gaskell; Michael D. Mozuch; Philip J. Kersten; Grzegorz Sabat; Diego Martinez; Daniel Cullen

2009-01-01

The wood decay basidiomycete Phanerochaete chrysosporium was grown under standard ligninolytic or cellulolytic conditions and subjected to whole-genome expression microarray analysis and liquid chromatography-tandem mass spectrometry of extracellular proteins. A total of 545 genes were flagged on the basis of significant changes in transcript accumulation and/or...

Exploring the Civic Identities of Latina/o High School Students: Reframing the Historical Narrative

ERIC Educational Resources Information Center

Salinas, Cinthia; Alarcón, Jeannette D.

2016-01-01

Notions of citizenship, as taught through the official state curriculum, are narrow and fail to consider the importance of histories that reveal a composite of diverse races/ethnicities, multiple languages, and complex patterns of immigration and transnationalism. The richness of such histories embodies the experiences and contributions of…

Evaluating Treatment and Generalization Patterns of Two Theoretically Motivated Sentence Comprehension Therapies.

PubMed

Des Roches, Carrie A; Vallila-Rohter, Sofia; Villard, Sarah; Tripodis, Yorghos; Caplan, David; Kiran, Swathi

2016-12-01

The current study examined treatment outcomes and generalization patterns following 2 sentence comprehension therapies: object manipulation (OM) and sentence-to-picture matching (SPM). Findings were interpreted within the framework of specific deficit and resource reduction accounts, which were extended in order to examine the nature of generalization following treatment of sentence comprehension deficits in aphasia. Forty-eight individuals with aphasia were enrolled in 1 of 8 potential treatment assignments that varied by task (OM, SPM), complexity of trained sentences (complex, simple), and syntactic movement (noun phrase, wh-movement). Comprehension of trained and untrained sentences was probed before and after treatment using stimuli that differed from the treatment stimuli. Linear mixed-model analyses demonstrated that, although both OM and SPM treatments were effective, OM resulted in greater improvement than SPM. Analyses of covariance revealed main effects of complexity in generalization; generalization from complex to simple linguistically related sentences was observed both across task and across movement. Results are consistent with the complexity account of treatment efficacy, as generalization effects were consistently observed from complex to simpler structures. Furthermore, results provide support for resource reduction accounts that suggest that generalization can extend across linguistic boundaries, such as across movement type.

Quantitative imaging reveals real-time Pou5f3–Nanog complexes driving dorsoventral mesendoderm patterning in zebrafish

PubMed Central

Perez-Camps, Mireia; Tian, Jing; Chng, Serene C; Sem, Kai Pin; Sudhaharan, Thankiah; Teh, Cathleen; Wachsmuth, Malte; Korzh, Vladimir; Ahmed, Sohail; Reversade, Bruno

2016-01-01

Formation of the three embryonic germ layers is a fundamental developmental process that initiates differentiation. How the zebrafish pluripotency factor Pou5f3 (homologous to mammalian Oct4) drives lineage commitment is unclear. Here, we introduce fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy to assess the formation of Pou5f3 complexes with other transcription factors in real-time in gastrulating zebrafish embryos. We show, at single-cell resolution in vivo, that Pou5f3 complexes with Nanog to pattern mesendoderm differentiation at the blastula stage. Later, during gastrulation, Sox32 restricts Pou5f3–Nanog complexes to the ventrolateral mesendoderm by binding Pou5f3 or Nanog in prospective dorsal endoderm. In the ventrolateral endoderm, the Elabela / Aplnr pathway limits Sox32 levels, allowing the formation of Pou5f3–Nanog complexes and the activation of downstream BMP signaling. This quantitative model shows that a balance in the spatiotemporal distribution of Pou5f3–Nanog complexes, modulated by Sox32, regulates mesendoderm specification along the dorsoventral axis. DOI: http://dx.doi.org/10.7554/eLife.11475.001 PMID:27684073

Complexity and dynamics of topological and community structure in complex networks

NASA Astrophysics Data System (ADS)

Berec, Vesna

2017-07-01

Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

Prioritising lexical patterns to increase axiomatisation in biomedical ontologies. The role of localisation and modularity.

PubMed

Quesada-Martínez, M; Fernández-Breis, J T; Stevens, R; Mikroyannidi, E

2015-01-01

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". In previous work, we have defined methods for the extraction of lexical patterns from labels as an initial step towards semi-automatic ontology enrichment methods. Our previous findings revealed that many biomedical ontologies could benefit from enrichment methods using lexical patterns as a starting point.Here, we aim to identify which lexical patterns are appropriate for ontology enrichment, driving its analysis by metrics to prioritised the patterns. We propose metrics for suggesting which lexical regularities should be the starting point to enrich complex ontologies. Our method determines the relevance of a lexical pattern by measuring its locality in the ontology, that is, the distance between the classes associated with the pattern, and the distribution of the pattern in a certain module of the ontology. The methods have been applied to four significant biomedical ontologies including the Gene Ontology and SNOMED CT. The metrics provide information about the engineering of the ontologies and the relevance of the patterns. Our method enables the suggestion of links between classes that are not made explicit in the ontology. We propose a prioritisation of the lexical patterns found in the analysed ontologies. The locality and distribution of lexical patterns offer insights into the further engineering of the ontology. Developers can use this information to improve the axiomatisation of their ontologies.

Explosive avian radiations and multi-directional dispersal across Wallacea: evidence from the Campephagidae and other Crown Corvida (Aves).

PubMed

Jønsson, Knud A; Irestedt, Martin; Fuchs, Jérôme; Ericson, Per G P; Christidis, Les; Bowie, Rauri C K; Norman, Janette A; Pasquet, Eric; Fjeldså, Jon

2008-04-01

The systematic relationships among avian families within Crown Corvida have been poorly studied so far and as such been of limited use for biogeographic interpretations. The group has its origin in Australia and is thought to have colonized Africa and the New World via Asia beginning some 35 Mya when terranes of Australian origin approached Asian landmasses. Recent detailed tectonic mapping of the origin of land masses in the region around Wallace's line have revealed a particularly complex movement of terranes over the last 20-30 Myr. Thus the biogeographic dispersal pattern of Crown Corvida is a particularly exciting case for linking vicariance and dispersal events with Earth history. Here we examine phylogenetic affinities among 72 taxa covering a broad range of genera in the basal radiations within Crown Corvida with an emphasis on Campephagidae and Pachycephalidae. Bayesian analyses of nuclear DNA sequence data identified the family Campephagidae as monophyletic but the large genus Coracina is not. Within the family Pachycephalidae the genera Pachycephala and Colluricincla are paraphyletic with respect to each other. The resulting phylogeny suggests that patterns of dispersal across Wallace's line are complex and began at least 25 Mya. We find evidence of explosive radiations and multi-directional dispersal within the last 10 Myr, and three independent long distance ocean dispersal events between Wallacea and Africa at 10-15 Mya. Furthermore, the study reveals that in the Campephagidae a complex series of dispersal events rather than vicariance is the most likely explanation for the current biogeographic pattern in the region.

Postnatal changes in the growth dynamics of the human face revealed from bone modelling patterns.

PubMed

Martinez-Maza, Cayetana; Rosas, Antonio; Nieto-Díaz, Manuel

2013-09-01

Human skull morphology results from complex processes that involve the coordinated growth and interaction of its skeletal components to keep a functional and structural balance. Previous histological works have studied the growth of different craniofacial regions and their relationship to functional spaces in humans up to 14 years old. Nevertheless, how the growth dynamics of the facial skeleton and the mandible are related and how this relationship changes through the late ontogeny remain poorly understood. To approach these two questions, we have compared the bone modelling activities of the craniofacial skeleton from a sample of subadult and adult humans. In this study, we have established for the first time the bone modelling pattern of the face and the mandible from adult humans. Our analyses reveal a patchy distribution of the bone modelling fields (overemphasized by the presence of surface islands with no histological information) reflecting the complex growth dynamics associated to the individual morphology. Subadult and adult specimens show important differences in the bone modelling patterns of the anterior region of the facial skeleton and the posterior region of the mandible. These differences indicate developmental changes in the growth directions of the whole craniofacial complex, from a predominantly downward growth in subadults that turns to a forward growth observed in the adult craniofacial skeleton. We hypothesize that these ontogenetic changes would respond to the physiological and physical requirements to enlarge the oral and nasal cavities once maturation of the brain and the closure of the cranial sutures have taken place during craniofacial development. © 2013 Anatomical Society.

Aftershocks of the 2010 Mw 7.2 El Mayor-Cucapah earthquake revealcomplex faulting in the Yuha Desert, California

USGS Publications Warehouse

Kroll, K.; Cochran, Elizabeth S.; Richards-Dinger, K.; Sumy, Danielle

2013-01-01

We detect and precisely locate over 9500 aftershocks that occurred in the Yuha Desert region during a 2 month period following the 4 April 2010 Mw 7.2 El Mayor-Cucapah (EMC) earthquake. Events are relocated using a series of absolute and relative relocation procedures that include Hypoinverse, Velest, and hypoDD. Location errors are reduced to ~40 m horizontally and ~120 m vertically.Aftershock locations reveal a complex pattern of faulting with en echelon fault segments trending toward the northwest, approximately parallel to the North American-Pacific plate boundary and en echelon, conjugate features trending to the northeast. The relocated seismicity is highly correlated with published surface mapping of faults that experienced triggered surface slip in response to the EMC main shock. Aftershocks occurred between 2 km and 11 km depths, consistent with previous studies of seismogenic thickness in the region. Three-dimensional analysis reveals individual and intersecting fault planes that are limited in their along-strike length. These fault planes remain distinct structures at depth, indicative of conjugate faulting, and do not appear to coalesce onto a throughgoing fault segment. We observe a complex spatiotemporal migration of aftershocks, with seismicity that jumps between individual fault segments that are active for only a few days to weeks. Aftershock rates are roughly consistent with the expected earthquake production rates of Dieterich (1994). The conjugate pattern of faulting and nonuniform aftershock migration patterns suggest that strain in the Yuha Desert is being accommodated in a complex manner.

Monitoring of Freezing Dynamics in Trees: A Simple Phase Shift Causes Complexity1[OPEN

PubMed Central

Charra-Vaskou, Katline

2017-01-01

During winter, trees have to cope with harsh conditions, including extreme freeze-thaw stress. This study focused on ice nucleation and propagation, related water shifts and xylem cavitation, as well as cell damage and was based on in situ monitoring of xylem (thermocouples) and surface temperatures (infrared imaging), ultrasonic emissions, and dendrometer analysis. Field experiments during late winter on Picea abies growing at the alpine timberline revealed three distinct freezing patterns: (1) from the top of the tree toward the base, (2) from thin branches toward the main stem’s top and base, and (3) from the base toward the top. Infrared imaging showed freezing within branches from their base toward distal parts. Such complex freezing causes dynamic and heterogenous patterns in water potential and probably in cavitation. This study highlights the interaction between environmental conditions upon freezing and thawing and demonstrates the enormous complexity of freezing processes in trees. Diameter shrinkage, which indicated water fluxes within the stem, and acoustic emission analysis, which indicated cavitation events near the ice front upon freezing, were both related to minimum temperature and, upon thawing, related to vapor pressure deficit and soil temperature. These complex patterns, emphasizing the common mechanisms between frost and drought stress, shed new light on winter tree physiology. PMID:28242655

Changing the spatial pattern of TFL1 expression reveals its key role in the shoot meristem in controlling Arabidopsis flowering architecture

PubMed Central

Baumann, Kim; Venail, Julien; Berbel, Ana; Domenech, Maria Jose; Money, Tracy; Conti, Lucio; Hanzawa, Yoshie; Madueno, Francisco; Bradley, Desmond

2015-01-01

Models for the control of above-ground plant architectures show how meristems can be programmed to be either shoots or flowers. Molecular, genetic, transgenic, and mathematical studies have greatly refined these models, suggesting that the phase of the shoot reflects different genes contributing to its repression of flowering, its vegetativeness (‘veg’), before activators promote flower development. Key elements of how the repressor of flowering and shoot meristem gene TFL1 acts have now been tested, by changing its spatiotemporal pattern. It is shown that TFL1 can act outside of its normal expression domain in leaf primordia or floral meristems to repress flower identity. These data show how the timing and spatial pattern of TFL1 expression affect overall plant architecture. This reveals that the underlying pattern of TFL1 interactors is complex and that they may be spatially more widespread than TFL1 itself, which is confined to shoots. However, the data show that while TFL1 and floral genes can both act and compete in the same meristem, it appears that the main shoot meristem is more sensitive to TFL1 rather than floral genes. This spatial analysis therefore reveals how a difference in response helps maintain the ‘veg’ state of the shoot meristem. PMID:26019254

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations.

PubMed

Schüler, D; Alonso, S; Torcini, A; Bär, M

2014-12-01

Pattern formation often occurs in spatially extended physical, biological, and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue, we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexisting static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular, revealing for the Swift-Hohenberg equations, a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of a weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.

Chimera patterns in the Kuramoto-Battogtokh model

NASA Astrophysics Data System (ADS)

Smirnov, Lev; Osipov, Grigory; Pikovsky, Arkady

2017-02-01

Kuramoto and Battogtokh (2002 Nonlinear Phenom. Complex Syst. 5 380) discovered chimera states represented by stable coexisting synchrony and asynchrony domains in a lattice of coupled oscillators. After a reformulation in terms of a local order parameter, the problem can be reduced to partial differential equations. We find uniformly rotating, spatially periodic chimera patterns as solutions of a reversible ordinary differential equation, and demonstrate a plethora of such states. In the limit of neutral coupling they reduce to analytical solutions in the form of one- and two-point chimera patterns as well as localized chimera solitons. Patterns at weakly attracting coupling are characterized by virtue of a perturbative approach. Stability analysis reveals that only the simplest chimeras with one synchronous region are stable.

Sodium channel blockade with QRS widening after an escitalopram overdose.

PubMed

Schreffler, Susan M; Marraffa, Jeanna M; Stork, Christine M; Mackey, Jennifer

2013-09-01

Escitalopram is rarely associated with prolongation of the QTc interval; however, there are no reported cases of QRS complex widening associated with escitalopram overdose. We report a case of a patient who presented with both QRS complex widening and QTc interval prolongation after an escitalopram overdose. A 16-year-old girl presented to the emergency department after ingestion of escitalopram, tramadol/acetaminophen, and hydrocodone/acetaminophen. Laboratory results were significant for 4-hour acetaminophen 21.1 μg/mL. Serum electrolytes including potassium, magnesium, and calcium were all normal. Initial electrocardiogram (ECG) revealed a widened QRS with an incomplete right bundle branch pattern. After administration of 100-mEq sodium bicarbonate, a repeat ECG revealed narrowing of the QRS complex and a prolonged QTc interval. Magnesium sulfate 2 g intravenous and sodium bicarbonate drip were initiated. A repeat ECG, 1 hour after the second, revealed normalization of the QRS complex and QTc interval. Prolongation of the QTc interval is an expected effect of escitalopram. Both escitalopram and citalopram are metabolized to the cardiotoxic metabolite S-didesmethylcitalopram and didesmethylcitalopram, respectively, which have been implicated in numerous cardiac abnormalities including widening of the QRS complex. Although never previously described with escitalopram, this mechanism provides a reasonable explanation for the QRS complex widening and incomplete right bundle branch block that occurred in our patient. Both QRS complex widening and QTc interval prolongation should be monitored in cases of escitalopram and citalopram overdoses.

Synthesis, structural characterization, DFT studies and in-vitro antidiabetic activity of new mixed ligand oxovanadium(IV) complex with tridentate Schiff base

NASA Astrophysics Data System (ADS)

Patel, R. N.; Singh, Yogendra Pratap

2018-02-01

The mixed ligand oxovanadium(IV) complex [VO(L1)(L2)] [L1 = N'-[(Z)-phenyl(pyridin-2-yl)methylidene]benzohydrazide and L2 = Benzohydrazide] has been synthesized in aerobic condition. The complex was characterized by elemental analysis spectroscopic (UV-vis, IR, epr) and electrochemical methods. X-ray diffraction pattern was also used to characterize this complex, which has a distorted octahedral structure. Single crystal diffraction analysis reveals that Csbnd H⋯π (aryl/metal chelate rings) interactions contribute to the stabilization of the crystal structure in given dimension. The room temperature magnetic susceptibility data shows paramagnetic nature of the complex. The complex was also tested for in-vitro antidiabetic activity. Moderate α-glucosidase inhibition is shown by this complex, which may be considered as α-glucosidase inhibitors.

Embracing heterothermic diversity: non-stationary waveform analysis of temperature variation in endotherms.

PubMed

Levesque, Danielle L; Menzies, Allyson K; Landry-Cuerrier, Manuelle; Larocque, Guillaume; Humphries, Murray M

2017-07-01

Recent research is revealing incredible diversity in the thermoregulatory patterns of wild and captive endotherms. As a result of these findings, classic thermoregulatory categories of 'homeothermy', 'daily heterothermy', and 'hibernation' are becoming harder to delineate, impeding our understanding of the physiological and evolutionary significance of variation within and around these categories. However, we lack a generalized analytical approach for evaluating and comparing the complex and diversified nature of the full breadth of heterothermy expressed by individuals, populations, and species. Here we propose a new approach that decomposes body temperature time series into three inherent properties-waveform, amplitude, and period-using a non-stationary technique that accommodates the temporal variability of body temperature patterns. This approach quantifies circadian and seasonal variation in thermoregulatory patterns, and uses the distribution of observed thermoregulatory patterns as a basis for intra- and inter-specific comparisons. We analyse body temperature time series from multiple species, including classical hibernators, tropical heterotherms, and homeotherms, to highlight the approach's general usefulness and the major axes of thermoregulatory variation that it reveals.

Differential subcellular distribution of ion channels and the diversity of neuronal function.

PubMed

Nusser, Zoltan

2012-06-01

Following the astonishing molecular diversity of voltage-gated ion channels that was revealed in the past few decades, the ion channel repertoire expressed by neurons has been implicated as the major factor governing their functional heterogeneity. Although the molecular structure of ion channels is a key determinant of their biophysical properties, their subcellular distribution and densities on the surface of nerve cells are just as important for fulfilling functional requirements. Recent results obtained with high resolution quantitative localization techniques revealed complex, subcellular compartment-specific distribution patterns of distinct ion channels. Here I suggest that within a given neuron type every ion channel has a unique cell surface distribution pattern, with the functional consequence that this dramatically increases the computational power of nerve cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration

PubMed Central

Lobo, Daniel; Levin, Michael

2015-01-01

Transformative applications in biomedicine require the discovery of complex regulatory networks that explain the development and regeneration of anatomical structures, and reveal what external signals will trigger desired changes of large-scale pattern. Despite recent advances in bioinformatics, extracting mechanistic pathway models from experimental morphological data is a key open challenge that has resisted automation. The fundamental difficulty of manually predicting emergent behavior of even simple networks has limited the models invented by human scientists to pathway diagrams that show necessary subunit interactions but do not reveal the dynamics that are sufficient for complex, self-regulating pattern to emerge. To finally bridge the gap between high-resolution genetic data and the ability to understand and control patterning, it is critical to develop computational tools to efficiently extract regulatory pathways from the resultant experimental shape phenotypes. For example, planarian regeneration has been studied for over a century, but despite increasing insight into the pathways that control its stem cells, no constructive, mechanistic model has yet been found by human scientists that explains more than one or two key features of its remarkable ability to regenerate its correct anatomical pattern after drastic perturbations. We present a method to infer the molecular products, topology, and spatial and temporal non-linear dynamics of regulatory networks recapitulating in silico the rich dataset of morphological phenotypes resulting from genetic, surgical, and pharmacological experiments. We demonstrated our approach by inferring complete regulatory networks explaining the outcomes of the main functional regeneration experiments in the planarian literature; By analyzing all the datasets together, our system inferred the first systems-biology comprehensive dynamical model explaining patterning in planarian regeneration. This method provides an automated, highly generalizable framework for identifying the underlying control mechanisms responsible for the dynamic regulation of growth and form. PMID:26042810

[X-ray semiotics of the morphological and functional changes in chronic bronchitis].

PubMed

Khomenko, A G; Dmitrieva, L I; Polak, J; Gapon'ko, G A; Starilova, I P

1985-01-01

The authors analysed structural disorders of a pulmonary pattern in patients with non-obstructive, obstructive and purulent bronchitis. Characteristic x-ray symptom-complexes were singled out for each clinical variant of the disease. In addition to roentgenomorphological changes functional disorders showing changes of biomechanics in patients with chronic bronchitis were revealed at roentgenopneumopolygraphy.

Organizational Commitment Patterns in Higher Education: A Study of Selected Midlevel Student Services Professionals

ERIC Educational Resources Information Center

Baker-Tate, Ixchel M.

2010-01-01

The student services profession was designed to create a commitment to the "whole student" and as such, the professionals who serve in this profession recognize the importance of this complex relationship. A review of the literature revealed that student services professionals are unsung professionals who generally feel a sense of calling to their…

Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation

PubMed Central

2011-01-01

Background To make sense out of gene expression profiles, such analyses must be pushed beyond the mere listing of affected genes. For example, if a group of genes persistently display similar changes in expression levels under particular experimental conditions, and the proteins encoded by these genes interact and function in the same cellular compartments, this could be taken as very strong indicators for co-regulated protein complexes. One of the key requirements is having appropriate tools to detect such regulatory patterns. Results We have analyzed the global adaptations in gene expression patterns in the budding yeast when the Hsp90 molecular chaperone complex is perturbed either pharmacologically or genetically. We integrated these results with publicly accessible expression, protein-protein interaction and intracellular localization data. But most importantly, all experimental conditions were simultaneously and dynamically visualized with an animation. This critically facilitated the detection of patterns of gene expression changes that suggested underlying regulatory networks that a standard analysis by pairwise comparison and clustering could not have revealed. Conclusions The results of the animation-assisted detection of changes in gene regulatory patterns make predictions about the potential roles of Hsp90 and its co-chaperone p23 in regulating whole sets of genes. The simultaneous dynamic visualization of microarray experiments, represented in networks built by integrating one's own experimental with publicly accessible data, represents a powerful discovery tool that allows the generation of new interpretations and hypotheses. PMID:21672238

Differences in the Visual Perception of Symmetric Patterns in Orangutans (Pongo pygmaeus abelii) and Two Human Cultural Groups: A Comparative Eye-Tracking Study.

PubMed

Mühlenbeck, Cordelia; Liebal, Katja; Pritsch, Carla; Jacobsen, Thomas

2016-01-01

Symmetric structures are of importance in relation to aesthetic preference. To investigate whether the preference for symmetric patterns is unique to humans, independent of their cultural background, we compared two human populations with distinct cultural backgrounds (Namibian hunter-gatherers and German town dwellers) with one species of non-human great apes (Orangutans) in their viewing behavior regarding symmetric and asymmetric patterns in two levels of complexity. In addition, the human participants were asked to give their aesthetic evaluation of a subset of the presented patterns. The results showed that humans of both cultural groups fixated on symmetric patterns for a longer period of time, regardless of the pattern's complexity. On the contrary, Orangutans did not clearly differentiate between symmetric and asymmetric patterns, but were much faster in processing the presented stimuli and scanned the complete screen, while both human groups rested on the symmetric pattern after a short scanning time. The aesthetic evaluation test revealed that the fixation preference for symmetric patterns did not match with the aesthetic evaluation in the Hai//om group, whereas in the German group aesthetic evaluation was in accordance with the fixation preference in 60 percent of the cases. It can be concluded that humans prefer well-ordered structures in visual processing tasks, most likely because of a positive processing bias for symmetry, which Orangutans did not show in this task, and that, in humans, an aesthetic preference does not necessarily accompany the fixation preference.

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

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

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna

Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. In this paper, we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated themore » identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. Finally, these efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.« less

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

DOE PAGES

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; ...

2015-04-09

Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. In this paper, we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated themore » identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. Finally, these efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.« less

Phylogeography and Sex-Biased Dispersal across Riverine Manatee Populations (Trichechus inunguis and Trichechus manatus) in South America

PubMed Central

Satizábal, Paula; Mignucci-Giannoni, Antonio A.; Duchêne, Sebastián; Caicedo-Herrera, Dalila; Perea-Sicchar, Carlos M.; García-Dávila, Carmen R.; Trujillo, Fernando; Caballero, Susana J.

2012-01-01

Phylogeographic patterns and sex-biased dispersal were studied in riverine populations of West Indian (Trichechus manatus) and Amazonian manatees (T. inunguis) in South America, using 410bp D-loop (Control Region, Mitochondrial DNA) sequences and 15 nuclear microsatellite loci. This multi-locus approach was key to disentangle complex patterns of gene flow among populations. D-loop analyses revealed population structuring among all Colombian rivers for T. manatus, while microsatellite data suggested no structure. Two main populations of T. inunguis separating the Colombian and Peruvian Amazon were supported by analysis of the D-loop and microsatellite data. Overall, we provide molecular evidence for differences in dispersal patterns between sexes, demonstrating male-biased gene flow dispersal in riverine manatees. These results are in contrast with previously reported levels of population structure shown by microsatellite data in marine manatee populations, revealing low habitat restrictions to gene flow in riverine habitats, and more significant dispersal limitations for males in marine environments. PMID:23285054

Deconstructing the brain’s moral network: dissociable functionality between the temporoparietal junction and ventro-medial prefrontal cortex

PubMed Central

Mobbs, Dean; Dalgleish, Tim

2014-01-01

Research has illustrated that the brain regions implicated in moral cognition comprise a robust and broadly distributed network. However, understanding how these brain regions interact and give rise to the complex interplay of cognitive processes underpinning human moral cognition is still in its infancy. We used functional magnetic resonance imaging to examine patterns of activation for ‘difficult’ and ‘easy’ moral decisions relative to matched non-moral comparators. This revealed an activation pattern consistent with a relative functional double dissociation between the temporoparietal junction (TPJ) and ventro-medial prefrontal cortex (vmPFC). Difficult moral decisions activated bilateral TPJ and deactivated the vmPFC and OFC. In contrast, easy moral decisions revealed patterns of activation in the vmPFC and deactivation in bilateral TPJ and dorsolateral PFC. Together these results suggest that moral cognition is a dynamic process implemented by a distributed network that involves interacting, yet functionally dissociable networks. PMID:23322890

Molecular Networking and Pattern-Based Genome Mining Improves discovery of biosynthetic gene clusters and their products from Salinispora species

PubMed Central

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; Sarkar, Anindita; Li, Jie; Ziemert, Nadine; Wang, Mingxun; Bandeira, Nuno; Moore, Bradley S.; Dorrestein, Pieter C.; Jensen, Paul R.

2015-01-01

Summary Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches. PMID:25865308

Phylogeography and sex-biased dispersal across riverine manatee populations (Trichechus inunguis and Trichechus manatus) in South America.

PubMed

Satizábal, Paula; Mignucci-Giannoni, Antonio A; Duchêne, Sebastián; Caicedo-Herrera, Dalila; Perea-Sicchar, Carlos M; García-Dávila, Carmen R; Trujillo, Fernando; Caballero, Susana J

2012-01-01

Phylogeographic patterns and sex-biased dispersal were studied in riverine populations of West Indian (Trichechus manatus) and Amazonian manatees (T. inunguis) in South America, using 410bp D-loop (Control Region, Mitochondrial DNA) sequences and 15 nuclear microsatellite loci. This multi-locus approach was key to disentangle complex patterns of gene flow among populations. D-loop analyses revealed population structuring among all Colombian rivers for T. manatus, while microsatellite data suggested no structure. Two main populations of T. inunguis separating the Colombian and Peruvian Amazon were supported by analysis of the D-loop and microsatellite data. Overall, we provide molecular evidence for differences in dispersal patterns between sexes, demonstrating male-biased gene flow dispersal in riverine manatees. These results are in contrast with previously reported levels of population structure shown by microsatellite data in marine manatee populations, revealing low habitat restrictions to gene flow in riverine habitats, and more significant dispersal limitations for males in marine environments.

Quantification of fetal heart rate regularity using symbolic dynamics

NASA Astrophysics Data System (ADS)

van Leeuwen, P.; Cysarz, D.; Lange, S.; Geue, D.; Groenemeyer, D.

2007-03-01

Fetal heart rate complexity was examined on the basis of RR interval time series obtained in the second and third trimester of pregnancy. In each fetal RR interval time series, short term beat-to-beat heart rate changes were coded in 8bit binary sequences. Redundancies of the 28 different binary patterns were reduced by two different procedures. The complexity of these sequences was quantified using the approximate entropy (ApEn), resulting in discrete ApEn values which were used for classifying the sequences into 17 pattern sets. Also, the sequences were grouped into 20 pattern classes with respect to identity after rotation or inversion of the binary value. There was a specific, nonuniform distribution of the sequences in the pattern sets and this differed from the distribution found in surrogate data. In the course of gestation, the number of sequences increased in seven pattern sets, decreased in four and remained unchanged in six. Sequences that occurred less often over time, both regular and irregular, were characterized by patterns reflecting frequent beat-to-beat reversals in heart rate. They were also predominant in the surrogate data, suggesting that these patterns are associated with stochastic heart beat trains. Sequences that occurred more frequently over time were relatively rare in the surrogate data. Some of these sequences had a high degree of regularity and corresponded to prolonged heart rate accelerations or decelerations which may be associated with directed fetal activity or movement or baroreflex activity. Application of the pattern classes revealed that those sequences with a high degree of irregularity correspond to heart rate patterns resulting from complex physiological activity such as fetal breathing movements. The results suggest that the development of the autonomic nervous system and the emergence of fetal behavioral states lead to increases in not only irregular but also regular heart rate patterns. Using symbolic dynamics to examine the cardiovascular system may thus lead to new insight with respect to fetal development.

The complexity of gene expression dynamics revealed by permutation entropy

PubMed Central

2010-01-01

Background High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical systems theory. The analysis of gene expression data has so far focused primarily on the identification of differentially expressed genes, or on the elucidation of pathway and regulatory relationships. We aim to study gene expression time series data from the viewpoint of complexity. Results Applying the PE complexity metric to abiotic stress response time series data in Arabidopsis thaliana, genes involved in stress response and signaling were found to be associated with the highest complexity not only under stress, but surprisingly, also under reference, non-stress conditions. Genes with house-keeping functions exhibited lower PE complexity. Compared to reference conditions, the PE of temporal gene expression patterns generally increased upon stress exposure. High-complexity genes were found to have longer upstream intergenic regions and more cis-regulatory motifs in their promoter regions indicative of a more complex regulatory apparatus needed to orchestrate their expression, and to be associated with higher correlation network connectivity degree. Arabidopsis genes also present in other plant species were observed to exhibit decreased PE complexity compared to Arabidopsis specific genes. Conclusions We show that Permutation Entropy is a simple yet robust and powerful approach to identify temporal gene expression profiles of varying complexity that is equally applicable to other types of molecular profile data. PMID:21176199

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.

PubMed

Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini

2016-01-01

Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

A phylogenetic assessment of the polyphyletic nature and intraspecific color polymorphism in the Bactrocera dorsalis complex (Diptera, Tephritidae)

PubMed Central

Leblanc, Luc; San Jose, Michael; Barr, Norman; Rubinoff, Daniel

2015-01-01

Abstract The Bactrocera dorsalis complex (Tephritidae) comprises 85 species of fruit flies, including five highly destructive polyphagous fruit pests. Despite significant work on a few key pest species within the complex, little has been published on the majority of non-economic species in the complex, other than basic descriptions and illustrations of single specimens regarded as typical representatives. To elucidate the species relationships within the Bactrocera dorsalis complex, we used 159 sequences from one mitochondrial (COI) and two nuclear (elongation factor-1α and period) genes to construct a phylogeny containing 20 described species from within the complex, four additional species that may be new to science, and 26 other species from Bactrocera and its sister genus Dacus. The resulting concatenated phylogeny revealed that most of the species placed in the complex appear to be unrelated, emerging across numerous clades. This suggests that they were placed in the Bactrocera dorsalis complex based on the similarity of convergent characters, which does not appear to be diagnostic. Variations in scutum and abdomen color patterns within each of the non-economic species are presented and demonstrate that distantly-related, cryptic species overlap greatly in traditional morphological color patterns used to separate them in keys. Some of these species may not be distinguishable with confidence by means other than DNA data. PMID:26798267

Algebraic Topology of Multi-Brain Connectivity Networks Reveals Dissimilarity in Functional Patterns during Spoken Communications

PubMed Central

Tadić, Bosiljka; Andjelković, Miroslav; Boshkoska, Biljana Mileva; Levnajić, Zoran

2016-01-01

Human behaviour in various circumstances mirrors the corresponding brain connectivity patterns, which are suitably represented by functional brain networks. While the objective analysis of these networks by graph theory tools deepened our understanding of brain functions, the multi-brain structures and connections underlying human social behaviour remain largely unexplored. In this study, we analyse the aggregate graph that maps coordination of EEG signals previously recorded during spoken communications in two groups of six listeners and two speakers. Applying an innovative approach based on the algebraic topology of graphs, we analyse higher-order topological complexes consisting of mutually interwoven cliques of a high order to which the identified functional connections organise. Our results reveal that the topological quantifiers provide new suitable measures for differences in the brain activity patterns and inter-brain synchronisation between speakers and listeners. Moreover, the higher topological complexity correlates with the listener’s concentration to the story, confirmed by self-rating, and closeness to the speaker’s brain activity pattern, which is measured by network-to-network distance. The connectivity structures of the frontal and parietal lobe consistently constitute distinct clusters, which extend across the listener’s group. Formally, the topology quantifiers of the multi-brain communities exceed the sum of those of the participating individuals and also reflect the listener’s rated attributes of the speaker and the narrated subject. In the broader context, the presented study exposes the relevance of higher topological structures (besides standard graph measures) for characterising functional brain networks under different stimuli. PMID:27880802

Common brain regions underlying different arithmetic operations as revealed by conjunct fMRI-BOLD activation.

PubMed

Fehr, Thorsten; Code, Chris; Herrmann, Manfred

2007-10-03

The issue of how and where arithmetic operations are represented in the brain has been addressed in numerous studies. Lesion studies suggest that a network of different brain areas are involved in mental calculation. Neuroimaging studies have reported inferior parietal and lateral frontal activations during mental arithmetic using tasks of different complexities and using different operators (addition, subtraction, etc.). Indeed, it has been difficult to compare brain activation across studies because of the variety of different operators and different presentation modalities used. The present experiment examined fMRI-BOLD activity in participants during calculation tasks entailing different arithmetic operations -- addition, subtraction, multiplication and division -- of different complexities. Functional imaging data revealed a common activation pattern comprising right precuneus, left and right middle and superior frontal regions during all arithmetic operations. All other regional activations were operation specific and distributed in prominently frontal, parietal and central regions when contrasting complex and simple calculation tasks. The present results largely confirm former studies suggesting that activation patterns due to mental arithmetic appear to reflect a basic anatomical substrate of working memory, numerical knowledge and processing based on finger counting, and derived from a network originally related to finger movement. We emphasize that in mental arithmetic research different arithmetic operations should always be examined and discussed independently of each other in order to avoid invalid generalizations on arithmetics and involved brain areas.

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations

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

Schüler, D.; Alonso, S.; Bär, M.

2014-12-15

Pattern formation often occurs in spatially extended physical, biological, and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue, we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexistingmore » static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular, revealing for the Swift-Hohenberg equations, a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of a weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.« less

The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data

PubMed Central

Sun, Keping; Kimball, Rebecca T.; Liu, Tong; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Lin, Aiqing; Feng, Jiang

2016-01-01

Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization. PMID:27748429

Evaluating Treatment and Generalization Patterns of Two Theoretically Motivated Sentence Comprehension Therapies

PubMed Central

Des Roches, Carrie A.; Vallila-Rohter, Sofia; Villard, Sarah; Tripodis, Yorghos; Caplan, David

2016-01-01

Purpose The current study examined treatment outcomes and generalization patterns following 2 sentence comprehension therapies: object manipulation (OM) and sentence-to-picture matching (SPM). Findings were interpreted within the framework of specific deficit and resource reduction accounts, which were extended in order to examine the nature of generalization following treatment of sentence comprehension deficits in aphasia. Method Forty-eight individuals with aphasia were enrolled in 1 of 8 potential treatment assignments that varied by task (OM, SPM), complexity of trained sentences (complex, simple), and syntactic movement (noun phrase, wh-movement). Comprehension of trained and untrained sentences was probed before and after treatment using stimuli that differed from the treatment stimuli. Results Linear mixed-model analyses demonstrated that, although both OM and SPM treatments were effective, OM resulted in greater improvement than SPM. Analyses of covariance revealed main effects of complexity in generalization; generalization from complex to simple linguistically related sentences was observed both across task and across movement. Conclusions Results are consistent with the complexity account of treatment efficacy, as generalization effects were consistently observed from complex to simpler structures. Furthermore, results provide support for resource reduction accounts that suggest that generalization can extend across linguistic boundaries, such as across movement type. PMID:27997950

Global terrestrial water storage connectivity revealed using complex climate network analyses

NASA Astrophysics Data System (ADS)

Sun, A. Y.; Chen, J.; Donges, J.

2015-07-01

Terrestrial water storage (TWS) exerts a key control in global water, energy, and biogeochemical cycles. Although certain causal relationship exists between precipitation and TWS, the latter quantity also reflects impacts of anthropogenic activities. Thus, quantification of the spatial patterns of TWS will not only help to understand feedbacks between climate dynamics and the hydrologic cycle, but also provide new insights and model calibration constraints for improving the current land surface models. This work is the first attempt to quantify the spatial connectivity of TWS using the complex network theory, which has received broad attention in the climate modeling community in recent years. Complex networks of TWS anomalies are built using two global TWS data sets, a remote sensing product that is obtained from the Gravity Recovery and Climate Experiment (GRACE) satellite mission, and a model-generated data set from the global land data assimilation system's NOAH model (GLDAS-NOAH). Both data sets have 1° × 1° grid resolutions and cover most global land areas except for permafrost regions. TWS networks are built by first quantifying pairwise correlation among all valid TWS anomaly time series, and then applying a cutoff threshold derived from the edge-density function to retain only the most important features in the network. Basinwise network connectivity maps are used to illuminate connectivity of individual river basins with other regions. The constructed network degree centrality maps show the TWS anomaly hotspots around the globe and the patterns are consistent with recent GRACE studies. Parallel analyses of networks constructed using the two data sets reveal that the GLDAS-NOAH model captures many of the spatial patterns shown by GRACE, although significant discrepancies exist in some regions. Thus, our results provide further measures for constraining the current land surface models, especially in data sparse regions.

Complex pattern of colon cancer recurrence including a kidney metastasis: A case report

PubMed Central

Waleczek, Helfried; Wente, Moritz N; Kozianka, Jürgen

2005-01-01

We report a case of a 77-year-old female with a local recurrence of cancer after right hemicolectomy which infiltrated the pancreatic head affording pancrea-toduodenectomy, who developed 3 years later recurrent tumor masses localized in the mesentery of the jejunum and in the lower pole of the left kidney. Partial nephrectomy and a segment resection of the small bowel were performed. Histological examination of both specimens revealed a necrotic metastasis of the primary carcinoma of the colon. Although intraluminal implantation of colon cancer cells in the renal pelvic mucosa from ureteric metastasis has been described, metastasis of a colorectal cancer in the kidney parenchyma is extremely rare and can be treated in an organ preserving manner. A complex pattern of colon cancer recurrence with unusual and rare sites of metastasis is reported. PMID:16222759

Complex Dynamics in Nonequilibrium Economics and Chemistry

NASA Astrophysics Data System (ADS)

Wen, Kehong

Complex dynamics provides a new approach in dealing with economic complexity. We study interactively the empirical and theoretical aspects of business cycles. The way of exploring complexity is similar to that in the study of an oscillatory chemical system (BZ system)--a model for modeling complex behavior. We contribute in simulating qualitatively the complex periodic patterns observed from the controlled BZ experiments to narrow the gap between modeling and experiment. The gap between theory and reality is much wider in economics, which involves studies of human expectations and decisions, the essential difference from natural sciences. Our empirical and theoretical studies make substantial progress in closing this gap. With the help from the new development in nonequilibrium physics, i.e., the complex spectral theory, we advance our technique in detecting characteristic time scales from empirical economic data. We obtain correlation resonances, which give oscillating modes with decays for correlation decomposition, from different time series including S&P 500, M2, crude oil spot prices, and GNP. The time scales found are strikingly compatible with business experiences and other studies in business cycles. They reveal the non-Markovian nature of coherent markets. The resonances enhance the evidence of economic chaos obtained by using other tests. The evolving multi-humped distributions produced by the moving-time -window technique reveal the nonequilibrium nature of economic behavior. They reproduce the American economic history of booms and busts. The studies seem to provide a way out of the debate on chaos versus noise and unify the cyclical and stochastic approaches in explaining business fluctuations. Based on these findings and new expectation formulation, we construct a business cycle model which gives qualitatively compatible patterns to those found empirically. The soft-bouncing oscillator model provides a better alternative than the harmonic oscillator or the random walk model as the building block in business cycle theory. The mathematical structure of the model (delay differential equation) is studied analytically and numerically. The research pave the way toward sensible economic forecasting.

Chess players' eye movements reveal rapid recognition of complex visual patterns: Evidence from a chess-related visual search task.

PubMed

Sheridan, Heather; Reingold, Eyal M

2017-03-01

To explore the perceptual component of chess expertise, we monitored the eye movements of expert and novice chess players during a chess-related visual search task that tested anecdotal reports that a key differentiator of chess skill is the ability to visualize the complex moves of the knight piece. Specifically, chess players viewed an array of four minimized chessboards, and they rapidly searched for the target board that allowed a knight piece to reach a target square in three moves. On each trial, there was only one target board (i.e., the "Yes" board), and for the remaining "lure" boards, the knight's path was blocked on either the first move (the "Easy No" board) or the second move (i.e., "the Difficult No" board). As evidence that chess experts can rapidly differentiate complex chess-related visual patterns, the experts (but not the novices) showed longer first-fixation durations on the "Yes" board relative to the "Difficult No" board. Moreover, as hypothesized, the task strongly differentiated chess skill: Reaction times were more than four times faster for the experts relative to novices, and reaction times were correlated with within-group measures of expertise (i.e., official chess ratings, number of hours of practice). These results indicate that a key component of chess expertise is the ability to rapidly recognize complex visual patterns.

Correlates of Marijuana and Alcohol Use Among College Students

ERIC Educational Resources Information Center

Biggs, Donald A.; And Others

1974-01-01

a questionnaire on marijuana was completed by 460 students; one on alcohol was completed by 465 students. Results reveal that the relationship between the use of these two drugs is complex. Students' attitudes toward their parents are related to their use of marijuana but not to their use of alcohol. The use of alcohol is a pattern of continuity…

Molecular Dynamics Study of HIV-1 RT-DNA-Nevirapine Complexes Explains NNRTI Inhibition, and Resistance by Connection Mutations

PubMed Central

Vijayan, R.S.K.; Arnold, Eddy; Das, Kalyan

2015-01-01

HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that is targeted by nucleoside analogs (NRTIs) and nonnucleoside inhibitors (NNRTIs). NNRTIs are allosteric inhibitors of RT, and constitute an integral part of the highly active antiretroviral therapy (HAART) regimen. Under selective pressure, HIV-1 acquires resistance against NNRTIs primarily by selecting mutations around the NNRTI pocket. Complete RT sequencing of clinical isolates revealed that spatially distal mutations arising in connection and the RNase H domain also confer NNRTI resistance and contribute to NRTI resistance. However, the precise structural mechanism by which the connection domain mutations confer NNRTI resistance is poorly understood. We performed 50-ns MD simulations, followed by essential dynamics, free-energy landscape analyses and network analyses of RT-DNA, RT-DNA-nevirapine, and N348I/T369I mutant RT-DNA-nevirapine complexes. MD simulation studies revealed altered global motions and restricted conformational landscape of RT upon nevirapine binding. Analysis of protein structure network parameters demonstrated a dissortative hub pattern in the RT-DNA complex and an assortative hub pattern in the RT-DNA-nevirapine complex suggesting enhanced rigidity of RT upon nevirapine binding. The connection subdomain mutations N348I/T369I did not induce any significant structural change; rather, these mutations modulate the conformational dynamics and alter the long-range allosteric communication network between the connection subdomain and NNRTI pocket. Insights from the present study provide a structural basis for the biochemical and clinical findings on drug resistance caused by the connection and RNase H mutations. PMID:24174331

Decoding the spatial signatures of multi-scale climate variability - a climate network perspective

NASA Astrophysics Data System (ADS)

Donner, R. V.; Jajcay, N.; Wiedermann, M.; Ekhtiari, N.; Palus, M.

2017-12-01

During the last years, the application of complex networks as a versatile tool for analyzing complex spatio-temporal data has gained increasing interest. Establishing this approach as a new paradigm in climatology has already provided valuable insights into key spatio-temporal climate variability patterns across scales, including novel perspectives on the dynamics of the El Nino Southern Oscillation or the emergence of extreme precipitation patterns in monsoonal regions. In this work, we report first attempts to employ network analysis for disentangling multi-scale climate variability. Specifically, we introduce the concept of scale-specific climate networks, which comprises a sequence of networks representing the statistical association structure between variations at distinct time scales. For this purpose, we consider global surface air temperature reanalysis data and subject the corresponding time series at each grid point to a complex-valued continuous wavelet transform. From this time-scale decomposition, we obtain three types of signals per grid point and scale - amplitude, phase and reconstructed signal, the statistical similarity of which is then represented by three complex networks associated with each scale. We provide a detailed analysis of the resulting connectivity patterns reflecting the spatial organization of climate variability at each chosen time-scale. Global network characteristics like transitivity or network entropy are shown to provide a new view on the (global average) relevance of different time scales in climate dynamics. Beyond expected trends originating from the increasing smoothness of fluctuations at longer scales, network-based statistics reveal different degrees of fragmentation of spatial co-variability patterns at different scales and zonal shifts among the key players of climate variability from tropically to extra-tropically dominated patterns when moving from inter-annual to decadal scales and beyond. The obtained results demonstrate the potential usefulness of systematically exploiting scale-specific climate networks, whose general patterns are in line with existing climatological knowledge, but provide vast opportunities for further quantifications at local, regional and global scales that are yet to be explored.

Prior activity of olfactory receptor neurons is required for proper sensory processing and behavior in Drosophila larvae.

PubMed

Utashiro, Nao; Williams, Claire R; Parrish, Jay Z; Emoto, Kazuo

2018-06-05

Animal responses to their environment rely on activation of sensory neurons by external stimuli. In many sensory systems, however, neurons display basal activity prior to the external stimuli. This prior activity is thought to modulate neural functions, yet its impact on animal behavior remains elusive. Here, we reveal a potential role for prior activity in olfactory receptor neurons (ORNs) in shaping larval olfactory behavior. We show that prior activity in larval ORNs is mediated by the olfactory receptor complex (OR complex). Mutations of Orco, an odorant co-receptor required for OR complex function, cause reduced attractive behavior in response to optogenetic activation of ORNs. Calcium imaging reveals that Orco mutant ORNs fully respond to optogenetic stimulation but exhibit altered temporal patterns of neural responses. These findings together suggest a critical role for prior activity in information processing upon ORN activation in Drosophila larvae, which in turn contributes to olfactory behavior control.

High-resolution mapping reveals topologically distinct cellular pools of phosphatidylserine

PubMed Central

Fairn, Gregory D.; Schieber, Nicole L.; Ariotti, Nicholas; Murphy, Samantha; Kuerschner, Lars; Webb, Richard I.; Grinstein, Sergio

2011-01-01

Phosphatidylserine (PS) plays a central role in cell signaling and in the biosynthesis of other lipids. To date, however, the subcellular distribution and transmembrane topology of this crucial phospholipid remain ill-defined. We transfected cells with a GFP-tagged C2 domain of lactadherin to detect by light and electron microscopy PS exposed on the cytosolic leaflet of the plasmalemma and organellar membranes. Cytoplasmically exposed PS was found to be clustered on the plasma membrane, and to be associated with caveolae, the trans-Golgi network, and endocytic organelles including intraluminal vesicles of multivesicular endosomes. This labeling pattern was compared with the total cellular distribution of PS as visualized using a novel on-section technique. These complementary methods revealed PS in the interior of the ER, Golgi complex, and mitochondria. These results indicate that PS in the lumenal monolayer of the ER and Golgi complex becomes exposed cytosolically at the trans-Golgi network. Transmembrane flipping of PS may contribute to the exit of cargo from the Golgi complex. PMID:21788369

Lineament and polygon patterns on Europa

NASA Technical Reports Server (NTRS)

Pieri, D. C.

1981-01-01

A classification scheme is presented for the lineaments and associated polygonal patterns observed on the surface of Europa, and the frequency distribution of the polygons is discussed in terms of the stress-relief fracturing of the surface. The lineaments are divided on the basis of albedo, morphology, orientation and characteristic geometry into eight groups based on Voyager 2 images taken at a best resolution of 4 km. The lineaments in turn define a system of polygons varying in size from small reticulate patterns the limit of resolution to 1,000,000 sq km individuals. Preliminary analysis of polygon side frequency distributions reveals a class of polygons with statistics similar to those found in complex terrestrial terrains, particularly in areas of well-oriented stresses, a class with similar statistics around the antijovian point, and a class with a distribution similar to those seen in terrestrial tensional fracture patterns. Speculations concerning the processes giving rise to the lineament patterns are presented.

On the diffraction pattern of bundled rare-earth silicide nanowires on Si(0 0 1).

PubMed

Timmer, F; Bahlmann, J; Wollschläger, J

2017-11-01

Motivated by the complex diffraction pattern observed for bundled rare-earth silicide nanowires on the Si(0 0 1) surface, we investigate the influence of the width and the spacing distribution of the nanowires on the diffraction pattern. The diffraction pattern of the bundled rare-earth silicide nanowires is analyzed by the binary surface technique applying a kinematic approach to diffraction. Assuming a categorical distribution for the (individual) nanowire size and a Poisson distribution for the size of the spacing between adjacent nanowire-bundles, we are able to determine the parameters of these distributions and derive an expression for the distribution of the nanowire-bundle size. Additionally, the comparison of our simulations to the experimental diffraction pattern reveal that a (1  ×  1)-periodicity on top of the nanowires has to be assumed for a good match.

Visibility in the topology of complex networks

NASA Astrophysics Data System (ADS)

Tsiotas, Dimitrios; Charakopoulos, Avraam

2018-09-01

Taking its inspiration from the visibility algorithm, which was proposed by Lacasa et al. (2008) to convert a time-series into a complex network, this paper develops and proposes a novel expansion of this algorithm that allows generating a visibility graph from a complex network instead of a time-series that is currently applicable. The purpose of this approach is to apply the idea of visibility from the field of time-series to complex networks in order to interpret the network topology as a landscape. Visibility in complex networks is a multivariate property producing an associated visibility graph that maps the ability of a node "to see" other nodes in the network that lie beyond the range of its neighborhood, in terms of a control-attribute. Within this context, this paper examines the visibility topology produced by connectivity (degree) in comparison with the original (source) network, in order to detect what patterns or forces describe the mechanism under which a network is converted to a visibility graph. The overall analysis shows that visibility is a property that increases the connectivity in networks, it may contribute to pattern recognition (among which the detection of the scale-free topology) and it is worth to be applied to complex networks in order to reveal the potential of signal processing beyond the range of its neighborhood. Generally, this paper promotes interdisciplinary research in complex networks providing new insights to network science.

Predictive ethoinformatics reveals the complex migratory behaviour of a pelagic seabird, the Manx Shearwater

PubMed Central

Freeman, Robin; Dean, Ben; Kirk, Holly; Leonard, Kerry; Phillips, Richard A.; Perrins, Chris M.; Guilford, Tim

2013-01-01

Understanding the behaviour of animals in the wild is fundamental to conservation efforts. Advances in bio-logging technologies have offered insights into the behaviour of animals during foraging, migration and social interaction. However, broader application of these systems has been limited by device mass, cost and longevity. Here, we use information from multiple logger types to predict individual behaviour in a highly pelagic, migratory seabird, the Manx Shearwater (Puffinus puffinus). Using behavioural states resolved from GPS tracking of foraging during the breeding season, we demonstrate that individual behaviours can be accurately predicted during multi-year migrations from low cost, lightweight, salt-water immersion devices. This reveals a complex pattern of migratory stopovers: some involving high proportions of foraging, and others of rest behaviour. We use this technique to examine three consecutive years of global migrations, revealing the prominence of foraging behaviour during migration and the importance of highly productive waters during migratory stopover. PMID:23635496

Origins of Aminergic Regulation of Behavior in Complex Insect Social Systems

PubMed Central

Kamhi, J. Frances; Arganda, Sara; Moreau, Corrie S.; Traniello, James F. A.

2017-01-01

Neuromodulators are conserved across insect taxa, but how biogenic amines and their receptors in ancestral solitary forms have been co-opted to control behaviors in derived socially complex species is largely unknown. Here we explore patterns associated with the functions of octopamine (OA), serotonin (5-HT) and dopamine (DA) in solitary ancestral insects and their derived functions in eusocial ants, bees, wasps and termites. Synthesizing current findings that reveal potential ancestral roles of monoamines in insects, we identify physiological processes and conserved behaviors under aminergic control, consider how biogenic amines may have evolved to modulate complex social behavior, and present focal research areas that warrant further study. PMID:29066958

DNA barcoding reveals new insights into the diversity of Antarctic species of Orchomene sensu lato (Crustacea: Amphipoda: Lysianassoidea)

NASA Astrophysics Data System (ADS)

Havermans, C.; Nagy, Z. T.; Sonet, G.; De Broyer, C.; Martin, P.

2011-03-01

Recent molecular analyses revealed that several so-called "circum-Antarctic" benthic crustacean species appeared to be complexes of cryptic species with restricted distributions. In this study we used a DNA barcoding approach based on mitochondrial cytochrome oxidase I gene sequences in order to detect possible cryptic diversity and to test the circumpolarity of some lysianassoid species. The orchomenid genus complex consists of the genera Abyssorchomene, Falklandia, Orchomenella, Orchomenyx and Pseudorchomene. Species of this genus complex are found throughout the Southern Ocean and show a high species richness and level of endemism. In the majority of the studied species, a genetic homogeneity was found even among specimens from remote sampling sites, which indicates a possible circum-Antarctic and eurybathic distribution. In four investigated species ( Orchomenella ( Orchomenopsis) acanthurus, Orchomenella ( Orchomenopsis) cavimanus, Orchomenella ( Orchomenella) franklini and Orchomenella ( Orchomenella) pinguides), genetically divergent lineages and possible cryptic taxa were revealed. After a detailed morphological analysis, O. ( O.) pinguides appeared to be composed of two distinct species, formerly synonymized under O. ( O.) pinguides. The different genetic patterns observed in these orchomenid species might be explained by the evolutionary histories undergone by these species and by their different dispersal and gene flow capacities.

The landscape of fear as an emergent property of heterogeneity: Contrasting patterns of predation risk in grassland ecosystems.

PubMed

Atuo, Fidelis Akunke; O'Connell, Timothy John

2017-07-01

The likelihood of encountering a predator influences prey behavior and spatial distribution such that non-consumptive effects can outweigh the influence of direct predation. Prey species are thought to filter information on perceived predator encounter rates in physical landscapes into a landscape of fear defined by spatially explicit heterogeneity in predation risk. The presence of multiple predators using different hunting strategies further complicates navigation through a landscape of fear and potentially exposes prey to greater risk of predation. The juxtaposition of land cover types likely influences overlap in occurrence of different predators, suggesting that attributes of a landscape of fear result from complexity in the physical landscape. Woody encroachment in grasslands furnishes an example of increasing complexity with the potential to influence predator distributions. We examined the role of vegetation structure on the distribution of two avian predators, Red-tailed Hawk ( Buteo jamaicensis ) and Northern Harrier ( Circus cyaneus ), and the vulnerability of a frequent prey species of those predators, Northern Bobwhite ( Colinus virginianus ). We mapped occurrences of the raptors and kill locations of Northern Bobwhite to examine spatial vulnerability patterns in relation to landscape complexity. We use an offset model to examine spatially explicit habitat use patterns of these predators in the Southern Great Plains of the United States, and monitored vulnerability patterns of their prey species based on kill locations collected during radio telemetry monitoring. Both predator density and predation-specific mortality of Northern Bobwhite increased with vegetation complexity generated by fine-scale interspersion of grassland and woodland. Predation pressure was lower in more homogeneous landscapes where overlap of the two predators was less frequent. Predator overlap created areas of high risk for Northern Bobwhite amounting to 32% of the land area where landscape complexity was high and 7% where complexity was lower. Our study emphasizes the need to evaluate the role of landscape structure on predation dynamics and reveals another threat from woody encroachment in grasslands.

Cross-slope Movement Patterns in Landslides

NASA Astrophysics Data System (ADS)

Petley, D.; Murphy, W.; Bulmer, M. H.; Keefer, D.

2002-12-01

There is growing evidence that there is a significant element of cross-slope movement in many large landslide systems. These movements may result in changing states of stress between landslide blocks that can establish complex displacement patterns. Such motions, which are not considered in traditional two-dimensional limit-equilibrium analyses, are important in the investigation of a variety of landslide types, such as those triggered by earthquakes. In addition, these movements may introduce considerable errors into the interpretation of strain patterns as derived from InSAR studies. Finally, even traditional interpretation techniques may lead to the amount of total displacement being underestimated. These observations suggest that a three dimensional form of analysis may be more appropriate for large landslide complexes. The significance of such cross-slope movements are being investigated using a detailed investigation of the Lishan landslide complex in Central Taiwan. This landslide system, which was reactivated in 1990 related to the construction of a hotel. The total recorded movements have been approximately 1.5 m over an area of sliding that is estimated to be 450 m wide and 200 m long. Extensive damage has been caused to roads and buildings within the town. Remediation work has resulted largely in the stabilization of the landslide complex. Detailed geomorphological mapping has revealed that the landslide complex is composed of two main components. The first, immediately upslope of the hotel construction site, is a relatively shallow earthflow. The second, which has formed a large headscarp upslope from the main road in the centre of the town, is a deeper translational slide. Both appear to have been reactivations of previous failures. While the displacement patterns of the earthflow indicate a relatively simple downslope movement, the vectors derived from kinematic analysis of surface features have indicated that the movement of the deeper-seated landslide was more complex. Though the dominant movement vector is downslope, there is evidence to suggest that there has been a cross-slope component of motion that corresponds to the bedding orientation.

Spatial organization of xylem cell walls by ROP GTPases and microtubule-associated proteins.

PubMed

Oda, Yoshihisa; Fukuda, Hiroo

2013-12-01

Proper patterning of cellulosic cell walls is critical for cell shaping and differentiation of plant cells. Cortical microtubule arrays regulate the deposition patterns of cellulose microfibrils by controlling the targeting and trajectory of cellulose synthase complexes. Although some microtubule-associated proteins (MAPs) regulate the arrangement of cortical microtubules, knowledge about the overall mechanism governing the spacing of cortical microtubules is still limited. Recent studies reveal that ROP GTPases and MAPs spatially regulate the assembly and disassembly of cortical microtubules in developing xylem cells, in which localized secondary cell walls are deposited. Here, we review recent insights into the regulation of xylem cell wall patterning by cortical microtubules, ROP GTPases, and MAPs. Copyright © 2013 Elsevier Ltd. All rights reserved.

Putting humans in ecology: consistency in science and management.

PubMed

Hobbs, Larry; Fowler, Charles W

2008-03-01

Normal and abnormal levels of human participation in ecosystems can be revealed through the use of macro-ecological patterns. Such patterns also provide consistent and objective guidance that will lead to achieving and maintaining ecosystem health and sustainability. This paper focuses on the consistency of this type of guidance and management. Such management, in sharp contrast to current management practices, ensures that our actions as individuals, institutions, political groups, societies, and as a species are applied consistently across all temporal, spatial, and organizational scales. This approach supplants management of today, where inconsistency results from debate, politics, and legal and religious polarity. Consistency is achieved when human endeavors are guided by natural patterns. Pattern-based management meets long-standing demands for enlightened management that requires humans to participate in complex systems in consistent and sustainable ways.

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed Central

Jezkova, Tereza; Wiens, John J.

2016-01-01

Animal phyla vary dramatically in species richness (from 1 species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g. sponges), parasitic worms (e.g. nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ~74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, non-marine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (~67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g. head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species. PMID:28221832

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed

Jezkova, Tereza; Wiens, John J

2017-03-01

Animal phyla vary dramatically in species richness (from one species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g., sponges), parasitic worms (e.g., nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ∼74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, nonmarine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (∼67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g., head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species.

Effect of gamma-irradiation on thermal decomposition kinetics, X-ray diffraction pattern and spectral properties of tris(1,2-diaminoethane)nickel(II)sulphate

NASA Astrophysics Data System (ADS)

Jayashri, T. A.; Krishnan, G.; Rema Rani, N.

2014-12-01

Tris(1,2-diaminoethane)nickel(II)sulphate was prepared, and characterised by various chemical and spectral techniques. The sample was irradiated with 60Co gamma rays for varying doses. Sulphite ion and ammonia were detected and estimated in the irradiated samples. Non-isothermal decomposition kinetics, X-ray diffraction pattern, Fourier transform infrared spectroscopy, electronic, fast atom bombardment mass spectra, and surface morphology of the complex were studied before and after irradiation. Kinetic parameters were evaluated by integral, differential, and approximation methods. Irradiation enhanced thermal decomposition, lowering thermal and kinetic parameters. The mechanism of decomposition is controlled by R3 function. From X-ray diffraction studies, change in lattice parameters and subsequent changes in unit cell volume and average crystallite size were observed. Both unirradiated and irradiated samples of the complex belong to trigonal crystal system. Decrease in the intensity of the peaks was observed in the infrared spectra of irradiated samples. Electronic spectral studies revealed that the M-L interaction is unaffected by irradiation. Mass spectral studies showed that the fragmentation patterns of the unirradiated and irradiated samples are similar. The additional fragment with m/z 256 found in the irradiated sample is attributed to S8+. Surface morphology of the complex changed upon irradiation.

