Miracle-dz/UniFAR-FTUs huggingface dataset:
TESTING IN SITU ASSEMBLY WITH THE KEPLER PLANET CANDIDATE SAMPLE

We present a Monte Carlo model for the structure of low-mass (total mass <25 M⊕) planetary systems that form by the in situ gravitational assembly of planetary embryos into final planets. Our model includes distributions of mass, eccentricity, inclination, and period spacing that are based on the simulation of a disk of 20 M⊕, forming planets around a solar-mass star, and assuming a power-law surface density distribution that drops with distance a as ∝ a−1.5. The output of the Monte Carlo model is then subjected to the selection effects that mimic the observations of a transiting planet search such as that performed by the Kepler satellite. The resulting comparison of the output to the properties of the observed sample yields an encouraging agreement in terms of the relative frequencies of multiple-planet systems and the distribution of the mutual inclinations when moderate tidal circularization is taken into account. The broad features of the period distribution and radius distribution can also be matched within this framework, although the model underpredicts the distribution of small period ratios. This likely indicates that some dissipation is still required in the formation process. The most striking deviation between the model and observations is in the ratio of single to multiple systems in that there are roughly 50% more single-planet candidates observed than are produced in any model population. This suggests that some systems must suffer additional attrition to reduce the number of planets or increase the range of inclinations.
The origin of the tilted disc in the low-mass X-ray binary GR Mus (XB 1254−690)

We present photometric and spectroscopic observations of the low mass X-ray binary GRMus (XB1254 690), and find strong evidence for the presence of a negative superhump with a period that is 2.4±0.3% shorter than the orbital. This provides further support that GRMus indeed harbours a precessing accretion disk (with a period of 6.74±0.07 day) that has retrograde precession and is completely tilted out of the orbital plane along its line of nodes. This tilt causes a large fraction of the gas in the accretion stream to either over- or underflow the accretion disk instead of hitting the disk rim, and could be a feature of all low mass X-ray binaries with characteristics similar to GRMus (i.e. the so-called atoll sources). Furthermore, we also find marginal evidence for the presence of a positive superhump, suggesting that the accretion disk in GRMus is eccentric due to tidal resonances. If true, than the relationship between the positive superhump period excess and the mass ratio (q) provides a constraint of q=Mdonor/MNS=0.33-0.36. Together with the radial velocity semi-amplitude measurements of the compact object, and previous modeling of the inclination we obtain a mass for the neutron star of 1.26MNS/M⊙61.8 (95% confidence).
Helminth exposure protects against murine SARS-CoV-2 infection through macrophage dependent T cell activation

Helminth endemic regions report lower COVID-19 morbidity and mortality. Here, we show that lung remodeling from a prior infection with a lung migrating helminth, Nippostrongylus brasiliensis, enhances viral clearance and survival of human-ACE2 transgenic mice challenged with SARS-CoV-2 (SCV2). This protection is associated with a lymphocytic infiltrate including an increased accumulation of pulmonary SCV2-specific CD8+ T cells and anti-CD8 antibody depletion abrogated the N. brasiliensis-mediated reduction in viral loads. Pulmonary macrophages with a type-2 transcriptional signature persist in the lungs of N. brasiliensis exposed mice after clearance of the parasite and establish a primed environment for increased antigen presentation. Accordingly, depletion of macrophages ablated the augmented viral clearance and accumulation of CD8+ T cells driven by prior N. brasiliensis infection. Together, these findings support the concept that lung migrating helminths can limit disease severity during SCV2 infection through macrophage-dependent enhancement of anti-viral CD8+ T cell responses.
Probabilistic entailment and iterated conditionals

