Miracle-dz/UniFAR-FTUs huggingface dataset:
A HYBRID SCENARIO FOR THE FORMATION OF BROWN DWARFS AND VERY LOW MASS STARS

We present a calculation of protostellar disk formation and evolution in which gaseous clumps (essentially, the first Larson cores formed via disk fragmentation) are ejected from the disk during the early stage of evolution. This is a universal process related to the phenomenon of ejection in multiple systems of point masses. However, it occurs in our model entirely due to the interaction of compact, gravitationally bound gaseous clumps and is free from the smoothing-length uncertainty that is characteristic of models using sink particles. Clumps that survive ejection span a mass range of 0.08–0.35 M☉, and have ejection velocities 0.8 ± 0.35 km s−1, which are several times greater than the escape speed. We suggest that, upon contraction, these clumps can form substellar or low-mass stellar objects with notable disks, or even close-separation very low mass binaries. In this hybrid scenario, allowing for ejection of clumps rather than finished protostars/proto-brown-dwarfs, disk formation and the low velocity dispersion of low-mass objects are naturally explained, while it is also consistent with the observation of isolated low-mass clumps that are ejection products. We conclude that clump ejection and the formation of isolated low-mass stellar and substellar objects is a common occurrence, with important implications for understanding the initial mass function, the brown dwarf desert, and the formation of stars in all environments and epochs.
Systematic study of multifragmentation in asymmetric colliding nuclei

We present a complete systematically theoretical study of multifragmentation for asymmetric colliding nuclei for heavy-ion reactions in the energy range between 50 MeV/nucleon and 600 MeV/nucleon by using soft and hard equations of state. This study is performed within an isospin-dependent quantum-molecular dynamics model. To see the effect of mass asymmetry, simulations are carried out in the absence of Coulomb interactions. Coulomb interactions enhance the production of fragments by about 20%. We envision an interesting outcome for large asymmetric colliding nuclei. Although nearly symmetric nuclei depict a well-known trend for rising and falling with a peak around E=100 MeV/nucleon, this trend, however, is completely missing for large asymmetric nuclei. Therefore, experiments are needed to verify this prediction.
Entropy Current for the Fluid/Gravity Model of the Chiral Magnetic Effect

We construct long wavelength asymptotically locally AdS_5 spacetimes with slowly varying (background) gauge fields which are solutions to the U(1)^n Einstein-Maxwell-Chern-Simons system. These bulk spacetimes are dual to (3+1)-dimensional fluid flows with n anomalous currents in the presence of external electromagnetic fields. We utilise the area form on the outer horizon to holographically compute an entropy current for the dual fluid to first order in boundary derivatives. Our resulting expression contains additional terms proportional to the vorticity and magnetic field and thus provides holographic confirmation of the entropy current calculated by Son and Surowka for hydrodynamics with triangle anomalies. We then restrict our bulk metric to describe the fluid/gravity model of the chiral magnetic effect (CME) and again holographically obtain the entropy current. As expected, our calculation replicates the result produced using standard hydrodynamic/thermodynamic arguments.
Asymptotic evolution of quantum walks with random coin

We study the asymptotic position distribution of general quantum walks on a lattice, including walks with a random coin, which is chosen from step to step by a general Markov chain. In the unitary (i.e., nonrandom) case, we allow any unitary operator which commutes with translations and couples only sites at a finite distance from each other. For example, a single step of the walk could be composed of any finite succession of different shift and coin operations in the usual sense, with any lattice dimension and coin dimension. We find ballistic scaling and establish a direct method for computing the asymptotic distribution of position divided by time, namely as the distribution of the discrete time analog of the group velocity. In the random case, we let a Markov chain (control process) pick in each step one of finitely many unitary walks, in the sense described above. In ballistic order, we find a nonrandom drift which depends only on the mean of the control process and not on the initial state. In diffu.
Structure analysis of simulated molecular clouds with the Δ-variance

