Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver

Chickens are one of the most important sources of meat worldwide, and the occurrence of fatty liver syndrome (FLS) is closely related to production efficiency. However, the potential mechanism of FLS remains poorly understood. An integrated analysis of data from whole-genome bisulfite sequencing and long noncoding RNA (lncRNA) sequencing was conducted. A total of 1177 differentially expressed genes (DEGs) and 1442 differentially methylated genes (DMGs) were found. There were 72% of 83 lipid- and glucose-related genes upregulated; 81% of 150 immune-related genes were downregulated in fatty livers. Part of those genes was within differentially methylated regions (DMRs). Besides, sixty-seven lncRNAs were identified differentially expressed and divided into 13 clusters based on their expression pattern. Some lipid- and glucose-related lncRNAs (e.g., LNC_006756, LNC_012355, and LNC_005024) and immune-related lncRNAs (e.g., LNC_010111, LNC_010862, and LNC_001272) were found through a co-expression network and functional annotation. From the expression and epigenetic profiles, 23 target genes (e.g., HAO1, ABCD3, and BLMH) were found to be hub genes that were regulated by both methylation and lncRNAs. We have provided comprehensive epigenetic and transcriptomic profiles on FLS in chicken, and the identification of key genes and epigenetic markers will expand our understanding of the molecular mechanism of chicken FLS.
Determinants of prelacteal feeding practices among mothers of children aged less than 24 months in Ile-Ife Southwest Nigeria: a community cross-sectional study

Introduction Prelacteal feeding remains an obstacle in achieving the best breastfeeding practices in the country. The growing poor breastfeeding practices are made worse by the continued engagement of the communities in prelacteal feeding practices. This study aimed at assessing the determinants of prelacteal feeding among mothers of children aged less than 24 months in Ile-Ife Southwest, Nigeria. Methods A community-based cross-sectional study that employed quantitative and qualitative methods. Two hundred and fifty-five (255) mother with children aged 0-23 months were recruited into the study using a multistage sampling technique. SPSS version 20 was used for data analysis Descriptive statistics, bivariate and multivariable logistic regression analysis was done. Results In this study, 26.3% of children were given prelacteal feeds. Glucose water (46.3%), sugar water (25.4%) and infant formula (17.9%) were commonly given prelacteal feeds. On multivariate analysis initiating breastfeeding after one hour (Adjusted Odds Ratio (AOR): 2.74, 95% CI 1.43, 5.23), not attending antenatal clinic (AOR = 2.52, 95% CI 1.05, 5.33), delivery via caesarian section 52% (AOR = 1.52, 95 % CI 1.10, 6.34) were associated with increased odds of giving prelacteal feeds. Delivery attended by health professional 25% (AOR = 0.75. 95% CI 0.42, 0.97), highest wealth quintiles 21% (AOR =0.79, 95 % CI 0.51, 0.94) were associated with lowers odds of giving prelacteal feeds. Conclusion Prelacteal feeding was prevalent in the study community and associated with community, individual and health service-related factors. Intervention that strengthens individual and community access to appropriate health information and maternal health services is vital in reducing prelacteal feeding practices.
Manipulation of Ascorbate Biosynthetic, Recycling, and Regulatory Pathways for Improved Abiotic Stress Tolerance in Plants

Abiotic stresses, such as drought, salinity, and extreme temperatures, are major limiting factors in global crop productivity and are predicted to be exacerbated by climate change. The overproduction of reactive oxygen species (ROS) is a common consequence of many abiotic stresses. Ascorbate, also known as vitamin C, is the most abundant water-soluble antioxidant in plant cells and can combat oxidative stress directly as a ROS scavenger, or through the ascorbate–glutathione cycle—a major antioxidant system in plant cells. Engineering crops with enhanced ascorbate concentrations therefore has the potential to promote broad abiotic stress tolerance. Three distinct strategies have been utilized to increase ascorbate concentrations in plants: (i) increased biosynthesis, (ii) enhanced recycling, or (iii) modulating regulatory factors. Here, we review the genetic pathways underlying ascorbate biosynthesis, recycling, and regulation in plants, including a summary of all metabolic engineering strategies utilized to date to increase ascorbate concentrations in model and crop species. We then highlight transgene-free strategies utilizing genome editing tools to increase ascorbate concentrations in crops, such as editing the highly conserved upstream open reading frame that controls translation of the GDP-L-galactose phosphorylase gene.
Clinical vs Microscopic Extranodal Extension and Survival in Oropharyngeal Carcinoma in the Human Papillomavirus Era

