HippUnfold: Automated hippocampal unfolding, morphometry, and subfield segmentation

The archicortical hippocampus differs, like the neocortex, in its folding patterns between individuals. Here, we present an automated and robust BIDS-App, HippUnfold, for defining and indexing subject-specific hippocampal folding in MRI, analogous to popular tools used in neocortical reconstruction. This is critical for inter-individual alignment, with topology as the basis for homology. This topological framework enables qualitatively new analyses of morphological and laminar structure in the hippocampus or hippocampal subfields, and is critical for the advancement of neuroimaging analyses at a meso- or micro-scale. HippUnfold uses state-of-the-art deep learning combined with previously developed topological constraints on hippocampal tissue. It is designed to work with commonly employed sub-millimetric MRI acquisitions, with extensibility to microscopic resolutions as well. In this paper we illustrate the power of HippUnfold in feature extraction, and its construct validity compared to several extant hippocampal subfield analysis methods.

Polynomial Invariant of Molecular Circuit Topology

The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic acids, often fold into 3D conformations with critical chain entanglements and local or global structural symmetries stabilised by formation contacts between different parts of the chain. Circuit topology captures the arrangements of intra-chain contacts within a given folded linear chain and allows for the classification and comparison of chains. Contacts keep chain segments in physical proximity and can be either mechanically hard attachments or soft entanglements that constrain a physical chain. Contrary to knot theory, which offers many established knot invariants, circuit invariants are just being developed. Here, we present polynomial invariants that are both efficient and sufficiently powerful to deal with any combination of soft and hard contacts. A computer implementation and table of chains with up to three contacts is also provided.

Otro lado. An inquiry into the conceptual topology of animism among the Moré (Itene) of the Bolivian Amazonia

This paper is based on ethnographic fieldwork among the Moré (Itene) who, together with Wari’ and Oro Win, are the descendants of the last Chapacura speaking groups in Amazonia. I analyze, hunting story and elderly people stories (los cuentos) where the Moré explicitly conceptualize the notion of “the other side” as the realm of reality inhabited by non-human persons (the Deads, Spirits, Mothers of game, etc.). I focus on some topological aspects of Moré animism, such as conception of surface, boundary, space-time, distance markers, inside/outside distinctions. In conclusion I sketch some possible directions for further research in this topological framework for animism. I hope this paper can contribute to the renewed debate about animism in Amazonia and more broadly to the onto-logical turn in anthropology.

On the Loop Homology of a Certain Complex of RNA Structures

In this paper, we establish a topological framework of τ-structures to quantify the evolutionary transitions between two RNA sequence–structure pairs. τ-structures developed here consist of a pair of RNA secondary structures together with a non-crossing partial matching between the two backbones. The loop complex of a τ-structure captures the intersections of loops in both secondary structures. We compute the loop homology of τ-structures. We show that only the zeroth, first and second homology groups are free. In particular, we prove that the rank of the second homology group equals the number γ of certain arc-components in a τ-structure and that the rank of the first homology is given by γ−χ+1, where χ is the Euler characteristic of the loop complex.

On the Loop Homology of a Certain Complex of RNA Structures

In this paper we establish a topological framework of τ-structures to quantify the evolutionary transitions between two RNA sequence-structure pairs. τ-structures developed here consist of a pair of RNA secondary structures together with a non-crossing partial matching between the two backbones. The loop complex of a τ-structure captures the intersections of loops in both secondary structures. We compute the loop homology of τ-structures. We show that only the zeroth, first and second homology groups are free. In particular, we prove that the rank of the second homology group equals the number γ of certain arc-components in a τ-structure, and the rank of the first homology is given by γ−χ+1, where χ is the Euler characteristic of the loop complex.

Deep Graph Mapper: Seeing Graphs Through the Neural Lens

Graph summarization has received much attention lately, with various works tackling the challenge of defining pooling operators on data regions with arbitrary structures. These contrast the grid-like ones encountered in image inputs, where techniques such as max-pooling have been enough to show empirical success. In this work, we merge the Mapper algorithm with the expressive power of graph neural networks to produce topologically grounded graph summaries. We demonstrate the suitability of Mapper as a topological framework for graph pooling by proving that Mapper is a generalization of pooling methods based on soft cluster assignments. Building upon this, we show how easy it is to design novel pooling algorithms that obtain competitive results with other state-of-the-art methods. Additionally, we use our method to produce GNN-aided visualisations of attributed complex networks.

The Effect of ‘Datafication’ on Knowledge Diffusion: A Topological Framework

This paper begins by distinguishing between data infrastructure, data entry and data points as three distinct, but interrelated situations. Data practices are understood in the general sense of the word here, i.e., such as actions, actions, and consequences, of introducing data-generating technologies for knowledge codification. This paper will investigate both the generics and specificities of data practices to explore the disentanglement of the liveness of data practices, i.e. how such practices are happening with regard to knowledge codification. Within this regard, this study seeks to account for the ‘fluid and heterogeneous ontology’ of such practices. In other words, the framework conceptualizes data processing as correlational, and aims to provide a technique to explore they disentanglement of these relationships.

Evaluating the Interoperability of Urban Air Mobility Systems and Airports

This paper investigates how existing arrival and departure procedures can be directly used or adapted to enable high-volume instrument and visual urban air mobility (UAM) flight operations at major airports in the United States. Viable procedures are restricted to those that enable simultaneous and non-interfering UAM flights with conventional aircraft operations. Air traffic controller workload is proposed as the critical integration barrier to scale UAM operations in visual conditions whereas separation minima, especially for approach procedures, is proposed as the critical barrier in instrument conditions. A systems approach is taken to evaluate potential integration strategies for UAM in which the location of UAM runways or vertipads and flight procedures are presented in a topological framework. The benefits, challenges, and notional application of five integration schemes are discussed. Four promising procedures for UAM are introduced through case studies at three airports. Findings indicate that multiple procedures exist to support high-volume UAM integration at major airports under current regulations with additional controller staffing, especially if UAM aircraft exhibit helicopter-like performance.

Different Benzendicarboxylate-Directed Structural Variations and Properties of Four New Porous Cd(II)-Pyridyl-Triazole Coordination Polymers

Four new different porous crystalline Cd(II)-based coordination polymers (CPs), i. e., [Cd(mdpt)2]·2H2O (1), [Cd2(mdpt)2(m-bdc)(H2O)2] (2), [Cd(Hmdpt)(p-bdc)]·2H2O (3), and [Cd3(mdpt)2(bpdc)2]·2.5NMP (4), were obtained successfully by the assembly of Cd(II) ions and bitopic 3-(3-methyl-2-pyridyl)-5-(4-pyridyl)-1,2,4-triazole (Hmdpt) in the presence of various benzendicarboxylate ligands, i.e., 1,3/1,4-benzenedicarboxylic acid (m-H2bdc, p-H2bdc) and biphenyl-4,4′-bicarboxylate (H2bpdc). Herein, complex 1 is a porous 2-fold interpenetrated four-connected 3D NbO topological framework based on the mdpt− ligand; 2 reveals a two-dimensional (2D) hcb network. Interestingly, 3 presents a three-dimensional (3D) rare interpenetrated double-insertion supramolecular net via 2D ···ABAB··· layers and can be viewed as an fsh topological net, while complex 4 displays a 3D sqc117 framework. Then, the different gas sorption performances were carried out carefully for complexes 1 and 4, the results of which showed 4 has preferable sorption than that of 1 and can be the potential CO2 storage and separation material. Furthermore, the stability and luminescence of four complexes were performed carefully in the solid state.