Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structure of Schizosaccharomyces pombe Rho1 Reveals Its Evolutionary Relationship with Other Rho GTPases

Simple Summary Rho family of proteins are involved in cytoskeletal organization, cell mobility and polarity, and are implicated in cancer morphogenesis. The structure and function of the Rho homologs from higher-level organisms are well studied, but not from the lower-level organisms. Such as over 95% of the known structures of Rho GTPases are from higher-order mammalian organisms, with only three structures of Rho homologs reported to date from lower-level, single-celled organisms. In this paper we report the crystal structure of Rho1 from Schizosaccharomyces pombe, also called fission yeast (SpRho1), in complex with GDP in the presence of Mg2+ at 2.63-Å resolution, to broaden our understanding of Rho homologs in lower-level organisms. Although the overall structure is similar to that of known Rho homologs, we observed subtle differences at the Switch I and II regions, in β2 and β3, and in the Rho insert domain and loop from Phe107 to Pro112. Combined with literature and sequence analyses, we suggest that the Switch regions and Rho insert domain may contribute to downstream kinase activation in different species through their interactions with different effectors and regulators; and the conservation and divergence of Rho GTPases among difference species and provide evolutionary insight for SpRho1. While many studies have reported the evolutionary development of Rho GTPases based on their amino acid sequences, the present study, for the first time, explores these evolutionary aspects based on structure. Our analysis indicates that SpRho is evolutionarily closer to HsRhoC than HsRhoA, as previously believed. Abstract The Rho protein, a homolog of Ras, is a member of the Ras superfamily of small GTPases. Rho family proteins are involved in cytoskeletal organization, cell mobility, and polarity, and are implicated in cancer morphogenesis. Although Rho homologs from higher-order mammalian organisms are well studied, there are few studies examining Rho proteins in lower-level single-celled organisms. Here, we report on the crystal structure of Rho1 from Schizosaccharomyces pombe (SpRho1) in complex with GDP in the presence of Mg2+ at a 2.78 Å resolution. The overall structure is similar to that of known Rho homologs, including human RhoA, human RhoC, and Aspergillus fumigatus Rho1 (AfRho1), with some exceptions. We observed subtle differences at the Switch I and II regions, in β2 and β3, and in the Rho insert domain and loop from Phe107 to Pro112. Our analysis suggests that SpRho is evolutionarily closer to HsRhoC than HsRhoA, as previously believed.
Entropic uncertainties for joint quantum measurements

We investigate the uncertainty associated with a joint quantum measurement of two spin components of a spin-$\frac{1}{2}$ particle and quantify this in terms of entropy. We consider two entropic quantities, the joint entropy and the sum of the marginal entropies, and obtain lower bounds for each of these quantities. For the case of joint measurements where we measure each spin observable equally well, these lower bounds are tight.
Relativistic orbits with gravitomagnetic corrections

Corrections to the relativistic orbits are studied considering higher order approximations induced by gravitomagnetic effects. We discuss in details how such corrections come out taking into account ‘magnetic’ components in the weak field limit of gravitational field and then the theory of orbits is developed starting from the Newtonian one, the lowest order in the approximation. Finally, the orbital structure and the stability conditions are discussed giving numerical examples. Beside the standard periastron corrections of General Relativity, a new nutation effect is due to the c−3 corrections. The transition to chaotic behavior strictly depends on the initial conditions. The orbital phase space portrait is discussed.
Biomimetic Hierarchical Nanocomposite Hydrogels: From Design to Biomedical Applications

