Miracle-dz/UniFAR-FTUs huggingface dataset:
Self-similar and disordered front propagation in a radial Hele-Shaw channel with time-varying cell depth

The displacement of a viscous fluid by an air bubble in the narrow gap between two parallel plates can readily drive complex interfacial pattern formation known as viscous fingering. We focus on a modified system suggested recently by [1], in which the onset of the fingering instability is delayed by introducing a time-dependent (power-law) plate separation. We perform a complete linear stability analysis of a depth-averaged theoretical model to show that the plate separation delays the onset of non-axisymmetric instabilities, in qualitative agreement with the predictions obtained from a simplified analysis by [1]. We then employ direct numerical simulations to show that in the parameter regime where the axisymmetrically expanding air bubble is unstable to nonaxisymmetric perturbations, the interface can evolve in a self-similar fashion such that the interface shape at a given time is simply a rescaled version of the shape at an earlier time. These novel, self-similar solutions are linearly stable but they only develop if the initially circular interface is subjected to unimodal perturbations. Conversely, the application of non-unimodal perturbations (e.g. via the superposition of multiple linearly unstable modes) leads to the development of complex, constantly evolving finger patterns similar to those that are typically observed in constant-width Hele-Shaw cells. [1] Z. Zheng, H. Kim, and H. A. Stone, Controlling viscous fingering using time-dependent strategies, Phys. Rev. Lett. 115, 174501 (2015).
Allelopathic Toxicity of Cyanamide Could Control Amaranth (Amaranthus retroflexus L.) in Alfalfa (Medicago sativa L.) Field

The inclination toward natural products has led to the onset of the discovery of new bioactive metabolites that could be targeted for specific therapeutic or agronomic applications. Despite increasing knowledge coming to light of allelochemicals as leads for new herbicides, relatively little is known about the mode of action of allelochemical-based herbicides on herbicide-resistant weeds. Cyanamide is an allelochemical produced by hairy vetch (Vicia villosa Roth.). This study aimed to detect the toxicity of cyanamide to alfalfa and amaranth. Seed germination experiments were carried out by the filter paper culture, and the seedling growth inhibition experiment was carried out by spraying alfalfa (Medicago sativa L.) and amaranth (Amaranthus retroflexus L.) seedlings with cyanamide. The results showed that when the concentration of cyanamide was 0.1 g·L−1, the germination of amaranth seeds could be completely inhibited without affecting the germination of alfalfa seeds. At the concentration of 0.5 g·L−1, cyanamide could significantly inhibit the growth of the root and stem of amaranth seedlings but did not affect the growth of alfalfa. This effect was associated with the induction of oxidative stress. The ascorbate peroxidase (APX) and catalase (CAT) activity of amaranth decreased by 6.828 U/g FW and 290.784 U/g FW, respectively. The malondialdehyde (MDA) content, peroxidase (POD), and superoxide dismutase (SOD) activity of amaranth firstly increased and then decreased with the increasing concentration of CA. These enzyme activities of amaranth changed more than that of alfalfa. Activities of the antioxidant enzymes APX, CAT, POD, and SOD and the content of MDA varied dramatically, thereby demonstrating the great influence of reactive oxygen species upon identified allelochemical exposure. In addition, cyanamide can also inhibit the production of chlorophyll, thereby affecting the growth of plants. From the above experiments, we know that cyanamide can inhibit the growth of amaranth in alfalfa fields. Thus, the changes caused by cyanamide described herein can contribute to a better understanding of the actions of allelochemical and the potential use of cyanamide in the production of bioherbicides.
Noise-induced non-Markovianity

We have studied the non-Markovianity of dichotomously driven spin-boson model in the strong coupling regime in both memory kernel and time convolutionless master equation formulations. A strong correlation between the decay time of the environmental correlation function and the non-zero non-Markovianity is found in the absence of the external noise. Stochastic driving is shown to create strong non-Markovianity when the dynamics of the system without driving is Markovian. Also, exact analytical expressions for the trace distance distinguishability and the non-Markovianity were obtained for the certain range of the parameters that describe the system and its environment.
The true nature of Swift J0746.3-1608: a possible Intermediate Polar showing accretion state changes

