Miracle-dz/UniFAR-FTUs huggingface dataset:
Sensemaking in the early stages of the COVID‐19 pandemic: A narrative exploration of polarised morality in an NHS Trust

Abstract This article presents an analysis of personal diaries kept by health‐care staff within a specialist NHS Trust in England during the initial 3 months of the COVID‐19 pandemic. It adopts a moral sensemaking perspective to explore how NHS employees mobilised and reframed ideas of right and wrong in order to make sense of unprecedented uncertainty and displacement. By focussing on how the macro and micro politics of the pandemic were played out in the organisation, the study finds that polarised moral judgements were invoked in order to justify and rationalise a broad array of associated emergent emotions, intuitions, behaviours and practices. This polarisation of moral responses could be seen as a desire to bring order out of chaos and put matters back into place following displacement. This is inevitably an ongoing, complex and variegated enterprise whose results can be as often discomforting as they can be reassuring. Indeed, while moral sensemaking was partly beneficial for staff in that it promoted a greater sense of camaraderie and support for others, it also appeared to have darker consequences in terms of staff wellbeing and the development of more impermeable social boundaries across the organisation through processes of moral ‘othering’.
Gestational exposure to triphenyl phosphate induces epigenetic modifications in C57Bl/6 fetal liver

Triphenyl phosphate (TPHP) is a chemical flame retardant and plasticizer which is added to consumer and industrial products. The developmental origins of health and disease hypothesis postulate that in utero exposures can have later‐in‐life effects on the developing fetus and can alter fetal gene expression. This study aimed to determine whether epigenetic modifications occurred following in utero TPHP exposure in mice and whether these changes were dose and/or sex‐dependent.
KINEMATICALLY IDENTIFIED RECOILING SUPERMASSIVE BLACK HOLE CANDIDATES IN SDSS QSOs WITH z < 0.25

We have performed a spectral decomposition to search for recoiling supermassive black holes (rSMBHs) in Sloan Digital Sky Survey (SDSS) quasi-stellar objects (QSOs) with z < 0.25. Out of 1271 QSOs, we have identified 26 rSMBH candidates that are recoiling toward us. The projected recoil velocities range from −76 to −307 km s−1 with a mean of −149 ± 58 km s−1. Most of the rSMBH candidates are hosted by gas-rich luminous infrared galaxies (LIRGs)/ultra-luminous infrared galaxies (ULIRGs), but only 23% of them show signs of tidal features, which suggests that a majority of them are advanced mergers. We find that the black hole masses MBH of the rSMBH candidates are on average ∼5 times smaller than those of their stationary counterparts and cause a scatter in the relation. The Eddington ratios of all of the rSMBH candidates are larger than 0.1, with a mean of 0.52 ± 0.27, suggesting that they are actively accreting mass. Velocity shifts in high-excitation coronal lines suggest that the rSMBH candidates are recoiling with an average velocity of about −265 km s−1. The electron density in the narrow line region of the H ii rSMBH candidates is about 1/10 of that in active galactic nucleus (AGN) rSMBH candidates, probably because the AGN in the former was more spatially offset than that in the latter. The estimated spatial offsets between the rSMBH candidate and the center of the host galaxy range from 0. ″21 to 1. ″97 and need to be confirmed spatially with high-resolution adaptive optics imaging observations.
MlrA, a MerR family regulator in Vibrio cholerae, senses the anaerobic signal in the small intestine of the host to promote bacterial intestinal colonization

ABSTRACT Vibrio cholerae (V. cholerae), one of the most important bacterial pathogens in history, is a gram-negative motile bacterium that causes fatal pandemic disease in humans via oral ingestion of contaminated water or food. This process involves the coordinated actions of numerous regulatory factors. The MerR family regulators, which are widespread in prokaryotes, have been reported to be associated with pathogenicity. However, the role of the MerR family regulators in V. cholerae virulence remains unknown. Our study systematically investigated the influence of MerR family regulators on intestinal colonization of V. cholerae within the host. Among the five MerR family regulators, MlrA was found to significantly promote the colonization capacity of V. cholerae in infant mice. Furthermore, we revealed that MlrA increases bacterial intestinal colonization by directly enhancing the expression of tcpA, which encodes one of the most important virulence factors in V. cholerae, by binding to its promoter region. In addition, we revealed that during infection, mlrA is activated by anaerobic signals in the small intestine of the host through Fnr. In summary, our findings reveal a MlrA-mediated virulence regulation pathway that enables V. cholerae to sense environmental signals at the infection site to precisely activate virulence gene expression, thus providing useful insights into the pathogenic mechanisms of V. cholerae.
CAMPR4: a database of natural and synthetic antimicrobial peptides

