Newly or already diagnosed cancer might significantly influence the clinical presentation, outcome, and therapy of acute pulmonary embolism (PE).

The current state of research on the anti-SARS-CoV-2 potential of artemisinin-related compounds has identified arteannuin B as a potent inhibitor of the nCoV-2019BetaCov/Wuhan/WiV04/2019 and BetaCov/Italy/CDG1/2020 strains of the virus. The aim of this work was to fractionate the targeted sesquiterpenoid compounds, arteannuin B and artemisinin, from the complex matrix of the crude ethanolic leaf extract of Artemisia annua L. using high-speed countercurrent chromatography (HSCCC) and to test the simplified or purified fractions against the genomically characterized Alpha SARS-CoV-2 variant in vitro. This is the first detailed in vitro anti-SARS-CoV-2 study using an analytically characterized supercritical fluid extract of A. annua L. The preparative HSCCC method enabled the isolation of purified arteannuin B in a single chromatographic step, which was confirmed by LC-ESI-QTOF-MS/MS. The MS data confirmed the selectivity of the HSCCC method for the targeted fractionation of artemisinin from the complex matrix, as it was successfully separated from the EtOH crude extract without co-elution with arteannuin B. Antiviral activity determined by quantitative real-time PCR (qRT-PCR) yielded half-maximal effective concentrations (EC50) of 93.7 µg/mL (SC-CO2 extract), 173.5 µg/mL (EtOH extract), 187.3 µg/mL (artemisinin knockout fraction), 38.1 µg/mL (arteannuin B fraction), and >100 µg/mL (artemisinin). The arteannuin B fraction was highly active at 50 µg/mL (p < 0.0001) and 100 µg/mL (p < 0.0001), and inhibited the amplification of the SARS-CoV-2 N and RdRp genes by 84% and 100%, respectively. An important contribution of this study is the demonstration of the antiviral activity of arteannuin B against the Alpha variant of SARS-CoV-2, which is known to have increased infectivity and transmissibility.

This study aimed to examine the habits, attitudes, and consumption patterns of food supplements (FS) among gym users in Sarajevo, Bosnia and Herzegovina, with respect to gender, age, and training experience. Understanding these behaviors is essential given the rising global trend in FS use, often without professional guidance, which can have implications for individual health and public awareness. By investigating local patterns, this study seeks to provide valuable insights into the motivations and risks associated with supplement consumption, contributing to evidence-based recommendations and policy-making in the field of fitness and nutrition. Methods: Cross-sectional data were collected from various fitness centers using an online questionnaire composed of 21 questions divided into three segments. A total of 614 participants (mean ± SD: 32.77 ± 9.82 years), including both male (67.8%) and female (32.2%) gym users, took part in the study. Results: Participants predominantly belonged to the 36–45 age group, with 70.0% (p < 0.001) reporting more than one year of regular gym attendance, and 40.4% indicating regular FS consumption (p < 0.05). Supplements were mainly used to support faster recovery (29.1%, p < 0.05) and muscle growth (25%, p < 0.05). Magnesium was the most commonly used supplement, equally favored across genders and age groups. Creatine, fish oil capsules, and multivitamins were also frequently consumed (p < 0.05). Self-prescription emerged as the predominant method of FS use (40.3%, p < 0.05), followed by advice from gym coaches (21.8%), with only 5.6% of participants receiving guidance from a nutritionist. Conclusions: The findings highlight a societal trend toward self-directed FS use, often influenced by informal sources, underscoring the importance of further research and the development of targeted, evidence-based educational strategies. Males reported higher FS consumption, with younger users more focused on muscle gain and older individuals prioritizing health maintenance. The reliance on non-expert recommendations raises concerns about the safety and effectiveness of FS usage in the fitness community.

