Miracle-dz/UniFAR-FTUs huggingface dataset:
Promiscuous Inflammasomes: The False Dichotomy of RNA/DNA Virus-Induced Inflammasome Activation and Pyroptosis

It is well-known that viruses activate various inflammasomes, which can initiate the programmed cell death pathway known as pyroptosis, subsequently leading to cell lysis and release of inflammatory cytokines IL-1β and IL-18. This pathway can be triggered by various sensors, including, but not limited to, NLRP3, AIM2, IFI16, RIG-I, and NLRC4. Many viruses are known either to activate or inhibit inflammasomes as a part of the innate immune response or as a mechanism of pathogenesis. Early research in the field of virus-induced pyroptosis suggested a dichotomy, with RNA viruses activating the NLRP3 inflammasome and DNA viruses activating the AIM2 inflammasome. More recent research has shown that this dichotomy may not be as distinct as once thought. It seems many viruses activate multiple inflammasome sensors. Here, we detail which viruses fit the dichotomy as well as many that appear to defy this clearly false dichotomy. It seems likely that most, if not all, viruses activate multiple inflammasome sensors, and future research should focus on expanding our understanding of inflammasome activation in a variety of tissue types as well as virus activation of multiple inflammasomes, challenging biases that stemmed from early literature in this field. Here, we review primarily research performed on human viruses but also include details regarding animal viruses whenever possible.
The effects of QCD equation of state on the relic density of WIMP dark matter

Weakly Interactive Massive Particles (WIMPs) are the most widely studied candidate particles forming the cold dark matter (CDM) whose existence can be inferred from a wealth of astrophysical and cosmological observations. In the framework of the minimal cosmological model detailed measurements on the cosmic microwave background by the PLANCK collaboration fix the scaled CDM relic density to Ωch2=0.1193±0.0014, with an error of less than 1.5%. In order to fully exploit this observational precision, theoretical calculations should have a comparable or smaller error. In this paper we use recent lattice QCD calculations to improve the description of the thermal plasma. This affects the predicted relic density of ``thermal WIMPs'', which once were in chemical equilibrium with Standard Model particles. For WIMP masses between 3 and 15 GeV, where QCD effects are most important, our predictions differ from earlier results by up to 9% (12%) for pure S-wave (P-wave) annihilation. We use these results to compute the thermally averaged WIMP annihilation cross section that reproduces the correct CDM relic density, for WIMP masses between 0.1 GeV and 10 TeV.
Finite temperature study of the axial U(1) symmetry on the lattice with overlap fermion formulation

We examine the axial U(1) symmetry near and above the finite temperature phase transition in two-flavor QCD using lattice QCD simulations. Although the axial U(1) symmetry is always violated by quantization, (i.e.) the chiral anomaly, the correlation functions may manifest effective restoration of the symmetry in the high temperature phase. We explicitly study this possibility by calculating the meson correlators as well as the Dirac operator spectral density near the critical point. Our numerical simulations are performed on a $16^3\times 8$ lattice with two flavors of dynamical quarks represented by the overlap fermion formalism. Chiral symmetry and its violation due to the axial anomaly is manifestly realized with this formulation, which is a prerequisite for the study of the effective restoration of the axial U(1) symmetry. In order to avoid discontinuity in the gauge configuration space, which occurs for the exactly chiral lattice fermions, the simulation is confined in a fixed topological sector. It induces finite volume effect, which is well described by a formula based on the Fourier transform from the $\theta$-vacua. We confirm this formula at finite temperature by calculating the topological susceptibility in the quenched theory. Our two flavor simulations show degeneracy of the meson correlators and a gap in the Dirac operator spectral density, which implies that the axial U(1) symmetry is effectively restored in the chirally symmetric phase.
PHOTOMETRIC REDSHIFT WITH BAYESIAN PRIORS ON PHYSICAL PROPERTIES OF GALAXIES

