Search Results (7,314)

Automatic Identification System (AIS) data provide valuable insights into ship behavior, supporting maritime safety, situational awareness, and operational efficiency capabilities that are increasingly required for autonomous ship functions and harbor maneuvering assistance. This review synthesizes recent research on AIS-based ship behavior analysis and modeling published between 2022 and 2024 using a structured literature search and screening process informed by PRISMA principles. The review presents a five-stage workflow, spanning data processing, data analysis, knowledge extraction, modeling, and runtime applications with emphasis on how these stages contribute to perception, prediction, and decision support in automated navigation. Four dimensions are considered in data analysis, including statistical analysis, safety indicators, situational awareness, and anomaly detection. The modeling approaches are categorized into classification, regression, and optimization, highlighting current limitations such as data quality, algorithmic transparency, and real-time performance, while also assessing runtime feasibility for onboard or edge deployment. Three runtime application directions are identified: autonomous vessel functions, remote monitoring and control operations, and onboard decision-support tools, with numerous studies focusing on constrained waterways and port-approach scenarios. Future directions suggest integrating multi-source data and advancing machine learning models to improve robustness in complex traffic and harbor environments. By linking theoretical insights with practical onboard needs, this study provides guidance for developing intelligent, adaptive, and safety-enhancing maritime systems. Full article

This study investigated the microbiological composition and antimicrobial resistance (AMR) profiles of artisanal goat and sheep milk cheeses produced in Poland. Ten raw milk cheeses (five each from goat and sheep milk) were analyzed using a combined approach involving culture-dependent enumeration, 16S rRNA gene sequencing, and antibiotic susceptibility testing. Microbial counts revealed substantial variability among the samples, with lactic acid bacteria (LAB) dominating the microbiota. Taxonomic analysis confirmed the predominance of Lactococcus, Streptococcus, and lactobacilli, although marked intra-group heterogeneity was observed. Multivariate analyses indicated that sample-specific factors had a greater influence on microbiome composition than milk origin. Among 170 isolates, 28.7% were classified as multidrug-resistant (MDR), being most prevalent in Enterobacterales (100%) and Enterococcus spp. (73%), whereas LAB exhibited low resistance levels (16.2%). Resistance was most frequently associated with aminoglycosides and β-lactams. The resistance results were interpreted according to CLSI guidelines. These findings demonstrate that artisanal cheeses harbor complex, dynamic microbial ecosystems that may serve as reservoirs of antimicrobial resistance. The results highlight that environmental and technological factors, rather than milk source alone, are key drivers of both microbiome structure and resistance distribution, underscoring the need for targeted AMR monitoring in traditional dairy products. Full article

