Miracle-dz/UniFAR-FTUs huggingface dataset:
Manifold Mixup: Better Representations by Interpolating Hidden States

Deep neural networks excel at learning the training data, but often provide incorrect and confident predictions when evaluated on slightly different test examples. This includes distribution shifts, outliers, and adversarial examples. To address these issues, we propose Manifold Mixup, a simple regularizer that encourages neural networks to predict less confidently on interpolations of hidden representations. Manifold Mixup leverages semantic interpolations as additional training signal, obtaining neural networks with smoother decision boundaries at multiple levels of representation. As a result, neural networks trained with Manifold Mixup learn class-representations with fewer directions of variance. We prove theory on why this flattening happens under ideal conditions, validate it on practical situations, and connect it to previous works on information theory and generalization. In spite of incurring no significant computation and being implemented in a few lines of code, Manifold Mixup improves strong baselines in supervised learning, robustness to single-step adversarial attacks, and test log-likelihood.
Increasing the Difference in Decision Making for Oneself and for Others by Stimulating the Right Temporoparietal Junction

The right temporoparietal junction (rTPJ) has been thought to be associated with the difference in self-other decision making. In the present study, using noninvasive transcranial direct current stimulation (tDCS), we examined whether stimulating the rTPJ could modulate the self-other decision-making difference. We found that after receiving anodal stimulation of the rTPJ, participants were more likely to choose a high-value item for others than for themselves in the situations where the win probability of the high-value item was equal to or greater than that of a low-value item, indicating that elevating the cortical excitability of the rTPJ might increase the self-other decision-making difference in certain decision contexts. Our results suggest that decision making for others depends on neural activity in the rTPJ and regulation of the excitability of the rTPJ can influence the self-other decision-making difference.
Caldendrin and Calneurons—EF-Hand CaM-Like Calcium Sensors With Unique Features and Specialized Neuronal Functions

The calmodulin (CaM)-like Ca2+-sensor proteins caldendrin, calneuron-1 and -2 are members of the neuronal calcium-binding protein (nCaBP)-family, a family that evolved relatively late during vertebrate evolution. All three proteins are abundant in brain but show a strikingly different subcellular localization. Whereas caldendrin is enriched in the postsynaptic density (PSD), calneuron-1 and -2 accumulate at the trans-Golgi-network (TGN). Caldendrin exhibit a unique bipartite structure with a basic and proline-rich N-terminus while calneurons are the only EF-Hand CaM-like transmembrane proteins. These uncommon structural features come along with highly specialized functions of calneurons in Golgi-to-plasma-membrane trafficking and for caldendrin in actin-remodeling in dendritic spine synapses. In this review article, we will provide a synthesis of available data on the structure and biophysical properties of all three proteins. We will then discuss their cellular function with special emphasis on synaptic neurotransmission. Finally, we will summarize the evidence for a role of these proteins in neuropsychiatric disorders.
The Importance of the Validation of M/EEG With Current Biomarkers in Alzheimer's Disease

Current biomarkers used in research and in clinical practice in Alzheimer's Disease (AD) are the analysis of cerebral spinal fluid (CSF) to detect levels of Aβ42 and phosphorylated-tau, amyloid and FDG-PET, and MRI volumetry. Some of these procedures are still invasive for patients or expensive. Electroencephalography (EEG) and Magnetoencephalography (MEG) are two non-invasive techniques able to detect the early synaptic dysfunction and track the course of the disease. However, in spite of its added value they are not part of the standard of care in clinical practice in dementia. In this paper we review what these neurophysiological techniques can add to the early diagnosis of AD, whether results in both modalities are related to each other or not, as well as the need of its validation against current biomarkers. We discuss their potential implications for the better understanding of the pathophysiological mechanisms of the disease as well as the need of performing simultaneous M/EEG recordings to better understand discrepancies between these two techniques. Finally, more studies are needed studying M/EEG with amyloid and Tau biomarkers.
Ferulic Acid Protects Hyperglycemia-Induced Kidney Damage by Regulating Oxidative Insult, Inflammation and Autophagy

