Search Results (4,686)

Beef production is an important component of the world’s food supply, with production being near 59 million tons in 2023 (USDA, 2023). Enhancing our understanding of the factors influencing metabolism will lead to improvements in production efficiency. Using RNA-seq and WGCNA of longissimus muscle samples, gene expression and metabolic pathway analyses were performed to examine relationships with ultrasound and body mass variables. In this study, body weight (BW), ultrasound back fat (BF), ultrasound muscle depth (MD), and body condition score (BCS) were traits recorded for 18 cull beef cows. As expected, all production-related traits monitored (WT, BF, MD, and BCS) in this study exhibited a positive correlation with each other. Large-scale transcriptome analyses were performed using RNA extracted from longissimus dorsi muscles. Weighted correlation network analysis (WGCNA) was employed to associate changes in traits with gene expression. In WGCNA, the dark-green module demonstrated a positive correlation (cor) with all traits, with the highest observed for BF (cor = 0.45, p = 0.07) and MD (cor = 0.45, p = 0.07). Functional analysis of the dark-green module highlighted olfactory transduction (p = 0.03) and RNA processing as significantly correlated (p = 0.08) with production traits. Additionally, the hematopoietic cell lineage pathway was reported as the most significant negative correlation with muscle depth (cor = −0.71, p = 0.001). We identified four hub genes (i.e., SEPTIN9, NONO, CCDC88C, and CACNA2D3) showing relationships with the traits measured. These findings provide further understanding of the molecular mechanisms influencing muscle and fat accretion in cull beef cows. Full article

The organelle genomes of N. jatamansi were sequenced and examined to explore their structure, evolution, and possible functional implications. The chloroplast genome was constructed as a singular circular entity of 155,225 bp, whereas the mitochondrial genome exhibited considerable complexity, divided into 14 contigs totaling 1,229,747 bp, along with several sub-circular formations. Comparative analysis within the Caprifoliaceae family revealed that four genes (rps19, rpl22, rpl20, and matK) exhibited high sequence variability, suggesting their potential as molecular markers for the identification of species. In addition, three genes (clpP, ycf1, and ycf2) exhibited ka/ks ratios greater than one, which implies positive selection. Intracellular (between chloroplast and mitochondria) gene transfer analysis revealed the integration of six chloroplast-derived genes, and repeat analysis identified 47,980 repeat pairs in the mitochondrial genome, which spans 2.64 Mb. It is likely that these traits add to the structural complexity of the mitochondrial genome. Predictions based on climate show that N. jatamansi may be able to find more ideal habitat over the next 60 years. These results give us a useful genetic resource for studying evolution and set the stage for future research into how the species can be used in medicinal applications. Full article

As apex predators, felids (Felidae) face unresolved phylogenetic controversies due to their recent rapid speciation and remarkable morphological conservatism. Previous studies, often relying on a limited number of genetic markers, were constrained by insufficient data and conflicting phylogenetic signals, leaving these disputes unresolved. Therefore, establishing a robust phylogenetic framework based on larger-scale genomic data is crucial. This study integrated complete mitogenomes from 37 species representing all major felid genera to characterize genomic diversity, selection pressures, and phylogenetic relationships. Results revealed conserved gene content and arrangement patterns but significant intergenic variation in nucleotide composition, with the light-strand encoded ND6 exhibiting pronounced strand-specific bias. Nucleotide diversity was highest in ND4L (Pi = 0.132) and ATP6 (Pi = 0.131), suggesting their utility as novel markers for species delimitation and population studies. Selection pressure analysis indicated strong purifying selection on cytochrome oxidase subunits (e.g., COX1 Ka/Ks = 0.00327) but relaxed constraints on ATP8 (Ka/Ks = 0.12304). Phylogenies reconstructed from the complete 13PCGs + 2rRNAs dataset (showing high congruence between maximum likelihood and Bayesian methods) clearly delineated Felidae into two primary clades (Pantherinae and Felinae), confirming monophyly of all genera and positioning Neofelis nebulosa as the basal lineage within Pantherinae. Crucially, exclusion of ND6 (12PCGs + 2rRNAs) yielded topologies congruent with the complete 13PCGs + 2rRNAs dataset, whereas single-gene or limited multi-gene datasets produced inconsistent trees (particularly at genus-level nodes). This demonstrates that near-complete mitogenomic data (≥12PCGs + 2rRNAs) are essential for reconstructing robust felid phylogenetic frameworks. Our study provides insights into carnivoran mitogenome evolution. Full article

