Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation Analysis between AK1 mRNA Expression and Inosine Monophosphate Deposition in Jingyuan Chickens

Simple Summary China is rich in livestock and poultry resources, but the development of animal husbandry in different regions is uneven, and excellent livestock and poultry resources have to be developed. Jingyuan chicken is a national-level protected breed of livestock and poultry and a genetically protected breed in the Ningxia Hui Autonomous Region. It is rich in amino acids and fatty acids, with a high nutritional value. It is the first choice of “green nutrition and health care” in chicken food. Meat flavor is the main factor affecting meat quality. Meat flavor is characterized by umami and aroma properties. Inosine acid (inosincacid, inosinemonphosphate, IMP) has the greatest influence on meat flavor and is an important indicator of the freshness of meat. The purpose of this study was to screen out differentially expressed genes related to IMP content in different parts of the Ningxia local breed of Jingyuan chicken on the basis of transcriptome sequencing, and select adenylate kinase 1 (AK1) for quantitative fluorescence verification and Pearson correlation analysis. These findings provide a theoretical basis for further discovery and screening of IMP-specific deposition regulation mechanisms, as well as scientific basis for the development and utilization of local varieties and the development of new approaches to molecular breeding. Abstract In this study, we examined correlations between the deposition of inosine monophosphate (IMP) and mRNA expression of the adenylate kinase 1 (AK1) gene in Jingyuan chicken. The IMP content was determined by high-performance liquid chromatography. Transcriptome sequencing was used to screen the differentially expressed gene AK1 and real-time quantitative polymerase chain reaction (PCR) to determine the expression level of AK1 mRNA associated with IMP synthesis. IMP and inosine content in the breast muscles of both Jingyuan cocks and hens was found to be significantly higher than that in the leg muscles. Similarly, the expression of AK1 mRNA in the breast muscles of cocks and hens was significantly higher than that in the leg muscles. Moreover, AK1 mRNA expression in cock breast muscles was negatively correlated with IMP content, whereas its expression in cock leg muscles was positively correlated with IMP content. In contrast, the expression of AK1 mRNA in hen breast and leg muscles was significantly positively correlated with IMP content. These findings provide a scientific basis for enhancing the meat flavor of Jingyuan chicken and promoting the development and utilization of local variety resources, as well as constituting a basis for screening IMP-regulated genes. Our study will advance our current understanding of AK1 function.
Coevolution analysis of amino-acids reveals diversified drug-resistance solutions in viral sequences: a case study of hepatitis B virus

Abstract The study of mutational landscapes of viral proteins is fundamental for the understanding of the mechanisms of cross-resistance to drugs and the design of effective therapeutic strategies based on several drugs. Antiviral therapy with nucleos(t)ide analogues targeting the hepatitis B virus (HBV) polymerase protein (Pol) can inhibit disease progression by suppression of HBV replication and makes it an important case study. In HBV, treatment may fail due to the emergence of drug-resistant mutants. Primary and compensatory mutations have been associated with lamivudine resistance, whereas more complex mutational patterns are responsible for resistance to other HBV antiviral drugs. So far, all known drug-resistance mutations are located in one of the four Pol domains, called reverse transcriptase. We demonstrate that sequence covariation identifies drug-resistance mutations in viral sequences. A new algorithmic strategy, BIS2TreeAnalyzer, is designed to apply the coevolution analysis method BIS2, successfully used in the past on small sets of conserved sequences, to large sets of evolutionary related sequences. When applied to HBV, BIS2TreeAnalyzer highlights diversified viral solutions by discovering thirty-seven positions coevolving with residues known to be associated with drug resistance and located on the four Pol domains. These results suggest a sequential mechanism of emergence for some mutational patterns. They reveal complex combinations of positions involved in HBV drug resistance and contribute with new information to the landscape of HBV evolutionary solutions. The computational approach is general and can be applied to other viral sequences when compensatory mutations are presumed.
Histone deacetylases facilitate the accurate repair of broken forks

