Miracle-dz/UniFAR-FTUs huggingface dataset:
SHARPIN at the nexus of integrin, immune, and inflammatory signaling in human platelets

Significance Platelets are professional hemostatic and immune cells. Integrin αIIbβ3 is required for fibrinogen-dependent platelet aggregation, but its role in immune/inflammatory responses is poorly understood. We identified interactions between αIIbβ3 and SHARPIN, a requisite member of the linear ubiquitin chain assembly complex (LUBAC), which mediates Met1 ubiquitination of signaling proteins. Using human platelets and megakaryocyte-lineage cells derived from human induced pluripotent stem cells, we find that SHARPIN is expressed in platelets and associates either with αIIb to suppress αIIbβ3 activation or with LUBAC to promote Met1 ubiquitination and NF-κB activation. Knockdown of SHARPIN in the megakaryocyte/platelet lineage not only primes αIIbβ3 for fibrinogen binding, but also increases MHC class I presentation and proinflammatory sCD40L release. Thus, SHARPIN functions at the nexus of αIIbβ3 and immune/inflammatory signaling in platelets. Platelets mediate primary hemostasis, and recent work has emphasized platelet participation in immunity and inflammation. The function of the platelet-specific integrin αIIbβ3 as a fibrinogen receptor in hemostasis is well defined, but the roles of αIIbβ3 or integrin-associated proteins in nonhemostatic platelet functions are poorly understood. Here we show that human platelets express the integrin-associated protein SHARPIN with functional consequences. In leukocytes, SHARPIN interacts with integrin α cytoplasmic tails, and it is also an obligate member of the linear ubiquitin chain assembly complex (LUBAC), which mediates Met1 linear ubiquitination of proteins leading to canonical NF-κB activation. SHARPIN interacted with αIIb in pull-down and coimmunoprecipitation assays. SHARPIN was partially localized, as was αIIbβ3, at platelet edges, and thrombin stimulation induced more central SHARPIN localization. SHARPIN also coimmunoprecipitated from platelets with the two other proteins comprising LUBAC, the E3 ligase HOIP and HOIL-1. Platelet stimulation with thrombin or inflammatory agonists, including lipopolysaccharide or soluble CD40 ligand (sCD40L), induced Met1 linear ubiquitination of the NF-κB pathway protein NEMO and serine-536 phosphorylation of the p65 RelA subunit of NF-κB. In human megakaryocytes and/or platelets derived from induced pluripotent stem (iPS) cells, SHARPIN knockdown caused increased basal and agonist-induced fibrinogen binding to αIIbβ3 as well as reduced Met1 ubiquitination and RelA phosphorylation. Moreover, these SHARPIN knockdown cells exhibited increased surface expression of MHC class I molecules and increased release of sCD40L. These results establish that SHARPIN functions in the human megakaryocyte/platelet lineage through protein interactions at the nexus of integrin and immune/inflammatory signaling.
Toward Development of a Fibromyalgia Responder Index and Disease Activity Score: OMERACT Module Update

Following development of the core domain set for fibromyalgia (FM) in Outcome Measures in Rheumatology Clinical Trials (OMERACT) meetings 7 to 9, the FM working group has progressed toward the development of an FM responder index and a disease activity score based on these domains, utilizing outcome indices of these domains from archived randomized clinical trials in FM. Possible clinical domains that could be included in a responder index and disease activity score include pain, fatigue, sleep disturbance, cognitive dysfunction, mood disturbance, tenderness, stiffness, and functional impairment. Outcome measures for these domains demonstrate good to adequate psychometric properties, although measures of cognitive dysfunction need to be further developed. The approach used in the development of responder indices and disease activity scores for rheumatoid arthritis and ankylosing spondylitis represents heuristic models for our work, but FM is challenging in that there is no clear algorithm of treatment that defines disease activity based on treatment decisions, nor are there objective markers that define thresholds of severity or response to treatment. The process of developing candidate dichotomous responder definitions and continuous quantitative disease activity measures is described, along with participant discussions from OMERACT 10. Final results of this work will be published in a separate report pending completion of analyses.
Mechanistic Assessment of Extrahepatic Contributions to Glucuronidation of Integrase Strand Transfer Inhibitors

