Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping of the Classical Mutation rosette Highlights a Role for Calcium in Wound-induced Rooting

Removal of the root system induces the formation of new roots from the remaining shoot. This process is primarily controlled by the phytohormone auxin which interacts with other signals in a yet unresolved manner. Here, we study the classical tomato mutation rosette (ro) which lacks shoot-borne roots. ro plants were severely inhibited in the formation of wound-induced roots and have reduced rates of auxin transport. We mapped ro to the tomato ortholog of the Arabidopsis thaliana BIG and the mammalians UBR4/p600. RO/BIG is a large protein of unknown biochemical function. In A. thaliana, BIG was implicated in the regulation of auxin transport and calcium homeostasis. We show that exogenous calcium inhibits wound-induced root formation in both tomato and A. thaliana ro/big mutants. Exogenous calcium antagonized the root-promoting effects of the auxin IAA, but not of 2,4-D, an auxin analog that is not recognized by the polar transport machinery, and accumulation of the auxin transporter PIN1 was sensitive to calcium levels in the ro/big mutants. Consistent with a role for calcium in mediating auxin transport, both ro/big mutants and calcium-treated wild-type plants were hypersensitive to treatment with polar auxin transport inhibitors. Subcellular localization of BIG suggests that like its mammalian ortholog, it is associated with the endoplasmic reticulum (ER). Analysis of subcellular morphology revealed that ro/big mutants exhibited disruption in cytoplasmic streaming. We suggest that RO/BIG maintain auxin flow by stabilizing PIN membrane localization, possibly by attenuating the inhibitory effect of Ca2+ on cytoplasmic streaming.
Changes in capture availability due to infection can lead to correctable biases in population-level infectious disease parameters

Correctly identifying the strength of selection parasites impose on hosts is key to predicting epidemiological and evolutionary outcomes. However, behavioral changes due to infection can alter the capture probability of infected hosts and thereby make selection difficult to estimate by standard sampling techniques. Mark-recapture approaches, which allow researchers to determine if some groups in a population are less likely to be captured than others, can mitigate this concern. We use an individual-based simulation platform to test whether changes in capture rate due to infection can alter estimates of three key outcomes: 1) reduction in offspring numbers of infected parents, 2) the relative risk of infection for susceptible genotypes compared to resistant genotypes, and 3) change in allele frequencies between generations. We find that calculating capture probabilities using mark-recapture statistics can correctly identify biased relative risk calculations. For detecting fitness impact, the bounded nature of the distribution possible offspring numbers results in consistent underestimation of the impact of parasites on reproductive success. Researchers can mitigate many of the potential biases associated with behavioral changes due to infection by using mark-recapture techniques to calculate capture probabilities and by accounting for the shapes of the distributions they are attempting to measure.
Mechanical and Surface Characterization of Diamond-Like Carbon Coatings onto Polymeric Substrate

In this master thesis, diamond-like carbon DLC/Cr bilayer systems, with thickness up to 1278 nm were formed on ABS, glass and Si substrates. Substrates surface were prepared by oxygen plasma cleaning process. The chromium thin film, which acts as a buffer layer, was grown by magnetron sputtering deposition. Diamond-like carbon was deposited by pulsed-DC PECVD, with methane and hydrogen as reactants. A Plackett-Burman experimental design was carried out in order to determine the influence of technological parameters of the deposition process on the thickness, deposition rate, intrinsic stress, contact angle, roughness, friction coefficient and wear rate of the obtained coatings. The independent variables were power, chamber pressure, time of deposition, total flux of the gases, composition of the reactant gases and oxygen plasma cleaning conditions. Values of intrinsic stress between 0.13-0.78 GPa were reported. Wear resistance measurements were performed by grinding calottes with a defined geometry. Low wear rate was achieved in the range of 1E-14 to 1E-15 m^3/Nm. The friction of the obtained coatings under different relative humidities, ranging 20 to 80% in a nitrogen environment, was measured using a nanotribometer with tungsten carbide ball. Results showed that friction coefficient increases with the increasing relativity humidity. Values from 0.12 to 0.24 for friction coefficient were reported. The main objective of the DLC coating is to improve the wear resistance and tribological behavior of ABS in order to increase his durability for automotive, medical, household and textile applications, among others.
Human-Like Modulation Sensitivity Emerging through Optimization to Natural Sound Recognition

