Investigating the Temporal Patterns within and between Intrinsic Connectivity Networks under Eyes-Open and Eyes-Closed Resting States: A Dynamical Functional Connectivity Study Based on Phase Synchronization

The brain active patterns were organized differently under resting states of eyes open (EO) and eyes closed (EC). The altered voxel-wise and regional-wise resting state active patterns under EO/EC were found by static analysis. More importantly, dynamical spontaneous functional connectivity has been observed in the resting brain. To the best of our knowledge, the dynamical mechanisms of intrinsic connectivity networks (ICNs) under EO/EC remain largely unexplored. The goals of this paper were twofold: 1) investigating the dynamical intra-ICN and inter-ICN temporal patterns during resting state; 2) analyzing the altered dynamical temporal patterns of ICNs under EO/EC. To this end, a cohort of healthy subjects with scan conditions of EO/EC were recruited from 1000 Functional Connectomes Project. Through Hilbert transform, time-varying phase synchronization (PS) was applied to evaluate the inter-ICN synchrony. Meanwhile, time-varying amplitude was analyzed as dynamical intra-ICN temporal patterns. The results found six micro-states of inter-ICN synchrony. The medial visual network (MVN) showed decreased intra-ICN amplitude during EC relative to EO. The sensory-motor network (SMN) and auditory network (AN) exhibited enhanced intra-ICN amplitude during EC relative to EO. Altered inter-ICN PS was found between certain ICNs. Particularly, the SMN and AN exhibited enhanced PS to other ICNs during EC relative to EO. In addition, the intra-ICN amplitude might influence the inter-ICN synchrony. Moreover, default mode network (DMN) might play an important role in information processing during EO/EC. Together, the dynamical temporal patterns within and between ICNs were altered during different scan conditions of EO/EC. Overall, the dynamical intra-ICN and inter-ICN temporal patterns could benefit resting state fMRI-related research, and could be potential biomarkers for human functional connectome.     

Deconstruction and Dynamical Robustness of Regulatory Networks: Application to the Yeast Cell Cycle Networks

Analyzing all the deterministic dynamics of a Boolean regulatory network is a difficult problem since it grows exponentially with the number of nodes. In this paper, we present mathematical and computational tools for analyzing the complete deterministic dynamics of Boolean regulatory networks. For this, the notion of alliance is introduced, which is a subconfiguration of states that remains fixed regardless of the values of the other nodes. Also, equivalent classes are considered, which are sets of updating schedules which have the same dynamics. Using these techniques, we analyze two yeast cell cycle models. Results show the effectiveness of the proposed tools for analyzing update robustness as well as the discovery of new information related to the attractors of the yeast cell cycle models considering all the possible deterministic dynamics, which previously have only been studied considering the parallel updating scheme.     

Organized Cell Swimming Motions in Bacillus subtilis Colonies: Patterns of Short-Lived Whirls and Jets

The swimming motions of cells within Bacillus subtilis colonies, as well as the associated fluid flows, were analyzed from video films produced during colony growth and expansion on wet agar surfaces. Individual cells in very wet dense populations moved at rates between 76 and 116 μm/s. Swimming cells were organized into patterns of whirls, each approximately 1,000 μm², and jets of about 95 by 12 μm. Whirls and jets were short-lived, lasting only about 0.25 s. Patterns within given areas constantly repeated with a periodicity of approximately 1 s. Whirls of a given direction became disorganized and then re-formed, usually into whirls moving in the opposite direction. Pattern elements were also organized with respect to one another in the colony. Neighboring whirls usually turned in opposite directions. This correlation decreased as a function of distance between whirls. Fluid flows associated with whirls and jets were measured by observing the movement of marker latex spheres added to colonies. The average velocity of markers traveling in whirls was 19 μm/s, whereas those traveling in jets moved at 27 μm/s. The paths followed by markers were aligned with the direction of cell motion, suggesting that cells create flows moving with them into whirls and along jets. When colonies became dry, swimming motions ceased except in regions close to the periphery and in isolated islands where cells traveled in slow whirls at about 4 μm/s. The addition of water resulted in immediate though transient rapid swimming (> 80 μm/s) in characteristic whirl and jet patterns. The rate of swimming decreased to 13 μm/s within 2 min, however, as the water diffused into the agar. Organized swimming patterns were nevertheless preserved throughout this period. These findings show that cell swimming in colonies is highly organized.     