O-RAN (Open-Radio Access Network) offers a flexible, open architecture for next-generation wireless networks. Network slicing within O-RAN allows network operators to create customized virtual networks, each tailored to meet the specific needs of a particular application or service. Efficiently managing these slices is crucial for future 6G networks. O-RAN introduces specialized software applications called xApps that manage different network functions. In network slicing, an xApp can be responsible for managing a separate network slice. To optimize resource allocation across numerous network slices, these xApps must coordinate. Traditional methods where all xApps communicate freely can lead to excessive overhead, hindering network performance. In this paper, we address the issue of xApp conflict mitigation by proposing an innovative Zero-Touch Management (ZTM) solution for radio resource management in O-RAN. Our approach leverages Multi-Agent Reinforcement Learning (MARL) to enable xApps to learn and optimize resource allocation without the need for constant manual intervention. We introduce a Graph Convolutional Network (GCN)-based attention mechanism to streamline communication among xApps, reducing overhead and improving overall system efficiency. Our results compare traditional MARL, where all xApps communicate, against our MARL GCN-based attention method. The findings demonstrate the superiority of our approach, especially as the number of xApps increases, ultimately providing a scalable and efficient solution for optimal network slicing management in O-RAN.

Introduction: Despite the presence of various constraints, Bosnia and Herzegovina has managed to establish healthcare services in the field of spinal surgery. Limiting factors associated with resource scarcity and a shortage of neurosurgeons may pose challenges, but they are not insurmountable in the context of spinal tumor surgery. This study aims to provide a comprehensive 10-year analysis of intradural spinal tumors in resource-constrained healthcare settings and assess surgical outcomes in these challenging environments. Methods: A retrospective study was conducted involving 39 patients with intradural spinal tumors in Zenica-Doboj Canton, Bosnia and Herzegovina, from 2011 to 2021. Patients underwent neurological examinations and spinal magnetic resonance imaging scans, followed by post-surgery assessments at 3 and 6 months using the McCormick scale. Results: Among the 39 patients, tumor distribution was as follows: meningioma (15, 38.5%), ependymoma (3, 7.7%), schwannoma (11, 28.2%), neurenteric cyst (1, 2.6%), primary melanoma (2, 5.1%), lipoma (1, 2.6%), and metastasis (6, 15.4%) (p < 0.001). A majority of patients reported localized and radicular pain (37, 94.9%, p < 0.001) and paresthesia (33, 84.6%, p < 0.001). Motor weakness was noted in 20 (51.3%) patients, while sphincteric dysfunction was reported by 17 (43.6%) patients. The average symptom duration was 397.9 ± 380.9 days, ranging from 14 to 1460 days (p < 0.001). Pneumonia and liquorrhea were reported by 1 (2.6%) patient each. Regarding mortality, 1 (2.6%) patient passed away within a 6-month follow-up period (p < 0.001), and 2 (5.1%) patients were diagnosed with primary malignant melanoma. Significant improvements in McCormick scores were observed between postoperative and 3-month assessments (p < 0.001) and between 3-month and 6-month assessments (p = 0.024). Conclusions: This study offers valuable insights into the management of intradural spinal tumors in resource-constrained healthcare settings. Timely diagnosis and surgical intervention are essential for achieving positive patient outcomes in these challenging environments.

To better understand the genetic architecture and adaptability of native sheep, 22 breeds were genotyped using ovine50K SNP chips. Eleven additional populations from open-source repositories were included. Cross population Extended Haplotype Homozygosity (XP-EHH) and Relative Scaled Haplotype Homozygosity (Rsb) haplotype-based approaches were used to identify genetic variations influencing the adaptation of local sheep breeds to different climatic zones. The results indicate that all breeds exhibited high but declining genetic diversity levels, with a larger proportion of genetic variation explained by development history and refined by geographical origin, as shown by principal component analysis and Neighbor Net graphs. Admixture analysis revealed high admixture levels in European and North African breeds. Using XP-EHH and Rsb methods, 371 genes were putatively under selection, with only nine common among all population pairs, highlighting unique adaptability. Most identified genes, including Interleukin (IL) and cluster differentiation (CD) gene families underlie immune responses, emphasizing their role in resilience to climate change effects. These findings support that indigenous sheep breeds have retained significant genetic diversity, but improper genetic management may threaten it. Additionally, the research emphasizes that indigenous sheep breeds’ unique adaptability to specific climatic zones makes them valuable genetic assets for developing climate-resilient breeds.

