Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical evolution of giant molecular clouds in simulations of galaxies

We present an analysis of Giant Molecular Clouds (GMCs) within hydrodynamic simulations of isolated, low-mass (M* ~ 10^9 M_sol) disc galaxies. We study the evolution of molecular abundances and the implications for CO emission and the X_CO conversion factor in individual clouds. We define clouds either as regions above a density threshold n_H,min = 10 cm^-3, or using an observationally motivated CO intensity threshold of 0.25 K km s^-1. Our simulations include a non-equilibrium chemical model with 157 species, including 20 molecules. We also investigate the effects of resolution and pressure floors (i.e. Jeans limiters). We find cloud lifetimes up to ~40 Myr, with a median of 13 Myr, in agreement with observations. At one tenth solar metallicity, young clouds (<10-15 Myr) are underabundant in H2 and CO compared to chemical equilibrium, by factors of ~3 and 1-2 orders of magnitude, respectively. At solar metallicity, GMCs reach chemical equilibrium faster (within ~1 Myr). We also compute CO emission from individual clouds. The mean CO intensity, I_CO, is strongly suppressed at low dust extinction, A_v, and possibly saturates towards high A_v, in agreement with observations. The I_CO - A_v relation shifts towards higher A_v for higher metallicities and, to a lesser extent, for stronger UV radiation. At one tenth solar metallicity, CO emission is weaker in young clouds (<10-15 Myr), consistent with the underabundance of CO. Consequently, X_CO decreases by an order of magnitude from 0 to 15 Myr, albeit with a large scatter.
Detection of Spatial and Temporal Influences on Bacterial Communities in an Urban Stream by Automated Ribosomal Intergenic Ribosomal Spacer Analysis

The Yarqon is the largest urban river in Israel, and is a slow-flowing stream whose water originates mostly from wastewater treatment plants. Thus, its microbial community is expected to be heavily impacted both by anthropogenic factors and by seasonal temporal variation. In order to identify the main factors that influence the bacterial community, and their spatial-temporal variation, 50 samples were collected representing five different time points and eleven locations. Samples were analyzed for biotic and a-biotic parameters and the bacterial populations were analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial richness and diversity were calculated and compared across samples. Canonical Correspondence Analysis (CCA) showed that ARISA clustered the samples according to temporal variation. Molecular fingerprinting analysis provided a snapshot of the microbial community and showed good correlation with geochemical parameters, despite the rapid changes of the Mediterranean environment and the anthropogenic impact. Molecular fingerprinting methods based on natural fragment length polymorphisms may therefore represent a supplementary approach for stream monitoring, alongside physico-chemical measurements.
Mechanism of nucleic-acid-driven LLPS of TDP-43 PLD

Most membrane-less organelles (MLOs) formed by LLPS contain both nucleic acids and IDR-rich proteins. Currently while IDRs are well-recognized to drive LLPS, nucleic acids are thought to exert non-specific electrostatic/salt effects. TDP-43 functions by binding RNA/ssDNA and its LLPS was characterized without nucleic acids to be driven mainly by PLD-oligomerization, which may further transit into aggregation characteristic of various neurodegenerative diseases. Here by NMR, we discovered unexpectedly for TDP-43 PLD: 1) ssDNAs drive and then dissolve LLPS by multivalently and specifically binding Arg/Lys. 2) LLPS is driven by nucleic-acid-binding coupled with PLD-oligomerization. 3) ATP and nucleic acids universally interplay in modulating LLPS by competing for binding Arg/Lys. However, the unique hydrophobic region within PLD renders LLPS to exaggerate into aggregation. The study not only unveils the first residue-resolution mechanism of the nucleic-acid-driven LLPS of TDP-43 PLD, but also decodes a general principle that not just TDP-43 PLD, all Arg/Lys-containing IDRs are cryptic nucleic-acid-binding domains that may phase separate upon binding nucleic acids. Strikingly, ATP shares a common mechanism with nucleic acids in binding IDRs, thus emerging as a universal mediator for interactions between IDRs and nucleic acids, which may underlie previously-unrecognized roles of ATP at mM in physiology and pathology.
Spin-orbit coupling in curved graphene, fullerenes, nanotubes, and nanotube caps

