Search Results (250)

Background: Centromeric alpha satellite DNA is organized into higher-order repeats (HORs), whose precise structure is often difficult to resolve in standard genome assemblies. The recent telomere-to-telomere (T2T) assembly of the human genome enables complete analysis of centromeric regions, including the full structure of HOR arrays. Methods: We applied the novel high-precision GRMhor algorithm to the complete T2T-CHM13 assembly of human chromosome 21. GRMhor integrates global repeat map (GRM) and monomer distance (MD) diagrams to accurately identify, classify, and visualize HORs and their subfragments. Results: The analysis revealed a novel Cascading 11mer HOR array, in which each canonical HOR copy comprises 11 monomers belonging to 10 different monomer types. Subfragments with periodicities of 4, 7, 9, and 20 were identified within the array. A second, complex 23/25mer HOR array of mixed Willard’s/Cascading type was also detected. In contrast to the hg38 assembly, where a dominant 8mer and 33mer HOR were previously annotated, these structures were absent in the T2T-CHM13 assembly, highlighting the limitations of hg38. Notably, we discovered a novel 52mer HOR—the longest alpha satellite HOR unit reported in the human genome to date. Several subfragment repeats correspond to alphoid subfamilies previously identified using restriction enzyme digestion, but are here resolved with higher structural precision. Conclusions: Our findings demonstrate the power of GRMhor in resolving complex and previously undetected alpha satellite architectures, including the longest canonical HOR unit identified in the human genome. The precise delineation of superHORs, Cascading structures, and HOR subfragments provides unprecedented insight into the fine-scale organization of the centromeric region of chromosome 21. These results highlight both the inadequacy of earlier assemblies, such as hg38, and the critical importance of complete telomere-to-telomere assemblies for accurately characterizing centromeric DNA. Full article

Hippophae rhamnoides subsp. sinensis is extensively found in China, where the annual precipitation ranges from 400 to 800 mm. It is the most dominant species in natural sea buckthorn forests and the primary cultivar for artificial ecological plantations. Additionally, it exhibits significant nutritional and medicinal value, making it a renowned eco-economic tree species. Despite extensive research into its ecological functions and health benefits, the mitochondrial genome of this widespread species has not yet been published, and knowledge of the mitochondrial genome is crucial for understanding plant environmental adaptation, evolution, and maternal inheritance. Therefore, the complete mitochondrial genome was successfully assembled by aligning third-generation sequencing data to the reference genome sequence using the Illumina NovaSeq 6000 platform and Nanopore Prometh ION technologies. Additionally, the gene structure, composition, repeat sequences, codon usage bias, homologous fragments, and phylogeny-related indicators were also analyzed. The results showed that the length of the mitochondrial genome is 454,489 bp, containing 30 tRNA genes, three rRNA genes, 40 PCGs, and two pseudogenes. A total of 411 C-to-U RNA editing sites were identified in 33 protein-coding genes (PCGs), with higher frequencies observed in ccmFn, ccmB, nad5, ccmC, nad2, and nad7 genes. Moreover, 31 chloroplast-derived fragments were detected, accounting for 11.86% of the mitochondrial genome length. The ccmB, nad4L, and nad7 genes related to energy metabolism exhibited positive selection pressure. The mitochondrial genome sequence similarity between H. rhamnoides subsp. sinensis and H. tibetana or H. salicifolia was 99.34% and 99.40%, respectively. Fifteen shared gene clusters were identified between H. rhamnoides subsp. sinensis and H. tibetana. Phylogenetically, the Rosales order showed close relationships with Fagales, Fabales, Malpighiales, and Celastrales. These findings provide fundamental data for exploring the widespread distribution of H. rhamnoides subsp. sinensis and offer theoretical support for understanding the evolutionary mechanisms within the Hippophae genus and the selection of molecular breeding targets. Full article