Natural extracellular matrix (ECM) is highly heterogeneous and anisotropic due to the existence of biomacromolecule bundles and pores. Hydrogels have been proposed as ideal carriers for therapeutic cells and drugs in tissue engineering and regenerative medicine. However, most of the homogeneous and isotropic hydrogels cannot fully emulate the hierarchical properties of natural ECM, including the dynamically spatiotemporal distributions of biochemical and biomechanical signals. Biomimetic hierarchical nanocomposite hydrogels have emerged as potential candidates to better recapitulate natural ECM by introducing various nanostructures, such as nanoparticles, nanorods, and nanofibers. Moreover, the nanostructures in nanocomposite hydrogels can be engineered as stimuli-responsive actuators to realize the desirable control of hydrogel properties, thereby manipulating the behaviors of the encapsulated cells upon appropriate external stimuli. In this review, we present a comprehensive summary of the main strategies to construct biomimetic hierarchical nanocomposite hydrogels with an emphasis on the rational design of local hydrogel properties and their stimuli-responsibility. We then highlight cell fate decisions in engineered nanocomposite niches and their recent development and challenges in biomedical applications.
Timing and spectral studies of the transient X-ray pulsar GX 304−1 during an outburst

We present the timing and spectral properties of the transient X-ray pulsar GX 304−1 during its recent outburst in 2010 August, using observations carried out with the Proportional Counter Array (PCA) instrument on board the Rossi X-ray Timing Explorer (RXTE) satellite. We detected strong intensity- and energy-dependent variations in the pulse profiles during the outburst. The pulse profile showed significant evolution over the outburst. It showed complex structures consisting of a main peak with steps on both sides during the start of the outburst. On some days, a sharp dip-like feature was seen which disappeared at the end of the outburst when the profile evolved into a sinusoidal shape. At low energies, the pulse profiles appeared complex, consisting of multiple peaks and a narrow minimum. The amplitude of the second brightest peak in low energies decreased with energy, and above 12 keV the shape of the pulse profile changed to a single broad peak with a dip-like feature. The dip had energy dependence, both in phase and in width. We detected quasi-periodic oscillations (QPOs) at 0.125 Hz with a harmonic. The QPO feature had a low rms value of 2.9 per cent and it showed a positive energy dependence up to 40 keV with the rms value increasing to 9 per cent at 40 keV. The QPO frequency decreased from 0.128 to 0.108 Hz in 12 days. During most of the outburst, the 3–30 keV spectrum of GX 304−1 can be well fitted with a partial covering power-law model with a high-energy cut-off and iron fluorescent line emission. For a few of the observations carried out during the decay of the outburst, the partial covering absorption component is found to change to single-component absorption. We also found that the partial covering and high-energy cut-off parameters vary significantly with the pulse phase.
Metastable clusters and channels formed by active particles with aligning interactions

We introduce a novel model for active particles with short-range position-dependent aligning interactions and study their behaviour in crowded environments using numerical simulations. When only active particles are present, we observe a transition from a gaseous state to the emergence of metastable clusters as the level of orientational noise is reduced. When passive particles are also present, we observe the emergence of a network of metastable channels.
The Impact of Selected Film Productions on the Development of Film Tourism and the Tourism Attractiveness of the Region

This paper examines how a Polish television drama series Father Matthew is used for promoting the town of Sandomierz and its vicinity. It aims to identify the tourism values presented in the film production and to describe promotional activities related to film tourism based on the results of surveys. The empirical part presents the results of surveys conducted in 2022 investigating the respondents’ interest in film and its effect on travelling for tourism. It was established which cultural and natural values were used to promote the town by exhibiting them in the TV drama series. Reference was made to the quantity and nature of information directly regarding the plot of Father Matthew published by national and regional media in Poland. It was demonstrated that the indicated film production is the main form of the town’s promotion – used for building a complete tourism product. It enhances the town’s attractiveness and recognisability and increases the use of its tourism facilities – thus stimulating the development of film tourism.
Behavior of a vacuum and naked singularity under a smooth gauge function in Lyra geometry

