Miracle-dz/UniFAR-FTUs huggingface dataset:
Methicillin- and Vancomycin-Resistant Staphylococcus aureus From Humans and Ready-To-Eat Meat: Characterization of Antimicrobial Resistance and Biofilm Formation Ability

Methicillin-resistant and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA) are zoonotic life-threatening pathogens, and their presence in food raises a public health concern. Yet, scarce data are available regarding MRSA and VRSA in both ready-to-eat (RTE) meat and food handlers. This study was undertaken to determine the frequency, antimicrobial resistance, and biofilm-forming ability of MRSA and VRSA isolated from RTE meat (shawarma and burger) and humans (food handlers, and hospitalized patients) in Zagazig city, Sharkia Governorate, Egypt. We analyzed 176 samples (112 human samples: 72 from hospitalized patients and 40 from food handlers, 64 RTE meat samples: 38 from shawarma and 26 from burger). Using phenotypic, PCR-based identification of nuc gene and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), 60 coagulase-positive S. aureus (COPS) isolates were identified in the samples as follow: RTE meat (15/64, 23.4%), hospitalized patients (33/72, 45.8%) and food handlers (12/40, 30%). All the COPS isolates were mecA positive (and thus were classified as MRSA) and multidrug resistant with multiple antibiotic resistance indices ranging from 0.25 to 0.92. Overall, resistance to cefepime (96.7%), penicillin (88.3%), were common, followed by ampicillin-sulbactam (65%), ciprofloxacin (55%), nitrofurontoin (51.7%), and gentamicin (43.3%). VRSA was detected in 30.3% of COPS hospitalized patient’s isolates, 26.7% of COPS RTE meat isolates and 25% of COPS food handler’s isolates. VanA, vanB, or both genes were detected in 64.7, 5.9, and 29.4% of all VAN-resistant isolates, respectively. The majority of the COPS isolates (50/60, 83.3%) have biofilm formation ability and harbored icaA (76%), icaD (74%), icaC (50%), and icaB (46%) biofilm-forming genes. The bap gene was not detected in any of the isolates. The ability of MRSA and VRSA isolates to produce biofilms in addition to being resistant to antimicrobials highlight the danger posed by these potentially virulent microorganisms persisting in RTE meat, food handlers, and patients. Taken together, good hygiene practices and antimicrobial surveillance plans should be strictly implemented along the food chain to reduce the risk of colonization and dissemination of MRSA and VRSA biofilm-producing strains.
Application of Flow-Ecology Analysis to Inform Prioritization for Stream Restoration and Management Actions

A key challenge in managing flow alteration is determining the severity and pattern of alteration associated with the degradation of biological communities. Understanding these patterns helps managers prioritize locations for restoration and flow management actions. However, the choices made about how to use these flow-ecology relationships can have profound implications on management decisions (e.g., which biological endpoints, which thresholds, which seasonal flow components to use). We describe a process for using flow-ecology relationships to prioritize management actions that 1) Represents the most relevant components of the annual hydrograph, 2) Demonstrates an appropriate level of sensitivity in order to discriminate locations to inform decision making, 3) Aims to protect multiple biological assemblages, 4) Reduces misclassification of priority areas (i.e., error of omission). Our approach is based on the functional flows approach which uses multiple flow metrics that describe the frequency, timing, magnitude, duration, and rate of change of seasonal process-based components of the annual hydrograph. Using this approach, we performed a flow-ecology analysis of regional bioassessment data, through which we determined where flow alteration impacts biology and prioritized reaches for changes in flow management to protect aquatic resources in a highly urbanized region of southern California, where managing scarce water resources leads to difficult decisions about tradeoffs that require technical information. We identified three important functional flow metrics for each of two bioassessment indices, one based on benthic macroinvertebrates, and another based on benthic algae. Based on thresholds that describe levels of alteration as well as thresholds describing the probability of achieving a healthy biological condition, we compared nine biological threshold combinations for each index. We found instances of flow alteration that impact biological condition highly variable (0–100% of subbasins) between combinations and we present a method for finding the most appropriate combination for prioritizing locations for flow management. We apply the final thresholds to the study region and propose 16 subbasins of high priority for implementing flow management and restoration. Importantly, we show that focusing on a single biological group would result in biologically altered locations being effectively ignored.
Development and External Validation of a Dynamic Nomogram With Potential for Risk Assessment of Ruptured Multiple Intracranial Aneurysms

