Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-cell microencapsulation improves lung retention of endothelial colony forming cells after intravascular delivery and unmasks therapeutic benefit in severe pulmonary arterial hypertension

Background Pulmonary arterial hypertension (PAH) is triggered by pulmonary vascular endothelial cell apoptosis and microvascular loss; therefore, therapies that can regenerate lost vasculature may offer therapeutic benefit. Endothelial colony forming cells (ECFCs) can directly repair damaged blood vessels and may have therapeutic potential for the treatment of PAH. However, poor retention of ECFCs in the lungs following intravenous delivery greatly limits their therapeutic application. Therefore, we studied whether cellular microencapsulation could enhance ECFCs viability and retention in the lung after systemic delivery and improve therapeutic efficacy of ECFCs in a rat monocrotaline (MCT) PAH model. Methods ECFCs were encapsulated by vortex-emulsion using various concentrations of agarose, and capsule size and initial cell viability were assessed. Encapsulated and free ECFCs were transduced with luciferase and administered to Sprague-Dawley rats three days after injection of MCT. ECFCs were tracked in vivo by bioluminescence imaging (BLI) to assess cell persistence and bio-distribution. At end-study, right ventricular systolic pressure (RVSP) and right ventricular hypertrophy were assessed for therapeutic efficacy. Results Microgel encapsulation using 3.5% agarose improved cells survival and supported cell migration from capsules. At 15 minutes after delivery, BLI radiance were similar for free and microencapsulated ECFCs; however, only encapsulated cells could be detected by BLI at 4 and 24 hours. Transplantation of microencapsulated ECFCs led to significant improvement in RVSP three weeks after delivery compared to non-encapsulated ECFCs. Conclusion Together, microencapsulation increased retention of ECFCs within the lungs. Furthermore, even a modest increase in ECFCs persistence over 24 hours can provide an important therapeutic benefit in the rat MCT model of PAH.
Alpha and beta-diversities performance comparison between different normalization methods and centered log-ratio transformation in a microbiome public dataset

Microbiome data obtained after ribosomal RNA or shotgun sequencing represent a challenge for their ecological and statistical interpretation. Microbiome data is compositional data, with a very different sequencing depth between sequenced samples from the same experiment and harboring many zeros. To overcome this scenario, several normalizations and transformation methods have been developed to correct the microbiome data’s technical biases, statistically analyze these data more optimally, and obtain more confident biological conclusions. Most existing studies have compared the performance of different normalization methods mainly linked to microbial differential abundance analysis methods but without addressing the initial statistical task in microbiome data analysis: alpha and beta-diversities. Furthermore, most of the studies used simulated microbiome data. The present study attempted to fill this gap. A public whole shotgun metagenomic sequencing dataset from a USA cohort related to gastrointestinal diseases has been used. Moreover, the performance comparison of eleven normalization methods and the transformation method based on the centered log ratio (CLR) has been addressed. Two strategies were followed to attempt to evaluate the aptitude of the normalization methods between them: the centered residuals obtained for each normalization method and their coefficient of variation. Concerning alpha diversity, the Shannon-Weaver index has been used to compare its output to the normalization methods. Regarding beta-diversity (multivariate analysis), it has been explored three types of analysis: principal coordinate analysis (PCoA) as an exploratory method; distance-based redundancy analysis (db-RDA) as interpretative analysis; and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) as machine learning discriminatory multivariate method. Moreover, other microbiome statistical approaches were compared along the normalization and transformation methods: permutational multivariate analysis of variance (PERMANOVA), analysis of similarities (ANOSIM), beta-dispersion and multi-level pattern analysis in order to associate specific species to each type of diagnosis group in the dataset used. The GMPR (geometric mean of pairwise ratios) normalization method presented the best results regarding the dispersion of the new matrix obtained after being scaled. For the case of α diversity, no differences were detected among the normalization methods compared. In terms of β diversity, the db-RDA and the sPLS-DA analysis have allowed us to detect the most meaningful differences between the normalization methods. The CLR transformation method was the most informative in biological terms, allowing us to make more predictions. Nonetheless, it is important to emphasize that the CLR method and the UQ normalization method have been the only ones that have allowed us to make predictions from the sPLS-DA analysis, so their use could be more encouraged.
Properties of graphene: a theoretical perspective