Lyra geometry is a conformal geometry that originated from Weyl geometry. In this article, we derive the exterior field equation under a spherically symmetric gauge function x0(r) and metric in Lyra geometry. When we impose a specific form of the gauge function x0(r), the radial differential equation of the metric component g00 will possess an irregular singular point (ISP) at r = 0. Moreover, we can apply the method of dominant balance to get the asymptotic behavior of the new space–time solution. The significance of this work is that we can use a series of smooth gauge functions x0(r) to modulate the degree of divergence of the singularity at r = 0, which will become a naked singularity under certain conditions. Furthermore, we investigate the physical meaning of this novel behavior of space–time in Lyra geometry and find out that no spaceship with finite integrated acceleration can arrive at this singularity at r = 0. The physical meaning of the gauge function and integrability is also discussed.
Sfermion loop contribution to the two-loop level fermion electric dipole moment in R-parity violating supersymmetric models

The supersymmetric extension of the standard model is one of the favored candidates of new physics. It has many advantages which resolve theoretical and observational problems of the standard model (SM), and has been exhaustively studied over decades [1]. The supersymmetric SM allows also baryon number or lepton number violating interactions, known as the R-parity violating (RPV) interactions. The RPV effects have also been constrained from the analysis of various phenomena [2]. In searching for new physics beyond the SM, the electric dipole moment (EDM) plays a very important role. The EDM is an observable sensitive to the P and CP violations of the underlying theory, and provides excellent information about the new physics for many reasons. First, it can be measured in many systems and many accurate experimental data are available [3]. Second, it has a very small SM contribution [4], so that any observation of finite EDM will be a direct indication of new physics. Finally, the EDM is sensitive to many new physics, in particular the supersymmetry, and many supersymmetric models with [5–8] and without [9–16] the conservation of R-parity have been studied. In the RPV supersymmetric model with trilinear RPV interactions, it has been found that the fermion (quark or lepton) EDM does not receive any one-loop level contribution [10], and the two-loop level contribution has been analyzed in detail to give the Barr-Zee type diagram [17] with fermion loops as the leading contribution [12, 15]. In previous works however, Barr-Zee type process with sfermion loops has not been considered so far, although it involves the same set of coupling constants. In this paper we will evaluate the Barr-Zee type diagrams with sfermion loop generated by RPV interactions to clarify the relative size between the currently known fermion loop contribution. It is actually found that the sfermion loop effect acts destructively to the fermion loop one, and that it can be significant in some situation. The RPV interactions are generated by the following superpotential:
Spin measurement using cycling transitions of a two-electron quantum dot molecule

Two-electron charged self-assembled quantum dot molecules exhibit a decoherence-avoiding singlet-triplet qubit subspace and an efficient spin-photon interface. Here, we demonstrate that the cycling transitions originating from auxiliary ground states in the same system allow for an efficient optical read-out of a singlet-triplet qubit. By implementing a spin-selective state transfer to the auxiliary state using a resonant laser field, we observe an improvement approaching two orders of magnitude in fidelity as compared to spin measurement by light scattering directly from the qubit states. Embedding the quantum dot molecule inside a low quality-factor micro-cavity structure should enable single-shot qubit read-out.
Maximum entropy states of collisionless systems with long-range interaction and different degrees of mixing

Dynamics of many-particle systems with long-range interaction is collisionless and governed by the Vlasov equation. This dynamics is a flow of a six-dimensional incompressible liquid with uncountable integrals of motion. If the flow possesses the statistical property of mixing, each liquid element spreads over the entire accessible space. I derive the equilibrium microcanonical maximum entropy states of this liquid for different degrees of mixing $M$. This $M$ is the number of liquid elements which are statistically independent. To count microstates of a liquid, I develop analog of the discrete combinatorics for continuous systems by introducing the ensemble of phase subspaces and making contact with the Shannon-McMillan-Breiman theorem from the ergodic theory. If $M$ is much larger than the total number of particles $N$, then the equilibrium distribution function (DF) is found to be exactly of the Fermi-Dirac form. If the system is ergodic but without mixing, $M=0$, the DF is a formal expression which coincides with the famous DF obtained by Lynden-Bell. If the mixing is incomplete and $M\sim N$, the exponentials, which are present in Lynden-Bell's DF, appear with certain weight given by the entropy of mixing. For certainty, the \ long-range interaction is taken in the form of the Newton and Coulomb potential in three dimensional space, but the applicability of the method developed in the paper is not restricted to this case. The analogy of the obtained statistics to the Fermi-Dirac statistics allows for expressing the entropy of the system via its total energy and chemical potentials of liquid's elements. The effect of the long-range interaction to the basic thermodynamic relations is demonstrated.
Toward an artificial Mott insulator: Correlations in confined high-density electron liquids in SrTiO3

