Miracle-dz/UniFAR-FTUs huggingface dataset:
A Heterozygous Genotype-Dependent Branched-Spike Wheat and the Potential Genetic Mechanism Revealed by Transcriptome Sequencing

Simple Summary This paper reported a novel type of branched spike wheat from a natural mutation event. The branched spike was controlled by a heterozygous genotype. The genetic patterns showed that gametophytic male sterility probably contributed to the heterozygous genotype responsible for the branched spike trait. Expressional levels and Wheat FRIZZY PANICLE (WFZP) sequencing between the mutant with the branched spike and the wild-type with the normal spike showed that WFZP was not the causal gene for the branched spike. Data from transcriptome sequencing indicated that carbohydrate metabolism might be involved in the formation of the branched spike trait. Abstract Wheat (Triticum aestivum L.) spike architecture is an important trait associated with spike development and grain yield. Here, we report a naturally occurring wheat mutant with branched spikelets (BSL) from its wild-type YD-16, which has a normal spike trait and confers a moderate level of resistance to wheat Fusarium head blight (FHB). The lateral meristems positioned at the basal parts of the rachis node of the BSL mutant develop into ramified spikelets characterized as multiple spikelets. The BSL mutant shows three to four-day longer growth period but less 1000-grain weight than the wild type, and it becomes highly susceptible to FHB infection, indicating that the locus controlling the BSL trait may have undergone an intensively artificial and/or natural selection in modern breeding process. The self-pollinated descendants of the lines with the BSL trait consistently segregated with an equal ratio of branched and normal spikelets (NSL) wheat, and homozygotes with the BSL trait could not be achieved even after nine cycles of self-pollination. Distinct segregation patterns both from the self-pollinated progenies of the BSL plants and from the reciprocal crosses between the BSL plants with their sister NSL plants suggested that gametophytic male sterility was probably associated with the heterozygosity for the BSL trait. Transcriptome sequencing of the RNA bulks contrasting in the two types of spike trait at the heading stage indicated that the genes on chromosome 2DS may be critical for the BSL trait formation since 329 out of 2540 differentially expressed genes (DEGs) were located on that chromosome, and most of them were down-regulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that carbohydrate metabolism may be involved in the BSL trait expression. This work provides valuable clues into understanding development and domestication of wheat spike as well as the association of the BSL trait with FHB susceptibility.
Activity Patterns and Functioning. A Contextual–Functional Approach to Pain Catastrophizing in Women with Fibromyalgia

Background: The psychological flexibility model states that activity patterns are not deemed to be intrinsically functional or dysfunctional; it is considered that underlying factors, such as personal goals and contextual factors, are what will determine their effects on disability. Pain catastrophizing has frequently been associated with several important pain-related outcomes. Despite its recent conceptualization within affective–motivational approaches, its moderating role between activity patterns and dysfunction has not been analyzed. Methods: This study analyzes the moderating role of pain catastrophizing and its dimensions (Pain Catastrophizing Scale) between activity patterns (Activity Patterns Scale) and disease impact (Fibromyalgia Impact Questionnaire—Revised) in 491 women with fibromyalgia. Results: Activity avoidance (p < 0.001), excessive persistence (p < 0.001) and pacing (p < 0.01) patterns were positively associated with fibromyalgia impact. Helplessness shows a moderating role between pain avoidance (B = 0.100, t =2.30, p = 0.021, [0.01, 0.18]), excessive persistence (B = −0.09, t = −2.24, p = 0.02, [−0.18, −0.01]), pain persistence (B = −0.10, t = −2.04, p = 0.04, [−0.19, −0.004]) and functioning. Conclusion: Helplessness (within pain catastrophizing) is a relevant variable within psychological flexibility models applied to activity patterns. Specifically, pain avoidance is especially dysfunctional in patients with high helplessness. To improve excessive persistence and pain persistence, it is necessary to reduce helplessness before regulating activity patterns.
The Effect of Sport Practice on Enhanced Cognitive Processing of Bodily Indices: A Study on Volleyball Players and Their Ability to Predict Hand Gestures