Background/Objectives: Staphylococcus aureus (S. aureus) intramammary infection remains a major global dairy problem due to its contagious nature, its ability to persist and colonize teat/skin and mucosal niches, and the often-limited bacteriological cure achieved with antimicrobial therapy. Beyond udder health, it is relevant to public health because it can enter raw milk chains and serve as a reservoir for antimicrobial resistance determinants that may circulate between dairy animals and humans. Methods: We assessed S. aureus’ ecology in raw ewe milk from 75 sheep farms in Epirus (Greece) by sampling clinically healthy controls (group A) and clinical mastitis cases pre-treatment (group B), followed by resampling at the first post-withdrawal milking after penicillin/streptomycin treatment (group C1—therapeutic protocol 1), oxytetracycline treatment (group C2—therapeutic protocol 2), or enrofloxacin treatment (group C3—therapeutic protocol 3). Results: S. aureus detection was high and comparable across groups (A 23.0%, B 22.0–30.0%, C 20.0–22.0%), and paired analyses showed no significant pre–post shifts in detection/burden within therapeutic protocols (all p > 0.05). Nevertheless, persistence remained evident. The chromosomal gene mecA was detected in S. aureus strains in all groups, ranging from 13.6% in controls to 54.5% post-withdrawal in group C1, and was also present in the pre-treatment group. In paired sampling animals, mecA was mostly stable, with rare emergence or loss. Across antibiotic classes, within-animal resistance transitions were generally uncommon and non-significant (p > 0.05); β-lactam resistance was fully stable (p = 1.00). Descriptively, resistance to protein synthesis inhibitors tended to decline after therapy in protocol 1 and protocol 3, while protocol 3 showed post-treatment gains in fluoroquinolone resistance. By contrast, virulence-associated phenotype traits shifted after therapy: enterotoxigenicity increased post-withdrawal (especially in the C3 group), Staphylococcal Enterotoxin A (SEA) and Staphylococcal Enterotoxin B (SEB) appeared only post-therapy, Staphylococcal Enterotoxin D (SED) increased significantly in paired isolates (p = 0.002), and strong biofilm adherence increased (in C3, p = 1.5 × 10⁻⁵). Conclusions: The detection of S. aureus after therapy suggests that one possibility is that antimicrobial exposure may select for, or otherwise reshape, the residual intramammary population, rather than reliably eliminating it—an outcome that remains clinically relevant for udder health. Moreover, the persistence of mecA/methicillin-resistant Staphylococcus aureus (MRSA)-compatible profiles indicates that milk released to the food chain after withdrawal compliance may still harbor S. aureus with enhanced preservation capacity and significant food safety relevance. Full article

Background/Objectives: Loss of nuclear BAP1 (BRCA1-associated protein 1) expression is a well-established adverse prognostic marker in uveal melanoma (UM). However, data from Central and Southeastern European populations are limited. This descriptive study aimed to evaluate BAP1 immunohistochemical expression in a Croatian enucleation-based UM cohort, characterize its associations with clinicopathological parameters, and contextualize the findings within the published literature. Methods: Formalin-fixed, paraffin-embedded tumor tissue from 58 consecutive patients with primary choroidal and ciliary body melanoma treated with enucleation at University Hospital Centre Zagreb (2006–2016) was analyzed immunohistochemically for BAP1 nuclear expression. Associations with clinicopathological parameters were assessed using chi-square and Fisher’s exact tests. Survival analysis was performed using Kaplan–Meier estimation, log-rank tests, and Cox proportional hazards regression with a median follow-up of 11.2 years. Results: Loss of nuclear BAP1 expression was observed in 53/58 (91.4%) specimens, resulting in a severely imbalanced distribution (53 versus 5 patients) precluding meaningful comparative survival analysis. Five-year and 10-year overall survival rates were 72.4% and 51.7%, respectively, with a median overall survival of 14.5 years. BAP1 loss was associated with longer disease-free survival (log-rank p = 0.020); however, this finding likely reflects a statistical artifact attributable to the extremely small BAP1-retained group (n = 5) harboring concurrent adverse features and should not be interpreted biologically. The study was underpowered to draw prognostic inferences regarding BAP1 status. Exploratory survival analyses are presented for transparency but should not be interpreted inferentially. Conclusions: The exceptionally high prevalence of BAP1 loss reflects the selection bias inherent in enucleation-based cohorts, which are enriched for large, molecularly high-risk tumors. This study provides the first comprehensive BAP1 immunohistochemical data from Croatia, contributing to the growing evidence that enucleation cohorts represent a distinct, biologically high-risk subgroup in which BAP1 immunohistochemistry offers limited discriminatory value. The extended follow-up of 11.2 years confirms the prolonged natural history of UM. Future multi-center studies incorporating molecular validation and diverse treatment modalities are needed to establish the prognostic utility of BAP1 across the full spectrum of UM disease. Full article