In this paper we exploit the notions of conjoined and iterated conditionals, which are defined in the setting of coherence by means of suitable conditional random quantities with values in the interval $[0,1]$. We examine the iterated conditional $(B|K)|(A|H)$, by showing that $A|H$ p-entails $B|K$ if and only if $(B|K)|(A|H) = 1$. Then, we show that a p-consistent family $\mathcal{F}=\{E_1|H_1,E_2|H_2\}$ p-entails a conditional event $E_3|H_3$ if and only if $E_3|H_3=1$, or $(E_3|H_3)|QC(\mathcal{S})=1$ for some nonempty subset $\mathcal{S}$ of $\mathcal{F}$, where $QC(\mathcal{S})$ is the quasi conjunction of the conditional events in $\mathcal{S}$. Then, we examine the inference rules $And$, $Cut$, $Cautious $ $Monotonicity$, and $Or$ of System~P and other well known inference rules ($Modus$ $Ponens$, $Modus$ $Tollens$, $Bayes$). We also show that $QC(\mathcal{F})|\mathcal{C}(\mathcal{F})=1$, where $\mathcal{C}(\mathcal{F})$ is the conjunction of the conditional events in $\mathcal{F}$. We characterize p-entailment by showing that $\mathcal{F}$ p-entails $E_3|H_3$ if and only if $(E_3|H_3)|\mathcal{C}(\mathcal{F})=1$. Finally, we examine \emph{Denial of the antecedent} and \emph{Affirmation of the consequent}, where the p-entailment of $(E_3|H_3)$ from $\mathcal{F}$ does not hold, by showing that $(E_3|H_3)|\mathcal{C}(\mathcal{F})\neq1. $
THE SIMPLE SURVEY: OBSERVATIONS, REDUCTION, AND CATALOG

We present the Spitzer IRAC/MUSYC Public Legacy Survey in the Extended CDF-South (SIMPLE), which consists of deep IRAC observations covering the ∼1600 arcmin2 area surrounding GOODS-S. The limiting magnitudes of the SIMPLE IRAC mosaics typically are 23.8, 23.6, 21.9, and 21.7, at 3.6 μm, 4.5 μm, 5.8 μm, and 8.0 μm, respectively (5σ total point source magnitudes in AB). The SIMPLE IRAC images are combined with the 10′ × 15′ GOODS IRAC mosaics in the center. We give detailed descriptions of the observations, data reduction, and properties of the final images, as well as the detection and photometry methods used to build a catalog. Using published optical and near-infrared data from the Multiwavelength Survey by Yale-Chile (MUSYC), we construct an IRAC-selected catalog, containing photometry in UBVRIz′JHK, [3.6 μm], [4.5 μm], [5.8 μm], and [8.0 μm]. The catalog contains 43,782 sources with S/N >5 at 3.6 μm, 19,993 of which have 13-band photometry. We compare this catalog to the publicly available MUSYC and FIREWORKS catalogs and discuss the differences. Using a high signal-to-noise sub-sample of 3391 sources with ([3.6] + [4.5])/2 < 21.2, we investigate the star formation rate history of massive galaxies out to z ∼ 1.8. We find that at z ∼ 1.8 at least 30% ± 7% of the most massive galaxies (M* >1011M☉) are passively evolving, in agreement with earlier results from surveys covering less area.
Balancing selection at a wing pattern locus is associated with major shifts in 1 genome-wide patterns of diversity and gene flow in a butterfly 2

: Selection shapes genetic diversity around target mutations, yet little is known about how 28 selection on specific loci affects the genetic trajectories of populations, including their genome- 29 wide patterns of diversity and demographic responses. Here we study the patterns of genetic 30 variation and geographic structure in a neotropical butterfly, Heliconius numata , and its closely 31 related allies in the so-called melpomene-silvaniform clade. H. numata is known to have evolved an 32 inversion supergene which controls variation in wing patterns involved in mimicry associations 33 with distinct groups of co-mimics. Butterflies show disassortative mate preferences and 34 heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) 35 among extant polymorphic and monomorphic populations of H. numata , 2) between H. numata and 36 its close relatives, and 3) between ancestral lineages. We show that H. numata populations which 37 carry the inversions as a balanced polymorphism show markedly distinct patterns of diversity 38 compared to all other taxa. They show the highest genetic diversity and effective population size 39 estimates in the entire clade, as well as a low level of geographic structure and isolation by distance 40 across the entire Amazon basin. By contrast, monomorphic populations of H. numata as well as its 41 sister species and their ancestral lineages all show lower effective population sizes and genetic 42 diversity, and higher levels of geographical structure across the continent. One hypothesis is that the 43 large effective population size of polymorphic populations could be caused by the shift to a regime 44 of balancing selection due to the genetic load and disassortative preferences associated with 45 inversions. Testing this hypothesis with forward simulations supported the observation of increased 46 diversity in populations with the supergene. Our results are consistent with the hypothesis that the 47 formation of a supergene triggered a change in gene flow, causing a general increase in genetic 48 diversity and the homogenisation of genomes at the continental scale.
An image cryptography method in highly error-prone DNA storage channel

