Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Fusion and Syncytium Formation in Betaherpesvirus Infection

Cell–cell fusion is a fundamental and complex process that occurs during reproduction, organ and tissue growth, cancer metastasis, immune response, and infection. All enveloped viruses express one or more proteins that drive the fusion of the viral envelope with cellular membranes. The same proteins can mediate the fusion of the plasma membranes of adjacent cells, leading to the formation of multinucleated syncytia. While cell–cell fusion triggered by alpha- and gammaherpesviruses is well-studied, much less is known about the fusogenic potential of betaherpesviruses such as human cytomegalovirus (HCMV) and human herpesviruses 6 and 7 (HHV-6 and HHV-7). These are slow-growing viruses that are highly prevalent in the human population and associated with several diseases, particularly in individuals with an immature or impaired immune system such as fetuses and transplant recipients. While HHV-6 and HHV-7 are strictly lymphotropic, HCMV infects a very broad range of cell types including epithelial, endothelial, mesenchymal, and myeloid cells. Syncytia have been observed occasionally for all three betaherpesviruses, both during in vitro and in vivo infection. Since cell–cell fusion may allow efficient spread to neighboring cells without exposure to neutralizing antibodies and other host immune factors, viral-induced syncytia may be important for viral dissemination, long-term persistence, and pathogenicity. In this review, we provide an overview of the viral and cellular factors and mechanisms identified so far in the process of cell–cell fusion induced by betaherpesviruses and discuss the possible consequences for cellular dysfunction and pathogenesis.
Automated plankton image analysis using convolutional neural networks

The rise of in situ plankton imaging systems, particularly high‐volume imagers such as the In Situ Ichthyoplankton Imaging System, has increased the need for fast processing and accurate classification tools that can identify a high diversity of organisms and nonliving particles of biological origin. Previous methods for automated classification have yielded moderate results that either can resolve few groups at high accuracy or many groups at relatively low accuracy. However, with the advent of new deep learning tools such as convolutional neural networks (CNNs), the automated identification of plankton images can be vastly improved. Here, we describe an image processing procedure that includes preprocessing, segmentation, classification, and postprocessing for the accurate identification of 108 classes of plankton using spatially sparse CNNs. Following a filtering process to remove images with low classification scores, a fully random evaluation of the classification showed that average precision was 84% and recall was 40% for all groups. Reliably classifying rare biological classes was difficult, so after excluding the 12 rarest taxa, classification accuracy for the remaining biological groups became > 90%. This method provides proof of concept for the effectiveness of an automated classification scheme using deep‐learning methods, which can be applied to a range of plankton or biological imaging systems, with the eventual application in a variety of ecological monitoring and fisheries management contexts.
Midterm survival of imaging-assisted robotic lung segmentectomy for non-small-cell lung cancer

Abstract OBJECTIVES Our goal was to report our midterm results using imaging-assisted modalities with robotic segmentectomies for non-small-cell lung cancer (NSCLC). METHODS This was a retrospective study of all robotic segmentectomies, with confirmed NSCLC, performed at our general and thoracic surgery unit in the Rouen University Hospital (France), from January 2012 through December 2019. Benign and metastatic lesions were excluded. Data were extracted from the EPITHOR French nationwide database. RESULTS A total of 121 robotic segmentectomies were performed for 118 patients with a median age of 65 (interquartile range: 60, 69) years. The majority had clinical stage T1aN0M0 (71.9%) or T1bN0M0 (13.2%). The mean (standard deviation) number of resected segments was 1.93 (1.09) with 80.2% imaging-assisted segmentectomies. Oriented (according to tumour location) or systematic lymphadenectomy or sampling was performed for 72.7%, 23.1% and 4.1% of patients. The postoperative course was uneventful for 94 patients (77.7%), whereas 34 complications occurred for 27 patients (22.3%), including 2 patients (1.7%) with Clavien-Dindo ≥III complications. The mean thoracic drainage duration was 4.12 days, and the median hospital stay was 4 days (interquartile range: 3, 5) after the operation. The 2-year survival rate was 93.9% (95% confidence interval: 86.4–97.8%). Excluding stage IV (n = 3) and stage 0 tumours (n = 6), the 2-year survival rate was 95.7% (95% confidence interval: 88.4–98.8%) compared to an expected survival rate of 94.0% according to stage-specific survival rates found in a large external reference cohort. CONCLUSIONS Imaging-guided robotic-assisted thoracic surgery segmentectomy seems to be useful and oncological with good midterm results, especially for patients with early-stage NSCLC.
Clinical utility of liquid biopsy in breast cancer: A systematic review

