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Keywords = RP11-1023L17.1

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21 pages, 430 KB  
Article
Evaluation of Patient-Assessed Quality of Life Questionnaires Following Operative Treatment of Pelvic Fractures
by Piotr Walus, Jakub Ohla, Benson Akinola, Michał Wesołowski, Jakub Bulski, Maria Zabrzyńska, Rafał Wójcicki, Tomasz Pielak, Bartłomiej Małkowski and Jan Zabrzyński
J. Clin. Med. 2025, 14(19), 7036; https://doi.org/10.3390/jcm14197036 - 4 Oct 2025
Abstract
Objective: To evaluate patient-assessed quality of life (QoL) following operative treatment of acetabular fractures and pelvic ring injuries and identify differences in their assessment of QoL depending on sex and age group. Methods: The study included 75 patients, 41 who had suffered acetabular [...] Read more.
Objective: To evaluate patient-assessed quality of life (QoL) following operative treatment of acetabular fractures and pelvic ring injuries and identify differences in their assessment of QoL depending on sex and age group. Methods: The study included 75 patients, 41 who had suffered acetabular fractures and 34 pelvic ring fractures, who had been treated operatively over a 6-year period (2017–2022). Post-operative HRQOL scores were evaluated using the World Health Organization Quality of Life BREF scale (WHQOL-BREF) and RAND Short Form 36 (SF-36). Separate analyses were completed for men and women, and we compared the data between five age groups. Results: The male patients scored slightly higher in all domains than the women in the acetabular fracture group. In the ring fracture group women reported higher scores in the psychological (72.67 vs. 69.44) and social domains (81.67 vs. 77.08). The men (80%) reported more significant overall satisfaction with their health in the acetabular group compared with the women (p = 0.0306). In the SF36 analysis, for both acetabular and ring fracture groups the lowest average QoL was recorded in the physical health composite summary (PHC) with a score of 41.34 ± 9.49 and 41.21 ± 9.19, respectively. Men scored higher for all eight scales in the ring fracture and all except general health in the acetabular fracture group (p = 0.0166). For the mental health composite (MHC), men had a better mean score in both fracture groups with significant differences for between both genders for the acetabular group (p = 0.0352). For age group analysis of the SF36, in the acetabular group, the youngest age group (<40 years) reported a significant decline in their performance due to role limitations due to physical health (RP) and emotional problems (RE) compared with the oldest group (>70 years) (p = 0.0306 and p = 0.0069, respectively), similarly to the PHC (p = 0.0279). Additionally, for the overall mental health summary of the acetabular group for the five age groups, there were significant differences between the youngest age group and the oldest age group (p = 0.0372). In contrast, for the ring fracture group, the oldest age group (>70 years) scored the worst in all four scales of the physical health composite and the <40 years patients had the highest score for the physical functioning (PF) scale, with statistical significance when compared with the oldest group (85 (17.53), p = 0.01501). Additionally, the lowest mean score for the PHC was recorded in >70 years and the highest in the 61–70 years age group, with a statistical significance (p = 0.0367). Conclusions: Patients that sustain a pelvic fracture and are treated operatively are at a higher risk of deterioration in quality of life. Using both functional assessments, male patients emphasized improved quality in more spheres that was evaluated than women. Full article
(This article belongs to the Section Orthopedics)
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17 pages, 4171 KB  
Article
Biochemical Methane Potential of Potato Chip Processing Waste, Process Mechanisms, and Microbial Community Shifts
by Abdelrahman G. Goda, Gamal K. Hassan, Karim M. Aboelghait, Dong-Fang Deng, Eunsung Kan, Eman Y. Tohamy and Saber A. El-Shafai
Processes 2025, 13(10), 3120; https://doi.org/10.3390/pr13103120 - 29 Sep 2025
Abstract
Anaerobic digestion (AD) is an environmentally friendly, promising solution for the recycling of agro-industrial wastes. However, overloading an anaerobic digester with substrate may cause the inhibition of the AD process. The present study investigated the effects of the substrate/inoculum (S/I) ratio on the [...] Read more.