Integrase strand transfer inhibitor (INSTI)–based regimens dominate initial human immunodeficiency virus treatment. Most INSTIs are metabolized predominantly via UDP-glucuronosyltransferases (UGTs). For drugs predominantly metabolized by UGTs, including INSTIs, in vitro data recovered from human liver microsomes (HLMs) alone often underpredict human oral clearance. While several factors may contribute, extrahepatic glucuronidation may contribute to this underprediction. Thus, we comprehensively characterized the kinetics for the glucuronidation of INSTIs (cabotegravir, dolutegravir, and raltegravir) using pooled human microsomal preparations from liver (HLMs), intestine (HIMs), and kidney (HKMs) tissues; human embryonic kidney 293 cells expressing individual UGTs; and recombinant UGTs. In vitro glucuronidation of cabotegravir (HLMs≈HKMs>>>HIMs), dolutegravir (HLMs>HIMs>>HKMs), and raltegravir (HLMs>HKMs>> HIMs) occurred in hepatic and extrahepatic tissues. The kinetic data from expression systems suggested the major enzymes in each tissue: hepatic UGT1A9 > UGT1A1 (dolutegravir and raltegravir) and UGT1A1 (cabotegravir), intestinal UGT1A3 > UGT1A8 > UGT1A1 (dolutegravir) and UGT1A8 > UGT1A1 (raltegravir), and renal UGT1A9 (dolutegravir and raltegravir). Enzymes catalyzing cabotegravir glucuronidation in the kidney and intestine could not be identified unequivocally. Using data from dolutegravir glucuronidation as a prototype, a “bottom-up” physiologically based pharmacokinetic model was developed in a stepwise approach and predicted dolutegravir oral clearance within 4.5-fold (hepatic data only), 2-fold (hepatic and intestinal data), and 32% (hepatic, intestinal, and renal data). These results suggest clinically meaningful glucuronidation of dolutegravir in tissues other than the liver. Incorporation of additional novel mechanistic and physiologic underpinnings of dolutegravir metabolism along with in silico approaches appears to be a powerful tool to accurately predict the clearance of dolutegravir from in vitro data.
Training and Competition Activity Profiles of Australian Football Field Umpires.

Jessiman, SW, Harvey, B, Corrigan, SL, and Gastin, PB. Training and competition activity profiles of Australian football field umpires. J Strength Cond Res XX(X): 000-000, 2019-The purpose of this study was to determine the activity profiles of Australian football (AF) field umpires during training and competition, and subsequently assess the specificity to competition of locomotor training sessions. Microtechnology incorporating a 5-Hz (interpolated to 15 Hz) global positioning system sensor tracked the movements of 24 field umpires during matches at the Melbourne Cricket Ground and fitness and skill-based training sessions before competition. Paired t-tests or Wilcoxon signed-rank tests determined whether significant differences existed between single training session and competition paired samples, with Cohen's d effect size and percent differences describing the magnitude of the training-competition differences. Absolute measures of total (d = 5.4; percent difference = 85.8%) and high-speed distance (>14.4 km·h) (1.0; 36.9%), as well as accelerations (3.3; 106.3%) and decelerations (3.2; 107.5%) were significantly greater during competition compared with training (p < 0.001). When standardized for time, high-speed distance (1.4; 52.0%), sprint distance (>23.0 km·h) (0.9; 121.5%), sprint efforts (1.0; 107.4%), and high acceleration (1.1; 114.3%) and deceleration (0.6; 66.7%) events (≥3 m·s) were greater during training (p < 0.001). No difference between training and competition was observed for relative distance. A single training session did not match the volume of work during competition, due primarily to large differences in duration. By contrast, training sessions were higher in intensity, likely to compensate for the shorter duration of training. Further research is required to determine whether the total weekly training load is sufficient to maintain and develop the competition-specific fitness of AF field umpires.
Diagnostic Value of Non-Invasive Prenatal Screening of β-thalassemia by Cell Free Fetal DNA and Fetal NRBC.

