Miracle-dz/UniFAR-FTUs huggingface dataset:
Artificial Rearing of Atlantic Salmon Juveniles for Supportive Breeding Programs Induces Long-Term Effects on Gut Microbiota after Stocking

In supportive breeding programs for wild salmon populations, stocked parr experience higher mortality rates than wild ones. Among other aspects of phenotype, the gut microbiota of artificially raised parr differs from that of wild parr before stocking. Early steps of microbiota ontogeny are tightly dependent upon environmental conditions, both of which exert long-term effects on host physiology. Therefore, our objective was to assess to what extent the resilience capacity of the microbiota of stocked salmon may prevent taxonomic convergence with that of their wild congeners after two months in the same natural environment. Using the 16S SSU rRNA marker gene, we tested the general hypothesis that environmental conditions during the very first steps of microbiota ontogeny imprint a permanent effect on later stages of microbiota recruitment. Our results first showed that gut microbiota composition of stocked and wild parr from the same genetic population, and sharing the same environment, was dependent on the early rearing environment. In contrast, skin microbiota in stocked individuals converged to that of wild individuals. Taxonomic composition and co-occurrence network analyses suggest an impairment of wild bacteria recruitment and a higher instability for the gut microbiota of stocked parr. This study is the first to demonstrate the long-term effect of early microbiota ontogeny in artificial rearing for natural population conservation programs, raising the need to implement microbial ecology.
Assessing Self-Efficacy and Communication Regarding Sexual Agreements among Men Who Have Sex with Men in the USA: Development and Validation of Two Novel Scales

HIV disproportionately impacts men who have sex with men (MSM) in the USA. Building upon research on relationship constructs unique to MSM couples’ HIV-prevention needs, we developed two new scales measuring sexual agreement self-efficacy (SASE) and importance of sexual agreement communication (ISAC). Following qualitative item development, we used two large independent samples of MSM couples (N1 = 441, N2 = 388) to conduct scale validation. Exploratory factor analyses indicated both SASE and ISAC to be unidimensional with 7 and 5 items (eigenvalues = 5.68 and 3.50), respectively, with strong factor loadings. Confirmatory factor analyses yielded satisfactory model fit for SASE (CFI = 0.99; SRMR = 0.03) and ISAC (CFI = 0.99; SRMR = 0.05). Reliability was high for SASE (ω = 0.92) and ISAC (ω = 0.84). Predictive validity analysis revealed a protective association between higher scores on both scales and the outcomes of sexual risk behavior and agreement breaks. Convergent and discriminant validity analyses demonstrated associations in the expected directions between these scales and multiple measures of relationship quality. Therefore, SASE and ISAC are two brief, valid, and reliable scales that can facilitate more in-depth explorations of sexual agreements in MSM and thereby contribute greatly to improving our understanding of and ability to intervene on sexual agreements to improve health and relationship outcomes.
Surface Magnetization Reversal of Wiegand Wire Measured by the Magneto-Optical Kerr Effect

The Wiegand wire is known to exhibit a unique feature of fast magnetization reversal in the magnetically soft region accompanied by a large Barkhausen jump. We clarified a significant difference between the magnetization reversals at the surface and at the entire cross section of a Wiegand wire. We conducted magnetization measurements based on the magneto-optical Kerr effect and applied conventional methods to determine the magnetization curves. The switching field of the magnetization reversal at the surface was greater than that at the initiation of a large Barkhausen jump. Our analysis suggests that the outer surface layer exhibits low coercivity.
Combating the Infodemic: A Chinese Infodemic Dataset for Misinformation Identification

Misinformation posted on social media during COVID-19 is one main example of infodemic data. This phenomenon was prominent in China when COVID-19 happened at the beginning. While a lot of data can be collected from various social media platforms, publicly available infodemic detection data remains rare and is not easy to construct manually. Therefore, instead of developing techniques for infodemic detection, this paper aims at constructing a Chinese infodemic dataset, “infodemic 2019”, by collecting widely spread Chinese infodemic during the COVID-19 outbreak. Each record is labeled as true, false or questionable. After a four-time adjustment, the original imbalanced dataset is converted into a balanced dataset by exploring the properties of the collected records. The final labels achieve high intercoder reliability with healthcare workers’ annotations and the high-frequency words show a strong relationship between the proposed dataset and pandemic diseases. Finally, numerical experiments are carried out with RNN, CNN and fastText. All of them achieve reasonable performance and present baselines for future works.
TLR3 and TLR7 RNA Sensor Activation during SARS-CoV-2 Infection