Anaerobic digestion (AD) is an environmentally friendly, promising solution for the recycling of agro-industrial wastes. However, overloading an anaerobic digester with substrate may cause the inhibition of the AD process. The present study investigated the effects of the substrate/inoculum (S/I) ratio on the AD of potato chip processing (PCP) waste from the potato chip processing industry (PCPI). The PCP waste included expired potato chips (EPCs), recovered potato starch (RPS), and potato peel (PP). Mesophilic AD was carried out in batch-wise static reactors at 35 ± 1 °C using four different S/I ratios (0.5, 1.0, 1.5, and 2.0 g VS/g VS) for each type of waste. Different optimum S/I ratios were obtained for the different wastes; however, the pH ranges were comparable (7.0 to 7.5) for all batches. The optimum S/I ratios for EPCs, RPS, and PP were 1.0, 1.5, and 2.0, respectively. The cumulative biogas yields for EPCs, RPS, and PP were 367.5 ± 6.3, 310.0 ± 5.5, and 202.5 ± 4.9 mL/g VS added, respectively. The methane content of the biogas yields ranged between 60% and 70%. There was a variable remarkable shift in the microbial population at the optimum S/I ratio of each type of waste. The abundance of Firmicutes increased in the case of EPCs and RPS but decreased in the case of PP. Conversely, Proteobacteria increased when using PP as a substrate and decreased in the case of EPCs. Herein, the results of the AD of PCP wastes confirm its potential for the onsite production of renewable bioenergy and reductions in energy bills in the PCPI. In addition, this study provides guidance for optimizing the AD of PCP wastes for large-scale applications. Full article
(This article belongs to the Special Issue Biomass Treatment and Pyrolysis Processes)
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18 pages, 4993 KB  
Article
Stable Non-Competitive DPP-IV Inhibitory Hexapeptide from Parkia timoriana Seeds: A Candidate for Functional Food Development in Type 2 Diabetes
by Sakinah Hilya Abida, Christoper Caesar Yudho Sutopo, Wei-Ting Hung, Nhung Thi Phuong Nong, Tunjung Mahatmanto and Jue-Liang Hsu
Processes 2025, 13(10), 3079; https://doi.org/10.3390/pr13103079 - 26 Sep 2025
Abstract
The tree bean (Parkia timoriana), an underutilized legume valued for its nutritional profile, represents a potential source of bioactive peptides for diabetes management. To our knowledge, this is the first study to identify and characterize DPP-IV inhibitory peptides derived from tree [...] Read more.
The tree bean (Parkia timoriana), an underutilized legume valued for its nutritional profile, represents a potential source of bioactive peptides for diabetes management. To our knowledge, this is the first study to identify and characterize DPP-IV inhibitory peptides derived from tree bean seed protein hydrolysates. The tree bean proteins were digested with trypsin, thermolysin, chymotrypsin, pepsin, and simulated gastrointestinal (SGI) enzymes, among which SGI hydrolysis yielded the highest degree of hydrolysis (14%) and strongest DPP-IV inhibitory activity (IC50 = 1289 ± 58 µg/mL). Guided by DPP-IV inhibitory assays, sequential fractionation using strong cation exchange and RP-HPLC yielded the most potent fraction, H5, with an IC50 of 949 ± 50 µg/mL. After peptide identification and synthesis, APLGPF (AF6) emerged as the most potent inhibitor, with an IC50 of 396 ± 18 µM. Enzyme kinetics revealed a non-competitive inhibition mechanism, corroborated by molecular docking, which indicated binding at an allosteric site of DPP-IV. Furthermore, AF6 remained stable under simulated gastrointestinal digestion and enzymatic exposure, highlighting its resistance to proteolysis. Taken together, these findings highlight P. timoriana as an underexplored source of peptides with DPP-IV inhibitory activity and identify AF6 as a promising lead for developing functional foods or nutraceuticals aimed at type 2 diabetes management. Full article
(This article belongs to the Special Issue Peptides: Advances and Innovations from Discovery to Application)
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21 pages, 3713 KB  
Article
Unraveling the Chemical Composition and Biological Activity of Geum aleppicum Jacq.: Insights from Plants Collected in Kazakhstan
by Gulnur N. Kuntubek, Martyna Kasela, Kaldanay K. Kozhanova, Wirginia Kukula-Koch, Łukasz Świątek, Kinga Salwa, Piotr Okińczyc, Aleksandra Józefczyk, Jarosław Widelski, Gulnara M. Kadyrbayeva, Aigerim Z. Mukhamedsadykova, Zuriyadda B. Sakipova and Anna Malm
Molecules 2025, 30(19), 3888; https://doi.org/10.3390/molecules30193888 - 26 Sep 2025
Abstract
Geum aleppicum Jacq. (yellow avens), a species traditionally used in folk medicine, remains understudied in the ethnopharmacological aspects. In this study, we comprehensively evaluated the phytochemical composition and biological activity of a hydroethanolic (50:50, v/v) extract from the aerial parts [...] Read more.