Background and Purpose About 20.1% of intracranial aneurysms (IAs) carriers are multiple intracranial aneurysms (MIAs) patients with higher rupture risk and worse prognosis. A prediction model may bring some potential benefits. This study attempted to develop and externally validate a dynamic nomogram to assess the rupture risk of each IA among patients with MIA. Method We retrospectively analyzed the data of 262 patients with 611 IAs admitted to the Hunan Provincial People's Hospital between November 2015 and November 2021. Multivariable logistic regression (MLR) was applied to select the risk factors and derive a nomogram model for the assessment of IA rupture risk in MIA patients. To externally validate the nomogram, data of 35 patients with 78 IAs were collected from another independent center between December 2009 and May 2021. The performance of the nomogram was assessed in terms of discrimination, calibration, and clinical utility. Result Size, location, irregular shape, diabetes history, and neck width were independently associated with IA rupture. The nomogram showed a good discriminative ability for ruptured and unruptured IAs in the derivation cohort (AUC = 0.81; 95% CI, 0.774–0.847) and was successfully generalized in the external validation cohort (AUC = 0.744; 95% CI, 0.627–0.862). The nomogram was calibrated well, and the decision curve analysis showed that it would generate more net benefit in identifying IA rupture than the “treat all” or “treat none” strategies at the threshold probabilities ranging from 10 to 60% both in the derivation and external validation set. The web-based dynamic nomogram calculator was accessible on https://wfs666.shinyapps. io/onlinecalculator/. Conclusion External validation has shown that the model was the potential to assist clinical identification of dangerous aneurysms after longitudinal data evaluation. Size, neck width, and location are the primary risk factors for ruptured IAs.
Mutation of MUC16 Is Associated With Tumor Mutational Burden and Lymph Node Metastasis in Patients With Gastric Cancer

Background Lymph node metastasis (LNM) is a critical factor in determining the prognosis of gastric cancer (GC), but its underlying mechanism remains unclear. The tumor mutational burden (TMB) has recently been recognized as a biomarker for predicting prognosis and response to immune checkpoint inhibitors, while mucin 16, cell surface associated (MUC16) is frequently mutated in GC. This study explored whether MUC16 mutation status is associated with TMB, LNM, and prognosis in patients with GC. Methods Somatic mutation data were downloaded from three GC cohorts. TMB values were calculated and associations between the TMB and clinical characteristics were analyzed. The mutational landscapes of these three GC cohorts were individually explored and visualized using waterfall diagrams. Univariate logistic regression and Kaplan-Meier survival analysis were performed to screen for mutated genes associated with LNM and overall survival (OS). Associations between MUC16 mutations and TMB, microsatellite instability (MSI), LNM, and tumor microenvironment signatures were explored. Results TMB was associated with LNM and OS in patients with GC. Analyzing the three GC cohorts (The Cancer Genome Atlas-Stomach Adenocarcinoma, International Cancer Genome Consortium [ICGC]-China, and ICGC-Japan) revealed that MUC16 was one of the most frequently mutated genes in patients with GC. MUC16 mutations were associated with better prognosis, including lower LNM rates and improved OS rates. In addition, MUC16 mutation status was associated with TMB and MSI statuses. Fifteen upregulated and 222 downregulated genes were identified in patients with MUC16 mutations, compared to in those in patients with wild-type MUC16. An altered tumor microenvironment signature was also identified in GC samples with MUC16 mutations; it was characterized by significantly decreased infiltration regarding stromal cells, CD4+ T cells, and macrophages. Conclusion MUC16 mutation status was associated with TMB, microsatellite status, LNM, and survival in patients with GC. These findings may provide new insights into the mechanism of LNM and could act as a signpost for prognostic predictions and immunotherapy guidance for patients with GC.
Phytogenics From Sage and Lemon Verbena Promote Growth, Systemic Immunity and Disease Resistance in Atlantic Salmon (Salmo salar)

