Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effects of Anterior Cruciate Ligament Reconstruction on Individual Quadriceps Muscle Thickness and Circulating Biomarkers

Anterior cruciate ligament reconstruction (ACLR) frequently results in quadriceps atrophy. The present study investigated the effect of ACLR on the muscle thickness of the different constituent muscles of the quadriceps and circulating biomarkers related to muscle atrophy and hypertrophy. Fourteen subjects underwent anterior cruciate ligament reconstruction following injury. Quadriceps muscle thicknesses were measured using ultrasound, and circulating biomarkers in the blood were measured using enzyme-linked immunosorbent assays (ELISAs) at the preoperative visit (PRE) and at two postoperative visits (PO1, PO2) in the early stages post-surgery. Differences between time points were analyzed using one-way repeated measures analysis of variance (ANOVA) tests. The most important finding was that severe muscle atrophy occurred in the vastus intermedius (VI) after ACLR (PRE: 20.45 ± 6.82 mm, PO1: 16.05 ± 6.13 mm, PO2: 13.18 ± 4.7 mm, F = 59.0, p < 0.001). Furthermore, the myostatin level was slightly increased, and IGF-1 was significantly reduced throughout the entire period. Therefore, we suggest that inducing selective hypertrophy in the vastus intermedius during the process of rehabilitation would be important for athletes and individuals who engage in explosive sports. Moreover, inhibiting myostatin level increases and maintaining IGF-1 levels in the early phase of recovery after ACLR to prevent muscle atrophy may provide a pharmaceutical option for rehabilitation after anterior cruciate ligament injury.
Caspase-4 Mediates Restriction of Burkholderia pseudomallei in Human Alveolar Epithelial Cells

Melioidosis is an infectious disease with a high mortality rate responsible for community-acquired sepsis in Southeast Asia and Northern Australia. The causative agent of this disease is Burkholderia pseudomallei, a Gram-negative bacterium that resides in soil and contaminated natural water. After entering into host cells, the bacteria escape into the cytoplasm, which has numerous cytosolic sensors, including the noncanonical inflammatory caspases. ABSTRACT Melioidosis is an infectious disease with a high mortality rate responsible for community-acquired sepsis in Southeast Asia and Northern Australia. The causative agent of this disease is Burkholderia pseudomallei, a Gram-negative bacterium that resides in soil and contaminated natural water. After entering into host cells, the bacteria escape into the cytoplasm, which has numerous cytosolic sensors, including the noncanonical inflammatory caspases. Although the noncanonical inflammasome (caspase-11) has been investigated in a murine model of B. pseudomallei infection, its role in humans, particularly in lung epithelial cells, remains unknown. We, therefore, investigated the function of caspase-4 (ortholog of murine caspase-11) in intracellular killing of B. pseudomallei. The results showed that B. pseudomallei induced caspase-4 activation at 12 h postinfection in human alveolar epithelial A549 cells. The number of intracellular B. pseudomallei bacteria was increased in the absence of caspase-4, suggesting its function in intracellular bacterial restriction. In contrast, a high level of caspase-4 processing was observed when cells were infected with lipopolysaccharide (LPS) mutant B. pseudomallei. The enhanced bacterial clearance in LPS-mutant-infected cells is also correlated with a higher degree of caspase-4 activation. These results highlight the susceptibility of the LPS mutant to caspase-4-mediated intracellular bacterial killing.
Genetic Characteristics and Pathogenicity Analysis in Chickens and Mice of Three H9N2 Avian Influenza Viruses