A continuum model for the effective spin-orbit interaction in graphene is derived from a tight-binding model which includes the $\ensuremath{\pi}$ and $\ensuremath{\sigma}$ bands. We analyze the combined effects of the intra-atomic spin-orbit coupling, curvature, and applied electric field, using perturbation theory. We recover the effective spin-orbit Hamiltonian derived recently from group theoretical arguments by Kane and Mele. We find, for flat graphene, that the intrinsic spin-orbit coupling ${\ensuremath{\Delta}}_{\mathrm{int}}\ensuremath{\propto}{\ensuremath{\Delta}}^{2}$ and the Rashba coupling due to a perpendicular electric field $\mathcal{E}$, ${\ensuremath{\Delta}}_{\mathcal{E}}\ensuremath{\propto}\ensuremath{\Delta}$, where $\ensuremath{\Delta}$ is the intra-atomic spin-orbit coupling constant for carbon. Moreover we show that local curvature of the graphene sheet induces an extra spin-orbit coupling term ${\ensuremath{\Delta}}_{\mathrm{curv}}\ensuremath{\propto}\ensuremath{\Delta}$. For the values of $\mathcal{E}$ and curvature profile reported in actual samples of graphene, we find that ${\ensuremath{\Delta}}_{\mathrm{int}}l{\ensuremath{\Delta}}_{\mathcal{E}}\ensuremath{\lesssim}{\ensuremath{\Delta}}_{\mathrm{curv}}$. The effect of spin-orbit coupling on derived materials of graphenelike fullerenes, nanotubes, and nanotube caps, is also studied. For fullerenes, only ${\ensuremath{\Delta}}_{\mathrm{int}}$ is important. Both for nanotubes and nanotube caps ${\ensuremath{\Delta}}_{\mathrm{curv}}$ is in the order of a few Kelvins. We reproduce the known appearance of a gap and spin-splitting in the energy spectrum of nanotubes due to the spin-orbit coupling. For nanotube caps, spin-orbit coupling causes spin-splitting of the localized states at the cap, which could allow spin-dependent field-effect emission.
Endoplasmic reticulum calnexins participate in the primary root growth response to phosphate deficiency

Accumulation of incompletely folded proteins in the endoplasmic reticulum (ER) leads to ER stress, activates ER protein degradation pathways, and upregulates genes involved in protein folding (Unfolded Protein Response; UPR). ER stress has been associated with abiotic stress conditions that affect protein folding, including salt stress. However, the role of ER protein folding in plant responses to nutrient deficiencies is unclear. We analyzed several Arabidopsis thaliana mutants affected in ER protein quality control and established that both CALNEXIN (CNX) genes function in the primary root’s response to phosphate (Pi) deficiency. CNX and calreticulin (CRT) are homologous ER lectins that bind to N-glycosylated proteins to promote their folding. Growth of cnx1-1 and cnx2-2 single mutants was similar to that of the wild type under high and low Pi conditions, but the cnx1-1 cnx2-2 double mutant showed decreased primary root growth under low Pi conditions due to reduced meristematic cell division. This phenotype was specific to Pi deficiency; the double mutant responded normally to osmotic and salt stress. The root growth phenotype was Fe dependent and was associated with Fe accumulation in the root. Two genes involved in Fe-dependent inhibition of root growth under Pi deficiency, the ferroxidase gene LPR1 and P5-type ATPase PDR2, are epistatic to CNX1/CNX2. Overexpressing PDR2 failed to complement the cnx1-1 cnx2-2 root phenotype. cnx1-1 cnx2-2 showed no evidence of UPR activation, indicating a limited effect on ER protein folding. CNX might process a set of N-glycosylated proteins specifically involved in the response to Pi deficiency. One sentence summary Calnexin, a lectin chaperone engaged in the folding of N-glycosylated proteins in the ER, participates in primary root adaptation to low phosphate conditions.
Dynamic growth re-orientation orchestrates flatness in the Arabidopsis leaf