We present a proof-of-concept analysis of photometric redshifts with Bayesian priors on physical properties of galaxies. This concept is particularly suited for upcoming/on-going large imaging surveys, in which only several broadband filters are available and it is hard to break some of the degeneracies in the multi-color space. We construct model templates of galaxies using a stellar population synthesis code and apply Bayesian priors on physical properties such as stellar mass and star formation rate. These priors are a function of redshift and they effectively evolve the templates with time in an observationally motivated way. We demonstrate that the priors help reduce the degeneracy and deliver significantly improved photometric redshifts. Furthermore, we show that a template error function, which corrects for systematic flux errors in the model templates as a function of rest-frame wavelength, delivers further improvements. One great advantage of our technique is that we simultaneously measure redshifts and physical properties of galaxies in a fully self-consistent manner, unlike the two-step measurements with different templates often performed in the literature. One may rightly worry that the physical priors bias the inferred galaxy properties, but we show that the bias is smaller than systematic uncertainties inherent in physical properties inferred from the spectral energy distribution fitting and hence is not a major issue. We will extensively test and tune the priors in the on-going Hyper Suprime-Cam survey and will make the code publicly available in the future.
DYNAMIC COUPLING OF CONVECTIVE FLOWS AND MAGNETIC FIELD DURING FLUX EMERGENCE

We simulate the buoyant rise of a magnetic flux rope from the solar convection zone into the corona to better understand the energetic coupling of the solar interior to the corona. The magnetohydrodynamic model addresses the physics of radiative cooling, coronal heating, and ionization, which allow us to produce a more realistic model of the solar atmosphere. The simulation illustrates the process by which magnetic flux emerges at the photosphere and coalesces to form two large concentrations of opposite polarities. We find that the large-scale convective motion in the convection zone is critical to form and maintain sunspots, while the horizontal converging flows in the near-surface layer prevent the concentrated polarities from separating. The footpoints of the sunspots in the convection zone exhibit a coherent rotation motion, resulting in the increasing helicity of the coronal field. Here, the local configuration of the convection causes the convergence of opposite polarities of magnetic flux with a shearing flow along the polarity inversion line. During the rising of the flux rope, the magnetic energy is first injected through the photosphere by the emergence, followed by energy transport by horizontal flows, after which the energy is subducted back to the convection zone by the submerging flows.
A Bayesian test for periodic signals in red noise

Many astrophysical sources, especially compact accreting sources, show strong, random brightness fluctuations with broad power spectra in addition to periodic or quasi-periodic oscillations (QPOs) that have narrower spectra. The random nature of the dominant source of variance greatly complicates the process of searching for possible weak periodic signals. We have addressed this problem using the tools of Bayesian statistics; in particular, using Markov Chain Monte Carlo techniques to approximate the posterior distribution of model parameters, and posterior predictive model checking to assess model fits and search for periodogram outliers that may represent periodic signals. The methods developed are applied to two example data sets, both long XMM–Newton observations of highly variable Seyfert 1 galaxies: RE J1034 + 396 and Mrk 766. In both cases, a bend (or break) in the power spectrum is evident. In the case of RE J1034 + 396, the previously reported QPO is found but with somewhat weaker statistical significance than reported in previous analyses. The difference is due partly to the improved continuum modelling, better treatment of nuisance parameters and partly to different data selection methods.
Biotransformation of Modified Benzylisoquinoline Alkaloids: Boldine and Berberine and In Silico Molecular Docking Studies of Metabolites on Telomerase and Human Protein Tyrosine Phosphatase 1B

