Miracle-dz/UniFAR-FTUs huggingface dataset:
From letters to composed concepts: A magnetoencephalography study of reading

Language comprehension requires the recognition of individual words and the combination of their meanings to yield complex concepts or interpretations. Rather than simple concatenation, this combinatory process often requires the insertion of unstated semantic material between words, based on thematic or feature knowledge of the concepts. For example, the phrase horse barn is not interpreted as a blend of a horse and a barn, but specifically a barn in which horses are kept. Mounting evidence suggests two cortical semantic hubs, in left temporoparietal and anterior temporal cortex, underpin thematic and feature concept knowledge, but much remains unclear about how these putative hubs contribute to combinatory language processing. Using magnetoencephalography, we contrasted source-localized responses to modifier-noun phrases involving thematic relations vs. feature modifications, while also examining how lower-level orthographic processing fed into responses supporting word combination. Twenty-eight participants completed three procedures examining responses to letter-strings, adjective-noun phrases, and noun-noun combinations that varied the semantic relations between words. We found that while color + noun phrases engaged the left anterior temporal lobe (150-300 ms after phrasal head), posterior temporal lobe (150-300 ms), and angular gyrus (300-450 ms), only left posterior temporal lobe responses were sensitive to implicit thematic relations between composing nouns (150-300 ms). We additionally identified a left temporo-occipital progression from orthographic to lexical processing, feeding into ventral anterior areas engaged in the combination of word meanings. Finally, by examining source signal leakage, we characterized the degree to which these responses could be distinguished from one another, using linear source estimation.
L'impatto emotivo della comunicazione istituzionale durante la pandemia di COVID-19: uno studio di Twitter Sentiment Analysis

This paper aims at investigating the impact of institutional communications during the health crisis due to Covid-19 pandemic in Italy, through the analysis of micro-blogging activities on Twitter by means of NLP techniques We performed a Sentiment Analysis on the TWITA corpus, to pinpoint potential correlations between opinion polarity (positive or negative) of the users and public speeches during the outbreak Our findings show changes in sentiment polarity related to three institutional speeches delivered by the Italian Prime Minister Giuseppe Conte on March, 4th, March, 9th, and April, 26th 2020 Copyright © 2020 for this paper by its authors
A new hypothesis for type 1 diabetes risk: The at-risk allele at rs3842753 associates with increased beta cell INS mRNA in a meta-analysis of single cell RNA sequencing data

Type 1 diabetes is characterized by the autoimmune destruction of insulin secreting β cells. Genetic variations upstream at the insulin (INS) locus contribute to ~10% of type 1 diabetes heritable risk. Multiple studies showed an association between rs3842753 C/C genotype and type 1 diabetes susceptibility, but the molecular mechanisms remain unclear. To date, no large-scale studies have looked at the effect of genetic variation at rs3842753 on INS mRNA at the single cell level. We aligned all human islet single cell RNA sequencing datasets available to us in 2020 to the reference genome GRCh38.98 and genotyped rs3842753, integrating 2315 β cells and 1223 β-like cells from 13 A/A protected donors, 23 A/C heterozygous donors, and 35 C/C at-risk donors, including adults without diabetes and with type 2 diabetes. INS expression mean and variance were significantly higher in single β cells from females compared with males. Comparing across β cells and β-like cells, we found that rs3842753 C containing cells (either homozygous or heterozygous) had the highest INS expression. We also found that β cells with the rs3842753 C allele had significantly higher ER stress marker gene expression compared to the A/A homozygous genotype. These findings support the emerging concept that inherited risk of type 1 diabetes may be associated with inborn, persistent elevated insulin production which may lead to β cell ER stress and fragility.
ItaliaNLP @ TAG-IT: UmBERTo for Author Profiling at TAG-it 2020 (short paper)

In this paper we describe the systems we used to participate in the task TAG-it of EVALITA 2020. The first system we developed uses linear Support Vector Machine as learning algorithm. The other two systems are based on the pretrained Italian Language Model UmBERTo: one of them has been developed following the Multi-Task Learning approach, while the other following the Single-Task Learning approach. These systems have been evaluated on TAG-it official test sets and ranked first in all the TAG-it subtasks, demonstrating the validity of the approaches we followed.
Aiming off the target: studying repetitive DNA using target capture sequencing reads

