Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: a randomized crossover trial.

BACKGROUND A whole-grain (WG)-rich diet has shown to have potential for both prevention and treatment of the metabolic syndrome (MetS), which is a cluster of risk factors that increase the risk of type 2 diabetes and cardiovascular disease. Different WGs may have different health effects. WG rye, in particular, may improve glucose homeostasis and blood lipids, possibly mediated through fermentable dietary fiber and lignans. Recent studies have also suggested a crucial role of the gut microbiota in response to WG. OBJECTIVES The aim was to investigate WG rye, alone and with lignan supplements [secoisolariciresinol diglucoside (SDG)], and WG wheat diets on glucose tolerance [oral-glucose-tolerance test (OGTT)], other cardiometabolic outcomes, enterolignans, and microbiota composition. Moreover, we exploratively evaluated the role of gut microbiota enterotypes in response to intervention diets. METHODS Forty men with MetS risk profile were randomly assigned to WG diets in an 8-wk crossover study. The rye diet was supplemented with 280 mg SDG at weeks 4-8. Effects of treatment were evaluated by mixed-effects modeling, and effects on microbiota composition and the role of gut microbiota as a predictor of response to treatment were analyzed by random forest plots. RESULTS The WG rye diet (± SDG supplements) did not affect the OGTT compared with WG wheat. Total and LDL cholesterol were lowered (-0.06 and -0.09 mmol/L, respectively; P < 0.05) after WG rye compared with WG wheat after 4 wk but not after 8 wk. WG rye resulted in higher abundance of Bifidobacterium [fold-change (FC) = 2.58, P < 0.001] compared with baseline and lower abundance of Clostridium genus compared with WG wheat (FC = 0.54, P = 0.02). The explorative analyses suggest that baseline enterotype is associated with total and LDL-cholesterol response to diet. CONCLUSIONS WG rye, alone or with SDG supplementation, compared with WG wheat did not affect glucose metabolism but caused transient LDL-cholesterol reduction. The effect of WG diets appeared to differ according to enterotype. This trial was registered at www.clinicaltrials. gov as NCT02987595.
Alterations in chromatin at antigen receptor loci define lineage progression during B lymphopoiesis

Significance Antigen receptor genes are assembled during lymphoid development from gene fragments by the process known as variable (diversity) joining (V[D]J) recombination. This process, which is initiated by the RAG1/RAG2 recombinase, is fundamental to the generation antigen receptor diversity required to respond to a virtually limitless array of pathogens. We show that chromatin at antigen receptor loci is subject to change during lymphoid development. We hypothesize that these developmentally regulated alterations of chromatin state may help to guide RAG1/RAG2 to the correct sites in recombinationally active cells. These changes represent key features of antigen receptor genes during lineage progression, serving either to facilitate or to impose a barrier to V(D)J recombination depending on cell lineage and developmental stage. Developing lymphocytes diversify their antigen receptor (AgR) loci by variable (diversity) joining (V[D]J) recombination. Here, using the micrococcal nuclease (MNase)-based chromatin accessibility (MACC) assay with low-cell count input, we profile both small-scale (kilobase) and large-scale (megabase) changes in chromatin accessibility and nucleosome occupancy in primary cells during lymphoid development, tracking the changes as different AgR loci become primed for recombination. The three distinct chromatin structures identified in this work define unique features of immunoglobulin H (IgH), Igκ, and T cell receptor-α (TCRα) loci during B lymphopoiesis. In particular, we find locus-specific temporal changes in accessibility both across megabase-long AgR loci and locally at the recombination signal sequences (RSSs). These changes seem to be regulated independently and can occur prior to lineage commitment. Large-scale changes in chromatin accessibility occur without significant change in nucleosome density and represent key features of AgR loci not previously described. We further identify local dynamic repositioning of individual RSS-associated nucleosomes at IgH and Igκ loci while they become primed for recombination during B cell commitment. These changes in chromatin at AgR loci are regulated in a locus-, lineage-, and stage-specific manner during B lymphopoiesis, serving either to facilitate or to impose a barrier to V(D)J recombination. We suggest that local and global changes in chromatin openness in concert with nucleosome occupancy and placement of histone modifications facilitate the temporal order of AgR recombination. Our data have implications for the organizing principles that govern assembly of these large loci as well as for mechanisms that might contribute to aberrant V(D)J recombination and the development of lymphoid tumors.
Mitotic cell responses to substrate topological cues are independent of the molecular nature of adhesion