The growth and division of cells in plant leaves is highly dynamic in time and space, all while the cells cannot move relative to their neighbors. Given these constraints, models predict that long range regulatory systems must exist to maintain flat forms. Juxtaposed microRNA (miR-NA) networks could serve as one of these regulatory systems. One of these miRNAs, miR319 is thought to be expressed from the base of leaves and to promote growth by degrading class II TCP transcription factor mRNAs. A miR319 overexpression mutant, jagged and wavy (jaw-D) exhibits rippling and undulating leaves, consistent with biomechanical predictions that without genetic spatial coordination, tissues will deform. It has been theorized that jaw-D rippling results from overgrowth at the margins, however this does not fully address how miR319 expression from the base of wild-type (WT) leaves allows them to flatten. Here, we track the growth, cell division and cell maturation in live WT and jaw-D leaves to ask how miR319 expression in WT promotes flattening. This data revealed the importance of spatially distinct growth, division and differentiation patterns in WT leaves, which are missing in jaw-D. We propose that WT leaf cells respond to differentiation cues to dynamically re-orient growth in specific tissue locations and regulate flattening.
Multilevel human secondary lymphoid immune system compartmentalization revealed by complementary multiplexing and mass spectrometry imaging approaches

Secondary human lymphoid tissue immune reactions take place in a highly coordinated environment with compartmentalization representing a fundamental feature of this organization. In situ profiling methodologies are indispensable for the understanding of this compartmentalization. Here, we propose a complementary experimental approach aiming to reveal different aspects of this process. The analysis of human tonsils, using a combination of single cell phenotypic analysis based on flow cytometry and multiplex imaging and mass spectrometry-based methodologies, revealed a compartmentalized organization at cellular and molecular level. More specifically, the skewed distribution of highly specialized immune cell subsets and relevant soluble mediators was accompanied by a compartmentalized localization of several lipids across different anatomical areas of the tonsillar tissue. The performance of such combinatorial experimental approaches could lead to the identification of novel in situ interactions and molecular targets for the in vivo manipulation of lymphoid organ, particularly the germinal center, immune reactions.
Model-driven optimal experimental design for calibrating cardiac electrophysiology models

Models of the cardiomyocyte action potential (AP) have contributed immensely to the understanding of heart function, pathophysiology, and the origin of heart rhythm disturbances. However, AP models are nonlinear, complex, and can contain more than a hundred differential equations, making them difficult to parameterise. Therefore, cellular cardiac models have been limited to describing ‘average cell’ dynamics, when cell-specific models would be ideal to uncover inter-cell variability but are too experimentally challenging to be achieved. Here, we focus on automatically designing experimental protocols that allow us to better identify cell-specific maximum conductance values for each major current type—optimal experimental designs—for both voltage-clamp and current-clamp experiments. We show that optimal designs are able to perform better than many of the existing experiment designs in the literature in terms of identifying model parameters and hence model predictive power. For cardiac cellular electrophysiology, this approach will allow researchers to define their hypothesis of the dynamics of the system and automatically design experimental protocols that will result in theoretically optimal designs.
Coupling gene expression dynamics to cell size dynamics and cell cycle events: Exact and approximate solutions of the extended telegraph model

The standard model describing the fluctuations of mRNA numbers in single cells is the telegraph model which includes synthesis and degradation of mRNA, and switching of the gene between active and inactive states. While commonly used, this model does not describe how fluctuations are influenced by the cell cycle phase, cellular growth and division, and other crucial aspects of cellular biology. Here we derive the analytical time-dependent solution of an extended telegraph model that explicitly considers the doubling of gene copy numbers upon DNA replication, dependence of the mRNA synthesis rate on cellular volume, gene dosage compensation, partitioning of molecules during cell division, cell-cycle duration variability, and cell-size control strategies. Based on the time-dependent solution, we obtain the analytical distributions of transcript numbers for lineage and population measurements in steady-state growth and also find a linear relation between the Fano factor of mRNA fluctuations and cell volume fluctuations. We show that generally the lineage and population distributions in steady-state growth cannot be accurately approximated by the steady-state solution of extrinsic noise models, i.e. a telegraph model with parameters drawn from probability distributions. This is because the mRNA lifetime is often not small enough compared to the cell cycle duration to erase the memory of division and replication. Accurate approximations are possible when this memory is weak, e.g. for genes with bursty expression and for which there is sufficient gene dosage compensation when replication occurs.
Phenolic Content and Antioxidant Activity of Young and Mature Mango (Mangifera indica) and Avocado (Persea americana) Leaves Extracts

