Miracle-dz/UniFAR-FTUs huggingface dataset:
Diet Potentially Drives the Differentiation of Eating Behaviours via Alterations to the Gut Microbiome in Infants

Certain infant eating behaviours are associated with adverse health outcomes such as obesity. While a diet consisting of infant formula has been linked to higher-risk eating behaviours and changes in the gut microbiome, little is known about what role the gut microbiome plays in mediating eating behaviours. Using 16S rRNA sequences extracted from 96 fecal samples collected from 58 infants, we identified a subset of bacterial taxa that were more abundant in formula-fed infants, primarily composed of the phylum Firmicutes. The presence of these taxa correlated with a lower drive to eat (i.e., lower food responsiveness). Furthermore, short-chain fatty acid production pathways were significantly more abundant in formula-fed infants, negatively correlated with food responsiveness, and positively associated with relative abundance of the Firmicutes subset. Our results suggest that higher abundances of Firmicutes in formula-fed infants may decrease their food responsiveness through short-chain fatty acid production in the first four months of life. Taken together, these findings suggest a potential role for the infant’s diet in impacting eating behaviour via changes to the gut microbiome, which may lead to the development of novel interventions for the prevention of childhood obesity.
Non-structural carbohydrate concentrations in woody organs, but not leaves, of temperate and tropical tree angiosperms are independent of the ‘fast-slow’ plant economic spectrum

Background and Aims Carbohydrate reserves play a vital role in plant survival during periods of negative carbon balance. Considering active storage of reserves, there is a trade-off between carbon allocation to growth and to reserves and defense. A resulting hypothesis is that allocation to reserves exhibits a coordinated variation with functional traits associated with the ‘fast-slow’ plant economics spectrum. Methods We tested the relationship between non-structural carbohydrates (NSC) of tree organs and functional traits using 61 angiosperm tree species from temperate and tropical forests with phylogenetic hierarchical Bayesian models. Key Results Our results provide evidence that NSC concentrations in woody organs and plant functional traits are largely decoupled, meaning that species’ resilience is unrelated to their position on the ‘fast-slow’ plant economics spectrum. In contrast, we found that variation between NSC concentrations in leaves and the fast-slow continuum was coordinated, as species with higher leaf NSC had traits values associated with resource conservative species such as lower SLA, lower Amax, and high wood density. We did not detect an influence of leaf habit on the variation of NSC concentrations in tree organs. Conclusions Efforts to predict the response of ecosystems to global change will need to integrate a suite of plant traits, such as NSC concentrations in woody organs, that are independent of the ‘fast-slow’ spectrum and that capture how species respond to a broad range of global change factors.
Spatial alignment between faces and voices improves selective attention to audio-visual speech

The ability to see a talker’s face has long been known to improve speech intelligibility in noise. This perceptual benefit depends on approximate temporal alignment between the auditory and visual speech components. However, the practical role that cross-modal spatial alignment plays in integrating audio-visual (AV) speech remains unresolved, particularly when competing talkers are present. In a series of online experiments, we investigated the importance of spatial alignment between corresponding faces and voices using a paradigm that featured both acoustic masking (speech-shaped noise) and attentional demands from a competing talker. Participants selectively attended a Target Talker’s speech, then identified a word spoken by the Target Talker. In Exp. 1, we found improved task performance when the talkers’ faces were visible, but only when corresponding faces and voices were presented in the same hemifield (spatially aligned). In Exp. 2, we tested for possible influences of eye position on this result. In auditory-only conditions, directing gaze toward the distractor voice reduced performance as predicted, but this effect could not fully explain the cost of AV spatial misalignment. Finally, in Exp. 3 and 4, we show that the effect of AV spatial alignment changes with noise level, but this was limited by a floor effect: due to the use of closed-set stimuli, participants were able to perform the task relatively well using lipreading alone. However, comparison between the results of Exp. 1 and Exp. 3 suggests that the cost of AV misalignment is larger at high noise levels. Overall, these results indicate that spatial alignment between corresponding faces and voices is important for AV speech integration in attentionally demanding communication settings.
WRKY33-mediated indole glucosinolate metabolic pathway confers host resistance against Alternaria brassicicola

