Search Results (3,727)

Background: Cunninghamia lanceolata (Lamb.) Hook. (C. lanceolata) is an important timber tree species in southern China. However, the molecular regulatory mechanisms underlying adventitious root formation during cutting propagation remain largely unclear. The lack of genetic resources has hindered molecular breeding efforts in this species. Methods: In this study, transcriptome analysis was performed on the root systems of scions from elite C. lanceolata clones at 7, 30, and 60 d after cutting. Results: Approximately 69.30 Gb of clean data were obtained. De novo assembly and gene prediction yielded 43,433 protein-coding genes, of which 32,886 (75.7%) were functionally annotated. Temporal clustering and comparative functional enrichment analyses revealed a distinct temporal functional shift during adventitious root development in C. lanceolata. Early stages were dominated by metabolic processes such as pyrimidine metabolism and carbohydrate biosynthesis, whereas later stages were governed by phytohormone signal transduction. Key components of the auxin pathway, including AUX1, AFB, IAA, and SAUR, exhibited dynamic and differential expression, which may be associated with adventitious root growth. Based on the transcriptome data, we identified nine members of the PIN gene family. Both transcriptomic expression profiles and qRT-PCR validation demonstrated that these PIN genes showed divergent expression trends across developmental stages, suggesting that they may participate in rooting by regulating polar auxin transport. Conclusions: This study systematically elucidates the molecular network underlying adventitious root formation in C. lanceolata cuttings. It enriches the omics resources for conifers and provides a theoretical foundation and omics basis for molecular breeding and efficient propagation of elite C. lanceolata clones. Full article

This study develops a multidimensional, indicator-based framework for assessing whether the expansion of research and development (R&D) resources in Türkiye is accompanied by broadly distributed innovation capacity, digital market integration, and ecosystem dynamism. The analysis uses the latest available official TurkStat tables, whose reference periods span 2015–2025, and treats them as a diagnostic profile rather than a longitudinal or causal dataset. Gross domestic R&D expenditure reached TRY 651.8 billion in 2024, and the business enterprise sector accounted for 64.8% of the total. R&D expenditure was geographically concentrated: İstanbul and Ankara together represented 61.2% of national expenditure. During 2022–2024, product innovation rates rose from 21.6% among small enterprises to 45.1% among large enterprises, while information and communication and scientific R&D activities each recorded a product specialisation ratio of 2.19. In 2025, 93.6% of enterprises had fixed-line internet access, but only 8.6% had a connection of at least 1 Gbit/s; in 2024, 12.4% made web sales and 27.8% of web sellers sold abroad. The proposed Strategic Innovation and R&D Capacity Index (SIRDCI) is therefore presented as a transparent conceptual diagnostic. A partial firm-size proxy is demonstrated only with indicators available at a common firm-size level; ecosystem dynamism remains a national contextual dimension because it cannot be disaggregated by firm size. The descriptive results reveal a positive firm-size gradient, marked sectoral and regional concentration, and a gap between digital access and commercialisation. These patterns do not establish causal mechanisms; instead, they identify areas that may warrant further capability-oriented policy attention and evaluation. Full article

G. barbadense represents an indispensable germplasm resource for high-quality textile fiber and disease resistance; nevertheless, systematic information regarding its ZRT/IRT-like protein (ZIP) gene family remains limited. Here, a total of 46 GbZIP genes were identified across the G. barbadense genome. Comprehensive bioinformatic investigations revealed uneven chromosomal distribution and confirmed that segmental/whole-genome duplications, supplemented by localized tandem duplications, drove family expansion. Members clustered within the same phylogenetic clades shared conserved motif organization and gene architecture, while promoter regions harbored abundant cis-acting elements associated with phytohormone and stress signaling. Transcriptome profiling indicated distinct expression patterns across vegetative/reproductive tissues, fiber and ovule developmental stages, and diverse abiotic stress conditions (cold, hot, drought, and salt). Quantitative Real-Time PCR (qRT-PCR) further validated that several GbZIP candidates exhibited temporal expression variations upon exposure to cadmium toxicity, V. dahliae infection, and combined Cd-V. dahliae stress. Specifically, GbZIP13, GbZIP18, GbZIP27, and GbZIP36 displayed prominent broad-spectrum responses to all three stress conditions, whereas GbZIP16, GbZIP29, and GbZIP30 showed stress-specific regulatory divergence. Overall, this study aims to systematically analyze the evolutionary characteristics and expression patterns of the GbZIP family, and to specifically evaluate the response differences under Cd stress, V. dahliae stress, and combined stress, in order to identify potential key candidate genes. Full article