H9N2 avian influenza is a remarkable disease that has circulated in domestic poultry in large regions of China and posed a serious threat to the poultry industry. The H9N2 virus can not only infect mammals directly, but also provide gene segments to generate novel, but lethal human reassortants. Therefore, it is important to study the evolution, pathogenicity, and transmission of the H9N2 virus. In this study, three H9N2 viruses isolated from chickens in different layer farms were identified. Phylogenetic analysis revealed that these H9N2 viruses were all multiple genotype reassortants, with genes originating from Y280-like, F/98-like, and G1-like viruses. Animal studies indicated that the AV1535 and AV1548 viruses replicated efficiently in the lungs, tracheas, spleens, kidneys, and brains of chickens; the viruses shed for at least 11 days post-inoculation (DPI) and were transmitted efficiently among contact chickens. The AV1534 virus replicated poorly in chickens, shed for 7 DPI, and were not transmitted efficiently among contact chickens. The AV1534 virus replicated well in mice lungs and caused about 2% weight loss. The AV1535 and AV1548 viruses were not able to replicate in the lungs of mice. Our results indicate that we should pay attention to H9N2 avian influenza virus surveillance in poultry and changes in the pathogenicity of them to mammals.
Persistent, bioaccumulative, and toxic properties of liquid crystal monomers and their detection in indoor residential dust

Significance Liquid crystal devices, such as smartphones, televisions, and tablet computers, have become integral tools of modern society; however, people do not know the environmental effects of liquid crystal monomers (LCMs). The present study conducted an extensive survey on industries producing LCMs and generated a list containing 362 current-produced LCMs. Eighty-seven out of 362 LCMs showed potential as P&B chemicals, indicating that these LCMs would exhibit resistance to degradation and high mobility after entering the environment. Beyond that, we observed that exposure to LCMs resulted in adverse effects during in vitro screening, by use of cell culture and toxicogenomic evaluation, that were similar to effects observed for other persistent organic pollutants, and that some LCMs were detectable in samples of indoor dust. Liquid crystal monomers (LCMs) are used widely in liquid crystal displays (LCDs), which are dramatically changing the world due to the provision of convenient communication. However, there are essentially no published reports on the fate and/or effects of LCMs in the environment. Of 362 currently produced LCMs, 87 were identified as persistent and bioaccumulative (P&B) chemicals, which indicated that these chemicals would exhibit resistance to degradation and exhibit mobility after entering the environment. Following exposure to mixtures of LCM collected from 6 LCD devices, significant modulation of 5 genes, CYP1A4, PDK4, FGF19, LBFABP, and THRSP, was observed in vitro. Modulation of expressions of mRNAs coding for these genes has frequently been reported for toxic (T) persistent organic pollutants (POPs). In LCM mixtures, 33 individual LCMs were identified by use of mass spectrometry and screened for in 53 samples of dust from indoor environments. LCMs were detectable in 47% of analyzed samples, and 17 of the 33 LCMs were detectable in at least 1 sample of dust. Based on chemical properties, including P&B&T of LCMs and their ubiquitous detection in dust samples, the initial screening information suggests a need for studies to determine status and trends in concentrations of LCMs in various environmental matrices as well as tissues of humans and wildlife. There is also a need for more comprehensive in vivo studies to determine toxic effects and potencies of LCMs during chronic, sublethal exposures.
Mercury Exposure, Fish Consumption, and Perceived Risk among Pregnant Women in Coastal Florida

Seafood consumption is the primary source of mercury (Hg) exposure, particularly among coastal populations. Hg exposure during pregnancy has been associated with cognitive impairment, as well as decrements in memory, attention, fine motor skills, and other markers of delayed neurodevelopment, although results are conflicting. High Hg hair concentrations in persons from coastal Florida, USA, have been previously reported. The purpose of the current study was to determine the concentrations of total Hg (THg) in the hair of pregnant women from this area and to assess the relationships between THg concentration, knowledge of the risks of mercury exposure, and dietary patterns among participants. Participants (n = 229) were recruited at prenatal clinics. Their mean total hair Hg concentration was 0.31 + 0.54 µg/g, lower or similar to US data for women of child-bearing age. Hair THg concentration was associated with consumption of locally caught fish and all seafood, a higher level of education, and first pregnancy. Eighty-five percent of women were aware of the risks of mercury exposure during pregnancy; over half reported a decrease in seafood consumption during pregnancy. Awareness of Hg in fish was marginally associated with lower hair THg concentration (p = 0.06) but reduction in seafood consumption during pregnancy was not.
Quantification of bile acids: a mass spectrometry platform for studying gut microbe connection to metabolic diseases[S]