To program proper reactions, athletes must anticipate opponents’ actions on the basis of previous visuomotor experience. In particular, such abilities seem to rely on processing others’ intentions to act. We adopted a new approach based on an attentional spatial compatibility paradigm to investigate how elite volleyball players elaborate both spatial and motor information at upper-limb posture presentation. Forty-two participants (18 volleyball players and 17 nonathlete controls assigned to Experiments 1 a and b, and eight basketball players assigned to Experiment 2) were tested to study their ability to process the intentions to act conveyed by hands and extract motor primitives (i.e., significant components of body movements). Analysis looked for a spatial compatibility effect between direction of the spike action (correspondence factor) and response side for both palm and back of the hand (view factor). We demonstrated that volleyball players encoded spatial sport-related indices from bodily information and showed preparatory motor activation according to the direction of the implied spike actions for the palm view (Experiment 1; hand simulating a cross-court spike, p = 0.013, and a down-the-line spike, p = 0.026) but both nonathlete controls (Experiment 1; both p < 0.05) and other sports athletes (basketball players, Experiment 2; p = 0.34, only cross-court spike) did not. Results confirm that elite players’ supremacy lies in the predictive abilities of coding elementary motor primitives for their sport discipline.
Bioactive Sugarcane Lipids in a Circular Economy Context

Most of the global sugar and ethanol supply trade comes from the harvesting of Saccharum officinarum (i.e., sugarcane). Its industrial processing results in numerous by-products and waste streams, such as tops, straw, filter cake, molasses and bagasse. The recovery of lipids (i.e., octacosanol, phytosterols, long-chain aldehydes and triterpenoids) from these residues is an excellent starting point for the development of new products for various application fields, such as health and well-being, representing an important feature of the circular economy. By selecting green scalable extraction procedures, industry can reduce its environmental impact. Refluxed ethanol extraction methods have been demonstrated to meet these characteristics. On the other hand, effective non-solvent methodologies such as molecular distillation and supercritical CO2 extraction can fractionate lipids based on high temperature and pressure application with similar yields. Sugarcane lipophilic extracts are usually analyzed through gas chromatography (GC) and liquid chromatography (LC) techniques. In many cases, the identification of such compounds involves the development of high-temperature GC–MS/FID techniques. On the other hand, for the identification and quantification of thermolabile lipids, LC–MS techniques are suitable for the separation and identification of major lipid classes. Generically, its composition includes terpenes, phytosterols, tocopherol, free fatty acids, fatty alcohols, wax esters, triglycerides, diglycerides and monoglycerides. These compounds are already known for their interesting application in various fields such as pharma and cosmetics due to their anti-hypercholesterolemic, anti-hyperglycemic, antioxidant and anti-inflammatory properties.
Phthalates and Their Impacts on Human Health

Phthalates are a series of widely used chemicals that demonstrate to be endocrine disruptors and are detrimental to human health. Phthalates can be found in most products that have contact with plastics during producing, packaging, or delivering. Despite the short half-lives in tissues, chronic exposure to phthalates will adversely influence the endocrine system and functioning of multiple organs, which has negative long-term impacts on the success of pregnancy, child growth and development, and reproductive systems in both young children and adolescents. Several countries have established restrictions and regulations on some types of phthalates; however, we think that more countries should establish constraints or substitute measures for phthalates to reduce health risks. This article aims to summarize the adverse impacts of phthalates on human health, analyze the toxicity mechanism, assess the risks, and finally provide feasible strategies to reduce exposure of the public to phthalates.
Effects of Berberine on Circular RNA Expression Profiles in Human Gastric Cancer Cells