Objective Extranodal extension (ENE) is known to be associated with poor outcomes in head and neck squamous cell carcinoma. The objective of this study is to examine the impact of extent of ENE on survival in oropharyngeal carcinoma in the human papillomavirus (HPV) era. Study Design Retrospective database review. Setting Review of the National Cancer Database. Subjects and Methods The National Cancer Database was used to examine surgically treated head and neck squamous cell carcinoma of the tonsil and base of tongue from 2010 to 2015. Nodes available for pathologic examination were classified as ENE negative (–), ENE clinically (+), or ENE (+) on pathology only. The primary outcome was overall survival. Cox regression modeling was used to examine the effect of ENE on survival while controlling for patient demographics, HPV status, stage, adjuvant radiation, and chemotherapy. Results Of the 66,106 patients identified, 16,845 were treated with surgery ± adjuvant therapy, 8780 of whom were known HPV+. Overall 5-year survival for this group was 86%. Documented ENE was associated with over a 60% decrease in survival for clinical (hazard ratio [HR], 1.63) and pathologic (HR, 1.62) ENE compared to negative ENE, after adjustment for stage, adjuvant radiation ± chemotherapy, HPV, and other variables. No significant differences were found between clinical and pathologic ENE (HR, 1.001). Conclusion While both surgically resected clinical and pathologic ENE are associated with decreased survival, no significant differences are observed between the two. The impact of these observations on potential de-escalation therapeutic strategies requires further study.
Molecular and Clinical Characterization of Multidrug-Resistant and Hypervirulent Klebsiella pneumoniae Strains from Liver Abscess in Taiwan

Hypervirulent Klebsiella pneumoniae strains are the major cause of liver abscesses throughout East Asia, and these strains are usually antibiotic susceptible. Recently, multidrug-resistant and hypervirulent (MDR-HV) K. pneumoniae strains have emerged due to hypervirulent strains acquiring antimicrobial resistance determinants or the transfer of a virulence plasmid into a classic MDR strain. In this study, we characterized the clinical and microbiological properties of K. pneumoniae liver abscess (KPLA) caused by MDR-HV strains in Taiwan. ABSTRACT Hypervirulent Klebsiella pneumoniae strains are the major cause of liver abscesses throughout East Asia, and these strains are usually antibiotic susceptible. Recently, multidrug-resistant and hypervirulent (MDR-HV) K. pneumoniae strains have emerged due to hypervirulent strains acquiring antimicrobial resistance determinants or the transfer of a virulence plasmid into a classic MDR strain. In this study, we characterized the clinical and microbiological properties of K. pneumoniae liver abscess (KPLA) caused by MDR-HV strains in Taiwan. Patients with community onset KPLA were retrospectively identified at Taipei Veterans General Hospital during January 2013 to May 2018. Antimicrobial resistance mechanisms, capsular types, and sequence types were determined. MDR-HV strains and their parental antimicrobial-susceptible strains further underwent whole-genome sequencing (WGS) and in vivo mice lethality tests. Thirteen MDR-HV strains were identified from a total of 218 KPLA episodes. MDR-HV strains resulted in similar outcomes to antimicrobial-susceptible strains. All MDR-HV strains were traditional hypervirulent clones carrying virulence capsular types. The major resistance mechanisms were the overexpression of efflux pumps and/or the acquisition of ESBL or AmpC β-lactamase genes. WGS revealed that two hypervirulent strains had evolved to an MDR phenotype due to mutation in the ramR gene and the acquisition of an SHV-12-bearing plasmid, respectively. Both these MDR-HV strains retained high virulence compared to their parental strains. The spread of MDR-HV K. pneumoniae strains in the community raises significant public concerns, and measures should be taken to prevent the further acquisition of carbapenemase and other resistance genes among these strains in order to avoid the occurrence of untreatable KPLA.
Bone Adaptation in Adult Women Is Related to Loading Dose: A 12‐Month Randomized Controlled Trial