Numerical models of caldera deformation: Effects of multiphase and multicomponent hydrothermal fluid flow

USGS Publications Warehouse

Hutnak, M.; Hurwitz, S.; Ingebritsen, S.E.; Hsieh, P.A.

2009-01-01

Ground surface displacement (GSD) in large calderas is often interpreted as resulting from magma intrusion at depth. Recent advances in geodetic measurements of GSD, notably interferometric synthetic aperture radar, reveal complex and multifaceted deformation patterns that often require complex source models to explain the observed GSD. Although hydrothermal fluids have been discussed as a possible deformation agent, very few quantitative studies addressing the effects of multiphase flow on crustal mechanics have been attempted. Recent increases in the power and availability of computing resources allow robust quantitative assessment of the complex time-variant thermal interplay between aqueous fluid flow and crustal deformation. We carry out numerical simulations of multiphase (liquid-gas), multicomponent (H 2O-CO2) hydrothermal fluid flow and poroelastic deformation using a range of realistic physical parameters and processes. Hydrothermal fluid injection, circulation, and gas formation can generate complex, temporally and spatially varying patterns of GSD, with deformation rates, magnitudes, and geometries (including subsidence) similar to those observed in several large calderas. The potential for both rapid and gradual deformation resulting from magma-derived fluids suggests that hydrothermal fluid circulation may help explain deformation episodes at calderas that have not culminated in magmatic eruption.

Differences and Commonalities: Farmer Stratifications in the San Luis Valley Research/Extension Project Area. ARE Research Report.

ERIC Educational Resources Information Center

Eckert, Jerry B.

A research project in the San Luis Valley of Colorado sought to isolate a few unique farm types that could become target groups for the design and implementation of agricultural research and extension programs. Questionnaires were completed by 44 of 65 farmers in one watershed area of Conejos County. Analysis revealed a complex pattern of…

Gulf of California, Mexico

NASA Technical Reports Server (NTRS)

1982-01-01

Sunglint on the water's surface reveals the complex pattern of currents in the Gulf of California in the vicinity of Tiburon and Angel de la Guarda Islands (29.0N, 113.0W). Mexico's state of Sonora and the Sonora Desert is on the mainland and the state of Baja California consists of the entire peninsula. The Pacific Ocean is under the coastal cloud cover on the Baja peninsula.

Dynamic Battlefield Visualization: Knowledge Management in a Complex, Emergent PMESII-PT Battlefield

DTIC Science & Technology

2009-06-01

organizations was articulated over two decades ago by Jerome Bruner (1986). Specifically, he argued that humans employ two distinctive modes of...narrative knowledge underscored by the writings of Jerome Bruner , Karl Weick, Laurence Prusak, and John Seely Brown. Finally, it consistently supports...a known battle calculus) and ambiguity (pattern/trend analysis to reveal operational variances or to discover influence mechanisms that can be

Rethinking the longitudinal stream temperature paradigm: region-wide comparison of thermal infrared imagery reveals unexpected complexity of river temperatures

Treesearch

Aimee H. Fullerton; Christian E. Torgersen; Joshua J. Lawler; Russell N. Faux; Ashley Steel; Timothy J. Beechie; Joseph L. Ebersole; Scott G. Leibowitz

2015-01-01

Prevailing theory suggests that stream temperature warms asymptotically in a downstream direction, beginning at the temperature of the source in the headwaters and levelling off downstream as it converges to matchmeteorological conditions.However, there have been few empirical examples of longitudinal patterns of temperature in large rivers due to a paucity of data. We...

Assessing Species-specific Contributions To Craniofacial Development Using Quail-duck Chimeras

PubMed Central

Fish, Jennifer L.; Schneider, Richard A.

2014-01-01

The generation of chimeric embryos is a widespread and powerful approach to study cell fates, tissue interactions, and species-specific contributions to the histological and morphological development of vertebrate embryos. In particular, the use of chimeric embryos has established the importance of neural crest in directing the species-specific morphology of the craniofacial complex. The method described herein utilizes two avian species, duck and quail, with remarkably different craniofacial morphology. This method greatly facilitates the investigation of molecular and cellular regulation of species-specific pattern in the craniofacial complex. Experiments in quail and duck chimeric embryos have already revealed neural crest-mediated tissue interactions and cell-autonomous behaviors that regulate species-specific pattern in the craniofacial skeleton, musculature, and integument. The great diversity of neural crest derivatives suggests significant potential for future applications of the quail-duck chimeric system to understanding vertebrate development, disease, and evolution. PMID:24962088

Effect of Rho-kinase inhibition on complexity of breathing pattern in a guinea pig model of asthma

PubMed Central

Pazhoohan, Saeed; Javan, Mohammad; Hajizadeh, Sohrab

2017-01-01

Asthma represents an episodic and fluctuating behavior characterized with decreased complexity of respiratory dynamics. Several evidence indicate that asthma severity or control is associated with alteration in variability of lung function. The pathophysiological basis of alteration in complexity of breathing pattern in asthma has remained poorly understood. Regarding the point that Rho-kinase is involved in pathophysiology of asthma, in present study we investigated the effect of Rho-kinase inhibition on complexity of respiratory dynamics in a guinea pig model of asthma. Male Dunkin Hartley guinea pigs were exposed to 12 series of inhalations with ovalbumin or saline. Animals were treated by the Rho-kinase inhibitor Y-27632 (1mM aerosols) prior to each allergen challenge. We recorded respiration of conscious animals using whole-body plethysmography. Exposure to ovalbumin induced lung inflammation, airway hyperresponsiveness and remodeling including goblet cell hyperplasia, increase in the thickness of airways smooth muscles and subepithelial collagen deposition. Complexity analysis of respiratory dynamics revealed a dramatic decrease in irregularity of respiratory rhythm representing less complexity in asthmatic guinea pigs. Inhibition of Rho-kinase reduced the airway remodeling and hyperreponsiveness, but had no significant effect on lung inflammation and complexity of respiratory dynamics in asthmatic animals. It seems that airway hyperresponsiveness and remodeling do not significantly affect the complexity of respiratory dynamics. Our results suggest that inflammation might be the probable cause of shift in the respiratory dynamics away from the normal fluctuation in asthma. PMID:29088265

Sentence-Based Attentional Mechanisms in Word Learning: Evidence from a Computational Model

PubMed Central

Alishahi, Afra; Fazly, Afsaneh; Koehne, Judith; Crocker, Matthew W.

2012-01-01

When looking for the referents of novel nouns, adults and young children are sensitive to cross-situational statistics (Yu and Smith, 2007; Smith and Yu, 2008). In addition, the linguistic context that a word appears in has been shown to act as a powerful attention mechanism for guiding sentence processing and word learning (Landau and Gleitman, 1985; Altmann and Kamide, 1999; Kako and Trueswell, 2000). Koehne and Crocker (2010, 2011) investigate the interaction between cross-situational evidence and guidance from the sentential context in an adult language learning scenario. Their studies reveal that these learning mechanisms interact in a complex manner: they can be used in a complementary way when context helps reduce referential uncertainty; they influence word learning about equally strongly when cross-situational and contextual evidence are in conflict; and contextual cues block aspects of cross-situational learning when both mechanisms are independently applicable. To address this complex pattern of findings, we present a probabilistic computational model of word learning which extends a previous cross-situational model (Fazly et al., 2010) with an attention mechanism based on sentential cues. Our model uses a framework that seamlessly combines the two sources of evidence in order to study their emerging pattern of interaction during the process of word learning. Simulations of the experiments of (Koehne and Crocker, 2010, 2011) reveal an overall pattern of results that are in line with their findings. Importantly, we demonstrate that our model does not need to explicitly assign priority to either source of evidence in order to produce these results: learning patterns emerge as a result of a probabilistic interaction between the two clue types. Moreover, using a computational model allows us to examine the developmental trajectory of the differential roles of cross-situational and sentential cues in word learning. PMID:22783211

Measuring floodplain spatial patterns using continuous surface metrics at multiple scales

USGS Publications Warehouse

Scown, Murray W.; Thoms, Martin C.; DeJager, Nathan R.

2015-01-01

Interactions between fluvial processes and floodplain ecosystems occur upon a floodplain surface that is often physically complex. Spatial patterns in floodplain topography have only recently been quantified over multiple scales, and discrepancies exist in how floodplain surfaces are perceived to be spatially organised. We measured spatial patterns in floodplain topography for pool 9 of the Upper Mississippi River, USA, using moving window analyses of eight surface metrics applied to a 1 × 1 m2 DEM over multiple scales. The metrics used were Range, SD, Skewness, Kurtosis, CV, SDCURV,Rugosity, and Vol:Area, and window sizes ranged from 10 to 1000 m in radius. Surface metric values were highly variable across the floodplain and revealed a high degree of spatial organisation in floodplain topography. Moran's I correlograms fit to the landscape of each metric at each window size revealed that patchiness existed at nearly all window sizes, but the strength and scale of patchiness changed within window size, suggesting that multiple scales of patchiness and patch structure exist in the topography of this floodplain. Scale thresholds in the spatial patterns were observed, particularly between the 50 and 100 m window sizes for all surface metrics and between the 500 and 750 m window sizes for most metrics. These threshold scales are ~ 15–20% and 150% of the main channel width (1–2% and 10–15% of the floodplain width), respectively. These thresholds may be related to structuring processes operating across distinct scale ranges. By coupling surface metrics, multi-scale analyses, and correlograms, quantifying floodplain topographic complexity is possible in ways that should assist in clarifying how floodplain ecosystems are structured.

Dynamic analysis and pattern visualization of forest fires.

PubMed

Lopes, António M; Tenreiro Machado, J A

2014-01-01

This paper analyses forest fires in the perspective of dynamical systems. Forest fires exhibit complex correlations in size, space and time, revealing features often present in complex systems, such as the absence of a characteristic length-scale, or the emergence of long range correlations and persistent memory. This study addresses a public domain forest fires catalogue, containing information of events for Portugal, during the period from 1980 up to 2012. The data is analysed in an annual basis, modelling the occurrences as sequences of Dirac impulses with amplitude proportional to the burnt area. First, we consider mutual information to correlate annual patterns. We use visualization trees, generated by hierarchical clustering algorithms, in order to compare and to extract relationships among the data. Second, we adopt the Multidimensional Scaling (MDS) visualization tool. MDS generates maps where each object corresponds to a point. Objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to identify forest fire patterns.

Dynamic Analysis and Pattern Visualization of Forest Fires

PubMed Central

Lopes, António M.; Tenreiro Machado, J. A.

2014-01-01

This paper analyses forest fires in the perspective of dynamical systems. Forest fires exhibit complex correlations in size, space and time, revealing features often present in complex systems, such as the absence of a characteristic length-scale, or the emergence of long range correlations and persistent memory. This study addresses a public domain forest fires catalogue, containing information of events for Portugal, during the period from 1980 up to 2012. The data is analysed in an annual basis, modelling the occurrences as sequences of Dirac impulses with amplitude proportional to the burnt area. First, we consider mutual information to correlate annual patterns. We use visualization trees, generated by hierarchical clustering algorithms, in order to compare and to extract relationships among the data. Second, we adopt the Multidimensional Scaling (MDS) visualization tool. MDS generates maps where each object corresponds to a point. Objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to identify forest fire patterns. PMID:25137393

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

Pattern transitions in spatial epidemics: Mechanisms and emergent properties.

PubMed

Sun, Gui-Quan; Jusup, Marko; Jin, Zhen; Wang, Yi; Wang, Zhen

2016-12-01

Infectious diseases are a threat to human health and a hindrance to societal development. Consequently, the spread of diseases in both time and space has been widely studied, revealing the different types of spatial patterns. Transitions between patterns are an emergent property in spatial epidemics that can serve as a potential trend indicator of disease spread. Despite the usefulness of such an indicator, attempts to systematize the topic of pattern transitions have been few and far between. We present a mini-review on pattern transitions in spatial epidemics, describing the types of transitions and their underlying mechanisms. We show that pattern transitions relate to the complexity of spatial epidemics by, for example, being accompanied with phenomena such as coherence resonance and cyclic evolution. The results presented herein provide valuable insights into disease prevention and control, and may even be applicable outside epidemiology, including other branches of medical science, ecology, quantitative finance, and elsewhere. Copyright © 2016 Elsevier B.V. All rights reserved.

Myositis, Ganglioneuritis, and Myocarditis with Distinct Perifascicular Muscle Atrophy in a 2-Year-Old Male Boxer

PubMed Central

Rossman, Paul M.; Thomovsky, Stephanie A.; Schafbuch, Ryan M.; Guo, Ling T.; Shelton, G. D.

2018-01-01

A 2-year-old male, intact Boxer was referred for chronic diarrhea, hyporexia, labored breathing, weakness and elevated creatine kinase, and alanine aminotransferase activities. Initial examination and diagnostics revealed a peripheral nervous system neurolocalization, atrial premature complexes, and generalized megaesophagus. Progressive worsening of the dog’s condition was noted after 36 h; the dog developed aspiration pneumonia, was febrile and oxygen dependent. The owners elected humane euthanasia. Immediately postmortem biopsies of the left cranial tibial and triceps muscles and the left peroneal nerve were obtained. Postmortem histology revealed concurrent myositis, myocarditis, endocarditis, and ganglioneuritis. Mixed mononuclear cell infiltrations and a distinct perifascicular pattern of muscle fiber atrophy was present in both muscles. This is a novel case of diffuse inflammatory myopathy with a distinct perifascicular pattern of atrophy in addition to endocarditis, myocarditis, and epicarditis. PMID:29516006

Proteome and Secretome Analysis Reveals Differential Post-transcriptional Regulation of Toll-like Receptor Responses*

PubMed Central

Koppenol-Raab, Marijke; Sjoelund, Virginie; Manes, Nathan P.; Gottschalk, Rachel A.; Dutta, Bhaskar; Benet, Zachary L.; Fraser, Iain D. C.

2017-01-01

The innate immune system is the organism's first line of defense against pathogens. Pattern recognition receptors (PRRs) are responsible for sensing the presence of pathogen-associated molecules. The prototypic PRRs, the membrane-bound receptors of the Toll-like receptor (TLR) family, recognize pathogen-associated molecular patterns (PAMPs) and initiate an innate immune response through signaling pathways that depend on the adaptor molecules MyD88 and TRIF. Deciphering the differences in the complex signaling events that lead to pathogen recognition and initiation of the correct response remains challenging. Here we report the discovery of temporal changes in the protein signaling components involved in innate immunity. Using an integrated strategy combining unbiased proteomics, transcriptomics and macrophage stimulations with three different PAMPs, we identified differences in signaling between individual TLRs and revealed specifics of pathway regulation at the protein level. PMID:28235783

Inherited crustal deformation along the East Gondwana margin revealed by seismic anisotropy tomography

NASA Astrophysics Data System (ADS)

Pilia, S.; Arroucau, P.; Rawlinson, N.; Reading, A. M.; Cayley, R. A.

2016-12-01

The mechanisms of continental growth are a crucial part of plate tectonic theory, yet a clear understanding of the processes involved remains elusive. Here we determine seismic Rayleigh wave phase anisotropy variations in the crust beneath the southern Tasmanides of Australia, a Paleozoic accretionary margin. Our results reveal a complex, thick-skinned pervasive deformation that was driven by the tectonic interaction between the proto-Pacific Ocean and the ancient eastern margin of Gondwana. Stress-induced effects triggered by the collision and entrainment of a microcontinent into the active subduction zone are evident in the anisotropy signature. The paleofracturing trend of failed rifting between Australia and Antarctica is also recorded in the anisotropy pattern as well as a tightly curved feature in central Tasmania. The observed patterns of anisotropy correlate well with recent geodynamic and kinematic models of the Tasmanides and provide a platform from which the spatial extent of deformational domains can be refined.

Anatomy and growth pattern of Amazon deep-sea fan as revealed by long-range side-scan sonar (GLORIA) and high-resolution seismic studies

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

Damuth, J.E.; Flood, R.D.; Kowsmann, R.O.

1988-08-01

Imaging of the Amazon deep-sea fan with long-range side-scan sonar (GLORIA) has, for the first time, revealed the anatomy, trends, and growth pattern of distributary channels on this fan. Only one channel-levee system was active at any given time and extended from the Amazon Submarine Canyon downslope onto the lower fan (> 4,200 m). Formation of new channel-levee systems occurred when a currently active channel-levee system was cut off and abandoned through avulsion, and a new channel-levee system was established nearby. Through time, successive channel-levee formation and abandonment built two broad levee complexes consisting of groups of overlapping, coalescing segmentsmore » of channel-levee systems across the present fan surface. These, plus older, now buried levee complexes, indicate that fan growth is radially outward and downslope through development of successive levee complexes. The most striking characteristic of the distributary channels is their intricate, often recurving, meanders with sinuosities of up to 2.5. Cutoffs and abandoned meander loops indicate that the channels migrate laterally through time. Channel bifurcation results predominantly from avulsion when flows breach a channel levee, thereby abandoning the present channel and establishing a new channel-levee segment nearby. No clear evidence of channel branching (i.e., division of a single channel into two active segments) or braiding was observed. 22 figs.« less

Prasinoviruses reveal a complex evolutionary history and a patchy environmental distribution

NASA Astrophysics Data System (ADS)

Finke, J. F.; Suttle, C.

2016-02-01

Prasinophytes constitute a group of eukaryotic phytoplankton that has a global distribution and is a major component of coastal and oceanic communities. Members of this group are infected by large double-stranded DNA viruses that can be significant agents of mortality, and which show evidence of substantial horizontal transfer of genes from their hosts and other organisms. However, information on the genetic diversity of these viruses and their environmental distribution is limited. This study examines the genetic repertoire, phylogeny and environmental distribution of large double-stranded DNA viruses infecting Micromonas pusilla and other prasinophytes. The genomes of viruses infecting M. pusilla were sequenced and compared to those of viruses infecting other prasinophytes, revealing a relatively small set of core genes and a larger flexible pan genome. Comparing genomes among prasinoviruses highlights their variable genetic content and complex evolutionary history. While some of the pan genome is clearly host derived, many open reading frames are most similar to those found in other eukaryotes and bacteria. Gene content of the viruses is is congruent with phylogenetic analysis of viral DNA polymerase sequences and indicates that two clades of M. pusilla viruses are less related to each other than to other prasinoviruses. Moreover, the environmental distribution of prasinovirus DNA polymerase sequences indicates a complex pattern of virus-host interactions in nature. Ultimately, these patterns are influenced by the genetic repertoire encoded by prasinoviruses, and the distribution of the hosts they infect.

Distinct mutations in yeast TAF(II)25 differentially affect the composition of TFIID and SAGA complexes as well as global gene expression patterns.

PubMed

Kirschner, Doris B; vom Baur, Elmar; Thibault, Christelle; Sanders, Steven L; Gangloff, Yann-Gaël; Davidson, Irwin; Weil, P Anthony; Tora, Làszlò

2002-05-01

The RNA polymerase II transcription factor TFIID, composed of the TATA-binding protein (TBP) and TBP-associated factors (TAF(II)s), nucleates preinitiation complex formation at protein-coding gene promoters. SAGA, a second TAF(II)-containing multiprotein complex, is involved in transcription regulation in Saccharomyces cerevisiae. One of the essential protein components common to SAGA and TFIID is yTAF(II)25. We define a minimal evolutionarily conserved 91-amino-acid region of TAF(II)25 containing a histone fold domain that is necessary and sufficient for growth in vivo. Different temperature-sensitive mutations of yTAF(II)25 or chimeras with the human homologue TAF(II)30 arrested cell growth at either the G(1) or G(2)/M cell cycle phase and displayed distinct phenotypic changes and gene expression patterns. Immunoprecipitation studies revealed that TAF(II)25 mutation-dependent gene expression and phenotypic changes correlated at least partially with the integrity of SAGA and TFIID. Genome-wide expression analysis revealed that the five TAF(II)25 temperature-sensitive mutant alleles individually affect the expression of between 18 and 33% of genes, whereas taken together they affect 64% of all class II genes. Thus, different yTAF(II)25 mutations induce distinct phenotypes and affect the regulation of different subsets of genes, demonstrating that no individual TAF(II) mutant allele reflects the full range of its normal functions.

Digital microfabrication of user-defined 3D microstructures in cell-laden hydrogels.

PubMed

Soman, Pranav; Chung, Peter H; Zhang, A Ping; Chen, Shaochen

2013-11-01

Complex 3D interfacial arrangements of cells are found in several in vivo biosystems such as blood vasculature, renal glomeruli, and intestinal villi. Current tissue engineering techniques fail to develop suitable 3D microenvironments to evaluate the concurrent effects of complex topography and cell encapsulation. There is a need to develop new fabrication approaches that control cell density and distribution within complex 3D features. In this work, we present a dynamic projection printing process that allows rapid construction of complex 3D structures using custom-defined computer-aided-design (CAD) files. Gelatin-methacrylate (GelMA) constructs featuring user-defined spiral, pyramid, flower, and dome micro-geometries were fabricated with and without encapsulated cells. Encapsulated cells demonstrate good cell viability across all geometries both on the scaffold surface and internal to the structures. Cells respond to geometric cues individually as well as collectively throughout the larger-scale patterns. Time-lapse observations also reveal the dynamic nature of mechanical interactions between cells and micro-geometry. When compared to conventional cell-seeding, cell encapsulation within complex 3D patterned scaffolds provides long-term control over proliferation, cell morphology, and geometric guidance. Overall, this biofabrication technique offers a flexible platform to evaluate cell interactions with complex 3D micro-features, with the ability to scale-up towards high-throughput screening platforms. © 2013 Wiley Periodicals, Inc.

Local control of globally competing patterns in coupled Swift-Hohenberg equations

NASA Astrophysics Data System (ADS)

Becker, Maximilian; Frenzel, Thomas; Niedermayer, Thomas; Reichelt, Sina; Mielke, Alexander; Bär, Markus

2018-04-01

We present analytical and numerical investigations of two anti-symmetrically coupled 1D Swift-Hohenberg equations (SHEs) with cubic nonlinearities. The SHE provides a generic formulation for pattern formation at a characteristic length scale. A linear stability analysis of the homogeneous state reveals a wave instability in addition to the usual Turing instability of uncoupled SHEs. We performed weakly nonlinear analysis in the vicinity of the codimension-two point of the Turing-wave instability, resulting in a set of coupled amplitude equations for the Turing pattern as well as left- and right-traveling waves. In particular, these complex Ginzburg-Landau-type equations predict two major things: there exists a parameter regime where multiple different patterns are stable with respect to each other and that the amplitudes of different patterns interact by local mutual suppression. In consequence, different patterns can coexist in distinct spatial regions, separated by localized interfaces. We identified specific mechanisms for controlling the position of these interfaces, which distinguish what kinds of patterns the interface connects and thus allow for global pattern selection. Extensive simulations of the original SHEs confirm our results.

Complex Degradation Processes Lead to Non-Exponential Decay Patterns and Age-Dependent Decay Rates of Messenger RNA

PubMed Central

Deneke, Carlus; Lipowsky, Reinhard; Valleriani, Angelo

2013-01-01

Experimental studies on mRNA stability have established several, qualitatively distinct decay patterns for the amount of mRNA within the living cell. Furthermore, a variety of different and complex biochemical pathways for mRNA degradation have been identified. The central aim of this paper is to bring together both the experimental evidence about the decay patterns and the biochemical knowledge about the multi-step nature of mRNA degradation in a coherent mathematical theory. We first introduce a mathematical relationship between the mRNA decay pattern and the lifetime distribution of individual mRNA molecules. This relationship reveals that the mRNA decay patterns at steady state expression level must obey a general convexity condition, which applies to any degradation mechanism. Next, we develop a theory, formulated as a Markov chain model, that recapitulates some aspects of the multi-step nature of mRNA degradation. We apply our theory to experimental data for yeast and explicitly derive the lifetime distribution of the corresponding mRNAs. Thereby, we show how to extract single-molecule properties of an mRNA, such as the age-dependent decay rate and the residual lifetime. Finally, we analyze the decay patterns of the whole translatome of yeast cells and show that yeast mRNAs can be grouped into three broad classes that exhibit three distinct decay patterns. This paper provides both a method to accurately analyze non-exponential mRNA decay patterns and a tool to validate different models of degradation using decay data. PMID:23408982

Differences in the Visual Perception of Symmetric Patterns in Orangutans (Pongo pygmaeus abelii) and Two Human Cultural Groups: A Comparative Eye-Tracking Study

PubMed Central

Mühlenbeck, Cordelia; Liebal, Katja; Pritsch, Carla; Jacobsen, Thomas

2016-01-01

Symmetric structures are of importance in relation to aesthetic preference. To investigate whether the preference for symmetric patterns is unique to humans, independent of their cultural background, we compared two human populations with distinct cultural backgrounds (Namibian hunter-gatherers and German town dwellers) with one species of non-human great apes (Orangutans) in their viewing behavior regarding symmetric and asymmetric patterns in two levels of complexity. In addition, the human participants were asked to give their aesthetic evaluation of a subset of the presented patterns. The results showed that humans of both cultural groups fixated on symmetric patterns for a longer period of time, regardless of the pattern’s complexity. On the contrary, Orangutans did not clearly differentiate between symmetric and asymmetric patterns, but were much faster in processing the presented stimuli and scanned the complete screen, while both human groups rested on the symmetric pattern after a short scanning time. The aesthetic evaluation test revealed that the fixation preference for symmetric patterns did not match with the aesthetic evaluation in the Hai//om group, whereas in the German group aesthetic evaluation was in accordance with the fixation preference in 60 percent of the cases. It can be concluded that humans prefer well-ordered structures in visual processing tasks, most likely because of a positive processing bias for symmetry, which Orangutans did not show in this task, and that, in humans, an aesthetic preference does not necessarily accompany the fixation preference. PMID:27065184

Perspectives on object manipulation and action grammar for percussive actions in primates

PubMed Central

Hayashi, Misato

2015-01-01

The skill of object manipulation is a common feature of primates including humans, although there are species-typical patterns of manipulation. Object manipulation can be used as a comparative scale of cognitive development, focusing on its complexity. Nut cracking in chimpanzees has the highest hierarchical complexity of tool use reported in non-human primates. An analysis of the patterns of object manipulation in naive chimpanzees after nut-cracking demonstrations revealed the cause of difficulties in learning nut-cracking behaviour. Various types of behaviours exhibited within a nut-cracking context can be examined in terms of the application of problem-solving strategies, focusing on their basis in causal understanding or insightful intentionality. Captive chimpanzees also exhibit complex forms of combinatory manipulation, which is the precursor of tool use. A new notation system of object manipulation was invented to assess grammatical rules in manipulative actions. The notation system of action grammar enabled direct comparisons to be made between primates including humans in a variety of object-manipulation tasks, including percussive-tool use. PMID:26483528

Courtship display dynamics, iridescent structural color and nanostructural pattern formation in ocellated pheasants

NASA Astrophysics Data System (ADS)

Kane, Suzanne Amador; Dakin, Roslyn; Fang, Rui; Lu, Yabin

Peacocks court females by tilting a fan-like array of feathers decorated with multicolored eyespots (ocelli). Previous research has shown that half of the variation in peacock mating success can be attributed to eyespot iridescence. Several closely-related pheasant species perform similar, but less complex, courtship displays using ocellated feathers with less complex coloration, patterns and underlying nanostructures. This study explores the relationship between the dynamics of male courtship behavior and optical properties and nanostructure of each species' iridescent feather ornaments. In particular, we examined videos of courting males and of individual feathers to measure how the angles used during displays compared to those corresponding to optimal eyespot reflected intensity and iridescent contrast. Bidirectional reflectance spectroscopy was used to measure how the spectrum of reflected light depends on the characteristic angles used during displays, and hence how displays stimulate the four classes of cones found in the color vision systems of these birds. This work reveals a close correlation between the complexity of the angular dependence of iridescent feather reflectance properties and that of the motions used by males of each species.

Perspectives on object manipulation and action grammar for percussive actions in primates.

PubMed

Hayashi, Misato

2015-11-19

The skill of object manipulation is a common feature of primates including humans, although there are species-typical patterns of manipulation. Object manipulation can be used as a comparative scale of cognitive development, focusing on its complexity. Nut cracking in chimpanzees has the highest hierarchical complexity of tool use reported in non-human primates. An analysis of the patterns of object manipulation in naive chimpanzees after nut-cracking demonstrations revealed the cause of difficulties in learning nut-cracking behaviour. Various types of behaviours exhibited within a nut-cracking context can be examined in terms of the application of problem-solving strategies, focusing on their basis in causal understanding or insightful intentionality. Captive chimpanzees also exhibit complex forms of combinatory manipulation, which is the precursor of tool use. A new notation system of object manipulation was invented to assess grammatical rules in manipulative actions. The notation system of action grammar enabled direct comparisons to be made between primates including humans in a variety of object-manipulation tasks, including percussive-tool use. © 2015 The Author(s).

Quantitative proteomic analysis reveals evolutionary divergence and species-specific peptides in the Alexandrium tamarense complex (Dinophyceae).

PubMed

Li, Cheng; Zhang, Yong; Xie, Zhang-Xian; He, Zhi-Ping; Lin, Lin; Wang, Da-Zhi

2013-06-28

The Alexandrium tamarense/catenella/fundyense complex is the major causative agent responsible for harmful algal blooms and paralytic shellfish poisoning around the world. However, taxonomy of the A. tamarense complex is contentious and the evolutionary relationships within the complex are unclear. This study compared protein profiles of the A. tamarense complex collected from different geographic regions using the two dimensional fluorescence difference gel electrophoresis (2-D DIGE) approach, and identified species-specific peptides using MALDI-TOF/TOF mass spectrometry. The results showed that three Alexandrium morphotypes presented significantly different protein expression patterns with about 30-40% shared proteins. However, ecotypes from different geographic regions within a species exhibited the same expression patterns, although a few proteins were altered in abundance. Several proteins, i.e. ribulose-1,5-bisphosphate carboxylase oxygenase form II, plastid protein NAP50, methionine S-adenosyltransferase, and peridinin-chlorophyll a-binding protein, were identified and presented different shift patterns in isoelectric point and/or molecular weight in the 2-D DIGE gels, indicating that amino acid mutation and/or posttranslational modification of these proteins had occurred. The species-specific peptide mass fingerprint and amino acid sequence of ribulose-1,5-bisphosphate carboxylase oxygenase were characterized in the A. tamarense complex, and amino acid substitution occurred among them. This study indicated that evolutionary divergence had occurred at the proteomic level in the A. tamarense complex, and that the species-specific peptides could be used as potential biomarkers to distinguish the three morphotypes. Scientific question: The Alexandrium tamarense/catenella/fundyense complex is the major causative agent responsible for harmful algal blooms and paralytic shellfish poisoning around the world. However, taxonomy of the A. tamarense complex is contentious and the evolutionary relationships within the complex are unclear, which has seriously impeded our understanding of Alexandrium-causing HABs and, consequently, the monitoring, mitigation and prevention. Technical significance: This study, for the first time, compared the global protein expression patterns of eight ecotypes from the A. tamarense complex and identified species-specific peptides using a quantitative proteomic approach combining 2-D DIGE and MALDI-TOF/TOF MS. This study demonstrated that the evolutionary divergence had occurred in the A. tamarense complex at the proteomic level, and the complex should be classified into three species, i.e. A. tamarense, A. catenella, and A. fundyense. Moreover, the species-specific peptide mass fingerprints could be used as potential biomarkers to distinguish the three morphotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and resistance by connection mutations.

PubMed

Vijayan, R S K; Arnold, Eddy; Das, Kalyan

2014-05-01

HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that is targeted by nucleoside analogs (NRTIs) and non-nucleoside RT inhibitors (NNRTIs). NNRTIs are allosteric inhibitors of RT, and constitute an integral part of several highly active antiretroviral therapy regimens. Under selective pressure, HIV-1 acquires resistance against NNRTIs primarily by selecting mutations around the NNRTI pocket. Complete RT sequencing of clinical isolates revealed that spatially distal mutations arising in connection and the RNase H domain also confer NNRTI resistance and contribute to NRTI resistance. However, the precise structural mechanism by which the connection domain mutations confer NNRTI resistance is poorly understood. We performed 50-ns molecular dynamics (MD) simulations, followed by essential dynamics, free-energy landscape analyses, and network analyses of RT-DNA, RT-DNA-nevirapine (NVP), and N348I/T369I mutant RT-DNA-NVP complexes. MD simulation studies revealed altered global motions and restricted conformational landscape of RT upon NVP binding. Analysis of protein structure network parameters demonstrated a dissortative hub pattern in the RT-DNA complex and an assortative hub pattern in the RT-DNA-NVP complex suggesting enhanced rigidity of RT upon NVP binding. The connection subdomain mutations N348I/T369I did not induce any significant structural change; rather, these mutations modulate the conformational dynamics and alter the long-range allosteric communication network between the connection subdomain and NNRTI pocket. Insights from the present study provide a structural basis for the biochemical and clinical findings on drug resistance caused by the connection and RNase H mutations. Copyright © 2013 Wiley Periodicals, Inc.

Contrasting Phylogeography of Sandy vs. Rocky Supralittoral Isopods in the Megadiverse and Geologically Dynamic Gulf of California and Adjacent Areas

PubMed Central

Hurtado, Luis A.; Lee, Eun Jung; Mateos, Mariana

2013-01-01

Phylogeographic studies of animals with low vagility and restricted to patchy habitats of the supralittoral zone, can uncover unknown diversity and shed light on processes that shaped evolution along a continent’s edge. The Pacific coast between southern California and central Mexico, including the megadiverse Gulf of California, offers a remarkable setting to study biological diversification in the supralittoral. A complex geological history coupled with cyclical fluctuations in temperature and sea level provided ample opportunities for diversification of supralittoral organisms. Indeed, a previous phylogeographic study of Ligia, a supralittoral isopod that has limited dispersal abilities and is restricted to rocky patches, revealed high levels of morphologically cryptic diversity. Herein, we examined phylogeographic patterns of Tylos, another supralittoral isopod with limited dispersal potential, but whose habitat (i.e., sandy shores) appears to be more extensive and connected than that of Ligia. We conducted Maximum Likelihood and Bayesian phylogenetic analyses on mitochondrial and nuclear DNA sequences. These analyses revealed multiple highly divergent lineages with discrete regional distributions, despite the recognition of a single valid species for this region. A traditional species-diagnostic morphological trait distinguished several of these lineages. The phylogeographic patterns of Tylos inside the Gulf of California show a deep and complex history. In contrast, patterns along the Pacific region between southern California and the Baja Peninsula indicate a recent range expansion, probably postglacial and related to changes in sea surface temperature (SST). In general, the phylogeographic patterns of Tylos differed from those of Ligia. Differences in the extension and connectivity of the habitats occupied by Tylos and Ligia may account for the different degrees of population isolation experienced by these two isopods and their contrasting phylogeographic patterns. Identification of divergent lineages of Tylos in the study area is important for conservation, as some populations are threatened by human activities. PMID:23844103

Defective ciliogenesis, embryonic lethality and severe impairment of the Sonic Hedgehog pathway caused by inactivation of the mouse complex A intraflagellar transport gene Ift122/Wdr10, partially overlapping with the DNA repair gene Med1/Mbd4

PubMed Central

Cortellino, Salvatore; Wang, Chengbing; Wang, Baolin; Bassi, Maria Rosaria; Caretti, Elena; Champeval, Delphine; Calmont, Amelie; Jarnik, Michal; Burch, John; Zaret, Kenneth; Larue, Lionel; Bellacosa, Alfonso

2009-01-01

Primary cilia are assembled and maintained by evolutionarily conserved intraflagellar transport (IFT) proteins that are involved in the coordinated movement of macromolecular cargo from the basal body to the cilium tip and back. The IFT machinery is organized in two structural complexes named complex A and complex B. Recently, inactivation in the mouse germline of Ift genes belonging to complex B revealed a requirement of ciliogenesis, or proteins involved in ciliogenesis, for Sonic Hedgehog (Shh) signaling in mammals. Here we report on a complex A mutant mouse, defective for the Ift122 gene. Ift122-null embryos show multiple developmental defects (exencephaly, situs viscerum inversus, delay in turning, hemorrhage and defects in limb development) that result in lethality. In the node, primary cilia were absent or malformed in homozygous mutant and heterozygous embryos, respectively. Impairment of the Shh pathway was apparent in both neural tube patterning (expansion of motoneurons and rostro-caudal level-dependent contraction or expansion of the dorso-lateral interneurons), and limb patterning (ectrosyndactyly). These phenotypes are distinct from both complex B IFT mutant embryos and embryos defective for the ciliary protein hennin/Arl13b, and suggest reduced levels of both Gli2/Gli3 activator and Gli3 repressor functions. We conclude that complex A and complex B factors play similar but distinct roles in ciliogenesis and Shh/Gli3 signaling. PMID:19000668

Self-organization of a periodic structure between amorphous and crystalline phases in a GeTe thin film induced by femtosecond laser pulse amorphization

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

Katsumata, Y.; Morita, T.; Morimoto, Y.

A self-organized fringe pattern in a single amorphous mark of a GeTe thin film was formed by multiple femtosecond pulse amorphization. Micro Raman measurement indicates that the fringe is a periodic alternation between crystalline and amorphous phases. The period of the fringe is smaller than the irradiation wavelength and the direction is parallel to the polarization direction. Snapshot observation revealed that the fringe pattern manifests itself via a complex but coherent process, which is attributed to crystallization properties unique to a nonthermally amorphized phase and the distinct optical contrast between crystalline and amorphous phases.

The chromosomal distribution of Mus musculus-like AT-rich heterochromatin in the M. dunni complex as revealed by AluI digestion of metaphase chromosomes.

PubMed

Balajee, A S; Sharma, T

1994-01-01

In situ digestion of metaphase chromosomes with AluI revealed differences in the distribution of Mus musculus-like AT-rich heterochromatin in the complements of the Indian pygmy field mice, M. booduga and M. dunni. In M. booduga, although the banding pattern was almost comparable to that of M. musculus, AluI-resistant bands were much reduced in size at the centromeric regions. In all three chromosome types of the M. dunni complex, M. musculus-like AT-rich heterochromatin was found to be confined mainly to two small segments on the short arm of the X chromosome. This AT-rich heterochromatin varied greatly in both position and quantity in the two X chromosomes. In addition to the polymorphism, a whole block of M. musculus-like AT-rich heterochromatin was found at the centromeric region of an autosome in one individual of M. dunni.

A density functional study of silicon fullerene endohedral X@Si20F20 and exohedral X-Si20F20 (X=O2-, S2-, Se2-) complexes

NASA Astrophysics Data System (ADS)

Behzadi, Hadi; Esrafili, Mehdi D.; Manzetti, Sergio; Roonasi, Payman

2014-02-01

This study reports the structure and electronic properties of three stable endohedral X@Si20F20 and exohedral X-Si20F20 (X=O2-, S2-, Se2-) complexes. The study revealed that the endohedral complexes with S2- and Se2- result as energy minimum structures, with the guest anion located in the cage center. In the case of endohedral O2--complexes, the pattern is quite different whereas the O2- complexes dramatically deviated from the architecture of S2- and Se2-, by having O2- located toward one of silicon atoms in the cage. With respect to the exohedral form, the energy minimized structure is obtained by positioning the anion between two silicon atoms and forming two Si-X bonds. For both cases, the strength of the interactions is calculated to increase accordingly to the pattern: Se2-@Si20F20 (Se2--Si20F20)

Formulation, characterization and evaluation of cyclodextrin-complexed bendamustine-encapsulated PLGA nanospheres for sustained delivery in cancer treatment.

PubMed

Gidwani, Bina; Vyas, Amber

2016-03-01

PLGA nanospheres are considered to be promising drug carrier in the treatment of cancer. Inclusion complex of bendamustine (BM) with epichlorohydrin beta cyclodextrin polymer was prepared by freeze-drying method. Phase solubility study revealed formation of AL type complex with stability constant (Ks = 645 M(-1)). This inclusion complex was encapsulated into PLGA nanospheres using solid-in-oil-in-water (S/O/W) technique. The particle size and zeta potential of PLGA nanospheres loaded with cyclodextrin-complexed BM were about 151.4 ± 2.53 nm and - 31.9 ± (-3.08) mV. In-vitro release study represented biphasic release pattern with 20% burst effect and sustained slow release. DSC studies indicated that inclusion complex incorporated in PLGA nanospheres was not in a crystalline state but existed in an amorphous or molecular state. The cytotoxicity experiment was studied in Z-138 cells and IC50 value was found to be 4.3 ± 0.11 µM. Cell viability studies revealed that the PLGA nanospheres loaded with complex exerts a more pronounced effect on the cancer cells as compared to the free drug. In conclusion, PLGA nanospheres loaded with inclusion complex of BM led to sustained drug delivery. The nanospheres were stable after 3 months of storage conditions with slight change in their particle size, zeta potential and entrapment efficiency.

Hierarchical and Complex System Entropy Clustering Analysis Based Validation for Traditional Chinese Medicine Syndrome Patterns of Chronic Atrophic Gastritis.

PubMed

Zhang, Yin; Liu, Yue; Li, Yannan; Zhao, Xia; Zhuo, Lin; Zhou, Ajian; Zhang, Li; Su, Zeqi; Chen, Cen; Du, Shiyu; Liu, Daming; Ding, Xia

2018-03-22

Chronic atrophic gastritis (CAG) is the precancerous stage of gastric carcinoma. Traditional Chinese Medicine (TCM) has been widely used in treating CAG. This study aimed to reveal core pathogenesis of CAG by validating the TCM syndrome patterns and provide evidence for optimization of treatment strategies. This is a cross-sectional study conducted in 4 hospitals in China. Hierarchical clustering analysis (HCA) and complex system entropy clustering analysis (CSECA) were performed, respectively, to achieve syndrome pattern validation. Based on HCA, 15 common factors were assigned to 6 syndrome patterns: liver depression and spleen deficiency and blood stasis in the stomach collateral, internal harassment of phlegm-heat and blood stasis in the stomach collateral, phlegm-turbidity internal obstruction, spleen yang deficiency, internal harassment of phlegm-heat and spleen deficiency, and spleen qi deficiency. By CSECA, 22 common factors were assigned to 7 syndrome patterns: qi deficiency, qi stagnation, blood stasis, phlegm turbidity, heat, yang deficiency, and yin deficiency. Combination of qi deficiency, qi stagnation, blood stasis, phlegm turbidity, heat, yang deficiency, and yin deficiency may play a crucial role in CAG pathogenesis. In accord with this, treatment strategies by TCM herbal prescriptions should be targeted to regulating qi, activating blood, resolving turbidity, clearing heat, removing toxin, nourishing yin, and warming yang. Further explorations are needed to verify and expand the current conclusions.

Verb and Noun Word Retrieval in Bilingual Aphasia: A Case Study of Language- and Modality-Specific Levels of Breakdown

ERIC Educational Resources Information Center

Kambanaros, Maria

2016-01-01

This study reports on the pattern of performance on spoken and written naming, spelling to dictation, and oral reading of single verbs and nouns in a bilingual speaker with aphasia in two first languages that differ in morphological complexity, orthographic transparency, and script: Greek (L1a) and English (L1b). The results reveal no verb/noun…

Post-Self-Assembly Cross-Linking to Integrate Molecular Nanofibers with Copolymers in Oscillatory Hydrogels

DTIC Science & Technology

2013-05-09

The BZ reaction provides a model system to mimic a variety of complex processes, such as biological morphogenesis, in monodisperse microemulsions .15...surfaces, ion-exchange resins, membranes, and microemulsions . For example, in addition to minimizing the hydrodynamic effects and formation of bubbles...Reaction-Diffusion Microemulsions Reveals Three-Dimensional Tu- ring Patterns. Science (Washington, DC, U.S.) 2011, 331, 1309−1312. (16) Agladze, K. I

Discover mouse gene coexpression landscapes using dictionary learning and sparse coding.

PubMed

Li, Yujie; Chen, Hanbo; Jiang, Xi; Li, Xiang; Lv, Jinglei; Peng, Hanchuan; Tsien, Joe Z; Liu, Tianming

2017-12-01

Gene coexpression patterns carry rich information regarding enormously complex brain structures and functions. Characterization of these patterns in an unbiased, integrated, and anatomically comprehensive manner will illuminate the higher-order transcriptome organization and offer genetic foundations of functional circuitry. Here using dictionary learning and sparse coding, we derived coexpression networks from the space-resolved anatomical comprehensive in situ hybridization data from Allen Mouse Brain Atlas dataset. The key idea is that if two genes use the same dictionary to represent their original signals, then their gene expressions must share similar patterns, thereby considering them as "coexpressed." For each network, we have simultaneous knowledge of spatial distributions, the genes in the network and the extent a particular gene conforms to the coexpression pattern. Gene ontologies and the comparisons with published gene lists reveal biologically identified coexpression networks, some of which correspond to major cell types, biological pathways, and/or anatomical regions.

Quantitative locomotion study of freely swimming micro-organisms using laser diffraction.

PubMed

Magnes, Jenny; Susman, Kathleen; Eells, Rebecca

2012-10-25

Soil and aquatic microscopic organisms live and behave in a complex three-dimensional environment. Most studies of microscopic organism behavior, in contrast, have been conducted using microscope-based approaches, which limit the movement and behavior to a narrow, nearly two-dimensional focal field.(1) We present a novel analytical approach that provides real-time analysis of freely swimming C. elegans in a cuvette without dependence on microscope-based equipment. This approach consists of tracking the temporal periodicity of diffraction patterns generated by directing laser light through the cuvette. We measure oscillation frequencies for freely swimming nematodes. Analysis of the far-field diffraction patterns reveals clues about the waveforms of the nematodes. Diffraction is the process of light bending around an object. In this case light is diffracted by the organisms. The light waves interfere and can form a diffraction pattern. A far-field, or Fraunhofer, diffraction pattern is formed if the screen-to-object distance is much larger than the diffracting object. In this case, the diffraction pattern can be calculated (modeled) using a Fourier transform.(2) C. elegans are free-living soil-dwelling nematodes that navigate in three dimensions. They move both on a solid matrix like soil or agar in a sinusoidal locomotory pattern called crawling and in liquid in a different pattern called swimming.(3) The roles played by sensory information provided by mechanosensory, chemosensory, and thermosensory cells that govern plastic changes in locomotory patterns and switches in patterns are only beginning to be elucidated.(4) We describe an optical approach to measuring nematode locomotion in three dimensions that does not require a microscope and will enable us to begin to explore the complexities of nematode locomotion under different conditions.

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

PubMed Central

de Mendoza, Alex; Sebé-Pedrós, Arnau; Šestak, Martin Sebastijan; Matejčić, Marija; Torruella, Guifré; Domazet-Lošo, Tomislav; Ruiz-Trillo, Iñaki

2013-01-01

Transcription factors (TFs) are the main players in transcriptional regulation in eukaryotes. However, it remains unclear what role TFs played in the origin of all of the different eukaryotic multicellular lineages. In this paper, we explore how the origin of TF repertoires shaped eukaryotic evolution and, in particular, their role into the emergence of multicellular lineages. We traced the origin and expansion of all known TFs through the eukaryotic tree of life, using the broadest possible taxon sampling and an updated phylogenetic background. Our results show that the most complex multicellular lineages (i.e., those with embryonic development, Metazoa and Embryophyta) have the most complex TF repertoires, and that these repertoires were assembled in a stepwise manner. We also show that a significant part of the metazoan and embryophyte TF toolkits evolved earlier, in their respective unicellular ancestors. To gain insights into the role of TFs in the development of both embryophytes and metazoans, we analyzed TF expression patterns throughout their ontogeny. The expression patterns observed in both groups recapitulate those of the whole transcriptome, but reveal some important differences. Our comparative genomics and expression data reshape our view on how TFs contributed to eukaryotic evolution and reveal the importance of TFs to the origins of multicellularity and embryonic development. PMID:24277850

Learning and transfer in motor-respiratory coordination.

PubMed

Hessler, Eric E; Amazeen, Polemnia G

2014-02-01

Motor-respiratory coordination occurs naturally during exercise, but the number of coordination patterns performed between movement and breathing is limited. We investigated whether participants could acquire novel ratios (either 5:2 or 5:3). To examine complex temporal relationships between movement and breathing, we used lagged return plots that were produced by graphing relative phase against relative phase after a time delay. By the end of practice, participants performed 5:2 consistently and performed 5:3 using more stable ratios (3:2 and 2:1). Lagged return plots revealed that 5:3 learners harnessed the stable inphase and antiphase patterns to stabilize the required ratio. That strategy resulted in the performance of smaller-integer ratios in the production of 5:3 but not 5:2. Despite those differences, there was positive transfer to unpracticed ratios that was similar in both learning conditions. The time series analysis of lagged return plots revealed differences in ratio performance at transfer. Ratios whose component frequencies were farther apart, like 7:2, were performed consistently, while ratios whose component frequencies were more similar, like 5:4, elicited attraction to inphase and antiphase. The implication is that participants can combine more stable chunks of rhythmic behavior to produce more complex ratios. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of WY 14,643 and its Complex with Aldose Reductase

PubMed Central

Sawaya, Michael R.; Verma, Malkhey; Balendiran, Vaishnavi; Rath, Nigam P.; Cascio, Duilio; Balendiran, Ganesaratnam K.

2016-01-01

The peroxisome proliferator, WY 14,643 exhibits a pure non-competitive inhibition pattern in the aldehyde reduction and in alcohol oxidation activities of human Aldose reductase (hAR). Fluorescence emission measurements of the equilibrium dissociation constants, Kd, of oxidized (hAR•NADP+) and reduced (hAR•NADPH) holoenzyme complexes display a 2-fold difference between them. Kd values for the dissociation of WY 14,643 from the oxidized (hAR•NADP+•WY 14,643) and reduced (hAR•NADPH•WY 14,643) ternary complexes are comparable to each other. The ternary complex structure of hAR•NADP+•WY 14,643 reveals the first structural evidence of a fibrate class drug binding to hAR. These observations demonstrate how fibrate molecules such as WY 14,643, besides being valued as agonists for PPAR, also inhibit hAR. PMID:27721416

Mass spectrometric profiling reveals association of N-glycan patterns with epithelial ovarian cancer progression.

PubMed

Chen, Huanhuan; Deng, Zaian; Huang, Chuncui; Wu, Hongmei; Zhao, Xia; Li, Yan

2017-07-01

Aberrant changes of N-glycan modifications on proteins have been linked to various diseases including different cancers, suggesting possible avenue for exploring their etiologies based on N-glycomic analysis. Changes in N-glycan patterns during epithelial ovarian cancer development have so far been investigated mainly using serum, plasma, ascites, and cell lines. However, changes in patterns of N-glycans in tumor tissues during epithelial ovarian cancer progression have remained largely undefined. To investigate whether changes in N-glycan patterns correlate with oncogenesis and progression of epithelial ovarian cancer, we profiled N-glycans from formalin-fixed paraffin-embedded tissue slides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and quantitatively compared among different pathological grades of epithelial ovarian cancer and healthy controls. Our results show that among the 80 compositions of N-glycan detected, expression levels of high-mannose type were higher in epithelial ovarian cancer samples than that observed in healthy controls, accompanied by reduced levels of hybrid-type glycans. By applying receiver operating characteristic analysis, we show that a combined panel composed of four high-mannose and three fucosylated neutral complex N-glycans allows for good discrimination of epithelial ovarian cancer from healthy controls. Furthermore, using a statistical analysis of variance assay, we found that different N-glycan patterns, including 2 high-mannose-type, 2 fucosylated and sialylated complex structures, and 10 fucosylated neutral complex N-glycans, exhibited specific changes in N-glycan abundance across epithelial ovarian cancer grades. Together, our results provide strong evidence that N-glycomic changes are a strong indicator for epithelial ovarian cancer pathological grades and should provide avenues to identify novel biomarkers for epithelial ovarian cancer diagnosis and monitoring.

THE ROLE OF SELF-INJURY IN THE ORGANIZATION OF BEHAVIOUR

PubMed Central

Sandman, Curt A.; Kemp, Aaron S.; Mabini, Christopher; Pincus, David; Magnusson, Magnus

2012-01-01

Background Self-injuring acts are among the most dramatic behaviours exhibited by human beings. There is no known single cause and there is no universally agreed upon treatment. Sophisticated sequential and temporal analysis of behaviour has provided alternative descriptions of self-injury that provide new insights into its initiation and maintenance. Method Forty hours of observations for each of 32 participants were collected in a contiguous two-week period. Twenty categories of behavioural and environmental events were recorded electronically that captured the precise time each observation occurred. Temporal behavioural/environmental patterns associated with self-injurious events were revealed with a method (t-patterns; THEME) for detecting non-linear, real-time patterns. Results Results indicated that acts of self-injury contributed both to more patterns and to more complex patterns. Moreover, self-injury left its imprint on the organization of behaviour even when counts of self-injury were expelled from the continuous record. Conclusions Behaviour of participants was organized in a more diverse array of patterns with SIB was present. Self-injuring acts may function as singular points, increasing coherence within self-organizing patterns of behaviour. PMID:22452417

A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves

PubMed Central

Digiuni, Simona; Schellmann, Swen; Geier, Florian; Greese, Bettina; Pesch, Martina; Wester, Katja; Dartan, Burcu; Mach, Valerie; Srinivas, Bhylahalli Purushottam; Timmer, Jens; Fleck, Christian; Hulskamp, Martin

2008-01-01

Trichome patterning in Arabidopsis serves as a model system for de novo pattern formation in plants. It is thought to typify the theoretical activator–inhibitor mechanism, although this hypothesis has never been challenged by a combined experimental and theoretical approach. By integrating the key genetic and molecular data of the trichome patterning system, we developed a new theoretical model that allows the direct testing of the effect of experimental interventions and in the prediction of patterning phenotypes. We show experimentally that the trichome inhibitor TRIPTYCHON is transcriptionally activated by the known positive regulators GLABRA1 and GLABRA3. Further, we demonstrate by particle bombardment of protein fusions with GFP that TRIPTYCHON and CAPRICE but not GLABRA1 and GLABRA3 can move between cells. Finally, theoretical considerations suggest promoter swapping and basal overexpression experiments by means of which we are able to discriminate three biologically meaningful variants of the trichome patterning model. Our study demonstrates that the mutual interplay between theory and experiment can reveal a new level of understanding of how biochemical mechanisms can drive biological patterning processes. PMID:18766177

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies.

PubMed

Youn, Ji-Young; Dunham, Wade H; Hong, Seo Jung; Knight, James D R; Bashkurov, Mikhail; Chen, Ginny I; Bagci, Halil; Rathod, Bhavisha; MacLeod, Graham; Eng, Simon W M; Angers, Stéphane; Morris, Quaid; Fabian, Marc; Côté, Jean-François; Gingras, Anne-Claude

2018-02-01

mRNA processing, transport, translation, and ultimately degradation involve a series of dedicated protein complexes that often assemble into large membraneless structures such as stress granules (SGs) and processing bodies (PBs). Here, systematic in vivo proximity-dependent biotinylation (BioID) analysis of 119 human proteins associated with different aspects of mRNA biology uncovers 7424 unique proximity interactions with 1,792 proteins. Classical bait-prey analysis reveals connections of hundreds of proteins to distinct mRNA-associated processes or complexes, including the splicing and transcriptional elongation machineries (protein phosphatase 4) and the CCR4-NOT deadenylase complex (CEP85, RNF219, and KIAA0355). Analysis of correlated patterns between endogenous preys uncovers the spatial organization of RNA regulatory structures and enables the definition of 144 core components of SGs and PBs. We report preexisting contacts between most core SG proteins under normal growth conditions and demonstrate that several core SG proteins (UBAP2L, CSDE1, and PRRC2C) are critical for the formation of microscopically visible SGs. Copyright © 2017 Elsevier Inc. All rights reserved.

Sugar-Based Polyamides: Self-Organization in Strong Polar Organic Solvents.

PubMed

Rosu, Cornelia; Russo, Paul S; Daly, William H; Cueto, Rafael; Pople, John A; Laine, Roger A; Negulescu, Ioan I

2015-09-14

Periodic patterns resembling spirals were observed to form spontaneously upon unassisted cooling of d-glucaric acid- and d-galactaric acid-based polyamide solutions in N-methyl-N-morpholine oxide (NMMO) monohydrate. Similar observations were made in d-galactaric acid-based polyamide/ionic liquid (IL) solutions. The morphologies were investigated by optical, polarized light and confocal microscopy assays to reveal pattern details. Differential scanning calorimetry was used to monitor solution thermal behavior. Small- and wide-angle X-ray scattering data reflected the complex and heterogeneous nature of the self-organized patterns. Factors such as concentration and temperature were found to influence spiral dimensions and geometry. The distance between rings followed a first-order exponential decay as a function of polymer concentration. Fourier-Transform Infrared Microspectroscopy analysis of spirals pointed to H-bonding between the solvent and the pendant hydroxyl groups of the glucose units from the polymer backbone. Tests on self-organization into spirals of ketal-protected d-galactaric acid polyamides in NMMO monohydrate confirmed the importance of the monosaccharide's pendant free hydroxyl groups on the formation of these patterns. Rheology performed on d-galactaric-based polyamides at high concentration in NMMO monohydrate solution revealed the optimum conditions necessary to process these materials as fibers by spinning. The self-organization of these sugar-based polyamides mimics certain biological materials.

Syllable acoustics, temporal patterns, and call composition vary with behavioral context in Mexican free-tailed bats

PubMed Central

Bohn, Kirsten M.; Schmidt-French, Barbara; Ma, Sean T.; Pollak, George D.

2008-01-01

Recent research has shown that some bat species have rich vocal repertoires with diverse syllable acoustics. Few studies, however, have compared vocalizations across different behavioral contexts or examined the temporal emission patterns of vocalizations. In this paper, a comprehensive examination of the vocal repertoire of Mexican free-tailed bats, T. brasiliensis, is presented. Syllable acoustics and temporal emission patterns for 16 types of vocalizations including courtship song revealed three main findings. First, although in some cases syllables are unique to specific calls, other syllables are shared among different calls. Second, entire calls associated with one behavior can be embedded into more complex vocalizations used in entirely different behavioral contexts. Third, when different calls are composed of similar syllables, distinctive temporal emission patterns may facilitate call recognition. These results indicate that syllable acoustics alone do not likely provide enough information for call recognition; rather, the acoustic context and temporal emission patterns of vocalizations may affect meaning. PMID:19045674

Rethinking pattern formation in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Halatek, J.; Frey, E.

2018-05-01

The present theoretical framework for the analysis of pattern formation in complex systems is mostly limited to the vicinity of fixed (global) equilibria. Here we present a new theoretical approach to characterize dynamical states arbitrarily far from (global) equilibrium. We show that reaction-diffusion systems that are driven by locally mass-conserving interactions can be understood in terms of local equilibria of diffusively coupled compartments. Diffusive coupling generically induces lateral redistribution of the globally conserved quantities, and the variable local amounts of these quantities determine the local equilibria in each compartment. We find that, even far from global equilibrium, the system is well characterized by its moving local equilibria. We apply this framework to in vitro Min protein pattern formation, a paradigmatic model for biological pattern formation. Within our framework we can predict and explain transitions between chemical turbulence and order arbitrarily far from global equilibrium. Our results reveal conceptually new principles of self-organized pattern formation that may well govern diverse dynamical systems.

Monitoring Urban Greenness Dynamics Using Multiple Endmember Spectral Mixture Analysis

PubMed Central

Gan, Muye; Deng, Jinsong; Zheng, Xinyu; Hong, Yang; Wang, Ke

2014-01-01

Urban greenness is increasingly recognized as an essential constituent of the urban environment and can provide a range of services and enhance residents’ quality of life. Understanding the pattern of urban greenness and exploring its spatiotemporal dynamics would contribute valuable information for urban planning. In this paper, we investigated the pattern of urban greenness in Hangzhou, China, over the past two decades using time series Landsat-5 TM data obtained in 1990, 2002, and 2010. Multiple endmember spectral mixture analysis was used to derive vegetation cover fractions at the subpixel level. An RGB-vegetation fraction model, change intensity analysis and the concentric technique were integrated to reveal the detailed, spatial characteristics and the overall pattern of change in the vegetation cover fraction. Our results demonstrated the ability of multiple endmember spectral mixture analysis to accurately model the vegetation cover fraction in pixels despite the complex spectral confusion of different land cover types. The integration of multiple techniques revealed various changing patterns in urban greenness in this region. The overall vegetation cover has exhibited a drastic decrease over the past two decades, while no significant change occurred in the scenic spots that were studied. Meanwhile, a remarkable recovery of greenness was observed in the existing urban area. The increasing coverage of small green patches has played a vital role in the recovery of urban greenness. These changing patterns were more obvious during the period from 2002 to 2010 than from 1990 to 2002, and they revealed the combined effects of rapid urbanization and greening policies. This work demonstrates the usefulness of time series of vegetation cover fractions for conducting accurate and in-depth studies of the long-term trajectories of urban greenness to obtain meaningful information for sustainable urban development. PMID:25375176

Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures

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

Oyama, Takuji; Toyota, Kenji; Waku, Tsuyoshi

2009-08-01

The structures of the ligand-binding domains (LBDs) of human peroxisome proliferator-activated receptors (PPARα, PPARγ and PPARδ) in complexes with a pan agonist, an α/δ dual agonist and a PPARδ-specific agonist were determined. The results explain how each ligand is recognized by the PPAR LBDs at an atomic level. Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone receptor family, which is defined as transcriptional factors that are activated by the binding of ligands to their ligand-binding domains (LBDs). Although the three PPAR subtypes display different tissue distribution patterns and distinct pharmacological profiles, they all are essentially related to fatty-acid andmore » glucose metabolism. Since the PPARs share similar three-dimensional structures within the LBDs, synthetic ligands which simultaneously activate two or all of the PPARs could be potent candidates in terms of drugs for the treatment of abnormal metabolic homeostasis. The structures of several PPAR LBDs were determined in complex with synthetic ligands, derivatives of 3-(4-alkoxyphenyl)propanoic acid, which exhibit unique agonistic activities. The PPARα and PPARγ LBDs were complexed with the same pan agonist, TIPP-703, which activates all three PPARs and their crystal structures were determined. The two LBD–ligand complex structures revealed how the pan agonist is adapted to the similar, but significantly different, ligand-binding pockets of the PPARs. The structures of the PPARδ LBD in complex with an α/δ-selective ligand, TIPP-401, and with a related δ-specific ligand, TIPP-204, were also determined. The comparison between the two PPARδ complexes revealed how each ligand exhibits either a ‘dual selective’ or ‘single specific’ binding mode.« less

Geo-Distinctive Comorbidity Networks of Pediatric Asthma.