ABSTRACT We have recently uncovered that loss of the yeast histone deacetylases Rpd3 (Reduced Potassium Dependency 3) and Hda1 (Histone DeAcetylase 3) affects the cohesion between sister chromatids thus impairing repair of DNA damage at replication forks and enhancing genetic instability. Here we discuss the possible implications of our findings given that histone deacetylases are a promising chemotherapeutic target often used in combination with DNA damaging agents.
Prognostic Impact of Postoperative Complications following Salvage Esophagectomy for Esophageal Cancer after Definitive Chemoradiotherapy

Background: Recent studies have reported that the occurrence of postoperative complications after esophagectomy for esophageal cancer has a negative impact on long-term survival. Although salvage esophagectomy is associated with higher rates of morbidity and mortality, the impact of postoperative complications on long-term survival following salvage esophagectomy has not been fully investigated. Methods: We retrospectively analyzed 73 patients with thoracic esophageal cancer who underwent salvage esophagectomy between January 1997 and December 2017 after definitive chemoradiotherapy. We investigated the clinical impact of postoperative complications on long-term survival after salvage esophagectomy. Results: Postoperative complications, pulmonary complications, and anastomotic leakage occurred in 34 (47%), 14 (13%), and 14 (19%) of the patients, respectively. Patients with complications had significantly poorer survival than patients who did not have complications (HR [hazard ratio], 2.06; p = 0.017), but there were no significant differences in overall survival between patients with and those without pulmonary complications or anastomotic leakage (HR, 1.48, p = 0.318, and HR, 1.37, p = 0.377, respectively). Multivariate analysis revealed that pathological T3–4 disease (HR, 4.63; p = 0.001), residual disease (HR, 5.09; p = 0.001), and postoperative complications (HR, 3.85; p = 0.001) were significant independent prognostic factors. In particular, the frequency of death from other diseases among patients with postoperative complications was nonsignificantly higher than among patients without postoperative complications (26 vs. 10%; p = 0.071). Conclusion: The occurrence of complications leads to a poor prognosis for patients with esophageal cancer after salvage esophagectomy. Prevention of postoperative complications and long-term postoperative general supportive care might be important for improving patients’ prognosis.
Malnutrition in all its forms and socioeconomic status in Bolivia

Abstract Objective: To estimate the prevalence of malnutrition (undernutrition and excess BMI) among children under the age of 5 years and women of reproductive age in Bolivia considering three socioeconomic indicators: wealth, education and ethnicity. Design: We used the 2008 nationally representative Bolivian Demographic and Health Survey (DHS). Malnutrition’s prevalence was estimated by wealth, ethnicity and educational level. Wealth index was measured based on the DHS methodology and nutritional status by using WHO standards and indicators. Education level (EL) was categorized by years of formal education. Setting: Bolivia. Participants: In total, 5·903 children <5 years, 3·345 adolescent women (15–19 years) and 12·297 women (20–49 years) with available information on anthropometric measurements· Results: A disproportionate prevalence of malnutrition was observed among different wealth groups: lower wealth tertiles show the higher prevalence of stunting (>30 %) and anaemia (>40 %) in all ages· The prevalence of overweight and obesity tends to rise with age from childhood (10·02–11·60) to adolescence (27·9–31·03), reaching highest levels in women of reproductive age (56·02–57·76). According to wealth tertiles, higher prevalence of overweight and obesity was found in children of high tertile (12·23), adolescent women of low (32·56) and adult women of medium tertile (63·08). Conclusions: The present study shows that currently Bolivia is in a transitional stage, faces not only the problem of undernutrition but also those of overnutrition, showing strong inequalities according to socioeconomic and education status. This study calls for state-specific policies keeping in view of the nature of inequality in malnutrition in the country and its differential characteristics across wealth status.
Information System Project of the Smart City Clinic

It is proposed a new approach to healthcare research, considering the dynamic interaction of all subsystems. It is created a model of a modified operation of the health care institution in a smart city, which will allow to evaluate the effectiveness of correcting the effects of various risk factors on their functioning and to offer the most favorable ways of modifying the system both from the medical point of view (reduction of the sickness rate), and financial one (efficient use of funds)
Decitabine Response in Breast Cancer Requires Efficient Drug Processing and Is Not Limited by Multidrug Resistance