With the advance of high-throughput sequencing (HTS), reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information. As the off-target reads from such sequencing are expected to be similar to genome skims (GS), we assessed the quality of repeat characterization using this data. For this, repeat composition from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. All the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01% in the GS data. Rank correlation between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS was also reliable to develop a cytogenetic probe and solve phylogenetic relationships of Rhynchospora species with high support. In light of our results, TCS data can be effectively used for cyto- and phylogenomic investigations of repetitive DNA. Given the growing availability of HTS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.
vHULK, a new tool for bacteriophage host prediction based on annotated genomic features and deep neural networks

The experimental determination of a bacteriophage host is a laborious procedure. For this reason, there is a pressing need for reliable computational predictions of bacteriophage hosts in phage research in general and in phage therapy in particular. Here, we present a new program called vHULK for phage host prediction based on 9,504 phage genome features. These features take into account alignment significance scores between predicted-protein sequences in the phage genomes and a curated database of viral protein families. The features were fed to a deep neural network, and four distinct models were trained to predict 61 different host genera and 52 host species. In random controlled test sets, the program obtained 99% and 98% accuracy values at the genus and species levels, respectively. On a validation dataset with 2,178 phage genomes, mean accuracies were 82% and 52% at the genus and species levels, respectively. When compared against other phage host prediction programs on the same validation dataset, vHULK achieved substantially better performance, therefore demonstrating that the program is an advance on the state-of-art in phage host prediction. vHULK is freely available at https://github.com/LaboratorioBioinformatica/vHULK.
Can we conjointly record direct interactions between neurons in vivo in anatomically-connected brain areas? Probabilistic analyses and further implications

Large-scale simultaneous in vivo recordings of neurons in multiple brain regions raises the question of the probability of recording direct interactions of neurons within, and between, multiple brain regions. In turn, identifying inter-regional communication rules between neurons during behavioural tasks might be possible, assuming conjoint activity between neurons in connected brain regions can be detected. Using the hypergeometric distribution, and employing anatomically-tractable connection mapping between regions, we derive a method to calculate the probability distribution of ‘recordable’ connections between groups of neurons. This mathematically-derived distribution is validated by Monte Carlo simulations of directed graphs representing the underlying anatomical connectivity structure. We apply this method to simulated graphs with multiple neurons, based on counts in rat brain regions, and to connection matrices from the Blue Brain model of the mouse neocortex connectome. Overall, we find low probabilities of simultaneously-recording directly interacting neurons in vivo in anatomically-connected regions with standard (tetrode-based) approaches. We suggest alternative approaches, including new recording technologies and summing neuronal activity over larger scales, offer promise for testing hypothesised interregional communication and source transformation rules.
Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure. ABSTRACT While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure. From October 2019 to March 2020, we conducted a home-based cross-sectional study in the greater Seattle, WA, area, utilizing electronic consent and data collection instruments. Participants received nasal swab collection kits via rapid delivery within 24 hours of self-reporting respiratory symptoms. Samples were returned to the laboratory and were screened for 26 respiratory pathogens and a housekeeping gene. Participant data were recorded via online survey at the time of sample collection and 1 week later. Of the 4,572 consented participants, 4,359 (95.3%) received a home swab kit and 3,648 (83.7%) returned a nasal specimen for respiratory pathogen screening. The 3,638 testable samples had a mean RNase P relative cycle threshold (Crt) value of 19.0 (SD, 3.4), and 1,232 (33.9%) samples had positive results for one or more pathogens, including 645 (17.7%) influenza-positive specimens. Among the testable samples, the median time between shipment of the home swab kit and completion of laboratory testing was 8.0 days (interquartile range [IQR], 7.0 to 14.0). A single adverse event occurred and did not cause long-term effects or require medical attention. Home-based surveillance using online participant enrollment and specimen self-collection is a safe and feasible method for community-level monitoring of influenza and other respiratory pathogens, which can readily be adapted for use during pandemics.
Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Significance Green/red CBCRs are one of the most important CBCR subfamilies owing to their physiological roles in cyanobacteria phylum and optogenetic applications. They are known to utilize a change in the bilin protonation state to cause the marked change in green/red absorption, but the structural bases of the protochromic photocycle are not well understood. Here, we have determined the crystal structure of the chromatic acclimation sensor RcaE of this subfamily in the Pr photoproduct state, identifying a unique conformation of the bilin and its interacting residues. In addition, we provide direct evidence of the protonation state of the bilin via NMR analysis. These findings bring insight to our understanding of the molecular mechanisms underlying the spectral diversity of CBCRs. Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. It is suggested that the absorption change of this subfamily is caused by the bilin C15-Z/C15-E photoisomerization and a subsequent change in the bilin protonation state. However, structural information and direct evidence of the bilin protonation state are lacking. Here, we report a high-resolution (1.63Å) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a “bucket” consisting of hydrophobic residues, in which the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A- through C-rings coplanar and the D-ring tilted. Three pyrrole nitrogens of the A- through C-rings are covered in the α-face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen bonded in the β-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the bucket, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the “leaky bucket” structure functions as a proton exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs.
The predatory strike of Odonata larvae – A temperature dependent spring actuated system