PubMed

Shin, Eun Kyong; Shaban-Nejad, Arash

2018-01-01

Most pediatric asthma cases occur in complex interdependencies, exhibiting complex manifestation of multiple symptoms. Studying asthma comorbidities can help to better understand the etiology pathway of the disease. Albeit such relations of co-expressed symptoms and their interactions have been highlighted recently, empirical investigation has not been rigorously applied to pediatric asthma cases. In this study, we use computational network modeling and analysis to reveal the links and associations between commonly co-observed diseases/conditions with asthma among children in Memphis, Tennessee. We present a novel method for geo-parsed comorbidity network analysis to show the distinctive patterns of comorbidity networks in urban and suburban areas in Memphis.

The neurobiology of psychopathy.

PubMed

Glenn, Andrea L; Raine, Adrian

2008-09-01

Numerous studies have tackled the complex challenge of understanding the neural substrates of psychopathy, revealing that brain abnormalities exist on several levels and in several structures. As we discover more about complex neural networks, it becomes increasingly difficult to clarify how these systems interact with each other to produce the distinct pattern of behavioral and personality characteristics observed in psychopathy. The authors review the recent research on the neurobiology of psychopathy, beginning with molecular neuroscience work and progressing to the level of brain structures and their connectivity. Potential factors that may affect the development of brain impairments, as well as how some systems may be targeted for potential treatment, are discussed.

Endophyte Microbiome Diversity in Micropropagated Atriplex canescens and Atriplex torreyi var griffithsii

PubMed Central

Lucero, Mary E.; Unc, Adrian; Cooke, Peter; Dowd, Scot; Sun, Shulei

2011-01-01

Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP) analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities. PMID:21437280

Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns

PubMed Central

Cruchet, Steeve; Gustafson, Kyle; Benton, Richard; Floreano, Dario

2015-01-01

The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs—locomotor bouts—matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior. PMID:26600381

Three perspectives on complexity: entropy, compression, subsymmetry

NASA Astrophysics Data System (ADS)

Nagaraj, Nithin; Balasubramanian, Karthi

2017-12-01

There is no single universally accepted definition of `Complexity'. There are several perspectives on complexity and what constitutes complex behaviour or complex systems, as opposed to regular, predictable behaviour and simple systems. In this paper, we explore the following perspectives on complexity: effort-to-describe (Shannon entropy H, Lempel-Ziv complexity LZ), effort-to-compress (ETC complexity) and degree-of-order (Subsymmetry or SubSym). While Shannon entropy and LZ are very popular and widely used, ETC is relatively a new complexity measure. In this paper, we also propose a novel normalized complexity measure SubSym based on the existing idea of counting the number of subsymmetries or palindromes within a sequence. We compare the performance of these complexity measures on the following tasks: (A) characterizing complexity of short binary sequences of lengths 4 to 16, (B) distinguishing periodic and chaotic time series from 1D logistic map and 2D Hénon map, (C) analyzing the complexity of stochastic time series generated from 2-state Markov chains, and (D) distinguishing between tonic and irregular spiking patterns generated from the `Adaptive exponential integrate-and-fire' neuron model. Our study reveals that each perspective has its own advantages and uniqueness while also having an overlap with each other.

On the origins of Balkan endemics: the complex evolutionary history of the Cyanus napulifer group (Asteraceae).

PubMed

Olšavská, Katarína; Slovák, Marek; Marhold, Karol; Štubňová, Eliška; Kučera, Jaromír

2016-11-01

The Balkan Peninsula is one of the most important centres of plant diversity in Europe. Here we aim to fill the gap in the current knowledge of the evolutionary processes and factors modelling this astonishing biological richness by applying multiple approaches to the Cyanus napulifer group. To reconstruct the mode of diversification within the C. napulifer group and to uncover its relationships with potential relatives with x = 10 from Europe and Northern Africa, we examined variation in genetic markers (amplified fragment length polymorphisms [AFLPs]; 460 individuals), relative DNA content (4',6-diamidino-2-phenylindole [DAPI] flow cytometry, 330 individuals) and morphology (multivariate morphometrics, 40 morphological characters, 710 individuals). To elucidate its evolutionary history, we analysed chloroplast DNA (cpDNA) sequences of the genus Cyanus deposited in the GenBank database. The AFLPs revealed a suite of closely related entities with variable levels of differentiation. The C. napulifer group formed a genetically well-defined unit. Samples outside the group formed strongly diversified and mostly species-specific genetic lineages with no further geographical patterns, often characterized also by a different DNA content. AFLP analysis of the C. napulifer group revealed extensive radiation and split it into nine allopatric (sub)lineages with varying degrees of congruence among genetic, DNA-content and morphological patterns. Genetic admixture was usually detected in contact zones between genetic lineages. Plastid data indicated extensive maintenance of ancestral variation across Cyanus perennials. The C. napulifer group is an example of a rapidly and recently diversified plant group whose genetic lineages have evolved in spatio-temporal isolation on the topographically complex Balkan Peninsula. Adaptive radiation, accompanied in some cases by long-term isolation and hybridization, has contributed to the formation of this species complex and its mosaic pattern. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study.

PubMed

Mudedla, Sathish Kumar; Azhagiya Singam, Ettayapuram Ramaprasad; Balamurugan, Kanagasabai; Subramanian, Venkatesan

2015-11-11

The complexation of small interfering RNA (siRNA) with positively charged gold nanoclusters has been studied in the present investigation with the help of classical molecular dynamics and steered molecular dynamics simulations accompanied by free energy calculations. The results show that gold nanoclusters form a stable complex with siRNA. The wrapping of siRNA around the gold nanocluster depends on the size and charge on the surface of the gold cluster. The binding pattern of the gold nanocluster with siRNA is also influenced by the presence of another cluster. The interaction between the positively charged amines in the gold nanocluster and the negatively charged phosphate group in the siRNA is responsible for the formation of complexes. The binding free energy value increases with the size of the gold cluster and the number of positive charges present on the surface of the gold nanocluster. The results reveal that the binding energy of small gold nanoclusters increases in the presence of another gold nanocluster while the binding of large gold nanoclusters decreases due to the introduction of another gold nanocluster. Overall, the findings have clearly demonstrated the effect of size and charge of gold nanoclusters on their interaction pattern with siRNA.

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

Deficits on irregular verbal morphology in Italian-speaking Alzheimer's disease patients

PubMed Central

Walenski, Matthew; Sosta, Katiuscia; Cappa, Stefano; Ullman, Michael T.

2010-01-01

Studies of English have shown that temporal-lobe patients, including those with Alzheimer's disease, are spared at processing real and novel regular inflected forms (e.g., blick → blicked; walk → walked), but impaired at real and novel irregular forms (e.g., spling → splang; dig → dug). Here we extend the investigation cross-linguistically to the more complex system of Italian verbal morphology, allowing us to probe the generality of the previous findings in English, as well as to test different explanatory accounts of inflectional morphology. We examined the production of real and novel regular and irregular past-participle and present-tense forms by native Italian-speaking healthy control subjects and patients with probable Alzheimer's disease. Compared to the controls, the patients were impaired at inflecting real irregular verbs but not real regular verbs both for past-participle and present-tense forms, but were not impaired at real regular verbs either for past-participle or present-tense forms. For novel past participles, the patients exhibited this same pattern of impaired production of class II (irregular) forms but spared class I (regular) production. In the present tense, patients were impaired at the production of class II forms (which are regular in the present tense), but spared at production of class I (regular) forms. Contrary to the pattern observed in English, the errors made by the patients on irregulars did not reveal a predominance of regularization errors (e.g., dig → digged). The findings thus partly replicate prior findings from English, but also reveal new patterns from a language with a more complex morphological system that includes verb classes (which are not possible to test in English). The demonstration of an irregular deficit following temporal-lobe damage in a language other than English reveals the cross-linguistic generality of the basic effect, while also elucidating important language-specific differences in the neuro-cognitive basis of regular and irregular morphological forms. PMID:19428387

Causality analysis of leading singular value decomposition modes identifies rotor as the dominant driving normal mode in fibrillation

NASA Astrophysics Data System (ADS)

Biton, Yaacov; Rabinovitch, Avinoam; Braunstein, Doron; Aviram, Ira; Campbell, Katherine; Mironov, Sergey; Herron, Todd; Jalife, José; Berenfeld, Omer

2018-01-01

Cardiac fibrillation is a major clinical and societal burden. Rotors may drive fibrillation in many cases, but their role and patterns are often masked by complex propagation. We used Singular Value Decomposition (SVD), which ranks patterns of activation hierarchically, together with Wiener-Granger causality analysis (WGCA), which analyses direction of information among observations, to investigate the role of rotors in cardiac fibrillation. We hypothesized that combining SVD analysis with WGCA should reveal whether rotor activity is the dominant driving force of fibrillation even in cases of high complexity. Optical mapping experiments were conducted in neonatal rat cardiomyocyte monolayers (diameter, 35 mm), which were genetically modified to overexpress the delayed rectifier K+ channel IKr only in one half of the monolayer. Such monolayers have been shown previously to sustain fast rotors confined to the IKr overexpressing half and driving fibrillatory-like activity in the other half. SVD analysis of the optical mapping movies revealed a hierarchical pattern in which the primary modes corresponded to rotor activity in the IKr overexpressing region and the secondary modes corresponded to fibrillatory activity elsewhere. We then applied WGCA to evaluate the directionality of influence between modes in the entire monolayer using clear and noisy movies of activity. We demonstrated that the rotor modes influence the secondary fibrillatory modes, but influence was detected also in the opposite direction. To more specifically delineate the role of the rotor in fibrillation, we decomposed separately the respective SVD modes of the rotor and fibrillatory domains. In this case, WGCA yielded more information from the rotor to the fibrillatory domains than in the opposite direction. In conclusion, SVD analysis reveals that rotors can be the dominant modes of an experimental model of fibrillation. Wiener-Granger causality on modes of the rotor domains confirms their preferential driving influence on fibrillatory modes.

Network morphospace

PubMed Central

Avena-Koenigsberger, Andrea; Goñi, Joaquín; Solé, Ricard; Sporns, Olaf

2015-01-01

The structure of complex networks has attracted much attention in recent years. It has been noted that many real-world examples of networked systems share a set of common architectural features. This raises important questions about their origin, for example whether such network attributes reflect common design principles or constraints imposed by selectional forces that have shaped the evolution of network topology. Is it possible to place the many patterns and forms of complex networks into a common space that reveals their relations, and what are the main rules and driving forces that determine which positions in such a space are occupied by systems that have actually evolved? We suggest that these questions can be addressed by combining concepts from two currently relatively unconnected fields. One is theoretical morphology, which has conceptualized the relations between morphological traits defined by mathematical models of biological form. The second is network science, which provides numerous quantitative tools to measure and classify different patterns of local and global network architecture across disparate types of systems. Here, we explore a new theoretical concept that lies at the intersection between both fields, the ‘network morphospace’. Defined by axes that represent specific network traits, each point within such a space represents a location occupied by networks that share a set of common ‘morphological’ characteristics related to aspects of their connectivity. Mapping a network morphospace reveals the extent to which the space is filled by existing networks, thus allowing a distinction between actual and impossible designs and highlighting the generative potential of rules and constraints that pervade the evolution of complex systems. PMID:25540237

Understanding Activist Leadership Effort in the Movement Opposing Drinking and Driving

PubMed Central

Dorius, Cassandra R.; McCarthy, John D.

2012-01-01

Why do some social movement leaders work harder than others? And, how does gender affect the patterns we uncover? Utilizing historical case study evidence of local chapters in the emerging movement opposing drinking and driving we are able to develop and test theoretical expectations about predictors of weekly effort among MADD and RID leaders. Taken together, our model explains 45 percent of the variation in leadership effort. We find bureaucratic complexity and victim support activities are more powerful predictors of effort than are individual leader characteristics, although all are important. Further analysis reveals that gender almost wholly conditions the strong effect of bureaucratic complexity on leadership effort so that increasingly complex chapter structures are associated with substantial increases in work hours for women but not men. PMID:22993454

X-ray diffraction, FTIR, UV-VIS and SEM studies on chromium (III) complexes

NASA Astrophysics Data System (ADS)

Mishra, Ashutosh; Dwivedi, Jagrati; Shukla, Kritika

2015-06-01

Five Chromium (III) complexes have been prepared using Schiff base ligands which derived from benzoin and five different amino acids (H2N-R). Samples were characterized by XRD, FTIR, UV-VIS and SEM method. X-Ray diffraction pattern analyzed that all chromium (III) complexes have hexagonal structure and crystalline, in nature, using Bruker D8 Advance instrument. Using VERTAX 70, FTIR spectroscopy reveals that Samples have (C=N), (C-O), (M-N) and (M-O) bonds in the range of 4000-400cm-1. UV-VIS spectroscopy give information that samples absorb the visible light which is in the range of 380-780nm. For this, Lambda 960 spectrometer used. SEM is designed for studying of the solid objects, using JEOL JSM 5600 instrument.

Characterization of Mycobacterium tuberculosis Complex DNAs from Egyptian Mummies by Spoligotyping

PubMed Central

Zink, Albert R.; Sola, Christophe; Reischl, Udo; Grabner, Waltraud; Rastogi, Nalin; Wolf, Hans; Nerlich, Andreas G.

2003-01-01

Bone and soft tissue samples from 85 ancient Egyptian mummies were analyzed for the presence of ancient Mycobacterium tuberculosis complex DNA (aDNA) and further characterized by spoligotyping. The specimens were obtained from individuals from different tomb complexes in Thebes West, Upper Egypt, which were used for upper social class burials between the Middle Kingdom (since ca. 2050 BC) and the Late Period (until ca. 500 BC). A total of 25 samples provided a specific positive signal for the amplification of a 123-bp fragment of the repetitive element IS6110, indicating the presence of M. tuberculosis DNA. Further PCR-based tests for the identification of subspecies failed due to lack of specific amplification products in the historic tissue samples. Of these 25 positive specimens, 12 could be successfully characterized by spoligotyping. The spoligotyping signatures were compared to those in an international database. They all show either an M. tuberculosis or an M. africanum pattern, but none revealed an M. bovis-specific pattern. The results from a Middle Kingdom tomb (used exclusively between ca. 2050 and 1650 BC) suggest that these samples bear an M. africanum-type specific spoligotyping signature. The samples from later periods provided patterns typical for M. tuberculosis. This study clearly demonstrates that spoligotyping can be applied to historic tissue samples. In addition, our results do not support the theory that M. tuberculosis originated from the M. bovis type but, rather, suggest that human M. tuberculosis may have originated from a precursor complex probably related to M. africanum. PMID:12517873

Minimal perceptrons for memorizing complex patterns

NASA Astrophysics Data System (ADS)

Pastor, Marissa; Song, Juyong; Hoang, Danh-Tai; Jo, Junghyo

2016-11-01

Feedforward neural networks have been investigated to understand learning and memory, as well as applied to numerous practical problems in pattern classification. It is a rule of thumb that more complex tasks require larger networks. However, the design of optimal network architectures for specific tasks is still an unsolved fundamental problem. In this study, we consider three-layered neural networks for memorizing binary patterns. We developed a new complexity measure of binary patterns, and estimated the minimal network size for memorizing them as a function of their complexity. We formulated the minimal network size for regular, random, and complex patterns. In particular, the minimal size for complex patterns, which are neither ordered nor disordered, was predicted by measuring their Hamming distances from known ordered patterns. Our predictions agree with simulations based on the back-propagation algorithm.

Two Parallel Olfactory Pathways for Processing General Odors in a Cockroach

PubMed Central

Watanabe, Hidehiro; Nishino, Hiroshi; Mizunami, Makoto; Yokohari, Fumio

2017-01-01

In animals, sensory processing via parallel pathways, including the olfactory system, is a common design. However, the mechanisms that parallel pathways use to encode highly complex and dynamic odor signals remain unclear. In the current study, we examined the anatomical and physiological features of parallel olfactory pathways in an evolutionally basal insect, the cockroach Periplaneta americana. In this insect, the entire system for processing general odors, from olfactory sensory neurons to higher brain centers, is anatomically segregated into two parallel pathways. Two separate populations of secondary olfactory neurons, type1 and type2 projection neurons (PNs), with dendrites in distinct glomerular groups relay olfactory signals to segregated areas of higher brain centers. We conducted intracellular recordings, revealing olfactory properties and temporal patterns of both types of PNs. Generally, type1 PNs exhibit higher odor-specificities to nine tested odorants than type2 PNs. Cluster analyses revealed that odor-evoked responses were temporally complex and varied in type1 PNs, while type2 PNs exhibited phasic on-responses with either early or late latencies to an effective odor. The late responses are 30–40 ms later than the early responses. Simultaneous intracellular recordings from two different PNs revealed that a given odor activated both types of PNs with different temporal patterns, and latencies of early and late responses in type2 PNs might be precisely controlled. Our results suggest that the cockroach is equipped with two anatomically and physiologically segregated parallel olfactory pathways, which might employ different neural strategies to encode odor information. PMID:28529476

Convergent functional architecture of the superior parietal lobule unraveled with multimodal neuroimaging approaches.

PubMed

Wang, Jiaojian; Yang, Yong; Fan, Lingzhong; Xu, Jinping; Li, Changhai; Liu, Yong; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

2015-01-01

The superior parietal lobule (SPL) plays a pivotal role in many cognitive, perceptive, and motor-related processes. This implies that a mosaic of distinct functional and structural subregions may exist in this area. Recent studies have demonstrated that the ongoing spontaneous fluctuations in the brain at rest are highly structured and, like coactivation patterns, reflect the integration of cortical locations into long-distance networks. This suggests that the internal differentiation of a complex brain region may be revealed by interaction patterns that are reflected in different neuroimaging modalities. On the basis of this perspective, we aimed to identify a convergent functional organization of the SPL using multimodal neuroimaging approaches. The SPL was first parcellated based on its structural connections as well as on its resting-state connectivity and coactivation patterns. Then, post hoc functional characterizations and connectivity analyses were performed for each subregion. The three types of connectivity-based parcellations consistently identified five subregions in the SPL of each hemisphere. The two anterior subregions were found to be primarily involved in action processes and in visually guided visuomotor functions, whereas the three posterior subregions were primarily associated with visual perception, spatial cognition, reasoning, working memory, and attention. This parcellation scheme for the SPL was further supported by revealing distinct connectivity patterns for each subregion in all the used modalities. These results thus indicate a convergent functional architecture of the SPL that can be revealed based on different types of connectivity and is reflected by different functions and interactions. © 2014 Wiley Periodicals, Inc.

Characterization of Fatigue Damage for Bonded Composite Skin/Stringer Configurations

NASA Technical Reports Server (NTRS)

Paris, Isabelle; Cvitkovich, Michael; Krueger, Ronald

2008-01-01

The fatigue damage was characterized in specimens which consisted of a tapered composite flange bonded onto a composite skin. Quasi-static tension tests were performed first to determine the failure load. Subsequently, tension fatigue tests were performed at 40%, 50%, 60% and 70% of the failure load to evaluate the debonding mechanisms. For four specimens, the cycling loading was stopped at intervals. Photographs of the polished specimen edges were taken under a light microscope to document the damage. At two diagonally opposite corners of the flange, a delamination appeared to initiate at the flange tip from a matrix crack in the top 45deg skin ply and propagated at the top 45deg/-45deg skin ply interface. At the other two diagonally opposite corners, a delamination running in the bondline initiated from a matrix crack in the adhesive pocket. In addition, two specimens were cut longitudinally into several sections. Micrographs revealed a more complex pattern inside the specimen where the two delamination patterns observed at the edges are present simultaneously across most of the width of the specimen. The observations suggest that a more sophisticated nondestructive evaluation technique is required to capture the complex damage pattern of matrix cracking and multi-level delaminations.

Computerized morphometry as an aid in distinguishing recurrent versus nonrecurrent meningiomas.

PubMed

Noy, Shawna; Vlodavsky, Euvgeni; Klorin, Geula; Drumea, Karen; Ben Izhak, Ofer; Shor, Eli; Sabo, Edmond

2011-06-01

To use novel digital and morphometric methods to identify variables able to better predict the recurrence of intracranial meningiomas. Histologic images from 30 previously diagnosed meningioma tumors that recurred over 10 years of follow-up were consecutively selected from the Rambam Pathology Archives. Images were captured and morphometrically analyzed. Novel algorithms of digital pattern recognition using Fourier transformation and fractal and nuclear texture analyses were applied to evaluate the overall growth pattern complexity of the tumors, as well as the chromatin texture of individual tumor nuclei. The extracted parameters were then correlated with patient prognosis. Kaplan-Meier analyses revealed statistically significant associations between tumor morphometric parameters and recurrence times. Tumors with less nuclear orientation, more nuclear density, higher fractal dimension, and less regular chromatin textures tended to recur faster than those with a higher degree of nuclear order, less pattern complexity, lower density, and more homogeneous chromatin nuclear textures (p < 0.01). To our knowledge, these digital morphometric methods were used for the first time to accurately predict tumor recurrence in patients with intracranial meningiomas. The use of these methods may bring additional valuable information to the clinician regarding the optimal management of these patients.

Descriptive Characteristics of Surface Water Quality in Hong Kong by a Self-Organising Map

PubMed Central

An, Yan; Zou, Zhihong; Li, Ranran

2016-01-01

In this study, principal component analysis (PCA) and a self-organising map (SOM) were used to analyse a complex dataset obtained from the river water monitoring stations in the Tolo Harbor and Channel Water Control Zone (Hong Kong), covering the period of 2009–2011. PCA was initially applied to identify the principal components (PCs) among the nonlinear and complex surface water quality parameters. SOM followed PCA, and was implemented to analyze the complex relationships and behaviors of the parameters. The results reveal that PCA reduced the multidimensional parameters to four significant PCs which are combinations of the original ones. The positive and inverse relationships of the parameters were shown explicitly by pattern analysis in the component planes. It was found that PCA and SOM are efficient tools to capture and analyze the behavior of multivariable, complex, and nonlinear related surface water quality data. PMID:26761018

Descriptive Characteristics of Surface Water Quality in Hong Kong by a Self-Organising Map.

PubMed

An, Yan; Zou, Zhihong; Li, Ranran

2016-01-08

In this study, principal component analysis (PCA) and a self-organising map (SOM) were used to analyse a complex dataset obtained from the river water monitoring stations in the Tolo Harbor and Channel Water Control Zone (Hong Kong), covering the period of 2009-2011. PCA was initially applied to identify the principal components (PCs) among the nonlinear and complex surface water quality parameters. SOM followed PCA, and was implemented to analyze the complex relationships and behaviors of the parameters. The results reveal that PCA reduced the multidimensional parameters to four significant PCs which are combinations of the original ones. The positive and inverse relationships of the parameters were shown explicitly by pattern analysis in the component planes. It was found that PCA and SOM are efficient tools to capture and analyze the behavior of multivariable, complex, and nonlinear related surface water quality data.

Characterization of WY 14,643 and its Complex with Aldose Reductase

DOE PAGES

Sawaya, Michael R.; Verma, Malkhey; Balendiran, Vaishnavi; ...

2016-10-10

The peroxisome proliferator, WY 14,643 exhibits a pure non-competitive inhibition pattern in the aldehyde reduction and in alcohol oxidation activities of human Aldose reductase (hAR). Fluorescence emission measurements of the equilibrium dissociation constants, Kd, of oxidized (hAR•NADP+) and reduced (hAR•NADPH) holoenzyme complexes display a 2-fold difference between them. Kd values for the dissociation of WY 14,643 from the oxidized (hAR•NADP+•WY 14,643) and reduced (hAR•NADPH•WY 14,643) ternary complexes are comparable to each other. The ternary complex structure of hAR•NADP+•WY 14,643 reveals the first structural evidence of a fibrate class drug binding to hAR. These observations demonstrate how fibrate molecules such asmore » WY 14,643, besides being valued as agonists for PPAR, also inhibit hAR.« less

Characterization of WY 14,643 and its Complex with Aldose Reductase

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

Sawaya, Michael R.; Verma, Malkhey; Balendiran, Vaishnavi

The peroxisome proliferator, WY 14,643 exhibits a pure non-competitive inhibition pattern in the aldehyde reduction and in alcohol oxidation activities of human Aldose reductase (hAR). Fluorescence emission measurements of the equilibrium dissociation constants, Kd, of oxidized (hAR•NADP+) and reduced (hAR•NADPH) holoenzyme complexes display a 2-fold difference between them. Kd values for the dissociation of WY 14,643 from the oxidized (hAR•NADP+•WY 14,643) and reduced (hAR•NADPH•WY 14,643) ternary complexes are comparable to each other. The ternary complex structure of hAR•NADP+•WY 14,643 reveals the first structural evidence of a fibrate class drug binding to hAR. These observations demonstrate how fibrate molecules such asmore » WY 14,643, besides being valued as agonists for PPAR, also inhibit hAR.« less

Experimental and quantum-chemical studies on the three-particle fragmentation of neutral triatomic hydrogen

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

Galster, Ulrich; Baumgartner, Frank; Mueller, Ulrich

2005-12-15

Dissociation of well-defined H{sub 3} Rydberg states into three ground state hydrogen atoms reveals characteristic correlation patterns in the center-of-mass motion of the three fragments. We present an extensive experimental dataset of momentum correlation maps for all lower Rydberg states of H{sub 3} and D{sub 3}. In particular the states with principal quantum number n=2 feature simple correlation patterns with regular occurence of mutual affinities. Energetically higher-lying states typically show more complex patterns which are unique for each state. Quantum-chemical calculations on adiabatic potential energy surfaces of H{sub 3} Rydberg states are presented to illuminate the likely origin of thesemore » differences. We discuss the likely dissociation mechanisms and paths which are responsible for the observed continuum correlation.« less

Fragmented patterns of flood change across the United States

PubMed Central

Hirsch, R. M.; Viglione, A.; Blöschl, G.

2016-01-01

Abstract Trends in the peak magnitude, frequency, duration, and volume of frequent floods (floods occurring at an average of two events per year relative to a base period) across the United States show large changes; however, few trends are found to be statistically significant. The multidimensional behavior of flood change across the United States can be described by four distinct groups, with streamgages experiencing (1) minimal change, (2) increasing frequency, (3) decreasing frequency, or (4) increases in all flood properties. Yet group membership shows only weak geographic cohesion. Lack of geographic cohesion is further demonstrated by weak correlations between the temporal patterns of flood change and large‐scale climate indices. These findings reveal a complex, fragmented pattern of flood change that, therefore, clouds the ability to make meaningful generalizations about flood change across the United States. PMID:27917010

Fragmented patterns of flood change across the United States

USGS Publications Warehouse

Archfield, Stacey A.; Hirsch, Robert M.; Viglione, A.; Blöschl, G.

2016-01-01

Trends in the peak magnitude, frequency, duration, and volume of frequent floods (floods occurring at an average of two events per year relative to a base period) across the United States show large changes; however, few trends are found to be statistically significant. The multidimensional behavior of flood change across the United States can be described by four distinct groups, with streamgages experiencing (1) minimal change, (2) increasing frequency, (3) decreasing frequency, or (4) increases in all flood properties. Yet group membership shows only weak geographic cohesion. Lack of geographic cohesion is further demonstrated by weak correlations between the temporal patterns of flood change and large-scale climate indices. These findings reveal a complex, fragmented pattern of flood change that, therefore, clouds the ability to make meaningful generalizations about flood change across the United States.

Sequential establishment of stripe patterns in an expanding cell population.

PubMed

Liu, Chenli; Fu, Xiongfei; Liu, Lizhong; Ren, Xiaojing; Chau, Carlos K L; Li, Sihong; Xiang, Lu; Zeng, Hualing; Chen, Guanhua; Tang, Lei-Han; Lenz, Peter; Cui, Xiaodong; Huang, Wei; Hwa, Terence; Huang, Jian-Dong

2011-10-14

Periodic stripe patterns are ubiquitous in living organisms, yet the underlying developmental processes are complex and difficult to disentangle. We describe a synthetic genetic circuit that couples cell density and motility. This system enabled programmed Escherichia coli cells to form periodic stripes of high and low cell densities sequentially and autonomously. Theoretical and experimental analyses reveal that the spatial structure arises from a recurrent aggregation process at the front of the continuously expanding cell population. The number of stripes formed could be tuned by modulating the basal expression of a single gene. The results establish motility control as a simple route to establishing recurrent structures without requiring an extrinsic pacemaker.

Bacterial Trapping in Porous Media Flows

NASA Astrophysics Data System (ADS)

Dehkharghani, Amin; Waisbord, Nicolas; Dunkel, Jörn; Guasto, Jeffrey

2016-11-01

Swimming bacteria inhabit heterogeneous, microstructured environments that are often characterized by complex, ambient flows. Understanding the physical mechanisms underlying cell transport in these systems is key to controlling important processes such as bioremediation in porous soils and infections in human tissues. We study the transport of swimming bacteria (Bacillus subtilis) in quasi-two-dimensional porous microfluidic channels with a range of periodic microstructures and flow strengths. Measured cell trajectories and the local cell number density reveal the formation of filamentous cell concentration patterns within the porous structures. The local cell densification is maximized at shear rates in the range 1-10 s-1, but widely varies with pore geometry and flow topology. Experimental observations are complemented by Langevin simulations to demonstrate that the filamentous patterns result from a coupling of bacterial motility to the complex flow fields via Jeffery orbits, which effectively 'trap' the bacteria on streamlines. The resulting microscopic heterogeneity observed here suppresses bacterial transport and likely has implications for both mixing and cell nutrient uptake in porous media flows. NSF CBET-1511340.

Learning complex temporal patterns with resource-dependent spike timing-dependent plasticity.

PubMed

Hunzinger, Jason F; Chan, Victor H; Froemke, Robert C

2012-07-01

Studies of spike timing-dependent plasticity (STDP) have revealed that long-term changes in the strength of a synapse may be modulated substantially by temporal relationships between multiple presynaptic and postsynaptic spikes. Whereas long-term potentiation (LTP) and long-term depression (LTD) of synaptic strength have been modeled as distinct or separate functional mechanisms, here, we propose a new shared resource model. A functional consequence of our model is fast, stable, and diverse unsupervised learning of temporal multispike patterns with a biologically consistent spiking neural network. Due to interdependencies between LTP and LTD, dendritic delays, and proactive homeostatic aspects of the model, neurons are equipped to learn to decode temporally coded information within spike bursts. Moreover, neurons learn spike timing with few exposures in substantial noise and jitter. Surprisingly, despite having only one parameter, the model also accurately predicts in vitro observations of STDP in more complex multispike trains, as well as rate-dependent effects. We discuss candidate commonalities in natural long-term plasticity mechanisms.

Complex codon usage pattern and compositional features of retroviruses.

PubMed

RoyChoudhury, Sourav; Mukherjee, Debaprasad

2013-01-01

Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition.

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

PubMed

Arteaga, Alejandro; Pyron, R Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H; Guayasamin, Juan M

2016-01-01

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

PubMed Central

Pyron, R. Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H.; Guayasamin, Juan M.

2016-01-01

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history. PMID:27120100

Adaptive and selective seed abortion reveals complex conditional decision making in plants.

PubMed

Meyer, Katrin M; Soldaat, Leo L; Auge, Harald; Thulke, Hans-Hermann

2014-03-01

Behavior is traditionally attributed to animals only. Recently, evidence for plant behavior is accumulating, mostly from plant physiological studies. Here, we provide ecological evidence for complex plant behavior in the form of seed abortion decisions conditional on internal and external cues. We analyzed seed abortion patterns of barberry plants exposed to seed parasitism and different environmental conditions. Without abortion, parasite infestation of seeds can lead to loss of all seeds in a fruit. We statistically tested a series of null models with Monte Carlo simulations to establish selectivity and adaptiveness of the observed seed abortion patterns. Seed abortion was more frequent in parasitized fruits and fruits from dry habitats. Surprisingly, seed abortion occurred with significantly greater probability if there was a second intact seed in the fruit. This strategy provides a fitness benefit if abortion can prevent a sibling seed from coinfestation and if nonabortion of an infested but surviving single seed saves resources invested in the fruit coat. Ecological evidence for complex decision making in plants thus includes a structural memory (the second seed), simple reasoning (integration of inner and outer conditions), conditional behavior (abortion), and anticipation of future risks (seed predation).

An empirical assessment of driver motivation and emotional states in perceived safety margins under varied driving conditions.

PubMed

Zhang, Yu; Kaber, David B

2013-01-01

Motivation models in driving behaviour postulate that driver motives and emotional states dictate risk tolerance under various traffic conditions. The present study used time and driver performance-based payment systems to manipulate motivation and risk-taking behaviour. Ten participants drove to a predefined location in a simulated driving environment. Traffic patterns (density and velocity) were manipulated to cause driver behaviour adjustments due to the need to conform with the social norms of the roadway. The driving environment complexity was investigated as a mediating factor in risk tolerance. Results revealed the performance-based payment system to closely relate to risk-taking behaviour as compared with the time-based payment system. Drivers conformed with social norms associated with specific traffic patterns. Higher roadway complexity led to a more conservative safety margins and speeds. This research contributes to the further development of motivational models of driver behaviour. This study provides empirical justification for two motivation factors in driver risk-taking decisions, including compliance with social norm and emotions triggered by incentives. Environment complexity was identified as a mediating factor in motivational behaviour model. This study also recommended safety margin measures sensitive to changes in driver risk tolerance.

Dynamic analysis of heartbeat rate signals of epileptics using multidimensional phase space reconstruction approach

NASA Astrophysics Data System (ADS)

Su, Zhi-Yuan; Wu, Tzuyin; Yang, Po-Hua; Wang, Yeng-Tseng

2008-04-01

The heartbeat rate signal provides an invaluable means of assessing the sympathetic-parasympathetic balance of the human autonomic nervous system and thus represents an ideal diagnostic mechanism for detecting a variety of disorders such as epilepsy, cardiac disease and so forth. The current study analyses the dynamics of the heartbeat rate signal of known epilepsy sufferers in order to obtain a detailed understanding of the heart rate pattern during a seizure event. In the proposed approach, the ECG signals are converted into heartbeat rate signals and the embedology theorem is then used to construct the corresponding multidimensional phase space. The dynamics of the heartbeat rate signal are then analyzed before, during and after an epileptic seizure by examining the maximum Lyapunov exponent and the correlation dimension of the attractors in the reconstructed phase space. In general, the results reveal that the heartbeat rate signal transits from an aperiodic, highly-complex behaviour before an epileptic seizure to a low dimensional chaotic motion during the seizure event. Following the seizure, the signal trajectories return to a highly-complex state, and the complex signal patterns associated with normal physiological conditions reappear.

Direct laser interference patterning for decreased bacterial attachment

NASA Astrophysics Data System (ADS)

Guenther, Denise; Valle, Jaoine; Burgui, Saioa; Gil, Carmen; Solano, Cristina; Toledo-Arana, Alejandro; Helbig, Ralf; Werner, Carsten; Lasa, Inigo; Lasagni, Andrés. F.

2016-03-01

In the past 15 years, many efforts were made to create functionalized artificial surfaces showing special anti-bacterial and anti-biofouling properties. Thereby, the topography of medical relevant materials plays an important role. However, the targeted fabrication of promising surface structures like hole-, lamella- and pyramid-like patterns with feature sizes in the sub-micrometer range in a one-step process is still a challenge. Optical and e-beam lithography, molding and selfassembly layers show a great potential to design topographies for this purpose. At the same time, most of these techniques are based on sequential processes, require masks or molds and thus are very device relevant and time consuming. In this work, we present the Direct Laser Interference Patterning (DLIP) technology as a capable method for the fast, flexible and direct fabrication of periodic micrometer- and submicrometer structures. This method offers the possibility to equip large plain areas and curved devices with 1D, 2D and 3D patterns. Simple 1D (e.g. lines) and complex 3D (e.g. lamella, pillars) patterns with periodic distances from 0.5 μm to 5 μm were fabricated on polymeric materials (polyimide, polystyrene). Subsequently, we characterized the adhesion behavior of Staphylococcus epidermidis and S. aureus bacteria under in vitro and in vivo conditions. The results revealed that the topographies have a significant impact on bacteria adhesion. On the one side, one-dimensional line-like structures especially with dimensions of the bacteria enhanced microbe attachment. While on the other hand, complex three-dimensional patterns prevented biofilm formation even after implantation and contamination in living organisms.

Spatial mapping reveals multi-step pattern of wound healing in Physarum polycephalum

NASA Astrophysics Data System (ADS)

Bäuerle, Felix K.; Kramar, Mirna; Alim, Karen

2017-11-01

Wounding is a severe impairment of function, especially for an exposed organism like the network-forming true slime mould Physarum polycephalum. The tubular network making up the organism’s body plan is entirely interconnected and shares a common cytoplasm. Oscillatory contractions of the enclosing tube walls drive the shuttle streaming of the cytoplasm. Cytoplasmic flows underlie the reorganization of the network for example by movement toward attractive stimuli or away from repellants. Here, we follow the reorganization of P. polycephalum networks after severe wounding. Spatial mapping of the contraction changes in response to wounding reveal a multi-step pattern. Phases of increased activity alternate with cessation of contractions and stalling of flows, giving rise to coordinated transport and growth at the severing site. Overall, severing surprisingly acts like an attractive stimulus enabling healing of severed tubes. The reproducible cessation of contractions arising during this wound-healing response may open up new venues to investigate the biochemical wiring underlying P. polycephalum’s complex behaviours.

Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses

PubMed Central

2012-01-01

Background Gene duplications play an important role in the evolution of functional protein diversity. Some models of duplicate gene evolution predict complex forms of paralog divergence; orthologous proteins may diverge as well, further complicating patterns of divergence among and within gene families. Consequently, studying the link between protein sequence evolution and duplication requires the use of flexible substitution models that can accommodate multiple shifts in selection across a phylogeny. Here, we employed a variety of codon substitution models, primarily Clade models, to explore how selective constraint evolved following the duplication of a green-sensitive (RH2a) visual pigment protein (opsin) in African cichlids. Past studies have linked opsin divergence to ecological and sexual divergence within the African cichlid adaptive radiation. Furthermore, biochemical and regulatory differences between the RH2aα and RH2aβ paralogs have been documented. It thus seems likely that selection varies in complex ways throughout this gene family. Results Clade model analysis of African cichlid RH2a opsins revealed a large increase in the nonsynonymous-to-synonymous substitution rate ratio (ω) following the duplication, as well as an even larger increase, one consistent with positive selection, for Lake Tanganyikan cichlid RH2aβ opsins. Analysis using the popular Branch-site models, by contrast, revealed no such alteration of constraint. Several amino acid sites known to influence spectral and non-spectral aspects of opsin biochemistry were found to be evolving divergently, suggesting that orthologous RH2a opsins may vary in terms of spectral sensitivity and response kinetics. Divergence appears to be occurring despite intronic gene conversion among the tandemly-arranged duplicates. Conclusions Our findings indicate that variation in selective constraint is associated with both gene duplication and divergence among orthologs in African cichlid RH2a opsins. At least some of this variation may reflect an adaptive response to differences in light environment. Interestingly, these patterns only became apparent through the use of Clade models, not through the use of the more widely employed Branch-site models; we suggest that this difference stems from the increased flexibility associated with Clade models. Our results thus bear both on studies of cichlid visual system evolution and on studies of gene family evolution in general. PMID:23078361

Metal Complexes of a Novel Schiff Base Based on Penicillin: Characterization, Molecular Modeling, and Antibacterial Activity Study.

PubMed

Chaudhary, Narendra Kumar; Mishra, Parashuram

2017-01-01

A novel Schiff base ligand of type HL was prepared by the condensation of amoxicillin trihydrate and nicotinaldehyde. The metal complexes of Co +2 , Ni +2 , Cu +2 , and Zn +2 were characterized and investigated by physical and spectral techniques, namely, elemental analysis, melting point, conductivity, 1 H NMR, IR, UV-Vis spectra, ESR, SEM, and mass spectrometry measurements. They were further analyzed by thermal technique (TGA/DTA) to gain better insight about the thermal stability and kinetic properties of the complexes. Thermal data revealed high thermal stability and nonspontaneous nature of the decomposition steps. The Coats-Redfern method was applied to extract thermodynamic parameters to explain the kinetic behavior. The molar conductance values were relatively low, showing their nonelectrolytic nature. The powder XRD pattern revealed amorphous nature except copper complex (1c) that crystallized in the triclinic crystal system. The EPR study strongly recommends the tetrahedral geometry of 1c. The structure optimization by MM force field calculation through ArgusLab 4.0.1 software program supports the concerned geometry of the complexes. The in vitro antibacterial activity of all the compounds, at their two different concentrations, was screened against four bacterial pathogens, namely, E. coli, P. vulgaris, K. pneumoniae, and S. aureus, and showed better activity compared to parent drug and control drug.

Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners

PubMed Central

Strübbe, Gero; Popp, Christian; Schmidt, Alexander; Pauli, Andrea; Ringrose, Leonie; Beisel, Christian; Paro, Renato

2011-01-01

The maintenance of specific gene expression patterns during cellular proliferation is crucial for the identity of every cell type and the development of tissues in multicellular organisms. Such a cellular memory function is conveyed by the complex interplay of the Polycomb and Trithorax groups of proteins (PcG/TrxG). These proteins exert their function at the level of chromatin by establishing and maintaining repressed (PcG) and active (TrxG) chromatin domains. Past studies indicated that a core PcG protein complex is potentially associated with cell type or even cell stage-specific sets of accessory proteins. In order to better understand the dynamic aspects underlying PcG composition and function we have established an inducible version of the biotinylation tagging approach to purify Polycomb and associated factors from Drosophila embryos. This system enabled fast and efficient isolation of Polycomb containing complexes under near physiological conditions, thereby preserving substoichiometric interactions. Novel interacting proteins were identified by highly sensitive mass spectrometric analysis. We found many TrxG related proteins, suggesting a previously unrecognized extent of molecular interaction of the two counteracting chromatin regulatory protein groups. Furthermore, our analysis revealed an association of PcG protein complexes with the cohesin complex and showed that Polycomb-dependent silencing of a transgenic reporter depends on cohesin function. PMID:21415365

DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

PubMed

Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

2015-10-01

The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (p<2.2e-16) than HK gene promoters. The entropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

Spots and stripes: ecology and colour pattern evolution in butterflyfishes

PubMed Central

Kelley, Jennifer L.; Fitzpatrick, John L.; Merilaita, Sami

2013-01-01

The incredible diversity of colour patterns in coral reef fishes has intrigued biologists for centuries. Yet, despite the many proposed explanations for this diversity in coloration, definitive tests of the role of ecological factors in shaping the evolution of particular colour pattern traits are absent. Patterns such as spots and eyespots (spots surrounded by concentric rings of contrasting colour) have often been assumed to function for predator defence by mimicking predators' enemies' eyes, deflecting attacks or intimidating predators, but the evolutionary processes underlying these functions have never been addressed. Striped body patterns have been suggested to serve for both social communication and predator defence, but the impact of ecological constraints remains unclear. We conducted the first comparative analysis of colour pattern diversity in butterflyfishes (Family: Chaetodontidae), fishes with conspicuous spots, eyespots and wide variation in coloration. Using a dated molecular phylogeny of 95 species (approx. 75% of the family), we tested whether spots and eyespots have evolved characteristics that are consistent with their proposed defensive function and whether the presence of spots and body stripes is linked with species' body length, dietary complexity, habitat diversity or social behaviour. Contrary to our expectations, spots and eyespots appeared relatively recently in butterflyfish evolution and are highly evolutionarily labile, suggesting that they are unlikely to have played an important part in the evolutionary history of the group. Striped body patterns showed correlated evolution with a number of ecological factors including habitat type, sociality and dietary complexity. Our findings question the prevailing view that eyespots are an evolutionary response to predation pressure, providing a valuable counter example to the role of these markings as revealed in other taxa. PMID:23427170

Automated analysis of calcium spiking profiles with CaSA software: two case studies from root-microbe symbioses.

PubMed

Russo, Giulia; Spinella, Salvatore; Sciacca, Eva; Bonfante, Paola; Genre, Andrea

2013-12-26

Repeated oscillations in intracellular calcium (Ca2+) concentration, known as Ca2+ spiking signals, have been described in plants for a limited number of cellular responses to biotic or abiotic stimuli and most notably the common symbiotic signaling pathway (CSSP) which mediates the recognition by their plant hosts of two endosymbiotic microbes, arbuscular mycorrhizal (AM) fungi and nitrogen fixing rhizobia. The detailed analysis of the complexity and variability of the Ca2+ spiking patterns which have been revealed in recent studies requires both extensive datasets and sophisticated statistical tools. As a contribution, we have developed automated Ca2+ spiking analysis (CaSA) software that performs i) automated peak detection, ii) statistical analyses based on the detected peaks, iii) autocorrelation analysis of peak-to-peak intervals to highlight major traits in the spiking pattern.We have evaluated CaSA in two experimental studies. In the first, CaSA highlighted unpredicted differences in the spiking patterns induced in Medicago truncatula root epidermal cells by exudates of the AM fungus Gigaspora margarita as a function of the phosphate concentration in the growth medium of both host and fungus. In the second study we compared the spiking patterns triggered by either AM fungal or rhizobial symbiotic signals. CaSA revealed the existence of different patterns in signal periodicity, which are thought to contribute to the so-called Ca2+ signature. We therefore propose CaSA as a useful tool for characterizing oscillatory biological phenomena such as Ca2+ spiking.

Highly Cooperative Tetrametallic Ruthenium-μ-Oxo-μ-Hydroxo Catalyst for the Alcohol Oxidation Reaction

PubMed Central

Yi, Chae S.; Zeczycki, Tonya N.; Guzei, Ilia A.

2008-01-01

The tetrametallic ruthenium-oxo-hydroxo-hydride complex {[(PCy3)(CO)RuH]4(μ4-O)(μ3-OH)(μ2-OH)} (1) was synthesized in two steps from the monomeric complex (PCy3)(CO)RuHCl (2). The tetrameric complex 1 was found to be a highly effective catalyst for the transfer dehydrogenation of alcohols. Complex 1 showed a different catalytic activity pattern towards primary and secondary benzyl alcohols, as indicated by the Hammett correlation for the oxidation reaction of p-X-C6H4CH2OH (ρ = −0.45) and p-X-C6H4CH(OH)CH3 (ρ = +0.22) (X = OMe, CH3, H, Cl, CF3). Both a sigmoidal curve from the plot of initial rate vs [PhCH(OH)CH3] (K0.5 = 0.34 M; Hill coefficient, n = 4.2±0.1) and the phosphine inhibition kinetics revealed the highly cooperative nature of the complex for the oxidation of secondary alcohols. PMID:18726005

T-Pattern Analysis and Cognitive Load Manipulation to Detect Low-Stake Lies: An Exploratory Study.

PubMed

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare; Realdon, Olivia; Jonsson, Gudberg K; Anguera, M Teresa

2018-01-01

Deception has evolved to become a fundamental aspect of human interaction. Despite the prolonged efforts in many disciplines, there has been no definite finding of a univocally "deceptive" signal. This work proposes an approach to deception detection combining cognitive load manipulation and T-pattern methodology with the objective of: (a) testing the efficacy of dual task-procedure in enhancing differences between truth tellers and liars in a low-stakes situation; (b) exploring the efficacy of T-pattern methodology in discriminating truthful reports from deceitful ones in a low-stakes situation; (c) setting the experimental design and procedure for following research. We manipulated cognitive load to enhance differences between truth tellers and liars, because of the low-stakes lies involved in our experiment. We conducted an experimental study with a convenience sample of 40 students. We carried out a first analysis on the behaviors' frequencies coded through the observation software, using SPSS (22). The aim was to describe shape and characteristics of behavior's distributions and explore differences between groups. Datasets were then analyzed with Theme 6.0 software which detects repeated patterns (T-patterns) of coded events (non-verbal behaviors) that regularly or irregularly occur within a period of observation. A descriptive analysis on T-pattern frequencies was carried out to explore differences between groups. An in-depth analysis on more complex patterns was performed to get qualitative information on the behavior structure expressed by the participants. Results show that the dual-task procedure enhances differences observed between liars and truth tellers with T-pattern methodology; moreover, T-pattern detection reveals a higher variety and complexity of behavior in truth tellers than in liars. These findings support the combination of cognitive load manipulation and T-pattern methodology for deception detection in low-stakes situations, suggesting the testing of directional hypothesis on a larger probabilistic sample of population.

T-Pattern Analysis and Cognitive Load Manipulation to Detect Low-Stake Lies: An Exploratory Study

PubMed Central

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare; Realdon, Olivia; Jonsson, Gudberg K.; Anguera, M. Teresa

2018-01-01

Deception has evolved to become a fundamental aspect of human interaction. Despite the prolonged efforts in many disciplines, there has been no definite finding of a univocally “deceptive” signal. This work proposes an approach to deception detection combining cognitive load manipulation and T-pattern methodology with the objective of: (a) testing the efficacy of dual task-procedure in enhancing differences between truth tellers and liars in a low-stakes situation; (b) exploring the efficacy of T-pattern methodology in discriminating truthful reports from deceitful ones in a low-stakes situation; (c) setting the experimental design and procedure for following research. We manipulated cognitive load to enhance differences between truth tellers and liars, because of the low-stakes lies involved in our experiment. We conducted an experimental study with a convenience sample of 40 students. We carried out a first analysis on the behaviors’ frequencies coded through the observation software, using SPSS (22). The aim was to describe shape and characteristics of behavior’s distributions and explore differences between groups. Datasets were then analyzed with Theme 6.0 software which detects repeated patterns (T-patterns) of coded events (non-verbal behaviors) that regularly or irregularly occur within a period of observation. A descriptive analysis on T-pattern frequencies was carried out to explore differences between groups. An in-depth analysis on more complex patterns was performed to get qualitative information on the behavior structure expressed by the participants. Results show that the dual-task procedure enhances differences observed between liars and truth tellers with T-pattern methodology; moreover, T-pattern detection reveals a higher variety and complexity of behavior in truth tellers than in liars. These findings support the combination of cognitive load manipulation and T-pattern methodology for deception detection in low-stakes situations, suggesting the testing of directional hypothesis on a larger probabilistic sample of population. PMID:29551986

Two-dimensional spectra of electron collisions with acrylonitrile and methacrylonitrile reveal nuclear dynamics

NASA Astrophysics Data System (ADS)

Regeta, K.; Allan, M.

2015-05-01

Detailed experimental information on the motion of a nuclear packet on a complex (resonant) anion potential surface is obtained by measuring 2-dimensional (2D) electron energy loss spectra. The cross section is plotted as a function of incident electron energy, which determines which resonant anion state is populated, i.e., along which normal coordinate the wave packet is launched, and of the electron energy loss, which reveals into which final states each specific resonant state decays. The 2D spectra are presented for acrylonitrile and methacrylonitrile, at the incident energy range 0.095-1.0 eV, where the incoming electron is temporarily captured in the lowest π∗ orbital. The 2D spectra reveal selectivity patterns with respect to which vibrations are excited in the attachment and de-excited in the detachment. Further insight is gained by recording 1D spectra measured along horizontal, vertical, and diagonal cuts of the 2D spectrum. The methyl group in methacrylonitrile increases the resonance width 7 times. This converts the sharp resonances of acrylonitrile into boomerang structures but preserves the essence of the selectivity patterns. Selectivity of vibrational excitation by higher-lying shape resonances up to 8 eV is also reported.

Managerial leadership assessment - Personality correlates of and sex differences in ratings by leaders, peers, and followers

NASA Technical Reports Server (NTRS)

Gibson, Robert H.; Wilhelm, John

1989-01-01

A performance appraisal was conducted at a Fortune 500 airline. Evaluations of each manager were taken from his or her management, peers and subordinates. These ratings were related to personality clusters revealing patterns for males similar to those found between personality and performance in pilot populations. A case is made that piloting aircraft requires similar skills to managing other complex enterprises and that similar profiles predict success in each.

What does the Sr-substituted 2.1 Å resolution crystal structure of photosystem II reveal about the water oxidation mechanism?

PubMed

Terrett, Richard; Petrie, Simon; Pace, Ron J; Stranger, Robert

2014-03-25

A density functional study of the Sr-substituted photosystem II water oxidising complex demonstrates that its recent X-ray crystal structure is consistent with a (Mn(III))4 oxidation state pattern, and with a Sr-bound hydroxide ion. The Sr-water-hydroxide interactions rationalize differences in the exchange rates of substrate water and kinetics of dioxygen bond formation relative to the Ca-containing structure.

Decreased complexity of glucose dynamics in diabetes: evidence from multiscale entropy analysis of continuous glucose monitoring system data.

PubMed

Chen, Jin-Long; Chen, Pin-Fan; Wang, Hung-Ming

2014-07-15

Parameters of glucose dynamics recorded by the continuous glucose monitoring system (CGMS) could help in the control of glycemic fluctuations, which is important in diabetes management. Multiscale entropy (MSE) analysis has recently been developed to measure the complexity of physical and physiological time sequences. A reduced MSE complexity index indicates the increased repetition patterns of the time sequence, and, thus, a decreased complexity in this system. No study has investigated the MSE analysis of glucose dynamics in diabetes. This study was designed to compare the complexity of glucose dynamics between the diabetic patients (n = 17) and the control subjects (n = 13), who were matched for sex, age, and body mass index via MSE analysis using the CGMS data. Compared with the control subjects, the diabetic patients revealed a significant increase (P < 0.001) in the mean (diabetic patients 166.0 ± 10.4 vs. control subjects 93.3 ± 1.5 mg/dl), the standard deviation (51.7 ± 4.3 vs. 11.1 ± 0.5 mg/dl), and the mean amplitude of glycemic excursions (127.0 ± 9.2 vs. 27.7 ± 1.3 mg/dl) of the glucose levels; and a significant decrease (P < 0.001) in the MSE complexity index (5.09 ± 0.23 vs. 7.38 ± 0.28). In conclusion, the complexity of glucose dynamics is decreased in diabetes. This finding implies the reactivity of glucoregulation is impaired in the diabetic patients. Such impairment presenting as an increased regularity of glycemic fluctuating pattern could be detected by MSE analysis. Thus, the MSE complexity index could potentially be used as a biomarker in the monitoring of diabetes.

Temporal motifs reveal homophily, gender-specific patterns, and group talk in call sequences.

PubMed

Kovanen, Lauri; Kaski, Kimmo; Kertész, János; Saramäki, Jari

2013-11-05

Recent studies on electronic communication records have shown that human communication has complex temporal structure. We study how communication patterns that involve multiple individuals are affected by attributes such as sex and age. To this end, we represent the communication records as a colored temporal network where node color is used to represent individuals' attributes, and identify patterns known as temporal motifs. We then construct a null model for the occurrence of temporal motifs that takes into account the interaction frequencies and connectivity between nodes of different colors. This null model allows us to detect significant patterns in call sequences that cannot be observed in a static network that uses interaction frequencies as link weights. We find sex-related differences in communication patterns in a large dataset of mobile phone records and show the existence of temporal homophily, the tendency of similar individuals to participate in communication patterns beyond what would be expected on the basis of their average interaction frequencies. We also show that temporal patterns differ between dense and sparse neighborhoods in the network. Because also this result is independent of interaction frequencies, it can be seen as an extension of Granovetter's hypothesis to temporal networks.

The role of self-injury in the organisation of behaviour.

PubMed

Sandman, C A; Kemp, A S; Mabini, C; Pincus, D; Magnusson, M

2012-05-01

Self-injuring acts are among the most dramatic behaviours exhibited by human beings. There is no known single cause and there is no universally agreed upon treatment. Sophisticated sequential and temporal analysis of behaviour has provided alternative descriptions of self-injury that provide new insights into its initiation and maintenance. Forty hours of observations for each of 32 participants were collected in a contiguous 2-week period. Twenty categories of behavioural and environmental events were recorded electronically that captured the precise time each observation occurred. Temporal behavioural/environmental patterns associated with self-injurious events were revealed with a method (t-patterns; THEME) for detecting non-linear, real-time patterns. Results indicated that acts of self-injury contributed both to more patterns and to more complex patterns. Moreover, self-injury left its imprint on the organisation of behaviour even when counts of self-injury were expelled from the continuous record. Behaviour of participants was organised in a more diverse array of patterns when self-injurious behaviour was present. Self-injuring acts may function as singular points, increasing coherence within self-organising patterns of behaviour. © 2012 The Authors. Journal of Intellectual Disability Research © 2012 Blackwell Publishing Ltd.

Temporal motifs reveal homophily, gender-specific patterns, and group talk in call sequences

PubMed Central

Kovanen, Lauri; Kaski, Kimmo; Kertész, János; Saramäki, Jari

2013-01-01

Recent studies on electronic communication records have shown that human communication has complex temporal structure. We study how communication patterns that involve multiple individuals are affected by attributes such as sex and age. To this end, we represent the communication records as a colored temporal network where node color is used to represent individuals’ attributes, and identify patterns known as temporal motifs. We then construct a null model for the occurrence of temporal motifs that takes into account the interaction frequencies and connectivity between nodes of different colors. This null model allows us to detect significant patterns in call sequences that cannot be observed in a static network that uses interaction frequencies as link weights. We find sex-related differences in communication patterns in a large dataset of mobile phone records and show the existence of temporal homophily, the tendency of similar individuals to participate in communication patterns beyond what would be expected on the basis of their average interaction frequencies. We also show that temporal patterns differ between dense and sparse neighborhoods in the network. Because also this result is independent of interaction frequencies, it can be seen as an extension of Granovetter’s hypothesis to temporal networks. PMID:24145424

Network Catastrophe: Self-Organized Patterns Reveal both the Instability and the Structure of Complex Networks

PubMed Central

Moon, Hankyu; Lu, Tsai-Ching

2015-01-01

Critical events in society or biological systems can be understood as large-scale self-emergent phenomena due to deteriorating stability. We often observe peculiar patterns preceding these events, posing a question of—how to interpret the self-organized patterns to know more about the imminent crisis. We start with a very general description — of interacting population giving rise to large-scale emergent behaviors that constitute critical events. Then we pose a key question: is there a quantifiable relation between the network of interactions and the emergent patterns? Our investigation leads to a fundamental understanding to: 1. Detect the system's transition based on the principal mode of the pattern dynamics; 2. Identify its evolving structure based on the observed patterns. The main finding of this study is that while the pattern is distorted by the network of interactions, its principal mode is invariant to the distortion even when the network constantly evolves. Our analysis on real-world markets show common self-organized behavior near the critical transitions, such as housing market collapse and stock market crashes, thus detection of critical events before they are in full effect is possible. PMID:25822423

Network Catastrophe: Self-Organized Patterns Reveal both the Instability and the Structure of Complex Networks

NASA Astrophysics Data System (ADS)

Moon, Hankyu; Lu, Tsai-Ching

2015-03-01

Critical events in society or biological systems can be understood as large-scale self-emergent phenomena due to deteriorating stability. We often observe peculiar patterns preceding these events, posing a question of--how to interpret the self-organized patterns to know more about the imminent crisis. We start with a very general description -- of interacting population giving rise to large-scale emergent behaviors that constitute critical events. Then we pose a key question: is there a quantifiable relation between the network of interactions and the emergent patterns? Our investigation leads to a fundamental understanding to: 1. Detect the system's transition based on the principal mode of the pattern dynamics; 2. Identify its evolving structure based on the observed patterns. The main finding of this study is that while the pattern is distorted by the network of interactions, its principal mode is invariant to the distortion even when the network constantly evolves. Our analysis on real-world markets show common self-organized behavior near the critical transitions, such as housing market collapse and stock market crashes, thus detection of critical events before they are in full effect is possible.

Exploration of dynamics in a complex person-centred intervention process based on health professionals' perspectives.

PubMed

Friberg, Febe; Wallengren, Catarina; Håkanson, Cecilia; Carlsson, Eva; Smith, Frida; Pettersson, Monica; Kenne Sarenmalm, Elisabeth; Sawatzky, Richard; Öhlén, Joakim

2018-06-13

The assessment and evaluation of practical and sustainable development of health care has become a major focus of investigation in health services research. A key challenge for researchers as well as decision-makers in health care is to understand mechanisms influencing how complex interventions work and become embedded in practice, which is significant for both evaluation and later implementation. In this study, we explored nurses' and surgeons' perspectives on performing and participating in a complex multi-centre person-centred intervention process that aimed to support patients diagnosed with colorectal cancer to feel prepared for surgery, discharge and recovery. Data consisted of retrospective interviews with 20 professionals after the intervention, supplemented with prospective conversational data and field notes from workshops and follow-up meetings (n = 51). The data were analysed to construct patterns in line with interpretive description. Although the participants highly valued components of the intervention, the results reveal influencing mechanisms underlying the functioning of the intervention, including multiple objectives, unclear mandates and competing professional logics. The results also reveal variations in processing the intervention focused on differences in using and talking about intervention components. The study indicates there are significant areas of ambiguity in understanding how theory-based complex clinical interventions work and in how interventions are socially constructed and co-created by professionals' experiences, assumptions about own professional practice, contextual conditions and the researchers' intentions. This process evaluation reveals insights into reasons for success or failure and contextual aspects associated with variations in outcomes. Thus, there is a need for further interpretive inquiry, and not only descriptive studies, of the multifaceted characters of complex clinical interventions and how the intervention components are actually shaped in constantly shifting contexts.