Background/Objectives: Non-invasive central nervous system (CNS) therapies are limited by complex mechanisms and the blood–brain barrier, but nasal delivery offers a promising alternative. The study planned to develop a non-invasive in situ intranasal mucoadhesive thermosensitive gel to deliver CNS-active risperidone via nose-to-brain targeting. Risperidone, a second-generation antipsychotic, has shown efficacy in managing both psychotic and mood-related symptoms. The mucoadhesive gel formulations help to prolong the residence time at the nasal absorption site, thereby facilitating the uptake of the drug. Methods: The poloxamer 407 (18.0% w/v), HPMC K100M and K15M (0.3–0.5% w/v), and benzalkonium chloride (0.1% v/v) were used as thermosensitive polymers, a mucoadhesive agent, and a preservative, respectively, for the development of in situ thermosensitive gel. The developed formulations were evaluated for various parameters. Results: The pH, gelation temperature, gelation time, and drug content were found to be 6.20 ± 0.026–6.37 ± 0.015, 34.25 ± 1.10–37.50 ± 1.05 °C, 1.65 ± 0.30–2.50 ± 0.55 min, and 95.58 ± 2.37–98.03 ± 1.68%, respectively. Furthermore, the optimized F3 formulation showed satisfactory gelling capacity (9.52 ± 0.513 h) and an acceptable mucoadhesive strength (1110.65 ± 6.87 dyne/cm²). Diffusion of the drug through the egg membrane depended on the formulation’s viscosity, and the F3 formulation explained the first-order release kinetics, indicating concentration-dependent drug diffusion with n < 0.45 (0.398) value, indicating the Fickian-diffusion (diffusional case I). The pharmacokinetic study was performed with male Wistar albino rats, and the F3 in situ thermosensitive risperidone gel confirmed significantly (p < 0.05) ~5.4 times higher brain AUC_0–∞ when administered intranasally compared to the oral solution. Conclusions: Based on physicochemical, in vitro, and in vivo parameters, it can be concluded that in situ thermosensitive gel is suitable for administration of risperidone through the nasal route and can enhance patient compliance through ease of application and with less repeated administration. Full article

This study aimed to compare stroke rate (SR), stroke length (SL), and stroke index (SI) during aerobic-dominated training sets applied at speed corresponding to lactate threshold (LT) or to maximum aerobic speed (MAS) and following repeated sprints (SPR). Twelve male swimmers performed four sessions in a randomized order: (i) LT, (ii) SPR-LT, (iii) MAS, and (iv) SPR-MAS. Set LT consisted of 8 × 200 m at a speed corresponding to the lactate threshold (30 s recovery). Set MAS included 8 × 100 m at the maximal aerobic speed (30 s recovery). Set SPR included 8 × 25 m at maximal intensity (2 min recovery). Blood lactate (BL), SR, SL, SI, and rate of perceived exertion (RPE) were measured. SR, SL, and SI did not differ between LT and SPR-LT sessions (p > 0.05). In the SPR-MAS session, SR was higher and SL was lower compared to the MAS session (p < 0.05), while SI did not differ between the sessions (p > 0.05). BL at the start of LT and MAS and RPE at the end of sets were higher in the SPR-LT and SPR-MAS sessions (p < 0.05). BL and RPE were correlated with SR in 8 × 200 m during the SPR-LT session (p < 0.05). Repeated sprints may change the biomechanical and physiological response during a subsequent training set performed at MAS while preserving technical efficiency. Full article

This study highlights the significant environmental and health risks associated with heavy metal contamination (As, Cd, Cr, and Pb) in Oreochromis niloticus (Nile tilapia) from two locations: the Khon Kaen municipal landfill (study site) and the Thapra commercial fish farm (reference site). It also evaluates potential human health risks and investigates genotoxicity and oxidative stress markers, including malondialdehyde, hydrogen peroxide (H₂O₂), catalase (CAT), and superoxide dismutase (SOD) in fish. Heavy metal concentrations were analyzed using inductively coupled plasma optical emission spectrometry. To determine genetic differentiation, inter-simple sequence repeats with dendrogram construction and genomic template stability (%GTS) were applied. The results showed that the average concentrations of As, Cd, Cr, and Pb in water samples were 0.0848, 0.536, 1.23, and 0.73 mg/L, respectively. These values exceeded safety limits, and the average Cd in sediment (1.162 mg/kg) was above regulatory thresholds. In fish muscle, the average metal concentrations (mg/kg) followed the order Cr (1.83) > Pb (0.69) > Cd (0.096) > As (0.0758), with Pb exceeding food quality standards. The bioaccumulation factor ranked as Cr > Pb > As > Cd. Health risk assessments, including health risk index and carcinogenic risk, suggested Pb contamination poses significant health risks through fish consumption. From dendrogram results, the %GTS of O. niloticus from the landfill and reference sites were 46.34 to 71.67% and 87.34 to 96.00%, respectively. This suggests that fish from the landfill site exhibited greater genetic diversity compared to those from the reference site. Specific oxidative stress markers revealed higher levels of H₂O₂ and significantly lower activities of CAT and SOD in landfill O. niloticus than in the reference site. These results emphasize the urgent need for environmental monitoring, stricter pollution controls, and improved waste management strategies to protect aquatic ecosystems and human health. Full article