Rapid development in synthetic technologies has boosted DNA as a potential medium for large-scale data storage. Meanwhile, how to implement data security in DNA storage system is still an unsolved problem. In this paper, we propose an image encryption method based on the modulation-based storage architecture. The key idea is to take advantage of the unpredictable modulation signals to encrypt image in highly error-prone DNA storage channel. Numerical results demonstrate that our image encryption method is feasible and effective with excellent security against various attacks (statistical, differential, noise and data loss, etc.). Compared with other methods by DNA molecules hybridization reaction, the proposed method is more reliable and feasible for large-scale applications.
Local and global information and equations with left and right invertible operators in the free Fock space

The subject of the work is short description of huge amount of n-point information (n-pi) about the system. Methods for solving equations that satisfy such information are considered. Possible interpretation of left and right invertible operators appearing in these equations is also proposed. For local information, the creation and annihilation operators satisfying the Cuntz relations are introduced. It is also introduced the vector describing the local vacuum which completes the equation for n-pi with a global information. An important components of the work are examples of local operator-valued functions.
Persulfidation of DJ-1: Mechanism and Consequences

DJ-1 (also called PARK7) is a ubiquitously expressed protein involved in the etiology of Parkinson disease and cancers. At least one of its three cysteine residue is functionally essential, and its oxidation state determines the specific function of the enzyme. DJ-1 was recently reported to be persulfidated in mammalian cell lines, but the implications of this post-translational modification have not yet been analyzed. Here, we report that recombinant DJ-1 is reversibly persulfidated at cysteine 106 by reaction with various sulfane donors and subsequently inhibited. Strikingly, this reaction is orders of magnitude faster than C106 oxidation by H2O2, and persulfidated DJ-1 behaves differently than sulfinylated DJ-1. Both these PTM most likely play a dedicated role in DJ-1 signaling or protective pathways.
Elasticity control of entangled chromosomes: crosstalk between condensin complexes and nucleosomes

Condensin-mediated loop extrusion is now considered as the main driving force of mitotic chromosome assembly. Recent experiments have shown, however, that a class of mutant condensin complexes deficient in loop extrusion can assemble chromosome-like structures in Xenopus egg extracts, although these structures are somewhat different from those assembled by wild-type condensin complexes. In the absence of topoisomerase II (topo II), the mutant condensin complexes produce an unusual round-shaped structure termed a ‘bean’, which consists of a DNA-dense central core surrounded by a DNA-sparse halo. The mutant condensin complexes accumulate in the core whereas histones are more concentrated in the halo than in the core. We consider that this peculiar structure serves as a model system to study how DNA entanglements, nucleosomes, and condensin functionally crosstalk with each other. To gain insight into how the bean structure is formed, here we construct a theoretical model. Our theory predicts that the core is formed by attractive interactions between mutant condensin complexes whereas the halo is stabilized by the energy reduction through the selective accumulation of nucleosomes. The formation of the halo increases the elastic free energy due to the DNA entanglement in the core, but the latter free energy is compensated by condensin complexes that suppress the assembly of nucleosomes.
Cell autonomous requirement of imprinted XCI in extra-embryonic polar trophoblast cells