Background: Enterobacter hormaechei, a member of the Enterobacter cloacae complex (ECC), is increasingly recognized as a multidrug-resistant (MDR) nosocomial pathogen. However, subspecies-level genomic data from Ecuador remain limited. Methods: Four clinical E. hormaechei isolates from a hospital in northern Ecuador were analyzed using antimicrobial susceptibility testing and whole-genome sequencing (WGS). Genomic characterization included multilocus sequence typing (MLST), resistome profiling, plasmid replicon detection, integron screening, genomic island analysis, and phylogenetic comparison with publicly available Ecuadorian genomes. Results: WGS identified three isolates as subsp. xiangfangensis (ST136 and ST337) and one as subsp. hoffmannii (ST145). Two ST136 isolates exhibited extensive MDR phenotypes associated with bla_CTX-M-15, bla_OXA-1, bla_ACT-16, and additional aminoglycoside and fluoroquinolone resistance genes. ST145 showed moderate resistance, whereas ST337 remained largely susceptible despite harboring bla_ACT-16. Multiple genomic islands and plasmid replicons (IncF/IncR or IncHI2) were detected. Phylogenetic analysis demonstrated clustering with previously reported Ecuadorian lineages. Conclusions: This study provides subspecies-level genomic characterization of clinical E. hormaechei in Ecuador and describes heterogeneous resistance profiles and associated mobile genetic elements, contributing baseline data for regional surveillance. Full article

Background and Objectives: Serum carcinoembryonic antigen (CEA) is a widely used biomarker in non-small cell lung cancer (NSCLC). However, its association with oncogenic driver alterations and prognostic significance across molecular subtypes in metastatic disease remains insufficiently defined. Materials and Methods: This retrospective multicenter study included 332 patients with metastatic NSCLC harboring oncogenic alterations (EGFR, ALK, ROS1, KRAS, and others) from eight oncology centers in Türkiye. Baseline serum CEA levels measured at metastatic diagnosis were analyzed on the natural logarithmic scale. Associations between CEA levels, molecular subtypes, clinical features, and overall survival (OS) were evaluated using generalized linear models and Cox proportional hazards regression. Results: Baseline CEA levels differed significantly across molecular subtypes (p = 0.001), with EGFR-mutant tumors showing the highest median levels. Multivariable analysis identified driver alteration, histology, and metastatic burden as independent determinants of baseline CEA. Higher baseline CEA and metastatic site count were independently associated with increased mortality risk (HR 1.151 and 1.279 per unit increase, respectively; p < 0.001), while female sex was protective (HR 0.626; p = 0.004). KRAS mutations were associated with poorer survival compared with EGFR (HR 2.370; p < 0.001). Kaplan–Meier analyses showed a consistent trend toward longer OS in patients with CEA < 5 ng/mL, with significance only in the rare alteration subgroup. Conclusions: Baseline CEA may reflect underlying tumor biology across molecular subtypes and are associated with survival outcomes in metastatic NSCLC. However, given the variability across subgroups and modest effect sizes, these findings should be interpreted with caution. Prospective studies evaluating longitudinal CEA dynamics are warranted. Full article

To improve Chrysanthemum tolerance to low temperatures and its adaptability to low autumn temperatures in Northeast China, we conducted the first genome-wide identification of the heat shock transcription factors (Hsfs) in Chrysanthemum indicum under low-temperature stress. Based on genome-wide analyses, we identified 14 CiHsf genes in Chrysanthemum indicum. Based on structural characteristics, the genes were grouped into two subfamilies, comprising 10 HsfA and four HsfB members, with no representatives of the HsfC subfamily detected. CiHsf1~CiHsf14 were located on seven chromosomes, and their promoter regions harbored numerous cis-acting elements associated with responses to low temperature, hormones, and light. Tissue-specific expression profiling revealed that seven CiHsf genes were predominantly expressed in roots, two in stems, three in leaves, and two in flowers. The analysis of low-temperature expression characteristics showed that CiHsf2, CiHsf5, CiHsf8, and CiHsf10 were significantly upregulated following cold acclimation, indicating that these genes may participate in the low-temperature response mechanism of Chrysanthemum indicum. Here, we demonstrated that transient transformation of Chrysanthemum indicum with 35S:CiHsf10 reduced reactive oxygen species (ROS) accumulation under low-temperature stress, which may contribute to enhanced cold tolerance. Full article

