Search Results (809)

Microscopy is a fundamental tool in biological research. However, conventional microscopes require manual operation and depend on user and equipment availability, limiting their suitability for continuous observation. Moreover, their size and complexity make them impractical for in situ experimentation. In this work, we present a novel, compact, affordable, and portable microscope that enables continuous in situ monitoring by being placed directly on biological samples. This chip-sized lensless holographic microscope (CLHM) is specifically designed to overcome the limitations of traditional microscopy. The device consists solely of an ultra-compact, state-of-the-art micro-LED display and a CMOS sensor, all enclosed within a 3D-printed housing. This unique light source enables a size that is markedly smaller than any comparable technology, allowing a resolution of 2.19 μm within a 7 mm distance between the light source and the camera. This paper demonstrates the CLHM’s versatility by monitoring in vitro models and performing whole-organism morphological analyses of small specimens. These experiments underscore its potential as an on-platform sensing device for continuous, in situ biological monitoring across diverse models. Full article

Background: Major geopolitical events and structural shocks are thought to play a significant role in shaping HIV epidemics by influencing individual behaviours, reshaping social networks, and impacting HIV prevention and treatment programs. Here, we describe individual-level measures of estimated time since HIV infection (ETI) from viral next-generation sequencing data among female sex workers and their clients in relation to significant geopolitical events in Ukraine. Methods: The Dynamics Study is a cross-sectional integrated biological and behavioural survey conducted among female sex workers and their clients in Dnipro, Ukraine (December 2017 to March 2018). We were able to successfully sequence a portion of the HIV pol gene on dried blood spot specimens among n = 5/9 clients and n = 5/16 female sex workers who tested positive for HIV (total n = 10/25) using an in-house drug resistance genotyping assay. The “HIV EVO” Intrapatient HIV Evolution web-based tool was used to infer ETI from viral diversity. Results: The median ETIs for female sex workers and their clients were 5.4 years (IQR = 2.9, 6.6) and 6.5 years (IQR = 5.4, 10.8), respectively. Nearly all HIV acquisition events (n = 7/10; 70%) were estimated to have occurred between the Great Recession (2008–2009) and the War in Donbas (May 2014–February 2022). In general, ETI suggests that HIV acquisition occurred earlier among clients (2012 [IQR = 2007, 2013]) compared to sex workers (2013 [IQR = 2012, 2016]). Conclusion: Our findings suggest that most HIV acquisition in this small subset of female sex workers and clients living with HIV occurred during periods of economic decline. Molecular studies on timing of HIV acquisition against timing of major geopolitical events offer a novel way to contextualize how such events may shape transmission patterns. Full article

Stone cleaning for cultural heritage monuments is a critical conservation intervention that must effectively eliminate harmful surface contaminants while preserving the material’s physical, chemical, and historical integrity. This study investigated the removal of tenacious black biofilms formed by Nocardia species previously isolated from deteriorated limestone from the Bastet tomb in Tell Basta, Zagazig City, Egypt, using a Q-switched 1064 nm Nd:YAG laser. Experimental limestone specimens were systematically inoculated with Nocardia sp. under controlled laboratory conditions to simulate biodeterioration processes. Comprehensive testing revealed that a laser fluence of 0.03 J/cm² with a 5 ns pulse duration, applied under wet conditions with 500 pulses, achieved the complete elimination of the biological black film without damaging the underlying stone substrate. The cleaning efficacy was evaluated through an integrated analytical framework combining stereomicroscopy, scanning electron microscopy coupled with energy-dispersive X-ray analysis (SEM-EDX), X-ray diffraction (XRD), and laser-induced plasma spectroscopy (LIPS). These analyses demonstrated a remarkable transformation from a compromised mineralogical composition dominated by gypsum (62%) and anhydrite (13%) to a restored state of 98% calcite, confirming the laser treatment’s effectiveness in reversing biodeterioration processes. SEM micrographs revealed the complete elimination of mycelial networks that had penetrated to depths between 984 μm and 1.66 mm, while LIPS analysis confirmed the restoration of elemental signatures to near-control levels. The successful application of LIPS for real-time monitoring during cleaning provides a valuable tool for preventing overcleaning, addressing a significant concern in laser conservation interventions. This research establishes evidence-based protocols for the non-invasive removal of Nocardia-induced black biofilms from limestone artifacts, offering conservation professionals a precise, effective, and environmentally sustainable alternative to traditional chemical treatments for preserving irreplaceable cultural heritage. Full article

