Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effects of a Varied Gold Shell Thickness on Iron Oxide Nanoparticle Cores in Magnetic Manipulation, T1 and T2 MRI Contrasting, and Magnetic Hyperthermia

Fe3O4–Au core–shell magnetic-plasmonic nanoparticles are expected to combine both magnetic and light responsivity into a single nanosystem, facilitating combined optical and magnetic-based nanotheranostic (therapeutic and diagnostic) applications, for example, photothermal therapy in conjunction with magnetic resonance imaging (MRI) imaging. To date, the effects of a plasmonic gold shell on an iron oxide nanoparticle core in magnetic-based applications remains largely unexplored. For this study, we quantified the efficacy of magnetic iron oxide cores with various gold shell thicknesses in a number of popular magnetic-based nanotheranostic applications; these included magnetic sorting and targeting (quantifying magnetic manipulability and magnetophoresis), MRI contrasting (quantifying benchtop nuclear magnetic resonance (NMR)-based T1 and T2 relaxivity), and magnetic hyperthermia therapy (quantifying alternating magnetic-field heating). We observed a general decrease in magnetic response and efficacy with an increase of the gold shell thickness, and herein we discuss possible reasons for this reduction. The magnetophoresis speed of iron oxide nanoparticles coated with the thickest gold shell tested here (ca. 42 nm) was only ca. 1% of the non-coated bare magnetic nanoparticle, demonstrating reduced magnetic manipulability. The T1 relaxivity, r1, of the thick gold-shelled magnetic particle was ca. 22% of the purely magnetic counterpart, whereas the T2 relaxivity, r2, was 42%, indicating a reduced MRI contrasting. Lastly, the magnetic hyperthermia heating efficiency (intrinsic loss power parameter) was reduced to ca. 14% for the thickest gold shell. For all applications, the efficiency decayed exponentially with increased gold shell thickness; therefore, if the primary application of the nanostructure is magnetic-based, this work suggests that it is preferable to use a thinner gold shell or higher levels of stimuli to compensate for losses associated with the addition of the gold shell. Moreover, as thinner gold shells have better magnetic properties, have previously demonstrated superior optical properties, and are more economical than thick gold shells, it can be said that “less is more”.
Whole Genome Characterization and Evolutionary Analysis of G1P[8] Rotavirus A Strains during the Pre- and Post-Vaccine Periods in Mozambique (2012–2017)

Mozambique introduced the Rotarix® vaccine (GSK Biologicals, Rixensart, Belgium) into the National Immunization Program in September 2015. Although G1P[8] was one of the most prevalent genotypes between 2012 and 2017 in Mozambique, no complete genomes had been sequenced to date. Here we report whole genome sequence analysis for 36 G1P[8] strains using an Illumina MiSeq platform. All strains exhibited a Wa-like genetic backbone (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Phylogenetic analysis showed that most of the Mozambican strains clustered closely together in a conserved clade for the entire genome. No distinct clustering for pre- and post-vaccine strains were observed. These findings may suggest no selective pressure by the introduction of the Rotarix® vaccine in 2015. Two strains (HJM1646 and HGM0544) showed varied clustering for the entire genome, suggesting reassortment, whereas a further strain obtained from a rural area (MAN0033) clustered separately for all gene segments. Bayesian analysis for the VP7 and VP4 encoding gene segments supported the phylogenetic analysis and indicated a possible introduction from India around 2011.7 and 2013.0 for the main Mozambican clade. Continued monitoring of rotavirus strains in the post-vaccine period is required to fully understand the impact of vaccine introduction on the diversity and evolution of rotavirus strains.
Photons to Formate: A Review on Photocatalytic Reduction of CO2 to Formic Acid

Rising levels of atmospheric carbon dioxide due to the burning and depletion of fossil fuels is continuously raising environmental concerns about global warming and the future of our energy supply. Renewable energy, especially better utilization of solar energy, is a promising method for CO2 conversion and chemical storage. Research in the solar fuels area is focused on designing novel catalysts and developing new conversion pathways. In this review, we focus on the photocatalytic reduction of CO2 primarily in its neutral pH species of carbonate to formate. The first two-electron photoproduct of carbon dioxide, a case for formate (or formic acid) is made in this review based on its value as; an important chemical feedstock, a hydrogen storage material, an intermediate to methanol, a high-octane fuel and broad application in fuel cells. This review focuses specifically on the following photocatalysts: semiconductors, phthalocyanines as photosensitizers and membrane devices and metal-organic frameworks.
Pharmacogenetic Study of Trabectedin-Induced Severe Hepatotoxicity in Patients with Advanced Soft Tissue Sarcoma

