Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary rate variation among genes involved in galactomannan biosynthesis in Coffea canephora

Abstract The endosperm cell walls of mature coffee seeds accumulate large amounts of mannan storage polysaccharides, which serve as nutrient reserve for embryo and contribute to beverage quality. Our study investigated the evolutionary patterns of key galactomannan (GM) biosynthesis genes using d N/d S ratio, synteny, and phylogenetic analysis and detected heterogeneity in rate of evolution among gene copies. Selection ratio index revealed evidence of positive selection in the branch editing gene Coffea canephora alpha (α) galactosidase (Cc‐alpha Gal) at Cc11_g15950 copy (ω = 1.12), whereas strong purifying selection on deleterious mutations was observed in the Coffea canephora uridine diphosphate (UDP)‐glucose 4′‐epimerase (Cc‐UG4E) and Coffea canephora mannose‐1P guanylytransferase (Cc‐MGT) genes controlling the crucial nucleotide carbon sugar building blocks flux in the pathway. Relatively low sequence diversity and strong syntenic linkages were detected in all GM pathway genes except in Cc‐alpha Gal, which suggests a correlation between selection pressure and nucleotide diversity or synteny analysis. In addition, phylogenetic analysis revealed independent evolution or expansion of GM pathway genes in different plant species, with no obvious inferable clustering patterns according to either gene family or congruent with evolutionary plants lineages tested due to high dynamic nature and specific biochemical cell wall modification requirements. Altogether, our study shows a significant high rate of evolutionary variation among GM pathway genes in the diploid C. canephora and demonstrates the inherent variation in evolution of gene copies and their potential role in understanding selection rates in a homogenously connected metabolic pathway.
Comparative Metabolomic Analysis Reveals Distinct Flavonoid Biosynthesis Regulation for Leaf Color Development of Cymbidium sinense ‘Red Sun’

The colorful leaf is an important ornamental character of Cymbidium sinense (C. sinense), especially the red leaf, which has always been attracted by breeders and consumers. However, little is documented on the formation mechanism of the red leaf of C. sinense. In this study, the changing patterns of flavonoid-related metabolites, corresponding enzyme activities and genes expression in the leaves of C. sinense ‘Red Sun’ from red to yellow and finally to green was investigated. A total of 196 flavonoid-related metabolites including 11 anthocyanins metabolites were identified using UPLC-MS/MS-based approach. In the process of leaf color change, 42 metabolites were identified as having significantly different contents and the content of 28 differential metabolites turned to zero. In anthocyanin biosynthetic pathway, content of all 15 identified metabolites showed downregulation trend in the process of leaf color change. Among the 15 metabolites, the contents of Naringenin chalcone, Pelargonidin O-acetylhexoside and Anthocyanin 3-O-beta-d-glucoside decreased to zero in the green leaf stage. The changing pattern of enzyme activity of 10 enzymes involved in the anthocyanin biosynthetic pathway showed different trends from red leaves that have turned yellow and finally green, while the expression of genes encoding these enzymes was all down-regulated in the process of leaf color change. The results of this study revealed the types of flavonoid-related metabolites and the comprehensive analysis of metabolites content, enzyme activities and genes expression providing a new reference for breeders to improve the leaf color of C. sinense ‘Red Sun’.
The Interrelations between Biological and Targeted Synthetic Agents Used in Inflammatory Joint Diseases, and Obesity or Body Composition

