Miracle-dz/UniFAR-FTUs huggingface dataset:
Lacon-, Shrub- and Parity-Decompositions: Characterizing Transductions of Bounded Expansion Classes

The concept of bounded expansion provides a robust way to capture sparse graph classes with interesting algorithmic properties. Most notably, every problem definable in first-order logic can be solved in linear time on bounded expansion graph classes. First-order interpretations and transductions of sparse graph classes lead to more general, dense graph classes that seem to inherit many of the nice algorithmic properties of their sparse counterparts. In this paper, we show that one can encode graphs from a class with structurally bounded expansion via lacon-, shrub- and parity-decompositions from a class with bounded expansion. These decompositions are useful for lifting properties from sparse to structurally sparse graph classes.
Mass of $1^{-+}$ four-quark--hybrid mixed states

The study of exotic meson states has a long history. Glueball, hybrid meson (quark-antiquark with excited gluon), and multi-quark were predicted after the establishment of quantum chromodynamics. Many heavy exotic hadrons have been confirmed experimentally in the last decade. There are also two light exotic mesons with J = 1 have been found since the end of the last century. However, the structure of these two mesons is still unclear. Lattice QCD and most phenomenological methods show that the mass of 1 hybrid is around 1.7-2.1GeV [1–4], and it prefers to decay into Sand P-wave mesons. However, the corresponding candidates π1(1400) and π1(1600)[5] are lighter than predictions. Besides, π1(1400) only decays into ηπ, while Ref [6] indicates that in the limit of SU(3) flavor symmetry, the 1 hybrid decay into ηπ is forbidden. This result implies π1(1400) may be a multi-quark state. Some authors consider the 1 exotic mesons as tetraquark (diquark-antidiquark structure) or four-quark molecule (mesons bound state). Ref [7] exhaust all 1 tetraquark configurations and get two masses around 1.6GeV and 2.0GeV for two types of quark contents. Ref [8] gives 1 four-quark molecule mass around 1.4-1.5GeV, but the result receives large uncertainty from the instanton density. Ref [3] re-examines the studies about 1 exotic mesons, and predicts 1.7GeV for tetraquark configuration and 1.3GeV for molecule configuration. However, if π1(1400) is a four-quark state , then there should be unobserved mesons with strangeness 2 and 2 units of charge[6]. Besides, there is a subtle problem for the study about four-quark state. The four-quark current, usually can be identified as two meson currents, may easily couple to two mesons. It then causes difficulty
A 15-year follow-up study of hip bone mineral density and associations with leisure time physical activity. The Tromsø Study 2001–2016

Aims The aim was to investigate the long-term association between leisure time physical activity and hip areal bone mineral density (aBMD), in addition to change in hip aBMD over time, in 32–86 years old women and men. Methods Data were retrieved from the 2001, 2007–2008, and 2015–2016 surveys of the Tromsø Study, a longitudinal population study in Norway. Leisure time physical activity was assessed by the four-level Saltin-Grimby Physical Activity Level Scale which refers to physical exertion in the past twelve months. Hip aBMD was assessed by Dual-Energy X-ray Absorptiometry. Linear Mixed Model analysis was used to examine long-term associations between physical activity and hip aBMD (n = 6324). In addition, the annual change in hip aBMD was analyzed in a subsample of 3199 participants. Results Physical activity was significantly and positively associated with total hip aBMD in the overall cohort (p<0.005). Participants who reported vigorous activity had 28.20 mg/cm2 higher aBMD than those who were inactive (95% CI 14.71; 41.69, controlled for confounders), and even light physical activity was associated with higher aBMD than inactivity (8.32 mg/cm2, 95% CI 4.89; 11.76). Associations between physical activity and femoral neck aBMD yielded similar results. Hip aBMD decreased with age in both sexes, although more prominently in women. From 2001 to 2007–2008, aBMD changed by –5.76 mg/cm2 per year (95% CI –6.08; –5.44) in women, and –2.31 mg/cm2 (95% CI –2.69; –1.93), in men. From 2007–2008 to 2015–2016, the change was –4.45 mg/cm2 per year (95% CI –4.84; –4.06) in women, and –1.45 mg/cm2 (95% CI –1.92; –0.98) in men. Conclusions In this cohort of adult men and women, physical activity levels were positively associated with hip aBMD in a dose-response relationship. Hip aBMD decreased with age, although more pronounced in women than men.
EEG-Based Multiword Imagined Speech Classification for Persian Words

