Search Results (241)

Influenza A(H1N1)pdm09 remains one of the predominant seasonal influenza viruses worldwide and continues to evolve under the combined effects of host immunity, vaccination, and changing epidemiological conditions. However, the long-term impact of the COVID-19 pandemic on its evolutionary dynamics remains poorly understood. We investigated the genetic variability and phylodynamic evolution of the hemagglutinin (HA) and neuraminidase (NA) genes of Italian A(H1N1)pdm09 viruses collected between 2009 and 2026. Time-calibrated phylodynamic analyses, Bayesian Skyline Plots (BSPs), Lineages Through Time (LTT) graphs, principal component analysis (PCA), and codon-based selection analyses were used to characterize long-term evolutionary patterns. Both HA and NA followed continuous evolutionary trajectories, with a marked post-2020 genetic shift associated with the emergence of 6B.1A.5a.2-related clades. HA showed greater evolutionary variability than NA, whereas selection analyses identified only one positively selected site in HA and none in NA, consistent with reduced adaptive diversification in recent strains. Phylodynamic analyses revealed a marked decline in effective population size and lineage accumulation during the COVID-19 pandemic, followed by renewed expansion after 2022. Overall, Italian A(H1N1)pdm09 viruses exhibited reduced genetic diversity, limited evidence of positive selection, and coordinated genomic restructuring following the pandemic. These findings provide new insights into the long-term evolutionary dynamics of A(H1N1)pdm09 in Italy and reinforce the importance of sustained genomic surveillance for anticipating evolutionary changes and informing evidence-based public health strategies. Full article

Confucian ethics are widely credited with shaping Guangfu ancestral halls, yet existing scholarship approaches their façades from two disconnected ends: macro-cultural studies treat the façade as an undifferentiated emblem of lineage order, while craft studies document individual motifs without asking how the composition addresses a viewer. This study bridges the two with a transparent, auditable, and replicable semiotic-coding framework, demonstrated on the main ceremonial façade of the Chen Clan Ancestral Hall in Guangzhou [广州] (1894). A semiotic reading identifies three legibility bands: a doorway band at eye level that regulates entry, a mid-register readable from the forecourt, and a crown that frames the long view. MAXQDA-assisted coding then classifies 88 carrier items screened by explicit inclusion rules. Confucian themes dominate (59.1%) over Taoist-related (22.7%), local Guangzhou (13.6%), and foreign (4.5%) repertoires; textual carriers are confined to the doorway band, narratives concentrate in the mid-register, emblems dominate the crown, and cross-validation shows each reading band is met by its coded distribution. Theoretically, the analysis reveals the façade as a graduated moral curriculum that reserves threshold and skyline for Confucian claims while domesticating other repertoires into subordinate positions; methodologically, the framework gives every value claim a traceable carrier, rule, and audit trail; practically, it equips heritage interpretation, conservation prioritisation, and cross-site comparison of Guangfu ancestral hall façades. Full article

Mumps virus (MuV) genotype G is widely represented among circulating strains, but the evolutionary patterns of the hemagglutinin–neuraminidase (HN) gene remain incompletely understood. In this study, we analyzed publicly available full-length genotype G HN sequences using phylogenetic, phylodynamic, codon-based selection, and structure-guided epitope prediction approaches. The genotype G HN sequences were categorized into Clade 1, an operationally defined Diverse group, and Clade 2. Clade 1, which was composed mainly of Japanese strains, showed a relatively structured pattern over time. In contrast, Clade 2 showed more recent diversification and an overall increase in relative genetic diversity, although this phylodynamic pattern was sensitive to sampling structure. The Diverse group was phylogenetically heterogeneous, and its Bayesian skyline estimates were not used for biological interpretation because repeated analyses showed unstable posterior behavior. Root-to-tip regression supported temporal structure in the complete dataset, with the strongest signal in Clade 2. Bayesian molecular dating estimated the time to the most recent common ancestor of the sampled genotype G HN sequences at approximately 1932, and the mean evolutionary rate was 4.925 × 10⁻⁴ substitutions/site/year. Although the HN protein is a major surface antigen and a target of neutralizing antibodies, codon-based analyses showed no robust evidence of positive selection using multiple methods. Instead, many codon sites were inferred to be under purifying selection, suggesting that genotype G HN evolution is largely constrained by the need to maintain protein function. Predicted B-cell epitope regions were broadly similar among representative genotype G strains. Overall, these findings indicate that genotype G HN lineages have followed distinct evolutionary patterns, while the HN gene remains mainly shaped by purifying selection. These findings may help improve our understanding of MuV genotype G HN gene evolution and support future molecular surveillance. Full article

