Search Results (300)

Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14–0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin–Benson–Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32–4.60). Its black variety scales were dominated by Campylobacterota (67.01–80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order “Endothiobacterales,” were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin–Benson–Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails’ adaptation to vent ecosystems. Full article

Malignant mediastinal tumors are a group representing some of the most demanding oncological challenges for early, multi-level, and successful management. The timely identification of any suspicious clinical symptomatology is urgent in achieving an accurate, staged histological diagnosis, in order to follow up with an equally detailed medical therapeutic plan (interventional or not) and determine the principal goals regarding efficient overall treatment in these patients. We report a case of a 24-year-old male patient with an incident-free prior medical history. An initial chest X-ray was performed after the patient reported short-term, consistent moderate chest pain symptomatology, early work fatigue, and shortness of breath. The following imaging procedures (chest CT, PET-CT) indicated the presence of an anterior mediastinal mass (meas. ~11 cm × 10 cm × 13 cm, SUV: 8.7), applying additional pressure upon both right heart chambers. The Alpha-Fetoprotein (aFP) blood levels had exceeded at least 50 times their normal range. Two consecutive diagnostic attempts with non-specific histological results, a negative-for-malignancy fine-needle aspiration biopsy (FNA-biopsy), and an additional tumor biopsy, performed via mini anterior (R) thoracotomy with “suspicious” cellular gatherings, were performed elsewhere. After admission to our department, an (R) Video-Assisted Thoracic Surgery (VATS) was performed, along with multiple tumor biopsies and moderate pleural effusion drainage. The tumor’s measurements had increased to DMax: 16 cm × 9 cm × 13 cm, with a severe degree of atelectasis of the Right Lower Lobe parenchyma (RLL) and a pressure-displacement effect upon the Superior Vena Cava (SVC) and the (R) heart sinus, based on data from the preoperative chest MRA. The histological report indicated elements of a combined, non-seminomatous germ-cell mediastinal tumor, posthuberal-type teratoma, and embryonal carcinoma. The imminent chemotherapeutic plan included a “BEP” (Bleomycin^®/Cisplatin^®/Etoposide^®) scheme, which needed to be modified to a “VIP” (Cisplatin^®/Etoposide^®/Ifosfamide^®) scheme, due to an acute pulmonary embolism incident. While the aFP blood levels declined, even reaching normal measurements, the tumor’s size continued to increase significantly (DMax: 28 cm × 25 cm × 13 cm), with severe localized pressure effects, rapid weight loss, and a progressively worsening clinical status. Thus, an emergency surgical intervention took place via median sternotomy, extended with a complementary “T-Shaped” mini anterior (R) thoracotomy. A large, approx. 4 Kg mediastinal tumor was extracted, with additional RML and RUL “en-bloc” segmentectomy and partial mediastinal pleura decortication. The following histological results, apart from verifying the already-known posthuberal-type teratoma, indicated additional scattered small lesions of combined high-grade rabdomyosarcoma, chondrosarcoma, and osteosarcoma, as well as numerous high-grade glioblastoma cellular gatherings. No visible findings of the previously discovered non-seminomatous germ-cell and embryonal carcinoma elements were found. The patient’s postoperative status progressively improved, allowing therapeutic management to continue with six “TIP” (Cisplatin^®/Paclitaxel^®/Ifosfamide^®) sessions, currently under his regular “follow-up” from the oncological team. This report underlines the importance of early, accurate histological identification, combined with any necessary surgical intervention, diagnostic or therapeutic, as well as the appliance of any subsequent multimodality management plan. The diversity of mediastinal tumors, especially for young patients, leaves no place for complacency. Such rare examples may manifest, with equivalent, unpredictable evolution, obliging clinical physicians to stay constantly alert and not take anything for granted. Full article

This study aims to analyze the differences in soil bacterial community structure under different vegetation restoration types, and to explore the role of microorganisms in the process of vegetation restoration on the soil ecosystem of the Grain for Green area in the Loess Plateau. High-throughput sequencing technology was used to analyze the alpha diversity of soil bacteria, community structure characteristics, and the correlation between soil environmental factors and bacterial communities in different artificial Hippophae rhamnoides forests. Soil microbial C and N show a decreasing trend with an increase in the 0–100 cm soil layers. The results indicated that the bacterial communities comprised 24 phyla, 55 classes, 110 orders, 206 families, 348 genera, 680 species, and 1989 OTUs. Additionally, the richness indices and diversity indices of the bacterial community in arbor shrub mixed forest are higher than those in shrub pure forest, and the indices of shrub forest on sunny slope are higher than those on shady slope. Across all samples, the dominant groups were Actinobacteria (37.27% on average), followed by Proteobacteria (23.91%), Acidobacteria (12.75%), and Chloroflexi (12.27%). Soil nutrient supply, such as TOC, TN, AN, AP, and AK, had crucial roles in shaping the composition and diversity of the bacterial communities. The findings reveal that vegetation restoration significantly affected soil bacterial community richness and diversity. Furthermore, based on the results, our data provide a starting point for establishing soil bacterial databases in the Loess Plateau, as well as for the plants associated with the vegetation restoration. Full article