Advancements in genetic sequencing techniques along with the identification of specific mutations and structural changes in multiple cancer genes, make it possible to identify circulating tumor cells and cell free nucleic acids as blood‐based biomarkers, serving as a liquid biopsy (LB) with great utility for the diagnosis, treatment and follow‐up of patients with neoplasms. This systematic review focuses on the clinical utility of LB in patients with breast cancer (BC). Articles published between 1990 and 2021 were included. Databases searched: Trip Database, WoS, EMBASE, PubMed, SCOPUS, and Clinical Keys. Variables studied: Publication year, country, number of cases, primary study design, LB detection methods, genes found, overall survival, disease‐free survival, stage, response to treatment, clinical utility, BC molecular type, systemic treatment and methodological quality of primary studies. Of 2619 articles, 74 were retained representing 12 658 patients, mainly cohort studies (66.2%), the majority were from China (15%) and Japan (12.2%). All primary studies described clinical stage and type of systemic treatment used. Most used biomarker detection method: DNA (52.7%) and type of analysis: quantification of total cfDNA (35.1%). PIK3CA mutation was most frequent (62.9%). Evidence suggests clinically useful applications of BC. Though heterogeneous, publications suggest that LB will constitute part of the standard diagnostic‐therapeutic process of BC.
The tarnished silver spoon? Trade‐off between prenatal growth and telomere length in wild boar

Life‐history theory predicts a trade‐off between growth rates and lifespan, which is reflected by telomere length, a biomarker of somatic state. We investigated the correlation between telomere length and early‐life growth of wild boar piglets, Sus scrofa, kept under semi‐natural conditions with high food availability to examine our hypothesis that increased pre‐ and postnatal growth will lead to telomere length attrition, but that a high supply of nutrient may provide the possibility to compensate telomere loss via telomere repair mechanisms. As predicted, our data showed a clear negative correlation between birth body mass and initial telomere length: heavier neonates had shorter telomeres at birth, and we did not find an influence of the mother on initial telomere length. Body mass at birth correlated with body mass later in life and postnatal growth rate did not affect telomere length. We observed an increase in telomere length during postnatal development, suggesting that high food availability allowed piglets to invest into both, growth and telomere restoration. The increase in telomere length over the duration of the study was not accompanied by telomerase activity; thus, telomere elongation was caused either by alternative mechanisms or by short pulses of telomerase activity that we missed. Taken together, this study suggests a trade‐off between investment into growth and telomere maintenance even before birth and the possibility to compensate telomere attrition during growth under high amounts of available energy.
Poor protective potential of influenza nucleoprotein antibodies despite wide prevalence

Humans are exposed to influenza virus through periodic infections. Due to these repeated exposures, human populations commonly have elevated antibody titers targeting the conserved internal influenza virus nucleoprotein (NP). Despite the presence of anti‐NP antibodies, humans are acutely susceptible to drifted influenza viruses with antigenically different surface proteins and the protective potential of human NP antibodies is unclear. In this study, high levels of anti‐NP antibody and NP‐specific B cells were detected in both adult humans and influenza‐infected mice, confirming that NP is a major target of humoral immunity. Through sorting single B cells from influenza‐exposed human adults, we generated a panel of 11 anti‐NP monoclonal antibodies (mAbs). The majority of anti‐NP human mAbs generated were capable of engaging cellular Fc receptors and bound NP on the surface of influenza‐infected cell lines in vitro, suggesting that anti‐NP mAbs have the potential to mediate downstream Fc effector functions such as antibody‐dependent cellular cytotoxicity and antibody‐dependent phagocytosis. However, human anti‐NP mAbs were not protective in vivo when passively transferred into a murine influenza challenge model. Future in vivo studies examining the synergistic effect of anti‐NP mAbs infused with other influenza‐specific mAbs are warranted.
N‐myc downstream regulated family member 1 (NDRG1) is enriched in myelinating oligodendrocytes and impacts myelin degradation in response to demyelination