Transformation of environmental conditions in large former Soviet countries: regional analysis

NASA Astrophysics Data System (ADS)

Bityukova, V. R.; Borovikov, M. S.

2018-01-01

The article studies changes in the structure of environmental conditions of regions in the large former Soviet countries (case study of Russia and Kazakhstan) that have formed considerable contrasts in the placement of industrial complex and population settlement during the previous development stages. The changes related to the transition to market economy have led to essential transformation of environmental conditions. A complex index allowing to assess changes at the regional level in Kazakhstan and Russia and to reveal main similarities and differences between those changes is applied to studying the transformation of regional and industry structure. The article examines both industry-specific and spatial patterns forming environmental conditions at the regional level.

Results of complex annual parasitological monitoring in the coastal area of Kola Bay

NASA Astrophysics Data System (ADS)

Kuklin, V. V.; Kuklina, M. M.; Kisova, N. E.; Maslich, M. A.

2009-12-01

The results of annual parasitological monitoring in the coastal area near the Abram-mys (Kola Bay, Barents Sea) are presented. The studies were performed in 2006-2007 and included complex examination of the intermediate hosts (mollusks and crustaceans) and definitive hosts (marine fish and birds) of the helminths. The biodiversity of the parasite fauna, seasonal dynamics, and functioning patterns of the parasite systems were investigated. The basic regularities in parasite circulation were assessed in relation to their life cycle strategies and the ecological features of the intermediate and definitive hosts. The factors affecting the success of parasite circulation in the coastal ecosystems were revealed through analysis of parasite biodiversity and abundance dynamics.

Already at the Table: Patterns of Play and Gambling Involvement Prior to Gambling Expansion.

PubMed

Nelson, Sarah E; LaPlante, Debi A; Gray, Heather M; Tom, Matthew A; Kleschinsky, John H; Shaffer, Howard J

2018-03-01

During 2011, the Governor of Massachusetts signed a bill to allow casino gambling in the state (Commonwealth of Massachusetts 2011). As a result, two resort casinos will begin operations during 2018 and 2019; a smaller slots parlor began operations during June 2015. Prior to this expansion, gambling was widely available in Massachusetts, through the state lottery, off-track betting, and gambling opportunities available in neighboring states. Within this context, it is important to understand the patterns of gambling involvement in the population prior to gambling expansion. The current study examined gambling involvement, patterns of play, and gambling-related problems prior to gambling expansion among a sample of 511 Massachusetts residents who were members of a statewide Internet panel. To measure patterns of play, we asked questions about past-year games played and frequency of play. To measure breadth of involvement, we assessed the number of different games played. To measure depth of involvement, we measured time spent gambling, amount wagered, and amount won or lost. Principal component analysis revealed four play pattern components accounting for more than 50% of the variance in game play frequency. Multiple regression analyses revealed that component scores composed of casino gambling and skill-based gambling (e.g., poker, sports) variables uniquely contributed to the prediction of gambling-related problems, even when depth of involvement was controlled. However, the addition of breadth of involvement to the model resulted in a model where no set of variables contributed significantly, suggesting a complex relationship among play patterns, depth, and breadth of involvement. The study established discrete and distinguishable gambling play patterns associated with gambling-related problems and identified groups of individuals potentially vulnerable to the effects of gambling expansion.

Exploratory Movement Generates Higher-Order Information That Is Sufficient for Accurate Perception of Scaled Egocentric Distance

PubMed Central

Mantel, Bruno; Stoffregen, Thomas A.; Campbell, Alain; Bardy, Benoît G.

2015-01-01

Body movement influences the structure of multiple forms of ambient energy, including optics and gravito-inertial force. Some researchers have argued that egocentric distance is derived from inferential integration of visual and non-visual stimulation. We suggest that accurate information about egocentric distance exists in perceptual stimulation as higher-order patterns that extend across optics and inertia. We formalize a pattern that specifies the egocentric distance of a stationary object across higher-order relations between optics and inertia. This higher-order parameter is created by self-generated movement of the perceiver in inertial space relative to the illuminated environment. For this reason, we placed minimal restrictions on the exploratory movements of our participants. We asked whether humans can detect and use the information available in this higher-order pattern. Participants judged whether a virtual object was within reach. We manipulated relations between body movement and the ambient structure of optics and inertia. Judgments were precise and accurate when the higher-order optical-inertial parameter was available. When only optic flow was available, judgments were poor. Our results reveal that participants perceived egocentric distance from the higher-order, optical-inertial consequences of their own exploratory activity. Analysis of participants’ movement trajectories revealed that self-selected movements were complex, and tended to optimize availability of the optical-inertial pattern that specifies egocentric distance. We argue that accurate information about egocentric distance exists in higher-order patterns of ambient energy, that self-generated movement can generate these higher-order patterns, and that these patterns can be detected and used to support perception of egocentric distance that is precise and accurate. PMID:25856410

Application of Factor Analysis to Identify Dietary Patterns and Use of Factor Scores to Study Their Relationship with Nutritional Status of Adult Rural Populations

PubMed Central

Brahmam, G.N.V.; Vijayaraghavan, K.

2011-01-01

The prevalence of chronic energy deficiency (CED) among one-third of the Indian population is attributed to inadequacy of consumption of nutrients. However, considering the complexity of diets among Indians, the relationship between a particular dietary pattern and the nutritional status of the population has not been established so far. A community-based cross-sectional study was undertaken to assess estimates, at district level, of diet and nutritional status in Orissa State, India. Factor analysis was used for exploring the existence of consumption pattern of food and nutrients and their relationship with the nutritional status of rural adult population. Data on 2,864 adult men and 3,525 adult women in Orissa state revealed that there exists six patterns among food-groups explaining 59% of the total variation and three patterns among nutrients that explain 73% of the total variation among both adult men and women. The discriminant function analysis revealed that, overall, 53% of the men were correctly classified as either with chronic energy deficiency (CED) or without CED. Similarly, overall, 54% of the women were correctly classified as either with CED or without CED. The sensitivity of the model was 65% for both men and women, and the specificity was 46% and 41% respectively for men and women. In the case of classification of overweight/obesity, the prediction of the model was about 75% among both men and women, along with high sensitivity. Using factor analysis, the dietary patterns were identified from the food and nutrient intake data. There exists a strong relationship between the dietary patterns and the nutritional status of rural adults. These results will help identify the community people with CED and help planners formulate nutritional interventions accordingly. PMID:21957671

Phylogenetic and morphological investigation of the Mochlus afer-sundevallii species complex (Squamata: Scincidae) across the arid corridor of sub-Saharan Africa.

PubMed

Freitas, Elyse S; Bauer, Aaron M; Siler, Cameron D; Broadley, Donald G; Jackman, Todd R

2018-06-02

The aridification of Africa resulted in the fragmentation of forests and the expansion of an arid corridor stretching from the northeast to southwest portion of sub-Saharan Africa, but the role this corridor has had in species-level diversification of southern African vertebrates is poorly understood. The skink species Mochlus afer and M. sundevallii inhabit wide areas of the arid corridor and are therefore an ideal species pair for studying patterns of genetic and phenotypic diversity associated with this landscape. However, species boundaries between these taxa have been controversial. Using multi-locus molecular and morphological datasets, we investigate diversification patterns of the M. afer-sundevallii Species Complex across the arid corridor. Although analyses of genetic data reveals some genetic structure among geographic populations, results of phylogenetic and morphological analyses provide little support for two distinct evolutionary lineages, suggesting that populations previously referred to as M. afer and M. sundevallii represent a single species, Mochlus sundevallii. Genetic diversity is unequally distributed across the arid corridor, with observed patterns consistent with aridification-facilitated diversification southward across southern Africa. Additional geographic and population-level sampling is necessary before more conclusive inferences can be drawn about the role historical climate transitions have played in skink diversification patterns across southern Africa. Copyright © 2018 Elsevier Inc. All rights reserved.

Idiosyncratic characteristics of saccadic eye movements when viewing different visual environments.

PubMed

Andrews, T J; Coppola, D M

1999-08-01

Eye position was recorded in different viewing conditions to assess whether the temporal and spatial characteristics of saccadic eye movements in different individuals are idiosyncratic. Our aim was to determine the degree to which oculomotor control is based on endogenous factors. A total of 15 naive subjects viewed five visual environments: (1) The absence of visual stimulation (i.e. a dark room); (2) a repetitive visual environment (i.e. simple textured patterns); (3) a complex natural scene; (4) a visual search task; and (5) reading text. Although differences in visual environment had significant effects on eye movements, idiosyncrasies were also apparent. For example, the mean fixation duration and size of an individual's saccadic eye movements when passively viewing a complex natural scene covaried significantly with those same parameters in the absence of visual stimulation and in a repetitive visual environment. In contrast, an individual's spatio-temporal characteristics of eye movements during active tasks such as reading text or visual search covaried together, but did not correlate with the pattern of eye movements detected when viewing a natural scene, simple patterns or in the dark. These idiosyncratic patterns of eye movements in normal viewing reveal an endogenous influence on oculomotor control. The independent covariance of eye movements during different visual tasks shows that saccadic eye movements during active tasks like reading or visual search differ from those engaged during the passive inspection of visual scenes.

The evolving content of meals in Great Britain. Results of a survey in 2012 in comparison with the 1950s.

PubMed

Yates, Luke; Warde, Alan

2015-01-01

This paper examines food eaten at meals in Great Britain. It presents findings about contemporary meal content, reflecting on the relationship between meal content and occasion, and makes comparison with an earlier study. Drawing on an online survey (N = 2784), conducted in September 2012, it describes the food consumed at daily eating events in terms of content, volume and complexity, common components and combinations, and sequence. Socio-demographic and economic differences are examined. Conceptual tools for analysing the association between food content and meal occasions are refined. The paper first explores the regularity of meal patterns. This is followed by description of the contours of the three principal daily eating events, with a brief section on snacks. The paper interprets distinctive features of current patterns by way of comparison with a similar study of eating habits in the 1950s. Findings reveal morning and midday eating events as simple and homogeneous in content, particularly on weekdays, with respondents breakfasting on cereal or toast, and lunching on sandwiches. Evening meals are more complex, structured and varied in content. Common patterns and systematic differentiation can be discerned, particularly across age cohort. Significant historical change can also be observed in relation to meal content and, to a lesser extent, meal pattern. Copyright © 2014 Elsevier Ltd. All rights reserved.

Complexity of spatiotemporal traffic phenomena in flow of identical drivers: Explanation based on fundamental hypothesis of three-phase theory

NASA Astrophysics Data System (ADS)

Kerner, Boris S.

2012-03-01

Based on numerical simulations of a stochastic three-phase traffic flow model, we reveal the physics of the fundamental hypothesis of three-phase theory that, in contrast with a fundamental diagram of classical traffic flow theories, postulates the existence of a two-dimensional (2D) region of steady states of synchronized flow where a driver makes an arbitrary choice of a space gap (time headway) to the preceding vehicle. We find that macroscopic and microscopic spatiotemporal effects of the entire complexity of traffic congestion observed up to now in real measured traffic data can be explained by simulations of traffic flow consisting of identical drivers and vehicles, if a microscopic model used in these simulations incorporates the fundamental hypothesis of three-phase theory. It is shown that the driver's choice of space gaps within the 2D region of synchronized flow associated with the fundamental hypothesis of three-phase theory can qualitatively change types of congested patterns that can emerge at a highway bottleneck. In particular, if drivers choose long enough spaces gaps associated with the fundamental hypothesis, then general patterns, which consist of synchronized flow and wide moving jams, do not emerge independent of the flow rates and bottleneck characteristics: Even at a heavy bottleneck leading to a very low speed within congested patterns, only synchronized flow patterns occur in which no wide moving jams emerge spontaneously.

Complexity of spatiotemporal traffic phenomena in flow of identical drivers: explanation based on fundamental hypothesis of three-phase theory.

PubMed

Kerner, Boris S

2012-03-01

Based on numerical simulations of a stochastic three-phase traffic flow model, we reveal the physics of the fundamental hypothesis of three-phase theory that, in contrast with a fundamental diagram of classical traffic flow theories, postulates the existence of a two-dimensional (2D) region of steady states of synchronized flow where a driver makes an arbitrary choice of a space gap (time headway) to the preceding vehicle. We find that macroscopic and microscopic spatiotemporal effects of the entire complexity of traffic congestion observed up to now in real measured traffic data can be explained by simulations of traffic flow consisting of identical drivers and vehicles, if a microscopic model used in these simulations incorporates the fundamental hypothesis of three-phase theory. It is shown that the driver's choice of space gaps within the 2D region of synchronized flow associated with the fundamental hypothesis of three-phase theory can qualitatively change types of congested patterns that can emerge at a highway bottleneck. In particular, if drivers choose long enough spaces gaps associated with the fundamental hypothesis, then general patterns, which consist of synchronized flow and wide moving jams, do not emerge independent of the flow rates and bottleneck characteristics: Even at a heavy bottleneck leading to a very low speed within congested patterns, only synchronized flow patterns occur in which no wide moving jams emerge spontaneously.

Transcriptome analysis of the painted lady butterfly, Vanessa cardui during wing color pattern development.

PubMed

Connahs, Heidi; Rhen, Turk; Simmons, Rebecca B

2016-03-31

Butterfly wing color patterns are an important model system for understanding the evolution and development of morphological diversity and animal pigmentation. Wing color patterns develop from a complex network composed of highly conserved patterning genes and pigmentation pathways. Patterning genes are involved in regulating pigment synthesis however the temporal expression dynamics of these interacting networks is poorly understood. Here, we employ next generation sequencing to examine expression patterns of the gene network underlying wing development in the nymphalid butterfly, Vanessa cardui. We identified 9, 376 differentially expressed transcripts during wing color pattern development, including genes involved in patterning, pigmentation and gene regulation. Differential expression of these genes was highest at the pre-ommochrome stage compared to early pupal and late melanin stages. Overall, an increasing number of genes were down-regulated during the progression of wing development. We observed dynamic expression patterns of a large number of pigment genes from the ommochrome, melanin and also pteridine pathways, including contrasting patterns of expression for paralogs of the yellow gene family. Surprisingly, many patterning genes previously associated with butterfly pattern elements were not significantly up-regulated at any time during pupation, although many other transcription factors were differentially expressed. Several genes involved in Notch signaling were significantly up-regulated during the pre-ommochrome stage including slow border cells, bunched and pebbles; the function of these genes in the development of butterfly wings is currently unknown. Many genes involved in ecdysone signaling were also significantly up-regulated during early pupal and late melanin stages and exhibited opposing patterns of expression relative to the ecdysone receptor. Finally, a comparison across four butterfly transcriptomes revealed 28 transcripts common to all four species that have no known homologs in other metazoans. This study provides a comprehensive list of differentially expressed transcripts during wing development, revealing potential candidate genes that may be involved in regulating butterfly wing patterns. Some differentially expressed genes have no known homologs possibly representing genes unique to butterflies. Results from this study also indicate that development of nymphalid wing patterns may arise not only from melanin and ommochrome pigments but also the pteridine pigment pathway.

Sex differences in functional activation patterns revealed by increased emotion processing demands.

PubMed

Hall, Geoffrey B C; Witelson, Sandra F; Szechtman, Henry; Nahmias, Claude

2004-02-09

Two [O(15)] PET studies assessed sex differences regional brain activation in the recognition of emotional stimuli. Study I revealed that the recognition of emotion in visual faces resulted in bilateral frontal activation in women, and unilateral right-sided activation in men. In study II, the complexity of the emotional face task was increased through tje addition of associated auditory emotional stimuli. Men again showed unilateral frontal activation, in this case to the left; whereas women did not show bilateral frontal activation, but showed greater limbic activity. These results suggest that when processing broader cross-modal emotional stimuli, men engage more in associative cognitive strategies while women draw more on primary emotional references.

The spatiotemporal order of signaling events unveils the logic of development signaling.

PubMed

Zhu, Hao; Owen, Markus R; Mao, Yanlan

2016-08-01

Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recognized that combinatorial use of and dynamic interactions among signaling pathways follow specific logic to control complex and accurate developmental signaling and patterning, but it remains elusive what such logic is, or even, what it looks like. We have developed a computational model for Drosophila eye development with innovated methods to reveal how interactions among multiple pathways control the dynamically generated hexagonal array of R8 cells. We obtained two novel findings. First, the coupling between the long-range inductive signals produced by the proneural Hh signaling and the short-range restrictive signals produced by the antineural Notch and EGFR signaling is essential for generating accurately spaced R8s. Second, the spatiotemporal orders of key signaling events reveal a robust pattern of lateral inhibition conducted by Ato-coordinated Notch and EGFR signaling to collectively determine R8 patterning. This pattern, stipulating the orders of signaling and comparable to the protocols of communication, may help decipher the well-appreciated but poorly defined logic of developmental signaling. The model is available upon request. hao.zhu@ymail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Mapping similarities in temporal parking occupancy behavior based on city-wide parking meter data

NASA Astrophysics Data System (ADS)

Bock, Fabian; Xia, Karen; Sester, Monika

2018-05-01

The search for a parking space is a severe and stressful problem for drivers in many cities. The provision of maps with parking space occupancy information assists drivers in avoiding the most crowded roads at certain times. Since parking occupancy reveals a repetitive pattern per day and per week, typical parking occupancy patterns can be extracted from historical data. In this paper, we analyze city-wide parking meter data from Hannover, Germany, for a full year. We describe an approach of clustering these parking meters to reduce the complexity of this parking occupancy information and to reveal areas with similar parking behavior. The parking occupancy at every parking meter is derived from a timestamp of ticket payment and the validity period of the parking tickets. The similarity of the parking meters is computed as the mean-squared deviation of the average daily patterns in parking occupancy at the parking meters. Based on this similarity measure, a hierarchical clustering is applied. The number of clusters is determined with the Davies-Bouldin Index and the Silhouette Index. Results show that, after extensive data cleansing, the clustering leads to three clusters representing typical parking occupancy day patterns. Those clusters differ mainly in the hour of the maximum occupancy. In addition, the lo-cations of parking meter clusters, computed only based on temporal similarity, also show clear spatial distinctions from other clusters.

Spatial Variation in Development of Epibenthic Assemblages in a Coastal Lagoon

NASA Astrophysics Data System (ADS)

Benedetti-Cecchi, L.; Rindi, F.; Bertocci, I.; Bulleri, F.; Cinelli, F.

2001-05-01

Spatial and temporal patterns in colonization of epibenthic assemblages were measured in a coastal lagoon on the west coast of Italy using recruitment panels. It was proposed that if the ecological processes influencing development of assemblages were homogeneous within the lagoon, then there should be no differences in mean cover of colonists nor in spatial patterns of variance in abundance in different areas of the lagoon. In contrast, heterogeneity in ecological processes affecting development would be revealed by spatial variability in colonization. To test these hypotheses, two sticks each with five replicate panels were placed 3-5 m apart in each of two sites 30-100 m apart in each of three locations 500-100 m apart; the experiment was repeated three times between April and December 1999, using new sites at each location each time. The results revealed considerable spatial variation in the structure of developing assemblages across locations. There were significant Location or Time×Location effects in the mean abundance of common taxa, such as Enteromorpha intestinalis , Ulva rigida, Cladophora spp., bryozoans and serpulids. Patterns in spatial variation differed among locations for these organisms. Collectively, the results supported a model of spatial heterogeneity in intensity of processes influencing patterns of recruitment and development of epibenthic assemblages in the Lagoon of Orbetello. The implications of these results for management of environmental problems in complex, variable habitats such as coastal lagoons, are discussed.

Molecular Cytogenetic Characterization of Multiple Intrachromosomal Rearrangements in Two Representatives of the Genus Turdus (Turdidae, Passeriformes)

PubMed Central

Kretschmer, Rafael; Gunski, Ricardo José; Garnero, Analía Del Valle; Furo, Ivanete de Oliveira; O'Brien, Patricia C. M.; Ferguson-Smith, Malcolm A.; de Oliveira, Edivaldo Herculano Corrêa

2014-01-01

Turdus rufiventris and Turdus albicollis, two songbirds belonging to the family Turdidae (Aves, Passeriformes) were studied by C-banding, 18S rDNA, as well as the use of whole chromosome probes derived from Gallus gallus (GGA) and Leucopternis albicollis (LAL). They showed very similar karyotypes, with 2n = 78 and the same pattern of distribution of heterochromatic blocks and hybridization patterns. However, the analysis of 18/28S rDNA has shown differences in the number of NOR-bearing chromosomes and ribosomal clusters. The hybridization pattern of GGA macrochromosomes was similar to the one found in songbirds studied by Fluorescent in situ hybridization, with fission of GGA 1 and GGA 4 chromosomes. In contrast, LAL chromosome paintings revealed a complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) on chromosome 2, which corresponds to GGA1q. The first inversion changed the chromosomal morphology and the second and third inversions changed the order of chromosome segments. Karyotype analysis in Turdus revealed that this genus has derived characteristics in relation to the putative avian ancestral karyotype, highlighting the importance of using new tools for analysis of chromosomal evolution in birds, such as the probes derived from L. albicollis, which make it possible to identify intrachromosomal rearrangements not visible with the use of GGA chromosome painting solely. PMID:25058578

The spatiotemporal order of signaling events unveils the logic of development signaling

PubMed Central

Zhu, Hao; Owen, Markus R.; Mao, Yanlan

2016-01-01

Motivation: Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recognized that combinatorial use of and dynamic interactions among signaling pathways follow specific logic to control complex and accurate developmental signaling and patterning, but it remains elusive what such logic is, or even, what it looks like. Results: We have developed a computational model for Drosophila eye development with innovated methods to reveal how interactions among multiple pathways control the dynamically generated hexagonal array of R8 cells. We obtained two novel findings. First, the coupling between the long-range inductive signals produced by the proneural Hh signaling and the short-range restrictive signals produced by the antineural Notch and EGFR signaling is essential for generating accurately spaced R8s. Second, the spatiotemporal orders of key signaling events reveal a robust pattern of lateral inhibition conducted by Ato-coordinated Notch and EGFR signaling to collectively determine R8 patterning. This pattern, stipulating the orders of signaling and comparable to the protocols of communication, may help decipher the well-appreciated but poorly defined logic of developmental signaling. Availability and implementation: The model is available upon request. Contact: hao.zhu@ymail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153573

Self-Organization of Embryonic Genetic Oscillators into Spatiotemporal Wave Patterns

PubMed Central

Tsiairis, Charisios D.; Aulehla, Alexander

2016-01-01

Summary In vertebrate embryos, somites, the precursor of vertebrae, form from the presomitic mesoderm (PSM), which is composed of cells displaying signaling oscillations. Cellular oscillatory activity leads to periodic wave patterns in the PSM. Here, we address the origin of such complex wave patterns. We employed an in vitro randomization and real-time imaging strategy to probe for the ability of cells to generate order from disorder. We found that, after randomization, PSM cells self-organized into several miniature emergent PSM structures (ePSM). Our results show an ordered macroscopic spatial arrangement of ePSM with evidence of an intrinsic length scale. Furthermore, cells actively synchronize oscillations in a Notch-signaling-dependent manner, re-establishing wave-like patterns of gene activity. We demonstrate that PSM cells self-organize by tuning oscillation dynamics in response to surrounding cells, leading to collective synchronization with an average frequency. These findings reveal emergent properties within an ensemble of coupled genetic oscillators. PMID:26871631

Effects of behavioral patterns and network topology structures on Parrondo’s paradox

PubMed Central

Ye, Ye; Cheong, Kang Hao; Cen, Yu-wan; Xie, Neng-gang

2016-01-01

A multi-agent Parrondo’s model based on complex networks is used in the current study. For Parrondo’s game A, the individual interaction can be categorized into five types of behavioral patterns: the Matthew effect, harmony, cooperation, poor-competition-rich-cooperation and a random mode. The parameter space of Parrondo’s paradox pertaining to each behavioral pattern, and the gradual change of the parameter space from a two-dimensional lattice to a random network and from a random network to a scale-free network was analyzed. The simulation results suggest that the size of the region of the parameter space that elicits Parrondo’s paradox is positively correlated with the heterogeneity of the degree distribution of the network. For two distinct sets of probability parameters, the microcosmic reasons underlying the occurrence of the paradox under the scale-free network are elaborated. Common interaction mechanisms of the asymmetric structure of game B, behavioral patterns and network topology are also revealed. PMID:27845430

Effects of behavioral patterns and network topology structures on Parrondo’s paradox

NASA Astrophysics Data System (ADS)

Ye, Ye; Cheong, Kang Hao; Cen, Yu-Wan; Xie, Neng-Gang

2016-11-01

A multi-agent Parrondo’s model based on complex networks is used in the current study. For Parrondo’s game A, the individual interaction can be categorized into five types of behavioral patterns: the Matthew effect, harmony, cooperation, poor-competition-rich-cooperation and a random mode. The parameter space of Parrondo’s paradox pertaining to each behavioral pattern, and the gradual change of the parameter space from a two-dimensional lattice to a random network and from a random network to a scale-free network was analyzed. The simulation results suggest that the size of the region of the parameter space that elicits Parrondo’s paradox is positively correlated with the heterogeneity of the degree distribution of the network. For two distinct sets of probability parameters, the microcosmic reasons underlying the occurrence of the paradox under the scale-free network are elaborated. Common interaction mechanisms of the asymmetric structure of game B, behavioral patterns and network topology are also revealed.

Pattern formation in mass conserving reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Brauns, Fridtjof; Halatek, Jacob; Frey, Erwin

We present a rigorous theoretical framework able to generalize and unify pattern formation for quantitative mass conserving reaction-diffusion models. Mass redistribution controls chemical equilibria locally. Separation of diffusive mass redistribution on the level of conserved species provides a general mathematical procedure to decompose complex reaction-diffusion systems into effectively independent functional units, and to reveal the general underlying bifurcation scenarios. We apply this framework to Min protein pattern formation and identify the mechanistic roles of both involved protein species. MinD generates polarity through phase separation, whereas MinE takes the role of a control variable regulating the existence of MinD phases. Hence, polarization and not oscillations is the generic core dynamics of Min proteins in vivo. This establishes an intrinsic mechanistic link between the Min system and a broad class of intracellular pattern forming systems based on bistability and phase separation (wave-pinning). Oscillations are facilitated by MinE redistribution and can be understood mechanistically as relaxation oscillations of the polarization direction.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PubMed

Mo, Delin; Zhu, Zhengmao; te Pas, Marinus F W; Li, Xinyun; Yang, Shulin; Wang, Heng; Wang, Huanling; Li, Kui

2008-06-30

In a previous screen to identify differentially expressed genes associated with embryonic development, the porcine PNAS-4 gene had been found. Considering differentially expressed genes in early stages of muscle development are potential candidate genes to improve meat quality and production efficiency, we determined how porcine PNAS-4 gene regulates meat production. Therefore, this gene has been sequenced, expression analyzed and associated with meat production traits. We cloned the full-length cDNA of porcine PNAS-4 gene encoding a protein of 194 amino acids which was expressed in the Golgi complex. This gene was mapped to chromosome 10, q11-16, in a region of conserved synteny with human chromosome 1 where the human homologous gene was localized. Real-time PCR revealed that PNAS-4 mRNA was widely expressed with highest expression levels in skeletal muscle followed by lymph, liver and other tissues, and showed a down-regulated expression pattern during prenatal development while a up-regulated expression pattern after weaning. Association analysis revealed that allele C of SNP A1813C was prevalent in Chinese indigenous breeds whereas A was dominant allele in Landrace and Large White, and the pigs with homozygous CC had a higher fat content than those of the pigs with other genotypes (P < 0.05). Porcine PNAS-4 protein tagged with green fluorescent protein accumulated in the Golgi complex, and its mRNA showed a widespread expression across many tissues and organs in pigs. It may be an important factor affecting the meat production efficiency, because its down-regulated expression pattern during early embryogenesis suggests involvement in increase of muscle fiber number. In addition, the SNP A1813C associated with fat traits might be a genetic marker for molecular-assisted selection in animal breeding.

Discovering amino acid patterns on binding sites in protein complexes

PubMed Central

Kuo, Huang-Cheng; Ong, Ping-Lin; Lin, Jung-Chang; Huang, Jen-Peng

2011-01-01

Discovering amino acid (AA) patterns on protein binding sites has recently become popular. We propose a method to discover the association relationship among AAs on binding sites. Such knowledge of binding sites is very helpful in predicting protein-protein interactions. In this paper, we focus on protein complexes which have protein-protein recognition. The association rule mining technique is used to discover geographically adjacent amino acids on a binding site of a protein complex. When mining, instead of treating all AAs of binding sites as a transaction, we geographically partition AAs of binding sites in a protein complex. AAs in a partition are treated as a transaction. For the partition process, AAs on a binding site are projected from three-dimensional to two-dimensional. And then, assisted with a circular grid, AAs on the binding site are placed into grid cells. A circular grid has ten rings: a central ring, the second ring with 6 sectors, the third ring with 12 sectors, and later rings are added to four sectors in order. As for the radius of each ring, we examined the complexes and found that 10Å is a suitable range, which can be set by the user. After placing these recognition complexes on the circular grid, we obtain mining records (i.e. transactions) from each sector. A sector is regarded as a record. Finally, we use the association rule to mine these records for frequent AA patterns. If the support of an AA pattern is larger than the predetermined minimum support (i.e. threshold), it is called a frequent pattern. With these discovered patterns, we offer the biologists a novel point of view, which will improve the prediction accuracy of protein-protein recognition. In our experiments, we produced the AA patterns by data mining. As a result, we found that arginine (arg) most frequently appears on the binding sites of two proteins in the recognition protein complexes, while cysteine (cys) appears the fewest. In addition, if we discriminate the shape of binding sites between concave and convex further, we discover that patterns {arg, glu, asp} and {arg, ser, asp} on the concave shape of binding sites in a protein more frequently (i.e. higher probability) make contact with {lys} or {arg} on the convex shape of binding sites in another protein. Thus, we can confidently achieve a rate of at least 78%. On the other hand {val, gly, lys} on the convex surface of binding sites in proteins is more frequently in contact with {asp} on the concave site of another protein, and the confidence achieved is over 81%. Applying data mining in biology can reveal more facts that may otherwise be ignored or not easily discovered by the naked eye. Furthermore, we can discover more relationships among AAs on binding sites by appropriately rotating these residues on binding sites from a three-dimension to two-dimension perspective. We designed a circular grid to deposit the data, which total to 463 records consisting of AAs. Then we used the association rules to mine these records for discovering relationships. The proposed method in this paper provides an insight into the characteristics of binding sites for recognition complexes. PMID:21464838

Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated 'subtype I', reveals a unique complex A/G/H/K/? mosaic pattern.

PubMed

Paraskevis, D; Magiorkinis, M; Vandamme, A M; Kostrikis, L G; Hatzakis, A

2001-03-01

Human immunodeficiency virus type 1 (HIV-1) has been classified into three main groups and 11 distinct subtypes. Moreover, several circulating recombinant forms (CRFs) of HIV-1 have been recently documented to have spread widely causing extensive HIV-1 epidemics. A subtype, initially designated I (CRF04_cpx), was documented in Cyprus and Greece and was found to comprise regions of sequence derived from subtypes A and G as well as regions of unclassified sequence. Re-analysis of the three full-length CRF04_cpx sequences that were available revealed a mosaic genomic organization of unique complexity comprising regions of sequence from at least five distinct subtypes, A, G, H, K and unclassified regions. These strains account for approximately 2% of the total HIV-1-infected population in Greece, thus providing evidence of the great capability of HIV-1 to recombine and produce highly divergent strains which can be spread successfully through different infection routes.

Narrow-Front Loop Migration in a Population of the Common Cuckoo Cuculus canorus, as Revealed by Satellite Telemetry

PubMed Central

Willemoes, Mikkel; Strandberg, Roine; Klaassen, Raymond H. G.; Tøttrup, Anders P.; Vardanis, Yannis; Howey, Paul W.; Thorup, Kasper; Wikelski, Martin; Alerstam, Thomas

2014-01-01

Narrow migration corridors known in diurnal, social migrants such as raptors, storks and geese are thought to be caused by topographical leading line effects in combination with learning detailed routes across generations. Here, we document narrow-front migration in a nocturnal, solitary migrant, the common cuckoo Cuculus canorus, using satellite telemetry. We tracked the migration of adult cuckoos from the breeding grounds in southern Scandinavia (n = 8), to wintering sites in south-western Central Africa (n = 6) and back to the breeding grounds (n = 3). Migration patterns were very complex; in addition to the breeding and wintering sites, six different stopover sites were identified during the 16,000 km annual route that formed a large-scale clockwise loop. Despite this complexity, individuals showed surprisingly similar migration patterns, with very little variation between routes. We compared observed tracks with simulated routes based on vector orientation (with and without effects of barriers on orientation and survival). Observed distances between routes were often significantly smaller than expected if the routes were established on the basis of an innate vector orientation programme. Average distance between individuals in eastern Sahel after having migrated more than 5,000 km for example, was merely 164 km. This implies that more sophisticated inherent guiding mechanisms, possibly involving elements of intermediate goal area navigation or more elaborate external cues, are necessary to explain the complex narrow-front migration pattern observed for the cuckoos in this study. PMID:24421890

Patterns of task and network actions performed by navigators to facilitate cancer care.

PubMed

Clark, Jack A; Parker, Victoria A; Battaglia, Tracy A; Freund, Karen M

2014-01-01

Patient navigation is a widely implemented intervention to facilitate access to care and reduce disparities in cancer care, but the activities of navigators are not well characterized. The aim of this study is to describe what patient navigators actually do and explore patterns of activity that clarify the roles they perform in facilitating cancer care. We conducted field observations of nine patient navigation programs operating in diverse health settings of the national patient navigation research program, including 34 patient navigators, each observed an average of four times. Trained observers used a structured observation protocol to code as they recorded navigator actions and write qualitative field notes capturing all activities in 15-minute intervals during observations ranging from 2 to 7 hours; yielding a total of 133 observations. Rates of coded activity were analyzed using numerical cluster analysis of identified patterns, informed by qualitative analysis of field notes. Six distinct patterns of navigator activity were identified, which differed most relative to how much time navigators spent directly interacting with patients and how much time they spent dealing with medical records and documentation tasks. Navigator actions reveal a complex set of roles in which navigators both provide the direct help to patients denoted by their title and also carry out a variety of actions that function to keep the health system operating smoothly. Working to navigate patients through complex health services entails working to repair the persistent challenges of health services that can render them inhospitable to patients. The organizations that deploy navigators might learn from navigators' efforts and explore alternative approaches, structures, or systems of care in addressing both the barriers patients face and the complex solutions navigators create in helping patients.

Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

PubMed

Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

2015-01-01

Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional) states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported) face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people) cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits) of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

Stability of spermine oxidase to thermal and chemical denaturation: comparison with bovine serum amine oxidase.

PubMed

Cervelli, Manuela; Leonetti, Alessia; Cervoni, Laura; Ohkubo, Shinji; Xhani, Marla; Stano, Pasquale; Federico, Rodolfo; Polticelli, Fabio; Mariottini, Paolo; Agostinelli, Enzo

2016-10-01

Spermine oxidase (SMOX) is a flavin-containing enzyme that specifically oxidizes spermine to produce spermidine, 3-aminopropanaldehyde and hydrogen peroxide. While no crystal structure is available for any mammalian SMOX, X-ray crystallography showed that the yeast Fms1 polyamine oxidase has a dimeric structure. Based on this scenario, we have investigated the quaternary structure of the SMOX protein by native gel electrophoresis, which revealed a composite gel band pattern, suggesting the formation of protein complexes. All high-order protein complexes are sensitive to reducing conditions, showing that disulfide bonds were responsible for protein complexes formation. The major gel band other than the SMOX monomer is the covalent SMOX homodimer, which was disassembled by increasing the reducing conditions, while being resistant to other denaturing conditions. Homodimeric and monomeric SMOXs are catalytically active, as revealed after gel staining for enzymatic activity. An engineered SMOX mutant deprived of all but two cysteine residues was prepared and characterized experimentally, resulting in a monomeric species. High-sensitivity differential scanning calorimetry of SMOX was compared with that of bovine serum amine oxidase, to analyse their thermal stability. Furthermore, enzymatic activity assays and fluorescence spectroscopy were used to gain insight into the unfolding process.

Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration

PubMed Central

Li, Song; Avera, Bethany N.; Strahm, Brian D.; Badgley, Brian D.

2017-01-01

ABSTRACT Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages. PMID:28476769

Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration.

PubMed

Sun, Shan; Li, Song; Avera, Bethany N; Strahm, Brian D; Badgley, Brian D

2017-07-15

Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages. Copyright © 2017 American Society for Microbiology.

Direct modulation of aberrant brain network connectivity through real-time NeuroFeedback.

PubMed

Ramot, Michal; Kimmich, Sara; Gonzalez-Castillo, Javier; Roopchansingh, Vinai; Popal, Haroon; White, Emily; Gotts, Stephen J; Martin, Alex

2017-09-16

The existence of abnormal connectivity patterns between resting state networks in neuropsychiatric disorders, including Autism Spectrum Disorder (ASD), has been well established. Traditional treatment methods in ASD are limited, and do not address the aberrant network structure. Using real-time fMRI neurofeedback, we directly trained three brain nodes in participants with ASD, in which the aberrant connectivity has been shown to correlate with symptom severity. Desired network connectivity patterns were reinforced in real-time, without participants' awareness of the training taking place. This training regimen produced large, significant long-term changes in correlations at the network level, and whole brain analysis revealed that the greatest changes were focused on the areas being trained. These changes were not found in the control group. Moreover, changes in ASD resting state connectivity following the training were correlated to changes in behavior, suggesting that neurofeedback can be used to directly alter complex, clinically relevant network connectivity patterns.

Animating streamlines with repeated asymmetric patterns for steady flow visualization

NASA Astrophysics Data System (ADS)

Yeh, Chih-Kuo; Liu, Zhanping; Lee, Tong-Yee

2012-01-01

Animation provides intuitive cueing for revealing essential spatial-temporal features of data in scientific visualization. This paper explores the design of Repeated Asymmetric Patterns (RAPs) in animating evenly-spaced color-mapped streamlines for dense accurate visualization of complex steady flows. We present a smooth cyclic variable-speed RAP animation model that performs velocity (magnitude) integral luminance transition on streamlines. This model is extended with inter-streamline synchronization in luminance varying along the tangential direction to emulate orthogonal advancing waves from a geometry-based flow representation, and then with evenly-spaced hue differing in the orthogonal direction to construct tangential flow streaks. To weave these two mutually dual sets of patterns, we propose an energy-decreasing strategy that adopts an iterative yet efficient procedure for determining the luminance phase and hue of each streamline in HSL color space. We also employ adaptive luminance interleaving in the direction perpendicular to the flow to increase the contrast between streamlines.

Gemella sanguinis endocarditis with c-ANCA/anti-PR-3-associated immune complex necrotizing glomerulonephritis with a ‘full-house’ pattern on immunofluorescence microscopy

PubMed Central

Rousseau-Gagnon, Mathieu; Riopel, Julie; Desjardins, Anne; Garceau, Daniel; Agharazii, Mohsen; Desmeules, Simon

2013-01-01

A 67-year-old man was evaluated for haematuria, with a rising creatinine level from 88 to 906 µmol/L and positive c-anti-neutrophil cytoplasm antibody (ANCA)/anti-proteinase 3 (anti-PR3). A kidney biopsy revealed necrotizing glomerulonephritis with a ‘full-house’ pattern on immunofluorescence microscopy. Echocardiography and blood cultures growing Gemella sanguinis diagnosed endocarditis. Dialysis was required for a month. Three months later, following valve replacement, glucocorticoids and 2 months of antibiotic therapy, the creatinine level decreased to 62 µmol/L and c-ANCA/anti-PR3 disappeared. This first case of c-ANCA/anti-PR3 positive glomerulonephritis with a ‘full-house’ immunofluorescence pattern due to bacterial endocarditis underlines the importance of ruling out infection with ANCA positivity or kidney biopsy suggestive of lupus nephritis. PMID:26064489

The Oncoprotein BRD4-NUT Generates Aberrant Histone Modification Patterns.

PubMed

Zee, Barry M; Dibona, Amy B; Alekseyenko, Artyom A; French, Christopher A; Kuroda, Mitzi I

2016-01-01

Defects in chromatin proteins frequently manifest in diseases. A striking case of a chromatin-centric disease is NUT-midline carcinoma (NMC), which is characterized by expression of NUT as a fusion partner most frequently with BRD4. ChIP-sequencing studies from NMC patients revealed that BRD4-NUT (B4N) covers large genomic regions and elevates transcription within these domains. To investigate how B4N modulates chromatin, we performed affinity purification of B4N when ectopically expressed in 293-TREx cells and quantified the associated histone posttranslational modifications (PTM) using proteomics. We observed significant enrichment of acetylation particularly on H3 K18 and of combinatorial patterns such as H3 K27 acetylation paired with K36 methylation. We postulate that B4N complexes override the preexisting histone code with new PTM patterns that reflect aberrant transcription and that epigenetically modulate the nucleosome environment toward the NMC state.

The Oncoprotein BRD4-NUT Generates Aberrant Histone Modification Patterns

PubMed Central

Zee, Barry M.; Dibona, Amy B.; Alekseyenko, Artyom A.; French, Christopher A.; Kuroda, Mitzi I.

2016-01-01

Defects in chromatin proteins frequently manifest in diseases. A striking case of a chromatin-centric disease is NUT-midline carcinoma (NMC), which is characterized by expression of NUT as a fusion partner most frequently with BRD4. ChIP-sequencing studies from NMC patients revealed that BRD4-NUT (B4N) covers large genomic regions and elevates transcription within these domains. To investigate how B4N modulates chromatin, we performed affinity purification of B4N when ectopically expressed in 293-TREx cells and quantified the associated histone posttranslational modifications (PTM) using proteomics. We observed significant enrichment of acetylation particularly on H3 K18 and of combinatorial patterns such as H3 K27 acetylation paired with K36 methylation. We postulate that B4N complexes override the preexisting histone code with new PTM patterns that reflect aberrant transcription and that epigenetically modulate the nucleosome environment toward the NMC state. PMID:27698495

Gas-water two-phase flow characterization with Electrical Resistance Tomography and Multivariate Multiscale Entropy analysis.

PubMed

Tan, Chao; Zhao, Jia; Dong, Feng

2015-03-01

Flow behavior characterization is important to understand gas-liquid two-phase flow mechanics and further establish its description model. An Electrical Resistance Tomography (ERT) provides information regarding flow conditions at different directions where the sensing electrodes implemented. We extracted the multivariate sample entropy (MSampEn) by treating ERT data as a multivariate time series. The dynamic experimental results indicate that the MSampEn is sensitive to complexity change of flow patterns including bubbly flow, stratified flow, plug flow and slug flow. MSampEn can characterize the flow behavior at different direction of two-phase flow, and reveal the transition between flow patterns when flow velocity changes. The proposed method is effective to analyze two-phase flow pattern transition by incorporating information of different scales and different spatial directions. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

A deployment of fine-grained sensor network and empirical analysis of urban temperature.

PubMed

Thepvilojanapong, Niwat; Ono, Takahiro; Tobe, Yoshito

2010-01-01

Temperature in an urban area exhibits a complicated pattern due to complexity of infrastructure. Despite geographical proximity, structures of a group of buildings and streets affect changes in temperature. To investigate the pattern of fine-grained distribution of temperature, we installed a densely distributed sensor network called UScan. In this paper, we describe the system architecture of UScan as well as experience learned from installing 200 sensors in downtown Tokyo. The field experiment of UScan system operated for two months to collect long-term urban temperature data. To analyze the collected data in an efficient manner, we propose a lightweight clustering methodology to study the correlation between the pattern of temperature and various environmental factors including the amount of sunshine, the width of streets, and the existence of trees. The analysis reveals meaningful results and asserts the necessity of fine-grained deployment of sensors in an urban area.

Three-dimensional visualization of cultural clusters in the 1878 yellow fever epidemic of New Orleans

PubMed Central

Curtis, Andrew J

2008-01-01

Background An epidemic may exhibit different spatial patterns with a change in geographic scale, with each scale having different conduits and impediments to disease spread. Mapping disease at each of these scales often reveals different cluster patterns. This paper will consider this change of geographic scale in an analysis of yellow fever deaths for New Orleans in 1878. Global clustering for the whole city, will be followed by a focus on the French Quarter, then clusters of that area, and finally street-level patterns of a single cluster. The three-dimensional visualization capabilities of a GIS will be used as part of a cluster creation process that incorporates physical buildings in calculating mortality-to-mortality distance. Including nativity of the deceased will also capture cultural connection. Results Twenty-two yellow fever clusters were identified for the French Quarter. These generally mirror the results of other global cluster and density surfaces created for the entire epidemic in New Orleans. However, the addition of building-distance, and disease specific time frame between deaths reveal that disease spread contains a cultural component. Same nativity mortality clusters emerge in a similar time frame irrespective of proximity. Italian nativity mortalities were far more densely grouped than any of the other cohorts. A final examination of mortalities for one of the nativity clusters reveals that further sub-division is present, and that this pattern would only be revealed at this scale (street level) of investigation. Conclusion Disease spread in an epidemic is complex resulting from a combination of geographic distance, geographic distance with specific connection to the built environment, disease-specific time frame between deaths, impediments such as herd immunity, and social or cultural connection. This research has shown that the importance of cultural connection may be more important than simple proximity, which in turn might mean traditional quarantine measures should be re-evaluated. PMID:18721469

Three-dimensional visualization of cultural clusters in the 1878 yellow fever epidemic of New Orleans.

PubMed

Curtis, Andrew J

2008-08-22

An epidemic may exhibit different spatial patterns with a change in geographic scale, with each scale having different conduits and impediments to disease spread. Mapping disease at each of these scales often reveals different cluster patterns. This paper will consider this change of geographic scale in an analysis of yellow fever deaths for New Orleans in 1878. Global clustering for the whole city, will be followed by a focus on the French Quarter, then clusters of that area, and finally street-level patterns of a single cluster. The three-dimensional visualization capabilities of a GIS will be used as part of a cluster creation process that incorporates physical buildings in calculating mortality-to-mortality distance. Including nativity of the deceased will also capture cultural connection. Twenty-two yellow fever clusters were identified for the French Quarter. These generally mirror the results of other global cluster and density surfaces created for the entire epidemic in New Orleans. However, the addition of building-distance, and disease specific time frame between deaths reveal that disease spread contains a cultural component. Same nativity mortality clusters emerge in a similar time frame irrespective of proximity. Italian nativity mortalities were far more densely grouped than any of the other cohorts. A final examination of mortalities for one of the nativity clusters reveals that further sub-division is present, and that this pattern would only be revealed at this scale (street level) of investigation. Disease spread in an epidemic is complex resulting from a combination of geographic distance, geographic distance with specific connection to the built environment, disease-specific time frame between deaths, impediments such as herd immunity, and social or cultural connection. This research has shown that the importance of cultural connection may be more important than simple proximity, which in turn might mean traditional quarantine measures should be re-evaluated.

Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition

PubMed Central

Blatter, Markus; Cléry, Antoine; Damberger, Fred F.

2017-01-01

Abstract The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes. PMID:28505313

Elucidation of Hydrogen Bonding Patterns in Ligand-Free, Lactose- and Glycerol-Bound Galectin-3C by Neutron Crystallography to Guide Drug Design.

PubMed

Manzoni, Francesco; Wallerstein, Johan; Schrader, Tobias E; Ostermann, Andreas; Coates, Leighton; Akke, Mikael; Blakeley, Matthew P; Oksanen, Esko; Logan, Derek T

2018-05-24

The medically important drug target galectin-3 binds galactose-containing moieties on glycoproteins through an intricate pattern of hydrogen bonds to a largely polar surface-exposed binding site. All successful inhibitors of galectin-3 to date have been based on mono- or disaccharide cores closely resembling natural ligands. A detailed understanding of the H-bonding networks in these natural ligands will provide an improved foundation for the design of novel inhibitors. Neutron crystallography is an ideal technique to reveal the geometry of hydrogen bonds because the positions of hydrogen atoms are directly detected rather than being inferred from the positions of heavier atoms as in X-ray crystallography. We present three neutron crystal structures of the C-terminal carbohydrate recognition domain of galectin-3: the ligand-free form and the complexes with the natural substrate lactose and with glycerol, which mimics important interactions made by lactose. The neutron crystal structures reveal unambiguously the exquisite fine-tuning of the hydrogen bonding pattern in the binding site to the natural disaccharide ligand. The ligand-free structure shows that most of these hydrogen bonds are preserved even when the polar groups of the ligand are replaced by water molecules. The protonation states of all histidine residues in the protein are also revealed and correlate well with NMR observations. The structures give a solid starting point for molecular dynamics simulations and computational estimates of ligand binding affinity that will inform future drug design.

Subduction zone locking, strain partitioning, intraplate deformation and their implications to Seismic Hazards in South America

NASA Astrophysics Data System (ADS)

Galgana, G. A.; Mahdyiar, M.; Shen-Tu, B.; Pontbriand, C. W.; Klein, E.; Wang, F.; Shabestari, K.; Yang, W.

2014-12-01

We analyze active crustal deformation in South America (SA) using published GPS observations and historic seismicity along the Nazca Trench and the active Ecuador-Colombia-Venezuela Plate boundary Zone. GPS-constrained kinematisc models that incorporate block and continuum techniques are used to assess patterns of regional tectonic deformation and its implications to seismic potential. We determine interplate coupling distributions, fault slip-rates, and intraplate crustal strain rates in combination with historic earthquakes within 40 seismic zones crust to provide moment rate constraints. Along the Nazca subduction zone, we resolve a series of highly coupled patches, interpreted as high-friction producing "asperities" beneath the coasts of Ecuador, Peru and Chile. These include areas responsible for the 2010 Mw 8.8 Maule Earthquake and the 2014 Mw 8.2 Iquique Earthquake. Predicted tectonic block motions and fault slip rates reveal that the northern part of South America deforms rapidly, with crustal fault slip rates as much as ~20 mm/a. Fault slip and locking patterns reveal that the Oca Ancón-Pilar-Boconó fault system plays a key role in absorbing most of the complex eastward and southward convergence patterns in northeastern Colombia and Venezuela, while the near-parallel system of faults in eastern Colombia and Ecuador absorb part of the transpressional motion due to the ~55 mm/a Nazca-SA plate convergence. These kinematic models, in combination with historic seismicity rates, provide moment deficit rates that reveal regions with high seismic potential, such as coastal Ecuador, Bucaramanga, Arica and Antofagasta. We eventually use the combined information from moment rates and fault coupling patterns to further constrain stochastic seismic hazard models of the region by implementing realistic trench rupture scenarios (see Mahdyiar et al., this volume).

Genomic Analyses Reveal the Common Occurrence and Complexity of Plasmodium vivax Relapses in Cambodia

PubMed Central

Popovici, Jean; Friedrich, Lindsey R.; Kim, Saorin; Bin, Sophalai; Run, Vorleak; Lek, Dysoley

2018-01-01

ABSTRACT Plasmodium vivax parasites have a unique dormant stage that can cause relapses weeks or months after the initial infection. These dormant parasites are among the main challenges of vivax malaria control as they constitute a reservoir that is difficult to eliminate. Since field studies are confounded by reinfections and possible recrudescence of drug-resistant parasites, most analyses of P. vivax relapses have focused on travelers returning from regions of malaria endemicity. However, it is not clear whether these individuals accurately recapitulate the relapse patterns of repeatedly infected individuals residing in areas of endemicity. Here, we present analyses of vivax malaria patients enrolled in a tightly controlled field study in Cambodia. After antimalarial drug treatment was administered, we relocated 20 individuals to a nontransmission area and followed them for 60 days, with blood collection performed every second day. Our analyses reveal that 60% of the patients relapsed during the monitoring period. Using whole-genome sequencing and high-throughput genotyping, we showed that relapses in Cambodia are often polyclonal and that the relapsing parasites harbor various degrees of relatedness to the parasites present in the initial infection. Our analyses also showed that clone populations differed dynamically, with new clones emerging during the course of the relapsing infections. Overall, our study data show that it is possible to investigate the patterns, dynamics, and diversity of P. vivax relapses of individuals living in a region of malaria endemicity and reveal that P. vivax relapses are much more pervasive and complex than previously considered. (This study has been registered at ClinicalTrials.gov under registration no. NCT02118090.) PMID:29362233

Advances on molecular mechanism of the adaptive evolution of Chiroptera (bats).

PubMed

Yunpeng, Liang; Li, Yu

2015-01-01

As the second biggest animal group in mammals, Chiroptera (bats) demonstrates many unique adaptive features in terms of flight, echolocation, auditory acuity, feeding habit, hibernation and immune defense, providing an excellent system for understanding the molecular basis of how organisms adapt to the living environments encountered. In this review, we summarize the researches on the molecular mechanism of the adaptive evolution of Chiroptera, especially the recent researches at the genome levels, suggesting a far more complex evolutionary pattern and functional diversity than previously thought. In the future, along with the increasing numbers of Chiroptera species genomes available, new evolutionary patterns and functional divergence will be revealed, which can promote the further understanding of this animal group and the molecular mechanism of adaptive evolution.

Numerical Simulation of the ``Fluid Mechanical Sewing Machine''

NASA Astrophysics Data System (ADS)

Brun, Pierre-Thomas; Audoly, Basile; Ribe, Neil

2011-11-01

A thin thread of viscous fluid falling onto a moving conveyor belt generates a wealth of complex ``stitch'' patterns depending on the belt speed and the fall height. To understand the rich nonlinear dynamics of this system, we have developed a new numerical code for simulating unsteady viscous threads, based on a discrete description of the geometry and a variational formulation for the viscous stresses. The code successfully reproduces all major features of the experimental state diagram of Morris et al. (Phys. Rev. E 2008). Fourier analysis of the motion of the thread's contact point with the belt suggests a new classification of the observed patterns, and reveals that the system behaves as a nonlinear oscillator coupling the pendulum modes of the thread.

Spatial Distribution of Cyanobacteria in Modern Stromatolites

NASA Technical Reports Server (NTRS)

Prufert-Bebout, Lee; Dacles-Mariani, Jennifer; Herbert, Alice; DeVincenzi, Donald (Technical Monitor)

2001-01-01

Living stromatolites consist of complex microbial communities with distinct distribution patterns for different microbial groups. The cyanobacterial populations of Highborne Cay Bahamas exemplify this phenomenon. Field observations reveal distinct distribution patterns for several of these cyanobacterial species. To date 10 different cyanobacterial cultures, including both filamentous and endolithic species, have been isolated from these stromatolites. We will present data on the growth and motility characteristics as well as on the nutritional requirements of these isolates. These data will then be correlated with the field observed distributions for these species. Lastly laboratory simulations of stromatolites grown under various conditions of irradiance, flow and cyanobacterial community composition will be presented. These experiments allow us to evaluate our predictions regarding controls on cyanobacterial distribution.

Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

PubMed

Sturgis, James N; Niederman, Robert A

2008-01-01

Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

New water soluble heterometallic complex showing unpredicted coordination modes of EDTA

NASA Astrophysics Data System (ADS)

Mudsainiyan, R. K.; Jassal, A. K.; Chawla, S. K.

2015-10-01

A mesoporous 3D polymeric complex (I) having formula {[Zr(IV)O-μ3-(EDTA)Fe(III)OH]·H2O}n has been crystallized and characterized by various techniques. Single-crystal X-ray diffraction analysis revealed that complex (I) crystallized in chiral monoclinic space group Cc (space group no. 9) with unexpected coordination modes of EDTA and mixture of two transition metal ions. In this complex, the coordination number of Zr(IV) ion is seven where four carboxylate oxygen atoms, two nitrogen atoms, one oxide atom are coordinating with Zr(IV). Fe(III) is four coordinated and its coordination environment is composed of three different carboxylic oxygen atoms from three different EDTA and one oxygen atom of -OH group. The structure consists of 4-c and 16-c (2-nodal) net with new topology and point symbol for net is (336·454·530)·(36). TGA study and XRPD pattern showed that the coordination polymer is quite stable even after losing water molecule and -OH ion. Quenching behavior in fluorescence of ligand is observed by complexation with transition metal ions is due to n-π* transition. The SEM micrograph shows the morphology of complex (I) exhibits spherical shape with size ranging from 50 to 280 nm. The minimum N2 (SBET=8.7693 m2/g) and a maximum amount of H2 (high surface area=1044.86 m2/g (STP)) could be adsorbed at 77 K. From DLS study, zeta potential is calculated i.e. -7.94 shows the negative charges on the surface of complex. Hirshfeld surface analysis and fingerprint plots revealed influence of weak or non bonding interactions in crystal packing of complex.

Reconfiguration of Brain Network Architectures between Resting-State and Complexity-Dependent Cognitive Reasoning.

PubMed

Hearne, Luke J; Cocchi, Luca; Zalesky, Andrew; Mattingley, Jason B

2017-08-30

Our capacity for higher cognitive reasoning has a measurable limit. This limit is thought to arise from the brain's capacity to flexibly reconfigure interactions between spatially distributed networks. Recent work, however, has suggested that reconfigurations of task-related networks are modest when compared with intrinsic "resting-state" network architecture. Here we combined resting-state and task-driven functional magnetic resonance imaging to examine how flexible, task-specific reconfigurations associated with increasing reasoning demands are integrated within a stable intrinsic brain topology. Human participants (21 males and 28 females) underwent an initial resting-state scan, followed by a cognitive reasoning task involving different levels of complexity, followed by a second resting-state scan. The reasoning task required participants to deduce the identity of a missing element in a 4 × 4 matrix, and item difficulty was scaled parametrically as determined by relational complexity theory. Analyses revealed that external task engagement was characterized by a significant change in functional brain modules. Specifically, resting-state and null-task demand conditions were associated with more segregated brain-network topology, whereas increases in reasoning complexity resulted in merging of resting-state modules. Further increments in task complexity did not change the established modular architecture, but affected selective patterns of connectivity between frontoparietal, subcortical, cingulo-opercular, and default-mode networks. Larger increases in network efficiency within the newly established task modules were associated with higher reasoning accuracy. Our results shed light on the network architectures that underlie external task engagement, and highlight selective changes in brain connectivity supporting increases in task complexity. SIGNIFICANCE STATEMENT Humans have clear limits in their ability to solve complex reasoning problems. It is thought that such limitations arise from flexible, moment-to-moment reconfigurations of functional brain networks. It is less clear how such task-driven adaptive changes in connectivity relate to stable, intrinsic networks of the brain and behavioral performance. We found that increased reasoning demands rely on selective patterns of connectivity within cortical networks that emerged in addition to a more general, task-induced modular architecture. This task-driven architecture reverted to a more segregated resting-state architecture both immediately before and after the task. These findings reveal how flexibility in human brain networks is integral to achieving successful reasoning performance across different levels of cognitive demand. Copyright © 2017 the authors 0270-6474/17/378399-13$15.00/0.

Temporal patterns of rat behaviour in the central platform of the elevated plus maze. Comparative analysis between male subjects of strains with different basal levels of emotionality.

PubMed

Casarrubea, M; Faulisi, F; Caternicchia, F; Santangelo, A; Di Giovanni, G; Benigno, A; Magnusson, M S; Crescimanno, G

2016-08-01

We have analyzed the temporal patterns of behaviour of male rats of the Wistar and DA/Han strains on the central platform of the elevated plus maze. The ethogram encompassed 10 behavioural elements. Durations, frequencies and latencies showed quantitative differences as to walking and sniffing activities. Wistar rats displayed significantly lower latency and significantly higher durations and frequencies of walking activities. DA/Han rats showed a significant increase of sniffing duration. In addition, DA/Han rats showed a significantly higher amount of time spent in the central platform. Multivariate T-pattern analysis revealed differences in the temporal organization of behaviour of the two rat strains. DA/Han rats showed (a) higher behavioural complexity and variability and (b) a significantly higher mean number of T-patterns than Wistar rats. Taken together, T-pattern analysis of behaviour in the centre of the elevated plus maze can noticeably improve the detection of subtle features of anxiety related behaviour. We suggest that T-pattern analysis could be used as sensitive tool to test the action of anxiolytic and anxiogenic manipulations. Copyright © 2015 Elsevier B.V. All rights reserved.

Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia.

PubMed

Chávez-Galarza, Julio; Henriques, Dora; Johnston, J Spencer; Carneiro, Miguel; Rufino, José; Patton, John C; Pinto, M Alice

2015-06-01

Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern-southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity. © 2015 John Wiley & Sons Ltd.

Comprehensive Expression Map of Transcription Regulators in the Adult Zebrafish Telencephalon Reveals Distinct Neurogenic Niches

PubMed Central

Diotel, Nicolas; Rodriguez Viales, Rebecca; Armant, Olivier; März, Martin; Ferg, Marco; Rastegar, Sepand; Strähle, Uwe

2015-01-01

The zebrafish has become a model to study adult vertebrate neurogenesis. In particular, the adult telencephalon has been an intensely studied structure in the zebrafish brain. Differential expression of transcriptional regulators (TRs) is a key feature of development and tissue homeostasis. Here we report an expression map of 1,202 TR genes in the telencephalon of adult zebrafish. Our results are summarized in a database with search and clustering functions to identify genes expressed in particular regions of the telencephalon. We classified 562 genes into 13 distinct patterns, including genes expressed in the proliferative zone. The remaining 640 genes displayed unique and complex patterns of expression and could thus not be grouped into distinct classes. The neurogenic ventricular regions express overlapping but distinct sets of TR genes, suggesting regional differences in the neurogenic niches in the telencephalon. In summary, the small telencephalon of the zebrafish shows a remarkable complexity in TR gene expression. The adult zebrafish telencephalon has become a model to study neurogenesis. We established the expression pattern of more than 1200 transcription regulators (TR) in the adult telencephalon. The neurogenic regions express overlapping but distinct sets of TR genes suggesting regional differences in the neurogenic potential. J. Comp. Neurol. 523:1202–1221, 2015. © 2015 Wiley Periodicals, Inc. PMID:25556858

Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches.