BACKGROUND Beta thalassemia is a common disorder with autosomal recessive inheritance. The most prenatal diagnostic methods are the invasive techniques that have the risk of miscarriage. Now the non-invasive methods will be gradually alternative for these invasive techniques. OBJECTIVE The aim of this study is to evaluate and compare the diagnostic value of two non-invasive diagnostic methods for fetal thalassemia using cell free fetal DNA (cff-DNA) and nucleated RBC (NRBC) in one sampling community. METHODS 10 ml of blood was taken in two k3EDTA tube from 32 pregnant women (mean of gestational age = 11 weeks), who themselves and their husbands had minor thalassemia. One tube was used to enrich NRBC and other was used for cff-DNA extraction. NRBCs were isolated by MACS method and immunohistochemistry; the genome of stained cells was amplified by multiple displacement amplification (MDA) procedure. These products were used as template in b-globin segments PCR. cff-DNA was extracted by THP method and 300 bp areas were recovered from the agarose gel as fetus DNA. These DNA were used as template in touch down PCR to amplify b-globin gen. The amplified b-globin segments were sequenced and the results compared with CVS resul. RESULTS The data showed that sensitivity and specificity of thalassemia diagnosis by NRBC were 100% and 92% respectively and sensitivity and specificity of thalassemia diagnosis by cff-DNA were 100% and 84% respectively. CONCLUSION These methods with high sensitivity can be used as screening test but due to their lower specificity than CVS, they cannot be used as diagnostic test.
Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila

Acquisition of chromatin modifications during embryogenesis distinguishes different regions of an initially naïve genome. In many organisms, repetitive DNA is packaged into constitutive heterochromatin that is marked by di/tri methylation of histone H3K9 and the associated protein HP1a. These modifications enforce the unique epigenetic properties of heterochromatin. However, in the early Drosophila melanogaster embryo the heterochromatin lacks these modifications which only appear later when rapid embryonic cell cycles slow down at the Mid-Blastula Transition or MBT. Here we focus on the initial steps restoring heterochromatic modifications in the embryo. We describe the JabbaTrap, a technique for inactivating maternally provided proteins in embryos. Using the JabbaTrap we reveal a major requirement for the methyltransferase Eggless/SetDB1 in the establishment of heterochromatin. In contrast, other methyltransferases contribute minimally. Live-imaging reveals that endogenous Eggless gradually accumulates on chromatin in interphase, but then dissociates in mitosis and its accumulation must restart in the next cell cycle. Cell cycle slowing as the embryo approaches the MBT permits increasing accumulation and action of Eggless at its targets. Experimental manipulation of interphase duration shows that cell cycle speed regulates Eggless. We propose that developmental slowing of the cell cycle times embryonic heterochromatin formation.
Toughened Poly (Lactic Acid)—PLA Formulations by Binary Blends with Poly(Butylene Succinate-co-Adipate)—PBSA and Their Shape Memory Behaviour

This study reports the effect of poly(butylene succinate-co-adipate) (PBSA) on the mechanical performance and shape memory behavior of poly(lactic acid) (PLA) specimens that were manufactured by injection molding and hot-press molding. The poor miscibility between PLA and PBSA was minimized by the addition of an epoxy styrene-acrylic oligomer (ESAO), which was commercially named Joncryl®. It was incorporated during the extrusion process. Tensile, impact strength, and hardness tests were carried out following international standards. PLA/PBSA blends with improved mechanical properties were obtained, which highlighted the sample that was compatibilized with ESAO, leading to a remarkable enhancement in elongation at break, but showing poor shape memory behaviour. Field Emission Scanning Electron Microscopy (FESEM) images showed how the ductile properties were improved, while PBSA loading increased, thus leading to minimizing the brittleness of neat PLA. The differential scanning calorimetry (DSC) analysis revealed the low miscibility between these two polymers and the improving effect of PBSA in PLA crystallization. The bending test carried out on the sheets of PLA/PBSA blends showed the direct influence that the PBSA has on the reduction of the shape memory that is intrinsically offered by neat PLA.
Macular choroidal thickness and volume in healthy pediatric individuals measured by swept-source optical coherence tomography.