Background and Objectives: Postoperative atrial fibrillation (POAF) is a common complication following cardiac surgery, associated with increased morbidity and prolonged hospital stays. Oxidative stress has been implicated in POAF pathogenesis, with malondialdehyde (MDA), a marker of lipid peroxidation, proposed as a potential biomarker. However, conflicting evidence exists regarding its predictive value. This study aimed to assess the association between serum MDA levels and POAF incidence in patients undergoing cardiac surgery. Materials and Methods: This prospective observational study included 99 consecutive patients undergoing elective on-pump cardiac surgery. Patients with preoperative atrial fibrillation, chronic kidney disease requiring dialysis, or emergency surgery were excluded. Blood samples for MDA measurement were collected at six perioperative time points: preoperatively, intraoperatively after aortic clamp release, and at 8, 24, 48, and 72 h postoperatively. Patients were monitored for new-onset POAF during the first three postoperative days. Statistical analyses included independent samples t-tests, Mann–Whitney U-tests, and Fisher’s exact tests, with significance set at p < 0.05. Results: POAF occurred in 33 (33%) patients. Patients who developed POAF were significantly older (p = 0.017) and had higher EuroSCORE II values (p = 0.019). No significant differences were observed in serum MDA concentrations between POAF and non-POAF patients at any measured time point. The incidence of POAF was higher in patients undergoing valvular surgery (p = 0.014). Conclusions: Serum MDA levels were not associated with POAF development, suggesting that lipid peroxidation alone may not play a central role in POAF pathogenesis. These findings challenge the predictive value of MDA for POAF risk stratification. Future research should explore alternative oxidative stress markers and their potential therapeutic implications in POAF prevention.

Abstract Basal cell carcinoma (BCC) is the most common type of skin cancer that usually appears in sun-exposed body regions such as the head, trunk, and extremities. There are four main clinicopathological subtypes of BCC: nodular, superficial, morpheaform, and fibroepithelial. BCC’s molecular basis includes inherited genetic susceptibility and somatic mutations, often induced by exposure to UV radiation. The aberrant activation of the hedgehog (Hh) signalling pathway, caused by mutations in the Hh components, plays a central role in the molecular pathogenesis of this carcinoma. This led to the development of Hh signalling pathway inhibitors as a new treatment option for patients with advanced disease. In this review, we summarise BCC’s clinical presentation and histopathology and present knowledge on the most studied Hh signalling inhibitors, vismodegib and sonidegib, and other inhibitors of this signalling, such as itraconazole, patidegib, taladegib, and arsenic trioxide, in the treatment of BCC. We also present the most common Hh signalling inhibitor adverse events and their management options, which could improve patients’ quality of life during treatment.

Background and Objectives: Carotid artery stenosis is a significant risk factor for ischemic stroke due to impaired cerebral blood flow (CBF). Even asymptomatic unilateral stenosis can induce subclinical cerebrovascular changes, potentially affecting both hemispheres through collateral circulation. This study aimed to systematically assess cerebral perfusion in asymptomatic individuals with unilateral carotid artery stenosis by comparing ipsilateral and contralateral hemispheres with healthy controls, challenging the assumption that the contralateral hemisphere remains unaffected. Materials and Methods: This cross-sectional study included 114 participants, comprising 54 asymptomatic individuals (mean age 65.5) with significant unilateral carotid stenosis and 60 age-matched controls (mean age 64.8). Cerebral perfusion was assessed using 1.5T Magnetic Resonance Imaging (MRI) with pseudo-continuous arterial spin labeling (pCASL). CBF was measured bilaterally in four predefined middle cerebral artery (MCA) regions: precentral gyrus, lentiform nucleus, insular cortex, and temporal cortex. Statistical analyses included multivariate analysis of variance (MANOVA), analysis of variance (ANOVA), paired t-tests, and discriminant analysis (DA). Results: Significant bilateral reductions in CBF were observed in individuals with carotid stenosis compared to controls (MANOVA and ANOVA, p < 0.001). The greatest perfusion deficit was in the ipsilateral insular cortex (49.88 ± 10.83 mL/100 g/min), followed by intermediate contralateral perfusion (51.49 ± 8.86 mL/100 g/min) and higher control values (58.78 ± 10.44 mL/100 g/min). DA indicated the insular cortex as the region with the highest discriminative contribution (64.7%). Conclusions: Unilateral carotid artery stenosis in asymptomatic individuals is associated with significant bilateral cerebral hypoperfusion, suggesting widespread hemodynamic effects. Pronounced perfusion deficits in the insular cortex underline its vulnerability. The observed contralateral perfusion reductions challenge the traditional use of the contralateral hemisphere as a reference standard, underscoring the need for comprehensive perfusion assessment in carotid artery disease.