This work is based on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member States, with Swift, a NASA science mission with Italian participation, and with Gaia, a ESA mission. Gaia data are processed by the Data Processing and Analysis Consortium (DPAC).
Title The role of Sox 6 in zebrafish muscle fiber typespecification

Background: The transcription factor Sox6 has been implicated in regulating muscle fiber type-specific gene expression in mammals. In zebrafish, loss of function of the transcription factor Prdm1a results in a slow to fast-twitch fiber type transformation presaged by ectopic expression of sox6 in slow-twitch progenitors. Morpholino-mediated Sox6 knockdown can suppress this transformation but causes ectopic expression of only one of three slow-twitch specific genes assayed. Here, we use gain and loss of function analysis to analyse further the role of Sox6 in zebrafish muscle fiber type specification. Methods: The GAL4 binary misexpression system was used to express Sox6 ectopically in zebrafish embryos. Cis-regulatory elements were characterized using transgenic fish. Zinc finger nuclease mediated targeted mutagenesis was used to analyse the effects of loss of Sox6 function in embryonic, larval and adult zebrafish. Zebrafish transgenic for the GCaMP3 Calcium reporter were used to assay Ca2+ transients in wild-type and mutant muscle fibres. Results: Ectopic Sox6 expression is sufficient to downregulate slow-twitch specific gene expression in zebrafish embryos. Cis-regulatory elements upstream of the slow myosin heavy chain 1 (smyhc1) and slow troponin c (tnnc1b) genes contain putative Sox6 binding sites required for repression of the former but not the latter. Embryos homozygous for sox6 null alleles expressed tnnc1b throughout the fast-twitch muscle whereas other slow-specific muscle genes, including smyhc1, were expressed ectopically in only a subset of fast-twitch fibers. Ca2+ transients in sox6 mutant fast-twitch fibers were intermediate in their speed and amplitude between those of wild-type slowand fast-twitch fibers. sox6 homozygotes survived to adulthood and exhibited continued misexpression of tnnc1b as well as smaller slow-twitch fibers. They also exhibited a striking curvature of the spine. Conclusions: The Sox6 transcription factor is a key regulator of fast-twitch muscle fiber differentiation in the zebrafish, a role similar to that ascribed to its murine ortholog.
AX-GADGET: a new code for cosmological simulations of Fuzzy Dark Matter and Axion models

We present a new module of the parallel N-Body code P-GADGET3 for cosmological simulations of light bosonic non-thermal dark matter, often referred as Fuzzy Dark Matter (FDM). The dynamics of the FDM features a highly non-linear Quantum Potential (QP) that suppresses the growth of structures at small scales. Most of the previous attempts of FDM simulations either evolved suppressed initial conditions, completely neglecting the dynamical effects of QP throughout cosmic evolution, or resorted to numerically challenging full-wave solvers. The code provides an interesting alternative, following the FDM evolution without impairing the overall performance. This is done by computing the QP acceleration through the Smoothed Particle Hydrodynamics (SPH) routines, with improved schemes to ensure precise and stable derivatives. As an extension of the P-GADGET3 code, it inherits all the additional physics modules implemented up to date, opening a wide range of possibilities to constrain FDM models and explore its degeneracies with other physical phenomena. Simulations are compared with analytical predictions and results of other codes, validating the QP as a crucial player in structure formation at small scales.
Institutional barriers to climate change and health adaptation in Burkina Faso