Oxidative insult, inflammation, apoptosis and autophagy play a pivotal role in the etiology of diabetic nephropathy, a global health concern. Ferulic acid, a phytochemical, is reported to protect against varied diseased conditions. However, the ameliorative role and mechanisms of ferulic acid in averting STZ-mediated nephrotoxicity largely remains unknown. For in vivo study, a single intraperitoneal injection of streptozotocin (50 mg kg-1 body wt.) was administered in experimental rats to induce diabetes. The diabetic rats exhibited a rise in blood glucose level as well as kidney to body weight ratio, a decrease in serum insulin level, severe kidney tissue damage and dysfunction. Elevation of intracellular ROS level, altered mitochondrial membrane potential and cellular redox balance impairment shown the participation of oxidative stress in hyperglycemia-triggered renal injury. Treatment with ferulic acid (50 mg kg-1 body wt., orally for 8 weeks), post-diabetic induction, could markedly ameliorate kidney injury, renal cell apoptosis, inflammation and defective autophagy in the kidneys. The underlying mechanism for such protection involved the modulation of AGEs, MAPKs (p38, JNK, and ERK 1/2), NF-κB mediated inflammatory pathways, mitochondria-dependent and -independent apoptosis as well as autophagy induction. In cultured NRK-52E cells, ferulic acid (at an optimum dose of 75 μM) could counter excessive ROS generation, induce autophagy and inhibit apoptotic death of cells under high glucose environment. Blockade of autophagy could significantly eradicate the protective effect of ferulic acid in high glucose-mediated cell death. Together, the study confirmed that ferulic acid, exhibiting hypoglycemic, antioxidant, anti-inflammatory, anti-apoptotic activities and role in autophagy, could circumvent oxidative stress-mediated renal cell damage.
A Systems Approach to Performance Analysis in Women’s Netball: Using Work Domain Analysis to Model Elite Netball Performance

Netball is a newly professional women’s sport, as such there has been little research conducted investigating performance analysis (PA) in elite netball. The aim of this study was to develop a model of the elite netball performance system to identify the complex relationships among key performance indicators. Eleven elite subject matter experts (SMEs) participated in workshops to produce a systems model of the netball match performance. The model was developed using the work domain analysis (WDA) method. A model of the netball match performance system was produced showing the interrelated objects, processes, functions, values, and purposes involved in elite level netball matches. The model identified the components of elite level netball performance and the interactions and relationships between them. The output of this research has identified novel PA measures including passing and possession measures, measures of cognitive performance, and measures related to physical activity. Netball is a complex sport, involving multiple dynamic and interrelated components. Consequently, there is an opportunity to develop holistic PA measures that focus on interacting components, as opposed to components in isolation.
Neural Correlates of Visuospatial Attention to Unseen Stimuli in Hemianopic Patients. A Steady-State Visual Evoked Potential Study

The relationship between attention and awareness is a topic of great interest in cognitive neuroscience. Some studies in healthy participants and hemianopic patients have shown dissociation between these two processes. In contrast, others confirmed the classic notion that the two processes are mutually exclusive. To try and cast further light on this fascinating dilemma, in the present study we have investigated the neural mechanisms of visual spatial attention when perceptual awareness is totally lacking. To do that, we monitored with steady-state visual evoked potentials (SSVEPs) the neurophysiological correlates of endogenous spatial attention to unseen stimuli presented to the blind field of hemianopic patients. Behaviourally, stimulus detection (a brief change in the orientation of a gabor grating) was absent in the blind hemifield while in the sighted field there was a lower, but non-significant, performance in hit rate with respect to a healthy control group. Importantly, however, in both blind and sighted hemifield of hemianopics (as well as in healthy participants) SSVEP recordings showed an attentional effect with higher frequency power in the attended than unattended condition. The scalp distribution of this effect was broadly in keeping with the location of the dorsal system of endogenous spatial attention. In conclusion, the present results provide evidence that the neural correlates of spatial attention are present regardless of visual awareness and this is in accord with the general hypothesis of a possible dissociation between attention and awareness.
Brain Activation Time-Locked to Sleep Spindles Associated With Human Cognitive Abilities