Wastewater analysis has emerged as a powerful tool for wastewater-based epidemiology, environmental surveillance, and monitoring of emerging contaminants. While most studies rely on targeted approaches focusing on predefined compound lists, untargeted metabolomics offers potential to capture a broader and less biased chemical snapshot. However, the complexity of wastewater matrices and the chemical diversity of small molecules pose analytical challenges. In this study, we apply a multi-platform, untargeted metabolomics workflow to profile the influent wastewater metabolome of five wastewater treatment plants in Spain, differing in geographic context, population size, and industrial activity. Twenty-four-hour composite samples were collected in three seasons and analyzed using gas chromatography, reversed-phase liquid chromatography, and hydrophilic interaction liquid chromatography, all coupled to mass spectrometry. A total of 828 unique compounds were annotated across platforms, with minimal overlap, highlighting the complementarity of analytical approaches and extraction strategies. Multivariate analyses revealed reproducible site-associated chemical patterns consistent across seasons and platforms. Dominant contributors included lipids, organic acids, organic oxygen compounds, organoheterocyclic compounds, and benzenoids, reflecting differences in population and human activity. This work demonstrates the feasibility of a multi-platform untargeted workflow for generating complementary and reproducible comparative profiles of wastewater influent. The resulting public dataset is intended as a methodological and exploratory comparative resource, and broader spatial and longitudinal validation is required before generalization or use for source attribution. Full article

The spread of Bursaphelenchus xylophilus has caused a critical shortage of traditional Poria cocos cultivation materials, making bag-based substrates an urgent alternative. Yet, how substrate stoichiometry shapes nutritional quality remains unclear. Using non-targeted metabolomics combined with redundancy analysis (RDA) and weighted gene co-expression network analysis (WGCNA), we profiled P. cocos cultivated on four substrates: healthy pine logs, pine wilt wood bags, oak bags, and pine needle/branch bags. Bag-cultivated P. cocos showed significantly elevated total amino acids, poria cocos acid, and total triterpenoids, with pine wilt wood bags (P1) performing best overall. Nitrogen, phosphorus, and the N/P ratio independently drove metabolomic variation (pairwise overlap < 5%). Nitrogen-line hub metabolites were negatively correlated with amino acid content, suggesting that suppressed lipid metabolism may free carbon skeletons for the accumulation of nitrogenous nutrients. Phosphorus-line hub metabolites were positively associated with polysaccharide indices, whereas the N/P ratio in line lipid amides showed strong negative correlations with polysaccharides under phosphorus limitation. These correlational patterns are consistent with a stoichiometric resource allocation model, although direct validation through controlled-element experiments is required. These findings provide quantitative guidance for optimizing bag-substrate formulations in P. cocos cultivation. Full article

Large-scale administrative hospital discharge data is a key resource for secondary health systems research, yet reuse is constrained by barriers of access, quality, interoperability, and semantic comparability. This paper presents and validates a reproducible, declarative, loss-aware harmonization framework for public discharge data that avoids full migration to a comprehensive common data model. The framework comprises a lightweight 14-field canonical model, versioned JSON crosswalks, a shared execution engine, a resilient file reader, schema validation, idempotency tests, value-domain checks, and an information-loss map. It was evaluated on public record-level discharge data from five jurisdictions on three continents (Korea, Brazil, Mexico, Chile, and New York State), comprising 561,966,231 harmonized records from 2001 to 2025. Validation demonstrated conformance to the declared source profiles for 82 of 99 files and full canonical conformance for 39, idempotency across all 99 files, 99.99% conformance with permitted value domains under an explicitly stated aggregation, and detection of source-level defects such as truncated files, malformed rows, and completeness anomalies. A marker-condition query for ischemic stroke (ICD-10 I63) showed that a single case definition executes consistently on the four sources retaining raw ICD-10 codes. The results show that, for heterogeneous administrative data, the key value lies not in scale alone but in the auditability of transformations, explicit loss documentation, and reproducibility of the harmonization process. Full article