Pet owners have become more aware of how their pet’s nutrition can influence the pet’s life expectancy, wellness, and energy. Evaluating the new ingredients claiming better pet health for nutrient contributions requires significant investment and targeted animal commitment while current research aims to find alternative approaches. Research on pet foods in universities is overseen by the Institutional Animal Care and Use Committee, which has restrictions on the use of vertebrates in testing but places no restrictions on the use of insects. The research reported here studied three species of beetles (Coleoptera: Dermestidae), Trogoderma variabile (Ballion), Trogoderma inclusum (LeConte), and Dermestes maculatus (DeGeer) as potential model organisms to evaluate pet food nutrient bioavailability. The larvae of all three species were fed a balanced pet food diet under various laboratory conditions to determine their protein efficiency ratios (PERs) over a 144 h period. Results suggested that D. maculatus larvae reared at 27 °C, 60–65% R.H. (relative humidity), and a photoperiod of 16:8 L:D were the most efficient at converting ingested protein into weight gain with an average protein efficiency ratio (PER) of 1.439. Further experiments were conducted using only D. maculatus larvae with shorter time windows of 48 h and 24 h. The 24 h feeding time was successful and yielded an average PER of 2.476. These findings suggest that D. maculatus larvae may be a useful model organism for pet food bioavailability studies. Full article

There is limited research that addresses microplastics (MPs) contamination on the surfaces of fruits and vegetables. This study quantifies and characterizes MPs on the surface of tomatoes, apples, grapes, and cucumbers purchased from three markets (A, C, L). MPs were examined by stereomicroscopy, hot needle tests, and Scanning Electron Microscopy with Energy Dispersion Detector (SEM-EDX), and the results were reported by abundance, shape, color, and composition. Grapes in market A had the highest surface MPs concentration with a maximum of 0.891 particles/mm², while tomatoes in the same market had the lowest, at 0.030 particles/mm². The majority of MPs (> 85%) were transparent. Tomato, grape, and cucumber surfaces in all markets predominantly contained fragments, while apple surfaces primarily contained fibers. SEM-EDX analysis revealed MPs were primarily composed of carbon and oxygen and provided insights into the surface structures, elemental compositions, and sizes. Exposure assessment revealed the highest estimated daily intake (EDI) occurred in grapes from market A, at 9.24 × 10⁻⁵ MPs/kg/day for adults and 4.04 × 10⁻⁴ MPs/kg/day for children. Although the values appear low, no regulatory limits exist. Surface contamination remains an overlooked exposure route, emphasizing the need for food safety policies addressing MPs contamination and their effect on human health and the environment. Full article

Polycomb group (PcG) proteins are pivotal in maintaining gene silencing through epigenetic mechanisms, particularly by catalyzing Histone H3 lysine 27 trimethylation (H3K27me3) via the Polycomb Repressive Complex 2 (PRC2) complex. These modifications are crucial for regulating developmental pathways and environmental stress responses in plants. Despite their importance, the PcG gene family has not been systematically explored in rice (Oryza sativa). In this study, 15 OsPcG genes were identified in the Nipponbare genome, spanning 12 chromosomes and classified into distinct phylogenetic groups. Structural and conserved motif analyses revealed high sequence conservation, while collinearity and Ka/Ks analyses indicated gene family expansion through segmental duplication under purifying selection. Promoter element prediction suggested that many OsPcG genes are responsive to plant hormones and abiotic stress cues. Transcriptome analysis under salt treatment highlighted OsPcG5 as a key salt-responsive gene, with qRT-PCR confirming its dynamic expression. Subcellular localization showed OsPcG5 residing in both the nucleus and plasma membrane, suggesting multifunctional roles. Additionally, overexpression of OsFIE2—a PRC2 component—resulted in elevated H3K27me3 levels and abnormal plant height, linking it to chromatin modification and development. These findings contribute to our understanding of PcG gene functions in rice and offer potential genetic resources for enhancing salt tolerance through epigenetic approaches. Full article