Multiday Recordings from Olfactory Bulb Neurons in Awake Freely Moving Rats: Spatially and Temporally Organized Variability in Odorant Response Properties

Chronic single-unit recordings were obtained from the mitral celllayer of the olfactory bulbs of awake freely moving rats placed in anodorant stream. Over periods up to five days, 618 recordings from 186single neurons were obtained. Responses of individual neurons werefound to be quite variable over time, although this variability wasbelow chance and was not incremental. The responses of nearbyneurons were more similar than expected by chance but less similarthan individual neurons recorded at different times. However,responses of spatially well-separated neurons were more differentthan chance over short time periods. During rapid sniffing,single-unit responses became more variable, and the spatialorganization of responses became less apparent. These results suggestthat neuronal responses in the olfactory bulb are generally quitevariable over time, with this variability increasing during periodsof rapid sniffing. These results are interpreted in the context of adistributed, centrally modulated model of olfactoryprocessing.     

UCSF Chimera, MODELLER, and IMP: an integrated modeling system

Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several modeling tools into UCSF Chimera. These include comparative modeling by MODELLER, simultaneous fitting of multiple components into electron microscopy density maps by IMP MultiFit, computing of small-angle X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera.     

Frequent Pattern Discovery in Multiple Biological Networks: Patterns and Algorithms

The rapid accumulation of biological network data is creating an urgent need for computational methods capable of integrative network analysis. This paper discusses a suite of algorithms that we have developed to discover biologically significant patterns that appear frequently in multiple biological networks: coherent dense subgraphs, frequent dense vertex-sets, generic frequent subgraphs, differential subgraphs, and recurrent heavy subgraphs. We demonstrate these methods on gene co-expression networks, using the identified patterns to systematically annotate gene functions, map genome to phenome, and perform high-order cooperativity analysis.     

Chemical Patterns, Compartments and a Binary Epigenetic Code in Drosophila

I propose a model which accounts for the geometries and sequencein which compartmental boundary lines arise on the differentimaginal discs, and on the blastoderm of Drosophila melanogaster;and propose that successive lines are recorded by differentbinary switches, to create a binary epigenetic code word specifyingeach disc, and disc compartment. I suppose a biochemical systemundergoing reaction and diffusion acts throughout development.As an imaginal disc grows, a succession of differently shapedchemical concentration patterns form at a discrete set of discsizes. I suppose a specific concentration of one chemical isa threshold. Concentrations above or below threshold switchcells to one or another of two commitments. Then the line acrossthe imaginal disc with the threshold concentration is a predictedcompartmental boundary. The sequence and geometries of suchlines predict the compartmental boundaries seen on the wingdisc, the other discs, and on the blastoderm stage egg. Thecompartmental lines on the wing disc suggest that a terminalcompartment is specified by a combination of binary names recordinga sequence of binary commitments: anterior, not posterior; dorsal,not ventral; wing, not thorax; proximal, not distal. Each combinationcomprises a binary epigenetic code word. Recently I constructedan independent model for transdetermination in Drosophila whichproposed a similar binary epigenetic code for the differentdiscs. The clone restriction lines predicted on the blastodermby my transdetermination model, the chemical pattern model,and analogy with the wing disc, are nearly identical. Severalare already confirmed. The resultant binary code scheme correctlypredicts many relative transdetermination frequencies and accountssimply for the action of most homeotic mutants as genes whichalter a single switch state in one or more discs.     

滇西北地区种子植物地理分布及区系分化

以大尺度的物种分布信息为基础,对滇西北地区种子植物物种多样性的地理分布格局及其与植物区系分化之间的关系进行分析.结果表明:(1)滇西北地区的种子植物物种多样性从南到北呈递增趋势;(2)无论是在属的水平上,还是在科的水平上,植物区系分化强度从南到北均呈单调递增格局;(3)区系分化强度较大的区域主要集中在地形复杂的北部地区;(4)物种多样性随着区系分化强度的增强而增加;(5)物种多样性地理分布格局的形成可能与滇西北地区的地质历史、地形以及由此引起的植物区系分化有关.     

