Curvature of Co-Links Uncovers Hidden Thematic Layers in the World Wide Web

Beyond the information stored in pages of the World Wide Web, novel types of ``meta-information'' are created when they connect to each other. This information is a collective effect of independent users writing and linking pages, hidden from the casual user. Accessing it and understanding the inter-relation of connectivity and content in the WWW is a challenging problem. We demonstrate here how thematic relationships can be located precisely by looking only at the graph of hyperlinks, gleaning content and context from the Web without having to read what is in the pages. We begin by noting that reciprocal links (co-links) between pages signal a mutual recognition of authors, and then focus on triangles containing such links, since triangles indicate a transitive relation. The importance of triangles is quantified by the clustering coefficient (Watts) which we interpret as a curvature (Gromov,Bridson-Haefliger). This defines a Web-landscape whose connected regions of high curvature characterize a common topic. We show experimentally that reciprocity and curvature, when combined, accurately capture this meta-information for a wide variety of topics. As an example of future directions we analyze the neural network of C. elegans (White, Wood), using the same methods.Comment: 8 pages, 5 figures, expanded version of earlier submission with more example

Uncovering temporal structure in hippocampal output patterns.

Place cell activity of hippocampal pyramidal cells has been described as the cognitive substrate of spatial memory. Replay is observed during hippocampal sharp-wave-ripple-associated population burst events (PBEs) and is critical for consolidation and recall-guided behaviors. PBE activity has historically been analyzed as a phenomenon subordinate to the place code. Here, we use hidden Markov models to study PBEs observed in rats during exploration of both linear mazes and open fields. We demonstrate that estimated models are consistent with a spatial map of the environment, and can even decode animals' positions during behavior. Moreover, we demonstrate the model can be used to identify hippocampal replay without recourse to the place code, using only PBE model congruence. These results suggest that downstream regions may rely on PBEs to provide a substrate for memory. Additionally, by forming models independent of animal behavior, we lay the groundwork for studies of non-spatial memory

Connectivity differences between Gulf War Illness (GWI) phenotypes during a test of attention

One quarter of veterans returning from the 1990–1991 Persian Gulf War have developed Gulf War Illness (GWI) with chronic pain, fatigue, cognitive and gastrointestinal dysfunction. Exertion leads to characteristic, delayed onset exacerbations that are not relieved by sleep. We have modeled exertional exhaustion by comparing magnetic resonance images from before and after submaximal exercise. One third of the 27 GWI participants had brain stem atrophy and developed postural tachycardia after exercise (START: Stress Test Activated Reversible Tachycardia). The remainder activated basal ganglia and anterior insulae during a cognitive task (STOPP: Stress Test Originated Phantom Perception). Here, the role of attention in cognitive dysfunction was assessed by seed region correlations during a simple 0-back stimulus matching task (“see a letter, push a button”) performed before exercise. Analysis was analogous to resting state, but different from psychophysiological interactions (PPI). The patterns of correlations between nodes in task and default networks were significantly different for START (n = 9), STOPP (n = 18) and control (n = 8) subjects. Edges shared by the 3 groups may represent co-activation caused by the 0-back task. Controls had a task network of right dorsolateral and left ventrolateral prefrontal cortex, dorsal anterior cingulate cortex, posterior insulae and frontal eye fields (dorsal attention network). START had a large task module centered on the dorsal anterior cingulate cortex with direct links to basal ganglia, anterior insulae, and right dorsolateral prefrontal cortex nodes, and through dorsal attention network (intraparietal sulci and frontal eye fields) nodes to a default module. STOPP had 2 task submodules of basal ganglia–anterior insulae, and dorsolateral prefrontal executive control regions. Dorsal attention and posterior insulae nodes were embedded in the default module and were distant from the task networks. These three unique connectivity patterns during an attention task support the concept of Gulf War Disease with recognizable, objective patterns of cognitive dysfunction

The Kinetic Basis of Self-Organized Pattern Formation

In his seminal paper on morphogenesis (1952), Alan Turing demonstrated that different spatio-temporal patterns can arise due to instability of the homogeneous state in reaction-diffusion systems, but at least two species are necessary to produce even the simplest stationary patterns. This paper is aimed to propose a novel model of the analog (continuous state) kinetic automaton and to show that stationary and dynamic patterns can arise in one-component networks of kinetic automata. Possible applicability of kinetic networks to modeling of real-world phenomena is also discussed.Comment: 8 pages, submitted to the 14th International Conference on the Synthesis and Simulation of Living Systems (Alife 14) on 23.03.2014, accepted 09.05.201

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

How attention and knowledge modulate memory: The differential impact of cognitive conflicts on subsequent memory—A review of a decade of research

In order to cope with cognitive conflicts, attention and knowledge are required. In some conditions, cognitive conflicts can boost subsequent memory and in other conditions, they can attenuate subsequent memory. The goal of the present study is to provide a narrative review of studies from the last decade in which Stroop or flanker conflicts, task switching, perceptual disfluency or semantic incongruence were manipulated at study. We propose an integrative framework considering attentional mechanisms and knowledge structures. Attentional mechanisms can refer to conflict resolution, which is required to explain the memory benefit for incongruent stimuli in Stroop and Flanker paradigms. Attentional mechanisms can also refer to attention allocation, which is required to explain the memory cost for targets and the memory benefit for task-irrelevant distractors in task-switching paradigms. Moreover, attention allocation policies can also account for the inconsistent results for perceptual disfluency manipulations. Prior knowledge is required to explain effects of semantic congruency and incongruency: Information that is expected, or congruent with prior knowledge, is better remembered, namely by pre-existing schemata. Moreover, information that is unexpected or incongruent with prior knowledge attracts attention and is better remembered. The impact of prior knowledge on memory performance thus results in a U-shape function. We integrate the findings according to this framework and suggest directions for future research

Lost in translation: Toward a formal model of multilevel, multiscale medicine

For a broad spectrum of low level cognitive regulatory and other biological phenomena, isolation from signal crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts of interacting physiological processes at multiple scales. The argument is similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological subsystems. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative larger scale broadcasts that link selected subsets of functional modules to address problems. This multilevel dynamical viewpoint has implications for initiatives in translational medicine that have followed the implosive collapse of pharmaceutical industry 'magic bullet' research. In short, failure to respond to the inherently multilevel, multiscale nature of human pathophysiology will doom translational medicine to a similar implosion