The larvae of Odonata are limnic predators capable of catching their prey using a highly modified mouthpart - the labium. Driven by a unique dual catapult mechanism, the apparatus can reach peak accelerations of up to 114.5m/s2. Yet little is known about the kinematics of the predatory strike in an ecological context. Here we show how different ambient temperatures affect the predatory strike and the avoidance reaction of prey items of Odonata larvae. We found that the extension velocity of the labial mask decreases significantly with the ambient temperature both in dragonflies and damselflies. However, temperature has lesser impact on the predatory strike itself than on directly muscle driven movements in both the predator and prey items. This contradicts the previous assumption that catapult mechanisms in insects are unaffected by temperature. Our results indicate that the prehensile labial mask is driven by a series-elastic catapult; a mechanism similar to the temperature dependent jump of frogs, where muscle and spring action are tightly linked. Our study provides novel insights into the predatory strike of Odonata larvae and offers a new ecological perspective on catapult mechanisms in arthropods in general.
Assessment Of Critical Care Nurses Knowledge and Practice Regarding Patient Safety in Intensive Care Units

Back ground: Patient safety is an essential and vital element in good nursing care which goals are patient identification, Communication between caregivers, safety of use of medication, prevention of infection, prevention of falls, prevention of pressure ulcers, prevention of wrong site, incorrect procedure, wrong person surgery, reduction of damage associated with clinical alarm systems Aim: this study was carried out to identify nursing knowledge and practice regarding patient safety in intensive care units . Methods: descriptive research design was used. Setting: Assiut University Hospital and Elmabara Hospital and convenient sample of 100 nurse working in the above mentioned setting, data was collected by utilizingTool1:Nurses'knowledge questionnaire, Tool II: Observation checklist to assess nurses' practice. Results: Most of nurses were aware of infection prevention and patient identification (0.98 ± 0.14,1.51 ± 0.61) respectively,64.0% of nurses had inadequate practice about all items of patient safety . Conclusion: The study sample showed about (38.0%) of nurses had good level of knowledge and nearly one-fourth (26.0%) of nurses had poor level of knowledge and about two -thirds of them had inadequate practice about patient safety Recommendation : Providing critical care nurses training courses regarding patient safety
Critical Thermal maximum measurements and its biological relevance: the case of ants