Although strong evidence exists that certain activities can increase bone density and structure in people, it is unclear what specific mechanical factors govern the response. This is important because understanding the effect of mechanical signals on bone could contribute to more effective osteoporosis prevention methods and efficient clinical trial design. The degree to which strain rate and magnitude govern bone adaptation in humans has never been prospectively tested. Here, we studied the effects of a voluntary upper extremity compressive loading task in healthy adult women during a 12‐month prospective period. A total of 102 women age 21 to 40 years participated in one of two experiments: (i) low (n = 21) and high (n = 24) strain magnitude; or (ii) low (n = 21) and high (n = 20) strain rate. Control (n = 16) no intervention. Strains were assigned using subject‐specific finite element models. Load cycles were recorded digitally. The primary outcome was change in ultradistal radius integral bone mineral content (iBMC), assessed with QCT. Interim time points and secondary outcomes were assessed with high resolution pQCT (HRpQCT) at the distal radius. Sixty‐six participants completed the intervention, and interim data were analyzed for 77 participants. Likely related to improved compliance and higher received loading dose, both the low‐strain rate and high‐strain rate groups had significant 12‐month increases to ultradistal iBMC (change in control: −1.3 ± 2.7%, low strain rate: 2.7 ± 2.1%, high strain rate: 3.4 ± 2.2%), total iBMC, and other measures. “Loading dose” was positively related to 12‐month change in ultradistal iBMC, and interim changes to total BMD, cortical thickness, and inner trabecular BMD. Participants who gained the most bone completed, on average, 128 loading bouts of (mean strain) 575 με at 1878 με/s. We conclude that signals related to strain magnitude, rate, and number of loading bouts contribute to bone adaptation in healthy adult women, but only explain a small amount of variance in bone changes. © 2020 The Authors. Journal of Bone and Mineral Research published by American Society for Bone and Mineral Research.
In Vivo Positive Magnetic Resonance Imaging Applications of Poly(methyl vinyl ether-alt-maleic acid)-coated Ultra-small Paramagnetic Gadolinium Oxide Nanoparticles

The study of ultra-small paramagnetic gadolinium oxide (Gd2O3) nanoparticles (NPs) as in vivo positive (T1) magnetic resonance imaging (MRI) contrast agents is one of the most attractive fields in nanomedicine. The performance of the Gd2O3 NP imaging agents depends on the surface-coating materials. In this study, poly(methyl vinyl ether-alt-maleic acid) (PMVEMA) was used as a surface-coating polymer. The PMVEMA-coated paramagnetic ultra-small Gd2O3 NPs with an average particle diameter of 1.9 nm were synthesized using the one-pot polyol method. They exhibited excellent colloidal stability in water and good biocompatibility. They also showed a very high longitudinal water proton spin relaxivity (r1) value of 36.2 s−1mM−1 (r2/r1 = 2.0; r2 = transverse water proton spin relaxivity) under a 3.0 tesla MR field which is approximately 10 times higher than the r1 values of commercial molecular contrast agents. High positive contrast enhancements were observed in in vivo T1 MR images after intravenous administration of the NP solution sample, demonstrating its potential as a T1 MRI contrast agent.
Oxygen and SO2 Consumption of Different Enological Tannins in Relationship to Their Chemical and Electrochemical Characteristics

The oxidative behavior of five commercial enological tannins of different sources (tea, grape marc, grape seed, untoasted oak, and toasted oak) was investigated in model wine solutions in the presence or absence of SO2. Solutions of the tannins were also analyzed for total phenolics, methyl cellulose precipitable tannins, high-performance liquid chromatography, and linear sweep voltammetry. Tea and oak-derived tannin solutions were characterized by the highest oxygen consumption rates, with oak-derived tannins exhibiting the highest oxygen consumption rates per milligram of phenolic material present. Linear sweep and derivative voltammetry parameters were well-correlated with oxygen consumption rates, whereas total phenolics or total tannins were not. All tannins were associated with consumption of SO2 upon reaction with oxygen, with the lowest rate of SO2 lost per milligram of O2 reacted being observed for oak tannins.
Beneficial effects of paricalcitol on cardiac dysfunction and remodelling in a model of established heart failure