Designed ankyrin repeat protein (DARPin) Ec1, a small scaffold protein (18 kDa), binds with high affinity the epithelial cell adhesion molecule (EpCAM) that is overexpressed in several carcinomas. To enhance the targeted delivery of cytotoxic drugs using Ec1, we investigated the potential of fusing Ec1 with an albumin-binding domain (ABD) to improve its circulation time and decrease renal uptake. Two fusion proteins were created, Ec1-ABD, with the ABD at the C-terminus, and ABD-Ec1, with the ABD at the N-terminus. Both variants were labeled with ¹¹¹In. ABD-fused variants bound specifically to EpCAM-expressing cells with picomolar affinity. Adding human albumin reduced the affinity. This effect was more pronounced for Ec1-ABD; however, the affinity remained in the subnanomolar range. The position of the ABD did not influence the internalization rate of both variants by human cancer cells. In mouse models with human cancer xenografts, both variants demonstrated over 10-fold lower renal uptake compared to the Ec1. Tumor uptake of the ABD-fused variants was higher than the uptake of Ec1. ABD-Ec1 provided two-fold higher tumor uptake, indicating fusion with an ABD as a promising way to modulate the targeting properties of an Ec1-based construct. However, the effect of fusion depends on the order of the domains. Full article

Portland cement is the primary barrier material for well abandonment. However, the limitations of cement, especially under harsh downhole conditions, are necessitating research into alternative barrier materials. While several alternatives have been proposed, the screening process leading to their selection is scarcely discussed in the literature, resulting in the non-repeatability of the selection process. This study develops a dynamic multi-criteria decision-making technique for assessing the material options for the abandonment of high-pressure high-temperature (HPHT) wells with exposure to harsh reservoir fluids. The material screening process is performed in ANSYS Granta and a combined technique for order of preference by similarity to ideal solution (TOPSIS) and analytical hierarchy process (AHP) approach is used for ranking the shortlisted material alternatives based on seven material properties proven in the literature to be critical to the long-term integrity of well barrier materials. Nine alternative materials are ranked against Portland cement and high alumina cement. The results show that the top-ranking materials are from the phenol formaldehyde and polyamide–imide groups. Of these, the primary production CO₂ of the polyamide–imide is, on average, about 25 times higher than the primary production CO₂ of the phenol formaldehyde material. A sensitivity analysis of the methodology confirms that the criteria with the highest initial weights are the most impactful in terms of the final rank. The material property values also have an impact on the extent to which variations in their weights affect the hierarchical position of the materials in the TOPSIS-AHP analysis. Despite their higher cost per unit volume, the alternative materials consistently outperformed cement—even when average price was weighted more heavily than the most influential mechanical property. Full article

Simulative and experimental studies were carried out to address multi-dimensional particle fractionation of non-biological particles according to size, shape, and density inside a high-throughput DLD array. Density sensitive separation was achieved for melamine and polystyrene particles at a diameter of 5 µm at a Reynolds number (Re) of 82, corresponding to an overall flow rate of 11.3 mL/min. This process is very sensitive, as no fractionation occurred for Re = 85 (11.7 mL/min). For the first time, the fractionation of elliptical polystyrene particles (5 × 10 µm) at Re > 1 was investigated up to Re = 80 (11 mL/min). A separation of elliptical particles from spherical melamine particles (5 µm) was observed in single experiments at all investigated Reynolds numbers. However, the separation is not reliably repeatable due to partial clogging of ellipsoidal particles along the posts. In addition, higher concentrations of polydisperse silica suspensions were experimentally investigated by using polydisperse silica particles at concentrations up to 0.4% (m/V) up to Re = 80 (20 mL/min). The separation size generally decreased with increasing Reynolds number and increased with increasing concentration. Separation efficiency decreased with increasing concentration, independent of the Reynolds number. In order to investigate the material-dependent separation in a contactless dielectrophoresis system (cDEP), the resolved CFD-DEM software was extended to calculate dielectrophoretic forces on particles. With this, the second stage of a serial-combined DLD-DEP system was simulated, showing good separation at lower flow rates. For these systems, different fabrication methods to minimize the distance between the electrodes and the fluid as well as the requirement to withstand high-throughput applications, were investigated. Full article

