Identifying super-feminine,super-masculine and sex-defining connections in the human braingraph

For more than a decade now, we can discover and study thousands of cerebral connections with the application of diffusion magnetic resonance imaging (dMRI) techniques and the accompanying algorithmic workflow. While numerous connectomical results were published enlightening the relation between the braingraph and certain biological, medical, and psychological properties, it is still a great challenge to identify a small number of brain connections closely related to those conditions. In the present contribution, by applying the 1200 Subjects Release of the Human Connectome Project (HCP) and Support Vector Machines, we identify just 102 connections out of the total number of 1950 connections in the 83-vertex graphs of 1064 subjects, which—by a simple linear test—precisely, without any error determine the sex of the subject. Next, we re-scaled the weights of the edges—corresponding to the discovered fibers—to be between 0 and 1, and, very surprisingly, we were able to identify two graph edges out of these 102, such that, if their weights are both 1, then the connectome always belongs to a female subject, independently of the other edges. Similarly, we have identified 3 edges from these 102, whose weights, if two of them are 1 and one is 0, imply that the graph belongs to a male subject—again, independently of the other edges. We call the former 2 edges superfeminine and the first two of the 3 edges supermasculine edges of the human connectome. Even more interestingly, the edge, connecting the right Pars Triangularis and the right Superior Parietal areas, is one of the 2 superfeminine edges, and it is also the third edge, accompanying the two supermasculine connections if its weight is 0; therefore, it is also a “switching” edge. Identifying such edge-sets of distinction is the unprecedented result of this work.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11571-021-09687-w.     

Orienteering in Knowledge Spaces: The Hyperbolic Geometry of Wikipedia Mathematics

In this paper we show how the coupling of the notion of a network with directions with the adaptation of the four-point probe from materials testing gives rise to a natural geometry on such networks. This four-point probe geometry shares many of the properties of hyperbolic geometry wherein the network directions take the place of the sphere at infinity, enabling a navigation of the network in terms of pairs of directions: the geodesic through a pair of points is oriented from one direction to another direction, the pair of which are uniquely determined. We illustrate this in the interesting example of the pages of Wikipedia devoted to Mathematics, or “The MathWiki.” The applicability of these ideas extends beyond Wikipedia to provide a natural framework for visual search and to prescribe a natural mode of navigation for any kind of “knowledge space” in which higher order concepts aggregate various instances of information. Other examples would include genre or author organization of cultural objects such as books, movies, documents or even merchandise in an online store.     

What are lightness illusions and why do we see them?

Lightness illusions are fundamental to human perception, and yet why we see them is still the focus of much research. Here we address the question by modelling not human physiology or perception directly as is typically the case but our natural visual world and the need for robust behaviour. Artificial neural networks were trained to predict the reflectance of surfaces in a synthetic ecology consisting of 3-D “dead-leaves” scenes under non-uniform illumination. The networks learned to solve this task accurately and robustly given only ambiguous sense data. In addition—and as a direct consequence of their experience—the networks also made systematic “errors” in their behaviour commensurate with human illusions, which includes brightness contrast and assimilation—although assimilation (specifically White's illusion) only emerged when the virtual ecology included 3-D, as opposed to 2-D scenes. Subtle variations in these illusions, also found in human perception, were observed, such as the asymmetry of brightness contrast. These data suggest that “illusions” arise in humans because (i) natural stimuli are ambiguous, and (ii) this ambiguity is resolved empirically by encoding the statistical relationship between images and scenes in past visual experience. Since resolving stimulus ambiguity is a challenge faced by all visual systems, a corollary of these findings is that human illusions must be experienced by all visual animals regardless of their particular neural machinery. The data also provide a more formal definition of illusion: the condition in which the true source of a stimulus differs from what is its most likely (and thus perceived) source. As such, illusions are not fundamentally different from non-illusory percepts, all being direct manifestations of the statistical relationship between images and scenes.     