The electronic properties of graphene, a two-dimensional crystal of carbon atoms, are exceptionally novel. For instance, the low-energy quasiparticles in graphene behave as massless chiral Dirac fermions which has led to the experimental observation of many interesting effects similar to those predicted in the relativistic regime. Graphene also has immense potential to be a key ingredient of new devices, such as single molecule gas sensors, ballistic transistors and spintronic devices. Bilayer graphene, which consists of two stacked monolayers and where the quasiparticles are massive chiral fermions, has a quadratic low-energy band structure which generates very different scattering properties from those of the monolayer. It also presents the unique property that a tunable band gap can be opened and controlled easily by a top gate. These properties have made bilayer graphene a subject of intense interest. In this review, we provide an in-depth description of the physics of monolayer and bilayer graphene from a theorist's perspective. We discuss the physical properties of graphene in an external magnetic field, reflecting the chiral nature of the quasiparticles near the Dirac point with a Landau level at zero energy. We address the unique integer quantum Hall effects, the role of electron correlations, and the recent observation of the fractional quantum Hall effect in the monolayer graphene. The quantum Hall effect in bilayer graphene is fundamentally different from that of a monolayer, reflecting the unique band structure of this system. The theory of transport in the absence of an external magnetic field is discussed in detail, along with the role of disorder studied in various theoretical models. Recent experminental observations of a metal–insulator transition in hydrogenated graphene is discussed in terms of a self-consistent theory and compared with related numerical simulations. We highlight the differences and similarities between monolayer and bilayer graphene, and focus on thermodynamic properties such as the compressibility, the plasmon spectra, the weak localization correction, quantum Hall effect and optical properties. Confinement of electrons in graphene is non-trivial due to Klein tunnelling. We review various theoretical and experimental studies of quantum confined structures made from graphene. The band structure of graphene nanoribbons and the role of the sublattice symmetry, edge geometry and the size of the nanoribbon on the electronic and magnetic properties are very active areas of research, and a detailed review of these topics is presented. Also, the effects of substrate interactions, adsorbed atoms, lattice defects and doping on the band structure of finite-sized graphene systems are discussed. We also include a brief description of graphane–gapped material obtained from graphene by attaching hydrogen atoms to each carbon atom in the lattice.
SEARCHING FOR OVERTURNING CONVECTION IN PENUMBRAL FILAMENTS: SLIT SPECTROSCOPY AT 0.″2 RESOLUTION

Recent numerical simulations of sunspots suggest that overturning convection is responsible for the existence of penumbral filaments and the Evershed flow, but there is little observational evidence of this process. Here, we carry out a spectroscopic search for small-scale convective motions in the penumbra of a sunspot located 5° away from the disk center. The position of the spot is very favorable for the detection of overturning downflows at the edges of penumbral filaments. Our analysis is based on measurements of the Fe i 709.0 nm line taken with the Littrow spectrograph of the Swedish 1 m Solar Telescope under excellent seeing conditions. We compute line bisectors at different intensity levels and derive Doppler velocities from them. The velocities are calibrated using a nearby telluric line, with systematic errors smaller than 150 m s−1. Deep in the photosphere, as sampled by the bisectors at the 80%–88% intensity levels, we always observe blueshifts or zero velocities. The maximum blueshifts reach 1.2 km s−1 and tend to be cospatial with bright penumbral filaments. In the line core, we detect blueshifts for the most part, with small velocities not exceeding 300 m s−1. Redshifts also occur, but at the level of 100–150 m s−1, and only occasionally. The fact that they are visible in high layers casts doubts on their convective origin. Overall, we do not find indications of downflows that could be associated with overturning convection at our detection limit of 150 m s−1. Either no downflows exist, or we have been unable to observe them because they occur beneath τ = 1 or the spatial resolution/height resolution of the measurements is still insufficient.
Abjad numerals recognition in medieval arabic mathematical texts