The synthetic vitamin D3 analogue paricalcitol acts as a selective activator of the vitamin D receptor (VDR). While there is evidence for cardioprotective effects of paricalcitol associated with the VDR pathway, less information is available about the structural and functional cardiac effects of paricalcitol on established heart failure (HF) and particularly its effects on associated electrophysiological or Ca2+ handling remodelling.
Pathological characterization of keel bone fractures in laying hens does not support external trauma as the underlying cause

Keel bone fractures in laying hens have been described with increasing prevalence from several countries over the last twenty years and are considered one of the greatest welfare problems to the layer industry. In Denmark we have observed fracture prevalence in the range of 53% to 100% in flocks from cage-free systems whereas flock prevalences in birds from enriched cages ranged between 50–98%. Previous research have speculated that the underlying reason for the development of keel bone fractures is trauma in relation to impact of the bird with furniture, other equipment etc. However, little evidence of this theory has been provided. Predisposing factors have also been suggested including genetics of the bird, lack of specific feedstuff components, high egg production, management factors and layer fatigue. This study has addressed the possible pathogenesis of these fractures by pathological characterization of fractures in birds from different production systems. More than 60 keel bones with fractures have been characterized histo-pathologically and by CT scan. This included an assessment of damage to muscles and soft tissues, the bone and the healing process including callus formation. This investigation has shown that high energy collisions cannot be responsible for the majority of fractures, located at the caudal tip of the keel bone, observed in laying birds as markers associated trauma were not observed in the majority of the cases just as few recognized healing processes were observed. These results suggest an alternative pathogenesis to trauma.
Study of the Phase Transitions in the Binary System NPG-TRIS for Thermal Energy Storage Applications

Neopentylglycol (NPG) and tris(hydroxymethyl)aminomethane (TRIS) are promising phase change materials (PCMs) for thermal energy storage (TES) applications. These molecules undergo reversible solid-solid phase transitions that are characterized by high enthalpy changes. This work investigates the NPG-TRIS binary system as a way to extend the use of both compounds in TES, looking for mixtures that cover transition temperatures different from those of pure compounds. The phase diagram of NPG-TRIS system has been established by thermal analysis. It reveals the existence of two eutectoids and one peritectic invariants, whose main properties as PCMs (transition temperature, enthalpy of phase transition, specific heat and density) have been determined. Of all transitions, only the eutectoid at 392 K shows sufficiently high enthalpy of solid-solid phase transition (150–227 J/g) and transition temperature significantly different from that of the solid-state transitions of pure compounds (NPG: 313 K; TRIS: 407 K). Special attention has also been paid to the analysis of metastability issues that could limit the usability of NPG, TRIS and their mixtures as PCMs. It is proven that the addition of small amounts of expanded graphite microparticles contributes to reduce the subcooling phenomena that characterizes NPG and TRIS and solve the reversibility problems observed in NPG/TRIS mixtures.
Meeting Calorie and Protein Needs in the Critical Care Unit: A Prospective Observational Pilot Study

Background: Inadequate calorie and protein intake during critical illness is associated with poor clinical outcomes. Unfortunately, most critically ill patients do not consume adequate levels of these nutrients. An enteral formula with appropriate macronutrient composition may assist patients in meeting nutritional goals. Design: This study was a single center, prospective, observational study of 29 adults in the medical intensive care unit who required enteral nutrition for at least 3 days. Subjects received a calorically dense, enzymatically hydrolyzed 100% whey peptide-based enteral formula for up to 5 days to assess the ability to achieve 50% of caloric goals within the first 3 days (primary outcome), the daily percentage of protein goals attained and gastrointestinal tolerance (secondary outcomes). Result: A total of 29 subjects consented and began the study. Four subjects dropped out before first day and 25 subjects were included in analyses. Subjects were aged 55.5 ± 16.9 years with mean body mass index (BMI) of 27.9 ± 7.5 kg/m2. Most (92%) subjects were on a mechanical ventilator and experienced organ failure. At least 50% of caloric and protein goals were achieved in 78.9% and 73.7% of the subjects, respectively, during the first 3 days. Overall, 75.0 ± 26.3% and 69.3 ± 26.7% of calorie and protein goals were achieved using the study formula. Conclusions: Subjects fed enterally with a calorically dense, enzymatically hydrolyzed 100% whey peptide-based enteral formula exceeded 50% of caloric and protein goals in most critically ill subjects included in this study. Use of study formula did not lead to severe gastrointestinal intolerance.
Effect of Recycled Iron Powder as Fine Aggregate on the Mechanical, Durability, and High Temperature Behavior of Mortars