Bile acids (BAs) serve multiple biological functions, ranging from the absorption of lipids and fat-soluble vitamins to serving as signaling molecules through the direct activation of dedicated cellular receptors. Synthesized by both host and microbial pathways, BAs are increasingly understood as participating in the regulation of numerous pathways relevant to metabolic diseases, including lipid and glucose metabolism, energy expenditure, and inflammation. Quantitative analyses of BAs in biological matrices can be problematic due to their unusual and diverse physicochemical properties, making optimization of a method that shows good accuracy, precision, efficiency of extraction, and minimized matrix effects across structurally distinct human and murine BAs challenging. Herein we develop and clinically validate a stable-isotope-dilution LC/MS/MS method for the quantitative analysis of numerous primary and secondary BAs in both human and mouse biological matrices. We also utilize this tool to investigate gut microbiota participation in the generation of structurally specific BAs in both humans and mice. We examine circulating levels of specific BAs and in a clinical case-control study of age- and gender-matched type 2 diabetes mellitus (T2DM) versus nondiabetics. BAs whose circulating levels are associated with T2DM include numerous 12α-hydroxyl BAs (taurocholic acid, taurodeoxycholic acid, glycodeoxycholic acid, deoxycholic acid, and 3-ketodeoxycholic acid), while taurohyodeoxycholic acid was negatively associated with diabetes. The LC/MS/MS-based platform described should serve as a robust, high-throughput investigative tool for studying the potential involvement of structurally specific BAs and the gut microbiome on both physiological and disease processes.
Variable Effects Of LDL Subclasses Of Cholesterol On Endothelial Nitric Oxide/Peroxynitrite Balance – The Risks And Clinical Implications For Cardiovascular Disease

Background Elevated levels of low density lipoprotein (LDL), “bad cholesterol”, is not an accurate indicator of coronary disease. About 75% of patients with heart attacks have cholesterol levels that do not indicate a high risk for a cardiovascular event. LDL is comprised of three subclasses, with particles of different size and density. We used nanomedical systems to elucidate the noxious effects of LDL subclasses on endothelium. Experimental Nanosensors were employed to measure the concentrations of nitric oxide (NO) and peroxynitrite (ONOO−) stimulated by LDL subclasses in HUVECs. N-LDL and ox-LDL (subclass A: 1.016–1.019 g/mL, subclass I: 1.024–1.029 g/mL, and subclass B: 1.034–1.053 g/mL) stimulated NO and ONOO− release. The concentrations ratio of (NO)/(ONOO−) was used to evaluate the noxious effects of the subclasses on endothelium. Results In HUVECs, the (NO)/(ONOO−) ratio for normal endothelium is about 5, but shifts to 2.7±0.4, 0.5±0.1, and 0.9±0.1 for subclasses A, B, and I, respectively. Ratios below 1.0 indicate an imbalance between NO and ONOO−, affecting endothelial function. LDL of 50% B and 50% I produced the most severe imbalance (0.45±0.04), whereas LDL of 60% A, 20% B, and 20% I had the most favorable balance of 5.66±0.69. Subclass B significantly elevated the adhesion of molecules and monocytes. The noxious effect was significantly higher for ox-LDL than n-LDL. Conclusion Subclass B of “bad cholesterol” is the most damaging to endothelial function and can contribute to the development of atherosclerosis. Contrary to the current national guidelines, this study suggests that it’s not the total LDL, rather it is the concentration of subclass B in relation to subclasses A and/or I, that should be used for diagnosis of atherosclerosis and the risk of heart attack. By utilizing specific pharmacological therapy to address the concentration of subclass B, there is a potential to significantly reduce the risk of heart attack and atherosclerosis.
Association Between Breastfeeding and Postpartum Multiple Sclerosis Relapses: A Systematic Review and Meta-analysis.