The structural analysis of shelterbelts forms the foundation of their planning and management, yet the scientific and effective quantification of shelterbelt structures requires further investigation. This study developed an innovative heterogeneous analytical framework, integrating three key methodologies: the LeWoS algorithm for wood–leaf separation, TreeQSM for structural reconstruction, and 3D alpha-shape spatial quantification, using terrestrial laser scanning (TLS) technology. This framework was applied to three typical farmland shelterbelts in the Ulan Buh Desert oasis, enabling the first precise quantitative characterization of structural components during the leaf-on stage. The results showed the following to be true: (1) The combined three-algorithm method achieved ≥90.774% relative accuracy in extracting structural parameters for all measured traits except leaf surface area. (2) Branch length, diameter, surface area, and volume decreased progressively from first- to fourth-order branches, while branch angles increased with ascending branch order. (3) The trunk, branch, and leaf components exhibited distinct vertical stratification. Trunk volume and surface area decreased linearly with height, while branch and leaf volumes and surface areas followed an inverted U-shaped distribution. (4) Horizontally, both surface area density (Scd) and volume density (Vcd) in each cube unit exhibited pronounced edge effects. Specifically, the Scd and Vcd were greatest between 0.33 and 0.60 times the shelterbelt’s height (H, i.e., mid-canopy). In contrast, the optical porosity (Op) was at a minimum of 0.43 H to 0.67 H, while the volumetric porosity (Vp) was at a minimum at 0.25 H to 0.50 H. (5) The proposed volumetric stratified porosity (Vsp) metric provides a scientific basis for regional farmland shelterbelt management strategies. This three-dimensional structural analytical framework enables precision silviculture, with particular relevance to strengthening ecological barrier efficacy in arid regions. Full article

Background/Objectives: Caesarean section (CS) accounts for over 20% of global births and routinely involves perioperative antibiotic prophylaxis (PAP) to reduce surgical site infections. While the impact of such prophylaxis on neonatal microbiome development is well described, effects on the maternal gut microbiome remain underexplored. This systematic review synthesizes current evidence on how antibiotic prophylaxis during CS affects maternal gut microbiome composition and diversity—an underrepresented, but clinically relevant aspect of maternal–fetal medicine. Methods: A systematic literature search was conducted in Medline (PubMed), the Cochrane Library, and the WHO International Clinical Trials Registry Platform (ICTRP) through November 2024. Inclusion criteria were defined according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Eligible studies used molecular techniques to report maternal gut microbiome outcomes (alpha- and beta-diversity). The search concentrated on beta-lactam antibiotics. Reference lists were screened, but no additional grey literature was searched. Synthesis followed the Synthesis Without meta-analysis (SWiM) approach. No review protocol was registered. The review received no external funding. Results: Out of 1011 records, three studies (total 286 mothers) met the inclusion criteria. All reported maternal microbiome outcomes secondarily to infant-focused research. Only one study provided pre- and post-birth stool samples. Applied antibiotic regimens, sequencing methods, and reported microbiome metrics for alpha- and beta-diversity varied considerably, thus limiting comparability of results. Due to high heterogeneity, no formal risk of bias was assessed. While taxonomic diversity changes were inconsistent, significant shifts in functional diversity metrics were observed postpartum. Conclusions: Evidence on maternal microbiome disruption following perioperative antibiotic prophylaxis in CS is methodologically fragmented and limited by small sample sizes and inconsistent antibiotic protocols. Nonetheless, functional diversity appears sensitive to antibiotic exposure. To improve clinical understanding and safety, maternal-focused studies using standardized protocols are urgently needed. The maternal microbiome may play a key role in both recovery and shaping the newborn’s early microbial environment. Full article

