Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving Social Interactive Learning through Dual Brain Stimulation

Social interactive learning denotes the ability to acquire new information from a conspecific – a prerequisite for cultural evolution and survival. As inspired by recent neurophysiological research, here we tested whether social interactive learning can be augmented by exogenously synchronizing oscillatory brain activity across an instructor and a learner engaged in a naturalistic song-learning task. We used a dual brain stimulation protocol entailing the trans-cranial delivery of synchronized electric currents in two individuals simultaneously. When we stimulated inferior frontal brain regions, with 6 Hz alternating currents being in-phase between the instructor and the learner, the dyad exhibited spontaneous and synchronized body movement. Remarkably, this stimulation also led to enhanced learning performance. A mediation analysis further disclosed that interpersonal movement synchrony acted as a partial mediator of the effect of dual brain stimulation on learning performance, i.e. possibly facilitating the effect of dual brain stimulation on learning. Our results provide a causal demonstration that inter-brain synchrony is a sufficient condition to improve real-time information transfer between pairs of individuals. Significance The study of social behavior, including but not limited to social learning, is undergoing a paradigm shift moving from single- to multi-person brain research. Yet, nearly all evidence in this area is purely correlational: inter-dependencies between brains’ signals are used to predict success in social behavior. For instance, inter-brain synchrony has been shown to be associated with successful communication, cooperation, and joint attention. Here we took a radically different approach. We stimulated two brains simultaneously, hence manipulating inter-brain synchrony, and measured the resulting effect upon behavior in the context of a social learning task. We report that frequency- and phase-specific dual brain stimulation can lead to the emergence of spontaneous synchronized body movement between an instructor and a learner. Remarkably, this can also augment learning performance.
MAP Kinase inhibition reshapes tumor microenvironment of mouse pancreatic cancer by depleting anti-inflammatory macrophages

The RAF/MEK/ERK (MAP Kinase) pathway is the index oncogenic signaling towards which many compounds have been developed and tested for the treatment of KRAS-driven cancers, including pancreatic ductal adenocarcinoma (PDA). Here, we explored the immunological changes induced by targeted MEK1/2 inhibition (MEKi) using trametinib in preclinical mouse models of PDA. We evaluated the dynamic changes in the immune contexture of mouse PDA upon MEKi using a multidimensional approach (mRNA analyses, flow cytometry, and immunophenotyping). Effect of MEKi on the viability and metabolism of macrophages was investigated in vitro. We showed that transcriptional signatures of MAP Kinase activation are enriched in aggressive human PDA subtype (squamous/basal-like/quasimesenchymal), while short term MEKi treatment in mouse PDA induced subtype switching. Integrative mRNA expression and immunophenotypic analyses showed that MEKi reshapes the immune landscape of PDA by depleting rather than reprogramming macrophages, while augmenting infiltration by neutrophils. Depletion of macrophages is observed early in the course of in vivo treatment and is at least partially due to their higher sensitivity to MEKi. Tumor-associated macrophages were consistently reported to interfere with gemcitabine uptake by PDA cells. Here, our in vivo studies show a superior antitumor activity upon combination of MEKi and gemcitabine using a sequential rather than simultaneous dosing protocol. Our results show that MEK inhibition induces a dramatic remodeling of the tumor microenvironment of mouse PDA through depletion of macrophages, which substantially improves the antitumor activity of gemcitabine.
LA-VOCE: LOW-SNR Audio-Visual Speech Enhancement Using Neural Vocoders

