Miracle-dz/UniFAR-FTUs huggingface dataset:
Emotion Classification from Speech by an Ensemble Strategy

Humans are prepared to comprehend each other's emotions through subtle body movements and speech expressions, and from those, they change the way they deliver/understand messages when communicating between them. Socially assistive robots need to empower their ability in recognizing emotions in a way to change the interaction with humans, especially with elders. This paper presents a framework for speech emotion prediction supported by an ensemble of distinct out-of-the-box methods, being the main contribution of the integration of the outputs of those methods in a single prediction consistent with the expression presented by the system's user. Results show a classification accuracy of 75.56% over the RAVDESS dataset and 86.43% in a group of datasets constituted by RAVDESS, SAVEE, and TESS.
Attention-Aware Pedagogical Agent for Smart Book Reading

The paradigm of Internet of Things (IoT), it is known to allow people and things to be connected anytime, anyplace, with anything, and anyone, and through any path or service. Embodied cognition, which is a new current of body thinking understanding understands the body and mind as a single unit in which there is no separation, can be inserted in learning experiences including Artificial Intelligence (AI). Thus, a form of implementation of AI is by using embodied agents, i.e. a software agent that interacts with the environment through a body. An application scenario can be the learning environment in which students’ attention is crucial since it is a facilitator of cognitive and behavioural performance, such as attention and learning performance. Embodied Pedagogical Agents, specifically might adapt according to student attentional states such as through attitudes and behaviours. Additionally, it enriches in social learning environment.
Skin microbiome dysbiosis and the role of Staphylococcus aureus in atopic dermatitis in adults and children: A narrative review

A dysfunctional epidermal barrier, which may be associated with mutations in the filaggrin gene in genetically predisposed individuals or harmful effects of environmental agents and allergens, contributes to the development of atopic dermatitis (AD) due to an interplay between the epithelial barrier, immune defence and the cutaneous microbiome. The skin of patients with AD is frequently over‐colonized by biofilm‐growing Staphylococcus aureus, especially during flares, causing dysbiosis of the cutaneous microbiota and a decrease in bacterial diversity that inversely correlates with AD severity. Specific changes in the skin microbiome can be present before clinical AD onset in infancy. Additionally, local skin anatomy, lipid content, pH, water activity and sebum secretion differ between children and adults and generally correlate with the predominant microbiota. Considering the importance of S. aureus in AD, treatments aimed at reducing over‐colonization to rebalance microbial diversity may help manage AD and reduce flares. Anti‐staphylococcal interventions in AD will contribute to a decrease in S. aureus superantigens and proteases that cause damage and inflammation of the skin barrier while concomitantly increasing the proportion of commensal bacteria that secrete antimicrobial molecules that protect healthy skin from invading pathogens. This review summarizes the latest data on targeting skin microbiome dysbiosis and S. aureus over‐colonization to treat AD in adults and children. Indirect AD therapies, including emollients ‘plus’, anti‐inflammatory topicals and monoclonal antibodies, may have an impact on S. aureus and help control bacterial diversity. Direct therapies, including antibacterial treatments (antiseptics/topical or systemic antibiotics), and innovative treatments specifically targeting S. aureus (e.g. anti‐S. aureus endolysin, and autologous bacteriotherapy), may be effective alternatives to mitigate against an increase in microbial resistance and allow a proportionate increase in the commensal microbiota.
Vascularized organ bioprinting: From strategy to paradigm

Over the past two decades, 3D bioprinting has become a popular research topic worldwide, as it is the most promising approach for manufacturing vascularized organs in vitro. However, transitioning from bioprinting of simple tissue models to real biomedical applications is still a challenge due to incomplete interdisciplinary theoretical knowledge and imperfect multi‐technology integration. This review examines the goals of vasculature manufacturing and proposes new strategic objectives in three stages. We then outline a bidirectional manufacturing strategy consisting of top‐down reconstruction (bioprinting) and bottom‐up regeneration (cellular behaviour). We also provide an in‐depth analysis of the four aspects of design, ink, printing and culture. Furthermore, we present the ‘construction‐comprehension cycle’ research paradigm and the ‘math‐model‐based batch insights generator’ research paradigm for the future, which may have the potential to revolutionize the biomedical field.
Effect of the Insecticide Chlorpyrifos on Behavioral and Metabolic Aspects of the Spider Polybetes pythagoricus