Edging along a Warming Coast: A Range Extension for a Common Sandy Beach Crab

Determining the position of range edges is the first step in developing an understanding of the ecological and evolutionary dynamics in play as species’ ranges shift in response to climate change. Here, we study the leading (poleward) range edge of Ocypode cordimanus, a ghost crab that is common along the central to northern east coast of Australia. Our study establishes the poleward range edge of adults of this species to be at Merimbula (36.90°S, 149.93°E), 270 km (along the coast) south of the previous southernmost museum record. We also establish that dispersal of pelagic larvae results in recruitment to beaches 248 km (along the coast; 0.9° of latitude) beyond the adult range edge we have documented here. Although we cannot conclusively demonstrate that the leading range edge for this species has moved polewards in response to climate change, this range edge does fall within a “hotspot” of ocean warming, where surface isotherms are moving southwards along the coast at 20–50 km.decade^-1; coastal air temperatures in the region are also warming. If these patterns persist, future range extensions could be anticipated. On the basis of their ecology, allied with their occupancy of ocean beaches, which are home to taxa that are particularly amenable to climate-change studies, we propose that ghost crabs like O. cordimanus represent ideal model organisms with which to study ecological and evolutionary processes associated with climate change. The fact that “hotspots” of ocean warming on four other continents correspond with poleward range edges of ghost crab species suggests that results of hypothesis tests could be generalized, yielding excellent opportunities to rapidly progress knowledge in this field.     

Collective predator evasion: Putting the criticality hypothesis to the test

According to the criticality hypothesis, collective biological systems should operate in a special parameter region, close to so-called critical points, where the collective behavior undergoes a qualitative change between different dynamical regimes. Critical systems exhibit unique properties, which may benefit collective information processing such as maximal responsiveness to external stimuli. Besides neuronal and gene-regulatory networks, recent empirical data suggests that also animal collectives may be examples of self-organized critical systems. However, open questions about self-organization mechanisms in animal groups remain: Evolutionary adaptation towards a group-level optimum (group-level selection), implicitly assumed in the “criticality hypothesis”, appears in general not reasonable for fission-fusion groups composed of non-related individuals. Furthermore, previous theoretical work relies on non-spatial models, which ignore potentially important self-organization and spatial sorting effects. Using a generic, spatially-explicit model of schooling prey being attacked by a predator, we show first that schools operating at criticality perform best. However, this is not due to optimal response of the prey to the predator, as suggested by the “criticality hypothesis”, but rather due to the spatial structure of the prey school at criticality. Secondly, by investigating individual-level evolution, we show that strong spatial self-sorting effects at the critical point lead to strong selection gradients, and make it an evolutionary unstable state. Our results demonstrate the decisive role of spatio-temporal phenomena in collective behavior, and that individual-level selection is in general not a viable mechanism for self-tuning of unrelated animal groups towards criticality.     

People Efficiently Explore the Solution Space of the Computationally Intractable Traveling Salesman Problem to Find Near-Optimal Tours

Humans need to solve computationally intractable problems such as visual search, categorization, and simultaneous learning and acting, yet an increasing body of evidence suggests that their solutions to instantiations of these problems are near optimal. Computational complexity advances an explanation to this apparent paradox: (1) only a small portion of instances of such problems are actually hard, and (2) successful heuristics exploit structural properties of the typical instance to selectively improve parts that are likely to be sub-optimal. We hypothesize that these two ideas largely account for the good performance of humans on computationally hard problems. We tested part of this hypothesis by studying the solutions of 28 participants to 28 instances of the Euclidean Traveling Salesman Problem (TSP). Participants were provided feedback on the cost of their solutions and were allowed unlimited solution attempts (trials). We found a significant improvement between the first and last trials and that solutions are significantly different from random tours that follow the convex hull and do not have self-crossings. More importantly, we found that participants modified their current better solutions in such a way that edges belonging to the optimal solution (“good” edges) were significantly more likely to stay than other edges (“bad” edges), a hallmark of structural exploitation. We found, however, that more trials harmed the participants'' ability to tell good from bad edges, suggesting that after too many trials the participants “ran out of ideas.” In sum, we provide the first demonstration of significant performance improvement on the TSP under repetition and feedback and evidence that human problem-solving may exploit the structure of hard problems paralleling behavior of state-of-the-art heuristics.     

Controllability of Deterministic Networks with the Identical Degree Sequence

Controlling complex network is an essential problem in network science and engineering. Recent advances indicate that the controllability of complex network is dependent on the network''s topology. Liu and Barabási, et.al speculated that the degree distribution was one of the most important factors affecting controllability for arbitrary complex directed network with random link weights. In this paper, we analysed the effect of degree distribution to the controllability for the deterministic networks with unweighted and undirected. We introduce a class of deterministic networks with identical degree sequence, called (x,y)-flower. We analysed controllability of the two deterministic networks ((1, 3)-flower and (2, 2)-flower) by exact controllability theory in detail and give accurate results of the minimum number of driver nodes for the two networks. In simulation, we compare the controllability of (x,y)-flower networks. Our results show that the family of (x,y)-flower networks have the same degree sequence, but their controllability is totally different. So the degree distribution itself is not sufficient to characterize the controllability of deterministic networks with unweighted and undirected.     