Audio-visual speech enhancement aims to extract clean speech from a noisy environment by leveraging not only the audio itself but also the target speaker’s lip movements. This approach has been shown to yield improvements over audio-only speech enhancement, particularly for the removal of interfering speech. Despite recent advances in speech synthesis, most audio-visual approaches continue to use spectral mapping/masking to reproduce the clean audio, often resulting in visual backbones added to existing speech enhancement architectures. In this work, we propose LA-VocE, a new two-stage approach that predicts mel-spectrograms from noisy audio-visual speech via a transformer-based architecture, and then converts them into waveform audio using a neural vocoder (HiFi-GAN). We train and evaluate our framework on thousands of speakers and 11+ different languages, and study our model’s ability to adapt to different levels of background noise and speech interference. Our experiments show that LA-VocE outperforms existing methods according to multiple metrics, particularly under very noisy scenarios.
Environmentally induced lipidome adaptation in the bacterial model organism M. extorquens

Cells, from microbes to man, adapt their membranes in response to the environment to maintain their properties and functions. To adapt, lipid composition is homeostatically regulated to conserve optimal membrane properties. Global patterns of lipidome remodelling are poorly understood, particularly in model organisms with simple lipid compositions that can provide insight into fundamental principles underlying membrane adaptation. Using shotgun lipidomics, we examined the simple yet adaptive lipidome of the plant-associated Gram-negative bacterium Methylobacterium extorquens over varying temperature, hyperosmotic and detergent stress, carbon sources, and cell density. We observed that as few as ten lipids account for 90% of the total changes, thus constraining the upper limit of variable lipids required for an adaptive living membrane. Across all conditions, the highest degree of lipidomic variability was observed for changing growth temperature. We also revealed that variations in lipid structural features are not monotonic over a given range of conditions and are heterogeneous across lipid classes. Interestingly, phosphotidylcholine showed the most extreme acyl chain remodeling among all lipid classes, suggesting a new link to its importance in bacterial-host interactions and pathogenicity. These patterns in lipidomic remodeling suggest a highly adaptive mechanism with many degrees of freedom and constrain the lipidomic requirements for an adaptive membrane.
Insect Defoliators in Recovering Industrial Landscapes: Effects of Landscape Degradation and Remediation Near an Abandoned Metal Smelter on Gypsy Moth (Lepidoptera: Lymantriidae) Feeding, Frass Production, and Frass Properties

Abstract Although insect defoliators are recognized as major agents of ecological change in North American forests, their ecology in industrially degraded landscapes with poor-quality soils, metal contamination, and marginal vegetation growth is largely unknown. We fed gypsy moth larvae (Lymantria dispar L.) paper birch leaves (Betula papyrifera Marsh) (Fagales: Betulaceae) collected from four forested catchment areas near an abandoned Cu/Ni smelter in Sudbury (Ontario, Canada) with different histories of industrial degradation and remediation (reference, remediated, natural recovery, and degraded). We measured caterpillar feeding, frass properties and decomposability, and the effects of frass on the growth of ticklegrass (Agrostis scabra Willd.) (Poales: Poaceae). Caterpillars generally ate more (+25–50%) and produced more frass (+30–40 %) on a diet of leaves from the more industrially degraded sites. Frass had an overall positive effect on plant survivorship (+4.1–10.8 effect size) and growth (+0.1–0.5 effect size), although the smallest benefits came from frass derived from vegetation from the more heavily degraded sites. Our results suggest that defoliating insects respond to differences in environmental degradation and remediation and that industrial landscapes may be particularly susceptible to more extensive defoliation and increased conversion of foliar biomass into frass, which could alter plant growth and survivorship, soil development, and nutrient and metal cycling. Some of these effects may pose additional challenges to landscape recovery (e.g., increased defoliation) while others may be beneficial (e.g., enhanced plant growth and soil development).
Equilibrium patterns of genetic diversity shuffled by migration and recombination

