SerpinA3N limits cartilage destruction in osteoarthritis by inhibiting macrophage-derived leucocyte elastase.

Objectives: Inflammatory mediators such as interleukin 6 (IL-6) are known to activate catabolic responses in chondrocytes during osteoarthritis (OA). This study aimed to investigate the role of a downstream target gene of IL-6, the serine protease inhibitor SerpinA3N, in the development of cartilage damage in OA.

Methods: RNA sequencing was performed in murine primary chondrocytes treated with IL-6, and identified target genes were confirmed in human and murine OA cartilage samples.

Direct Observation of Enhanced Electron-Phonon Coupling in Copper Nanoparticles in the Warm-Dense Matter Regime.

Warm dense matter (WDM) represents a highly excited state that lies at the intersection of solids, plasmas, and liquids and that cannot be described by equilibrium theories. The transient nature of this state when created in a laboratory, as well as the difficulties in probing the strongly coupled interactions between the electrons and the ions, make it challenging to develop a complete understanding of matter in this regime. In this work, by exciting isolated ∼8  nm copper nanoparticles with a femtosecond laser below the ablation threshold, we create uniformly excited WDM.

Analysis of Ancient Microbial DNA.

The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens.

Direct evaluation of the phase diagrams of dense multicomponent plasmas by integration of the Clapeyron equations.

Accurate phase diagrams of multicomponent plasmas are required for the modeling of dense stellar plasmas, such as those found in the cores of white dwarf stars and the crusts of neutron stars. Those phase diagrams have been computed using a variety of standard techniques, which suffer from physical and computational limitations. Here we present an efficient and accurate method that overcomes the drawbacks of previously used approaches.

Friction force in strongly magnetized plasmas.

A charged particle moving through a plasma experiences a friction force that commonly acts antiparallel to its velocity. It was recently predicted that in strongly magnetized plasmas, in which the plasma particle gyrofrequency exceeds the plasma frequency, the friction also includes a transverse component that is perpendicular to both the velocity and Lorentz force. Here, this prediction is confirmed using molecular-dynamics simulations, and it is shown that the relative magnitude of the transverse component increases with plasma coupling strength.

Nature of Non-Adiabatic Electron-Ion Forces in Liquid Metals.

An accurate description of electron-ion interactions in materials is crucial for our understanding of their equilibrium and nonequilibrium properties. Here we assess the properties of frictional forces experienced by ions in noncrystalline metallic systems, including liquid metals and warm dense plasmas, that arise from electronic excitations driven by the nuclear motion due to the presence of a continuum of low-lying electronic states. To this end, we perform detailed ab initio calculations of the full friction tensor that characterizes the set of friction forces.

Calculation of electron-ion temperature equilibration rates and friction coefficients in plasmas and liquid metals using quantum molecular dynamics.

We discuss a method to calculate with quantum molecular dynamics simulations the rate of energy exchanges between electrons and ions in two-temperature plasmas, liquid metals, and hot solids. Promising results from this method were recently reported for various materials and physical conditions [Simoni and Daligault, Phys. Rev.

Theory of the electron-ion temperature relaxation rate spanning the hot solid metals and plasma phases.

We present a theory for the rate of energy exchange between electrons and ions-also known as the electron-ion coupling factor-in physical systems ranging from hot solid metals to plasmas, including liquid metals and warm dense matter. The paper provides the theoretical foundations of a recent work [J. Simoni and J.

First-Principles Determination of Electron-Ion Couplings in the Warm Dense Matter Regime.

We present first-principles calculations of the rate of energy exchanges between electrons and ions in nonequilibrium warm dense plasmas, liquid metals, and hot solids, a fundamental property for which various models offer diverging predictions. To this end, a Kubo relation for the electron-ion coupling parameter is introduced, which includes self-consistently the quantum, thermal, nonlinear, and strong coupling effects that coexist in materials at the confluence of solids and plasmas. Most importantly, like other Kubo relations widely used for calculating electronic conductivities, the expression can be evaluated using quantum molecular dynamics simulations.

Transport regimes spanning magnetization-coupling phase space.

The manner in which transport properties vary over the entire parameter-space of coupling and magnetization strength is explored. Four regimes are identified based on the relative size of the gyroradius compared to other fundamental length scales: the collision mean free path, Debye length, distance of closest approach, and interparticle spacing. Molecular dynamics simulations of self-diffusion and temperature anisotropy relaxation spanning the parameter space are found to agree well with the predicted boundaries.

Crossover from Classical to Fermi Liquid Behavior in Dense Plasmas.