ABSTRACT West African countries, such as Burkina Faso are particularly vulnerable to an array of health impacts due to climate change. Consequently, Burkina Faso has drafted and implemented adaptation plans and programmes, with varying levels of success. This exploratory qualitative study examines the institutional barriers faced by policymakers in this process, particularly in the health system of concern. We applied in-depth interviews with policymakers, using framework analysis. We identified the barriers to implementing climate change and health programmes and categorized the barriers according to the Framework to diagnose barriers to climate change adaptation. Policymakers identified eight interconnected barriers through the framework: Four barriers in the management phase (insufficient financial resources, frequent turnover, policy-politics disconnect /weak structural support, unsustainable programming), three in the planning phase (heft of bureaucracy/lack of political will, diverging development priorities, insufficient cooperation), one in the larger context of Burkina Faso’s environment (national security). The respondents mentioned no barriers in the understanding phase. These barriers are indicative of weak institutional support systems and limited resource allocation to climate and health work in Burkina Faso.
Imaging through glass diffusers using densely connected convolutional networks

Computational imaging through scatter generally is accomplished by first characterizing the scattering medium so that its forward operator is obtained; and then imposing additional priors in the form of regularizers on the reconstruction functional so as to improve the condition of the originally ill-posed inverse problem. In the functional, the forward operator and regularizer must be entered explicitly or parametrically (e.g. scattering matrices and dictionaries, respectively.) However, the process of determining these representations is often incomplete, prone to errors, or infeasible. Recently, deep learning architectures have been proposed to instead learn both the forward operator and regularizer through examples. Here, we propose for the first time, to our knowledge, a convolutional neural network architecture called "IDiffNet" for the problem of imaging through diffuse media and demonstrate that IDiffNet has superior generalization capability through extensive tests with well-calibrated diffusers. We found that the Negative Pearson Correlation Coefficient loss function for training is more appropriate for spatially sparse objects and strong scattering conditions. Our results show that the convolutional architecture is robust to the choice of prior, as demonstrated by the use of multiple training and testing object databases, and capable of achieving higher space-bandwidth product reconstructions than previously reported.
Modelling mass distribution of the Milky Way galaxy using Gaia billion-star map

The Milky Way galaxy is a typical spiral galaxy which consists of a black hole in its centre, a barred bulge and a disk which contains spiral arms. The complex structure of the Galaxy makes it extremely difficult and challenging to model its mass distribution, particularly for the Galactic disk which plays the most important role in the dynamics and evolution of the Galaxy. Conventionally an axisymmetric disk model with an exponential brightness distribution and a constant mass-to-light ratio is assumed for the Galactic disk. In order to generate a flat rotation curve, a dark halo has also to be included. Here, by using the recently released Gaia billion-star map, we propose a Galactic disk mass distribution model which is based on the star density distribution rather than the brightness and mass-to-light ratio. The model is characterized by two parameters, a bulge radius and a characteristic length. Using the mass distribution model and solving the Poisson equation of the Galaxy, we obtain a flat rotation curve which reproduces the key observed features with no need for a dark halo.
Effects of Irradiation on the Evolution of Ultracompact X-Ray Binaries

Using the Modules for Experiments in Stellar Astrophysics code, we investigate the influences of irradiation on ultracompact X-ray binary (UCXB) evolution. Although the persistent UCXBs have short orbital periods that result in high irradiation flux, the irradiation hardly affects the evolution of persistent sources because the white dwarfs (WDs) in these binaries have large masses that lead to very low irradiation depth. The irradiation has a significant effect on the transient sources during outburst phase. At the beginning of the outburst, high X-ray luminosity produces high radiation flux, which results in the significant expansion of WDs. Then, the irradiation triggers high mass-transfer rates, which can last several days for the transient sources with WDs whose masses are larger than or several hundred years for those sources with WDs whose masses are less than . The observed three persistent UCXBs, XTE J0929-314, 4U 1916-05, and SWIFT J1756.9-2508, may belong to the latter.
Supramolecular Protein-Polyelectrolyte Assembly at Near Physiological Conditions—Water Proton NMR, ITC, and DLS Study

