Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Respiratory Syncytial Virus Infection in a Human T Cell Line Is Hampered at Multiple Steps

Human respiratory syncytial virus (HRSV) is the most frequent cause of severe respiratory disease in children. The main targets of HRSV infection are epithelial cells of the respiratory tract, and the great majority of the studies regarding HRSV infection are done in respiratory cells. Recently, the interest on respiratory virus infection of lymphoid cells has been growing, but details of the interaction of HRSV with lymphoid cells remain unknown. Therefore, this study was done to assess the relationship of HRSV with A3.01 cells, a human CD4+ T cell line. Using flow cytometry and fluorescent focus assay, we found that A3.01 cells are susceptible but virtually not permissive to HRSV infection. Dequenching experiments revealed that the fusion process of HRSV in A3.01 cells was nearly abolished in comparison to HEp-2 cells, an epithelial cell lineage. Quantification of viral RNA by RT-qPCR showed that the replication of HRSV in A3.01 cells was considerably reduced. Western blot and quantitative flow cytometry analyses demonstrated that the production of HRSV proteins in A3.01 was significantly lower than in HEp-2 cells. Additionally, using fluorescence in situ hybridization, we found that the inclusion body-associated granules (IBAGs) were almost absent in HRSV inclusion bodies in A3.01 cells. We also assessed the intracellular trafficking of HRSV proteins and found that HRSV proteins colocalized partially with the secretory pathway in A3.01 cells, but these HRSV proteins and viral filaments were present only scarcely at the plasma membrane. HRSV infection of A3.01 CD4+ T cells is virtually unproductive as compared to HEp-2 cells, as a result of defects at several steps of the viral cycle: Fusion, genome replication, formation of inclusion bodies, recruitment of cellular proteins, virus assembly, and budding.
Too Much of a Good Thing: Defining Antimicrobial Therapeutic Targets to Minimize Toxicity

Antimicrobials are a common cause of drug toxicity. Understanding the relationship between systemic antimicrobial exposure and toxicity is necessary to enable providers to take a proactive approach to prevent undesired drug effects. When an exposure threshold has been defined that predicts drug toxicity, therapeutic drug monitoring (TDM) can be performed to assure drug exposure does not exceed the defined threshold. Although some antimicrobials have well‐defined dose‐dependent toxicities, many other exposure‐toxicity relationships have either not been well‐defined or, in some cases, not been evaluated at all. In this review, we examine the relationship between exposures and toxicities for antibiotic, antifungal, and antiviral agents. Furthermore, we classify these relationships into four categories: known association between drug exposure and toxicity such that clinical implementation of a specific exposure threshold associated with toxicity for TDM is supported (category 1), known association between drug exposure and toxicity but the specific exposure threshold associated with toxicity is undefined (category 2), association between drug exposure and toxicity has been suggested but relationship is poorly defined (category 3), and no known association between drug exposure and toxicity (category 4). Further work to define exposure‐toxicity thresholds and integrate effective TDM strategies has the potential to minimize many of the observed antimicrobial toxicities.
Dipeptidyl peptidase‐4 inhibitor‐related bullous pemphigoid: A comparative study of 100 patients with bullous pemphigoid and diabetes mellitus

