Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms.

Topologically associating domains (TADs) are sub-Megabase regions in vertebrate genomes with enriched intradomain interactions that restrict enhancer-promoter contacts across their boundaries. However, the mechanisms that separate TADs remain incompletely understood. Most boundaries between TADs contain CTCF binding sites (CBSs), which individually contribute to the blocking of Cohesin-mediated loop extrusion.

Unraveling microglial spatial organization in the developing human brain with DeepCellMap, a deep learning approach coupled with spatial statistics.

Mapping cellular organization in the developing brain presents significant challenges due to the multidimensional nature of the data, characterized by complex spatial patterns that are difficult to interpret without high-throughput tools. Here, we present DeepCellMap, a deep-learning-assisted tool that integrates multi-scale image processing with advanced spatial and clustering statistics. This pipeline is designed to map microglial organization during normal and pathological brain development and has the potential to be adapted to any cell type.

Production of the adjective and possessive markers in Chinese post-stroke aphasia.

Research has shown that patients with post-stroke aphasia may encounter difficulties in producing inflectional morphemes. Interestingly, they also show distinct challenges with the inflectional morphemes of homophones, such as the plural marker and the possessive marker in English. However, previous studies have predominantly focused on morphemes in European languages.

Embedded Ethics in Practice: A Toolbox for Integrating the Analysis of Ethical and Social Issues into Healthcare AI Research.

Integrating artificial intelligence (AI) into critical domains such as healthcare holds immense promise. Nevertheless, significant challenges must be addressed to avoid harm, promote the well-being of individuals and societies, and ensure ethically sound and socially just technology development. Innovative approaches like Embedded Ethics, which refers to integrating ethics and social science into technology development based on interdisciplinary collaboration, are emerging to address issues of bias, transparency, misrepresentation, and more.

Voltage mapping in subcellular nanodomains using electro-diffusion modeling.

Voltage distribution in sub-cellular micro-domains such as neuronal synapses, small protrusions, or dendritic spines regulates the opening and closing of ionic channels, energy production, and thus, cellular homeostasis and excitability. Yet how voltage changes at such a small scale in vivo remains challenging due to the experimental diffraction limit, large signal fluctuations, and the still limited resolution of fast voltage indicators. Here, we study the voltage distribution in nano-compartments using a computational approach based on the Poisson-Nernst-Planck equations for the electro-diffusion motion of ions, where inward and outward fluxes are generated between channels.

Synapsin 2a tetramerisation selectively controls the presynaptic nanoscale organisation of reserve synaptic vesicles.

Neurotransmitter release relies on the regulated fusion of synaptic vesicles (SVs) that are tightly packed within the presynaptic bouton of neurons. The mechanism by which SVs are clustered at the presynapse, while preserving their ability to dynamically recycle to support neuronal communication, remains unknown. Synapsin 2a (Syn2a) tetramerization has been suggested as a potential clustering mechanism.

Analyzing Photoactivation with Diffusion Models to Study Transport in the Endoplasmic Reticulum Network.

Photoactivation is a paradigm consisting in local molecular fluorescent activation by laser illumination in a chosen region (source) while measuring the concentration at a target region. Data-driven modeling is concerned with the following questions: how from the measurement in these two regions is it possible to infer the properties of molecular propagation? How is it possible to use such responses to infer motions occurring in networks such as the endoplasmic reticulum? In this book chapter, we shall review the data-driven analysis based on diffusion-transport models and numerical simulations to interpret the photoactivation dynamics and extract biophysical parameters. We will discuss modeling approaches to reconstruct local network properties from photoactivation transients.

Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories.

Phase separated domains (PSDs) are ubiquitous in cell biology, representing nanoregions of high molecular concentration. PSDs appear at diverse cellular domains, such as neuronal synapses but also in eukaryotic cell nucleus, limiting the access of transcription factors and thus preventing gene expression. We develop a generalized cross-linker polymer model, to study PSDs: we show that increasing the number of cross-linkers induces a polymer condensation, preventing access of diffusing molecules.

Mapping general anesthesia states based on electro-encephalogram transition phases.

Cortical electro-encephalography (EEG) served as the clinical reference for monitoring unconsciousness during general anesthesia. The existing EEG-based monitors classified general anesthesia states as underdosed, adequate, or overdosed, lacking predictive power due to the absence of transition phases among these states. In response to this limitation, we undertook an analysis of the EEG signal during isoflurane-induced general anesthesia in mice.

Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.

Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs.

Spinteract: a program to refine magnetic interactions to diffuse scattering data.

Magnetic diffuse scattering-the broad magnetic scattering features observed in neutron-diffraction data above a material's magnetic ordering temperature-provides a rich source of information about the material's magnetic Hamiltonian. However, this information has often remained under-utilised due to a lack of available computer software that can fit values of magnetic interaction parameters to such data. Here, an open-source computer program, Spinteract, is presented, which enables straightforward refinement of magnetic interaction parameters to powder and single-crystal magnetic diffuse scattering data.

Diversity of dynamic voltage patterns in neuronal dendrites revealed by nanopipette electrophysiology.

Dendrites and dendritic spines are the essential cellular compartments in neuronal communication, conveying information through transient voltage signals. Our understanding of these compartmentalized voltage dynamics in fine, distal neuronal dendrites remains poor due to the difficulties inherent to accessing and stably recording from such small, nanoscale cellular compartments for a sustained time. To overcome these challenges, we use nanopipettes that permit long and stable recordings directly from fine neuronal dendrites.

Translating theories of justice into a practice model for triage of scarce intensive care resources during a pandemic.