Simple Summary Trabectedin is a cytotoxic drug used for the treatment of advanced soft tissue sarcoma. One of the most frequent side effects is hepatotoxicity, which occurs in nearly 40% of patients. In this pharmacogenetic study, we aimed to identify genetic polymorphisms that could impair the functionality of liver proteins—as metabolic enzymes or membrane transporters—involved in the production and the elimination of trabectedin and/or its metabolites from hepatocytes. In a prospective cohort of 63 patients, we showed that some variants of P-gp and MRP2 transporters and the well-known CYP3A5*3 variant were associated with hepatotoxicity. With these findings, we provide new biomarkers that might be useful to prevent the risk of hepatotoxicity in patients treated with trabectedin. However, this study is limited by the low number of patients included and should be validated on larger cohorts before any clinical application. Abstract Hepatotoxicity is an important concern for nearly 40% of the patients treated with trabectedin for advanced soft tissue sarcoma (ASTS). The mechanisms underlying these liver damages have not yet been elucidated but they have been suggested to be related to the production of reactive metabolites. The aim of this pharmacogenetic study was to identify genetic variants of pharmacokinetic genes such as CYP450 and ABC drug transporters that could impair the trabectedin metabolism in hepatocytes. Sixty-three patients with ASTS from the TSAR clinical trial (NCT02672527) were genotyped by next-generation sequencing for 11 genes, and genotype–toxicity association analyses were performed with R package SNPassoc. Among the results, ABCC2 c.1249A allele (rs2273697) and ABCG2 intron variant c. -15994T (rs7699188) were associated with an increased risk of severe cytolysis, whereas ABCC2 c.3563A allele had a protective effect, as well as ABCB1 variants rs2032582 and rs1128503 (p-value < 0.05). Furthermore, CYP3A5*1 rs776746 (c.6986A > G) increased the risk of severe overall hepatotoxicity (p = 0.012, odds ratio (OR) = 5.75), suggesting the implication of metabolites in the hepatotoxicity. However, these results did not remain significant after multiple analysis correction. These findings need to be validated on larger cohorts of patients, with mechanistic studies potentially being able to validate the functional consequences of these variants.
Promoting parkrun to patients using the general practice website: a qualitative exploration of ‘parkrun practice’ websites

Background The parkrun practice initiative is a widely accessible and low-cost approach in primary care, which promotes patient and staff health and wellbeing through increased physical activity and volunteering opportunities. The parkrun practice Toolkit offers guidance to practices on how to promote parkrun. One recommendation is to include a parkrun page on the practice website, or a link to the parkrun website. How practices are presenting this information is unknown. Aim To explore how parkrun practices are using their websites to promote parkrun, including the content and format of information presented and variety of promotion methods used, in order to provide recommendations for inclusion in the Toolkit. Design & setting Qualitative content analysis of a sample of parkrun practice websites. Method The websites of 114 practices that reported using their websites for parkrun promotion were systematically searched and the content analysed. Results Five main types of content were identified, namely: what parkrun or parkrun practice is; activities and events; addressing patients’ concerns; benefits of parkrun; and practical information. While there were similarities in the information provided, there were variations in presentation. Websites ranged from being extensive and highly informative, to minimal amounts of text or solely images. Conclusion Findings highlight the variability that currently exists across parkrun practice websites. Including a link on the homepage would assist patients to find information on parkrun and clarify the information that can be found. Suggestions are made on the type of information and how it could be presented to be further developed for inclusion in the Toolkit.
Chronic cigarette smoke exposure and pneumococcal infection induce oropharyngeal microbiota dysbiosis and contribute to long-lasting lung damage in mice

Environmental factors, such as cigarette smoking or lung infections, may influence chronic obstructive pulmonary disease (COPD) progression by modifying the respiratory tract microbiome. However, whether the disease itself induces or maintains dysbiosis remains undefined. In this longitudinal study, we investigated the oropharyngeal microbiota composition and disease progression of mice (in cages of 5–10 mice per cage) before, during and up to 3 months after chronic cigarette smoke exposure or exposure to room air for 6 months. Cigarette smoke exposure induced pulmonary emphysema measurable at the end of exposure for 6 months, as well as 3 months following smoke exposure cessation. Using both classical culture methods and 16S rRNA sequencing, we observed that cigarette smoke exposure altered the relative composition of the oropharyngeal microbiota and reduced its diversity (P <0.001). More than 60 taxa were substantially reduced after 6 months of smoke exposure (P <0.001) However, oropharyngeal microbiota disordering was reversed 3 months after smoke exposure cessation and no significant difference was observed compared to age-matched control mice. The effects of lung infection with Streptococcus pneumoniae on established smoke-induced emphysema and on the oropharyngeal microbiota were also evaluated. Inoculation with S. pneumoniae induced lung damage and altered the microbiota composition for a longer time compared to control groups infected but not previously exposed to smoke (P=0.01). Our data demonstrate effects of cigarette smoke and pneumococcus infection leading to altered microbiota and emphysema development. The reversal of the disordering of the microbiota composition, but not lung damage, following smoke exposure cessation and after clearance of infection suggest that changes in lung structure are not sufficient to sustain a disordered microbiota in mice. Whether changes in the airway microbiota contribute to inducing emphysema requires further investigation.
The Optimization of a Novel Hydrogel—Egg White-Alginate for 2.5D Tissue Engineering of Salivary Spheroid-Like Structure