Importance Multiple sclerosis (MS) relapses may be increased in the postpartum period, and whether breastfeeding is associated with reduction in the risk of postpartum relapses remains controversial. Objective To perform a systematic review and meta-analysis to evaluate whether breastfeeding is associated with reduction in postpartum MS relapses compared with not breastfeeding. Data Sources PubMed and Embase were searched for studies assessing the association between breastfeeding and MS disease activity published between January 1, 1980, and July 11, 2018, as well as reference lists of selected articles. Study Selection All study designs assessing the association between breastfeeding and postpartum relapses in MS relative to a comparator group were included. Data Extraction and Synthesis Study eligibility assessment and extraction of study characteristics, methods, and outcomes, were performed independently by 2 reviewers following PRISMA guidelines. Risk of bias was evaluated by 2 independent reviewers with the ROBINS-I tool for nonrandomized, interventional studies. Findings from studies with data available for the number of women with postpartum relapses in the breastfeeding and nonbreastfeeding groups were combined with a random-effects model. Main Outcomes and Measures Postpartum MS relapse. Results The search identified 462 unique citations, and 24 (2974 women) satisfied eligibility criteria and were included, of which 16 were included in the quantitative meta-analysis. The pooled summary odds ratio for the association of breastfeeding with postpartum relapses was 0.63 (95% CI, 0.45-0.88; P = .006) compared with a reference of nonbreastfeeding. Pooled adjusted hazard ratio across 4 studies that reported this finding was 0.57 (95% CI, 0.38-0.85; P = .006). There was moderate heterogeneity (I2 = 48%), which was explained by variable prepregnancy relapse rate, postpartum follow-up duration, and the publication year. A stronger association was seen in studies of exclusive rather than nonexclusive breastfeeding, although both demonstrated an association. Studies were rated at moderate and serious risk of bias, with concern for residual confounding, although sensitivity analysis including only moderate quality studies was consistent with a protective outcome of breastfeeding. Conclusions and Relevance These findings suggest that breastfeeding is protective against postpartum relapses in MS, although high-quality prospective studies to date are limited and well-designed observational studies that aim to emulate a randomized trial would be of benefit.
The "core" of the dark triad: A test of competing hypotheses.

As research on the dark triad (DT; the interrelated constructs of Machiavellianism, narcissism, and psychopathy) has accumulated, a subset of this research has focused on explicating what traits may account for the overlap among the DT members. Various candidate traits have been investigated, with evidence supporting several of them, including antagonism (vs. agreeableness), honesty-humility, and callousness and interpersonal manipulation (the latter 2 as a set). The present study sought to test the leading candidates against one another in their ability to account for the shared variance among the DT members. Using a preregistered analytical plan, we found that agreeableness (as measured by the International Personality Item Pool-NEO-120), honesty-humility (H/H) from the HEXACO-Personality Inventory, and the Self-Report Psychopathy Scale subscales of Callous Affect and Interpersonal Manipulation accounted for all or nearly all of the shared variance among the DT members. Big Five Inventory (BFI)-based measures of Agreeableness (BFI and BFI-2) accounted for notably less variance in most cases. The results were consistent across 2 large samples (Ns of 627 and 628) and across various DT measurement approaches. We argue that the most parsimonious explanation for findings on the core of the DT is that such traits all fall under the umbrella of antagonism. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Fluorescence Polarization Immunoassay for Determination of Enrofloxacin in Pork Liver and Chicken

Enrofloxacin (ENR) is a widely used fluoroquinolone (FQ) antibiotic for antibacterial treatment of edible animal. In this study, a rapid and highly specific fluorescence polarization immunoassay (FPIA) was developed for monitoring ENR residues in animal foods. First, ENR was covalently coupled to bovine serum albumin (BSA) to produce specific polyclonal antibodies (pAbs). Three fluorescein-labeled ENR tracers (A, B, and C) with different spacers were synthesized and compared to obtain higher sensitivity. Tracer C with the longest arm showed the best sensitivity among the three tracers. The developed FPIA method showed an IC50 (50% inhibitory concentration) of 21.49 ng·mL−1 with a dynamic working range (IC20–IC80) of 4.30–107.46 ng·mL−1 and a limit of detection (LOD, IC10) of 1.68 ng·mL−1. The cross-reactivity (CR) of several structurally related compounds was less than 2%. The recoveries of spiked pork liver and chicken samples varied from 91.3% to 112.9%, and the average coefficients of variation were less than 3.83% and 5.13%, respectively. The immunoassay took only 8 min excluding sample pretreatment. This indicated that the established method had high sensitivity, specificity, and the advantages of simplicity. Therefore, the proposed FPIA provided a useful screening method for the rapid detection of ENR residues in pork liver and chicken.
Associations between Dairy Intake, Body Composition, and Cardiometabolic Risk Factors in Spanish Schoolchildren: The Cuenca Study