Despite significant advancements, prosthetic hernia repair continues to face unacceptably high complication rates. These likely stem from poor biological responses, such as stiff scar tissue leading to mesh shrinkage. To overcome these issues, the Stenting and Shielding (S&S) Hernia System, a newly designed 3D dynamic device, has been developed for dissection-free laparoscopic placement to permanently obliterate hernia defects. Unlike conventional meshes, this device induces a regenerative biological response, promoting viable tissue growth rather than fibrotic plaque formation. In a porcine experimental model, the S&S device demonstrated the development of a great amount of muscle fibers, alongside nervous and vascular structures, within well-perfused connective tissue. Histological analysis of biopsy specimens excised from the experimental animals revealed progressive muscle fiber maturation from early myocyte development in the short term to fully developed muscle bundles in the long term. The enhanced biological response observed with the S&S device suggests a promising shift in hernia repair, potentially reversing the degenerative processes of hernia formation and promoting tissue regeneration. The S&S Hernia System described here can be classified not merely as a conventional hernia implant, but as part of a new category of hernia devices: the dynamic regenerative scaffold. Full article

This study conducted a multi-directional evaluation of the chemical potential and biological properties of selected European fungal species of the genus Phellinus. We investigated 30 samples belonging to 22 Phellinus species. Fruiting bodies were collected, among other specimens, in the Białowieża Forest (Poland); Village Kozhle (North Macedonia); Estremadura, Sesimbra, and Lagoa de Albufeira (Portugal); Zlatari close to Prishtina (Kosovo); and Spoleto and the Bosco Siro Negri State Nature Reserve (Italy). Morphological identification of the collected fungi was carried out, and genetic tests were performed to confirm the identity of the collected specimens. Methanol extracts for biological activity tests were prepared. Screening of antimicrobial activity of 30 methanolic extracts was performed on strains of bacteria (Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, and Kocuria rhizophila) and fungi (Candida albicans). Antioxidant activity tests (DPPH and ABTS) were also performed. The three most biologically active fungi species were selected (Phellinus igniarius, Fomitiporia robusta, and Porodaedalea pini) for further research. The chemical composition of the extracts was determined using GC-MS analysis. Thermal decomposition studies and spectroscopic analysis of the dry fruiting bodies were performed. The extracts were tested for their antimicrobial activity against antibiotic-resistant bacteria. Cytotoxic activity was also tested. Full article

A wide range of microorganisms, including endophytes, frequently interact with forest trees. The role of endophytes in industrial conifers has not been fully investigated. The Yezo spruce Picea jezoensis is widely used for logging in Russia and Japan. In this work, the endophytic communities of bacteria and fungi in healthy needles, branches, and fresh wood of P. jezoensis from Primorsky Territory were analyzed using metagenomic analysis. The results indicate that the diversity of endophytic communities in P. jezoensis is predominantly influenced by the specific tree parts (for both bacteria and fungi) and by different tree specimens (for fungi). The most abundant bacterial classes were Alphaproteobacteria, Gammaproteobacteria and Actinobacteria. Functional analysis of KEGG orthologs (KOs) in endophytic bacterial community using PICRUSt2 and the PLaBAse PGPT ontology revealed that 59.5% of the 8653 KOs were associated with plant growth-promoting traits (PGPTs), mainly, colonization, stress protection, bio-fertilization, bio-remediation, vitamin production, and competition. Metagenomic analysis identified a high abundance of the genera Pseudomonas and Methylobacterium-Methylorubrum in P. jezoensis, which are known for their potential growth-promoting activity in other coniferous species. The dominant fungal classes in P. jezoensis were Dothideomycetes, Sordariomycetes, and Eurotiomycetes. Notably, the genus Penicillium showed a pronounced increase in relative abundance within the fresh wood and needles of Yezo spruce, while Aspergillus displayed elevated abundance specifically in the fresh wood. It is known that some of these fungi exhibit antagonistic activity against phytopathogenic fungi. Thus, our study describes endophytic communities of the Yezo spruce and provides a basis for the production of biologicals with potential applications in forestry and agriculture. Full article