Natural sounds contain rich patterns of amplitude modulation (AM), which is one of the essential sound dimensions for auditory perception. The sensitivity of human hearing to AM measured by psychophysics takes diverse forms depending on the experimental conditions. Here, we address with a single framework the questions of why such patterns of AM sensitivity have emerged in the human auditory system and how they are realized by our neural mechanisms. Assuming that optimization for natural sound recognition has taken place during human evolution and development, we examined its effect on the formation of AM sensitivity by optimizing a computational model, specifically, a multilayer neural network, for natural sound (namely, everyday sounds and speech sounds) recognition and simulating psychophysical experiments in which the AM sensitivity of the model was assessed. Relatively higher layers in the model optimized to sounds with natural AM statistics exhibited AM sensitivity similar to that of humans, although the model was not designed to reproduce human-like AM sensitivity. Moreover, simulated neurophysiological experiments on the model revealed a correspondence between the model layers and the auditory brain regions. The layers in which human-like psychophysical AM sensitivity emerged exhibited substantial neurophysiological similarity with the auditory midbrain and higher regions. These results suggest that human behavioral AM sensitivity has emerged as a result of optimization for natural sound recognition in the course of our evolution and/or development and that it is based on a stimulus representation encoded in the neural firing rates in the auditory midbrain and higher regions. SIGNIFICANCE STATEMENT This study provides a computational paradigm to bridge the gap between the behavioral properties of human sensory systems as measured in psychophysics and neural representations as measured in nonhuman neurophysiology. This was accomplished by combining the knowledge and techniques in psychophysics, neurophysiology, and machine learning. As a specific target modality, we focused on the auditory sensitivity to sound AM. We built an artificial neural network model that performs natural sound recognition and simulated psychophysical and neurophysiological experiments in the model. Quantitative comparison of a machine learning model with human and nonhuman data made it possible to integrate the knowledge of behavioral AM sensitivity and neural AM tunings from the perspective of optimization to natural sound recognition.
Foxes engineer hotspots of wildlife activity on the nutrient-limited Arctic tundra

Predators largely affect ecosystems through trophic interactions, but they also can have indirect effects by altering nutrient dynamics and acting as ecosystem engineers. Arctic foxes (Vulpes lagopus) are ecosystem engineers that concentrate nutrients on their dens, creating biogeochemical hotspots with lush vegetation on the nutrient-limited tundra. Red foxes (V. vulpes) similarly engineer subarctic environments through their denning behavior, and have recently expanded onto the tundra where they now often occupy historical Arctic fox dens. We evaluated the impact of fox denning activity on the spatial behavior of other tundra wildlife by comparing predator and herbivore visits to 12 natal dens and adjacent control sites over two years using camera traps in northeastern Manitoba, where both fox species are sympatric. Both the capture rates and species richness of wildlife were significantly greater at fox dens relative to control sites. Predators were detected almost exclusively on dens occupied by foxes, where they were observed investigating and scavenging prey remains (carrion, feathers), suggesting carcass presence or fox presence attracts predators to den sites. Caribou (Rangifer tarandus) also visited dens more often than control sites, likely attracted by the enhanced vegetation typically found on dens. Our results suggest fox ecosystem engineering affects the spatial distribution of herbivores by enriching vegetation at dens, and other predators by providing carrion. Understanding how predators affect other organisms via non-trophic interactions provides an enriched view of their functional roles within ecosystems.
Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

Adaptation in protein-coding sequences can be detected from multiple sequence alignments across species, or alternatively by leveraging polymorphism data inside a population. Across species, quantification of the adaptive rate relies on phylogenetic codon models, classically formulated in terms of the ratio of non-synonymous over synonymous substitution rates. Evidence of an accelerated non-synonymous substitution rate is considered a signature of pervasive adaptation. However, because of the background of purifying selection, these models are potentially limited in their sensitivity. Recent developments have led to more sophisticated mutation-selection codon models aimed at making a more detailed quantitative assessment of the interplay between mutation, purifying and positive selection. In this study, we conducted a large-scale exome-wide analysis of placental mammals with mutation-selection models, assessing their performance at detecting proteins and sites under adaptation. Importantly, mutation-selection codon models are based on a population-genetic formalism and thus are directly comparable to McDonald & Kreitman tests at the population level to quantify adaptation. Taking advantage of this relationship between phylogenetic and population genetics, we integrated divergence and polymorphism data across the entire exome for 29 populations across 7 genera, and showed that proteins and sites detected to be under adaptation at the phylogenetic scale are also under adaptation at the population-genetic scale. Altogether, our exome-wide analysis shows that phylogenetic mutation-selection codon models and population-genetic test of adaptation can be reconciled and are congruent, paving the way for integrative models and analyses across individuals and populations. Significance Statement Detecting genes under adaptation represents a key step in the decoding of genomes. Several methods have been proposed, focussing either on the short time scale (population genetics, e.g. human populations), or on the long time scale (phylogenetics, e.g. across mammals). However, the accuracy of these methods is still under debate, and it is still unclear whether the signatures of adaptation are congruent across evolutionary scales. In this study, using novel phylogenetic methods and gathering genome data across and within species, we show that the signatures of adaptation at the phylogenetic and population-genetic scales can be reconciled. While providing a mutual confirmation of the two approaches, our work paves the way for further methodological integration between micro- and macro-evolutionary genomics.
An FGF timer for zygotic genome activation