We employ the Delta-variance analysis and study the turbulent gas dynamics of simulated molecular clouds (MCs). Our models account for a simplified treatment of time-dependent chemistry and the non-isothermal nature of the gas. We investigate simulations using three different initial mean number densities of n_0 = 30, 100 and 300 cm^{-3} that span the range of values typical for MCs in the solar neighbourhood. Furthermore, we model the CO line emission in a post-processing step using a radiative transfer code. We evaluate Delta-variance spectra for centroid velocity (CV) maps as well as for integrated intensity and column density maps for various chemical components: the total, H2 and 12CO number density and the integrated intensity of both the 12CO and 13CO (J = 1 -> 0) lines. The spectral slopes of the Delta-variance computed on the CV maps for the total and H2 number density are significantly steeper compared to the different CO tracers. We find slopes for the linewidth-size relation ranging from 0.4 to 0.7 for the total and H2 density models, while the slopes for the various CO tracers range from 0.2 to 0.4 and underestimate the values for the total and H2 density by a factor of 1.5-3.0. We demonstrate that optical depth effects can significantly alter the Delta-variance spectra. Furthermore, we report a critical density threshold of ~100 cm^{-3} at which the Delta-variance slopes of the various CO tracers change sign. We thus conclude that carbon monoxide traces the total cloud structure well only if the average cloud density lies above this limit.
Topological in-plane polarized piezo actuation for compact adaptive lenses with aspherical correction

In this contribution, we investigate the effects of using in-plane polarized piezo actuators with topological buckling displacement to drive glass-piezo composite membranes for adaptive lenses with aspherical control. We find that the effects on the focal power and aspherical tuning range are relatively small, whereas the tuning speed is improved significantly with a first resonance of 1 kHz for a 13 mm aperture lens.
Putative Transcription Factor Genes Associated with Regulation of Carotenoid Biosynthesis in Chili Pepper Fruits Revealed by RNA-Seq Coexpression Analysis

During the ripening process, the pericarp of chili pepper (Capsicum spp.) fruits accumulates large amounts of carotenoids. Although the carotenoid biosynthesis pathway in the Capsicum genus has been widely studied from different perspectives, the transcriptional regulation of genes encoding carotenoid biosynthetic enzymes has not been elucidated in this fruit. We analyzed RNA-Seq transcriptomic data from the fruits of 12 accessions of Capsicum annuum during the growth, development, and ripening processes using the R package named Salsa. We performed coexpression analyses between the standardized expression of genes encoding carotenoid biosynthetic enzymes (target genes (TGs)) and the genes of all expressed transcription factors (TFs). Additionally, we analyzed the promoter region of each biosynthetic gene to identify putative binding sequences for each selected TF candidate. We selected 83 TFs as putative regulators of the carotenogenic structural genes. From them, putative binding sites in the promoters of the carotenoid-biosynthesis-related structural genes were found for only 54 TFs. These results could guide the search for transcription factors involved in the regulation of the carotenogenic pathway in chili pepper fruits and might facilitate the collection of corresponding experimental evidence to corroborate their participation in the regulation of this biosynthetic pathway in Capsicum spp.
Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins

Using data from 183 public human data sets from PRIDE, a machine learning model was trained to identify tissue and cell-type specific protein patterns. PRIDE projects were searched with ionbot and tissue/cell type annotation was manually added. Data from physiological samples were used to train a Random Forest model on protein abundances to classify samples into tissues and cell types. Subsequently, a one-vs-all classification and feature importance were used to analyse the most discriminating protein abundances per class. Based on protein abundance alone, the model was able to predict tissues with 98% accuracy, and cell types with 99% accuracy. The F-scores describe a clear view on tissue-specific proteins and tissue-specific protein expression patterns. In-depth feature analysis shows slight confusion between physiologically similar tissues, demonstrating the capacity of the algorithm to detect biologically relevant patterns. These results can in turn inform downstream uses, from identification of the tissue of origin of proteins in complex samples such as liquid biopsies, to studying the proteome of tissue-like samples such as organoids and cell lines.
Phosphorylation chemistry of the Bordetella PlrSR TCS and its contribution to bacterial persistence in the lower respiratory tract