In female mice the gene dosage from X chromosomes is adjusted by a process called X chromosome inactivation (XCI) that occurs in two steps. An imprinted form of XCI (iXCI) silencing the paternally inherited X chromosome (Xp) is initiated at the 2-4 cell stages. As extraembryonic cells including trophoblasts keep the Xp silenced, epiblast cells that give rise to the embryo proper reactivate the Xp and undergo a random form of XCI (rXCI) during peri-implantation stages. Lack of X dosage compensation leads to peri-implantation lethality due to inhibition of trophoblast stem cells. However, as the epiblast regulates the trophoblast lineage, the roles of iXCI vs rXCI in the early lethal phenotype remains unclear. We have investigated functions and expression of Rlim (Rnf12), an E3 ubiquitin ligase, and its target protein Rex1 (Zfp42) that control iXCI. Consistent with functions specifically for iXCI, we show an inverse correlation in the expression of Rlim and Rex1 throughout pre-implantation development, but an Rlim-independent downregulation of Rex1 in epiblast cells upon implantation. Moreover, disturbing the functional Rlim-Rex1 dynamics in females leads to cell fate confusion and premature differentiation specifically of the polar trophoblast stem cell pool. Thus, controlled by the Rlim-Rex1 axis, female mouse development requires iXCI in the polar trophoblast cell lineage.
NSC-derived exosomes enhance therapeutic effects of NSC transplantation on cerebral ischemia in mice

Transplantation of neural stem cells (NSCs) has been proved to promote functional rehabilitation of brain lesions including ischemic stroke. However, the therapeutic effects of NSC transplantation is limited by the low survival and differentiation rates of NSCs due to the harsh environment in the brain after ischemic stroke. Here, we employed NSCs derived from human induced pluripotent stem cells (iPSCs) together with exosomes extracted from NSCs to treat cerebral ischemia induced by middle cerebral artery occlusion/reperfusion (MCAO/R) in mice. The results showed that NSC-derived exosomes significantly reduced the inflammatory response, alleviated oxidative stress after NSC transplantation, and facilitated NSCs differentiation in vivo. The combination of NSCs with exosomes ameliorated the injury of brain tissue including cerebral infarct, neuronal death and glial scarring, and promoted the motor function recovery. To explore the underlying mechanisms, we analyzed the miRNA profiles of NSC-derived exosomes and the potential downstream genes. Our study provided the rationale for the clinical application of NSC-derived exosomes as a supportive adjuvant for NSC transplantation after stroke.
A Dynamic Bayesian Actor Model explains Endpoint Variability in Homing Tasks

Goal-directed navigation requires integrating information from a variety of internal and external spatial cues, representing them internally, planning, and executing motor actions sequentially. However, a comprehensive computational account of how these processes interact in an ambiguous, uncertain, and noisy environment giving rise to biases and variability observed in navigation behavior is currently unavailable. In this paper, we introduce an optimal control under uncertainty model, which provides a computational-level explanation of how landmarks and path integration interact and are combined to reduce variability in navigation. We apply our model to trajectory and end-point data from three previously published studies that employ a variant of the triangle completion task with landmarks. Contrary to observer models, which attribute human end-point variability to perceptual cue combination processes only, this dynamic Bayesian actor model provides a unifying account of a wide range of phenomena found in this task by considering variability in perception, action, and internal representations jointly. Taken together, these findings have wide-ranging implications for the analysis and interpretation of human navigation behavior, including resolution of seemingly contradictory results on cue integration in navigation.
Quantum dynamics of attractive versus repulsive bosonic Josephson junctions: Bose-Hubbard and full-Hamiltonian results

The quantum dynamics of one-dimensional bosonic Josephson junctions with attractive and repulsive interparticle interactions is studied by using the Bose-Hubbard model and by numerically exact computations of the full many-body Hamiltonian. A symmetry present in the Bose-Hubbard Hamiltonian dictates an equivalence between the evolution in time of the survival probability and the fragmentation of attractive and repulsive Josephson junctions with attractive and repulsive interactions of equal magnitude. The full many-body Hamiltonian does not possess this symmetry and, consequently, the dynamics of the attractive and repulsive junctions are different.
Electromagnetic Emission from Supermassive Binary Black Holes Approaching Merger