Dipeptidyl peptidase‐4 inhibitor (DPP4i)‐associated bullous pemphigoid (BP) has been emerging but whether it has genotype or phenotype differences from idiopathic BP (IBP) remains to be determined. We aimed to compare clinical characteristics, genetic susceptibility, laboratory features, disease activity, and outcomes between DPP4i‐associated BP (DBP) and IBP occurring among patients with diabetes mellitus type 2 (T2DM). Medical records of patients diagnosed with BP and T2DM from January 2009 to December 2019 were retrospectively reviewed, and patients were categorized into DBP or IBP groups. Of 100 patients, 23 had DBP and 77 had IBP. There was no difference in the Bullous Pemphigoid Disease Activity Index score between the two groups; however, the score for urticaria and erythema was less in DBP (p < 0.001), indicating a non‐inflammatory phenotype. The HLA‐DQB1*03:01 allele was more commonly present in the DBP than IBP cases (odds ratio = 5.33 [95% confidence interval, 1.11–28.59], p = 0.016). The absolute eosinophil count was significantly lower in the DBP group (p = 0.002). Likewise, eosinophilic spongiosis was found less frequently in DBP cases (p = 0.005). Patients in the DBP group had a significantly higher percentage of complete remission on therapy compared to the IBP counterpart (p = 0.026) after DPP4i discontinuation. Moreover, the mean maximum dosage of prednisolone administrated per patient was significantly lower in drug‐related cases (p = 0.012). In conclusion, our cohort in Thai patients with T2DM confirms the differences between phenotype and genotype characteristics of DBP and IBP. We emphasize the importance of drug discontinuation in all DPP4i‐related cases because doing so may lead to a better disease outcome.
Phaseolus vulgaris-rhizobia symbiosis increases the phosphorus uptake and symbiotic N2 fixation under insoluble phosphorus

Five north Tunisian native rhizobia were tested in symbiosis with ‘Coco-blanc’ variety under two phosphorus (P) supplies [P-sufficient and insoluble P (IP)] at 250 μmol P plant−1. At flowering stage, responses against IP were assessed and indicated that inoculation with P.Ps. 09 produced a high nodule biomass (0.12g). Similarly, P.Tb. 09 produced 0.08 g nodule biomass under both P and P.Bj. 09 that significantly increased nodule number under IP. Shoot biomass exhibited high dry weight with P.Tb. 09 and CIAT899 (1.6 g plant−1). Inoculation with CIAT899 produced a high root biomass under both P. Analysis of a halo diameter of clear zone rounding each colony under IP indicated that P.Tb. 09 has developed high halo Ø (1.7cm). These variations were associated under IP with a decrease of pH by P.Ar. 09 and with increase in shoot phosphatase activity by P.Ar. 09, P.Bj. 09, P.OM. 09 and P.Ps. 09. The use of P-efficient rhizobia may constitute an adaptive mechanism against P-deficiency tolerance.
Development of an Aerosol System for Uniformly Depositing Bacillus Anthracis Spore Particles on Surfaces

After the anthrax incidents in October 2001, several techniques used for sampling surfaces for biological agents were found to be inadequately validated, especially at low surface loadings. Therefore a test chamber was developed to produce sample sets having targeted surface concentrations of dry biological agent simulant. Dry spore aerosols were initially dispersed into the chamber at relatively high air concentrations, and monitored in real time. The concentration decay (due to stirred settling and dilution) was measured and when the targeted air concentration was reached, the sampling surfaces were uncovered and exposed to the settling particles until >99% of the particles had settled. Multiple agar plates were used to estimate the true colony-forming-unit (CFU) surface concentration. The uniformity of surface loadings was limited by random deposition of small numbers of particles on the surfaces (Poisson distribution) and was characterized by how much greater the observed variability was than that predicted by Poisson statistics. The flow-enhanced powder mixture appeared to affect the spores' ability to grow on the agar medium. Three ways of analyzing the agar plates were used to evaluate the effect of spore coatings on viability and to differentiate between number of spore-containing particles and the number of spores. The presence of spore agglomerates re-suspended by various sample handling activities in the chamber further increased the variability of deposited particles. Based on estimated airborne particle concentration, it was possible to predict mean agar plate concentrations within narrow confidence intervals (CI) at low (4.8 CFU, 95% CI 3.5–6.4), medium (20 CFU, 95% CI 17–23), and high (160 CFU, 95% CI 140–190) concentrations.
Inflammatory Response Mechanisms of the Dentine–Pulp Complex and the Periapical Tissues

