Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation in supplemental lighting quality influences key aroma volatiles in hydroponically grown ‘Italian Large Leaf’ basil

The spectral quality of supplemental greenhouse lighting can directly influence aroma volatiles and secondary metabolic resource allocation (i.e., specific compounds and classes of compounds). Research is needed to determine species-specific secondary metabolic responses to supplemental lighting (SL) sources with an emphasis on variations in spectral quality. The primary objective of this experiment was to determine the impact of supplemental narrowband blue (B) and red (R) LED lighting ratios and discrete wavelengths on flavor volatiles in hydroponic basil (Ocimum basilicum var. Italian Large Leaf). A natural light (NL) control and different broadband lighting sources were also evaluated to establish the impact of adding discrete and broadband supplements to the ambient solar spectrum. Each SL treatment provided 8.64 mol . m-2. d-1 (100 µmol . m-2. s-1, 24 h . d-1) photon flux. The daily light integral (DLI) of the NL control averaged 11.75 mol . m-2.d-1 during the growth period (ranging from 4 to 20 mol . m-2.d-1). Basil plants were harvested 45 d after seeding. Using GC-MS, we explored, identified, and quantified several important volatile organic compounds (VOCs) with known influence on sensory perception and/or plant physiological processes of sweet basil. We found that the spectral quality from SL sources, in addition to changes in the spectra and DLI of ambient sunlight across growing seasons, directly influence basil aroma volatile concentrations. Further, we found that specific ratios of narrowband B/R wavelengths, combinations of discrete narrowband wavelengths, and broadband wavelengths directly and differentially influence the overall aroma profile as well as specific compounds. Based on the results of this study, we recommend supplemental 450 and 660 nm (± 20 nm) wavelengths at a ratio of approximately 10B/90R at 100-200 µmol . m-2.s-1, 12-24 h . d-1 for sweet basil grown under standard greenhouse conditions, with direct consideration of the natural solar spectrum and DLI provided for any given location and growing season. This experiment demonstrates the ability to use discrete narrowband wavelengths to augment the natural solar spectrum to provide an optimal light environment across variable growing seasons. Future experiments should investigate the spectral quality for the optimization of sensory compounds in other high-value specialty crops.
Gene expression of peripheral blood mononuclear cells and CD8+ T cells from gilts after PRRSV infection

Porcine reproductive and respiratory syndrome virus (PRRSV) is a positive-stranded RNA virus, which emerged in Europe and U.S.A. in the late 1980s and has since caused huge economic losses. Infection with PRRSV causes mild to severe respiratory and reproductive clinical symptoms in pigs. Alteration of the host immune response by PRRSV is associated with the increased susceptibility to secondary viral and bacterial infections resulting in more serious and chronic disease. However, the expression profiles underlying innate and adaptive immune responses to PRRSV infection are yet to be further elucidated. In this study, we investigated gene expression profiles of PBMCs and CD8+ T cells after PRRSV AUT15-33 infection. We identified the highest number of differentially expressed genes in PBMCs and CD8+ T cells at 7 dpi and 21 dpi, respectively. The gene expression profile of PBMCs from infected animals was dominated by a strong innate immune response at 7 dpi which persisted through 14 dpi and 21 dpi and was accompanied by involvement of adaptive immunity. The gene expression pattern of CD8+ T cells showed a strong adaptive immune response to PRRSV, leading to the formation of highly differentiated CD8+ T cells starting from 14 dpi. The hallmark of the CD8+ T-cell response was the increased expression of effector and cytolytic genes (PRF1, GZMA, GZMB, GZMK, KLRK1, KLRD1, FASL, NKG7), with the highest levels observed at 21 dpi. Temporal clustering analysis of DEGs of PBMCs and CD8+ T cells from PRRSV-infected animals revealed three and four clusters, respectively, suggesting tight transcriptional regulation of both the innate and the adaptive immune response to PRRSV. The main cluster of PBMCs was related to the innate immune response to PRRSV, while the main clusters of CD8+ T cells represented the initial transformation and differentiation of these cells in response to the PRRSV infection. Together, we provided extensive transcriptomics data explaining gene signatures of the immune response of PBMCs and CD8+ T cells after PRRSV infection. Additionally, our study provides potential biomarker targets useful for vaccine and therapeutics development.
Effects of leaf age during drought and recovery on photosynthesis, mesophyll conductance and leaf anatomy in wheat leaves

