Miracle-dz/UniFAR-FTUs huggingface dataset:
K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes

The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole‐genome alignment, promoter analysis, or pangenome exploration. Although homology‐based annotation methods are computationally expensive, k‐mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two‐step approach, where repeats were first called by k‐mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k‐mer‐based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red‐masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant‐scripts.
Optimization of wheat flour by product films: A technological and sustainable approach for bio-based packaging material.

This study aimed to evaluate the feasibility of the production of sustainable and biodegradable packages made from a little-explored by product of wheat-milling, the glue flour (GF). Films were produced by the casting method and the effect of the incorporation of glycerol, sorbitol, and GF in the properties of the films was investigated following the central composite rotational design (CCRD) approach. The results have been statistically analyzed by the response surface methodology and the desirability function. Due to the rich composition in amylaceous reserve (64.81%; 26% of amylose content), considerable protein content (11.23%), and fibers (8.28%), the GF proved to be suitable for use as a matrix in biopolymer films. All the properties were mainly influenced by the plasticizer type and GF concentration. Film plasticized with glycerol (run 13) was more flexible, had higher moisture (28.39%) content, and was more adhesive than the formulation made with sorbitol (run 11). Film elongation (ELO) ranged from 25.84% to 56.71%, and tensile strength (TS) from 0.10 to 2.8 MPa. The optimized process conditions were 8% for Cf, 0% for Cg, and 4% for Cs. Under these conditions, the films presented low moisture (12.1%), moderate solubility (35.5%) and TS (1.64 MPa), and high ELO (72.06%). This study showed that GF is a promising source for the development of biodegradable films. PRACTICAL APPLICATION: Films made from a by product of wheat flour (glue flour) have technological potential to be used as packaging for food products. The valorization of a by product of the agribusiness without pre-treatment for the production of biodegradable films was made possible. The study by casting technique is a previous for scale-up production.
No antinociceptive synergy between morphine and delta-9-tetrahydrocannabinol in male and female rats with persistent inflammatory pain

Studies have demonstrated antinociceptive synergy between morphine and delta-9-tetrahydrocannabinol (THC) in animals, but whether such synergy occurs against all types of pain and in humans is unclear. Because a majority of chronic pain patients are women, and sex differences in morphine and THC potencies have been observed in rodents, the present study examined sex-specific effects of morphine and THC given alone and in combination, in rats with persistent inflammatory pain. On day 1, baseline mechanical and thermal response thresholds, hindpaw weight-bearing, locomotor activity, and hindpaw thickness were determined. Inflammation was then induced via hindpaw injection of complete Freund’s adjuvant (CFA). Three days later, morphine (s.c.), THC (i.p) or a morphine-THC combination (1:1, 3:1 and 1:3 dose ratios) was administered, and behavioral testing was conducted at 30–240 min postinjection. Morphine alone was antiallodynic and antihyperalgesic, with no sex differences, but at some doses increased weight-bearing on the CFA-treated paw more in males than females. THC alone reduced mechanical allodynia with similar potency in both sexes, but reduced thermal hyperalgesia and locomotor activity with greater potency in females than males. All morphine-THC combinations reduced allodynia and hyperalgesia, but isobolographic analysis of mechanical allodynia data showed no significant morphine-THC synergy in either sex. Additionally, whereas morphine alone was antinociceptive at doses that did not suppress locomotion, morphine-THC combinations suppressed locomotion and did not increase weight-bearing on the inflamed paw. These results suggest that THC is unlikely to be a beneficial adjuvant when given in combination with morphine for reducing established inflammatory pain.
Distinct single-component adjuvants steer human DC-mediated T-cell polarization via Toll-like receptor signaling toward a potent antiviral immune response