Abjad numerals, also called his¯ab al-jumal , is a numeral system based on the twenty eight letters of Arabic but not in the dictionary order. In ancient Arabic mathematics, all problems and solutions sentences were completely expressed in natural language with no mathematical symbolism. The present paper is the first attempt to automatically analyze and recognize Abjad numerals in medieval Arabic mathematical texts. Since that his¯ab al-jumal system has no ambiguity, we also translate Abjad numeral written in natural language to modern numeral system. We construct a new dataset named Hj-Tagged corpus to facilitate our study. According to the experimental results, the proposed method is efficient for automatically analyze and recognize Abjad numerals and mathematical components (such as numerical constants, Abjad numbers, mathematical operations,. etc). We also translate Abjad terms detected in the previous step to modern numeral system, where it achieves an F1 score of 98.1%.
Thermodynamic anomaly above the superconducting critical temperature in the quasi-one-dimensional superconductor Ta4Pd3Te16

We study the intrinsic transport anisotropy and fermiology of the quasi one-dimensional superconductor Ta$_4$Pd$_3$Te$_{16}$. Below $T^*=20$ K we detect a thermodynamic phase transition that predominantly affects the conductivity perpendicular to the quasi one-dimensional chains, consistent with a thermodynamic transition related to the presence of charge order that precedes superconductivity. Remarkably the Fermi surface pockets detected by de Haas-van Alphen (dHvA) oscillations are unaffected by this transition, suggesting that the ordered state does not break any translational symmetries but rather alters the scattering of the quasiparticles themselves.
Pulse properties of terrestrial gamma‐ray flashes detected by the Fermi Gamma‐Ray Burst Monitor

The Gamma‐ray Burst Monitor (GBM) on board the Fermi Gamma‐ray Space Telescope has triggered on over 300 terrestrial gamma‐ray flashes (TGFs) since its launch in June 2008. With 14 detectors, GBM collects on average ∼100 counts per triggered TGF, enabling unprecedented studies of the time profiles of TGFs. Here we present the first rigorous analysis of the temporal properties of a large sample of TGFs (278), including the distributions of the rise and fall times of the individual pulses and their durations. A variety of time profiles are observed with 19% of TGFs having multiple pulses separated in time and 31 clear cases of partially overlapping pulses. The effect of instrumental dead time and pulse pileup on the temporal properties are also presented. As the observed gamma ray pulse structure is representative of the electron flux at the source, TGF pulse parameters are critical to distinguish between relativistic feedback discharge and lightning leader models. We show that at least 67% of TGFs at satellite altitudes are significantly asymmetric. For the asymmetric pulses, the rise times are almost always shorter than the fall times. Those which are not are consistent with statistical fluctuations. The median rise time for asymmetric pulses is ∼3 times shorter than for symmetric pulses while their fall times are comparable. The asymmetric shapes observed are consistent with the relativistic feedback discharge model when Compton scattering of photons between the source and Fermi is included, and instrumental effects are taken into account.
THE DISTRIBUTION OF FAINT SATELLITES AROUND CENTRAL GALAXIES IN THE CANADA–FRANCE–HAWAII TELESCOPE LEGACY SURVEY

We investigate the radial number density profile and the abundance distribution of faint satellites around central galaxies in the low-redshift universe using the Canada–France–Hawaii Telescope (CFHT) Legacy Survey. We consider three samples of central galaxies with magnitudes of Mr = −21, −22, and −23 selected from the Sloan Digital Sky Survey group catalog of Yang et al. The satellite distribution around these central galaxies is obtained by cross-correlating these galaxies with the photometric catalog of the CFHT Legacy Survey. The projected radial number density of the satellites obeys a power-law form with the best-fit logarithmic slope of −1.05, independent of both the central galaxy luminosity and the satellite luminosity. The projected cross-correlation function between central and satellite galaxies exhibits a non-monotonic trend with satellite luminosity. It is most pronounced for central galaxies with Mr = −21, where the decreasing trend of clustering amplitude with satellite luminosity is reversed when satellites are fainter than central galaxies by more than 2 mag. A comparison with the satellite luminosity functions in the Milky Way (MW) and M31 shows that the MW/M31 system has about twice as many satellites as around a typical central galaxy of similar luminosity. The implications for theoretical models are briefly discussed.
Validation of the Distress Thermometer in Parkinson's disease

