Miracle-dz/UniFAR-FTUs huggingface dataset:
Beauty and the brain: Investigating the neural and musical attributes of beauty during a naturalistic music listening experience

Evaluative beauty judgments are very common, but in spite of this commonality, are rarely studied in cognitive neuroscience. Here we investigated the neural and musical attributes of musical beauty using a naturalistic free-listening paradigm applied to behavioral and neuroimaging recordings and validated by experts’ judgments. In Study 1, 30 Western healthy adult participants rated continuously the perceived beauty of three musical pieces using a motion sensor. This allowed us to identify the passages in the three musical pieces that were inter-subjectively judged as beautiful or ugly. This informed the analysis for Study 2, where additional 36 participants were recorded with functional magnetic resonance imaging (fMRI) while they listened attentively to the same musical pieces as in Study 1. In Study 3, in order to identify the musicological features characterizing the passages that were consistently rated as beautiful or ugly in Study 1, we collected post-hoc questionnaires from 12 music-composition experts. Results from Study 2 evidenced focal regional activity in the orbitofrontal brain structure when listening to beautiful passages of music, irrespectively of the subjective reactions and individual listening biographies. In turn, the moments in the music that were consistently rated as ugly were associated with bilateral supratemporal activity. Effective connectivity analysis also discovered inhibition of auditory activation and neural communication with orbitofrontal cortex, especially in the right hemisphere, during listening to beautiful musical passages as opposed to intrinsic activation of auditory cortices and decreased coupling to orbitofrontal cortex during listening to ugly musical passages. Experts’ questionnaires indicated that the beautiful passages were more melodic, calm, sad, slow, tonal, traditional and simple than the ones negatively valenced. In sum, we identified a neural mechanism for inter-subjective beauty judgments of music in the supratemporal-orbitofrontal circuit, irrespectively of individual taste and listening biography. Furthermore, some invariance in objective musical attributes of beautiful and ugly passages was evidenced. Future studies might address the generalizability of the findings to non-Western listeners.
Signature morpho-electric, transcriptomic, and dendritic properties of extratelencephalic-projecting human layer 5 neocortical pyramidal neurons

In the neocortex, subcerebral axonal projections originate largely from layer 5 (L5) extratelencephalic-projecting (ET) neurons. The highly distinctive morpho-electric properties of these neurons have mainly been described in rodents, where ET neurons can be labeled by retrograde tracers or transgenic lines. Similar labeling strategies are not possible in the human neocortex, rendering the translational relevance of findings in rodents unclear. We leveraged the recent discovery of a transcriptomically-defined L5 ET neuron type to study the properties of human L5 ET neurons in neocortical brain slices derived from neurosurgeries. Patch-seq recordings, where transcriptome, physiology and morphology are assayed from the same cell, revealed many conserved morpho-electric properties of human and rodent L5 ET neurons. Divergent properties were also apparent but were often smaller than differences between cell types within these two species. These data suggest a conserved function of L5 ET neurons in the neocortical hierarchy, but also highlight marked phenotypic divergence possibly related to functional specialization of human neocortex.
Mechanosensitive Expression of Lamellipodin Governs Cell Cycle Progression and Intracellular Stiffness