The transcriptomic response of the head kidney, the main lymphohematopoietic tissue of the body, was evaluated in Atlantic salmon (Salmo salar) smolts fed a functional feed containing a phytogenic rich in verbascoside and triterpenic compounds like ursolic acid. Fish (initial body weight = 55.0 ± 0.1 g) were fed two experimental diets (40% crude protein, 22% crude fat; 21.6 MJ/kg gross energy) that only differed in the phytogenic content (0.1% inclusion). Each diet has six replicates and was tested over a period of 133 days. The tested zootechnical feed additive a medicinal plant leaf extract (MPLE) obtained from sage (Salvia officinalis) and lemon verbena (Lippia citriodora). At the end of the trial, smolts fed the MPLE diet were heavier than their congeners from the control group (271.5 ± 7.9 g vs. 240.2 ± 19.3 g, respectively; P < 0.05). Feed conversion ratio (FCR) values in fish fed the control diet were higher than those in fish fed the MPLE diet (FCRcontrol diet = 1.27 ± 0.08 vs. FCR0.1% MPLE diet = 1.08 ± 0.05; P < 0.05). The immunomodulatory properties of the functional diet were evaluated by means of an in vivo challenge with Aeromonas salmonicida subsp. salmonicida (1 × 107 CFU mL–1). The microarray analysis of head kidney samples from both dietary groups revealed 1,178 differentially expressed genes (802 upregulated and 376 downregulated). Among them, several biological processes related to immunity were identified in fish fed the MPLE diet (i.e., interferon-gamma-mediated signaling pathway, antigen processing and presentation of peptide antigen via MHC class II, autophagy, regulation of i-kappaB kinase/NF-kappaB signaling, and leukocyte activation). Results from the bacterial challenge showed that survival rates were higher in smolts from the MPLE group (90.6 ± 6.4%) in comparison to the control group (60.7 ± 13.5%), confirming the functional benefits of the phytogenic in terms of host’s immunity and disease resistance. Biological processes such as cytoskeleton organization and regulation of cellular protein metabolic process detected in fish fed the MPLE diet supported the metabolic changes related to increased somatic growth promoted. The present findings showed that the inclusion at 0.1% of the tested MPLE obtained from sage and lemon verbena in diets for Atlantic salmon smolts promoted somatic growth, and enhanced their systemic immune response and reduced mortality when fish were challenged with A. salmonicida cumulative, the causative agent of furunculosis in salmonids.
Deciphering the Relationship Between Free and Vesicular Hemoglobin in Stored Red Blood Cell Units

Red blood cells (RBCs) release hemoglobin (Hb)-containing extracellular vesicles (EVs) throughout their lifespan in the circulation, and especially during senescence, by spleen-facilitated vesiculation of their membrane. During ex vivo aging under blood bank conditions, the RBCs lose Hb, both in soluble form and inside EVs that accumulate as a part of storage lesion in the supernatant of the unit. Spontaneous hemolysis and vesiculation are increasingly promoted by the storage duration, but little is known about any physiological linkage between them. In the present study, we measured the levels of total extracellular and EV-enclosed Hb (EV-Hb) in units of whole blood (n = 36) or packed RBCs stored in either CPDA-1 (n = 99) or in CPD-SAGM additive solution (n = 46), in early, middle, and late storage. The spectrophotometry data were subjected to statistical analysis to detect possible correlation(s) between storage hemolysis and EV-Hb, as well as the threshold (if any) that determines the area of this dynamic association. It seems that the percentage of EV-Hb is negatively associated with hemolysis levels from middle storage onward by showing low to moderate correlation profiles in all strategies under investigation. Moreover, 0.17% storage hemolysis was determined as the potential cut-off, above which this inverse correlation is evident in non-leukoreduced CPDA units. Notably, RBC units with hemolysis levels > 0.17% are characterized by higher percentage of nanovesicles (<100 nm) over typical microvesicles (100–400 nm) compared with the lower hemolysis counterparts. Our results suggest an ordered loss of Hb during RBC accelerated aging that might fuel targeted research to elucidate its mechanistic basis.
PREDIÇÃO DA ADUBAÇÃO NITROGENADA ATRAVÉS DA UTILIZAÇÃO DO ÍNDICE SPAD PARA O ALGODOEIRO NO SEMI-ÁRIDO.