Accurate identification of microplastic polymers in marine environments is essential for tracing pollution sources, understanding ecological impacts, and guiding mitigation strategies. This study presents a comprehensive, explainable-AI framework that uses Raman spectroscopy to classify pristine and weathered microplastics versus biological materials. Using a curated spectral library of 78 polymer specimens—including pristine, weathered, and biological materials—we benchmark seven supervised machine learning models (Decision Trees, Random Forest, k-Nearest Neighbours, Neural Networks, LightGBM, XGBoost and Support Vector Machines) without and with Principal Component Analysis for binary classification. Although k-Nearest Neighbours and Support Vector Machines achieved the highest single metric accuracy (82.5%), k NN also recorded the highest recall both with and without PCA, thereby offering the most balanced overall performance. To enhance interpretability, we employed SHapley Additive exPlanations, which revealed chemically meaningful spectral regions (notably near 700 cm⁻¹ and 1080 cm⁻¹) as critical to model predictions. Notably, models trained without Principal Component Analysis provided clearer feature attributions, suggesting improved interpretability in raw spectral space. This pipeline surpasses traditional spectral matching techniques and also delivers transparent insights into classification logic. Our findings can support scalable, real-time deployment of AI-based tools for oceanic microplastic monitoring and environmental policy development. Full article

Seed amplification assays (SAA) targeting misfolded α-synuclein have emerged as powerful tools for the diagnosis and study of synucleinopathies, including Parkinson’s disease (PD), dementia with Lewy bodies, and multipßle system atrophy. These assays exploit the prion-like seeding properties of pathological α-synuclein to detect minute amounts of misfolded protein in biological specimens. the PubMed database was searched according to our study criteria, and 55 clinical studies comprised the final literature review. the majority of studies have focused on patients at various stages of PD, with cerebrospinal fluid (CSF) being the most commonly investigated biological specimen. Diagnostic utility was most pronounced in the CSF of PD patients, whereas results from other biological samples and across different synucleinopathies have been more modest. α-syn SAA demonstrate significant diagnostic potential in synucleinopathies. Additional applications may include monitoring disease progression. Future studies should explore the utility of α-syn SAA in alternative biological specimens, assess its performance across various synucleinopathies and other neurodegenerative diseases, and determine its comparative diagnostic value. Full article

Background: Upper tract urothelial carcinoma (UTUC) is a rare and aggressive malignancy with limited prognostic tools to predict disease progression. Due to its low incidence, the molecular pathogenesis of UTUC remains poorly understood, and few studies have explored transcriptomic profiling in this setting. Identifying gene expression biomarkers associated with progression may help improve risk stratification and guide postoperative management. Methods: In this study, we applied a machine learning approach to gene expression data from radical nephroureterectomy (RNU) specimens of 17 consecutive patients with pT2 or pT3 UTUC treated at our institution. RNA was extracted from formalin-fixed paraffin-embedded tissues and sequenced using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit on an Illumina HiSeq 2500 platform. Differential gene expression was assessed using DESeq2, and results were visualized with volcano plots. Predictive power was evaluated through logistic regression and receiver operating characteristic (ROC) analysis. Gene Ontology enrichment analysis was used to explore biological pathways. Results: A total of 76 genes were differentially expressed between progressive and non-progressive patients. A random forest classifier identified ten key genes with prognostic potential. Validation with logistic regression yielded an area under the ROC curve (AUC) of 0.88, indicating high discriminative ability. These genes were associated with immune regulation, cell cycle control, and tumor progression. Conclusions: This pilot study demonstrates the potential of integrating machine learning with transcriptomic analysis to identify prognostic biomarkers in UTUC. Further validation in larger, independent cohorts is needed to confirm these findings and support their clinical application. Full article