Phytoene, a colorless precursor of carotenoids, has attracted increasing attention because of its favorable bioavailability, antioxidant activity, and potential applications in functional foods, nutraceuticals, and animal nutrition. However, its industrial utilization remains limited by low natural abundance and the dependence of current production strategies on genetic engineering or metabolic pathway manipulation. In this study, we identified and characterized a naturally occurring Brevundimonas vesicularis strain (Bv-xms2024) exhibiting pronounced phytoene accumulation without genetic modification. The strain was comprehensively characterized using morphological, biochemical, molecular, genomic, metabolomic, and transcriptional analyses. Quantitative LC–MS/MS analysis demonstrated that Bv-xms2024 accumulated phytoene to 420.42 ± 98.11 μg/g dry biomass after 96 h of cultivation, substantially exceeding the levels of downstream carotenoids, including β-carotene and astaxanthin. Optimization of cultivation parameters identified 25 °C, pH 7.0, and 96 h as the optimal conditions for phytoene accumulation, while serial passaging confirmed stable production over 20 generations. Genome annotation identified the carotenoid biosynthetic gene repertoire, while RT-qPCR analysis revealed a temporal shift from early upregulation of crtE and crtB to later upregulation of downstream pathway genes, consistent with the observed phytoene-dominant carotenoid profile. Short-term tolerance evaluations in mice and chickens revealed no observable adverse effects under the tested conditions. Collectively, these findings identify Bv-xms2024 as a promising natural microbial resource for phytoene production and provide a basis for further process development and strain-level safety evaluation. Full article

Acorns represent a traditional seasonal feed resource for pigs in Mediterranean production systems; however, comparative information on the nutritional composition and safety of acorns from Central European oak species remains scarce. The present study comprehensively characterized acorns of Quercus robur, Q. petraea, and Q. rubra to assess their potential relevance to pig nutrition based on their chemical composition. Proximate composition, mineral content, fatty acid and amino acid profiles, phenolic compounds, tannins, triterpenoid acids, and heavy metal concentrations were determined using analytical methods. Differences among the analyzed acorn samples were observed in nutritional composition and phytochemical profile. Acorns from all three species were characterized by a high proportion of unsaturated fatty acids, particularly oleic acid, a favourable amino acid profile, and the presence of phenolic compounds, tannins, and triterpenoid acids. Heavy metal concentrations remained below the maximum levels established by European legislation for feed materials, indicating that the analyzed acorns showed no heavy-metal-related exceedances of the applicable European limits for feed materials. The results indicate that acorns from Central European oak species represent a locally available feed resource of potential relevance to pig nutrition. This comprehensive chemical characterization provides a scientific basis for future nutritional studies and further evaluation of acorns as sustainable feed materials. Full article

This study aimed to identify socioenvironmental vulnerability profiles among Mexican households and analyze their association with health expenditure. Data from 86,102 households included in the 2024 National Household Income and Expenditure Survey were analyzed. Socioenvironmental profiles were constructed using housing, basic services, sanitation, household energy, socioeconomic stratum, and overcrowding through factor analysis of mixed data and k-means. Internal validation, stability analyses, algorithm comparisons, and sensitivity analyses supported a three-profile solution representing low, intermediate, and high vulnerability. Health expenditure was examined using survey-weighted descriptive estimates, exploratory nonparametric comparisons, and a survey-adjusted two-part model. The intermediate vulnerability profile showed higher odds of reporting health expenditure than the low vulnerability profile (OR = 1.129, 95% CI: 1.048 to 1.217, p = 0.002), whereas the high vulnerability profile showed no significant difference. Among households with positive expenditure, high vulnerability was associated with lower logarithmic expenditure ($\beta =-0.341$, 95% CI: $-0.490$ to $-0.192$, p < $0.001$), whereas the intermediate profile was not significantly different in the main model. The association for high vulnerability remained significant in sensitivity analyses, while results for the intermediate profile were more sensitive to model specification and income adjustment. Despite several statistically significant associations, effect sizes in the exploratory comparisons were small and the regression models explained a limited proportion of the variability in health expenditure. The findings therefore indicate modest associations between socioenvironmental vulnerability and health expenditure, with household economic resources and other unmeasured health-related factors likely contributing to the observed differences. Full article