Obesity is a comorbidity that plays a role in the development and severity of inflammatory joint diseases, including rheumatoid arthritis, psoriatic arthritis and axial spondyloarthritis. The relationships between obesity and adipose tissue and the treatments given for inflammatory joint diseases are bidirectional. In fact, biological agents (bDMARDs) and targeted synthetic agents (tsDMARDs) may influence body weight and body composition of treated patients, while obesity in turn may influence clinical response to these agents. Obesity is a prevalent comorbidity mainly affecting patients with rheumatoid arthritis (RA) and psoriatic arthritis (PsA) with specific phenotypes. Tumour necrosis factor alpha (TNFα) inhibitors have been associated with changes in body composition by improving lean mass, but also by significantly increasing fat mass, which localized toward the abdominal/visceral region. The IL-6 inhibitor tocilizumab is associated with an increase in lean mass without change in fat mass. The clinical response to TNFα inhibitors is attenuated by obesity, an effect that is less pronounced with IL-6 inhibitors and the B-cell depletion agent rituximab. Conversely, body weight has no influence on the response to the costimulation inhibitor abatacept. These effects may be of help to the physician in personalized medicine, and may guide the therapeutic choice in obese/overweight patients.
Genomic Insight into the Spread of Meropenem-Resistant Streptococcus pneumoniae Spain23F-ST81, Taiwan

Incidence of invasive pneumococcal disease caused by antimicrobial-resistant Streptococcus pneumoniae types not included in pneumococcal conjugate vaccines has increased, including a penicillin- and meropenem-resistant serotype 15A-ST63 clone in Japan. During 2013–2017, we collected 206 invasive pneumococcal isolates in Taiwan for penicillin and meropenem susceptibility testing. We found serotypes 15B/C-ST83 and 15A-ST63 were the most prevalent penicillin- and meropenem-resistant clones. A transformation study confirmed that penicillin-binding protein (PBP) 2b was the primary meropenem resistance determinant, and PBP1a was essential for high-level resistance. The rate of serotype 15B/C-ST83 increased during the study. All 15B/C-ST83 isolates showed an ermB macrolide resistance genotype. Prediction analysis of recombination sites revealed 12 recombination regions in 15B/C-ST83 compared with the S. pneumoniae Spain23F-ST81 genome. Pneumococcal clones rapidly recombine to acquire survival advantages and undergo local expansion under the selective pressure exerted by vaccines and antimicrobial drugs. The spread of 15B/C-ST83 is alarming for countries with high antimicrobial pressure.
Sense of Coherence in Nurses: A Systematic Review

Background: Nurses experience high levels of distress due to the nature of their work and workplaces; Antonovsky’s salutogenic theory shows that individual and work-related factors can influence human health. The aim of this paper is to analyze the possible correlations with different work-related and individual variables, which influence or are influenced by Sense of Coherence (SOC) and verify the possible use of SOC scales to prevent negative health determinants in workplaces. Methods: Electronic databases were searched with selected studies compared for sample, sample size, study design and basic results. Cross-sectional studies were reviewed for correlations between individual physical and mental health, distress, burnout, job satisfaction and SOC, with intervention studies used to assess the possible impact of training on nurses’ SOC. Results: The review found several correlations between SOC and different work-related variables; but also with several individual characteristics. Conclusion: The review found that SOC was predictor of depressive state, burnout, job dissatisfaction among female nurses; therefore, SOC could be a health promoting resource.
Effect of caffeine on Alzheimer’s molecular factors in correlation with involved cell communication systems in developing zebrafish Danio rerio

Abstract Background: Epidemiological studies suggested that caffeine/coffee could be an effective therapeutic agent against Alzheimer disease (AD). The mechanism has not been well established; however, molecular genetic analyses suggest that many genes influence it. Methods: Using developing zebrafish (Danio rerio), we studied the regulatory effect of caffeine on AD molecular factors, APP, Psen1, Psen2, ApoE, and Sorl1, and on receptor expression of two cell communication systems involved in the disease, adenosine (AR) and dopamine receptors (DR). Results: All genes are already expressed at early developmental stages. No morphological changes were found at tested concentrations and control. Caffeine significantly down-regulated the expression of all AD tested genes at 24 h post-fertilization (hpf) and APP, Sorl1, and Psen1 at 96 and 168 hpf. A2aa and A2ab receptors have higher affinity for caffeine than A2b. Significant down-regulation occurred in A2b at 168 hpf in both concentrations. Caffeine blocked the expression of drd2a and drd2c at 24 hpf but significantly stimulated the expression at 96 and 168 hpf. Conclusions: Zebrafish is a promising organism in studying AD at the molecular level because all tested factors are already expressed at early developmental stages. Caffeine has a regulatory effect on all tested genes and may protect against the disease via amyloid pathway as well as AR and DR.
EMERGENT INPATIENT ADMISSIONS AND DELAYED HOSPITAL DISCHARGES

