Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Facets of the Liver Transcriptome Are Associated with the Susceptibility and Resistance to Lipid-Related Metabolic Disorders in Periparturient Holstein Cows

Simple Summary Energy and nutrient demands of the early lactation period can result in the development of metabolic disorders, such as ketosis and fatty liver, in dairy cows. Variability in the incidence of these disorders suggests that some cows have an ability to adapt. The objective of this study was to discover differences in liver gene expression that are associated with a cow’s susceptibility (disposition to disorder during typical conditions) or resistance (disposition to disorder onset and severity when presented a challenge) to metabolic disorders. Cows in a control treatment and a ketosis induction protocol treatment were retrospectively grouped into susceptibility and resistance groups, respectively, by a machine learning algorithm using lipid biomarker concentrations. Whole-transcriptome RNA sequencing was performed on liver samples from these cows. More susceptible cows had lower expression of glutathione metabolism genes, while less resistant cows had greater expression of eicosanoid-metabolism-related genes. Additionally, differentially expressed genes suggested a role for immune-response-related genes in conferring susceptibility and resistance to metabolic disorders. The overall inferred metabolism suggests that responses to oxidative stress may determine susceptibility and resistance to metabolic disorders, with novel implications for immunometabolism. Abstract Lipid-related metabolic disorders (LRMD) are prevalent in early lactation dairy cows, and have detrimental effects on productivity and health. Our objectives were to identify cows resistant or susceptible to LRMD using a ketosis induction protocol (KIP) to discover differentially expressed liver genes and metabolic pathways associated with disposition. Clustering cows based on postpartum lipid metabolite concentrations within dietary treatments identified cows more or less susceptible (MS vs. LS) to LRMD within the control treatment, and more or less resistant (MR vs. LR) within the KIP treatment. Whole-transcriptome RNA sequencing was performed on liver samples (−28, +1, and +14 days relative to calving) to assess differential gene and pathway expression (LS vs. MS; MR vs. LR; n = 3 cows per cluster). Cows within the MS and LR clusters had evidence of greater blood serum β-hydroxybutyrate concentration and liver triglyceride content than the LS and MR clusters, respectively. The inferred metabolism of differentially expressed genes suggested a role of immune response (i.e., interferon-inducible proteins and major histocompatibility complex molecules). Additionally, unique roles for glutathione metabolism and eicosanoid metabolism in modulating susceptibility and resistance, respectively, were implicated. Overall, this research provides novel insight into the role of immunometabolism in LRMD pathology, and suggests the potential for unique control points for LRMD progression and severity.
Tuning Reconstruction Level of Precatalysts to Design Advanced Oxygen Evolution Electrocatalysts

Surface reconstruction engineering is an effective strategy to promote the catalytic activities of electrocatalysts, especially for water oxidation. Taking advantage of the physicochemical properties of precatalysts by manipulating their structural self-reconstruction levels provide a promising methodology for achieving suitable catalysts. In this review, we focus on recent advances in research related to the rational control of the process and level of surface transformation ultimately to design advanced oxygen evolution electrocatalysts. We start by discussing the original contributions to surface changes during electrochemical reactions and related factors that can influence the electrocatalytic properties of materials. We then present an overview of current developments and a summary of recently proposed strategies to boost electrochemical performance outcomes by the controlling structural self-reconstruction process. By conveying these insights, processes, general trends, and challenges, this review will further our understanding of surface reconstruction processes and facilitate the development of high-performance electrocatalysts beyond water oxidation.
Comprehensive Analysis of External Dependency in Terms of Material Criticality by Employing Total Material Requirement: Sulfuric Acid Production in Japan as a Case Study