Precision agriculture applies data-driven strategies to manage spatial and temporal variability within fields, aiming to increase productivity while minimizing pressure on natural resources. As interest in smart tillage systems expands, this study explores a central question: Can tillage tools be used to measure soil compaction during regular field operations? To investigate this, vibration data measurements were collected from a cultivator shank in the northeast of Kansas using the AVDAQ system. The test field soils were Reading silt loam and Eudora–Bismarck Grove silt loams. The relationship between shank vibrations, soil moisture (measured by a Hydrosense II soil–water sensor), and soil compaction (measured by a cone penetrometer) was evaluated using machine learning models. Both XGBoost and Random Forest demonstrated strong predictive performance, with Random Forest achieving a slightly higher correlation of 93.8% compared to 93.7% for XGBoost. Statistical analysis confirmed no significant difference between predicted and measured values, validating the accuracy and reliability of both models. Overall, the results demonstrate that combining vibration data with soil moisture data as model inputs enables accurate estimation of soil compaction, providing a foundation for future in situ soil sensing, reduced tillage intensity, and more sustainable cultivation practices. Full article

This study aims to bridge the critical knowledge gap in understanding the dynamic microstructural evolution during high-solid-fraction semi-solid rheo-die casting process, including slurry preparation (0.1–0.3 K/s) and rheo-die casting (10–150 K/s). A novel phase-field model coupling continuous cooling with explicit nucleation was developed, enabling the dynamic simulation of continuous solidification microstructure evolution, considering two-stage cooling rate transition characteristics. Integrated the Swirled Enthalpy Equilibration Device (SEED) slurry preparation and graded-cooling mold experiments established variable cooling rate and solid fraction conditions for quantitative analysis of α-Al morphological evolution during rheo-die casting solidification. Through experimental and simulation investigations of the Al-7Si alloy, it is concluded that during Stage I slurry preparation, the primary α₁-Al phase coarsened due to Ostwald ripening. In Stage II rheo-die casting, primary α₁-Al undergoes continued growth under a moderate cooling rate (15 K/s). Meanwhile, secondary α₂-Al formation exhibits a cooling-rate and solid fraction dependence: a high cooling rate (150 K/s) promotes explosive nucleation with the volume fraction decreasing from 4.78% to 0.33% as the solid fraction rises, whereas a mid-cooling rate (15 K/s) substantially suppresses its formation. Mechanistically, a high cooling rate promotes solute trapping, which intensifies constitutional undercooling, thereby elevating both the nucleation and growth driving forces to facilitate the formation of secondary α₂-Al, whereas higher solid fractions restrict secondary phase formation by narrowing the solidification windows from 22 °C to 7 °C. Full article

Background/Objectives: DNA-damaging agents can contribute to genetic instability, and such agents are often used in cancer chemotherapeutic regimens due to their cytotoxicity. Thus, understanding the mechanisms involved in DNA damage processing can not only enhance our knowledge of basic DNA repair mechanisms but may also be used to develop improved chemotherapeutic strategies to treat cancer. The high-mobility group box protein 1 (HMGB1) is a known nucleotide excision repair (NER) cofactor, and its family member HMGB3 has been implicated in chemoresistance in ovarian cancer. Here, we aim to understand the potential role(s) of HMGB3 in processing DNA damage. Methods: A potential role in NER was investigated using HMGB3 knockout human cell lines in response to UV damage. Subsequently, potential roles in DNA interstrand crosslink (ICL) and DNA double-strand break (DSB) repair were investigated using mutagenesis assays, metaphase spreads, foci formation, a variety of DNA repair assays, and TagSeq analyses in human cells. Results: Interestingly, unlike HMGB1, HMGB3 does not appear to play a role in NER. We found evidence to suggest that HMGB3 is involved in the processing of both DSBs and ICLs in human cells. Conclusions: These novel results elucidate a role for HMGB3 in DNA damage repair and, surprisingly, also indicate a distinct role of HMGB3 in DNA damage repair from that of HMGB1. These findings advance our understanding of the role of HMGB3 in chemotherapeutic drug resistance and as a target for new chemotherapeutic strategies in the treatment of cancer. Full article