We present the first relativistic prediction of the electromagnetic emission from the surrounding gas of a supermassive binary black hole system approaching merger. Using a ray-tracing code to post-process data from a general relativistic 3D magnetohydrodynamic simulation, we generate images and spectra, and analyze the viewing angle dependence of the light emitted. When the accretion rate is relatively high, the circumbinary disk, accretion streams, and mini-disks combine to emit light in the UV/extreme-UV bands. We posit a thermal Compton hard X-ray spectrum for coronal emission; at high accretion rates, it is almost entirely produced in the mini-disks, but at lower accretion rates it is the primary radiation mechanism in the mini-disks and accretion streams as well. Due to relativistic beaming and gravitational lensing, the angular distribution of the power radiated is strongly anisotropic, especially near the equatorial plane.
Many-body corrections to cyclotron resonance in monolayer and bilayer graphene

Cyclotron resonance in graphene is studied with focus on many-body corrections to the resonance energies, which evade Kohn's theorem. The genuine many-body corrections turn out to derive from vacuum polarization, specific to graphene, which diverges at short wavelengths. Special emphasis is placed on the need for renormalization, which allows one to determine many-body corrections uniquely from one resonance to another. For bilayer graphene, in particular, both intralayer and interlayer coupling strengths undergo infinite renormalization; as a result, the renormalized velocity and interlayer coupling strength run with the magnetic field. A comparison of theory with the experimental data is made for both monolayer and bilayer graphene.
Type III and N solutions to quadratic gravity

We study exact vacuum solutions to quadratic gravity (QG) of the Weyl types N and III. We show that in an arbitrary dimension all Einstein spacetimes of the Weyl type N with an appropriately chosen effective cosmological constantare exact solutions to QG and we refer to explicitly known metrics within this class. For type III Einstein spacetimes, an additional constraint follows from the field equations of QG and examples of spacetimes obeying such constraint are given. However, type III pp-waves do not satisfy this constraint and thus do not solve QG. For type N, we also study a wider class of spacetimes admitting a pure radiation term in the Ricci tensor. In contrast to the Einstein case, the field equations of generic QG determine optical properties of the geometry and restrict such exact solutions to the Kundt class. We provide examples of these metrics.
Spectral theory of electromagnetic scattering by a coated sphere

In this paper, we introduce an alternative representation of the electromagnetic field scattered from a homogeneous sphere coated with a homogeneous layer of uniform thickness. Specifically, we expand the scattered field using a set of modes that are independent of the permittivity of the coating, while the expansion coefficients are simple rational functions of the permittivity. The theory we develop represents both a framework for the analysis of plasmonic and photonic modes and a straightforward methodology to design the permittivity of the coating to pursue a prescribed tailoring of the scattered field. To illustrate the practical implications of this method, we design the permittivity of the coating to zero either the backscattering or a prescribed multipolar order of the scattered field, and to maximize an electric field component in a given point of space.
ON THE CENTRAL HELIUM-BURNING VARIABLE STARS OF THE LeoI DWARF SPHEROIDAL GALAXY

We present a study of short-period, central helium-burning variable stars in the Local Group dwarf spheroidal galaxy LeoI, including 106 RR Lyrae stars and 51 Cepheids. So far, this is the largest sample of Cepheids and the largest Cepheids to RR Lyrae ratio found in such a kind of galaxy. Comparison with other Local Group dwarf spheroidals, Carina and Fornax, shows that the period distribution of RR Lyrae stars is quite similar, suggesting similar properties of the parent populations, whereas the Cepheid period distribution in LeoI peaks at longer periods (P ∼ 1.26 days instead of ∼0.5 days) and spans over a broader range, from 0.5 to 1.78 days. Evolutionary and pulsation predictions indicate, assuming a mean metallicity peaked within −1.5 ≲ [Fe/H] ≲ −1.3, that the current sample of LeoI Cepheids traces a unique mix of anomalous Cepheids (blue extent of the red-clump, partially electron-degenerate central helium-burning stars) and short-period classical Cepheids (blue-loop, quiescent central helium-burning stars). Current evolutionary prescriptions also indicate that the transition mass between the two different groups of stars is MHeF ∼ 2.1 M☉, and it is constant for stars metal-poorer than [Fe/H] ∼ −0.7. Finally, we briefly outline the different implications of the current findings on the star formation history of LeoI.