Bordetella species cause lower respiratory tract infections in mammals. B. pertussis and B. bronchiseptica are the causative agents of whooping cough and kennel cough, respectively. The current acellular vaccine for B. pertussis protects against the pertussis toxin but does not prevent transmission or colonization. Cases of B. pertussis infections are on the rise even in areas of high vaccination. The PlrSR two-component system, is required for persistence in the mouse lung. A partial plrS deletion strain and a plrS H521Q strain cannot survive past three days in the lung, suggesting PlrSR works in a phosphorylation dependent mechanism. We characterized the biochemistry of B. bronchiseptica PlrSR and found that both proteins function as a canonical two-component system. His521 and Glu522 were essential for PlrS autophosphorylation. Asn525 was essential for phosphatase activity. The PAS domain was critical for both PlrS autophosphorylation and phosphatase activities. PlrS can both phosphotransfer to and exert phosphatase activity towards PlrR. Unexpectedly, PlrR forms a tetramer when unphosphorylated and a dimer upon phosphorylation. Finally, we demonstrated the importance of PlrS phosphatase activity for persistence within the murine lung. By characterizing PlrSR we hope to guide future in vivo investigation for development of new vaccines and therapeutics. 10 GRAPHICAL ABSTRACT
Host Phylogeny Shapes Viral Transmission Networks in an Island Ecosystem

Viral transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator-prey relationships, may govern cross-species virus transmission and zoonotic risk, although their relative impact is unknown. By characterising the virome of a relatively isolated island ecological community linked through a food web we show that phylogenetic barriers result in distantly related host species sharing fewer viruses. Host ecology had a much smaller influence on overall virome composition. Network analysis revealed that hosts with a high diversity of viruses were more likely to gain new viruses, and that generalist viruses were more likely to infect new hosts. Such a highly connected ecological community heightens the risk of disease emergence, particularly among closely related species. One-Sentence Summary Sequencing of an entire island virome reveals that closely related hosts have highly connected virus communities, increasing emergence risk.
Assessing the influence of distinct culture media on human pre-implantation development using single-embryo transcriptomics

The use of assisted reproductive technologies is consistently rising across the world. However, making an informed choice on which embryo culture medium should be preferred to ensure satisfactory pregnancy rates and the health of future children critically lacks scientific background. In particular, embryos within their first days of development are highly sensitive to their micro-environment, and it is unknown how their transcriptome adapts to different embryo culture compositions. Here, we determined the impact of culture media composition on gene expression in human pre-implantation embryos. By employing single-embryo RNA-sequencing after 2 or 5 days of the post-fertilization culture in different commercially available media (Ferticult, Global, and SSM), we revealed medium-specific differences in gene expression changes. Embryos cultured pre-compaction until day 2 in Ferticult or Global media notably displayed 266 differentially expressed genes, which were related to essential developmental pathways. Herein, 19 of them could have a key role in early development, based on their previously described dynamic expression changes across development. When embryos were cultured after day 2 in the same media considered more suitable because of its amino acid enrichment, 18 differentially expressed genes thought to be involved in the transition from early to later embryonic stages were identified. Overall, the differences were reduced at the blastocyst stage, highlighting the ability of embryos conceived in a suboptimal in vitro culture medium to mitigate the transcriptomic profile acquired under different pre-compaction environments.
Epigenetically distinct synaptic architecture in clonal compartments in the teleostean dorsal pallium

The dorsal telencephalon (i.e. the pallium) exhibits high anatomical diversity across vertebrate classes. The mammalian dorsal pallium accommodates a six layered-structure, the neocortex, whereas the teleostean dorsal pallium possesses various compartmentalized structures among species. The development, function and evolution of the fish dorsal pallium remain unillustrated. Here, we analyzed the structure and epigenetic landscapes of cell lineages in the telencephalon of medaka fish (Oryzias latipes) which possesses a clearly delineated dorsal pallium (the Dd2 region). We found that different pallial regions, including Dd2, are formed by mutually exclusive clonal units, and that each pallium compartment exhibits a distinct epigenetic landscape. In particular, Dd2 possesses a unique open chromatin pattern that preferentially targets synapse-related genes. Indeed, Dd2 shows a high density of synapses, which might reflect strong plasticity. Finally, we identified several transcription factors as candidate regulators for the Dd2, which are partially shared with the human neocortex and hippocampus.
A human-specific motif facilitates CARD8 inflammasome activation after HIV-1 infection