Emergency Department (ED) congestion can be better understood by examining overall system impacts, in particular inpatient admissions and discharges. This study first investigates trends of inpatient admissions, volume of patients in the ED who have been admitted (ED “boarders”), length of stay, and bed resources of three major admitting services at our teaching institution. It was found that patients admitted to the General Internal Medicine (GIM) service constituted the majority of ED boarders by default rather than design, as GIM served as a safety net for specialty services. This study investigates operational factors that impact discharge and found that day of the week and holidays followed by team organization and scheduling are significant predictors of daily variation in discharge rates. Based on these results, next, a system dynamics computer simulation was built to test the impact of various discharge smoothing strategies on the number of ED boarders. Next, this study uses the framework and tools of system dynamics methodology to design a conceptual model of the ED boarder problem that may be used as a generalizable roadmap to create sustainable improvements in ED congestion. Finally, this study introduces a novel real time metric of hospital operational discharge efficiencydaily discharge rate – to bring focus on the underlying causes of discharge variation and help indicate opportunities for improvement.
Statistical optimization of simultaneous saccharification fermentative hydrogen production from corn stover

ABSTRACT Corn stovers are rich in carbohydrates and can be used by anaerobic bacteria to produce hydrogen by fermentation. In the present study, using hydrogen production as the main experimental index, the effect of different influential factors on hydrogen production from corn stover saccharification and fermentation was studied, using the response surface method BBD model. The significance of interactions between different influential factors on hydrogen production by simultaneous saccharification and fermentation of corn stover material were investigated and optimized. Results showed that there were several factors affecting simultaneous saccharification fermentative hydrogen production from corn stover, including substrate concentration, inoculation amount, pH value and enzyme concentration. In linear terms, substrate concentration had the greatest influence on hydrogen production by anaerobic simultaneous saccharification and fermentation. In terms of multi-factor interactions, the interaction between pH and enzyme concentration was the most significant. The optimal hydrogen production conditions established from the BBD model were as follows: substrate concentration of 25 mg/mL, inoculation amount proportion of 32.62%, initial pH value of 6.50 and enzyme concentration of 172.08 mg/g, resulting in the maximum hydrogen production of 55.29 mL/g TS. The actual maximum hydrogen production reached 56.66 mL/g TS, with these experimental results consistent with the predicted value established from equation fitting. This study provides a reference for hydrogen production by anaerobic synchronous saccharification fermentation using corn stover as substrate and lays a foundation and provides technical support for the industrialization of biological hydrogen production using corn stover as substrate. Graphical abstract
IoT Smart Parking System Based on the Visual-Aided Smart Vehicle Presence Sensor: SPIN-V

Humanity is currently experiencing one of the short periods of transition thanks to novel sensing solutions for smart cities that bring the future to today. Overpopulation of cities demands the development of solid strategic plannings that uses infrastructure, innovation, and technology to adapt to rapid changes. To improve mobility in cities with a larger and larger vehicle fleet, a novel sensing solution that is the cornerstone of a smart parking system, the smart vehicular presence sensor (SPIN-V, in its Spanish abbreviation), is presented. The SPIN-V is composed of a small single-board computer, distance sensor, camera, LED indicator, buzzer, and battery and devoted to obtain the status of a parking space. This smart mobility project involves three main elements, namely the SPIN-V, a mobile application, and a monitoring center, working together to monitor, control, process, and display the parking space information in real-time to the drivers. In addition, the design and implementation of the three elements of the complete architecture are presented.
Recent updates on purine and pyrimidine metabolism in physiological and pathological settings