(1) Background: Acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent for the coronavirus disease (COVID-19) that has led to a pandemic that began in March 2020. The role of the SARS-CoV-2 components on innate and adaptive immunity is still unknown. We investigated the possible implication of pathogen-associated molecular patterns (PAMPs)–pattern recognition receptors (PRRs) interaction. (2) Methods: We infected Calu-3/MRC-5 multicellular spheroids (MTCSs) with a SARS-CoV-2 clinical strain and evaluated the activation of RNA sensors, transcription factors, and cytokines/interferons (IFN) secretion, by quantitative real-time PCR, immunofluorescence, and ELISA. (3) Results: Our results showed that the SARS-CoV-2 infection of Calu-3/MRC-5 multicellular spheroids induced the activation of the TLR3 and TLR7 RNA sensor pathways. In particular, TLR3 might act via IRF3, producing interleukin (IL)-1α, IL-1β, IL-4, IL-6, and IFN-α and IFN-β, during the first 24 h post-infection. Then, TLR3 activates the NFκB transduction pathway, leading to pro-inflammatory cytokine secretion. Conversely, TLR7 seems to mainly act via NFκB, inducing type 1 IFN, IFN-γ, and IFN-λ3, starting from the 48 h post-infection. (4) Conclusion: We showed that both TLR3 and TLR7 are involved in the control of innate immunity during lung SARS-CoV-2 infection. The activation of TLRs induced pro-inflammatory cytokines, such as IL-1α, IL-1β, IL-4, and IL-6, as well as interferons. TLRs could be a potential target in controlling the infection in the early stages of the disease.
The Role of Mitochondria in Oocyte Maturation

With the nucleus as an exception, mitochondria are the only animal cell organelles containing their own genetic information, called mitochondrial DNA (mtDNA). During oocyte maturation, the mtDNA copy number dramatically increases and the distribution of mitochondria changes significantly. As oocyte maturation requires a large amount of ATP for continuous transcription and translation, the availability of the right number of functional mitochondria is crucial. There is a correlation between the quality of oocytes and both the amount of mtDNA and the amount of ATP. Suboptimal conditions of in vitro maturation (IVM) might lead to changes in the mitochondrial morphology as well as alternations in the expression of genes encoding proteins associated with mitochondrial function. Dysfunctional mitochondria have a lower ability to counteract reactive oxygen species (ROS) production which leads to oxidative stress. The mitochondrial function might be improved with the application of antioxidants and significant expectations are laid on the development of new IVM systems supplemented with mitochondria-targeted reagents. Different types of antioxidants have been tested already on animal models and human rescue IVM oocytes, showing promising results. This review focuses on the recent observations on oocytes’ intracellular mitochondrial distribution and on mitochondrial genomes during their maturation, both in vivo and in vitro. Recent mitochondrial supplementation studies, aiming to improve oocyte developmental potential, are summarized.
Erlotinib Promotes Ligand-Induced EGFR Degradation in 3D but Not 2D Cultures of Pancreatic Ductal Adenocarcinoma Cells

