Miracle-dz/UniFAR-FTUs huggingface dataset:
First wave of COVID-19 did not reach the homeless population in Aarhus.

INTRODUCTION The deadly coronavirus disease 2019 (COVID-19) has rapidly become a pandemic affecting the whole world. Lower health literacy and higher mortality rates in the homeless and vulnerable population compared with the background population potentially leaves this group or people more exposed to COVID-19. This study assessed the vulnerable population of Aarhus in relation to COVID-19 infection. METHODS Participants were tested during a six-day period in April and a four-day period in June at drop-in centres, injection rooms and homeless shelters in Aarhus. Oropharyngeal swab tests were performed and analysed with real-time quantitative polymerase chain reaction. Test days in June were supplemented with lateral flow tests for immunoglobulin (Ig) G and IgM. Prevalence and corresponding Wilson 95% confidence intervals were computed. RESULTS We tested 295 individuals in April and 141 individuals in June. All oropharyngeal swabs were COVID-19 negative. The lateral flow tests were IgM-positive in six of 129 individuals (4.7%) and IgG-positive less than five of 129 (less than 3.9%) individuals. On the day of testing, COVID-19 symptoms such as fever, coughing and/or sore throat were found in 63 of 240 (26.3%) of the participants in April and in 26 of 123 (21.1%) in June. In the April testing round, 175 of 291 (59.9%) reported to be born in Denmark. The corresponding number for the June testing round was 84 of 138 (60.9%). CONCLUSIONS Despite their vulnerable profile, the vulnerable citizens tested in Aarhus were not infected with COVID-19 at the testing day and very few participants carried antibodies. FUNDING Testing was funded by Aarhus University Hospital. TRIAL REGISTRATION not relevant.
A non‐radioactive DNA synthesis assay demonstrates that elements of the Sigma 1278b Mip1 mitochondrial DNA polymerase domain and C‐terminal extension facilitate robust enzyme activity

The yeast DNA polymerase gamma, Mip1, is a useful tool to investigate the impact of orthologous human disease variants on mitochondrial DNA (mtDNA) replication. However, Mip1 is characterized by a C‐terminal extension (CTE) that is not found on orthologous metazoan DNA polymerases, and the CTE is required for robust enzymatic activity. Two MIP1 alleles exist in standard yeast strains, encoding Mip1[S] or Mip1[Σ]. Mip1[S] is associated with reduced mtDNA stability and increased error rates in vivo. Although the Mip1[S] allele was initially identified in S288c, the Mip1[Σ] allele is widely present among available yeast genome sequences, suggesting that it is the wild‐type (WT) allele. We developed a novel non‐radioactive polymerase gamma assay to assess Mip1 functioning at its intracellular location, the mitochondrial membrane. Membrane fractions were isolated from yeast cells expressing full‐length or CTE truncation variants of Mip1[S] or a chimeric Mip1[S] isoform harboring the Mip1[Σ]‐specific T661 residue (cMip1 T661). Relative incorporation of digoxigenin (DIG)‐11‐deoxyuridine monophosphate (DIG‐dUMP) by cMip1 T661 was higher than that by Mip1[S]. A cMip1 T661variant lacking 175 C‐terminal residues maintained WT levels of DIG‐dUMP incorporation, whereas the C‐terminal variant lacking 205 residues displayed a significant decrease in incorporation. Newly synthesized DIG‐labeled DNA decreased during later phases of reactions carried out at 37°C, suggesting temperature‐sensitive destabilization of the polymerase domain and/or increased shuttling of the nascent DNA into the exonuclease domain. Comparative analysis of Mip1 enzyme functions using our novel assay has further demonstrated the importance of the CTE and T661 encoded by MIP1[Σ] in yeast mtDNA replication.
Use of Essential Oils in Veterinary Medicine to Combat Bacterial and Fungal Infections