SUMMARY In June 2019, the Purine and Pyrimidine Society (PPS) organized the 18th biennial symposium on Purine and Pyrimidine Metabolism at the International Agency for Research on Cancer in Lyon, France. This meeting went over 3 days and gathered students and researchers working in various specialties such as inborn errors, hyper- and hypouricemia and gout, cancer, enzymology, and cardiovascular diseases to exchange and discuss recent advances in the field of purine and pyrimidine metabolism. Here, we give an overview of oral presentations given during the symposium.
Nutrient Extraction Lowers Postprandial Glucose Response of Fruit in Adults with Obesity as well as Healthy Weight Adults

Fruit consumption is recommended as part of a healthy diet. However, consumption of fruit in the form of juice is positively associated with type 2 diabetes risk, possibly due to resulting hyperglycemia. In a recent study, fruit juice prepared by nutrient extraction, a process that retains the fiber component, was shown to elicit a favorable glycemic index (GI), compared to eating the fruit whole, in healthy weight adults. The current study expanded on this to include individuals with obesity, and assessed whether the nutrient extraction of seeded fruits reduced GI in a higher disease risk group. Nutrient extraction was shown to significantly lower GI, compared to eating fruit whole, in subjects with obesity (raspberry/mango: 25.43 ± 18.20 vs. 44.85 ± 20.18, p = 0.034 and passion fruit/mango (26.30 ± 25.72 vs. 42.56 ± 20.64, p = 0.044). Similar results were found in those of a healthy weight. In summary, the current study indicates that the nutrient-extraction of raspberries and passionfruit mixed with mango lowers the GI, not only in healthy weight individuals, but also in those with obesity, and supports further investigation into the potential for nutrient extraction to enable increased fruit intake without causing a high glycemic response.
Non-invasive proteome-wide quantification of skin barrier-related proteins using label-free LC-MS/MS analysis

A number of epidermal proteins are closely related to skin barrier function, the abnormalities of which can lead to specific skin diseases. These proteins must be quantified to further investigate the changes in the skin barrier between healthy and disease states. However, the non-invasive and proteome-wide quantification of skin proteins without any labelling steps remains a challenge. In this study, 3M medical adhesive tapes were used to obtain skin samples from volunteers. Proteins were extracted from fresh skin samples and digested with trypsin. Each tryptic peptide was analysed in three replicates using liquid chromatography with tandem mass spectrometry analysis and label-free quantification. The data were searched against the Human Universal Protein Resource (UniProt) to match with known proteins. Using this method, 1,157 skin proteins recorded in the UniProt were quantified. A total of 50 identical proteins were identified in the three replicate analyses of all samples with no significant differences in abundance. The results provided an objective metric for further study of skin ageing and various skin diseases. Specifically, the non-invasive proteome-wide method used in this study can be applied to future studies of skin diseases related to barrier destruction by monitoring the changes in the levels of epidermal proteins.
Temperature-Responsive Molecular Assemblies Using Oligo(Ethylene Glycol)-Attached Polyamidoamine Dendron Lipids and their Functions as Drug Carriers

Temperature-responsive nanocarrier systems using external stimuli are one of the most widely investigated stimuli-responsive strategies because heat is easy and safe to use for hyperthermia and controlled drug delivery. Polyamidoamine dendron lipids (PAMAM-DLs) composed of PAMAM dendron as head group and two alkyl chains can exhibit temperature-responsive morphological change through the attachment of suitable moieties to terminal of PAMAM dendron. In this study, oligo(ethylene glycol)s including ethoxy- or methoxy-diethylene glycols were attached to the terminals of PAMAM-DL, and temperature-responsive properties of their self-assemblies were evaluated by calorimetric and turbidity measurements. In the evaluation of temperature-responsive properties, ethoxy diethylene glycol (EDEG)-attached PAMAM-DL composed of two saturated alkyl chains and PAMAM dendron with 1st generation had lipid bilayer structure and suitable cloud point for the application as drug carrier. In vitro performances of the assemblies combining EDEG-attached PAMAM-DLs with cholesteryl-oxy-poly(ethylene glycol) (PEG-Chol) was evaluated using doxorubicin (DOX) as an anticancer drug. Cellular uptake of DOX-loaded EDEG-attached PAMAM-DL/PEG-Chol assemblies was promoted at 42 °C rather than 37 °C, resulting in an effective decrease in cell viability.
Interstitial microRNA miR-214 attenuates inflammation and polycystic kidney disease progression.