We investigate correlation physics in high-density, two-dimensional electron liquids that reside in narrow SrTiO3 quantum wells. The quantum wells are remotely doped via an interfacial polar discontinuity and the three-dimensional (3D) carrier density is modulated by changing the width of the quantum well. It is shown that even at 3D densities well below one electron per site, short-range Coulomb interactions become apparent in transport, and an insulating state emerges at a critical density. We also discuss the role of disorder in the insulating state.
MAGiiCAT VI. The Mg ii Intragroup Medium Is Kinematically Complex

By comparing Mg ii absorption in the circumgalactic medium (CGM) of group environments to isolated galaxies, we investigated the impact of environment on the CGM. An Mg ii absorber is associated with a group if there are two or more galaxies at the absorption redshift within a projected distance of D = 200 kpc from a background quasar and a line-of-sight velocity separation of 500 km s−1. We compiled a sample of 29 group environments consisting of 74 galaxies (two to five galaxies per group) at . The group absorber median equivalent width ( Å) and covering fraction ( ) are larger than isolated absorbers (1.27σ and 2.2σ, respectively), but median column densities are statistically consistent. A pixel-velocity two-point correlation function analysis shows that group environment kinematics are statistically comparable to isolated environments (0.8σ), but with more power for high velocity dispersions similar to outflow kinematics. Group absorbers display more optical depth at larger velocities. A superposition model in which multiple galaxies contribute to the observed gas matches larger equivalent width group absorbers but significantly overpredicts the kinematics owing to large velocity separations between member galaxies. Finally, galaxy–galaxy groups (similar member galaxy luminosities) may have larger absorber median equivalent widths (1.7σ) and velocity dispersions (2.5σ) than galaxy–dwarf groups (disparate luminosities). We suggest that the observed gas is coupled to the group rather than individual galaxies, forming an intragroup medium. Gas may be deposited into this medium by multiple galaxies via outflowing winds undergoing an intergalactic transfer between member galaxies or from tidal stripping of interacting members.
GALEX ULTRAVIOLET IMAGING OF DWARF GALAXIES AND STAR FORMATION RATES

We present ultraviolet-integrated and azimuthally averaged surface photometric properties of a sample of 44 dwarf irregular (dIm), blue compact dwarf, and Sm galaxies measured from archival near-ultraviolet (NUV) and far-ultraviolet (FUV) images obtained with the Galaxy Evolution Explorer (GALEX). We compare the UV to Hα and V-band properties and convert FUV, Hα, and V-band luminosities into star formation rates (SFRs). We also model the star formation history from colors and compare the integrated SFRs and SFR profiles with radius for these methods. In most galaxies, the UV photometry extends beyond Hα in radius, providing a better measure of the star formation activity in the outer disks. The Hα appears to be lacking in the outer disk because of faintness in low-density gas. The FUV and V-band profiles are continuous with radius, although they sometimes have a kink from a double exponential disk. There is no obvious difference in star formation properties between the inner and outer disks. No disk edges have been observed, even to stellar surface densities as low as 0.1 M☉ pc−2 and SFRs as low as 10−4 M☉ yr−1 kpc−2. Galaxies with low H i to luminosity ratios have relatively low FUV compared to V-band emission in the outer parts, suggesting a cessation of star formation there. Galaxies with relatively high H i apparently have fluctuating star formation with a gigayear timescale.
A NEW JEANS RESOLUTION CRITERION FOR (M)HD SIMULATIONS OF SELF-GRAVITATING GAS: APPLICATION TO MAGNETIC FIELD AMPLIFICATION BY GRAVITY-DRIVEN TURBULENCE