Spindle orientation in nonpolarized adherent cells does not depend on specific adhesion signaling mechanisms. Adhesion signaling not required Adherent cells position their spindle poles parallel to the plane of the substrate and orient the spindle within that plane depending on cell shape–dependent mechanical forces. Both integrins, which mediate adhesion to the extracellular matrix (ECM), and cadherins, which mediate cell-cell interactions, are implicated in establishing spindle position. Anastasiou et al. found that both cadherin- and integrin-mediated adhesion supported proper spindle positioning in cultured cells. Although adhesion-dependent integrin activation was not required to position spindles parallel to the plane of the substrate, force-dependent integrin activation at the cell cortex was required to orient the spindle in response to mechanical cues generated by adhesion topology. Thus, spindle positioning does not depend on the molecular nature of adhesion and does not specifically require integrin-based adhesion, but integrin signaling is required to transduce mechanical cues that orient the spindle. Correct selection of the cell division axis is important for cell differentiation, tissue and organ morphogenesis, and homeostasis. Both integrins, which mediate interactions with extracellular matrix (ECM) components such as fibronectin, and cadherins, which mediate interactions between cells, are implicated in the determination of spindle orientation. We found that both cadherin- and integrin-based adhesion resulted in cell divisions parallel to the attachment plane and elicited identical spindle responses to spatial adhesive cues. This suggests that adhesion topology provides purely mechanical spatial cues that are independent of the molecular nature of the interaction or signaling from adhesion complexes. We also demonstrated that cortical integrin activation was indispensable for correct spindle orientation on both cadherin and fibronectin substrates. These data suggest that spindle orientation responses to adhesion topology are primarily a result of force anisotropy on the cell cortex and show that integrins play a central role in this process that is distinct from their role in cell-ECM interactions.
The Efficacy of Medical Marijuana in the Treatment of Cancer-Related Pain.

Background: The opioid epidemic has spurred investigations for nonopioid options, yet limited research persists on medical marijuana's (MMJ) efficacy in managing cancer-related symptoms. Objective: We sought to characterize MMJ's role on symptomatic relief and opioid consumption in the oncologic population. Design: Retrospective chart review of MMJ-certified oncology patients was performed. Divided patients into MMJ use [MMJ(+)] versus no use [MMJ(-)], and Edmonton Symptom Assessment System (ESAS)-reported pain cohorts: "mild-moderate" versus "severe. " Measurements: Medical records were reviewed for ESAS, to measure physical and emotional symptoms, and opiate consumption, converted into morphine milligram equivalents (MME). Minimal clinically important differences were determined. Wilcoxon signed-rank tests determined statistical significance between MMJ-certification and most recent palliative care visit. Results: Identified 232 patients [95/232 MMJ(-); 137/232 MMJ(+)]. Pain, physical and total ESAS significantly improved for total MMJ(-) and MMJ(+); however, only MMJ(+) significantly improved emotional ESAS. MMJ(-) opioid consumption increased by 23% (97.5-120 mg/day MME, p = 0.004), while it remained constant (45-45 mg/day MME, p = 0.522) in MMJ(+). Physical and total ESAS improved in mild-moderate-MMJ(-) and MMJ(+). Pain and emotional symptoms worsened in MMJ(-); while MMJ(+)'s pain remained unchanged and emotional symptoms improved. MMJ(-) opioid consumption increased by 29% (90-126 mg/day MME, p = 0.012); while MMJ(+)'s decreased by 33% (45-30 mg/day MME, p = 0.935). Pain, physical, emotional, and total ESAS scores improved in severe-MMJ(-) and MMJ(+); opioid consumption reduced by 22% in MMJ(-) (135-106 mg/day MME, p = 0.124) and 33% in MMJ(+) (90-60 mg/day MME, p = 0.421). Conclusions: MMJ(+) improved oncology patients' ESAS scores despite opioid dose reductions and should be considered a viable adjuvant therapy for palliative management.
Combined therapy of photobiomodulation and adipose-derived stem cells synergistically improve healing in an ischemic, infected and delayed healing wound model in rats with type 1 diabetes mellitus