Cells exhibit pathological behaviors in response to increased extracellular matrix (ECM) stiffness, including accelerated cell proliferation and migration [1–9], which are correlated with increased intracellular stiffness and tension [2, 3, 10–12]. The biomechanical signal transduction of ECM stiffness into relevant molecular signals and resultant cellular processes is mediated through multiple proteins associated with the actin cytoskeleton in lamellipodia [2, 3, 10, 11, 13]. However, the molecular mechanisms by which lamellipodial dynamics regulate cellular responses to ECM stiffening remain unclear. Previous work described that lamellipodin, a phosphoinositide- and actin filament-binding protein that is known mostly for controlling cell migration [14–21], promotes ECM stiffness-mediated early cell cycle progression [2], revealing a potential commonality between the mechanisms controlling stiffness-dependent cell migration and those controlling cell proliferation. However, i) whether and how ECM stiffness affects the levels of lamellipodin expression and ii) whether stiffness-mediated lamellipodin expression is required throughout cell cycle progression and for intracellular stiffness have not been explored. Here, we show that the levels of lamellipodin expression in cells are significantly increased by a stiff ECM and that this stiffness-mediated lamellipodin upregulation persistently stimulates cell cycle progression and intracellular stiffness throughout the cell cycle, from the early G1 phase to M phase. Finally, we show that both Rac activation and intracellular stiffening are required for the mechanosensitive induction of lamellipodin. More specifically, inhibiting Rac1 activation in cells on stiff ECM reduces the levels of lamellipodin expression, and this effect is reversed by the overexpression of activated Rac1 in cells on soft ECM. We thus propose that lamellipodin is a critical molecular lynchpin in the control of mechanosensitive cell cycle progression and intracellular stiffness.
Evaluation of the antiviral effect of chlorine dioxide (ClO2) using a vertebrate model inoculated with avian coronavirus

Background The need for safe and effective antiviral treatments is pressing given the number of viral infections that are prevalent in animal and human populations, often causing devastating economic losses and mortality. Informal accounts of anecdotal use of chlorine dioxide (ClO2), a well-known disinfectant and antiseptic, in COVID-19 patients has raised concern about potential toxicity, but also raises the question that ClO2 might elicit antiviral effects, a possibility that has never been examined in vivo in any animal model. Here, we challenged the hypothesis that ClO2 decreases the viral load and virus-induced mortality in a vertebrate model. For this, we determined viral load, virus-induced lesions and mortality in 10-day old chick embryos inoculated with 104 mean EID50/mL of attenuated Massachusetts and Connecticut avian coronavirus (IBV) strains. Results The ClO2 treatment had a marked impact on IBV infection. Namely, viral titres were 2.4-fold lower and mortality was reduced by half in infected embryos that were treated with ClO2. Infection led to developmental abnormalities regardless of treatment. Lesions typical of IBV infections were observed in all inoculated embryos, but severity tended to be significantly lower in ClO2-treated embryos. We found no gross or microscopic evidence of toxicity caused by ClO2 at the doses used herein. Conclusions Our study shows that ClO2 could be a safe and viable way of treating and mitigating the effects of avian coronavirus infections, and raises the possibility that similar effects could be observed in other organisms. Graphical abstract
A memory-based theory of emotional disorders

Learning and memory play a central role in emotional disorders, particularly in depression and posttraumatic stress disorder. We present a new, transdiagnostic theory of how memory and mood interact in emotional disorders. Drawing upon retrieved-context models of episodic memory, we propose that memories form associations with the contexts in which they are encoded, including emotional valence and arousal. Later, encountering contextual cues retrieves their associated memories, which in turn reactivate the context that was present during encoding. We first show how our retrieved-context model accounts for findings regarding the organization of emotional memories in list-learning experiments. We then show how this model predicts clinical phenomena, including persistent negative mood after chronic stressors, intrusive memories of painful events, and the efficacy of cognitive-behavioral therapies.
Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates

We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequilibrium in the pan-genome of L. monocytogenes. Our analysis revealed the presence of strong linkage disequilibrium in L. monocytogenes, with ∼99% of genes showing significant non-random associations with a large majority of other genes in the genome. Twenty-seven loci having lower levels of association with other genes were considered to be potential “hot spots” for horizontal gene transfer (i.e., recombination via conjugation, transduction, and/or transformation). The patterns of linkage disequilibrium in L. monocytogenes suggest limited exchange of foreign genetic material in the genome and can be used as a tool for identifying new recombinant strains. This can help understand processes contributing to the diversification and evolution of this pathogenic bacteria, thereby facilitating development of effective control measures.
PHYTOCHROMES B1/B2 ARE KEY REGULATORS OF EPIGENOME REPROGRAMMING DURING TOMATO FRUIT DEVELOPMENT