The toxicity of pesticides to organisms depends on the total amount of chemical exposure. Toxicity can be minimized if the organism recognizes the pesticide and alters its behavior. Furthermore, the physical barrier of cuticular hydrocarbons can prevent the entrance of the pesticide into the organism. Finally, if the pesticide enters the body, the organism experiences physiological changes favoring detoxification and the maintenance of homeostasis. We analyzed the behavioral and metabolic response of the spider Polybetes pythagoricus at different times of exposure to the organophosphate pesticide chlorpyrifos. First we observed that the individuals are capable of recognizing and avoiding surfaces treated with pesticides based on a behavioral analysis. Subsequently, we characterized cuticular hydrocarbons as a possible barrier against pesticides. Then we observed that the pesticide provoked histological damage, mainly at the level of the midgut diverticula. Finally, we analyzed the activity of several of the spider's enzymes linked to oxidative stress after exposure to chlorpyrifos for different lengths of time (6, 24, and 48 h). We observed that catalase activity was high at the start, whereas the activity of superoxide dismutase and glutathione S‐transferase changed significantly at 48 h. Lipid peroxidation became high at 6 h, but decreased at 48 h. In conclusion, although P. pythagoricus can avoid contact with chlorpyrifos, this pesticide causes activation of the antioxidant system when it enters the body. Our results make a significant contribution to the ecotoxicology of spiders. Environ Toxicol Chem 2023;42:1293–1308. © 2023 SETAC
Interaction between two magnetic dipoles in a uniform magnetic field

A new formula for the interaction force between two magnetic dipoles in a uniform magnetic field is derived taking their mutual magnetic interaction into consideration and used to simulate their relative motion. Results show that when the angle β between the direction of external magnetic field and the centerline of two magnetic dipoles is 0 ° or 90 °, magnetic dipoles approach each other or move away from each other in a straight line, respectively. And the time required for them to contact each other from the initial position is related to the specific susceptibility and the diameter of magnetic particles, medium viscosity and magnetic field strength. When β is between 0 ° and 90 °, magnetic dipole pair performs approximate elliptical motion, and the motion trajectory is affected by the specific susceptibility, diameter and medium viscosity but not magnetic field strength. However, time required for magnetic dipoles to complete the same motion trajectory is shorter when adopting stronger magnetic field.
Membrane potential phase shifts differ for excitation vs. inhibition in resonant pyramidal neurons: a computer modeling study

Rhythmic activity is ubiquitous in neural systems, and impedance analysis has been widely used to examine frequency-dependent responses of neuronal membranes to rhythmic inputs. Impedance analysis assumes the neuronal membrane is a linear system, requiring the use of small signals to stay in a near-linear regime. However, postsynaptic potentials are often large and trigger nonlinear mechanisms. We therefore augmented impedance analysis to evaluate membrane responses in this nonlinear domain, analyzing responses to injected current for subthreshold membrane voltage (Vmemb), suprathreshold spike-blocked Vmemb, and spiking in a validated neocortical pyramidal neuron computer model. Responses in these output regimes were asymmetrical, with different phase shifts during hyperpolarizing and depolarizing half-cycles. Suprathreshold chirp stimulation gave equivocal results due to nonstationarity of response, requiring us to use fixed-frequency sinusoids. Sinusoidal inputs produced phase retreat: action potentials occurred progressively later in cycles of the input stimulus, resulting from adaptation. Conversely, sinusoidal current with increasing amplitude over cycles produced a pattern of phase advance: action potentials occurred progressively earlier. Phase retreat was dependent on Ih and IAHP currents; phase advance was modulated by these currents. Our results suggest differential responses of cortical neurons depending on the frequency of oscillatory input in the delta – beta range, which will play a role in neuronal responses to shifts in network state. We hypothesize that intrinsic cellular properties complement network properties and contribute to in vivo phase-shift phenomena such as phase precession, seen in place and grid cells, and phase roll, observed in hippocampal CA1 neurons. New & Noteworthy We augmented electrical impedance analysis to characterize phase shifts between large amplitude current stimuli and nonlinear, asymmetric membrane potential responses. We predict different frequency-dependent phase shifts in response excitation versus inhibition, as well as shifts in spike timing over multiple input cycles, in resonant pyramidal neurons. We hypothesize that these effects contribute to navigation-related phenomena like phase precession and phase roll. Our neuron-level hypothesis complements, rather than falsifies, prior network-level explanations of these phenomena.
Pelvic irradiation induces behavioral and neuronal damage through gut dysbiosis in a rat model

