Miracle-dz/UniFAR-FTUs huggingface dataset:
Chitosan edible coating incorporated with resveratrol and Satureja bachtiarica essential oil as natural active packaging: In vitro antibacterial and antioxidant properties, and its impact on the shelf life of fresh chicken fillet and growth of inoculated Escherichia coli O157:H7

Abstract The purpose of this study was to investigate the effects of chitosan coating containing resveratrol (RES) and Satureja bachtiarica essential oil (SEO) on the microbial quality, oxidative stability, and sensory properties of chicken meat as well as inoculated Escherichia coli O157:H7 during 12 day storage at 4 °C. The synergistic in vitro antioxidant effects between RES and SEO in chitosan coatings were observed. Moreover, chicken coated with chitosan solution containing RES 0.001% + SEO 2% indicated better results compared with the control group with the following scores (p≤0.05): Total viable count (6.11 log10 CFU/g), total psychrotrophic count (5.39 log10 CFU/g), Lactic acid bacteria (5.36 log10 CFU/g), pH (6.25), peroxide value (4.32 meq/kg lipid), thiobarbituric acid reactive substance (1.03 mg MDA/kg), sensory analysis (overall acceptability: 5.5), and inoculated E.coli O157:H7 (6.01 log10 CFU/g). The finding of the present study can contribute to the meat industry as a natural active packaging system.
Thermal vacancy formation energies of random solid solutions

Vacancy mechanism plays a dominant role in the atomic migration when a close-packed disordered alloy undergoes ordering transition. However, the calculation of thermal vacancy formation energies (VFEs) of random solid solutions is usually cumbersome due to the difficulty in considering various local atomic environments. Here, we propose a transparent way that combines coherent potential approximation and supercell-local cluster expansion to investigate VFEs of random solid solutions. This method is used to study the effects of temperature, strain and magnetism on the VFEs of random A1-FePt alloy. The results show that the mean VFE increases with increasing temperature, decreases under (001) in-plane tensile and compressive strains, and can be further reduced by the magnetic excitation. These effects are explained by discussing the dependence of VFE on local atomic environments and the overall bond strength within.
The theoretical mass-magnitude relation of low mass stars and its metallicity dependence

We investigate the dependence of theoretically generated mass - (absolute magnitude) relations on stellar models. Using up to date physics we compute models in the mass range 0.1 [Fe/H] > -2.3) shows a maximum in -dm/dM_bol, which moves to brighter bolometric magnitudes with decreasing metallicity. The change in location of the maximum, as a function of [Fe/H], follows the location of structure in luminosity functions for stellar populations with different metal abundances. This structure seen in all observed stellar populations can be accounted for by the mass--luminosity relation.
Optimized Three Deep Learning Models Based-PSO Hyperparameters for Beijing PM2.5 Prediction

Deep learning is a machine learning approach that produces excellent performance in various applications, including natural language processing, image identification, and forecasting. Deep learning network performance depends on the hyperparameter settings. This research attempts to optimize the deep learning architecture of Long short term memory (LSTM), Convolutional neural network (CNN), and Multilayer perceptron (MLP) for forecasting tasks using Particle swarm optimization (PSO), a swarm intelligence-based metaheuristic optimization methodology: Proposed M-1 (PSO-LSTM), M-2 (PSO-CNN), and M-3 (PSO-MLP). Beijing PM2.5 datasets was analyzed to measure the performance of the proposed models. PM2.5 as a target variable was affected by dew point, pressure, temperature, cumulated wind speed, hours of snow, and hours of rain. The deep learning network inputs consist of three different scenarios: daily, weekly, and monthly. The results show that the proposed M-1 with three hidden layers produces the best results of RMSE and MAPE compared to the proposed M-2, M-3, and all the baselines. A recommendation for air pollution management could be generated by using these optimized models.
Impact of speckle disorder on a superfluid Fermi system