PURPOSE We evaluated the choroidal thickness and volume in healthy pediatric individuals by swept-source optical coherence tomography (SS-OCT) and compared the findings to those of adults. METHODS We examined 100 eyes of 100 healthy pediatric volunteers (3-15 years) and 83 eyes of 83 healthy adult volunteers (24-87 years) by SS-OCT with a tunable long wavelength laser source. The three-dimensional raster scan protocol was used to construct a choroidal thickness map. When the built-in software delineated an erroneous chorioscleral border in the B-scan images, manual segmentation was used. RESULTS The central choroidal thickness and volume within a 1.0-mm circle were significantly larger in the children (260.4 ± 57.2 μm, 0.205 ± 0.045 mm(3)) than in the adults (206.1 ± 72.5 μm, 0.160 ± 0.056 mm(3), both P < 0.0001). In the children, the mean choroidal thickness of the nasal area was significantly thinner than that of all other areas (P < 0.005). Pediatric choroidal thinning with increasing age in the central area was faster than that in the outer areas. Stepwise regression analysis showed that the axial length and body mass index had the highest correlation with the choroidal thickness (R(2) = 0.313, P < 0.0001). CONCLUSIONS The macular choroidal thickness and volume in the pediatric individuals were significantly larger than those in the adults. The pediatric choroidal thinning with increasing age is more rapid in the central area. Pediatric choroidal thickness is associated with several systemic or ocular parameters, especially the axial length and body mass index. These differences should be remembered when the choroidal thickness is evaluated in pediatric patients with retinochoroidal diseases.
Human CD8+CD25
+CD127
low regulatory T cells: microRNA signature and impact on TGF‐β and IL‐10 expression

Regulatory T cells (Tregs) are central for maintaining immune balance and their dysfunction drives the expansion of critical immunologic disorders. During the past decade, microRNAs (miRNAs) have emerged as potent regulators of gene expression among which immune‐related genes and their immunomodulatory properties have been associated with different immune‐based diseases. The miRNA signature of human peripheral blood (PB) CD8+CD25 +CD127 low Tregs has not been described yet. We thus identified, using TaqMan low‐density array (TLDA) technique followed by individual quantitative real‐time polymerase chain reaction (qRT‐PCR) confirmation, 14 miRNAs, among which 12 were downregulated whereas two were upregulated in CD8 +CD25 +CD127 low Tregs in comparison to CD8 +CD25 − T cells. In the next step, microRNA Data Integration Portal (mirDIP) was used to identify potential miRNA target sites in the 3′‐untranslated region (3′‐UTR) of key Treg cell‐immunomodulatory genes with a special focus on interleukin 10 (IL‐10) and transforming growth factor β (TGF‐β). Having identified potential miR target sites in the 3′‐UTR of IL‐10 (miR‐27b‐3p and miR‐340‐5p) and TGF‐β (miR‐330‐3p), we showed through transfection and transduction assays that the overexpression of two underexpressed miRNAs, miR‐27b‐3p and miR‐340‐5p, downregulated IL‐10 expression upon targeting its 3′‐UTR. Similarly, overexpression of miR‐330‐3p negatively regulated TGF‐β expression. These results highlighted an important impact of the CD8 + Treg mirnome on the expression of genes with significant implication on immunosuppression. These observations could help in better understanding the mechanism(s) orchestrating Treg immunosuppressive function toward unraveling new targets for treating autoimmune pathologies and cancer.
Dietary β-Sitosterol Improves Growth Performance, Meat Quality, Antioxidant Status, and Mitochondrial Biogenesis of Breast Muscle in Broilers

Simple Summary Fast growth of modern broilers induces their muscle abnormality and myopathy, and therefore could compromise meat quality attributes. Antibiotic growth promoters have been banned by European Union and restricted by other countries in livestock production due to the public concern about food safety and antibiotic resistance. The search for efficacious, environmentally friendly, safe, and consumer favorable feed additives have become a necessity to poultry meat production. β-sitosterol—the most abundant phytosterol similar to cholesterol in chemical structure—is found in several plant products. It was incorporated at four levels into broiler diets (40, 60, 80, and 100 mg/kg). Dietary β-sitosterol supplementation improved growth performance and breast muscle meat quality of broilers, and the improved meat quality may be related with the simultaneously enhanced oxidative status and mitochondrial biogenesis in the breast muscle. The β-sitosterol dietary supplementation at the level of 80 mg/kg is recommended in broilers Abstract The present study evaluated effects of β-sitosterol on growth performance, meat quality, oxidative status, and mitochondrial biogenesis of breast muscle in broilers. One-day-old chicks were allocated to five treatments of six replicates. Broilers were fed a basal diet supplemented either with 0 (control), 40, 60, 80, or 100 mg/kg β-sitosterol for 42 days. β-sitosterol linearly and quadratically reduced feed/gain ratio, lightness24h and cooking loss24h in breast muscle, whereas 2, 2-diphenyl-1-picrylhydrazyl scavenging activity of breast muscle followed an opposite trend. β-sitosterol linearly decreased drip loss24h and malondialdehyde content, whereas linearly increased pH24h, superoxide dismutase activity, and mRNA abundances of peroxisome proliferator-activated receptor γ coactivator 1α (PCG-1α) and mitochondrial transcription factor A (TFAM) in breast muscle. Compared with control, levels of β-sitosterol higher than 40 mg/kg reduced feed/gain ratio, muscular lightness24h, cooking loss24h, and malondialdehyde level, whereas increased muscular 2, 2-diphenyl-1-picrylhydrazyl scavenging activity, and mRNA abundances (except 60 mg/kg) of PCG-1α and TFAM. Eighty milligram/kilogram β-sitosterol increased muscular pH24h and superoxide dismutase activity, but decreased its drip loss24h. Therefore, β-sitosterol could improve growth performance and meat quality, oxidative status, and mitochondrial biogenesis of breast muscle in broilers. Furthermore, supplementation level of 80 mg/kg β-sitosterol is recommended for broiler diets.
Reverse Engineering Cancer: Inferring Transcriptional Gene Signatures from Copy Number Aberrations with ICAro