Geum aleppicum Jacq. (yellow avens), a species traditionally used in folk medicine, remains understudied in the ethnopharmacological aspects. In this study, we comprehensively evaluated the phytochemical composition and biological activity of a hydroethanolic (50:50, v/v) extract from the aerial parts of G. aleppicum collected in Kazakhstan. Using the high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (HPLC-ESI-QTOF-MS/MS), we identified 24 compounds, predominantly phenolic acids, flavonoids, tannins, and triterpenoids. The major compound was ellagic acid (2.28 mg/g dry extract) as revealed by the reverse phase high-performance liquid chromatography–diode array detector (RP-HPLC-DAD). The extract exhibited a high polyphenol content (131.45 mg GAE/g) and strong antioxidant activity in Ferric Reducing Antioxidant Power (FRAP) assay and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay (3.82 ± 0.07 mmol Fe2+/g and 106.61 ± 0.89 mg GAE/g, respectively). Antimicrobial assay of the extract revealed notable antifungal activity against Candida spp., especially against C. glabrata and C. tropicalis with minimum inhibitory concentration (MIC) of as low as 0.125 mg/mL, showing fungistatic effect. Although the extract inhibited the cytopathic effect induced by Human Herpesvirus 1 (HHV-1) in VERO cells, it did not significantly reduce viral replication. Moreover, among human cancer cell lines studied, the extract exerted moderate and selective cytotoxicity against A549 lung cancer cells (CC50 = 75.51 µg/mL, SI = 9). These findings highlight G. aleppicum as a rich source of bioactive compounds, especially phenolics, supporting its potential for development of pharmaceutical and cosmetic applications. Full article
(This article belongs to the Special Issue Biological Evaluation of Plant Extracts)
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17 pages, 1270 KB  
Article
Molecular Diversification of the Genus Clinopodium (Lamiaceae) from the Balkans with an Emphasis on the Transferred Groups Calamintha, Acinos, and the Sect. Pseudomelissa
by Smiljana Janković, Tanja Dodoš, Petar D. Marin, Jelica Obradović Novaković and Nemanja Rajčević
Plants 2025, 14(18), 2940; https://doi.org/10.3390/plants14182940 - 22 Sep 2025
Viewed by 210
Abstract
Clinopodium is a morphologically highly diverse and taxonomically intricate genus. Molecular studies have demonstrated high divergence within the genus, and there is no consensus on the taxonomic treatment of some groups classified as Clinopodium. The current phylogenetic understanding of the genus relies [...] Read more.
Clinopodium is a morphologically highly diverse and taxonomically intricate genus. Molecular studies have demonstrated high divergence within the genus, and there is no consensus on the taxonomic treatment of some groups classified as Clinopodium. The current phylogenetic understanding of the genus relies almost exclusively on the analysis of the trnK and trnL-trnF sequences. In Clinopodium s.s., there is no phylogenetic backbone based on nuclear sequences. Therefore, in this study, we included a larger number of plastid and nuclear markers to better understand the diversification of natural populations of the genus Clinopodium from the Balkans. We encompassed the wild-growing taxa from former genera that have now been integrated into Clinopodium: Calamintha, Acinos, and section Pseudomelissa from the genus Micromeria. The markers that displayed the highest informativeness in the in silico analysis were selected. Four nuclear loci (ITS1, 5.8S rDNA, ITS2, ETS) and seven plastid loci (rps16-trnKUUU, rpl32-trnLUAG, rps15-ycf1, psbA-trnHGUG, rps16-trnQUUG, petN-psbM, psbK-trnSUGA) were used to analyse the phylogenetic relationships between the Balkan species and subspecies currently classified into Clinopodium. Phylogenetic reconstructions showed the divergence of the two lineages with different diversification patterns. Nuclear markers have shown that the three groups within the clade Clinopodium s.s. have evolved separately, which is consistent with earlier phenetic systems. Full article
(This article belongs to the Section Plant Systematics, Taxonomy, Nomenclature and Classification)
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25 pages, 4979 KB  
Article
Single Super Phosphate Improves Lolium perenne Quality and Rhizosphere Microorganism Structure Under Combined Cadmium and Arsenic Stress
by Toe Toe Maw, Jiangdi Deng, Bo Li, Yanqun Zu and Zuran Li
Toxics 2025, 13(9), 805; https://doi.org/10.3390/toxics13090805 - 22 Sep 2025
Viewed by 281
Abstract
Cadmium and arsenic co-contamination found in mining actions indicates major effluence in adjacent farmland soils, disturbing the plant physiology and soil’s microbial community. Phosphorus (P) plays a vital role in reducing soil contamination from Cd and As bioavailability and uptake by plants. However, [...] Read more.