Simultaneous electroencephalography and functional magnetic resonance imaging (EEG–fMRI) studies have revealed brain activations time-locked to spindles. Yet, the functional significance of these spindle-related brain activations is not understood. EEG studies have shown that inter-individual differences in the electrophysiological characteristics of spindles (e.g., density, amplitude, duration) are highly correlated with “Reasoning” abilities (i.e., “fluid intelligence”; problem solving skills, the ability to employ logic, identify complex patterns), but not short-term memory (STM) or verbal abilities. Spindle-dependent reactivation of brain areas recruited during new learning suggests night-to-night variations reflect offline memory processing. However, the functional significance of stable, trait-like inter-individual differences in brain activations recruited during spindle events is unknown. Using EEG–fMRI sleep recordings, we found that a subset of brain activations time-locked to spindles were specifically related to Reasoning abilities but were unrelated to STM or verbal abilities. Thus, suggesting that individuals with higher fluid intelligence have greater activation of brain regions recruited during spontaneous spindle events. This may serve as a first step to further understand the function of sleep spindles and the brain activity which supports the capacity for Reasoning.
The Differential Roles of T Cells in Non-alcoholic Fatty Liver Disease and Obesity

Non-alcoholic fatty liver disease (NAFLD) constitutes a spectrum of disease states characterized by hepatic steatosis and is closely associated to obesity and the metabolic syndrome. In non-alcoholic steatohepatitis (NASH), additionally, inflammatory changes and hepatocellular damage are present, representing a more severe condition, for which the treatment is an unmet medical need. Pathophysiologically, the immune system is one of the main drivers of NAFLD progression and other obesity-related comorbidities, and both the innate and adaptive immune system are involved. T cells form the cellular component of the adaptive immune system and consist of multiple differentially active subsets, i.e., T helper (Th) cells, regulatory T (Treg) cells, and cytotoxic T (Tc) cells, as well as several innate T-cell subsets. This review focuses on the role of these T-cell subsets in the pathogenesis of NAFLD, as well as the association with obesity and type 2 diabetes mellitus, reviewing the available evidence from both animal and human studies. Briefly, Th1, Th2, Th17, and Th22 cells seem to have an attenuating effect on adiposity. Th2, Th22, and Treg cells seem to decrease insulin resistance, whereas Th1, Th17, and Tc cells have an aggravating effect. Concerning NAFLD, both Th22 and Treg cells appear to have an overall tempering effect, whereas Th17 and Tc cells seem to induce more liver damage and fibrosis progression. The evidence regarding the role of the innate T-cell subsets is more controversial and warrants further exploration.
Combined Transcriptome and Proteome Analysis of RpoS Regulon Reveals Its Role in Spoilage Potential of Pseudomonas fluorescens

Microbial contamination is considered the main cause of food spoilage. Pseudomonas fluorescens is a typical spoilage bacterium contributing to a large extent to the spoilage process of proteinaceous foods. RpoS is known as an alternative sigma factor controlling stress resistance and virulence in many pathogens. Our previous work revealed that RpoS contributes to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. RNA-seq transcriptomics analysis combined with quantitative proteomics analysis based on multiplexed isobaric tandem mass tag (TMT) labeling was performed in the P. fluorescens wild-type strain UK4 and its derivative carrying an rpoS mutation. A total of 375 differentially expressed coding sequences (DECs) and 212 differentially expressed proteins (DEPs) were identified. The DECs were further verified by qRT-PCR. The combined transcriptome and proteome analyses revealed the involvement of this regulator in several cellular processes, mainly including polysaccharide metabolism, intracellular secretion, extracellular structures, cell wall biogenesis, stress responses, and amino acid and biogenic amine metabolism, which may contribute to the biofilm formation, stress resistance, and spoilage activities of P. fluorescens. Moreover, we indeed observed that RpoS contributed to the production of the macrocolony biofilm's matrix. Our results provide insights into the regulatory network of RpoS and expand the knowledge about the role of RpoS in the functioning of P. fluorescens in food spoilage.
How Pre-tenure and Tenured Faculty Can Engage Undergraduates in Publishable Research