Purified water from vending machines offers consumers an alternative source of clean, safe water. However, data regarding its microbiological quality are limited, particularly concerning the prevalence of Pseudomonas aeruginosa harboring virulence traits. This study aimed to evaluate the microbiological quality of 125 purified water samples collected from vending machines across six cities of Michoacan, Mexico. Additionally, it sought to assess the occurrence of Pseudomonas aeruginosa and characterize its antimicrobial resistance profiles and biofilm-forming capacity. Aerobic mesophilic bacteria (AMB) were detected in all analyzed samples. A total of 71 (56.8%), 40 (32.0%), and 31 (24.8%) samples were positive for total coliforms (TC), fecal coliforms (FC), and Escherichia coli, respectively. Among the samples, 43 (34.4%) were positive for P. aeruginosa. There were significant correlations between the presence of P. aeruginosa and AMB (rho = 0.4445; p < 0.0001), TC (rho = 0.4094; p < 0.0001), FC (rho = 0.3389; p = 0.0001), and E. coli (rho = 0.3242; p = 0.0002). Moreover, the presence of TC in purified water samples increased the risk of P. aeruginosa nearly seven-fold (odds ratio = 6.91; p < 0.001). The resistance rate among P. aeruginosa strains to the most tested antibiotics ranged from 2.3 to 16.3%, and two (4.6%) of the isolates were multidrug-resistant. All P. aeruginosa strains were strong biofilm producers. Consequently, we recommend periodic maintenance of vending machines, the establishment of P. aeruginosa control protocols, and enhanced regulatory monitoring of the water vending industry. Full article

Acinetobacter baumannii remains a significant nosocomial infectious agent, with its ability to acquire antimicrobial resistance posing a global public health concern. Over time, substantial knowledge has been amassed regarding A. baumannii in human clinical cases. Recently, research has shifted to non-human A. baumannii. Therefore, the current work aimed to investigate the occurrence of A. baumannii carrying carbapenem resistance genes in broiler chickens via molecular detection and its public health significance. Two hundred cloacal swabs were collected from broiler chickens and grouped into 40 pools. DNA extraction was conducted on these pools, followed by molecular detection of the A. baumannii bla_OXA-51-like gene. Among the 40 pools, 31 (77.5%) tested positive for the bla_OXA-51-like gene and were further screened for additional carbapenemase genes, including bla_OXA-58, bla_OXA-23, and bla_OXA-24. The bla_OXA-58 gene was identified in eight pools (25.8%), whereas bla_OXA-23 and bla_OXA-24 were not detected. Subsequently, partial DNA sequencing was performed on two PCR amplicons of the A. baumannii bla_OXA-51-like gene derived from broiler chickens, followed by a phylogenetic analysis. The analysis revealed genetic similarity between the A. baumannii sequences obtained in this work and those retrieved from humans, birds, animals, and environmental sources. In conclusion, the occurrence of A. baumannii harboring genes coding for carbapenem resistance in broiler chickens highlights a potential new path of transmission, which may require further investigation to better understand the dynamics of transmission and to guide effective strategies for preventing and controlling A. baumannii infections. Full article