Objective We assessed the therapeutic effects of photobiomodulation (PBM) and adipose-derived stem cell (ADS) treatments individually and together on the maturation step of repairing of a delayed healing wound model in rats with type 1 diabetes mellitus (DM1). Research design and methods We randomly assigned 24 rats with DM1 to four groups (n=6 per group). Group 1 was the control (placebo) group. In group 2, allograft human ADSs were transplanted. Group 3 was subjected to PBM (wavelength: 890 nm, peak power output: 80 W, pulse frequency: 80 Hz, pulsed duration: 180 ns, duration of exposure for each point: 200 s, power density: 0.001 W/cm2, energy density: 0.2 J/cm2) immediately after surgery, which continued for 6 days per week for 16 days. Group 4 received both the human ADS and PBM. In addition, we inflicted an ischemic, delayed healing, and infected wound simulation in all of the rats. The wounds were infected with methicillin-resistant Staphylococcus aureus (MRSA). Results All three treatment regimens significantly decreased the amount of microbial flora, significantly increased wound strength and significantly modulated inflammatory response and significantly increased angiogenesis on day 16. Microbiological analysis showed that PBM+ADS was significantly better than PBM and ADS alone. In terms of wound closure rate and angiogenesis, PBM+ADS was significantly better than the PBM, ADS and control groups. Conclusions Combination therapy of PBM+ADS is more effective that either PBM or ADS in stimulating skin injury repair, and modulating inflammatory response in an MRSA-infected wound model of rats with DM1.
The Influence of the Welding Process on the Ultrasonic Inspection of 9%Ni Steel Pipe Circumferential Welded Joints

This work aims to compare the ultrasonic inspection of 9%Ni steel joints welded with the Gas Metal Arc Welding (GMAW) process and Shielded Metal Arc Welding (SMAW) process. These are the two most widely used processes used to weld pipes for CO2 injection units for floating production storage and offloading (FPSO) in the Brazilian oil and gas industry. The SMAW equipment is simple and portable, which is convenient for the FPSO; however, the GMAW process has the advantage of welding with high productivity. In this study we performed a numerical simulation using the software CIVA, 11th version, to analyze the behavior of ultrasonic longitudinal wave beams through GMAW and SMAW dissimilar weld joints. Ultrasonic tests were performed on calibration blocks drawn from both welded joints to evaluate the simulation results. The results are discussed with regard to the microstructure of the weld metal via electron backscatter diffraction (EBSD) analyses. The SMAW process presented better inspection performance than the GMAW process in terms of attenuation and dispersion effects. Although the SMAW had a better outcome, for both processes the configuration of 16 active elements and a scanning angle of 48° resulted in an optimized inspection of the entire joint.
Differential gene regulation in selected lines for high and low sperm production in male guppies

In species where females mate with more than one male during the same reproductive event, males typically increase the number of sperm produced to boost their fertilization share. Sperm is not limitless, however, and theory predicts that their production will come at the cost of other fitness‐related traits, such as body growth or immunocompetence, although these evolutionary trade‐offs are notoriously difficult to highlight. To this end, we combined artificial selection for sperm production with a transcriptome analysis using Poecilia reticulata, a fish characterized by intense sperm competition in which the number of sperm transferred during mating is the most important predictor of fertilization success, yet sperm production is highly variable among males. We compared the brain and testes transcriptome in male guppies of lines artificially selected for high and low sperm production by identifying pivotal differentially expressed gene sets that may regulate spermatogenesis and immune function in this species. Despite the small differences in single genes' expression, gene set enrichment analysis showed coordinated gene expression differences associated with several pathways differentially regulated in the two selection lines. High sperm production males showed an upregulation of pathways related to immunosuppression and development of spermatozoa indicating a possible immunological cost of sperm production.
Expanding and understanding the CRISPR toolbox for Bacillus subtilis with MAD7 and dMAD7