Securing stable material supply is of paramount importance since materials are fundamental to the economy and human well-being. The domestic production to consumption ratio has conventionally been utilized as a main index for external dependency in terms of material supply security and its criticality. However, the conventional approach confines its application to raw materials, which potentially risks reaching short-sighted conclusions in the policy-making process. Beyond the conventional analysis of external dependency, the development of a more applicable approach for every material is of paramount importance to consider the diversification of external dependency more comprehensively and to aid the analysis of overall material criticality. As such, this paper establishes a new methodology for analyzing external dependency related to every material and product by using the concept of total material requirement (TMR). Applying the methodology, the external dependency of sulfuric acid production in Japan is evaluated as a case study. Previously unexamined elements associated with external dependency in the conventional approach are revealed by this new comprehensive approach. The new approach may be of use to policymakers in designing more sophisticated and well-grounded material securement policy.
Recognition Rate Advancement and Data Error Improvement of Pathology Cutting with H-DenseUNet for Hepatocellular Carcinoma Image

Due to the fact that previous studies have rarely investigated the recognition rate discrepancy and pathology data error when applied to different databases, the purpose of this study is to investigate the improvement of recognition rate via deep learning-based liver lesion segmentation with the incorporation of hospital data. The recognition model used in this study is H-DenseUNet, which is applied to the segmentation of the liver and lesions, and a mixture of 2D/3D Hybrid-DenseUNet is used to reduce the recognition time and system memory requirements. Differences in recognition results were determined by comparing the training files of the standard LiTS competition data set with the training set after mixing in an additional 30 patients. The average error value of 9.6% was obtained by comparing the data discrepancy between the actual pathology data and the pathology data after the analysis of the identified images imported from Kaohsiung Chang Gung Memorial Hospital. The average error rate of the recognition output after mixing the LiTS database with hospital data for training was 1%. In the recognition part, the Dice coefficient was 0.52 after training 50 epochs using the standard LiTS database, while the Dice coefficient was increased to 0.61 after adding 30 hospital data to the training. After importing 3D Slice and ITK-Snap software, a 3D image of the lesion and liver segmentation can be developed. It is hoped that this method could be used to stimulate more research in addition to the general public standard database in the future, as well as to study the applicability of hospital data and improve the generality of the database.
A Co-Culture Model of IPEC-J2 and Swine PBMC to Study the Responsiveness of Intestinal Epithelial Cells: The Regulatory Effect of Arginine Deprivation

Simple Summary The interest in amino acids comes from their involvement in research on alternative strategies for the utilization of antibiotics on farms. Among several substances used to replace antibiotics, there is arginine, an essential amino acid in newborns and piglets. This amino acid has a protective role in intestinal immune cells and improves intestinal immunity. The purpose of this research was to define a co-culture model, in which intestinal epithelial cells can communicate with peripheral blood mononuclear cells (PBMC) to deepen the effects of arginine deprivation on intestinal epithelial cells over time. The main finding was that the lack of arginine highly impacts on intestinal and immune cells by way of immuno-regulation mediated by the expression of pro- and anti-inflammatory cytokines. The use of this experimental model could allow us to investigate the impact of and interactions between specific nutrients and the complex intestinal environment and, in addition, to assess feed additives to improve health and animal production. Abstract Arginine is a semi-essential amino acid, supplementation with which induces a reduction of intestinal damage and an improvement of intestinal immunity in weaned piglets, but the mechanism is not yet entirely clear. The aim of this study was to characterise a co-culture model by measuring changes in gene expression over time (24 and 48 h) in intestinal IPEC-J2 cells in the presence of immune cells activated with phytohemagglutinin and, consequently, to assess the effectiveness of arginine deprivation or supplementation in modulating the expression of certain cytokines related to the regulation of intestinal cells’ function. The main results show the crucial role of arginine in the viability/proliferation of intestinal cells evaluated by an MTT assay, and in the positive regulation of the expression of pro-inflammatory (TNF-α, IL-1α, IL-6, IL-8) and anti-inflammatory (TGF-β) cytokines. This experimental model could be important for analysing and clarifying the role of nutritional conditions in intestinal immune cells’ functionality and reactivity in pigs as well as the mechanisms of the intestinal defence system. Among the potential applications of our in vitro model of interaction between IEC and the immune system there is the possibility of studying the effect of feed additives to improve animal health and production.
Socioeconomic Inequalities in Physical Activity and Sedentary Behaviour among the Chilean Population: A Systematic Review of Observational Studies

