Non-utopian optical properties computed of a tomographically reconstructed real photonic nanostructure.

State-of-the-art computational methods combined with common idealized structural models provide an incomplete understanding of experimental observations on real nanostructures, since manufacturing introduces unavoidable deviations from the design. We propose to close this knowledge gap by using the real structure of a manufactured nanostructure as input in computations to obtain a realistic comparison with measurements on the same nanostructure. We demonstrate this approach on the structure of a real inverse woodpile photonic bandgap crystal made from silicon, as previously obtained by synchrotron X-ray imaging.

Antimicrobial-Resistant Bacteria Carriage in Rodents According to Habitat Anthropization.

It is increasingly suggested that the dynamics of antimicrobial-resistant bacteria in the wild are mostly anthropogenically driven, but the spatial and temporal scales at which these phenomena occur in landscapes are only partially understood. Here, we explore this topic by studying antimicrobial resistance in the commensal bacteria from micromammals sampled at 12 sites from a large heterogenous landscape (the Carmargue area, Rhone Delta) along a gradient of anthropization: natural reserves, rural areas, towns, and sewage-water treatment plants. There was a positive relationship between the frequency of antimicrobial-resistant bacteria and the level of habitat anthropization.

DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces.

Motivation: Gaining structural insights into the protein-protein interactome is essential to understand biological phenomena and extract knowledge for rational drug design or protein engineering. We have previously developed DeepRank, a deep-learning framework to facilitate pattern learning from protein-protein interfaces using convolutional neural network (CNN) approaches. However, CNN is not rotation invariant and data augmentation is required to desensitize the network to the input data orientation which dramatically impairs the computation performance.

High B-value diffusion tensor imaging for early detection of hippocampal microstructural alteration in a mouse model of multiple sclerosis.

Several studies have highlighted the value of diffusion tensor imaging (DTI) with strong diffusion weighting to reveal white matter microstructural lesions, but data in gray matter (GM) remains scarce. Herein, the effects of b-values combined with different numbers of diffusion-encoding directions (NDIRs) on DTI metrics to capture the normal hippocampal microstructure and its early alterations were investigated in a mouse model of multiple sclerosis (experimental autoimmune encephalomyelitis [EAE]). Two initial DTI datasets (B2700-43Dir acquired with b = 2700 s.

Multiresistant Enterobacteriaceae in yellow-legged gull chicks in their first weeks of life.

Wild animal species living in anthropogenic areas are commonly carriers of antimicrobial-resistant bacteria (AMRB), but their role in the epidemiology of these bacteria is unclear. Several studies on AMRB in wildlife have been cross-sectional in design and sampled individual animals at only one point in time. To further understand the role of wildlife in maintaining and potentially transmitting these bacteria to humans and livestock, longitudinal studies are needed in which samples are collected from individual animals over multiple time periods.

PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes.

Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks. T-cells are activated when they recognize foreign peptides that are presented on the cell surface by Major Histocompatibility Complexes (MHC), forming peptide:MHC (pMHC) complexes. 3D structures of pMHC complexes provide fundamental insight into T-cell recognition mechanism and aids immunotherapy design.

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces.

Three-dimensional (3D) structures of protein complexes provide fundamental information to decipher biological processes at the molecular scale. The vast amount of experimentally and computationally resolved protein-protein interfaces (PPIs) offers the possibility of training deep learning models to aid the predictions of their biological relevance. We present here DeepRank, a general, configurable deep learning framework for data mining PPIs using 3D convolutional neural networks (CNNs).

Changes Over Time of Diffusion MRI in the White Matter of Aging Brain, a Good Predictor of Verbal Recall.

: Extensive research using water-diffusion MRI reported age-related modifications of cerebral White Matter (WM). Moreover, water-diffusion parameter modifications have been frequently associated with cognitive performances in the elderly sample, reinforcing the idea of aging inducing microstructural disconnection of the brain which in turn impacts cognition. However, only few studies really assessed over-time modifications of these parameters and their relationship with episodic memory outcome of elderly.

Embolus Retriever with Interlinked Cages (ERIC) versus conventional stent retrievers for thrombectomy: a propensity score-based analysis.

Background: The Embolus Retriever with Interlinked Cages (ERIC) is one of the latest devices for thrombectomies. It has several architectural features that are supposed to enhance its ability to remove clots and prevent distal emboli. We aimed to compare ERIC with standard stent retrievers (SRs) using propensity score (PS) matching.

iScore: An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines.

Computational docking is a promising tool to model three-dimensional (3D) structures of protein-protein complexes, which provides fundamental insights of protein functions in the cellular life. Singling out near-native models from the huge pool of generated docking models (referred to as the scoring problem) remains as a major challenge in computational docking. We recently published iScore, a novel graph kernel based scoring function.

Experimental sepsis-associated encephalopathy is accompanied by altered cerebral blood perfusion and water diffusion and related to changes in cyclooxygenase-2 expression and glial cell morphology but not to blood-brain barrier breakdown.

Sepsis-associated encephalopathy (SAE) refers to brain dysfunction, including delirium, occurs during severe infection and is associated with development of post-traumatic stress disorder. SAE has been proposed to be related to reduced cerebral blood flow (CBF), blood-brain barrier breakdown (BBB), white matter edema and disruption and glia cell activation, but their exact relationships remain to be determined. In the present work, we set out to study CBF using Arterial Spin Labeling (ASL) and grey and white matter structure with T2- and diffusion magnetic resonance imaging (dMRI) in rats with cecal ligation and puncture (CLP)-induced encephalopathy.

The effect of the magnitude and direction of the dipoles of organic cations on the electronic structure of hybrid halide perovskites.

