Miracle-dz/UniFAR-FTUs huggingface dataset:
The properties of the extended warm ionised gas around low-redshift QSOs and the lack of extended high-velocity outflows

(Abridged) We present a detailed analysis of a large sample of 31 low-redshift, mostly radio-quiet type 1 QSOs observed with integral field spectroscopy to study their extended emission-line regions (EELRs). We focus on the ionisation state of the gas, size and luminosity of extended narrow line regions (ENLRs), which corresponds to those parts of the EELR dominated by ionisation from the QSO, as well as the kinematics of the ionised gas. We detect EELRs around 19 of our 31 QSOs (61%) after deblending the unresolved QSO emission and the extended host galaxy light in the integral field data. We identify 13 EELRs to be entirely ionised by the QSO radiation, 3 EELRs are composed of HII regions and 3 EELRs display signatures of both ionisation mechanisms at different locations. The typical size of the ENLR is 10kpc at a median nuclear [OIII] luminosity of log(L([OIII])/[erg/s])=42.7+-0.15. We show that the ENLR sizes are least a factor of 2 larger than determined with HST, but are consistent with those of recently reported type 2 QSOs at matching [OIII] luminosities. The ENLR of type 1 and type 2 QSOs appear to follow the same size-luminosity relation. Furthermore, we show for the first time that the ENLR size is much better correlated with the QSO continuum luminosity than with the total/nuclear [OIII] luminosity. We show that ENLR luminosity and radio luminosity are correlated, and argue that radio jets even in radio-quiet QSOs are important for shaping the properties of the ENLR. Strikingly, the kinematics of the ionised gas is quiescent and likely gravitationally driven in the majority of cases and we find only 3 objects with radial gas velocities exceeding 400km/s in specific regions of the EELR that can be associate with radio jets. In general, these are significantly lower outflow velocities and detection rates compared to starburst galaxies or radio-loud QSOs.
Cosmology of modified (but second order) gravity

This is a brief review of applications of extended gravity theories to cosmology, in particular to the dark energy problem. Generically extensions of gravity action involve higher derivative terms, which can result in ghosts and instabilities. We consider three ways to circumvent this: Chern‐Simons terms, first order variational principle and nonlocality. We consider some recent cosmological applications within these three classes of modified gravity models avoiding introduction of extra degrees of freedom. The viable parameter space can be very efficiently bounded by taking into account cosmological constraints from all epochs in addition to bounds from Solar system tests and stability considerations. We make some new remarks concerning so called algebraic scalar‐tensor theories, biscalar reformulation of nonlocal actions involving the inverse d’Alembertian, and a possible covariant formulation holographic cosmology with nonperturbative gravity.
Anti-Apoptotic c-FLIP Reduces the Anti-Tumour Activity of Chimeric Antigen Receptor T Cells