Natural nitrogen heterocycles biotransformation has been extensively used to prepare synthetic drugs and explore the fate of therapeutic agents inside the body. Herein, the ability of filamentous fungi to biotransform boldine and berberine was investigated. Docking simulation studies of boldine, berberine and their metabolites on the target enzymes: telomerase (TERT) and human protein tyrosine phosphatase 1B (PTP-1B) were also performed to investigate the anticancer and antidiabetic potentials of compounds in silico. The biotransformation of boldine and berberine with Cunninghamella elegans NRRL 2310, Rhodotorula rubra NRRL y1592, Penicillium chrysogeneum ATCC 10002, Cunninghamella blackesleeana MR198 and Cunninghamella blackesleeana NRRL 1369 via demethylation, N- oxidation, glucosidation, oxidation and hydroxylation reactions produced seven metabolites, namely: 1,10-didesmethyl-boldine (1), laurolitsine (2), 1,10-didesmethyl-norboldine (3), boldine-9-O-β-D-glucoside (4), tridesmethyl berberine (5), demethylene berberine (6), and lambertine (7). Primarily, the structures of the metabolites were established by one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) analyses and mass spectrometry. In silico molecular docking simulation of the metabolites of boldine and berberine to the proteins TERT and PTP-1B, respectively, revealed good binding MolDock scores comparable to boldine and berberine and favorable interactions with the catalytic sites of the proteins. In conclusion, this study presented promising biologically prepared nitrogen scaffolds (isoquinolines) of boldine and berberine.
MAGNETAR-POWERED SUPERNOVAE IN TWO DIMENSIONS. I. SUPERLUMINOUS SUPERNOVAE

Previous studies have shown that the radiation emitted by a rapidly rotating magnetar embedded in a young supernova can greatly amplify its luminosity. These one-dimensional studies have also revealed the existence of an instability arising from the piling up of radiatively accelerated matter in a thin dense shell deep inside the supernova. Here, we examine the problem in two dimensions and find that, while instabilities cause mixing and fracture this shell into filamentary structures that reduce the density contrast, the concentration of matter in a hollow shell persists. The extent of the mixing depends upon the relative energy input by the magnetar and the kinetic energy of the inner ejecta. The light curve and spectrum of the resulting supernova will be appreciably altered, as will the appearance of the supernova remnant, which will be shellular and filamentary. A similar pile up and mixing might characterize other events where energy is input over an extended period by a centrally concentrated source, e.g., a pulsar, radioactive decay, a neutrino-powered wind, or colliding shells. The relevance of our models to the recent luminous transient ASASSN-15lh is briefly discussed.
THREE-DIMENSIONAL SIMULATIONS OF LONG DURATION GAMMA-RAY BURST JETS: TIMESCALES FROM VARIABLE ENGINES

Gamma-ray burst (GRB) light curves are characterized by marked variability, each showing unique properties. The origin of this variability, at least for a fraction of long GRBs, may be the result of an unsteady central engine. It is thus important to study the effects that an episodic central engine has on the jet propagation and, eventually, on the prompt emission within the collapsar scenario. Thus, in this study we follow the interaction of pulsed outflows with their progenitor stars with hydrodynamic numerical simulations in both two and three dimensions. We show that the propagation of unsteady jets is affected by the interaction with the progenitor material well after the break-out time, especially for jets with long quiescent times comparable to or larger than a second. We also show that this interaction can lead to an asymmetric behavior in which pulse durations and quiescent periods are systematically different. After the pulsed jets drill through the progenitor and the interstellar medium, we find that, on average, the quiescent epochs last longer than the pulses (even in simulations with symmetrical active and quiescent engine times). This could explain the asymmetry detected in the light curves of long quiescent time GRBs.
Basic properties of Fermi blazars and the `blazar sequence'

By statistically analysing a large sample that includes Fermi-detected blazars (FBs) and non-Fermi-detected blazars (NFBs), we find that there are significant differences between FBs and NFBs in redshift, black hole mass, jet kinetic power from cavity power, broad-line luminosity and the ratio of core luminosity to absolute V-band magnitude (R-v), but not in the ratio of the radio core to extended flux (R-c) and the Eddington ratio. Compared with NFBs, FBs have larger mean jet power, R-c and R-v, while having smaller mean redshift, black hole mass and broad-line luminosity. These results support the fact that the beaming effect is the main reason for differences between FBs and NFBs, and that FBs are likely to have a more powerful jet. For both FBs and NFBs, there are significant correlations between the jet power and the accretion rate (traced by the broad-emission line luminosity), and between the jet power and the black hole mass. For FBs, the black hole mass does not have a significant influence on jet power, while for NFBs, both the accretion rate and black hole mass contribute to the jet power. Our results support the 'blazar sequence' and show that the synchrotron peak frequency (nu(peak)) is associated with the accretion rate but not with the black hole mass.
THE M31 NEAR-INFRARED PERIOD–LUMINOSITY RELATION AND ITS NON-LINEARITY FOR δ Cep VARIABLES WITH 0.5 ⩽ log (P) ⩽ 1.7

