Miracle-dz/UniFAR-FTUs huggingface dataset:
Principal Components Analysis Using Data Collected From Healthy Individuals on Two Robotic Assessment Platforms Yields Similar Behavioral Patterns

Background Kinarm Standard Tests (KSTs) is a suite of upper limb tasks to assess sensory, motor, and cognitive functions, which produces granular performance data that reflect spatial and temporal aspects of behavior (>100 variables per individual). We have previously used principal component analysis (PCA) to reduce the dimensionality of multivariate data using the Kinarm End-Point Lab (EP). Here, we performed PCA using data from the Kinarm Exoskeleton Lab (EXO), and determined agreement of PCA results across EP and EXO platforms in healthy participants. We additionally examined whether further dimensionality reduction was possible by using PCA across behavioral tasks. Methods Healthy participants were assessed using the Kinarm EXO (N = 469) and EP (N = 170–200). Four behavioral tasks (six assessments in total) were performed that quantified arm sensory and motor function, including position sense [Arm Position Matching (APM)] and three motor tasks [Visually Guided Reaching (VGR), Object Hit (OH), and Object Hit and Avoid (OHA)]. The number of components to include per task was determined from scree plots and parallel analysis, and rotation type (orthogonal vs. oblique) was decided on a per-task basis. To assess agreement, we compared principal components (PCs) across platforms using distance correlation. We additionally considered inter-task interactions in EXO data by performing PCA across all six behavioral assessments. Results By applying PCA on a per task basis to data collected using the EXO, the number of behavioral parameters were substantially reduced by 58–75% while accounting for 76–87% of the variance. These results compared well to the EP analysis, and we found good-to-excellent agreement values (0.75–0.99) between PCs from the EXO and those from the EP. Finally, we were able to reduce the dimensionality of the EXO data across tasks down to 16 components out of a total of 76 behavioral parameters, which represents a reduction of 79% while accounting for 73% of the total variance. Conclusion PCA of Kinarm robotic assessment appears to capture similar relationships between kinematic features in healthy individuals and is agnostic to the robotic platform used for collection. Further work is needed to investigate the use of PCA-based data reduction for the characterization of neurological deficits in clinical populations.
A Balancing Act During Covid-19: Teachers' Self-Efficacy, Perception of Stress in the Distance Learning Experience

One of the many drastic changes caused by Covid-19 was the quick implementation of distance learning which represented a great technological challenge to many teachers and students. In fact, Italy ranks 24th amongst the 27-EU member countries in digital competitiveness which testifies to the significant delays and gaps in basic digital skills amongst the population. Based on the difficulties encountered in organizing distance learning, we assumed that teachers' perceived stress increased. Given that transversal skills can be associated with this relationship, we hypothesized that among these skills, self-efficacy mediated the relationship between the difficulties in organizing distance learning and perceived stress. Since we targeted teachers from Italy and other European countries, we also hypothesized that this mediator effect would be different for both samples. Our sample was composed of a total of 366 primary/middle school teachers of which 86% female. After doing a mediation analyses with Process, Hayes' Model 4, we confirmed H1 but not H2: resulting in a partial mediation effect of self-efficacy for each individual group of teachers. Since difficulties of distance learning can affect the perception of stress, we believe that the promotion of transversal skills, such as self-efficacy, can better equip teachers when facing stressful situations.
Osthole Ameliorates Estrogen Deficiency-Induced Cognitive Impairment in Female Mice

Loss of endogenous estrogen and dysregulation of the estrogen receptor signaling pathways are associated with an increase in risk for cognitive deficit and depression in women after menopause. Estrogen therapy for menopause increases the risk of breast and ovarian cancers, and stroke. Therefore, it is critical to find an alternate treatment for menopausal women. Osthole (OST), a coumarin, has been reported to have neuroprotective effects. This study examined whether OST improves ovariectomy (OVX)-induced cognitive impairment, and alleviates anxiety- and depression-like behaviors induced by OVX in mice. Adult female C57BL/6J mice were ovariectomized and then treated with OST at a dose of 30 mg/kg for 14 days. At the end of the treatment period, behavioral tests were used to evaluate spatial learning and memory, recognition memory, anxiety- and depression-like behaviors. A cohort of the mice were sacrificed after 14 days of OST treatment and their hippocampi were collected for measurement of the proteins of interest using western blot. OVX-induced alteration in the levels of proteins was accompanied by cognitive deficit, anxiety- and depression-like behaviors. OST treatment improved cognitive deficit, alleviated anxiety- and depression-like behaviors induced by OVX, and reversed OVX-induced alterations in the levels of synaptic proteins and ERα, BDNF, TrKB, p-CREB, p-Akt and Rac1 in the hippocampus. Therefore, reversal of OVX-induced decrease in the levels of hippocampal proteins by OST might contribute to the effects of OST on improving cognitive deficit and alleviating anxiety- and depression-like behaviors induced by OVX.
Characterization of Reproductive and Morphological Variables in Female Elite Futsal Players

