Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between Prevalent Flagellated Bacteria in Gut Microbiota and Cardiovascular Benefits in Humans

Background Increasing evidence has shown associations between gut microbiota and cardiovascular risks. However, whether sex influences the cardiovascular outcome of gut microbiota remains elusive. Methods The gut microbiota metagenomic data from two previous population-based cohorts and the proteomics data from human liver samples were analyzed. Results Through a sex-based analysis of 500 Functional Genomics Project (500FG) cohort, we found that the capacity of producing flagellin in Eubacterium rectale, Roseburia Intestinalis and Roseburia inulinivorans partially explained the levels of high-density lipoprotein-cholesterol (HDL-C) and apolipoprotein A1 in female participants. By comparing the bacterial species showing positive correlations with HDL-C and the flagellin species found in human liver samples, we found that E. rectale and R. inulinivorans appeared to be the major prevalent flagellated species in gut microbiota contributed to the host’s HDL-C level. The analysis of the Chinese-based cohort in which the male participants had relatively higher abundance of these two bacteria, the abovementioned positive correlation was also observed. Conclusions The flagellin-producing function of E. rectale and R. inulinivorans in the gut microbiota partially explained the HDL-C level in the host, and there is a sex-specific difference in the sensitivity of this beneficial interaction. Our findings suggest a potential interaction between commensal bacteria and the host that yields a cardiovascular benefit. Clinical Perspective What is new? The flagellin-producing capacity of certain species in gut microbiota is positively associated with the HDL-C and ApoA1 levels in human. By comparing the flagellated bacteria in the gut and flagellin species in the liver, Eubacterium rectale and Roseburia inulinivorans are shown to be the most prevalent species contributing to such cardiovascular benefits. The sensitivity of such beneficial interaction with the gut flagellated bacteria is different between male and female. What are the clinical implications? (maximum 100 words, formatted as 2-3 bullets) Beside the role in metabolic inflammation, gut microbiota can be beneficial against cardiovascular risk by modulating HDL-C level through certain flagellated species. The interaction between flagellated bacteria in the gut and the host provide a different insight in exploring potential therapeutic targets to increase HDL-C level.
Time optimal problems with boundary controls

We consider time optimal control problems governed by semilinear parabolic equations with pointwise state constraints and unbounded controls. We derive a Pontryagin’s principle for boundary controls. We prove a regularity result for the gradient of the state variable and by this way we are able to define a Hamiltonian functional which intervenes in an optimality condition satisfied by the optimal terminal time.
RELAMINARIZATION OF WALL TURBULENCE BY HIGH-PRESSURE RAMPS AT LOW REYNOLDS NUMBERS

Reverse transition from the turbulent towards the laminar flow regime was investigated experimentally by progressively increasing the pressure up to 400 MPa in a fully developed pipe flow operated with silicone oil as the working fluid. Using hot-wire anemometry, it is shown indirectly that at low Reynolds numbers a rapid increase in pressure modifies the turbulence dynamics owing to the processes which induce the effects caused by fluid compressibility in the region very close to the wall. The experimental results confirm that under such circumstances, the traditional mechanism responsible for self-maintenance of turbulence in wall-bounded flows is altered in such a way as to lead towards a state in which turbulence cannot persist any longer.
Asymptotic properties of the periodic orbits of the cat maps

The author studies the periodic orbits of the hyperbolic automorphisms of the unit 2-torus. These are also known as the cat maps, and may be viewed as completely chaotic Hamiltonian dynamical systems. Properties of the orbits of rational points with a given denominator g are considered. Combining results from the theory of numbers with methods from probability theory, he derives an explicit approximation to the distribution of the periods of those orbits which correspond to prime values of g. This result is then used to investigate the asymptotic behaviour of certain properties of the orbits in the limit as g to infinity .
Equity in the Turkish education system: A multilevel analysis of social background influences on the mathematics performance of 15-year-old students

This paper aims to discover the level of equity in the Turkish education system using maths outcomes of 15-year-old students in the Programme for International Student Assessment (PISA) exam. In order to do that, associations between various social background variables and student performance are analysed via multilevel models. Female pupils, students from lower socio-economic backgrounds and students from eastern regions are all found to be disadvantaged in terms of maths outcomes. The biggest gap between students in Turkey is due to school types. The difference between selective academic schools and other types of schools is more than 100 points, which is equal to the difference between almost four grade years. However, the positive effect of attending selective academic schools is smaller for girls. Further investigations indicate that, in the Turkish education system, school type at secondary level represents the effects of socio-economic background and educational and physical resources at school in addition to previous achievements of pupils. Results of the analyses show that it is very hard to claim that the education system in Turkey is operating in a way that mitigates existing inequalities in the society. To the contrary, there are indications that the Turkish education system itself reproduces inequalities.
Measurement of Atmospheric Turbulence by 2-μm Doppler Lidar

