Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding Contextual Factors Effects and Their Implications for Italian Physiotherapists: Findings from a National Cross-Sectional Study

An online cross-sectional survey was conducted using Google Docs software. The aim was to understand the management of contextual factors and to identify which are most relevant and which clinicians underestimate. A total of 1250 physiotherapists were chosen from the database of the Manual Therapists group mailing list (GTM-IFOMPT MO) from July to August 2020. A total of 699 responses were received that were considered valid (56%). Participants (40.83%) identified contextual factors (CFs) as “any element, even involuntary, with which the patient interacts during treatment”. Physiotherapists individually chose the representation of CF with the “therapeutic relationship” (82.9%), followed by “therapeutic setting” (75.8%). This choice differed between participants belonging to different age groups. Participants favor communication strategies (76.93%). More than half (57.88%) pay attention to patient involvement during the course of care; and in response to the patients’ doubts about the use of treatments with limited scientific efficacy, they suggest different medical treatments. The patient’s previous clinical experience is not considered significant and does not influence the choice of treatment. Subsequently, however, the participants reported that they stimulate the patients’ positive expectations of the success of the clinical outcome (45.27%). Knowledge of contextual factors in physiotherapy appears limited and very heterogeneous. Future research could increase the focus on professional development.
Characterization of Immune Responses to SARS-CoV-2 and Other Human Pathogenic Coronaviruses Using a Multiplex Bead-Based Immunoassay

Serological assays that simultaneously detect antibodies to multiple targets of SARS-CoV-2 and to other structurally related coronaviruses provide a holistic picture of antibody response patterns. Well-validated multiplex immunoassays are scarce. Here, we evaluated the performance of an 11-plex serological assay capable of detecting antibodies directed to four antigenic targets of SARS-CoV-2 and to S1 proteins of other human pathogenic coronaviruses. We used 620 well-characterized sera (n = 458 seropositive and n = 110 seronegative for SARS-CoV-2 in the pre-SARS-CoV-2 era and n = 52 seronegative for SARS-CoV-2 in the era of SARS-CoV-2) as positive and negative standards. We calculated the sensitivity, specificity, as well as positive and negative predictive values, including a 95% confidence interval. The difference in mean fluorescence intensity (95% CI) was used to assess a potential cross-reaction between antibodies to SARS-CoV-2 and the other coronaviruses. The sensitivity (95% CI) of detecting anti-SARS-CoV-2 antibodies to four antigenic targets ranged from 83.4% (76.7–86.7) to 93.7% (91.0–95.7) and the specificity from 98.2% (93.6–99.8) to 100% (96.7–100). We observed no obvious cross-reaction between anti-SARS-CoV-2 antibodies and antibodies to the other coronaviruses except for SARS-CoV-1. The high sensitivity and specificity warrant a reliable utilization of the assay in population-based seroprevalence surveys or vaccine efficacy studies.
Stable Isotope Abundance and Fractionation in Human Diseases

The natural abundance of heavy stable isotopes (13C, 15N, 18O, etc.) is now of considerable importance in many research fields, including human physiology. In fact, it varies between tissues and metabolites due to isotope effects in biological processes, that is, isotope discriminations between heavy and light isotopic forms during enzyme or transporter activity. The metabolic deregulation associated with many diseases leads to alterations in metabolic fluxes, resulting in changes in isotope abundance that can be identified easily with current isotope ratio technologies. In this review, we summarize the current knowledge on changes in natural isotope composition in samples (including various tissues, hair, plasma, saliva) found in patients compared to controls, caused by human diseases. We discuss the metabolic origin of such isotope fractionations and highlight the potential of using isotopes at natural abundance for medical diagnosis and/or prognostic.
A Reliable and Standardizable Differential PCR and qPCR Methodology Assesses HER2 Gene Amplification in Gastric Cancer