The significance of the matrix morphology of vermicular cast iron for the alloy’s thermal shock resistance was determined. The study included vermicular cast iron subjected to heat treatment in order to obtain an ausferritic matrix. Heat treatment involved austenitization at 960 °C for 90 min, followed by two different austempering variants at 290 °C and 390 °C, each for 90 min. Austempering at 390 °C resulted in a higher content of retained austenite compared to austempering at 290 °C. A test stand was used to determine thermal shock resistance, enabling repeated heating and cooling of the samples. The samples were heated inductively and subsequently cooled in water at a constant temperature of approximately 30 °C. The total length of cracks formed on the wedge-shaped surfaces of the tested samples was adopted as a characteristic value inversely proportional to the material’s thermal shock resistance. The samples heated to 500 °C were subjected to 2000 heating–cooling test cycles. It was found that in as-cast iron, structural changes were minor, whereas in the heat-treated material, changes in the structure were more noticeable. Under the influence of thermal shocks, ausferrite transforms into ferrite with carbides. Among the analyzed materials, the most resistant cast iron was the one austempered at 290 °C. Oxide precipitates were observed near cracks and graphite regions. Full article

Oxidative stress (OS) occurs when there is an imbalance between the production of reactive oxygen species (ROS) and the body’s antioxidant defenses, causing damage to lipids, proteins, and DNA. In marine mammals, physiological adaptation to aquatic life conditions, such as prolonged and repeated dives resulting in cycles of hypoxia followed by reperfusion, is associated with increased production of ROS. This study examines the relationship between oxidative stress, muscular stress, and metabolic damage in the blood serum of eleven captive bottlenose dolphins (Tursiops truncatus), six males and five females. This relationship is investigated using oxidative stress markers (d-ROMs, OXY, and Oxidative Stress index, OSi) and biochemical parameter measurements, including glucose (GLU), aspartate aminotransferase (AST), creatine kinase (CK), and lactate dehydrogenase (LDH). Pearson’s sex correlation was performed, and males exhibited significantly higher pro-oxidant levels than females, suggesting a potential protective role of female hormones. Also, a positive correlation between pro-oxidants and antioxidants has been observed in relation to age, as older dolphins produced more ROS but also exhibited higher antioxidant capacity, likely to compensate for oxidative damage. Results show no significant correlation between biochemical parameters and oxidative stress markers. However, a moderately positive correlation between LDH and antioxidant (OXY) capacity was observed (r = 0.458), suggesting a possible association between tissue turnover and antioxidant defenses. The results indicate that the biochemical markers analyzed are not strong predictors of oxidative stress in bottlenose dolphins. However, the correlation between LDH and antioxidant capacity suggests that tissue turnover may affect antioxidant defenses. This is a preliminary study, and further research is needed to clarify these relationships in order to better understand physiological adaptations in dolphins and their implications for management, health, and welfare. Full article

Background: Chronic kidney disease-associated pruritus (CKD-aP) is a common condition in dialysis patients, and is associated with lower quality of life, depression, and sleep problems. CKD-aP is under-recognized and undertreated. While question 20 of the KDQOL is used for CKD-aP assessment in the clinical setting, recent studies testing novel drugs for CKD-aP have used the WI-NRS. Therefore, evaluating the correlation between KDQOL-Q20 and the WI-NRS may enable the identification of patients who could potentially benefit from these treatments. Methods: This was an observational cohort study of patients receiving in-center hemodialysis from the Mount Sinai Kidney Center. Patients completed a baseline survey on CKD-aP (KDQOL-Q20 and WI-NRS), depression, and sleep quality. A repeat survey was conducted at 4 weeks, with the order of the CKD-aP surveys reversed. We defined moderate/severe CKD-aP as a KDQOL-Q20 score ≥2 and a WI-NRS score ≥ 4. Our outcomes of interest were the correlations of KDQOL-Q20 with the WI-NRS, missed HD treatments, depression, and sleep quality. Correlation analysis was performed with Spearman correlation analysis. Association testing between CKD-aP and outcomes was conducted by relative risk estimation with robust error variance. Results: A total of 112 patients completed the study. According to the WI-NRS, 42% of patients reported itching (score of ≥4) while according to KDQOL-Q20, 57% of patients reported itching (score of ≥2). KDQOL-Q20 and the WI-NRS were strongly correlated (r = 0.7; p < 0.001). Patients who had moderate/severe CKD-aP according to KDQOL-Q20 had a non-statistically significant trend towards a lower risk of missed HD treatments and a higher risk of depression, and a statistically significantly higher risk of sleep-related problems, compared to those with no or mild CKD-aP. Conclusions: CKD-aP is a common condition, and is associated with various clinical outcomes. We found a strong correlation between two CKD-aP measures. These results can help to identify patients for CKD-aP treatment. Full article