We present the largest M31 near-infrared (F110W (close to J band), F160W (H band)) Cepheid sample so far. The sample consists of 371 Cepheids with photometry obtained from the Hubble Space Telescope PHAT program. The sample of 319 fundamental mode Cepheids, 16 first overtone Cepheids, and 36 type II Cepheids was identified using the median absolute deviation outlier rejection method we develop here. This method does not rely on priors and allows us to obtain this clean Cepheid sample without rejecting a large fraction of Cepheids. The obtained period–luminosity relations (PLRs) have a very small dispersion, i.e., 0.155 mag in F160W, despite using random phased observations. This remarkably small dispersion allows us to determine that the PLRs are significantly better described by a broken slope at 10 days than a linear slope. The use of our sample as an anchor to determine the Hubble constant gives a 3.2% larger Hubble constant compared to the Riess et al. sample.
Differences in Fish Abundance in Rivers under the Influence of Open-Pit Gold Mining in the Santiago-Cayapas Watershed, Esmeraldas, Ecuador

Illegal gold mining is on the rise in the tropical Andes. The Santiago-Cayapas watershed is located in the north of the Pacific basin of Ecuador, in the Chocó biogeographical region. It is recognized for its high biodiversity, as 62 fish species have been described in the area, and because it contains two of the largest protected areas in the Pacific coast of Ecuador: the mangroves of the Cayapas and Mataje Rivers and the Cotacachi-Cayapas Ecological Reserve. Open-pit gold mining has been described in the area since 2006 and most mining fronts operate illegally and lack any environmental control. Heavy-metal concentrations and fish communities were studied in streams that drain active and abandoned mines, in larger rivers located downstream of the mined areas and in control sites without mining activities. Open-pit mining causes a reduction of dissolved oxygen concentrations and an increase of water temperature, turbidity, and concentrations of Al, Cr, Co, Cu, Fe, Mn, and V. Fish abundance decreased in streams that drain active mines, however, metrics of taxonomic diversity remain unchanged among the study sites. The response of fish communities to open-pit gold mining was complex and driven by the pollution tolerance of each species, the presence of specific adaptions to turbid waters, and changes in the fishing pressure as locals avoid fishing activities in mined areas. Finally, streams that drain abandoned mines showed chemical characteristics, metal concentrations, and fish communities that were similar to control sites, but maintained higher water temperatures than control sites.
Diagnosis of COVID-19 from X-ray images using deep learning techniques

Abstract In this study, we searched for the latest literature on the use of deep learning applications to combat COVID-19 and these were identified from several search engines including IEEE Xplore, Google Scholar, PubMed, and Scopus. This involved a comprehensive analysis of the studies to identify the challenges associated with the use of deep learning models with a view to highlight the possible future trends in the development of deep learning systems that are efficient and more reliable for the diagnosis of COVID-19 patients. This paper provides information related to the deep learning techniques used to detect COVID-19. This paper discusses the Convolutional Neural Networks’ (CNNs) structure, how to train CNNs, and highlights the different pre-trained models of CNNs that can be used for the detection of COVID-19. This paper explores the latest developments in the diagnosis of COVID-19 using deep learning applications that rely on the use of X-ray images taken from medical imaging samples. A review of the different models developed to facilitate effective diagnosis of COVID-19 provides information regarding the experimental data, the data splitting techniques used, as well as the proposed architecture for detecting COVID-19 and the different evaluation metrics for each model. This paper is a useful resource for medical and technical experts, as it helps them to develop a sound understanding of how deep learning techniques can be harnessed to stop the spread of COVID-19.
Roles of TOPO Coordinating Solvent on Prepared Nano-Flower/Star and Nano-Rods Nickel Sulphides for Solar Cells Applications