Socioeconomic inequalities in physical (in)activity and sedentary behaviours are key mediators in obesity and health socioeconomic inequalities. Considering the high and uneven obesity rates in Chile, this review aims to systematically assess the socioeconomic inequalities in physical activity (PA) and sedentary behaviour (SB) among the Chilean population from different age groups. Peer-reviewed and grey literature were searched from inception until 31st December 2019 in PubMed, Scopus, PsycINFO, Web of Sciences and LILACS. Publications in English and Spanish, from observational studies that reported the comparison of at least one indicator of PA or SB between at least two groups of different socioeconomic positions (SEP), from the general Chilean population, were included. Data searches, screening, extraction, and quality assessment, using the Newcastle Ottawa Quality Assessment Scale for observational studies, were conducted by two independent researchers. Seventeen articles (from 16 studies) met the inclusion criteria (14 cross-sectional; two cohort). Across these, quality was considered low, medium and high for 19%, 69% and 13%, respectively. Results showed consistent evidence for a lower leisure-time PA and sitting time, and higher physical inactivity among adults from the lower, compared to the highest, SEP groups. Associations between SEP and total PA, moderate-to-vigorous PA, low PA, and transport and work-related PA were inconsistent. These findings provide insights to public health and physical activity researchers and policymakers aiming to reduce socioeconomic inequalities in PA and SB in Chile and other countries.
Sensitivity of Rapid Antigen Testing and RT-PCR Performed on Nasopharyngeal Swabs versus Saliva Samples in COVID-19 Hospitalized Patients: Results of a Prospective Comparative Trial (RESTART)

Saliva sampling could serve as an alternative non-invasive sample for SARS-CoV-2 diagnosis while rapid antigen tests (RATs) might help to mitigate the shortage of reagents sporadically encountered with RT-PCR. Thus, in the RESTART study we compared antigen and RT-PCR testing methods on nasopharyngeal (NP) swabs and salivary samples. We conducted a prospective observational study among COVID-19 hospitalized patients between 10 December 2020 and 1 February 2021. Paired saliva and NP samples were investigated by RT-PCR (Cobas 6800, Roche-Switzerland, Basel, Switzerland) and by two rapid antigen tests: One Step Immunoassay Exdia® COVID-19 Ag (Precision Biosensor, Daejeon, Korea) and Standard Q® COVID-19 Rapid Antigen Test (Roche-Switzerland). A total of 58 paired NP-saliva specimens were collected. A total of 32 of 58 (55%) patients were hospitalized in the intensive care unit, and the median duration of symptoms was 11 days (IQR 5-19). NP and salivary RT-PCR exhibited sensitivity of 98% and 69% respectively, whereas the specificity of these RT-PCRs assays was 100%. The NP RATs exhibited much lower diagnostic performance, with sensitivities of 35% and 41% for the Standard Q® and Exdia® assays, respectively, when a wet-swab approach was used (i.e., when the swab was diluted in the viral transport medium (VTM) before testing). The sensitivity of the dry-swab approach was slightly better (47%). These antigen tests exhibited very low sensitivity (4% and 8%) when applied to salivary swabs. Nasopharyngeal RT-PCR is the most accurate test for COVID-19 diagnosis in hospitalized patients. RT-PCR on salivary samples may be used when nasopharyngeal swabs are contraindicated. RATs are not appropriate for hospitalized patients.
Validation and Selection of New Reference Genes for RT-qPCR Analysis in Pediatric Glioma of Different Grades