This paper introduces a novel and flexible class of continuous probability distributions, termed the Alpha Power Survival Ratio-X (APSR-X) family. Unlike many existing transformation-based families, the APSR-X class integrates an alpha power transformation with a survival ratio structure, offering a new mechanism for enhancing shape flexibility while maintaining mathematical tractability. This construction enables fine control over both the tail behavior and the symmetry properties, distinguishing it from traditional alpha power or survival-based extensions. We focus on a key member of this family, the two-parameter Alpha Power Survival Ratio Exponential (APSR-Exp) distribution, deriving essential mathematical properties including moments, quantile functions and hazard rate structures. We estimate the model parameters using eight frequentist methods: the maximum likelihood (MLE), maximum product of spacings (MPSE), least squares (LSE), weighted least squares (WLSE), Anderson–Darling (ADE), right-tailed Anderson–Darling (RADE), Cramér–von Mises (CVME) and percentile (PCE) estimation. Through comprehensive Monte Carlo simulations, we evaluate the estimator performance using bias, mean squared error and mean relative error metrics. The proposed APSR-X framework uniquely enables preservation or controlled modification of the symmetry in probability density and hazard rate functions via its shape parameter. This capability is particularly valuable in reliability and survival analyses, where symmetric patterns represent balanced risk profiles while asymmetric shapes capture skewed failure behaviors. We demonstrate the practical utility of the APSR-Exp model through three real-world applications: economic (tax revenue durations), engineering (mechanical repair times) and medical (infection durations) datasets. In all cases, the proposed model achieves a superior fit over that of the conventional alternatives, supported by goodness-of-fit statistics and visual diagnostics. These findings establish the APSR-X family as a unique, symmetry-aware modeling framework for complex lifetime data. Full article

Phyllosphere microbial communities influence the growth and productivity of plants, particularly in epiphytic plants, which are disconnected from nutrients available in the soil. We characterized the phyllosphere of 30 individuals of the epiphytic cycad, Zamia pseudoparasitica, collected from three forest sites during the rainy and dry seasons in the Republic of Panama. We used DNA metabarcoding to describe the total bacteria community with the 16S rRNA gene and the diazotrophic community with nifH gene. Common taxa included members of the Rhizobiales, Frankiales, Pseudonocardiales, Acetobacteriales, and the diazotrophic community was dominated by Cyanobacateria. We observed similar patterns of alpha diversity across sites and seasons, and no community differences were seen within sites between the rainy and dry seasons for either the 16S rRNA or nifH genes. However, pairwise comparisons showed some statistically significant differences in community composition between sites and seasons, but these explained only a small portion of the variation. Beta diversity partitioning indicated that communities were more phylogenetically closely related than expected by chance, indicative of strong environmental or host filtering shaping these phyllosphere communities. These results highlight the influence of host-driven selection and habitat stability in shaping phyllosphere microbiota, offering new insights into microbial assembly in tropical canopy ecosystems. Full article

The coastal zone presents complex hydrodynamic interactions among inland groundwater, reservoir water, and intruding seawater, with important implications for ecosystem functioning and water quality. However, the relative roles of hydraulic connectivity and seawater-driven salinity gradients in shaping microbial communities at the aquifer–reservoir interface remain unclear. Here, we integrated hydrochemical analyses with high-throughput 16S rRNA gene sequencing to investigate bacterial community composition, assembly processes, and co-occurrence network patterns across groundwater_in (entering the reservoir), groundwater_out (exiting the reservoir), and reservoir water in a coastal system. Our findings reveal that seawater intrusion exerts a stronger influence on groundwater_out, leading to distinct chemical profiles and salinity-driven environmental filtering, whereas hydraulic connectivity promotes greater microbial similarity between groundwater_in and reservoir water. Groundwater samples exhibited higher alpha and beta diversity compared to the reservoir, with dominant taxa such as Comamonadaceae, Flavobacteriaceae, and Rhodobacteraceae serving as indicators of seawater intrusion. Community assembly analyses showed that homogeneous selection predominated, especially under strong salinity gradients, while dispersal limitation and spatial distance also contributed in areas of reduced connectivity. Key chemical factors, including TDS, Na⁺, Cl⁻, Mg²⁺, and K⁺, strongly shaped groundwater communities. Additionally, groundwater bacterial networks were more complex and robust than those in reservoir water, suggesting enhanced resilience to salinity stress. Collectively, this study demonstrates that salinity gradients can override the effects of hydraulic connectivity in structuring bacterial communities and their networks at coastal interfaces. Our findings provide novel microbial insights relevant for understanding biogeochemical processes and support the use of microbial indicators for more sensitive monitoring and management of coastal groundwater resources. Full article