Background Berberine has been demonstrated to have anticancer effects against gastric cancer (GC), but the mechanism of these actions is unclear. Objectives To explore the impact of berberine on circular RNA (circRNA) expression profiles in GC and investigate the potential molecular mechanisms associated with circRNAs in GC. Methods AGS and HGC27 GC cells were treated with various concentrations of berberine. Cell viability was measured using a Cell Counting Kit-8 assay. Cell proliferation was measured using a cell colony formation assay. Cell apoptosis was measured using flow cytometry. The mitochondrial membrane potential (Δψm) was determined using a JC-1 probe. RNA-seq was performed to identify circRNA expression profiles in AGS cells after berberine treatment. Selected differentially expressed (DE) circRNAs were verified using RT-qPCR. Bioinformatics analysis was performed to predict target miRNAs and mRNAs and construct a circRNA-miRNA-mRNA network. Pathway and process enrichment analyses were performed to explore the potential biological roles of DE circRNAs. Results Berberine decreased GC cell viability, cell proliferation, and Δψm and induced cell apoptosis. Thirty-one DE circRNAs were identified in the berberine-treated group compared to the control group, among which circRNA2499, hsa_circ_0003423, and hsa_circ_0006702 were validated using RT-qPCR. Enrichment analyses, based on the host genes of these 31 DE circRNAs and putative target mRNAs in the circRNA-miRNA-mRNA network of the validated circRNAs, indicated that berberine exerts anti-GC effects in multiple pathways including the Notch, MAPK, and NF-κB signaling pathways via specific circRNAs. Conclusion This study elucidated the expression profile of circRNAs in human GC cells after berberine treatment. Our results demonstrate that berberine has the potential to influence cancer-related pathways by regulating circRNA expression and their corresponding target genes in GC cells.
Ranking-Oriented Quantitative Structure–Activity Relationship Modeling Combined with Assay-Wise Data Integration

In ligand-based drug design, quantitative structure–activity relationship (QSAR) models play an important role in activity prediction. One of the major end points of QSAR models is half-maximal inhibitory concentration (IC50). Experimental IC50 data from various research groups have been accumulated in publicly accessible databases, providing an opportunity for us to use such data in predictive QSAR models. In this study, we focused on using a ranking-oriented QSAR model as a predictive model because relative potency strength within the same assay is solid information that is not based on any mechanical assumptions. We conducted rigorous validation using the ChEMBL database and previously reported data sets. Ranking support vector machine (ranking-SVM) models trained on compounds from similar assays were as good as support vector regression (SVR) with the Tanimoto kernel trained on compounds from all the assays. As effective ways of data integration, for ranking-SVM, integrated compounds should be selected from only similar assays in terms of compounds. For SVR with the Tanimoto kernel, entire compounds from different assays can be incorporated.
Cold Atmospheric-Pressure Plasma Caused Protein Damage in Methicillin-Resistant Staphylococcus aureus Cells in Biofilms

Biofilms formed by multidrug-resistant bacteria are a major cause of hospital-acquired infections. Cold atmospheric-pressure plasma (CAP) is attractive for sterilization, especially to disrupt biofilms formed by multidrug-resistant bacteria. However, the underlying molecular mechanism is not clear. In this study, CAP effectively reduced the living cells in the biofilms formed by methicillin-resistant Staphylococcus aureus, and 6 min treatment with CAP reduced the S. aureus cells in biofilms by 3.5 log10. The treatment with CAP caused the polymerization of SaFtsZ and SaClpP proteins in the S. aureus cells of the biofilms. In vitro analysis demonstrated that recombinant SaFtsZ lost its self-assembly capability, and recombinant SaClpP lost its peptidase activity after 2 min of treatment with CAP. Mass spectrometry showed oxidative modifications of a cluster of peaks differing by 16 Da, 31 Da, 32 Da, 47 Da, 48 Da, 62 Da, and 78 Da, induced by reactive species of CAP. It is speculated that the oxidative damage to proteins in S. aureus cells was induced by CAP, which contributed to the reduction of biofilms. This study elucidates the biological effect of CAP on the proteins in bacterial cells of biofilms and provides a basis for the application of CAP in the disinfection of biofilms.
The Relationship between Changes in GRIT, Taekwondo Ability, and Academic Achievement of University Students Majoring in Science and Engineering and Participating in Taekwondo Class