Optical lattice experiments which probe the effect of disorder on superfluidity often use a speckle pattern for generating the disorder. Such speckle disorder is spatially correlated. While fermionic superfluidity in the presence of uncorrelated disorder is well studied, the impact of correlated disorder, particularly on thermal properties of the superfluid, is poorly understood. We provide a detailed study of the impact of speckle disorder, for varying speckle size and disorder magnitude, on the ground state and thermal properties of a Fermi superfluid. We work in the coupling regime of BCS-BEC crossover in a two-dimensional lattice. For a fixed disorder strength, an increase in speckle size leads to smoothening of the self-consistent background potential, increase in the critical disorder needed for a superfluid-insulator transition, and an increase in superfluid ${T}_{c}$. Along with these hints at decrease in effective disorder, speckle correlations also suppress the superfluid gap and the gap formation temperature---effects normally associated with increasing disorder. We correlate these effects with the effective potential and the single-particle localization effects in the ground state.
Variation in mate competition favors phenotypic plasticity in male coloration of an African cichlid

Sexual selection is thought to be a potent evolutionary force giving rise to diversity in sexual traits that enhance mating success, such as ornament, sexual display, and weapons. The expression of sexual traits is often influenced by environmental conditions, suggesting that phenotypic plasticity may precede and facilitate evolutionary divergence in sexual traits by sexual selection. However, the mechanisms that promote plasticity in sexual traits remain poorly understood. Using the cichlid fish Astatotilapia burtoni, we show that sexual selection may promote plasticity in sexual traits. In this species, males change between yellow and blue color and exhibit intense male contest competition over breeding territories to attract females. We found that experimentally increased competition over territories led to a higher proportion of males expressing the yellow phenotype. Furthermore, we found that expression of yellow coloration is beneficial to males in territorial disputes. Specifically, yellow males won more staged dyadic contests than blue males, and yellow males had a lower level of oxidative stress than blue males, especially when engaging in more territorial display. However, females spawned more with blue males than with yellow males, suggesting that expression of blue coloration is sexually more attractive. The ability to adjust color phenotype according to the local competitive environment could therefore promote the persistence of plastic changes in coloration. Our findings challenge the view that phenotypic plasticity sets the stage for the evolution of genetically fixed changes via sexual selection, and instead suggest that sexual selection may favor plasticity in sexual traits.
Removing the Ostrogradski ghost from degenerate gravity theories

The Ostrogradski ghost problem that appears in higher derivative system is considered for systems with constraints. A prescription for removal of the ghost creating momenta is described based on the Dirac's constraint analysis. It is shown how one can make the canonical Hamiltonian bounded from below by systematically removing the constraints appearing in the system thereby reducing the effective dimension of the phase space. To show the effect of higher derivative terms we consider the singularity free Gauss-Bonnet theory coupled via a matter field to the Einstein Hilbert action. Finally we construct the ghost free canonical Hamiltonian for the theory that is bounded from below.
Molecular evolution of non-visual opsin genes across environmental, developmental, and morphological adaptations in frogs

Non-visual opsins are transmembrane proteins expressed in the eyes, skin, and brain of many animals. When paired with a light-sensitive chromophore, non-visual opsins form photopigment systems involved in various non-visual, light-detection functions, including circadian rhythm regulation, light-seeking behavior, and detection of seasonality. Previous research has primarily explored the diversity and function of non-visual opsins in model organisms, with few studies investigating their molecular evolution in non-model species. Here we explored molecular evolution of non-visual opsin genes in anuran amphibians (frogs and toads). With diverse lifestyles ranging from fossorial to aquatic, anurans inhabit a diverse array of light environments, which makes them a compelling system for studying the evolution of light detection mechanisms. Using whole-eye transcriptomes from 79 anuran species, as well as genomes and multi-tissue transcriptomes from an additional 15 species, we 1) identify which non-visual opsin genes are expressed in the eyes of anurans; 2) compare selective constraint (ω, or dN/dS) among non-visual opsin genes; and 3) test for potential adaptive evolution by comparing selection between discrete ecological classes in anurans (e.g. diurnal versus non-diurnal). We consistently recovered 14 non-visual opsin genes from anuran eye transcriptomes, compared to 18 genes that we recovered genome wide, and detected positive selection in a subset of these genes. We also found variation in selective constraint between discrete ecological and life-history classes, which may reflect functional adaptation in non-visual opsin genes. Although non-visual opsins remain poorly understood, these findings provide insight into their molecular evolution and set the stage for future research on their potential function across taxa with diverse environmental, developmental, and morphological adaptations.
Contemporary human H3N2 influenza A viruses require a low threshold of suitable glycan receptors for efficient infection