Significance Vaccines profit from the addition of adjuvants to better and more specifically initiate, amplify, and shape immune responses. Although the number of adjuvant candidates has steadily increased, peaking in the current SARS-CoV-2 pandemic, little is known about their inherent mode of action. Using human blood immune cells, we established a multilayer method to systematically assess the adjuvants’ effects on innate and adaptive immune cells. By employing a multiplex analysis with cells from 30 different donors, we determined important patterns of adjuvant function. Moreover, we demonstrate correlates of an antiviral immune response using a Toll-like receptor 7/8 ligand adjuvant and single-stranded RNA. This knowledge about adjuvants’ distinct immune signatures supports the selection of safe and effective adjuvants for future vaccines. The COVID-19 pandemic highlights the importance of efficient and safe vaccine development. Vaccine adjuvants are essential to boost and tailor the immune response to the corresponding pathogen. To allow for an educated selection, we assessed the effect of different adjuvants on human monocyte-derived dendritic cells (DCs) and their ability to polarize innate and adaptive immune responses. In contrast to commonly used adjuvants, such as aluminum hydroxide, Toll-like receptor (TLR) agonists induced robust phenotypic and functional DC maturation. In a DC-lymphocyte coculture system, we investigated the ensuing immune reactions. While monophosphoryl lipid A synthetic, a TLR4 ligand, induced checkpoint inhibitors indicative for immune exhaustion, the TLR7/8 agonist Resiquimod (R848) induced prominent type-1 interferon and interleukin 6 responses and robust CTL, B-cell, and NK-cell proliferation, which is particularly suited for antiviral immune responses. The recently licensed COVID-19 vaccines, BNT162b and mRNA-1273, are both based on single-stranded RNA. Indeed, we could confirm that the cytokine profile induced by lipid-complexed RNA was almost identical to the pattern induced by R848. Although this awaits further investigation, our results suggest that their efficacy involves the highly efficient antiviral response pattern stimulated by the RNAs’ TLR7/8 activation.
A novel, eco-friendly bio-nanocomposite (Alg-Cst/Kal) for the adsorptive removal of crystal violet dye from its aqueous solutions

Abstract Herein, we report the synthesis of a novel bio-nanocomposite (Alg-Cst/Kal) for the effective removal of the dye “Crystal Violet” from its aqueous solutions. In order to observe the surface morphology and functional groups, the bio-nanocomposite was characterized using various techniques such as SEM, EDX, TEM, FTIR, XRD, and TGA. The effect of parameters like contact time, pH, concentration and temperature on the adsorption of the dye over adsorbent has been studied in detail. The dye – adsorbent system has been tested over various isotherm models and found to follow the Freundlich adsorption isotherm model at 303 K. The developed bio-nanocomposite material exhibits an excellent adsorption toward Crystal Violet with a maximum adsorption capacity of 169.49 mg.g−1. The experimental data has been further validated by applying various kinetic models and the pseudo-second order kinetic model was the best suited model. The calculated rate constant values ranged from 0.0046 to 0.0204 g.mg−1.min−1 for different dye concentrations. The positive values of change in enthalpy, ΔH° (9.765 kJ.mol−1) and change in entropy, ΔS° (0.0565 kJ.mol−1.K−1) obtained through thermodynamic studies demonstrate the endothermic nature and spontaneity of the adsorption process, respectively. The adsorption capacity of the adsorbent for the removal of the Crystal Violet dye was also compared with other adsorbents and found maximum. Novelty statement A novel bio-nanocomposite is synthesized by modifying the biopolymer alginate, cysteine and mixing the clay, kaolinite (Kal). The adsorption abilities of the material was tested the on the cationic hazardous dye, Crystal Violet. The material is novel and no attempt has so far been made to examine its batch adsorption abilities to remove hazardous dyes from the wastewater. The results are highly encouraging as out of all the adsorbents tested so far highest adsorption of the dye is observed in the present studies.
Abrogation of STAT3 activation cascade by Ginkgolide C mitigates tumourigenesis in lung cancer preclinical model.