Avaliacoes precisas dos teores foliares de nitrogenio sao necessarias no gerenciamento de uma cultura para garantir alta produtividade e evitar danos ambientais. Entretanto, metodos laboratoriais para quantificar o N foliar, alem de caros sao demorados. O objetivo desse trabalho foi avaliar a precisao das leituras do SPAD-502 da Minolta, na determinacao precoce do teor foliar de N e na produtividade do algodoeiro, proporcionando subsidios para recomendacao da adubacao nitrogenada em tempo real. Adotou-se delineamento de blocos casualizados com 3 repeticoes. Os tratamentos foram dispostos em esquema de parcela subdividida no tempo, tendo nas parcelas os efeitos de quatro doses de N, (0, 90, 180 e 270 kg ha-1) e nas subparcelas quatro epocas de avaliacao, (40, 60, 80, 100 DAE). Foram determinados teores foliares de N, indice SPAD e a produtividade. As leituras obtidas com o SPAD-502 possibilitaram a obtencao de modelos matematicos para a predicao do teor de N nas folhas do algodoeiro de maneira simples e com elevado grau de precisao. E possivel corrigir a deficiencia de nitrogenio na cultura e restaurar total ou parcialmente sua produtividade, usando doses suplementares delimitadas a partir do indice SPAD entre os 40 e 90 dias apos a emergencia aplicada via fertirrigacao. Palavras-chaves: Gossypium hirsutum, nutricao mineral, oxido nitroso, danos ambientais, produtividade. ABSTRACT Accurate assessments of leaf nitrogen content are needed to ensure high productivity in crop management and prevent environmental damages. However, laboratory methods of quantifying N content are costly and time consuming. The objective of this study was to evaluate the accuracy of the Minolta SPAD-502 readings for early assessing of leaf N content and cotton yield, providing subsidies for real-time recommendation of nitrogen fertilization. It was used a randomized block design with 3 replications. The treatments were arranged in a split-plot in time, where was evaluated the effects of four N doses, (0, 90, 180 and 270 kg ha-1) into plots, and the effects of four evaluation seasons, (40, 60, 80, 100 DAE) in the subplots. Were done assessments when was determined the leaf nitrogen content and the SPAD index during the evaluation seasons and at the harvest the yield. The readings of the SPAD-502 allowed figure out mathematical models for predicting the content of N in cotton leaves in a simple way and with high precision. It’s possible to correct the crop nitrogen deficiency and restore partially or totally the yield, using nitrogen supplementation rates obtained with SPAD index from 40 until 90 days after emergence applied by fertirigation. Keywords: Gossypium hirsutum, mineral nutrition, nitrous oxide, environmental damages, yield.
An Experiment of Two Dimensional Roughness Effect on Hypersonic Boundary-Layer Transition

tripping method of the hypersonic boundary layer is conducted at a freestream Mach number of 7.1 and a wide range of stagnation conditions with a 5 deg half angle sharp cone at Hypersonic Wind Tunnel #1, JAXA. Aerodynamic heating distributions and fluctuations of the surface pressure are measured both with and without roughness elements. A wavy-wall roughness with a wave length of 2 99%, intending to introduce ‘right’ frequency disturbances into the boundary layer, resulted in delaying the transition at nominal conditions instead of expediting it. Comparisons in power spectrum densities of the surface pressure fluctuations between test conditions as well as roughness types were made to discuss the roll of the wavy-wall roughness. Based on the accurate repeatability results obtained in the present tests, it is concluded that the wavy-wall roughness has a delaying eect on transition at a specific condition.
Gut Mucosal Microbiome Signatures of Colorectal Cancer Differ According to BMI Status

Background Carrying excess body weight is a strong risk factor for colorectal cancer (CRC) development with ~11% of CRC cases in Europe linked to being overweight. The mechanisms through which excess body weight influences CRC development are not well understood but studies suggest the involvement of the presence of chronic low-grade inflammation and changes in the gut microbiota are involved. Aim To compare the mucosal associated microbiota of patients with CRC to understand whether carrying excess body weight was associated with a unique CRC microbial signature. Methods Microbiota signatures from colonic mucosal biopsies of CRC lesions and adjacent normal mucosal samples from 20 patients with overt CRC were compared with 11 healthy controls to see if having a BMI of >25 kg/m2 influenced colonic microbial composition. Results Colonic mucosa samples from patients with CRC confirmed previously reported over-abundance of Fusobacteria associated with CRC but also an increase in Fusobacteria and Prevotella were associated with a BMI of >25 kg/m2. Correlation analysis of bacterial taxa indicated co-exclusive relationships were more common in CRC patients with a BMI >25 kg/m2 with an increase in transphylum relationships also seen in this patient group. Conclusions The findings suggest that gut microbiota composition in patients with CRC is influenced by BMI status. Further understanding/defining these differences will provide valuable information in terms of developing novel pre-onset screening and providing post-manifestation therapeutic intervention.
Effects of switching from a metered dose inhaler to a dry powder inhaler on climate emissions and asthma control: post-hoc analysis

