Search Results (843)

A woman in her 40s with a history of ER/PR+, HER2-negative breast cancer presented with a seizure three years after mastectomy. Magnetic resonance imaging (MRI) revealed a right caudate head mass, which was concerning for either high-grade glioma or metastatic disease, but biopsy was deemed too high risk. Cerebrospinal fluid (CSF) tumor-derived DNA (tDNA) analysis by next-generation sequencing (NGS) was ordered, revealing a gain-of-function variant in PIK3CA, ERBB2 copy number gain, and high aneuploidy, findings consistent with breast cancer brain metastasis. Based on these results, the patient was treated with stereotactic radiosurgery (SRS) followed by trastuzumab deruxtecan, a HER2-targeted therapy. This case highlights the diagnostic and therapeutic value of CSF tDNA analysis in central nervous system (CNS) lesions when biopsy is not feasible. The report also illustrates how clonal evolution, such as acquired ERBB2 amplification, can occur in metastatic disease and influence treatment decisions. Full article

Bolivian hemorrhagic fever (BHF) is a zoonotic disease caused by Mammarenavirus machupoense (MACV) featuring severe neurological and hemorrhagic symptoms and a high mortality rate. BHF is usually diagnosed by serological tests or real-time polymerase chain reaction (RT-PCR); these methods are often inaccessible in endemic regions due to a lack of laboratory infrastructure, creating a demand for sensitive and rapid equipment-free alternatives. Here, we present an isothermal method for MACV nucleic acid detection based on the Cas12a-based DETECTR system combined with recombinase polymerase amplification (RPA) in a single tube: the RT-RPA/DETECTR assay. We demonstrate the possibility of using more than one primer set for the simultaneous detection of MACV genetic variants containing multiple point mutations. The method was optimized and tested using specially developed virus-like armored particles containing the target sequence. The multiplex RT-RPA/DETECTR method achieved a limit of detection of approximately 5 × 10⁴ copies/ mL (80 aM) of armored particles. The method was validated using clinical samples spiked with virus-like particles. The assay proved to be selective and reliable in detecting certain nucleotide substitutions simultaneously. Full article

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) nucleases enable precise genome editing, but off-target cleavage remains a critical challenge. Here, we report the development of MAD7_HF, a high-fidelity variant of the MAD7 nuclease engineered through a bacterial screening system leveraging the DNA gyrase-targeting toxic gene ccdB. This system couples survival to efficient on-target cleavage and minimal off-target activity, mimicking the transient action required for high-precision editing. Through iterative selection and sequencing validation, we identified MAD7_HF, harboring three substitutions (R187C, S350T, K1019N) that enhanced discrimination between on- and off-target sites. In Escherichia coli assays, MAD7_HF exhibited a >20-fold reduction in off-target cleavage across multiple mismatch contexts while maintaining on-target efficiency comparable to wild-type MAD7. Structural modeling revealed that these mutations stabilize the guide RNA-DNA hybrid at on-target sites and weaken interactions with mismatched sequences. This work establishes a high-throughput bacterial screening strategy that allows the identification of Cas12a variants with improved specificity at a given target site, providing a useful framework for future efforts to develop precision genome-editing tools. Full article

Introduction: Epidermal growth factor receptor (EGFR) alterations exist in 15–50% of non-small cell lung cancer (NSCLC) diagnoses. Although effective therapeutics have been developed in the form of tyrosine kinase inhibitors (TKI), various mechanisms of resistance lead to treatment failure after exposure to EGFR TKI-based therapy. Of these, histologic transformation (HT) into small cell lung cancer (SCLC) represents approximately 14% of cases. Methods: Within a single institution, we retrospectively reviewed longitudinal data from both tissue and liquid biopsies of patients with histologic transformation after a diagnosis of EGFR-mutant NSCLC. We sought to further characterize the baseline and emergent genomic alterations after HT to SCLC in the context of TKI exposure, along with germline alterations that may contribute to lineage plasticity and outcomes. Results: Fifteen patients were included in our analysis. Of these, EGFR exon 19 deletions were the most frequent (n = 11, 73.3%), followed by L858R (n = 3, 20%) and L861Q (n = 1, 6.7%). The median time for transformation was 17 months (95%CI, 8.9–41.9 months). The median OS of our cohort was 51.6 months (95%CI, 26.3—NE) with a median OS post-transformation of 13.4 months. Recurrent genomic alterations included TP53, Rb1, PIK3CA, and BRAF. Germline testing revealed a pathogenic alteration in FBN1, with a recurrent variant of unknown significance (VUS) in PALLD. Conclusion: Post-transformation somatic mutation testing and germline testing at presentation revealed unique mutational profiles not previously reported in the setting of HT to SCLC. Further investigations are required to determine the optimal treatment and sequencing following HT. Full article