This thesis presents two different models to study how recombination and migration shuffle genetic diversity. In the first model, recombination is the only evolutionary force. At time 0, each individual has her unique chromosome painted in a distinct color. By the blending effect of recombination, the genomes of the descending individuals look like mosaics of colors, each color representing the genetic material inherited from a different ancestral individual. Each segment of the same color is called an identical-by-descent (IBD) segment. We have been able to characterize the sizes and positions of the segments that are IBD to a given locus in the chromosome of a randomly sampled individual in the population. The second model is devoted to the study of the effects of geographic structure, migration, mutation and recombination in the genetic composition of a metapopulation. The metapopulation is modelled as a graph where vertices correspond to subpopulations and edges are associated to migration rates. The idea behind this project is to study speciation: when two subpopulations accumulate enough genetic differences they may become separate species. We have been able to characterize the distribution of the genetic distances between subpopulations in a low mutation - low migration regime, depending on the geographic structure, and to show that some geographic configurations can promote speciation.
High-resolution melt curve analysis for rapid detection of rifampicin resistance in mycobacterium tuberculosis: A single-center study in Iran

Introduction Tuberculosis (TB) remains a leading cause of death worldwide, especially in developing countries. Early detection of resistance is extremely important to reduce the risk of death. This study was aimed to compare the diagnostic accuracy of high resolution melting (HRM) analysis in comparison with Xpert MTB/RIF as well as conventional drug susceptibility testing (DST) for the detection of rifampicin (RIF) resistance in Mycobacterium tuberculosis in Iran. Materials and methods A comparative cross-sectional study was carried out from April 2017 to September 2018. A total of 80 culture-positive clinical samples selected during the study period were analyzed for detection of RIF-resistant TB by conventional DST, Xpert MTB/RIF, and sequencing. Sensitivity and specificity of the HRM calculated according to DST as our gold standard test in this study. Results The overall sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of HRM assay were found to be 100%, 89.33%, 38.46%, and 100% respectively. Conclusions The analysis has demonstrated that the diagnostic accuracy of HRM tests is insufficient to replace Xpert MTB/RIF and conventional DST. HRM test may be used in combination with culture due to the advantage of the time to result. Further work to improve molecular tests would benefit from standardized reference standards and the methodology.
A Note on Associations Observed between Sharks and Teleosts

Abstract We report herein on novel observations of associations between 2 teleost species and a variety of shark species in the Gulf of Mexico. Using underwater video, we observed Decapterus punctatus (Round Scad) and Chloroscombrus chrysurus (Atlantic Bumper) associating with both Carcharhinus limbatus (Blacktip Shark) and Carcharhinus brevipinna (Spinner Shark). We also observed Round Scad associating with Carcharhinus acronotus (Blacknose Shark). Both Round Scad and Atlantic Bumpers schooled around and followed these sharks. We observed Round Scad in schools averaging 54 individuals that tended to stay posterior to the pectoral fins of the shark. These observations prompted a novel on-line image survey wherein we found that Round Scad were associated with 3 additional shark species. Online media platforms have not been commonly utilized for data collection, and to our knowledge, this is the first study to conduct a Google Image survey to obtain data supporting interspecific associations. This paper is also the first report of an apparent symbiosis between various shark species with Round Scad and with Atlantic Bumpers. There are few reports of associations with sharks aside from well-known examples, such as Echeneis naucrates (Sharksucker), Naucrates ductor (Pilotfish), and Labroides spp. (cleaner wrasses). These results provide additional information to the body of literature about symbioses between top predators, such as sharks, and teleosts.
A Modular Master Regulator Landscape Determines the Impact of Genetic Alterations on the Transcriptional Identity of Cancer Cells

Despite considerable pan-cancer efforts, the link between genomics and transcriptomics in cancer remains relatively weak and mostly based on statistical rather than mechanistic principles. By performing integrative analysis of transcriptomic and mutational profiles on a sample-by-sample basis, via regulatory/signaling networks, we identified a repertoire of 407 Master-Regulator proteins responsible for canalizing the genetics of 20 TCGA cohorts into 112 transcriptionally-distinct tumor subtypes. Further analysis highlighted a highly-recurrent regulatory architecture (oncotecture) with Master-Regulators organized into 24 modular MR-Blocks, regulating highly-specific tumor-hallmark functions and predictive of patient outcome. Critically, >50% of the somatic alterations identified in individual samples were in proteins affecting Master-Regulator activity, thus yielding novel insight into mechanisms linking tumor genetics and transcriptional identity and establishing novel non-oncogene dependencies. Experimental validation of functional mutations upstream of the most conserved MR-Block confirmed their ability to affect MR-protein activity, suggesting that the proposed methodology may effectively complement and extend current pan-cancer knowledge.
Oral absorption and lymphatic transport of baicalein following drug–phospholipid complex incorporation in self-microemulsifying drug delivery systems