Forming Patterns in Development without Morphogen Gradients: Scattered Differentiation and Sorting Out

Few mechanisms provide alternatives to morphogen gradients for producing spatial patterns of cells in development. One possibility is based on the sorting out of cells that initially differentiate in a salt and pepper mixture and then physically move to create coherent tissues. Here, we describe the evidence suggesting this is the major mode of patterning in Dictyostelium. In addition, we discuss whether convergent evolution could have produced a conceptually similar mechanism in other organisms.A limited number of processes are thought to regulate the differentiation of specialized cell types and their organization to form larger scale structures, such as organs or limbs, during embryonic development. First, early embryological experiments revealed a patterning process that depends on special “organizing” regions in the embryo. This idea was encapsulated as “positional information” and led to the concept of morphogen gradients (Fig. 1) (Wolpert 1996). In addition, cytoplasmic determinants have been shown to direct development along different lines when they are partitioned unequally between daughter cells by asymmetric cell division (Betschinger and Knoblich 2004). Finally, short-range inductive signaling can specify cells at a local level and when reiterated produces highly ordered structures (Simpson 1990; Freeman 1997; Meinhardt and Gierer 2000).Open in a separate windowFigure 1.Alternative ways of patterning cells during development. (A) Patterning by “positional information”: A group of undifferentiated cells is patterned by a morphogen diffusing from a pre-established source, producing a concentration gradient. Cells respond according to the local morphogen concentration, becoming red, white, or blue. (B, C) Patterning without positional information: This is a two-step process in which different cell types first differentiate mixed up with each other, and then sort out. The initial differentiation can be controlled by strictly local interactions between the cells, as in lateral inhibition (B), or by a global signal to which cells respond with different sensitivities and whose concentration they regulate by negative feedback (C). Once sorting has occurred, the global inducer forms a reverse gradient, which could then convey positional information for further patterning events.The question then arises of whether evolution has devised any further global patterning mechanisms. One possibility that has been repeatedly considered, but not firmly established as a general mechanism, is based on sorting out. In this process, pattern is produced in two steps: (1) Different cell types are initially specified from a precursor pool independent of their position to produce a salt and pepper mixture and (2) the mixture of cell types is resolved into discrete tissues by the physical movement and sorting out of the cells (Fig. 1). Consequently, this mechanism does not involve positional information. However, it can actually provide the conditions under which positional signaling and morphogen gradients can arise, if the resolved tissues then act as sources and sinks for signal molecules.We first describe the powerful evidence that this alternative patterning process is used during the developmental cycle of the social amoeba Dictyostelium discoideum, and then consider the possibility that this patterning strategy may be used more widely.     

VA-Index: Quantifying Assortativity Patterns in Networks with Multidimensional Nodal Attributes

Network connections have been shown to be correlated with structural or external attributes of the network vertices in a variety of cases. Given the prevalence of this phenomenon network scientists have developed metrics to quantify its extent. In particular, the assortativity coefficient is used to capture the level of correlation between a single-dimensional attribute (categorical or scalar) of the network nodes and the observed connections, i.e., the edges. Nevertheless, in many cases a multi-dimensional, i.e., vector feature of the nodes is of interest. Similar attributes can describe complex behavioral patterns (e.g., mobility) of the network entities. To date little attention has been given to this setting and there has not been a general and formal treatment of this problem. In this study we develop a metric, the vector assortativity index (VA-index for short), based on network randomization and (empirical) statistical hypothesis testing that is able to quantify the assortativity patterns of a network with respect to a vector attribute. Our extensive experimental results on synthetic network data show that the VA-index outperforms a baseline extension of the assortativity coefficient, which has been used in the literature to cope with similar cases. Furthermore, the VA-index can be calibrated (in terms of parameters) fairly easy, while its benefits increase with the (co-)variance of the vector elements, where the baseline systematically over(under)estimate the true mixing patterns of the network.     