Objective: Yttria-stabilized tetragonal zirconia polycrystal (Y-TZP), a variant of zirconia (ZrO₂), has attracted interest as a substitute for titanium in dental and orthopedic implants, valued for its biocompatibility and aesthetics that resemble natural teeth. However, its bioinert surface limits osseointegration, making surface modifications such as calcium phosphate (CaP) coatings highly relevant. Materials and methods: The review process adhered to the PRISMA guidelines. Electronic searches of PubMed, Scopus, Web of Science, Embase, and Cochrane Library (July 2025) identified studies evaluating CaP-coated zirconia implants. Eligible studies included in vitro, in vivo, and preclinical investigations with a control group. Data on coating type, deposition method, and biological outcomes were extracted and analyzed. Results: A total of 27 studies were analyzed, featuring different calcium phosphate (CaP) coatings including β-tricalcium phosphate (β-TCP), hydroxyapatite (HA), octacalcium phosphate (OCP), and various composites. These coatings were applied using diverse techniques such as RF magnetron sputtering, sol–gel processing, biomimetic methods, and laser-based approaches. In multiple investigations, calcium phosphate coatings enhanced osteoblast attachment, proliferation, alkaline phosphatase (ALP) expression, and bone-to-implant contact (BIC) relative to unmodified zirconia surfaces. Multifunctional coatings incorporating growth factors, antibiotics, or nanoparticles showed additional benefits. Conclusion: CaP coatings enhance the bioactivity of zirconia implants and represent a promising strategy to overcome their inertness. Further standardized approaches and long-term studies are essential to verify their translational relevance. Full article

The BEST1 gene encodes a transmembrane protein in the retinal pigment epithelium (RPE) in the eye, that functions as a calcium-dependent chloride channel (CaCC). Pathogenic variants in BEST1 are the underlying cause for bestrophinopathies, a group of inherited retinal disorders that vary in their pattern of inheritance, clinical appearance, and underlying molecular disease mechanisms. Currently, there are no treatments available for any of the bestrophinopathies, and gene therapy represents an attractive strategy due to the accessibility of the eye and slow disease progression. While gene augmentation may be effective for a subset of bestrophinopathies, others require allele-specific silencing or correction of the disease-causing variant to reconstitute expression of the BEST1 protein. This review aims to give an overview of the clinical diversity of bestrophinopathies and proposes the molecular disease mechanism of the pathogenic BEST1 variant as an important parameter for the choice of treatment strategy. Furthermore, we discuss the potential of different mutation-specific and mutation-independent CRISPR/Cas9-based gene editing strategies as a future treatment approach for bestrophinopathies. Full article

The CA125 epitope within the MUC16 tandem repeat region is detected via the CA125 II test for ovarian cancer surveillance. This test utilizes the M11 and OC125 antibodies. A revised model of MUC16 with 19 tandem repeats has recently been identified, including splice variants that exclude entire repeats. Additionally, OC125 has exhibited gaps in coverage of the tandem repeat region. To identify antibodies that bind more repeats and are suitable for spliceoform detection, more antibodies must be characterized using the revised model. This study characterized the binding of two M11-like and two OC125-like antibodies against the updated tandem repeat numbering system. 16 individual tandem repeats were expressed and purified. Binding interactions between each of the antibodies and recombinant repeats were examined by indirect enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR). The M11-like antibodies displayed different binding patterns when compared to each other, while the two OC125-like antibodies exhibited similar binding patterns. M11-like clone M77161 bound to all 16 repeats tested, indicating that it may be suitable for accurate detection of CA125. These findings demonstrate how different antibodies vary in their binding to CA125, contributing to ongoing development of improved clinical and research tools for ovarian cancer. Full article