Renal cysts are the defining feature of autosomal dominant polycystic kidney disease (ADPKD); however, the substantial interstitial inflammation is an often-overlooked aspect of this disorder. Recent studies suggest that immune cells in the cyst microenvironment impact ADPKD progression. Here we report that microRNAs (miRNAs) are new molecular signals in this crosstalk. We found that miR-214 and its host long non-coding RNA Dnm3os are upregulated in orthologous ADPKD mouse models and cystic kidneys from humans with ADPKD. In situ hybridization revealed that interstitial cells in the cyst microenvironment are the primary source of miR-214. While genetic deletion of miR-214 does not affect kidney development or homeostasis, surprisingly, its inhibition in Pkd2 and Pkd1 mutant mice aggravates cyst growth. Mechanistically, the pro-inflammatory TLR4/INF-γ/STAT1 pathways transactivate the miR-214 host gene. miR-214, in turn as a negative feedback loop, directly inhibits Tlr4. Accordingly, miR-214 deletion is associated with increased Tlr4 expression and enhanced peri-cystic macrophage accumulation. Thus, miR-214 upregulation is a compensatory protective response in the cyst microenvironment that restrains inflammation and cyst growth.
A Guide to Human Zinc Absorption: General Overview and Recent Advances of In Vitro Intestinal Models

Zinc absorption in the small intestine is one of the main mechanisms regulating the systemic homeostasis of this essential trace element. This review summarizes the key aspects of human zinc homeostasis and distribution. In particular, current knowledge on human intestinal zinc absorption and the influence of diet-derived factors on bioaccessibility and bioavailability as well as intrinsic luminal and basolateral factors with an impact on zinc uptake are discussed. Their investigation is increasingly performed using in vitro cellular intestinal models, which are continually being refined and keep gaining importance for studying zinc uptake and transport via the human intestinal epithelium. The vast majority of these models is based on the human intestinal cell line Caco-2 in combination with other relevant components of the intestinal epithelium, such as mucin-secreting goblet cells and in vitro digestion models, and applying improved compositions of apical and basolateral media to mimic the in vivo situation as closely as possible. Particular emphasis is placed on summarizing previous applications as well as key results of these models, comparing their results to data obtained in humans, and discussing their advantages and limitations.
Updated Evaluation of Dupilumab in the Treatment of Asthma: Patient Selection and Reported Outcomes

Abstract Uncontrolled asthma continues to be a problem for many patients with moderate-to-severe allergic asthma. Dupilumab, which blocks the receptors for interleukin-4 and interleukin-13, has been effective in reducing asthma exacerbations, improving forced expiratory volume in one second (FEV1), and reducing oral corticosteroid use. When selecting patients for dupilumab, it is important to consider entry criteria for the original studies, subgroups that have responded best, and the presence of comorbid diseases that may also respond to dupilumab. Factors that were considered when selecting patients likely to respond to dupilumab in asthma studies include: failure of moderate or high dose inhaled steroids in combination with an additional controller medication, baseline FEV1 reversibility of 12% or greater, and Asthma Control Questionnaire > 1.5. The baseline characteristics that predicted a better response to dupilumab included blood eosinophils > 150 cells/mm3 and fractional exhaled nitric oxide > 25 parts per billion. Comorbidities that may also respond to treatment with dupilumab include atopic dermatitis, chronic rhinosinusitis, and allergic rhinitis. A combination of these factors should be considered when selecting the patients most likely to benefit from dupilumab.