Abstract Two methods for the estimation of the turbulence energy dissipation rate (TEDR) from data measured by a 2-μm coherent Doppler lidar are described in this paper. Based on data measured at the Tarbes-Lourdes-Pyrenees International Airport in summer 2003, height profiles of TEDR have been retrieved. The results of TEDR estimation both from the Doppler spectrum width and from the velocity structure function are compared. Moreover, the experiment has been treated by numerical simulation and the theoretical results have been used for verification of the described methods.
Dissipativity analysis of memristive neural networks with time‐varying delays and randomly occurring uncertainties

Dissipativity theory is a very important concept in the field of control system. In this paper, we pay attention to the problem of dissipativity analysis of memristive neural networks with time‐varying delay and randomly occurring uncertainties(ROUs). Under the framework of Filippov solution, differential inclusion theory, by employing a proper Lyapunov functional, and some inequality techniques, the dissipativity criteria are obtained in terms of LMIs. It should be noteworthy that the uncertainty terms as well as the ROUs are separately taken into consideration, in which the uncertainties are norm‐bounded and the ROUs obey certain mutually uncorrelated Bernoulli‐distributed white noise sequences. Finally, the effectiveness of the proposed method will be verified via numerical example. Copyright © 2015 John Wiley & Sons, Ltd.
Observing Collectivities as Simplex Systems: The Combinatory Systems Approach

My paper aims to present a particular class of complex systems made up of collectivities of non- interconnected similar agents, acting on the basis of global information which they directly produce and update by the combination of their analogous micro behaviours, and that directs the subsequent micro behaviours as a result of a micro- macro feedback that produces self-organization in the agents' micro be- haviours. Due to their operative logic these systems can in general be called Combinatory Systems. I have provocatively defined the simplest class of them as Simplex Systems, since the similarity of the agents and the micro behaviours, the absence of direct interactions among the agents, and the simplicity of their structure and operative logic make these collectivities a particular simplified class of complex systems, as usually conceived. If we accept the traditional definition of self-or- ganization as the macro behaviour of a collectivity of agents in which the micro behaviours appear to be directed, or organized, by an Invisible Hand, or Supreme Authority, in order to produce the emerging phenome- non represented by the formation of ordered structures, or recognizable patterns, then it is easy to recognize the synergetic effect of a micro- macro feedback action (or circular causality) acting between the agents' micro behaviours and a global system's macro behaviour or effect.
Analysis and forecast impact of the main humidity observing systems

The global analysis and forecast impact of observed humidity has been assessed by means of observing system experiments with the ECMWF 4D‐Var data assimilation system. It is found that humidity data have a significant impact extending into the medium range (5–6 day forecasts), with a marked impact also on the wind and temperature fields. This contradicts some previous studies that have shown insignificant impact of humidity observations in general. The current, greater benefit of the humidity analysis may be due to improved model and data assimilation methods, and vastly increased availability of atmospheric moisture observations. The results show that each tested data type provides benefit to the analysis and forecast performance, which indicates that the humidity analysis is effective in extracting information from a wide variety of humidity observations. Data from the microwave sounding instruments (SSMI and AMSU‐B) dominate the humidity analysis over the sea, whereas radiosondes, surface stations (SYNOP) and AMSU‐B dominate over land. The infrared sounders (GOES, HIRS and AIRS) dominate in the upper troposphere, at 200–300 hPa.
Stochastic ODEs and PDEs for interacting multi-type populations

This thesis consists of the manuscripts of three research papers studying stochastic ODEs (ordinary differential equations) and PDEs (partial differential equations) that arise in biological models of interacting multi-type populations. In the first paper I prove uniqueness of the martingale problem for a degenerate SDE (stochastic differential equation) modelling a catalytic branching network. This work is an extension of a paper by Dawson and Perkins to arbitrary networks. The proof is based upon the semigroup perturbation method of Stroock and Varadhan. In the proof estimates on the corresponding semigroup are given in terms of weighted Hölder norms, which are equivalent to a semigroup norm in this generalized setting. An explicit representation of the semigroup is found and estimates using cluster decomposition techniques are derived. In the second paper I investigate the long-term behaviour of a special class of the SDEs considered above, involving catalytic branching and mutation between types. I analyse the behaviour of the overall sum of masses and the relative distribution of types in the limit using stochastic analysis. For the latter existence, uniqueness and convergence to a stationary distribution are proved by the reasoning of Dawson, Greven, den Hollander, Sun and Swart. One-dimensional diffusion theory allows for a complete analysis of the two-dimensional case. In the third paper I show that one can construct a sequence of rescaled perturbations of voter processes in d = 1 whose approximate densities are tight. This is an extension of the results of Mueller and Tribe for the voter model. We combine critical long-range and fixed kernel interactions in the perturbations. In the long-range case, the approximate densities converge to a continuous density solving a class of SPDEs (stochastic PDEs). For integrable initial conditions, weak uniqueness of the limiting SPDE is shown by a Girsanov theorem. A special case includes a class of stochastic spatial competing species models in mathematical ecology. Tightness is established via a Kolmogorov tightness criterion. Here, estimates on the moments of small increments for the approximate densities are derived via an approximate martingale problem and Green’s function representation.
The Eightfold Way to Dissipation: Classification of Hydrodynamic Transport