The N‐myc downstream regulated gene family member 1 (NDRG1) is a gene whose mutation results in peripheral neuropathy with central manifestations. While most of previous studies characterized NDRG1 role in Schwann cells, the detection of central nervous system symptoms and the identification of NDRG1 as a gene silenced in the white matter of multiple sclerosis brains raise the question regarding its role in oligodendrocytes. Here, we show that NDRG1 is enriched in oligodendrocytes and myelin preparations, and we characterize its expression using a novel reporter mouse (TgNdrg1‐EGFP). We report NDRG1 expression during developmental myelination and during remyelination after cuprizone‐induced demyelination of the adult corpus callosum. The transcriptome of Ndrg1‐EGFP+ cells further supports the identification of late myelinating oligodendrocytes, characterized by expression of genes regulating lipid metabolism and bioenergetics. We also generate a lineage specific conditional knockout (Olig1cre/+;Ndrg1fl/fl) line to study its function. Null mice develop normally, and despite similar numbers of progenitor cells as wild type, they have fewer mature oligodendrocytes and lower levels of myelin proteins than controls, thereby suggesting NDRG1 as important for the maintenance of late myelinating oligodendrocytes. In addition, when control and Ndrg1 null mice are subject to cuprizone‐induced demyelination, we observe a higher degree of demyelination in the mutants. Together these data identify NDRG1 as an important molecule for adult myelinating oligodendrocytes, whose decreased levels in the normal appearing white matter of human MS brains may result in greater susceptibility of myelin to damage.
In silico genome‐wide gene‐based association analysis reveals new genes predisposing to coronary artery disease

Genome‐wide association study (GWAS) have identified more than 300 single nucleotide polymorphisms at 163 independent loci associated with coronary artery disease (CAD). However, there is no full understanding about the causal genes for CAD and the mechanisms of their action. We aimed to perform a post GWAS analysis to identify genes whose polymorphism may influence the risk of CAD. Using the UK Biobank GWAS summary statistics, we performed a gene‐based association analysis. We found 63 genes significantly associated with CAD due to their within‐gene polymorphisms. Many of these genes are well known. Some known CAD genes such as FURIN and SORT1 did not show the gene‐based association because their variants had low GWAS signals or gene‐based association was inflated by the strong GWAS signal outside the gene. For several known CAD genes, we demonstrated that their effects could be explained not only or not at all by their own variants but by the variants within the neighboring genes controlling their expression. Using several bioinformatics techniques, we suggested potential mechanisms underlying gene‐CAD associations. Three genes, CDK19, NCALD, and ARHGEF12 were not previously associated with CAD. The role of these genes should be clarified in further studies.
The effect of apple cultivars and yeast strains on selected quality parameters and antioxidant activity of fermented apple beverages

ABSTRACT The aim of the study was to evaluate the impact of selected apple cultivars (Rubin, Topaz, Elise) and selected strains of wine, cider, distiller yeast, and wild-type yeast on the dynamics of the fermentation process as well as on the chemical composition and antioxidant properties (AOX) of fermented apple beverages. The quality parameters of the fermented beverages depend mainly on the apple cultivar used. The beverages from the Rubin cultivar met all the requirements for fruit wines, but in the beverages from the Topaz cultivar, the limit values for total acidity were exceeded (> 7g/L). The beverages from the Elise cultivar were characterized by low ethanol content and degree of fermentation. The process of fermentation resulted in a reduction of the total polyphenol content (TPC) in the beverages of the Rubin and Topaz cultivars, while in beverages from the Elise cultivar, in an increase of both TPC and AOX. Abbreviations: AOX - antioxidant activity; TPC - total polyphenol content; FAN - free amino nitrogen; ABTS - diammonium salt of the 2,2ʹ-azino-bis(3-ethylbenzothiazoline-6-sulfonic) acid.
AIT_FHSTP at GermEval 2021: Automatic Fact Claiming Detection with Multilingual Transformer Models