Simple Summary Chimeric antigen receptor (CAR) T cell treatment is a promising adoptive cell therapy that utilises CAR-expressing primary T cells to target specific tumour antigens. Since its first approval in 2017, the FDA has approved six CAR T cell therapies for blood cancer treatment. Despite their success in treating B cell malignancies, solid-tumour-directed CAR T cells face multifactorial challenges, often resulting in a lack of anti-tumour response in tumour elimination. The aim of this study was to evaluate the potency of expressing anti-apoptotic gene FLICE-like inhibitory protein p43 (c-FLIPp43) in Her2-CAR T cells to resist activation-induced cell death (AICD). This study confirmed the anti-apoptotic activity of c-FLIPp43. However, the expression of c-FLIPp43 reduced the CAR activity in a Her-2 breast cancer xenograft model relative to the control Her2-CAR T cells. This work provides insight into the role of c-FLIP in T cells and its impact on anti-tumour immunity in CAR T cells. Abstract CAR T cell treatment of solid tumours is limited by poor persistence partly due to CD95 ligand (CD95L)-induced apoptosis. Both T cells and cells within the tumour microenvironment (TME) may express CD95L, triggering apoptosis in CD95-receptor-positive CAR T cells. Tonic signalling of CAR T cells may also increase CD95-dependent AICD. Because the intracellular protein c-FLIP protects T cells from AICD, we expressed c-FLIPp43 within a Her-2 targeted CAR cassette and evaluated the potential of c-FLIPp43 through in vitro functional assays and in vivo tumour-bearing xenograft model. cFLIP expression protected against CD95L-induced cell death in the Jurkat T cell lines. However, in primary human CAR T cells containing CAR-CD28 domains, c-FLIPp43 overexpression had minimal additional impact on resistance to CD95L-induded cell death. In vitro cytotoxicity against a breast cancer tumour cell line was not altered by c-FLIPp43 expression, but the expression of c-FLIPp43 in Her2-CAR T cells lowered interferon-γ secretion, without markedly affecting IL-2 levels, and c-FLIPp43-Her2-CAR T cells showed reduced anti-tumour activity in immunodeficient mice with breast cancer. The findings of this study provide a new understanding of the effects of controlling extrinsic apoptosis pathway suppression in CAR T cells, suggesting that c-FLIPp43 expression reduces anti-tumour immunity through the modulation of effector T cell pathways.
ECO-FRIENDLY, NON-TOXIC, AND HIGHLY ANTIMICROBIALBIOSYNTHESIZED OF Silver NANOPARTICLES (PAgNPs) FROM POMEGRANATE(PUNICA GRANATUM) PEEL (WASTE) EXTRACT (PPE) WITH MANY APPLICATIONS IN NANO INDUSTRIES AND PATHOGEN ELIMINATION FROM WATER

The green synthesis of silver nanoparticles (AgNPs) regarded as the most significant field of nanotechnology science because of the cost-effective and environmentally friendly. Methodology used in the process of the fundamentals of green nanotechnology is the use of reductive by products in the food and fruit processing industry as a cheap and dependable source of green reducing agents due to their favorable physicochemical properties and applications potential
Discovery of Compton-thick quasars in the Sloan Digital Sky Survey

We present new and archival Chandra snapshot (≈10 ks each) observations of 15 optically identified [from the Sloan Digital Sky Survey (SDSS)] Type 2 quasars at z = 0.40-0.73. When combined with existing X-ray data, this work provides complete X-ray coverage for all 25 radio-quiet Type 2 quasars with log L [O III] > 9.28 L ☉ from Zakamska et al. Two targets out of 15 were not detected by Chandra and most of the remaining sources are X-ray weak, with nine having less than 10 counts in the 0.5-8 keV band. Low- to moderate-quality spectral analysis was limited to three sources, whose properties are consistent with the pres- ence of column densities in the range N H ≈ 10 22 -10 23 cm -2 in the source rest frame. If the [O III] luminosity is a reliable proxy for the intrinsic X-ray luminosity, the current X-ray data indicate that Compton-thick quasars may hide among ≈65 per cent of the SDSS Type 2 quasar population (L X,meas/ L X,[O III] < 0.01); however, since the Type 2 quasar sample is selected on [O III] luminosity, the estimated Compton-thick quasar fraction may be overestimated. Using archival Spitzer observations, we find that ≈50 per cent of SDSS Type 2 quasars appear to be obscured by Compton-thick material based on both the L X,meas /L X,mid-IR (where mid-IR corresponds to rest frame 12.3 μm) and L X,meas /L X,[O III] ratios. We use this information to provide an estimate of the Compton-thick quasar number density at z ≈ 0.3-0.8, which we find is in broad agreement with the expectations from X-ray background models.
Nusinersen Induces Disease-Severity-Specific Neurometabolic Effects in Spinal Muscular Atrophy

Intrathecal delivery of Nusinersen–an antisense oligonucleotide that promotes survival motor neuron (SMN) protein induction–is an approved therapy for spinal muscular atrophy (SMA). Here, we employed nuclear magnetic resonance (NMR) spectroscopy to longitudinally characterize the unknown metabolic effects of Nusinersen in the cerebrospinal fluid (CSF) of SMA patients across disease severity. Modulation of amino acid metabolism is a common denominator of biochemical changes induced by Nusinersen, with distinct downstream metabolic effects according to disease severity. In severe SMA1 patients, Nusinersen stimulates energy-related glucose metabolism. In intermediate SMA2 patients, Nusinersen effects are also related to energy homeostasis but involve ketone body and fatty acid biosynthesis. In milder SMA3 patients, Nusinersen mainly modulates amino acid metabolism. Moreover, Nusinersen modifies the CSF metabolome of a more severe clinical group towards the profile of untreated SMA patients with milder disease. These findings reveal disease severity-specific neurometabolic signatures of Nusinersen treatment, suggesting a selective modulation of peripheral organ metabolism by this CNS-directed therapy in severe SMA patients.
Parallelization of the maximum likelihood approach to phylogenetic inference