The two closely related Oriental species of the genus Rhynocoris, R. costalis (Stål, 1867) and R. fuscipes (Fabricius, 1787), exhibit remarkable morphological similarity, particularly in their overall red and black body coloration, including the head, thorax, and abdomen. Based on the examination of type specimens and non-type material collected from various localities of southern China, we found these two congeners were misidentified in many previous publications. Due to the restricted distribution and limited population size of R. fuscipes in China, most taxonomic, biological, and biocontrol studies conducted under the name Harpactor fuscipes or Rhynocoris fuscipes should be instead attributed to R. costalis. To address this confusion regarding these two species, the present study clarifies the taxonomic status of the two controversial species—R. costalis and R. fuscipes. Additionally, a new species, Rhynocoris minutus Liu, Zhao & Cai sp. nov., collected from southwestern China, is described and illustrated. A key to the 13 species in Rhynocoris currently recorded in China is provided. Full article

Background/Objectives: In recent years, lipids have emerged as critical regulators of different disease processes, being involved in cancer pathogenesis, progression, and outcome. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) has significantly expanded the technology’s reach, enabling spatially resolved profiling of lipids directly from tissue, including formalin-fixed paraffin-embedded (FFPE) specimens. In this context, MALDI matrix selection is crucial for lipid extraction and ionization, influencing key aspects such as molecular coverage and sensitivity, especially in such specimens with already depleted lipid content. Thus, in this work, we aim to explore the feasibility of mapping lipid species in FFPE clinical samples with MALDI-MSI using 6-aza-2-thiothymine (ATT) as a matrix of choice. Methods: To do so, ATT performances were first compared to those two other matrices commonly used for lipidomic analyses, 2′,5′-dihydroxybenzoic acid (DHB) and Norharmane (NOR), on lipid standards. Results: As a proof-of-concept, we then assessed ATT’s performance for the MALDI-MSI analysis of lipids in FFPE brain sections, both in positive and negative ion modes, comparing results with those obtained from other commonly used dual-polarity matrices. In this context, ATT enabled the putative annotation of 98 lipids while maintaining a well-balanced detection of glycerophospholipids (60.2%) and sphingolipids (32.7%) in positive ion mode. It outperformed both DHB and NOR in the identification of glycolipids (3%) and fatty acids (4%). Additionally, ATT exceeded DHB in terms of total lipid count (62 vs. 21) and class diversity and demonstrated performance comparable to NOR in negative ion mode. Moreover, ATT was applied to a FFPE glioblastoma tissue microarray (TMA) evaluating the ability of this matrix to reveal biologically relevant lipid features capable of distinguishing normal brain tissue from glioblastoma regions. Conclusions: Altogether, the results presented in this work suggest that ATT is a suitable matrix for pathology imaging applications, even at higher lateral resolutions of 20 μm, not only for proteomic but also for lipidomic analysis. This could enable the use of the same matrix type for the analysis of both lipids and peptides on the same tissue section, offering a unique strategic advantage for multi-omics studies, while also supporting acquisition in both positive and negative ionization modes. Full article

This study presents an integrated approach combining molecular, phytochemical, and biological analyses to characterize a newly discovered Zizania specimen from the northern Nile Delta, Egypt. Genetic fingerprinting using RAPD and ISSR markers revealed 85% band-sharing similarity with Zizania texana (Z. texana), though distinct morphological and genetic traits suggested potential intraspecific variation. Phytochemical profiling identified high concentrations of bioactive compounds, including quercetin (42.1 µg/mL), β-caryophyllene (11.21%), and gallic acid (23.4 µg/mL), which are pertinent and correlated with robust biological activities. The ethanolic leaf extract exhibited significant antioxidant capacity (IC₅₀ = 38.6 µg/mL in DPPH assay), potent antimicrobial effects against Candida albicans (C. albicans) (IC₅₀ = 4.9 ± 0.6 µg/mL), and dose-dependent cytotoxicity against cancer cell lines. MCF-7 has the lowest IC₅₀ (28.3 ± 1.5 µg/mL), indicating the highest potency among the tested cell lines. In contrast, HepG2 demonstrates moderate sensitivity (IC₅₀ = 31.4 ± 1.8 µg/mL), while A549 shows the highest IC₅₀ value (36.9 ± 2.0 µg/mL), indicating greater resistance. These findings underscore the taxonomic novelty of the specimen and its potential as a source of natural antioxidants, antimicrobials, and anticancer agents. The study highlights the importance of interdisciplinary approaches in resolving taxonomic uncertainties and unlocking the medicinal value of understudied aquatic plants. Full article

