Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.

Multiple Sclerosis and Serotonin: Potential Therapeutic Applications.

Multiple sclerosis (MS) is a neurodegenerative disease with a complex autoimmune component, and it has a high prevalence among middle-aged females. The manifestations of the disease range from episodic somatosensory dysfunction to progressive and permanent central nervous system (CNS) damage. Due to a high prevalence of psychiatric comorbidities and proven abnormalities in serotonin (5-HT) levels among MS patients, they are usually on drugs that modify the serotonergic system. Through a comprehensive literature review of studies published in the last 10 years related to 5-HT in MS and its therapeutic applications, we aimed to elucidate the mechanism behind the neurotransmitter (NT) levels' abnormalities. Most importantly, we endeavored to gather the most up-to-date information about the full therapeutic potential of agents acting on this system. We discovered that multiple processes cause low levels of 5-HT in MS patients. The varying levels of the availability of the 5-HT transporter (SERT) in the CNS decreasing overall tryptophan (TRP) levels, and diversion of the amino acid away from its synthetic pathway constitute some of those. Studies in animals have shown that 5-HT levels' elevations could cause immune-modulating effects and could probably slow down the disease progression rate. Human studies have shown a more diverse and complex response. Promising results have been obtained in the last 10 years regarding 5-HT's immune-modulatory role in MS patients and its therapeutic applications. Human studies with a larger population and feasible designs are still needed to fully ascertain the effects of serotonin on the immune system and disease progression in patients with MS.

Statins Versus Proprotein Convertase Subtilisin/Kexin Type 9 Inhibitors- Are We Doing Better? A Systematic Review on Treatment Disparity.

Coronary artery disease (CAD) is a significant contributor to mortality in America. A common risk factor of CAD is hyperlipidemia. Treatment guidelines of hyperlipidemia are well established. Statins are the cornerstone of treating hyperlipidemia. New medications such as proprotein convertase subtilisin/kexin type 9 inhibitors (PCSK9 inhibitors) have also illustrated significant results in treating hyperlipidemia. While multiple studies exemplify the disparities in statin and PCSK9 inhibitors utilization to reduce CAD mortality and risk factors, there are no systematic reviews to validate these disparities. We conducted a search on PubMed, including Medline and PubMed Central, and Google Scholar. For this analysis, we selected articles published between 2000 and 2020 and those that fit the inclusion and exclusion criteria. Based on the type of study, we performed appropriate quality assessments and deleted studies with a score of less than seven or with a high risk of biases. The search strategy resulted in 322 studies. After inclusion and exclusion criteria were applied, we included 20 articles in the analysis of this review. This systematic review demonstrates that non-white races and women were less likely to receive the correct, clinically indicated, therapy for hyperlipidemia. A multi-faceted approach is required to solve this inequality in healthcare.

Equation of state of warm dense deuterium and its isotopes from density-functional theory molecular dynamics.

Of the two approaches of density-functional theory molecular dynamics, quantum molecular dynamics is limited at high temperature by computational cost whereas orbital-free molecular dynamics, based on an approximation of the kinetic electronic free energy, can be implemented in this domain. In the case of deuterium, it is shown how orbital-free molecular dynamics can be regarded as the limit of quantum molecular dynamics at high temperature for the calculation of the equation of state. To this end, accurate quantum molecular dynamics calculations are performed up to 20 eV at mass densities as low as 0.5g/cm^{3} and up to 10 eV at mass densities as low as 0.2g/cm^{3}. As a result, the limitation in temperature so far attributed to quantum molecular dynamics is overcome and an approach combining quantum and orbital-free molecular dynamics is used to construct an equation of state of deuterium. The thermodynamic domain addressed is that of the fluid phase above 1 eV and 0.2g/cm^{3}. Both pressure and internal energy are calculated as functions of temperature and mass density, and various exchange-correlation contributions are compared. The generalized gradient approximation of the exchange-correlation functional, corrected to approximately include the influence of temperature, is retained and the results obtained are compared to other approaches and to experimental shock data; in parts of the thermodynamic domain addressed, these results significantly differ from those obtained in other first-principles investigations which themselves disagree. The equations of state of hydrogen and tritium above 1 eV and above, respectively, 0.1g/cm^{3} and 0.3g/cm^{3}, can be simply obtained by mass density scaling from the results found for deuterium. This ab initio approach allows one to consistently cover a very large domain of temperature on the domain of mass density outlined above.