Summary statement: Mesophyll conductance (g m) was negatively correlated with wheat leaf age but was positively correlated with the surface area of chloroplasts exposed to intercellular airspaces (S c). The rate of decline in photosynthetic rate and g m as leaves aged was slower for water-stressed than well-watered plants. Upon rewatering, the degree of recovery from water-stress depended on the age of the leaves, with the strongest recovery for mature leaves, rather than young or old leaves. Diffusion of CO2 from the intercellular airspaces to the site of Rubisco within C3 plant chloroplasts (gm ) governs photosynthetic CO2 assimilation (A). However, variation in g m in response to environmental stress during leaf development remains poorly understood. Age-dependent changes in leaf ultrastructure and potential impacts on g m, A, and stomatal conductance to CO2 (g sc) were investigated for wheat (Triticum aestivum L.) in well-watered and water-stressed plants, and after recovery by re-watering of droughted plants. Significant reductions in A and g m were found as leaves aged. The oldest plants (15 days and 22 days) in water-stressed conditions showed higher A and gm compared to irrigated plants. The rate of decline in A and g m as leaves aged was slower for water-stressed compared to well-watered plants. When droughted plants were rewatered, the degree of recovery depended on the age of the leaves, but only for g m. The surface area of chloroplasts exposed to intercellular airspaces (S c) and the size of individual chloroplasts declined as leaves aged, resulting in a positive correlation between g m and S c. Leaf age significantly affected cell wall thickness (t cw), which was higher in old leaves compared to mature/young leaves. Greater knowledge of leaf anatomical traits associated with g m partially explained changes in physiology with leaf age and plant water status, which in turn should create more possibilities for improving photosynthesis using breeding/biotechnological strategies.
Identification and validation of aging-related gene signatures and their immune landscape in diabetic nephropathy

Background Aging and immune infiltration have essential role in the physiopathological mechanisms of diabetic nephropathy (DN), but their relationship has not been systematically elucidated. We identified aging-related characteristic genes in DN and explored their immune landscape. Methods Four datasets from the Gene Expression Omnibus (GEO) database were screened for exploration and validation. Functional and pathway analysis was performed using Gene Set Enrichment Analysis (GSEA). Characteristic genes were obtained using a combination of Random Forest (RF) and Support Vector Machine Recursive Feature Elimination (SVM-RFE) algorithm. We evaluated and validated the diagnostic performance of the characteristic genes using receiver operating characteristic (ROC) curve, and the expression pattern of the characteristic genes was evaluated and validated. Single-Sample Gene Set Enrichment Analysis (ssGSEA) was adopted to assess immune cell infiltration in samples. Based on the TarBase database and the JASPAR repository, potential microRNAs and transcription factors were predicted to further elucidate the molecular regulatory mechanisms of the characteristic genes. Results A total of 14 differentially expressed genes related to aging were obtained, of which 10 were up-regulated and 4 were down-regulated. Models were constructed by the RF and SVM-RFE algorithms, contracted to three signature genes: EGF-containing fibulin-like extracellular matrix (EFEMP1), Growth hormone receptor (GHR), and Vascular endothelial growth factor A (VEGFA). The three genes showed good efficacy in three tested cohorts and consistent expression patterns in the glomerular test cohorts. Most immune cells were more infiltrated in the DN samples compared to the controls, and there was a negative correlation between the characteristic genes and most immune cell infiltration. 24 microRNAs were involved in the transcriptional regulation of multiple genes simultaneously, and Endothelial transcription factor GATA-2 (GATA2) had a potential regulatory effect on both GHR and VEGFA. Conclusion We identified a novel aging-related signature allowing assessment of diagnosis for DN patients, and further can be used to predict immune infiltration sensitivity.
Editorial: Extremophiles: tolerance mechanisms and use in crop improvement