Dysregulation of DNA methylation is an established feature of breast cancers. DNA demethylating therapies like decitabine are proposed for the treatment of triple-negative breast cancers (TNBC) and indicators of response need to be identified. For this purpose, we characterized the effects of decitabine in a panel of 10 breast cancer cell lines and observed a range of sensitivity to decitabine that was not subtype specific. Knockdown of potential key effectors demonstrated the requirement of deoxycytidine kinase (DCK) for decitabine response in breast cancer cells. In treatment-naïve breast tumors, DCK was higher in TNBCs, and DCK levels were sustained or increased post chemotherapy treatment. This suggests that limited DCK levels will not be a barrier to response in patients with TNBC treated with decitabine as a second-line treatment or in a clinical trial. Methylome analysis revealed that genome-wide, region-specific, tumor suppressor gene–specific methylation, and decitabine-induced demethylation did not predict response to decitabine. Gene set enrichment analysis of transcriptome data demonstrated that decitabine induced genes within apoptosis, cell cycle, stress, and immune pathways. Induced genes included those characterized by the viral mimicry response; however, knockdown of key effectors of the pathway did not affect decitabine sensitivity suggesting that breast cancer growth suppression by decitabine is independent of viral mimicry. Finally, taxol-resistant breast cancer cells expressing high levels of multidrug resistance transporter ABCB1 remained sensitive to decitabine, suggesting that the drug could be used as second-line treatment for chemoresistant patients.
Comparison of the effects of hemodialysis and hemodiafiltration on left ventricular hypertrophy in end‐stage renal disease patients: A systematic review and meta‐analysis

Whether hemodiafiltration (HDF) is better than conventional hemodialysis (HD) in improving left ventricular hypertrophy (LVH), defined as reduction of the left ventricular mass index (LVMi) and increasing the ejection fraction (EF), is unclear. A systematic literature search was performed. Primary outcome was the mean difference between pre‐ and post‐procedural LVMi. Secondary outcome was the mean difference in EF. Seven studies with a total of 845 patients were included. The pooled mean difference between pre‐and post‐procedural LVMi was −8.0 g/m2 (95% confidence interval [CI] −13.1, −2.8). On subgroup analysis, the mean differences between pre‐ and post‐procedural LVMi for HD and HDF were −6.7 g/m2 (95% CI −14.5, 1.1) and −9.3 g/m2 (95% CI −16.3, −2.3), respectively (P for subgroups = .62). Pooled mean difference between pre‐ and post‐procedural EF was 2.4% (95% CI −1.8, 6.5). On subgroup analysis, the mean differences between pre‐ and post‐procedural EF for HD and HDF were 3.6% (95% CI −2.7, 9.8) and 2.0% (95% CI 2.9, 6.8), respectively (P for subgroups = .68). On meta‐regression, age (Beta −0.35 ± 0.05, P < .001) and longer dialysis duration (Beta −0.12 ± 0.02, P < .001) were associated with lower mean difference between pre‐and post‐procedural EF. No significant effects on changes in LVMi and EF were observed with HDF compared with conventional HD.
Preparation and characterization of poly(3-hydroxybutyrate-co-4-hydroxybutyrate)/pullulan-gelatin electrospun nanofibers with shell-core structure

In this study, hydrophilic pullulan, which is favorable for cell adhesion, proliferation, and differentiation, was selected as a modifier for the preparation of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-co-4HB))/pullulan nanofibers via electrospinning to improve the biocompatibility of P(3HB-co-4HB) and increase the drug loading of composite fibers. Alkyl polyglycoside was used as the emulsifying agent to promote emulsification and stabilize the P(3HB-co-4HB)/pullulan composite solution. Drug-loading property of the nanofibers with a shell-core structure is increased because gelatin was not formed into fibers via electrospinning, thereby forming a stable drug-containing gelatin solution in the core layer. Finally, P(3HB-co-4HB)/pullulan-gelatin shell-core nanofibers were prepared. The intermolecular interaction, morphology, crystallization properties, mechanical properties, morphology, sustained release, and biocompatibility of composite nanofibers were characterized. Results show that the crystallization property of P(3HB-co-4HB)/pullulan composite nanofibers increases continuously with an increase in the pullulan content. As the pullulan content increases, the strain and stress of P(3HB-co-4HB)/pullulan nanofibers increase initially and decrease later. At the mass ratio of P(3HB-co-4HB) to pullulan of 10:2, P(3HB-co-4HB)/pullulan composite nanofibers exhibit a uniform morphology with an average diameter of 590 nm and porosity of 70.71%. At this mass ratio, the P(3HB-co-4HB)/pullulan-gelatin/drug shell-core structure, which sustained a release effect for more than 180 h, has potential applications as biomaterials without cytotoxicity.
Antimicrobial Activity of a Phage Mixture and a Lactic Acid Bacterium against Staphylococcus aureus from Bovine Mastitis