The coming era of quantum supremacy has created an existential threat to critical information infrastructures (CIIs). This threat is realized through delayed attack vectors of the “Harvest Now, Decrypt Later” (HNDL) class. Existing security paradigms dictate forced migration to post-quantum cryptography (PQC) algorithms. However, in the context of legacy architectures, and in particular in the ICS and SCADA segments, such a strategy generates quantum technological friction. This friction can trigger cascading failures of legitimate CII services. This article proposes addressing the PQC transformation problem not as a linear IT modernization task, but as a general-sum differential Stackelberg game. The concept of “active deception” (Cyber Deception) is described as a Leader (Defender) strategy, i.e., the variable redistribution of budgets between real cryptographic migration and the generation of resource-intensive decoy infrastructures. Using the Forward-Backward Sweep Method algorithm, optimal software controls are obtained for three typical architectural profiles, calibrated using statistical data from the critical information infrastructure of the Republic of Kazakhstan. Numerical simulations have demonstrated that in high-inertia and strategic networks, maximizing active deception creates the necessary “temporal buffer”, minimizing the damage from an HNDL compromise while maintaining operational continuity. The results support the need to revise rigid cryptographic transition regulations in favor of flexible, mathematically sound hybrid strategies. Full article

Species belonging to the genus Seseli have long been known to be used as herbal remedies in traditional medicine for various purposes such as colds, inflammation, pain, and gastrointestinal disorders. Therefore, in this study, the flower parts of Seseli transcaucasicum (Schischk.) Pimenov & Sdobnina were extracted using methanol and acetone to investigate their phytochemical composition and antioxidant, antimicrobial, and cytotoxic activities. For this purpose, total phenolic content (TPC), DPPH free radical scavenging activity (RSA), phenolic component (PCs) profile, volatile component composition, antimicrobial effect, and cytotoxic potential on the HT29 human colorectal adenocarcinoma cell line were evaluated. When the results were examined, HPLC analysis of phenolic components revealed that both extracts contained particularly high levels of rosmarinic acid, catechin, and quercetin. Among these, rosmarinic acid was detected in the highest amount, with 15.195 mg/g in the methanol extract and 14.929 mg/g in the acetone extract. The volatile components of this plant were determined by GC-MS, and a total of 29 volatile compounds were identified. Among these, β-pinene (220.792 mg/kg), Δ3-carotene (81.898 mg/kg), α-sedrene (63.331 mg/kg), elixen (44.535 mg/kg), sabinene (40.822 mg/kg), and D-limonene (38.422 mg/kg) were identified as the most dominant compounds. It was observed that the methanol extract had a higher total phenolic content (77.389 ± 1.389 mg gallic acid equivalent/g extract) and higher free radical scavenging activity (40.933 ± 0.067 mg trolox equivalent/g extract) compared to the acetone extract. Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans strains were used to determine the antimicrobial activities of plant extracts, and moderate inhibitory effects were observed against these microorganisms. The highest antimicrobial activity was determined by the 16 mm inhibition zone created against S. aureus by the methanol extract at a concentration of 100 mg/mL. The cytotoxic activity of the plant was determined by measuring its dose-dependent antiproliferative effect on HT29 cells. When the difference between solvents was examined, it was observed that the acetone extract at a concentration of 500 µg/mL reduced cell viability by 18.03%, while the methanol extract at the same concentration reduced viability by 30.56%. According to the results, S. transcaucasicum is rich in phenolic and terpenic compounds and exhibits antioxidant, antimicrobial, and cytotoxic effects. Therefore, this plant species is considered a promising resource for the development of naturally occurring biologically active compounds. Full article