Zygotic genome activation has been extensively studied in a variety of systems including flies, frogs, and mammals. However, there is comparatively little known about the precise timings of gene induction during the earliest phases of embryogenesis. Here we employ high-resolution in situ detection methods, along with genetic and experimental manipulations, to study the timing of zygotic activation in the simple model chordate, Ciona intestinalis with minute-scale temporal precision. We found that two Prdm1 homologs in Ciona are the earliest genes that respond to FGF signaling. We present evidence for a FGF timing mechanism that is driven by derepression of the ERF repressor by ERK activity, which works in concert with localized activators such as Foxa.a. Absence of ERF results in derepression of target genes throughout the embryo. A highlight of this timer is the sharp transition in FGF responsiveness between the 8- and 16-cell stages of development. We propose that this timer is an innovation of chordates that is also employed by other vertebrates.
Experimental and Numerical Assessment of Iso-Flux Cooling with Low Reynolds Pulsating Water Flow

Almost every scale in thermal engineering requires performance optimization to lessen energy demand. The possibility of using pulsating flow for water cooling was investigated both experimentally and numerically. The experiments were conducted below a 60 mL∙min−1 flow rate and frequencies of 3.3, 4, 5, 6.6, and 10 Hz. The flow rate and temperatures were monitored while the solenoid valve was actuated and cooled with thermoelectric coolers. The measurements were replicated by using commercially available software capable of doing large-eddy simulations with coupled thermal modelling. Thermal boundaries were created by using steady inflow temperature and iso-flux conditions. The experimental and numerical results were compared and evaluated. The results show that the Nusselt number of the examined pulsating flow was lower when compared to constant flow scenarios at the corresponding averaged flow rate.
Integration of Machine Learning Algorithms and Discrete-Event Simulation for the Cost of Healthcare Resources

A healthcare resource allocation generally plays a vital role in the number of patients treated (pnt) and the patient waiting time (wt) in healthcare institutions. This study aimed to estimate pnt and wt as output variables by considering the number of healthcare resources employed and analyze the cost of health resources to the hospital depending on the cost coefficient (δi) in an emergency department (ED). The integration of the discrete-event simulation (DES) model and machine learning (ML) algorithms, namely random forest (RF), gradient boosting (GB), and AdaBoost (AB), was used to calculate the estimation of the output variables depending on the δi of resources cost. The AB algorithm performed best in almost all scenarios based on the results of the analysis. According to the AB algorithm based on the δ0. 0, δ0. 1, δ0. 2, and δ0. 3, the accuracy data were calculated as 0.9838, 0.9843, 0.9838, and 0.9846 for pnt; 0.9514, 0.9517, 0.9514, and 0.9514 for wt, respectively in the training stage. The GB algorithm had the best performance value, except for the results of the δ0. 2 (AB had a better accuracy at 0.8709 based on the value of δ0.2 for pnt) in the test stage. According to the AB algorithm based on the δ0. 0, δ0. 1, δ0. 2, and δ0. 3, the accuracy data were calculated as 0.7956, 0.9298, 0.8288, and 0.7394 for pnt; 0.8820, 0.8821, 0.8819, and 0.8818 for wt in the training phase, respectively. All scenarios created by the δi coefficient should be preferred for ED since the income provided by the pnt value to the hospital was more than the cost of healthcare resources. On the contrary, the wt estimation results of ML algorithms based on the δi coefficient differed. Although wt values in all ML algorithms with δ0. 0 and δ0. 1 coefficients reduced the cost of the hospital, wt values based on δ0. 2 and δ0. 3 increased the cost of the hospital.
Central Stars of Galactic Planetary Nebulae II New OB-type and emission-line stars

Context. There are more than 3000 confirmed and probable known Galactic planetary nebulae, but central star spectroscopic information is available for only 13% of them. Aims. We undertook a spectroscopic survey of central stars of PNe to identify their spectral types. Methods. We performed spectroscopic observations, at low resolution, with the 2-m telescope at CASLEO, Argentina. Results. We present the spectra of 46 central stars of PNe, most of them are OB-type and emission-line stars.
Temporal Deep Learning for Video Smoke Detection

In the proposed paper, temporal approaches based on Deep Learning are applied to Video Smoke Detection. Two Deep Learning methods are investigated: Firstly, a combination of convolutional neural networks (CNN) and long-short-term-memory networks (LSTM), secondly the inflated 3D architecture (i3D), which consists of 3D convolutions. These are two state of the art approaches to extract spatial and temporal information out of video sequences. These temporal approaches are compared to a single frame CNN method. Based on these information, a new way to detect and localize smoke within such sequences is presented, called cell-wise classification. It is shown that the temporal approaches work better for smoke than single frame approaches and that the cell-wise classification approach is suitable for Video Smoke Detection. A dataset consisting of about 350 hours of sequences is utilized. This is the first large scale dataset for the purpose of Video Smoke Detection, on which temporal Deep Learning methods are applied.
MISCLASSIFIED TYPE 1 AGNS IN THE LOCAL UNIVERSE