This study focuses on providing a simple, extensible, and multiclass classifier for imagined words using EEG signals. Six Persian words, along with the silence (or idle state), were selected as input classes. The words can be used to control a mouse/robot movement or fill a simple computer form. The data set of this study was 10 recordings of five participants collected in five sessions. Each record had 20 repetitions of all words and the silence. Feature sets consist of normalized, 1 Hz resolution frequency spectrum of 19 EEG channels in 1 to 32 Hz bands. Majority rule on a bank of binary SVM classifiers was used to determine the corresponding class of a feature set. Mean accuracy and confusion matrix of the classifiers were estimated by Monte-Carlo cross-validation. According to recording the time difference of inter- and intraclass samples, three classification modes were defined. In the long-time mode, where all instances of a word in the whole database are involved, average accuracies were about 58% for Word-Silence, 60% for Word-Word, 40% for Word-Word-Silence, and 32% for the seven-class classification (6 Words+Silence). For the short-time mode, when only instances of the same record are used, the accuracies were 96, 75, 79, and 55%, respectively. Finally, in the mixed-time classification, where samples of every class are taken from a different record, the highest performance achieved with average accuracies was about 97, 97, 92, and 62%. These results, even in the worst case of the long-time mode, are meaningfully better than random and are comparable with the best reported results of previously conducted studies in this area.
Cytohesin-2/ARNO: A Novel Bridge Between Cell Migration and Immunoregulation in Synovial Fibroblasts

The guanine nucleotide exchange factor cytohesin-2 (ARNO) is a major activator of the small GTPase ARF6 that has been shown to play an important role(s) in cell adhesion, migration and cytoskeleton reorganization in various cell types and models of disease. Interestingly, dysregulated cell migration, in tandem with hyper-inflammatory responses, is one of the hallmarks associated with activated synovial fibroblasts (SFs) during chronic inflammatory joint diseases, like rheumatoid arthritis. The role of ARNO in this process has previously been unexplored but we hypothesized that the pro-inflammatory milieu of inflamed joints locally induces activation of ARNO-mediated pathways in SFs, promoting an invasive cell phenotype that ultimately leads to bone and cartilage damage. Thus, we used small interference RNA to investigate the impact of ARNO on the pathological migration and inflammatory responses of murine SFs, revealing a fully functional ARNO-ARF6 pathway which can be rapidly activated by IL-1β. Such signalling promotes cell migration and formation of focal adhesions. Unexpectedly, ARNO was also shown to modulate SF-inflammatory responses, dictating their precise cytokine and chemokine expression profile. Our results uncover a novel role for ARNO in SF-dependent inflammation, that potentially links pathogenic migration with initiation of local joint inflammation, offering new approaches for targeting the fibroblast compartment in chronic arthritis and joint disease.
Impact of the COVID-19 pandemic and work-related stress in Umbrian healthcare workers during Phase 1 in Italy

Background: Depression, anxiety, psychological distress, and poor sleep quality increased in healthcare workers (HCWs) during the COVID-19 pandemic. The aim of the study was to assess levels of psychological distress in Umbrian HCWs during the COVID-19 Phase 1 lockdown along with exploring the relationship between sociodemographic/occupational factors. Methods: Data on sociodemographic and occupational characteristics, change of job description, economic losses and emergency involvement and SARS-CoV2 infections in the workplace were collected using an anonymous online survey sent by healthcare professional associations. Data concerning psychological healthcare distress, were collected anonymously using BIAS 20 (stress balance) and Depression Anxiety Stress Scales (DASS-21). Results: One thousand and one healthcare workers responded to the questionnaire. Biological risk at work was perceived by all HCWs, less so from psychologists and more so from those working in hospitals. Stress symptoms (DASS21 >14) were associated with a younger age group (OR 0.98; 95% CI 0.97-0.99) and less work experience (OR 0.98; 95% CI 0.96-0.99). Younger age was also associated with anxiety symptoms (DASS 21 >7) (OR 0.98; 95% CI 0.97-0.99), as well as graduate/post graduate education level (OR 2.04; 95% CI 1.14-3.63). Working as an independent contractor was a risk factor for high stress health impact (OR 2.00; CI 1.40-2.86) and stress (OR 1.87; CI 1.20-2.92), anxiety (OR 1.89; CI 1.22-2.92) and depression (OR 1.57; CI 1.10-2.22) symptoms. Conclusions: Our study showed a possible relationship between healthcare type of employment and distress symptoms during Covid19 pandemic phase 1. Results of our study should be confirmed in other Italian healthcare settings and could serve as a preliminarily baseline for multidisciplinary Italian collaboration.
Role of Salivary Biomarkers in Cystic Fibrosis: A Systematic Review