Full-fat dairy has been traditionally associated with obesity and cardiovascular disease (CVD); however, recent evidence shows that the amount of dairy intake might have a beneficial effect over these pathologies, regardless of their fat content. The aim of this study was to examine the association between the intake of dairy products (including milk with different fat contents) with both adiposity and serum lipid concentration, adjusted by cardiorespiratory fitness (CRF), in Spanish schoolchildren. A cross-sectional study of 1088 children, aged 8 to 11 years, was conducted in which anthropometric variables (body mass index (BMI), waist circumference (WC), fat mass percentage (FM%) and fat mass index (FMI)), blood lipid profile, and dairy intake (using a food frequency questionnaire), and CRF (through a 20-m shuttle run test) were measured. Results showed that children with lower BMI, WC, FM%, and FMI had higher whole-fat milk intake and lower skimmed and semi-skimmed milk intake than children with higher BMI, WC, FM%, and FMI. Children with normal levels of triglycerides and high density lipoproteins (HLD) cholesterol consumed more whole-fat milk and less reduced-fat milk than children with dyslipidemic patterns. These relationships persisted after adjustment for CRF. Our findings suggest that full-fat milk intake should be promoted in children without obesity or high cardiometabolic risk.
The Induction and Roles Played by Phi Thickenings in Orchid Roots

Phi thickenings are specialised secondary wall thickenings present in the root cortex of many plant species, including both angiosperms and gymnosperms. While environmental stresses induce phi thickenings, their role(s) in the root remain unclear. Suggested functions include regulation of transport through the apoplast in a manner similar to the Casparian strip, limiting fungal infections, and providing mechanical support to the root. We investigated phi thickening induction and function in Miltoniopsis sp. , an epiphytic orchid. As movement of a fluorescent tracer through the apoplast was not blocked by phi thickenings, and as phi thickenings developed in the roots of sterile cultures in the absence of fungus and did not prevent fungal colonisation of cortical cells, the phi thickenings in Miltoniopsis did not function as a barrier. Phi thickenings, absent in roots grown on agar, remained absent when plants were transplanted to moist soil, but were induced when plants were transplanted to well-drained media, and by the application of water stress. We suggest that it is likely that phi thickenings stabilise to the root during water stress. Nevertheless, the varied phi thickening induction responses present in different plant species suggest that the phi thickenings may play multiple adaptive roles depending on species.
Modelling the Effects of Beverage Substitution during Adolescence on Later Obesity Outcomes in Early Adulthood: Results from the Raine Study

High sugar-sweetened beverage (SSB) consumption has been linked with obesity. The present study examined the associations between adolescent SSB intake and body mass index (BMI), waist circumference (WC), and overweight status in early adulthood, and modelled the association of alternative beverage substitution with BMI and WC. Data of offspring from the Western Australian Pregnancy Cohort (Raine) Study at ages 14 and 22 years were used (n = 667). SSB intake at 14 years (100 g/day) was associated with higher BMI (β = 0.19 kg/m2, 95% CI 0.04, 0.33), WC (β = 0.41cm, 95% CI 0.04, 0.78), and being overweight at 22 years (OR 1.10, 95% CI 1.02, 1.18). Every 100g modelled substitution of SSB with milk at age 14 years was associated with lower BMI (−0.19 kg/m2) and WC (−0.52 cm) at age 22 years. Replacement of SSB with diet drink was associated with higher BMI and WC. No association was found for substitutions of SSB with water, tea/coffee, or 100% fruit juice with BMI or WC. SSB intake during adolescence was associated with higher BMI, WC, and being overweight in early adulthood. Milk as an alternative to SSB was associated with less adiposity. Caution is necessary in recommending diet drinks as a SSB alternative.
Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a “DNA remodeling mechanism”. The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.