Differences in career stage may influence work stress and job satisfaction (Olsen and Crawford, 1998), which in turn can impact attitudes about recruiting, managing, and mentoring undergraduates in publishable research endeavors. Written from the perspectives of a pre-tenure faculty member (i.e., in 4th year) at a primarily teaching institution (PTI) and a tenured faculty member (i.e., in 38th year) from a large research university (RU), this paper discusses obstacles faced by professors at different career stages and institutions while working on publishable research with undergraduates as well as strategies to overcome these obstacles.
Audiovisual Processing of Chinese Characters Elicits Suppression and Congruency Effects in MEG

Learning to associate written letters/characters with speech sounds is crucial for reading acquisition. Most previous studies have focused on audiovisual integration in alphabetic languages. Less is known about logographic languages such as Chinese characters, which map onto mostly syllable-based morphemes in the spoken language. Here we investigated how long-term exposure to native language affects the underlying neural mechanisms of audiovisual integration in a logographic language using magnetoencephalography (MEG). MEG sensor and source data from 12 adult native Chinese speakers and a control group of 13 adult Finnish speakers were analyzed for audiovisual suppression (bimodal responses vs. sum of unimodal responses) and congruency (bimodal incongruent responses vs. bimodal congruent responses) effects. The suppressive integration effect was found in the left angular and supramarginal gyri (205–365 ms), left inferior frontal and left temporal cortices (575–800 ms) in the Chinese group. The Finnish group showed a distinct suppression effect only in the right parietal and occipital cortices at a relatively early time window (285–460 ms). The congruency effect was only observed in the Chinese group in left inferior frontal and superior temporal cortex in a late time window (about 500–800 ms) probably related to modulatory feedback from multi-sensory regions and semantic processing. The audiovisual integration in a logographic language showed a clear resemblance to that in alphabetic languages in the left superior temporal cortex, but with activation specific to the logographic stimuli observed in the left inferior frontal cortex. The current MEG study indicated that learning of logographic languages has a large impact on the audiovisual integration of written characters with some distinct features compared to previous results on alphabetic languages.
Evolution of Mechanical Properties of Lava Dome Rocks Across the 1995–2010 Eruption of Soufrière Hills Volcano, Montserrat

Lava dome collapses pose a hazard to surrounding populations, but equally represent important processes for deciphering the eruptive history of a volcano. Models examining lava dome instability rely on accurate physical and mechanical properties of volcanic rocks. Here we focus on determining the physical and mechanical properties of a suite of temporally-constrained rocks from different phases of the 1995-2010 eruption at Soufriere Hills volcano in Montserrat. We determine the uniaxial compressive strength, tensile strength, density, porosity, permeability, and Young’s modulus using laboratory measurements, complemented by Schmidt hammer testing in the field. By viewing a snapshot of each phase, we find the highest tensile and compressive strength in the samples attributed to Phase 4, corresponding to a lower permeability and an increasing proportion of isolated porosity. Samples from Phase 5 show lower compressive and tensile strengths, corresponding to the highest permeability and porosity of the tested materials. Overall, this demonstrates a reliance of mechanical properties primarily on porosity, however, a shift towards increasing prevalence of pore connectivity in weaker samples identified by microtextural analysis demonstrates that here, pore connectivity also contributes to the strength and Young’s Modulus, as well as controlling permeability. The range in UCS strengths are supported using Schmidt hammer field testing. We determine a narrow range in mineralogy across the sample suite, but identify a correlation between increasing crystallinity and increasing strength. We correlate these changes to residency-time in the growing lava dome during the eruption, where stronger rocks have undergone more crystallization. In addition, subsequent recrystallization of silica polymorphs from the glass phase may further strengthen the material. We suggest the variation in physical and mechanical rock properties shown within the Soufriere Hills eruptive products be included in future structural stability models of the remaining over-steepened dome on Montserrat, and that consideration of rock heterogeneity and its temporal variation if possible, be made in other, similar systems.
Antibacterial Activity of Kalanchoe mortagei and K. fedtschenkoi Against ESKAPE Pathogens