The macroscopic and microscopic anatomy of the oral cavity is complex and unique in the human body. Soft-tissue structures are in close interaction with mineralized bone, but also dentine, cementum and enamel of our teeth. These are exposed to intense mechanical and chemical stress as well as to dense microbiologic colonization. Teeth are susceptible to damage, most commonly to caries, where microorganisms from the oral cavity degrade the mineralized tissues of enamel and dentine and invade the soft connective tissue at the core, the dental pulp. However, the pulp is well-equipped to sense and fend off bacteria and their products and mounts various and intricate defense mechanisms. The front rank is formed by a layer of odontoblasts, which line the pulp chamber towards the dentine. These highly specialized cells not only form mineralized tissue but exert important functions as barrier cells. They recognize pathogens early in the process, secrete antibacterial compounds and neutralize bacterial toxins, initiate the immune response and alert other key players of the host defense. As bacteria get closer to the pulp, additional cell types of the pulp, including fibroblasts, stem and immune cells, but also vascular and neuronal networks, contribute with a variety of distinct defense mechanisms, and inflammatory response mechanisms are critical for tissue homeostasis. Still, without therapeutic intervention, a deep carious lesion may lead to tissue necrosis, which allows bacteria to populate the root canal system and invade the periradicular bone via the apical foramen at the root tip. The periodontal tissues and alveolar bone react to the insult with an inflammatory response, most commonly by the formation of an apical granuloma. Healing can occur after pathogen removal, which is achieved by disinfection and obturation of the pulp space by root canal treatment. This review highlights the various mechanisms of pathogen recognition and defense of dental pulp cells and periradicular tissues, explains the different cell types involved in the immune response and discusses the mechanisms of healing and repair, pointing out the close links between inflammation and regeneration as well as between inflammation and potential malignant transformation.
Electronic Health Interventions in the Case of Multiple Sclerosis: From Theory to Practice

(1) Background: eHealth interventions play a growing role in shaping the future healthcare system. The integration of eHealth interventions can enhance the efficiency and quality of patient management and optimize the course of treatment for chronically ill patients. In this integrative review, we discuss different types of interventions, standards and advantages of quality eHealth approaches especially for people with multiple sclerosis (pwMS). (2) Methods: The electronic databases PubMed, Cochrane and Web of Science were searched to identify potential articles for eHealth interventions in pwMS; based on 62 articles, we consider different ways of implementing health information technology with various designs. (3) Results: There already exist some eHealth interventions for single users with a single-use case, interventions with a social setting, as well as eHealth interventions that integrate various single and social interventions and even those that may be used additionally for complex use cases. A key determinant of consumer acceptance is a high-quality user-centric design for healthcare practitioners and pwMS. In pwMS, the different neurological disabilities should be considered, and particular attention must be paid to the course of the treatment and the safety processes of each treatment option. (4) Conclusion: Depending on the field of application and the respective users, interventions are designed for single, social, integrated or complex use. In order to be accepted by their target group, interventions must be beneficial and easy to use.
A Supervised Segmentation Network for Hyperspectral Image Classification

Recently, deep learning has drawn broad attention in the hyperspectral image (HSI) classification task. Many works have focused on elaborately designing various spectral-spatial networks, where convolutional neural network (CNN) is one of the most popular structures. To explore the spatial information for HSI classification, pixels with its adjacent pixels are usually directly cropped from hyperspectral data to form HSI cubes in CNN-based methods. However, the spatial land-cover distributions of cropped HSI cubes are usually complicated. The land-cover label of a cropped HSI cube cannot simply be determined by its center pixel. In addition, the spatial land-cover distribution of a cropped HSI cube is fixed and has less diversity. For CNN-based methods, training with cropped HSI cubes will result in poor generalization to the changes of spatial land-cover distributions. In this paper, an end-to-end fully convolutional segmentation network (FCSN) is proposed to simultaneously identify land-cover labels of all pixels in a HSI cube. First, several experiments are conducted to demonstrate that recent CNN-based methods show the weak generalization capabilities. Second, a fine label style is proposed to label all pixels of HSI cubes to provide detailed spatial land-cover distributions of HSI cubes. Third, a HSI cube generation method is proposed to generate plentiful HSI cubes with fine labels to improve the diversity of spatial land-cover distributions. Finally, a FCSN is proposed to explore spectral-spatial features from finely labeled HSI cubes for HSI classification. Experimental results show that FCSN has the superior generalization capability to the changes of spatial land-cover distributions.
Investigation of some numerical issues in a chemistry-transport model: Gas-phase simulations