Hydrodynamics is the low-energy effective field theory of any interacting quantum theory, capturing the long-wavelength fluctuations of an equilibrium Gibbs density matrix. Conventionally, one views the effective dynamics in terms of the conserved currents, which should be expressed in terms of the fluid velocity and the intensive parameters such as the temperature and chemical potential. However, not all currents allowed by symmetry are physically acceptable; one has to ensure that the second law of thermodynamics is satisfied on all physical configurations. We provide a complete solution to hydrodynamic transport at all orders in the gradient expansion compatible with the second law constraint. The key new ingredient we introduce is the notion of adiabaticity, which allows us to take hydrodynamics off-shell. Adiabatic fluids are such that off-shell dynamics of the fluid compensates for entropy production. The space of adiabatic fluids admits a decomposition into seven distinct classes. Together with the dissipative class this establishes the eightfold way of hydrodynamic transport. Furthermore, recent results guarantee that dissipative terms beyond leading order in the gradient expansion are agnostic of the second law. After completing the transport taxonomy, we go on to argue for a new symmetry principle, an Abelian gauge invariance that guarantees adiabaticity in hydrodynamics and serves as the emergent version of microscopic KMS conditions. We demonstrate its utility by explicitly constructing effective actions for adiabatic transport (i.e., seven out of eight classes). The theory of adiabatic fluids, we speculate, provides a useful starting point for a new framework to describe non-equilibrium dynamics. We outline briefly the crucial role of the proposed symmetry of gauged thermal translations in the construction of a Schwinger-Keldysh effective action that encompasses all of hydrodynamic transport.
Free Will with Afterthoughts: A Quasichemical Model

A model of free will is proposed, appealing to the similarity with simple, two-body chemical reactions where the energy curves for the reagents and for the products cross. The system at the crossing point has a freedom of choice to perform the reaction or not. The Landau-Zener formula, corresponding to the opportunity of meeting twice the crossing point, is interpreted as free will with an afterthought and generalized to the cases when a subject thinks about a choice times. If the probability distribution of afterthoughts is known, the probability of a final yes decision is given. The results are generalized to situations where a preference for or against a change exists or where the freedom is only partial, has to fight with conditioning factors, and possibly decreases with increasing instances of free choice.
Radiative-Convective Equilibrium: Atmospheric Simulations in DALES

Using the Dutch Atmospheric Large-Eddy Simulation model (DALES) the atmosphere in both a pure radiative and a radiative-convective equilibrium is investigated. These simulations are performed on a domain which top is located at 30 kilometres. This high altitude requires some modifications of the radiative transfer code used in DALES. The effects of the imposed surface temperature on the resulting surface heat flux and evaporation, temperature profiles and cloud fields are investigated. The results of this thesis show that DALES can be well used to study equilibrium states of deep convective clouds, paving the way for future research.
A relativistic eikonal description of nucleon propagation through nuclei

The main focus of my PhD thesis is on exclusive proton-induced A(p,pN) reactions. A relativistic and cross-section factorized framework for computing quasielastic $A(p,pN)$ observables is presented. To model the propagation of the nucleons through the nuclear medium, the eikonal approximation is used. Our eikonal model is very flexible as it can be used either in conjunction with relativistic optical potentials (relativistic optical model eikonal approximation, ROMEA) or within its Glauber multiple-scattering extension (relativistic multiple-scattering Glauber approximation, RMSGA). The major difference between both approaches is that the ROMEA framework describes the initial- and final-state interactions (IFSI) in terms of a nucleon-nucleus picture, whereas the RMSGA framework is essentially a nucleon-nucleon model. At lower nucleon energies, the former is preferred; while the latter is more suitable at higher energies. The ROMEA formalism has been put to a stringent test by comparing the calculations with A(p,pN) cross-section data from a wide variety of experiments. A fair description of the data is obtained, thereby demonstrating that the ROMEA model can be applied in a wide energy range. The RMSGA approach has been used to account for the IFSI in the study of A(p,2p) nuclear transparencies at GeV energies. To explain the oscillatory energy dependence of the nuclear transparency data, the A(p,2p) formalism has been extended to incorporate the Ralston-Pire model for the pp scattering amplitude and the concepts of color transparency (CT) and nuclear filtering (NF). Introducing the concept of NF brings the calculations in qualitative agreement with the data. Furthermore, the calculations indicate that CT is imperative to increase the predictions to the level of the data. The quantitative description of the data, however, is far from perfect and a number of uncertainties involving the A(p,2p) transparency remain. Finally, we have studied the accuracy of the eikonal approximation at lower energies by developing an extension of the ROMEA model which accounts for second-order eikonal corrections. The calculations show that the effect of the second-order eikonal corrections on A(e,e'p) observables is rather limited for Q^2 >= 0.2 (GeV/c)^2.
Inhibition of miR-221-3p promotes axonal regeneration and repair of primary sensory neurons via regulating p27 expression