OBJECTIVES Ginkgolide C (GGC) isolated from Ginkgo biloba (Ginkgoaceae) leaf can demonstrate pleiotropic pharmacological actions. However, its anti-oncogenic impact in non-small cell lung cancer (NSCLC) model has not been reconnoitered. As signal transducer and activator of transcription 3 (STAT3) cascade can promote tumour growth and survival, we contemplated that GGC may interrupt this signalling cascade to expend its anti-cancer actions in NSCLC. METHODS The effect of GGC on STAT3 activation, associated protein kinases, STAT3-regulated gene products, cellular proliferation and apoptosis was examined. The in-vivo effect of GGC on the growth of human NSCLC xenograft tumours in athymic nu/nu female mice was also investigated. KEY FINDINGS GGC attenuated the phosphorylation of STAT3 and STAT3 upstream kinases effectively. Exposure to pervanadate modulated GGC-induced down-regulation of STAT3 activation and promoted an elevation in the level of PTPε protein. Indeed, silencing of the PTPε gene reversed the GGC-promoted abrogation of STAT3 activation and apoptosis. Moreover, GGC exposure significantly reduced NSCLC tumour growth without demonstrating significant adverse effects via decreasing levels of p-STAT3 in mice tissues. CONCLUSIONS Overall, the findings support that GGC may exhibit anti-neoplastic actions by mitigation of STAT3 signalling cascade in NSCLC.
Soluble interleukin-2 receptor as a predictive and prognostic marker for patients with familial breast cancer

The incidence of breast cancer increases annually, and it has become common within families of breast cancer patients. Interleukin-2 activates cytotoxic T lymphocytes, which are important for cancer immunity. To identify markers of increased familial breast cancer risk, soluble interleukin-2 receptor levels and immunologic factors were investigated in familial breast cancer and non-familial breast cancer patients. Of 106 untreated breast cancer patients in this study, 24 had familial breast cancer and 82 had non-familial breast cancer. The patients’ soluble interleukin-2 receptor, interleukin-10, vascular endothelial growth factor, interleukin-17, regulatory T cell, myeloid-derived suppressor cell, white blood cell, and C-reactive protein levels, and their neutrophil-to-lymphocyte ratios were measured, and their prognoses were compared according to the soluble interleukin-2 receptor levels. Additionally, postoperative tissues from the patients with high soluble interleukin-2 receptor levels were stained with programmed cell death ligand 1 and cluster of differentiation 8. The soluble interleukin-2 receptor level in the familial breast cancer patients was significantly higher, and it showed significantly stronger correlations with the neutrophil-to-lymphocyte ratio and the interleukin-10, vascular endothelial growth factor, interleukin-17, regulatory T cell, myeloid-derived suppressor cell, white blood cell, and C-reactive protein levels, than in the non-familial breast cancer patients. The regulatory T cell and myeloid-derived suppressor cell levels were significantly higher in the patients with high soluble interleukin-2 receptor levels, and the overall survival and disease-free-survival rates were significantly worse for the familial breast cancer patients than for the non-familial breast cancer patients. Triple-negative breast cancer tissues from the familial breast cancer patients with high soluble interleukin-2 receptor levels stained well for programmed cell death ligand 1 and cluster of differentiation 8. Soluble interleukin-2 receptor levels can be used to predict the prognosis of familial breast cancer patients. Prospectively identifying patients who are less likely to have non-familial breast cancer is vital for improving their overall survival.
In vitro Antioxidant and Antibacterial activity of Bridelia atroviridis (Arasado)

Aim: Bridelia atroviridis methanolic leaf extracts was assessed for antioxidant and antibacterial activity. Place and Duration of Study: The study was carried out in the Microbiology Laboratory, Department of Science Laboratory Technology, School of Pure and Applied Science, Lagos State Polytechnic, Ikorodu, LagosNigeria for the period of three months between September and November 2015. Methodology: Antioxidant compounds lycophene, β-carotene, total phenolic and total flavonoid content were evaluated using the method described by Nagata and Yamashita, aluminum chloride colorimetric assay and Folin-Ciocalteau assay respectively. DPPH radical scavenging activity method was utilized in assessing the antioxidant capacity of the plant extract while the antimicrobial activity was evaluated by the agar diffusion technique. Original Research Article Sokefun et al.; JOCAMR, 2(4): 1-7, 2017; Article no.JOCAMR. 29305 2 Results: The Bridelia atroviridis methanolic leaf extracts assessed in this study possessed significant amount of antioxidant compounds lycophene, β-carotene, total phenol and flavonoids. The extract exhibited antioxidant activity by scavenging DPPH radicals in a dose dependent pattern with IC50 of 51.24 μg/mL compared to vitamin C with IC50 of 41.67 μg/mL. Conclusion: Bridelia atroviridis methanolic leaf extracts is a potential source of drugs with antioxidant and antimicrobial activity.
Exercise-induced Bronchodilation Equalizes Exercise Ventilatory Mechanics despite Variable Baseline Airway Function in Asthma