Cadmium and arsenic co-contamination found in mining actions indicates major effluence in adjacent farmland soils, disturbing the plant physiology and soil’s microbial community. Phosphorus (P) plays a vital role in reducing soil contamination from Cd and As bioavailability and uptake by plants. However, the right P sources for remediation approaches are critical and still require further research in Cd- and As-contaminated soil. This study aimed to explore the effects of different phosphorus fertilizer sources on Lolium perenne growth and its physiological and rhizosphere microbial diversity under combined contamination with Cd and As. Pot experiments were performed with seven treatments including SSP (single super phosphate), DAP (diammonium phosphate), MAP (monoammonium phosphate), CaP (calcium phosphate), HighCaP (high calcium phosphate), RP (rock phosphate), and no phosphorus fertilizer application (CK) with five replications in the RCB design. The SSP treatment showed the greatest plant height (15.7 cm), hay yield (3567.6 kg·ha−1), and enhanced antioxidant defense activities. It also achieved the highest phosphorus accumulation rate (0.63 g·kg−1) with reduced Cd and As uptake. In addition, SSP promoted higher non-protein sulfhydryl (NPT) and phytochelatin synthetase (PCs) contents along with γ-glutamylcysteine synthetase (γ-ECS) activity, and enriched the rhizosphere microbial community, where the Sphingomonas abundance was 7.08% higher than for other treatments. Therefore, this result indicates that SSP can improve the yield and physiology in L. perenne, as well as soil the rhizosphere microbial community structure, while reducing Cd and As accumulation in plants under Cd and As stress. Full article
(This article belongs to the Special Issue Plant Responses to Heavy Metal)
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20 pages, 4824 KB  
Article
Assembly and Analysis of the Complete Mitochondrial Genome of Eryngium foetidum L. (Apiaceae)
by Lihong Zhang, Wenhu Zhang, Yongjian Luo, Jun Liu, Qing Li and Qiongheng Liu
Biology 2025, 14(9), 1296; https://doi.org/10.3390/biology14091296 - 19 Sep 2025
Viewed by 346
Abstract
Eryngium foetidum L. belongs to the Apiaceae family and is a perennial herb. The entire plant is rich in essential oils, which have a distinctive aroma similar to cilantro. This plant exhibits significant biological activity and possesses characteristics such as disease resistance and [...] Read more.
Eryngium foetidum L. belongs to the Apiaceae family and is a perennial herb. The entire plant is rich in essential oils, which have a distinctive aroma similar to cilantro. This plant exhibits significant biological activity and possesses characteristics such as disease resistance and antimicrobial properties, showing great potential in medical and food applications. Additionally, its essential oil has substantial commercial value. Mitochondria play a crucial role as organelles within plant cells; however, the mitochondrial genome of E. foetidum remains underexplored. To fill this research gap, we conducted sequencing and assembly of the mitochondrial genome of E. foetidum, aiming to uncover its genetic mechanisms and evolutionary trajectories. Our investigation reveals that the mitochondrial genome of E. foetidum is a circular structure, similar to that of other species, with a length of 241,660 bp and a GC content of 45.35%, which is within the range observed in other organisms. This genome encodes 59 genes, comprising 37 protein-coding sequences, 18 tRNA genes, and 4 rRNA genes. Comparative analysis highlighted 16 homologous regions between the mitochondrial and chloroplast genomes, with the longest segment spanning 992 bp. By analyzing 37 protein-coding genes (PCGs), we identified 479 potential RNA editing sites, which induce the formation of stop codons in the nad3 and atp6 genes, as well as start codons in the ccmFC, atp8, nad4L, cox2, cox1, and nad7 genes. Meanwhile, the genome shows a preference for A/T bases and A/T-ending codons, with 32 codons having a relative synonymous codon usage (RSCU) value greater than 1. The codon usage bias is relatively weak and mainly influenced by natural selection. Most PCGs are under purifying selection (Ka/Ks < 1), while only a few genes, such as rps7 and matR, may be under positive selection. Phylogenetic analysis of mitochondrial PCGs from 21 species showed E. foetidum at the basal node of Apiaceae, consistent with the latest APG angiosperm classification and chloroplast genome-based phylogenetic relationships. In summary, our comprehensive characterization of the E. foetidum mitochondrial genome not only provides novel insights into its evolutionary history and genetic regulation but also establishes a critical genomic resource for future molecular breeding efforts targeting mitochondrial-associated traits in this economically important species. Full article
(This article belongs to the Section Genetics and Genomics)
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15 pages, 3045 KB  
Article
Cloning and Characterization of the Mycovirus MpChrV2 from Macrophomina phaseolina
by Peimeng Sun, Luyang Song, Mengyuan Mu, Jiayi Ma, Xinyu Li, Kunni Tian, Mengyuan Zhang, Mingyue Zhang, Yuanyuan Zhang, Caiyi Wen, Jing Wang and Ying Zhao
J. Fungi 2025, 11(9), 675; https://doi.org/10.3390/jof11090675 - 12 Sep 2025
Viewed by 392
Abstract
Macrophomina phaseolina is a widely distributed soilborne phytopathogenic fungus that causes destructive diseases such as charcoal rot and stem canker, posing serious threats to crop yield and quality. In recent years, mycoviruses have gained attention as potential biological control agents. In this study, [...] Read more.