Melanoma incidence rates have also been steadily increasing, emphasizing the need for improved prognostic and diagnostic tools with the goal of enhancing patients’ outcomes. Biomarkers in melanoma have emerged as an important component of melanoma management, offering insight into disease progression, tumor biology, and the potential for judging treatment responses. Traditionally, blood and immunohistochemical markers such as lactate dehydrogenase (LDH), S100 calcium-binding protein (S100B), human melanoma black-45 (HMB-45), and SRY-box transcription factor 10 (SOX10) have been widely used in melanoma diagnosis, staging, and monitoring. However, their clinical use has been limited because of their low specificity, especially in patients with early-stage disease. This has led to the development of molecular and genetic biomarkers, including BRAF, NRAS, and KIT mutations, which improved patients’ risk stratification and enabled targeted therapies, and gene expression signature assays such as DecisionDx (Castle Biosciences) and SkylineDx (Merlin) that are already used in clinics to help with surgical decisions and to assess patients’ prognosis. Other circulating biomarkers, including microRNAs, circulating tumor DNA and circulating tumor cells, have been developed to provide minimally invasive approaches to monitor tumor evolution and detect recurrence. However, none of these new approaches are used in clinics due to their low specificity and/or sensitivity. Additionally, nomograms or predictive models have been created using biomarkers and clinicopathologic data to assess patients’ outcomes and survival. While significant progress has been made, the integration of melanoma biomarkers into routine clinical practice remains limited. This review summarizes current advancements in melanoma biomarkers, including traditional serum and immunohistochemical markers, as well as developments in molecular, genetic, circulating, and predictive biomarker approaches. Full article

Roughly 100,000 new cases of melanoma are diagnosed yearly in the United States, the majority of which are early-stage disease with excellent prognosis. However, a subset of patients harbors clinically occult aggressive biology that can go undetected on standard clinicopathologic analyses. Gene expression profiling (GEP) assays have emerged as molecular adjuncts to risk stratification, aiming to improve sentinel lymph node biopsy (SLNB) decision-making and surveillance planning. Two commercial tests are widely available: the 31-gene expression profile (31-GEP, DecisionDx-Melanoma, Castle Biosciences) and the clinicopathologic gene expression profile (CP-GEP, Merlin, SkylineDx). This review summarizes the current evidence for each assay regarding their performance and utility, with a focus on potentially actionable use cases, limitations, and the practical context in which these tools are most valuable. Full article

The Garisenda Tower, along with the neighboring Asinelli Tower, is arguably the symbol of the city of Bologna. They are the sole remnants of about one hundred towers that formed the city’s skyline in medieval times. As such, the monitoring of their state of health has been of great interest to the scientific community for more than a century—one example being the studies of Prof. Cavani in the early 1900s. The Garisenda Tower, famous for its impressive lean, is the object of Structural Health Monitoring (SHM) involving a multitude of devices. Some examples are a 30 m long pendulum installed on the inside of the tower to measure the planar displacement of the tower’s top; Fiber-Optical Strings (FOSs) installed in the walls of the basement to measure their vertical deformation; and piezoelectric acoustic emission (AE) sensors, also installed on the walls of the tower’s basement to detect elastic waves generated by micro-cracking. This rich experimental setup allows for the investigation of the tower’s stability and damage assessment. In this work, attention is focused on two analyses: The first is a Principal Component Analysis (PCA) study that investigates the correlation between AE data and other SHM data, such as in situ temperature, pendulum displacement, and AE rate. The second analysis corresponds with numerical finite element (FE) studies that assess damage in the base of the tower. Initially, the Smeared Cracking material model is used to understand which zones of the tower are more damaged. Moreover, a possible critical scenario due to increasing tower tilt is investigated. Finally, a viscoelastic formulation of the materials at the base of the tower is used to account for creep to understand the possible viscous effects at the base of the tower. Full article