Colorectal cancer (CRC) is driven by a complex spectrum of somatic mutations and structural variants that contribute to tumor heterogeneity and therapy resistance. In this study, we performed a comparative analysis of short-read Illumina and long-read Nanopore sequencing technologies across multiple CRC sample groups, encompassing diverse tissue morphologies. Our evaluation included general base-level metrics—such as nucleotide ratios, sequence match rates, and coverage—as well as variant calling performance, including variant allele frequency (VAF) distributions and pathogenic mutation detection rates. Focusing on clinically relevant genes (KRAS, BRAF, TP53, APC, PIK3CA, and others), we characterized platform-specific detection profiles and completed the ground truth validation of somatic KRAS and BRAF mutations. Structural variant (SV) analysis revealed Nanopore’s enhanced ability to resolve large and complex rearrangements, with consistently high precision across SV types, though recall varied by variant class and size. To enable direct comparison with the Illumina exome panel, we applied an exonic position reference file. To assess the impact of depth and PCR amplification, we completed an additional high-coverage Nanopore sequencing run. This analysis confirmed that PCR-free protocols preserve methylation signals more accurately, reinforcing Nanopore’s utility for integrated genomic and epigenomic profiling. Together, these findings underscore the complementary strengths of short- and long-read sequencing platforms in high-resolution cancer genomics, and we highlight the importance of coverage normalization, epigenetic fidelity, and rigorous benchmarking in variant discovery. Full article

Fat volume and obesity-related genes (e.g., the FTO gene) are important candidate genes affecting energy metabolism. Single nucleotide polymorphisms (SNPs) in the FTO gene are associated with carcass, growth and meat quality traits of pigs, cattle, sheep, rabbits and ducks. The purpose of this study was to detect the single nucleotide polymorphisms in the chicken FTO gene coding region by DNA sequencing and analyze its association with the carcass and growth traits of Heying black chickens. We detected polymorphisms in exons 5, 7, 8 and 9, respectively, g.57337C>A, g.64757T>G, g.97213G>A and g.220985G>A, which are synonymous mutations. g.57337C>A mutation site CA and AA genotype individuals were significantly higher than CC genotype individuals in live weights, head weights, breast muscle weights and leg muscle weights (p < 0.05), AA genotype individuals were significantly higher than CC genotype individuals in slaughter live weights and liver weights (p < 0.05) and CA and AA genotype individuals were significantly higher than CC genotype individuals in heart weights (p < 0.01). In terms of growth traits, the weights of individuals with genotype CA at 8 weeks were significantly higher than that of individuals with genotype CC (p < 0.05), and the weights of individuals with genotype AA and CA at 10 weeks and 16 weeks were significantly higher than that of individuals with genotype CC (p < 0.05). For the g.64757T > G mutation, individuals with the TT genotype exhibited significantly higher values (p < 0.05) than those with the TG genotype across multiple traits, including slaughter weight, live weight, eviscerated weight and semi-eviscerated weight. Individuals with GG genotypes were significantly higher than individuals with TG genotypes (p < 0.05) in slaughter weights and wing weights. In terms of growth traits, the 16-week-old body weight of individuals with TT genotype was significantly higher than that of individuals with TG genotype (p < 0.01). The GA genotype exhibited significantly higher slaughter weights in the g.97213G>A variant compared to the GG genotype (p < 0.01), and in live weights, eviscerated weights, semi-eviscerated weights, leg muscle weights and wing weights, GA genotype was significantly higher than in GG genotype (p < 0.05). In terms of growth traits, GA genotype was significantly higher in individuals 8 weeks old, 10 weeks old and 16 weeks old than GG genotype (p < 0.05). g.220985G>A was significantly higher in individuals with GG genotype than GA genotype (p < 0.05). In terms of growth traits, the weight of GG genotype was significantly higher than that of GA genotype (p < 0.05). The results showed that the FTO gene may be a candidate gene related to chicken growth and slaughter traits and lays a foundation for Heying black chicken assisted breeding. Full article