Background/Objectives: Dietary patterns vary with age and sex. The aim of this study was to clarify the differences in dietary patterns among young and middle-aged Japanese individuals by age group and sex via statistical methods such as alpha diversity and beta diversity analyses. Methods: Using data from a dietary survey of 10 food items during health checkups of 2743 Fujita Health University employees, we examined the effects of age and sex on alpha diversity (Shannon index) and beta diversity (nonmetric multidimensional scaling (NMDS) and RDA). Unlike principal component analysis which assumes linear relationships, redundancy analysis (RDA) incorporates explanatory variables to directly assess how external factors shape multivariate patterns. Results: The Shannon index increased with age and was greater in males across age groups. Type III ANOVA revealed significant main effects of age (p < 0.001) and sex (p < 0.001), and the effect of the interaction between age and sex approached significance (p = 0.08). Visualization of the NMDS data revealed that women aged 20–29 years and women aged 30 years and older and men aged 20–39 years and men aged 50–59 years have different dietary patterns. The RDA model accounted for 2.01% of the variance (adjusted R² = 1.94%), with age and sex contributing 56.7% and 43.3%, respectively. RDA1 and RDA2 were correlated with age (r = 0.26, −0.14) and sex (r = 0.15, 0.21). The RDA1 values increased with age and were greater in females, whereas the RDA2 values decreased with age and were greater in females. RDA1 (1.41% of the total variance in food group intake, 70.1% of the constrained variance) was positively associated with fruits, milk, and seaweed and negatively associated with meat and eggs. In RDA2 (0.60% of total variance, 29.9% contribution), fruits, potatoes, and vegetables had positive effects, whereas fish had negative effects. Conclusions: Dietary patterns vary by age and sex, with meat, fish, eggs, and fruit as key determinants. Nutritional guidance must account for variations in dietary patterns influenced by age and sex. Full article

Infections with cytomegalovirus (CMV) can result in increased morbidity and mortality in immunocompromised patients. The pUL97 kinase is a critical enzyme in the regulation of CMV replication. Although it does not phosphorylate deoxynucleosides, this enzyme is involved in the first phosphorylation step of ganciclovir (GCV), a viral DNA polymerase inhibitor. In contrast, maribavir (MBV) is a specific inhibitor of pUL97 kinase activity. In this paper, we analyzed the already-reported amino acid changes, conferring resistance to MBV and cross-resistance to GCV, in the pUL97 protein structure, predicted with AlphaFold2. Docking experiments suggest that MBV is a dual-site inhibitor, targeting ATP binding and substrate phosphorylation. Substitutions that confer resistance to MBV only may directly or indirectly alter the shape of the cavity in the vicinity of the invariant K355 in the putative ATP binding site, without affecting the viral growth. The most frequently encountered T409M substitution may correspond to a gatekeeper mutation. Substitutions that induce cross-resistance to MBV and GCV may directly or indirectly affect the environment of D456 and N461 residues in the catalytic loop, with reduced viral replicative capacity. These results have implications for the clinical use of MBV as well as for the design of novel pUL97 kinase inhibitors. Full article

Many studies have recognized that individual variability shapes user experience in virtual reality (VR), yet little is known about how these differences influence objective cognitive engagement and performance outcomes. This study investigates how cognitive factors (IQ, age) and technological familiarity (tech enthusiasm, tech fluency, first-time VR experience) influence EEG-derived cognitive responses (alpha and theta activity) and task performance (trial duration) during VR interactions. Sixteen autistic and sixteen neurotypical participants engaged with various VR interactions while their neural activity was recorded using a Muse S EEG. Correlational analyses showed distinct group-specific patterns: higher IQ correlated with elevated average alpha and theta power in autistic participants, while tech fluency significantly influenced performance outcomes only in neurotypical group. Prior VR experience correlated with better performance in the neurotypical group but slower adaptation in the autistic group. These results highlight the role of individual variability in shaping VR engagement and underscore the importance of personalized design approaches. This work provides foundational insights toward advancing inclusive, user-centered VR systems. Full article