COPYRIGHT © 2023 Uzilday and Ganie. This is an openaccess article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 20 June 2023 DOI 10.3389/fpls.2023. 1233202
A meta-analysis of the validity of the Head-Toes-Knees-Shoulders task in predicting young children's academic performance

The present study represents the first meta-analytic synthesis of the utility of a widely used early-childhood self-regulation measure, the Head-Toes-Knees-Shoulders task, in predicting children's academic achievement. A systematic review of the literature yielded 69 studies accessed from peer reviewed journals representing 413 effect sizes and 19,917 children meeting the complete set of inclusion and exclusion criteria. Robust variance analysis demonstrated that the Head-Toes-Knees-Shoulders task was a consistent predictor of children's academic achievement across literacy, oral language, and mathematical outcomes. A moderator analysis indicated that in accordance with prior research, the Head-Toes-Knees-Shoulders task was more strongly associated with children's mathematics performance relative to their performance on language and literacy measures. The results of this meta-analysis suggest that the Head-Toes-Knees-Shoulders task demonstrated statistically significant, positive associations with children's overall academic performance. These associations remained stable across different participant and measurement factors and are comparable to meta-analyses examining the self-regulation and academic association with multiple measures of self-regulation and executive function.
Comparison of intraoperative radiotherapy as a boost vs. simultaneously integrated boosts after breast-conserving therapy for breast cancer

Background Currently, there are no data from randomized trials on the use of intraoperative radiotherapy (IORT) as a tumor bed boost in women at high risk of local recurrence. The aim of this retrospective analysis was to compare the toxicity and oncological outcome of IORT or simultaneous integrated boost (SIB) with conventional external beam radiotherapy (WBI) after breast conserving surgery (BCS). Methods Between 2009 and 2019, patients were treated with a single dose of 20 Gy IORT with 50 kV photons, followed by WBI 50 Gy in 25 or 40.05 in 15 fractions or WBI 50 Gy with SIB up to 58.80–61.60 Gy in 25–28 fractions. Toxicity was compared after propensity score matching. Overall survival (OS) and progression-free survival (PFS) were calculated using the Kaplan–Meier method. Results A 1:1 propensity-score matching resulted in an IORT + WBI and SIB + WBI cohort of 60 patients, respectively. The median follow-up for IORT + WBI was 43.5 vs. 32 months in the SIB + WBI cohort. Most women had a pT1c tumor: IORT group 33 (55%) vs. 31 (51.7%) SIB group (p = 0.972). The luminal-B immunophenotype was most frequently diagnosed in the IORT group 43 (71.6%) vs. 35 (58.3%) in the SIB group (p = 0.283). The most reported acute adverse event in both groups was radiodermatitis. In the IORT cohort, radiodermatitis was grade 1: 23 (38.3%), grade 2: 26 (43.3%), and grade 3: 6 (10%) vs. SIB cohort grade 1: 3 (5.1%), grade 2: 21 (35%), and grade 3: 7 (11.6%) without a meaningful difference (p = 0.309). Fatigue occurred more frequently in the IORT group (grade 1: 21.7% vs. 6.7%; p = 0.041). In addition, intramammary lymphedema grade 1 occurred significantly more often in the IORT group (11.7% vs. 1.7%; p = 0.026). Both groups showed comparable late toxicity. The 3- and 5-year local control (LC) rates were each 98% in the SIB group vs. 98% and 93% in the IORT group (LS: log rank p = 0.717). Conclusion Tumor bed boost using IORT and SIB techniques after BCS shows excellent local control and comparable late toxicity, while IORT application exhibits a moderate increase in acute toxicity. These data should be validated by the expected publication of the prospective randomized TARGIT-B study.
Microbial interactions and metabolisms in response to bacterial wilt and black shank pathogens in the tobacco rhizosphere