Simple Summary Patients with gastric cancer may present variations in the copy number of the HER2 gene in their primary tumors. The techniques used to detect these variations and HER2 overexpression render false positive and negative results with high frequency, and robust methodologies are required to assess this amplification and confidently select patients who may benefit from HER2-specific monoclonal antibody-based therapies. We addressed this issue by molecular biology techniques using DNA samples from tumor or distal tissue of gastric cancer patients. The HER2 and a control (IFNG) gene were subjected to differential (diffPCR) and quantitative PCR (qPCR). A cut-off point above which patients can be deemed positive was set based on the HER2/IFNG ratio, achieved using DNA from 30 healthy donors. Both, diffPCR and qPCR, identified the presence of somatic HER2 amplifications in 25% of patients in DNA from tumoral tissue, but not distal, paired tissue samples. Immunohistochemistry and immunofluorescence detected HER2 overexpression in tumor, but not distal, tissue of the patients previously identified as HER2+ by diffPCR and qPCR. Thus, the molecular biology-based techniques herein reported can identify patients with HER2 gene amplification and suitable for immune-based therapies. Abstract We have applied two PCR techniques, differential PCR (diffPCR) and qPCR for the identification of HER2 gene amplifications in genomic DNA of tumor and distal gastric samples from patients with gastric cancer. The diffPCR technique consists of the simultaneous amplification of the HER2 gene and a housekeeping gene by conventional PCR and the densitometric analysis of the bands obtained. We established a cut-off point based on the mean and standard deviation analyzing the DNA of 30 gastric tissues from patients undergoing non-cancer gastrectomy. diffPCR and qPCR yielded consistent results. HER2-overexpression was detected in 25% of patients and was further confirmed by immunohistochemistry and immunofluorescence. The approaches herein described may serve as complementary and reliable methods to assess HER2 amplification.
Cerebrolysin Combined with Rehabilitation Enhances Motor Recovery and Prevents Neural Network Degeneration in Ischemic Stroke Patients with Severe Motor Deficits

The objective of this study was to evaluate whether Cerebrolysin combined with rehabilitation therapy supports additional motor recovery in stroke patients with severe motor impairment. This study analyzed the combined data from the two phase IV prospective, multicenter, randomized, double-blind, placebo-controlled trials. Stroke patients were included within seven days after stroke onset and were randomized to receive a 21-day treatment course of either Cerebrolysin or placebo with standardized rehabilitation therapy. Assessments were performed at baseline, immediately after the treatment course, and 90 days after stroke onset. The plasticity of the motor system was assessed by diffusion tensor imaging and resting state fMRI. In total, 110 stroke patients were included for the full analysis set (Cerebrolysin n = 59, placebo n = 51). Both groups showed significant motor recovery over time. Repeated-measures analysis of varianceshowed a significant interaction between time and type of intervention as measured by the Fugl–Meyer Assessment (p < 0.05). The Cerebrolysin group demonstrated less degenerative changes in the major motor-related white matter tracts over time than the placebo group. In conclusion, Cerebrolysin treatment as an add-on to a rehabilitation program is a promising pharmacologic approach that is worth considering in order to enhance motor recovery in ischemic stroke patients with severe motor impairment.
Patterns of Gene Expression in Cutaneous T-Cell Lymphoma: Systematic Review of Transcriptomic Studies in Mycosis Fungoides

Mycosis fungoides (MF) is the most prevalent type of skin lymphoma. In its early stages, it has a favorable prognosis. However, in its late stages, it is associated with an increased risk of mortality. This systematic review aimed to identify the transcriptomic changes involved in MF pathogenesis and progression. A literature search was conducted using the database PubMed, followed by the extraction of 2245 genes which were further filtered to 150 recurrent genes that appeared in two or more publications. Categorization of these genes identified activated pathways involved in pathways such as cell cycle and proliferation, chromosomal instability, and DNA repair. We identified 15 genes implicated in MF progression, which were involved in cell proliferation, immune checkpoints, resistance to apoptosis, and immune response. In highlighting the discrepancies in the way MF transcriptomic data is obtained, further research can focus on not only unifying their approach but also focus on the 150 pertinent genes identified in this review.
3D Clumps/Extracellular Matrix Complexes of Periodontal Ligament Stem Cells Ameliorate the Attenuating Effects of LPS on Proliferation and Osteogenic Potential