The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic bacterial communities of dominant desert plants in the Arabian Peninsula have not been comprehensively characterized. Here, we investigated the endophytic microbiota of five co-adapted desert species, namely, Schweinfurthia papilionacea, Sesuvium verrucosum, Ochtocloa compressa, Helianthemum nummularium, and Convolvulus arvensis. These plants coexist in hyper-arid habitats and exhibit exceptional tolerance to drought, salinity, and nutrient scarcity. We hypothesized that, despite their phylogenetic divergence, these plants host functionally convergent microbial communities shaped by desert selection pressures. Using 16S rRNA gene amplicon sequencing, we obtained 3.4 million high-quality reads from 25 samples. Clustering at 97% similarity revealed 35 phyla and 17 dominant genera, highlighting notable microbial richness and ecological complexity. Alpha-diversity indices showed comparable species richness across hosts, while beta-diversity indicated community differentiation driven by environmental filtering. The dominant phyla included Pseudomonadota, Actinomycetota, Cyanobacteriota, and Bacillota, reflecting microbial adaptation to extreme desert conditions. Functional pathway prediction revealed enrichment of genes associated with DNA repair and protein turnover, suggesting metabolic flexibility and enhanced survival under stress. Overall, this study provides a comparative metagenomic insight into the endophytic bacterial communities of five desert plant species, uncovering a consistent pattern of functional convergence across diverse hosts. The findings suggest the presence of shared functional traits among the endophytic microbiota examined here, offering preliminary evidence for microbial contributions to plant resilience in arid environments. Full article

Background: Perivascular adipose tissue (PVAT) contains adipocytes and a stromal-vascular fraction with immune cells that modulate the adjacent vasculature. The presence of immune cells in PVAT of vascular beds is poorly understood—are they resident or recruited? We propose a novel resident microbiome present in PVAT, given the immune-rich stromal environment. Hypothesis: We hypothesized the existence of distinct bacterial and viral communities in healthy PVAT compared to non-PVAT adipose tissues. Methods: PVAT samples from thoracic and abdominal aorta, mesenteric resistance arteries, non-PVAT tissues (subscapular brown adipose tissue, retroperitoneal white adipose tissue), and fecal samples were collected one year apart from male Dahl SS rats, split into two cohorts (2023 and 2024, n = 3 each). Whole-genome shotgun sequencing (CosmosID) and 16S rRNA gene analysis assessed microbial relative abundance. Results: PVAT harbored bacterial and viral sequences, and species composition varied significantly between cohorts. Bacterial and viral fecal samples showed lower variability. Conclusions: PVAT microbiome differed dramatically from the fecal microbiome, with temporal influences on bacterial and viral diversity, marking the first such report. Despite inherent limitations, these findings establish the potential of PVAT microbiota in vascular biology and immune modulation, paving the development of microbiome-targeted drugs to address vascular dysfunctions. Full article

Background/Objectives: Lung cancer remains the leading cause of cancer-related mortality globally. Approximately 45% of these tumors harbor oncogenic mutations that drive carcinogenesis and are amenable to targeted therapies. Other predictive biomarkers—e.g., PD-L1, TMB, and MSI—play a crucial role in patients’ management. This study aims to investigate the existence of mutation clusters (co-mutations) and evaluate the correlation of these clusters with various clinical and laboratory parameters. Methods: A retrospective study was conducted utilizing pathological samples from lung cancer patients harboring mutations in EGFR, KRAS, ALK, BRAF, MET, HER2, ROS1, NTRK, and NRG1. Data were collected from the Institute of Pathology at Carmel Medical Center between the years 2022 and 2024. Patients were stratified using a Two-Step Cluster Analysis algorithm based on actionable mutations and co-mutations. Heatmaps and dendrograms were generated to assess the correlation between these genomic clusters, clinical metrics, and predictive biomarkers. Results: The study cohort included 129 patients with actionable mutations. Five distinct clusters were identified: Clusters 1, 2, and 3 exhibited a high expression of STK11 and TP53 co-mutations alongside KRAS drivers (n = 38, n = 12, and n = 23, respectively). Clusters 4 and 5 demonstrated high expression of ALK alterations and tumor suppressor gene mutations (n = 31 and n = 25, respectively). Cluster comparisons demonstrated statistically significant differences between clusters regarding age, gender, PD-L1 expression, and tumor mutational burden. No significant associations were found regarding ethnicity or microsatellite instability status. Conclusions: By constructing clusters based on the aggregate of genomic alterations in patients with actionable mutations, it is possible to predict associations with distinct demographic and clinical characteristics. Future research should apply this analytical approach to larger cohorts to further characterize these subgroups and investigate potential correlations with therapeutic efficacy. Full article