Recent human H3N2 influenza A viruses (IAV) have evolved to employ elongated glycans terminating in α2,6-linked sialic acid as their receptors. These glycans are displayed in low abundancies by cells commonly employed to propagate these viruses (MDCK and hCK), resulting in low or no viral propagation. Here, we examined whether the overexpression of the glycosyltransferases B3GNT2 and B4GALT1, which are responsible for the elongation of poly-N-acetyllactosamines (LacNAc), would result in improved A/H3N2 propagation. Stable overexpression of B3GNT2 and B4GALT1 in MDCK and hCK cells was achieved by lentiviral integration and subsequent antibiotic selection and confirmed by qPCR and protein mass spectrometry experiments. Flow cytometry and glycan mass spectrometry experiments using the B3GNT2 and/or B4GALT1 knock-in cells demonstrated increased binding of viral hemagglutinins and the presence of a larger number of LacNAc repeating units, especially on hCK-B3GNT2 cells. An increase in the number of glycan receptors did, however, not result in a greater infection efficiency of recent human H3N2 viruses. Based on these results, we propose that H3N2 IAVs require a low number of suitable glycan receptors to infect cells and that an increase in the glycan receptor display above this threshold does not result in improved infection efficiency.
Possible Chiral Phase Transition in Two-Dimensional Solid {sup 3}He

We study a spin system with two- and four-spin exchange interactions on the triangular lattice, which is a possible model for the nuclear magnetism of solid {sup 3}He layers. It is found that a novel spin structure with scalar chiral order appears if the four-spin interaction is dominant. Ground-state properties are studied using the spin-wave approximation. A phase transition concerning the scalar chirality occurs at a finite temperature, even though the dimensionality of the system is two and the interaction has isotropic spin symmetry. Critical properties of this transition are studied with Monte Carlo simulations in the classical limit. {copyright} {ital 1997} {ital The American Physical Society}
DrFARM: Identification and inference for pleiotropic gene in GWAS

In a standard analysis, pleiotropic variants are identified by running separate genome-wide association studies (GWAS) and combining results across traits. But such two-stage statistical approach may lead to spurious results. We propose a new statistical approach, Debiased-regularized Factor Analysis Regression Model (DrFARM), through a joint regression model for simultaneous analysis of high-dimensional genetic variants and multilevel dependencies. This joint modeling strategy controls overall error to permit universal false discovery rate (FDR) control. DrFARM uses the strengths of the debiasing technique and the Cauchy combination test, both being theoretically justified, to establish a valid post selection inference on pleiotropic variants. Through extensive simulations, we show that DrFARM appropriately controls overall FDR. Applying DrFARM to data on 1,031 metabolites measured on 6,135 men from the Metabolic Syndrome in Men (METSIM) study, we identify 288 new metabolite associations at loci that did not reach statistical significance in prior METSIM metabolite GWAS.
Starlight in the Universe

There has been remarkable progress recently in both observational and theoretical studies of galaxy formation and evolution. Largely due to a combination of deep Hubble Space Telescope (HST) imaging, Keck spectroscopy and COBE far-IR background measurements, new constraints have emerged on the emission history of the galaxy population as a whole. The global ultraviolet, optical, near- and far-IR photometric properties of the universe as a function of cosmic time cannot be reproduced by a simple stellar evolution model defined by a constant (comoving) star-formation density and a universal (Salpeter) initial mass function, and require instead a substantial increase in the stellar birthrate with lookback time. While the bulk of the stars present today appears to have formed relatively recently, the existence of a decline in the star-formation density above z ≈ 2 remains uncertain. The study of the transition from cosmic `dark age' to an ionized universe populated with luminous sources can shed new light on the star formation activity at high redshifts, and promises answers to some fundamental questions on the formation of cosmic structures. If stellar sources are responsible for photoionizing the intergalatic medium at z ≈ 5, the rate of star formation at this epoch must be comparable or greater than the one inferred from optical observations of galaxies at z ≈ 3. A population of quasars at z ≲ 2 could make a significant contribution to the extragalactic background light if dust-obscured accretion onto supermassive black holes is an efficient process.
A Peroxiredoxin-P38 MAPK scaffold increases MAPK activity by MAP3K-independent mechanisms