During the COVID-19 pandemic, national triage guidelines were developed to address the anticipated shortage of life-saving resources, should ICU capacities be overloaded. Rationing and triage imply that in addition to individual patient interests, interests of population health have to be integrated. The transfer of theoretical and empirical knowledge into feasible and useful practice models and their implementation in clinical settings need to be improved.

O37: one of the exceptions that prove the rule.

Between 1965 and 1968, outbreaks of cholera in Sudan and former Czechoslovakia provoked considerable public health concern. These still represent important historical events that need to be linked to the growing genomic evidence describing the aetiological agent of cholera, . Whilst O1 serogroup are canonically associated with epidemic and pandemic cholera, these events were caused by a clone of toxigenic O37 that may be more globally distributed than just to Europe and North Africa.

Spectral EEG correlations from the different phases of general anesthesia.

Introduction: Electroencephalography (EEG) signals contain transient oscillation patterns commonly used to classify brain states in responses to action, sleep, coma or anesthesia.

Methods: Using a time-frequency analysis of the EEG, we search for possible causal correlations between the successive phases of general anesthesia. We hypothesize that it could be possible to anticipate recovery patterns from the induction or maintenance phases.

Interactive nanocluster compaction of the ELKS scaffold and Cacophony Ca channels drives sustained active zone potentiation.

At presynaptic active zones (AZs), conserved scaffold protein architectures control synaptic vesicle (SV) release by defining the nanoscale distribution and density of voltage-gated Ca channels (VGCCs). While AZs can potentiate SV release in the minutes range, we lack an understanding of how AZ scaffold components and VGCCs engage into potentiation. We here establish dynamic, intravital single-molecule imaging of endogenously tagged proteins at AZs undergoing presynaptic homeostatic potentiation.

How large the number of redundant copies should be to make a rare event probable.

The redundancy principle provides a framework to study how rare events are made possible with probability 1 in accelerated time, by making many copies of similar random searchers. However, what is a large n? To estimate large n with respect to the geometrical properties of a domain and the dynamics, we present here a criterion based on splitting probabilities between a small fraction of the exploration space associated with an activation process and other absorbing regions where trajectories can be terminated. We obtain explicit computations especially when there is a killing region located inside the domain that we compare with stochastic simulations.

High-throughput super-resolution single-particle trajectory analysis reconstructs organelle dynamics and membrane reorganization.

Super-resolution imaging can generate thousands of single-particle trajectories. These data can potentially reconstruct subcellular organization and dynamics, as well as measure disease-linked changes. However, computational methods that can derive quantitative information from such massive datasets are currently lacking.

Physiological Robustness of Model Gram-Negative Bacteria in Response to Genome Rewiring.

DNA supercoiling and nucleoid-associated proteins (NAPs) are two of the factors that govern the architecture of the bacterial genome, influencing the expression of the genetic information that it contains. Alterations to DNA topology, and to the numbers and types of NAPs, have pleiotropic effects on gene expression, suggesting that modifications to the production patterns of DNA topoisomerases and/or NAPs are likely to result in marked impacts on bacterial physiology. Knockout mutations in the genes encoding these proteins (where the mutants remain viable) result in clear physiological effects.

Systemising triage: COVID-19 guidelines and their underlying theories of distributive justice.

The COVID-19 pandemic has been overwhelming public health-care systems around the world. With demand exceeding the availability of medical resources in several regions, hospitals have been forced to invoke triage. To ensure that this difficult task proceeds in a fair and organised manner, governments scrambled experts to draft triage guidelines under enormous time pressure.

Geometric Frustration on the Trillium Lattice in a Magnetic Metal-Organic Framework.

In the dense metal-organic framework Na[Mn(HCOO)_{3}], Mn^{2+} ions (S=5/2) occupy the nodes of a "trillium" net. We show that the system is strongly magnetically frustrated: the Néel transition is suppressed well below the characteristic magnetic interaction strength; short-range magnetic order persists far above the Néel temperature; and the magnetic susceptibility exhibits a pseudo-plateau at 1/3-saturation magnetization. A simple model of nearest-neighbor Heisenberg antiferromagnetic and dipolar interactions accounts quantitatively for all observations, including an unusual 2-k magnetic ground state.

Harold Wilson, 'Selsdon Man', and the defence of social democracy in 1970s Britain.

Harold Wilson's attack on 'Selsdon Man' in the run-up to the 1970 general election has generally been seen as a flawed rhetorical gambit, which inadvertently gave coherence to Edward Heath's policies. The subsequent invocation of 'Selsdon' by critics of Heath's 'u-turns' has meant that the episode has mainly attracted scrutiny from historians of the Conservative Party. Yet the debate over Selsdon can also be seen as a landmark in Wilson's transition from the 'modernizing' politics of the 1960s to a more defensive posture, in which he presented Labour as a bulwark against regressive market-liberal policies.

Emergence and fragmentation of the alpha-band driven by neuronal network dynamics.

Rhythmic neuronal network activity underlies brain oscillations. To investigate how connected neuronal networks contribute to the emergence of the α-band and to the regulation of Up and Down states, we study a model based on synaptic short-term depression-facilitation with afterhyperpolarization (AHP). We found that the α-band is generated by the network behavior near the attractor of the Up-state.

The Reduction of Visible Spaces of Sex Work in Europe.

Introduction: Visible spaces of sex work are controversial and contested spaces. This paper explores the relationship between the legal framing of sex work and local policy and how this impacts upon the health and safety of sex workers who use those spaces.

Methods: This paper is based on data collected from a Winston Churchill Memorial Trust Travel Fellowship in 2016.