The Antarctic continent hosts highly specialized microbial ecosystems, particularly within endolithic habitats, where microorganisms colonize the interior of rocks in order to withstand conditions that otherwise cannot support life. Previous studies have characterized the composition and abundance of these communities, as well as their different degrees of stress power; furthermore, the effect of different lithic substrates in shaping their associated bacterial assemblages has been extensively investigated. By contrast, how rock typology exerts fungal endolithic colonization still remains unexplored. In this study, we have considered and compared fungal communities inhabiting granite and sandstone rocks collected across Victoria Land, Antarctica, using high-throughput sequencing of the Internal Transcribed Spacer (ITS) region. Our analyses revealed that both rock types were dominated by Ascomycota, with a marked prevalence of lichen-forming fungi, particularly within the class Lecanoromycetes. However, granite-supported communities exhibited significantly higher species richness, likely driven by the structural heterogeneity of the substrate and the presence of fissures enabling chasmoendolithic colonization. In contrast, sandstone communities were more specialized and dominated by strict cryptoendolithic taxa capable of surviving within the rock’s pore spaces. Differential abundance analysis identified key species associated with each substrate, including the lichen Buellia frigida in granite and the black fungus Friedmanniomyces endolithicus in sandstone, two endemic species in Antarctica. Moreover, the use of presence/absence- versus abundance-based diversity metrics revealed contrasting ecological patterns; substrate type had a stronger influence on species presence, whereas geographic location more significantly shaped abundance profiles, highlighting the complex interplay between both factors in determining fungal community composition. Additionally, alpha diversity analyses showed significantly higher species richness in granite compared to sandstone, suggesting that structural heterogeneity and chasmoendolithism may promote a more diverse fungal assemblage. Full article

The COVID-19 pandemic has revealed the profound and lasting impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the nervous system. Beyond acute infection, SARS-CoV-2 acts as a potent immunomodulatory agent, disrupting immune homeostasis and contributing to persistent inflammation, autoimmunity, and neurodegeneration. Long COVID, or post-acute sequelae of SARS-CoV-2 infection (PASC), is characterized by a spectrum of neurological symptoms, including cognitive dysfunction, fatigue, neuropathy, and mood disturbances. These are linked to immune dysregulation involving cytokine imbalance, blood–brain barrier (BBB) disruption, glial activation, and T-cell exhaustion. Key biomarkers such as interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), glial fibrillary acidic protein (GFAP), and neurofilament light chain (NFL) correlate with disease severity and chronicity. This narrative review examines the immunopathological mechanisms underpinning the neurological sequelae of long COVID, focusing on neuroinflammation, endothelial dysfunction, and molecular mimicry. We also assess the role of viral variants in shaping neuroimmune outcomes and explore emerging diagnostic and therapeutic strategies, including biomarker-guided and immune-targeted interventions. By delineating how SARS-CoV-2 reshapes neuroimmune interactions, this review aims to support the development of precision-based diagnostics and targeted therapies for long COVID-related neurological dysfunction. Emerging approaches include immune-modulatory agents (e.g., anti-IL-6), neuroprotective drugs, and strategies for repurposing antiviral or anti-inflammatory compounds in neuro-COVID. Given the high prevalence of comorbidities, personalized therapies guided by biomarkers and patient-specific immune profiles may be essential. Advancements in vaccine technologies and targeted biologics may also hold promise for prevention and disease modification. Finally, continued interdisciplinary research is needed to clarify the complex virus–immune–brain axis in long COVID and inform effective clinical management. Full article

Dendritic cells (DCs) play a central role in the immunopathogenesis of rheumatoid arthritis (RA), yet their regulation by tumor necrosis factor alpha (TNF) and associated receptors remains poorly characterized. We applied a single-cell multi-omics approach (CITE-seq) to profile peripheral blood mononuclear cells (PBMCs) from RA patients and healthy donors, before and after in vitro TNF stimulation. Using integrated analysis of surface protein expression and transcriptomic data, we focused on phenotypic and transcriptional changes in dendritic cell populations. DCs from RA patients exhibited elevated surface expression of CD14 and CD16, indicative of an inflammatory phenotype, and showed marked responsiveness to TNF. Upon stimulation, RA-derived DCs upregulated genes involved in antigen presentation (CD83, LAMP3), lymph node migration (CCR7, ADAM19), and inflammation (TRAF1, IL24) whereas such activation was absent in healthy controls. Our data reveal a TNF-responsive, pro-inflammatory transcriptional program in dendritic cells from RA patients and underscore the relevance of the TNF receptor profile in shaping DC function. These findings provide new insights into the immunobiology of RA and identify dendritic cells as potential targets for personalized immunomodulatory therapy. Full article

This review investigates the novel idea that proteins catalyze chemical reactions through conformational changes driven by energy derived from their collisions with water molecules. Recent studies have suggested that proteins in solution undergo constant deformation due to collisions with water molecules, generating potential energy that can be harnessed for catalytic functions. We detail the existing evidence supporting this idea, including how structures in proteins such as α-helices and β-sheets facilitate energy conversion, how conformational changes can affect the ways in which substrates attach, and how reactions occur. Combining information from computer-based methods—such as molecular dynamics simulations and machine learning models (e.g., AlphaFold)—we suggest a more complete model for understanding how proteins function beyond simply looking at their fixed shapes. This emerging view has implications for drug design, enzyme engineering, and our fundamental understanding of biological catalysis. Full article