The tryptophan (Trp)-derived plant secondary metabolites, including camalexin, 4-hydroxy-indole-3-carbonylnitrile (4OH-ICN), and indole glucosinolate (IGS), show broad-spectrum antifungal activity. However, the upstream regulators of these metabolic pathways among different plant species in response to fungus infection are rarely studied. In this study, our results revealed a positive role of WRKY33 in host resistance to Alternaria brassicicola by directly regulating the transcription of genes involved in the biosynthesis and atypical hydrolysis of IGS both in Arabidopsis and Chinese kale. Indole-3-yl-methylglucosinolate (I3G) and 4-methoxyindole-3-yl-methylglucosinolate (4MI3G) are the main components of IGS. WRKY33 induces the expression of MYB51 and CYP83B1 which promotes the biosynthesis of I3G, the precursor of 4MI3G. Moreover, it also directly activates the expression of CYP81F2, IGMT1, and IGMT2 to drive side chain modification of I3G to produce 4MI3G, which is in turn hydrolyzed by PEN2. However, Chinese kale showed a more severe symptom than Arabidopsis when infected by Alternaria brassicicola. Comparative analyses of the origin and evolution of Trp-metabolism indicate that the loss of camalexin biosynthesis in Brassica crops during evolution might attenuate the resistance of crops to Alternaria brassicicola. As a result, IGS metabolic pathway mediated by WRKY33 becomes essential for Chinese kale to deter Alternaria brassicicola. Our results highlight the differential regulation of Trp-derived camalexin and IGS biosynthetic pathways in plant immunity between Arabidopsis and Brassica crops. One-sentence Summary Pathogen-responsive WRKY33 directly regulates indole glucosinolates biosynthesis and atypical hydrolysis, conferring to host resistance to Alternaria brassicicola in Arabidopsis and Brassica crops.
Modeling-Based Design of Memristive Devices for Brain-Inspired Computing

Resistive switching random access memory (RRAM) has emerged for non-volatile memory application with the features of simple structure, low cost, high density, high speed, low power, and CMOS compatibility. In recent years, RRAM technology has made significant progress in brain-inspired computing paradigms by exploiting its unique physical characteristics, which attempts to eliminate the energy-intensive and time-consuming data transfer between the processing unit and the memory unit. The design of RRAM-based computing paradigms, however, requires a detailed description of the dominant physical effects correlated with the resistive switching processes to realize the interaction and optimization between devices and algorithms or architectures. This work provides an overview of the current progress on device-level resistive switching behaviors with detailed insights into the physical effects in the resistive switching layer and the multifunctional assistant layer. Then the circuit-level physics-based compact models will be reviewed in terms of typical binary RRAM and the emerging analog synaptic RRAM, which act as an interface between the device and circuit design. After that, the interaction between device and system performances will finally be addressed by reviewing the specific applications of brain-inspired computing systems including neuromorphic computing, in-memory logic, and stochastic computing.
High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens

Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. ABSTRACT Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated with the mating-type locus sizes, which is up to ~560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results in substitutions that often lead to amino acid alterations. IMPORTANCE Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. They also impact genome evolution as their repetitive nature facilitates nonhomologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, Ustilago hordei. This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. We hypothesize that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.
Wnt-Dependent Activation of ERK Mediates Repression of Chondrocyte Fate during Calvarial Development

Wnt signaling regulates cell fate decisions in diverse contexts during development, and loss of Wnt signaling in the cranial mesenchyme results in a robust and binary cell fate switch from cranial bone to ectopic cartilage. The Extracellular signal-regulated protein kinase 1 and 2 (ERK1/2) and Wnt signaling pathways are activated during calvarial osteoblast cell fate selection. Here, we test the hypothesis that ERK signaling is a mediator of Wnt-dependent cell fate decisions in the cranial mesenchyme. First, we show that loss of Erk1/2 in the cranial mesenchyme results in a diminished domain of osteoblast marker expression and increased expression of cartilage fate markers and ectopic cartilage formation in the frontal bone primordia. Second, we show that mesenchyme Wnt/β-catenin signaling and Wntless are required for ERK activation in calvarial osteoblasts. Third, we demonstrate that Wnt and ERK signaling pathways function together to repress Sox9 expression in mouse cranial mesenchyme. Our results demonstrate a link between the Wnt and ERK signaling pathways in regulating lineage selection in a subset of calvarial cells and provide new insights into Wnt-dependent cell fate decisions.
Optoception: perception of optogenetic brain stimulation

How do animals experience brain manipulations? Optogenetics has allowed us to manipulate selectively and interrogate neural circuits underlying brain function in health and disease. However, it is currently unknown whether mice could perceive arbitrary optogenetic stimulation in addition to their evoked physiological functions. To address this issue, mice were trained to report an optogenetic stimulation as a cue to obtain rewards and avoid punishments. It was found that mice could perceive optogenetic manipulations regardless of the brain area modulated, their rewarding effects, or the stimulation of glutamatergic, GABAergic, and dopaminergic cell types. We named this phenomenon optoception. Using optoception, mice could learn to execute two different sets of instructions based on the laser frequency. Importantly, optoception can occur either activating or silencing a single cell type. Our findings revealed that mice’s brains are capable of “monitoring” their self-activity, albeit indirectly, perhaps via interoception or as a discriminative stimulus, opening a new way to introduce information to the brain and control brain-computer interfaces.
Targeted Enrichment of rRNA Gene Tandem Arrays for Ultra-Long Sequencing by Selective Restriction Endonuclease Digestion