Phytochrome-mediated light and temperature perception has been shown to be a major regulator of fruit development. Furthermore, chromatin remodelling via DNA demethylation has been described as a crucial mechanism behind the fruit ripening process; however, the molecular basis underlying the triggering of this epigenetic modification remains largely unknown. Here, an integrative analyses of the methylome, siRNAome and transcriptome of tomato fruits from phyA and phyB1B2 null mutants was performed, revealing that PHYB1 and PHYB2 influences genome-wide DNA methylation during fruit development and ripening. The experimental evidence indicates that PHYB1B2 signal transduction relies on a gene expression network that includes chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes and remodelling factors) and transcriptional regulators, ultimately leading to altered mRNA profile of photosynthetic and ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits in fleshy fruits.
Minding The Gap: Range Size And Economic Use Drive Functional Trait Data Shortfall In The Atlantic Forest

Biodiversity shortfalls are knowledge gaps that may result from uneven sampling through time and space and human interest biases. Gaps in data of functional traits of species may add uncertainty in functional diversity and structure measures and hinder inference on ecosystem functioning and ecosystem services, with negative implications for conservation and restoration practices, such as in Atlantic Forest hotspot. Here we investigate which are the potential drivers of trait data gaps and where geographically they are in the Atlantic Forest. We quantified trait gaps for four key plant functional traits of 2335 trees species, and evaluated which factors drive trait gap at the species and at the geographical level. At the species level, we found larger trait gaps for small-ranged and with no economic use. At the geographical level, we found larger gaps at the Atlantic Forest east coast. Trait gaps were higher away from urban areas, and among species with smaller mean range size and smaller mean economic use of wood, and smaller near protected areas. Efforts on reducing trait gaps of small-ranged and of species with economic use of wood can further advance theory-driven studies and improve knowledge coverage
Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes

Effects of metformin, the first-line drug for type 2 diabetes therapy, on gut microbiome composition in type 2 diabetes have been described in various studies both in human subjects and animals. However, the details of the molecular mechanisms of metformin action have not been fully understood. Moreover, there is a significant lack of information on how metformin affects gut microbiome composition in female mice models, as most of the existing studies have focused on males only. Our study aimed to examine metformin-induced alterations in gut microbiome diversity and composition of high-fat diet-induced type 2 diabetes mouse model, employing a randomized block, factorial study design, and including 24 experimental units allocated to 8 treatment groups. We performed shotgun metagenomic sequencing using DNA obtained from fecal samples representing gut microbiome before and after ten weeks-long metformin treatment. We identified 100 metformin-related differentially abundant species in high-fat diet-fed mice before and after the treatment, with most of the species abundances increased. In contrast, no significant changes were observed in control diet-fed mice.We also observed sex-specific differences in response to metformin treatment. Males experienced more pronounced changes in metabolic markers, while, in females, the extent of changes in gut microbiome representatives was more marked, indicated by 53 differentially abundant species with more remarkable Log fold changes compared to the combined-sex analysis. Our results suggest that both sexes of animals should be included in future studies focusing on metformin effects on the gut microbiome.
Amino acid transporter B0AT1 influence on ADAM17 interactions with SARS-CoV-2 receptor ACE2 putatively expressed in intestine, kidney, and cardiomyocytes