Cosmic structure formation is characterized by the complex interplay between gravity, turbulence, and magnetic fields. The processes by which gravitational energy is converted into turbulent and magnetic energies, however, remain poorly understood. Here, we show with high-resolution, adaptive-mesh simulations that MHD turbulence is efficiently driven by extracting energy from the gravitational potential during the collapse of a dense gas cloud. Compressible motions generated during the contraction are converted into solenoidal, turbulent motions, leading to a natural energy ratio of Esol/Etot ≈ 2/3. We find that the energy injection scale of gravity-driven turbulence is close to the local Jeans scale. If small seeds of the magnetic field are present, they are amplified exponentially fast via the small-scale dynamo process. The magnetic field grows most efficiently on the smallest scales, for which the stretching, twisting, and folding of field lines, and the turbulent vortices are sufficiently resolved. We find that this scale corresponds to about 30 grid cells in the simulations. We thus suggest a new minimum resolution criterion of 30 cells per Jeans length in (magneto)hydrodynamical simulations of self-gravitating gas, in order to resolve turbulence on the Jeans scale, and to capture minimum dynamo amplification of the magnetic field. Due to numerical diffusion, however, any existing simulation today can at best provide lower limits on the physical growth rates. We conclude that a small, initial magnetic field can grow to dynamically important strength on timescales significantly shorter than the free-fall time of the cloud.
Human Dose Assessment of 68Ga-NODAGA-RGD-BBN Heterodimer Peptide based on Animal Data

Aims: Calculation of the absorbed dose in human organs is one of the first steps for developing new radiopharmaceuticals. The aim of this study is to estimate the human absorbed dose of a newly developed 68Ga-NODAGA-RGD-BBN radiolabeled compound. Materials and Methods: 68Ga-NODAGA-RGD-BBN was prepared by varying different parameters at optimized conditions. The stability of the radiolabeled peptide in phosphate-buffered saline (PBS) and in human serum was evaluated for 120 min. Afterward, the biodistribution of the complex was assessed in normal and tumor-bearing mice, at least for 120 min postinjection. Finally, the human absorbed dose of 68Ga-NODAGA-RGD-BBN was estimated based on mice data using Radiation Dose Assessment Resource and Spark method. Results: 68Ga-NODAGA-RGD-BBN was produced with radiochemical purity of more than 98% (high-performance liquid chromatography/ radio thin layer chromatography (RTLC)) with high stability in PBS buffer and in human serum at least for 2 h. The complex demonstrated high uptake in gastrin-releasing peptide receptor-expressing tumors compared to other nontarget organs. Furthermore, the dose assessment for the complex showed that the kidneys receive the highest absorbed dose in comparison with other organs. Conclusion: The result of this study showed that 68Ga-NODAGA-RGD-BBN is an effective and radiolabeled ligand for tumor detection, however more studies are still needed.
Stable contraction in Brans-Dicke cosmology

Contracting Universe (including bouncing models) solution generally depends on the initial conditions and hence possesses an extreme fine-tuning problem. In order to probe the stability of those solutions, in this work, we consider the Brans-Dicke theory with the power law potential in the presence of an additional barotropic matter in the homogeneous and isotropic background. We study the phase space and obtain critical points. We find that the quadratic potential is a special case where one of the solutions always gives rise to de-Sitter solution in all conformally connected frame. We generalize the condition for arbitrary power law potential and find that contracting Universe solution can indeed lead to an attractor solution. In doing so, we also provide an example of a matter contracting Universe that leads to near scale-invariant spectra and study the behavior near the fixed point. In the vicinity of this point, the system behaves as the Universe contains three different types of matter. Amongst them, with time, energy densities of two effective fluids decay down and only the leading order solution survives. Therefore, the non-minimal coupling can address and solve the problem of fine-tuning of the contraction models and may open a different outlook.