Hydrogels have been used for a variety of biomedical applications; in tissue engineering, they are commonly used as scaffolds to cultivate cells in a three-dimensional (3D) environment allowing the formation of organoids or cellular spheroids. Egg white-alginate (EWA) is a novel hydrogel which combines the advantages of both egg white and alginate; the egg white material provides extracellular matrix (ECM)-like proteins that can mimic the ECM microenvironment, while alginate can be tuned mechanically through its ionic crosslinking property to modify the scaffold’s porosity, strength, and stiffness. In this study, a frozen calcium chloride (CaCl2) disk technique to homogenously crosslink alginate and egg white hydrogel is presented for 2.5D culture of human salivary cells. Different EWA formulations were prepared and biologically evaluated as a spheroid-like structure platform. Although all five EWA hydrogels showed biocompatibility, the EWA with 1.5% alginate presented the highest cell viability, while EWA with 3% alginate promoted the formation of larger size salivary spheroid-like structures. Our EWA hydrogel has the potential to be an alternative 3D culture scaffold that can be used for studies on drug-screening, cell migration, or as an in vitro disease model. In addition, EWA can be used as a potential source for cell transplantation (i.e., using this platform as an ex vivo environment for cell expansion). The low cost of producing EWA is an added advantage.
Challenging behavior of nursing home residents during COVID-19 measures in the Netherlands

Abstract Objectives From the perspective of the nursing home (NH) practitioners, to gain understanding of (1) whether challenging behavior in NH residents changed during the COVID-19 measures, (2) whether the practitioners’ involvement in the treatment of challenging behavior changed, (3) what can be learned from the experience of NH staff. Methods A mixed methods study with a survey in 323 NH practitioners (psychologists, elderly care physicians, nurse practitioners) in the Netherlands, and in-depth interviews in 16 NH practitioners. Nonparametric analyses were used to compare estimated proportions of residents with increased and with decreased challenging behavior. Content analyses were conducted for open-ended questions and in-depth interviews. Results Participants reported changes in challenging behavior with slightly higher proportions for increased (Q1/Mdn/Q3: 12.5%, 21.7%, 30.8%) than for decreased (8.7%, 14.8%, 27.8%, Z = –2.35, p = .019) challenging behavior. Half of the participants reported that their work load increased and work satisfaction worsened during the measures. Different strategies were described to respond to the effects of COVID-19 measures, such as video calls, providing special areas for residents to meet their loved ones, adjusting activities, and reducing the exposure to negative news. Conclusions Because COVID-19 measures resulted in both increased and decreased challenging behavior in NH residents, it is important to monitor for their potential long lasting effects. Increased work load and worsened work satisfaction of the NH staff, together with the changes in type of challenging behavior, indicate that the harmful effects of the anti-pandemic measures should be taken seriously.
The Benefits of Vitamin D Supplementation for Athletes: Better Performance and Reduced Risk of COVID-19

The COVID-19 pandemic is having major economic and personal consequences for collegiate and professional sports. Sporting events have been canceled or postponed, and even when baseball and basketball seasons resumed in the United States recently, no fans were in attendance. As play resumed, several players developed COVID-19, disrupting some of the schedules. A hypothesis now under scientific consideration is that taking vitamin supplements to raise serum 25-hydroxyvitamin D [25(OH)D] concentrations could quickly reduce the risk and/or severity of COVID-19. Several mechanisms have been identified through which vitamin D could reduce the risks of infection and severity, death, and long-haul effects of COVID-19: (1) inducing production of cathelicidin and defensins to reduce the survival and replication of the SARS-CoV-2 virus; (2) reducing inflammation and the production of proinflammatory cytokines and risk of the “cytokine storm” that damages the epithelial layer of the lungs, heart, vascular system, and other organs; and (3) increasing production of angiotensin-converting enzyme 2, thus limiting the amount of angiotensin II available to the virus to cause damage. Clinical trials have confirmed that vitamin D supplementation reduces risk of acute respiratory tract infections, and approximately 30 observational studies have shown that incidence, severity, and death from COVID-19 are inversely correlated with serum 25(OH)D concentrations. Vitamin D supplementation is already familiar to many athletes and sports teams because it improves athletic performance and increases playing longevity. Thus, athletes should consider vitamin D supplementation to serve as an additional means by which to reduce risk of COVID-19 and its consequences.
Prediction of putative epitope‐based vaccine against all corona virus strains for the Chinese population: Approach toward development of vaccine