Discriminating Different Classes of Biological Networks by Analyzing the Graphs Spectra Distribution

The brain''s structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world topology. Recent studies indicate that some pathologies present topological network alterations relative to norms seen in the general population. Therefore, methods to discriminate the processes that generate the different classes of networks (e.g., normal and disease) might be crucial for the diagnosis, prognosis, and treatment of the disease. It is known that several topological properties of a network (graph) can be described by the distribution of the spectrum of its adjacency matrix. Moreover, large networks generated by the same random process have the same spectrum distribution, allowing us to use it as a “fingerprint”. Based on this relationship, we introduce and propose the entropy of a graph spectrum to measure the “uncertainty” of a random graph and the Kullback-Leibler and Jensen-Shannon divergences between graph spectra to compare networks. We also introduce general methods for model selection and network model parameter estimation, as well as a statistical procedure to test the nullity of divergence between two classes of complex networks. Finally, we demonstrate the usefulness of the proposed methods by applying them to (1) protein-protein interaction networks of different species and (2) on networks derived from children diagnosed with Attention Deficit Hyperactivity Disorder (ADHD) and typically developing children. We conclude that scale-free networks best describe all the protein-protein interactions. Also, we show that our proposed measures succeeded in the identification of topological changes in the network while other commonly used measures (number of edges, clustering coefficient, average path length) failed.     

Efficiency and cost of economical brain functional networks

Brain anatomical networks are sparse, complex, and have economical small-world properties. We investigated the efficiency and cost of human brain functional networks measured using functional magnetic resonance imaging (fMRI) in a factorial design: two groups of healthy old (N = 11; mean age = 66.5 years) and healthy young (N = 15; mean age = 24.7 years) volunteers were each scanned twice in a no-task or “resting” state following placebo or a single dose of a dopamine receptor antagonist (sulpiride 400 mg). Functional connectivity between 90 cortical and subcortical regions was estimated by wavelet correlation analysis, in the frequency interval 0.06–0.11 Hz, and thresholded to construct undirected graphs. These brain functional networks were small-world and economical in the sense of providing high global and local efficiency of parallel information processing for low connection cost. Efficiency was reduced disproportionately to cost in older people, and the detrimental effects of age on efficiency were localised to frontal and temporal cortical and subcortical regions. Dopamine antagonism also impaired global and local efficiency of the network, but this effect was differentially localised and did not interact with the effect of age. Brain functional networks have economical small-world properties—supporting efficient parallel information transfer at relatively low cost—which are differently impaired by normal aging and pharmacological blockade of dopamine transmission.     

Cellulose as an Architectural Element in Spatially Structured Escherichia coli Biofilms

Morphological form in multicellular aggregates emerges from the interplay of genetic constitution and environmental signals. Bacterial macrocolony biofilms, which form intricate three-dimensional structures, such as large and often radially oriented ridges, concentric rings, and elaborate wrinkles, provide a unique opportunity to understand this interplay of “nature and nurture” in morphogenesis at the molecular level. Macrocolony morphology depends on self-produced extracellular matrix components. In Escherichia coli, these are stationary phase-induced amyloid curli fibers and cellulose. While the widely used “domesticated” E. coli K-12 laboratory strains are unable to generate cellulose, we could restore cellulose production and macrocolony morphology of E. coli K-12 strain W3110 by “repairing” a single chromosomal SNP in the bcs operon. Using scanning electron and fluorescence microscopy, cellulose filaments, sheets and nanocomposites with curli fibers were localized in situ at cellular resolution within the physiologically two-layered macrocolony biofilms of this “de-domesticated” strain. As an architectural element, cellulose confers cohesion and elasticity, i.e., tissue-like properties that—together with the cell-encasing curli fiber network and geometrical constraints in a growing colony—explain the formation of long and high ridges and elaborate wrinkles of wild-type macrocolonies. In contrast, a biofilm matrix consisting of the curli fiber network only is brittle and breaks into a pattern of concentric dome-shaped rings separated by deep crevices. These studies now set the stage for clarifying how regulatory networks and in particular c-di-GMP signaling operate in the three-dimensional space of highly structured and “tissue-like” bacterial biofilms.     