The Distress Thermometer (DT) has been validated across various medical conditions, but no studies have investigated its performance in people with Parkinson's disease (PD). In this study, the authors aimed to determine if the DT is valid and reliable in a sample of participants with PD recruited from a movement disorder clinic. Use of a tool such as the DT allows staff to identify and address the most distressing symptoms and refer patients on for specialist input when needed.
HUBBLE SPACE TELESCOPE OBSERVATIONS OF THE STELLAR DISTRIBUTION NEAR Sgr A*

Sgr A* is embedded within the nuclear cluster, which consists of a mixture of evolved and young populations of stars dominating the light over a wide range of angular scales. Here we present Hubble Space Telescope/NICMOS data to study the surface brightness distribution of stellar light within the inner 10″ of Sgr A* at 1.45 μm, 1.7 μm, and 1.9 μm. We use these data to independently examine the surface brightness distribution that had been measured previously with NICMOS and to determine whether there is a drop in the surface density of stars very near Sgr A*. Our analysis confirms that a previously reported drop in the surface brightness within 0. ″8 of Sgr A* is an artifact of bright and massive stars near that radius. We also show that the surface brightness profile within 5″ or ∼0.2 pc of Sgr A* can be fitted with broken power laws. The power laws are consistent with previous measurements, in that the profile becomes shallower at small radii. For radii >0. ″7, the slope is β = −0.34 ± 0.04, where Σ is ∝rβ and becomes flatter at smaller radii with β = −0.13 ± 0.04. Modeling of the surface brightness profile gives a stellar density that increases roughly as r−1 within the inner 1″ of Sgr A*. This slope confirms earlier measurements in that it is not consistent with that expected from an old, dynamically relaxed stellar cluster with a central supermassive black hole. Assuming that the diffuse emission is not contaminated by a faint population of young stars down to the 17.1 mag limit of our imaging data at 1.70μm, the shallow cusp profile is not consistent with a decline in stellar density in the inner arcsecond. In addition, converting our measured diffuse light profile to a stellar mass profile, with the assumption that the light is dominated by K0 dwarfs, the enclosed stellar mass within radius r ≲ 0.1 pc of Sgr A* is ≈3.2 × 104 M☉(r/0.1 pc)2.1.
THE APACHE POINT OBSERVATORY GALACTIC EVOLUTION EXPERIMENT: FIRST DETECTION OF HIGH-VELOCITY MILKY WAY BAR STARS

Commissioning observations with the Apache Point Observatory Galactic Evolution Experiment (APOGEE), part of the Sloan Digital Sky Survey III, have produced radial velocities (RVs) for ∼4700 K/M-giant stars in the Milky Way (MW) bulge. These high-resolution (R ∼ 22, 500), high-S/N (>100 per resolution element), near-infrared (NIR; 1.51–1.70 μm) spectra provide accurate RVs (ϵV ∼ 0.2 km s−1) for the sample of stars in 18 Galactic bulge fields spanning −1° −32°. This represents the largest NIR high-resolution spectroscopic sample of giant stars ever assembled in this region of the Galaxy. A cold (σV ∼ 30 km s−1), high-velocity peak (VGSR ≈ +200 km s−1) is found to comprise a significant fraction (∼10%) of stars in many of these fields. These high RVs have not been detected in previous MW surveys and are not expected for a simple, circularly rotating disk. Preliminary distance estimates rule out an origin from the background Sagittarius tidal stream or a new stream in the MW disk. Comparison to various Galactic models suggests that these high RVs are best explained by stars in orbits of the Galactic bar potential, although some observational features remain unexplained.
Induced-gravity inflation in no-scale supergravity and beyond