Background Pelvic radiotherapy is the endorsed course of treatment for pelvic malignancies, which frequently cover pelvic primary tumor lesions as well as non-cancerous lymphatic drainage sites in the pelvic area. As a result, pelvic irradiation may indiscriminately cause harm to healthy tissues and organs in the pelvic area in individuals undergoing treatment. Some studies suggest that gut microbial dysbiosis can be correlated with the incidence of radiation-induced toxicities in cancer patients. Since, the consequences were earlier thought to be solely due to the targeted or non-targeted effect of radiation, the role of gut microbiota in the non-targeted effects of radiation and the mechanistic role of the gut-brain axis in the pelvic irradiation scenario is not well explored. Hence, the current study was carried out to explore implication of gut dysbiosis in behavioral and neuronal changes induced by pelvic irradiation. Materials and Methods 3-4-month-old Sprague Dawley rats were given a single dose of 6 Gy pelvic irradiation. Fecal samples of control and treated mice were collected at different timepoints to assess microbial abundance and diversity using 16S rRNA-based metagenomic sequencing. Behavioral analysis, histological analysis of intestine, brain and gene expression analysis of brain hippocampus was performed to ascertain the indirect impact of microbial dysbiosis on cognition. Results Following pelvic irradiation, significant microbial dysbiosis and behavioral alterations were observed with distinct changes in the microbial diversity and a significant decline in the locomotor effect and anxiety level at each time point following radiation. Histological analysis revealed a significant reduction in villus distortion as well as a significant decrease in neuronal cells, matured neurons, and an increase in reactive astrocytes, suggesting that pelvic irradiation promotes neuroinflammation. Gene expression analysis revealed a significant reduction in neural plasticity. Altogether, this study demonstrated that gut dysbiosis caused by pelvic irradiation alters behavior, intestinal morphology, integrity, and brain neuronal maturation, as well as lowers the levels of neural plasticity expression. Conclusion Current study provides evidence for the influence of gut dysbiosis on pelvic irradiation induced cognitive impairment in a rat model.
Mapping Niche-specific Two-Component System Requirements in Uropathogenic Escherichia coli