We present ab initio calculations (DFT and SOC-GW) of the optoelectronic properties of different hybrid-halide perovskites, namely X-PbI (X = methylamonimum, formamidinium, guanidinium, hydrazinium, and hydroxylammonium). These calculations shed new light on how the substitution of different organic cations in the material influences its optoelectronic properties. Our simulations show a significant modification of the lattice parameter and band gap of the material upon cation substitution.

iScore: a novel graph kernel-based function for scoring protein-protein docking models.

Motivation: Protein complexes play critical roles in many aspects of biological functions. Three-dimensional (3D) structures of protein complexes are critical for gaining insights into structural bases of interactions and their roles in the biomolecular pathways that orchestrate key cellular processes. Because of the expense and effort associated with experimental determinations of 3D protein complex structures, computational docking has evolved as a valuable tool to predict 3D structures of biomolecular complexes.

Computational Design of Two-Dimensional Perovskites with Functional Organic Cations.

Two-dimensional (2D) halide perovskites are a class of materials in which 2D layers of perovskite are separated by large organic cations. Conventionally, the 2D perovskites incorporate organic cations as spacers, but these organic cations also offer a route to introduce specific functionality in the material. In this work, we demonstrate, by density functional theory calculations, that the introduction of electron withdrawing and electron donating molecules leads to the formation of localized states, either in the organic or the inorganic part.

Hot-electron transfer in quantum-dot heterojunction films.

Thermalization losses limit the photon-to-power conversion of solar cells at the high-energy side of the solar spectrum, as electrons quickly lose their energy relaxing to the band edge. Hot-electron transfer could reduce these losses. Here, we demonstrate fast and efficient hot-electron transfer between lead selenide and cadmium selenide quantum dots assembled in a quantum-dot heterojunction solid.

Signatures of Conformational Dynamics and Electrode-Molecule Interactions in the Conductance Profile During Pulling of Single-Molecule Junctions.

We demonstrate that conductance can act as a sensitive probe of conformational dynamics and electrode-molecule interactions during the equilibrium and nonequilibrium pulling of molecular junctions. To do so, we use a combination of classical molecular dynamics simulations and Landauer electron transport computations to investigate the conductance of a family of Au-alkanedithiol-Au junctions as they are mechanically elongated. The simulations show an overall decay of the conductance during pulling that is due to a decrease in the through-space electrode-molecule interactions, and that sensitivity depends on the electrode geometry.

Interconversion between Free Charges and Bound Excitons in 2D Hybrid Lead Halide Perovskites.

The optoelectronic properties of hybrid perovskites can be easily tailored by varying their components. Specifically, mixing the common short organic cation (methylammonium (MA)) with a larger one (e.g.

Temperature Dependent Charge Carrier Dynamics in Formamidinium Lead Iodide Perovskite.

The fundamental opto-electronic properties of organic-inorganic hybrid perovskites are strongly affected by their structural parameters. These parameters are particularly critical in formamidinium lead iodide (FAPbI), in which its large structural disorder leads to a non-perovskite yellow phase that hinders its photovoltaic performance. A clear understanding of how the structural parameters affect the opto-electronic properties is currently lacking.

Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life.

Few studies have analyzed the gut microbiota of child in unindustrialized countries, but none during the first month of life. Stool samples were collected from healthy newborns in hospitals of Gabon (n = 6) and Republic of the Congo (n = 9) at different time points during the first month of life: meconium, day 2 (D02), day 7 (D07) and day 28 (D28). In addition, one fecal sample was collected from each mother after delivery.

Design and Characterization of an Electrically Powered Single Molecule on Gold.

The surface diffusion of individual molecules is of paramount importance in self-assembly processes and catalytic processes. However, the fundamental understanding of molecule diffusion peculiarities considering conformations and adsorption sites remain poorly known at the atomic scale. Here, we probe the 4'-(4-tolyl)-2,2':6',2″-terpyridine adsorbed on the Au(111) herringbone structure combining scanning tunneling microscopy and atomic force microscopy.

Ga for Zn Cation Exchange Allows for Highly Luminescent and Photostable InZnP-Based Quantum Dots.

In this work, we demonstrate that a preferential Ga-for-Zn cation exchange is responsible for the increase in photoluminescence that is observed when gallium oleate is added to InZnP alloy QDs. By exposing InZnP QDs with varying Zn/In ratios to gallium oleate and monitoring their optical properties, composition, and size, we conclude that Ga preferentially replaces Zn, leading to the formation of InZnP/InGaP core/graded-shell QDs. This cation exchange reaction results in a large increase of the QD photoluminescence, but only for InZnP QDs with Zn/In ≥ 0.

VIM-1 carbapenemase-producing in gulls from southern France.

Acquired carbapenemases currently pose one of the most worrying public health threats related to antimicrobial resistance. A NDM-1-producing Corvallis was reported in 2013 in a wild raptor. Further research was needed to understand the role of wild birds in the transmission of bacteria resistant to carbapenems.

High Electronic Conductance through Double-Helix DNA Molecules with Fullerene Anchoring Groups.

Determining the mechanism of charge transport through native DNA remains a challenge as different factors such as measuring conditions, molecule conformations, and choice of technique can significantly affect the final results. In this contribution, we have used a new approach to measure current flowing through isolated double-stranded DNA molecules, using fullerene groups to anchor the DNA to a gold substrate. Measurements were performed at room temperature in an inert environment using a conductive AFM technique.

Mechanically controlled quantum interference in individual π-stacked dimers.

Recent observations of destructive quantum interference in single-molecule junctions confirm the role of quantum effects in the electronic conductance properties of molecular systems. These effects are central to a broad range of chemical and biological processes and may be beneficial for the design of single-molecule electronic components to exploit the intrinsic quantum effects that occur at the molecular scale. Here we show that destructive interference can be turned on or off within the same molecular system by mechanically controlling its conformation.