We aimed to characterize the age of onset of training, age at menarche, menstrual periodicity, and performance perception during the menstrual cycle and examined the impact of these reproductive variables on body composition, morphology, and body weight satisfaction in Brazilian elite futsal players. The study consisted of 115 female Brazilian elite futsal players from the top national teams. Data were collected during the twentieth Women’s Brazil Futsal Cup. Players were interviewed and self-reported their age of onset of training, age at menarche, menstrual periodicity, and the menstrual period, where they performed best. We also asked for what they considered to be their ideal body weight as well as information related to their training (i.e., volume and frequency). Subsequently, anthropometric measurements (i.e., body mass, height, circumferences, diameters, and skinfold thickness) were performed to estimate the body composition and determine morphological characteristics (e.g., somatotype). Fifty-nine (53.2%) players were postmenarche-trained and 52 (46.8%) were premenarche-trained. Eighteen (16.2%), 65 (58.6%), and 28 (25.2%) were classified as early, normal, and late menarche, respectively. Only 11 (9.6%) and 1 (0.9%) had irregular menstrual cycles and were amenorrheic, respectively. Seventy-three (69.5%), 23 (21.9%), and 9 (8.6%) reported that their game performance was the best at the follicular phase, menses, and luteal phase of the menstrual cycle, respectively. No associations between the four reproductive-related variables were found. Postmenarche-trained players had significant lower age at menarche and higher percentage body fat. The somatotype profile registered lower ectomorphy rate for the postmenarche-trained participants after controlling for covariates. Early menarche group presented higher sum of six skinfold thickness and endomorphy rate compared to normal and late menarche groups. No differences were found when menstrual periodicity groups and best performance groups were compared, except for higher femur width in the regular menstrual cycle group compared to the irregular one. The association between body weight satisfaction and the four reproductive-related variables were not observed. Premenarche-trained Brazilian elite futsal players had the menarche later than the postmenarche-trained athletes. Most of the participants had menarche age classified as “normal,” presented “regular” menstrual cycles and perceived to perform better during the follicular phase of the menstrual cycle.
Phytochemical evaluation of leaf extracts of Naringi crenulata (roxb.) Nicolson

The use of traditional medicines holds a great promise as an easily available source as effective medicinal agents to cure a wide range of ailments among the people particularly in tropical developing countries like India. The present study investigates the qualitative and quantitative analysis of the major bioactive constituents of N. crenulata leaf extracts. The extractive values of aqueous, acetone and chloroform extracts were found to be 11.34, 4.24 and 6.06 respectively. Qualitative phytochemical analysis of these three solvent extracts confirm the presence of Alkaloids, Saponins, Flavonoids and Phenolic compounds in all the three extracts; however, these phytochemicals were more significant in aqueous extract. Quantitative analysis was carried out using TLC method by different solvent system. Amongst various solvent systems, Butanol: acetic acid: water (9: 0.9: 0.1 v/v/v) shows maximum resolution and number of spots produced at long UV (365 nm) and under iodine vapours. The TLC chromatograms constituted different coloured phytochemical compounds with different Rf values. It can be conveniently used to evaluate the quality of different area samples. This indicates that the leaves can be useful for treating different diseases because the therapeutic activity of a plant is due to the presence of particular class of compounds and thus can serve as potential sources of useful drugs in future .
Differential Contributions of Ventral Striatum Subregions to the Motivational and Hedonic Components of the Affective Processing of Reward