Simple Summary The EGFR is a tyrosine kinase receptor that responds to different stresses such as UV irradiation, hypoxia and drug treatment by internalizing into endosomal compartments. Receptor trafficking and degradation due to tyrosine kinase inhibitors has been widely studied in two- dimensional (2D) cell culture systems, but little is known about how cells respond to these types of drugs in more physiologically relevant models such as three-dimensional (3D) cultures, whose nanostructured properties allow cells to grow, proliferate, migrate and extend cellular processes in their 3D space. In this study, we show that EGFR suffers degradation in response to erlotinib treatment in 3D-cultured cancer cells but not in classic 2D culture systems, demonstrating that dimensionality strongly affects cell drug response. This 3D model may pave the way for the development of more physiological culture platforms to obtain mechanistic insights into how cells respond to chemotherapy. Abstract The epithelial growth factor receptor (EGFR) is a tyrosine kinase receptor that participates in many biological processes such as cell proliferation. In addition, EGFR is overexpressed in many epithelial cancers and therefore is a target for cancer therapy. Moreover, EGFR responds to lots of stimuli by internalizing into endosomes from where it can be recycled to the membrane or further sorted into lysosomes where it undergoes degradation. Two-dimensional cell cultures have been classically used to study EGFR trafficking mechanisms in cancer cells. However, it has been widely demonstrated that in 2D cultures cells are exposed to a non-physiological environment as compared to 3D cultures that provide the normal cellular conformation, matrix dimensionality and stiffness, as well as molecular gradients. Therefore, the microenvironment of solid tumors is better recreated in 3D culture models, and this is why they are becoming a more physiological alternative to study cancer physiology. Here, we develop a new model of EGFR internalization and degradation upon erlotinib treatment in pancreatic ductal adenocarcinoma (PDAC) cells cultured in a 3D self-assembling peptide scaffold. In this work, we show that treatment with the tyrosine kinase inhibitor erlotinib promotes EGFR degradation in 3D cultures of PDAC cell lines but not in 2D cultures. We also show that this receptor degradation does not occur in normal fibroblast cells, regardless of culture dimensionality. In conclusion, we demonstrate not only that erlotinib has a distinct effect on tumor and normal cells but also that pancreatic ductal adenocarcinoma cells respond differently to drug treatment when cultured in a 3D microenvironment. This study highlights the importance of culture systems that can more accurately mimic the in vivo tumor physiology.
Kaempferol Blocks the Skin Fibroblastic Interleukin 1β Expression and Cytotoxicity Induced by 12-O-tetradecanoylphorbol-13-acetate by Suppressing c-Jun N-terminal Kinase

Kaempferol, a bioflavonoid present in fruits and vegetables, has a variety of antioxidant and anti-inflammatory capacities, but the functional role of kaempferol in oxidative skin dermal damage has yet to be well studied. In this study, we examine the role of kaempferol during the inflammation and cell death caused by 12-O-tetradecanoylphorbol-13-acetate (TPA) in normal human dermal fibroblasts (NHDF). TPA (5 μM) significantly induced cytotoxicity of NHDF, where a robust increase in the interleukin (IL)-1β mRNA among the various pro-inflammatory cytokines. The skin fibroblastic cytotoxicity and IL-1β expression induced by TPA were significantly ameliorated by a treatment with 100 nM of kaempferol. Kaempferol blocked the production of the intracellular reactive oxygen species (ROS) responsible for the phosphorylation of c-Jun N-terminal kinase (JNK) induced by TPA. Interestingly, we found that kaempferol inhibited the phosphorylation of nuclear factor-kappa B (NF-κB) and the inhibitor NF-κB (IκBα), which are necessary for the expression of cleaved caspase-3 and the IL-1β secretion in TPA-treated NHDF. These results suggest that kaempferol is a functional agent that blocks the signaling cascade of the skin fibroblastic inflammatory response and cytotoxicity triggered by TPA.
Continuous Manufacturing of Cocrystals Using Solid State Shear Milling Technology

Solid state shear milling (S3M) is reported as a scalable, continuous, polymer-assisted cocrystallization technique. A specially designed milling pan was employed to provide high levels of applied shear, and the addition of a polymeric processing aid enabled generation of high stress fields. Carbamazepine–salicylic acid cocrystals were produced with 5–25 wt % of poly(ethylene oxide) (PEO). A systematic study was carried out to understand the effect of process variables on properties and performance of the cocrystals. S3M offers an important new route for continuous manufacturing of pharmaceutical cocrystals.
Burden of Malnutrition among Children and Adolescents with Cerebral Palsy in Arabic-Speaking Countries: A Systematic Review and Meta-Analysis