Background: Multiple Myeloma (MM) is the most common type of blood cancer among black individuals. CAR-T therapy is crucial, but often inaccessible to many black patients and those from underserved communities. The University of Kansas Health System administers over 100 CAR-T treatments annually and aims to evaluate barriers to CAR-T therapy access related to the social determinants of health in the Midwest area. Methods: This study examined patients with MM referred for CAR-T therapy from January 2021 to December 2023, assessing how race, socioeconomic status, and insurance influenced eligibility for leukapheresis. Data on income and travel were gathered from the 2022 US Census and analyzed using R software. Results: The study included 271 referrals for MM CAR-T therapy involving 179 patients, with a median age of 66 years (51% male). Demographics: 80% white, 16% black, 2.2% other races, 1.8% Asian, with a median income of $70,644. Nearly half lived more than 30 min from the center (Mainly from Kansas, Missouri and Nebraska). Apheresis rates were similar across racial groups: 54% for whites, 54% for blacks, and 50% for others, while none of the three Asian patients proceeded. Nine patients (5%) could not proceed because of caregiver or insurance barriers, and cell collection rates were comparable regardless of distance (34% vs. 35%). Conclusion: This study showed that black representation in CAR-T access matches local demographics, indicating less disparity among minorities. Unlike national reports, distance, income, and insurance do not significantly affect access, suggesting the need for a national study on the social determinants impacting CAR-T access for multiple myeloma. Full article

Background/Objectives: G protein-coupled receptors (GPCRs) can promote ligand-biased signaling, yet the mechanisms that promote bias are not well understood. We have shown that C-C Chemokine Ligand 19 (CCL19) and CCL21 promote ligand-biased internalization and signaling of C-C Chemokine Receptor 7 (CCR7) in T cells. The roles of GPCR kinases (GRKs) in regulating biased CCR7 internalization and biased signaling in T cells are unclear. GRK2 is a serine/threonine kinase that phosphorylates GPCRs in response to ligand binding and is recruited to the plasma membrane via its C-terminal pleckstrin homology domain to phosphatidylinositol 4,5-bisphosphate (PIP₂). Methods: Human embryonic kidney cells (HEK293) transfected to express wild-type and mutant GRK2 and human CCR7, human T cell lines harboring heterozygous deletions of GRK2, and naïve primary T cells from GRK2 heterozygous (GRK2^+/−) or GRK2^f/f CD4-Cre mice were used to examine the effects of GRK2 on ligand-induced CCR7 signaling in T cells. We used flow cytometry to assay the effect of GRK2 on CCR7 internalization, Fluorescence Resonance Energy Transfer (FRET) to define the effect of GRK2 on CCR7 activation of Gα_i isoforms and transwell migration assays to examine the effect of GRK2 on chemotaxis. Since chemotaxis via CCR7 is mediated by phospholipase Cγ1 (PLCγ1), Western blot assays were used to measure the effect of GRK2 during downstream signaling via phosphorylation of PLCγ1. Results: We found that following CCL19 binding, GRK2 promoted kinase-dependent CCR7 recruitment of arrestin-3, rapid CCR7 internalization and Gα_i3 recruitment to CCR7. In contrast, following binding of CCL21 to CCR7, GRK2 slowed CCR7 internalization, induced recruitment of Gα_i2 to the activated receptor_, and promoted chemotaxis. Since we have shown that CCL21 promotes chemotaxis via PLCγ1, we examined the effect of GRK2 on PLCγ1 activation and found that GRK2 had no effect on CCL21-mediated PLCγ1 phosphorylation. Conclusions: GRK2 promotes differential signaling downstream of CCR7 activation by CCL19 and CCL21 and provides a model for biased signaling downstream of a GPCR driven by GRK2. Full article

Probable Maximum Storms (PMS) are synthetic design storms represented by idealized hyetographs. They play a critical role in assessing extreme rainfall events over extended durations and are widely applied in the hydraulic design of infrastructure such as dams, culverts, and bridges. PMS provide essential input for estimating Probable Maximum Floods (PMF), vital for analyzing worst-case flood scenarios with the potential to cause catastrophic loss of life and property. Despite their importance, the estimation of design storms at ungauged locations, particularly across synoptic scales, remains a major scientific and engineering challenge. This study addresses this gap by utilizing the Integrated Multi-satellitE Retrievals for Global Precipitation Measurement (IMERG) dataset, which provides near-global estimated precipitation coverage. IMERG’s 24 h design storm hyetographs (expressed as cumulative percentage of precipitation throughout a 24 h period) were modeled and compared with similar reference data from NOAA Atlas 14 across twenty-eight regions and seven larger zones covering most of the conterminous United States (CONUS). Across the regions, the average root mean square error (RMSE) was 3.7%, with a mean relative bias (RB) of 1.4%. The mean normalized storm loading index (NSLI) from NOAA Atlas 14 was −7.7%, indicating that 57.7% of the total precipitation was received during the first 12 h of the storm, whereas IMERG storms exhibited a mean NSLI of −4.1%, suggesting they are also frontloaded but to a lesser extent. Across the broader zones, the mean RMSE was 4.8% and the mean RB was 1.1%. The mean NSLI values were −9.7% for NOAA Atlas 14 and −5.7% for IMERG, again indicating that IMERG storms are less frontloaded. When design storm families were estimated corresponding with different degrees of frontloading (corresponding to the 10, 20, …, 90% deciles of NSLI), the 40th to 60th percentile range exhibited the strongest agreement between IMERG and NOAA Atlas 14 hyetographs. Full article