PARALLELIZATION OF THE MAXIMUM LIKELIHOOD APPROACH TO PHYLOGENETIC INFERENCE by Janine B. Garnham Supervising Professor: Dr. Muhammad Shaaban Department of Computer Engineering Phylogenetic inference refers to the reconstruction of evolutionary relationships among various species, usually presented in the form of a tree. DNA sequences are most often used to determine these relationships. The results of phylogenetic inference have many important applications, including protein function determination, drug discovery, disease tracking and forensics. There are several popular computational methods used for phylogenetic inference, among them distance-based (i.e. neighbor joining), maximum parsimony, maximum likelihood, and Bayesian methods. This thesis focuses on the maximum likelihood method, which is regarded as one of the most accurate methods, with its computational demand being the main hindrance to its widespread use. Maximum likelihood is generally considered to be a heuristic method providing a statistical evaluation of the results, where potential tree topologies are judged by how well they predict the observed sequences. While there have been several previous efforts to parallelize the maximum likelihood method, sequential implementations are more widely used in the biological research community. This is due to a lack of confidence in the results produced by the more recent, parallel programs. However, because phylogenetic inference can be extremely computationally intensive, with the number of v possible tree topologies growing exponentially with the number of species, parallelization is necessary to reduce the computation time to a reasonable amount. A parallel program was developed for phylogenetic inference based on the trusted algorithms of fastDNAml, a sequential program for phylogenetic inference utilizing the maximum likelihood approach. Parallelization is achieved using the popular master/workers scheme, where workers evaluate potential tree topologies in parallel. Three innovative optimizations are employed to alleviate the associated communication bottleneck encountered when using the master/workers technique with large-scale systems and problems. First, message packing reduces the number of messages sent out by the master, along with the associated overheads. Secondly, allowing workers to keep the best trees evaluated reduces the number of messages received by the master, as lowscoring results are discarded by the workers. Finally, multiple masters are utilized to parallelize the responsibilities of what is traditionally a single master process. These last two optimizations led to a dramatic improvement in performance over the unoptimized parallelization under the conditions tested. Message packing, however, demonstrated a slight reduction in performance. Although testing with large-scale systems and problems was not possible, results for all three optimizations suggested likely performance enhancement under such conditions, potentially leading to relief of the bottleneck.
THE INSIDIOUS BOOSTING OF THERMALLY PULSING ASYMPTOTIC GIANT BRANCH STARS IN INTERMEDIATE-AGE MAGELLANIC CLOUD CLUSTERS

In the recent controversy about the role of thermally pulsing asymptotic giant branch (TP-AGB) stars in evolutionary population synthesis (EPS) models of galaxies, one particular aspect is puzzling: TP-AGB models aimed at reproducing the lifetimes and integrated fluxes of the TP-AGB phase in Magellanic Cloud (MC) clusters, when incorporated into EPS models, are found to overestimate, to various extents, the TP-AGB contribution in resolved star counts and integrated spectra of galaxies. In this paper, we call attention to a particular evolutionary aspect, linked to the physics of stellar interiors, that in all probability is the main cause of this conundrum. As soon as stellar populations intercept the ages at which red giant branch stars first appear, a sudden and abrupt change in the lifetime of the core He-burning phase causes a temporary “boost” in the production rate of subsequent evolutionary phases, including the TP-AGB. For a timespan of about 0.1 Gyr, triple TP-AGB branches develop at slightly different initial masses, causing their frequency and contribution to the integrated luminosity of the stellar population to increase by a factor of ∼2. The boost occurs for turn-off masses of ∼1.75 M☉, just in the proximity of the expected peak in the TP-AGB lifetimes (for MC metallicities), and for ages of ∼1.6 Gyr. Coincidently, this relatively narrow age interval happens to contain the few very massive MC clusters that host most of the TP-AGB stars used to constrain stellar evolution and EPS models. This concomitance makes the AGB-boosting particularly insidious in the context of present EPS models. As we discuss in this paper, the identification of this evolutionary effect brings about three main consequences. First, we claim that present estimates of the TP-AGB contribution to the integrated light of galaxies derived from MC clusters are biased toward too large values. Second, the relative TP-AGB contribution of single-burst populations falling in this critical age range cannot be accurately derived by approximations such as the fuel consumption theorem, which ignore, by construction, the above evolutionary effect. Third, a careful revision of AGB star populations in intermediate-age MC clusters is urgently demanded, promisingly with the aid of detailed sets of stellar isochrones.
Triggered fragmentation in self-gravitating discs: forming fragments at small radii