The ventral striatum is implicated in the affective processing of reward, which can be divided into a motivational and a hedonic component. Here, we examined whether these two components rely on distinct neural substrates within the ventral striatum in humans (11 females and 13 males). We used a high-resolution fMRI protocol targeting the ventral striatum combined with a pavlovian-instrumental task and a hedonic reactivity task. Both tasks involved an olfactory reward, thereby allowing us to measure pavlovian-triggered motivation and sensory pleasure for the same reward within the same participants. Our findings show that different subregions of the ventral striatum are dissociable in their contributions to the motivational versus the hedonic component of the affective processing of reward. Parsing the neural mechanisms of the interplay between pavlovian incentive and hedonic processes may have important implications for understanding compulsive reward-seeking behaviors such as addiction, binge eating, or gambling.
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills. Significance Statement The primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.
Quantifying the tissue-specific regulatory information within enhancer DNA sequences

Recent efforts to measure epigenetic marks across a wide variety of different cell types and tissues provide insights into the cell type-specific regulatory landscape. We use this data to study if there exists a correlate of epigenetic signals in the DNA sequence of enhancers and explore with computational methods to what degree such sequence patterns can be used to predict cell type-specific regulatory activity. By constructing classifiers that predict in which tissues enhancers are active, we are able to identify sequence features that might be recognized by the cell in order to regulate gene expression. While classification performances vary greatly between tissues, we show examples where our classifiers correctly predict tissue specific regulation from sequence alone. We also show that many of the informative patterns indeed harbor transcription factor footprints.
The predictive potential of key adaptation parameters and proxy fitness traits between benign and stressful thermal environments

Understanding the adaptive potential of a species is key when predicting whether a species can contend with climate change. Adaptive capacity depends on the amount of genetic variation within a population for relevant traits. However, genetic variation changes in different environments, making it difficult to predict whether a trait will respond to selection when not measured directly in that environment. Here, we investigated how genetic variances, and phenotypic and genetic covariances, between a fitness trait and morphological traits changed between thermal environments in two closely-related Drosophila. If morphological traits strongly correlate with fitness, they may provide an easy-to-measure proxy of fitness to aid in understanding adaptation potential. We used a parent-offspring quantitative genetic design to test the effect of a benign (23°C) and stressful (28°C) thermal environment on genetic variances of fecundity and wing size and shape, and their phenotypic and genetic covariances. We found genetic variances were higher within the stressful environment for fecundity but lower within the stressful environment for wing size. We did not find evidence for significant phenotypic correlations. Phenotypic and genetic correlations did not reveal a consistent pattern between thermal environments or within or between species. This corroborates previous research and reiterates that conclusions drawn in one environment about the adaptive potential of a trait, and the relationship of that trait with fitness, cannot be extrapolated to other environments or within or between closely-related species. This confirms that researchers should use caution when generalising findings across environments in terms of genetic variation and adaptive potential.
Disease‐linked TDP‐43 hyperphosphorylation suppresses TDP‐43 condensation and aggregation

Post-translational modifications (PTMs) have emerged as key modulators of protein phase separation and have been linked to protein aggregation in neurodegenerative disorders. The major aggregating protein in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), the RNA-binding protein TDP-43, is hyperphosphorylated in disease on several C-terminal serine residues, which is generally believed to promote TDP-43 aggregation. Here, we show that hyperphosphorylation by Casein kinase 1δ or C-terminal phosphomimetic mutations surprisingly reduce TDP-43 phase separation and aggregation and render TDP-43 condensates more liquid-like and dynamic. Multi-scale simulations reveal reduced homotypic interactions of TDP-43 low complexity domains through enhanced solvation of phosphomimetic residues. Cellular experiments show that phosphomimetic substitutions do not affect nuclear import or RNA regulatory functions of TDP-43, but suppress accumulation of TDP-43 in membrane-less organelles and promote its solubility in neurons. We propose that TDP-43 hyperphosphorylation may be a protective cellular response to counteract TDP-43 aggregation.
Protein Secondary Structure Affects Glycan Clustering in Native Mass Spectrometry