Background Saliva biomarkers could be easily used as a noninvasive alternative tool for diagnosing cystic fibrosis (CF) disease. In this study, the significance of changes in salivary compositions in patients with CF was systematically reviewed. Methods An electronic search was utilized to include studies published in English, with case-control, cohort, or cross-sectional design. The evaluated salivary components were extracted and summarized. The included studies were assessed using the Strengthening the Reporting of Observational Studies in Epidemiology checklist. Results Out of 498 identified studies, nine met the eligibility criteria. Salivary electrolytes showed a substantial alteration in the CF group, especially with chloride and sodium. Total protein concentration was higher in patients with CF. However, SCN– concentration was lower in patients with CF. In addition, a reduction in the salivary flow rate and amylase levels was found in patients with CF. Conclusion Alterations in salivary biomarkers among patients with CF could be used as a promising diagnostic tool for cystic fibrosis.
Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity

Abstract Both ligand binding and nanocavity can increase the stability of a biomolecular structure. Using mechanical unfolding in optical tweezers, here we found that a DNA origami nanobowl drastically increased the stability of a human telomeric G-quadruplex bound with a pyridostatin (PDS) ligand. Such a stability change is equivalent to >4 orders of magnitude increase (upper limit) in binding affinity (Kd: 490 nM → 10 pM (lower limit)). Since confined space can assist the binding through a proximity effect between the ligand-receptor pair and a nanoconfinement effect that is mediated by water molecules, we named such a binding as mechanochemical binding. After minimizing the proximity effect by using PDS that can enter or leave the DNA nanobowl freely, we attributed the increased affinity to the nanoconfinement effect (22%) and the proximity effect (78%). This represents the first quantification to dissect the effects of proximity and nanoconfinement on binding events in nanocavities. We anticipate these DNA nanoassemblies can deliver both chemical (i.e. ligand) and mechanical (i.e. nanocavity) milieus to facilitate robust mechanochemical binding in various biological systems.
Stimulus-Induced Narrowband Gamma Oscillations are Test–Retest Reliable in Human EEG

Abstract Visual stimulus-induced gamma oscillations in electroencephalogram (EEG) recordings have been recently shown to be compromised in subjects with preclinical Alzheimer’s Disease (AD), suggesting that gamma could be an inexpensive biomarker for AD diagnosis provided its characteristics remain consistent across multiple recordings. Previous magnetoencephalography studies in young subjects have reported consistent gamma power over recordings separated by a few weeks to months. Here, we assessed the consistency of stimulus-induced slow (20–35 Hz) and fast gamma (36–66 Hz) oscillations in subjects (n = 40) (age: 50–88 years) in EEG recordings separated by a year, and tested the consistency in the magnitude of gamma power, its temporal evolution and spectral profile. Gamma had distinct spectral/temporal characteristics across subjects, which remained consistent across recordings (average intraclass correlation of ~0.7). Alpha (8–12 Hz) and steady-state-visually evoked-potentials were also reliable. We further tested how EEG features can be used to identify 2 recordings as belonging to the same versus different subjects and found high classifier performance (AUC of ~0.89), with temporal evolution of slow gamma and spectral profile being most informative. These results suggest that EEG gamma oscillations are reliable across sessions separated over long durations and can also be a potential tool for subject identification.
ASPICov: An automated pipeline for identification of SARS-Cov2 nucleotidic variants

ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or Ion Torrent technology. To ensure FAIR data analysis, this Nextflow pipeline follows nf-core guidelines and use Singularity containers. Pipeline is implemented and available at https://gitlab.com/vtilloy/aspicov.
Landscape and Climatic Variations Shaped Secondary Contacts amid Barn Owls of the Western Palearctic

Abstract The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
OKN-007 Alters Protein Expression Profiles in High-Grade Gliomas: Mass Spectral Analysis of Blood Sera

Current therapies for high-grade gliomas, particularly glioblastomas (GBM), do not extend patient survival beyond 16–22 months. OKN-007 (OKlahoma Nitrone 007), which is currently in phase II (multi-institutional) clinical trials for GBM patients, and has demonstrated efficacy in several rodent and human xenograft glioma models, shows some promise as an anti-glioma therapeutic, as it affects most aspects of tumorigenesis (tumor cell proliferation, angiogenesis, migration, and apoptosis). Combined with the chemotherapeutic agent temozolomide (TMZ), OKN-007 is even more effective by affecting chemo-resistant tumor cells. In this study, mass spectrometry (MS) methodology ESI-MS, mass peak analysis (Leave One Out Cross Validation (LOOCV) and tandem MS peptide sequence analyses), and bioinformatics analyses (Ingenuity® Pathway Analysis (IPA®)), were used to identify up- or down-regulated proteins in the blood sera of F98 glioma-bearing rats, that were either untreated or treated with OKN-007. Proteins of interest identified by tandem MS-MS that were decreased in sera from tumor-bearing rats that were either OKN-007-treated or untreated included ABCA2, ATP5B, CNTN2, ITGA3, KMT2D, MYCBP2, NOTCH3, and VCAN. Conversely, proteins of interest in tumor-bearing rats that were elevated following OKN-007 treatment included ABCA6, ADAMTS18, VWA8, MACF1, and LAMA5. These findings, in general, support our previous gene analysis, indicating that OKN-007 may be effective against the ECM. These findings also surmise that OKN-007 may be more effective against oligodendrogliomas, other brain tumors such as medulloblastoma, and possibly other types of cancers.
Activity- and Enrichment-Based Metaproteomics Insights into Active Urease from the Rumen Microbiota of Cattle