Large regions of nearly identical repeats, such as the 45S ribosomal RNA (rRNA) genes of Nucleolus Organizer Regions (NORs), can account for major gaps in sequenced genomes. To assemble these regions, ultra-long sequencing reads that span multiple repeats have the potential to reveal sets of repeats that collectively have sufficient sequence variation to unambiguously define that interval and recognize overlapping reads. Because individual repetitive loci typically represent a small proportion of the genome, methods to enrich for the regions of interest are desirable. Here we describe a simple method that achieves greater than tenfold enrichment of Arabidopsis thaliana 45S rRNA gene sequences among ultra-long Oxford Nanopore Technology sequencing reads. This method employs agarose-embedded genomic DNA that is subjected to restriction endonucleases digestion using a cocktail of enzymes predicted to be non-cutters of rRNA genes. Most of the genome is digested into small fragments that diffuse out of the agar plugs, whereas rRNA gene arrays are retained. In principle, the approach can also be adapted for sequencing other repetitive loci for which gaps exist in a reference genome.
Informational masking vs. crowding — A mid-level trade-off between auditory and visual processing

In noisy or cluttered environments, sensory cortical mechanisms help combine auditory or visual features into perceived objects. Knowing that individuals vary greatly in their ability to suppress unwanted sensory information, and knowing that the sizes of auditory and visual cortical regions are correlated, we wondered whether there might be a corresponding relation between an individual’s ability to suppress auditory vs. visual interference. In auditory masking, background sound makes spoken words unrecognizable. When masking arises due to interference at central auditory processing stages, beyond the cochlea, it is called informational masking (IM). A strikingly similar phenomenon in vision, called visual crowding, occurs when nearby clutter makes a target object unrecognizable, despite being resolved at the retina. We here compare susceptibilities to auditory IM and visual crowding in the same participants. Surprisingly, across participants, we find a negative correlation (R = −0.7) between IM susceptibility and crowding susceptibility: Participants who have low susceptibility to IM tend to have high susceptibility to crowding, and vice versa. This reveals a mid-level trade-off between auditory and visual processing.
A Solid-State Fluorescence Switch Based on Triphenylethene-Functionalized Dithienylethene With Aggregation-Induced Emission

The development of novel dithienylethene-based fluorescence switches in the aggregated state, and the solid state is highly desirable for potential application in the fields of optoelectronics and photopharmacology. In this contribution, three novel triphenylethene-functionalized dithienylethenes (1–3) have been designed and prepared by appending triphenylethene moieties at one end of dithienylethene unit. Their chemical structures are confirmed by 1H NMR, 13C NMR, and HRMS (ESI). They display good photochromic behaviors with excellent fatigue resistance upon irradiation with UV or visible light in Tetrahydrofuran (THF) solution. Before irradiation with UV light, they exhibit Aggregation Induced Emission (AIE) properties and luminescence behaviors in the solid state. Moreover, upon alternating irradiation with UV/visible light, they display effective fluorescent switching behaviors in the aggregated state and the solid state. The experimental results have been validated by the Density Functional Theory (DFT) calculations. Thus, they can be utilized as novel fluorescence switches integrated in smart, solid-state optoelectronic materials and photopharmacology.
The Relationship Between Quarantine Length and Negative Affect During the COVID-19 Epidemic Among the General Population in China: The Roles of Negative Cognition and Protective Factors

Quarantine and isolation at extended length, although considered as highly effective countermeasures for the novel coronavirus (COVID-19) which started at the end of 2019, can have great impact on individual's mental health, especially emotional state. The present research recruited 5,115 participants from the general public across 32 provinces and autonomous regions in China in an online survey study, about 20 days after the lockdown of the epicenter (Wuhan), to investigate the relationship between the length of the quarantine and negative affect (including depression and anxiety), as well as the mediating roles of negative cognition (including worry and anticipation), and the moderating roles of dispositional optimism, tolerance of uncertainty, social support, and healthy behavior. The results showed that: (1) Worry and anticipation mediated the relationship between quarantine length and depression and anxiety; (2) Dispositional optimism moderated the path coefficients of quarantine length to worry, worry to anxiety, and anticipation to depression; (3) Tolerance of uncertainty moderated the path coefficient of worry to anxiety; (4) Social support moderated the path coefficient of anticipation to anxiety. In conclusion, during quarantine, dispositional optimism, uncertainty tolerance, and social support can buffer the direct or indirect effects of quarantine length on depression and anxiety. These findings could have profound implications on the societal responses to COVID-19 and future pandemics.
Sero-Prevalence and Risk Factor of Peste Des Petits Ruminants in Sheep and Goats of Ethiopia: Systematic Review and Meta-Analysis