The antimicrobial activity of a phage mixture and a lactic acid bacterium against Staphylococcus aureus isolates from bovine origin was investigated in vitro with regard to possible applications in the therapy of udder inflammation (mastitis) caused by bacterial infections. The S. aureus isolates used for inoculation derived from quarter foremilk samples of mastitis cases. For the examination of the antimicrobial activity, the reduction of the S. aureus germ density was determined [log10 cfu/mL]. The phage mixture consisted of the three obligatory lytic and S. aureus-specific phages STA1.ST29, EB1.ST11 and EB1.ST27 (1:1:1). The selected Lactobacillus plantarum strain with proven antimicrobial properties and the phage mixture were tested against S. aureus in milk, both alone and in combination. The application of the lactic acid bacterium showed only a low reduction ability for a 24 h incubation period. The bacteriophage mixture as well as its combination with the lactic acid bacterium showed high antimicrobial activity against S. aureus for a 24 h incubation period at 37 °C, with only the phage mixture showing significance.
The Interfacial Adhesion Performance and Mechanism of a Modified Asphalt–Steel Slag Aggregate

The interfacial adhesion between asphalt and steel slag aggregate is a decisive factor in the formation of an asphalt–steel slag mixture and significantly affects the quality stability of steel slag–asphalt mixtures. In this study, the adhesion between an asphalt and steel slag aggregate, the interfacial microstructure, the adsorption and desorption characteristics, and chemical reactions were, respectively, explored by a PosiTestAT–A adhesion puller, a scanning electron microscope, a net adsorption test, an infrared spectrometer, and a dynamic shear rheometer. The mechanism of adhesion between the asphalt and steel slag aggregate was analyzed from the perspectives of physical adsorption and chemical reactions. The results showed that different factors had different effects on the adhesion of asphalt–steel slag aggregate interface. The freeze–thaw cycle and steel slag aggregate particle size had significant effects on interfacial adhesion, while the asphalt heating temperature, water bath time, and stirring time had relatively weak effects on interfacial adhesion. Compared to a limestone aggregate, the steel slag–asphalt mixture had greater adhesion and better adhesion performance because the pits and textures on the surface of the steel slag aggregate produced a skeleton–like effect that strengthened the phase strength of the asphalt–slag aggregate interface, thereby improving the adhesion and increasing the physical adsorption between the asphalt and steel slag aggregate. In addition, due to the N–H stretching vibrations of the amines and amides, as well as SiO–H stretching vibrations, a chemical reaction occurred between the asphalt and steel slag aggregate, thus improving the adhesion performance between the asphalt and steel slag. Based on the shape of the adsorption isotherm, it was determined that the adsorption type was multi–molecular layer adsorption, indicating that the adhesion between the asphalt and steel slag mainly involved physical adsorption.
Molecular Epidemiological Survey of Prophages in MRSA Isolates in Taiwan