Macrophomina phaseolina is a widely distributed soilborne phytopathogenic fungus that causes destructive diseases such as charcoal rot and stem canker, posing serious threats to crop yield and quality. In recent years, mycoviruses have gained attention as potential biological control agents. In this study, a novel double-stranded RNA (dsRNA) virus was identified from M. phaseolina strain 22C-8, isolated from sesame (Sesamum indicum L.) charcoal rot samples in Fuyang, Anhui Province, China. The viral genome comprised four dsRNA segments, each encoding a single open reading frame (ORF) predicted to encode RNA-dependent RNA polymerase (RdRp), coat protein (CP), and two hypothetical proteins. Phylogenetic analysis classified the virus as a new member of the genus Betachrysovirus in the family Chrysoviridae, and it was designated Macrophomina phaseolina chrysovirus 2 (MpChrV2). Pathogenicity assays in sesame seedlings revealed that MpChrV2 infection significantly reduced the virulence of M. phaseolina strain 22C-8. In contrast, virus-free derivatives (22C-8-VF18), obtained via protoplast regeneration, caused more severe symptoms and exhibited enhanced growth rates, indicating that MpChrV2 alters fungal physiology and pathogenicity. These findings suggest that MpChrV2 possesses a typical hypovirulence phenotype and holds promise as a biocontrol agent for sesame charcoal rot. Full article
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17 pages, 2298 KB  
Article
Influence of the Process-Related Surface Structure of L-PBF Manufactured Components on Residual Stress Measurement Using the Incremental Hole Drilling Method
by Sebastian Gersch, Ulf Noster, Carsten Schulz and Jörg Bagdahn
Appl. Sci. 2025, 15(18), 9861; https://doi.org/10.3390/app15189861 - 9 Sep 2025
Viewed by 365
Abstract
Laser Powder Bed Fusion (L-PBF) parts combine geometric freedom with process-induced rough surfaces that challenge residual-stress metrology. We evaluated the accuracy of the incremental hole-drilling (IHD) method with electronic speckle pattern interferometry (ESPI) by applying defined stresses via four-point bending to stress-relieved AlSi10Mg [...] Read more.
Laser Powder Bed Fusion (L-PBF) parts combine geometric freedom with process-induced rough surfaces that challenge residual-stress metrology. We evaluated the accuracy of the incremental hole-drilling (IHD) method with electronic speckle pattern interferometry (ESPI) by applying defined stresses via four-point bending to stress-relieved AlSi10Mg coupons, rather than measuring unknown process stresses. Flat specimens (2 mm, thin per ASTM E837) were analyzed on up-skin, side-skin, and CNC-milled surfaces; thin-specimen calibration coefficients were used. After a preliminary inter-specimen check (three specimens per surface; spread < 8 MPa), one representative specimen per surface was tested with three drill sites to assess intra-specimen uniformity. Measured IHD–ESPI stresses agreed best at 70 MPa: deviations were ~4.1% (up-skin), 6.0% (side-skin), and 6.24% (CNC-milled). At 10 MPa the relative errors increased (23.6%, 18.4%, and 1.40%), consistent with reduced ESPI signal-to-noise and fixture compliance in the low-stress regime. At 140 MPa, deviations rose again (21.1%, 14.3%, and 13.1%), reflecting operation near the ~60% Rp0.2 elastic limit of hole-drilling and potential local plasticity. Surface-dependent artifacts also mattered as follows: the side-skin required no coating and performed comparably to CNC-milled, whereas the up-skin’s roughness plus matting spray introduced fringe distortions and chip/coating debris near the hole. This controlled study indicates that IHD–ESPI can provide reliable results on L-PBF AlSi10Mg in the mid-stress range when surface preparation, coating, and rig compliance are carefully managed. Limitations include excluding down-skin surfaces and testing only one specimen per condition; thus, results should be generalized cautiously. Full article
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13 pages, 1028 KB  
Article
Population PK Modeling of Denosumab Biosimilar MB09 and Reference Denosumab to Establish PK Similarity
by Sara Sánchez-Vidaurre, Alexandra Paravisini and Javier Queiruga-Parada
Pharmaceutics 2025, 17(9), 1146; https://doi.org/10.3390/pharmaceutics17091146 - 1 Sep 2025
Viewed by 650
Abstract
Background/Objectives: MB09 is a denosumab biosimilar to the reference products (RPs) Xgeva and Prolia. A population pharmacokinetic (popPK) meta-analysis was conducted to characterize the denosumab PK profile and to support MB09 biosimilarity. Methods: Pooled denosumab PK data from one phase I [...] Read more.