Background: We aimed to estimate the burden and underlying risk factors of malnutrition among children and adolescents with cerebral palsy in Arabic-speaking countries. Methods: OVID Medline, OVID Embase, CINAHL via EBSCO, Cochrane Library, and SCOPUS databases were searched up to 3 July 2021. Publications were reviewed to identify relevant papers following pre-defined inclusion/exclusion criteria. Two reviewers independently assessed the studies for inclusion. Data extraction was independently completed by two reviewers. Descriptive and pooled analysis has been reported. Results: From a total of 79 records screened, nine full-text articles were assessed for eligibility, of which seven studies met the inclusion criteria. Study characteristics, anthropometric measurements used, and nutritional outcome reported varied between the studies. The included studies contained data of total 400 participants aged 1–18 years. Overall, (mean: 71.46%, 95% confidence interval: 55.52–85.04) of children with cerebral palsy had at least one form of malnutrition. Severe gross motor function limitation, feeding difficulties, cognitive impairment and inadequate energy intake were the commonly reported underlying risk factors for malnutrition among children with cerebral palsy. Conclusions: The burden of malnutrition is high among children with cerebral palsy in Arabic-speaking countries. More research is needed for better understanding of this public health issue in these countries.
Common and Unique Genetic Background between Attention-Deficit/Hyperactivity Disorder and Excessive Body Weight

Comorbidity studies show that children with ADHD have a higher risk of being overweight and obese than healthy children. This study aimed to assess the genetic alternations that differ between and are shared by ADHD and excessive body weight (EBW). The sample consisted of 743 Polish children aged between 6 and 17 years. We analyzed a unique set of genes and polymorphisms selected for ADHD and/or obesity based on gene prioritization tools. Polymorphisms in the KCNIP1, SLC1A3, MTHFR, ADRA2A, and SLC6A2 genes proved to be associated with the risk of ADHD in the studied population. The COMT gene polymorphism was one that specifically increased the risk of EBW in the ADHD group. Using the whole-exome sequencing technique, we have shown that the ADHD group contains rare and protein-truncating variants in the FBXL17, DBH, MTHFR, PCDH7, RSPH3, SPTBN1, and TNRC6C genes. In turn, variants in the ADRA2A, DYNC1H1, MAP1A, SEMA6D, and ZNF536 genes were specific for ADHD with EBW. In this way, we confirmed, at the molecular level, the existence of genes specifically predisposing to EBW in ADHD patients, which are associated with the biological pathways involved in the regulation of the reward system, intestinal microbiome, and muscle metabolism.
A Health Technology Assessment in Maxillofacial Cancer Surgery by Using the Six Sigma Methodology

Squamous cell carcinoma represents the most common cancer affecting the oral cavity. At the University of Naples “Federico II”, two different antibiotic protocols were used in patients undergoing oral mucosa cancer surgery from 2006 to 2018. From 2011, there was a shift; the combination of Cefazolin plus Clindamycin as a postoperative prophylactic protocol was chosen. In this paper, a health technology assessment (HTA) is performed by using the Six Sigma and DMAIC (Define, Measure, Analyse, Improve, Control) cycle in order to compare the performance of the antibiotic protocols according to the length of hospital stay (LOS). The data (13 variables) of two groups were collected and analysed; overall, 136 patients were involved. The American Society of Anaesthesiologist score, use of lymphadenectomy or tracheotomy and the presence of infections influenced LOS significantly (p-value < 0.05) in both groups. Then, the groups were compared: the overall difference between LOS of the groups was not statistically significant, but some insights were provided by comparing the LOS of the groups according to each variable. In conclusion, in light of the insights provided by this study regarding the comparison of two antibiotic protocols, the utilization of DMAIC cycle and Six Sigma tools to perform HTA studies could be considered in future research.
Aptasensor for the Detection of Mycobacterium tuberculosis in Sputum Utilising CFP10-ESAT6 Protein as a Selective Biomarker