The in vivo potency of polyphosphazene immunoadjuvants is inherently linked to the ability of these ionic macromolecules to assemble with antigenic proteins in aqueous solutions and form physiologically stable supramolecular complexes. Therefore, in-depth knowledge of interactions in this biologically relevant system is a prerequisite for a better understanding of mechanism of immunoadjuvant activity. Present study explores a self-assembly of polyphosphazene immunoadjuvant—PCPP and a model antigen—lysozyme in a physiologically relevant environment—saline solution and neutral pH. Three analytical techniques were employed to characterize reaction thermodynamics, water-solute structural organization, and supramolecular dimensions: isothermal titration calorimetry (ITC), water proton nuclear magnetic resonance (wNMR), and dynamic light scattering (DLS). The formation of lysozyme–PCPP complexes at near physiological conditions was detected by all methods and the avidity was modulated by a physical state and dimensions of the assemblies. Thermodynamic analysis revealed the dissociation constant in micromolar range and the dominance of enthalpy factor in interactions, which is in line with previously suggested model of protein charge anisotropy and small persistence length of the polymer favoring the formation of high affinity complexes. The paper reports advantageous use of wNMR method for studying protein-polymer interactions, especially for low protein-load complexes.
On a relational theory of biological systems: a natural model for complex biological behavior

In this paper, we develop a natural (empirical) relational theory for describing and modeling complex biological phenomena. We have as stepping stone the assertion: function implies structure. The theory is built upon a graph's theory structure in which a diffusion model of information takes place, and where dynamics can be investigated in order to generate steady quantifiers. In this context, we improve a seminal work by adding a free context biological importance measure given by the Shannon's Entropy. We also introduce the concept of biological loci. Such concept stands for closely related biological agents which plays a role as an agent by itself. Our results allow us to synthesize a natural model for complex biological behavior that takes into account: system's update, irreducibility, and exploit of the dynamical behavior mounted over a diffusion model. The model deals in final terms to its natural capacity to model plasticity and environmental changes, which has an intrinsic relationship with Shannon's Entropy and the sort of dynamics that biological systems can display.
Weakly Isolated horizons: first order actions and gauge symmetries

The notion of Isolated Horizons has played an important role in gravitational physics, being useful from the characterization of the endpoint of black hole mergers to (quantum) black hole entropy. With an eye towards a canonical formulation we consider general relativity in terms of connection and vierbein variables and their corresponding first order actions. We focus on two main issues: (i) The role of the internal gauge freedom that exists, in the consistent formulations of the action principle, and (ii) the role that a 3 + 1 canonical decomposition has in the allowed internal gauge freedom. More concretely, we clarify in detail how the requirement of having well posed variational principles compatible with general weakly isolated horizons (WIHs) as internal boundaries does lead to a partial gauge fixing in the first order descriptions used previously in the literature. We consider the standard Hilbert–Palatini action together with the Holst extension (needed for a consistent 3 + 1 decomposition), with and without boundary terms at the horizon. We show in detail that, for the complete configuration space—with no gauge fixing—, while the Palatini action is differentiable without additional surface terms at the inner WIH boundary, the more general Holst action is not. The introduction of a surface term at the horizon—that renders the action for asymptotically flat configurations differentiable—does make the Holst action differentiable, but only if one restricts the configuration space and partially reduces the internal Lorentz gauge. For the second issue at hand, we show that upon performing a 3 + 1 decomposition and imposing the time gauge, there is a further gauge reduction of the Hamiltonian theory in terms of Ashtekar–Barbero variables to a U(1)-gauge theory on the horizon. We also extend our analysis to the more restricted boundary conditions of (strongly) isolated horizons as inner boundary. We show that even when the Holst action is indeed differentiable without the need of additional surface terms or any gauge fixing for Type I spherically symmetric (strongly) isolated horizons—and a preferred foliation—, this result does not go through for more general isolated or weakly isolated horizons. Our results represent the first comprehensive study of these issues and clarify some contradictory statements found in the literature.
Surface Wave Isotropic and Azimuthally Anisotropic Dispersion Across Alaska and the Alaska‐Aleutian Subduction Zone