Currently, the whole world is facing the coronavirus disease‐19 pandemic. As of now, approximately 0.15 million people around the globe are infected with the novel coronavirus. In the last decade, two strains of the coronavirus family, severe acute respiratory syndrome‐related coronavirus and Middle East respiratory syndrome coronavirus, also resulted in epidemics in south Asian and the Middle Eastern countries with high mortality rate. This scenario demands the development of a putative vaccine which may provide immunity against all current and new evolving coronavirus strains. In this study, we designed an epitope‐based vaccine using an immunoinformatic approach. This vaccine may protect against all coronavirus strains. The vaccine is developed by considering the geographical distribution of coronavirus strains and host genetics (Chinese population). Nine experimentally validated epitopes sequences from coronavirus strains were used to derive the variants considering the conservancy in all strains. Further, the binding affinities of all derived variants were checked with most abundant human leukocyte antigen alleles in the Chinese population. Three major histocompatibility complex (MHC) Class I epitopes from spike glycoprotein and nucleoprotein showed sufficient binding while one MHC Class II epitope from spike glycoprotein was found to be an effective binder. A cocktail of these epitopes gave more than 95% population coverage in the Chinese population. Moreover, molecular dynamics simulation supported the aforementioned predictions. Further, in vivo studies are needed to confirm the immunogenic potential of these vaccines.
Rejoinder to “Nonparametric variable importance assessment using machine learning techniques”

IL highlight the relationship between our proposed measures and the Breiman-Cutler family of variable importance measures (BC-VIMs). Indeed, apart from how the reducedmodel is defined, our procedures do fall under the umbrella of BC-VIMs. However, we arrive at these procedures from a somewhat different perspective than in the existing literature, and this distinction has important repercussions on both interpretation and inference. While we make this point explicit and expand on it in various directions in WGSC, we summarize it below. For this, it is useful to delineate the various definitions and objectives of variable importance assessment—in this discussion, we focus on what we believe are the two predominant perspectives on variable importance. Traditionally, the objective in variable importance assessment is to quantify the importance of a variable (or set of variables) within the confines of a given (possibly black box) prediction algorithm. For example, BC-VIMs play a key role in helping to interpret a fitted algorithm, leading to their tremendous popularity in the machine learning literature. The BC-VIM estimand must be interpreted relative to the fitted algorithm, and helps us to understand the extent to which a fitted model makes use of features. In the notation of IL, a BC-VIM is typically given by
Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes

The pneumococcus causes serious diseases such as pneumonia, sepsis, and meningitis and is a major cause of morbidity and mortality worldwide. Serotype 1 accounts for the majority of invasive pneumococcal disease cases in sub-Saharan Africa but is rarely found during nasopharyngeal carriage. ABSTRACT Streptococcus pneumoniae is a frequent colonizer of the human nasopharynx and a major cause of life-threating invasive infections such as pneumonia, meningitis and sepsis. Over 1 million people die every year due to invasive pneumococcal disease (IPD), mainly in developing countries. Serotype 1 is a common cause of IPD; however, unlike other serotypes, it is rarely found in the carrier state in the nasopharynx, which is often considered a prerequisite for disease. The aim of this study was to understand this dichotomy. We used murine models of carriage and IPD to characterize the pathogenesis of African serotype 1 (sequence type 217) pneumococcal strains obtained from the Queen Elizabeth Central Hospital in Blantyre, Malawi. We found that ST217 pneumococcal strains were highly virulent in a mouse model of invasive pneumonia, but in contrast to the generally accepted assumption, can also successfully establish nasopharyngeal carriage. Interestingly, we found that cocolonizing serotypes may proliferate in the presence of serotype 1, suggesting that acquisition of serotype 1 carriage could increase the risk of developing IPD by other serotypes. RNA sequencing analysis confirmed that key virulence genes associated with inflammation and tissue invasiveness were upregulated in serotype 1. These data reveal important new insights into serotype 1 pathogenesis, with implications for carriage potential and risk of invasive disease through interactions with other cocolonizing serotypes, an often-overlooked factor in transmission and disease progression. IMPORTANCE The pneumococcus causes serious diseases such as pneumonia, sepsis, and meningitis and is a major cause of morbidity and mortality worldwide. Serotype 1 accounts for the majority of invasive pneumococcal disease cases in sub-Saharan Africa but is rarely found during nasopharyngeal carriage. Understanding the mechanisms leading to nasopharyngeal carriage and invasive disease by this serotype can help reduce its burden on health care systems worldwide. In this study, we also uncovered the potential impact of serotype 1 on disease progression of other coinfecting serotypes, which can have important implications for vaccine efficacy. Understanding the interactions between different serotypes during nasopharyngeal carriage may lead to improved intervention methods and therapies to reduce pneumococcal invasive disease levels.