Polyphenols are groups of secondary metabolites in plants, known with their various biological activities, including their ability to act as antioxidants. Due to the side effects of the use of synthetic antioxidants on human health, the search for natural less toxic compounds has significantly increased. This study was carried out to evaluate the phenolic content and antioxidant activity of young and mature avocado ( Persea americana ) and mango leaves ( Mangifera indica ). Different extracts were prepared by maceration in methanol, ethanol, cold and hot water. The phenolic content of the extracts was determined using the Folic-Ciocalteu Method. A total of three antioxidant tests were done on the extracts; the 2, 2-diphenyl-1-picrylhydrazyl test (DPPH test), the Ferric reducing antioxidant power and the Hydroxyl radical scavenging activity. Results of these investigation showed that the mature mango leaves and young avocado leaves exhibited the highest phenolic and flavonoid contents. They were also very efficient as antioxidants in reducing the ferric ions and in scavenging the DPPH and hydroxyl radicals.
Transport in nanoscale systems: the microcanonical versus grand-canonical picture

We analyse a picture of transport in which two large but finite charged electrodes discharge across a nanoscale junction. We identify a functional whose minimization, within the space of all bound many-body wavefunctions, defines an instantaneous steady state. We also discuss factors that favour the onset of steady-state conduction in such systems, make a connection with the notion of entropy, and suggest a novel source of steady-state noise. Finally, we prove that the true many-body total current in this closed system is given exactly by the one-electron total current, obtained from time-dependent density-functional theory.
Magnetic activity of seismic solar analogs

We present our latest results on the solar-stellar connection by studying 18 solar analogs that we identified among the Kepler seismic sample (Salabert et al., 2016a). We measured their magnetic activity properties using observations collected by the Kepler satellite and the ground-based, high-resolution Hermes spectrograph. The photospheric (Sph) and chromospheric (S) magnetic activity proxies of these seismic solar analogs are compared in relation to solar activity. We show that the activity of the Sun is actually comparable to the activity of the seismic solar analogs. Furthermore, we report on the discovery of temporal variability in the acoustic frequencies of the young (1 Gyr-old) solar analog KIC10644253 with a modulation of about 1.5 years, which agrees with the derived photospheric activity (Salabert et al., 2016b). It could actually be the signature of the short-period modulation, or quasi-biennal oscillation, of its magnetic activity as observed in the Sun and the 1-Gyr-old solar analog HD30495. In addition, the lithium abundance and the chromospheric activity estimated from Hermes confirms that KIC10644253 is a young and more active star than the Sun.
Tension-Type Headache of Longer Duration is associated With Higher Frequency of Nausea and Vomiting in Temporomandibular Disorder Individuals

Introduction: Nausea and vomiting are common disorders reported with different frequencies by patients with different headache disorders. Aim: Evaluate frequency of nausea and vomiting in subjects with craniomadibular disorders, bruxing behavior and tension-type headache, test the hypothesis that both disorders increase in frequency with longer pain duration. Methods: Clinical evaluation, pain history, questionnaires, palpation of muscles and joints, criteria for craniomandibular disorders, bruxing behavior and tension-type headache and self-report in 208 subjects with tension-type headache. Outcome: Frequencies of nausea in different pain duration ranges were as follows: 0-1 year: 14/39=35,9%; 2-4 years:17/54=31,5%; 5-7 years: 13/36=36,1%; 8-10 years:20/26=38,5%; 11-15 years: 20/25=80%; 16 years or longer: 21/28=75%. As for vomiting, the frequencies in different pain duration ranges were about 01 year: 4/39=10,3%; 2-4 years: 5/54= 9,3%; 5-7 years: 7/36= 19,4%; 8-10 years: 5/26=19,2%; 11-15 years: 11/25= 44%; 16 years/longer pain duration: 15/28=53.6%. The frequency of nausea increased with longer duration of headache (Chi-squared for independence p<0,0004, for trends p<0,0001). The frequency of vomiting increased with longer duration of pain: Chi-squared for independence p<0.0001, for trends p<0.0001. Conclusions: Nausea and vomiting may be reported frequently in patients with tension-type headache and their frequency increases with longer chronicity of tension-type headache. Multiple neurophysiologic mechanisms including those associated with the parasympathetic one, are involved in the development of nausea and vomiting.
TESTING THE WAVELENGTH DEPENDENCE OF COSMOLOGICAL REDSHIFT DOWN TO Δz ∼ 10−6