Infection with human noroviruses (hNoV) for the vast majority of strains requires attachment of the viral capsid to histo blood group antigens (HBGA). The HBGA binding pocket is formed by dimers of the protruding domain (P dimers) of the capsid protein VP1. Several studies have focused on HBGA binding to P dimers, reporting binding affinities and stoichiometries. However, nuclear magnetic resonance spectroscopy (NMR) and native mass spectrometry (MS) analyses yielded incongruent dissociation constants (KD) for binding of HBGAs to P dimers and, in some cases, disagreed whether glycans bind at all. We hypothesized that glycan clustering during electrospray ionization in native MS critically depends on the physicochemical properties of the protein studied. It follows that the choice of the reference protein is crucial. We analyzed carbohydrate clustering using various P dimers and eight non-glycan binding proteins serving as possible references. Data from native and ion mobility MS indicate that the mass fraction of β-sheet has a strong influence on the degree of glycan clustering. Therefore, the determination of specific glycan binding affinities from native MS must be interpreted cautiously.
Terrestrial force production by the limbs of a semi-aquatic salamander provides insight into the evolution of terrestrial locomotor mechanics

Amphibious fishes and salamanders are valuable functional analogs for vertebrates that spanned the water-to-land transition. However, investigations of walking mechanics have focused on terrestrial salamanders and, thus, may better reflect the capabilities of stem tetrapods that were already terrestrial. The earliest tetrapods were aquatic, so salamanders that are not primarily terrestrial may yield more appropriate data for modelling the incipient stages of terrestrial locomotion. In the present study, locomotor biomechanics were quantified from semi-aquatic Pleurodeles waltl, a salamander that spends most of its adult life in water, and then compared to a primarily terrestrial salamander (Ambystoma tigrinum) and semi-aquatic fish (Periophthalmus barbarus) to evaluate whether walking mechanics show greater similarity between species with ecological versus phylogenetic similarities. Ground reaction forces (GRFs) from individual limbs or fins indicated that the pectoral appendages of each taxon had distinct patterns of force production, but hind limb forces were comparable between the salamanders. The rate of force development (‘yank’) was sometimes slower in P. waltl but generally comparable between the three species. Finally, medial inclination of the GRF in P. waltl was intermediate between semi-aquatic fish and terrestrial salamanders, potentially elevating bone stresses among more aquatic taxa as they move on land. These data provide a framework for modelling stem tetrapods using an earlier stage of quadrupedal locomotion that was powered primarily by the hind limbs (i.e., “rear-wheel drive”), and reveal mechanisms for appendages to generate propulsion in three locomotor strategies that are presumed to have occurred across the water-to-land transition in vertebrate evolution. Summary statement Semi-aquatic salamanders had limb mechanics that were intermediate in magnitude yet steadier than the appendages of terrestrial salamanders and semi-aquatic fish, providing a framework to model semi-aquatic early tetrapods.
Classification of non-coding variants with high pathogenic impact

Whole genome sequencing is increasingly used to diagnose medical conditions of genetic origin. While both coding and non-coding DNA variants contribute to a wide range of diseases, most patients who receive a WGS-based diagnosis today harbour a protein-coding mutation. Functional interpretation and prioritization of non-coding variants represents a persistent challenge, and disease-causing non-coding variants remain largely unidentified. Depending on the disease, WGS fails to identify a candidate variant in 20-80% of patients, severely limiting the usefulness of sequencing for personalised medicine. Here we present FINSURF, a machine-learning approach to predict the functional impact of non-coding variants in regulatory regions. FINSURF outperforms state-of-the-art methods, owing to control optimisation during training. In addition to ranking candidate variants, FINSURF also delivers diagnostic information on functional consequences of mutations. We applied FINSURF to a diverse set of 30 diseases with described causative non-coding mutations, and correctly identified the disease-causative non-coding variant within the ten top hits in 22 cases. FINSURF is implemented as an online server to as well as custom browser tracks, and provides a quick and efficient solution to prioritize candidate non-coding variants in realistic clinical settings.
THE GRAPHENE OXIDE EFFECT ON THE OPTICAL PROPERTIES OF NIPA-GO COMPOSITES

Poly (N-isopropylacrylamide) (NIPA)-Graphene oxide (GO) composites were polymerizated radically with various contents of GO solution. The gelation process was performed by Steady State Fluorescence Spectroscopy. The results of gelation were modelled by Percolation and Classical Model, respectively. Our results show that the critical exponent of gel fraction is agree with percolation model till 25 µl content of GO solution. On the other hand, the optical energy band gap of the NIPA-GO composite was decided by using UV spectroscopy from the absorbance measurement in the range of 200-800 nm. The effect of graphene oxide dopant on the gap has been examined for NIPA-GO composites. In conclusion, their gelation process and optical energy band gap behavior were investigated and correlated to the GO content in the composites.