Equation of state of a dense plasma by orbital-free and quantum molecular dynamics: examination of two isothermal-isobaric mixing rules.

We test two isothermal-isobaric mixing rules, respectively based on excess-pressure and total-pressure equilibration, applied to the equation of state of a dense plasma. While the equation of state is generally known for pure species, that of arbitrary mixtures is not available so that the validation of accurate mixing rules, that implies resorting to first-principles simulations, is very useful. Here we consider the case of a plastic with composition C(2)H(3) and we implement two complementary ab initio approaches adapted to the dense plasma domain: quantum molecular dynamics, limited to low temperature by its computational cost, and orbital-free molecular dynamics, that can be implemented at high temperature. The temperature and density range considered is 1-10 eV and 0.6-10 g/cm(3) for quantum molecular dynamics, and 5-1000 eV and 1-10 g/cm(3) for orbital-free molecular dynamics. Simulations for the full C(2)H(3) mixture are the benchmark against which to assess the mixing rules, and both pressure and internal energy are compared. We find that the mixing rule based on excess-pressure equilibration is overall more accurate than that based on total-pressure equilibration; except for quantum molecular dynamics and a thermodynamic domain characterized by very low or negative excess pressures, it gives pressures which are generally within statistical error or within 1% of the exact ones. Besides, its superiority is amplified in the calculation of a principal Hugoniot.

Numerical convergence of the self-diffusion coefficient and viscosity obtained with Thomas-Fermi-Dirac molecular dynamics.

Computations of the self-diffusion coefficient and viscosity in warm dense matter are presented with an emphasis on obtaining numerical convergence and a careful evaluation of the standard deviation. The transport coefficients are computed with the Green-Kubo relation and orbital-free molecular dynamics at the Thomas-Fermi-Dirac level. The numerical parameters are varied until the Green-Kubo integral is equal to a constant in the t→+∞ limit; the transport coefficients are deduced from this constant and not by extrapolation of the Green-Kubo integral. The latter method, which gives rise to an unknown error, is tested for the computation of viscosity; it appears that it should be used with caution. In the large domain of coupling constant considered, both the self-diffusion coefficient and viscosity turn out to be well approximated by simple analytical laws using a single effective atomic number calculated in the average-atom model.

Orbital-free molecular dynamics simulations of a warm dense mixture: examination of the excess-pressure matching rule.

A form of the linear mixing rule involving the equality of excess pressures is tested with various mole fractions and various types of orbital-free molecular dynamics simulations. For all the cases considered, this mixing rule yields, within statistical error, the pressure of a mixture of helium and iron obtained by a direct simulation. In an attempt to interpret the robustness of the mixing rule, we show that it can be derived from thermodynamic stability if the system is regarded as a mixture of independent effective average atoms. The success of the mixing rule applied with equations of state including various degrees of approximation leads us to suggest its use in the thermodynamic domain where quantum molecular dynamics can be implemented.

Direct verification of mixing rules in the hot and dense regime.

We perform orbital-free molecular dynamics simulations in the hot and dense regime for two mixtures: equimolar helium-iron and asymmetric deuterium-copper plasmas. For thermodynamic properties, we test two isobaric-isothermal mixing rules whose definitions involve either the equality of total pressures or the equality of the so-defined excess pressures of the components; the pressure and internal energy obtained by direct simulations are in very good agreement with those given by the mixing rule involving the equality of excess pressures. The viscosity of the deuterium-copper mixture is also extracted from a direct simulation and compared to the result given by a mixing rule applied to the viscosities of the pure elements. Finally, for structural properties, the effective charges given by the isobaric-isothermal mixing rule for the average atom model, used in the binary ionic mixture model, yield partial pair distribution functions in good agreement with those obtained by a direct simulation.