Essential oils (EOs) are secondary metabolites of plants employed in folk medicine for a long time thanks to their multiple properties. In the last years, their use has been introduced in veterinary medicine, too. The study of the antibacterial properties of EOs is of increasing interest, because therapies with alternative drugs are welcome to combat infections caused by antibiotic-resistant strains. Other issues could be resolved by EOs employment, such as the presence of antibiotic residues in food of animal origin and in environment. Although the in vitro antimicrobial activity of EOs has been frequently demonstrated in studies carried out on bacterial and fungal strains of different origins, there is a lack of information about their effectiveness in treating infections in animals. The scientific literature reports some studies about in vitro EOs’ activity against animal clinical bacterial and fungal isolates, but in vivo studies are very scanty. The use of EOs in therapy of companion and farm animals should follow careful studies on the toxicity of these natural products in relation to animal species and route of administration. Moreover, considering the different behavior of EOs in relation to both species and strain pathogen, before starting a therapy, an aromatogram should be executed to choose the oil with the best antimicrobial activity.
Electronic Sun Journal Versus Self‐report Sun Diary: A Comparison of Recording Personal Sunlight Exposure Methods

This research compared personal sunlight exposure times monitored electronically within suburban Australian environments against self‐report paper journals for determining the timing and total duration of individual exposure to daily solar radiation. A total of 90 Electronic Sun Journal (ESJ) daily readings and self‐report timing and duration estimates of exposure for weekend and weekdays were compared. A Wilcoxon ranked sign test showed a significant difference (V = 157, P < 0.001) between the duration of exposure recorded electronically and the duration of exposure that was self‐reported in a diary. There was also found to be a statistically significant difference between total exposure time measured using both methods for weekends (V = 10, P < 0.001) and weekdays (V = 87, P < 0.001). General trends in outdoor exposure timing confirmed that the most frequent daily exposures received over the weekend occurred between 1 and 2 h earlier than the most frequent exposures received on weekdays. This preliminary research found that exposure durations as recorded by the ESJ were longer on the weekends compared to weekdays (W = 402, P < 0.001) and confirmed that the ESJ is a viable alternative to self‐reporting diaries.
How Hormones and MADS-Box Transcription Factors Are Involved in Controlling Fruit Set and Parthenocarpy in Tomato

Fruit set is the earliest phase of fruit growth and represents the onset of ovary growth after successful fertilization. In parthenocarpy, fruit formation is less affected by environmental factors because it occurs in the absence of pollination and fertilization, making parthenocarpy a highly desired agronomic trait. Elucidating the genetic program controlling parthenocarpy, and more generally fruit set, may have important implications in agriculture, considering the need for crops to be adaptable to climate changes. Several phytohormones play an important role in the transition from flower to fruit. Further complexity emerges from functional analysis of floral homeotic genes. Some homeotic MADS-box genes are implicated in fruit growth and development, displaying an expression pattern commonly observed for ovary growth repressors. Here, we provide an overview of recent discoveries on the molecular regulatory gene network underlying fruit set in tomato, the model organism for fleshy fruit development due to the many genetic and genomic resources available. We describe how the genetic modification of components of this network can cause parthenocarpy, discussing the contribution of hormonal signals and MADS-box transcription factors.
Microbiological and Chemical Assessment of Wastewater Discharged by Infiltration Trenches in Fractured and Karstified Limestone (SCA.Re.S. Project 2019–2020)

This study investigated the environmental contamination of groundwater as a consequence of the discharge of treated wastewater into the soil. The investigation focused on a wastewater treatment plant located in an area fractured by karst in the Salento peninsula (Apulia, Italy). Water samples were collected at four sites (raw wastewater, treated wastewater, infiltration trench, and monitoring well), monthly from May to December 2019 (with the exception of August), and were tested for (1) panel of bacteria; (2) enteric viruses; and (3) chemical substances. A gradual reduction in the concentration of bacteria, viruses and contaminants of emerging concern was observed across the profile of soil fissured by karst. All monitored bacteria were absent from the monitoring well, except for Pseudomonas aeruginosa. Pepper mild mottle virus and adenovirus were detected at all sampling sites. Personal care products and X-ray contrast media showed the greatest decrease in concentration from infiltration trench to the monitoring well, while the highest residual concentrations in the monitoring well were found for anticonvulsants (78.5%), antimicrobials (41.3%), and antipsychotic drugs (38.6%). Our results show that parameters provided by current law may not always be sufficient to evaluate the sanitary risk relating to the discharge of treated wastewater to the soil.
18F-Sodium Fluoride Positron Emission Tomography Activity Predicts the Development of New Coronary Artery Calcifications