The purpose of this paper is to evaluate the nutritional, functional, and technological potential of whey resulting as a by-product in the dairy industry, as such or mixed with berries (blueberries, strawberries, and raspberries) to obtain healthy jellies with added value. In this regard, the following parameters were analyzed: protein content, total amino acids, total mineral substances, macro- and microelements, antioxidant capacity, and total polyphenols. Also, the storage stability, textural and color parameters, FTIR spectra, and microstructures of jellies were analyzed. The results obtained showed that the protein content ranged from 4.18% to 4.51%, with a general increase observed in the variants with added whey and berries. Regarding total mineral substances, a significant increase was noted in jellies with added whey (0.34%) and strawberries (0.35%), compared to the control (0.15%). Whey jellies presented the highest levels of K, Ca, Mg, Zn, and Fe, while samples with added fruits completed the microelement (Mn, Cu, Ni, and Cr) content. The storage stability at 4 °C and the evolution of pH and acidity confirm that the products maintain their structure, while when stored at ambient temperature an acceleration of the decrease in pH and an increase in acidity are observed after 14 days. The jellies with combined additions (whey and berries) presented the most favorable microstructure, which supports the use of synergistic functional ingredients in the development of innovative products with high nutritional and sensory value. The FTIR spectra reflect the composition of the ingredients used. Based on obtained results, it can be concluded that whey represents a versatile and sustainable resource for obtaining functional jellies, offering both nutritional benefits and favorable economic and ecological perspectives. Full article

Na⁺/Ca²⁺ exchangers (NCXs) are membrane transporters crucial for calcium homeostasis in excitable tissues, particularly in the central nervous system. Growing evidence indicates that NCX dysfunction contributes to calcium overload and neuronal damage in several neurological conditions. Thus, pharmacological modulation of NCX isoforms (NCX1, NCX2, and NCX3) has emerged as a potential therapeutic strategy for disorders such as stroke, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD), and Parkinson’s disease (PD). However, the identification of selective modulators directed at specific NCX isoforms, or even different splice variants, remains challenging and limits their clinical validation. This Review aims to provide an updated overview of small-molecule NCX modulators, described over the last two decades. Chemical structures, mechanisms of action, and isoform specificity are discussed, along with the most commonly used biological assays for their functional evaluation. Full article

Background: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive neoplasm often diagnosed at advanced stages. Immune checkpoint molecules, particularly programmed cell death protein-1 (PD-1) and its ligand PD-L1, are pivotal in tumor immune evasion. Genetic polymorphisms in PD-1/PD-L1 and their soluble isoforms (sPD-1/sPD-L1) may influence individual susceptibility to cancer and disease progression. Therefore, this study was conducted to examine the correlation between PD-1/PD-L1 gene polymorphisms, serum levels of sPD-1/sPD-L1, and their association with PDAC susceptibility, severity, and prognostication. Methods: This case–control study was performed with 150 PDAC patients and 150 controls. Clinical and laboratory data, including tumor markers (CA19-9 and CEA), were recorded. Allele-specific PCR was utilized to genotype PD-1 (rs6749527 and rs7421861) and PD-L1 (rs2297136, and rs4143815). sPD-1/sPD-L1 were quantified with ELISA. Mapping of the Kaplan–Meier survival curve of mutant genes was performed. Results: The rs7421861 AG and GG and rs4143815 GG genotypes, together with their G-alleles, were linked to increased PDAC risk and greater tumor burden. In contrast, the rs2297136 GG genotype and G-allele conferred protection against PDAC development. Serum sPD-L1 levels, rather than sPD-1, were markedly elevated in PDAC patients, progressively increased with tumor grade, and correlated with tumor markers. Also, higher PD-L1 gene expression was associated with lower overall survival. Conclusions: PD-1/PD-L1 genetic variants, particularly rs7421861 and rs4143815, along with sPD-L1 levels, correlate with PDAC susceptibility and disease severity. These findings endorse the prospects of integrating immune checkpoint genetic variants and soluble biomarkers for early identification, risk stratification, prognostication, and personalized therapeutic strategies in PDAC management. Full article

The exponential growth of AI applications has intensified the demand for efficient inference hardware capable of delivering low-latency, high-throughput, and energy-efficient performance. This study presents a systematic, empirical comparison of GPU- and NPU-based server platforms across key AI inference domains: text-to-text, text-to-image, multimodal understanding, and object detection. We configure representative models—LLama-family for text generation, Stable Diffusion variants for image synthesis, LLaVA-NeXT for multimodal tasks, and YOLO11 series for object detection—on a dual NVIDIA A100 GPU server and an eight-chip RBLN-CA12 NPU server. Performance metrics including latency, throughput, power consumption, and energy efficiency are measured under realistic workloads. Results demonstrate that NPUs match or exceed GPU throughput in many inference scenarios while consuming 35–70% less power. Moreover, optimization with the vLLM library on NPUs nearly doubles the tokens-per-second and yields a 92% increase in power efficiency. Our findings validate the potential of NPU-based inference architectures to reduce operational costs and energy footprints, offering a viable alternative to the prevailing GPU-dominated paradigm. Full article