Melanoma, a highly heterogeneous cancer, evolves through a complex interplay of genetic alterations, including both single nucleotide variants (SNVs) and structural variants (SVs). To study the evolutionary trajectory of melanoma, we established a model system composed of 24 single-cell-derived clonal sublines (C1-C24) from the M4 melanoma model, developed in a genetically engineered hepatocyte growth factor (HGF)-transgenic mouse. While SNVs have been extensively used to construct phylogenetic trees using Trisicell (Triple-toolkit for single-cell intratumor heterogeneity inference), a tool that analyzes intratumor heterogeneity and single-cell RNA mutations, the role and timing of SVs in melanoma evolution remain less well understood. This study integrates SV data with an SNV-driven phylogeny to investigate whether SV patterns align with SNV-based evolutionary trajectories in the mouse melanoma model, providing insights into the functional impact of SVs during tumor progression. We performed long-read sequencing on the 24 clonal sublines and detected SVs using Severus, a tool optimized for phasing in long-read sequencing. The SVs were mapped to the SNV-driven phylogeny using R and classified as either concordant (aligning with the SNV-based tree) or discordant (deviating from the SNV phylogeny). Gene ontology enrichment analysis revealed that concordant SVs were significantly enriched in genes associated with the hepatocyte growth factor receptor signaling pathway and the negative regulation of peptidyl-threonine phosphorylation, both of which represent core drivers of tumor progression. In contrast, discordant SVs were associated with a broader range of functional pathways, including the positive regulation of antigen receptor-mediated signaling and the regulation of natural killer cell-mediated cytotoxicity, though the exact mechanisms underlying these associations remain unclear. By integrating these SVs with an established SNV-driven phylogeny, this study highlights the distinct and critical roles SVs play in melanoma evolution. Concordant SVs appear to drive core oncogenic processes, while discordant SVs may contribute to other aspects of tumor evolution. These findings underscore the importance of considering SVs alongside SNVs to fully capture the complexity of melanoma evolution. Ongoing investigations will continue to explore the functional implications of these SVs and how the gene disruption patterns they cause shape the evolutionary trajectory of melanoma, offering potential targets for future therapeutic strategies. Xiwen Cui, Ayse G. Keskus, Salem Malikic, Yuelin Liu, Anton Goretsky, Chi-Ping Day, Farid R. Mehrabadi, Mikhail Kolmogorov, Glenn Merlino, S. Cenk Sahinalp. Integrating structural variants and single nucleotide variants to uncover evolutionary trajectories in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3898.

Most human cancers arise from somatic alterations, ranging from single nucleotide variations to structural variations (SVs) that can alter the genomic organization. Pathogenic SVs are identified in various cancer types and subtypes, and they play a crucial role in diagnosis and patient stratification. However, the studies on structural variations have been limited due to biological and computational challenges, including tumor heterogeneity, aneuploidy, and the diverse spectrum of SVs from simpler deletions and focal amplifications to catastrophic events shuffling large fragments from one or multiple chromosomes. Long-read sequencing provides the advantage of improved mappability and direct haplotype phasing. Yet, no tool currently exists to comprehensively analyze complex rearrangements within the cancer genome using long-read sequencing. Here, we present Severus, a tool for somatic SV calling and complex SV characterization using long reads. Severus first detects individual SV junctions from phased split alignments, then constructs a phased breakpoint graph to cluster junctions into complex rearrangement events. We first benchmarked the somatic SV calling performance using six tumor/normal cell line pairs (HCC1395, H1437, H2009, HCC1937, HCC1954, Hs578T). We sequenced all cell lines with Illumina, ONT, and PacBio HiFi. We then established a set of high-confidence calls supported by multiple technologies and tools. Severus consistently had the highest F1 scores compared to the HiFi, ONT, and Illumina methods against this high-confidence SV call set. We then extend our analysis to complex SVs. Severus accurately detected complex events, i.e., chromothripsis and chromoplexy, and templated insertion cycles/chains (TIC), reported for these cell lines. We then compared Severus’ performance with Jabba and Linx, two widely used tools for complex SV calling in short-read sequencing. Our comparison revealed that Severus showed higher agreement with Linx, while Jabba failed to detect most of the SV clusters identified by both Severus and Linx. Severus also outperformed the other tools in characterizing complex reciprocal translocations and TICs. Most of the junctions in complex SVs called by either of the tools but not Severus were either simple SVs with a single long-read junction or were not present in long-read sequencing. In contrast, Severus effectively resolved overlapping SVs by utilizing long-read connectivity, allowing for more accurate clustering of smaller genomic segments. We have also applied Severus to seventeen pediatric leukemia cases. Severus identified two chromoplexy and two cryptic translocations, which were missed by FISH and karyotype panels and were incomplete in Illumina SV calls, further validated by RNA-seq. This highlights the potential of the long-read whole genome sequencing approach for diagnosing complex cases driven by SVs. Ayse Keskus, Asher Bryant, Tanveer Ahmad, Anton Goretsky, Byunggil Yoo, Sergey Aganezov, Ataberk Donmez, Lisa A. Lansdon, Isabel Rodriguez, Jimin Park, Yuelin Liu, Xiwen Cui, Joshua Gardner, Brandy McNulty, Samuel Sacco, Jyoti Shetty, Yongmei Zhao, Bao Tran, Giuseppe Narzisi, Adrienne Helland, Daniel Cook, Pi-Chuan Chang, Alexey Kolesnikov, Andrew Carroll, Erin Molloy, Chengpeng Bi, Adam Walter, Margaret Gibson, Irina Pushel, Erin Guest, Tomi Pastinen, Kishwar Shafin, Karen Miga, Salem Malikic, Chi-Ping Day, Nicolas Robine, Cenk Sahinalp, Michael Dean, Midhat S. Farooqi, Benedict Paten, Mikhail Kolmogorov. Severus: A tool for detecting and characterizing complex structural variants in cancer using long-read sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2848.