The transition from conventional silica nanoparticle (SiNP) production based on purified alkoxysilanes and high-temperature flame hydrolysis of silicon tetrachloride to renewable and waste-derived silicon resources requires more than precursor substitution. It requires a mechanistic understanding of how feedstock mineralogy, silicon speciation, impurity chemistry, and processing history propagate through dissolution, nucleation, condensation, gelation, aging, drying, and pore evolution to determine material performance, environmental burden, and manufacturing feasibility. Although previous reviews have established the technical feasibility of producing silica from secondary resources, their predominant organization by feedstock, synthesis route, or application provides limited ability to explain why nominally similar processes generate materials with markedly different structural and functional properties. This review addresses these through a resource-pull, feedstock-to-function framework that links resource chemistry and process design to critical material attributes, application-specific specifications, sustainability, and scale-up requirements. Agricultural residues, industrial by-products, geothermal resources, waste glass, and fluorosilicate streams are critically compared according to silicon form and phase, reactivity, impurity profile, compositional variability, purification demand, and attainable product quality. Particular attention is given to waste-derived alkaline silicate systems, in which molecular, oligomeric, and colloidal silica coexist and therefore require characterization beyond bulk SiO₂ concentration. Established and emerging processing strategies, including controlled combustion and alkaline extraction, alkali fusion, ambient-pressure drying, microwave and mechanochemical activation, biogenic and biomimetic templating, and continuous processing, are evaluated according to their mechanistic effects, technological maturity, structural control, and demands for energy, reagents, water, solvents, effluent treatment, and capital. Across these routes, gelation and aging emerge as critical transfer stages through which feedstock composition is translated into network connectivity, pore architecture, shrinkage behavior, and ultimately functional performance. Evidence from secondary-source aerogels further shows that properly controlled waste-derived systems can attain BET surface areas of approximately 350–500 m² g⁻¹, within the textural range of many alkoxide-derived materials, indicating that feedstock variability, impurity management, and process control are more important constraints than an inherently lower performance ceiling. On this basis, this review proposes a minimum evidence framework comprising feedstock traceability, intermediate-speciation and colloidal characterization, silicon mass balance, gelation and aging metrics, application-specific qualification criteria, performance-normalized life cycle and techno-economic assessment, process analytical control, and staged pilot validation. Collectively, these principles provide a mechanistically grounded basis for moving sustainable silica synthesis beyond isolated proof-of-concept demonstrations toward reproducible, scalable, application-matched, and commercially credible manufacturing platforms. Full article

This review examines the clinical and practical implications of embedding molecular profiles directly into the 2023 FIGO staging system for endometrial carcinoma, in the context of the 2025 ESGO/ESTRO/ESP guidelines. The primary purpose is to navigate a central conflict in modern oncology: how to deliver increasingly personalized care while maintaining a globally accessible, equitable, and standardized cancer classification system. The 2023 FIGO update represents a paradigm shift from the traditional dualistic model (Type I versus Type II) by allowing molecular findings to redefine stage itself. While this integration offers clear benefits, it introduces significant challenges. First, the system depends on advanced molecular testing, creating a “rich-poor” divide where patients in resource-limited settings are systematically overtreated because testing is unavailable. Second, stage becomes unstable, changing with sequential histologic and molecular re-review, which causes confusion for patients and clinicians. Third, the system lumps prognostically distinct histotypes (Serous, Clear Cell, Carcinosarcoma, and Grade 3 Endometrioid) into a single aggressive stage, obscuring meaningful differences in survival. Fourth, it relies on subjective parameters such as “substantial” lymphovascular space invasion, for which no standardized definition exists, leading to high inter-observer variability. After analyzing these controversies, the review proposes a pragmatic solution: decouple anatomical staging from molecular risk stratification. Staging should remain a purely anatomical, universally applicable descriptor of tumor extent, while molecular and histologic data are used separately within a dynamic risk assessment model, as suggested by the European guidelines. This dual-track approach preserves global comparability, reduces inequity, and maintains diagnostic stability, while still enabling personalized treatment where advanced diagnostics are available. Full article