PubMed

Diotel, Nicolas; Rodriguez Viales, Rebecca; Armant, Olivier; März, Martin; Ferg, Marco; Rastegar, Sepand; Strähle, Uwe

2015-06-01

The zebrafish has become a model to study adult vertebrate neurogenesis. In particular, the adult telencephalon has been an intensely studied structure in the zebrafish brain. Differential expression of transcriptional regulators (TRs) is a key feature of development and tissue homeostasis. Here we report an expression map of 1,202 TR genes in the telencephalon of adult zebrafish. Our results are summarized in a database with search and clustering functions to identify genes expressed in particular regions of the telencephalon. We classified 562 genes into 13 distinct patterns, including genes expressed in the proliferative zone. The remaining 640 genes displayed unique and complex patterns of expression and could thus not be grouped into distinct classes. The neurogenic ventricular regions express overlapping but distinct sets of TR genes, suggesting regional differences in the neurogenic niches in the telencephalon. In summary, the small telencephalon of the zebrafish shows a remarkable complexity in TR gene expression. The adult zebrafish telencephalon has become a model to study neurogenesis. We established the expression pattern of more than 1200 transcription regulators (TR) in the adult telencephalon. The neurogenic regions express overlapping but distinct sets of TR genes suggesting regional differences in the neurogenic potential. © 2015 Wiley Periodicals, Inc.

Interactions between rate processes with different timescales explain counterintuitive foraging patterns of arctic wintering eiders

PubMed Central

Heath, Joel P.; Gilchrist, H. Grant; Ydenberg, Ronald C.

2010-01-01

To maximize fitness, animals must respond to a variety of processes that operate at different rates or timescales. Appropriate decisions could therefore involve complex interactions among these processes. For example, eiders wintering in the arctic sea ice must consider locomotion and physiology of diving for benthic invertebrates, digestive processing rate and a nonlinear decrease in profitability of diving as currents increase over the tidal cycle. Using a multi-scale dynamic modelling approach and continuous field observations of individuals, we demonstrate that the strategy that maximizes long-term energy gain involves resting during the most profitable foraging period (slack currents). These counterintuitive foraging patterns are an adaptive trade-off between multiple overlapping rate processes and cannot be explained by classical rate-maximizing optimization theory, which only considers a single timescale and predicts a constant rate of foraging. By reducing foraging and instead digesting during slack currents, eiders structure their activity in order to maximize long-term energetic gain over an entire tide cycle. This study reveals how counterintuitive patterns and a complex functional response can result from a simple trade-off among several overlapping rate processes, emphasizing the necessity of a multi-scale approach for understanding adaptive routines in the wild and evaluating mechanisms in ecological time series. PMID:20504814

Complex patterns of multivariate selection on the ejaculate of a broadcast spawning marine invertebrate.

PubMed

Fitzpatrick, John L; Simmons, Leigh W; Evans, Jonathan P

2012-08-01

Assessing how selection operates on several, potentially interacting, components of the ejaculate is a challenging endeavor. Ejaculates can be subject to natural and/or sexual selection, which can impose both linear (directional) and nonlinear (stabilizing, disruptive, and correlational) selection on different ejaculate components. Most previous studies have examined linear selection of ejaculate components and, consequently, we know very little about patterns of nonlinear selection on the ejaculate. Even less is known about how selection acts on the ejaculate as a functionally integrated unit, despite evidence of covariance among ejaculate components. Here, we assess how selection acts on multiple ejaculate components simultaneously in the broadcast spawning sessile invertebrate Mytilus galloprovincialis using the statistical tools of multivariate selection analyses. Our analyses of relative fertilization rates revealed complex patterns of selection on sperm velocity, motility, and morphology. Interestingly, the most successful ejaculates were made up of slower swimming sperm with relatively low percentages of motile cells, and sperm with smaller head volumes that swam in highly pronounced curved swimming trajectories. These results are consistent with an emerging body of literature on fertilization kinetics in broadcast spawners, and shed light on the fundamental nature of selection acting on the ejaculate as a functionally integrated unit. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Molecular Microbial Analysis of Lactobacillus Strains Isolated from the Gut of Calves for Potential Probiotic Use

PubMed Central

Soto, Lorena P.; Frizzo, Laureano S.; Bertozzi, Ezequiel; Avataneo, Elizabeth; Sequeira, Gabriel J.; Rosmini, Marcelo R.

2010-01-01

The intestinal microbiota has an influence on the growth and health status of the hosts. This is of particular interest in animals reared using intensive farming practices. Hence, it is necessary to know more about complexity of the beneficial intestinal microbiota. The use of molecular methods has revolutionized microbial identification by improving its quality and effectiveness. The specific aim of the study was to analyze predominant species of Lactobacillus in intestinal microbial ecosystem of young calves. Forty-two lactic acid bacteria (LAB) isolated from intestinal tract of young calves were characterized by: Amplified Ribosomal DNA Restriction Analysis (ARDRA), by using Hae III, Msp I, and Hinf I restriction enzymes, and 16S rDNA gene sequencing. ARDRA screening revealed nine unique patterns among 42 isolates, with the same pattern for 29 of the isolates. Gene fragments of 16S rDNA of 19 strains representing different patterns were sequenced to confirm the identification of these species. These results confirmed that ARDRA is a good tool for identification and discrimination of bacterial species isolated from complex ecosystem and between closely related groups. This paper provides information about the LAB species predominant in intestinal tract of young calves that could provide beneficial effects when administered as probiotic. PMID:20445780

Signatures of a globally optimal searching strategy in the three-dimensional foraging flights of bumblebees

NASA Astrophysics Data System (ADS)

Lihoreau, Mathieu; Ings, Thomas C.; Chittka, Lars; Reynolds, Andy M.

2016-07-01

Simulated annealing is a powerful stochastic search algorithm for locating a global maximum that is hidden among many poorer local maxima in a search space. It is frequently implemented in computers working on complex optimization problems but until now has not been directly observed in nature as a searching strategy adopted by foraging animals. We analysed high-speed video recordings of the three-dimensional searching flights of bumblebees (Bombus terrestris) made in the presence of large or small artificial flowers within a 0.5 m3 enclosed arena. Analyses of the three-dimensional flight patterns in both conditions reveal signatures of simulated annealing searches. After leaving a flower, bees tend to scan back-and forth past that flower before making prospecting flights (loops), whose length increases over time. The search pattern becomes gradually more expansive and culminates when another rewarding flower is found. Bees then scan back and forth in the vicinity of the newly discovered flower and the process repeats. This looping search pattern, in which flight step lengths are typically power-law distributed, provides a relatively simple yet highly efficient strategy for pollinators such as bees to find best quality resources in complex environments made of multiple ephemeral feeding sites with nutritionally variable rewards.

Sexual and reproductive behaviour of Drosophila melanogaster from a microclimatically interslope differentiated population of "Evolution Canyon" (Mount Carmel, Israel).

PubMed

Iliadi, K; Iliadi, N; Rashkovetsky, E; Minkov, I; Nevo, E; Korol, A

2001-11-22

The strong microscale interslope environmental differences in "Evolution Canyon" provide an excellent natural model for sympatric speciation. Our previous studies revealed significant slope-specific differences for a fitness complex of Drosophila. This complex involved either adaptation traits (tolerance to high temperature, different viability and longevity pattern) or behavioural differentiation, manifested in habitat choice and non-random mating. This remarkable differentiation has evolved despite a very small interslope distance (a few hundred metres only). Our hypothesis is that strong interslope microclimatic contrast caused differential selection for fitness-related traits accompanied by behavioural differentiation and reinforced by some sexual isolation, which started incipient speciation. Here we describe the results of a systematic analysis of sexual behaviour in a non-choice situation and several reproductive parameters of D. melanogaster populations from the opposite slopes of "Evolution Canyon". The evidence indicates that: (i) mate choice derives from differences in mating propensity and discrimination; (ii) females from the milder north-facing slope discriminate strongly against males of the opposite slope; (iii) both sexes of the south-facing slope display distinct reproductive and behavioural patterns with females showing increased fecundity, shorter time before remating and relatively higher receptivity, and males showing higher mating propensity. These patterns represent adaptive life strategies contributing to higher fitness.

How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches.

PubMed

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M; Jonsson, Gudberg K; Anguera, M Teresa

2017-01-01

The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013-First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann-Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

Beyond the continuum: a multi-dimensional phase space for neutral-niche community assembly.

PubMed

Latombe, Guillaume; Hui, Cang; McGeoch, Melodie A

2015-12-22

Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multi-dimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral-niche community dynamics. The neutral-niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology. © 2015 The Author(s).

Beyond the continuum: a multi-dimensional phase space for neutral–niche community assembly

PubMed Central

Latombe, Guillaume; McGeoch, Melodie A.

2015-01-01

Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multi-dimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral–niche community dynamics. The neutral–niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology. PMID:26702047

How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches

PubMed Central

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M.; Jonsson, Gudberg K.; Anguera, M. Teresa

2017-01-01

The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013—First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann–Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training. PMID:28878712

New water soluble heterometallic complex showing unpredicted coordination modes of EDTA

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

Mudsainiyan, R.K., E-mail: mudsainiyanrk@gmail.com; Jassal, A.K.; Chawla, S.K., E-mail: sukhvinder.k.chawla@gmail.com

2015-10-15

A mesoporous 3D polymeric complex (I) having formula ([Zr(IV)O-μ{sup 3}-(EDTA)Fe(III)OH]·H{sub 2}O){sub n} has been crystallized and characterized by various techniques. Single-crystal X-ray diffraction analysis revealed that complex (I) crystallized in chiral monoclinic space group Cc (space group no. 9) with unexpected coordination modes of EDTA and mixture of two transition metal ions. In this complex, the coordination number of Zr(IV) ion is seven where four carboxylate oxygen atoms, two nitrogen atoms, one oxide atom are coordinating with Zr(IV). Fe(III) is four coordinated and its coordination environment is composed of three different carboxylic oxygen atoms from three different EDTA and onemore » oxygen atom of –OH group. The structure consists of 4-c and 16-c (2-nodal) net with new topology and point symbol for net is (3{sup 36}·4{sup 54}·5{sup 30})·(3{sup 6}). TGA study and XRPD pattern showed that the coordination polymer is quite stable even after losing water molecule and –OH ion. Quenching behavior in fluorescence of ligand is observed by complexation with transition metal ions is due to n–π⁎ transition. The SEM micrograph shows the morphology of complex (I) exhibits spherical shape with size ranging from 50 to 280 nm. The minimum N{sub 2} (S{sub BET}=8.7693 m{sup 2}/g) and a maximum amount of H{sub 2} (high surface area=1044.86 m{sup 2}/g (STP)) could be adsorbed at 77 K. From DLS study, zeta potential is calculated i.e. −7.94 shows the negative charges on the surface of complex. Hirshfeld surface analysis and fingerprint plots revealed influence of weak or non bonding interactions in crystal packing of complex. - Graphical abstract: The complex (I) crystallized with unexpected coordination modes of EDTA having 4-c, 16-c net with new topology and point symbol is (3{sup 36}·4{sup 54}·5{sup 30})·(3{sup 6}). TGA study and XRPD pattern proved its stability with high preference of H{sub 2} uptake by complex. - Highlights: • 3D complex having unexpected coordination modes of EDTA with Zr(IV) and Fe(III). • The structure consists of 4-c and 16-c (2-nodal) net with new topology. • Reasonable S{sub BET} (8.7693 m{sup 2}/g) but high H{sub 2} uptake (1044.86 m{sup 2}/g) due to limited pore size. • Quenching behavior due to n–π⁎ transition by complexation with transition metal ions. • From DLS study, zeta potential value is −7.94.« less

Complex chromatin condensation patterns and nuclear protein transitions during spermiogenesis: examples from mollusks.

PubMed

Chiva, M; Saperas, N; Ribes, E

2011-12-01

In this paper we review and analyze the chromatin condensation pattern during spermiogenesis in several species of mollusks. Previously, we had described the nuclear protein transitions during spermiogenesis in these species. The results of our study show two types of condensation pattern: simple patterns and complex patterns, with the following general characteristics: (a) When histones (always present in the early spermatid nucleus) are directly replaced by SNBP (sperm nuclear basic proteins) of the protamine type, the spermiogenic chromatin condensation pattern is simple. However, if the replacement is not direct but through intermediate proteins, the condensation pattern is complex. (b) The intermediate proteins found in mollusks are precursor molecules that are processed during spermiogenesis to the final protamine molecules. Some of these final protamines represent proteins with the highest basic amino acid content known to date, which results in the establishment of a very strong electrostatic interaction with DNA. (c) In some instances, the presence of complex patterns of chromatin condensation clearly correlates with the acquisition of specialized forms of the mature sperm nuclei. In contrast, simple condensation patterns always lead to rounded, oval or slightly cylindrical nuclei. (d) All known cases of complex spermiogenic chromatin condensation patterns are restricted to species with specialized sperm cells (introsperm). At the time of writing, we do not know of any report on complex condensation pattern in species with external fertilization and, therefore, with sperm cells of the primitive type (ect-aquasperm). (e) Some of the mollusk an spermiogenic chromatin condensation patterns of the complex type are very similar (almost identical) to those present in other groups of animals. Interestingly, the intermediate proteins involved in these cases can be very different.In this study, we discuss the biological significance of all these features and conclude that the appearance of precursor (intermediate) molecules facilitated the development of complex patterns of condensation and, as a consequence, a great diversity of forms in the sperm cell nuclei Copyright © 2011 Elsevier Ltd. All rights reserved.

Process-Based Species Pools Reveal the Hidden Signature of Biotic Interactions Amid the Influence of Temperature Filtering.

PubMed

Lessard, Jean-Philippe; Weinstein, Ben G; Borregaard, Michael K; Marske, Katharine A; Martin, Danny R; McGuire, Jimmy A; Parra, Juan L; Rahbek, Carsten; Graham, Catherine H

2016-01-01

A persistent challenge in ecology is to tease apart the influence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining species pools and permits assessment of the relative influence of the main processes thought to shape assemblage structure: environmental filtering, dispersal limitations, and biotic interactions. We illustrate our approach using data on the assemblage composition and geographic distribution of hummingbirds, a comprehensive phylogeny and morphological traits. The implementation of several process-based species pool definitions in null models suggests that temperature-but not precipitation or dispersal limitation-acts as the main regional filter of assemblage structure. Incorporating this environmental filter directly into the definition of assemblage-specific species pools revealed an otherwise hidden pattern of phylogenetic evenness, indicating that biotic interactions might further influence hummingbird assemblage structure. Such hidden patterns of assemblage structure call for a reexamination of a multitude of phylogenetic- and trait-based studies that did not explicitly consider potentially important processes in their definition of the species pool. Our heuristic approach provides a transparent way to explore patterns and refine interpretations of the underlying causes of assemblage structure.

Race and Older Mothers’ Differentiation: A Sequential Quantitative and Qualitative Analysis

PubMed Central

Sechrist, Jori; Suitor, J. Jill; Riffin, Catherine; Taylor-Watson, Kadari; Pillemer, Karl

2011-01-01

The goal of this paper is to demonstrate a process by which qualitative and quantitative approaches are combined to reveal patterns in the data that are unlikely to be detected and confirmed by either method alone. Specifically, we take a sequential approach to combining qualitative and quantitative data to explore race differences in how mothers differentiate among their adult children. We began with a standard multivariate analysis examining race differences in mothers’ differentiation among their adult children regarding emotional closeness and confiding. Finding no race differences in this analysis, we conducted an in-depth comparison of the Black and White mothers’ narratives to determine whether there were underlying patterns that we had been unable to detect in our first analysis. Using this method, we found that Black mothers were substantially more likely than White mothers to emphasize interpersonal relationships within the family when describing differences among their children. In our final step, we developed a measure of familism based on the qualitative data and conducted a multivariate analysis to confirm the patterns revealed by the in-depth comparison of the mother’s narratives. We conclude that using such a sequential mixed methods approach to data analysis has the potential to shed new light on complex family relations. PMID:21967639

Productive engagement among older Americans: prevalence, patterns, and implications for public policy.

PubMed

Hinterlong, James E

2008-01-01

This study estimates the prevalence of productive engagement among adults aged 60 and over residing in the United States over a nine-year period. We analyze three waves of data from the Americans' Changing Lives Study, which allows the findings to describe the non-institutionalized older American population. Focusing upon five activities--formal paid employment, irregular paid work, unpaid volunteerism, caregiving, and informal assistance to others--we identify changes in the engagement rates, examine the extent to which engagement occurs through single or multiple concurrent activities, and document intra-individual patterns of engagement within and across forms of productive activity, including the continuity, initiation, and cessation of involvement. The findings reveal that late-life productive engagement is widespread, with the majority of older individuals involved in multiple forms of activity concurrently. Non-market-based activities such as caregiving, informal assistance, and volunteering are most prevalent. Initiation and cessation of activities are common and yield more complex patterns and lower rates of non-participation than are revealed in cross-sectional analyses. Time spent in productive engagement is highly variable and exhibits an overall decline across time. We conclude by highlighting policy strategies to increase the availability and quality of opportunities for productive engagement and promote planning for engagement in late life.

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

PubMed Central

Handfield, Louis-François; Chong, Yolanda T.; Simmons, Jibril; Andrews, Brenda J.; Moses, Alan M.

2013-01-01

Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images. PMID:23785265

Multi-voxel Patterns Reveal Functionally Differentiated Networks Underlying Auditory Feedback Processing of Speech

PubMed Central

Zheng, Zane Z.; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N.; Munhall, Kevin G.; Cusack, Rhodri; Johnsrude, Ingrid S.

2013-01-01

The everyday act of speaking involves the complex processes of speech motor control. An important component of control is monitoring, detection and processing of errors when auditory feedback does not correspond to the intended motor gesture. Here we show, using fMRI and converging operations within a multi-voxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was employed to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during vocalization, compared to during passive listening. One network of regions appears to encode an ‘error signal’ irrespective of acoustic features of the error: this network, including right angular gyrus, right supplementary motor area, and bilateral cerebellum, yielded consistent neural patterns across acoustically different, distorted feedback types, only during articulation (not during passive listening). In contrast, a fronto-temporal network appears sensitive to the speech features of auditory stimuli during passive listening; this preference for speech features was diminished when the same stimuli were presented as auditory concomitants of vocalization. A third network, showing a distinct functional pattern from the other two, appears to capture aspects of both neural response profiles. Taken together, our findings suggest that auditory feedback processing during speech motor control may rely on multiple, interactive, functionally differentiated neural systems. PMID:23467350

Automated analysis of calcium spiking profiles with CaSA software: two case studies from root-microbe symbioses

PubMed Central

2013-01-01

Background Repeated oscillations in intracellular calcium (Ca2+) concentration, known as Ca2+ spiking signals, have been described in plants for a limited number of cellular responses to biotic or abiotic stimuli and most notably the common symbiotic signaling pathway (CSSP) which mediates the recognition by their plant hosts of two endosymbiotic microbes, arbuscular mycorrhizal (AM) fungi and nitrogen fixing rhizobia. The detailed analysis of the complexity and variability of the Ca2+ spiking patterns which have been revealed in recent studies requires both extensive datasets and sophisticated statistical tools. Results As a contribution, we have developed automated Ca2+ spiking analysis (CaSA) software that performs i) automated peak detection, ii) statistical analyses based on the detected peaks, iii) autocorrelation analysis of peak-to-peak intervals to highlight major traits in the spiking pattern. We have evaluated CaSA in two experimental studies. In the first, CaSA highlighted unpredicted differences in the spiking patterns induced in Medicago truncatula root epidermal cells by exudates of the AM fungus Gigaspora margarita as a function of the phosphate concentration in the growth medium of both host and fungus. In the second study we compared the spiking patterns triggered by either AM fungal or rhizobial symbiotic signals. CaSA revealed the existence of different patterns in signal periodicity, which are thought to contribute to the so-called Ca2+ signature. Conclusions We therefore propose CaSA as a useful tool for characterizing oscillatory biological phenomena such as Ca2+ spiking. PMID:24369773

Measuring word complexity in speech screening: single-word sampling to identify phonological delay/disorder in preschool children.

PubMed

Anderson, Carolyn; Cohen, Wendy

2012-01-01

Children's speech sound development is assessed by comparing speech production with the typical development of speech sounds based on a child's age and developmental profile. One widely used method of sampling is to elicit a single-word sample along with connected speech. Words produced spontaneously rather than imitated may give a more accurate indication of a child's speech development. A published word complexity measure can be used to score later-developing speech sounds and more complex word patterns. There is a need for a screening word list that is quick to administer and reliably differentiates children with typically developing speech from children with patterns of delayed/disordered speech. To identify a short word list based on word complexity that could be spontaneously named by most typically developing children aged 3;00-5;05 years. One hundred and five children aged between 3;00 and 5;05 years from three local authority nursery schools took part in the study. Items from a published speech assessment were modified and extended to include a range of phonemic targets in different word positions in 78 monosyllabic and polysyllabic words. The 78 words were ranked both by phonemic/phonetic complexity as measured by word complexity and by ease of spontaneous production. The ten most complex words (hereafter Triage 10) were named spontaneously by more than 90% of the children. There was no significant difference between the complexity measures for five identified age groups when the data were examined in 6-month groups. A qualitative analysis revealed eight children with profiles of phonological delay or disorder. When these children were considered separately, there was a statistically significant difference (p < 0.005) between the mean word complexity measure of the group compared with the mean for the remaining children in all other age groups. The Triage 10 words reliably differentiated children with typically developing speech from those with delayed or disordered speech patterns. The Triage 10 words can be used as a screening tool for triage and general assessment and have the potential to monitor progress during intervention. Further testing is being undertaken to establish reliability with children referred to speech and language therapy services. © 2012 Royal College of Speech and Language Therapists.

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

Mishra, Ashutosh; Dwivedi, Jagrati, E-mail: hemu.dwi@gmail.com; Shukla, Kritika

Five Chromium (III) complexes have been prepared using Schiff base ligands which derived from benzoin and five different amino acids (H{sub 2}N-R). Samples were characterized by XRD, FTIR, UV-VIS and SEM method. X-Ray diffraction pattern analyzed that all chromium (III) complexes have hexagonal structure and crystalline, in nature, using Bruker D8 Advance instrument. Using VERTAX 70, FTIR spectroscopy reveals that Samples have (C=N), (C-O), (M-N) and (M-O) bonds in the range of 4000-400cm{sup −1}. UV-VIS spectroscopy give information that samples absorb the visible light which is in the range of 380-780nm. For this, Lambda 960 spectrometer used. SEM is designedmore » for studying of the solid objects, using JEOL JSM 5600 instrument.« less

Hydrodynamically induced oscillations and traffic dynamics in 1D microfludic networks

NASA Astrophysics Data System (ADS)

Bartolo, Denis; Jeanneret, Raphael

2011-03-01

We report on the traffic dynamics of particles driven through a minimal microfluidic network. Even in the minimal network consisting in a single loop, the traffic dynamics has proven to yield complex temporal patterns, including periodic, multi-periodic or chaotic sequences. This complex dynamics arises from the strongly nonlinear hydrodynamic interactions between the particles, that takes place at a junction. To better understand the consequences of this nontrivial coupling, we combined theoretical, numerical and experimental efforts and solved the 3-body problem in a 1D loop network. This apparently simple dynamical system revealed a rich and unexpected dynamics, including coherent spontaneous oscillations along closed orbits. Striking similarities between Hamiltonian systems and this driven dissipative system will be explained.

Envisioning migration: Mathematics in both experimental analysis and modeling of cell behavior

PubMed Central

Zhang, Elizabeth R.; Wu, Lani F.; Altschuler, Steven J.

2013-01-01

The complex nature of cell migration highlights the power and challenges of applying mathematics to biological studies. Mathematics may be used to create model equations that recapitulate migration, which can predict phenomena not easily uncovered by experiments or intuition alone. Alternatively, mathematics may be applied to interpreting complex data sets with better resolution—potentially empowering scientists to discern subtle patterns amid the noise and heterogeneity typical of migrating cells. Iteration between these two methods is necessary in order to reveal connections within the cell migration signaling network, as well as to understand the behavior that arises from those connections. Here, we review recent quantitative analysis and mathematical modeling approaches to the cell migration problem. PMID:23660413

Envisioning migration: mathematics in both experimental analysis and modeling of cell behavior.

PubMed

Zhang, Elizabeth R; Wu, Lani F; Altschuler, Steven J

2013-10-01

The complex nature of cell migration highlights the power and challenges of applying mathematics to biological studies. Mathematics may be used to create model equations that recapitulate migration, which can predict phenomena not easily uncovered by experiments or intuition alone. Alternatively, mathematics may be applied to interpreting complex data sets with better resolution--potentially empowering scientists to discern subtle patterns amid the noise and heterogeneity typical of migrating cells. Iteration between these two methods is necessary in order to reveal connections within the cell migration signaling network, as well as to understand the behavior that arises from those connections. Here, we review recent quantitative analysis and mathematical modeling approaches to the cell migration problem. Copyright © 2013 Elsevier Ltd. All rights reserved.

Integrating mechanisms of visual guidance in naturalistic language production.

PubMed

Coco, Moreno I; Keller, Frank

2015-05-01

Situated language production requires the integration of visual attention and linguistic processing. Previous work has not conclusively disentangled the role of perceptual scene information and structural sentence information in guiding visual attention. In this paper, we present an eye-tracking study that demonstrates that three types of guidance, perceptual, conceptual, and structural, interact to control visual attention. In a cued language production experiment, we manipulate perceptual (scene clutter) and conceptual guidance (cue animacy) and measure structural guidance (syntactic complexity of the utterance). Analysis of the time course of language production, before and during speech, reveals that all three forms of guidance affect the complexity of visual responses, quantified in terms of the entropy of attentional landscapes and the turbulence of scan patterns, especially during speech. We find that perceptual and conceptual guidance mediate the distribution of attention in the scene, whereas structural guidance closely relates to scan pattern complexity. Furthermore, the eye-voice span of the cued object and its perceptual competitor are similar; its latency mediated by both perceptual and structural guidance. These results rule out a strict interpretation of structural guidance as the single dominant form of visual guidance in situated language production. Rather, the phase of the task and the associated demands of cross-modal cognitive processing determine the mechanisms that guide attention.

Acoustofluidic waveguides for localized control of acoustic wavefront in microfluidics

PubMed Central

Bian, Yusheng; Guo, Feng; Yang, Shujie; Mao, Zhangming; Bachman, Hunter; Tang, Shi-Yang; Ren, Liqiang; Zhang, Bin; Gong, Jianying; Guo, Xiasheng

2017-01-01

The precise manipulation of acoustic fields in microfluidics is of critical importance for the realization of many biomedical applications. Despite the tremendous efforts devoted to the field of acoustofluidics during recent years, dexterous control, with an arbitrary and complex acoustic wavefront, in a prescribed, microscale region is still out of reach. Here, we introduce the concept of acoustofluidic waveguide, a three-dimensional compact configuration that is capable of locally guiding acoustic waves into a fluidic environment. Through comprehensive numerical simulations, we revealed the possibility of forming complex field patterns with defined pressure nodes within a highly localized, pre-determined region inside the microfluidic chamber. We also demonstrated the tunability of the acoustic field profile through controlling the size and shape of the waveguide geometry, as well as the operational frequency of the acoustic wave. The feasibility of the waveguide concept was experimentally verified via microparticle trapping and patterning. Our acoustofluidic waveguiding structures can be readily integrated with other microfluidic configurations and can be further designed into more complex types of passive acoustofluidic devices. The waveguide platform provides a promising alternative to current acoustic manipulation techniques and is useful in many applications such as single-cell analysis, point-of-care diagnostics, and studies of cell–cell interactions. PMID:29358901

Correlation between pairing initiation sites, recombination nodules and meiotic recombination in Sordaria macrospora.

PubMed

Zickler, D; Moreau, P J; Huynh, A D; Slezec, A M

1992-09-01

The decrease of meiotic exchanges (crossing over and conversion) in two mutants of Sordaria macrospora correlated strongly with a reduction of chiasmata and of both types of "recombination nodules." Serial section reconstruction electron microscopy was used to compare the synapsis pattern of meiotic prophase I in wild type and mutants. First, synapsis occurred but the number of synaptonemal complex initiation sites was reduced in both mutants. Second, this reduction was accompanied by, or resulted in, modifications of the pattern of synapsis. Genetic and synaptonemal complex maps were compared in three regions along one chromosome arm divided into well marked intervals. Reciprocal exchange frequencies and number of recombination nodules correlated in wild type in the three analyzed intervals, but disparity was found between the location of recombination nodules and exchanges in the mutants. Despite the twofold exchange decrease, sections of the genome such as the short arm of chromosome 2 and telomere regions were sheltered from nodule decrease and from pairing modifications. This indicated a certain amount of diversity in the control of these features and suggested that exchange frequency was dependent not only on the amount of effective pairing but also on the localization of the pairing sites, as revealed by the synaptonemal complex progression in the mutants.

Complex Patterns of Admixture across the Indonesian Archipelago

PubMed Central

Hudjashov, Georgi; Karafet, Tatiana M.; Lawson, Daniel J.; Downey, Sean; Savina, Olga; Sudoyo, Herawati; Lansing, J. Stephen; Hammer, Michael F.; Cox, Murray P.

2017-01-01

Abstract Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups. PMID:28957506

A contact photo-cross-linking investigation of the active site of the 8-17 deoxyribozyme.

PubMed

Liu, Yong; Sen, Dipankar

2008-09-12

The small RNA-cleaving 8-17 deoxyribozyme (DNAzyme) has been the subject of extensive mechanistic and structural investigation, including a number of recent single-molecule studies of its global folding. Little detailed insight exists, however, into this DNAzyme's active site; for instance, the identity of specific nucleotides that are proximal to or in contact with the scissile site in the substrate. Here, we report a systematic replacement of a number of bases within the magnesium-folded DNAzyme-substrate complex with thio- and halogen-substituted base analogues, which were then photochemically activated to generate contact cross-links within the complex. Mapping of the cross-links revealed a striking pattern of DNAzyme-substrate cross-links but an absence of significant intra-DNAzyme cross-links. Notably, the two nucleotides directly flanking the scissile phosphodiester cross-linked strongly with functionally important elements within the DNAzyme, the thymine of a G.T wobble base pair, a WCGR bulge loop, and a terminal AGC loop. Mutation of the wobble base pair to a G-C pair led to a significant folding instability of the DNAzyme-substrate complex. The cross-linking patterns obtained were used to generate a model for the DNAzyme's active site that had the substrate's scissile phosphodiester sandwiched between the DNAzyme's wobble thymine and its AGC and WCGR loops.

Correlation between Pairing Initiation Sites, Recombination Nodules and Meiotic Recombination in Sordaria Macrospora

PubMed Central

Zickler, D.; Moreau, PJF.; Huynh, A. D.; Slezec, A. M.

1992-01-01

The decrease of meiotic exchanges (crossing over and conversion) in two mutants of Sordaria macrospora correlated strongly with a reduction of chiasmata and of both types of ``recombination nodules.'' Serial section reconstruction electron microscopy was used to compare the synapsis pattern of meiotic prophase I in wild type and mutants. First, synapsis occurred but the number of synaptonemal complex initiation sites was reduced in both mutants. Second, this reduction was accompanied by, or resulted in, modifications of the pattern of synapsis. Genetic and synaptonemal complex maps were compared in three regions along one chromosome arm divided into well marked intervals. Reciprocal exchange frequencies and number of recombination nodules correlated in wild type in the three analyzed intervals, but disparity was found between the location of recombination nodules and exchanges in the mutants. Despite the twofold exchange decrease, sections of the genome such as the short arm of chromosome 2 and telomere regions were sheltered from nodule decrease and from pairing modifications. This indicated a certain amount of diversity in the control of these features and suggested that exchange frequency was dependent not only on the amount of effective pairing but also on the localization of the pairing sites, as revealed by the synaptonemal complex progression in the mutants. PMID:1398050

Historical and contemporary geographic data reveal complex spatial and temporal responses of vegetation to climate and land stewardship

USGS Publications Warehouse

Villarreal, Miguel L.; Norman, Laura M.; Webb, Robert H.; Turner, Raymond M.

2013-01-01

Vegetation and land-cover changes are not always directional but follow complex trajectories over space and time, driven by changing anthropogenic and abiotic conditions. We present a multi-observational approach to land-change analysis that addresses the complex geographic and temporal variability of vegetation changes related to climate and land use. Using land-ownership data as a proxy for land-use practices, multitemporal land-cover maps, and repeat photography dating to the late 19th century, we examine changing spatial and temporal distributions of two vegetation types with high conservation value in the southwestern United States: grasslands and riparian vegetation. In contrast to many reported vegetation changes, notably shrub encroachment in desert grasslands, we found an overall increase in grassland area and decline of xeroriparian and riparian vegetation. These observed change patterns were neither temporally directional nor spatially uniform over the landscape. Historical data suggest that long-term vegetation changes coincide with broad climate fluctuations while fine-scale patterns are determined by land-management practices. In some cases, restoration and active management appear to weaken the effects of climate on vegetation; therefore, if land managers in this region act in accord with on-going directional changes, the current drought and associated ecological reorganization may provide an opportunity to achieve desired restoration endpoints.

Complexity and time asymmetry of heart rate variability are altered in acute mental stress.

PubMed

Visnovcova, Z; Mestanik, M; Javorka, M; Mokra, D; Gala, M; Jurko, A; Calkovska, A; Tonhajzerova, I

2014-07-01

We aimed to study the complexity and time asymmetry of short-term heart rate variability (HRV) as an index of complex neurocardiac control in response to stress using symbolic dynamics and time irreversibility methods. ECG was recorded at rest and during and after two stressors (Stroop, arithmetic test) in 70 healthy students. Symbolic dynamics parameters (NUPI, NCI, 0V%, 1V%, 2LV%, 2UV%), and time irreversibility indices (P%, G%, E) were evaluated. Additionally, HRV magnitude was quantified by linear parameters: spectral powers in low (LF) and high frequency (HF) bands. Our results showed a reduction of HRV complexity in stress (lower NUPI with both stressors, lower NCI with Stroop). Pattern classification analysis revealed significantly higher 0V% and lower 2LV% with both stressors, indicating a shift in sympathovagal balance, and significantly higher 1V% and lower 2UV% with Stroop. An unexpected result was found in time irreversibility: significantly lower G% and E with both stressors, P% index significantly declined only with arithmetic test. Linear HRV analysis confirmed vagal withdrawal (lower HF) with both stressors; LF significantly increased with Stroop and decreased with arithmetic test. Correlation analysis revealed no significant associations between symbolic dynamics and time irreversibility. Concluding, symbolic dynamics and time irreversibility could provide independent information related to alterations of neurocardiac control integrity in stress-related disease.

Limbic encephalitis associated with anti-voltage-gated potassium channel complex antibodies as a cause of adult-onset mesial temporal lobe epilepsy.

PubMed

Toyota, Tomoko; Akamatsu, Naoki; Tsuji, Sadatoshi; Nishizawa, Shigeru

2014-06-01

Recently, some reports have indicated that limbic encephalitis associated with anti-voltage-gated potassium channel complex antibodies (VGKC-Ab) is a cause of adult-onset mesial temporal lobe epilepsy (MTLE). We report a 53-year-old woman who had her first epileptic seizure at the age of 50 years old. Examination by 3-Tesla brain MRI revealed left hippocampal high signal intensity and swelling on fluid-attenuated inversion recovery (FLAIR) and T2-weighted imaging at 2 months after her first seizure. The patient received intravenous methylprednisolone and carbamazepine 300 mg/day. One month later, MRI revealed improvement of her left hippocampal abnormalities. Thereafter, she had no seizures, however, three years after her first seizure, EEG revealed a seizure pattern in the left temporal region. Brain MRI revealed left hippocampal high signal intensity and brain fluorodeoxyglucose positron emission tomography revealed hypermetabolism. Her serum VGKC-Ab levels were 118 pM(normal < 100 pM). Intravenous methylprednisolone therapy was reinitiated. Two months later, her hippocampal abnormalities had improved and 3 months later her VGKC-Ab levels decreased to 4.4 pM. Remission of the epileptic seizures was also observed. This MTLE in the middle age was considered as limbic encephalitis associated with anti- VGKC-Ab. In cases of unexplained adult-onset MTLE, limbic encephalitis associated with anti-VGKC-Ab, which responds well to immunotherapy, should be considered in the differential diagnosis.

Entanglement complexity in quantum many-body dynamics, thermalization, and localization

NASA Astrophysics Data System (ADS)

Yang, Zhi-Cheng; Hamma, Alioscia; Giampaolo, Salvatore M.; Mucciolo, Eduardo R.; Chamon, Claudio

2017-07-01

Entanglement is usually quantified by von Neumann entropy, but its properties are much more complex than what can be expressed with a single number. We show that the three distinct dynamical phases known as thermalization, Anderson localization, and many-body localization are marked by different patterns of the spectrum of the reduced density matrix for a state evolved after a quantum quench. While the entanglement spectrum displays Poisson statistics for the case of Anderson localization, it displays universal Wigner-Dyson statistics for both the cases of many-body localization and thermalization, albeit the universal distribution is asymptotically reached within very different time scales in these two cases. We further show that the complexity of entanglement, revealed by the possibility of disentangling the state through a Metropolis-like algorithm, is signaled by whether the entanglement spectrum level spacing is Poisson or Wigner-Dyson distributed.

Clonal development and organization of the adult Drosophila central brain.

PubMed

Yu, Hung-Hsiang; Awasaki, Takeshi; Schroeder, Mark David; Long, Fuhui; Yang, Jacob S; He, Yisheng; Ding, Peng; Kao, Jui-Chun; Wu, Gloria Yueh-Yi; Peng, Hanchuan; Myers, Gene; Lee, Tzumin

2013-04-22

The insect brain can be divided into neuropils that are formed by neurites of both local and remote origin. The complexity of the interconnections obscures how these neuropils are established and interconnected through development. The Drosophila central brain develops from a fixed number of neuroblasts (NBs) that deposit neurons in regional clusters. By determining individual NB clones and pursuing their projections into specific neuropils, we unravel the regional development of the brain neural network. Exhaustive clonal analysis revealed 95 stereotyped neuronal lineages with characteristic cell-body locations and neurite trajectories. Most clones show complex projection patterns, but despite the complexity, neighboring clones often coinnervate the same local neuropil or neuropils and further target a restricted set of distant neuropils. These observations argue for regional clonal development of both neuropils and neuropil connectivity throughout the Drosophila central brain. Copyright © 2013 Elsevier Ltd. All rights reserved.

Uranyl mediated photofootprinting reveals strong E. coli RNA polymerase--DNA backbone contacts in the +10 region of the DeoP1 promoter open complex.

PubMed Central

Jeppesen, C; Nielsen, P E

1989-01-01

Employing a newly developed uranyl photofootprinting technique (Nielsen et al. (1988) FEBS Lett. 235, 122), we have analyzed the structure of the E. coli RNA polymerase deoP1 promoter open complex. The results show strong polymerase DNA backbone contacts in the -40, -10, and most notably in the +10 region. These results suggest that unwinding of the -12 to +3 region of the promoter in the open complex is mediated through polymerase DNA backbone contacts on both sides of this region. The pattern of bases that are hyperreactive towards KMnO4 or uranyl within the -12 to +3 region furthermore argues against a model in which this region is simply unwound and/or single stranded. The results indicate specific protein contacts and/or a fixed DNA conformation within the -12 to +3 region. Images PMID:2503811

Patterns and processes: Subaerial lava flow morphologies: A review

NASA Astrophysics Data System (ADS)

Gregg, Tracy K. P.

2017-08-01

Most lava flows have been emplaced away from the watchful eyes of volcanologists, so there is a desire to use solidified lava-flow morphologies to reveal important information about the eruption that formed them. Our current understanding of the relationship between solidified basaltic lava morphology and the responsible eruption and emplacement processes is based on decades of fieldwork, laboratory analyses and simulations, and computer models. These studies have vastly improved our understanding of the complex interactions between the solids, liquids, and gases that comprise cooling lava flows. However, the complex interactions (at millimeter and sub-millimeter scales) between the temperature-dependent abundances of the distinct phases that comprise a lava flow and the final morphology remain challenging to model and to predict. Similarly, the complex behavior of an active pahoehoe flow, although almost ubiquitous on Earth, remains difficult to quantitatively model and precisely predict.

A Corticothalamic Circuit Model for Sound Identification in Complex Scenes

PubMed Central

Otazu, Gonzalo H.; Leibold, Christian

2011-01-01

The identification of the sound sources present in the environment is essential for the survival of many animals. However, these sounds are not presented in isolation, as natural scenes consist of a superposition of sounds originating from multiple sources. The identification of a source under these circumstances is a complex computational problem that is readily solved by most animals. We present a model of the thalamocortical circuit that performs level-invariant recognition of auditory objects in complex auditory scenes. The circuit identifies the objects present from a large dictionary of possible elements and operates reliably for real sound signals with multiple concurrently active sources. The key model assumption is that the activities of some cortical neurons encode the difference between the observed signal and an internal estimate. Reanalysis of awake auditory cortex recordings revealed neurons with patterns of activity corresponding to such an error signal. PMID:21931668

An experimental investigation of the impingement of a planar shock wave on an axisymmetric body at Mach 3

NASA Technical Reports Server (NTRS)

Brosh, A.; Kussoy, M. I.

1983-01-01

An experimental study of the flow caused by a planar shock wave impinging obliquely on a cylinder is presented. The complex three dimensional shock wave and boundary layer interaction occurring in practical problems, such as the shock wave impingement from the shuttle nose on an external fuel tank, and store carriage interference on a supersonic tactical aircraft were investigated. A data base for numerical computations of complex flows was also investigated. The experimental techniques included pressure measurements and oil flow patterns on the surface of the cylinder, and shadowgraphs and total and static pressure surveys on the leeward and windward planes of symmetry. The complete data is presented in tabular form. The results reveal a highly complex flow field with two separation zones, regions of high crossflow, and multiple reflected shocks and expansion fans.

Defined-size DNA triple crossover construct for molecular electronics: modification, positioning and conductance properties.

PubMed

Linko, Veikko; Leppiniemi, Jenni; Paasonen, Seppo-Tapio; Hytönen, Vesa P; Toppari, J Jussi

2011-07-08

We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.

Confirming and denying in co-construction processes: a case study of an adult with cerebral palsy and two familiar partners.

PubMed

Hörmeyer, Ina; Renner, Gregor

2013-09-01

For individuals with complex communication needs, one of the most frequent communicative strategies is the co-construction of meaning with familiar partners. This preliminary single-case study gives insight into a special sequential pattern of co-construction processes - the search sequence - particularly in relation to the processes of confirming and denying meanings proposed by familiar interaction partners. Five different conversations between an adult with cerebral palsy and complex communication needs and two familiar co-participants were videotaped and analyzed using the methodology of conversation analysis (CA). The study revealed that confirmations and denials are not simply two alternative actions, but that several possibilities to realize confirmations and denials exist that differ in their frequency and that have different consequences for the sequential context. This study of confirmations and denials demonstrates that co-construction processes are more complex than have previously been documented.

Complex Seismic Anisotropy at the Edges of a Very-low Velocity Province in the Lowermost Mantle

NASA Astrophysics Data System (ADS)

Wang, Y.; Wen, L.

2005-12-01

A prominent very-low velocity province (VLVP) in the lowermost mantle is revealed, and has been extensively mapped out in recent seismic studies (e.g., Wang and Wen, 2004). Seismic evidence unambiguously indicates that the VLVP is compositionally distinct, and its seismic structure can be best explained by partial melting driven by a compositional change produced in the early Earth's history (Wen, 2001; Wen et. al, 2001; Wang and Wen, 2004). In this presentation, we study the seismic anisotropic behavior inside the VLVP and its surrounding area using SKS and SKKS waveform data. We collect 272 deep earthquakes recorded by more than 80 stations in the Kaapvaal seismic array in southern Africa from 1997 to 1999. Based on the data quality, we choose SKS and SKKS waveform data for 16 earthquakes to measure the anisotropic parameters: the fast polarization direction and the splitting time, using the method of Silver and Chan (1991). A total of 162 high-quality measurements are obtained based on the statistics analysis of shear wave splitting results. The obtained anisotropy exhibits different patterns for the SKS and SKKS phases sampling inside the VLVP and at the edges of the VLVP. When the SKS and SKKS phases sample inside the VLVP, their fast polarization directions exhibit a pattern that strongly correlates with stations, gradually changing from 11°N~to 80°N~across the seismic array from south to north and rotating back to the North direction over short distances for several northernmost stations. The anisotropy pattern obtained from the analysis of the SKKS phases is the same as that from the SKS phases. However, when the SKS and SKKS phases sample at the edges of the VLVP, the measured anisotropy exhibits a very complex pattern. The obtained fast polarization directions change rapidly over a small distance, and they no longer correlate with stations; the measurements obtained from the SKS analysis also differ with those from the SKKS analysis. As the SKS and SKKS phases have similar propagation paths in the lithosphere beneath the array, but different sampling points near the core mantle boundary. The anisotropy in the lithosphere should have a similar influence on SKS and SKKS phases. Therefore, the similar anisotropy obtained from the SKS and SKKS phases sampling inside the VLVP and its correlation with seismic stations suggest that the observed anisotropy variation across the seismic array is mainly due to the anisotropy in the lithosphere beneath the Kaapvaal seismic array, and the interior of the VLVP is isotropic or weakly anisotropic. On the other hand, for the SKS and SKKS phases sampling at the edges of the VLVP, the observed complex anisotropy pattern and the lack of correlation between the results from the SKS and SKKS analyses indicate that part of that anisotropy has to originate from the lowermost mantle near the exit points of these phases at the core mantle boundary, revealing a complex flow pattern at the edges of the VLVP.

International business cycle synchronization since the 1870s: Evidence from a novel network approach

NASA Astrophysics Data System (ADS)

Antonakakis, Nikolaos; Gogas, Periklis; Papadimitriou, Theophilos; Sarantitis, Georgios Antonios

2016-04-01

In this study, we examine the issue of business cycle synchronization from a historical perspective in 27 developed and developing countries. Based on a novel complex network approach, the Threshold-Minimum Dominating Set (T-MDS), our results reveal heterogeneous patterns of international business cycle synchronization during fundamental globalization periods since the 1870s. In particular, the proposed methodology reveals that worldwide business cycles de-coupled during the Gold Standard, though they were synchronized during the Great Depression. The Bretton Woods era was associated with a lower degree of synchronization as compared to that during the Great Depression, while worldwide business cycle synchronization increased to unprecedented levels during the latest period of floating exchange rates and the Great Recession.

Comparison of coseismic near-field and off-fault surface deformation patterns of the 1992 Mw 7.3 Landers and 1999 Mw 7.1 Hector Mine earthquakes: Implications for controls on the distribution of surface strain

NASA Astrophysics Data System (ADS)

Milliner, C. W. D.; Dolan, J. F.; Hollingsworth, J.; Leprince, S.; Ayoub, F.

2016-10-01

Subpixel correlation of preevent and postevent air photos reveal the complete near-field, horizontal surface deformation patterns of the 1992 Mw 7.3 Landers and 1999 Mw 7.1 Hector Mine ruptures. Total surface displacement values for both earthquakes are systematically larger than "on-fault" displacements from geologic field surveys, indicating significant distributed, inelastic deformation occurred along these ruptures. Comparison of these two data sets shows that 46 ± 10% and 39 ± 22% of the total surface deformation were distributed over fault zones averaging 154 m and 121 m in width for the Landers and Hector Mine events, respectively. Spatial variations of distributed deformation along both ruptures show correlations with the type of near-surface lithology and degree of fault complexity; larger amounts of distributed shear occur where the rupture propagated through loose unconsolidated sediments and areas of more complex fault structure. These results have basic implications for geologic-geodetic rate comparisons and probabilistic seismic hazard analysis.

The ventralizing activity of Radar, a maternally expressed bone morphogenetic protein, reveals complex bone morphogenetic protein interactions controlling dorso-ventral patterning in zebrafish.

PubMed

Goutel, C; Kishimoto, Y; Schulte-Merker, S; Rosa, F

2000-12-01

In Xenopus and zebrafish, BMP2, 4 and 7 have been implicated, after the onset of zygotic expression, in inducing and maintaining ventro-lateral cell fate during early development. We provide evidence here that a maternally expressed bone morphogenetic protein (BMP), Radar, may control early ventral specification in zebrafish. We show that Radar ventralizes zebrafish embryos and induces the early expression of bmp2b and bmp4. The analysis of Radar overexpression in both swirl/bmp2b mutants and embryos expressing truncated BMP receptors shows that Radar-induced ventralization is dependent on functional BMP2/4 pathways, and may initially rely on an Alk6-related signaling pathway. Finally, we show that while radar-injected swirl embryos still exhibit a strongly dorsalized phenotype, the overexpression of Radar into swirl/bmp2b mutant embryos restores ventral marker expression, including bmp4 expression. Our results suggest that a complex regulation of different BMP pathways controls dorso-ventral (DV) patterning from early cleavage stages until somitogenesis.

Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

NASA Astrophysics Data System (ADS)

Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun

2016-03-01

The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.

The roosting spatial network of a bird-predator bat.

PubMed

Fortuna, Miguel A; Popa-Lisseanu, Ana G; Ibáñez, Carlos; Bascompte, Jordi

2009-04-01

The use of roosting sites by animal societies is important in conservation biology, animal behavior, and epidemiology. The giant noctule bat (Nyctalus lasiopterus) constitutes fission-fusion societies whose members spread every day in multiple trees for shelter. To assess how the pattern of roosting use determines the potential for information exchange or disease spreading, we applied the framework of complex networks. We found a social and spatial segregation of the population in well-defined modules or compartments, formed by groups of bats sharing the same trees. Inside each module, we revealed an asymmetric use of trees by bats representative of a nested pattern. By applying a simple epidemiological model, we show that there is a strong correlation between network structure and the rate and shape of infection dynamics. This modular structure slows down the spread of diseases and the exchange of information through the entire network. The implication for management is complex, affecting differently the cohesion inside and among colonies and the transmission of parasites and diseases. Network analysis can hence be applied to quantifying the conservation status of individual trees used by species depending on hollows for shelter.

H4 replication-dependent diacetylation and Hat1 promote S-phase chromatin assembly in vivo

PubMed Central

Ejlassi-Lassallette, Aïda; Mocquard, Eloïse; Arnaud, Marie-Claire; Thiriet, Christophe

2011-01-01

While specific posttranslational modification patterns within the H3 and H4 tail domains are associated with the S-phase, their actual functions in replication-dependent chromatin assembly have not yet been defined. Here we used incorporation of trace amounts of recombinant proteins into naturally synchronous macroplasmodia of Physarum polycephalum to examine the function of H3 and H4 tail domains in replication-coupled chromatin assembly. We found that the H3/H4 complex lacking the H4 tail domain was not efficiently recovered in nuclei, whereas depletion of the H3 tail domain did not impede nuclear import but chromatin assembly failed. Furthermore, our results revealed that the proper pattern of acetylation on the H4 tail domain is required for nuclear import and chromatin assembly. This is most likely due to binding of Hat1, as coimmunoprecipitation experiments showed Hat1 associated with predeposition histones in the cytoplasm and with replicating chromatin. These results suggest that the type B histone acetyltransferase assists in shuttling the H3/H4 complex from cytoplasm to the replication forks. PMID:21118997

Postural Coordination during Socio-motor Improvisation

PubMed Central

Gueugnon, Mathieu; Salesse, Robin N.; Coste, Alexandre; Zhao, Zhong; Bardy, Benoît G.; Marin, Ludovic

2016-01-01

Human interaction often relies on socio-motor improvisation. Creating unprepared movements during social interaction is not a random process but relies on rules of synchronization. These situations do not only involve people to be coordinated, but also require the adjustment of their posture in order to maintain balance and support movements. The present study investigated posture in such a context. More precisely, we first evaluated the impact of amplitude and complexity of arm movements on posture in solo situation. Then, we assessed the impact of interpersonal coordination on posture using the mirror game in which dyads performed improvised and synchronized movements (i.e., duo situation). Posture was measured through ankle-hip coordination in medio-lateral and antero-posterior directions (ML and AP respectively). Our results revealed the spontaneous emergence of in-phase pattern in ML direction and antiphase pattern in AP direction for solo and duo situations. These two patterns respectively refer to the simultaneous flexion/extension of the ankles and the hips in the same or opposite direction. It suggests different functional roles of postural coordination patterns in each direction, with in-phase supporting task performance in ML (dynamical stability) and antiphase supporting postural control in AP (mechanical stability). Although amplitude of movement did not influence posture, movement complexity disturbed postural stability in both directions. Conversely, interpersonal coordination promoted postural stability in ML but not in AP direction. These results are discussed in terms of the difference in coupling strength between ankle-hip coordination and interpersonal coordination. PMID:27547193

Postural Coordination during Socio-motor Improvisation.

PubMed

Gueugnon, Mathieu; Salesse, Robin N; Coste, Alexandre; Zhao, Zhong; Bardy, Benoît G; Marin, Ludovic

2016-01-01

Human interaction often relies on socio-motor improvisation. Creating unprepared movements during social interaction is not a random process but relies on rules of synchronization. These situations do not only involve people to be coordinated, but also require the adjustment of their posture in order to maintain balance and support movements. The present study investigated posture in such a context. More precisely, we first evaluated the impact of amplitude and complexity of arm movements on posture in solo situation. Then, we assessed the impact of interpersonal coordination on posture using the mirror game in which dyads performed improvised and synchronized movements (i.e., duo situation). Posture was measured through ankle-hip coordination in medio-lateral and antero-posterior directions (ML and AP respectively). Our results revealed the spontaneous emergence of in-phase pattern in ML direction and antiphase pattern in AP direction for solo and duo situations. These two patterns respectively refer to the simultaneous flexion/extension of the ankles and the hips in the same or opposite direction. It suggests different functional roles of postural coordination patterns in each direction, with in-phase supporting task performance in ML (dynamical stability) and antiphase supporting postural control in AP (mechanical stability). Although amplitude of movement did not influence posture, movement complexity disturbed postural stability in both directions. Conversely, interpersonal coordination promoted postural stability in ML but not in AP direction. These results are discussed in terms of the difference in coupling strength between ankle-hip coordination and interpersonal coordination.

Neurite outgrowth at the interface of 2D and 3D growth environments

NASA Astrophysics Data System (ADS)

Kofron, Celinda M.; Fong, Vivian J.; Hoffman-Kim, Diane

2009-02-01

Growing neurons navigate complex environments, but in vitro systems for studying neuronal growth typically limit the cues to flat surfaces or a single type of cue, thereby limiting the resulting growth. Here we examined the growth of neurons presented with two-dimensional (2D) substrate-bound cues when these cues were presented in conjunction with a more complex three-dimensional (3D) architecture. Dorsal root ganglia (DRG) explants were cultured at the interface between a collagen I matrix and a glass coverslip. Laminin (LN) or chondroitin sulfate proteoglycans (CSPG) were uniformly coated on the surface of the glass coverslip or patterned in 50 µm tracks by microcontact printing. Quantitative analysis of neurite outgrowth with a novel grid system at multiple depths in the gel revealed several interesting trends. Most of the neurites extended at the surface of the gel when LN was presented whereas more neurites extended into the gel when CSPG was presented. Patterning of cues did not affect neurite density or depth of growth. However, neurite outgrowth near the surface of the gel aligned with LN patterns, and these extensions were significantly longer than neurites extended in other cultures. In interface cultures, DRG growth patterns varied with the type of cue where neurite density was higher in cultures presenting LN than in cultures presenting CSPG. These results represent an important step toward understanding how neurons integrate local structural and chemical cues to make net growth decisions.

Very-Long-Chain Fatty Acids Are Involved in Polar Auxin Transport and Developmental Patterning in Arabidopsis[W

PubMed Central

Roudier, François; Gissot, Lionel; Beaudoin, Frédéric; Haslam, Richard; Michaelson, Louise; Marion, Jessica; Molino, Diana; Lima, Amparo; Bach, Liên; Morin, Halima; Tellier, Frédérique; Palauqui, Jean-Christophe; Bellec, Yannick; Renne, Charlotte; Miquel, Martine; DaCosta, Marco; Vignard, Julien; Rochat, Christine; Markham, Jonathan E.; Moreau, Patrick; Napier, Johnathan; Faure, Jean-Denis

2010-01-01

Very-long-chain fatty acids (VLCFAs) are essential for many aspects of plant development and necessary for the synthesis of seed storage triacylglycerols, epicuticular waxes, and sphingolipids. Identification of the acetyl-CoA carboxylase PASTICCINO3 and the 3-hydroxy acyl-CoA dehydratase PASTICCINO2 revealed that VLCFAs are important for cell proliferation and tissue patterning. Here, we show that the immunophilin PASTICCINO1 (PAS1) is also required for VLCFA synthesis. Impairment of PAS1 function results in reduction of VLCFA levels that particularly affects the composition of sphingolipids, known to be important for cell polarity in animals. Moreover, PAS1 associates with several enzymes of the VLCFA elongase complex in the endoplasmic reticulum. The pas1 mutants are deficient in lateral root formation and are characterized by an abnormal patterning of the embryo apex, which leads to defective cotyledon organogenesis. Our data indicate that in both tissues, defective organogenesis is associated with the mistargeting of the auxin efflux carrier PIN FORMED1 in specific cells, resulting in local alteration of polar auxin distribution. Furthermore, we show that exogenous VLCFAs rescue lateral root organogenesis and polar auxin distribution, indicating their direct involvement in these processes. Based on these data, we propose that PAS1 acts as a molecular scaffold for the fatty acid elongase complex in the endoplasmic reticulum and that the resulting VLCFAs are required for polar auxin transport and tissue patterning during plant development. PMID:20145257

More than just drought: complexity of recruitment patterns in Mediterranean forests.

PubMed

Granda, Elena; Escudero, Adrián; Valladares, Fernando

2014-12-01

Understanding community dynamics during early life stages of trees is critical for the prediction of future species composition. In Mediterranean forests drought is a major constraint for regeneration, but likely not the only factor determining the observed spatial patterns. We carried out a sowing experiment aimed at identifying main filters during seed-seedling transition. Specifically, we studied seed fate (predation, fungi infection, emergence) and subsequent seedling performance (mortality during the first summer and overall recruitment after 2 years) of four co-occurring Mediterranean tree species (Quercus ilex, Quercus faginea, Juniperus thurifera, Pinus nigra). We related these processes to the dominant species composition, microhabitat heterogeneity, herb cover and seed mass. The identity of the dominant species in the forest canopy was more important for recruitment than the forest canopy being dominated by conspecific vs. heterospecific species. The patterns we found suggest that biotic interactions such as facilitation (lower mortality under the canopies) and herb competition (during emergence of J. thurifera) are relevant during recruitment. Moreover, our results pointed to ontogenetic conflicts regarding the seed mass of Q. faginea and to density-dependent seed mortality for Q. ilex, rarely described in Mediterranean ecosystems. We propose that our study species experience population growth in forests dominated by heterospecifics where the recruitment success depends on habitat heterogeneity and on moderated biotic and abiotic stresses created by each species. Our results reveal patterns and mechanisms involved in recruitment constraints that add complexity to the well-known drought-related processes in Mediterranean ecosystems.

Characterizing the correlations between local phase fractions of gas-liquid two-phase flow with wire-mesh sensor.

PubMed

Tan, C; Liu, W L; Dong, F

2016-06-28

Understanding of flow patterns and their transitions is significant to uncover the flow mechanics of two-phase flow. The local phase distribution and its fluctuations contain rich information regarding the flow structures. A wire-mesh sensor (WMS) was used to study the local phase fluctuations of horizontal gas-liquid two-phase flow, which was verified through comparing the reconstructed three-dimensional flow structure with photographs taken during the experiments. Each crossing point of the WMS is treated as a node, so the measurement on each node is the phase fraction in this local area. An undirected and unweighted flow pattern network was established based on connections that are formed by cross-correlating the time series of each node under different flow patterns. The structure of the flow pattern network reveals the relationship of the phase fluctuations at each node during flow pattern transition, which is then quantified by introducing the topological index of the complex network. The proposed analysis method using the WMS not only provides three-dimensional visualizations of the gas-liquid two-phase flow, but is also a thorough analysis for the structure of flow patterns and the characteristics of flow pattern transition. This article is part of the themed issue 'Supersensing through industrial process tomography'. © 2016 The Author(s).

Mammographic breast density patterns in asymptomatic mexican women.

PubMed

Calderón-Garcidueñas, Ana Laura; Sanabria-Mondragón, Mónica; Hernández-Beltrán, Lourdes; López-Amador, Noé; Cerda-Flores, Ricardo M

2012-01-01

Breast density (BD) is a risk factor for breast cancer. Aims. To describe BD patterns in asymptomatic Mexican women and the pathological mammographic findings. Methods and Material. Prospective, descriptive, and comparative study. Women answered a questionnaire and their mammograms were analyzed according to BI-RADS. Univariate (χ(2)) and conditional logistic regression analyses were performed. Results. In 300 women studied the BD patterns were fat 56.7% (170), fibroglandular 29% (87), heterogeneously dense 5.7% (17), and dense pattern 8.6% (26). Prevalence of fat pattern was significantly different in women under 50 years (37.6%, 44/117) and older than 50 (68.8%, 126/183). Patterns of high breast density (BD) (dense + heterogeneously dense) were observed in 25.6% (30/117) of women ≤50 years and 7.1% (13/183) of women >50. Asymmetry in BD was observed in 22% (66/300). Compression cone ruled out underlying disease in 56 cases. In the remaining 10, biopsy revealed one fibroadenoma, one complex cyst, and 6 invasive and 2 intraductal carcinomas. 2.6% (8/300) of patients had non-palpable carcinomas. Benign lesions were observed in 63.3% (190/300) of cases, vascular calcification in 150 cases (78.9%), and fat necrosis in 38 cases (20%). Conclusions. Mexican women have a low percentage of high-density patterns.