ABSTRACT Purpose We quantified the magnitude of exercise-induced bronchodilation in adult asthmatics under conditions of narrowed and dilated airways. We then assessed the effect of the bronchodilation on ventilatory capacity and the extent of ventilatory limitation during exercise. Methods Eleven asthmatics completed three exercise bouts on a cycle ergometer. Exercise was preceded by no treatment (trialCON), inhaled β2 agonist (trialBD), or a eucapnic voluntary hyperpnea challenge (trialBC). Maximal expiratory flow-volume maneuvers (MEFV) were performed before and within 40 s of exercise cessation. Exercise tidal flow-volume loops were placed within the preexercise and postexercise MEFV curve and used to determine expiratory flow limitation and maximum ventilatory capacity (V˙ECap). Results Preexercise airway function was different among the trials (forced expiratory volume 1 s during trialCON, trialBD, and trialBC = 3.3 ± 0.8 L, 3.8 ± 0.8 L, and 2.9 ± 0.8 L, respectively; P < 0.05). Maximal expired airflow increased with exercise during all three trials, but the increase was greatest during trialBC (delta forced expiratory volume 1 s during trialCON, trialBD, and trialBC = +12.2% ± 13.1%, +5.2% ± 5.7%, +28.1% ± 15.7%). Thus, the extent of expiratory flow limitation decreased, and V˙ECap increased, when the postexercise MEFV curve was used. During trialCON and trialBC, actual exercise ventilation exceeded V˙ECap calculated with the preexercise MEFV curve in seven and nine subjects, respectively. Conclusions These findings demonstrate the critical importance of exercise bronchodilation in the asthmatic with narrowed airways. Of clinical relevance, the results also highlight the importance of assessing airway function during or immediately after exercise in asthmatic persons; otherwise, mechanical limitations to exercise ventilation will be overestimated.
Exercise, Physical Activity, and Cardiometabolic Health: Insights into the Prevention and Treatment of Cardiometabolic Diseases

Physical activity (PA) and exercise are widely recognized as essential components of primary and secondary cardiovascular disease (CVD) prevention efforts and are emphasized in the health promotion guidelines of numerous professional societies and committees. The protean benefits of PA and exercise extend across the spectrum of CVD, and include the improvement and reduction of risk factors and events for atherosclerotic CVD (ASCVD), cardiometabolic disease, heart failure, and atrial fibrillation (AF), respectively. Here, we highlight recent insights into the salutary effects of PA and exercise on the primary and secondary prevention of ASCVD, including their beneficial effects on both traditional and nontraditional risk mediators; exercise “prescriptions” for ASCVD; the role of PA regular exercise in the prevention and treatment of heart failure; and the relationships between, PA, exercise, and AF. While our understanding of the relationship between exercise and CVD has evolved considerably, several key questions remain including the association between extreme volumes of exercise and subclinical ASCVD and its risk; high-intensity exercise and resistance (strength) training as complementary modalities to continuous aerobic exercise; and dose- and intensity-dependent associations between exercise and AF. Recent advances in molecular profiling technologies (ie, genomics, transcriptomics, proteomics, and metabolomics) have begun to shed light on interindividual variation in cardiometabolic responses to PA and exercise and may provide new opportunities for clinical prediction in addition to mechanistic insights.
Viscosity and normal stress forces of Lennard-Jones chains using reverse non-equilibrium molecular dynamics