Introduction The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) type SCCmec IV or V is increasing in Taiwan. It has been suggested that the surface protein SasX is responsible for their transmission. However, the sasX gene was not detected in our SCCmec IV or V isolates. Since sasX was originally found in S. epidermidis and believed to be transferred to S. aureus by a prophage, studies were conducted to detect and type this prophage in our clinical isolates. Materials and Methods A total of 1192 MRSA isolates collected from 2006 to 2014 were examined. Multiplex PCRs were performed to determine SCCmec, sasX, and prophage types. Results The prevalence of SCCmec IV and V isolates was increased in recent years (from 2006 to 2014). The sasX gene was present in most SCCmec III isolates but was absent in SCCmec IV or V isolates. The Sa5 prophage was found only in SCCmec IV and SCCmec V (or Vt) isolates, and the Sa6 prophage was mainly present in SCCmec III isolates. MRSA isolates harboring prophage combinations Sa1, Sa2, and Sa3; Sa2 and Sa3; Sa2, Sa3, and Sa7; or Sa2 and Sa7 were mainly of SCCmec II, and those that harbored prophage combinations Sa3 and Sa6; Sa3, Sa6, and Sa7; or Sa3 and Sa7 were mostly of SCCmec III. The numbers of SCCmec II isolates containing prophages Sa2, Sa3, and Sa7 and those of SCCmec III isolates containing prophages Sa3 and Sa6 or Sa3, Sa6, and Sa7 were decreased from 2010 to 2014. The number of SCCmec IV isolates with prophage Sa3 or prophages Sa3 and Sa5 was decreased, but that of those with prophage Sa6 or prophages Sa2 and Sa3 was increased from 2010 to 2014. Conclusion The sasX gene was found to play no role in clonal selection of MRSA. The finding that different SCCmec types of MRSA harbored different types of prophages suggests that these prophages may affect the survival and clonal expansion of certain types of MRSA.
PPARγ and Its Agonists in Chronic Kidney Disease

Chronic kidney disease (CKD) has become a global healthcare issue. CKD can progress to irreversible end-stage renal diseases (ESRD) or renal failure. The major risk factors for CKD include obesity, diabetes, and cardiovascular diseases. Understanding the key process involved in the disease development may lead to novel interventive strategies, which is currently lagging behind. Peroxisome proliferator-activated receptor γ (PPARγ) is one of the ligand-activated transcription factor superfamily members and is globally expressed in human tissues. Its agonists such as thiazolidinediones (TZDs) have been applied as effective antidiabetic drugs as they control insulin sensitivity in multiple metabolic tissues. Besides, TZDs exert protective effects in multiple other CKD risk disease contexts. As PPARγ is abundantly expressed in major kidney cells, its physiological roles in those cells have been studied in both cell and animal models. The function of PPARγ in the kidney ranges from energy metabolism, cell proliferation to inflammatory suppression, although major renal side effects of existing agonists (including TZDs) have been reported, which limited their application in treating CKD. In the current review, we systemically assess the function of PPARγ in CKDs and the benefits and current limitations of its agonists in the clinical applications.
Molecular and Morphological Characterization of Two Novel Species Collected from Soil in Korea

Abstract Two fungal species of ascomycetes were discovered during the screening of soil microflora from the Gangwon Province in Korea: Didymella chlamydospora sp. nov. (YW23-14) and Microdochium salmonicolor sp. nov. (NC14-294). Morphologically, YW23-14 produces smaller chlamydospores (8.0–17.0 × 7.0–15.0 µm) than D. glomerata and D. musae. The strain NC14-294 was characterized by smaller conidiogenous cells (4.9–8.8 × 2.0–3.2 µm) compared with the closest strains M. fisheri and M. phragmitis. The detailed descriptions, illustrations, and discussions regarding the morphological and phylogenetical analyses of the closely related species are provided to support the novelty of each species. Thus, YW23-14 and NC14-294 are described here as newly discovered species.
Location of neonatal microglia drives small extracellular vesicles content and biological functions in vitro

ABSTRACT Combining proteomics and systems biology approaches, we demonstrate that neonatal microglial cells derived from two different CNS locations, cortex and spinal cord, and cultured in vitro displayed different phenotypes upon different physiological or pathological conditions. These cells also exhibited greater variability in terms of cellular and small extracellular vesicles (sEVs) protein content and levels. Bioinformatic data analysis showed that cortical microglia exerted anti-inflammatory and neurogenesis/tumorigenesis properties, while the spinal cord microglia were more inflammatory. Interestingly, while both sEVs microglia sources enhanced growth of DRGs processes, only the spinal cord-derived sEVs microglia under LPS stimulation significantly attenuated glioma proliferation. These results were confirmed using the neurite outgrowth assay on DRGs cells and glioma proliferation analysis in 3D spheroid cultures. Results from these in vitro assays suggest that the microglia localized at different CNS regions can ensure different biological functions. Together, this study indicates that neonatal microglia locations regulate their physiological and pathological functional fates and could affect the high prevalence of brain vs spinal cord gliomas in adults.