Background: The effects of lipopolysaccharide (LPS) on cell proliferation and osteogenic potential (OP) of MSCs have been frequently studied. Objective: to compare the effects of LPS on periodontal-ligament-derived mesenchymal stem cells (PDLSCs) in monolayer and 3D culture. Methods: The PDLSCs were colorimetrically assessed for proliferation and osteogenic potential (OP) after LPS treatment. The 3D cells were manually prepared by scratching and allowing them to clump up. The clumps (C-MSCs) were treated with LPS and assessed for Adenosine triphosphate (ATP) and OP. Raman spectroscopy was used to analyze calcium salts, DNA, and proline/hydroxyproline. Multiplexed ELISA was performed to assess LPS induced local inflammation. Results: The proliferation of PDLSCs decreased with LPS. On Day 28, LPS-treated cells showed a reduction in their OP. C-MSCs with LPS did not show a decrease in ATP production. Principal bands identified in Raman analysis were the P–O bond at 960 cm−1 of the mineral component, 785 cm−1, and 855 cm−1 showing qualitative changes in OP, proliferation, and proline/hydroxyproline content, respectively. ELISA confirmed increased levels of IL-6 and IL-8 but with the absence of TNF-α and IL-1β secretion. Conclusions: These observations demonstrate that C-MSCs are more resistant to the effects of LPS than cells in monolayer cell culture. Though LPS stimulation of C-MSCs creates an early pro-inflammatory milieu by secreting IL-6 and IL-8, PDLSCs possess inactivated TNF promoter and an ineffective caspase-1 activating process.
Molecular Characterization of Highly Pathogenic Avian Influenza Viruses H5N6 Detected in Denmark in 2018–2019

Beginning in late 2017, highly pathogenic avian influenza (HPAI) H5N6 viruses caused outbreaks in wild birds and poultry in several European countries. H5N6 viruses were detected in 43 wild birds found dead throughout Denmark. Most of the Danish virus-positive dead birds were found in the period from February to April 2018. However, unlike the rest of Europe, sporadic HPAI H5N6-positive dead wild birds were detected in Denmark in July, August, September, and December 2018, with the last positive bird being found in January 2019. HPAI viruses were not detected in active surveillance of apparently healthy wild birds. In this study, we use full genome sequencing and phylogenetic analysis to investigate the wild bird HPAI H5N6 viruses found in Denmark. The Danish viruses were found to be closely related to those of contemporary HPAI H5N6 viruses detected in Europe. Their sequences formed two clusters indicating that at least two or more introductions of H5N6 into Denmark occurred. Notably, all viruses detected in the latter half of 2018 and in 2019 grouped into the same cluster. The H5N6 viruses appeared to have been maintained undetected in the autumn 2018.
Characterisation of Aspergillus fumigatus Endocytic Trafficking within Airway Epithelial Cells Using High-Resolution Automated Quantitative Confocal Microscopy

The precise characterization of the mechanisms modulating Aspergillus fumigatus survival within airway epithelial cells has been impaired by the lack of live-cell imaging technologies and user-friendly quantification approaches. Here we described the use of an automated image analysis pipeline to estimate the proportion of A. fumigatus spores taken up by airway epithelial cells, those contained within phagolysosomes or acidified phagosomes, along with the fungal factors contributing to these processes. Coupling the use of fluorescent A. fumigatus strains and fluorescent epithelial probes targeting lysosomes, acidified compartments and cell membrane, we found that both the efficacy of lysosome recruitment to phagosomes and phagosome acidification determines the capacity of airway epithelial cells to contain A. fumigatus growth. Overall, the capability of the airway epithelium to prevent A. fumigatus survival was higher in bronchial epithelial than alveolar epithelial cells. Certain A. fumigatus cell wall mutants influenced phagosome maturation in airway epithelial cells. Taken together, this live-cell 4D imaging approach allows observation and measurement of the very early processes of A. fumigatus interaction within live airway epithelial monolayers.
How Does Mechanical Pearling Affect Quinoa Nutrients and Saponin Contents?