The CRISPR‐Cas9 system has become increasingly popular for genome engineering across all fields of biological research, including in the Gram‐positive model organism Bacillus subtilis. A major drawback for the commercial use of Cas9 is the IP landscape requiring a license for its use, as well as reach‐through royalties on the final product. Recently an alternative CRISPR nuclease, free to use for industrial R&D, MAD7 was released by Inscripta (CO). Here we report the first use of MAD7 for gene editing in B. subtilis, in which editing rates of 93% and 100% were established. Additionally, we engineer the first reported catalytically inactive MAD7 (dMAD7) variant (D877A, E962A, and D1213A) and demonstrate its utility for CRISPR interference (CRISPRi) at up to 71.3% reduction of expression at single and multiplexed target sites within B. subtilis. We also confirm the CRISPR‐based editing mode of action in B. subtilis providing evidence that the nuclease‐mediated DNA double‐strand break acts as a counterselection mechanism after homologous recombination of the donor DNA.
Limb dynamics in agility jumps of beginner and advanced dogs

ABSTRACT A considerable body of work has examined the dynamics of different dog gaits, but there are no studies that have focused on limb dynamics in jumping. Jumping is an essential part of dog agility, a dog sport in which handlers direct their dogs through an obstacle course in a limited time. We hypothesized that limb parameters like limb length and stiffness indicate the skill level of dogs. We analyzed global limb parameters in jumping for 10 advanced and 10 beginner dogs. In experiments, we collected 3D kinematics and ground reaction forces during dog jumping at high forward speeds. Our results revealed general strategies of limb control in jumping and highlighted differences between advanced and beginner dogs. In take-off, the spatially leading forelimb was 75% (P<0.001) stiffer than the trailing forelimb. In landing, the trailing forelimb was 14% stiffer (P<0.001) than the leading forelimb. This indicates a strut-like action of the forelimbs to achieve jumping height in take-off and to transfer vertical velocity into horizontal velocity in landing (with switching roles of the forelimbs). During landing, the more (24%) compliant forelimbs of beginner dogs (P=0.005) resulted in 17% (P=0.017) higher limb compression during the stance phase. This was associated with a larger amount of eccentric muscle contraction, which might in turn explain the soft tissue injuries that frequently occur in the shoulder region of beginner dogs. For all limbs, limb length at toe-off was greater for advanced dogs. Hence, limb length and stiffness might be used as objective measures of skill. Summary: Limb dynamics in agility jumps of beginner and advanced dogs reveal general strategies of limb control and highlight differences between levels of skill during landing.
Green Synthesis of Silver Nanoparticles Using Pseudoduganella eburnea MAHUQ-39 and Their Antimicrobial Mechanisms Investigation against Drug Resistant Human Pathogens

Silver nanoparticles (AgNPs) have shown great promise in biomedical applications. The exact mechanism and mode of action of AgNPs regarding antimicrobial activity are still not well known. Moreover, synthesis of nanoparticles by physical and chemical methods is expensive and not ecofriendly. This study highlights the green, rapid, facile, cost-effective and ecofriendly synthesis of AgNPs using Pseudoduganella eburnea MAHUQ-39 and also investigates their antibacterial mechanisms. The transmission electron microscopy (TEM) image revealed a spherical shape of the AgNPs. The size of the synthesized AgNPs was 8 to 24 nm. The elemental mapping and selected area electron diffraction (SAED) and X-ray diffraction (XRD) patterns revealed the crystalline structure of AgNPs. Fourier-transform infrared spectroscopy (FTIR) analysis identified the functional groups that are involved in the reduction of silver ion to AgNPs. The green synthesized AgNPs exhibited strong antimicrobial activity against multidrug-resistant pathogenic microbes. Minimal inhibitory concentrations (MICs) of Staphylococcus aureus and Pseudomonas aeruginosa were 100 μg/mL and 6.25 μg/mL, respectively, and the minimum bactericidal concentrations (MBCs) of S. aureus and P. aeruginosa were 200 μg/mL and 50 μg/mL, respectively. Our data demonstrated that synthesized AgNPs created structural changes of cells and destroyed the membrane integrity of strains S. aureus and P. aeruginosa. Therefore, AgNPs synthesized by strain MAHUQ-39 can be used as a powerful antimicrobial agent for various therapeutic applications.
Gastrointestinal stromal tumour of stomach: Feasibility of laparoscopic resection in large lesions and its long-term outcomes