GRIT, which was conceptualized by the American psychologist Duckworth, was designed by grouping growth (G), resilience (R), intrinsic motivation (I), and tenacity (T), which means continuing to be patient and put in effort to achieve goals without being frustrated by adversity or failures experienced in the process of striving toward one’s goals. The purpose of this study was to determine GRIT changes caused by participation of students majoring in science and engineering in taekwondo class. Effects of taekwondo ability on GRIT and academic achievement were also examined to determine structural relationships among taekwondo ability, GRIT, and academic achievement. We selected a total of 305 students (204 participants and 101 non-participants) as research subjects and conducted a GRIT (preliminary) measurement. After one-year of taekwondo class, we collected and statistically processed the data of GRIT (post) measurement, taekwondo ability, and academic achievement of the participants. Reliability analysis, technical statistics, paired sample t-test, correlation analysis, and path analysis were performed. Changes in the GRIT values of the participants were found to be greater than those of non-participants. It was also found that taekwondo ability, GRIT, and academic achievement had significant correlations with each other. Finally, it was found that the higher the taekwondo ability, the higher the academic achievement and the higher the GRIT. Moreover, the higher the GRIT, the higher the academic achievement. Taekwondo training increased the GRIT values of participants. In addition, the taekwondo ability had positive effects on GRIT and academic achievement. GRIT also had a positive effect on academic achievement. Thus, there were structural relationships among taekwondo ability, GRIT, and academic achievement.
Methylation and Expression of FTO and PLAG1 Genes in Childhood Obesity: Insight into Anthropometric Parameters and Glucose–Lipid Metabolism

The occurrence of childhood obesity is influenced by both genetic and epigenetic factors. FTO (FTO alpha-ketoglutarate dependent dioxygenase) is a gene of well-established connection with adiposity, while a protooncogene PLAG1 (PLAG1 zinc finger) has been only recently linked to this condition. We performed a cross-sectional study on a cohort of 16 obese (aged 6.6–17.7) and 10 healthy (aged 11.4–16.9) children. The aim was to evaluate the relationship between methylation and expression of the aforementioned genes and the presence of obesity as well as alterations in anthropometric measurements (including waist circumference (WC), body fat (BF_kg) and body fat percent (BF_%)), metabolic parameters (lipid profile, blood glucose and insulin levels, presence of insulin resistance) and blood pressure. Expression and methylation were measured in peripheral blood mononuclear cells using a microarray technique and a method based on restriction enzymes, respectively. Multiple regression models were constructed to adjust for the possible influence of age and sex on the investigated associations. We showed significantly increased expression of the FTO gene in obese children and in patients with documented insulin resistance. Higher FTO expression was also associated with an increase in WC, BF_kg, and BF_% as well as higher fasting concentration of free fatty acids (FFA). FTO methylation correlated positively with WC and BF_kg. Increase in PLAG1 expression was associated with higher BF%. Our results indicate that the FTO gene is likely to play an important role in the development of childhood adiposity together with coexisting impairment of glucose-lipid metabolism.
Detection of Renal Injury Following Primary Coronary Intervention among ST-Segment Elevation Myocardial Infarction Patients: Doubling the Incidence Using Neutrophil Gelatinase-Associated Lipocalin as a Renal Biomarker

Background: A subgroup of patients with acute kidney injury (AKI) do not fulfil the functional criteria for AKI diagnosis but show elevated levels of new biomarkers reflecting tubular injury, suggesting that these patients suffer “subclinical AKI”. We investigated the incidence and possible implications of “subclinical AKI”, compared to no and clinical AKI among ST elevation myocardial infarction patients (STEMI) treated with primary coronary intervention (PCI). Methods: We included 223 patients with STEMI treated with PCI. Neutrophil gelatinase-associated lipocalin (NGAL) was used as a marker of renal tubular damage in the absence of functional AKI, with NGAL levels ≥100 ng/mL suggesting subclinical AKI. Patients were assessed for the occurrence of in-hospital adverse outcomes. Results: Of the study patients, 45 (25%) had subclinical AKI. These patients were more likely to have left ventricular ejection fraction ≤45% (33% vs. 23%. p = 0.01), in-hospital adverse outcomes (73% vs. 48%; p = 0.005), and a combination of the two. The multivariate regression model demonstrated that subclinical AKI was independently associated with in-hospital adverse outcomes (OR 3.71, 95% CI 1.30–10.62, p = 0.02). Conclusions: Subclinical AKI is common among STEMI patients and is independently associated with adverse outcomes, even in the absence of functional AKI.
Antioxidant Status in the Vitreous of Eyes with Rhegmatogenous Retinal Detachment with and without Proliferative Vitreoretinopathy, Macular Hole and Epiretinal Membrane