Abstract There has been an exponential increase in the design of synthetic antimicrobial peptides (AMPs) for its use as novel antibiotics. Synthetic AMPs are substantially enriched in residues with physicochemical properties known to be critical for antimicrobial activity; such as positive charge, hydrophobicity, and higher alpha helical propensity. The current prediction algorithms for AMPs have been developed using AMP sequences from natural sources and hence do not perform well for synthetic peptides. In this version of CAMP database, along with updating sequence information of AMPs, we have created separate prediction algorithms for natural and synthetic AMPs. CAMPR4 holds 24243 AMP sequences, 933 structures, 2143 patents and 263 AMP family signatures. In addition to the data on sequences, source organisms, target organisms, minimum inhibitory and hemolytic concentrations, CAMPR4 provides information on N and C terminal modifications and presence of unusual amino acids, as applicable. The database is integrated with tools for AMP prediction and rational design (natural and synthetic AMPs), sequence (BLAST and clustal omega), structure (VAST) and family analysis (PRATT, ScanProsite, CAMPSign). The data along with the algorithms of CAMPR4 will aid to enhance AMP research. CAMPR4 is accessible at http://camp.bicnirrh. res.in/.
Probiotic Supplement for the Prevention of Gestational Diabetes: A Meta-Analysis of Randomized Controlled Trials

Abstract Background Probiotic supplements may have some potential in preventing gestational diabetes, and this meta-analysis aims to explore the efficacy of probiotic supplements to prevent gestational diabetes. Methods PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases were systematically searched, and we included randomized controlled trials (RCTs) assessing the effect of probiotic supplements on the incidence of gestational diabetes mellitus. Meta-analysis was performed using the fixed-effect or random-effect model as appropriate. Results Six RCTs were finally included in the meta-analysis. Overall, compared with control intervention in pregnant women, probiotic supplementation intervention showed no obvious impact on the incidence of gestational diabetes (OR=0.68; 95% CI=0.39 to 1.20; P=0.18), fasting plasma glucose (SMD=−0.05; 95% CI=−0.29 to 0.19; P=0.69), 2 h-OGTT (SMD=−0.07; 95% CI=−0.27 to 0.13; P=0.47), gestational age (SMD=0.04; 95% CI=−0.14 to 0.21; P=0.69) or preeclampsia (OR=1.22; 95% CI=0.83 to 1.78; P=0.31). Conclusions Probiotic supplementation was confirmed to have no benefits for the prevention of gestational diabetes.
New Transformative Possibilities for Ovonic Devices

The Ovonic Phase Change Memory is critical in the quest to meet the increasing commercial needs for new information systems. The important paper of DerChang Kau et al. [1], describing a stackable cross point phase change memory, resulting in a three dimensional device which includes the Ovonic Threshold Switch, therefore permits a significant expansion of our field. I will propose and show that our basic science allows for other transformative changes that combine both threshold and phase change mechanisms in a single device. The mechanisms that I will describe have already been proven. My aim is to provide the understanding of these mechanisms so that new devices based on them can become important components that illustrate the great potential of our field. I know of no better place to give this kind of talk than Italy where I have had some of my happiest memories of working together with Roberto Bez and his wonderful colleagues and collaborators.
UNLEASHING POSITIVE FEEDBACK: LINKING THE RATES OF STAR FORMATION, SUPERMASSIVE BLACK HOLE ACCRETION, AND OUTFLOWS IN DISTANT GALAXIES