Generalized anxiety disorder (GAD) is characterized by persistent, excessive, and difficult-to-control worry. The Contrast Avoidance Model (CAM) proposes that individuals with GAD use worry to sustain negative emotional arousal, thereby avoiding sharp negative emotional contrasts that would otherwise follow unexpected adverse events. A virtual reality (VR) protocol was developed to simulate such contrasts by alternating guided relaxation with brief anxiety-inducing scenarios (skyline plank, crowded elevator, and loose dog encounter). This study evaluated the usability and feasibility of this protocol in 20 subclinical adults aged 18–45 who met a screening threshold of GAD-7 ≥ 5, using a Meta Quest 3 headset and Polar H10 heart rate sensor. Exposure segments produced a significant decrease in RMSSD (β = −0.185, p < 0.001), consistent with reduced parasympathetic activity during exposure, whereas heart rate did not differ significantly between conditions. Subjectively, exposure increased SUDS (β = 2.23, p < 0.001) and SAM arousal (β = 1.95, p < 0.001), and decreased SAM valence (β = −2.68, p < 0.001) and dominance (β = −1.70, p = 0.005). Presence scores, cybersickness ratings, and qualitative feedback supported the usability of the protocol and identified concrete design refinements. These results support the feasibility of the protocol and provide a foundation for future controlled clinical evaluation. Full article

Residential valuation under the comparison principle requires systematic adjustment for material differences between comparable units. In high-density, high-rise housing markets, however, visual amenities such as harbour and skyline views are often treated qualitatively or implicitly embedded in comparable evidence, reducing transparency and auditability. This study examines whether view quality is systematically capitalized into transaction prices in Hong Kong and whether such premiums vary across market conditions. Using 352 secondary market transactions from six prime high-rise estates (2015–2024), we estimate hedonic models with the logarithm of price per saleable area as the dependent variable. View quality is specified as an ordered categorical variable (nil, partial, full), constructed from listing descriptions and cross-validated using map and street-view evidence. Controlling for floor level, estate age, monthly market movements proxied by the Centa-City Index (CCI), and estate fixed effects, the pooled estimates indicate that partial views command an approximate 11% premium and full views an approximate 22% premium relative to nil view, with a clear incremental premium for full over partial views. Split-sample estimation using GDP-defined regimes reveals partial state dependence: full view premiums remain economically meaningful across market conditions, whereas partial view effects become less precisely identified during weaker periods. The findings demonstrate that view quality is a material and systematically priced attribute in Hong Kong’s vertically differentiated housing market. By providing transparent percentage-based adjustment benchmarks grounded in within-estate variation, the study enhances the consistency, transparency, and evidential rigor of comparable-based valuation practice. Full article

Senecavirus A (SVA) has rapidly emerged as a globally distributed swine pathogen, with clinical signs mimicking vesicular diseases such as Foot-and-Mouth Disease, posing challenges for timely detection and control. Here, we analyzed 329 complete SVA genomes spanning multiple continents to provide a comprehensive view of its evolutionary dynamics, recombination patterns, haplotype diversity, and global dissemination. Phylogenetic analyses revealed two major lineages: Lineage 1, consisting mainly of early strains from the United States before 2007, and Lineage 2, which emerged post-2007 and subsequently spread across the Americas and East Asia. Recombination was confined to Lineage 2 and concentrated in nonstructural regions, particularly 2C, highlighting intra-lineage genetic exchange as a driver of recent diversification. Haplotype analysis of the 3AB gene identified 170 distinct haplotypes, revealing a star-like network structure consistent with rapid population expansion from a central ancestral variant, while secondary branches reflect ongoing regional diversification. Despite this high genetic variation, genome-wide dN/dS ratios remained below one, and purifying selection was strongest in the N-terminal domains of structural and nonstructural proteins, indicating functional constraints that maintain viral fitness. Time-scaled phylogenetic reconstruction and Bayesian Skyline analysis revealed rapid lineage diversification and a marked increase in effective population size in the early 2010s. Phylogeographic inference further identified repeated introductions from the Americas into East Asia, likely facilitated by swine trade and other anthropogenic factors. Collectively, SVA evolution is driven by frequent mutation and intra-lineage recombination yet constrained by pervasive purifying selection, generating extensive genetic diversity while maintaining functional integrity, with implications for genomic surveillance and targeted control. Full article