Sensory systems allow pathogens to differentiate between different niches and respond to stimuli within them. A major mechanism through which bacteria sense and respond to stimuli in their surroundings is two-component systems (TCSs). TCSs allow for the detection of multiple stimuli to lead to a highly controlled and rapid change in gene expression. Here, we provide a comprehensive list of TCSs important for the pathogenesis of uropathogenic Escherichia coli (UPEC). UPEC accounts for >75% of urinary tract infections (UTIs) worldwide. UTIs are most prevalent among people assigned female at birth, with the vagina becoming colonized by UPEC in addition to the gut and the bladder. In the bladder, adherence to the urothelium triggers E. coli invasion of bladder cells and an intracellular pathogenic cascade. Intracellular E. coli are safely hidden from host neutrophils, competition from the microbiota, and antibiotics that kill extracellular E. coli. To survive in these intimately connected, yet physiologically diverse niches E. coli must rapidly coordinate metabolic and virulence systems in response to the distinct stimuli encountered in each environment. We hypothesized that specific TCSs allow UPEC to sense these diverse environments encountered during infection with built-in redundant safeguards. Here, we created a library of isogenic TCS deletion mutants that we leveraged to map distinct TCS contributions to infection. We identify – for the first time – a comprehensive panel of UPEC TCSs that are critical for infection of the genitourinary tract and report that the TCSs mediating colonization of the bladder, kidneys, or vagina are distinct. IMPORTANCE While two-component system (TCS) signaling has been investigated at depth in model strains of E. coli, there have been no studies to elucidate – at a systems level – which TCSs are important during infection by pathogenic Escherichia coli. Here, we report the generation of a markerless TCS deletion library in a uropathogenic E. coli (UPEC) isolate that can be leveraged for dissecting the role of TCS signaling in different aspects of pathogenesis. We use this library to demonstrate, for the first time in UPEC, that niche-specific colonization is guided by distinct TCS groups.
Neuronal Synchrony and Critical Bistability: Mechanistic Biomarkers for Localizing the Epileptogenic Network

Objective Post-surgical seizure freedom in drug-resistant epilepsy (DRE) patients varies from 30 to 80%, implying that in many cases the current approaches fail to fully map the epileptogenic zone (EZ). This suggests that the EZ entails a broader epileptogenic brain network (EpiNet) beyond the seizure-zone (SZ) that show seizure activity. Methods We first used computational modeling to identify putative complex-systems- and systems-neuroscience-driven mechanistic biomarkers for epileptogenicity. We then extracted these epileptogenicity biomarkers from stereo-EEG (SEEG) resting-state data from DRE patients and trained supervised classifiers to localize the SZ with these biomarkers against gold-standard clinical localization. To further explore the prevalence of these pathological biomarkers in an extended network outside of the clinically-identified SZ, we also used unsupervised classification. Results Supervised SZ-classification trained on individual features achieved accuracies of 0.6–0.7 areaunder-the-receiver-operating-characteristics curve (AUC). However, combining all criticality and synchrony features improved the AUC up to 0.85. Unsupervised classification uncovered an EpiNet-like cluster of brain regions with 51% of regions outside of SZ. Brain regions in this cluster engaged in inter-areal hypersynchrony and locally exhibited high amplitude bistability and excessive inhibition, which was strikingly similar to the high seizure-risk regime revealed by computational modeling. Significance The finding that combining biomarkers improves EZ localization shows that the different mechanistic biomarkers of epileptogenicity assessed here yield synergistic information. On the other hand, the discovery of SZ-like pathophysiological brain dynamics outside of the clinically-defined EZ provides experimental localization of an extended EpiNet. Key points We advanced novel complex-systems- and systems-neuroscience-driven biomarkers for epileptogenicity Increased bistability, inhibition, and power-low scaling exponents characterized our model operating in a high seizure-risk regime and SEEG oscillations in the seizure-zone (SZ) Combining all biomarkers yielded more accurate supervised SZ-classification than using any individual biomarker alone Unsupervised classification revealed more extended pathological brain networks including the SZ and many non-seizure-zone areas that were previously considered healthy
Soybean-SCN duel: Novel insight into Soybean’s Resistant Responses to Heterodera glycines