Pressure-regulated star formation is a simple variant on the usual supernova-regulated star formation efficiency that controls the global star formation rate as a function of cold gas content in star-forming galaxies, and accounts for the Schmidt–Kennicutt law in both nearby and distant galaxies. Inclusion of active galactic nucleus (AGN) induced pressure, by jets and/or winds that flow back onto a gas-rich disk, can lead, under some circumstances, to significantly enhanced star formation rates, especially at high redshift and most likely followed by the more widely accepted phase of star formation quenching. Simple expressions are derived that relate supermassive black hole growth, star formation, and outflow rates. The ratios of black hole to spheroid mass and of both black hole accretion and outflow rates to star formation rate are predicted as a function of time. I suggest various tests of the AGN-triggered star formation hypothesis.
Synthetic extinction maps around intermediate-mass black holes in Galactic globular clusters

During the last decades, much effort has been devoted to explain the discrepancy between the amount of intracluster medium (ICM) estimated from stellar evolution theories and that emerging from observations in globular clusters (GCs). One possible scenario is the accretion of this medium by an intermediate-mass black hole (IMBH) at the centre of the cluster. In this work, we aim at modelling the cluster colour-excess profile as a tracer of the ICM density, both with and without an IMBH. Comparing the profiles with observations allows us to test the existence of IMBHs and their possible role in the cleansing of the ICM. We derive the intracluster density profiles from hydrodynamical models of accretion onto a central IMBH in a GC and we determine the corresponding dust density. This model is applied to a list of 25 Galactic GCs. We find that central IMBHs decrease the ICM by several orders of magnitude. In a subset of 9 clusters, the absence of the black hole combined with a low intracluster medium temperature would be at odds with present gas mass content estimations. As a result, we conclude that IMBHs are an effective cleansing mechanism of the ICM of GCs. We construct synthetic extinction maps for M 62 and ω Cen, two clusters in the small subset of 9 with observed 2D extinction maps. We find that under reasonable assumptions regarding the model parameters, if the gas temperature in M 62 is close to 8000 K, an IMBH needs to be invoked. Further ICM observations regarding both the gas and dust in GCs could help to settle this issue.
The case for primordial black holes as dark matter

The aim of this paper is to present the case that stellar mass primordial black holes make up the dark matter component of the Universe. A near critical density of compact bodies implies that most lines of sight will be gravitationally microlensed, and the paper focuses on looking for the predicted effects on quasar brightness and spectral variations. These signatures of microlensing include the shape of the Fourier power spectrum of the light curves, near achromatic and statistically symmetric variations, and the absence of time dilation in the time-scale of variability. For spectral changes it is predicted that as the continuum varies there is little corresponding change in the strength of the broad lines. In all these cases, the observations are found to be consistent with the predictions for microlensing by a population of stellar mass compact bodies. For multiply lensed quasar systems where the images vary independently and microlensing is the generally accepted explanation, the case is made that stellar populations are too small to produce the observed effects, and that the only plausible alternative is a population of compact dark matter bodies of around a stellar mass along the line of sight. The most serious objection to dark matter in the form of compact bodies has come from observations of microlensing of stars in the Magellanic clouds. In this paper, the expected event rate is re-analysed using more recent values for the structure and dynamics of the Galactic halo, and it is shown that there is then no conflict with the observations. Finally, the possible identity of a near critical density of dark matter in the form of stellar mass compact bodies is reviewed, with the conclusion that by far the most plausible candidates are primordial black holes formed during the QCD epoch. The overall conclusion of the paper is that primordial black holes should be seen alongside elementary particles as viable dark matter candidates.
Narrow escape: how ionizing photons escape from disc galaxies