This study evaluates the mechanical, durability, and residual compressive strength (after being exposed to 20, 120, 250, 400 and 600 °C) of mortar that uses recycled iron powder (RIP) as a fine aggregate. Within this context, mechanical strength, shrinkage, durability, and residual strength tests were performed on mortar made with seven different percentages (0%, 5%, 10%, 15%, 20%, 30% and 50%) of replacement of natural sand (NS) by RIP. It was found that the mechanical strength of mortar increased when replaced with up to 30% NS by RIP. In addition, the increase was 30% for compressive, 18% for tensile, and 47% for flexural strength at 28 days, respectively, compared to the reference mortar (mortar made with 100% NS). Shrinkage was observed for the mortar made with 100% NS, while both shrinkage and expansion occurred in the mortar made with RIP, especially for RIP higher than 5%. Furthermore, significantly lower porosity and capillary water absorption were observed for mortar made with up to 30% RIP, compared to that made with 100% NS, which decreased by 36% for porosity and 48% for water absorption. As the temperature increased, the strength decreased for all mixes, and the drop was more pronounced for the temperatures above 250 °C and 50% RIP. This study demonstrates that up to 30% RIP can be utilized as a fine aggregate in mortar due to its better mechanical and durability performances.
Liver enzyme variability and risk of heart disease and mortality: A nationwide population‐based study

Liver enzymes, such as alanine aminotransferase (ALT), aspartate aminotransferase (AST) and γ‐glutamyltransferase (GGT), have been suggested as surrogate markers of various cardiovascular diseases. However, previous studies assessed liver enzymes only once at baseline. We investigated the association between liver enzyme variability and the risk of mortality and cardiovascular outcomes in general population.
Predictors of chronic kidney disease in obstructive sleep apnea patients

Introduction Obstructive sleep apnea (OSA) is a common condition in patients with chronic kidney disease (CKD). It may worsen renal function in CKD patients and is associated with uncontrolled blood pressure. Although OSA is found in up to 80% of CKD patients, there are limited data available on its clinical features in patients with and without CKD. Objective This study aimed to identifying the differences in the clinical characteristics of OSA between CKD and non-CKD OSA patients and determine the clinical predictors for CKD in OSA patients. Methods This was a retrospective study conducted at Khon Kaen University's Srinagarind Hospital in Thailand between July and December 2018. The inclusion criteria were diagnosis with OSA via polysomnography and having undergone laboratory tests for CKD. Obstructive sleep apnea is diagnosed according to the apnea-hypopnea index (AHI) as experiencing ≥5 events/hour, while CKD diagnosed based on the KDOQI guidelines. Eligible patients were divided into two groups: OSA with CKD and OSA without CKD. Predictors of CKD in OSA patients were analyzed using multivariate logistic regression analysis. Results During the study period, there were 178 OSA patients who met the study criteria, 88 (49.44%) of whom were in the OSA with CKD group. Both age and body mass index were comparable between OSA patients with CKD and those without (age: 59 and 57 years, respectively; body mass index: 30 and 29 kg/m2, respectively. There were three significant factors that differed between those with and without CKD group including systolic blood pressure (147 vs 135 mmHg), proportion of patients with diabetes (55% vs 34%), and proportion of patients with Mallampati scores of 3-4 (73% vs 39%). There were three independent predictors for OSA in patients with CKD: female sex, high systolic blood pressure, and Mallampati score of 3 or 4, with adjusted odds ratios (95% confidence interval) of 4.624 (1.554, 13.750), 1.060 (1.020, 1.101), and 2.816 (1.356, 5.849), respectively. The Hosmer-Lemeshow chi-square statistic of the predictive model was 6.06 (p 0.640). Systolic blood pressure of more than 130 and 150 mmHg resulted in sensitivity of 84.21% and specificity of 81.40%, respectively. Conclusions Female sex, high systolic blood pressure, and Mallampati score of 3-4 were suggestive of OSA with CKD. Obstructive sleep apnea patients with one or more of these predictors may have a high risk of CKD.