Many numerical strategies have been specifically developed for chemistry-transport models. Since no exact solutions are available for 3-D real problems, there are only few insights to choose between alternative numerical schemes and approximations, or to estimate the performance discrepancy between two approaches. However it is possible to assess the importance of numerical approximations through the comparison of different strategies. We estimated the impact of several numerical schemes for advection, diffusion and stiff chemistry. We also addressed operator splitting with different methods and operator orders. The study is performed with a gas-phase Eulerian model from the modeling platform Polyphemus. It is applied to ozone forecasts mainly over Europe, with focus on a few key species: ozone, nitric oxide, nitrogen dioxide, sulfur dioxide and hydroxy radical. The outcome is a ranking of the most sensitive numerical choices. It stresses the prominent impact of the advection scheme and of the splitting time step.
Diagnosis and Treatment of Pediatric Brain Tumors.

OBJECTIVE Tumors of the brain and spine make up about 20% of all childhood cancers; they are the second most common form of childhood cancer after leukemia. Brain tumors are the most common solid tumor in children. Symptoms depend on a variety of factors, including location of the tumor, age of child, and rate of tumor growth. The aim of study was to present our experience with the diagnosis and treatment of brain tumors in children. PATIENTS AND METHODS The aim of this study is to analyze clinicopathological characteristics, treatments, complications, and outcomes in children with brain tumors. This study is a retrospective analysis of 27 consecutive patients younger than 16 years and hospitalized for surgical treatment of brain tumors. Intracranial hypertension, neurological status, radiological computerized tomography (CT) or magnetic resonance imaging (MRI) findings, tumor localization, type of resection, hydrocephalus treatment, histopathology, complications, and outcome were analyzed. RESULTS Twenty-seven surgeries were performed in patients for brain tumors. There were 9 females and 18 males. The average patient age was 7.8 years. There were 11 (40%) children with astrocytoma; of these, there were 9 (82%) pilocytic astrocytomas and 2 (18%) ordinary histopathological subtypes of high-grade tumors. CONCLUSION As with any cancer, prognosis and long-term survival vary greatly from child to child. Prompt medical attention and aggressive therapy are important for the best prognosis. Continuous follow-up care is essential for a child diagnosed with a brain tumor.
Co-Occurrence of Symptoms and Gut Microbiota Composition Before Neoadjuvant Chemotherapy and Radiation Therapy for Rectal Cancer: A Proof of Concept

Purpose: To examine a) whether there are significant differences in gut microbial diversity and in the abundance of gut microbial taxa; and b) differences in predicted functional pathways of the gut microbiome between those participants with high co-occurring symptoms and those with low co-occurring symptoms, prior to neoadjuvant chemotherapy and radiation therapy (CRT) for rectal cancer. Methods: Rectal cancer patients (n = 41) provided stool samples for 16 S rRNA gene sequencing and symptom ratings for fatigue, sleep disturbance, and depressive symptoms prior to CRT. Descriptive statistics were computed for symptoms. Gut microbiome data were analyzed using QIIME2, LEfSe, and the R statistical package. Results: Participants with high co-occurring symptoms (n = 19) had significantly higher bacterial abundances of Ezakiella, Clostridium sensu stricto, Porphyromonas, Barnesiella, Coriobacteriales Incertae Sedis, Synergistiaceae, Echerichia-Shigella, and Turicibacter compared to those with low co-occurring symptoms before CRT (n = 22). Biosynthesis pathways for lipopolysaccharide, L-tryptophan, and colanic acid building blocks were enriched in participants with high co-occurring symptoms. Participants with low co-occurring symptoms showed enriched abundances of Enterococcus and Lachnospiraceae, as well as pathways for β-D-glucoronosides, hexuronide/hexuronate, and nicotinate degradation, methanogenesis, and L-lysine biosynthesis. Conclusion: A number of bacterial taxa and predicted functional pathways were differentially abundant in patients with high co-occurring symptoms compared to those with low co-occurring symptoms before CRT for rectal cancer. Detailed examination of bacterial taxa and pathways mediating co-occurring symptoms is warranted.
Evidence for distinct mechanisms of small molecule inhibitors of filovirus entry