Plants in the genus Kalanchoe (Family: Crassulaceae) are used in traditional medicine throughout the tropics for treating a variety of conditions. Two species, Kalanchoe mortagei and K. fedtschenkoi, have established ethnobotanical usage but have been neglected in previous research concerning their potential bioactivity. Here, we provide a thorough review of the reported antimicrobial activities of Kalanchoe genus and evaluate the in vitro antibacterial effects of two previously unexplored species against a panel of multidrug-resistant bacteria, the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae). Plant specimens were collected and voucher specimens deposited in the Emory University Herbarium. Dried plant material was ground into a powder and extracted as ethanolic macerations or as aqueous decoctions. Extracts were tested against the ESKAPE pathogens for growth inhibitory activity. Cytotoxicity to human cells was assessed via a lactate dehydrogenase assay of treated human keratinocytes (HaCaTs). K. fedtschenkoi extracts demonstrated growth inhibitory effects against two Gram-negative species, A. baumannii (strain CDC-33) and P. aeruginosa (AH-71), as well as S. aureus (UAMS-1). In these cases, growth inhibition greater than 50% (IC50) was generally observed at concentrations of 256 μg mL-1, though one K. fedtschenkoi extract (1465, prepared from stems) exhibited an IC50 against A. baumannii at 128 μg mL-1. All extracts were well tolerated by HaCaTs (LD50 ≥ 256 μg mL-1). Chemical characterization using HPLC and chemical standards established the presence of caffeic acid and quercetin in both plant species, as well as kaempferol in K. fedtschenkoi. These results reveal K. fedtschenkoi to be a plant of medicinal interest, and future research should aim to characterize the bioactivity of this species and its active constituents through bioassay-guide fractionation. Effects on bacterial biofilm formation and quorum-sensing are also research topics of interest for this genus.
Quantitation of Six Alternaria Toxins in Infant Foods Applying Stable Isotope Labeled Standards

Alternaria fungi are widely distributed saprophytes and plant pathogens. As pathogens, Alternaria fungi infect crops and vegetables and cause losses in the fields and during postharvest storage. While farmers suffer from declining yields, consumers are endangered by the formation of secondary metabolites, because some of these exhibit a pronounced toxicological potential. The evaluation of the toxicological capabilities is still ongoing and will contribute to a valid risk assessment. Additionally, data on the incidence and the quantity of Alternaria mycotoxins found in food products is necessary for dietary exposure evaluations. A sensitive LC-MS/MS method for the determination of the Alternaria mycotoxins alternariol (AOH), alternariol monomethylether (AME), tentoxin (TEN), altertoxin I (ATX I), alterperylenol (ALTP), and tenuazonic acid (TA) was developed. AOH, AME, and TA were quantified using stable-isotopically labeled standards. TEN, ATX I, and ALTP were determined using matrix matched calibration. The developed method was validated by using starch and fresh tomato matrix and resulted in limits of detection ranging from 0.05 to 1.25 μg/kg for starch (as a model for cereals) and from 0.01 to 1.36 μg/kg for fresh tomatoes. Limits of quantification were determined between 0.16 and 4.13 μg/kg for starch and between 0.02 and 5.56 μg/kg for tomatoes. Recoveries varied between 83 and 108% for starch and between 95 and 111% for tomatoes. Intra-day precisions were below 4% and inter-day precisions varied from 3 to 8% in both matrices. Various cereal based infant foods, jars containing vegetables and fruits as well as tomato products for infants were analyzed for Alternaria mycotoxin contamination (n = 25). TA was the most frequently determined mycotoxin and was detected in much higher contents than the other toxins. AME and TEN were quantified in many samples, but in low concentrations, whereas AOH, ATX I, and ALTP were determined rarely, among which AOH had higher concentration. Some infant food products were highly contaminated with Alternaria mycotoxins and the consumption of these individual products might pose a risk to the health of infants. However, when the mean or median is considered, no toxicological risk was obvious.