Comprehensive observations of surface wave anisotropy across Alaska and the Aleutian subduction zone are needed to improve understanding of its tectonics, mantle dynamics, and earthquake risk. We produce such observations, using stations from the USArray Transportable Array and regional networks across Alaska and the Alaska Amphibious Community Seismic Experiment in the Alaska‐Aleutian subduction zone both onshore and offshore. Our data include Rayleigh and Love wave phase dispersion from earthquakes (28–85 s) and ambient noise two‐ and three‐station interferometry (8–50 s). Compared with using two‐station interferometry alone, three‐station interferometry significantly improves the signal‐to‐noise ratio and approximately doubles the number of measurements retained. Average differences between both isotropic and anisotropic tomographic maps constructed from different methods lie within their uncertainties, which is justification for combining the measurements. The composite tomographic maps include Rayleigh wave isotropy and azimuthal anisotropy from 8 to 85 s both onshore and offshore, and onshore Love wave isotropy from 8 to 80 s. In the Alaska‐Aleutian subduction zone, Rayleigh wave fast directions vary from trench parallel to perpendicular and back to parallel with increasing periods, apparently reflecting the effect of the subducted Pacific Plate. The tomographic maps provide a basis for inferring the 3‐D anisotropic crustal and uppermost mantle structure across Alaska and the Aleutian subduction zone.
Improving the efficiency of graph algorithm executions on high‐performance computing

The growing need for extracting information from large graphs has been pushing the development of parallel graph algorithms. However, the highly irregular structure of the real‐world graphs limits the performance and energy improvements of graph applications. In this paper, we show that, in most cases, using all the available cores of the multiprocessor is not the best option in terms of the aforementioned non‐functional requirements. Based on that, we propose GraphKat, a framework that enables the simultaneous processing of several algorithms/graphs instead of executing them serially (i.e., one after another), increasing efficiency in terms of performance and energy. GraphKat works in two steps: (i) it characterizes the graph applications with a specific number of threads based on their efficiency levels; and (ii) it defines the execution order of all graph applications in the target system. Experimental results on three multicore processors (Intel and AMD) show that GraphKat improves the overall system's efficiency related to performance (up to 434.26×$$ 434.26\times $$ ) and energy‐saving (up to 245.21 ×$$ \times $$ ), and reduces the graph applications' execution time (up to 17.70×$$ 17.70\times $$ ) and energy consumption (up to 6.64 ×$$ \times $$ ) compared to the default execution of parallel applications on HPC systems.
New Constraints on the Nature and Origin of the Leading Arm of the Magellanic Stream

We present a new precision measurement of gas-phase abundances of S, O, N, Si, Fe, P, Al, Ca as well as molecular hydrogen (H2) in the Leading Arm (region II, LA II) of the Magellanic Stream (MS) toward the Seyfert galaxy NGC 3783. The results are based on high-quality archival ultraviolet/optical/radio data from various different instruments (HST/STIS, FUSE, AAT, GBT, GB140 ft, ATCA). Our study updates previous results from lower-resolution data and provides for the first time a self-consistent component model of the complex multiphase absorber, delivering important constraints on the nature and origin of LA II. We derive a uniform, moderate α abundance in the two main absorber groups at +245 and +190 km s−1 of α/H = 0.30 ± 0.05 solar, a low nitrogen abundance of N/H = 0.05 ± 0.01 solar, and a high dust content with substantial dust depletion values for Si, Fe, Al, and Ca. These α, N, and dust abundances in LA II are similar to those observed in the Small Magellanic Cloud (SMC). From the analysis of the H2 absorption, we determine a high thermal pressure of P/k ≈ 1680 K cm−3 in LA II, in line with the idea that LA II is located in the inner Milky Way halo at a z-height of <20 kpc, where it hydrodynamically interacts with the ambient hot coronal gas. Our study supports a scenario in which LA II stems from the breakup of a metal- and dust-enriched progenitor cloud that was recently (200–500 Myr ago) stripped from the SMC.