Background Tobacco bacterial wilt (TBW) and black shank (TBS) are responsible for substantial economic losses worldwide; however, microbial interactions and metabolisms in response to TBW and TBS pathogens in the tobacco rhizosphere remain unclear. Methods We explored and compared the response of rhizosphere microbial communities to these two plant diseases with the incidences in moderate and heavy degrees by sequencing of 16S rRNA gene amplicons and bioinformatics analysis. Results and discussions We found that the structure of rhizosphere soil bacterial communities was significantly (p < 0.05) changed from the incidences of TBW and TBS, which also led to decreased Shannon diversity and Pielou evenness. Compared with the healthy group (CK), the OTUs with significantly (p < 0.05) decreased relative abundances were mostly affiliated with Actinobacteria (e.g., Streptomyces and Arthrobacter) in the diseased groups, and the OTUs with significantly (p < 0.05) increased relative abundances were mainly identified as Proteobacteria and Acidobacteria. Also, molecular ecological network analysis showed that the nodes (<467) and links (<641) were decreased in the diseased groups compared with the control group (572; 1056), suggesting that both TBW and TBS weakened bacterial interactions. In addition, the predictive functional analysis indicated that the relative abundance of genes related to the biosynthesis of antibiotics (e.g., ansamycins and streptomycin) was significantly (p < 0.05) decreased due to incidences of TBW and TBS, and antimicrobial tests showed that some Actinobacteria strains (e.g., Streptomyces) and their secreted antibiotics (e.g., streptomycin) could effectively inhibit the growth of these two pathogens.
Dissecting the mechanism of regulation of a ferroptosis-like form of cell death in Drosophila melanogaster

Ferroptosis is a specific form of non-apoptotic cell death that is driven by iron-dependent phospholipid peroxidation. Research over the past decade has contributed to our understanding of how this important cell death process is regulated in mammalian systems, especially with regard to the distinct modes of induction, the role of metabolic signals, the organelles involved, implications of ferroptosis for development and aging, and how our improved understanding of the process can be exploited for therapeutic purposes. Other studies have described variants of this ancient cell death process in cyanobacteria, plants and protozoans. Emerging evidence indicates that a ferroptosis-like form of cell death exists in fruit flies (Drosophila melanogaster). Due to the extensive homology of genes in Drosophila melanogaster and Drosophila suzukii, unique aspects of ferroptosis in Drosophila melanogaster may be of particular relevance for developing targeted pesticides against Drosophila suzukii—a major invasive agricultural pest of the berry and wine industry in Southeast Asia, Europe and America. Further, aspects of ferroptosis in Drosophila melanogaster that are conserved in insects in general may provide the basis for identifying new insecticides for controlling the spread of vector-borne diseases such as malaria. In this perspective, we highlight some of the studies in Drosophila melanogaster that have sought to improve our understanding of the ferroptosis-like form of cell death that operates in this organism and conclude with a discussion of the opportunities and challenges for studying this phenomenon in fruit flies.
Association of handgrip strength with new-onset CKD in Korean adults according to gender

Introduction Handgrip strength (HGS) is an indicator of many diseases such as pneumonia, cardiovascular disease and cancer. HGS can also predict renal function in chronic kidney disease (CKD) patients, but the value of HGS as a predictor of new-onset CKD is unknown. Methods 173,195 subjects were recruited from a nationwide cohort and were followed for 4.1 years. After exclusions, 35,757 participants remained in the final study, and CKD developed in 1063 individuals during the follow-up period. Lifestyle, anthropometric and laboratory data were evaluated in relation to the risk of CKD. Results The participants were subdivided into quartiles according to relative handgrip strength (RGS). Multivariate Cox regression demonstrated that RGS was inversely associated with incident CKD. Compared with the lowest quartile, the hazard ratios (HRs) [95% confidence intervals (CIs)] for incident CKD for the highest quartile (Q4) was 0.55 (0.34–0.88) after adjusting for covariates in men and 0.51 (0.31–0.85) in women. The incidence of CKD decreased as RGS increased. These negative associations were more significant in men than in women. The receiver operating characteristic (ROC) curve showed that baseline RGS had predictive power for new-onset CKD. Area under the curve (AUC) (95% CIs) was 0.739 (0.707–0.770) in men and 0.765 (0.729–0.801) in women. Conclusion This is the novel study demonstrating that RGS is associated with incident CKD in both men and women. The relationship between RGS and incident CKD is more significant in women than in men. RGS can be used in clinical practice to evaluate renal prognosis. Regular measurement of handgrip strength is essential to CKD detection.
Editorial: Risk and protective factors, family environment and (a)typical neurodevelopmental outcomes