Upper thermal limit (UTL) is a key trait in evaluating ectotherm fitness. Critical Thermal maximum CTmax, often used to characterize the UTL of an organism in laboratory setting, needs to be accurate to characterize this significant and field-relevant threshold. The lack of standardization in CTmax assays has, however, introduce methodological problems in its measurement and incorrect estimation of species upper thermal limit; with potential major implications on the use of CTmax in forecasting community dynamics under climate change. In this study we ask if a satisfactory ramping rate can be identified to produce accurate measures of CTmax for multiple species. We first identified the most commonly used ramping rates (i.e. 0.2, 0.5 and 1.0 °Cmin−1) based on a literature review, and determined the ramping rate effects on CTmax value measurements in 27 ant species (7 arboreal, 16 ground, 4 subterranean species) from eight subfamilies using both dynamic and static assays. In addition, we used field observations on multiple species foraging activity in function of ground temperatures to identify the most biologically relevant CTmax value to ultimately develop a standardized methodological approach. Integrating dynamic and static assays provided a powerful approach to identify a suitable ramping rate for the measurements of CTmax values in ants. Our results also showed that among the values tested the ramping rate of 1 °Cmin−1 is optimal, with convergent evidences from CTmax values measured in laboratory and from foraging thermal maximum measured in the field. Finally, we illustrate how methodological bias in terms of physiological trait measurements can also affect the detection of phylogenetic signal (Pagel’s λ and Bloomberg’s K) in subsequent analyses. Overall, this study presents a methodological framework allowing the identification of suitable and standardized ramping rates for the measurement of ant CTmax, which may be used for other ectotherms. Particular attention should be given to CTmax values retrieved from less suitable ramping rate, and the potential biases that functional trait based research may induce on topics such as global warming, habitat conversion or their impacts on analytical interpretations on phylogenetic conservatism.
Cardiac Gq Receptors and Calcineurin Activation Are Not Required for the Hypertrophic Response to Mechanical Left Ventricular Pressure Overload

Rationale Gq-coupled receptors are thought to play a critical role in the induction of left ventricular hypertrophy (LVH) secondary to pressure overload, although mechano-sensitive channel activation by a variety of mechanisms has also been proposed, and the relative importance of calcineurin- and calmodulin kinase II (CaMKII)-dependent hypertrophic pathways remains controversial. Objective To determine the mechanisms regulating the induction of LVH in response to mechanical pressure overload. Methods and Results Transgenic mice with cardiac-targeted inhibition of Gq-coupled receptors (GqI mice) and their non-transgenic littermates (NTL) were subjected to neurohumoral stimulation (continuous, subcutaneous angiotensin II (AngII) infusion for 14 days) or mechanical pressure overload (transverse aortic arch constriction (TAC) for 21 days) to induce LVH. Candidate signalling pathway activation was examined. As expected, LVH observed in NTL mice with AngII infusion was attenuated in heterozygous (GqI+/-) mice and absent in homozygous (GqI-/-) mice. In contrast, LVH due to TAC was unaltered by either heterozygous or homozygous Gq inhibition. Gene expression of atrial natriuretic peptide (ANP), B-type natriuretic peptide (BNP) and α-skeletal actin (α-SA) was increased 48 hours after AngII infusion or TAC in NTL mice; in GqI mice, the increases in ANP, BNP and α-SA in response to AngII were completely absent, as expected, but all three increased after TAC. Increased nuclear translocation of nuclear factor of activated T-cells c4 (NFATc4), indicating calcineurin pathway activation, occurred in NTL mice with AngII infusion but not TAC, and was prevented in GqI mice infused with AngII. Nuclear and cytoplasmic CaMKIIδ levels increased in both NTL and GqI mice after TAC but not AngII infusion, with increased cytoplasmic phospho- and total histone deacetylase 4 (HDAC4) and increased nuclear myocyte enhancer factor 2 (MEF2) levels. Conclusion Cardiac Gq receptors and calcineurin activation are required for neurohumorally mediated LVH but are not required for LVH induced by mechanical pressure overload (TAC); the latter is mediated by activation of the CaMKII-HDAC4-MEF2 pathway.
Noncanonical usage of stop codons in ciliates expands proteins with Q-rich motifs

Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 27 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, including Saccharomyces cerevisiae RNA-mediated transposition and pseudohyphal growth, Candida albicans filamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement, Tetrahymena thermophila xylan catabolism and meiosis, Dictyostelium discoideum development and sexual cycles, Plasmodium falciparum infection, and the nervous systems of Drosophila melanogaster, Mus musculus and Homo sapiens. We also show that Q-rich-motif proteins are expanded massively in ten ciliates with reassigned TAAQ and TAGQ codons. Notably, the usage frequency of CAGQ is much lower in ciliates with reassigned TAAQ and TAGQ codons than in organisms with expanded and unstable Q runs (e.g., D. melanogaster and H. sapiens), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.