Agriculture is facing many challenges, such as climate change, drought, and salinity, which call for urgent interventions for fast adaptation and crop diversification. The introduction of high-value and stress tolerant crops such as quinoa would be a judicious solution to overcome constraints related to abiotic stress and to increase land productivity and farmers’ incomes. The implementation of quinoa in Morocco has not been supported by a full valorization program to control the quality of quinoa seeds. The novelty of this work is to assess the pearling operation as an efficient method of saponins removal as well as the determination of total residual saponins. This study aimed to evaluate the effects of several pearling durations on nutrient and saponin content of quinoa seeds of three tested varieties (Puno, Titicaca, and ICBA-Q5). Five pearling durations were tested (0, 2, 4, 6, 7, and 8 min) using a locally manufactured pearling machine. The results indicated that a pearling duration of two minutes was enough to reduce total saponin content from 0.49% to 0.09% for Puno variety, from 0.37% to 0.07% for Titicaca variety, and from 0.57% to 0.1% for ICBA-Q5 variety. Our results showed that pearling slightly reduced protein, total fat, and moisture contents for all varieties except for Puno, where total fat content slightly increased with the pearling. Puno variety had the highest seed content in terms of protein and total fat; the ICBA-Q5 variety had the lowest. Titicaca had the highest bran content in terms of protein and total fat, ICBA-Q5 had the highest bran content in terms of ash and the lowest bran content in terms of protein and total fat, and Puno had the lowest bran content in terms of ash. Pearling had no significant effect on macronutrient contents in the processed seed, but it resulted in a very highly significant difference for most of them in the bran except for Mg and S. Regarding seed content in terms of micro-nutrients, statistical analysis showed significant differences between varieties in terms of Zn, Cu, and Mn contents, but no significant difference was recorded for Fe or B. Pearling had no significant effect on seed micronutrient contents. Therefore, to retain maximum nutritional content in the quinoa and maintain quinoa integrity, it is necessary to limit the pearling duration of quinoa to two minutes, which is enough to reduce saponin content below the Codex Standard threshold (0.12%).
Association between Visceral Adipose Tissue and Non-Alcoholic Steatohepatitis Histology in Patients with Known or Suspected Non-Alcoholic Fatty Liver Disease

(1) Purpose: To determine the association between visceral adipose tissue (VAT) and proton density fat fraction (PDFF) with magnetic resonance imaging (MRI), and hepatic steatosis (HS), non-alcoholic steatohepatitis (NASH) and hepatic fibrosis (HF) in patients with known or suspected non-alcoholic fatty liver disease (NAFLD). (2) Methods: 135 subjects that had a liver biopsy performed within 3 months (bariatric cohort) or 1 month (NAFLD cohort) of an MRI exam formed the study group. VAT volume was quantified at L2-L3 level on opposed-phase images with signal intensity-based painting using a semi-quantitative software. Liver PDFF and pancreas PDFF were calculated on fat fraction maps. Liver volume (Lvol) and spleen volume (Svol) were also calculated using a semi-automated 3D volume tool available on PACS. A histological analysis was performed by an expert hepatopathologist blinded to imaging findings. (3) Results: The mean Lvol, Svol, liver PDFF, pancreas PDFF and VAT of the study population were 2492.2 mL, 381.6 mL, 13.2%, 12.7% and 120.6 mL, respectively. VAT showed moderate correlation with liver PDFF (r = 0.41, p < 0.001) and weak correlation with Lvol (r = 0.38, p < 0.001), Svol (r = 0.20, p = 0.025) and pancreas PDFF (rs = 0.29, p = 0.001). VAT, Lvol and liver PDFF were significantly higher in patients with HS (p < 0.001), NASH (p < 0.05) and HF (p < 0.05). VAT was also significantly higher in the presence of lobular inflammation (p = 0.019) and hepatocyte ballooning (p = 0.001). The cut-off VAT volumes for predicting HS, NASH and HF were 101.8 mL (AUC, 0.7), 111.8 mL (AUC, 0.64) and 111.6 mL (AUC, 0.66), respectively. (4) Conclusion: The MRI determined VAT can be used for predicting the presence of HS, NASH and HF in patients with known or suspected NAFLD.
Could a New COVID-19 Mutant Strain Undermine Vaccination Efforts? A Mathematical Modelling Approach for Estimating the Spread of B.1.1.7 Using Ontario, Canada, as a Case Study