Transition to quorum sensing in an Agrobacterium population: A stochastic model

Understanding of the intracellular molecular machinery that is responsible for the complex collective behavior of multicellular populations is an exigent problem of modern biology. Quorum sensing, which allows bacteria to activate genetic programs cooperatively, provides an instructive and tractable example illuminating the causal relationships between the molecular organization of gene networks and the complex phenotypes they control. In this work we—to our knowledge for the first time—present a detailed model of the population-wide transition to quorum sensing using the example of Agrobacterium tumefaciens. We construct a model describing the Ti plasmid quorum-sensing gene network and demonstrate that it behaves as an “on–off” gene expression switch that is robust to molecular noise and that activates the plasmid conjugation program in response to the increase in autoinducer concentration. This intracellular model is then incorporated into an agent-based stochastic population model that also describes bacterial motion, cell division, and chemical communication. Simulating the transition to quorum sensing in a liquid medium and biofilm, we explain the experimentally observed gradual manifestation of the quorum-sensing phenotype by showing that the transition of individual model cells into the “on” state is spread stochastically over a broad range of autoinducer concentrations. At the same time, the population-averaged values of critical autoinducer concentration and the threshold population density are shown to be robust to variability between individual cells, predictable and specific to particular growth conditions. Our modeling approach connects intracellular and population scales of the quorum-sensing phenomenon and provides plausible answers to the long-standing questions regarding the ecological and evolutionary significance of the phenomenon. Thus, we demonstrate that the transition to quorum sensing requires a much higher threshold cell density in liquid medium than in biofilm, and on this basis we hypothesize that in Agrobacterium quorum sensing serves as the detector of biofilm formation.     

Intrinsic connectivity reveals functionally distinct cortico-hippocampal networks in the human brain

Episodic memory depends on interactions between the hippocampus and interconnected neocortical regions. Here, using data-driven analyses of resting-state functional magnetic resonance imaging (fMRI) data, we identified the networks that interact with the hippocampus—the default mode network (DMN) and a “medial temporal network” (MTN) that included regions in the medial temporal lobe (MTL) and precuneus. We observed that the MTN plays a critical role in connecting the visual network to the DMN and hippocampus. The DMN could be further divided into 3 subnetworks: a “posterior medial” (PM) subnetwork comprised of posterior cingulate and lateral parietal cortices; an “anterior temporal” (AT) subnetwork comprised of regions in the temporopolar and dorsomedial prefrontal cortex; and a “medial prefrontal” (MP) subnetwork comprised of regions primarily in the medial prefrontal cortex (mPFC). These networks vary in their functional connectivity (FC) along the hippocampal long axis and represent different kinds of information during memory-guided decision-making. Finally, a Neurosynth meta-analysis of fMRI studies suggests new hypotheses regarding the functions of the MTN and DMN subnetworks, providing a framework to guide future research on the neural architecture of episodic memory.

Episodic memory depends on interactions between the hippocampus and interconnected neocortical regions. This study uses network analyses of intrinsic brain networks at rest to identify and characterize brain networks that interact with the hippocampus and have distinct functions during memory-guided decision making.     

What Would Jaws Do? The Tyranny of Film and the Relationship between Gaze and Higher-Level Narrative Film Comprehension

What is the relationship between film viewers’ eye movements and their film comprehension? Typical Hollywood movies induce strong attentional synchrony—most viewers look at the same things at the same time. Thus, we asked whether film viewers’ eye movements would differ based on their understanding—the mental model hypothesis—or whether any such differences would be overwhelmed by viewers’ attentional synchrony—the tyranny of film hypothesis. To investigate this question, we manipulated the presence/absence of prior film context and measured resulting differences in film comprehension and eye movements. Viewers watched a 12-second James Bond movie clip, ending just as a critical predictive inference should be drawn that Bond’s nemesis, “Jaws,” would fall from the sky onto a circus tent. The No-context condition saw only the 12-second clip, but the Context condition also saw the preceding 2.5 minutes of the movie before seeing the critical 12-second portion. Importantly, the Context condition viewers were more likely to draw the critical inference and were more likely to perceive coherence across the entire 6 shot sequence (as shown by event segmentation), indicating greater comprehension. Viewers’ eye movements showed strong attentional synchrony in both conditions as compared to a chance level baseline, but smaller differences between conditions. Specifically, the Context condition viewers showed slightly, but significantly, greater attentional synchrony and lower cognitive load (as shown by fixation probability) during the critical first circus tent shot. Thus, overall, the results were more consistent with the tyranny of film hypothesis than the mental model hypothesis. These results suggest the need for a theory that encompasses processes from the perception to the comprehension of film.     