SARS-CoV-2 exhibits significant experimental and clinical gastrointestinal, renal, and cardiac muscle tropisms responsible for local tissue-specific and systemic pathophysiology capriciously occurring in about half of COVID-19 patients. The underlying COVID-19 mechanisms engaged by these extra-pulmonary organ systems are largely unknown. We approached this knowledge gap by recognizing that neutral amino acid transporter B0AT1 (alternately called NBB, B, B0 in the literature) is a common denominator expressed nearly exclusively by three particular cell types: intestinal epithelia, renal proximal tubule epithelium, and cardiomyocytes. B0AT1 provides uptake of glutamine and tryptophan. The gut is the main depot expressing over 90% of the body’s entire pool of SARS-CoV-2 receptor angiotensin converting enzyme-2 (ACE2) and B0AT1. Recent cryo-EM studies established that ACE2 forms a thermodynamically favored dimer-of-heterodimers complex with B0AT1 assembled in the form of a dimer of two ACE2:B0AT1 heterodimers anchored in plasma membranes. Prior epithelial cell studies demonstrated ACE2 chaperone trafficking of B0AT1. This contrasts with monomeric expression of ACE2 in lung pneumocytes, in which B0AT1 is undetectable. The cell types in question also express a disintegrin and metalloproteinase-17 (ADAM17) known to cleave and shed the ectodomain of monomeric ACE2 from the cell surface, thereby relinquishing protection against unchecked renin-angiotensin-system (RAS) events of COVID-19. The present study employed molecular docking modeling to examine the interplaying assemblage of ACE2, ADAM17 and B0AT1. We report that in the monomer form of ACE2, neck region residues R652-N718 provide unimpeded access to ADAM17 active site pocket, but notably R708 and S709 remained >10-15 Å distant. In contrast, interference of ADAM17 docking to ACE2 in a dimer-of-heterodimers arrangement was directly correlated with the presence of a neighboring B0AT1 subunit complexed to the partnering ACE2 subunit of the 2ACE2:2B0AT1] dimer of heterodimers, representing the expression pattern putatively exclusive to intestinal, renal and cardiomyocyte cell types. The monomer and dimer-of-heterodimers docking models were not influenced by the presence of SARS-CoV-2 receptor binding domain (RBD) complexed to ACE2. The results collectively provide the underpinnings for understanding the role of B0AT1 involvement in COVID-19 and the role of ADAM17 steering ACE2 events in intestinal and renal epithelial cells and cardiomyocytes, with implications useful for consideration in pandemic public hygiene policy and drug development.
Transcriptomic signature and metabolic programming of bovine classical and nonclassical monocytes indicate distinct functional specializations

Similar to human monocytes, bovine monocytes can be split into CD14+CD16− classical and CD14−CD16+ nonclassical monocytes (cM and ncM, respectively). Here, we present an in-depth analysis of their steady-state transcriptomes, highlighting pronounced functional specializations. Gene transcription indicates that pro-inflammatory and antibacterial processes are associated with cM, while ncM appear to be specialized in regulatory/anti-inflammatory functions and tissue repair, as well as antiviral responses and T-cell immunomodulation. In support of these functional differences, we found that oxidative phosphorylation prevails in ncM, whereas cM are clearly biased towards aerobic glycolysis. Furthermore, bovine monocyte subsets differed in their responsiveness to TLR ligands, supporting an antiviral role of ncM. Taken together, these data clearly indicate a variety of subset-specific functions in cM and ncM that are likely to be transferable to monocyte subsets of other species, including humans.
Quantifying signal persistence in the T cell signaling network using an optically controllable antigen receptor

T cells discriminate between healthy and infected cells with remarkable sensitivity when mounting an immune response. It has been hypothesized that this efficient detection requires combining signals from discrete antigen-presenting cell interactions into a more potent response, requiring T cells to maintain a ‘memory’ of previous encounters. To quantify the magnitude of this phenomenon, we have developed an antigen receptor that is both optically and chemically tunable, providing control over the initiation, duration, and intensity of intracellular T-cell signaling within physiological cell conjugates. We observe very limited persistence within the T cell intracellular network on disruption of receptor input, with signals dissipating entirely in ~15 minutes, and directly confirm that sustained proximal receptor signaling is required to maintain active gene transcription. Our data suggests that T cells are largely incapable of integrating discrete antigen receptor signals but instead simply accumulate the output of gene expression. By engineering optical control in a clinically relevant chimeric antigen receptor, we show that this limited signal persistence can be exploited to increase the activation of primary T cells by ~3-fold by using pulsatile stimulation. Our results are likely to apply more generally to the signaling dynamics of other cellular networks.
RESTORING CONNEXIN-36 FUNCTION IN DIABETOGENIC ENVIRONMENTS PRECLUDES MOUSE AND HUMAN ISLET DYSFUNCTION