The characterization of a gene product function is a process that involves multiple laboratory techniques in order to silence the gene itself and to understand the resulting cellular phenotype via several omics profiling. When it comes to tumor cells, usually the translation process from in vitro characterization results to human validation is a difficult journey. Here, we present a simple algorithm to extract mRNA signatures from cancer datasets, where a particular gene has been deleted at the genomic level, ICAro. The process is implemented as a two-step workflow. The first one employs several filters in order to select the two patient subsets: the inactivated one, where the target gene is deleted, and the control one, where large genomic rearrangements should be absent. The second step performs a signature extraction via a Differential Expression analysis and a complementary Random Forest approach to provide an additional gene ranking in terms of information loss. We benchmarked the system robustness on a panel of genes frequently deleted in cancers, where we validated the downregulation of target genes and found a correlation with signatures extracted with the L1000 tool, outperforming random sampling for two out of six L1000 classes. Furthermore, we present a use case correlation with a published transcriptomic experiment. In conclusion, deciphering the complex interactions of the tumor environment is a challenge that requires the integration of several experimental techniques in order to create reproducible results. We implemented a tool which could be of use when trying to find mRNA signatures related to a gene loss event to better understand its function or for a gene-loss associated biomarker research.
Alcohol Consumption and Incident Kidney Disease: Results From the Atherosclerosis Risk in Communities Study.

OBJECTIVE(S) Moderate alcohol consumption has been found to be associated with lower risk of coronary heart disease and myocardial infarction, which share similar risk factors and pathophysiology with chronic kidney disease (CKD). However, there is inconsistent evidence on the association between alcohol consumption and CKD. DESIGN AND METHODS We conducted a prospective analysis of 12,692 participants aged 45-64 years from the Atherosclerosis Risk in Communities (ARIC) study. We categorized participants into 6 alcohol consumption categories: never drinkers, former drinkers, ≤1 drink per week, 2 to 7 drinks per week, 8 to 14 drinks per week, and ≥15 drinks per week based on food frequency questionnaire responses at visit 1 (1987-1989). Incident CKD was defined as estimated glomerular filtration rate <60 mL/minute/1.73 m2 accompanied by ≥25% estimated glomerular filtration rate decline, a kidney disease-related hospitalization or death or end-stage renal disease. RESULTS During a median follow-up of 24 years, there were 3,664 cases of incident CKD. Current drinkers were more likely to be men, whites, and to have a higher income level and education level. After adjusting for total energy intake, age, sex, race-center, income, education level, health insurance, smoking, and physical activity, there was no significant association between being a former drinker and risk of incident CKD. Participants who drank ≤1 drink per week, 2 to 7 drinks per week, 8 to 14 drinks per week, and ≥15 drinks per week had, respectively, a 12% (hazard ratio [HR]: 0.88, 95% confidence interval [CI]: 0.79-0.97), 20% (HR: 0.80, 95% CI: 0.72-0.89), 29% (HR: 0.71, 95% CI: 0.62-0.83), and 23% (HR: 0.77, 95% CI: 0.65-0.91) lower risk of CKD compared with never drinkers. CONCLUSION(S) Consuming a low or moderate amount of alcohol may lower the risk of developing CKD. Therefore, moderate consumption of alcohol may not likely be harmful to the kidneys.