Background/Objectives: MB09 is a denosumab biosimilar to the reference products (RPs) Xgeva and Prolia. A population pharmacokinetic (popPK) meta-analysis was conducted to characterize the denosumab PK profile and to support MB09 biosimilarity. Methods: Pooled denosumab PK data from one phase I study [255 healthy adult men receiving a single 35 mg subcutaneous (SC) dose] and one phase III study (555 postmenopausal women with osteoporosis receiving two 60 mg SC doses, one every six months) were used. A one-compartment model with first-order absorption and elimination and parallel non-linear saturable clearance was used. Body weight was included on clearance as a structural covariate and treatment was tested as a covariate on all PK parameters. PK biosimilarity was assessed at 35 mg dose. Results: For a 70 kg subject, the apparent clearance and central volume of distribution for denosumab were 0.123 L/day [95% confidence interval (CI): 0.114, 0.132] and 9.33 L (95% CI: 9.11, 9.55), respectively. The Michaelis constant was 0.124 ng/mL and the maximum rate for the non-linear clearance was 0.139 ng/day. Model-based bioequivalence criteria were met for RP Xgeva, European and US-sourced, versus MB09 for a dose of 60 mg SC. The mean area under the plasma concentration curve (AUC) resultant from the simulation of MB09 120 mg SC was similar to the published mean AUC observed for Xgeva 120 mg SC every four weeks. Conclusions: This analysis provides a valuable assessment of denosumab PK characteristics and elucidates in more detail how the MB09 PK profile compares to the denosumab RPs, supporting the totality of evidence on MB09 biosimilarity. Full article
(This article belongs to the Special Issue Emerging Trends in Bioequivalence Research)
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16 pages, 2534 KB  
Article
Complete Chloroplast Genome Features and Phylogenetic Analysis of Linum usitatissimum L.
by Qingqing Ji, Guanghui Du, Xingcai An, Junyuan Dong, Xiahong Luo, Changli Chen, Tingting Liu, Lina Zou, Shaocui Li, Jikang Chen and Xia An
Genes 2025, 16(9), 1038; https://doi.org/10.3390/genes16091038 - 31 Aug 2025
Viewed by 582
Abstract
Background: The chloroplast genome provides rich genetic information for plant evolutionary studies. This study aimed to assemble, annotate, and analyze the complete chloroplast genome of flax cultivar ‘Longya 15’ (Linum usitatissimum L.) and clarify its phylogenetic relationships with other Linaceae species. Methods: [...] Read more.
Background: The chloroplast genome provides rich genetic information for plant evolutionary studies. This study aimed to assemble, annotate, and analyze the complete chloroplast genome of flax cultivar ‘Longya 15’ (Linum usitatissimum L.) and clarify its phylogenetic relationships with other Linaceae species. Methods: We assembled and annotated the chloroplast genome of ‘Longya 15’ and retrieved chloroplast genomes of related species (e.g., Linum grandiflorum NC_058845.1, Linum lewisii NC_058799.1) from the NCBI database for phylogenetic analysis. Results: The chloroplast genome of ‘Longya 15’ was a 157,074-bp quadripartite structure with 37.42% GC content, encoding 128 genes (83 mRNAs, 37 tRNAs, 8 rRNAs) without pseudogenes. It showed codon bias for leucine (28 codons with RSCU > 1, ending in A/U), 260 dispersed repeats, and 240 SSRs. Ka/Ks analysis revealed purifying selection for most genes, while rps18 and ycf2 had positive selection. ycf1 was identified as the hypervariable region (pi = 0.25024). Phylogenetically, it clustered closest with Linum grandiflorum, followed by L. lewisii and L. perenne, and was related to Hypericum species. Conclusions: This is the first fine assembly and annotation of ‘Longya 15’ chloroplast genome, confirming no pseudogenes in flax chloroplast. It elucidates flax chloroplast genome conservation and evolutionary dynamics, enriches the database, and provides a foundation for Linaceae phylogenetics, germplasm development, and stress-resistant breeding. Full article
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12 pages, 1870 KB  
Article
A Novel Cogu-like Virus Identified in Wine Grapes
by Jennifer Dahan, Gardenia E. Orellana, Edison Reyes-Proaño, Jungmin Lee and Alexander V. Karasev
Viruses 2025, 17(9), 1175; https://doi.org/10.3390/v17091175 - 28 Aug 2025
Viewed by 713
Abstract
A new negative-strand RNA virus was identified in grapevines from a 38-year-old ‘Chardonnay’ block in Idaho through high-throughput sequencing (HTS) of total RNA. This virus was tentatively named grapevine-associated cogu-like Idaho virus (GaCLIdV). GaCLIdV has three negative-sense, single-stranded RNA genome segments of ca. [...] Read more.