In this study, we investigated the long-term evolutionary dynamics of human norovirus GII.17[P17] using the RNA-dependent RNA polymerase (RdRp) region and the VP1 capsid gene, integrating phylogenetics, time-scaled inference, phylodynamics, and structure-based analyses. Maximum-likelihood phylogenies of both genomic regions consistently resolved four major clades (Clades 1–4). VP1 patristic-distance distributions indicated higher within-clade diversity in the phylogenetically basal Clades 1 and 3, whereas Clades 2 and 4 showed lower diversity, consistent with recent demographic expansion. Similarity-plot analysis identified pronounced variability in the VP1 P2 domain, while the S and P1 domains remained comparatively conserved, supporting P2 as the primary hotspot of diversification. Bayesian time-scaled analyses estimated the most recent common ancestor around 1993 (VP1) and 2000 (RdRp) and revealed two major lineages (Clade 1/2 and Clade 3/4), with the split between Clades 3 and 4 occurring around 2016–2017. Bayesian skyline plots showed a marked increase in effective population size after 2013, and substitution-rate estimates indicated faster evolution in VP1 than in RdRp, with higher VP1 rates in the Clade 3/4 lineage than in Clade 1/2. Capsid dimer modeling further mapped high-confidence conformational B-cell epitopes and positively selected residues predominantly to the distal surface of P2, with broadly conserved spatial patterns across clades. Compared with the Clade 1 reference (Kawasaki323), Clade 2 accumulated numerous P2 substitutions, whereas Clades 3 and 4 retained fewer changes and remained closer to Clade 1 at the amino-acid level. Together, these results suggest lineage turnover within GII.17[P17] driven by constrained diversification at the P2 surface, potentially contributing to the recent predominance of the Clade 3/4 lineage. Full article

This research is an analysis of the relationship between sustainable urbanization and economic inequality through smart city initiatives in developing countries such as India. Rapid urbanization in developing countries tends to have a detrimental impact on socioeconomic inequalities, and the effort to build smart cities may inadvertently increase exclusion when it is not planned with inclusiveness in mind. To reach this goal, an integrated Multi-Criteria Decision-Making (MCDM) approach using a combination of AHP, TOPSIS, and DEMATEL is adopted to systematically identify, assess, and identify the key criteria that affect the inclusive urban development. This study’s results show that infrastructure, governance, digital accessibility, and social inclusion play a key role in mitigating urban disparities and facilitating sustainable development. In particular, good governance and the availability of equitable digital infrastructure appear to be one of the critical factors in the reduction in inequalities and long-term urban resilience. This research provides policy-oriented insights for policymakers in designing inclusive smart city policies in accordance with the Sustainable Development Goals, as well as theoretical contributions to urban sustainability research. Full article

Background: In Pakistan, the number of Human immunodeficiency virus (HIV) cases is increasing significantly, attributed to risk factors such as injection drug use, sexual transmission, etc. However, transmission through hemodialysis units is not well documented. In 2024, an outbreak of HIV cases in Multan, Pakistan, drew alarm from local health authorities due to reports linking it to a large public hospital in South Punjab. Here, we report the molecular epidemiological investigation of the outbreak. Methods: Twenty-five hemodialysis patients identified during the outbreak were enrolled. Blood samples were subjected to DNA extraction and polymerase chain reaction (PCR) amplification. Phylogenetic analysis was conducted using the maximum-likelihood approach in IQ-TREE. For dating phylogenetics, a maximum clade credibility tree (MCC) was constructed using the BEAST tool. The MCC tree was constructed using the Bayesian Skyline model with an uncorrelated lognormal relaxed clock. The VESPA program was used to identify amino acid signatures unique to outbreak sequences compared with Pakistani reference sequences. Results: A total of 25 patients (identified as part of the HIV outbreak) were enrolled. 96% (24 out of 25) also tested positive for Hepatitis C, while none tested positive for Hepatitis B. The age range of patients in the study was 23 to 72 years (median age: 44.88 years). In terms of gender distribution, 13 out of 25 were male. All the sequences were identified as HIV subtype CRF02_AG. Phylogenetic analysis revealed that Multan sequences formed a well-supported monophyletic cluster, indicating shared recent origin. Signature pattern analysis identified a unique molecular fingerprint at 26 nucleotide positions, whereas molecular dating placed the emergence of the cluster between 2023 and 2024, consistent with the outbreak timing. Conclusions: Findings provide biologically plausible evidence of a point-source HIV outbreak linked to lapses in infection prevention and control practices at the hemodialysis unit. Full article