Background: Gastric gastrointestinal stromal tumours (GISTs) are rare neoplasms that require excision for cure. Although the feasibility of laparoscopic resection of smaller gastric GIST has been established, the feasibility and long-term efficacy of these techniques are unclear in larger lesions. This study is done to assess the feasibility of the laparoscopic resection of gastric GISTs and their long-term outcomes. Methods: Patients who underwent laparoscopic resection of gastric GISTs were identified in a prospectively collected database. Outcome measures included patient demographics, operative findings, morbidity and histopathologic characteristics of the tumour. Patient and tumour characteristics were analysed to identify risk factors for tumour recurrence. Results: There were 42 patients with a mean age of 56.7 years and had a mean tumour size was 4.5 ± 2.7 cm. Laparoscopic wedge resection was the most common procedure done. There were no major perioperative complications or mortalities. All lesions had negative resection margins. At a mean follow-up of 48 months, 36/39 (92.3%) patients were disease free and 3/39 (7.6%) had progressive disease. Univariate analysis showed that there was a statistically significant association of disease progression with tumour size, high mitotic index, tumour ulceration and tumour necrosis. The presence of >10 mitotic figures/50 high-power field was an independent predictor of disease progression. Conclusion: Our study establishes laparoscopic resection is feasible and safe in treating gastric GISTs for tumours >5 cm size. The long-term disease-free survival in our study shows acceptable oncological results in comparison to historical open resections.
Multilevel analyses of related public health indicators: The European Surveillance of Congenital Anomalies (EUROCAT) Public Health Indicators

Abstract Background Public health organisations use public health indicators to guide health policy. Joint analysis of multiple public health indicators can provide a more comprehensive understanding of what they are intended to evaluate. Objective To analyse variaitons in the prevalence of congenital anomaly‐related perinatal mortality attributable to termination of pregnancy for foetal anomaly (TOPFA) and prenatal diagnosis of congenital anomaly prevalence. Methods We included 55 363 cases of congenital anomalies notified to 18 EUROCAT registers in 10 countries during 2008‐12. Incidence rate ratios (IRR) representing the risk of congenital anomaly‐related perinatal mortality according to TOPFA and prenatal diagnosis prevalence were estimated using multilevel Poisson regression with country as a random effect. Between‐country variation in congenital anomaly‐related perinatal mortality was measured using random effects and compared between the null and adjusted models to estimate the percentage of variation in congenital anomaly‐related perinatal mortality accounted for by TOPFA and prenatal diagnosis. Results The risk of congenital anomaly‐related perinatal mortality decreased as TOPFA and prenatal diagnosis prevalence increased (IRR 0.79, 95% confidence interval [CI] 0.72, 0.86; and IRR 0.88, 95% CI 0.79, 0.97). Modelling TOPFA and prenatal diagnosis together, the association between congenital anomaly‐related perinatal mortality and TOPFA prevalence became stronger (RR 0.70, 95% CI 0.61, 0.81). The prevalence of TOPFA and prenatal diagnosis accounted for 75.5% and 37.7% of the between‐country variation in perinatal mortality, respectively. Conclusion We demonstrated an approach for analysing inter‐linked public health indicators. In this example, as TOPFA and prenatal diagnosis of congenital anomaly prevalence decreased, the risk of congenital anomaly‐related perinatal mortality increased. Much of the between‐country variation in congenital anomaly‐related perinatal mortality was accounted for by TOPFA, with a smaller proportion accounted for by prenatal diagnosis.