A new negative-strand RNA virus was identified in grapevines from a 38-year-old ‘Chardonnay’ block in Idaho through high-throughput sequencing (HTS) of total RNA. This virus was tentatively named grapevine-associated cogu-like Idaho virus (GaCLIdV). GaCLIdV has three negative-sense, single-stranded RNA genome segments of ca. 7 kb, 1.9 kb, and 1.3 kb, encoding L protein (RNA-dependent RNA polymerase, RdRP), a movement protein (MP), and a nucleocapsid protein (NC), respectively, identified based on pair-wise comparisons with other cogu- and cogu-like viruses. In phylogenetic analysis based on the RdRP, GaCLIdV grouped within the family Phenuiviridae and was placed in a lineage of plant-infecting phenuiviruses as a sister clade of the genus Laulavirus, clustering most closely with switchgrass phenui-like virus 1 (SgPLV-1) and more distantly related to grapevine-associated cogu-like viruses from the Laulavirus and Coguvirus clades. Both GaCLIdV and SgPhLV-1 are proposed to form a new genus, Switvirus, within the family Phenuiviridae. The presence of GaCLIdV in the original ‘Chardonnay’ samples was confirmed by RT-PCR amplification and Sanger sequencing. This new virus was found in five wine grape cultivars and in six vineyards sampled in Idaho and in Oregon during the 2020–2024 seasons. GaCLIdV may have contributed to the decline observed in the old ‘Chardonnay’ block, although the role of the virus in symptom development awaits further investigation. Full article
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22 pages, 4875 KB  
Article
Effect of Plant Protein Ingredients at a Range of Pre-Hydration Levels on Technological Properties of Hybrid Beef Patties
by Zuo Song, Joseph P. Kerry, Rahel Suchintita Das, Brijesh K. Tiwari, Antonia Santos and Ruth M. Hamill
Foods 2025, 14(17), 2957; https://doi.org/10.3390/foods14172957 - 25 Aug 2025
Viewed by 813
Abstract
Hybrid plant and meat (HPM) products, in which a portion of meat is substituted with alternative plant protein-containing ingredients, offer a promising option for flexitarian consumers seeking to increase plant protein consumption while continuing to enjoy the sensory qualities of meat products. This [...] Read more.
Hybrid plant and meat (HPM) products, in which a portion of meat is substituted with alternative plant protein-containing ingredients, offer a promising option for flexitarian consumers seeking to increase plant protein consumption while continuing to enjoy the sensory qualities of meat products. This study evaluated the effects of faba bean protein (FBP), pea protein (PP), and rice protein (RP) ingredients at a 12.5% meat protein substitution level, under varying pre-hydration conditions and, subsequently, on the technological properties of hybrid plant/beef patties (HPBP). Colour measurements indicated that plant protein ingredient addition to HPBP resulted in increased lightness (L*) and decreased redness (a*) values. HPBP showed reduced cooking loss compared to 100% beef patties, and cooking loss increased with higher pre-hydration levels of plant proteins. Faba bean hybrid patty (FBHP) exhibited lower texture scores, while the patty containing non-hydrated RP had the highest hardness values. The texture of patties with PP was comparable to the control, irrespective of the hydration status of the plant protein. Inclusion of plant proteins also reduced water mobility by restricting intracellular water. Overall, these findings provide valuable insights into the selection of suitable plant proteins and the requirement for optimal pre-hydration of plant proteins prior to incorporation into HPBP to ensure optimal technological properties. Full article
(This article belongs to the Section Meat)
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21 pages, 1126 KB  
Article
Reversed-Phase (RP) and Hydrophilic Interaction (HILIC) Separation Mechanisms for the Assay of Nicotine and E-Cigarette Liquids
by Răzvan Moisi, Mircea-Alexandru Comănescu and Andrei-Valentin Medvedovici
Molecules 2025, 30(16), 3443; https://doi.org/10.3390/molecules30163443 - 21 Aug 2025
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Abstract
Nicotine is a highly used addictive substance that has recently also become available through electronic cigarettes. Here we present a study of nicotine from e-cigarette liquids through reversed-phase (RP) and hydrophilic interaction (HILIC) liquid chromatography. Multiple aqueous mobile-phase additives are considered for the [...] Read more.