Inflammasomes are cytosolic innate immune complexes that play a critical role in host defense against pathogens but can also contribute to inflammatory pathogenesis. Here, we find that the human inflammasome-forming sensor CARD8 senses HIV-1 infection via site-specific cleavage of the CARD8 N-terminus by the HIV protease (HIV-1PR). HIV-1PR cleavage of CARD8 induces pyroptotic cell death and the release of pro-inflammatory cytokines from infected cells, processes that we find are dependent on Toll-like receptor stimulation prior to viral infection. Our evolutionary analyses reveal that the HIV-1PR cleavage site in CARD8 is unique to humans, and that chimpanzee CARD8 does not recognize proteases from HIV or simian immunodeficiency viruses from chimpanzees (SIVcpz). In contrast, SIVcpz does cleave human CARD8, suggesting that SIVcpz was poised to activate the human CARD8 inflammasome prior to its cross-species transmission into humans and implicating the CARD8 inflammasome as a potential driver of HIV pathogenesis.
Intracellular Helix-Loop-Helix Domain Modulates Inactivation Kinetics of Mammalian TRPV5 and TRPV6 Channels

TRPV5 and TRPV6 are calcium-selective ion channels expressed at the apical membrane of epithelial cells. Important for systemic calcium (Ca2+) homeostasis, these channels are considered as gatekeepers of this cation transcellular transport. Intracellular Ca2+ exerts a negative control over the activity of these channels by promoting inactivation. TRPV5 and TRPV6 inactivation has been divided into fast and slow phases based on their kinetics. While slow inactivation is common to both channels, fast inactivation is characteristic of TRPV6. It has been proposed that the fast phase depends on Ca2+ binding and that the slow phase depends on the binding of the Ca2+/Calmodulin complex to the internal gate of the channels. Here, by means of structural analyses, site-directed mutagenesis, electrophysiology, and molecular dynamic simulations, we identified a specific set of amino acids and interactions that determine the inactivation kinetics of mammalian TRPV5 and TRPV6 channels. We propose that the association between the intracellular helix-loop-helix (HLH) and the TRP helix (TDh) domains favors the faster inactivation kinetics observed in mammalian TRPV6 channels.
Broad Brain Networks Support Curiosity-Motivated Incidental Learning Of Naturalistic Dynamic Stimuli With And Without Monetary Incentives

Curiosity – the intrinsic desire to know – is a concept central to the human mind and knowledge acquisition. Experimental studies on information-seeking have found that curiosity facilitates memory encoding and exhibits similar reward,ng properties as extrinsic rewards/incentives by eliciting a dopaminergic response. However, it is not clear whether these findings hold with more naturalistic dynamic stimuli and how the joint effect of curiosity and extrinsic incentive manifests in learning and neural activation patterns. Herein, we presented participants with videos of magic tricks across two behavioural (N1 = 77, N2 = 78) and one fMRI study (N = 50) and asked them to rate subjective feelings of curiosity, while also performing a judgement task that was incentivised for the half of participants. Incidental memory for the magic trick was tested a week later. The integrated results showed that both curiosity and availability of extrinsic incentives enhanced encoding but did not interact with each other. However, exploratory analyses showed that curiosity and monetary incentives were associated with recollection and familiarity differently, suggesting the involvement of different encoding mechanisms. Analysis of the fMRI data using the intersubject synchronisation framework showed that, while the effects of curiosity on memory were located in the hippocampus and dopaminergic brain areas, neither the effects of curiosity nor incentives themselves were found in the often-implicated reward network, but instead were associated with cortical areas involved in processing uncertainly and attention. These results suggest that curiosity recruits broader brain networks than what was implicated in the previous literature when investigated with dynamic stimuli.
Ultrasonic measures of prestin (SLC26a5) charge movements in membrane patches