Gliomas are heterogeneous, solid, and intracranial tumors that originate from glial cells. Malignant cells from the tumor undergo metabolic alterations to obtain the energy required for proliferation and the invasion of the cerebral parenchyma. The alterations in the expression of the genes related to the metabolic pathways can be detected in biopsies of gliomas of different CNS WHO grades. In this study, we evaluated the expression of 16 candidate reference genes in the HMC3 microglia cell line. Then, statistical algorithms such as BestKeeper, the comparative ΔCT method, geNorm, NormFinder, and RefFinder were applied to obtain the genes most suitable to be considered as references for measuring the levels of expression in glioma samples. The results show that PKM and TPI1 are two novel genes suitable for genic expression studies on gliomas. Finally, we analyzed the expression of genes involved in metabolic pathways in clinical samples of brain gliomas of different CNS WHO grades. RT-qPCR analysis showed that in CNS WHO grade 3 and 4 gliomas, the expression levels of HK1, PFKM, GAPDH, G6PD, PGD1, IDH1, FASN, ACACA, and ELOVL2 were higher than those of CNS WHO grade 1 and 2 glioma biopsies. Hence, our results suggest that reference genes from metabolic pathways have different expression profiles depending on the stratification of gliomas and constitute a potential model for studying the development of this type of tumor and the search for molecular targets to treat gliomas.
Adherence to Mediterranean Diet, Alcohol Consumption and Emotional Eating in Spanish University Students

(1) Introduction: The university period may increase the risk of different unhealthy habits, such as low adherence to the Mediterranean diet, high alcohol consumption and eating in response to specific emotions. The aim of this study was to detect early-risk alcohol consumption and alcohol dependence (ADS), the degree of adherence to the Mediterranean diet and emotional eating in university students of the Madrid community. (2) Methods: For each individual, anthropometric parameters, the Alcohol Use Disorders Identification Test (AUDIT), AUDIT-Consumption (AUDIT-C), the Mediterranean Diet Adherence Screener (MEDAS) and the Emotional Eater Questionnaire (EEQ) were assessed. (3) Results: A total of 584 university students aged 20.5 (sex ratio = 0.39) were enrolled in a cross-sectional study. In total, 63.6% of students showed low adherence to the Mediterranean diet, with no differences by sex (64.3% female versus 61.5% male, p = 0.19). According to the AUDIT questionnaire, 26.2% of participants were categorized as high-risk drinkers and 7.7% as ADS. About 38.6% of the students were categorized as eating very emotionally or eating emotionally, and 37.2% were categorized as low emotional eaters. A weak positive correlation was observed between the EEQ and BMI in female students (rho= 0.15, p = 0.03). (4) Conclusions: University students in our sample showed a low adherence to the Mediterranean diet, an important high-risk alcohol consumption and low emotional eating.
The Problem of Fairness in Synthetic Healthcare Data

Access to healthcare data such as electronic health records (EHR) is often restricted by laws established to protect patient privacy. These restrictions hinder the reproducibility of existing results based on private healthcare data and also limit new research. Synthetically-generated healthcare data solve this problem by preserving privacy and enabling researchers and policymakers to drive decisions and methods based on realistic data. Healthcare data can include information about multiple in- and out- patient visits of patients, making it a time-series dataset which is often influenced by protected attributes like age, gender, race etc. The COVID-19 pandemic has exacerbated health inequities, with certain subgroups experiencing poorer outcomes and less access to healthcare. To combat these inequities, synthetic data must “fairly” represent diverse minority subgroups such that the conclusions drawn on synthetic data are correct and the results can be generalized to real data. In this article, we develop two fairness metrics for synthetic data, and analyze all subgroups defined by protected attributes to analyze the bias in three published synthetic research datasets. These covariate-level disparity metrics revealed that synthetic data may not be representative at the univariate and multivariate subgroup-levels and thus, fairness should be addressed when developing data generation methods. We discuss the need for measuring fairness in synthetic healthcare data to enable the development of robust machine learning models to create more equitable synthetic healthcare datasets.
Transient Congenital Complete Heart Block: A Case Report

Congenital complete heart block is defined as a complete atrioventricular block occurring prenatally, at birth, or within the first month of life. Congenital complete heart block has a high mortality rate, and in infants with normal heart morphology, it is often associated with maternal connective tissue disease. In these latter cases, neonatal congenital complete heart block is usually irreversible. We present a rare case of a female neonate who had bradycardia noted at a gestational age of 37 weeks. Her mother had no autoimmune disease history. She had no structural heart disease, and the serology surveys for autoantibodies including SSA/Ro and SSB/La were all negative. Without intervention or medication, her congenital complete heart block completely recovered to a normal sinus rhythm within 5 days. The cause of the transient congenital complete heart block was unknown in this case.
First Report of Antimicrobial Susceptibility and Virulence Gene Characterization Associated with Staphylococcus aureus Carriage in Healthy Camels from Tunisia