A portable electrochemical aptamer-antibody based sandwich biosensor has been designed and successfully developed using an aptamer bioreceptor immobilized onto a screen-printed electrode surface for Mycobacterium tuberculosis (M. tuberculosis) detection in clinical sputum samples. In the sensing strategy, a CFP10-ESAT6 binding aptamer was immobilized onto a graphene/polyaniline (GP/PANI)-modified gold working electrode by covalent binding via glutaraldehyde linkage. Upon interaction with the CFP10-ESAT6 antigen target, the aptamer will capture the target where the nano-labelled Fe3O4/Au MNPs conjugated antibody is used to complete the sandwich format and enhance the signal produced from the aptamer–antigen interaction. Using this strategy, the detection of CFP10-ESAT6 antigen was conducted in the concentration range of 5 to 500 ng/mL. From the analysis, the detection limit was found to be 1.5 ng/mL, thereby demonstrating the efficiency of the aptamer as a bioreceptor. The specificity study was carried out using bovine serum albumin (BSA), MPT64, and human serum, and the result demonstrated good specificity that is 7% higher than the antibody–antigen interaction reported in a previous study. The fabricated aptasensor for M. tuberculosis analysis shows good reproducibility with an relative standard deviation (RSD) of 2.5%. Further analysis of M. tuberculosis in sputum samples have shown good correlation with the culture method with 100% specificity and sensitivity, thus making the aptasensor a promising candidate for M. tuberculosis detection considering its high specificity and sensitivity with clinical samples.
Numerical Modeling of Phase Transformations in Dual-Phase Steels Using Level Set and SSRVE Approaches

Development of a reliable model of phase transformations in steels presents significant challenges, not only metallurgical but also connected to numerical solutions and implementation. The model proposed in this paper is dedicated to austenitic transformation during heating and ferritic transformation during cooling. The goal was to find a solution which allows for the decreasing of computing time without noticeable decreasing the accuracy and reliability of the model. Proceedings to achieve this goal were twofold. Statistically Similar Representative Volume Element was used as a representation of the microstructure. It allowed for the reducing of the complexity of the computational domain. For the purpose of the model, carbon diffusion was assumed to be the main driving force for both transformations. A coupled finite element–level set method was used to describe growth of a new phase. The model was verified and validated by comparing the results with the experimental data. Numerical tests of the model were performed for the industrial intercritical annealing process.
Molecular Interactions Driving Intermediate Filament Assembly

Given the role of intermediate filaments (IFs) in normal cell physiology and scores of IF-linked diseases, the importance of understanding their molecular structure is beyond doubt. Research into the IF structure was initiated more than 30 years ago, and some important advances have been made. Using crystallography and other methods, the central coiled-coil domain of the elementary dimer and also the structural basis of the soluble tetramer formation have been studied to atomic precision. However, the molecular interactions driving later stages of the filament assembly are still not fully understood. For cytoplasmic IFs, much of the currently available insight is due to chemical cross-linking experiments that date back to the 1990s. This technique has since been radically improved, and several groups have utilized it recently to obtain data on lamin filament assembly. Here, we will summarize these findings and reflect on the remaining open questions and challenges of IF structure. We argue that, in addition to X-ray crystallography, chemical cross-linking and cryoelectron microscopy are the techniques that should enable major new advances in the field in the near future.
Crosstalk between Autophagy and Inflammatory Processes in Cancer

Inflammation is an adaptive response to tissue injury, which is a critical process in order to restore tissue functionality and homeostasis. The association between inflammation and cancer has been a topic of interest for many years, not only inflammatory cells themselves but also the chemokines and cytokines they produce, which affect cancer development. Autophagy is an intracellular self-degradative process providing elimination of damaged or dysfunctional organelles under stressful conditions such as nutrient deficiency, hypoxia, or chemotherapy. Interestingly, the signaling pathways that are involved in cancer-associated inflammation may regulate autophagy as well. These are (1) the toll-like receptor (TLR) signaling cascade, (2) the reactive oxygen species (ROS) signaling pathway, (3) the inflammatory cytokine signaling pathway, and (4) the IκB kinase (IKK)/Nuclear factor-κB (NF-κB) signaling axis. Moreover, the studies on the context-specific functions of autophagy during inflammatory responses in cancer will be discussed here. On that basis, we focus on autophagy inhibitors and activators regulating inflammatory process in cancer as useful candidates for enhancing anticancer effects. This review summarizes how the autophagic process regulates these key inflammatory processes and vice versa in various cancers.