Background: Autophagy plays a central role in maintaining cellular homeostasis, regulating growth and development, and responding to multiple stresses. Autophagy-related genes (ATGs) play critical roles in autophagy, yet their functional diversity in soybean (Glycine max) remains underexplored. Methods: Genome-wide identification of GmATG genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, three-dimensional structural, and promoter cis-acting elements. Tissue-specific expression and multiple stresses response were examined using transcriptome data and profiled by RT-qPCR. Results: A total of 60 GmATG genes belonging to 20 subfamilies were identified in soybean. Gene family expansion was predominantly driven by fragment duplication (33 gene pairs), with the ATG8 family expanding to 12 members, and pan-genomic analysis uncovered prominent copy number variation (6–9 copies) in the ATG18 family. GmATG genes showed distinct expression patterns in response to multiple abiotic and biotic stresses. Specifically, GmATG18f was significantly induced by phosphorus deficiency in the low-phosphorus-tolerant soybean variety Nannong 94-156. GmATG8g, GmATG9d and GmATG13d showed a typical expression trend of initial increase followed by decrease, with expression levels peaking at 6–12 h after salt stress treatment. GmATG8g and GmATG9d were rapidly upregulated at the early drought stress stage, while GmATG13a maintained sustained upregulation. In response to Phomopsis stem rot, GmATG7a/8h/8i/11/13d/18e/18f displayed differential expression in resistant and susceptible soybean materials. Conclusions: This study systematically characterizes the composition, expansion and stress response patterns of the GmATG gene family, revealing functional differentiation among family members. The identified key candidate genes, including abiotic-stress-regulated GmATG8g/9d/13d/18f and biotic-stress-regulated GmATG7a/8h/8i/11/13d/18e/18f, provide valuable genetic resources for the molecular breeding of stress-tolerant soybean. Full article

Traditional fermented foods are important reservoirs of wild microorganisms with technological, sensory, protective, and functional potential. However, the performance of these isolates in controlled or compositionally different food matrices remains fragmented across microbial groups and food systems. This systematic review synthesized evidence on using wild microbial isolates from traditional fermented foods and beverages as starters or potential probiotic cultures. The conducted a systematic search exclusively in Scopus, following PRISMA 2020, to include original research articles published between 2021 and 2026, yielding 68 eligible studies. The included studies were analyzed by geographical origin, isolation source, recipient matrix, microbial group, and key physicochemical, technological, sensory, microbiological, nutritional, and functional outcomes. The evidence was organized into wild yeasts and filamentous fungi, lactic acid bacteria (LAB), Bacillus isolates, and defined mixed microbial cultures. Across food matrices, microbial incorporation frequently accelerated acidification, shortened fermentation time, modified volatile compound profiles, and altered texture, color, enzymatic activity, or substrate utilization. Sensory responses improved aroma, flavor, texture, and acceptance, whereas others produced profiles that deviated from the characteristic product and reduced overall liking. Functional effects included increases in phenolic compounds, antioxidant activity, GABA, folate, peptides, and resistant starch, along with reductions in phytates, nitrites, biogenic amines, aflatoxins, and nondigestible oligosaccharides. Researchers also reported antimicrobial, antifungal, protective, and preliminary probiotic properties. Defined mixed microbial cultures often provided complementary metabolic effects, although true synergistic interactions were demonstrated only sporadically. Overall, wild isolates from traditional fermentations represent promising resources for food bioprocessing; however, their performance varies widely across strains, recipient matrices, experimental conditions, and outcomes evaluated. Consequently, their application requires strain–matrix validation, comprehensive sensory assessment, safety characterization, and evaluation under processing and storage conditions relevant to industrial production. Full article