Purpose The aims of this study were to prepare a baicalein self-microemulsion with baicalein-phospholipid complex as the intermediate (BAPC-SMEDDS) and to compare its effects with those of conventional baicalein self-microemulsion (CBA-SMEDDS) on baicalein oral absorption and lymphatic transport. Methods Two SMEDDS were characterized by emulsifying efficiency, droplet size, zeta potential, cloud point, dilution stability, physical stability, and in vitro release and lipolysis. Different formulations of 40 mg/kg baicalein were orally administered to Sprague-Dawley rats to investigate their respective bioavailabilities. The chylomicron flow blocking rat model was used to evaluate their lymphatic transport. Results The droplet sizes of BAPC-SMEDDS and CBA-SMEDDS after 100x dilution were 9.6±0.2 nm and 11.3±0.4 nm, respectively. In vivo experiments indicated that the relative bioavailability of CBA-SMEDDS and BAPC-SMEDDS was 342.5% and 448.7% compared to that of free baicalein (BA). The AUC0–t and Cmax of BAPC-SMEDDS were 1.31 and 1.87 times higher than those of CBA-SMEDDS, respectively. The lymphatic transport study revealed that 81.2% of orally absorbed BA entered the circulation directly through the portal vein, whereas approximately 18.8% was transported into the blood via lymphatic transport. CBA-SMEDDS and BAPC-SMEDDS increased the lymphatic transport ratio of BA from 18.8% to 56.2% and 70.2%, respectively. Therefore, self-microemulsion not only significantly improves oral bioavailability of baicalein, but also increases the proportion lymphatically transported. This is beneficial to the direct interaction of baicalein with relevant immune cells in the lymphatic system and for proper display of its effects. Conclusion This study demonstrates the oral absorption and lymphatic transport characteristics of free baicalein and baicalein SMEDDS with different compositions. This is of great significance to studies on lymphatic targeted delivery of natural immunomodulatory compounds.
TinyQMIX: Distributed Access Control for mMTC via Multi-agent Reinforcement Learning

Distributed access control is a crucial component for massive machine type communication (mMTC). In this communication scenario, centralized resource allocation is not scalable because resource configurations have to be sent frequently from the base station to a massive number of devices. We investigate distributed reinforcement learning for resource selection without relying on centralized control. Another important feature of mMTC is the sporadic and dynamic change of traffic. Existing studies on distributed access control assume that traffic load is static or they are able to gradually adapt to the dynamic traffic. We minimize the adaptation period by training TinyQMIX, which is a lightweight multi-agent deep reinforcement learning model, to learn a distributed wireless resource selection policy under various traffic patterns before deployment. Therefore, the trained agents are able to quickly adapt to dynamic traffic and provide low access delay. Numerical results are presented to support our claims.
Quantifying the Relationship among Impact Factors of Shrub Layer Diversity in Chinese Pine Plantation Forest Ecosystems