Charged moieties in the outer hair cell (OHC) molecular motor protein, prestin, are driven by transmembrane voltage to ultimately provide for cochlear amplification. The speed of voltage-dependent conformational switching underlies its ability to influence micromechanics of the cell and the organ of Corti. Corresponding voltage-sensor charge movements in prestin, classically assessed as a voltage-dependent, nonlinear membrane capacitance (NLC), have been used to gauge its frequency response. Using megahertz sampling of prestin charge movements, we extend interrogations of prestin performance into the ultrasonic range (up to 120 kHz) and find response magnitude larger than previously reported. We also confirm kinetic model predictions of prestin by directly observing its cut-off frequency under voltage-clamp as the intersection frequency (Fis) of the real and imaginary components of complex NLC (cNLC), showing values near 19 kHz. At higher frequencies, the imaginary component roll-off exactly tracks that of Abs(cNLC). The frequency response of prestin displacement current noise determined from the Nyquist relation aligns with this cut-off. On the other hand, previous measures of stationary thermal-driven noise of prestin indicated that the cut-off was several fold greater than that of NLC, in violation of the fluctuation-dissipation theorem. We have attempted to confirm this apparent paradox, but find that low frequency (<10kHz), voltage-dependent 1/f noise, likely due to intrinsic prestin conductance, can limit the accessible bandwidth for stationary noise analysis. Nevertheless, within those bandwidths, frequency response comparisons of stationary measures and Nyquist relation measures are consistent. We conclude that voltage stimulation accurately assesses the spectral limits of prestin activity. Significance Using megahertz sampling, we extend measures of prestin charge movement into the ultrasonic range and find that the frequency roll-off is less than previously reported. Nevertheless, analysis of complex nonlinear capacitance confirms low-pass behavior, with a characteristic cut-off frequency near 19 kHz. The frequency response of prestin noise garnered by the admittance-based Nyquist relation confirms this cut-off frequency. In conflict with previous results, however, we find a similar low-pass frequency response using direct measures of prestin noise in the absence of voltage stimulation. Our data indicate that voltage perturbation provides an accurate assessment of prestin performance.
Altered Secretion, Constitution, and Functional Properties of the Gastrointestinal Mucus in a Rat Model of Sporadic Alzheimer’s Disease

Accumulating evidence supports the involvement of the gastrointestinal (GI) system in Alzheimer’s disease (AD), however, it is currently unknown whether GI alterations arise as a consequence of central nervous system (CNS) pathology or play a causal role in the pathogenesis of the disease. The GI mucus system is a possible mediator of GI dyshomeostasis in neurological disorders as CNS controls mucus production and secretion via the efferent arm of the brain-gut axis. The aim was to use a brain-first model of sporadic AD induced by intracerebroventricular streptozotocin (STZ-icv) to dissect the efferent (i.e. brain-to-gut) effects of isolated central neuropathology on the GI mucus system. Quantification and morphometric analysis of goblet cell mucigen granules revealed altered GI mucus secretion in the AD model possibly mediated by the insensitivity of AD goblet cells to neurally-evoked mucosal secretion confirmed by ex vivo cholinergic stimulation of isolated duodenal rings. The dysfunctional efferent control of the GI mucus secretion results in altered biochemical composition of the mucus associated with reduced glycoprotein aggregation and binding capacity in vitro. Finally, functional consequences of the reduced barrier-forming capacity of the AD mucus are demonstrated using the in vitro two-compartment caffeine diffusion interference model. Isolated central AD-like neuropathology results in the loss of efferent control of GI homeostasis via the brain-gut axis characterized by the insensitivity to neurally-evoked mucosal secretion, altered mucus constitution, and reduced barrier-forming capacity potentially increasing the susceptibility of STZ-icv rat model of AD to GI and systemic inflammation induced by intraluminal toxins, microorganisms, and drugs.