Serious games are powerful interactive environments that provide more authentic experiences for learning or training different skills. However, developing effective serious games is complex, and a more systematic approach is needed to create better evidence-based games. Learning analytics—based on the analysis of collected in-game user interactions—can support game development and the players’ learning process, providing assessment information to teachers, students, and other stakeholders. However, empirical studies applying and demonstrating the use of learning analytics in the context of serious games in real environments remain scarce. In this paper, we study the application of learning analytics throughout the whole lifecycle of a serious game, in order to assess the game’s design and players’ learning using a serious game that introduces basic programming concepts through a visual programming language. The game was played by N = 134 high school students in two 50-min sessions. During the game sessions, all player interactions were collected, including the time spent solving levels, their programming solutions, and the number of replays. We analyzed these interaction traces to gain insights that can facilitate teachers’ use of serious games in their lessons and assessments, as well as guide developers in making possible improvements to the game. Among these insights, knowing which tasks students struggle with is critical for both teachers and game developers, and can also reveal game design issues. Among the results obtained through analysis of the interaction data, we found differences between boys and girls when playing. Girls play in a more reflexive way and, in terms of acceptance of the game, a higher percentage of girls had neutral opinions. We also found the most repeated errors, the level each player reached, and how long it took them to reach those levels. These data will help to make further improvements to the game’s design, resulting in a more effective educational tool in the future. The process and results of this study can guide other researchers when applying learning analytics to evaluate and improve the educational design of serious games, as well as supporting teachers—both during and after the game activity—in applying an evidence-based assessment of the players based on the collected learning analytics. Full article

Backgrounds/Objectives: The aim of this study was to compare differences in the physical characteristics of lissamine green (LG) strips and the outcomes of using different staining techniques. Methods: Two separate complementary investigations were conducted. Physical study: Differences between four LG strips were evaluated in terms of material, dye concentration, and dye absorption. In vivo study: Bulbar conjunctival staining was compared for four application methods of I-DEW LG strips presented in a randomized order for twenty-two participants: (1) single application 5 s after wetting (also repeated using GreenGlo for comparison), (2) single application using two strips held together, 5 s after wetting, (3) two applications using a single LG strip 5 s after wetting, 1 minute apart, (4) the same as method 3, with a single fluorescein strip in between LG applications. White light imaging was performed immediately following application and after 30, 60, 90, and 300 s. Three masked practitioners independently evaluated the randomized staining images for spot count and staining intensity. Results: Physical study: Strip paper fibres demonstrated visible similarities, with no difference in saline absorption (p > 0.05). LG concentration increased as saline retention duration increased (F = 964.1, p < 0.001), and GreenGlo tips were significantly darker (F = 2775.2, p < 0.001). In vivo study: I-DEW application resulted in less conjunctival staining than GreenGlo (p < 0.001). Amongst I-DEW application techniques, staining levels were similar (p > 0.05); however, staining intensity was significantly higher following two applications of I-DEW, 1 min apart, compared to a single application (p = 0.042). Both spot count and staining intensity decreased with time (p < 0.001). Conclusions: Two applications of I-DEW using a single strip, 1 min apart, after wetting with a single drop of saline provided maximal staining. There was also a significant difference in staining intensity observed between LG products. Full article

The testing of rolling stock for the assessment of disturbance in signalling circuits is considered with a focus on the measurement process and the selection of operating conditions. The definition of interference limits is briefly reviewed, but they are considered an external input. The spectral behavior of acquired signals and the evaluation of repeatability are instead discussed with the help of three different real test cases, considering correspondence between similar operating points and differences as rolling stock operation evolves during a test run. Repeatability evaluated as standard deviation is in the order of 3% to 5% in the harmonic and audio frequency range for the different systems, slightly lower for AC railways; above about 10–15 kHz it increases to 30%. Uncorrelated components (with much lower amplitudes) may show much higher dispersion. Full article

Tragus racemosus often grows in close proximity to motorways. The aim of this work was to determine whether the seeds of the species can grow under salt (NaCl) stress, how the plants are able to accumulate heavy metals and what plant architecture prerequisites they have for spreading. It was found that the structure of the plant consists of a single rosette of the first order, from which shoots of the first order develop, on which rosettes of the second order grow, and this is repeated modularly. Higher-order rosettes can produce their own root systems. Research on this species revealed its small salt and heavy metal tolerances during germination and early development. The concentration of metals in the above-ground parts of plants was of the following rank: Fe >> Zn > Ni ≥ Pb > Cu; for soil, it was Fe >> Pb > Cu > Ni. The plant germinates successfully and grows in environments containing NaCl up to 0.50% (including solutions of 0.12% and 0.25%). However, higher salt contents of 0.99% and 1.96% proved lethal for seed germination. This tolerance to salt explains why T. racemosus commonly grows along motorways where winter road maintenance involves the application of salt. These adaptations give the species a competitive advantage in these human-modified environments. Furthermore, T. racemosus turned out to be a possible Ni hyperaccumulator. Full article