Shrub layer diversity is an essential component of the forest ecosystem diversity, that contributes significantly to structuring the community and maintaining diversity, especially in plantation forests. In previous studies, researchers have reported the strong relationship among various factors (i.e., soil composition, mean annual temperature, etc.) and shrub diversity. However, how these factors jointly influence shrub diversity and which factors could be considered the key factors is still unknown. In this study, we attempted to quantify the effect among environmental factors, soil factors and forest stand factors on shrub diversity. Twenty-seven variables were selected from 57 Chinese pine plantation plots in Huanglong Mountain, Yanan City, Shaanxi Province, China. The path models showed that latent variable of soil properties is the main effective factor of latent variable of shrub diversity (directly effect, path coefficient = 0.344) and the latent variable of site conditions is another effective factor of latent variable of shrub diversity (indirectly effect, path coefficient = 0.177); Besides, the latent variable of site conditions and forest properties directly affect the latent variable of soil properties (path coefficient = 0.514 and 0.326, respectively). Among the latent variable of soil properties, soil water content (SWC) has the biggest weight of 0.666, which indicated the most significant contribution of SWC to latent variables of shrub diversity. Total nitrogen, weighted 0.375, and total phosphorus, weighted 0.308, are also important factors and make a similar contribution to latent variable of shrub diversity. Soil organic matter (SOM) has a minimal impact (lowest weight, 0.059); among the objective variables of site condition, altitude contributes the most and is followed by litter thickness, weighted at 0.722 and 0.448, respectively. Furthermore, among all the variables affecting the latent variable of forest properties, forest age is recognized as the maximum impactor of soil property change, which weighted −0.941; and is followed by forest stock volume and diameter at breast height (DBH), weighted 0.795 and 0.788, respectively. The crowding index (C) has the lowest weight (−0.235) and demonstrated that spatial distribution and crowding of trees have minimal impact on the latent variable of Soil properties. diversity Overall, our study provides new insights into quantifying the relationships among different driving factors that potentially play a significant role in determining shrub layer diversity within the plantation forest.
Linker Histone H1 subtypes specifically regulate neutrophil differentiation

Neutrophils are important innate immune cells that tackle invading pathogens with different effector mechanisms. They acquire this antimicrobial potential during their maturation in the bone marrow, where they differentiate from hematopoietic stem cells in a process called granulopoiesis. Mature neutrophils are terminally differentiated and short-lived with a high turnover rate. Here, we show a critical role for linker histone H1 on the differentiation and function of neutrophils using a genome-wide CRISPR/Cas9 screen in the human cell line PLB-985. We systematically disrupted expression of somatic H1 subtypes to show that individual H1 subtypes affect PLB-985 maturation in opposite ways. Importantly, H1 subtypes also affect neutrophil differentiation of murine bone marrow stem cells, demonstrating an unexpected subtype-specific role for H1 in granulopoiesis.
Emergence of hystricognathous rodents: Palaeogene fossil record, phylogeny, dental evolution and historical biogeography

Although phylogenetic trees imply Asia as the ancestral homeland of the Hystricognathi clade (Rodentia: Ctenohystrica), curiously the oldest known fossil occurrences of hystricognathous rodents are not from Asia, but from Africa and South America, where they appear suddenly in the fossil record of both landmasses by the Late Middle Eocene. Here we performed cladistic and Bayesian (standard and tip-dating analyses) assessments of the dental evidence documenting early ctenohystricans, including several Asian ‘ctenodactyloids’, virtually all Palaeogene Asian and African hystricognaths known thus far and two representatives of the earliest known South American hystricognaths. Our results provide a phylogenetic context of early hystricognaths (with implications on systematics) and suggest that some Eocene Asian ‘ctenodactyloids’ could be considered as stem hystricognaths and pre-hystricognaths, although they were not recognized as such originally. However, this view does not fill the gap of the Eocene Asian hystricognath record, as the proposed results imply many ghost lineages extending back to the Middle Eocene for several Asian and African taxa. They also imply a complex early historical biogeography of the group, involving multiple dispersal events from Asia to Africa (and possibly from Africa back to Asia) and then to South America sometime during the Middle Eocene. Based on these phylogenetic considerations, we discuss the emergence of hystricognathous rodents from a morpho-anatomical perspective by analysing the differentiation of their masticatory apparatus and chewing movements, notably through the evolution of their dental patterns.