Early wildfire smoke detection is critical for preventing small ignitions from escalating into large-scale fires, yet early-stage smoke plumes are often faint, low-contrast, and spatially small. When full-resolution frames are resized to satisfy fixed-input detector architectures and enable efficient batched GPU inference, these subtle cues are further diminished, leading to missed detections and unreliable scores near deployment thresholds. Existing remedies such as multi-scale inference, slicing/tiling, or super-resolution could improve sensitivity, but typically incur substantial overhead from multiple forward passes or added network components, limiting real-time use on resource-constrained platforms. To mitigate these challenges, we propose a composite multi-resolution detection framework that improves sensitivity to small smoke regions while maintaining single-pass inference. Motivated by the fact that most operational wildfire monitoring systems rely on Unmanned Aerial Vehicle (UAV) platforms and mountain-top Closed-Circuit Television (CCTV) systems surveillance, their wide-field imagery typically contains a large sky region above the horizon where early smoke is most likely to first become visible. Accordingly, crop placement is guided by a skyline prior that prioritizes this high-probability sky band while retaining the remaining scene for global context. A dynamic compositing stage stacks a global view with a high-resolution, sky-aligned band into a standard square detector input, preserving context with minimal added cost. Detections from the two views are reconciled via coordinate restoration and non-maximum suppression. For deployment, a lightweight second-stage classifier selectively re-evaluates low-confidence detections to stabilize decisions near a fixed operating threshold without retraining the detector. Compared to the baseline detector, our approach improves detection performance on the Early Smoke dataset, achieving gains of +4.6 percentage points in AP @0.5:0.95, +3.4 percentage points in AP @0.5, +2.9 percentage points in precision, +5.3 percentage points in recall, and +4.3 percentage points in F1-score. Full article

Human metapneumovirus genotype B (HMPV-B) is an important respiratory pathogen, requiring detailed elucidation of the evolutionary and antigenic features of its fusion (F) gene. Using 500 sequences collected between 1982 and 2024, we investigated the molecular evolution, phylodynamics, and structural epitope landscape of the HMPV-B F gene. Time-scaled phylogeny dated the divergence of sublineages B1 and B2 to around 1937, and Bayesian Skyline Plot analysis showed that these sublineages exhibited distinct demographic trajectories over time. The F gene evolved at a rate of 1.01 × 10⁻³ substitutions/site/year; however, amino acid variation remained limited, consistent with pervasive purifying selection, with 39% of codons under strong negative selection and little consensus evidence for positive selection. Conformational B-cell epitope prediction demonstrated a high degree of conservation across neutralizing antibody binding regions (sites Ø and I–V), and amino acid substitutions occurring within these sites were not predicted to substantially alter epitope architecture. Together, these findings indicate that the HMPV-B F gene evolves under strong evolutionary constraint while maintaining stable antigenic features, supporting the potential for antibody-based strategies that target neutralizing antibody binding regions of the F protein. Full article

This prospective, analytical study aimed to measure and compare trochlear groove depth using skyline radiographic projection and ultrasonography at three stifle joint angles and four distinct anatomical regions, as well as to compare these findings with ex vivo measurements obtained using a caliper under the same conditions in canine cadavers without patellar luxation. A total of 67 limbs were evaluated. Ultrasonography demonstrated greater agreement with ex vivo measurements than radiography. Ultrasonographic assessment was considered appropriate for measuring trochlear groove depth with the stifle joint in maximal extension, with the transducer positioned distal to the patella, and at 90° of flexion, with the transducer positioned proximal to the patella. Full article