Patterns of Tracheary Differentiation in Lettuce Pith Explants: Positional Control and Temperature Effects

When lettuce pith explants were cultured for 14 d on a xylogenicmedium, tracheary elements differentiated in greatest numbersbetween 25 and 30 °C. Numbers were depressed at lower temperaturesby slower development and at higher temperatures by adverseprocesses. The data did not support previous suggestions ofa great stimulation of xylogenesis above 30 °C and of aspecial sensitivity to low temperatures. Tracheary elements differentiated in various spatial patterns:as clumps in the peripheral callus, as strands which extendedradially and longitudinally from some of these clumps, as individuallarge tracheids especially at the more extreme temperatures,and as short strands associated with nodules and roots thatformed at favourable temperatures. We suggest that indoleacetic acid (IAA) has various roles inthe positional control of these tracheary patterns: (1) IAAdestruction at the explant surface leads to concentration gradientsthat inhibit tracheary induction close to the surface; (2) IAAtransport from the source in the culture medium to sinks especiallyat the explant surface, coupled with autocatalytic flow facilitation,leads to canalization along pathways that become meristematicand then trachcary strands; (3) the IAA flux (and associatedproton flux) along these pathways tend to orient cortical microtubulesat right angles to the flow, by some mechanism as yet unknown,and hence to control the orientation of tracheary element elongationand secondary wall banding. These suggestions, supported bymorphometric studies of tracheary element dimensions and orientations,and by experiments with localized IAA application, lead to ageneral interpretation of the development of polarity in plants. IAA, Lactuca sativa, lettuce, pith explants, positional control, temperature effects, tracheary element differentiation     

Patterns and drivers for wetland connections in the Prairie Pothole Region,United States

Ecosystem function in rivers, lakes and coastal waters depends on the functioning of upstream aquatic ecosystems, necessitating an improved understanding of watershed-scale interactions including variable surface-water flows between wetlands and streams. As surface water in the Prairie Pothole Region expands in wet years, surface-water connections occur between many depressional wetlands and streams. Minimal research has explored the spatial patterns and drivers for the abundance of these connections, despite their potential to inform resource management and regulatory programs including the U.S. Clean Water Act. In this study, wetlands were identified that did not intersect the stream network, but were shown with Landsat images (1990–2011) to become merged with the stream network as surface water expanded. Wetlands were found to spill into or consolidate with other wetlands within both small (2–10 wetlands) and large (>100 wetlands) wetland clusters, eventually intersecting a stream channel, most often via a riparian wetland. These surface-water connections occurred over a wide range of wetland distances from streams (averaging 90–1400 m in different ecoregions). Differences in the spatial abundance of wetlands that show a variable surface-water connection to a stream were best explained by smaller wetland-to-wetland distances, greater wetland abundance, and maximum surface-water extent. This analysis demonstrated that wetland arrangement and surface water expansion are important mechanisms for depressional wetlands to connect to streams and provides a first step to understanding the frequency and abundance of these surface-water connections across the Prairie Pothole Region.     

Uniform Sampling of Steady States in Metabolic Networks: Heterogeneous Scales and Rounding

The uniform sampling of convex polytopes is an interesting computational problem with many applications in inference from linear constraints, but the performances of sampling algorithms can be affected by ill-conditioning. This is the case of inferring the feasible steady states in models of metabolic networks, since they can show heterogeneous time scales. In this work we focus on rounding procedures based on building an ellipsoid that closely matches the sampling space, that can be used to define an efficient hit-and-run (HR) Markov Chain Monte Carlo. In this way the uniformity of the sampling of the convex space of interest is rigorously guaranteed, at odds with non markovian methods. We analyze and compare three rounding methods in order to sample the feasible steady states of metabolic networks of three models of growing size up to genomic scale. The first is based on principal component analysis (PCA), the second on linear programming (LP) and finally we employ the Lovazs ellipsoid method (LEM). Our results show that a rounding procedure dramatically improves the performances of the HR in these inference problems and suggest that a combination of LEM or LP with a subsequent PCA perform the best. We finally compare the distributions of the HR with that of two heuristics based on the Artificially Centered hit-and-run (ACHR), gpSampler and optGpSampler. They show a good agreement with the results of the HR for the small network, while on genome scale models present inconsistencies.     

Transmission Mode Predicts Specificity and Interaction Patterns in Coral-Symbiodinium Networks

Most reef-building corals in the order Scleractinia depend on endosymbiotic algae in the genus Symbiodinium for energy and survival. Significant levels of taxonomic diversity in both partners result in numerous possible combinations of coral-Symbiodinium associations with unique functional characteristics. We created and analyzed the first coral-Symbiodinium networks utilizing a global dataset of interaction records from coral reefs in the tropical Indo-Pacific and Atlantic Oceans for 1991 to 2010. Our meta-analysis reveals that the majority of coral species and Symbiodinium types are specialists, but failed to detect any one-to-one obligate relationships. Symbiont specificity is correlated with a host’s transmission mode, with horizontally transmitting corals being more likely to interact with generalist symbionts. Globally, Symbiodinium types tend to interact with only vertically or horizontally transmitting corals, and only a few generalist types are found with both. Our results demonstrate a strong correlation between symbiont specificity, symbiont transmission mode, and community partitioning. The structure and dynamics of these network interactions underlie the fundamental biological partnership that determines the condition and resilience of coral reef ecosystems.     