Supplemental Digital Content is available in the text. Objective: The coronary calcium score (CCS) predicts cardiovascular disease risk in individuals with diabetes, and rate of progression of CCS is an additional and incremental marker of risk. 18F-sodium fluoride positron emission tomography (18F-NaF PET) detects early and active calcifications within the vasculature. We aimed to ascertain the relationship between 18F-NaF PET activity and CCS progression in patients with diabetes. Approach and Results: We identified individuals between 50 and 80 years with diabetes and no history of clinical coronary artery disease. Those with a CCS ≥10 were invited to undergo 18F-NaF PET scanning and then repeat CCS >2 years later. 18F-NaF PET and CCS analysis were performed on a per-coronary and a per-patient level. We compared the proportion of CCS progressors in 18F-NaF PET–positive versus 18F-NaF PET–negative coronary arteries. Forty-one participants with 163 coronary arteries underwent follow-up CCS 2.8±0.5 years later. 18F-NaF PET–positive coronary arteries (n=52) were more likely to be CCS progressors, compared with negative coronary arteries (n=111; 86.5% versus 52.3%, P<0.001). Adjusting for baseline CCS, 18F-NaF PET–positive disease was an independent predictor of subsequent CCS progression (odds ratio, 2.92 [95% CI, 1.32–6.45], P=0.008). All subjects (100%, 15/15) with ≥2 18F-NaF–positive coronary arteries progressed in CCS. Conclusions: In subjects with diabetes, 18F-NaF PET positivity at baseline, independently predicted the progression of calcifications within the coronary arteries 2.8 years later. These findings suggest 18F-NaF PET may be a promising technique for earlier identification of patients at higher risk of cardiovascular events.
A Variable Scheduling Maintenance Culture Platform for Mammalian Cells

Cell culturing is a basic experimental technique in cell biology and medical science. However, culturing high-quality cells with a high degree of reproducibility relies heavily on expert skills and tacit knowledge, and it is not straightforward to scale the production process due to the education bottleneck. Although many automated culture systems have been developed and a few have succeeded in mass production environments, very few robots are permissive of frequent protocol changes, which are often required in basic research environments. LabDroid is a general-purpose humanoid robot with two arms that performs experiments using the same tools as humans. Combining our newly developed AI software with LabDroid, we developed a variable scheduling system that continuously produces subcultures of cell lines without human intervention. The system periodically observes the cells on plates with a microscope, predicts the cell growth curve by processing cell images, and decides the best times for passage. We have succeeded in developing a system that maintains the cultures of two HEK293A cell plates with no human intervention for 192 h.
Self-Reported Impact of the COVID-19 Pandemic on Nutrition and Physical Activity Behaviour in Dutch Older Adults Living Independently