Peroxiredoxins (Prdx) utilize reversibly oxidized cysteine residues to reduce peroxides but also to promote H2O2 signal transduction, including H2O2-induced activation of P38 MAPK. Prdx form H2O2-induced disulfide complexes with many proteins, including multiple kinases involved in P38 MAPK signaling. Here we show that a genetically-encoded fusion between Prdx and the P38 MAPK is sufficient to hyperactivate the kinase in yeast and human cells by a mechanism that does not require the H2O2-sensing cysteine of the Prdx. In yeast, we demonstrate that a P38-Prdx fusion protein compensates for the loss of a scaffold protein and upstream MAP3K kinase activity, driving entry into mitosis. Based on our findings, we propose that the H2O2-induced formation of Prdx-MAPK disulfide complexes provides a scaffold and signaling platform for MAPKK-MAPK signaling. The demonstration that formation of a complex with a Prdx can be sufficient to modify the activity of a kinase has broad implications for peroxide-based signal transduction in eukaryotes. Highlights P38-Prdx complexes increase P38 (Sty1/MAPK14) phosphorylation in yeast and human cells The S. pombe Prdx promotes transient thioredoxin-mediated oxidation of a MAPK tyrosine phosphatase P38-Prdx complexes increase P38(Sty1) activity by phosphatase and MAP3K-independent mechanisms P38-Prdx complexes increase the stability and phosphorylation of the S. pombe P38 MAPKK (Wis1) Non-canonical, H2O2-induced autophosphorylation contributes to activation of the Wis1 MAPKK
Single-cell RNA-sequencing implicates venous endothelial cells as a source of VEGF-A-mediated neo-angiogenesis in neuroinflammation

Histopathological studies of multiple sclerosis (MS), a demyelinating disease of the central nervous system (CNS), and its animal model, experimental autoimmune encephalomyelitis (EAE), have found newly formed leaky vessels in demyelinated acute and chronic plaques, in addition to blood-brain barrier (BBB) damage in existing vessels, that exacerbate disease pathology by increasing infiltration of immune cells. Which vessel subtypes and signaling pathways generate these aberrant vessels is poorly understood. Using single-cell RNA-sequencing and in vivo validation, we find that transcriptome signatures of neo-angiogenesis arise in venous endothelial cells in both acute and chronic EAE, and correlate with upregulation in VEGF-A signaling. These neo-angiogenic markers are also increased in acute and chronic MS lesions. Treatment with a VEGF-A blocking antibody diminishes neo-angiogenic transcriptomic signatures and vascular proliferation in vivo, but does not restore BBB function or ameliorate significantly EAE pathology. Therefore, anti-angiogenic therapies in combination with immunomodulatory therapies may benefit MS progression.
Learning to predict based on self- versus externally induced prediction violations: a direct comparison using a Bayesian inference modelling approach

Predictive processing is quickly gaining ground as a theory of perception and attention. From this perspective the brain is cast as an organism’s predictive model of how its world works and will continue to work in the future. However, research on the brain’s predictive capacities remains beholden to traditional research practices in which participants are passively shown stimuli without their active involvement. The current study is an investigation into ways in which self-generated predictions may differ from externally induced predictions. Participants completed a volatile spatial attention task under both conditions on different days. We used the Hierarchical Gaussian Filter, an approximate Bayesian inference model, to determine subject-specific parameters of belief-updating and inferred volatility. We found preliminary evidence in support of self-generated predictions incurring a larger reaction time cost when violated compared to predictions induced by sensory cue, which translated to participants’ increased sensitivity to changes in environmental volatility. Our results suggest that internally generated predictions may be afforded more weight, but these results are complicated by session order and duration effects, as well as a lack of statistical power. We discuss the limitations of our study preventing us from replicating previous research, and ways to remedy these shortcomings in future studies.
Conscious perception and the role of the basal ganglia: preliminary findings from a deep brain stimulation study