This study aimed to explore the key microRNA (miRNA) playing a vital role in axonal regeneration with a hostile microenvironment after spinal cord injury. Based on the theory that sciatic nerve conditioning injury (SNCI) could promote the repair of the injured dorsal column. Differentially expressed miRNAs were screened according to the microarray, revealing that 47 known miRNAs were differentially expressed after injury and perhaps involved in nerve regeneration. Among the 47 miRNAs, the expression of miR-221-3p decreased sharply in the SNCI group compared with the simple dorsal column lesion (SDCL) group. Subsequently, it was confirmed that p27 was the target gene of miR-221-3p from luciferase reporter assay. Further, we found that inhibition of miR-221-3p expression could specifically target p27 to upregulate the expression of growth-associated protein 43 (GAP-43), α-tubulin acetyltransferase (α-TAT1) together with α-tubulin, and advance the regeneration of dorsal root ganglion (DRG) neuronal axons. Chondroitin sulfate proteoglycans (CSPGs) are the main components of glial scar, which can hinder the extension and growth of damaged neuronal axons. After CSPGs were used in this study, the results demonstrated that restrained miR-221-3p expression also via p27 promoted the upregulation of GAP-43, α-TAT1, and α-tubulin and enhanced the axonal growth of DRG neurons. Hence, miR-221-3p could contribute significantly to the regeneration of DRG neurons by specifically regulating p27 in the p27/CDK2/GAP-43 and p27/α-TAT1/α-tubulin pathways even in the inhibitory environment with CSPGs.
Platelets and SARS-CoV-2 During COVID-19: Immunity, Thrombosis, and Beyond

COVID-19 is characterized by dysregulated thrombosis and coagulation that can increase mortality in patients. Platelets are fast responders to pathogen presence, alerting the surrounding immune cells and contributing to thrombosis and intravascular coagulation. The SARS-CoV-2 genome has been found in platelets from patients with COVID-19, and its coverage varies according to the method of detection, suggesting direct interaction of the virus with these cells. Antibodies against Spike and Nucleocapsid have confirmed this platelet-viral interaction. This review discusses the immune, prothrombotic, and procoagulant characteristics of platelets observed in patients with COVID-19. We outline the direct and indirect interaction of platelets with SARS-CoV-2, the contribution of the virus to programmed cell death pathway activation in platelets and the consequent extracellular vesicle release. We discuss platelet activation and immunothrombosis in patients with COVID-19, the effect of Spike on platelets, and possible activation of platelets by classical platelet activation triggers as well as contribution of platelets to complement activation. As COVID-19-mediated thrombosis and coagulation are still not well understood in vivo, we discuss available murine models and mouse adaptable strains.
On the cuspless sub-Riemannian geodesics in $\mathbb{R}\rtimes S^2$

We study the cuspless curves in three dimensional Euclidean space that minimize the energy functional {formula omitted} defined for each spatial arc-length parameterized curve with curvature ? and length (free) L=0. To compute the stationary curves, we took the Lagrangian approach used by Bryant and Grifiths for similar minimization problems. We have also shown that two other approaches, a direct variational method in R3 and the Hamiltonian approach using the Pontryagin's Maximum Principle (PMP) give the same ODE's for the stationary curves (that are locally minimizing due to PMP). We show that using the spatial arc-length parameterizations is advantageous in our case over the sub-Riemannian arc-length parameterization. The Bryant and Griffiths approach leads us to explicit formulas for the stationary curves. The formulas allow us to extract geometrical properties of the cuspless sub-Riemannian geodesics, such as planarity conditions and explicit bounds on the torsion. Moreover, they allow a study of the symmetries of the associated exponential map, and they allow to numerically solve both the initial and the boundary value problem, and to numerically compute the range of the exponential map. As a result, we characterize necessary conditions on the boundary conditions for which our optimization is well-posed.