Objective To compare the effects of switching from a pressurised metered dose inhaler (pMDI)-based to a dry powder inhaler (DPI)-based maintenance therapy versus continued usual care on greenhouse gas emissions (carbon dioxide equivalents, CO2e) and asthma control. Methods This post-hoc analysis was based on a subset of 2236 (53%) patients from the Salford Lung Study in Asthma who at baseline were using a pMDI-based controller therapy. During the study patients were randomised to fluticasone furoate/vilanterol (FF/VI) via the ELLIPTA DPI (switched from pMDI to DPI) (n=1081) or continued their usual care treatment (n=1155), and were managed in conditions close to everyday clinical practice. Annual CO2e (kg) was calculated for the total number of maintenance and rescue inhalers prescribed. Asthma control was assessed by the proportion of ACT responders (composite of ACT total score ≥20 and/or increase from baseline ≥3). Results The groups were well matched for demographic characteristics and baseline Asthma Control Test (ACT) total score (mean age: 49 years; mean ACT score: usual care, 16.6; FF/VI, 16.5). Annual CO2e kg per patient (maintenance plus rescue therapy) was significantly lower with FF/VI DPI treatment (‘switch’ group) than usual care (least squares geometric mean 108 kg (95% CI 102 to 114) vs 240 kg (95% CI 229 to 252), p<0.001). Asthma control was consistently superior over the 12 months in the FF/VI DPI group compared with usual care. Conclusions Patients switching from a pMDI-based to a DPI-based maintenance therapy more than halved their inhaler carbon footprint without loss of asthma control. The remaining inhaler carbon footprint could be reduced through switches from pMDI to DPI rescue medications or alternative lower-carbon footprint rescue inhalers if available. Asthma control improved in both groups, with greater control demonstrated in those initiated on FF/VI DPI. Trial registration number NCT01706198.
Consumption and effects of caffeinated energy drinks in young people: an overview of systematic reviews and secondary analysis of UK data to inform policy

Background This overview and analysis of UK datasets was commissioned by the UK government to address concerns about children’s consumption of caffeinated energy drinks and their effects on health and behaviour. Methods We searched nine databases for systematic reviews, published between 2013 and July 2021, in English, assessing caffeinated energy drink consumption by people under 18 years old (children). Two reviewers rated or checked risk of bias using AMSTAR2, and extracted and synthesised findings. We searched the UK Data Service for country-representative datasets, reporting children’s energy-drink consumption, and conducted bivariate or latent class analyses. Results For the overview, we included 15 systematic reviews; six reported drinking prevalence and 14 reported associations between drinking and health or behaviour. AMSTAR2 ratings were low or critically low. Worldwide, across reviews, from 13% to 67% of children had consumed energy drinks in the past year. Only two of the 74 studies in the reviews were UK-based. For the dataset analysis, we identified and included five UK cross-sectional datasets, and found that 3% to 32% of children, across UK countries, consumed energy drinks weekly, with no difference by ethnicity. Frequent drinking (5 or more days per week) was associated with low psychological, physical, educational and overall well-being. Evidence from reviews and datasets suggested that boys drank more than girls, and drinking was associated with more headaches, sleep problems, alcohol use, smoking, irritability, and school exclusion. GRADE (Grading of Recommendations, Assessment, Development and Evaluation) assessment suggests that the evidence is weak. Conclusions Weak evidence suggests that up to a third of children in the UK consume caffeinated energy drinks weekly; and drinking 5 or more days per week is associated with some health and behaviour problems. Most of the evidence is from surveys, making it impossible to distinguish cause from effect. Randomised controlled trials are unlikely to be ethical; longitudinal studies could provide stronger evidence. PROSPERO registrations CRD42018096292 – no deviations. CRD42018110498 – one deviation - a latent class analysis was conducted.