Regulation of microbial urease activity plays a crucial role in improving the utilization efficiency of urea and reducing nitrogen emissions to the environment for ruminant animals. Dealing with the diversity of microbial urease and identifying highly active urease as the target is the key for future regulation. However, the identification of active urease in the rumen is currently limited due to large numbers of uncultured microorganisms. In the present study, we describe an activity- and enrichment-based metaproteomic analysis as an approach for the discovery of highly active urease from the rumen microbiota of cattle. We conducted an optimization method of protein extraction and purification to obtain higher urease activity protein. Cryomilling was the best choice among the six applied protein extraction methods (ultrasonication, bead beating, cryomilling, high-pressure press, freeze-thawing, and protein extraction kit) for obtaining protein with high urease activity. The extracted protein by cryomilling was further enriched through gel filtration chromatography to obtain the fraction with the highest urease activity. Then, by using SDS-PAGE, the gel band including urease was excised and analyzed using LC-MS/MS, searching against a metagenome-derived protein database. Finally, we identified six microbial active ureases from 2225 rumen proteins, and the identified ureases were homologous to those of Fibrobacter and Treponema. Moreover, by comparing the 3D protein structures of the identified ureases and known ureases, we found that the residues in the β-turn of flap regions were nonconserved, which might be crucial in influencing the flexibility of flap regions and urease activity. In conclusion, the active urease from rumen microbes was identified by the approach of activity- and enrichment-based metaproteomics, which provides the target for designing a novel efficient urease inhibitor to regulate rumen microbial urease activity.
Non-linear and Interaction Analyses of Biomarkers for Organ Dysfunctions as Predictive Markers for Sepsis: A Nationwide Retrospective Study

The Sequential Organ Failure Assessment (SOFA) score is predominantly used to assess the severity of organ dysfunction in sepsis. However, differences in prognostic value between SOFA subscores have not been sufficiently evaluated. This retrospective observational study used a large-scale database containing about 30 million patients. Among them, we included 38,869 adult patients with sepsis from 2006 to 2019. The cardiovascular and neurological subscores were calculated by a modified method. Associations between the biomarkers of the SOFA components and mortality were examined using restricted cubic spline analyses, which showed that an increase in the total modified SOFA score was linearly associated with increased mortality. However, the prognostic association of subscores varied widely: platelet count showed a J-shaped association, creatinine showed an inverted J-shaped association, and bilirubin showed only a weak association. We also evaluated interaction effects on mortality between an increase of one subscore and another. The joint odds ratios on mortality of two modified SOFA subscores were synergistically increased compared to the sum of the single odds ratios, especially in cardiovascular-neurological, coagulation-hepatic, and renal-hepatic combinations. In conclusion, total modified SOFA score was associated with increased mortality despite the varied prognostic associations of the subscores, possibly because interactions between subscores synergistically enhanced prognostic accuracy.
Melatonin Promotes Antler Growth by Accelerating MT1-Mediated Mesenchymal Cell Differentiation and Inhibiting VEGF-Induced Degeneration of Chondrocytes

The sika deer is one type of seasonal breeding animal, and the growth of its antler is affected by light signals. Melatonin (MLT) is a neuroendocrine hormone synthesized by the pineal gland and plays an important role in controlling the circadian rhythm. Although the MLT/MT1 (melatonin 1A receptor) signal has been identified during antler development, its physiological function remains almost unknown. The role of MLT on antler growth in vivo and in vitro is discussed in this paper. In vivo, MLT implantation was found to significantly increase the weight of antlers. The relative growth rate of antlers showed a remarkable increased trend as well. In vitro, the experiment showed MLT accelerated antler mesenchymal cell differentiation. Further, results revealed that MLT regulated the expression of Collage type II (Col2a) through the MT1 binding mediated transcription of Yes-associated protein 1 (YAP1) in antler mesenchymal cells. In addition, treatment with vascular endothelial growth factor (VEGF) promoted chondrocytes degeneration by downregulating the expression of Col2a and Sox9 (SRY-Box Transcription Factor 9). MLT effectively inhibited VEGF-induced degeneration of antler chondrocytes by inhibiting the Signal transducers and activators of transcription 5/Interleukin-6 (STAT5/IL-6) pathway and activating the AKT/CREB (Cyclin AMP response-element binding protein) pathway dependent on Sox9 expression. Together, our results indicate that MLT plays a vital role in the development of antler cartilage.