We carry out three dimensional radiation hydrodynamical simulations of gravitationally unstable discs to explore the movement of mass in a disc following its initial fragmentation. We find that the radial velocity of the gas in some parts of the disc increases by up to a factor of approximately 10 after the disc fragments, compared to before. While the movement of mass occurs in both the inward and outward directions, the inwards movement can cause the inner spirals of a self-gravitating disc to become sufficiently dense such that they can potentially fragment. This suggests that the dynamical behaviour of fragmented discs may cause subsequent fragmentation to occur at smaller radii than initially expected, but only after an initial fragment has formed in the outer disc.
Phase diagram of Yang-Mills theories in the presence of a θ term

We study the phase diagram of non-Abelian pure gauge theories in the presence of a topological theta term. The dependence of the deconfinement temperature on theta is determined on the lattice both by analytic continuation and by reweighting, obtaining consistent results. The general structure of the diagram is discussed on the basis of large-N considerations and of the possible analogies and dualities existing with the phase diagram of QCD in presence of an imaginary baryon chemical potential.
Glutathione and Glutaredoxin in Redox Regulation and Cell Signaling of the Lens

The ocular lens has a very high content of the antioxidant glutathione (GSH) and the enzymes that can recycle its oxidized form, glutathione disulfide (GSSG), for further use. It can be synthesized in the lens and, in part, transported from the neighboring anterior aqueous humor and posterior vitreous body. GSH is known to protect the thiols of the structural lens crystallin proteins from oxidation by reactive oxygen species (ROS) so the lens can maintain its transparency for proper visual function. Age-related lens opacity or senile cataract is the major visual impairment in the general population, and its cause is closely associated with aging and a constant exposure to environmental oxidative stress, such as ultraviolet light and the metabolic end product, H2O2. The mechanism for senile cataractogenesis has been hypothesized as the results of oxidation-induced protein-thiol mixed disulfide formation, such as protein-S-S-glutathione and protein-S-S-cysteine mixed disulfides, which if not reduced in time, can change the protein conformation to allow cascading modifications of various kinds leading to protein–protein aggregation and insolubilization. The consequence of such changes in lens structural proteins is lens opacity. Besides GSH, the lens has several antioxidation defense enzymes that can repair oxidation damage. One of the specific redox regulating enzymes that has been recently identified is thioltransferase (glutaredoxin 1), which works in concert with GSH, to reduce the oxidative stress as well as to regulate thiol/disulfide redox balance by preventing protein-thiol mixed disulfide accumulation in the lens. This oxidation-resistant and inducible enzyme has multiple physiological functions. In addition to protecting structural proteins and metabolic enzymes, it is able to regulate the redox signaling of the cells during growth factor-stimulated cell proliferation and other cellular functions. This review article focuses on describing the redox regulating functions of GSH and the thioltransferase enzyme in the ocular lens.
Efficacy of crustal superfluid neutrons in pulsar glitch models

