### Concept: Topological space

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##### Do girls with anorexia nervosa have elevated autistic traits?

- OPEN
- Molecular autism
- Published over 4 years ago
- Discuss

Patients with anorexia may have elevated autistic traits. In this study, we tested test whether patients with anorexia nervosa (anorexia) have an elevated score on a dimensional measure of autistic traits, the Autism Spectrum Quotient (AQ), as well as on trait measures relevant to the autism spectrum: the Empathy Quotient (EQ), and the Systemizing Quotient (SQ).

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Biology presents many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture containing closed loops at many different levels. Although a number of approaches have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework, the hierarchical loop decomposition, that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated graphs, such as artificial models and optimal distribution networks, as well as natural graphs extracted from digitized images of dicotyledonous leaves and vasculature of rat cerebral neocortex. We calculate various metrics based on the asymmetry, the cumulative size distribution and the Strahler bifurcation ratios of the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information (exact location of edges and nodes) from the metric topology (connectivity and edge weight) and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.

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##### Hippocampal and prefrontal processing of network topology to simulate the future

- Nature communications
- Published about 1 year ago
- Discuss

Topological networks lie at the heart of our cities and social milieu. However, it remains unclear how and when the brain processes topological structures to guide future behaviour during everyday life. Using fMRI in humans and a simulation of London (UK), here we show that, specifically when new streets are entered during navigation of the city, right posterior hippocampal activity indexes the change in the number of local topological connections available for future travel and right anterior hippocampal activity reflects global properties of the street entered. When forced detours require re-planning of the route to the goal, bilateral inferior lateral prefrontal activity scales with the planning demands of a breadth-first search of future paths. These results help shape models of how hippocampal and prefrontal regions support navigation, planning and future simulation.

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Humans can see and name thousands of distinct object and action categories, so it is unlikely that each category is represented in a distinct brain area. A more efficient scheme would be to represent categories as locations in a continuous semantic space mapped smoothly across the cortical surface. To search for such a space, we used fMRI to measure human brain activity evoked by natural movies. We then used voxelwise models to examine the cortical representation of 1,705 object and action categories. The first few dimensions of the underlying semantic space were recovered from the fit models by principal components analysis. Projection of the recovered semantic space onto cortical flat maps shows that semantic selectivity is organized into smooth gradients that cover much of visual and nonvisual cortex. Furthermore, both the recovered semantic space and the cortical organization of the space are shared across different individuals. VIDEO ABSTRACT:

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##### Information diffusion, Facebook clusters, and the simplicial model of social aggregation: a computational simulation of simplicial diffusers for community health interventions

- Health communication
- Published over 2 years ago
- Discuss

By integrating the simplicial model of social aggregation with existing research on opinion leadership and diffusion networks, this article introduces the constructs of simplicial diffusers (mathematically defined as nodes embedded in simplexes; a simplex is a socially bonded cluster) and simplicial diffusing sets (mathematically defined as minimal covers of a simplicial complex; a simplicial complex is a social aggregation in which socially bonded clusters are embedded) to propose a strategic approach for information diffusion of cancer screenings as a health intervention on Facebook for community cancer prevention and control. This approach is novel in its incorporation of interpersonally bonded clusters, culturally distinct subgroups, and different united social entities that coexist within a larger community into a computational simulation to select sets of simplicial diffusers with the highest degree of information diffusion for health intervention dissemination. The unique contributions of the article also include seven propositions and five algorithmic steps for computationally modeling the simplicial model with Facebook data.

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##### Mapping membrane activity in undiscovered peptide sequence space using machine learning

- Proceedings of the National Academy of Sciences of the United States of America
- Published over 1 year ago
- Discuss

There are some ∼1,100 known antimicrobial peptides (AMPs), which permeabilize microbial membranes but have diverse sequences. Here, we develop a support vector machine (SVM)-based classifier to investigate ⍺-helical AMPs and the interrelated nature of their functional commonality and sequence homology. SVM is used to search the undiscovered peptide sequence space and identify Pareto-optimal candidates that simultaneously maximize the distance σ from the SVM hyperplane (thus maximize its “antimicrobialness”) and its ⍺-helicity, but minimize mutational distance to known AMPs. By calibrating SVM machine learning results with killing assays and small-angle X-ray scattering (SAXS), we find that the SVM metric σ correlates not with a peptide’s minimum inhibitory concentration (MIC), but rather its ability to generate negative Gaussian membrane curvature. This surprising result provides a topological basis for membrane activity common to AMPs. Moreover, we highlight an important distinction between the maximal recognizability of a sequence to a trained AMP classifier (its ability to generate membrane curvature) and its maximal antimicrobial efficacy. As mutational distances are increased from known AMPs, we find AMP-like sequences that are increasingly difficult for nature to discover via simple mutation. Using the sequence map as a discovery tool, we find a unexpectedly diverse taxonomy of sequences that are just as membrane-active as known AMPs, but with a broad range of primary functions distinct from AMP functions, including endogenous neuropeptides, viral fusion proteins, topogenic peptides, and amyloids. The SVM classifier is useful as a general detector of membrane activity in peptide sequences.

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##### Meta-analysis of negative-pressure wound therapy for closed surgical incisions

- The British journal of surgery
- Published about 2 years ago
- Discuss

Postoperative wound complications are common following surgical procedures. Negative-pressure wound therapy (NPWT) is well recognized for the management of open wounds and has been applied recently to closed surgical incisions. The evidence base to support this intervention is limited. The aim of this study was to assess whether NPWT reduces postoperative wound complications when applied to closed surgical incisions.

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##### Multilayer Joint Gait-Pose Manifolds for Human Gait Motion Modeling

- IEEE transactions on cybernetics
- Published over 3 years ago
- Discuss

We present new multilayer joint gait-pose manifolds (multilayer JGPMs) for complex human gait motion modeling, where three latent variables are defined jointly in a low-dimensional manifold to represent a variety of body configurations. Specifically, the pose variable (along the pose manifold) denotes a specific stage in a walking cycle; the gait variable (along the gait manifold) represents different walking styles; and the linear scale variable characterizes the maximum stride in a walking cycle. We discuss two kinds of topological priors for coupling the pose and gait manifolds, i.e., cylindrical and toroidal, to examine their effectiveness and suitability for motion modeling. We resort to a topologically-constrained Gaussian process (GP) latent variable model to learn the multilayer JGPMs where two new techniques are introduced to facilitate model learning under limited training data. First is training data diversification that creates a set of simulated motion data with different strides. Second is the topology-aware local learning to speed up model learning by taking advantage of the local topological structure. The experimental results on the Carnegie Mellon University motion capture data demonstrate the advantages of our proposed multilayer models over several existing GP-based motion models in terms of the overall performance of human gait motion modeling.

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The use of accelerometers to objectively measure physical activity (PA) has become the most preferred method of choice in recent years. Traditionally, cutpoints are used to assign impulse counts recorded by the devices to sedentary and activity ranges. Here, hidden Markov models (HMM) are used to improve the cutpoint method to achieve a more accurate identification of the sequence of modes of PA.

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##### Paralog specific Hsp90 Inhibitors - a brief history and a bright future

- Current topics in medicinal chemistry
- Published about 2 years ago
- Discuss

The high sequence and structural homology among the hsp90 paralogs - Hsp90α, Hsp90β, Grp94, and Trap-1 - has made the development of paralog-specific inhibitors a challenging proposition.