At the core of the standard cosmological model lies the assumption that the redshift of distant galaxies is independent of photon wavelength. This invariance of cosmological redshift with wavelength is routinely found in all galaxy spectra with a precision of Δz ∼ 10−4. The combined use of approximately half a million high-quality galaxy spectra from the Sloan Digital Sky Survey (SDSS) allows us to explore this invariance down to a nominal precision in redshift of 10−6 (statistical). Our analysis is performed over the redshift interval 0.02 < z < 0.25. We use the centroids of spectral lines over the 3700–6800 Å rest-frame optical window. We do not find any difference in redshift between the blue and red sides down to a precision of 10−6 at z ≲ 0.1 and 10−5 at 0.1 ≲ z ≲ 0.25 (i.e., at least an order of magnitude better than with single galaxy spectra). This is the first time the wavelength-independence of the (1 + z) redshift law is confirmed over a wide spectral window at this precision level. This result holds independently of the stellar population of the galaxies and their kinematical properties. This result is also robust against wavelength calibration issues. The limited spectral resolution (R ∼ 2000) of the SDSS data, combined with the asymmetric wavelength sampling of the spectral features in the observed restframe due to the (1 + z) stretching of the lines, prevent our methodology from achieving a precision higher than 10−5, at z > 0.1. Future attempts to constrain this law will require high quality galaxy spectra at higher resolution (R ≳ 10,000).
Extending the Canada-France brown dwarfs survey to the near-infrared: first ultracool brown dwarfs from CFBDSIR

Aims. We present the first results of the ongoing Canada-France Brown Dwarfs Survey-InfraRed, hereafter CFBDSIR, a near infrared extension to the optical wide-field survey CFBDS. Our final objectives are to constrain ultracool atmosphere physics by finding a statistically significant sample of objects cooler than 650 K and to explore the ultracool brown dwarf mass function building on a well-defined sample of such objects. Methods. We identify candidates in CFHT/WIRCam J and CFHT/MegaCam z' images using optimised psf-fitting, and follow them up with pointed, near-infrared imaging with SOFI at the NTT. We finally obtain low-resolution spectroscopy of the coolest candidates to characterise their atmospheric physics. Results. We have so far analysed and followed up all candidates on the first 66 square degrees of the 335 square degree survey. We identified 55 T-dwarfs candidates with z' - J > 3.5 and have confirmed six of them as T-dwarfs, including 3 that are strong later-than-T8 candidates, based on their far-red and NIR colours. We also present here the NIR spectra of one of these ultracool dwarfs, CFBDSIR1458+1013, which confirms it as one of the coolest brown dwarf known, possibly in the 550-600 K temperature range. Conclusions. From the completed survey we expect to discover 10 to 15 dwarfs later than T8, more than doubling the known number of such objects. This will enable detailed studies of their extreme atmospheric properties and provide a stronger statistical basis for studies of their luminosity function.
X-ray bounds on the r-mode amplitude in millisecond pulsars

r-mode astroseismology provides a unique way to study the internal composition of compact stars. Due to their precise timing, recycled millisecond radio pulsars present a particularly promising class of sources. Although their thermal properties are still poorly constrained, X-ray data is very useful for astroseismology since r-modes could strongly heat a star. Using known and new upper bounds on the temperatures and luminosities of several non-accreting millisecond radio pulsars we derive bounds on the r-mode amplitude as low as $\alpha\lesssim10^{-8}$ and discuss the impact on scenarios for their internal composition.