Infections represent highly dynamic processes, characterized by evolutionary changes and events that involve both the pathogen and the host. Among infectious agents, viruses, such as Severe Acute Respiratory Syndrome-related Coronavirus type 2 (SARS-CoV-2), the infectious agent responsible for the currently ongoing Coronavirus disease 2019 (COVID-2019) pandemic, have a particularly high mutation rate. Taking into account the mutational landscape of an infectious agent, it is important to shed light on its evolution capability over time. As new, more infectious strains of COVID-19 emerge around the world, it is imperative to estimate when these new strains may overtake the wild-type strain in different populations. Therefore, we developed a general-purpose framework to estimate the time at which a mutant variant is able to take over a wild-type strain during an emerging infectious disease outbreak. In this study, we used COVID-19 as a case-study; however, the model is adaptable to any emerging pathogen. We devised a two-strain mathematical framework to model a wild- and a mutant-type viral population and fit cumulative case data to parameterize the model, using Ontario as a case study. We found that, in the context of under-reporting and the current case levels, a variant strain was unlikely to dominate until March/April 2021. The current non-pharmaceutical interventions in Ontario need to be kept in place longer even with vaccination in order to prevent another outbreak. The spread of a variant strain in Ontario will likely be observed by a widened peak of the daily reported cases. If vaccine efficacy is maintained across strains, then it is still possible to achieve high levels of immunity in the population by the end of 2021. Our findings have important practical implications in terms of public health as policy- and decision-makers are equipped with a mathematical tool that can enable the estimation of the take-over of a mutant strain of an emerging infectious disease.
Corneal Cross-Linking for Paediatric Keratoconus: A Systematic Review and Meta-Analysis

All corneal cross-linking techniques attenuated disease progression in patients with pediatric keratoconus for at least one year based on a meta-analysis. A standard and accelerated technique led to marked improvement in visual acuity. We determined the efficacy and safety of corneal cross-linking (CXL) in pediatric keratoconus by conducting a systematic review and meta-analysis. The PubMed and Cochrane databases were searched for relevant studies on the effects of standard, transepithelial, and/or accelerated CXL protocols in patients aged 18 years or younger. Standardized mean differences with 95% confidence intervals were calculated to compare the data collected at baseline and 12 months. The primary outcomes were maximum keratometry (Kmax) and uncorrected visual acuity (UCVA), and the secondary outcomes were the thinnest corneal thickness (TCT), best-corrected visual acuity (BCVA), and manifest refraction spherical equivalent or cylindrical refraction. Our search yielded 7913 publications, of which 26 were included in our systematic review and 21 were included in the meta-analysis. Standard CXL significantly improved the Kmax, UCVA, and BCVA, and significantly decreased the TCT. Accelerated CXL significantly improved UCVA and BCVA. In the transepithelial and accelerated-transepithelial CXL methods, each measurable parameter did not change after treatments. All CXL techniques attenuated disease progression in patients with pediatric keratoconus for at least one year. Standard and accelerated CXL led to marked improvement in visual acuity.