We explore the crossover from classical plasma to quantum Fermi liquid behavior of electrons in dense plasmas. To this end, we analyze the evolution with density and temperature of the momentum lifetime of a test electron introduced in a dense electron gas. This allows us (1) to determine the boundaries of the crossover region in the temperature-density plane and to shed light on the evolution of scattering properties across it, (2) to quantify the role of the fermionic nature of electrons on electronic collisions across the crossover region, and (3) to explain how the concept of the Coulomb logarithm emerges at a high enough temperature but disappears at a low enough temperature.

Effective potential theory for diffusion in binary ionic mixtures.

Self-diffusion and interdiffusion coefficients of binary ionic mixtures are evaluated using the effective potential theory (EPT), and the predictions are compared with the results of molecular dynamics simulations. We find that EPT agrees with molecular dynamics from weak coupling well into the strong-coupling regime, which is a similar range of coupling strengths as previously observed in comparisons with the one-component plasma. Within this range, typical relative errors of approximately 20% and worst-case relative errors of approximately 40% are observed.

A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa.

We present a cost-effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next-generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human- and/or climate-induced environmental changes.

Ionic Transport Coefficients of Dense Plasmas without Molecular Dynamics.

We present a theoretical model that allows a fast and accurate evaluation of ionic transport properties of realistic plasmas spanning from warm and dense to hot and dilute conditions, including mixtures. This is achieved by combining a recent kinetic theory based on effective interaction potentials with a model for the equilibrium radial density distribution based on an average atom model and the integral equations theory of fluids. The model should find broad use in applications where nonideal plasma conditions are traversed, including inertial confinement fusion, compact astrophysical objects, solar and extrasolar planets, and numerous present-day high energy density laboratory experiments.

Analysis of Ancient DNA in Microbial Ecology.

The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia.

Ionic and electronic transport properties in dense plasmas by orbital-free density functional theory.

We validate the application of our recent orbital-free density functional theory (DFT) approach [Phys. Rev. Lett.

A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites.

Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination.

Modified Enskog kinetic theory for strongly coupled plasmas.

Concepts underlying the Enskog kinetic theory of hard-spheres are applied to include short-range correlation effects in a model for transport coefficients of strongly coupled plasmas. The approach is based on an extension of the effective potential transport theory [S. D.

A novel platform based on immobilized histidine tagged olfactory receptors, for the amperometric detection of an odorant molecule characteristic of boar taint.

We report a dose-dependent detection of androstenone in solution, as one of the boar taint compounds, based on related OR7D4 olfactory receptors immobilized on a gold electrode through their 6-His tag and NTA-copper complex, as visualized through fluorescence microscopy. Square wave voltammetry (SWV) is for the first time, the method used to monitor the olfactory receptor/odorant recognition process. The relative variation of the Cu(I)-Cu(II) current peak increases linearly versus log (concentration of androstenone) from 10(-14)M to 10(-4)M, in buffer solution.

Pseudoatom molecular dynamics.

An approach to simulating warm and hot dense matter that combines density-functional-theory-based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The method, which we call pseudoatom molecular dynamics, can be applied to single-component or multicomponent plasmas. It gives equation of state and self-diffusion coefficients with an accuracy comparable to orbital-free molecular dynamics simulations but is computationally much more efficient.

Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes.

We develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state.

Integral equation model for warm and hot dense mixtures.

In a previous work [C. E. Starrett and D.

Determination of the shear viscosity of the one-component plasma.

The shear viscosity coefficient of the one-component plasma is calculated with unprecedented accuracy using equilibrium molecular dynamics simulations and the Green-Kubo relation. Numerical and statistical uncertainties and their mitigation for improving accuracy are analyzed. In the weakly coupled regime, our results agree with the Landau-Spitzer prediction.

Library construction for ancient genomics: single strand or double strand?

A novel method of library construction that takes advantage of a single-stranded DNA ligase has been recently described and used to generate high-resolution genomes from ancient DNA samples. While this method is effective and appears to recover a greater fraction of endogenous ancient material, there has been no direct comparison of results from different library construction methods on a diversity of ancient DNA samples. In addition, the single-stranded method is limited by high cost and lengthy preparation time and is restricted to the Illumina sequencing platform.

Effective potential theory for transport coefficients across coupling regimes.

A plasma transport theory that spans weak to strong coupling is developed from a binary collision picture, but where the interaction potential is taken to be an effective potential that includes correlation effects and screening self-consistently. This physically motivated approach provides a practical model for evaluating transport coefficients across coupling regimes. The theory is shown to compare well with classical molecular dynamics simulations of temperature relaxation in electron-ion plasmas as well as simulations and experiments of self-diffusion in one-component plasmas.