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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. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive high-throughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour-intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology. [ABSTRACT FROM AUTHOR]

The effective potential theory is a physically motivated method for extending traditional plasma transport theories to stronger coupling. It is practical in the sense that it is easily incorporated within the framework of the Chapman-Enskog or Grad methods that are commonly applied in plasma physics and it is computationally efficient to evaluate. The extension is to treat binary scatterers as interacting through the potential of mean force, rather than the bare Coulomb or Debye-screened Coulomb potential. This allows for aspects of many-body correlations to be included in the transport coefficients. Recent work has shown that this method accurately extends plasma theory to orders of magnitude stronger coupling when applied to the classical one-component plasma model. The present work shows that similar accuracy is realized for the Yukawa one-component plasma model and it provides a comparison with other approaches. (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [ABSTRACT FROM AUTHOR]

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. Male cartilage-specific Serpina3n -deficient mice and control mice underwent meniscectomy (MNX) or sham surgery at 10 weeks of age. Intra-articular injections of SerpinA3N or sivelestat (an inhibitor of leucocyte elastase (LE), a substrate for SerpinA3N) were performed in wild-type mice after MNX. Joint damage was assessed 3-9 weeks after surgery by histology and micro-CT. The effect of sivelestat was assessed in cartilage explants exposed to macrophage-derived conditioned media., Results: RNA sequencing revealed that SerpinA3N is a major target gene of IL-6 in chondrocytes. The expression of SerpinA3N is increased in OA cartilage. Conditional loss of SerpinA3N in chondrocytes aggravated OA in mice, while intra-articular injection of SerpinA3N limited joint damage. Chondrocytes did not produce serine proteases targeted by SerpinA3N. By contrast, macrophages produced LE on IL-6 stimulation. Sivelestat limited the cartilage catabolism induced by conditioned media derived from IL-6-stimulated macrophages. Additionally, an intra-articular injection of sivelestat is protected against OA in the MNX model., Conclusions: SerpinA3N protects cartilage against catabolic factors produced by macrophages, including LE. SerpinA3N and LE represent new therapeutic targets to dampen cartilage damage in OA., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ on behalf of EULAR.)

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. Using photoelectron spectroscopy, we measure the instantaneous electron temperature and extract the electron-ion coupling of the nanoparticle as it undergoes a solid-to-WDM phase transition. By comparing with state-of-the-art theories, we confirm that the superheated nanoparticles lie at the boundary between hot solids and plasmas, with associated strong electron-ion coupling. This is evidenced both by a fast energy loss of electrons to ions, and a strong modulation of the electron temperature induced by strong acoustic breathing modes that change the nanoparticle volume. This work demonstrates a new route for experimental exploration of the exotic properties of WDM.

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. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

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. In particular, finite-size effects are avoided as each phase is calculated separately; the plasma electrons and volume changes are explicitly taken into account; and arbitrary analytic fits to simulation data as well as particle insertions are avoided. Furthermore, no simulations at "uninteresting" state conditions, i.e., away from the phase coexistence curves, are required, which improves the efficiency of the technique. The method consists of an adaptation of the so-called Gibbs-Duhem integration approach to electron-ion plasmas, where the coexistence curve is determined by direct numerical integration of its underlying Clapeyron equation. The thermodynamics properties of the coexisting phases are evaluated separately using Monte Carlo simulations in the isobaric semigrand canonical ensemble (NPTΔμ). We describe this Monte Carlo-based Clapeyron integration method, including its basic physical and numerical principles, our extension to electron-ion plasmas, and our numerical implementation. We illustrate its applicability and benefits with the calculation of the melting curve of dense carbon-oxygen plasmas under conditions relevant for the cores of white dwarf stars and provide analytic fits to implement this new melting curve in white dwarf models. While this work focuses on the liquid-solid phase boundary of dense two-component plasmas, a wider range of physical systems and phase boundaries are within the scope of the Clapeyron integration method, which had until now only been applied to simple model systems of neutral particles.

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. The non-adiabatic electron-ion interactions introduce hydrodynamic couplings between the ionic degrees of freedom, which are sizable between nearest neighbors. The friction tensor is generally inhomogeneous, anisotropic, and nondiagonal, especially at lower densities.

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. This result influences single-particle motion and macroscopic transport in strongly magnetized plasmas found in a broad range of applications.

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. Lett. 122, 205001 (2019)PRLTAO0031-900710.1103/PhysRevLett.122.205001]. Like other ab initio calculations, the approach offers a very useful comparison with the experimental measurements and permits an extension into conditions not covered by the experiments. The energy relaxation rate is related to the friction coefficients felt by individual ions due to their nonadiabatic interactions with electrons. Each coefficient satisfies a Kubo relation given by the time integral of the autocorrelation function of the interaction force between an ion and the electrons. These Kubo relations are evaluated using the output of quantum molecular dynamics calculations in which electrons are treated in the framework of finite-temperature density functional theory. The calculation presents difficulties that are unlike those encountered with the Kubo formulas for the electrical and thermal conductivities. In particular, the widely used Kubo-Greenwood approximation is inapplicable here. Indeed, the friction coefficients and the energy relaxation rate diverge in this approximation since it does not properly account for the electronic screening of electron-ion interactions. The inclusion of screening effects considerably complicates the calculations. We discuss the physically motivated approximations we applied to deal with these complications in order to investigate a widest range of materials and physical conditions. Unlike the standard method used for the electronic conductivities, the Kubo formulas are evaluated directly in the time domain and not in the energy domain, which spares one from needing to introduce an extraneous undetermined numerical parameter to account for the discrete character of the numerical density of states. We highlight interesting properties of the energy relaxation rate not shared by other electronic properties, in particular its self-averaging character. We then present a detailed parametric and convergence study with the numerical parameters, including the system size, the number of bands and k points, and the physical approximations for the dielectric function and the exchange-correlation energy.

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. Daligault, Phys. Rev. Lett. 122, 205001 (2019)PRLTAO0031-900710.1103/PhysRevLett.122.205001], where first-principles quantum molecular dynamics calculations based on this theory were presented for representative materials and conditions. We first derive a general expression for the electron-ion coupling factor that includes self-consistently the quantum mechanical and statistical nature of electrons, the thermal and disorder effects, and the correlations between particles. The electron-ion coupling is related to the friction coefficients felt by individual ions due to their nonadiabatic interactions with the electrons. Each coefficient satisfies a Kubo relation given by the time integral of the autocorrelation function of the interaction force of an ion with the electrons. Exact properties and different representations of the general expressions are discussed. We then show that our theory reduces to well-known models in limiting cases. In particular, we show that it simplifies to the standard electron-phonon coupling formula in the limit of hot solids with lattice and electronic temperatures much greater than the Debye temperature, and that it extends the electron-phonon coupling formula beyond the harmonic phonon approximation. For plasmas, we show that the theory readily reduces to the well-known Spitzer formula in the hot plasma limit, to the Fermi "golden rule" formula in the limit of weak electron-ion interactions, and to other models proposed to go beyond the latter approximation. We explain that the electron-ion coupling is particularly well adapted to average atom models, which offer an effective way to include nonideal interaction effects to the standard models and at a much reduced computational cost in comparison to first-principles quantum molecular dynamics simulations.

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. Results are presented and compared to experimental and theoretical predictions for representative materials of various electronic complexity, including aluminum, copper, iron, and nickel.

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. Comparison with existing theories reveals regimes where they succeed, where they fail, and where no theory has yet been developed.

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.

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. We also examine the Darken model, which approximates the interdiffusion coefficients based on the self-diffusion coefficients.

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.

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. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.