In this paper we calculate the escape fraction (f(esc)) of ionizing photons from starburst galaxies. Using 2D axisymmetric hydrodynamic simulations, we study superbubbles created by overlapping supernovae in OB associations. We calculate the escape fraction of ionizing photons from the centre of the disc along different angles through the superbubble and the gas disc. After convolving with the luminosity function of OB associations, we show that the ionizing photons escape within a cone of similar to 40 degrees, consistent with observations of nearby galaxies. The evolution of the escape fraction with time shows that it falls initially as cold gas is accumulated in a dense shell. After the shell crosses a few scaleheights and fragments, the escape fraction through the polar regions rises again. The angle-averaged escape fraction cannot exceed similar to1 - cos (1 rad)] = 0.5 from geometrical considerations (using the emission cone opening angle). We calculate the dependence of the time-and angle-averaged escape fraction on the mid-plane disc gas density (in the range n(0) = 0.15-50 cm(-3)) and the disc scaleheight (between z(0) = 10 and 600 pc). We find that the escape fraction is related to the disc parameters (the mid-plane disc density and scaleheight) roughly so that f(esc)(alpha)n(0)(2)z(0)(3) (with alpha approximate to 2.2) is a constant. For discs with a given warm neutral medium temperature, massive discs have lower escape fraction than low-mass galaxies. For Milky Way ISM parameters, we find f(esc) similar to 5 per cent, and it increases to approximate to 10 per cent for a galaxy 10 times less massive. We discuss the possible effects of clumpiness of the ISM on the estimate of the escape fraction and the implications of our results for the reionization of the Universe.
An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays

Abstract In the adaptive immune system, V(D)J recombination initiates the production of a diverse antigen receptor repertoire in developing B and T cells. Recombination activating proteins, RAG1 and RAG2 (RAG1/2), catalyze V(D)J recombination by cleaving adjacent to recombination signal sequences (RSSs) that flank antigen receptor gene segments. Previous studies defined the consensus RSS as containing conserved heptamer and nonamer sequences separated by a less conserved 12 or 23 base-pair spacer sequence. However, many RSSs deviate from the consensus sequence. Here, we developed a cell-based, massively parallel assay to evaluate V(D)J recombination activity on thousands of RSSs where the 12-RSS heptamer and adjoining spacer region contained randomized sequences. While the consensus heptamer sequence (CACAGTG) was marginally preferred, V(D)J recombination was highly active on a wide range of non-consensus sequences. Select purine/pyrimidine motifs that may accommodate heptamer unwinding in the RAG1/2 active site were generally preferred. In addition, while different coding flanks and nonamer sequences affected recombination efficiency, the relative dependency on the purine/pyrimidine motifs in the RSS heptamer remained unchanged. Our results suggest RAG1/2 specificity for RSS heptamers is primarily dictated by DNA structural features dependent on purine/pyrimidine pattern, and to a lesser extent, RAG:RSS base-specific interactions.
Constraints on cosmic ray and PeV neutrino production in blazars

IceCube has detected a cumulative flux of PeV neutrinos, which origin is unknown. Blazars, active galactic nuclei with relativistic jets pointing to us, are long and widely expected to be one of the strong candidates of high energy neutrino sources. The neutrino production depends strongly on the cosmic ray power of blazar jets, which is largely unknown. The recent null results in stacking searches of neutrinos for several blazar samples by IceCube put upper limits on the neutrino fluxes from these blazars. Here we compute the cosmic ray power and PeV neutrino flux of Fermi-LAT blazars, and find that the upper limits for known blazar sources give stringent constraint on the cosmic ray loading factor of blazar jets (i.e., the ratio of the cosmic ray to bolometric radiation luminosity of blazar jets), ξcr ≲ (2–10)ζ−1 (with ζ ≲ 1 the remained fraction of cosmic ray energy when propagate into the blazar broad line region) for flat cosmic ray spectrum, and that the cumulative PeV neutrino flux contributed by all-sky blazars is a fraction ≲ (10–50)% of the IceCube detected flux.
Religiousness and Sexual Values Predict Sexual Incongruence: Results from a U.S. Nationally Representative Study

Abstract The present work aimed to clarify commonly endorsed sexual values in the general U.S. population as well as the association between sexual values and incongruence. Study 1 recruited adults (N = 923; 51.8% women; M age = 35.5, SD = 10.8) to answer a free response question about sexual values via Amazon’s Mechanical Turk, while Study 2 posed the same question to a weighted, nationally representative U.S. sample (N = 2,519; 51.4% women; M age = 48.2, SD = 17.8). Data collection was completed in 2017 and 2019, respectively. Results from these cross-sectional studies demonstrated that, although religiousness predicted sexual incongruence, conservative sexual values predicted variance in sexual incongruence, over and above the effects of religiousness.
Proton temperature-anisotropy-driven instabilities in weakly collisional plasmas: Hybrid simulations