Environmental stressors and host genetics influence gut microbiota and antimicrobial resistance, but their combined effects across intestinal niches remain poorly unexplored. We conducted a metagenomic analysis of 60 jejunal and cecal samples from 30 native Chinese pigs across three altitudes (500 m, 1400 m, and 3850 m). The aim was to disentangle the interactive impacts of altitude, breed, and intestinal site on microbiome structure and antibiotic resistome dynamics. The cecal microbiota was taxonomically conserved and strongly associated with breed. Conversely, while jejunal communities exhibited structural variations among the sampled cohorts, differences in alpha diversity (Shannon index, p < 0.01) appeared to be primarily associated with breed differences rather than an independent altitudinal effect. High-altitude Tibetan pigs showed an enrichment of Bifidobacterium and Pseudomonas, which may be linked to hypoxia adaptation. Despite a shared core resistome (88 ARG types), the cecum harbored significantly higher ARG abundance than the jejunum within-breed comparisons of Tibetan pigs across altitudes; this revealed stable ARG profiles (p > 0.05) suggesting that, although some descriptive differences were observed, the independent effect of altitude weakens when the genetic effect is taken into account. Furthermore, carbohydrate-active enzymes (e.g., CBM13, GH33) correlated positively with ARG abundance. In conclusion, the jejunum appears to act as an environmentally responsive niche, while the cecum exhibits a higher ARG abundance that is closely associated with the host breed. Full article

Kazakhstan harbors the richest flora in Central Asia. However, its current plant diversity faces significant challenges. We present an updated checklist of vascular plants for Kazakhstan, comprising 6035 taxa from 134 families and 1016 genera. This includes 485 endemic taxa (8.0% of the flora) from 38 families and 147 genera, and 359 threatened taxa (6.0%) from 66 families and 203 genera. Among them, the genera with the most endangered species are Tulipa, Astragalus, and Allium. Based on the latest available data, we describe and analyze the diversity and distribution of vascular plants at a phytogeographic regional scale of 29 regions and 7 subregions. Our analyses specifically quantify patterns of species richness, phylogenetic diversity, and the spatial distribution of both threatened and endemic species. Furthermore, floristic similarity analysis revealed clear patterns of species turnover: high similarity between adjacent mountain regions and low similarity between mountains and arid western regions. Analysis revealed five key biodiversity hotspots, including the Karatau Mountains and Western Tien Shan, which host high concentrations of threatened species yet have limited protected area coverage. Our findings underscore the need to align national and international conservation assessments, expand protected area networks, and enhance cross-border collaboration. These results provide important guidance for the conservation and sustainable management of plant diversity in Kazakhstan. Full article

Background: Reusable tourniquets are widely used across clinical settings, yet their role as reservoirs of microbial contamination and antimicrobial resistance remains poorly characterized. Methods: In this cross-sectional study, 53 polyester–elastane tourniquets were collected from an Emergency Department (SR) and Operating Theater (SBO) over a 28-day period to assess bacterial burden and resistome composition. A 180-target qPCR panel targeting antibiotic and disinfectant resistance determinants was used. qPCR analysis identified 112 distinct resistance genes across all samples, with SR tourniquets harboring significantly richer resistomes than SBO (median 34 vs. 15 genes; p < 0.001). Efflux pump- and disinfectant-associated genes were pervasive, and β-lactamase and quinolone-resistance determinants increased over time in SR samples. Results: Principal component analysis showed clear segregation of resistome profiles by clinical unit and progressive enrichment over time. These findings indicate that reusable, porous tourniquets can accumulate extensive resistance gene profiles under routine clinical use, particularly in high-contact environments. Conclusions: Enhanced decontamination strategies, development of new materials or transition to single-use alternatives may be necessary to mitigate their potential contribution to environmental antimicrobial resistance in hospitals. Full article