The aim was to explore the self-reported impact of the COVID-19 pandemic on nutrition and physical activity behaviour in Dutch older adults and to identify subgroups most susceptible to this impact. Participants (N = 1119, aged 62–98 y, 52.8% female) of the Longitudinal Aging Study Amsterdam living independently completed a COVID-19 questionnaire. Questions on diagnosis, quarantine and hospitalization were asked, as well as impact of the pandemic on ten nutrition and physical activity behaviours. Associations of pre-COVID-19 assessed characteristics (age, sex, region, household composition, self-rated health, BMI, physical activity, functional limitations) with reported impact were tested using logistic regression analyses. About half of the sample (48.3–54.3%) reported a decrease in physical activity and exercise due to the pandemic. An impact on nutritional behaviour predisposing to overnutrition (e.g., snacking more) was reported by 20.3–32.4%. In contrast, 6.9–15.1% reported an impact on behaviour predisposing to undernutrition (e.g., skipping warm meals). Those who had been in quarantine (n = 123) more often reported a negative impact. Subgroups with higher risk of impact could be identified. This study shows a negative impact of the COVID-19 pandemic on nutrition and physical activity behaviour of many older adults, which may increase their risk of malnutrition, frailty, sarcopenia and disability.
Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations

Abstract Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid–liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA and other polynucleotides play a key role in modulating protein phase separation. There is currently a dearth of modelling techniques which allow one to delve deeper into how polynucleotides play the role of a modulator/promoter of LLPS in cells using computational methods. Here, we present a coarse-grained polynucleotide model developed to fill this gap, which together with our recently developed HPS model for protein LLPS, allows us to capture the factors driving protein-polynucleotide phase separation. We explore the capabilities of the modelling framework with the LAF-1 RGG system which has been well studied in experiments and also with the HPS model previously. Further taking advantage of the fact that the HPS model maintains sequence specificity we explore the role of charge patterning on controlling polynucleotide incorporation into condensates. With increased charge patterning we observe formation of structured or patterned condensates which suggests the possible roles of polynucleotides in not only shifting the phase boundaries but also introducing microscopic organization in MLOs.
Effects of Raw and Fermented Rapeseed Cake on Growth Performance, Methane Production, and Breast Meat Fatty Acid Composition in Broiler Chickens

Simple Summary The addition of raw rapeseed cake (RRC) to broiler feed may avoid the negative effects of soybean meal (SBM), including its genetically modified origin, environmental impact, and nonprospective flexible price. Processing RRC through fermentation has also been shown to be beneficial: adding fermented rapeseed cake (FRC) to the broiler diet is a nutritional approach that addresses both the environmental issue of broiler enteric methane emission and the economic issues of soybean meal. The aim of this study was to assess the effects of partial replacement of soybean meal by a 15% addition of RRC or FRC to the diets of broiler chickens on methane emission, nitrogen retention, ether extract digestibility, growth performance, and breast muscle fatty acid composition. The FRC did not show any unfavorable effects on growth performance or nutrient utilization, and it improved the fatty acid profile of the breast muscle; additionally, both methanogens and methane emission from the fermentation of cecal contents were significantly limited. In conclusion, FRC as a partial substituent may be a valuable alternative to soybean meal in broiler chicken nutrition. Abstract The study was conducted to evaluate the effects of partial replacement of soybean meal (SBM) by 15% raw or fermented rapeseed cake (RRC or FRC) to broilers’ diets on growth performance, nutrient utilization, methane emission, and breast muscle fatty acid (FA) composition. A total of 420 one-day-old female Ros 308 broilers were used in three independent experiments (300 birds in the first experiment and 60 in the second and third experiments). In each trial, three treatments were set up: a control group (without rapeseed), and diets replaced soybean meal with 15% addition of RRC or FRC. Birds fed the FRC diet experienced no effect (p > 0.05) on performance or nutrients utilization. Methane emission and total methanogen population in the ceca was decreased (p < 0.05) with the FRC diet. The concentrations of n-3 and n-6 FAs in the breast tissue of fourteen-day-old birds were not affected (p > 0.05) by FRC. However, the n-6/n-3 ratio in the breast muscle of 28-day-old birds was reduced (p < 0.001). In conclusion, the replacement of SBM by FRC in the broiler diets did not show any unfavorable effects on performance or nutrient utilization. Furthermore, the breast meat FA profile was improved, methanogen counts significantly decreased, and methane emission was limited.
Association of the Modified Mediterranean Diet Score (mMDS) with Anthropometric and Biochemical Indices in US Career Firefighters