Supersymmetric versions of induced-gravity inflation are formulated within Supergravity (SUGRA) employing two gauge singlet chiral superfields. The proposed superpotential is uniquely determined by applying a continuous R and a discrete ℤn symmetry. We select two types of logarithmic Kähler potentials, one associated with a no-scale-type SU(2,1)/SU(2)× U(1)R×ℤn Kähler manifold and one more generic. In both cases, imposing a lower bound on the parameter cℛ involved in the coupling between the inflaton and the Ricci scalar curvature — e.g. cℛ≳ 76, 105, 310 for n=2,3 and 6 respectively —, inflation can be attained even for subplanckian values of the inflaton while the corresponding effective theory respects the perturbative unitarity. In the case of no-scale SUGRA we show that, for every n, the inflationary observables remain unchanged and in agreement with the current data while the inflaton mass is predicted to be 3·1013 GeV. Beyond no-scale SUGRA the inflationary observables depend mildly on n and crucially on the coefficient involved in the fourth order term of the Kähler potential which mixes the inflaton with the accompanying non-inflaton field.
Model estimates of metazoans’ contributions to the biological carbon pump

The daily vertical migrations of fish and other metazoans actively transport organic carbon from the ocean surface to depth, contributing to the biological carbon pump. We use an oxygen-constrained, game-theoretic food-web model to simulate diel vertical migrations and estimate global carbon fluxes and sequestration by fish and zooplankton due to respiration, fecal pellets, and deadfalls. Our model provides estimates of the carbon export and sequestration potential for a range of pelagic functional groups, despite uncertain biomass estimates of some functional groups. While the export production of metazoans and fish is modest (~20% of global total), we estimate that their contribution to carbon sequestered by the biological pump (~ 800 PgC) is conservatively more than 50% of the estimated global total (~1300 PgC) and have a significantly longer sequestration time scale (~250 years) than previously reported for other components of the biological pump. Fish and multicellular zooplankton contribute about equally to this sequestered carbon pool. This essential ecosystem service could be at risk from both unregulated fishing on the high seas and ocean deoxygenation due to climate change.
Percolate: an exponential family JIVE model to design DNA-based predictors of drug response

Motivation Anti-cancer drugs may elicit resistance or sensitivity through mechanisms which involve several genomic layers. Nevertheless, we have demonstrated that gene expression contains most of the predictive capacity compared to the remaining omic data types. Unfortunately, this comes at a price: gene expression biomarkers are often hard to interpret and show poor robustness. Results To capture the best of both worlds, i.e. the accuracy of gene expression and the robustness of other genomic levels, such as mutations, copy-number or methylation, we developed Percolate, a computational approach which extracts the joint signal between gene expression and the other omic data types. We developed an out-of-sample extension of Percolate which allows predictions on unseen samples without the necessity to recompute the joint signal on all data. We employed Percolate to extract the joint signal between gene expression and either mutations, copy-number or methylation, and used the out-of sample extension to perform response prediction on unseen samples. We showed that the joint signal recapitulates, and sometimes exceeds, the predictive performance achieved with each data type individually. Importantly, molecular signatures created by Percolate do not require gene expression to be evaluated, rendering them suitable to clinical applications where only one data type is available. Availability Percolate is available as a Python 3.7 package and the scripts to reproduce the results are available here.
GALEX FUV OBSERVATIONS OF COMET C/2004 Q2 (MACHHOLZ): THE IONIZATION LIFETIME OF CARBON

We present a measurement of the lifetime of ground state atomic carbon, C(3P), against ionization processes in interplanetary space and compare it to the lifetime expected from the dominant physical processes likely to occur in this medium. Our measurement is based on analysis of a far ultraviolet (FUV) image of comet C/2004 Q2 (Machholz) recorded by the Galaxy Evolution Explorer (GALEX) on 2005 March 1. The bright C i 1561 Å and 1657 Å multiplets dominate the GALEX FUV band. We used the image to create high signal-to-noise ratio radial profiles that extended beyond 1 × 106 km from the comet nucleus. Our measurements yielded a total carbon lifetime of (7.1–9.6) × 105 s (ionization rate of (1.0–1.4) × 10−6 s−1) when scaled to 1 AU. This compares favorably to calculations assuming solar photoionization, solar wind proton change exchange, and solar wind electron impact ionization are the dominant processes occurring in this medium and that comet Machholz was embedded in the slow solar wind. The shape of the C i profiles inside 3 × 105 km suggests that either the CO lifetime is shorter than previously thought and/or a shorter-lived carbon-bearing parent molecule, such as CH4, is providing the majority of the carbon in this region of the coma of comet Machholz.