Spreading ones opinion on the internet is becoming more and more important. A problem is that in many discussions people often argue with supposed facts. This year’s GermEval 2021 focuses on this topic by incorporating a shared task on the identification of fact-claiming comments. This paper presents the contribution of the AIT FHSTP team at the GermEval 2021 benchmark for task 3: “identifying fact-claiming comments in social media texts”. Our methodological approaches are based on transformers and incorporate 3 different models: multilingual BERT, GottBERT and XML-RoBERTa. To solve the fact claiming task, we fine-tuned these transformers with external data and the data provided by the GermEval task organizers. Our multilingual BERT model achieved a precision-score of 72.71%, a recall of 72.96% and an F1-Score of 72.84% on the GermEval test set. Our fine-tuned XML-RoBERTa model achieved a precision-score of 68.45%, a recall of 70.11% and a F1-Score of 69.27%. Our best model is GottBERT (i.e., a BERT transformer pre-trained on German texts) fine-tuned on the GermEval 2021 data. This transformer achieved a precision of 74.13%, a recall of 75.11% and an F1-Score of 74.62% on the test set.
QT variability unrelated to RR variability during stress testing for identification of coronary artery disease

Stress test electrocardiogram (ECG) analysis is widely used for coronary artery disease (CAD) diagnosis despite its limited accuracy. Alterations in autonomic modulation of cardiac electrical activity have been reported in CAD patients during acute ischemia. We hypothesized that those alterations could be reflected in changes in ventricular repolarization dynamics during stress testing that could be measured through QT interval variability (QTV). However, QTV is largely dependent on RR interval variability (RRV), which might hinder intrinsic ventricular repolarization dynamics. In this study, we investigated whether different markers accounting for low-frequency (LF) oscillations of QTV unrelated to RRV during stress testing could be used to separate patients with and without CAD. Power spectral density of QTV unrelated to RRV was obtained based on time-frequency coherence estimation. Instantaneous LF power of QTV and QTV unrelated to RRV were obtained. LF power of QTV unrelated to RRV normalized by LF power of QTV was also studied. Stress test ECG of 100 patients were analysed. Patients referred to coronary angiography were classified into non-CAD or CAD group. LF oscillations in QTV did not show significant differences between CAD and non-CAD groups. However, LF oscillations in QTV unrelated to RRV were significantly higher in the CAD group as compared with the non-CAD group when measured during the first phases of exercise and last phases of recovery. ROC analysis of these indices revealed area under the curve values ranging from 61 to 73%. Binomial logistic regression analysis revealed LF power of QTV unrelated to RRV, both during the first phase of exercise and last phase of recovery, as independent predictors of CAD. In conclusion, this study highlights the importance of removing the influence of RRV when measuring QTV during stress testing for CAD identification and supports the added value of LF oscillations of QTV unrelated to RRV to diagnose CAD from the first minutes of exercise. This article is part of the theme issue ‘Advanced computation in cardiovascular physiology: new challenges and opportunities’.
UPAppliedCL at GermEval 2021: Identifying Fact-Claiming and Engaging Facebook Comments Using Transformers

In this paper we present UPAppliedCL’s contribution to the GermEval 2021 Shared Task. In particular, we participated in Subtasks 2 (Engaging Comment Classification) and 3 (Fact-Claiming Comment Classification). While acceptable results can be obtained by using unigrams or linguistic features in combination with traditional machine learning models, we show that for both tasks transformer models trained on fine-tuned BERT embeddings yield best results.
Effect of the GeoGebra software-supported collaborative learning environment on seventh grade students’ geometry achievement, retention and attitudes