Characterizing the correlations between local phase fractions of gas–liquid two-phase flow with wire-mesh sensor

PubMed Central

Liu, W. L.; Dong, F.

2016-01-01

Understanding of flow patterns and their transitions is significant to uncover the flow mechanics of two-phase flow. The local phase distribution and its fluctuations contain rich information regarding the flow structures. A wire-mesh sensor (WMS) was used to study the local phase fluctuations of horizontal gas–liquid two-phase flow, which was verified through comparing the reconstructed three-dimensional flow structure with photographs taken during the experiments. Each crossing point of the WMS is treated as a node, so the measurement on each node is the phase fraction in this local area. An undirected and unweighted flow pattern network was established based on connections that are formed by cross-correlating the time series of each node under different flow patterns. The structure of the flow pattern network reveals the relationship of the phase fluctuations at each node during flow pattern transition, which is then quantified by introducing the topological index of the complex network. The proposed analysis method using the WMS not only provides three-dimensional visualizations of the gas–liquid two-phase flow, but is also a thorough analysis for the structure of flow patterns and the characteristics of flow pattern transition. This article is part of the themed issue ‘Supersensing through industrial process tomography’. PMID:27185959

Marine turtle mitogenome phylogenetics and evolution.

PubMed

Duchene, Sebastián; Frey, Amy; Alfaro-Núñez, Alonzo; Dutton, Peter H; Thomas P Gilbert, M; Morin, Phillip A

2012-10-01

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution. Published by Elsevier Inc.

Anaerobic microbial communities in Lake Pavin, a unique meromictic lake in France.

PubMed

Lehours, Anne-C; Bardot, Corinne; Thenot, Aurelie; Debroas, Didier; Fonty, Gerard

2005-11-01

The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.

Improvisation and the self-organization of multiple musical bodies.

PubMed

Walton, Ashley E; Richardson, Michael J; Langland-Hassan, Peter; Chemero, Anthony

2015-01-01

Understanding everyday behavior relies heavily upon understanding our ability to improvise, how we are able to continuously anticipate and adapt in order to coordinate with our environment and others. Here we consider the ability of musicians to improvise, where they must spontaneously coordinate their actions with co-performers in order to produce novel musical expressions. Investigations of this behavior have traditionally focused on describing the organization of cognitive structures. The focus, here, however, is on the ability of the time-evolving patterns of inter-musician movement coordination as revealed by the mathematical tools of complex dynamical systems to provide a new understanding of what potentiates the novelty of spontaneous musical action. We demonstrate this approach through the application of cross wavelet spectral analysis, which isolates the strength and patterning of the behavioral coordination that occurs between improvising musicians across a range of nested time-scales. Revealing the sophistication of the previously unexplored dynamics of movement coordination between improvising musicians is an important step toward understanding how creative musical expressions emerge from the spontaneous coordination of multiple musical bodies.

Improvisation and the self-organization of multiple musical bodies

PubMed Central

Walton, Ashley E.; Richardson, Michael J.; Langland-Hassan, Peter; Chemero, Anthony

2015-01-01

Understanding everyday behavior relies heavily upon understanding our ability to improvise, how we are able to continuously anticipate and adapt in order to coordinate with our environment and others. Here we consider the ability of musicians to improvise, where they must spontaneously coordinate their actions with co-performers in order to produce novel musical expressions. Investigations of this behavior have traditionally focused on describing the organization of cognitive structures. The focus, here, however, is on the ability of the time-evolving patterns of inter-musician movement coordination as revealed by the mathematical tools of complex dynamical systems to provide a new understanding of what potentiates the novelty of spontaneous musical action. We demonstrate this approach through the application of cross wavelet spectral analysis, which isolates the strength and patterning of the behavioral coordination that occurs between improvising musicians across a range of nested time-scales. Revealing the sophistication of the previously unexplored dynamics of movement coordination between improvising musicians is an important step toward understanding how creative musical expressions emerge from the spontaneous coordination of multiple musical bodies. PMID:25941499

The non-monotypic status of the neotropical fish genus Hemiodontichthys (Siluriformes, Loricariidae) evidenced by genetic approaches.

PubMed

Carvalho, Margarida Lima; Costa Silva, Guilherme José da; Melo, Silvana; Ashikaga, Fernando Yuldi; Shimabukuro-Dias, Cristiane Kioko; Scacchetti, Priscilla Cardim; Devidé, Renato; Foresti, Fausto; Oliveira, Claudio

2018-01-31

The combination of cytogenetic and molecular data with those traditionally obtained in areas like systematics and taxonomy created interesting perspectives for the analysis of natural populations under different aspects. In this context, this study aimed to evaluate the genetic differentiation among populations of the genus Hemiodontichthys Bleeker, 1862, through combined genetic techniques and included the analysis of populations sampled in the Araguaia River, Guamá River, Madeira River and two populations from the Purus River. Hemiodontichthys samples from the two localities in Purus River were also karyotyped in order to address the degree of chromosomal variation between populations. Through GMYC analysis of the COI tree, the patterns of genetic variation among local populations revealed to be higher than the ones found among distinct species from other genera of the subfamily Loricariinae, suggesting the existence of probable four cryptic species in this genus. The possible existence of a species complex in the genus is corroborated by the different cytogenetic patterns between Hemiodontichthys sp. 1 and sp. 2, revealing the necessity of a deep taxonomic review of the group.

Circular flow patterns induced by ciliary activity in reconstituted human bronchial epithelium

NASA Astrophysics Data System (ADS)

Viallat, Annie; Khelloufi, Kamel; Gras, Delphine; Chanez, Pascal; Aix Marseille Univ., CNRS, CINaM, Marseille, France Team; Aix Marseille Univ., CNRS, Inserm, LAI, Marseille, France Team

2016-11-01

Mucociliary clearance is the transport at the surface of airways of a complex fluid layer, the mucus, moved by the beats of microscopic cilia present on epithelial ciliated cells. We explored the coupling between the spatial organisation and the activity of cilia and the transport of surface fluids on reconstituted cultures of human bronchial epithelium at air-liquid interface, obtained by human biopsies. We reveal the existence of stable local circular surface flow patterns of mucus or Newtonian fluid at the epithelium surface. We find a power law over more than 3 orders of magnitude showing that the average ciliated cell density controls the size of these flow patterns, and, therefore the distance over which mucus can be transported. We show that these circular flow patterns result from the radial linear increase of the local propelling forces (due to ciliary beats) on each flow domain. This linear increase of local forces is induced by a fine self-regulation of both cilia density and orientation of ciliary beats. Local flow domains grow and merge during ciliogenesis to provide macroscopic mucus transport. This is possible only when the viscoelastic mucus continuously exerts a shear stress on beating cilia, revealing a mechanosensitive function of cilia. M. K. Khelloufi thanks the society MedBioMed for financial support. This work was supported by the ANR MUCOCIL project, Grant ANR-13-BSV5-0015 of the French Agence Nationale de la Recherche.

Defective pulmonary innervation and autonomic imbalance in congenital diaphragmatic hernia

PubMed Central

Lath, Nikesh R.; Galambos, Csaba; Rocha, Alejandro Best; Malek, Marcus; Gittes, George K.

2012-01-01

Congenital diaphragmatic hernia (CDH) is associated with significant mortality due to lung hypoplasia and pulmonary hypertension. The role of embryonic pulmonary innervation in normal lung development and lung maldevelopment in CDH has not been defined. We hypothesize that developmental defects of intrapulmonary innervation, in particular autonomic innervation, occur in CDH. This abnormal embryonic pulmonary innervation may contribute to lung developmental defects and postnatal physiological derangement in CDH. To define patterns of pulmonary innervation in CDH, human CDH and control lung autopsy specimens were stained with the pan-neural marker S-100. To further characterize patterns of overall and autonomic pulmonary innervation during lung development in CDH, the murine nitrofen model of CDH was utilized. Immunostaining for protein gene product 9.5 (a pan-neuronal marker), tyrosine hydroxylase (a sympathetic marker), vesicular acetylcholine transporter (a parasympathetic marker), or VIP (a parasympathetic marker) was performed on lung whole mounts and analyzed via confocal microscopy and three-dimensional reconstruction. Peribronchial and perivascular neuronal staining pattern is less complex in human CDH than control lung. In mice, protein gene product 9.5 staining reveals less complex neuronal branching and decreased neural tissue in nitrofen-treated lungs from embryonic day 12.5 to 16.5 compared with controls. Furthermore, nitrofen-treated embryonic lungs exhibited altered autonomic innervation, with a relative increase in sympathetic nerve staining and a decrease in parasympathetic nerve staining compared with controls. These results suggest a primary defect in pulmonary neural developmental in CDH, resulting in less complex neural innervation and autonomic imbalance. Defective embryonic pulmonary innervation may contribute to lung developmental defects and postnatal physiological derangement in CDH. PMID:22114150

Genotyping and drug susceptibility testing of mycobacterial isolates from population-based tuberculosis prevalence survey in Ghana.

PubMed

Addo, Kennedy Kwasi; Addo, Samuel Ofori; Mensah, Gloria Ivy; Mosi, Lydia; Bonsu, Frank Adae

2017-12-02

Mycobacterium tuberculosis complex (MTBC) and Non-tuberculosis Mycobacterium (NTM) infections differ clinically, making rapid identification and drug susceptibility testing (DST) very critical for infection control and drug therapy. This study aims to use World Health Organization (WHO) approved line probe assay (LPA) to differentiate mycobacterial isolates obtained from tuberculosis (TB) prevalence survey in Ghana and to determine their drug resistance patterns. A retrospective study was conducted whereby a total of 361 mycobacterial isolates were differentiated and their drug resistance patterns determined using GenoType Mycobacterium Assays: MTBC and CM/AS for differentiating MTBC and NTM as well MTBDRplus and NTM-DR for DST of MTBC and NTM respectively. Out of 361 isolates, 165 (45.7%) MTBC and 120 (33.2%) NTM (made up of 14 different species) were identified to the species levels whiles 76 (21.1%) could not be completely identified. The MTBC comprised 161 (97.6%) Mycobacterium tuberculosis and 4 (2.4%) Mycobacterium africanum. Isoniazid and rifampicin monoresistant MTBC isolates were 18/165 (10.9%) and 2/165(1.2%) respectively whiles 11/165 (6.7%) were resistant to both drugs. Majority 42/120 (35%) of NTM were M. fortuitum. DST of 28 M. avium complex and 8 M. abscessus complex species revealed that all were susceptible to macrolides (clarithromycin, azithromycin) and aminoglycosides (kanamycin, amikacin, and gentamicin). Our research signifies an important contribution to TB control in terms of knowledge of the types of mycobacterium species circulating and their drug resistance patterns in Ghana.

Characterization of craniofacial sutures using the finite element method.

PubMed

Maloul, Asmaa; Fialkov, Jeffrey; Wagner, Diane; Whyne, Cari M

2014-01-03

Characterizing the biomechanical behavior of sutures in the human craniofacial skeleton (CFS) is essential to understand the global impact of these articulations on load transmission, but is challenging due to the complexity of their interdigitated morphology, the multidirectional loading they are exposed to and the lack of well-defined suture material properties. This study aimed to quantify the impact of morphological features, direction of loading and suture material properties on the mechanical behavior of sutures and surrounding bone in the CFS. Thirty-six idealized finite element (FE) models were developed. One additional specimen-specific FE model was developed based on the morphology obtained from a µCT scan to represent the morphological complexity inherent in CFS sutures. Outcome variables of strain energy (SE) and von Mises stress (σvm) were evaluated to characterize the sutures' biomechanical behavior. Loading direction was found to impact the relationship between SE and interdigitation index and yielded varied patterns of σvm in both the suture and surrounding bone. Adding bone connectivity reduced suture strain energy and altered the σvm distribution. Incorporating transversely isotropic material properties was found to reduce SE, but had little impact on stress patterns. High-resolution µCT scanning of the suture revealed a complex morphology with areas of high and low interdigitations. The specimen specific suture model results were reflective of SE absorption and σvm distribution patterns consistent with the simplified FE results. Suture mechanical behavior is impacted by morphologic factors (interdigitation and connectivity), which may be optimized for regional loading within the CFS. © 2013 Elsevier Ltd. All rights reserved.

Lamina-specific contribution of glutamatergic and GABAergic potentials to hippocampal sharp wave-ripple complexes.

PubMed

Schönberger, Jan; Draguhn, Andreas; Both, Martin

2014-01-01

The mammalian hippocampus expresses highly organized patterns of neuronal activity which form a neuronal correlate of spatial memories. These memory-encoding neuronal ensembles form on top of different network oscillations which entrain neurons in a state- and experience-dependent manner. The mechanisms underlying activation, timing and selection of participating neurons are incompletely understood. Here we studied the synaptic mechanisms underlying one prominent network pattern called sharp wave-ripple complexes (SPW-R) which are involved in memory consolidation during sleep. We recorded SPW-R with extracellular electrodes along the different layers of area CA1 in mouse hippocampal slices. Contribution of glutamatergic excitation and GABAergic inhibition, respectively, was probed by local application of receptor antagonists into s. radiatum, pyramidale and oriens. Laminar profiles of field potentials show that GABAergic potentials contribute substantially to sharp waves and superimposed ripple oscillations in s. pyramidale. Inhibitory inputs to s. pyramidale and s. oriens are crucial for action potential timing by ripple oscillations, as revealed by multiunit-recordings in the pyramidal cell layer. Glutamatergic afferents, on the other hand, contribute to sharp waves in s. radiatum where they also evoke a fast oscillation at ~200 Hz. Surprisingly, field ripples in s. radiatum are slightly slower than ripples in s. pyramidale, resulting in a systematic shift between dendritic and somatic oscillations. This complex interplay between dendritic excitation and perisomatic inhibition may be responsible for the precise timing of discharge probability during the time course of SPW-R. Together, our data illustrate a complementary role of spatially confined excitatory and inhibitory transmission during highly ordered network patterns in the hippocampus.

Geomorphic controls of soil spatial complexity in a primeval mountain forest in the Czech Republic

NASA Astrophysics Data System (ADS)

Daněk, Pavel; Šamonil, Pavel; Phillips, Jonathan D.

2016-11-01

Soil diversity and complexity is influenced by a variety of factors, and much recent research has been focused on interpreting or modeling complexity based on soil-topography relationships, and effects of biogeomorphic processes. We aimed to (i) describe local soil diversity in one of the oldest forest reserves in Europe, (ii) employ existing graph theory concepts in pedocomplexity calculation and extend them by a novel approach based on hypothesis testing and an index measuring graph sequentiality (the extent to which soils have gradual vs. abrupt variations in underlying soil factors), and (iii) reveal the main sources of pedocomplexity, with a particular focus on geomorphic controls. A total of 954 soil profiles were described and classified to soil taxonomic units (STU) within a 46 ha area. We analyzed soil diversity using the Shannon index, and soil complexity using a novel graph theory approach. Pairwise tests of observed adjacencies, spectral radius and a newly proposed sequentiality index were used to describe and quantify the complexity of the spatial pattern of STUs. This was then decomposed into the contributions of three soil factor sequences (SFS), (i) degree of weathering and leaching processes, (ii) hydromorphology, and (iii) proportion of rock fragments. Six Reference Soil Groups and 37 second-level soil units were found. A significant portion of pedocomplexity occurred at distances shorter than the 22 m spacing of neighbouring soil profiles. The spectral radius (an index of complexity) of the pattern of soil spatial adjacency was 14.73, to which the individual SFS accounted for values of 2.0, 8.0 and 3.5, respectively. Significant sequentiality was found for degree of weathering and hydromorphology. Exceptional overall pedocomplexity was particularly caused by enormous spatial variability of soil wetness, representing a crucial soil factor sequence in the primeval forest. Moreover, the soil wetness gradient was partly spatially correlated with the gradient of soil weathering and leaching, suggesting synergistic influences of topography, climate, (hydro)geology and biomechanical and biochemical effects of individual trees. The pattern of stony soils, random in most respects, resulted probably from local geology and quaternary biogeomorphological processes. Thus, while geomorphology is the primary control over a very locally complex soil pattern, microtopography and local disturbances, mostly related to the effects of individual trees, are also critical. Considerable local pedodiversity seems to be an important component of the dynamics of old-growth mixed temperate mountain forests, with implications for decreasing pedodiversity in managed forests and deforested areas.

Patterned variation in prehistoric chiefdoms

PubMed Central

Drennan, Robert D.; Peterson, Christian E.

2006-01-01

Comparative study of early complex societies (chiefdoms) conjures visions of a cultural evolutionary emphasis on similarities and societal typology. Variation within the group has not been as systematically examined but offers an even more productive avenue of approach to fundamental principles of organization and change. Three widely separated trajectories of early chiefdom development are compared here: the Valley of Oaxaca (Mexico), the Alto Magdalena (Colombia), and Northeast China. Archaeological data from all three regions are analyzed with the same tools to reveal variation in human activities, relationships, and interactions as these change in the emergence of chiefly communities. Patterning in this variation suggests the operation of underlying general principles, which are offered as hypotheses that merit further investigation and evaluation in comparative study of a much larger number of cases. PMID:16473941

Redox Non-Innocence of Nitrosobenzene at Nickel

DOE PAGES

Kundu, Subrata; Stieber, S. Chantal; Ferrier, Maryline Ghislaine; ...

2016-08-22

Nitrosobenzene (PhNO) serves as a stable analogue of nitroxyl (HNO), a biologically relevant, redox-active nitric oxide derivative. Capture of nitrosobenzene at the electrondeficient β-diketiminato nickel(I) complex [ iPr 2NN F6]Ni results in reduction of the PhNO ligand to a (PhNO) ./ ⁻ species coordinated to a square planar Ni II center in [ iPr 2NN F6]Ni(η 2- ONPh). Ligand centered reduction leads to the (PhNO) -2 moiety bound to Ni II supported by XAS studies. Ultimately, systematic investigation of structure–reactivity patterns of (PhNO) ./ ⁻ and (PhNO) 2- ligands reveals parallels with superoxo (O 2) ./ ⁻ and peroxo (Omore » 2) 2- ligands, respectively, and forecasts reactivity patterns of the more transient HNO ligand.« less

Patterns of calcium oxalate monohydrate crystallization in complex biological systems

NASA Astrophysics Data System (ADS)

Golovanova, O. A.; Korol'kov, V. V.; Kuimova, M. V.

2017-01-01

The paper presents the features of calcium oxalate crystallization in the presence of additives revealed through experimental modeling. The patterns of phase formation are shown for the Ca2+ - C2O4 2- - H2O and Ca2+ - C2O4 2- - PO4 3- - H2O systems with the components and pH of the saline varying over a wide concentrations range. The effect of additives on crystallization of calcium oxalate monohydrate was investigated. It was found that the ionic strength and magnesium ions are inhibitors, and calcium oxalate and hydroxyapatite crystals are catalysts of calcium oxalate monohydrate crystallization. The basic calcium phosphate (apatite) was found to be most thermodynamically stable, which indicates its special role in kidney stone formation since it is found in virtually all stones.

Affinity communities in United Nations voting: Implications for democracy, cooperation, and conflict

NASA Astrophysics Data System (ADS)

Pauls, Scott D.; Cranmer, Skyler J.

2017-10-01

A network oriented examination of the co-voting network of the United Nations (UN) provides powerful insights into the international alignment of states, as well as normatively important processes such as democracy, defensive cooperation, and armed conflict. Here, we investigate the UN co-voting network using the tools of community detection and inductively identify "affinity communities" in which states articulate similar policy preferences through their voting patterns. Analysis of these communities reveals that there is more information contained in UN voting and co-voting patterns than has previously been thought. Affinity communities have complex relationships with some of the most normatively important international outcomes: they reflect transitions to democracy, have a feedback loop with the formation of defensive alliances, and actively help states avoid armed conflict.

Face adaptation improves gender discrimination.

PubMed

Yang, Hua; Shen, Jianhong; Chen, Juan; Fang, Fang

2011-01-01

Adaptation to a visual pattern can alter the sensitivities of neuronal populations encoding the pattern. However, the functional roles of adaptation, especially in high-level vision, are still equivocal. In the present study, we performed three experiments to investigate if face gender adaptation could affect gender discrimination. Experiments 1 and 2 revealed that adapting to a male/female face could selectively enhance discrimination for male/female faces. Experiment 3 showed that the discrimination enhancement induced by face adaptation could transfer across a substantial change in three-dimensional face viewpoint. These results provide further evidence suggesting that, similar to low-level vision, adaptation in high-level vision could calibrate the visual system to current inputs of complex shapes (i.e. face) and improve discrimination at the adapted characteristic. Copyright © 2010 Elsevier Ltd. All rights reserved.

Reconstructing Perceived and Retrieved Faces from Activity Patterns in Lateral Parietal Cortex.

PubMed

Lee, Hongmi; Kuhl, Brice A

2016-06-01

Recent findings suggest that the contents of memory encoding and retrieval can be decoded from the angular gyrus (ANG), a subregion of posterior lateral parietal cortex. However, typical decoding approaches provide little insight into the nature of ANG content representations. Here, we tested whether complex, multidimensional stimuli (faces) could be reconstructed from ANG by predicting underlying face components from fMRI activity patterns in humans. Using an approach inspired by computer vision methods for face recognition, we applied principal component analysis to a large set of face images to generate eigenfaces. We then modeled relationships between eigenface values and patterns of fMRI activity. Activity patterns evoked by individual faces were then used to generate predicted eigenface values, which could be transformed into reconstructions of individual faces. We show that visually perceived faces were reliably reconstructed from activity patterns in occipitotemporal cortex and several lateral parietal subregions, including ANG. Subjective assessment of reconstructed faces revealed specific sources of information (e.g., affect and skin color) that were successfully reconstructed in ANG. Strikingly, we also found that a model trained on ANG activity patterns during face perception was able to successfully reconstruct an independent set of face images that were held in memory. Together, these findings provide compelling evidence that ANG forms complex, stimulus-specific representations that are reflected in activity patterns evoked during perception and remembering. Neuroimaging studies have consistently implicated lateral parietal cortex in episodic remembering, but the functional contributions of lateral parietal cortex to memory remain a topic of debate. Here, we used an innovative form of fMRI pattern analysis to test whether lateral parietal cortex actively represents the contents of memory. Using a large set of human face images, we first extracted latent face components (eigenfaces). We then used machine learning algorithms to predict face components from fMRI activity patterns and, ultimately, to reconstruct images of individual faces. We show that activity patterns in a subregion of lateral parietal cortex, the angular gyrus, supported successful reconstruction of perceived and remembered faces, confirming a role for this region in actively representing remembered content. Copyright © 2016 the authors 0270-6474/16/366069-14$15.00/0.

The co-genetic evolution of metamorphic core complexes and drainage systems

NASA Astrophysics Data System (ADS)

Trost, Georg; Neubauer, Franz; Robl, Jörg

2016-04-01

Metamorphic core complexes (MCCs) are large scale geological features that globally occur in high strain zones where rocks from lower crustal levels are rapidly exhumed along discrete fault zones, basically ductile-low-angle normal faults recognizable by a metamorphic break between the cool upper plate and hot lower plate. Standard methods, structural analysis and geochronology, are applied to reveal the geodynamic setting of MCCs and to constrain timing and rates of their exhumation. Exhumation is abundantly accompanied by spatially and temporally variable vertical (uplift) and horizontal motions (lateral advection) representing the tectonic driver of topography formation that forces drainage systems and related hillslopes to adjust. The drainage pattern commonly develops in the final stage of exhumation and contributes to the decay of the forming topography. Astonishingly, drainage systems and their characteristic metrics (e.g. normalized steepness index) in regions coined by MCCs have only been sparsely investigated to determine distinctions between different MCC-types (A- and B-type MCCs according to Le Pourhiet et al., 2012). They however, should significantly differ in their topographic expression that evolves by the interplay of tectonic forcing and erosional surface processes. A-type MCCs develop in an overall extensional regime and are bounded partly by strike-slip faults showing transtensional or transpressional components. B-type MCCs are influenced by extensional dynamics only. Here, we introduce C-type MCCs that are updoming along oversteps of crustal-scale, often orogen-parallel strike-slip shear zones. In this study, we analyze drainage systems of several prominent MCCs, and compare their drainage patterns and channel metrics to constrain their geodynamic setting. The Naxos MCC represents an A-type MCC. The Dayman Dome located in Papua New Guinea a B-type MCC, whereas MCCs of the Red River Shear Zone, the Diancang, Ailao-Shan and Day Nui Con Voi complexes, show structural features of the C-type endmember. In the case of the Diancang complex, the MCC is even superimposed by late stage B-type dynamics. The Tauern window and Lepontine dome in the Alps are described as C-type MCCs. We extracted drainage systems and basins and calculated Strahler orders to explore asymmetries in the drainage pattern and to detect evidence for horizontal advection of rivers and catchments. We computed longitudinal river profiles and determined the normalized steepness indexes for channels to uncover regions of spatially variable uplift rates and to constrain the state of landscape adjustment at active MCCs. Furthermore, we analyzed the stability of watersheds by computing so called χ-maps. A-type MCCs show a drainage pattern, which is partly parallel to the stretching and elongation direction, potentially developing from grooves of the detachment. The B-type MCCs show preferences for a radial oriented drainage pattern along lateral terminations. The radial morphology is overprinted by fault systems and neighboring uplifted domes beside the investigation site. A clear preferred direction for further capturing of catchments can be described along detachment zones. The results show an asymmetric alignment of the drainage networks of C-type MCCs, caused by tilting and lateral offset of the streams. One side of the valley shows short streams, whereas the other side is characterized by long, deeply incised streams with a clear tendency to capture adjacent catchments. In C-type MCCs, the drainage pattern develops perpendicular to the trunk streams, which are subparallel to confining faults. The tributaries of the trunk valleys show often dragging in shear direction of the confining fault. The drainage pattern along ductile low-angle normal faults seemingly develops parallel to these faults and shows an asymmetry due to tilting towards the hangingwall block. The analysis reveals that the three types of MCCs can be distinguished by their drainage pattern. All three types have a distinct central drainage divide in common, which is getting elongated in the stretching direction in C-type MCCs and remains small in B-type MCCs. Further early results of our analysis show the high potential of employing morphometric tools in combination with methods from structural geology and low temperature geochronology to determine the type of MCCs, to reveal timing and rates of uplift and horizontal advection, and to constrain the state of landscape adjustment at active MCCs.

Settlement-Size Scaling among Prehistoric Hunter-Gatherer Settlement Systems in the New World

PubMed Central

Haas, W. Randall; Klink, Cynthia J.; Maggard, Greg J.; Aldenderfer, Mark S.

2015-01-01

Settlement size predicts extreme variation in the rates and magnitudes of many social and ecological processes in human societies. Yet, the factors that drive human settlement-size variation remain poorly understood. Size variation among economically integrated settlements tends to be heavy tailed such that the smallest settlements are extremely common and the largest settlements extremely large and rare. The upper tail of this size distribution is often formalized mathematically as a power-law function. Explanations for this scaling structure in human settlement systems tend to emphasize complex socioeconomic processes including agriculture, manufacturing, and warfare—behaviors that tend to differentially nucleate and disperse populations hierarchically among settlements. But, the degree to which heavy-tailed settlement-size variation requires such complex behaviors remains unclear. By examining the settlement patterns of eight prehistoric New World hunter-gatherer settlement systems spanning three distinct environmental contexts, this analysis explores the degree to which heavy-tailed settlement-size scaling depends on the aforementioned socioeconomic complexities. Surprisingly, the analysis finds that power-law models offer plausible and parsimonious statistical descriptions of prehistoric hunter-gatherer settlement-size variation. This finding reveals that incipient forms of hierarchical settlement structure may have preceded socioeconomic complexity in human societies and points to a need for additional research to explicate how mobile foragers came to exhibit settlement patterns that are more commonly associated with hierarchical organization. We propose that hunter-gatherer mobility with preferential attachment to previously occupied locations may account for the observed structure in site-size variation. PMID:26536241

The dynamics of folding instability in a constrained Cosserat medium

NASA Astrophysics Data System (ADS)

Gourgiotis, Panos A.; Bigoni, Davide

2017-04-01

Different from Cauchy elastic materials, generalized continua, and in particular constrained Cosserat materials, can be designed to possess extreme (near a failure of ellipticity) orthotropy properties and in this way to model folding in a three-dimensional solid. Following this approach, folding, which is a narrow zone of highly localized bending, spontaneously emerges as a deformation pattern occurring in a strongly anisotropic solid. How this peculiar pattern interacts with wave propagation in the time-harmonic domain is revealed through the derivation of an antiplane, infinite-body Green's function, which opens the way to integral techniques for anisotropic constrained Cosserat continua. Viewed as a perturbing agent, the Green's function shows that folding, emerging near a steadily pulsating source in the limit of failure of ellipticity, is transformed into a disturbance with wavefronts parallel to the folding itself. The results of the presented study introduce the possibility of exploiting constrained Cosserat solids for propagating waves in materials displaying origami patterns of deformation. This article is part of the themed issue 'Patterning through instabilities in complex media: theory and applications.'

Resting state fMRI entropy probes complexity of brain activity in adults with ADHD.

PubMed

Sokunbi, Moses O; Fung, Wilson; Sawlani, Vijay; Choppin, Sabine; Linden, David E J; Thome, Johannes

2013-12-30

In patients with attention deficit hyperactivity disorder (ADHD), quantitative neuroimaging techniques have revealed abnormalities in various brain regions, including the frontal cortex, striatum, cerebellum, and occipital cortex. Nonlinear signal processing techniques such as sample entropy have been used to probe the regularity of brain magnetoencephalography signals in patients with ADHD. In the present study, we extend this technique to analyse the complex output patterns of the 4 dimensional resting state functional magnetic resonance imaging signals in adult patients with ADHD. After adjusting for the effect of age, we found whole brain entropy differences (P=0.002) between groups and negative correlation (r=-0.45) between symptom scores and mean whole brain entropy values, indicating lower complexity in patients. In the regional analysis, patients showed reduced entropy in frontal and occipital regions bilaterally and a significant negative correlation between the symptom scores and the entropy maps at a family-wise error corrected cluster level of P<0.05 (P=0.001, initial threshold). Our findings support the hypothesis of abnormal frontal-striatal-cerebellar circuits in ADHD and the suggestion that sample entropy is a useful tool in revealing abnormalities in the brain dynamics of patients with psychiatric disorders. © 2013 Elsevier Ireland Ltd. All rights reserved.

Nuclear and chloroplast DNA phylogeny reveals complex evolutionary history of Elymus pendulinus.

PubMed

Yan, Chi; Hu, Qianni; Sun, Genlou

2014-02-01

Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo complex reticulate evolution. In this study, 13 accessions of tetraploid Elymus pendulinus were analyzed using two low-copy nuclear genes (RPB2 and PepC) and two regions of chloroplast genome (Rps16 and trnD-trnT). Previous studies suggested that Pseudoroegneria (St) and an unknown diploid (Y) were genome donors to E. pendulinus, and that Pseudoroegneria was the maternal donor. Our results revealed an extreme reticulate pattern, with at least four distinct gene lineages coexisting within this species that might be acquired through a possible combination of allotetraploidization and introgression from both within and outside the tribe Hordeeae. Chloroplast DNA data identified two potential maternal genome donors (Pseudoroegneria and an unknown species outside Hordeeae) to E. pendulinus. Nuclear gene data indicated that both Pseudoroegneria and an unknown Y diploid have contributed to the nuclear genome of E. pendulinus, in agreement with cytogenetic data. However, unexpected contributions from Hordeum and unknown aliens from within or outside Hordeeae to E. pendulinus without genome duplication were observed. Elymus pendulinus provides a remarkable instance of the previously unsuspected chimerical nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events.

Low latitude ionospheric TEC responses to dynamical complexity quantifiers during transient events over Nigeria

NASA Astrophysics Data System (ADS)

Ogunsua, Babalola

2018-04-01

In this study, the values of chaoticity and dynamical complexity parameters for some selected storm periods in the year 2011 and 2012 have been computed. This was done using detrended TEC data sets measured from Birnin-Kebbi, Torro and Enugu global positioning system (GPS) receiver stations in Nigeria. It was observed that the significance of difference (SD) values were mostly greater than 1.96 but surprisingly lower than 1.96 in September 29, 2011. The values of the computed SD were also found to be reduced in most cases just after the geomagnetic storm with immediate recovery a day after the main phase of the storm while the values of Lyapunov exponent and Tsallis entropy remains reduced due to the influence of geomagnetic storms. It was also observed that the value of Lyapunov exponent and Tsallis entropy reveals similar variation pattern during storm period in most cases. Also recorded surprisingly were lower values of these dynamical quantifiers during the solar flare event of August 8th and 9th of the year 2011. The possible mechanisms responsible for these observations were further discussed in this work. However, our observations show that the ionospheric effects of some other possible transient events other than geomagnetic storms can also be revealed by the variation of chaoticity and dynamical complexity.

Students Mental Representation of Biology Diagrams/Pictures Conventions Based on Formation of Causal Network

NASA Astrophysics Data System (ADS)

Sampurno, A. W.; Rahmat, A.; Diana, S.

2017-09-01

Diagrams/pictures conventions is one form of visual media that often used to assist students in understanding the biological concepts. The effectiveness of use diagrams/pictures in biology learning at school level has also been mostly reported. This study examines the ability of high school students in reading diagrams/pictures biological convention which is described by Mental Representation based on formation of causal networks. The study involved 30 students 11th grade MIA senior high school Banten Indonesia who are studying the excretory system. MR data obtained by Instrument worksheet, developed based on CNET-protocol, in which there are diagrams/drawings of nephron structure and urinary mechanism. Three patterns formed MR, namely Markov chain, feedback control with a single measurement, and repeated feedback control with multiple measurement. The third pattern is the most dominating pattern, differences in the pattern of MR reveal the difference in how and from which point the students begin to uncover important information contained in the diagram to establish a causal networks. Further analysis shows that a difference in the pattern of MR relate to how complex the students process the information contained in the diagrams/pictures.

Microbial colonization and lung function in adolescents with cystic fibrosis.

PubMed

Hector, Andreas; Kirn, Tobias; Ralhan, Anjali; Graepler-Mainka, Ute; Berenbrinker, Sina; Riethmueller, Joachim; Hogardt, Michael; Wagner, Marlies; Pfleger, Andreas; Autenrieth, Ingo; Kappler, Matthias; Griese, Matthias; Eber, Ernst; Martus, Peter; Hartl, Dominik

2016-05-01

With intensified antibiotic therapy and longer survival, patients with cystic fibrosis (CF) are colonized with a more complex pattern of bacteria and fungi. However, the clinical relevance of these emerging pathogens for lung function remains poorly defined. The aim of this study was to assess the association of bacterial and fungal colonization patterns with lung function in adolescent patients with CF. Microbial colonization patterns and lung function parameters were assessed in 770 adolescent European (German/Austrian) CF patients in a retrospective study (median follow-up time: 10years). Colonization with Pseudomonas aeruginosa and MRSA were most strongly associated with loss of lung function, while mainly colonization with Haemophilus influenzae was associated with preserved lung function. Aspergillus fumigatus was the only species that was associated with an increased risk for infection with P. aeruginosa. Microbial interaction analysis revealed three distinct microbial clusters within the longitudinal course of CF lung disease. Collectively, this study identified potentially protective and harmful microbial colonization patterns in adolescent CF patients. Further studies in different patient cohorts are required to evaluate these microbial patterns and to assess their clinical relevance. Copyright © 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Hits to the left, flops to the right: different emotions during listening to music are reflected in cortical lateralisation patterns.

PubMed

Altenmüller, Eckart; Schürmann, Kristian; Lim, Vanessa K; Parlitz, Dietrich

2002-01-01

In order to investigate the neurobiological mechanisms accompanying emotional valence judgements during listening to complex auditory stimuli, cortical direct current (dc)-electroencephalography (EEG) activation patterns were recorded from 16 right-handed students. Students listened to 160 short sequences taken from the repertoires of jazz, rock-pop, classical music and environmental sounds (each n=40). Emotional valence of the perceived stimuli were rated on a 5-step scale after each sequence. Brain activation patterns during listening revealed widespread bilateral fronto-temporal activation, but a highly significant lateralisation effect: positive emotional attributions were accompanied by an increase in left temporal activation, negative by a more bilateral pattern with preponderance of the right fronto-temporal cortex. Female participants demonstrated greater valence-related differences than males. No differences related to the four stimulus categories could be detected, suggesting that the actual auditory brain activation patterns were more determined by their affective emotional valence than by differences in acoustical "fine" structure. The results are consistent with a model of hemispheric specialisation concerning perceived positive or negative emotions proposed by Heilman [Journal of Neuropsychiatry and Clinical Neuroscience 9 (1997) 439].

Using factor analysis to identify neuromuscular synergies during treadmill walking

NASA Technical Reports Server (NTRS)

Merkle, L. A.; Layne, C. S.; Bloomberg, J. J.; Zhang, J. J.

1998-01-01

Neuroscientists are often interested in grouping variables to facilitate understanding of a particular phenomenon. Factor analysis is a powerful statistical technique that groups variables into conceptually meaningful clusters, but remains underutilized by neuroscience researchers presumably due to its complicated concepts and procedures. This paper illustrates an application of factor analysis to identify coordinated patterns of whole-body muscle activation during treadmill walking. Ten male subjects walked on a treadmill (6.4 km/h) for 20 s during which surface electromyographic (EMG) activity was obtained from the left side sternocleidomastoid, neck extensors, erector spinae, and right side biceps femoris, rectus femoris, tibialis anterior, and medial gastrocnemius. Factor analysis revealed 65% of the variance of seven muscles sampled aligned with two orthogonal factors, labeled 'transition control' and 'loading'. These two factors describe coordinated patterns of muscular activity across body segments that would not be evident by evaluating individual muscle patterns. The results show that factor analysis can be effectively used to explore relationships among muscle patterns across all body segments to increase understanding of the complex coordination necessary for smooth and efficient locomotion. We encourage neuroscientists to consider using factor analysis to identify coordinated patterns of neuromuscular activation that would be obscured using more traditional EMG analyses.

Phase separation driven by density-dependent movement: A novel mechanism for ecological patterns.

PubMed

Liu, Quan-Xing; Rietkerk, Max; Herman, Peter M J; Piersma, Theunis; Fryxell, John M; van de Koppel, Johan

2016-12-01

Many ecosystems develop strikingly regular spatial patterns because of small-scale interactions between organisms, a process generally referred to as spatial self-organization. Self-organized spatial patterns are important determinants of the functioning of ecosystems, promoting the growth and survival of the involved organisms, and affecting the capacity of the organisms to cope with changing environmental conditions. The predominant explanation for self-organized pattern formation is spatial heterogeneity in establishment, growth and mortality, resulting from the self-organization processes. A number of recent studies, however, have revealed that movement of organisms can be an important driving process creating extensive spatial patterning in many ecosystems. Here, we review studies that detail movement-based pattern formation in contrasting ecological settings. Our review highlights that a common principle, where movement of organisms is density-dependent, explains observed spatial regular patterns in all of these studies. This principle, well known to physics as the Cahn-Hilliard principle of phase separation, has so-far remained unrecognized as a general mechanism for self-organized complexity in ecology. Using the examples presented in this paper, we explain how this movement principle can be discerned in ecological settings, and clarify how to test this mechanism experimentally. Our study highlights that animal movement, both in isolation and in unison with other processes, is an important mechanism for regular pattern formation in ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

Venomic and antivenomic analyses of the Central American coral snake, Micrurus nigrocinctus (Elapidae).

PubMed

Fernández, Julián; Alape-Girón, Alberto; Angulo, Yamileth; Sanz, Libia; Gutiérrez, José María; Calvete, Juan J; Lomonte, Bruno

2011-04-01

The proteome of the venom of Micrurus nigrocinctus (Central American coral snake) was analyzed by a "venomics" approach. Nearly 50 venom peaks were resolved by RP-HPLC, revealing a complex protein composition. Comparative analyses of venoms from individual specimens revealed that such complexity is an intrinsic feature of this species, rather than the sum of variable individual patterns of simpler composition. Proteins related to eight distinct families were identified by MS/MS de novo peptide sequencing or N-terminal sequencing: phospholipase A(2) (PLA(2)), three-finger toxin (3FTx), l-amino acid oxidase, C-type lectin/lectin-like, metalloproteinase, serine proteinase, ohanin, and nucleotidase. PLA(2)s and 3FTxs are predominant, representing 48 and 38% of the venom proteins, respectively. Within 3FTxs, several isoforms of short-chain α-neurotoxins as well as muscarinic-like toxins and proteins with similarity to long-chain κ-2 bungarotoxin were identified. PLA(2)s are also highly diverse, and a toxicity screening showed that they mainly exert myotoxicity, although some are lethal and may contribute to the known presynaptic neurotoxicity of this venom. An antivenomic characterization of a therapeutic monospecific M. nigrocinctus equine antivenom revealed differences in immunorecognition of venom proteins that correlate with their molecular mass, with the weakest recognition observed toward 3FTxs.

Genotyping of clinical and environmental multidrug resistant Enterococcus faecium strains.

PubMed

Shokoohizadeh, Leili; Mobarez, Ashraf Mohabati; Alebouyeh, Masoud; Zali, Mohammad Reza; Ranjbar, Reza

2017-01-01

Multidrug resistant (MDR) Enterococcus faecium is a nosocomial pathogen and clonal complex 17 (CC17) is the main genetic subpopulation of E. faecium in hospitals worldwide. There has thus far been no report of major E. faecium clones in Iranian hospitals. The present study analyzed strains of MDR E. faecium obtained from patients and the Intensive Care Unit environments using pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) to determine the antibiotic resistance patterns and genetic features of the dominant. clones of E. faecium. PFGE and MLST analysis revealed the presence of 17and 15 different subtypes, respectively. Of these, 18 (86%) isolates belonged toCC17. Most strains in this clonal complex harbored the esp gene and exhibited resistance to vancomycin, teicoplanin, ampicillin, ciprofloxacin, gentamicin, and erythromycin. The MLST results revealed 12 new sequence types (ST) for the first time. Approximately 50% of the STs were associated with ST203. Detection of E. faecium strains belonging to CC17 on medical equipment and in clinical specimens verified the circulation of high-risk MDR clones among the patients and in hospital environments in Iran.

A Developmental Framework for Complex Plasmodesmata Formation Revealed by Large-Scale Imaging of the Arabidopsis Leaf Epidermis[W

PubMed Central

Fitzgibbon, Jessica; Beck, Martina; Zhou, Ji; Faulkner, Christine; Robatzek, Silke; Oparka, Karl

2013-01-01

Plasmodesmata (PD) form tubular connections that function as intercellular communication channels. They are essential for transporting nutrients and for coordinating development. During cytokinesis, simple PDs are inserted into the developing cell plate, while during wall extension, more complex (branched) forms of PD are laid down. We show that complex PDs are derived from existing simple PDs in a pattern that is accelerated when leaves undergo the sink–source transition. Complex PDs are inserted initially at the three-way junctions between epidermal cells but develop most rapidly in the anisocytic complexes around stomata. For a quantitative analysis of complex PD formation, we established a high-throughput imaging platform and constructed PDQUANT, a custom algorithm that detected cell boundaries and PD numbers in different wall faces. For anticlinal walls, the number of complex PDs increased with increasing cell size, while for periclinal walls, the number of PDs decreased. Complex PD insertion was accelerated by up to threefold in response to salicylic acid treatment and challenges with mannitol. In a single 30-min run, we could derive data for up to 11k PDs from 3k epidermal cells. This facile approach opens the door to a large-scale analysis of the endogenous and exogenous factors that influence PD formation. PMID:23371949

Preparation and properties of a monomeric high-spin Mn(V)-oxo complex.

PubMed

Taguchi, Taketo; Gupta, Rupal; Lassalle-Kaiser, Benedikt; Boyce, David W; Yachandra, Vittal K; Tolman, William B; Yano, Junko; Hendrich, Michael P; Borovik, A S

2012-02-01

Oxomanganese(V) species have been implicated in a variety of biological and synthetic processes, including their role as a key reactive center within the oxygen-evolving complex in photosynthesis. Nearly all mononuclear Mn(V)-oxo complexes have tetragonal symmetry, producing low-spin species. A new high-spin Mn(V)-oxo complex that was prepared from a well-characterized oxomanganese(III) complex having trigonal symmetry is now reported. Oxidation experiments with [FeCp(2)](+) were monitored with optical and electron paramagnetic resonance (EPR) spectroscopies and support a high-spin oxomanganese(V) complex formulation. The parallel-mode EPR spectrum has a distinctive S = 1 signal at g = 4.01 with a six-line hyperfine pattern having A(z) = 113 MHz. The presence of an oxo ligand was supported by resonance Raman spectroscopy, which revealed O-isotope-sensitive peaks at 737 and 754 cm(-1) assigned as a Fermi doublet centered at 746 cm(-1)(Δ(18)O = 31 cm(-1)). Mn Kβ X-ray emission spectra showed Kβ' and Kβ(1,3) bands at 6475.92 and 6490.50 eV, respectively, which are characteristic of a high-spin Mn(V) center. © 2012 American Chemical Society

A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes.

PubMed

Skourtanioti, Eirini; Kapli, Paschalia; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Ahmadzadeh, Faraham; Crnobrnja-Isailović, Jelka; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos

2016-10-01

Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East. Copyright © 2016 Elsevier Inc. All rights reserved.

Energy Landscape of Social Balance

NASA Astrophysics Data System (ADS)

Marvel, Seth A.; Strogatz, Steven H.; Kleinberg, Jon M.

2009-11-01

We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social “balance” allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.

Energy landscape of social balance.

PubMed

Marvel, Seth A; Strogatz, Steven H; Kleinberg, Jon M

2009-11-06

We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social "balance" allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.

On the pattern of black hole information release

NASA Astrophysics Data System (ADS)

Park, I. Y.; James, F.

2014-03-01

We propose a step towards a resolution to black hole information paradox by analyzing scattering amplitudes of a complex scalar field around a Schwarzschild black hole. The scattering cross-section reveals much information on the incoming state but exhibits flux loss at the same time. The flux loss should be temporary, and indicate mass growth of the black hole. The black hole should Hawking-radiate subsequently, thereby, compensating for the flux loss. By examining the purity issue, we comment on the possibility that information bleaching may be the key to the paradox.

Forest Connectivity Regions of Canada Using Circuit Theory and Image Analysis

PubMed Central

Pelletier, David; Lapointe, Marc-Élie; Wulder, Michael A.; White, Joanne C.; Cardille, Jeffrey A.

2017-01-01

Ecological processes are increasingly well understood over smaller areas, yet information regarding interconnections and the hierarchical nature of ecosystems remains less studied and understood. Information on connectivity over large areas with high resolution source information provides for both local detail and regional context. The emerging capacity to apply circuit theory to create maps of omnidirectional connectivity provides an opportunity for improved and quantitative depictions of forest connectivity, supporting the formation and testing of hypotheses about the density of animal movement, ecosystem structure, and related links to natural and anthropogenic forces. In this research, our goal was to delineate regions where connectivity regimes are similar across the boreal region of Canada using new quantitative analyses for characterizing connectivity over large areas (e.g., millions of hectares). Utilizing the Earth Observation for Sustainable Development of forests (EOSD) circa 2000 Landsat-derived land-cover map, we created and analyzed a national-scale map of omnidirectional forest connectivity at 25m resolution over 10000 tiles of 625 km2 each, spanning the forested regions of Canada. Using image recognition software to detect corridors, pinch points, and barriers to movements at multiple spatial scales in each tile, we developed a simple measure of the structural complexity of connectivity patterns in omnidirectional connectivity maps. We then mapped the Circuitscape resistance distance measure and used it in conjunction with the complexity data to study connectivity characteristics in each forested ecozone. Ecozone boundaries masked substantial systematic patterns in connectivity characteristics that are uncovered using a new classification of connectivity patterns that revealed six clear groups of forest connectivity patterns found in Canada. The resulting maps allow exploration of omnidirectional forest connectivity patterns at full resolution while permitting quantitative analyses of connectivity over broad areas, informing modeling, planning and monitoring efforts. PMID:28146573

Chaotic itinerancy within the coupled dynamics between a physical body and neural oscillator networks

PubMed Central

Mori, Hiroki; Okuyama, Yuji; Asada, Minoru

2017-01-01

Chaotic itinerancy is a phenomenon in which the state of a nonlinear dynamical system spontaneously explores and attracts certain states in a state space. From this perspective, the diverse behavior of animals and its spontaneous transitions lead to a complex coupled dynamical system, including a physical body and a brain. Herein, a series of simulations using different types of non-linear oscillator networks (i.e., regular, small-world, scale-free, random) with a musculoskeletal model (i.e., a snake-like robot) as a physical body are conducted to understand how the chaotic itinerancy of bodily behavior emerges from the coupled dynamics between the body and the brain. A behavior analysis (behavior clustering) and network analysis for the classified behavior are then applied. The former consists of feature vector extraction from the motions and classification of the movement patterns that emerged from the coupled dynamics. The network structures behind the classified movement patterns are revealed by estimating the “information networks” different from the given non-linear oscillator networks based on the transfer entropy which finds the information flow among neurons. The experimental results show that: (1) the number of movement patterns and their duration depend on the sensor ratio to control the balance of strength between the body and the brain dynamics and on the type of the given non-linear oscillator networks; and (2) two kinds of information networks are found behind two kinds movement patterns with different durations by utilizing the complex network measures, clustering coefficient and the shortest path length with a negative and a positive relationship with the duration periods of movement patterns. The current results seem promising for a future extension of the method to a more complicated body and environment. Several requirements are also discussed. PMID:28796797

Chaotic itinerancy within the coupled dynamics between a physical body and neural oscillator networks.

PubMed

Park, Jihoon; Mori, Hiroki; Okuyama, Yuji; Asada, Minoru

2017-01-01

Chaotic itinerancy is a phenomenon in which the state of a nonlinear dynamical system spontaneously explores and attracts certain states in a state space. From this perspective, the diverse behavior of animals and its spontaneous transitions lead to a complex coupled dynamical system, including a physical body and a brain. Herein, a series of simulations using different types of non-linear oscillator networks (i.e., regular, small-world, scale-free, random) with a musculoskeletal model (i.e., a snake-like robot) as a physical body are conducted to understand how the chaotic itinerancy of bodily behavior emerges from the coupled dynamics between the body and the brain. A behavior analysis (behavior clustering) and network analysis for the classified behavior are then applied. The former consists of feature vector extraction from the motions and classification of the movement patterns that emerged from the coupled dynamics. The network structures behind the classified movement patterns are revealed by estimating the "information networks" different from the given non-linear oscillator networks based on the transfer entropy which finds the information flow among neurons. The experimental results show that: (1) the number of movement patterns and their duration depend on the sensor ratio to control the balance of strength between the body and the brain dynamics and on the type of the given non-linear oscillator networks; and (2) two kinds of information networks are found behind two kinds movement patterns with different durations by utilizing the complex network measures, clustering coefficient and the shortest path length with a negative and a positive relationship with the duration periods of movement patterns. The current results seem promising for a future extension of the method to a more complicated body and environment. Several requirements are also discussed.

Receptive fields of locust brain neurons are matched to polarization patterns of the sky.

PubMed

Bech, Miklós; Homberg, Uwe; Pfeiffer, Keram

2014-09-22

Many animals, including insects, are able to use celestial cues as a reference for spatial orientation and long-distance navigation [1]. In addition to direct sunlight, the chromatic gradient of the sky and its polarization pattern are suited to serve as orientation cues [2-5]. Atmospheric scattering of sunlight causes a regular pattern of E vectors in the sky, which are arranged along concentric circles around the sun [5, 6]. Although certain insects rely predominantly on sky polarization for spatial orientation [7], it has been argued that detection of celestial E vector orientation may not suffice to differentiate between solar and antisolar directions [8, 9]. We show here that polarization-sensitive (POL) neurons in the brain of the desert locust Schistocerca gregaria can overcome this ambiguity. Extracellular recordings from POL units in the central complex and lateral accessory lobes revealed E vector tunings arranged in concentric circles within large receptive fields, matching the sky polarization pattern at certain solar positions. Modeling of neuronal responses under an idealized sky polarization pattern (Rayleigh sky) suggests that these "matched filter" properties allow locusts to unambiguously determine the solar azimuth by relying solely on the sky polarization pattern for compass navigation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Embryonic expression of endothelins and their receptors in lamprey and frog reveals stem vertebrate origins of complex Endothelin signaling

PubMed Central

Square, Tyler; Jandzik, David; Cattell, Maria; Hansen, Andrew; Medeiros, Daniel Meulemans

2016-01-01

Neural crest cells (NCCs) are highly patterned embryonic cells that migrate along stereotyped routes to give rise to a diverse array of adult tissues and cell types. Modern NCCs are thought to have evolved from migratory neural precursors with limited developmental potential and patterning. How this occurred is poorly understood. Endothelin signaling regulates several aspects of NCC development, including their migration, differentiation, and patterning. In jawed vertebrates, Endothelin signaling involves multiple functionally distinct ligands (Edns) and receptors (Ednrs) expressed in various NCC subpopulations. To test the potential role of endothelin signaling diversification in the evolution of modern, highly patterned NCC, we analyzed the expression of the complete set of endothelin ligands and receptors in the jawless vertebrate, the sea lamprey (Petromyzon marinus). To better understand ancestral features of gnathostome edn and ednr expression, we also analyzed all known Endothelin signaling components in the African clawed frog (Xenopus laevis). We found that the sea lamprey has a gnathsotome-like complement of edn and ednr duplicates, and these genes are expressed in patterns highly reminiscent of their gnathostome counterparts. Our results suggest that the duplication and specialization of vertebrate Endothelin signaling coincided with the appearance of highly patterned and multipotent NCCs in stem vertebrates. PMID:27677704

Isolation and characterization of major histocompatibility complex class II B genes in cranes.

PubMed

Kohyama, Tetsuo I; Akiyama, Takuya; Nishida, Chizuko; Takami, Kazutoshi; Onuma, Manabu; Momose, Kunikazu; Masuda, Ryuichi

2015-11-01

In this study, we isolated and characterized the major histocompatibility complex (MHC) class II B genes in cranes. Genomic sequences spanning exons 1 to 4 were amplified and determined in 13 crane species and three other species closely related to cranes. In all, 55 unique sequences were identified, and at least two polymorphic MHC class II B loci were found in most species. An analysis of sequence polymorphisms showed the signature of positive selection and recombination. A phylogenetic reconstruction based on exon 2 sequences indicated that trans-species polymorphism has persisted for at least 10 million years, whereas phylogenetic analyses of the sequences flanking exon 2 revealed a pattern of concerted evolution. These results suggest that both balancing selection and recombination play important roles in the crane MHC evolution.

Methods of identification employing antibody profiles

DOEpatents

Francoeur, Ann-Michele

1993-12-14

An identification method, applicable to the identification of animals or inanimate objects, is described. The method takes advantage of the set of individual-specific antibodies that are part of the unique antibody repertoire present in animals, by reacting an effective amount of such antibodies with a particular panel, of n-dimensional array (where n is typically one or two) consisting of an effective amount of many different antigens (typically greater than one thousand), to give antibody-antigen complexes. The profile or pattern formed by the antigen-antibody complexes, termed an antibody fingerprint, when revealed by an effective amount of an appropriate detector molecule, is uniquely representative of a particular individual. The method can similarly be used to distinguish genetically, or otherwise similar individuals, or their body parts containing individual-specific antibodies.

Diversity pattern in Sesamum mutants selected for a semi-arid cropping system.

PubMed

Murty, B R; Oropeza, F

1989-02-01

Due to the complex requirements of moisture stress, substantial genetic diversity with a wide array of character combinations and effective simultaneous selection for several variables is necessary for improving the productivity and adaptation of a component crop in order for it to fit into a cropping system under semi-arid tropical conditions. Sesamum indicum L. is grown in Venezuela after rice/sorghum/or maize under such conditions. A mutation breeding program was undertaken using six locally adapted varieties to develop genotypes suitable for the above system. The diversity pattern for nine variables was assessed by multivariate analysis in 301 M4 progenies. Analysis of the characteristic roots and principal components in three methods of selection, i.e., M2 bulks (A), individual plant selection throughout (B), and selection in M3 for single variable (C), revealed differences in the pattern of variation between varieties, selection methods, and varieties x methods interactions. Method B was superior to the others and gave 17 of the 21 best M5 progenies. 'Piritu' and 'CF' varieties yielded the most productive progenies in M5 and M6. Diversity was large and selection was effective for such developmental traits as earliness and synchrony, combined with multiple disease resistance, which could be related to their importance by multivariate analyses. Considerable differences in the variety of character combinations among the high yielding. M5 progenies of 'CF' and 'Piritu' suggested possible further yield improvement. The superior response of 'Piritu' and 'CF' over other varieties in yield and adaptation was due to major changes in plant type and character associations. Multilocation testing of M5 generations revealed that the mutant progenies had a 40%-100% yield superiority over the parents; this was combined with earliness, synchrony, and multiple disease resistance, and was confirmed in the M6 generation grown on a commercial scale. This study showed that multivariate analysis is an effective tool for assessing diversity patterns, choice of appropriate variety, and selection methodology in order to make rapid progress in meeting the complex requirements of semi-arid cropping systems.

Complex-ordered patterns in shaken convection.

PubMed

Rogers, Jeffrey L; Pesch, Werner; Brausch, Oliver; Schatz, Michael F

2005-06-01

We report and analyze complex patterns observed in a combination of two standard pattern forming experiments. These exotic states are composed of two distinct spatial scales, each displaying a different temporal dependence. The system is a fluid layer experiencing forcing from both a vertical temperature difference and vertical time-periodic oscillations. Depending on the parameters these forcing mechanisms produce fluid motion with either a harmonic or a subharmonic temporal response. Over a parameter range where these mechanisms have comparable influence the spatial scales associated with both responses are found to coexist, resulting in complex, yet highly ordered patterns. Phase diagrams of this region are reported and criteria to define the patterns as quasiperiodic crystals or superlattices are presented. These complex patterns are found to satisfy four-mode (resonant tetrad) conditions. The qualitative difference between the present formation mechanism and the resonant triads ubiquitously used to explain complex-ordered patterns in other nonequilibrium systems is discussed. The only exception to quantitative agreement between our analysis based on Boussinesq equations and laboratory investigations is found to be the result of breaking spatial symmetry in a small parameter region near onset.

Time-Series Analysis of Embodied Interaction: Movement Variability and Complexity Matching As Dyadic Properties

PubMed Central

Zapata-Fonseca, Leonardo; Dotov, Dobromir; Fossion, Ruben; Froese, Tom

2016-01-01

There is a growing consensus that a fuller understanding of social cognition depends on more systematic studies of real-time social interaction. Such studies require methods that can deal with the complex dynamics taking place at multiple interdependent temporal and spatial scales, spanning sub-personal, personal, and dyadic levels of analysis. We demonstrate the value of adopting an extended multi-scale approach by re-analyzing movement time-series generated in a study of embodied dyadic interaction in a minimal virtual reality environment (a perceptual crossing experiment). Reduced movement variability revealed an interdependence between social awareness and social coordination that cannot be accounted for by either subjective or objective factors alone: it picks out interactions in which subjective and objective conditions are convergent (i.e., elevated coordination is perceived as clearly social, and impaired coordination is perceived as socially ambiguous). This finding is consistent with the claim that interpersonal interaction can be partially constitutive of direct social perception. Clustering statistics (Allan Factor) of salient events revealed fractal scaling. Complexity matching defined as the similarity between these scaling laws was significantly more pronounced in pairs of participants as compared to surrogate dyads. This further highlights the multi-scale and distributed character of social interaction and extends previous complexity matching results from dyadic conversation to non-verbal social interaction dynamics. Trials with successful joint interaction were also associated with an increase in local coordination. Consequently, a local coordination pattern emerges on the background of complex dyadic interactions in the PCE task and makes joint successful performance possible. PMID:28018274

Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

PubMed

Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

2014-03-01

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg.

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins

PubMed Central

Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

2014-01-01

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg. PMID:24603469

Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine

PubMed Central

Pietak, Alexis; Levin, Michael

2016-01-01

Bioelectric cell properties have been revealed as powerful targets for modulating stem cell function, regenerative response, developmental patterning, and tumor reprograming. Spatio-temporal distributions of endogenous resting potential, ion flows, and electric fields are influenced not only by the genome and external signals but also by their own intrinsic dynamics. Ion channels and electrical synapses (gap junctions) both determine, and are themselves gated by, cellular resting potential. Thus, the origin and progression of bioelectric patterns in multicellular tissues is complex, which hampers the rational control of voltage distributions for biomedical interventions. To improve understanding of these dynamics and facilitate the development of bioelectric pattern control strategies, we developed the BioElectric Tissue Simulation Engine (BETSE), a finite volume method multiphysics simulator, which predicts bioelectric patterns and their spatio-temporal dynamics by modeling ion channel and gap junction activity and tracking changes to the fundamental property of ion concentration. We validate performance of the simulator by matching experimentally obtained data on membrane permeability, ion concentration and resting potential to simulated values, and by demonstrating the expected outcomes for a range of well-known cases, such as predicting the correct transmembrane voltage changes for perturbation of single cell membrane states and environmental ion concentrations, in addition to the development of realistic transepithelial potentials and bioelectric wounding signals. In silico experiments reveal factors influencing transmembrane potential are significantly different in gap junction-networked cell clusters with tight junctions, and identify non-linear feedback mechanisms capable of generating strong, emergent, cluster-wide resting potential gradients. The BETSE platform will enable a deep understanding of local and long-range bioelectrical dynamics in tissues, and assist the development of specific interventions to achieve greater control of pattern during morphogenesis and remodeling. PMID:27458581

Estimating the functional dimensionality of neural representations.