Melanoma is the most serious form of skin cancer, developed by the malignant evolution of melanocytes. Malignant melanoma incidence is increasing faster than most other cancers. While stage zero melanoma is highly treatable, survivability dramatically decreases in its advanced stages. Melanoma has shown to be one of the most heterogeneous cancers from RNA and exome analyses by The Cancer Genome Atlas and other groups. A better understanding of the key genomic and epigenomic events that characterize the diverse subclonal populations in melanoma may reveal key insights into what drives its progression and therapeutic resistance. In this study, we leveraged Nanopore long-read sequencing to study the evolution of the mouse B2905 melanoma cell line. Twenty-four distinct clonal sublines were derived in vitro from single cells of the cell line, and the genetically homogeneous population from each subline was sequenced using PromethION R10 flow cells. Enabled by long reads to perform haplotype phasing and accurate structural variation detection, our goal is to integrate small and structural variants to better our understanding of melanoma evolution, and build upon prior analyses of short-read sequenced sublines. We employed multiple SNV calling approaches, including DeepVariant and Clair, in order to provide highly accurate variants for phylogeny reconstruction using Trisicell. We performed structural variant calling with our cancer somatic structural variant (SV) caller Severus as well as copy-number alteration (CNA) analysis with our method Wakhan. Lastly, we placed SNVs, SVs, and CNAs on our reconstructed phylogeny to examine the progression of different types of variants during subline evolution. We identified approximately 560k unique SNVs and around 2, 400 unique SVs. The majority of SNVs (19%) are either clonal or private (73%); however, a meaningful fraction of subclonal variants were available for phylogenetic tree reconstruction. SVs are distributed across the phylogenetic tree branches similarly to SNVs. We identified loss of heterozygosity (LOH) events throughout the subline evolution as well as subclonal CNAs resulting from chromosomal translocations. We find clonal and subclonal evidence of densely clustered SNVs and SV, resembling kataegis; however, our analysis of mutational signatures did not reveal APOBEC-mediated mutations. By analyzing mutational signatures within individual branches of the phylogenetic tree, we observed relative timing of different mutational processes, such as early clonal signatures of UV damage. By incorporating structural variations, copy number changes, and small variant data in the phylogenetic reconstruction, our analysis offers a better characterization of the genetic landscape of subclonal evolution in melanoma. Anton Goretsky, Yuelin Liu, Ayse Keskus, Tanveer Ahmad, Salem Malikic, Glenn Merlino, Chi-Ping Day, Erin Molloy, S. Cenk Sahinalp, Mikhail Kolmogorov. Nanopore sequencing of single-cell derived sublines provides insights into melanoma heterogeneity and evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7497.