The secretion of insulin from β-cells in the islet of Langerhans is governed by a series of metabolic and electrical events, which can fail during the progression of type2 diabetes (T2D). β-cells are electrically coupled via Cx36 gap junction channels, which coordinates the pulsatile dynamics of [Ca2+] and insulin release across the islet. Factors such as pro-inflammatory cytokines and free fatty acids disrupt gap junction coupling under invitro conditions. Here we test whether gap junction coupling and coordinated [Ca2+] dynamics are disrupted in T2D, and whether recovery of gap junction coupling can recover islet function. We examine islets from donors with T2D, from db/db mice, and islets treated with proinflammatory cytokines (TNF-α, IL-1β, IFN-ɣ) or free fatty acids (palmitate). We modulate gap junction coupling using Cx36 over-expression or pharmacological activation via modafinil. We also develop a peptide mimetic (S293) of the c-terminal regulatory site of Cx36 designed to compete against its phosphorylation. Cx36 gap junction permeability and [Ca2+] dynamics were disrupted in islets from both human donors with T2D and db/db mice, and in islets treated with proinflammatory cytokines or palmitate. Cx36 over-expression, modafinil treatment and S293 peptide all enhanced Cx36 gap junction coupling and protected against declines in coordinated [Ca2+] dynamics. Cx36 over-expression and S293 peptide also reduced apoptosis induced by proinflammatory cytokines. Critically S293 peptide rescued gap junction coupling and [Ca2+] dynamics in islets from both db/db mice and a sub-set of T2D donors. Thus, recovering or enhancing Cx36 gap junction coupling can improve islet function in diabetes. KEY POINTS - Cx36 gap junction permeability and associated coordination of [Ca2+] dynamics is diminished in human type 2 diabetes (T2D) and mouse models of T2D. - Enhancing Cx36 gap junction permeability protects against disruptions to the coordination of [Ca2+] dynamics. - A novel peptide mimetic of the Cx36 c-terminal regulatory region protects against declines in Cx36 gap junction permeability. - Pharmacological elevation in Cx36 or Cx36 peptide mimetic recovers [Ca2+] dynamics and GSIS in human T2D and mouse models of T2D.
Control of neurogenic competence in mammalian hypothalamic tanycytes

Loss of function of NFI transcription factors in hypothalamic tanycytes generates diverse subtypes of functional neurons. Hypothalamic tanycytes, radial glial cells that share many features with neuronal progenitors, can generate small numbers of neurons in the postnatal hypothalamus, but the identity of these neurons and the molecular mechanisms that control tanycyte-derived neurogenesis are unknown. In this study, we show that tanycyte-specific disruption of the NFI family of transcription factors (Nfia/b/x) robustly stimulates tanycyte proliferation and tanycyte-derived neurogenesis. Single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) analysis reveals that NFI (nuclear factor I) factors repress Sonic hedgehog (Shh) and Wnt signaling in tanycytes and modulation of these pathways blocks proliferation and tanycyte-derived neurogenesis in Nfia/b/x-deficient mice. Nfia/b/x-deficient tanycytes give rise to multiple mediobasal hypothalamic neuronal subtypes that can mature, fire action potentials, receive synaptic inputs, and selectively respond to changes in internal states. These findings identify molecular mechanisms that control tanycyte-derived neurogenesis, which can potentially be targeted to selectively remodel the hypothalamic neural circuitry that controls homeostatic physiological processes.
A rapid and simple method for the determination of ethephon residue in agricultural products by GC with headspace sampling

Ethephon quickly decomposes to ethylene under alkaline and high temperature conditions. In this research, we developed a rapid and simple method suitable for routine analysis of ethephon residues in agricultural products using gas chromatography (GC) equipped with a flame ionization detector (FID). This method was based upon the headspace sampling and determined the ethylene formed. Average recoveries from a pples, tomatoes, grapes, kiwifruits and sugarcane, which were spiked with 1~3 ppm ethephon, were in the range of 88.3~98.6% and the coefficient of variation were ranged of 2.2~7.5%. The detection limit was 0.1 ppm.