Nicotine is a highly used addictive substance that has recently also become available through electronic cigarettes. Here we present a study of nicotine from e-cigarette liquids through reversed-phase (RP) and hydrophilic interaction (HILIC) liquid chromatography. Multiple aqueous mobile-phase additives are considered for the RP mechanism, focusing on chaotropic agents, mobile-phase concentrations and mixing ratios, and column temperature. Sample preparation was conducted by toluene liquid–liquid extraction of e-cigarette liquids diluted with aqueous 25 mM NaHCO3/Na2CO3. Optimal RP results for retention and peak symmetry were obtained using aqueous 0.1% formic acid and 20 mM ammonium hexafluorophosphate with 0.1% formic acid in acetonitrile, using a gradient profile with a C18 column, exploited at 40 °C and a 1.5 mL/min flow rate. A dilute-and-shoot alternative with automated flow reversal after isocratic elution is presented. For HILIC, aqueous 100 mM ammonium formate and 0.1% formic acid in acetonitrile were used as mobile-phase components, using a gradient profile, on a Thermo Scientific™ Acclaim™ Mixed-Mode HILIC-1 column, operated at 25 °C with a 1 mL/min flow rate. UV detection was at 260 nm. Absolute limits of quantitation in the 1 μg/mL range were obtained for all tested alternatives, with 1 μL injection volumes. Full article
(This article belongs to the Special Issue Chromatography—The Ultimate Analytical Tool, 3rd Edition)
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16 pages, 2800 KB  
Article
High Concordance Between SYBR Green and TaqMan PCR for SARS-CoV-2 Detection in Nasopharyngeal and Saliva Samples
by Muhareva Raekiansyah, Ratika Rahmasari, Fathan Baihaqy, Muhamad Irhamsyah, Nurul Izza Fajriani, Mila Meilani Putri, Botefilia Maharani, Rani Sauriasari, Takeshi Urano, Mya Myat Ngwe Tun and Kouichi Morita
Viruses 2025, 17(8), 1130; https://doi.org/10.3390/v17081130 - 18 Aug 2025
Viewed by 947
Abstract
During the COVID-19 pandemic, the standard diagnostic assay for SARS-CoV-2 detection was RT-qPCR using TaqMan probes, with samples primarily taken through nasal and oropharyngeal swabs. The TaqMan-based method is costly, highlighting the need for a more affordable alternative for SARS-CoV-2 diagnosis. As an [...] Read more.
During the COVID-19 pandemic, the standard diagnostic assay for SARS-CoV-2 detection was RT-qPCR using TaqMan probes, with samples primarily taken through nasal and oropharyngeal swabs. The TaqMan-based method is costly, highlighting the need for a more affordable alternative for SARS-CoV-2 diagnosis. As an alternative strategy, we developed and evaluated a SYBR Green-based RT-qPCR method targeting the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2. Under optimized RT-qPCR conditions, the sensitivity and linearity of the SYBR assays were assessed by using in vitro-transcribed RNA and RNA extracted from cultured SARS-CoV-2 isolates of the Wuhan reference strain and various circulating variants. Our results demonstrated that the SYBR Green-based RT-qPCR method was successfully developed with sufficient performance. The assay could detect up to 25 copies of in vitro-transcript RNA per reaction. Meanwhile, using the RNA extracted from cultured virus, the SYBR green assay was able to detect virus concentrations at least as low as 1 PFU/mL per reaction for all the variants tested. When tested on clinically relevant samples (88 naso-oropharyngeal swabs and 47 saliva samples), comparable results with the TaqMan assay were demonstrated. The Ct values of both methods for the positively detected samples were similar, with a difference in Ct of 0.72 ± 0.83 (p = 0.392) and −0.7765 ± 0.6107 (p = 0.209) for naso-oropharyngeal swab and saliva samples, respectively. These findings suggest that the SYBR method is reliable and thus offers an alternative assay for the detection of SARS-CoV-2. In particular, using saliva specimens could allow this assay to serve as a simple approach for SARS-CoV-2 detection. Full article
(This article belongs to the Section Coronaviruses)
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