Many small molecules have been identified as entry inhibitors of filoviruses. However, a lack of understanding of the mechanism of action for these molecules limits further their development as anti-filoviral agents. Here we provide evidence that toremifene and other small molecule entry inhibitors have at least three distinctive mechanisms of action and lay the groundwork for future development of anti-filoviral agents. The three mechanisms identified here include: (1) direct binding to the internal fusion loop region of Ebola virus glycoprotein (GP); (2) the HR2 domain is likely the main binding site for Marburg virus GP inhibitors and a secondary binding site for some EBOV GP inhibitors; (3) lysosome trapping of GP inhibitors increases drug exposure in the lysosome and further improves the viral inhibition. Importantly, small molecules targeting different domains on GP are synergistic in inhibiting EBOV entry suggesting these two mechanisms of action are distinct. Our findings provide important mechanistic insights into filovirus entry and rational drug design for future antiviral development.
Factors associated with clinical interpretation of tracheal wash fluid from dogs with respiratory disease: 281 cases (2012‐2017)

Abstract Background Clinicians face several dilemmas regarding tracheal washes (TWs) for the diagnosis of respiratory disease, including method and prediction of bacterial growth from cytology results. Objective To compare cytology and culture of endotracheal and transtracheal washes and identify factors associated with discordancy and bacterial growth. Animals Two hundred forty‐five dogs with respiratory disease. Methods Retrospective study. Tracheal wash submissions were included if cellularity was sufficient for cytologic interpretation and aerobic cultures were performed. Collection technique, cytology, bacterial growth, and antibiotic history were analyzed. Results Fewer transtracheal specimens (9/144, 6.3%) were excluded for hypocellularity than endotracheal (28/174, 16.1%); otherwise, results were similar and were combined. Of 281 specimens with cellularity sufficient for interpretation, 97 (34.5%) had bacteria on cytology and 191 (68.0%) had bacterial growth. Cytology positive/culture negative discordancy was uncommon (8/97, 8%). Cytology negative/culture positive discordancy was frequent (102/184, 55.4%), but occurred less often (28/184, 14.2%) when only 1+ growth or greater was considered positive. Oropharyngeal contamination was associated with bacterial growth, but not discordancy. No association was found between antibiotic administration and bacterial growth. Conclusions and Clinical Importance Endotracheal wash fluid, in particular, should be screened for gross mucus or turbidity to maximize the likelihood of an adequate specimen. Otherwise, endotracheal and transtracheal specimens were similar. Presence of bacteria on cytology was a good predictor of any growth, while their absence was a good predictor of the absence of growth of 1+ or more. Recent antibiotic usage should not discourage TW culture if there is compelling reason to avoid delay.
A partial skeleton of Carcharias gustrowensis ( Winkler , 1875 ) ( Chondrichthyes , Odontaspididae ) including embryos , a chi-maeriod dorsal fin spine and a myliobatoid tail spine from the Oligocene of Germany

Les restes d’un requin femelleenceinte et de ses huit embryons ont etc decouverts dans les Fischschiefer de 1’argiliere Frauenweiler pres de Rauenberg (Oligocene, Allemagne) ainsi q’une epine caudale de myliobatoide et une epine dorsale de chimaeroi'de. Le requin est identifie comme Carcharias gustrowensis (Winkler, 1875). La dentition et les vertebres du specimen adulte et de ses embryons, le squelette de la nageoire pectorale de Fadulte et la morphologic des denticules dermiques des embryons sont ddcrits et