Extensive research is underway on a variety of functional foods that support consumer health. A promising combination is milk (a drink with high nutritional value), fortified with spices (naturally rich in antioxidant compounds) and supplemented with low-calorie, health-promoting sweeteners. The aim was to analyze the antioxidant activity (AA), total polyphenol content (TPC), and mineral composition of milk beverages fortified with a mixture of spices and sweeteners and to verify the interactions between these ingredients. Twenty-four variants of milk drinks were prepared with the addition of three types of spice mixtures (1:1) of clove (Cl), cinnamon (Ci), and turmeric (Tu) with the shares of 2.5%, 5%, 7.5%, and 10%, and two types of sweeteners—erythritol (E) and stevia (S)—as well as six control samples, including three 10% aqueous solutions of spice mixtures. AA was measured using the ABTS, FRAP, and DPPH methods. TPC was determined using the Folin–Ciocalteu method. Mineral content (Ca, Mg, Fe, Cu, and Zn) was assessed using the FAAS/FAES method. The highest AA was demonstrated for beverages with Cl-Ci and Cl-Tu, whereas the highest TPC was found in those with Cl-Tu. AA and TPC values increased with the increase in the share of spices in the beverages, and both measurements were significantly higher in beverages with erythritol compared to those with stevia. Despite the 4–5 times lower TPC, 3–8 times higher AA was demonstrated in beverages with the addition of 10% spice mixtures than their corresponding control samples (aqueous solutions with the addition of 10% spice mixtures), which suggests the great role of interactions between nutrients in food. For beverages with 10% Cl-Ci/Cl-Tu mixtures, significantly higher ABTS, FRAP, and DPPH were observed than would result from the simple sum of AA of the components (synergistic effect). The opposite (antagonistic) effect was observed for beverages with Ci-Tu. AA was positively correlated with the content of Fe, Mg, and Cu; negatively with Ca; and not correlated with Zn. The results suggest that the most health-promoting properties are exhibited by the milk drink with the addition of 10% Cl-Tu and erythritol, demonstrating the highest AA and TPC, the strongest synergistic effect of the components, and the highest content of Mg and Zn. This study highlights the importance of carefully selecting and combining ingredients to maximize the antioxidant properties of functional beverages. However, further research is needed to expand knowledge on this issue. Full article

Background/Objectives: Tumor mutational burden (TMB) has emerged as a potential biomarker of response to immunotherapy across multiple solid tumors. However, its role in cervical cancer remains insufficiently defined. This study aimed to evaluate the genomic landscape and TMB profile in a cohort of patients with cervical cancer treated at a tertiary gynecologic oncology center, with a focus on TMB’s associations with clinical features, HPV infection, and treatment modalities. Methods: A total of 61 patients diagnosed with cervical cancer (82.0% ca. planoepitheliale, 18.0% adenocarcinoma) were retrospectively analyzed. Tumor samples were collected during primary surgery, biopsy, or conization and subjected to targeted next-generation sequencing using the ONCOaccuPanel™ and BRCAaccuTest PLUS™ (NGeneBio). TMB was calculated as non-synonymous mutations per megabase and analyzed using NGeneAnalySys^® software. Variant classification followed ACMG guidelines. Comparative analyses were conducted between TMB-high (≥10 mut/Mb) and TMB-low subgroups, and correlations with clinical and molecular variables were assessed using univariable statistics. Results: High TMB was identified in 36 patients (59.0%), while microsatellite instability was found in only 2 cases (3.3%). No significant associations were observed between TMB status and FIGO stage, histologic subtype, or HPV 16/18 infection. However, higher TMB values were observed in patients with nodal involvement, diabetes, and HPV52 infection. A diverse spectrum of mutations was detected, with PIK3CA and ARID1A being most frequently altered. Several variants of uncertain significance were identified in genes not classically associated with cervical cancer. Conclusions: TMB-high status is relatively frequent in cervical cancer and appears to be independent of FIGO stage or histological subtype. While not predictive of clinical stage, TMB correlates with specific molecular and comorbidity profiles, suggesting its potential relevance for future patient stratification in immunotherapy trials. Full article