The Mediterranean diet is associated with multiple health benefits, and the modified Mediterranean Diet Score (mMDS) has been previously validated as a measure of Mediterranean diet adherence. The aim of this study was to examine associations between the mMDS and anthropometric indices, blood pressure, and biochemical parameters in a sample of career firefighters. The participants were from Indiana Fire Departments, taking part in the “Feeding America’s Bravest” study, a cluster-randomized controlled trial that aimed to assess the efficacy of a Mediterranean diet intervention. We measured Mediterranean diet adherence using the mMDS. Anthropometric, blood pressure, and biochemical measurements were also collected. Univariate and multivariate linear regression models were used. In unadjusted analyses, many expected favorable associations between the mMDS and cardiovascular disease risk factors were found among the 460 firefighters. After adjustment for age, gender, ethnicity, physical activity, and smoking, a unitary increase in the mMDS remained associated with a decrease of the total cholesterol/HDL ratio (β-coefficient −0.028, p = 0.002) and an increase of HDL-cholesterol (β-coefficient 0.254, p = 0.004). In conclusion, greater adherence to the Mediterranean diet was associated with markers of decreased cardiometabolic risk. The mMDS score is a valid instrument for measuring adherence to the Mediterranean diet and may have additional utility in research and clinical practice.
Appetite Control across the Lifecourse: The Acute Impact of Breakfast Drink Quantity and Protein Content. The Full4Health Project

Understanding the mechanisms of hunger, satiety and how nutrients affect appetite control is important for successful weight management across the lifecourse. The primary aim of this study was to describe acute appetite control across the lifecourse, comparing age groups (children, adolescents, adults, elderly), weight categories, genders and European sites (Scotland and Greece). Participants (n = 391) consumed four test drinks, varying in composition (15% (normal protein, NP) and 30% (high protein, HP) of energy from protein) and quantity (based on 100% basal metabolic rate (BMR) and 140% BMR), on four separate days in a double-blind randomized controlled study. Ad libitum energy intake (EI), subjective appetite and biomarkers of appetite and metabolism (adults and elderly only) were measured. The adults’ appetite was significantly greater than that of the elderly across all drink types (p < 0.004) and in response to drink quantities (p < 0.001). There were no significant differences in EI between age groups, weight categories, genders or sites. Concentrations of glucagon-like peptide 1 (GLP-1) and peptide YY (PYY) were significantly greater in the elderly than the adults (p < 0.001). Ghrelin and fasting leptin concentrations differed significantly between weight categories, genders and sites (p < 0.05), while GLP-1 and PYY concentrations differed significantly between genders only (p < 0.05). Compared to NP drinks, HP drinks significantly increased postprandial GLP-1 and PYY (p < 0.001). Advanced age was concomitant with reduced appetite and elevated anorectic hormone release, which may contribute to the development of malnutrition. In addition, appetite hormone concentrations differed between weight categories, genders and geographical locations.
Mixed Methods Evaluation of Reasons Why Care Deviates From Clinical Guidelines Among Patients With Multimorbidity

Reasons why care does not conform to single-disease guideline recommendations for multimorbid patients have not been systematically measured in practice. Using a mixed methods approach, we identified and quantified types of reasons why care deviates from nine sets of disease guideline recommendations for multimorbid patients. Utilizing a focus group concept mapping technique, we built on a categorization of reasons explaining guideline deviation, and surveyed treating nurses about these reasons for patients’ specific care processes. Directed content analysis was conducted to classify the responses into reasons categories. Of 4,386 guideline-recommended care processes evaluated, 920 were not guideline-concordant (944 reasons). Three broad categories of reasons and 18 specific reasons were identified: Biomedical-related occurred 35.2% of the time, patient personal-related (30.4%), context-related (18.4%), and unknown (16.0%). Patient- and context-related factors are prevalent drivers for guideline deviation in multimorbidity, demonstrating that patient-centered aspects are as much a part of care decisions as biomedical aspects.