In order to assess the ability of purely crust-driven glitch models to match the observed glitch activity in the Vela pulsar, we conduct a systematic analysis of the dependence of the fractional moment of inertia of the inner crustal neutrons on the stiffness of the nuclear symmetry energy at saturation density $L$. We take into account both crustal entrainment and the fact that only a fraction $Y_{\rm g}$ of the core neutrons may couple to the crust on the glitch-rise timescale. We use a set of consistently-generated crust and core compositions and equations-of-state which are fit to results of low-density pure neutron matter calculations. When entrainment is included at the level suggested by recent microscopic calculations and the core is fully coupled to the crust, the model is only able to account for the Vela glitch activity for a 1.4$M_{\odot}$ star if the equation of state is particularly stiff $L>100$ MeV. However, an uncertainty of about 10\% in the crust-core transition density and pressure allows for the Vela glitch activity to be marginally accounted for in the range $L\approx30-60$MeV consistent with a range of experimental results. Alternatively, only a small amount of core neutrons need be involved. If less than 50\% of the core neutrons are coupled to the crust during the glitch, we can also account for the Vela glitch activity using crustal neutrons alone for EOSs consistent with the inferred range of $L$. We also explore the possibility of Vela being a high-mass neutron star, and of crustal entrainment being reduced or enhanced relative to its currently predicted values.
Electric breakdown effect in the current-voltage characteristics of amorphous indium oxide thin films near the superconductor-insulator transition

Current-voltage characteristics in the insulator bordering superconductivity in disordered thin films exhibit current jumps of several orders of magnitude due to the development of a thermally bistable electronic state at very low temperatures. In this high-resolution study we find that the jumps can be composed of many (up to 100) smaller jumps that appear to be random. This indicates that inhomogeneity develops near the transition to the insulator and that the current breakdown proceed via percolative paths spanning from one electrode to the other.
HIGH-RESOLUTION HELIOSEISMIC IMAGING OF SUBSURFACE STRUCTURES AND FLOWS OF A SOLAR ACTIVE REGION OBSERVED BY HINODE

We analyze a solar active region observed by the Hinode Ca ii H line using the time–distance helioseismology technique, and infer wave-speed perturbation structures and flow fields beneath the active region with a high spatial resolution. The general subsurface wave-speed structure is similar to the previous results obtained from Solar and Heliospheric Observatory/Michelson Doppler Imager observations. The general subsurface flow structure is also similar, and the downward flows beneath the sunspot and the mass circulations around the sunspot are clearly resolved. Below the sunspot, some organized divergent flow cells are observed, and these structures may indicate the existence of mesoscale convective motions. Near the light bridge inside the sunspot, hotter plasma is found beneath, and flows divergent from this area are observed. The Hinode data also allow us to investigate potential uncertainties caused by the use of phase-speed filter for short travel distances. Comparing the measurements with and without the phase-speed filtering, we find out that inside the sunspot, mean acoustic travel times are in basic agreement, but the values are underestimated by a factor of 20%–40% inside the sunspot umbra for measurements with the filtering. The initial acoustic tomography results from Hinode show a great potential of using high-resolution observations for probing the internal structure and dynamics of sunspots.
UNVEILING THE PHYSICS OF LOW-LUMINOSITY AGNs THROUGH X-RAY VARIABILITY: LINER VERSUS SEYFERT 2

X-ray variability is very common in active galactic nuclei (AGNs), but these variations may not occur similarly in different families of AGNs. We aim to disentangle the structure of low-ionization nuclear emission-line regions (LINERs) compared to Seyfert 2s by the study of their spectral properties and X-ray variations. We assembled the X-ray spectral parameters and variability patterns, which were obtained from simultaneous spectral fittings. Major differences are observed in the X-ray luminosities and the Eddington ratios, which are higher in Seyfert 2s. Short-term X-ray variations were not detected, while long-term changes are common in LINERs and Seyfert 2s. Compton-thick sources generally do not show variations, most probably because the AGN is not accesible in the 0.5–10 keV energy band. The changes are mostly related to variations in the nuclear continuum, but other patterns of variability show that variations in the absorbers and at soft energies can be present in a few cases. We conclude that the X-ray variations may occur similarly in LINERs and Seyfert 2s, i.e., they are related to the nuclear continuum, although they might have different accretion mechanisms. Variations at UV frequencies are detected in LINER nuclei but not in Seyfert 2s. This is suggestive of at least some LINERs having an unobstructed view of the inner disk where the UV emission might take place, with UV variations being common in them. This result might be compatible with the disappeareance of the torus and/or the broad-line region in at least some LINERs.