Background Peste des petits ruminant (PPR) is the most common prevalent viral disease of sheep and goats that impacts productivity and international animal trade in the world and also in Ethiopia. Despite the huge economic consequences related to PPR, little is known about the sero-prevalence of this disease at the country levels. The objective of this systematic review and meta-analysis was to estimate a single-group summary for sero-prevalence of PPR disease in small ruminants of Ethiopia and assess the potential risk factor to contribute the sero-prevalence estimate. Methodology Article on PPR in sheep and goats were searched in PubMed, Web of Science, Google Scholar, reference lists and African online source of articles that had been conducted between 1994 to 2020 and using inclusion and exclusion criteria with restricted to those studies published in English language. Results A total of 13 published papers containing 46 district level studies were included for analyses. The single-group summary of PPR disease sero-prevalence in small ruminant was estimated to be 27.71% (95 % CI: 21.46 - 33.96). Overall, the estimated pooled sero-prevalence at country level in sheep was 33.56% (95% CI: 18.72–48.41) and in goats 25.14% (95% CI: 15.68–34.59). Significant heterogeneity (I2 > 80%) was noted in all pooled estimates. The visual inspection of the funnel plot demonstrated the presence of possible publication bias which could be associated with the small number of studies and longtime interval. Conclusions This quantitative review showed that the pooled sero-prevalence to be high and regional prevalence estimates of PPR presented here will be useful in raising awareness and advocating the Governments to engage in initiatives PPR control and prevention.
Hydrogen sulfide blocks HIV rebound by maintaining mitochondrial bioenergetics and redox homeostasis

A fundamental challenge in HIV eradication is to understand how the virus establishes latency, maintains stable cellular reservoirs, and promotes rebound upon interruption of antiretroviral treatment (ART). Here, we discovered an unexpected role of the ubiquitous gasotransmitter hydrogen sulfide (H2S) in HIV latency and reactivation. We show that reactivation of HIV-1 is associated with down-regulation of the key H2S producing enzyme cystathionine-γ-lyase (CTH) and reduction in endogenous H2S. Genetic silencing of CTH disrupts redox homeostasis, impairs mitochondrial function, and remodels the transcriptome of latent cells to trigger HIV reactivation. Chemical complementation of CTH activity using a slow-releasing H2S donor, GYY4137, suppressed HIV reactivation and diminished virus replication. Mechanistically, GYY4137 blocked HIV reactivation by inducing the Keap1-Nrf2 pathway, inhibiting NF-κB, and recruiting the epigenetic silencer, YY1, to the HIV promoter. In latently infected CD4+ T cells from ART-suppressed human subjects, GYY4137 in combination with ART prevented viral rebound and improved mitochondrial bioenergetics. Moreover, prolonged exposure to GYY4137 exhibited no adverse influence on proviral content or CD4+ T cell subsets, indicating that diminished viral rebound is due to a loss of transcription rather than a selective loss of infected cells. In summary, this work provides mechanistic insight into H2S-mediated suppression of viral rebound and suggests the inclusion of an H2S donor in the current ART regimen to achieve a functional HIV-1 cure.
Multi-targeted therapy resistance via drug-induced secretome fucosylation

Cancer secretome is a reservoir for aberrant glycosylation. How therapies alter this post-translational cancer hallmark and the consequences thereof remain elusive. Here we show that an elevated secretome fucosylation is a pan-cancer signature of both response and resistance to multiple targeted therapies. Large-scale pharmacogenomics revealed that fucosylation genes display widespread association with resistance to these therapies. In both cancer cell cultures and patients, targeted kinase inhibitors distinctively induced core fucosylation of secreted proteins less than 60 kDa. Label-free proteomics of N-glycoproteomes revealed that fucosylation of the antioxidant PON1 is a critical component of the therapy-induced secretome. Core fucosylation in the Golgi impacts PON1 stability and folding prior to secretion, promoting a more degradation-resistant PON1. Non-specific and PON1-specific secretome de-N-glycosylation both limited the expansion of resistant clones in a tumor regression model. Our findings demonstrate that core fucosylation is a common modification indirectly induced by targeted therapies that paradoxically promotes resistance.