Conscious perception is thought to depend on global amplification of sensory input. In recent years, the basal ganglia have been implicated in gating conscious access due to their consistent involvement in thalamocortical loops. However, much of the evidence implicating the basal ganglia in these processes in humans is correlational. The current study is a preliminary investigation in four patients to explore whether deep brain stimulation (DBS) in the basal ganglia might improve conscious perception. In our study, treatment-resistant obsessive-compulsive disorder (OCD) patients with a striatal DBS implant completed two canonical conscious perception tasks: emotion-induced blindness and backward masking. We found preliminary evidence in support of a role played by the basal ganglia in conscious perception at the behavioral level: patients performed better when stimulation was active, but we could not establish neural effects corresponding to these behavioral findings, possibly due to our small sample size. We discuss the potential implications and limitations of our study and delineate avenues for future research.
Sex-Specific Changes in Neuronal Activity and Affective Behavior after Chronic Alcohol Consumption in CRF1-cre Transgenic Rats

Alcohol use disorders are complex conditions characterized in part by excessive ethanol (EtOH) drinking and withdrawal-induced malaise. The corticotropin releasing factor-1 receptor (CRF1) has been implicated in EtOH drinking, affective states, and pain sensitivity; often in a sex-dependent manner. The studies presented here investigate the associations between baseline behavior, chronic intermittent EtOH intake, and withdrawal-induced affective behavior in male and female CRF1:cre: td Tomato rats. There were no sex differences in basal affective state or thermal sensitivity, as measured by the splash test, novelty suppressed feeding test, and Hargreaves, respectively. However, female rats displayed increased mechanical sensitivity, measured by the Von Frey test. Following baseline testing, rats underwent voluntary EtOH or water drinking under intermittent access conditions. Female rats consumed significantly more EtOH, but only during the first week. There were no group effects of EtOH on behavioral tests, but all of the rats demonstrated increased malaise upon repeated testing. There were significant individual differences where affective behavior positively correlated with negative affect in both sexes. There were also significant correlations between EtOH intake and CRF1-cFos co-expression in the infralimbic cortex and basolateral amygdala. EtOH decreased CRF1+ expression in the lateral amygdala, but there were no significant group effects of EtOH on cFos or CRF1-cFos co-expression in the medial prefrontal cortex or amygdala. Together, these results illustrate the complex interplay between affect, pain sensitivity, EtOH drinking, and the role of CRF1 containing neurons in mediating these behaviors. the specific contributions of these cells to AUD and associated negative affect remains unclear. The present study uses behavioral testing, voluntary EtOH drinking, and immunofluorescence in a CRF1 transgenic rat line to investigate the interaction between EtOH drinking and affective behavior in a sex-specific manner. IL
Longitudinal Analysis of Retinal Ganglion Cell Damage at Individual Axon Bundle Level in Mice Using Visible-Light Optical Coherence Tomography Fibergraphy

We developed a new analytic tool based on visible-light optical coherence tomography fibergraphy (vis-OCTF) to longitudinally track individual axon bundle transformation following acute optic nerve crush injury (ONC) in mice. We analyzed four parameters: lateral bundle width, axial bundle height, cross-sectional area, and the shape of individual bundles. We showed that axon bundles became wider and thicker at 3-days post ONC. The bundle swelling at 3-days post-ONC has correlated with about 15% retinal ganglion cell (RGC) soma loss. At 6-days post-ONC, axon bundles showed a significant reduction in lateral width and cross-sectional area, followed by a reduction in bundle height at 9-days post-ONC. Bundle shrinking at 9-days post-ONC has correlated with about 68% RGC soma loss. Both experimental and simulated results suggested that the cross-sectional area of individual RGC axon bundles is more sensitive than the bundle width and height to indicate RGC soma loss. This study is the first to track and quantify individual RGC axon bundles in vivo following ONC injury and establish the correlation between the morphological changes of RGC axon bundles and RGC soma loss.