Entrainment of Lemna CO(2) Output Through Phytochrome

The entrainability of Lemna perpusilla CO₂ output by periodic 15 minute red (R) and far red (F) illuminations was tested in low nitrate medium. R every 8 hour, symbolized R/R/R, gives a flat output (no entrainment) as does F/F/F. However, R/—/— (R every 24 hour) entrains rapidly, and F/—/— does so as well, in a similar manner. The effects of R/R/— and F/F/— also resemble each other closely. Entrainment by R/F/F or R/R/F is rapid and indifferent to order of presentation, e.g., R/F/F and F/R/F lead to the same steady state. Typical phytochrome reversals occur, e.g., R,F/F/F holds output flat, while F,R/F/F entrains in the manner of R/F/F. Blue (B) light acts like R in schedules such as B/F/F but like F in schedules such as B/R/R. In all schedules studied, the zeitgeber (primary synchronizer) appears to be the sharpest transition from a low to a high level of far red-absorbing phytochrome that occurs with a 24-hr periodicity. Thus in entrainment, and by inference in photoperiodic timing, the level of far red-absorbing phytochrome at any time may be less significant than the succession of levels of which it is a part, a conclusion that implies the existence of a “scanning” mechanism that compares levels of far red-absorbing phytochrome at various times of day.     

Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene,the EnvV Syncytin,Captured for a Function in Placentation

Syncytins are envelope genes of retroviral origin that have been co-opted for a role in placentation. They promote cell–cell fusion and are involved in the formation of a syncytium layer—the syncytiotrophoblast—at the materno-fetal interface. They were captured independently in eutherian mammals, and knockout mice demonstrated that they are absolutely required for placenta formation and embryo survival. Here we provide evidence that these “necessary” genes acquired “by chance” have a definite lifetime with diverse fates depending on the animal lineage, being both gained and lost in the course of evolution. Analysis of a retroviral envelope gene, the envV gene, present in primate genomes and belonging to the endogenous retrovirus type V (ERV-V) provirus, shows that this captured gene, which entered the primate lineage >45 million years ago, behaves as a syncytin in Old World monkeys, but lost its canonical fusogenic activity in other primate lineages, including humans. In the Old World monkeys, we show—by in situ analyses and ex vivo assays—that envV is both specifically expressed at the level of the placental syncytiotrophoblast and fusogenic, and that it further displays signs of purifying selection based on analysis of non-synonymous to synonymous substitution rates. We further show that purifying selection still operates in the primate lineages where the gene is no longer fusogenic, indicating that degeneracy of this ancestral syncytin is a slow, lineage-dependent, and multi-step process, in which the fusogenic activity would be the first canonical property of this retroviral envelope gene to be lost.     

Cephalic and Limb Anatomy of a New Isoxyid from the Burgess Shale and the Role of “Stem Bivalved Arthropods” in the Disparity of the Frontalmost Appendage

We herein describe Surusicaris elegans gen. et sp. nov. (in Isoxyidae, amended), a middle (Series 3, Stage 5) Cambrian bivalved arthropod from the new Burgess Shale deposit of Marble Canyon (Kootenay National Park, British Columbia). Surusicaris exhibits 12 simple, partly undivided biramous trunk limbs with long tripartite caeca, which may illustrate a plesiomorphic “fused” condition of exopod and endopod. We construe also that the head is made of five somites (= four segments), including two eyes, one pair of anomalocaridid-like frontalmost appendages, and three pairs of poorly sclerotized uniramous limbs. This fossil may therefore be a candidate for illustrating the origin of the plesiomorphic head condition in euarthropods, and questions the significance of the “two-segmented head” in, e.g., fuxianhuiids. The frontalmost appendage in isoxyids is intriguingly disparate, bearing similarities with both dinocaridids and euarthropods. In order to evaluate the relative importance of bivalved arthropods, such as Surusicaris, in the hypothetical structuro-functional transition between the dinocaridid frontal appendage and the pre-oral—arguably deutocerebral—appendage of euarthropods, we chose a phenetic approach and computed morphospace occupancy for the frontalmost appendages of 36 stem and crown taxa. Results show different levels of evolutionary decoupling between frontalmost appendage disparity and body plans. Variance is greatest in dinocaridids and “stem bivalved” arthropods, but these groups do not occupy the morphospace homogeneously. Rather, the diversity of frontalmost appendages in “stem bivalved” arthropods, distinct in its absence of clear clustering, is found to link the morphologies of “short great appendages,” chelicerae and antennules. This find fits the hypothesis of an increase in disparity of the deutocerebral appendage prior to its diversification in euarthropods, and possibly corresponds to its original time of development. The analysis of this pattern, however, is sensitive to the—still unclear—extent of polyphyly of the “stem bivalved” taxa.