Abstract The purpose of this study was to examine the effects of using GeoGebra software in a computer-supported collaborative learning (CSCL) environment on seventh grade students’ geometry achievement, retention of learning, and attitudes toward geometry. The study was designed using a quasi-experimental research method with pretest, post-test and delayed post-test. This study was carried out with 62 seventh grade students in a city in western Turkey. CSCL activities using GeoGebra software were implemented in the experimental group, while instruction in the control group continued with textbook-based direct instruction. The Geometry Achievement Test (GAT) and Geometry Attitude Scale (GAS) were applied to groups as pretest and post-test. A retention test was applied to both groups eight weeks after the post-test. Data were analyzed through SPSS 17.0 statistical software by using a t-test and ANCOVA test. It was indicated in this study that CSCL using GeoGebra software significantly increased seventh grade students’ geometry achievement and retention of learning in comparison to textbook-based direct instruction. It was also determined that the CSCL environment with GeoGebra software significantly increased students’ attitudes toward geometry.
Comparison of Antimicrobial Substantivity of Six Root Canal Irrigants against Enterococcus faecalis

Introduction: The antimicrobial substantivity of Mixture of Doxycycline, Citric acid, and Tween 80 (MTAD), Tetraclean, Tetraclean NA, Q-Mix, 2% Chlorhexidine (CHX) and Octenisept was assessed in human root dentine blocks infected with Enterococcus (E.) faecalis. Methods and Materials: A total of 170 dentine tubes were prepared from human maxillary incisors. After crown and apical third removal, cementum was abraded. The remaining center-holed pieces were cut into 4-mm blocks, infected with E. faecalis in Brain Heart Infusion (BHI) broth for 28 days, then randomly divided into 6 experimental groups (n=25) and 2 controls (n=10). At 0, 7, 14, 21 and 28 days, dentine chips were removed from the canals, with sequential round burs with increasing diameters, and collected into freshly prepared BHI broth. After culturing, growing colonies were counted as colony forming units (CFU). Conventional non-parametric tests (Kruskal-Wallis and Mann-Whitney tests) were used to assess intra-group (at different time frames) and inter-group (at each experimental time) differences (P=0.05). Results: Tetraclean yielded the lowest CFU counts (P<0.001) at each observation time. Tetraclean NA and Q-Mix showed better (P<0.001) substantivity than 2% CHX and MTAD (except for Q-Mix versus MTAD at 14 days, P=0.21). Conclusions: In this in vitro study, Tetraclean NA and Q-Mix displayed the best antimicrobial substantivity against E. faecalis after Tetraclean in infected human root dentine. Considering the findings of our study and potential drawbacks of antibiotic-based irrigants, free-antibiotic irrigants may represent viable alternative for final rinse in root canal treatment.
Random Peptides Rich in Small and Disorder-Promoting Amino Acids Are Less Likely to Be Harmful

Proteins are the workhorses of the cell, yet they carry great potential for harm via misfolding and aggregation. Despite the dangers, proteins are sometimes born de novo from non-coding DNA. Proteins are more likely to be born from non-coding regions that produce peptides that do little to no harm when translated than from regions that produce harmful peptides. To investigate which newborn proteins are most likely to “first, do no harm”, we estimate fitnesses from an experiment that competed Escherichia coli lineages that each expressed a unique random peptide. A variety of peptide metrics significantly predict lineage fitness, but this predictive power stems from simple amino acid frequencies rather than the ordering of amino acids. Amino acids that are smaller and that promote intrinsic structural disorder have more benign fitness effects. We validate that the amino acids that indicate benign effects in random peptides expressed in E. coli also do so in an independent dataset of random N-terminal tags in which it is possible to control for expression level. The same amino acids are also enriched in young animal proteins. Significance statement Proteins are sometimes born de novo. In an experiment to reproduce this process in Escherichia coli, we were able to predict 15% of the variation in random peptide fitness effects from their amino acid frequencies. In contrast, which order the amino acids are in seems to make no difference, adding no predictive power on top of simple amino acid frequencies. Amino acids that are smaller and promote intrinsic structural disorder have more benign fitness effects.