We search for misclassified type 1 AGNs among type 2 AGNs identified with emission line flux ratios, and investigate the properties of the sample. Using 4113 local type 2 AGNs at 0.02 < z < 0.05 selected from Sloan Digital Sky Survey Data Release 7, we detected a broad component of the Hline with a Full-Width at Half-Maximum (FWHM) ranging from 1700 to 19090 km s −1 for 142 objects, based on the spectral decomposition and visual inspection. The fraction of the misclassified type 1 AGNs among type 2 AGN sample is �3.5%, implying that a large number of missing type 1 AGN population may exist. The misclassified type 1 AGNs have relatively low luminosity with a mean broad Hluminosity, log LH� = 40.50 ± 0.35 erg s −1 , while black hole mass of the sample is comparable to that of the local black hole population, with a mean black hole mass, log MBH = 6.94 ± 0.51 M⊙. The mean Eddington ratio of the sample is log Lbol/LEdd = 2.00±0.40, indicating that black hole activity is relatively weak, hence, AGN continuum is too weak to change the host galaxy color. We find that the Oiii lines show significant velocity offsets, presumably due to outflows in the narrow-line region, while the velocity offset of the narrow component of the Hline is not prominent, consistent with the ionized gas kinematics of general type 1 AGN population.
Chromo-natural model in anisotropic background

In this work we study the chromo-natural inflation model in the anisotropic setup. Initiating inflation from Bianchi type-I cosmology, we analyze the system thoroughly during the slow-roll inflation, from both analytical and numerical points of view. We show that the isotropic FRW inflation is an attractor of the system. In other words, anisotropies are damped within few e-folds and the chromo-natural model respects the cosmic no-hair conjecture. Furthermore, we demonstrate that in the slow-roll limit, the anisotropies in both chromo-natural and gauge-flation models share the same dynamics.
A de Sitter tachyon thick braneworld

Among the multiple 5D thick braneworld models that have been proposed in the last years, in order to address several open problems in modern physics, there is a specific one involving a tachyonic bulk scalar field. Delving into this framework, a thick braneworld with a cosmological background induced on the brane is here investigated. The respective field equations — derived from the model with a warped 5D geometry — are highly non-linear equations, admitting a non-trivial solution for the warp factor and the tachyon scalar field as well, in a de Sitter 4D cosmological background. Moreover, the non-linear tachyonic scalar field, that generates the brane in complicity with warped gravity, has the form of a kink-like configuration. Notwithstanding, the non-linear field equations restricting character does not allow one to easily find thick brane solutions with a decaying warp factor which leads to the localization of 4D gravity and other matter fields. We derive such a thick brane configuration altogether in this tachyon-gravity setup. When analyzing the spectrum of gravity fluctuations in the transverse traceless sector, the 4D gravity is shown to be localized due to the presence of a single zero mode bound state, separated by a continuum of massive Kaluza-Klein (KK) modes by a mass gap. It contrasts with previous results, where there is a KK massive bound excitation providing no clear physical interpretation. The mass gap is determined by the scale of the metric parameter H. Finally, the corrections to Newton's law in this model are computed and shown to decay exponentially. It is in full compliance to corrections reported in previous results (up to a constant factor) within similar braneworlds with induced 4D de Sitter metric, despite the fact that the warp factor and the massive modes have a different form.
EFFECT OF NON-LOCAL THERMODYNAMIC EQUILIBRIUM MODEL ATMOSPHERES ON PHOTOMETRIC AMPLITUDES AND PHASES OF EARLY B-TYPE PULSATING STARS

Amplitudes and phases of the light variation of a pulsating star in various photometric passbands contain information about the geometry of observed modes. Because oscillation spectra of early B-type main-sequence stars do not exhibit regular patterns, these observables are very often the only ones from which mode identification can be derived. Moreover, these data can yield valuable constraints on mean stellar parameters, subphotospheric convection, microphysics, and atmospheres. We study all possible sources of inaccuracy in theoretical values of the photometric observables, i.e., amplitude ratios and phase differences, of early B-type main-sequence pulsators. Here, we discuss the effects of parameters coming from both model atmospheres and linear nonadiabatic theory of stellar pulsation. In particular, we evaluate for the first time the effect of the departure from the local thermodynamic equilibrium (LTE) approximation. To this end, for non-LTE model atmospheres, we compute tables with the passband fluxes, flux derivatives over effective temperature and gravity, as well as the nonlinear limb-darkening coefficients in 12 passbands most often used. We make these tables publicly available at the Wrocław HELAS Web site.