Soybean cyst nematodes (SCN, Heterodera glycines Ichinohe) are a significant threat to soybean production globally, causing severe yield losses and necessitating the development of effective strategies to combat this devastating nematode disease. This study presents dual RNA-seq analyses of the three most common SCN-resistant lines (Plant Introduction (PI) 437654, 548402, and 88788) and the susceptible line Lee74 against the SCN HG type 1.2. 5.7 to identify the mechanisms of resistance and virulence genes involved in resistance breakdown. Transcriptomic and pathway analyses reveal the activation of the phenylpropanoid pathway, MAPK signaling pathway, plant hormone signal transduction, and secondary metabolite pathways in the resistance mechanisms. PI 437654, which exhibited robust resistance (female index, FI=0%), demonstrated unique gene expression associated with cell wall reinforcement, oxidative enzymes, ROS scavengers, and Ca+2 sensors governing the salicylic acid (SA) biosynthesis process, indicating its key defense mechanism. Moreover, using different hosts with varying levels of immunity and a susceptible line provided insights into SCN pathogenesis and how H. glycine overcomes different layers of host immunity by modulating its virulence genes. This research provides novel insights into the molecular mechanisms underlying soybean-SCN interactions and identifies potential targets for developing strategies to manage this devastating nematode disease.
Genomic potential and evolution of Dissimilatory Nitrate Reduction to Ammonium in Cyanobacteria

Cyanobacteria play an important role in primary production and nitrogen fixation. Although Cyanobacteria are well-known diazotrophic organisms, their role in other steps Nitrogen Cycle is obscure. Screening of Cyanobacterial genomes from cultured and unculturable species can help identify potentially novel functions. In this study, we assembled Cyanobacterial genomes from metagenomic data generated from environmental DNA isolated from a brackish water lagoon (Chilika, India). We annotated these Cyanobacterial metagenome-assembled genomes (MAG) for all the encoded functions using KEGG Orthology. We found two high-quality Cyanobacterial MAGs containing the nirBD gene and nifH and nifD genes involved in the nitrogen cycle. nirBD encodes for the Dissimilatory Nitrate Reduction to Ammonium (DNRA) activity, a function previously not ascribed to Cyanobacteria. We validated the presence of NirBD in publicly available isolate genomes of Cyanobacteria and examined its evolution in the phylum by phylogenetic reconciliation of species and gene trees. Our analysis revealed that both horizontal gene transfers and speciation events contributed to the dispersal of the nirBD gene in Cyanobacteria. We observed that mostly filamentous Cyanobacteria served as ancestral donors in horizontal gene transfer events. Further, we found that the nirBD gene is under a purifying selection pressure in Cyanobacteria. This study demonstrates the genomic potential and evolution of DNRA activity in Cyanobacteria for the utilisation of nitrate in the ecosystem which can help these organisms to cope with extreme environmental conditions. It expands our overall comprehension of the contribution of Cyanobacteria in the biogeochemical cycling in aquatic ecosystems.
Discovery of the apiosyltransferase, celery UGT94AX1 that catalyzes the biosynthesis of a flavone glycoside, apiin

Apiose is a unique branched-chain pentose found in plant glycosides and a key component of the cell wall-polysaccharide pectin and other specialized metabolites. More than 1,200 plant-specialized metabolites contain apiose residues, represented by apiin, a distinctive flavone glycoside found in celery and parsley in the family Apiaceae. The physiological functions of apiin remain obscure, partly due to our lack of knowledge on apiosyltransferase during apiin biosynthesis. Here, we identified celery UGT94AX1 (AgApiT) as a novel apiosyltransferase, responsible for catalyzing the last sugar-modification step in apiin biosynthesis. AgApiT showed strict substrate specificity for the sugar donor, UDP-apiose, and moderate specificity for acceptor substrates, thereby producing various apiose-containing flavone glycosides in celery. Homology modeling of AgApiT with UDP-apiose, followed by site-directed mutagenesis experiments, identified unique Ile139, Phe140, and Leu356 residues in AgApiT, which are seemingly crucial for the recognition of UDP-apiose in the sugar donor pocket. Sequence comparison and molecular phylogenetic analysis of celery glycosyltransferases paralogous to AgApiT suggested that AgApiT is the sole apiosyltransferase-encoding gene in the celery genome. This is the first report on the identification of a plant apiosyltransferase gene that will enhance our understanding of the physio-ecological functions of apiose and apiose-containing compounds.