ABSTRACT Reverse non-equilibrium molecular dynamics was applied for the calculation of the viscosity for different chain lengths. Each chain consisted of m tangent spherical sites, where m was 1, 2, 4, 8 or 16, respectively. From these results, shear thinning was observed at high shear rates. The normal stress forces were also estimated via the calculation of the total stress tensor, and they were related to the shear thinning effect depending on the length of the chain. Furthermore, a power law equation was used to fit the rheological curves of each chain, making possible the calculation of the viscoelasticity as a function of the sites involved in the chains.
Simultaneous detection of aqueous aluminum(III) and chromium(III) using Persea americana reduced and capped silver nanoparticles

Abstract There is a significant interest to develop sensing devices that detect water toxins, especially heavy metal ions. Although there have already been numerical reports on detecting toxic heavy metal ions, the use of adaptable devices could enable a broader range of sensing applications. Here, we used fresh peel extract (PeA) and dried peel extract (DPeA) of Persea americana (Avocado) as a reducing and capping agent to synthesize and stabilize AgNPs. The dimensions of NPs were controlled by tuning pH, temperature, and volume of the reducing agent. The sensitivity and selectivity of the AgNPs toward various metal ions viz. Ni(II), Cd(II), Al(III), Hg(II), Cr(III), Ba(II), Pb(II), Zn(II), Co(II), Mn(II), Cu(II), Ca(II), Mg(II), and K(I) were studied. The detection probe was found to be selective and sensitive toward Al(III) and Cr(III) ions with the detection limit of 0.04 ppm and 0.05 ppm, respectively. High-resolution transmission electron microscope (HRTEM), ultraviolet-visible (UV-Vis) spectroscopy, and dynamic light scattering (DLS) analysis results confirm an agglomeration-based mechanism for sensing both metal ions. This method can be exploited for the colorimetric detection of toxic heavy metals in real water samples. Novelty statement This is the first study to report the use of avocado peel extract to synthesize AgNPs in sensing aqueous Al(III) and Cr(III) at trace level concentration.
Beck Depression Inventory-II : A Study for Meta Analytical Reliability Generalization

Ab s t r Ac t The main aim of achieving with the reliability generalization is to investigate the variability related to the reliability estimates and to try to characterize the sources of this variability. As part of the research, a reliability generalization study was carried out on the basis of Beck Depression Inventory-II to investigate potential factors contributing to the variability of the reliability of the measurement results and to examine the sources of the measurement error. Within the scope of the study, it was published in English between 2011-2019 and only 40 articles in the type of article were examined. The Kappa coefficient for the coding form was determined to be 0.93 and it was concluded that the measurement results performed for the coding form were valid and reliable. Jamovi and R programs were used in the research. When the test results regarding publication bias are evaluated in a holistic way, it is concluded that there is no publication bias related to the studies included in the research. It was thought that the heterogeneity observed by the researchers may indicate an amount of heterogeneity to be examined and moderator analyzes were performed. As a result of the moderator analysis, it was determined that any of the continuous and categorical moderator variables did not have an explanatory role regarding the variability between the reliability estimates of the inventory. In order to carry out qualified RG studies in the future, it is recommended that researchers report their reliability estimates regarding the measurement results of their studies.
Profiling code cache behaviour via events

Virtual machine performance tuning for a given application is an arduous and challenging task. For example, parametrizing the behaviour of the JIT compiler machine code caches affects the overall performance of applications while being rather obscure for final users not knowledgeable about VM internals. Moreover, VM components are often heavily coupled and changes in some parameters may affect several seemingly unrelated components and may have unclear performance impacts. Therefore, choosing the best parametrization requires to have precise information. In this paper, we present Vicoca, a tool that allows VM users and developers to obtain detailed information about the behaviour of the code caches and their interactions with other virtual machine components. We present a complex optimization problem due to the heavy interaction of components in the Pharo VM, and we explain it using Vicoca. The information produced by the tool allows developers to produce an optimized configuration for the VM. Vicoca is based on event recording that are manipulated during off-line analysis. Vicoca not only allows us to understand this given problem, but it opens the door to future work such as automatic detection of application characteristics, identification of performance issues, and automatic hinting.