Poly(lactic acid) (PLA) is an aliphatic polyester considered a “green” material due to its natural-based origin and biodegradable properties. This is why PLA fibres may be compared with poly(ethylene terephthalate) (PET) fibres in an effort to partially replace the latter in industrial production. The purpose of this study is to investigate the dyeability of poly(lactic acid) fibres using six (6) commercially available disperse dyes with different energy levels, molecular weights and chemical structures, namely Disperse Red 59 (Serisol Fast Pink RFL), Disperse Red 60 (Serilene Red 2BL), Disperse Red 92 (Serilene Red TBLS), Disperse Orange 31 (Serisol Br Orange RGL), Disperse Yellow 54 (Serilene Yellow 3GL) and Disperse Blue 79 (Serilene Navy Blue GRLS). The dyeing characteristics, such as dye exhaustion, colour strength (K/S value), colorimetric values, wash fastness, light fastness and sublimation fastness of dyed fibres, were examined at dyeing temperatures of 110 and 130 °C, while the presence of carrier agent was also investigated. The dye exhaustion values of PLA fibres were found to be lower than those of PET fabrics; however, K/S values were higher than those of the corresponding PET fabrics in some cases. Dyed PLA fibres illustrated good colour fastness, light fastness and sublimation fastness properties, comparable to similarly dyed PET fibres. Full article

Plodia interpunctella is a globally significant pest of stored grains, posing a major threat to food safety. To explore its cold-adaptation mechanisms, this study evaluated the physiological and developmental responses of different life stages following short-term cold acclimation at 4 °C. Results showed that cold acclimation significantly reduced the supercooling points (SCPs) of larvae and pupae, with the greatest reduction observed in the second instar larvae. Antioxidant enzyme assays revealed marked increases in the activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), indicating enhanced oxidative stress resistance. Developmental durations were significantly shortened at lower temperatures in acclimated individuals, and fecundity was notably increased at 24 °C, although no significant changes were observed at higher temperatures. These findings suggest that cold acclimation improves the cold tolerance and reproductive performance of P. interpunctella under low-temperature conditions, offering insights into insect adaptability and providing theoretical support for the development of low-temperature-based pest management strategies in stored grain systems. Full article

The Riemann Hypothesis (RH) asserts that all non-trivial zeros of the Riemann zeta function lie on the critical line Re(s) = 0.5, yet no general proof exists despite extensive numerical verification. This study introduces a machine learning–based framework that combines classification, explainability, contradiction testing, and generative modeling to provide empirical evidence consistent with RH. First, discriminative models augmented with SHAP analysis reveal that the real and imaginary parts of ζ(s) contribute stable explanatory signals exclusively along the critical line, while off-line regions exhibit negligible attributions. Second, a contradiction-test framework, constructed from systematically sampled off-line points, shows no indication of spurious zero-like behavior. Finally, a mixture-density variational autoencoder (MDN-VAE) trained on 10,000 zero spacings produces synthetic distributions that closely match the empirical spacing law, with a Kolmogorov–Smirnov test (KS = 0.041, p = 0.075) confirming statistical indistinguishability. Together, these findings demonstrate that machine learning and explainable AI not only reproduce the known statistical properties of zeta zeros but also reinforce the absence of contradictions to RH under extended empirical exploration. While this framework does not constitute a formal proof, it offers a falsifiability-oriented, data-driven methodology for exploring deep mathematical conjectures. This empirical evaluation involved a baseline of 12,005 points, including 5 known zeros, and 15 off-line test points. The Random Forest classifier achieved high accuracy in distinguishing critical-line zeros, and consistently rejected off-line points. The generative models further corroborated these findings. Full article