The present study describes a cheap, safe, and stable chemical process for the formation of nickel sulphide (NiS) with the use of mixed and single molecular precursors. The production pathway is uncomplicated, energy-efficient, quick, and toxic-free, with large-scale commercialization potential. The obtained results show the effect of tri-N-octylphosphine oxide (TOPO) as a coordinating solvent on the reaction chemistry, size distributions, morphology, and optical properties of both precursors. Ni[N,N-benz-N-p-anisldtc] as NiSa, Ni[N,N-benzldtc] as NiSb, and Ni[N-p-anisldtc] as NiSc thermally decompose in a single step at 333–334 °C. The X-ray diffraction peaks for NiSa, NiSb, and NiSc matched well with the cubic NiS nanoparticles and corresponded to planes of (111), (220), and (311). The extrapolated linear part from the Tauc plots reveals band gap values of 3.12 eV, 2.95 eV, and 2.5 eV, which confirms the three samples as potential materials for solar cell applications. The transmission electron microscopy (TEM) technique affirmed the quantum dot size distribution at 19.69–28.19 nm for NISa, 9.08–16.63 nm for NISb, and 9.37–10.49 nm for NISc, respectively. NiSa and NiSc show a clearly distinguishable flower/star like morphology, while NiSb displays a compact nano-rod shape. To the best of the authors’ knowledge, very few studies have been reported on the flower/star like and nano-rod shapes, but none with the dithiocarbamate molecular precursor for NiS nanoparticles.
Social Capital in the Family Business Literature: A Systematic Review and Future Research Agenda

Using a systematic literature review, we address the topic of social capital in family firms. Based on 69 studies, we analyze the main findings, sampling and methodologies, theoretical approaches, definitions, and measurements of social capital in family firms. We also present how social capital is used as a model variable and present a conceptual framework of social capital in family firms. Subsequently, we identify the research gaps and develop research questions for further research.
Direct Evidence of Interchange Instabilities at Dipolarization Fronts

Using the high‐resolution measurements from magnetospheric multiscale mission, here we present the observational evidence of kinetic interchange instabilities (ICIs) at dipolarization fronts (DFs). Specifically, we present the observation of two DFs caused by ICI, and discover the sub‐ion scale magnetic depression caused by kinetic‐scale ICI at the second DF. By using multi‐spacecraft observation, the typical process inside the magnetic hole (MH)—by electron trapping process—is clearly shown in the magnetic depression, evidencing that the depression is a sub‐ion MH generated at DF by kinetic ICI. Based on observations and Minimum Variance Analysis (MVA) analysis, we present a two‐dimensional image of the ICI in the nonlinear stage. This observational study demonstrates the kinetic ICI at DFs, confirming the existence of MH generated by ICI at DF, and improves the understanding of dynamics at DFs.
The mass–metallicity relation in galaxy clusters: the relative importance of cluster membership versus local environment

Using a large (14 857), homogenously selected sample of cluster galaxies identified in the Sloan Digital Sky Survey Data Release 4, we investigate the impact of cluster membership and local density on the stellar mass-gas phase metallicity relation (MZR). We show that stellar metallicities are not suitable for this work, being relatively insensitive to subtle changes in the MZR. Accurate nebular abundances can be obtained for 1318 cluster galaxies in our sample and we show that these galaxies are drawn from clusters that are fully representative of the parent sample in terms of mass, size, velocity dispersion and richness. By comparing the MZR of the cluster galaxies with a sample of control galaxies matched in mass, redshift, fibre covering fraction and rest-frame g - r colour cluster galaxies are found to have, on average, higher metallicities by up to 0.04 dex. The magnitude of this offset does not depend strongly on galactic half-light radius or cluster properties such as velocity dispersion or cluster mass. The effect of local density on the MZR is investigated, using the presence of a near neighbour and both two- and three-dimensional density estimators. For all three metrics, it is found that the cluster galaxies in locally rich environments have higher median metallicities by up to ∼0.05 dex than those in locally poor environments (or without a near neighbour). Control (non-cluster) galaxies at locally high densities exhibit similar metal enhancements. Taken together, these results show that galaxies in clusters are, on average, slightly more metal rich than the field, but that this effect is driven by local overdensity and not simply cluster membership.