COPYRIGHT © 2023 Provenzi, Bussu and Riva. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Risk and protective factors, family environment and (a)typical neurodevelopmental outcomes
Computing within-study covariances, data visualization, and missing data solutions for multivariate meta-analysis with metavcov

Multivariate meta-analysis (MMA) is a powerful statistical technique that can provide more reliable and informative results than traditional univariate meta-analysis, which allows for comparisons across outcomes with increased statistical power. However, implementing appropriate statistical methods for MMA can be challenging due to the requirement of various specific tasks in data preparation. The metavcov package aims for model preparation, data visualization, and missing data solutions to provide tools for different methods that cannot be found in accessible software. It provides sufficient constructs for estimating coefficients from other well-established packages. For model preparation, users can compute both effect sizes of various types and their variance-covariance matrices, including correlation coefficients, standardized mean difference, mean difference, log odds ratio, log risk ratio, and risk difference. The package provides a tool to plot the confidence intervals for the primary studies and the overall estimates. When specific effect sizes are missing, single imputation is available in the model preparation stage; a multiple imputation method is also available for pooling the results in a statistically principled manner from models of users' choice. The package is demonstrated in two real data applications and a simulation study to assess methods for handling missing data.
Tislelizumab plus chemotherapy versus pembrolizumab plus chemotherapy for the first-line treatment of advanced non-small cell lung cancer: systematic review and indirect comparison of randomized trials

Purpose: Pembrolizumab and tislelizumab have demonstrated significant clinical benefits in first-line treatment for advanced NSCLC. However, no head-to-head clinical trial has ever compared the optimal choice. Therefore, we conducted an indirect comparison to explore the optimal choice for advanced NSCLC combined with chemotherapy. Methods: We conducted a systematic review of randomized trials; the clinical outcomes included overall survival (OS), progression-free survival (PFS), objective response rate (ORR), and adverse events (AEs). Indirect comparisons between tislelizumab and pembrolizumab were conducted with the Bucher method. Results: Data were abstracted from 6 randomized trials involving more than 2,000 participants. Direct meta-analysis showed that both treatment regimens improved clinical outcomes compared with chemotherapy alone (PFS: hazard ratio (HR)tis+chemo/chemo 0.55, 95% CI 0.45–0.67; HRpem+chemo/chemo 0.53, 95% CI 0.47–0.60; ORR: relative risk (RR)tis+chemo/chemo 1.50, 95% CI 1.32–1.71; RRpem+chemo/chemo 1.89, 95% CI 1.44–2.48). Regarding safety outcomes, tislelizumab and pembrolizumab have a higher risk in the incidence of grade 3 or higher AEs (RRtis+chemo/chemo 1.12, 95% CI 1.03–1.21; RRpem+chemo/chemo 1.13, 95% CI 1.03–1.24). The indirect comparison showed that there was no significant difference between tislelizumab plus chemotherapy and pembrolizumab plus chemotherapy in terms of PFS (HR: 1.04, 95% CI 0.82–1.31), ORR (RR: 0.79, 95% CI 0.59–1.07), the incidence of grade 3 or higher AEs (RR 0.99, 95% CI 0.87–1.12), and AEs leading to death (RR 0.70, 95% CI 0.23–2.09). In progression-free survival subgroup analysis, the results demonstrate no significant differences in PFS by PD-L1 TPS expression level, age, liver metastasis status, and smoking status between tislelizumab plus chemotherapy and pembrolizumab plus chemotherapy. Conclusion: The efficacy and safety of tislelizumab combination chemotherapy were not substantially different from pembrolizumab combination chemotherapy.