Kinetic instabilities in weakly collisional, high beta plasmas are investigated using two-dimensional hybrid expanding box simulations with Coulomb collisions modeled through the Langevin equation (corresponding to the Fokker-Planck one). The expansion drives a parallel or perpendicular temperature anisotropy (depending on the orientation of the ambient magnetic field). For the chosen parameters the Coulomb collisions are important with respect to the driver but are not strong enough to keep the system stable with respect to instabilities driven by the proton temperature anisotropy. In the case of the parallel temperature anisotropy the dominant oblique fire hose instability efficiently reduces the anisotropy in a quasilinear manner. In the case of the perpendicular temperature anisotropy the dominant mirror instability generates coherent compressive structures which scatter protons and reduce the temperature anisotropy. For both the cases the instabilities generate temporarily enough wave energy so that the corresponding (anomalous) transport coefficients dominate over the collisional ones and their properties are similar to those in collisionless plasmas.
Spontaneous Crystallization of Light and Ultracold Atoms

Coherent scattering of light from ultracold atoms involves an exchange of energy and momentum introducing a wealth of non-linear dynamical phenomena. As a prominent example particles can spontaneously form stationary periodic configurations which simultaneously maximize the light scattering and minimize the atomic potential energy in the emerging optical lattice. Such self-ordering effects resulting in periodic lattices via bimodal symmetry breaking have been experimentally observed with cold gases and Bose-Einstein condensates (BECs) inside an optical resonator. Here we study a new regime of periodic pattern formation for an atomic BEC in free space, driven by far off-resonant counterpropagating and non-interfering lasers of orthogonal polarization. In contrast to previous works, no spatial light modes are preselected by any boundary conditions and the transition from homogeneous to periodic order amounts to a crystallization of both light and ultracold atoms breaking a continuous translational symmetry. In the crystallized state the BEC acquires a phase similar to a supersolid with an emergent intrinsic length scale whereas the light-field forms an optical lattice allowing phononic excitations via collective back scattering, which are gapped due to the infinte-range interactions. The studied system constitutes a novel configuration allowing the simulation of synthetic solid state systems with ultracold atoms including long-range phonon dynamics.
Lipid saturation induces degradation of squalene epoxidase for sterol homeostasis and cell survival

The authors describe the ER-associated degradation of Erg1 under increased membrane lipid saturation and show its importance in balancing sterol levels for membrane integrity in budding yeast. A fluid membrane containing a mix of unsaturated and saturated lipids is essential for life. However, it is unclear how lipid saturation might affect lipid homeostasis, membrane-associated proteins, and membrane organelles. Here, we generate temperature-sensitive mutants of the sole fatty acid desaturase gene OLE1 in the budding yeast Saccharomyces cerevisiae. Using these mutants, we show that lipid saturation triggers the endoplasmic reticulum–associated degradation (ERAD) of squalene epoxidase Erg1, a rate-limiting enzyme in sterol biosynthesis, via the E3 ligase Doa10-Ubc7 complex. We identify the P469L mutation that abolishes the lipid saturation–induced ERAD of Erg1. Overexpressed WT or stable Erg1 mutants all mislocalize into foci in the ole1 mutant, whereas the stable Erg1 causes aberrant ER and severely compromises the growth of ole1, which are recapitulated by doa10 deletion. The toxicity of the stable Erg1 and doa10 deletion is due to the accumulation of lanosterol and misfolded proteins in ole1. Our study identifies Erg1 as a novel lipid saturation–regulated ERAD target, manifesting a close link between lipid homeostasis and proteostasis that maintains sterol homeostasis under the lipid saturation condition for cell survival.
Confinement and duality in supersymmetric gauge theories

In this thesis we review the Seiberg-Witten solution of four dimensional N=2 gauge theories, the six-dimensional construction of these models recently proposed by Gaiotto and the BPS quiver technique for the determination of the BPS spectrum of N=2 theories. We then study how these recent developments allow to better understand nonperturbative aspects such as confinement and dynamical symmetry breaking in the N=1 theories obtained starting from N=2 SQCD and adding a mass term for the chiral multiplet in the adjoint of the gauge group. We find an unusual realization of the 't Hooft-Mandelstam mechanism, in which confinement and dynamical symmetry breaking are due to the condensation of different degrees of freedom.