(1) Background: The aim of the study was to test the hypothesis that the antioxidant status in the vitreous body of eyes, which had been vitrectomized due to rhegmatogenous retinal detachment (RRD) with or without proliferative vitreoretinopathy (PVR), is higher than in eyes vitrectomized due to other retinal diseases. (2) Methods: four patient groups were analyzed: 22 eyes of patients with RRD without PVR, 27 eyes with RRD and PVR, 22 eyes with macular hole (MH) and 10 eyes with epiretinal membrane (ERM). Spectrophotometric methods were used to determine the total antioxidant status (TAS) values as well as superoxide dismutase (SOD) and glutathione reductase (GR) activities in the vitreous fluid samples. (3) Results: no significant differences in TAS values and antioxidant enzyme activities were observed among patient with RRD with and without PVR and with MH and ERM. The longer the duration of RRD leading to PVR and better postoperative visual acuity, the higher the TAS level. No significant differences were found between “macula on” and “macula off” subgroups within the RRD group and the RRD combined with PVR group. (4) Conclusions: The preliminary results do not support the thesis that the antioxidant status of vitrectomized eyes is different in patients with RRD with or without PVR in comparison to patients with MH and ERM. In patients with RRD, PVR presence and detached macula do not affect the values of TAS, SOD and GR in the vitreous fluid. The duration of the disease influences TAS in the vitreous in eyes with RRD complicated with PVR.
SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method

Long non-coding RNA (lncRNA)–microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs. Accordingly, predicting lncRNA–miRNA interactions provides an important basis for understanding the mechanisms of action of ncRNAs. However, the accuracy of the established prediction methods is still limited. In this study, we used structural consistency to measure the predictability of interactive links based on a bilayer network by integrating information for known lncRNA–miRNA interactions, an lncRNA similarity network, and an miRNA similarity network. In particular, by using the structural perturbation method, we proposed a framework called SPMLMI to predict potential lncRNA–miRNA interactions based on the bilayer network. We found that the structural consistency of the bilayer network was higher than that of any single network, supporting the utility of bilayer network construction for the prediction of lncRNA–miRNA interactions. Applying SPMLMI to three real datasets, we obtained areas under the curves of 0.9512 ± 0.0034, 0.8767 ± 0.0033, and 0.8653 ± 0.0021 based on 5-fold cross-validation, suggesting good model performance. In addition, the generalizability of SPMLMI was better than that of the previously established methods. Case studies of two lncRNAs (i.e., SNHG14 and MALAT1) further demonstrated the feasibility and effectiveness of the method. Therefore, SPMLMI is a feasible approach to identify novel lncRNA–miRNA interactions underlying complex biological processes.
Investigation on the Thermoforming of Pmsq-Hdpe for the Manufacture of a NACA Profile of Small Dimensions

Unmanned aerial vehicles (UAVs) or drones are attracting increasing interest in the aviation industry, both for military and civilian applications. The materials used so far in the manufacture of UAVs are wood, plastic, aluminum and carbon fiber. In this regard, a new family of high-density polyethylene (HDPE) nanocomposites reinforced with polymethylsilsesquioxane nanoparticles (PMSQ), with mechanical performances significantly superior to those of pure HPDE, has been prepared by a fusion-combination process. Their viscoelastic properties were determined by oscillatory shear tests and their viscoelastic behavior characterized by the Lodge integral model. Then, the Lagrangian formulation and the membrane theory assumption were used in the explicit implementation of the dynamic finite element formulation. For the forming phase, we considered the thermodynamic approach to express the external work in terms of closed volume. In terms of von Mises stress distribution and thickness in the blade, the results indicate that HDPE-PMSQ behaves like virgin HDPE. Furthermore, its materials, for all intents and purposes, require the same amount of energy to form as HDPE.