Simple Summary The one-humped camel (Camelus dromedarius) is an important livestock species and is present in more than 46 national entities, with 80% of the camel population inhabiting Africa. In these regions, the role of camels in the livestock economy is highly valuable and a part of this camel herd is valorized on national or international markets for meat production, live animal export or milk production. Even if camels are the species that is most adapted to the harsh conditions of arid/semi-arid rangelands, they can be susceptible to a high number of pathogens, including S. aureus. This latter is often associated with asymptomatic carriage but can also be responsible for several diseases, therefore causing considerable economical losses. Continued monitoring and control assume particular importance in containing the spread of the bacterium since it constitutes an important zoonotic disease. Abstract A total of 318 nasal and rectal swabs were collected from 159 apparently healthy camels (Camelus dromedarius) randomly selected from five regions in southern and central Tunisia and screened for Staphylococcus aureus carriage. Staphylococcus spp. were recovered from 152 of 159 camels studied (95.6%) and in total 258 swabs (81%) were positive. Among these isolates, 16 were coagulase positive Staphylococcus (CoPS) (6.2%) and were characterized by biochemical and molecular tests as S. aureus. These were isolated from 14 camels (8.8%) with co-carriage in nasal and rectal mucosa by two camels. All S. aureus isolates recovered were methicillin-susceptible Staphylococcus aureus (MSSA) and were characterized by spa typing and PFGE. Three different spa types were recovered: t729, t4013 and a spa type newly registered as t19687, which was the most common. PFGE analysis revealed seven different patterns and these were characterized by MLST, which revealed five different sequence types (ST6, ST88, ST3583 and two new sequences, ST6504 and ST6506). All isolates harbored different virulence genes, including hld, encoding delta hemolysin; lukE–lukD, encoding bicomponent leukotoxin LukE–LukD; the clfB gene, encoding clumping factor B; the laminin gene, encoding laminin-binding protein; and cap8, encoding capsule type 8. Fifteen isolates harbored hemolysin beta (hlb) and fourteen encoded hemolysin alpha (hla) and hemolysin G2 (hlgv). Adhesin factors, including clfA and fnbB, were detected in five and four isolates respectively. Binding proteins, including collagen (cbp) and elastin-binding protein (ebp), were detected in two S. aureus isolates while fibrinogen-binding protein (fib) was identified in four isolates. This study provides the first set of genotyping data on the population structure and presence of toxin genes of S. aureus strains in Tunisian camels.
Optimisation of a Microfluidic Method for the Delivery of a Small Peptide

Peptides hold promise as therapeutics, as they have high bioactivity and specificity, good aqueous solubility, and low toxicity. However, they typically suffer from short circulation half-lives in the body. To address this issue, here, we have developed a method for encapsulation of an innate-immune targeted hexapeptide into nanoparticles using safe non-toxic FDA-approved materials. Peptide-loaded nanoparticles were formulated using a two-stage microfluidic chip. Microfluidic-related factors (i.e., flow rate, organic solvent, theoretical drug loading, PLGA type, and concentration) that may potentially influence the nanoparticle properties were systematically investigated using dynamic light scattering and transmission electron microscopy. The pharmacokinetic (PK) profile and biodistribution of the optimised nanoparticles were assessed in mice. Peptide-loaded lipid shell-PLGA core nanoparticles with designated size (~400 nm) and a sustained in vitro release profile were further characterized in vivo. In the form of nanoparticles, the elimination half-life of the encapsulated peptide was extended significantly compared with the peptide alone and resulted in a much higher distribution into the lung. These novel nanoparticles with lipid shells have considerable potential for increasing the circulation half-life and improving the biodistribution of therapeutic peptides to improve their clinical utility, including peptides aimed at treating lung-related diseases.