PubMed

Ahlheim, Christiane; Love, Bradley C

2018-06-07

Recent advances in multivariate fMRI analysis stress the importance of information inherent to voxel patterns. Key to interpreting these patterns is estimating the underlying dimensionality of neural representations. Dimensions may correspond to psychological dimensions, such as length and orientation, or involve other coding schemes. Unfortunately, the noise structure of fMRI data inflates dimensionality estimates and thus makes it difficult to assess the true underlying dimensionality of a pattern. To address this challenge, we developed a novel approach to identify brain regions that carry reliable task-modulated signal and to derive an estimate of the signal's functional dimensionality. We combined singular value decomposition with cross-validation to find the best low-dimensional projection of a pattern of voxel-responses at a single-subject level. Goodness of the low-dimensional reconstruction is measured as Pearson correlation with a test set, which allows to test for significance of the low-dimensional reconstruction across participants. Using hierarchical Bayesian modeling, we derive the best estimate and associated uncertainty of underlying dimensionality across participants. We validated our method on simulated data of varying underlying dimensionality, showing that recovered dimensionalities match closely true dimensionalities. We then applied our method to three published fMRI data sets all involving processing of visual stimuli. The results highlight three possible applications of estimating the functional dimensionality of neural data. Firstly, it can aid evaluation of model-based analyses by revealing which areas express reliable, task-modulated signal that could be missed by specific models. Secondly, it can reveal functional differences across brain regions. Thirdly, knowing the functional dimensionality allows assessing task-related differences in the complexity of neural patterns. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Expression patterns of regulatory RNAs, including lncRNAs and tRNAs, during postnatal growth of normal and dystrophic (mdx) mouse muscles, and their response to taurine treatment.

PubMed

Butchart, Lauren C; Terrill, Jessica R; Rossetti, Giulia; White, Robert; Filipovska, Aleksandra; Grounds, Miranda D

2018-06-01

Post-natal skeletal muscle growth in mice is very rapid and involves complex changes in many cells types over the first 6 weeks of life. The acute onset of dystropathology also occurs around 3 weeks of age in the mdx mouse model of the human disease Duchenne Muscular Dystrophy (DMD). This study investigated (i) alterations in expression patterns of regulatory non-coding RNAs (ncRNAs) in vivo, including miRNAs, lncRNAs and tRNAs, during early growth of skeletal muscles in normal control C57Bl/10Scsn (C57) compared with dystrophic mdx mice from 2 to 6 weeks of postnatal age, and revealed inherent differences in vivo for levels of 3 ncRNAs between C57 and mdx muscles before the onset of dystropathology. Since the amino acid taurine has many benefits and reduces disease severity in mdx mice, this study also (ii) determined the impact of taurine treatment on these expression patterns in mdx muscles at the onset of dystropathology (3 weeks) and after several bouts of myonecrosis and regeneration (6 weeks). Taurine treatment of mdx mice only altered ncRNA levels when administered from 18 days to 6 weeks of age, but a deficiency in tRNA levels was rectified earlier in mdx skeletal muscles treated from 14 days to 3 weeks. Myogenesis in tissue culture was also used to (iii) compare ncRNA expression patterns for both strains, and (iv) the response to taurine treatment. These analyses revealed intrinsic differences in ncRNA expression patterns during myogenesis between strains, as well as increased sensitivity of mdx ncRNA levels to taurine treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Influence of lateral and in-depth metal segregation on the patterning of ohmic contacts for GaN-based devices

NASA Astrophysics Data System (ADS)

Redondo-Cubero, A.; Vázquez, L.; Alves, L. C.; Corregidor, V.; Romero, M. F.; Pantellini, A.; Lanzieri, C.; Muñoz, E.

2014-05-01

The lateral and in-depth metal segregation of Au/Ni/Al/Ti ohmic contacts for GaN-based high electron mobility transistors were analysed as a function of the Al barrier's thickness (d). The surface of the contacts, characterized by atomic force and scanning electron microscopy, shows a transition from a fractal network of rough and complex island-like structures towards smoother and cauliflower-like fronts with increasing d. Rutherford backscattering spectrometry and energy dispersive x-ray spectroscopy (EDXS) at different energies were used to confirm the in-depth intermixing of the metals relevant for the final contact resistance. EDXS mapping reveals a significant lateral segregation too, where the resulting patterns depend on two competing NiAlx and AuAlx phases, the intermixing being controlled by the available amount of Al. The optimum ohmic resistance is not affected by the patterning process, but is mainly dependent on the partial interdiffusion of the metals.

Role of visual and non-visual cues in constructing a rotation-invariant representation of heading in parietal cortex

PubMed Central

Sunkara, Adhira

2015-01-01

As we navigate through the world, eye and head movements add rotational velocity patterns to the retinal image. When such rotations accompany observer translation, the rotational velocity patterns must be discounted to accurately perceive heading. The conventional view holds that this computation requires efference copies of self-generated eye/head movements. Here we demonstrate that the brain implements an alternative solution in which retinal velocity patterns are themselves used to dissociate translations from rotations. These results reveal a novel role for visual cues in achieving a rotation-invariant representation of heading in the macaque ventral intraparietal area. Specifically, we show that the visual system utilizes both local motion parallax cues and global perspective distortions to estimate heading in the presence of rotations. These findings further suggest that the brain is capable of performing complex computations to infer eye movements and discount their sensory consequences based solely on visual cues. DOI: http://dx.doi.org/10.7554/eLife.04693.001 PMID:25693417

Polluted and turbid water masses in Osaka Bay and its vicinity revealed with ERTS-A imageries

NASA Technical Reports Server (NTRS)

Watanabe, K.

1973-01-01

ERTS-1 took very valuable MSS imageries of Osaka Bay and its vicinity on October 24, 1972. In the MSS-4 and MSS-5 imageries a complex grey pattern of water masses can be seen. Though some of grey colored patterns seen in black and white prints of the MSS-4 and MSS-5 imageries are easily identified from their shapes as cloud covers or polluted water masses characterized by their color tone in longer wavelengths in the visible region, any correct distribution pattern of polluted or turbid water masses can be hardly detected separately from thin cloud covers in a quick look analysis. In the present investigation, a simple photographic technique was applied using the fact that reflected sun light from cloud including smog and inclined water surfaces of wave have a certain component in the near infrared region, that MSS-7, whereas the light scattered from fine materials suspended in the sea water has nearly no component sensible in MSS-4 and MSS-5 channels.

Time-dependent scaling patterns in high frequency financial data

NASA Astrophysics Data System (ADS)

Nava, Noemi; Di Matteo, Tiziana; Aste, Tomaso

2016-10-01

We measure the influence of different time-scales on the intraday dynamics of financial markets. This is obtained by decomposing financial time series into simple oscillations associated with distinct time-scales. We propose two new time-varying measures of complexity: 1) an amplitude scaling exponent and 2) an entropy-like measure. We apply these measures to intraday, 30-second sampled prices of various stock market indices. Our results reveal intraday trends where different time-horizons contribute with variable relative amplitudes over the course of the trading day. Our findings indicate that the time series we analysed have a non-stationary multifractal nature with predominantly persistent behaviour at the middle of the trading session and anti-persistent behaviour at the opening and at the closing of the session. We demonstrate that these patterns are statistically significant, robust, reproducible and characteristic of each stock market. We argue that any modelling, analytics or trading strategy must take into account these non-stationary intraday scaling patterns.

Direct modulation of aberrant brain network connectivity through real-time NeuroFeedback

PubMed Central

Kimmich, Sara; Gonzalez-Castillo, Javier; Roopchansingh, Vinai; Popal, Haroon; White, Emily; Gotts, Stephen J; Martin, Alex

2017-01-01

The existence of abnormal connectivity patterns between resting state networks in neuropsychiatric disorders, including Autism Spectrum Disorder (ASD), has been well established. Traditional treatment methods in ASD are limited, and do not address the aberrant network structure. Using real-time fMRI neurofeedback, we directly trained three brain nodes in participants with ASD, in which the aberrant connectivity has been shown to correlate with symptom severity. Desired network connectivity patterns were reinforced in real-time, without participants’ awareness of the training taking place. This training regimen produced large, significant long-term changes in correlations at the network level, and whole brain analysis revealed that the greatest changes were focused on the areas being trained. These changes were not found in the control group. Moreover, changes in ASD resting state connectivity following the training were correlated to changes in behavior, suggesting that neurofeedback can be used to directly alter complex, clinically relevant network connectivity patterns. PMID:28917059

Spatiotemporal variability of rainfall extremes in monsoonal climates - examples from the South American Monsoon and the Indian Monsoon Systems (Invited)

NASA Astrophysics Data System (ADS)

Bookhagen, B.; Boers, N.; Marwan, N.; Malik, N.; Kurths, J.

2013-12-01

Monsoonal rainfall is the crucial component for more than half of the world's population. Runoff associated with monsoon systems provide water resources for agriculture, hydropower, drinking-water generation, recreation, and social well-being and are thus a fundamental part of human society. However, monsoon systems are highly stochastic and show large variability on various timescales. Here, we use various rainfall datasets to characterize spatiotemporal rainfall patterns using traditional as well as new approaches emphasizing nonlinear spatial correlations from a complex networks perspective. Our analyses focus on the South American (SAMS) and Indian (ISM) Monsoon Systems on the basis of Tropical Rainfall Measurement Mission (TRMM) using precipitation radar and passive-microwave products with horizontal spatial resolutions of ~5x5 km^2 (products 2A25, 2B31) and 25x25 km^2 (3B42) and interpolated rainfall-gauge data for the ISM (APHRODITE, 25x25 km^2). The eastern slopes of the Andes of South America and the southern front of the Himalaya are characterized by significant orographic barriers that intersect with the moisture-bearing, monsoonal wind systems. We demonstrate that topography exerts a first-order control on peak rainfall amounts on annual timescales in both mountain belts. Flooding in the downstream regions is dominantly caused by heavy rainfall storms that propagate deep into the mountain range and reach regions that are arid and without vegetation cover promoting rapid runoff. These storms exert a significantly different spatial distribution than average-rainfall conditions and assessing their recurrence intervals and prediction is key in understanding flooding for these regions. An analysis of extreme-value distributions of our high-spatial resolution data reveal that semi-arid areas are characterized by low-frequency/high-magnitude events (i.e., are characterized by a ';heavy tail' distribution), whereas regions with high mean annual rainfall have a less skewed distribution. In a second step, an analysis of the spatial characteristics of extreme rainfall synchronicity by means of complex networks reveals patterns of the propagation of extreme rainfall events. These patterns differ substantially from those obtained from the mean annual rainfall distribution. In addition, we have developed a scheme to predict rainfall extreme events in the eastern Central Andes based on event synchronization and spatial patterns of complex networks. The presented methods and result will allow to critically evaluate data and models in space and time.

Characteristics of pattern formation and evolution in approximations of Physarum transport networks.

PubMed

Jones, Jeff

2010-01-01

Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation.

Gradual and contingent evolutionary emergence of leaf mimicry in butterfly wing patterns.

PubMed

Suzuki, Takao K; Tomita, Shuichiro; Sezutsu, Hideki

2014-11-25

Special resemblance of animals to natural objects such as leaves provides a representative example of evolutionary adaptation. The existence of such sophisticated features challenges our understanding of how complex adaptive phenotypes evolved. Leaf mimicry typically consists of several pattern elements, the spatial arrangement of which generates the leaf venation-like appearance. However, the process by which leaf patterns evolved remains unclear. In this study we show the evolutionary origin and process for the leaf pattern in Kallima (Nymphalidae) butterflies. Using comparative morphological analyses, we reveal that the wing patterns of Kallima and 45 closely related species share the same ground plan, suggesting that the pattern elements of leaf mimicry have been inherited across species with lineage-specific changes of their character states. On the basis of these analyses, phylogenetic comparative methods estimated past states of the pattern elements and enabled reconstruction of the wing patterns of the most recent common ancestor. This analysis shows that the leaf pattern has evolved through several intermediate patterns. Further, we use Bayesian statistical methods to estimate the temporal order of character-state changes in the pattern elements by which leaf mimesis evolved, and show that the pattern elements changed their spatial arrangement (e.g., from a curved line to a straight line) in a stepwise manner and finally establish a close resemblance to a leaf venation-like appearance. Our study provides the first evidence for stepwise and contingent evolution of leaf mimicry.　 Leaf mimicry patterns evolved in a gradual, rather than a sudden, manner from a non-mimetic ancestor. Through a lineage of Kallima butterflies, the leaf patterns evolutionarily originated through temporal accumulation of orchestrated changes in multiple pattern elements.

Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene.

PubMed

Crees, Jennifer J; Carbone, Chris; Sommer, Robert S; Benecke, Norbert; Turvey, Samuel T

2016-03-30

The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18,700 mammalian zooarchaeological records for the last 11,700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of 'static' past baselines to inform current-day environmental management and restoration. © 2016 The Author(s).

Prepenetration Apparatus Assembly Precedes and Predicts the Colonization Patterns of Arbuscular Mycorrhizal Fungi within the Root Cortex of Both Medicago truncatula and Daucus carota[W

PubMed Central

Genre, Andrea; Chabaud, Mireille; Faccio, Antonella; Barker, David G.; Bonfante, Paola

2008-01-01

Arbuscular mycorrhizas (AM) are widespread, ancient endosymbiotic associations that contribute significantly to soil nutrient uptake in plants. We have previously shown that initial fungal penetration of the host root is mediated via a specialized cytoplasmic assembly called the prepenetration apparatus (PPA), which directs AM hyphae through the epidermis (Genre et al., 2005). In vivo confocal microscopy studies performed on Medicago truncatula and Daucus carota, host plants with different patterns of AM colonization, now reveal that subsequent intracellular growth across the root outer cortex is also PPA dependent. On the other hand, inner root cortical colonization leading to arbuscule development involves more varied and complex PPA-related mechanisms. In particular, a striking alignment of polarized PPAs can be observed in adjacent inner cortical cells of D. carota, correlating with the intracellular root colonization strategy of this plant. Ultrastructural analysis of these PPA-containing cells reveals intense membrane trafficking coupled with nuclear enlargement and remodeling, typical features of arbusculated cells. Taken together, these findings imply that prepenetration responses are both conserved and modulated throughout the AM symbiosis as a function of the different stages of fungal accommodation and the host-specific pattern of root colonization. We propose a model for intracellular AM fungal accommodation integrating peri-arbuscular interface formation and the regulation of functional arbuscule development. PMID:18515499

Exome sequencing of a colorectal cancer family reveals shared mutation pattern and predisposition circuitry along tumor pathways.

PubMed

Suleiman, Suleiman H; Koko, Mahmoud E; Nasir, Wafaa H; Elfateh, Ommnyiah; Elgizouli, Ubai K; Abdallah, Mohammed O E; Alfarouk, Khalid O; Hussain, Ayman; Faisal, Shima; Ibrahim, Fathelrahamn M A; Romano, Maurizio; Sultan, Ali; Banks, Lawrence; Newport, Melanie; Baralle, Francesco; Elhassan, Ahmed M; Mohamed, Hiba S; Ibrahim, Muntaser E

2015-01-01

The molecular basis of cancer and cancer multiple phenotypes are not yet fully understood. Next Generation Sequencing promises new insight into the role of genetic interactions in shaping the complexity of cancer. Aiming to outline the differences in mutation patterns between familial colorectal cancer cases and controls we analyzed whole exomes of cancer tissues and control samples from an extended colorectal cancer pedigree, providing one of the first data sets of exome sequencing of cancer in an African population against a background of large effective size typically with excess of variants. Tumors showed hMSH2 loss of function SNV consistent with Lynch syndrome. Sets of genes harboring insertions-deletions in tumor tissues revealed, however, significant GO enrichment, a feature that was not seen in control samples, suggesting that ordered insertions-deletions are central to tumorigenesis in this type of cancer. Network analysis identified multiple hub genes of centrality. ELAVL1/HuR showed remarkable centrality, interacting specially with genes harboring non-synonymous SNVs thus reinforcing the proposition of targeted mutagenesis in cancer pathways. A likely explanation to such mutation pattern is DNA/RNA editing, suggested here by nucleotide transition-to-transversion ratio that significantly departed from expected values (p-value 5e-6). NFKB1 also showed significant centrality along with ELAVL1, raising the suspicion of viral etiology given the known interaction between oncogenic viruses and these proteins.

Modeling carbachol-induced hippocampal network synchronization using hidden Markov models

NASA Astrophysics Data System (ADS)

Dragomir, Andrei; Akay, Yasemin M.; Akay, Metin

2010-10-01

In this work we studied the neural state transitions undergone by the hippocampal neural network using a hidden Markov model (HMM) framework. We first employed a measure based on the Lempel-Ziv (LZ) estimator to characterize the changes in the hippocampal oscillation patterns in terms of their complexity. These oscillations correspond to different modes of hippocampal network synchronization induced by the cholinergic agonist carbachol in the CA1 region of mice hippocampus. HMMs are then used to model the dynamics of the LZ-derived complexity signals as first-order Markov chains. Consequently, the signals corresponding to our oscillation recordings can be segmented into a sequence of statistically discriminated hidden states. The segmentation is used for detecting transitions in neural synchronization modes in data recorded from wild-type and triple transgenic mice models (3xTG) of Alzheimer's disease (AD). Our data suggest that transition from low-frequency (delta range) continuous oscillation mode into high-frequency (theta range) oscillation, exhibiting repeated burst-type patterns, occurs always through a mode resembling a mixture of the two patterns, continuous with burst. The relatively random patterns of oscillation during this mode may reflect the fact that the neuronal network undergoes re-organization. Further insight into the time durations of these modes (retrieved via the HMM segmentation of the LZ-derived signals) reveals that the mixed mode lasts significantly longer (p < 10-4) in 3xTG AD mice. These findings, coupled with the documented cholinergic neurotransmission deficits in the 3xTG mice model, may be highly relevant for the case of AD.

Kangaroo – A pattern-matching program for biological sequences

PubMed Central

2002-01-01

Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats. PMID:12150718

Spatio-temporal patterns of high summer ozone events in the Madrid Basin, Central Spain

NASA Astrophysics Data System (ADS)

Reche, C.; Moreno, T.; Amato, F.; Pandolfi, M.; Pérez, J.; de la Paz, D.; Diaz, E.; Gómez-Moreno, F. J.; Pujadas, M.; Artíñano, B.; Reina, F.; Orio, A.; Pallarés, M.; Escudero, M.; Tapia, O.; Crespo, E.; Vargas, R.; Alastuey, A.; Querol, X.

2018-07-01

Complex spatial and temporal patterns of ground-level O3 and NO2 concentrations have been revealed across an important southern European O3 exceedance area (Madrid Basin, central Spain). Data were obtained from 102 diffusion tube sites and 49 monitoring stations (25 urban/suburban, 12 urban/suburban-traffic, 7 remote, 3 rural, 2 urban-industrial) located through a wide area inside and beyond the city. This new, high-density database confirms that current locations of monitoring stations in the Madrid networks are well positioned to record representative levels of O3 across the area. Two air quality monitoring stations were identified as reference measurement points, based on their lower O3 and NO2 concentrations, and used as a proxy for regional and hemispheric background levels. Although a main regional contribution was evidenced, emissions of local precursors within the Madrid urban plume play a key role in the generation of O3 exceedances, which are higher and occur earlier near the city than at rural sites, where the effect of NO titration is lower. Despite the fact that weekend emissions of O3 precursors in Madrid are typically lower than on weekdays, mainly due to fewer road traffic emissions, there is little difference in average values of weekday and weekend O3. However, more subtle "weekend effect" differences are revealed by probability density analysis, with high O3 and low NO2 at the highest temperature range (30-35° C) at weekends reflecting lower NO titration. This analysis highlights the importance of NO timing with respect to the photochemical activity timing. The complexity of these O3 pollution patterns in and around the city is dependent on an ever-changing interplay between weather conditions, emission sources, and the timescale required for pollutant transport, chemical processing and recirculation in an evolving contaminated airmass.

The Role of Celestial Compass Information in Cataglyphis Ants during Learning Walks and for Neuroplasticity in the Central Complex and Mushroom Bodies

PubMed Central

Grob, Robin; Fleischmann, Pauline N.; Grübel, Kornelia; Wehner, Rüdiger; Rössler, Wolfgang

2017-01-01

Central place foragers are faced with the challenge to learn the position of their nest entrance in its surroundings, in order to find their way back home every time they go out to search for food. To acquire navigational information at the beginning of their foraging career, Cataglyphis noda performs learning walks during the transition from interior worker to forager. These small loops around the nest entrance are repeatedly interrupted by strikingly accurate back turns during which the ants stop and precisely gaze back to the nest entrance—presumably to learn the landmark panorama of the nest surroundings. However, as at this point the complete navigational toolkit is not yet available, the ants are in need of a reference system for the compass component of the path integrator to align their nest entrance-directed gazes. In order to find this directional reference system, we systematically manipulated the skylight information received by ants during learning walks in their natural habitat, as it has been previously suggested that the celestial compass, as part of the path integrator, might provide such a reference system. High-speed video analyses of distinct learning walk elements revealed that even exclusion from the skylight polarization pattern, UV-light spectrum and the position of the sun did not alter the accuracy of the look back to the nest behavior. We therefore conclude that C. noda uses a different reference system to initially align their gaze directions. However, a comparison of neuroanatomical changes in the central complex and the mushroom bodies before and after learning walks revealed that exposure to UV light together with a naturally changing polarization pattern was essential to induce neuroplasticity in these high-order sensory integration centers of the ant brain. This suggests a crucial role of celestial information, in particular a changing polarization pattern, in initially calibrating the celestial compass system. PMID:29184487

The Role of Celestial Compass Information in Cataglyphis Ants during Learning Walks and for Neuroplasticity in the Central Complex and Mushroom Bodies.

PubMed

Grob, Robin; Fleischmann, Pauline N; Grübel, Kornelia; Wehner, Rüdiger; Rössler, Wolfgang

2017-01-01

Central place foragers are faced with the challenge to learn the position of their nest entrance in its surroundings, in order to find their way back home every time they go out to search for food. To acquire navigational information at the beginning of their foraging career, Cataglyphis noda performs learning walks during the transition from interior worker to forager. These small loops around the nest entrance are repeatedly interrupted by strikingly accurate back turns during which the ants stop and precisely gaze back to the nest entrance-presumably to learn the landmark panorama of the nest surroundings. However, as at this point the complete navigational toolkit is not yet available, the ants are in need of a reference system for the compass component of the path integrator to align their nest entrance-directed gazes. In order to find this directional reference system, we systematically manipulated the skylight information received by ants during learning walks in their natural habitat, as it has been previously suggested that the celestial compass, as part of the path integrator, might provide such a reference system. High-speed video analyses of distinct learning walk elements revealed that even exclusion from the skylight polarization pattern, UV-light spectrum and the position of the sun did not alter the accuracy of the look back to the nest behavior. We therefore conclude that C. noda uses a different reference system to initially align their gaze directions. However, a comparison of neuroanatomical changes in the central complex and the mushroom bodies before and after learning walks revealed that exposure to UV light together with a naturally changing polarization pattern was essential to induce neuroplasticity in these high-order sensory integration centers of the ant brain. This suggests a crucial role of celestial information, in particular a changing polarization pattern, in initially calibrating the celestial compass system.

Hemodynamic Response Alteration As a Function of Task Complexity and Expertise—An fNIRS Study in Jugglers

PubMed Central

Carius, Daniel; Andrä, Christian; Clauß, Martina; Ragert, Patrick; Bunk, Michael; Mehnert, Jan

2016-01-01

Detailed knowledge about online brain processing during the execution of complex motor tasks with a high motion range still remains elusive. The aim of the present study was to investigate the hemodynamic responses within sensorimotor networks as well as in visual motion area during the execution of a complex visuomotor task such as juggling. More specifically, we were interested in how far the hemodynamic response as measured with functional near infrared spectroscopy (fNIRS) adapts as a function of task complexity and the level of the juggling expertise. We asked expert jugglers to perform different juggling tasks with different levels of complexity such as a 2-ball juggling, 3- and 5-ball juggling cascades. We here demonstrate that expert jugglers show an altered neurovascular response with increasing task complexity, since a 5-ball juggling cascade showed enhanced hemodynamic responses for oxygenated hemoglobin as compared to less complex tasks such as a 3- or 2-ball juggling pattern. Moreover, correlations between the hemodynamic response and the level of the juggling expertise during the 5-ball juggling cascade, acquired by cinematographic video analysis, revealed only a non-significant trend in primary motor cortex, indicating that a higher level of expertise might be associated with lower hemodynamic responses. PMID:27064925

Complex Patterns of Admixture across the Indonesian Archipelago.

PubMed

Hudjashov, Georgi; Karafet, Tatiana M; Lawson, Daniel J; Downey, Sean; Savina, Olga; Sudoyo, Herawati; Lansing, J Stephen; Hammer, Michael F; Cox, Murray P

2017-10-01

Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Synergetic and Redundant Information Flow Detected by Unnormalized Granger Causality: Application to Resting State fMRI.

PubMed

Stramaglia, Sebastiano; Angelini, Leonardo; Wu, Guorong; Cortes, Jesus M; Faes, Luca; Marinazzo, Daniele

2016-12-01

We develop a framework for the analysis of synergy and redundancy in the pattern of information flow between subsystems of a complex network. The presence of redundancy and/or synergy in multivariate time series data renders difficulty to estimate the neat flow of information from each driver variable to a given target. We show that adopting an unnormalized definition of Granger causality, one may put in evidence redundant multiplets of variables influencing the target by maximizing the total Granger causality to a given target, over all the possible partitions of the set of driving variables. Consequently, we introduce a pairwise index of synergy which is zero when two independent sources additively influence the future state of the system, differently from previous definitions of synergy. We report the application of the proposed approach to resting state functional magnetic resonance imaging data from the Human Connectome Project showing that redundant pairs of regions arise mainly due to space contiguity and interhemispheric symmetry, while synergy occurs mainly between nonhomologous pairs of regions in opposite hemispheres. Redundancy and synergy, in healthy resting brains, display characteristic patterns, revealed by the proposed approach. The pairwise synergy index, here introduced, maps the informational character of the system at hand into a weighted complex network: the same approach can be applied to other complex systems whose normal state corresponds to a balance between redundant and synergetic circuits.

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

PubMed Central

Wen, Dingqiao; Yu, Yun; Hahn, Matthew W.; Nakhleh, Luay

2016-01-01

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

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

NASA Technical Reports Server (NTRS)

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

1996-01-01

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

incurvata13, a Novel Allele of AUXIN RESISTANT6, Reveals a Specific Role for Auxin and the SCF Complex in Arabidopsis Embryogenesis, Vascular Specification, and Leaf Flatness1[W][OA

PubMed Central

Esteve-Bruna, David; Pérez-Pérez, José Manuel; Ponce, María Rosa; Micol, José Luis

2013-01-01

Auxin plays a pivotal role in plant development by modulating the activity of SCF ubiquitin ligase complexes. Here, we positionally cloned Arabidopsis (Arabidopsis thaliana) incurvata13 (icu13), a mutation that causes leaf hyponasty and reduces leaf venation pattern complexity and auxin responsiveness. We found that icu13 is a novel recessive allele of AUXIN RESISTANT6 (AXR6), which encodes CULLIN1, an invariable component of the SCF complex. Consistent with a role for auxin in vascular specification, the vascular defects in the icu13 mutant were accompanied by reduced expression of auxin transport and auxin perception markers in provascular cells. This observation is consistent with the expression pattern of AXR6, which we found to be restricted to vascular precursors and hydathodes in wild-type leaf primordia. AXR1, RELATED TO UBIQUITIN1-CONJUGATING ENZYME1, CONSTITUTIVE PHOTOMORPHOGENIC9 SIGNALOSOME5A, and CULLIN-ASSOCIATED NEDD8-DISSOCIATED1 participate in the covalent modification of CULLIN1 by RELATED TO UBIQUITIN. Hypomorphic alleles of these genes also display simple venation patterns, and their double mutant combinations with icu13 exhibited a synergistic, rootless phenotype reminiscent of that caused by loss of function of MONOPTEROS (MP), which forms an auxin-signaling module with BODENLOS (BDL). The phenotypes of double mutant combinations of icu13 with either a gain-of-function allele of BDL or a loss-of-function allele of MP were synergistic. In addition, a BDL:green fluorescent protein fusion protein accumulated in icu13, and BDL loss of function or MP overexpression suppressed the phenotype of icu13. Our results demonstrate that the MP-BDL module is required not only for root specification in embryogenesis and vascular postembryonic development but also for leaf flatness. PMID:23319550

Distributed recurrent neural forward models with synaptic adaptation and CPG-based control for complex behaviors of walking robots

PubMed Central

Dasgupta, Sakyasingha; Goldschmidt, Dennis; Wörgötter, Florentin; Manoonpong, Poramate

2015-01-01

Walking animals, like stick insects, cockroaches or ants, demonstrate a fascinating range of locomotive abilities and complex behaviors. The locomotive behaviors can consist of a variety of walking patterns along with adaptation that allow the animals to deal with changes in environmental conditions, like uneven terrains, gaps, obstacles etc. Biological study has revealed that such complex behaviors are a result of a combination of biomechanics and neural mechanism thus representing the true nature of embodied interactions. While the biomechanics helps maintain flexibility and sustain a variety of movements, the neural mechanisms generate movements while making appropriate predictions crucial for achieving adaptation. Such predictions or planning ahead can be achieved by way of internal models that are grounded in the overall behavior of the animal. Inspired by these findings, we present here, an artificial bio-inspired walking system which effectively combines biomechanics (in terms of the body and leg structures) with the underlying neural mechanisms. The neural mechanisms consist of (1) central pattern generator based control for generating basic rhythmic patterns and coordinated movements, (2) distributed (at each leg) recurrent neural network based adaptive forward models with efference copies as internal models for sensory predictions and instantaneous state estimations, and (3) searching and elevation control for adapting the movement of an individual leg to deal with different environmental conditions. Using simulations we show that this bio-inspired approach with adaptive internal models allows the walking robot to perform complex locomotive behaviors as observed in insects, including walking on undulated terrains, crossing large gaps, leg damage adaptations, as well as climbing over high obstacles. Furthermore, we demonstrate that the newly developed recurrent network based approach to online forward models outperforms the adaptive neuron forward models, which have hitherto been the state of the art, to model a subset of similar walking behaviors in walking robots. PMID:26441629

A Network of Networks Perspective on Global Trade.

PubMed

Maluck, Julian; Donner, Reik V

2015-01-01

Mutually intertwined supply chains in contemporary economy result in a complex network of trade relationships with a highly non-trivial topology that varies with time. In order to understand the complex interrelationships among different countries and economic sectors, as well as their dynamics, a holistic view on the underlying structural properties of this network is necessary. This study employs multi-regional input-output data to decompose 186 national economies into 26 industry sectors and utilizes the approach of interdependent networks to analyze the substructure of the resulting international trade network for the years 1990-2011. The partition of the network into national economies is observed to be compatible with the notion of communities in the sense of complex network theory. By studying internal versus cross-subgraph contributions to established complex network metrics, new insights into the architecture of global trade are obtained, which allow to identify key elements of global economy. Specifically, financial services and business activities dominate domestic trade whereas electrical and machinery industries dominate foreign trade. In order to further specify each national sector's role individually, (cross-)clustering coefficients and cross-betweenness are obtained for different pairs of subgraphs. The corresponding analysis reveals that specific industrial sectors tend to favor distinct directionality patterns and that the cross-clustering coefficient for geographically close country pairs is remarkably high, indicating that spatial factors are still of paramount importance for the organization of trade patterns in modern economy. Regarding the evolution of the trade network's substructure, globalization is well-expressed by trends of several structural characteristics (e.g., link density and node strength) in the interacting network framework. Extreme events, such as the financial crisis 2008/2009, are manifested as anomalies superimposed to these trends. The marked reorganization of trade patterns, associated with this economic crisis in comparison to "normal" annual fluctuations in the network structure is traced and quantified by a new widely applicable generalization of the Hamming distance to weighted networks.

A Network of Networks Perspective on Global Trade

PubMed Central

Maluck, Julian; Donner, Reik V.

2015-01-01

Mutually intertwined supply chains in contemporary economy result in a complex network of trade relationships with a highly non-trivial topology that varies with time. In order to understand the complex interrelationships among different countries and economic sectors, as well as their dynamics, a holistic view on the underlying structural properties of this network is necessary. This study employs multi-regional input-output data to decompose 186 national economies into 26 industry sectors and utilizes the approach of interdependent networks to analyze the substructure of the resulting international trade network for the years 1990–2011. The partition of the network into national economies is observed to be compatible with the notion of communities in the sense of complex network theory. By studying internal versus cross-subgraph contributions to established complex network metrics, new insights into the architecture of global trade are obtained, which allow to identify key elements of global economy. Specifically, financial services and business activities dominate domestic trade whereas electrical and machinery industries dominate foreign trade. In order to further specify each national sector’s role individually, (cross-)clustering coefficients and cross-betweenness are obtained for different pairs of subgraphs. The corresponding analysis reveals that specific industrial sectors tend to favor distinct directionality patterns and that the cross-clustering coefficient for geographically close country pairs is remarkably high, indicating that spatial factors are still of paramount importance for the organization of trade patterns in modern economy. Regarding the evolution of the trade network’s substructure, globalization is well-expressed by trends of several structural characteristics (e.g., link density and node strength) in the interacting network framework. Extreme events, such as the financial crisis 2008/2009, are manifested as anomalies superimposed to these trends. The marked reorganization of trade patterns, associated with this economic crisis in comparison to “normal” annual fluctuations in the network structure is traced and quantified by a new widely applicable generalization of the Hamming distance to weighted networks. PMID:26197439

Biogeography, phylogeny, and morphological evolution of central Texas cave and spring salamanders

PubMed Central

2013-01-01

Background Subterranean faunal radiations can result in complex patterns of morphological divergence involving both convergent or parallel phenotypic evolution and cryptic species diversity. Salamanders of the genus Eurycea in central Texas provide a particularly challenging example with respect to phylogeny reconstruction, biogeography and taxonomy. These predominantly aquatic species inhabit karst limestone aquifers and spring outflows, and exhibit a wide range of morphological and genetic variation. We extensively sampled spring and cave populations of six Eurycea species within this group (eastern Blepsimolge clade), to reconstruct their phylogenetic and biogeographic history using mtDNA and examine patterns and origins of cave- and surface-associated morphological variation. Results Genetic divergence is generally low, and many populations share ancestral haplotypes and/or show evidence of introgression. This pattern likely indicates a recent radiation coupled with a complex history of intermittent connections within the aquatic karst system. Cave populations that exhibit the most extreme troglobitic morphologies show no or very low divergence from surface populations and are geographically interspersed among them, suggesting multiple instances of rapid, parallel phenotypic evolution. Morphological variation is diffuse among cave populations; this is in contrast to surface populations, which form a tight cluster in morphospace. Unexpectedly, our analyses reveal two distinct and previously unrecognized morphological groups encompassing multiple species that are not correlated with spring or cave habitat, phylogeny or geography, and may be due to developmental plasticity. Conclusions The evolutionary history of this group of spring- and cave-dwelling salamanders reflects patterns of intermittent isolation and gene flow influenced by complex hydrogeologic dynamics that are characteristic of karst regions. Shallow genetic divergences among several species, evidence of genetic exchange, and nested relationships across morphologically disparate cave and spring forms suggests that cave invasion was recent and many troglobitic morphologies arose independently. These patterns are consistent with an adaptive-shift hypothesis of divergence, which has been proposed to explain diversification in other karst fauna. While cave and surface forms often do not appear to be genetically isolated, morphological diversity within and among populations may be maintained by developmental plasticity, selection, or a combination thereof. PMID:24044519

Molecular modeling studies of substrate binding by penicillin acylase.

PubMed

Chilov, G G; Stroganov, O V; Svedas, V K

2008-01-01

Molecular modeling has revealed intimate details of the mechanism of binding of natural substrate, penicillin G (PG), in the penicillin acylase active center and solved questions raised by analysis of available X-ray structures, mimicking Michaelis complex, which substantially differ in the binding pattern of the PG leaving group. Three MD trajectories were launched, starting from PDB complexes of the inactive mutant enzyme with PG (1FXV) and native penicillin acylase with sluggishly hydrolyzed substrate analog penicillin G sulfoxide (1GM9), or from the complex obtained by PG docking. All trajectories converged to a similar PG binding mode, which represented the near-to-attack conformation, consistent with chemical criteria of how reactive Michaelis complex should look. Simulated dynamic structure of the enzyme-substrate complex differed significantly from 1FXV, resembling rather 1GM9; however, additional contacts with residues bG385, bS386, and bN388 have been found, which were missing in X-ray structures. Combination of molecular docking and molecular dynamics also clarified the nature of extremely effective phenol binding in the hydrophobic pocket of penicillin acylase, which lacked proper explanation from crystallographic experiments. Alternative binding modes of phenol were probed, and corresponding trajectories converged to a single binding pattern characterized by a hydrogen bond between the phenol hydroxyl and the main chain oxygen of bS67, which was not evident from the crystal structure. Observation of the trajectory, in which phenol moved from its steady bound to pre-dissociation state, mapped the consequence of molecular events governing the conformational transitions in a coil region a143-a146 coupled to substrate binding and release of the reaction products. The current investigation provided information on dynamics of the conformational transitions accompanying substrate binding and significance of poorly structured and flexible regions in maintaining catalytic framework.

Multistage magma emplacement and progressive strain accumulation in the shallow-level Krkonoše-Jizera plutonic complex, Bohemian Massif

NASA Astrophysics Data System (ADS)

Žák, Jiří; Verner, Kryštof; Sláma, Jiří; Kachlík, Václav; Chlupáčová, Marta

2013-09-01

relationships combined with new U-Pb zircon geochronology suggest that the shallow-level Krkonoše-Jizera plutonic complex, northern Bohemian Massif, was assembled successively from bottom to top, starting with emplacement of the separately evolved S-type Tanvald granite (317.3 ± 2.1 Ma), followed by at least two voluminous batches of the I-type porphyritic Liberec (319.5 ± 2.3 Ma) and Jizera (320.1 ± 3.0 Ma and 319.3 ± 3.7 Ma) granites. The intrusive sequence was completed by uppermost, minor intrusions of the equigranular Harrachov (315.0 ± 2.7 Ma) and Krkonoše granites. The I-type granites exhibit an unusually complex pattern of superposed feldspar phenocryst and magnetic fabrics as revealed from the anisotropy of magnetic susceptibility (AMS). The outer Liberec granite preserves margin-parallel foliations and lineations, interpreted to record emplacement-related strain captured by cooling from the pluton floor and walls. In contrast, the inner Jizera, Harrachov, and Krkonoše granites were overprinted by synmagmatic strain resulting from dextral movements along regional strike-slip faults cutting the opposite ends of the plutonic complex. Late-stage felsic dikes in the Liberec and Jizera granites reorient from horizontal to vertical (lineation-perpendicular) attitude in response to changing the least principal stress direction, whereas mafic schlieren do not do so, representing only randomly oriented small-scale thermal-mechanical instabilities in the phenocryst framework. In general, this case example challenges the common approach of inferring pluton-wide magma flow from interpolated foliation, lineation, and schlieren patterns. More likely, magmatic fabrics in large plutons record complex temporal succession of superposed strains resulting from diverse processes at multiple scales.

Clonal evolution in myelodysplastic syndromes

PubMed Central

da Silva-Coelho, Pedro; Kroeze, Leonie I.; Yoshida, Kenichi; Koorenhof-Scheele, Theresia N.; Knops, Ruth; van de Locht, Louis T.; de Graaf, Aniek O.; Massop, Marion; Sandmann, Sarah; Dugas, Martin; Stevens-Kroef, Marian J.; Cermak, Jaroslav; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; de Witte, Theo; Blijlevens, Nicole M. A.; Muus, Petra; Huls, Gerwin; van der Reijden, Bert A.; Ogawa, Seishi; Jansen, Joop H.

2017-01-01

Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5–11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment. The application of disease-modifying therapy may create an evolutionary bottleneck after which more complex MDS, but also unrelated clones of haematopoietic cells, may emerge. In addition, subclones that acquired an additional mutation associated with treatment resistance (TP53) or disease progression (NRAS, KRAS) may be detected months before clinical changes become apparent. Monitoring the genetic landscape during the disease may help to guide treatment decisions. PMID:28429724

Unusual large-pitch banding in poly(L-lactic acid): Effects of composition and geometry confinement

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

Woo, Eamor M.; Lugito, Graecia; Hsieh, Ya-Ting

2014-02-24

Lamellar patterns and orientations in blends of two crystalline polymers: poly(ethylene oxide) (PEO) and low-molecular-weight poly(L-lactic acid) (PLLA) were investigated using polarizing light optical microscopy (POM), and atomic and scanning electron microscopy (AFM, SEM). Specific etching off of PEO was used to reveal the complex earlier-grown PLLA lamellae patterns with various PEO content in blends. Banding of extremely long pitch (50 μm) in crystallized PLLA spherulites was induced by two kinetic factors: geometry confinement by top cover and introduction of diluent such as PEO. The mechanisms and correlation among the lamellar assembly, ring bands, and cracks are exemplified. Lamellar patternsmore » and ring-band types in blends were found to vary with respect to not only blend compositions, but also confinement of top-cover.« less

Hierarchy of orofacial rhythms revealed through whisking and breathing

PubMed Central

Moore, Jeffrey D.; Deschênes, Martin; Furuta, Takahiro; Huber, Daniel; Smear, Matthew C.; Demers, Maxime; Kleinfeld, David

2014-01-01

Whisking and sniffing are predominant aspects of exploratory behavior in rodents, yet the neural mechanisms that generate their motor patterns remain largely uncharacterized. We use anatomical, behavioral, electrophysiological, and pharmacological tools to demonstrate that these patterns are coordinated by respiratory centers in the ventral medulla. We delineate a distinct region in the ventral medulla that provides rhythmic input to the facial motoneurons that drive protraction of the vibrissae. Neuronal output from this region is reset at each inspiration by direct input from the preBötzinger complex, such that high frequency sniffing has a one-to-one coordination with whisking while basal respiration is accompanied by intervening whisks that occur between breaths. We conjecture that the respiratory nuclei, which project to other premotor regions for oral and facial control, function as a master clock for behaviors that coordinate with breathing. PMID:23624373

Permutation Entropy Applied to Movement Behaviors of Drosophila Melanogaster

NASA Astrophysics Data System (ADS)

Liu, Yuedan; Chon, Tae-Soo; Baek, Hunki; Do, Younghae; Choi, Jin Hee; Chung, Yun Doo

Movement of different strains in Drosophila melanogaster was continuously observed by using computer interfacing techniques and was analyzed by permutation entropy (PE) after exposure to toxic chemicals, toluene (0.1 mg/m3) and formaldehyde (0.01 mg/m3). The PE values based on one-dimensional time series position (vertical) data were variable according to internal constraint (i.e. strains) and accordingly increased in response to external constraint (i.e. chemicals) by reflecting diversity in movement patterns from both normal and intoxicated states. Cross-correlation function revealed temporal associations between the PE values and between the component movement patterns in different chemicals and strains through the period of intoxication. The entropy based on the order of position data could be a useful means for complexity measure in behavioral changes and for monitoring the impact of stressors in environment.

Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum.

PubMed

Venkataramanan, Keerthi P; Min, Lie; Hou, Shuyu; Jones, Shawn W; Ralston, Matthew T; Lee, Kelvin H; Papoutsakis, E Terry

2015-01-01

Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation. The identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5'UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5'UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress. The integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.

Identification of complex metabolic states in critically injured patients using bioinformatic cluster analysis.

PubMed

Cohen, Mitchell J; Grossman, Adam D; Morabito, Diane; Knudson, M Margaret; Butte, Atul J; Manley, Geoffrey T

2010-01-01

Advances in technology have made extensive monitoring of patient physiology the standard of care in intensive care units (ICUs). While many systems exist to compile these data, there has been no systematic multivariate analysis and categorization across patient physiological data. The sheer volume and complexity of these data make pattern recognition or identification of patient state difficult. Hierarchical cluster analysis allows visualization of high dimensional data and enables pattern recognition and identification of physiologic patient states. We hypothesized that processing of multivariate data using hierarchical clustering techniques would allow identification of otherwise hidden patient physiologic patterns that would be predictive of outcome. Multivariate physiologic and ventilator data were collected continuously using a multimodal bioinformatics system in the surgical ICU at San Francisco General Hospital. These data were incorporated with non-continuous data and stored on a server in the ICU. A hierarchical clustering algorithm grouped each minute of data into 1 of 10 clusters. Clusters were correlated with outcome measures including incidence of infection, multiple organ failure (MOF), and mortality. We identified 10 clusters, which we defined as distinct patient states. While patients transitioned between states, they spent significant amounts of time in each. Clusters were enriched for our outcome measures: 2 of the 10 states were enriched for infection, 6 of 10 were enriched for MOF, and 3 of 10 were enriched for death. Further analysis of correlations between pairs of variables within each cluster reveals significant differences in physiology between clusters. Here we show for the first time the feasibility of clustering physiological measurements to identify clinically relevant patient states after trauma. These results demonstrate that hierarchical clustering techniques can be useful for visualizing complex multivariate data and may provide new insights for the care of critically injured patients.

Evolution and Conservation on Top of the World: Phylogeography of the Marbled Water Frog (Telmatobius marmoratus Species Complex; Anura, Telmatobiidae) in Protected Areas of Chile.

PubMed

Victoriano, Pedro F; Muñoz-Mendoza, Carla; Sáez, Paola A; Salinas, Hugo F; Muñoz-Ramírez, Carlos; Sallaberry, Michel; Fibla, Pablo; Méndez, Marco A

2015-01-01

The Andean Altiplano has served as a complex setting throughout its history, driving dynamic processes of diversification in several taxa. We investigated phylogeographic processes in the Telmatobius marmoratus species complex occurring in this region by studying the geographic patterns of genetic variability, genealogies, and historical migration, using the cytochrome b (cyt-b) gene as a marker. DNA sequences from Telmatobius gigas and Telmatobius culeus, Bolivian species with an uncertain taxonomic status, were also included. Additionally, we evaluated the phylogenetic diversity (PD) represented within Chilean protected areas and the complementary contribution from unprotected populations. Phylogenetic reconstructions from 148 cyt-b sequences revealed 4 main clades, one of which corresponded to T. culeus. T. gigas was part of T. marmoratus clade indicating paraphyletic relationships. Haplotypes from Chilean and Bolivian sites were not reciprocally monophyletic. Geographic distribution of lineages, spatial Bayesian analysis, and migration patterns indicated that T. marmoratus displays a weaker geographic structure than expected based on habitat distribution and physiological requirements. Demographic and statistical phylogeography analyses pointed out to a scenario of recent population expansion and high connectivity events of a more recent age than the post Last Glacial Maximum, probably associated to more humid events in Altiplano. PD of T. marmoratus populations within protected areas represents 55.6% of the total estimated PD. The unprotected populations that would contribute the most to PD are Caquena and Quebe (21%). Recent evolutionary processes and paleoclimatic changes, potentially driving shifts in habitat connectivity levels and population sizes, could explain the phylogeographic patterns recovered herein. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The 3of5 web application for complex and comprehensive pattern matching in protein sequences.

PubMed

Seiler, Markus; Mehrle, Alexander; Poustka, Annemarie; Wiemann, Stefan

2006-03-16

The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable, especially in protein sequences. They are frequently described using terms of regular expressions (RegEx) because of the user-friendly terminology. Limitations arise for queries with the increasing complexity of patterns and are accompanied by requirements for enhanced capabilities. This is especially true for patterns containing ambiguous characters and positions and/or length ambiguities. We have implemented the 3of5 web application in order to enable complex pattern matching in protein sequences. 3of5 is named after a special use of its main feature, the novel n-of-m pattern type. This feature allows for an extensive specification of variable patterns where the individual elements may vary in their position, order, and content within a defined stretch of sequence. The number of distinct elements can be constrained by operators, and individual characters may be excluded. The n-of-m pattern type can be combined with common regular expression terms and thus also allows for a comprehensive description of complex patterns. 3of5 increases the fidelity of pattern matching and finds ALL possible solutions in protein sequences in cases of length-ambiguous patterns instead of simply reporting the longest or shortest hits. Grouping and combined search for patterns provides a hierarchical arrangement of larger patterns sets. The algorithm is implemented as internet application and freely accessible. The application is available at http://dkfz.de/mga2/3of5/3of5.html. The 3of5 application offers an extended vocabulary for the definition of search patterns and thus allows the user to comprehensively specify and identify peptide patterns with variable elements. The n-of-m pattern type offers an improved accuracy for pattern matching in combination with the ability to find all solutions, without compromising the user friendliness of regular expression terms.

Possible evidence for contribution of arbuscular mycorrhizal fungi (AMF) in phytoremediation of iron-cyanide (Fe-CN) complexes.

PubMed

Sut, Magdalena; Boldt-Burisch, Katja; Raab, Thomas

2016-08-01

Arbuscular mycorrhizal fungi (AMF) are integral functioning parts of plant root systems and are widely recognized for enhancing contaminants uptake and metabolism on severely disturbed sites. However, the patterns of their influence on the phytoremediation of iron-cyanide (Fe-CN) complexes are unknown. Fe-CN complexes are of great common interest, as iron is one of the most abundant element in soil and water. Effect of ryegrass (Lolium perenne L.) roots inoculation, using mycorrhizal fungi (Rhizophagus irregularis and a mixture of R. irregularis, Funneliformis mosseae, Rhizophagus aggregatus, and Claroideoglomus etunicatum), on iron-cyanide sorption was studied. Results indicated significantly higher colonization of R. irregularis than the mixture of AMF species on ryegrass roots. Series of batch experiments using potassium hexacyanoferrate (II) solutions, in varying concentrations revealed significantly higher reduction of total CN and free CN content in the mycorrhizal roots, indicating greater cyanide decrease in the treatment inoculated with R. irregularis. Our study is a first indication of the possible positive contribution of AM fungi on the phytoremediation of iron-cyanide complexes.

Geomorphology of unique reefs on the western Canadian shelf: sponge reefs mapped by multibeam bathymetry

NASA Astrophysics Data System (ADS)

Conway, Kim W.; Barrie, J. Vaughn; Krautter, Manfred

2005-09-01

Multibeam imagery of siliceous sponge reefs (Hexactinellida, Hexactinosida) reveals the setting, form, and organization of five reef complexes on the western Canadian continental shelf. The reefs are built by framework skeleton sponges which trap clay-rich sediments resulting in a distinctive pattern of low intensity backscatter from the reefs that colonize more reflective glacial sediments of higher backscatter intensity. Bathymetry and backscatter maps show the distribution and form of reefs in two large complexes in the Queen Charlotte Basin (QCB) covering hundreds of km2, and three smaller reef complexes in the Georgia Basin (GB). Ridges up to 7 km long and 21 m in height, together with diversely shaped, coalescing bioherms and biostromes form the principal reef shape in the QCB whereas chains of wave-form, streamlined mounds up to 14 m in height have developed in the GB. Reef initiation is dependent on the distribution of high backscatter-intensity relict glacial surfaces, and the variation in reef complex morphology is probably the result of tidally driven, near seabed currents.

Topics in Complexity: From Physical to Life Science Systems

NASA Astrophysics Data System (ADS)

Charry, Pedro David Manrique

Complexity seeks to unwrap the mechanisms responsible for collective phenomena across the physical, biological, chemical, economic and social sciences. This thesis investigates real-world complex dynamical systems ranging from the quantum/natural domain to the social domain. The following novel understandings are developed concerning these systems' out-of-equilibrium and nonlinear behavior. Standard quantum techniques show divergent outcomes when a quantum system comprising more than one subunit is far from thermodynamic equilibrium. Abnormal photon inter-arrival times help fulfill the metabolic needs of a terrestrial photosynthetic bacterium. Spatial correlations within incident light can act as a driving mechanism for an organism's adaptation toward more ordered structures. The group dynamics of non-identical objects, whose assembly rules depend on mutual heterogeneity, yield rich transition dynamics between isolation and cohesion, with the cohesion regime reproducing a particular universal pattern commonly found in many real-world systems. Analyses of covert networks reveal collective gender superiority in the connectivity that provides benefits for system robustness and survival. Nodal migration in a network generates complex contagion profiles that lie beyond traditional approaches and yet resemble many modern-day outbreaks.

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum

PubMed Central

Alvarado-Sizzo, Hernán; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC. PMID:29342184

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum.

PubMed

Alvarado-Sizzo, Hernán; Casas, Alejandro; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

Stable carbon isotopic compositions of intact polar lipids reveal complex carbon flow patterns among hydrocarbon degrading microbial communities at the Chapopote asphalt volcano

NASA Astrophysics Data System (ADS)

Schubotz, Florence; Lipp, Julius S.; Elvert, Marcus; Hinrichs, Kai-Uwe

2011-08-01

Seepage of asphalt forms the basis of a cold seep system at 3000 m water depth at the Chapopote Knoll in the southern Gulf of Mexico. Anaerobic microbial communities are stimulated in the oil-impregnated sediments as evidenced by the presence of intact polar membrane lipids (IPLs) derived from archaea and Bacteria at depths up to 7 m below the seafloor. Detailed investigation of stable carbon isotope composition (δ 13C) of alkyl and acyl moieties derived from a range of IPL precursors with distinct polar head groups resolved the complexity of carbon metabolisms and utilization of diverse carbon sources by uncultured microbial communities. In surface sediments most of the polar lipid-derived fatty acids with phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG) head groups could be tentatively assigned to autotrophic sulfate-reducing bacteria, with a relatively small proportion involved in the anaerobic oxidation of methane. Derivatives of phosphatidyl-( N)-methylethanolamine (PME) were abundant and could be predominantly assigned to heterotrophic oil-degrading bacteria. Archaeal IPLs with phosphate-based hydroxyarchaeols and diglycosidic glyceroldibiphytanylglyceroltetraethers (GDGTs) were assigned to methanotrophic archaea of the ANME-2 and ANME-1 cluster, respectively, whereas δ 13C values of phosphate-based archaeols and mixed phosphate-based and diglycosidic GDGTs point to methanogenic archaea. At a 7 m deep sulfate-methane transition zone that is linked to the upward movement of gas-laden petroleum, a distinct increase in abundance of archaeal IPLs such as phosphate-based hydroxyarchaeols and diglycosidic archaeol and GDGTs is observed; their δ 13C values are consistent with their origin from both methanotrophic and methanogenic archaea. This study reveals previously hidden, highly complex patterns in the carbon-flow of versatile microbial communities involved in the degradation of heavy oil including hydrocarbon gases that would not have been evident from classical compound-specific isotope analyses of either bulk IPL or apolar lipid derivatives.

Enabling complex nanoscale pattern customization using directed self-assembly.

PubMed

Doerk, Gregory S; Cheng, Joy Y; Singh, Gurpreet; Rettner, Charles T; Pitera, Jed W; Balakrishnan, Srinivasan; Arellano, Noel; Sanders, Daniel P

2014-12-16

Block copolymer directed self-assembly is an attractive method to fabricate highly uniform nanoscale features for various technological applications, but the dense periodicity of block copolymer features limits the complexity of the resulting patterns and their potential utility. Therefore, customizability of nanoscale patterns has been a long-standing goal for using directed self-assembly in device fabrication. Here we show that a hybrid organic/inorganic chemical pattern serves as a guiding pattern for self-assembly as well as a self-aligned mask for pattern customization through cotransfer of aligned block copolymer features and an inorganic prepattern. As informed by a phenomenological model, deliberate process engineering is implemented to maintain global alignment of block copolymer features over arbitrarily shaped, 'masking' features incorporated into the chemical patterns. These hybrid chemical patterns with embedded customization information enable deterministic, complex two-dimensional nanoscale pattern customization through directed self-assembly.

Arnica (Asteraceae) phylogeny revisited using RPB2: complex patterns and multiple d-paralogues.

PubMed

Ekenäs, Catarina; Heidari, Nahid; Andreasen, Katarina

2012-08-01

The region coding for the second largest subunit of RNA polymerase II (RPB2) was explored for resolving interspecific relationships in Arnica and lower level taxa in general. The region between exons 17 and 23 was cloned and sequenced for 33 accessions of Arnica and four outgroup taxa. Three paralogues of the RPB2-d copy (RPB2-dA, B and C) were detected in Arnica and outgroup taxa, indicating that the duplications must have occurred before the divergence of Arnica. Parsimony and Bayesian analyses of separate alignments of the three copies reveal complex patterns in Arnica, likely reflecting a history of lineage sorting in combination with apomixis, polyploidization, and possibly hybridization. Cloned sequences of some taxa do not form monophyletic clades within paralogues, but form multiple strongly supported clades with sequences of other taxa. Some well supported groups are present in more than one paralogue and many groups are in line with earlier hypotheses regarding interspecific relationships within the genus. Low levels of homoplasy in combination with relatively high sequence variation indicates that the introns of the RPB2 region could be suitable for phylogenetic studies in low level taxonomy. Copyright © 2012. Published by Elsevier Inc.

First insights into circulating Mycobacterium tuberculosis complex lineages and drug resistance in Guinea

PubMed Central

Ejo, Mebrat; Gehre, Florian; Barry, Mamadou Dian; Sow, Oumou; Bah, Nene Mamata; Camara, Mory; Bah, Boubacar; Uwizeye, Cecile; Nduwamahoro, Elie; Fissette, Kristina; Rijk, Pim De; Merle, Corinne; Olliaro, Piero; Burgos, Marcos; Lienhardt, Christian; Rigouts, Leen; de Jong, Bouke C.

2015-01-01

In this study we assessed first-line anti-tuberculosis drug resistance and the genotypic distribution of Mycobacterium tuberculosis complex (MTBC) isolates that had been collected from consecutive new tuberculosis patients enrolled in two clinical trials conducted in Guinea between 2005 and 2010. Among the total 359 MTBC strains that were analyzed in this study, 22.8% were resistant to at least one of the first line anti-tuberculosis drugs, including 2.5% multidrug resistance and 17.5% isoniazid resistance, with or without other drugs. In addition, further characterization of isolates from a subset of the two trials (n = 184) revealed a total of 80 different spoligotype patterns, 29 “orphan” and 51 shared patterns. We identified the six major MTBC lineages of human relevance, with predominance of the Euro-American lineage. In total, 132 (71.7%) of the strains were genotypically clustered, and further analysis (using the DESTUS model) suggesting significantly faster spread of LAM10_CAM family (p = 0.00016). In conclusion, our findings provide a first insight into drug resistance and the population structure of the MTBC in Guinea, with relevance for public health scientists in tuberculosis control programs. PMID:26004194

First insights into circulating Mycobacterium tuberculosis complex lineages and drug resistance in Guinea.

PubMed

Ejo, Mebrat; Gehre, Florian; Barry, Mamadou Dian; Sow, Oumou; Bah, Nene Mamata; Camara, Mory; Bah, Boubacar; Uwizeye, Cecile; Nduwamahoro, Elie; Fissette, Kristina; De Rijk, Pim; Merle, Corinne; Olliaro, Piero; Burgos, Marcos; Lienhardt, Christian; Rigouts, Leen; de Jong, Bouke C

2015-07-01

In this study we assessed first-line anti-tuberculosis drug resistance and the genotypic distribution of Mycobacterium tuberculosis complex (MTBC) isolates that had been collected from consecutive new tuberculosis patients enrolled in two clinical trials conducted in Guinea between 2005 and 2010. Among the total 359 MTBC strains that were analyzed in this study, 22.8% were resistant to at least one of the first line anti-tuberculosis drugs, including 2.5% multidrug resistance and 17.5% isoniazid resistance, with or without other drugs. In addition, further characterization of isolates from a subset of the two trials (n = 184) revealed a total of 80 different spoligotype patterns, 29 "orphan" and 51 shared patterns. We identified the six major MTBC lineages of human relevance, with predominance of the Euro-American lineage. In total, 132 (71.7%) of the strains were genotypically clustered, and further analysis (using the DESTUS model) suggesting significantly faster spread of LAM10_CAM family (p = 0.00016). In conclusion, our findings provide a first insight into drug resistance and the population structure of the MTBC in Guinea, with relevance for public health scientists in tuberculosis control programs. Copyright © 2015. Published by Elsevier B.V.

Principal network analysis: identification of subnetworks representing major dynamics using gene expression data

PubMed Central

Kim, Yongsoo; Kim, Taek-Kyun; Kim, Yungu; Yoo, Jiho; You, Sungyong; Lee, Inyoul; Carlson, George; Hood, Leroy; Choi, Seungjin; Hwang, Daehee

2011-01-01

Motivation: Systems biology attempts to describe complex systems behaviors in terms of dynamic operations of biological networks. However, there is lack of tools that can effectively decode complex network dynamics over multiple conditions. Results: We present principal network analysis (PNA) that can automatically capture major dynamic activation patterns over multiple conditions and then generate protein and metabolic subnetworks for the captured patterns. We first demonstrated the utility of this method by applying it to a synthetic dataset. The results showed that PNA correctly captured the subnetworks representing dynamics in the data. We further applied PNA to two time-course gene expression profiles collected from (i) MCF7 cells after treatments of HRG at multiple doses and (ii) brain samples of four strains of mice infected with two prion strains. The resulting subnetworks and their interactions revealed network dynamics associated with HRG dose-dependent regulation of cell proliferation and differentiation and early PrPSc accumulation during prion infection. Availability: The web-based software is available at: http://sbm.postech.ac.kr/pna. Contact: dhhwang@postech.ac.kr; seungjin@postech.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21193522

Temperature-dependent behaviours are genetically variable in the nematode Caenorhabditis briggsae.