Patterns of Phylogenetic Differentiation in the Toxochelyid and Cheloniid Sea Turtles

The patterns of phylogenetic differentiation in the closelyrelated sea turtle families Toxochelyidae and Cheloniidae followedstrikingly different courses. In the Toxochelyidae there isa gradual increase in specialization toward a pelagic mode oflife with time. The phyletic picture is thus that of a shrub.In the Cheloniidae, by contrast, the geologically oldest representativesof the family are the most advanced, pelagic species, and theRecent species, except for Eretmochelys imbricata, are amongthe least specialized members of the family. There is good evidencethat the living species are the only cheloniids that have theirhind limbs modified as rudders, and the very close similaritybetween the limb skeletons of these species suggests that theyare more closely related to each other than any of them areto any earlier form. A similar case can be made for the earlyCaenozoic cheloniids. The phylogenetic pattern, therefore, suggestsrepeated episodes of pelagic specialization from a central,unspecialized stock, a pattern referred to as iterative evolution.     

Species Richness and Patterns of Invasion in Plants, Birds, and Fishes in the United States*

We quantified broad-scale patterns of species richness and species density (mean # species/km²) for native and non-indigenous plants, birds, and fishes in the continental USA and Hawaii. We hypothesized that the species density of native and non-indigenous taxa would generally decrease in northern latitudes and higher elevations following declines in potential evapotranspiration, mean temperature, and precipitation. County data on plants (n = 3004 counties) and birds (n=3074 counties), and drainage (6 HUC) data on fishes (n = 328 drainages) showed that the densities of native and non-indigenous species were strongly positively correlated for plant species (r = 0.86, P < 0.0001), bird species (r = 0.93, P<0.0001), and fish species (r = 0.41, P<0.0001). Multiple regression models showed that the densities of native plant and bird species could be strongly predicted (adj. R² = 0.66 in both models) at county levels, but fish species densities were less predictable at drainage levels (adj. R² = 0.31, P<0.0001). Similarly, non-indigenous plant and bird species densities were strongly predictable (adj. R² = 0.84 and 0.91 respectively), but non-indigenous fish species density was less predictable (adj. R² = 0.38). County level hotspots of native and non-indigenous plants, birds, and fishes were located in low elevation areas close to the coast with high precipitation and productivity (vegetation carbon). We show that (1) native species richness can be moderately well predicted with abiotic factors; (2) human populations have tended to settle in areas rich in native species; and (3) the richness and density of non-indigenous plant, bird, and fish species can be accurately predicted from biotic and abiotic factors largely because they are positively correlated to native species densities. We conclude that while humans facilitate the initial establishment, invasions of non-indigenous species, the spread and subsequent distributions of non-indigenous species may be controlled largely by environmental factors. The U.S. Government’s right to retain a non-exclusive, royalty-free licence in and to any copyright is acknowledged.     

Time Delay and Long-Range Connection Induced Synchronization Transitions in Newman-Watts Small-World Neuronal Networks

The synchronization transitions in Newman-Watts small-world neuronal networks (SWNNs) induced by time delay and long-range connection (LRC) probability have been investigated by synchronization parameter and space-time plots. Four distinct parameter regions, that is, asynchronous region, transition region, synchronous region, and oscillatory region have been discovered at certain LRC probability as time delay is increased. Interestingly, desynchronization is observed in oscillatory region. More importantly, we consider the spatiotemporal patterns obtained in delayed Newman-Watts SWNNs are the competition results between long-range drivings (LRDs) and neighboring interactions. In addition, for moderate time delay, the synchronization of neuronal network can be enhanced remarkably by increasing LRC probability. Furthermore, lag synchronization has been found between weak synchronization and complete synchronization as LRC probability is a little less than 1.0. Finally, the two necessary conditions, moderate time delay and large numbers of LRCs, are exposed explicitly for synchronization in delayed Newman-Watts SWNNs.