Background: The Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) was a 3-year, multicenter, randomized controlled trial to test the effects of the MIND diet on cognitive decline in 604 individuals at risk for Alzheimer’s dementia. Here, we describe the genotyping, imputation, and quality control (QC) procedures for the genetic data of trial participants. Methods: DNA was extracted from either whole blood or serum, and genotyping was performed using the Infinium Global Diversity Array. Established sample and SNP QC procedures were applied to the genotyping data, followed by imputation using the 1000 Genomes Phase 3 v5 reference panel. Results: Significant study-site, specimen type, and batch effects were observed. A total of 494 individuals of inferred European ancestry and 58 individuals of inferred African ancestry were included in the final imputed dataset. Evaluation of the imputed APOE genotype against gold-standard sequencing data showed high concordance (98.2%). We replicated several known genetic associations identified from previous genome-wide association studies, including SNPs previously linked to adiponectin (rs16861209, p = 1.5 × 10⁻⁵), alpha-linolenic acid (rs174547, p = 1.3 × 10⁻⁷), and alpha-tocopherol (rs964184, p = 0.003). Conclusions: This dataset represents the first genetic resource derived from a dietary intervention trial focused on cognitive outcomes. It enables investigation of genetic contributions to variability in cognitive response to the MIND diet and supports integrative analyses with other omics data types to elucidate the biological mechanisms underlying cognitive decline. These efforts may ultimately inform precision nutrition strategies to promote cognitive health. Full article

Autumn fern, Dryopteris erythrosora, is the most marketed temperate fern in the world. The rapid increase and spread of this recently naturalized fern in North America was determined and mapped using 76 herbarium specimen records and 2553 Research Grade iNaturalist posts. In 2008, it was recorded in two states, but by 2025, it was found in 25 states in the eastern United States and Ontario, Canada. At the end of 2017, there had been only 23 iNaturalist posts, but this grew to 511 by the end of 2020 and 2553 by May 2025. The great increase in the number of iNaturalist posts is thought to be due to the real geographic spread and an actual increase in the abundance of the fern, as well as recognition of the fern by iNaturalists, and the increase in the number of iNaturalists. The spread and great increase are probably related to the high level of marketing, which introduces plants to the environment, and to biological characteristics of the fern, including apogamy and polyploidy, and possibly natural enemy release, which allows it to flourish in new environments and to displace native plants. This novel study demonstrated citizen science’s (iNaturalist’s) great value in detecting the naturalization and spread of alien plants. Full article

To address the growing demand for sustainable materials in advanced manufacturing, the objective of this study was to develop and characterize a novel 3D-printable biocomposite using ruminant-digested corn stover (DCS) as a reinforcement for polylactic acid (PLA). The methodology involved systematically optimizing DCS particle size (80–140 mesh) and loading concentration (5–20 wt.%), followed by fabricating composite filaments via melt extrusion and 3D printing test specimens. The resulting materials were comprehensively characterized for their morphological, physical, and mechanical properties. The optimal formulation, achieved with 120-mesh particles at 15 wt.% loading, exhibited a 15.6% increase in tensile strength to 64.17 MPa and a 21.1% enhancement in flexural modulus to 4.19 GPa compared to neat PLA. In addition to the mechanical improvements, the biocomposite offers an advantageous density reduction, enabling the fabrication of lightweight structures for resource-efficient applications. Comprehensive characterization revealed effective interfacial integration and uniform fiber dispersion, validating biological preprocessing as a viable method for unlocking the reinforcement potential of this abundant biomass. While the composite exhibits characteristic trade-offs, such as reduced impact strength, the overall performance profile makes it a promising candidate for structural applications in sustainable manufacturing. This research establishes a viable pathway for agricultural waste valorization, demonstrating that biological preprocessing can convert agricultural residues into value-added engineering materials for the circular bioeconomy. Full article