PubMed

Stegeman, Gregory W; de Mesquita, Matthew Bueno; Ryu, William S; Cutter, Asher D

2013-03-01

Temperature-dependent behaviours in Caenorhabditis elegans, such as thermotaxis and isothermal tracking, are complex behavioural responses that integrate sensation, foraging and learning, and have driven investigations to discover many essential genetic and neural pathways. The ease of manipulation of the Caenorhabditis model system also has encouraged its application to comparative analyses of phenotypic evolution, particularly contrasts of the classic model C. elegans with C. briggsae. And yet few studies have investigated natural genetic variation in behaviour in any nematode. Here we measure thermotaxis and isothermal tracking behaviour in genetically distinct strains of C. briggsae, further motivated by the latitudinal differentiation in C. briggsae that is associated with temperature-dependent fitness differences in this species. We demonstrate that C. briggsae performs thermotaxis and isothermal tracking largely similar to that of C. elegans, with a tendency to prefer its rearing temperature. Comparisons of these behaviours among strains reveal substantial heritable natural variation within each species that corresponds to three general patterns of behavioural response. However, intraspecific genetic differences in thermal behaviour often exceed interspecific differences. These patterns of temperature-dependent behaviour motivate further development of C. briggsae as a model system for dissecting the genetic underpinnings of complex behavioural traits.

Vertical-axis rotations and deformation along the active strike-slip El Tigre Fault (Precordillera of San Juan, Argentina) assessed through palaeomagnetism and anisotropy of magnetic susceptibility

NASA Astrophysics Data System (ADS)

Fazzito, Sabrina Y.; Rapalini, Augusto E.; Cortés, José M.; Terrizzano, Carla M.

2017-03-01

Palaeomagnetic data from poorly consolidated to non-consolidated late Cenozoic sediments along the central segment of the active El Tigre Fault (Central-Western Precordillera of the San Juan Province, Argentina) demonstrate broad cumulative deformation up to 450 m from the fault trace and reveal clockwise and anticlockwise vertical-axis rotations of variable magnitude. This deformation has affected in different amounts Miocene to late Pleistocene samples and indicates a complex kinematic pattern. Several inherited linear structures in the shear zone that are oblique to the El Tigre Fault may have acted as block boundary faults. Displacement along these faults may have resulted in a complex pattern of rotations. The maximum magnitude of rotation is a function of the age of the sediments sampled, with largest values corresponding to middle Miocene-lower Pliocene deposits and minimum values obtained from late Pleistocene deposits. The kinematic study is complemented by low-field anisotropy of magnetic susceptibility data to show that the local strain regime suggests a N-S stretching direction, subparallel to the strike of the main fault.

Focal expression of mutant huntingtin in the songbird basal ganglia disrupts cortico-basal ganglia networks and vocal sequences

PubMed Central

Tanaka, Masashi; Singh Alvarado, Jonnathan; Murugan, Malavika; Mooney, Richard

2016-01-01

The basal ganglia (BG) promote complex sequential movements by helping to select elementary motor gestures appropriate to a given behavioral context. Indeed, Huntington’s disease (HD), which causes striatal atrophy in the BG, is characterized by hyperkinesia and chorea. How striatal cell loss alters activity in the BG and downstream motor cortical regions to cause these disorganized movements remains unknown. Here, we show that expressing the genetic mutation that causes HD in a song-related region of the songbird BG destabilizes syllable sequences and increases overall vocal activity, but leave the structure of individual syllables intact. These behavioral changes are paralleled by the selective loss of striatal neurons and reduction of inhibitory synapses on pallidal neurons that serve as the BG output. Chronic recordings in singing birds revealed disrupted temporal patterns of activity in pallidal neurons and downstream cortical neurons. Moreover, reversible inactivation of the cortical neurons rescued the disorganized vocal sequences in transfected birds. These findings shed light on a key role of temporal patterns of cortico-BG activity in the regulation of complex motor sequences and show how a genetic mutation alters cortico-BG networks to cause disorganized movements. PMID:26951661

Tropical Hydroclimate Change during Heinrich Stadial 1: An Integrative Proxy-Model Synthesis

NASA Astrophysics Data System (ADS)

Lawman, A. E.; Sun, T.; Shanahan, T. M.; Di Nezio, P. N.; Gomez, K.; Piatrunia, N.; Sun, C.; Wu, X.; Kageyama, M.; Merkel, U.; Otto-Bliesner, B. L.; Abe-Ouchi, A.; Lohmann, G.; Singarayer, J. S.

2017-12-01

We explore the response of tropical climate to abrupt cooling of the North Atlantic (NA) during Heinrich Stadial 1 (HS1) combining paleoclimate proxies with model simulations. A total of 146 published paleoclimate records from tropical locations are used to categorize whether HS1 was wetter, drier, or unchanged relative to a deglacial baseline state. Only records with sufficient resolution to resolve HS1 and sufficient length to characterize the deglacial trend are considered. This synthesis reveals large-scale patterns of hydroclimate change relative to glacial conditions, confirming previously reported weaker Indian summer monsoon, a wetter southern Africa, and drying over the Caribbean. Our synthesis also reveals large-scale drying over the Maritime continent as well as wetter conditions in northern Australia and southern tropical South America. Our reinterpretation of the available proxy data reveals far more complexity and uncertainties for equatorial East Africa, a region that appears to straddle a pattern of dryer conditions to the north and wetter conditions to the south. Overall, these patterns of hydroclimate change depart from a southward shift of the Inter Tropical Convergence Zone (ITCZ), particularly outside the tropical Atlantic. We explore mechanisms driving these changes using a multi-model ensemble of "hosing" simulations performed relative to glacial conditions. The models show robust weakening of the Afro-Asian Monsoon, which we attribute to ventilation of colder mid-latitude air. Not all models simulate the remaining patterns inferred from the proxy data. The best-agreeing models indicate that cooling over the tropical NA and the Caribbean may be essential to communicate the response to the global tropics. This response can induce warming over the tropical South Atlantic via the wind-evaporation-SST feedback, driving wetter conditions in South Africa and tropical South America. Cooling over the Caribbean is communicated to the Pacific over the Central American isthmus resulting in an El Niño-like pattern accompanied by drying over the Maritime Continent - as seen in the proxy data. Together these results show a dominant role for altered tropical SST gradients driving changes in tropical rainfall, and a lesser role for inter-hemispheric shifts in the ITCZ.

New 3D structuring process for non-integrated circuit related technologies (Conference Presentation)

NASA Astrophysics Data System (ADS)

Nouri, Lamia; Possémé, Nicolas; Landis, Stéfan; Milesi, Frédéric; Gaillard, Frédéric-Xavier

2017-04-01

Fabrication processes that microelectronic developed for Integrated circuit (IC) technologies for decades, do not meet the new emerging structuration's requirements, in particular non-IC related technologies one, such as MEMS/NEMS, Micro-Fluidics, photovoltaics, lenses. Actually complex 3D structuration requires complex lithography patterning approaches such as gray-scale electron beam lithography, laser ablation, focused ion beam lithography, two photon polymerization. It is now challenging to find cheaper and easiest technique to achieve 3D structures. In this work, we propose a straightforward process to realize 3D structuration, intended for silicon based materials (Si, SiN, SiOCH). This structuration technique is based on nano-imprint lithography (NIL), ion implantation and selective wet etching. In a first step a pattern is performed by lithography on a substrate, then ion implantation is realized through a resist mask in order to create localized modifications in the material, thus the pattern is transferred into the subjacent layer. Finally, after the resist stripping, a selective wet etching is carried out to remove selectively the modified material regarding the non-modified one. In this paper, we will first present results achieved with simple 2D line array pattern processed either on Silicon or SiOCH samples. This step have been carried out to demonstrate the feasibility of this new structuration process. SEM pictures reveals that "infinite" selectivity between the implanted areas versus the non-implanted one could be achieved. We will show that a key combination between the type of implanted ion species and wet etching chemistries is required to obtain such results. The mechanisms understanding involved during both implantation and wet etching processes will also be presented through fine characterizations with Photoluminescence, Raman and Secondary Ion Mass Spectrometry (SIMS) for silicon samples, and ellipso-porosimetry and Fourier Transform InfraRed spectroscopy (FTIR) for SiOCH samples. Finally the benefit of this new patterning approach will be presented on 3D patterns structures.

Complex transitions between spike, burst or chaos synchronization states in coupled neurons with coexisting bursting patterns

NASA Astrophysics Data System (ADS)

Gu, Hua-Guang; Chen, Sheng-Gen; Li, Yu-Ye

2015-05-01

We investigated the synchronization dynamics of a coupled neuronal system composed of two identical Chay model neurons. The Chay model showed coexisting period-1 and period-2 bursting patterns as a parameter and initial values are varied. We simulated multiple periodic and chaotic bursting patterns with non-(NS), burst phase (BS), spike phase (SS), complete (CS), and lag synchronization states. When the coexisting behavior is near period-2 bursting, the transitions of synchronization states of the coupled system follows very complex transitions that begins with transitions between BS and SS, moves to transitions between CS and SS, and to CS. Most initial values lead to the CS state of period-2 bursting while only a few lead to the CS state of period-1 bursting. When the coexisting behavior is near period-1 bursting, the transitions begin with NS, move to transitions between SS and BS, to transitions between SS and CS, and then to CS. Most initial values lead to the CS state of period-1 bursting but a few lead to the CS state of period-2 bursting. The BS was identified as chaos synchronization. The patterns for NS and transitions between BS and SS are insensitive to initial values. The patterns for transitions between CS and SS and the CS state are sensitive to them. The number of spikes per burst of non-CS bursting increases with increasing coupling strength. These results not only reveal the initial value- and parameter-dependent synchronization transitions of coupled systems with coexisting behaviors, but also facilitate interpretation of various bursting patterns and synchronization transitions generated in the nervous system with weak coupling strength. Project supported by the National Natural Science Foundation of China (Grant Nos. 11372224 and 11402039) and the Fundamental Research Funds for Central Universities designated to Tongji University (Grant No. 1330219127).

Noncoding RNAs of the Ultrabithorax Domain of the Drosophila Bithorax Complex

PubMed Central

Pease, Benjamin; Borges, Ana C.; Bender, Welcome

2013-01-01

RNA transcripts without obvious coding potential are widespread in many creatures, including the fruit fly, Drosophila melanogaster. Several noncoding RNAs have been identified within the Drosophila bithorax complex. These first appear in blastoderm stage embryos, and their expression patterns indicate that they are transcribed only from active domains of the bithorax complex. It has been suggested that these noncoding RNAs have a role in establishing active domains, perhaps by setting the state of Polycomb Response Elements A comprehensive survey across the proximal half of the bithorax complex has now revealed nine distinct noncoding RNA transcripts, including four within the Ultrabithorax transcription unit. At the blastoderm stage, the noncoding transcripts collectively span ∼75% of the 135 kb surveyed. Recombination-mediated cassette exchange was used to invert the promoter of one of the noncoding RNAs, a 23-kb transcript from the bxd domain of the bithorax complex. The resulting animals fail to make the normal bxd noncoding RNA and show no transcription across the bxd Polycomb Response Element in early embryos. The mutant flies look normal; the regulation of the bxd domain appears unaffected. Thus, the bxd noncoding RNA has no apparent function. PMID:24077301

Processing of simple and complex acoustic signals in a tonotopically organized ear

PubMed Central

Hummel, Jennifer; Wolf, Konstantin; Kössl, Manfred; Nowotny, Manuela

2014-01-01

Processing of complex signals in the hearing organ remains poorly understood. This paper aims to contribute to this topic by presenting investigations on the mechanical and neuronal response of the hearing organ of the tropical bushcricket species Mecopoda elongata to simple pure tone signals as well as to the conspecific song as a complex acoustic signal. The high-frequency hearing organ of bushcrickets, the crista acustica (CA), is tonotopically tuned to frequencies between about 4 and 70 kHz. Laser Doppler vibrometer measurements revealed a strong and dominant low-frequency-induced motion of the CA when stimulated with either pure tone or complex stimuli. Consequently, the high-frequency distal area of the CA is more strongly deflected by low-frequency-induced waves than by high-frequency-induced waves. This low-frequency dominance will have strong effects on the processing of complex signals. Therefore, we additionally studied the neuronal response of the CA to native and frequency-manipulated chirps. Again, we found a dominant influence of low-frequency components within the conspecific song, indicating that the mechanical vibration pattern highly determines the neuronal response of the sensory cells. Thus, we conclude that the encoding of communication signals is modulated by ear mechanics. PMID:25339727

Quantifying full phenological event distributions reveals simultaneous advances, temporal stability and delays in spring and autumn migration timing in long-distance migratory birds.

PubMed

Miles, Will T S; Bolton, Mark; Davis, Peter; Dennis, Roy; Broad, Roger; Robertson, Iain; Riddiford, Nick J; Harvey, Paul V; Riddington, Roger; Shaw, Deryk N; Parnaby, David; Reid, Jane M

2017-04-01

Phenological changes in key seasonally expressed life-history traits occurring across periods of climatic and environmental change can cause temporal mismatches between interacting species, and thereby impact population and community dynamics. However, studies quantifying long-term phenological changes have commonly only measured variation occurring in spring, measured as the first or mean dates on which focal traits or events were observed. Few studies have considered seasonally paired events spanning spring and autumn or tested the key assumption that single convenient metrics accurately capture entire event distributions. We used 60 years (1955-2014) of daily bird migration census data from Fair Isle, Scotland, to comprehensively quantify the degree to which the full distributions of spring and autumn migration timing of 13 species of long-distance migratory bird changed across a period of substantial climatic and environmental change. In most species, mean spring and autumn migration dates changed little. However, the early migration phase (≤10th percentile date) commonly got earlier, while the late migration phase (≥90th percentile date) commonly got later. Consequently, species' total migration durations typically lengthened across years. Spring and autumn migration phenologies were not consistently correlated within or between years within species and hence were not tightly coupled. Furthermore, different metrics quantifying different aspects of migration phenology within seasons were not strongly cross-correlated, meaning that no single metric adequately described the full pattern of phenological change. These analyses therefore reveal complex patterns of simultaneous advancement, temporal stability and delay in spring and autumn migration phenologies, altering species' life-history structures. Additionally, they demonstrate that this complexity is only revealed if multiple metrics encompassing entire seasonal event distributions, rather than single metrics, are used to quantify phenological change. Existing evidence of long-term phenological changes detected using only one or two metrics should consequently be interpreted cautiously because divergent changes occurring simultaneously could potentially have remained undetected. © 2016 John Wiley & Sons Ltd.

Balancing selection and genetic drift at major histocompatibility complex class II genes in isolated populations of golden snub-nosed monkey (Rhinopithecus roxellana)

PubMed Central

2012-01-01

Background Small, isolated populations often experience loss of genetic variation due to random genetic drift. Unlike neutral or nearly neutral markers (such as mitochondrial genes or microsatellites), major histocompatibility complex (MHC) genes in these populations may retain high levels of polymorphism due to balancing selection. The relative roles of balancing selection and genetic drift in either small isolated or bottlenecked populations remain controversial. In this study, we examined the mechanisms maintaining polymorphisms of MHC genes in small isolated populations of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) by comparing genetic variation found in MHC and microsatellite loci. There are few studies of this kind conducted on highly endangered primate species. Results Two MHC genes were sequenced and sixteen microsatellite loci were genotyped from samples representing three isolated populations. We isolated nine DQA1 alleles and sixteen DQB1 alleles and validated expression of the alleles. Lowest genetic variation for both MHC and microsatellites was found in the Shennongjia (SNJ) population. Historical balancing selection was revealed at both the DQA1 and DQB1 loci, as revealed by excess non-synonymous substitutions at antigen binding sites (ABS) and maximum-likelihood-based random-site models. Patterns of microsatellite variation revealed population structure. FST outlier analysis showed that population differentiation at the two MHC loci was similar to the microsatellite loci. Conclusions MHC genes and microsatellite loci showed the same allelic richness pattern with the lowest genetic variation occurring in SNJ, suggesting that genetic drift played a prominent role in these isolated populations. As MHC genes are subject to selective pressures, the maintenance of genetic variation is of particular interest in small, long-isolated populations. The results of this study may contribute to captive breeding and translocation programs for endangered species. PMID:23083308

Effect of cerulenin on fatty acid composition and gene expression pattern of DHA-producing strain Colwellia psychrerythraea strain 34H.

PubMed

Wan, Xia; Peng, Yun-Feng; Zhou, Xue-Rong; Gong, Yang-Min; Huang, Feng-Hong; Moncalián, Gabriel

2016-02-06

Colwellia psychrerythraea 34H is a psychrophilic bacterium able to produce docosahexaenoic acid (DHA). Polyketide synthase pathway is assumed to be responsible for DHA production in marine bacteria. Five pfa genes from strain 34H were confirmed to be responsible for DHA formation by heterogeneous expression in Escherichia coli. The complexity of fatty acid profile of this strain was revealed by GC and GC-MS. Treatment of cells with cerulenin resulted in significantly reduced level of C16 monounsaturated fatty acid (C16:1(Δ9t), C16:1(Δ7)). In contrast, the amount of saturated fatty acids (C10:0, C12:0, C14:0), hydroxyl fatty acids (3-OH C10:0 and 3-OH C12:0), as well as C20:4ω3, C20:5ω3 and C22:6ω3 were increased. RNA sequencing (RNA-Seq) revealed the altered gene expression pattern when C. psychrerythraea cells were treated with cerulenin. Genes involved in polyketide synthase pathway and fatty acid biosynthesis pathway were not obviously affected by cerulenin treatment. In contrast, several genes involved in fatty acid degradation or β-oxidation pathway were dramatically reduced at the transcriptional level. Genes responsible for DHA formation in C. psychrerythraea was first cloned and characterized. We revealed the complexity of fatty acid profile in this DHA-producing strain. Cerulenin could substantially change the fatty acid composition by affecting the fatty acid degradation at transcriptional level. Acyl-CoA dehydrogenase gene family involved in the first step of β-oxidation pathway may be important to the selectivity of degraded fatty acids. In addition, inhibition of FabB protein by cerulenin may lead to the accumulation of malonyl-CoA, which is the substrate for DHA formation.

How regularity representations of short sound patterns that are based on relative or absolute pitch information establish over time: An EEG study.

PubMed

Bader, Maria; Schröger, Erich; Grimm, Sabine

2017-01-01

The recognition of sound patterns in speech or music (e.g., a melody that is played in different keys) requires knowledge about pitch relations between successive sounds. We investigated the formation of regularity representations for sound patterns in an event-related potential (ERP) study. A pattern, which consisted of six concatenated 50 ms tone segments differing in fundamental frequency, was presented 1, 2, 3, 6, or 12 times and then replaced by another pattern by randomly changing the pitch of the tonal segments (roving standard paradigm). In an absolute repetition condition, patterns were repeated identically, whereas in a transposed condition, only the pitch relations of the tonal segments of the patterns were repeated, while the entire patterns were shifted up or down in pitch. During ERP measurement participants were not informed about the pattern repetition rule, but were instructed to discriminate rarely occurring targets of lower or higher sound intensity. EPRs for pattern changes (mismatch negativity, MMN; and P3a) and for pattern repetitions (repetition positivity, RP) revealed that the auditory system is able to rapidly extract regularities from unfamiliar complex sound patterns even when absolute pitch varies. Yet, enhanced RP and P3a amplitudes, and improved behavioral performance measured in a post-hoc test, in the absolute as compared with the transposed condition suggest that it is more difficult to encode patterns without absolute pitch information. This is explained by dissociable processing of standards and deviants as well as a back propagation mechanism to early sensory processing stages, which is effective after less repetitions of a standard stimulus for absolute pitch.

Spontaneous switching among multiple spatio-temporal patterns in three-oscillator systems constructed with oscillatory cells of true slime mold

NASA Astrophysics Data System (ADS)

Takamatsu, Atsuko

2006-11-01

Three-oscillator systems with plasmodia of true slime mold, Physarum polycephalum, which is an oscillatory amoeba-like unicellular organism, were experimentally constructed and their spatio-temporal patterns were investigated. Three typical spatio-temporal patterns were found: rotation ( R), partial in-phase ( PI), and partial anti-phase with double frequency ( PA). In pattern R, phase differences between adjacent oscillators were almost 120 ∘. In pattern PI, two oscillators were in-phase and the third oscillator showed anti-phase against the two oscillators. In pattern PA, two oscillators showed anti-phase and the third oscillator showed frequency doubling oscillation with small amplitude. Actually each pattern is not perfectly stable but quasi-stable. Interestingly, the system shows spontaneous switching among the multiple quasi-stable patterns. Statistical analyses revealed a characteristic in the residence time of each pattern: the histograms seem to have Gamma-like distribution form but with a sharp peak and a tail on the side of long period. That suggests the attractor of this system has complex structure composed of at least three types of sub-attractors: a “Gamma attractor”-involved with several Poisson processes, a “deterministic attractor”-the residence time is deterministic, and a “stable attractor”-each pattern is stable. When the coupling strength was small, only the Gamma attractor was observed and switching behavior among patterns R, PI, and PA almost always via an asynchronous pattern named O. A conjecture is as follows: Internal/external noise exposes each pattern of R, PI, and PA coexisting around bifurcation points: That is observed as the Gamma attractor. As coupling strength increases, the deterministic attractor appears then followed by the stable attractor, always accompanied with the Gamma attractor. Switching behavior could be caused by regular existence of the Gamma attractor.

How regularity representations of short sound patterns that are based on relative or absolute pitch information establish over time: An EEG study

PubMed Central

Schröger, Erich; Grimm, Sabine

2017-01-01

The recognition of sound patterns in speech or music (e.g., a melody that is played in different keys) requires knowledge about pitch relations between successive sounds. We investigated the formation of regularity representations for sound patterns in an event-related potential (ERP) study. A pattern, which consisted of six concatenated 50 ms tone segments differing in fundamental frequency, was presented 1, 2, 3, 6, or 12 times and then replaced by another pattern by randomly changing the pitch of the tonal segments (roving standard paradigm). In an absolute repetition condition, patterns were repeated identically, whereas in a transposed condition, only the pitch relations of the tonal segments of the patterns were repeated, while the entire patterns were shifted up or down in pitch. During ERP measurement participants were not informed about the pattern repetition rule, but were instructed to discriminate rarely occurring targets of lower or higher sound intensity. EPRs for pattern changes (mismatch negativity, MMN; and P3a) and for pattern repetitions (repetition positivity, RP) revealed that the auditory system is able to rapidly extract regularities from unfamiliar complex sound patterns even when absolute pitch varies. Yet, enhanced RP and P3a amplitudes, and improved behavioral performance measured in a post-hoc test, in the absolute as compared with the transposed condition suggest that it is more difficult to encode patterns without absolute pitch information. This is explained by dissociable processing of standards and deviants as well as a back propagation mechanism to early sensory processing stages, which is effective after less repetitions of a standard stimulus for absolute pitch. PMID:28472146

Complex Event Recognition Architecture

NASA Technical Reports Server (NTRS)

Fitzgerald, William A.; Firby, R. James

2009-01-01

Complex Event Recognition Architecture (CERA) is the name of a computational architecture, and software that implements the architecture, for recognizing complex event patterns that may be spread across multiple streams of input data. One of the main components of CERA is an intuitive event pattern language that simplifies what would otherwise be the complex, difficult tasks of creating logical descriptions of combinations of temporal events and defining rules for combining information from different sources over time. In this language, recognition patterns are defined in simple, declarative statements that combine point events from given input streams with those from other streams, using conjunction, disjunction, and negation. Patterns can be built on one another recursively to describe very rich, temporally extended combinations of events. Thereafter, a run-time matching algorithm in CERA efficiently matches these patterns against input data and signals when patterns are recognized. CERA can be used to monitor complex systems and to signal operators or initiate corrective actions when anomalous conditions are recognized. CERA can be run as a stand-alone monitoring system, or it can be integrated into a larger system to automatically trigger responses to changing environments or problematic situations.

Formation mechanism of complex pattern on fishes' skin

NASA Astrophysics Data System (ADS)

Li, Xia; Liu, Shuhua

2009-10-01

In this paper, the formation mechanism of the complex patterns observed on the skin of fishes has been investigated by a two-coupled reaction diffusion model. The effects of coupling strength between two layers play an important role in the pattern-forming process. It is found that only the epidermis layer can produce complicated patterns that have structures on more than one length scale. These complicated patterns including super-stripe pattern, mixture of spots and stripe, and white-eye pattern are similar to the pigmentation patterns on fishes' skin.

Rethinking the longitudinal stream temperature paradigm: region-wide comparison of thermal infrared imagery reveals unexpected complexity of river temperatures

USGS Publications Warehouse

Fullerton, Aimee H.; Torgersen, Christian E.; Lawler, Joshua J.; Faux, Russell N.; Steel, E. Ashley; Beechie, Timothy J.; Ebersole, Joseph L.; Leibowitz, Scott J.

2015-01-01

Prevailing theory suggests that stream temperature warms asymptotically in a downstream direction, beginning at the temperature of the source in the headwaters and leveling off downstream as it converges to match meteorological conditions. However, there have been few empirical examples of longitudinal patterns of temperature in large rivers due to a paucity of data. We constructed longitudinal thermal profiles (temperature versus distance) for 53 rivers in the Pacific Northwest (USA) using an extensive dataset of remotely sensed summertime river temperatures and classified each profile into one of five patterns of downstream warming: asymptotic (increasing then flattening), linear (increasing steadily), uniform (not changing), parabolic (increasing then decreasing), or complex (not fitting other classes). We evaluated (1) how frequently profiles warmed asymptotically downstream as expected, and (2) whether relationships between river temperature and common hydroclimatic variables differed by profile class. We found considerable diversity in profile shape, with 47% of rivers warming asymptotically, and 53% having alternative profile shapes. Water temperature did not warm substantially over the course of the river for coastal parabolic and uniform profiles, and for some linear and complex profiles. Profile classes showed no clear geographical trends. The degree of correlation between river temperature and hydroclimatic variables differed among profile classes, but there was overlap among classes. Water temperature in rivers with asymptotic or parabolic profiles was positively correlated with August air temperature, tributary temperature and velocity, and negatively correlated with elevation, August precipitation, gradient, and distance upstream. Conversely, associations were less apparent in rivers with linear, uniform, or complex profiles. Factors contributing to the unique shape of parabolic profiles differed for coastal and inland rivers, where downstream cooling was influenced locally by climate or cool water inputs, respectively. Potential drivers of shape for complex profiles were specific to each river. These thermal patterns indicate diverse thermal habitats that may promote resilience of aquatic biota to climate change. Without this spatial context, climate change models may incorrectly estimate loss of thermally suitable habitat.

Historical archaeology at the Clarkson Mine, an eastern Ohio mining complex

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

Keener, C.S.

2003-07-01

This study examines the Clarkson Mine (33BL333), an eastern Ohio coal mine complex dating to the 1910s to 1920s, situated along Wheeling Creek. The results of preliminary surveys and the subsequent mitigation of four structures at the site are presented. The historical archaeology conducted at the site demonstrates the significant research possibilities inherent at many of these early industrial mine complexes. Of particular interest is the findings of depositional patterning around residential structures that revealed the influence of architecture on where and how items were deposited on the land surface. The ceramic and faunal assemblage were analyzed and provide significantmore » details on socioeconomic attributes associated with the workers or staff. Artifacts recovered at the site provide an excellent diagnostic framework from which other similarly aged sites can be compared and dated. The findings at the Clarkson Mine are also placed into a more regional perspective and compared with other contemporary studies.« less

Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

PubMed Central

Gaiti, Federico; Jindrich, Katia; Fernandez-Valverde, Selene L; Roper, Kathrein E; Degnan, Bernard M; Tanurdžić, Miloš

2017-01-01

Combinatorial patterns of histone modifications regulate developmental and cell type-specific gene expression and underpin animal complexity, but it is unclear when this regulatory system evolved. By analysing histone modifications in a morphologically-simple, early branching animal, the sponge Amphimedonqueenslandica, we show that the regulatory landscape used by complex bilaterians was already in place at the dawn of animal multicellularity. This includes distal enhancers, repressive chromatin and transcriptional units marked by H3K4me3 that vary with levels of developmental regulation. Strikingly, Amphimedon enhancers are enriched in metazoan-specific microsyntenic units, suggesting that their genomic location is extremely ancient and likely to place constraints on the evolution of surrounding genes. These results suggest that the regulatory foundation for spatiotemporal gene expression evolved prior to the divergence of sponges and eumetazoans, and was necessary for the evolution of animal multicellularity. DOI: http://dx.doi.org/10.7554/eLife.22194.001 PMID:28395144

Fragmentation studies of fulvic acids using collision induced dissociation fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Witt, Matthias; Fuchser, Jens; Koch, Boris P

2009-04-01

The complex natural organic matter standard Suwannee river fulvic acid (SRFA) was analyzed by negative ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS) using on-resonance collision induced dissociation (CID) of single ultrahigh resolved mass peaks in the ICR cell. Molecular formula assignment of precursor masses resulted in exactly one molecular formula for each of the peaks. Analyses of the corresponding fragment spectra and comparison to different standard substances revealed specific neutral losses and fragmentation patterns which result in structures consisting of a high degree of carboxyl- and fewer hydroxyl groups. The comparison of fragmented mass peaks within different pseudohomologous series (CH(2)-series, and CH(4) vs O exchange) suggested structurally based differences between these series. CID FTICR MS allowed isolating single mass peaks in a very complex natural organic matter spectrum. Subsequently, fragmentation gave structural insights into this material. Our results suggest that the structural diversity in complex humic substances is not as high as expected.

Complex Patterns in Financial Time Series Through HIGUCHI’S Fractal Dimension

NASA Astrophysics Data System (ADS)

Grace Elizabeth Rani, T. G.; Jayalalitha, G.

2016-11-01

This paper analyzes the complexity of stock exchanges through fractal theory. Closing price indices of four stock exchanges with different industry sectors are selected. Degree of complexity is assessed through Higuchi’s fractal dimension. Various window sizes are considered in evaluating the fractal dimension. It is inferred that the data considered as a whole represents random walk for all the four indices. Analysis of financial data through windowing procedure exhibits multi-fractality. Attempts to apply moving averages to reduce noise in the data revealed lower estimates of fractal dimension, which was verified using fractional Brownian motion. A change in the normalization factor in Higuchi’s algorithm did improve the results. It is quintessential to focus on rural development to realize a standard and steady growth of economy. Tools must be devised to settle the issues in this regard. Micro level institutions are necessary for the economic growth of a country like India, which would induce a sporadic development in the present global economical scenario.

Instant noodles, processed food intake, and dietary pattern are associated with atopic dermatitis in an adult population (KNHANES 2009-2011).

PubMed

Park, Sunmin; Choi, Hyun-Seok; Bae, Ji-Hyun

2016-01-01

The incidence of atopic dermatitis (AD) is continuously increasing in industrialized countries, possibly due to dietary and lifestyle changes. However, the association between processed food intake and AD has not been studied in a large adult population. We investigated the association between dietary habits and AD in 17,497 adults in the 2009-2011 Korean National Health and Nutrition Examination Survey (KNHANES). We identified 4 dietary patterns using principal components analysis of a 63-item food frequency questionnaire: the "traditional dietary pattern", rich in rice and kimchi; the "processed food pattern", with more meat, instant noodles, soda, and processed foods; the "healthy dietary pattern", high in grains, vegetables, fruits, and seaweeds; and the "drinking dietary pattern", mainly drinking coffee and alcohol. Adjusted odds ratios (ORs) for AD were calculated according to dietary patterns after adjusting for potential confounders with incorporation of sample weights for the complex sample design. The "meat and processed food" pattern was associated with a significant 1.57 fold higher OR for atopic dermatitis than the low consumption group. Further analysis revealed that the increased atopic dermatitis was most closely associated with instant noodles. In contrast, the groups with high intake of rice and kimchi exhibited lower ORs, 0.38 and 0.43 folds, compared to the low intake group. Consuming instant noodles, meat and processed foods was associated with increased prevalence of atopic dermatitis, whereas consuming rice and kimchi, and coffee was associated with decreased prevalence of atopic dermatitis.

Visualizing fossilization using laser ablation-inductively coupled plasma-mass spectrometry maps of trace elements in Late Cretaceous bones

USGS Publications Warehouse

Koenig, A.E.; Rogers, R.R.; Trueman, C.N.

2009-01-01

Elemental maps generated by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) provide a previously unavailable high-resolution visualization of the complex physicochemical conditions operating within individual bones during the early stages of diagenesis and fossilization. A selection of LA-ICP-MS maps of bones collected from the Late Cretaceous of Montana (United States) and Madagascar graphically illustrate diverse paths to recrystallization, and reveal unique insights into geochemical aspects of taphonomic history. Some bones show distinct gradients in concentrations of rare earth elements and uranium, with highest concentrations at external bone margins. Others exhibit more intricate patterns of trace element uptake related to bone histology and its control on the flow paths of pore waters. Patterns of element uptake as revealed by LA-ICP-MS maps can be used to guide sampling strategies, and call into question previous studies that hinge upon localized bulk samples of fossilized bone tissue. LA-ICP-MS maps also allow for comparison of recrystallization rates among fossil bones, and afford a novel approach to identifying bones or regions of bones potentially suitable for extracting intact biogeochemical signals. ?? 2009 Geological Society of America.

Fine-scale phylogenetic architecture of a complex bacterial community.

PubMed

Acinas, Silvia G; Klepac-Ceraj, Vanja; Hunt, Dana E; Pharino, Chanathip; Ceraj, Ivica; Distel, Daniel L; Polz, Martin F

2004-07-29

Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored. Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.

The geographic mosaic of Ecuadorian Y-chromosome ancestry.

PubMed

Toscanini, U; Gaviria, A; Pardo-Seco, J; Gómez-Carballa, A; Moscoso, F; Vela, M; Cobos, S; Lupero, A; Zambrano, A K; Martinón-Torres, F; Carabajo-Marcillo, A; Yunga-León, R; Ugalde-Noritz, N; Ordoñez-Ugalde, A; Salas, A

2018-03-01

Ecuadorians originated from a complex mixture of Native American indigenous people with Europeans and Africans. We analyzed Y-chromosome STRs (Y-STRs) in a sample of 415 Ecuadorians (145 using the AmpFlSTR ® Yfiler™ system [Life Technologies, USA] and 270 using the PowerPlex ® Y23 system [Promega Corp., USA]; hereafter Yfiler and PPY23, respectively) representing three main ecological continental regions of the country, namely Amazon rainforest, Andes, and Pacific coast. Diversity values are high in the three regions, and the PPY23 exhibits higher discrimination power than the Yfiler set. While summary statistics, AMOVA, and R ST distances show low to moderate levels of population stratification, inferred ancestry derived from Y-STRs reveal clear patterns of geographic variation. The major ancestry in Ecuadorian males is European (61%), followed by an important Native American component (34%); whereas the African ancestry (5%) is mainly concentrated in the Northwest corner of the country. We conclude that classical procedures for measuring population stratification do not have the desirable sensitivity. Statistical inference of ancestry from Y-STRS is a satisfactory alternative for revealing patterns of spatial variation that would pass unnoticed when using popular statistical summary indices. Copyright © 2017 Elsevier B.V. All rights reserved.

Zebrin II compartmentation of the cerebellum in a basal insectivore, the Madagascan hedgehog tenrec Echinops telfairi

PubMed Central

Sillitoe, Roy V; Künzle, Heinz; Hawkes, Richard

2003-01-01

The mammalian cerebellum is histologically uniform. However, underlying the simple laminar architecture is a complex arrangement of parasagittal stripes and transverse zones that can be revealed by the expression of zebrin II/aldolase C. The cerebellar cortex of rodents, for example, is organized into four transverse zones: anterior, central, posterior and nodular. Within the anterior and posterior zones, parasagittal stripes of Purkinje cells expressing zebrin II alternate with those that do not. Zonal boundaries appear to be independent of cerebellar lobulation. To explore this model further, and to broaden our understanding of the evolution of cerebellar patterning, zebrin II expression has been studied in the cerebellum of the Madagascan hedgehog tenrec (Echinops telfairi), a basal insectivore with a lissiform cerebellum with only five lobules. Zebrin II expression in the tenrec reveals an array of four transverse zones as in rodents, two with homogeneous zebrin II expression, two further subdivided into stripes, that closely resembles the expression pattern described in other mammals. We conclude that a zone-and-stripe organization may be a common feature of the mammalian cerebellar vermis and hemispheres, and that zonal boundaries and cerebellar lobules and fissures form independently. PMID:14529046

Coastal currents and mass transport of surface sediments over the shelf regions of Monterey Bay, California

USGS Publications Warehouse

Wolf, S.C.

1970-01-01

In Monterey Bay, the highest concentrations of medium and fine sands occur nearshore between ten and thirty fathoms. Silt and clay accumulate in greater depths. Contours of median diameter roughly parallel the isobaths. Fine-grained materials are supplied to the bay region from erosion of cliffs which partly surround Monterey Bay, from sediment laden river discharge, and from continual reworking of widespread Pleistocene and Recent sea floor sediments. These sediments in turn are picked up by coastal currents and distributed over the shelf regions by present day current regimes. Studies of bottom currents over the shelf regions and in Monterey Canyon have revealed patterns which vary with seasonal changes. Current patterns during August and September exhibit remarkable symmetry about the axis of Monterey Submarine Canyon. Central Shelf currents north and south of Monterey Canyon flowed northwest at an average rate of 0.2 knots and south at 0.3 knots respectively. On the North Shelf between January and March currents flowed east to southeast at 0.3-0.5 knots with mirror image patterns above the South Shelf during the same period. Irregular current flow in the canyon indicates a complex current structure with frequent shifts in counterclockwise and clockwise direction over very short periods of time. Bottom topography of the canyon complex often causes localization of canyon currents. One particular observation at a depth of 51 fathoms indicated up-canyon flow at a rate of 0.2 knots. Most of the observed currents are related to seasonal variations, upwelling, ocean swell patterns, and to changes in the California and Davidson currents. Changes in current regimes are reflected in the patterns of sediment distribution and transport. Sediment transport is chiefly parallel to the isobaths, particularly on the North and South Shelf regions. Complex dispersal patterns are observed near Monterey Canyon and Moss Landing Harbor jetties. Longshore currents move sediments southward except near Monterey Canyon which acts as a physiographic barrier and the extreme southern end of the bay where currents are non persistent. Some sediments are also transported offshore by rip currents and other agencies and deposited in deeper, quieter waters. Supply of sediments to the canyon head results in over-filling and steepening with subsequent mass movement of sediments seaward followed by deposition in channels and on the broad deep sea fan. ?? 1970.

Modified nucleotides reveal the indirect role of the central base pairs in stabilizing the lac repressor-operator complex.

PubMed Central

Zhang, X; Gottlieb, P A

1995-01-01

Guanine residues in the lac operator were replaced by 2-aminopurine or purine analogues, pairing the modified nucleotides with C. The observed equilibrium dissociation constants for lac repressor binding to substituted operators were measured in 10 mM Tris, 150 mM KCl, 0.1 mM EDTA, 0.1 mM DTE, pH 7.6 at 25 degrees C. These measurements revealed five positions that destabilized the complex when substituted with either analogue. Two positions, which are related by a 2-fold symmetry, are in the major groove of the operator thought to directly interact with the protein. Three sites were in the central region of the operator. A purine analogue at a sixth site perturbed the local DNA structure and destabilized the complex. Alkylation interference experiments of the 2-aminopurine substituted operators demonstrated that, of the five affected, two substitutions displayed altered phosphate interference patterns at the phosphate adjacent to the substituted base. For these operators, complex formation was measured in different concentrations of KCl to assess the contribution of counterion release to the bimolecular process. The results indicated that both complexes were similar to wild-type, although minor changes were observed. The Kobs of the complex was then measured when 2-aminopurine or purine analogues were paired with uracil nucleotide, a base pair that serves to stabilize the DNA. The introduction of the new base pairs revealed two effects on the bimolecular interaction. For those operator sites that are thought to perturb the interaction directly, the affinity of the complex was weakened to levels observed for the singly-substituted operators. In contrast, the nucleotides of 2-aminopurine paired with uracil positioned in the central region of the operator served to enhance the stability of the complex. The purine-uracil base pair substitution on the other hand had a significant destabilizing effect on the interaction. We propose that the central base pairs modulate binding of the complex by altering the intrinsic properties of the DNA. Two specific attributes are required to achieve the lowest free energy of interaction. The DNA must have two interstrand hydrogen bonds to stabilize the duplex and it must have properties associated with directional bending or unwinding. This analysis does not rule out contributions by direct interactions between the protein and the central region of the operator but underscores how indirect effects play a major role in complex formation in this system. Images PMID:7784203

Silver clusters encapsulated in C{sub 60}: A density functional study

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

Dhiman, Shobhna; Kumar, Ranjan; Dharamvir, Keya

2015-08-28

We explore the possibility of formation of endohedral complexes of Ag{sub n} atoms (n=1-9) inside C{sub 60} molecule using density functional theory and molecular dynamics. The obtained results reveal that Ag{sub n} (n=8) atoms can form stable complexes with the C{sub 60} molecule. Encapsulation of large number of Ag{sub n} atoms (n>8) make C{sub 60} cage instable, showing distortion of cage. Binding energy/atom increases with the number of Ag atoms up to n=4, after that it increases. Ionization potential decreases till n=4 and then increases, electron affinity increases till n=4 and then shows oscillatory nature as a function of Agmore » atoms inside the cage. Homo –Lumo gap shows no systematic pattern. Our results agreed well with the data available.« less

Intermolecular symmetry-adapted perturbation theory study of large organic complexes.

PubMed

Heßelmann, Andreas; Korona, Tatiana

2014-09-07

Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.

Synthesis, structural characterization and DFT calculation on a square-planar Ni(II) complex of a compartmental Schiff base ligand

NASA Astrophysics Data System (ADS)

Biswas, Surajit; Dolai, Malay; Dutta, Arpan; Ali, Mahammad

2016-12-01

Reaction of a symmetric compartmental Schiff-base ligand, (H2L) with nickel(II) perchlorate hexahydrate in 1:1 M ratio in methanol gives rise to a mononuclear nickel(II) compound, NiL (1). The compound has been characterized by C, H, N microanalyses and UV-Vis spectra. The single crystal X-ray diffraction studies reveal a square planar geometry around the Ni(II) center. The compound crystallizes in monoclinic system with space group C2/c with a = 21.6425(6), b = 9.9481(3), c = 13.1958(4) Å, β = 107.728(2)°, V = 2706.16(14) Å3 and Z = 4. Ground state DFT optimization and TDDFT calculations on the ligand and complex were performed to get their UV-Vis spectral pattern.

Mecp2 truncation in male mice promotes affiliative social behavior

PubMed Central

Pearson, B.L.; Defensor, E.B.; Pobbe, R.L.H.; Yamamoto, L.H.L.; Bolivar, V.J.; Blanchard, D.C.; Blanchard, R.J.

2018-01-01

Mouse models of Rett syndrome, with targeted mutations in the Mecp2 gene, show a high degree of phenotypic consistency with the clinical syndrome. In addition to severe and age-specific regression in motor and cognitive abilities, a variety of studies have demonstrated that Mecp2 mutant mice display impaired social behavior. Conversely, other studies indicate complex enhancements of social behavior in Mecp2 mutant mice. Since social behavior is a complicated accumulation of constructs, we performed a series of classic and refined social behavior tasks and revealed a relatively consistent pattern of enhanced pro-social behavior in hypomorphic Mecp2308/Y mutant mice. Analyses of repetitive motor acts, and cognitive stereotypy did not reveal any profound differences due to genotype. Taken together, these results suggest that the mutations associated with Rett syndrome are not necessarily associated with autism-relevant social impairment in mice. However, this gene may be a valuable candidate for revealing basic mechanisms of affiliative behavior. PMID:21909962

Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development.

PubMed

Parker, Heidi G; Dreger, Dayna L; Rimbault, Maud; Davis, Brian W; Mullen, Alexandra B; Carpintero-Ramirez, Gretchen; Ostrander, Elaine A

2017-04-25

There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Room temperature chemical bath deposition of cadmium selenide, cadmium sulfide and cadmium sulfoselenide thin films with novel nanostructures

NASA Astrophysics Data System (ADS)

VanderHyde, Cephas A.; Sartale, S. D.; Patil, Jayant M.; Ghoderao, Karuna P.; Sawant, Jitendra P.; Kale, Rohidas B.

2015-10-01

A simple, convenient and low cost chemical synthesis route has been used to deposit nanostructured cadmium sulfide, selenide and sulfoselenide thin films at room temperature. The films were deposited on glass substrates, using cadmium acetate as cadmium ion and sodium selenosulfate/thiourea as a selenium/sulfur ion sources. Aqueous ammonia was used as a complex reagent and also to adjust the pH of the final solution. The as-deposited films were uniform, well adherent to the glass substrate, specularly reflective and red/yellow in color depending on selenium and sulfur composition. The X-ray diffraction pattern of deposited cadmium selenide thin film revealed the nanocrystalline nature with cubic phase; cadmium sulfide revealed mixture of cubic along with hexagonal phase and cadmium sulfoselenide thin film were grown with purely hexagonal phase. The morphological observations revealed the growth and formation of interesting one, two and three-dimensional nanostructures. The band gap of thin films was calculated and the results are reported.

Multiple Fermi pockets revealed by Shubnikov-de Haas oscillations in WTe2

NASA Astrophysics Data System (ADS)

Xiang, Fei-Xiang; Veldhorst, Menno; Dou, Shi-Xue; Wang, Xiao-Lin

2015-11-01

The recently discovered non-saturating and parabolic magnetoresistance and the pressure-induced superconductivity at low temperature in WTe2 imply its rich electronic structure and possible practical applications. Here we use magnetotransport measurements to investigate the electronic structure of WTe2 single crystals. A non-saturating and parabolic magnetoresistance is observed from low temperature to high temperature up to 200 K with magnetic fields up to 8 T. Shubnikov-de Haas (SdH) oscillations with beating patterns are observed, the fast Fourier transform of which reveals three oscillation frequencies, corresponding to three pairs of Fermi pockets with comparable effective masses, m* ∼ 0.31~me . By fitting the Hall resistivity, we infer that they can be attributed to one pair of electron pockets and two pairs of hole pockets, together with nearly perfect compensation of the electron-hole carrier concentration. These magnetotransport measurements reveal the complex electronic structure in WTe2, explaining the non-saturating magnetoresistance.

Holocene forest dynamics in central and western Mediterranean: periodicity, spatio-temporal patterns and climate influence.

PubMed

Di Rita, Federico; Fletcher, William J; Aranbarri, Josu; Margaritelli, Giulia; Lirer, Fabrizio; Magri, Donatella

2018-06-12

It is well-known that the Holocene exhibits a millennial-scale climate variability. However, its periodicity, spatio-temporal patterns and underlying processes are not fully deciphered yet. Here we focus on the central and western Mediterranean. We show that recurrent forest declines from the Gulf of Gaeta (central Tyrrhenian Sea) reveal a 1860-yr periodicity, consistent with a ca. 1800-yr climate fluctuation induced by large-scale changes in climate modes, linked to solar activity and/or AMOC intensity. We show that recurrent forest declines and dry events are also recorded in several pollen and palaeohydrological proxy-records in the south-central Mediterranean. We found coeval events also in several palaeohydrological records from the south-western Mediterranean, which however show generally wet climate conditions, indicating a spatio-temporal hydrological pattern opposite to the south-central Mediterranean and suggesting that different expressions of climate modes occurred in the two regions at the same time. We propose that these opposite hydroclimate regimes point to a complex interplay of the prevailing or predominant phases of NAO-like circulation, East Atlantic pattern, and extension and location of the North African anticyclone. At a larger geographical scale, displacements of the ITCZ, modulated by solar activity and/or AMOC intensity, may have also indirectly influenced the observed pattern.

Alkynyl-naphthalimide Fluorophores: Gold Coordination Chemistry and Cellular Imaging Applications.

PubMed

Langdon-Jones, Emily E; Lloyd, David; Hayes, Anthony J; Wainwright, Shane D; Mottram, Huw J; Coles, Simon J; Horton, Peter N; Pope, Simon J A

2015-07-06

A range of fluorescent alkynyl-naphthalimide fluorophores has been synthesized and their photophysical properties examined. The fluorescent ligands are based upon a 4-substituted 1,8-naphthalimide core and incorporate structural variations (at the 4-position) to tune the amphiphilic character: chloro (L1), 4-[2-(2-aminoethoxy)ethanol] (L2), 4-[2-(2-methoxyethoxy)ethylamino] (L3), piperidine (L4), morpholine (L5), 4-methylpiperidine (L6), and 4-piperidone ethylene ketal (L7) variants. The amino-substituted species (L2-L7) are fluorescent in the visible region at around 517-535 nm through a naphthalimide-localized intramolecular charge transfer (ICT), with appreciable Stokes' shifts of ca. 6500 cm(-1) and lifetimes up to 10.4 ns. Corresponding two-coordinate Au(I) complexes [Au(L)(PPh3)] were isolated, with X-ray structural studies revealing the expected coordination mode via the alkyne donor. The Au(I) complexes retain the visible fluorescence associated with the coordinated alkynyl-naphthalimide ligand. The ligands and complexes were investigated for their cytotoxicity across a range of cell lines (LOVO, MCF-7, A549, PC3, HEK) and their potential as cell imaging agents for HEK (human embryonic kidney) cells and Spironucleus vortens using confocal fluorescence microscopy. The images reveal that these fluorophores are highly compatible with fluorescence microscopy and show some clear intracellular localization patterns that are dependent upon the specific nature of the naphthalimide substituent.

Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.

PubMed

Beres, Stephen B; Carroll, Ronan K; Shea, Patrick R; Sitkiewicz, Izabela; Martinez-Gutierrez, Juan Carlos; Low, Donald E; McGeer, Allison; Willey, Barbara M; Green, Karen; Tyrrell, Gregory J; Goldman, Thomas D; Feldgarden, Michael; Birren, Bruce W; Fofanov, Yuriy; Boos, John; Wheaton, William D; Honisch, Christiane; Musser, James M

2010-03-02

Understanding the fine-structure molecular architecture of bacterial epidemics has been a long-sought goal of infectious disease research. We used short-read-length DNA sequencing coupled with mass spectroscopy analysis of SNPs to study the molecular pathogenomics of three successive epidemics of invasive infections involving 344 serotype M3 group A Streptococcus in Ontario, Canada. Sequencing the genome of 95 strains from the three epidemics, coupled with analysis of 280 biallelic SNPs in all 344 strains, revealed an unexpectedly complex population structure composed of a dynamic mixture of distinct clonally related complexes. We discovered that each epidemic is dominated by micro- and macrobursts of multiple emergent clones, some with distinct strain genotype-patient phenotype relationships. On average, strains were differentiated from one another by only 49 SNPs and 11 insertion-deletion events (indels) in the core genome. Ten percent of SNPs are strain specific; that is, each strain has a unique genome sequence. We identified nonrandom temporal-spatial patterns of strain distribution within and between the epidemic peaks. The extensive full-genome data permitted us to identify genes with significantly increased rates of nonsynonymous (amino acid-altering) nucleotide polymorphisms, thereby providing clues about selective forces operative in the host. Comparative expression microarray analysis revealed that closely related strains differentiated by seemingly modest genetic changes can have significantly divergent transcriptomes. We conclude that enhanced understanding of bacterial epidemics requires a deep-sequencing, geographically centric, comparative pathogenomics strategy.

Volcanic deformation of Atosanupuri volcanic complex in the Kussharo caldera, Japan, from 1993 to 2016 revealed by JERS-1, ALOS, and ALOS-2 radar interferometry

NASA Astrophysics Data System (ADS)

Fujiwara, Satoshi; Murakami, Makoto; Nishimura, Takuya; Tobita, Mikio; Yarai, Hiroshi; Kobayashi, Tomokazu

2017-06-01

A series of uplifts and subsidences of a volcanic complex in the Kussharo caldera in eastern Hokkaido (Japan) has been revealed by interferometric analysis using archived satellite synthetic aperture radar data. A time series of interferograms from 1993 to 1998 showed the temporal evolution of a ground deformation process. The horizontal dimension of the deformation field was about 10 km in diameter, and the maximum amplitude of the deformation was >20 cm. Uplift started in 1994, and concurrent earthquake swarm activity was observed around the uplift area; however, no other phenomena were observed during this period. A subsidence process then followed, with the shape of the deformation forming a mirror image of the uplift. Model simulations suggest deformation was caused by a source at the depth of about 6 km and that the position of the source remained static throughout the episode. Subsidence of the volcanic complex was also observed by another satellite from 2007 to 2010, and likely continued for more than 10 years. In addition to the main uplift-subsidence sequence, small deformation patterns with short spatial wavelengths were observed at the center of the deforming area. Data from three satellites recorded small-scale subsidence of the Atosanupuri and Rishiri lava domes at a constant rate of approx. 1 cm/year from 1993 to 2016.[Figure not available: see fulltext.

STED super-resolution microscopy reveals an array of MINOS clusters along human mitochondria

PubMed Central

Jans, Daniel C.; Wurm, Christian A.; Riedel, Dietmar; Wenzel, Dirk; Stagge, Franziska; Deckers, Markus; Rehling, Peter; Jakobs, Stefan

2013-01-01

The mitochondrial inner membrane organizing system (MINOS) is a conserved large hetero-oligomeric protein complex in the mitochondrial inner membrane, crucial for the maintenance of cristae morphology. MINOS has been suggested to represent the core of an extended protein network that controls mitochondrial function and structure, and has been linked to several human diseases. The spatial arrangement of MINOS within mitochondria is ill-defined, however. Using super-resolution stimulated emission depletion (STED) microscopy and immunogold electron microscopy, we determined the distribution of three known human MINOS subunits (mitofilin, MINOS1, and CHCHD3) in mammalian cells. Super-resolution microscopy revealed that all three subunits form similar clusters within mitochondria, and that MINOS is more abundant in mitochondria around the nucleus than in peripheral mitochondria. At the submitochondrial level, mitofilin, a core MINOS subunit, is preferentially localized at cristae junctions. In primary human fibroblasts, mitofilin labeling uncovered a regularly spaced pattern of clusters arranged in parallel to the cell growth surfaces. We suggest that this array of MINOS complexes might explain the observed phenomenon of largely horizontally arranged cristae junctions that connect the inner boundary membrane to lamellar cristae. The super-resolution images demonstrate an unexpectedly high level of regularity in the nanoscale distribution of the MINOS complex in human mitochondria, supporting an integrating role of MINOS in the structural organization of the organelle. PMID:23676277

A new universality class in corpus of texts; A statistical physics study

NASA Astrophysics Data System (ADS)

Najafi, Elham; Darooneh, Amir H.

2018-05-01

Text can be regarded as a complex system. There are some methods in statistical physics which can be used to study this system. In this work, by means of statistical physics methods, we reveal new universal behaviors of texts associating with the fractality values of words in a text. The fractality measure indicates the importance of words in a text by considering distribution pattern of words throughout the text. We observed a power law relation between fractality of text and vocabulary size for texts and corpora. We also observed this behavior in studying biological data.

Hedgehog signal transduction: key players, oncogenic drivers, and cancer therapy

PubMed Central

Pak, Ekaterina; Segal, Rosalind A.

2016-01-01

Summary The Hedgehog (Hh) signaling pathway governs complex developmental processes, including proliferation and patterning within diverse tissues. These activities rely on a tightly-regulated transduction system that converts graded Hh input signals into specific levels of pathway activity. Uncontrolled activation of Hh signaling drives tumor initiation and maintenance. However, recent entry of pathway-specific inhibitors into the clinic reveals mixed patient responses and thus prompts further exploration of pathway activation and inhibition. In this review, we share emerging insights on regulated and oncogenic Hh signaling, supplemented with updates on the development and use of Hh pathway-targeted therapies. PMID:27554855

The cosmic web in our own backyard.

PubMed

Ibata, Rodrigo A; Lewis, Geraint F

2008-01-04

On the largest scales, matter is strung out on an intricate pattern known as the cosmic web. The tendrils of this web should reach right into our own cosmic backyard, lacing the Galactic halo with lumps of dark matter. The search for these lumps, lit up by stars that formed within them, is a major astronomical endeavor, although it has failed to find the huge expected population. Is this a dark matter crisis, or does it provide clues to the complexities of gas physics in the early universe? New technologies in the coming decade will reveal the answer.

Molecular identification of Mycobacterium bovis from cattle and human host in Mali: expanded genetic diversity.

PubMed

Diallo, Mamadou; Diarra, Bassirou; Sanogo, Moumine; Togo, Antieme C G; Somboro, Anou M; Diallo, Mariam H; Traoré, Bréhima; Maiga, Mamoudou; Koné, Younoussa; Tounkara, Karim; Sarro, Yeya Dit Sadio; Baya, Bocar; Goita, Drissa; Kassambara, Hamadoun; Dembélé, Bindongo P P; Siddiqui, Sophia; Murphy, Robert L; Dao, Sounkalo; Diallo, Souleymane; Tounkara, Anatole; Niang, Mamadou

2016-07-20

Bovine tuberculosis (BTB) is a contagious, debilitating human and animal disease caused by Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex. The study objective were to estimate the frequency of BTB, examine genetic diversity of the M. bovis population in cattle from five regions in Mali and to determine whether M. bovis is involved in active tuberculosis (TB) in humans. Samples from suspected lesions on cattle at the slaughterhouses were collected. Mycobacterial smear, culture confirmation, and spoligotyping were used for diagnosis and species identification. Mycobacterium DNA from TB patients was spoligotyped to identify M. bovis. In total, 675 cattle have been examined for lesions in the five regions of Mali. Out of 675 cattle, 79 specimens presented lesions and then examined for the presence of M. bovis. Thus, 19 (24.1 %) were identified as M. bovis; eight (10.1 %) were non-tuberculous Mycobacterium (NTM). Nineteen spoligotype patterns were identified among 79 samples with five novel patterns. One case of M. bovis (spoligotype pattern SB0300) was identified among 67 TB patients. This study estimates a relatively true proportion of BTB in the regions of Mali and reveals new spoligotype patterns.

The complexity of organizational change: describing communication during organizational turbulence.

PubMed

Salem, Philip

2013-01-01

Organizational researchers and practitioners have been interested in organizational change for some time. Historically, they have directed most of their efforts at improving the efficiency of planned top-down change. These efforts were strategic attempts at altering parameters leading to transformational change. Most efforts failed to meet their intended purposes. Transformational organizational change has not been likely. The legitimate systems have been robust. There has been little systematic investigation of the communication occurring during these efforts. The purpose of this essay is to describe results of a mixed methods research project answering two research questions. (a) How do organizational members communicate during a time of turbulence? (b) What features of this communication suggest the potential for or resistance to transformative change? Comparing the results at the beginning of the period to other periods, gives insight into how social actors communicate and enact the organization during a threshold period where transformational change was possible. Results reveal identifiable patterns of communication as communication strategies, parameters, or basins of attraction. The overall pattern explains how micro communication patterns intersect and how the accumulation of these patterns may resist or accomplish change at a macro level.

Developmental Patterns of Adverse Childhood Experiences and Current Symptoms and Impairment in Youth Referred For Trauma-Specific Services.

PubMed

Grasso, Damion J; Dierkhising, Carly B; Branson, Christopher E; Ford, Julian D; Lee, Robert

2016-07-01

By the time children reach adolescence, most have experienced at least one type of severe adversity and many have been exposed to multiple types. However, whether patterns of adverse childhood experiences are consistent or change across developmental epochs in childhood is not known. Retrospective reports of adverse potentially traumatic childhood experiences in 3 distinct developmental epochs (early childhood, 0- to 5-years-old; middle childhood, 6- to 12-years-old; and adolescence, 13- to 18-years-old) were obtained from adolescents (N = 3485) referred to providers in the National Child Traumatic Stress Network (NCTSN) for trauma-focused assessment and treatment. Results from latent class analysis (LCA) revealed increasingly complex patterns of adverse/traumatic experiences in middle childhood and adolescence compared to early childhood. Depending upon the specific developmental epoch assessed, different patterns of adverse/traumatic experiences were associated with gender and with adolescent psychopathology (e.g., internalizing/externalizing behavior problems), and juvenile justice involvement. A multiply exposed subgroup that had severe problems in adolescence was evident in each of the 3 epochs, but their specific types of adverse/traumatic experiences differed depending upon the developmental epoch. Implications for research and clinical practice are identified.

Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae.

PubMed

Westneat, Mark W; Alfaro, Michael E; Wainwright, Peter C; Bellwood, David R; Grubich, Justin R; Fessler, Jennifer L; Clements, Kendall D; Smith, Lydia L

2005-05-22

The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes.

Respiration and heart rate complexity: Effects of age and gender assessed by band-limited transfer entropy

PubMed Central

Nemati, Shamim; Edwards, Bradley A.; Lee, Joon; Pittman-Polletta, Benjamin; Butler, James P.; Malhotra, Atul

2013-01-01

Aging and disease are accompanied with a reduction of complex variability in the temporal patterns of heart rate. This reduction has been attributed to a break down of the underlying regulatory feedback mechanisms that maintain a homeodynamic state. Previous work has established the utility of entropy as an index of disorder, for quantification of changes in heart rate complexity. However, questions remain regarding the origin of heart rate complexity and the mechanisms involved in its reduction with aging and disease. In this work we use a newly developed technique based on the concept of band-limited transfer entropy to assess the aging-related changes in contribution of respiration and blood pressure to entropy of heart rate at different frequency bands. Noninvasive measurements of heart beat interval, respiration, and systolic blood pressure were recorded from 20 young (21–34 years) and 20 older (68–85 years) healthy adults. Band-limited transfer entropy analysis revealed a reduction in high-frequency contribution of respiration to heart rate complexity (p < 0.001) with normal aging, particularly in men. These results have the potential for dissecting the relative contributions of respiration and blood pressure-related reflexes to heart rate complexity and their degeneration with normal aging. PMID:23811194