Tools for post-operative localization of deep brain stimulation (DBS) electrodes may be of major benefit in the evaluation of the stimulation area. However, little is known about their precision. This study compares 3 different software packages used for DBS electrode localization. T1-weighted MRI images before and after the implantation of the electrodes into the subthalamic nucleus for DBS in 105 Parkinson's disease patients were processed using the pipelines implemented in Lead-DBS, SureTune4, and Brainlab. Euclidean distance between active contacts determined by individual software packages and in repeated processing by the same and by a different operator was calculated. Furthermore, Dice coefficient for overlap of volume of tissue activated (VTA) was determined for Lead-DBS. Medians of Euclidean distances between estimated active contact locations in inter-software package comparison ranged between 1.5 mm and 2 mm. Euclidean distances in within-software package intra- and inter-rater assessments were 0.6-1 mm and 1-1.7 mm, respectively. Median intra- and inter-rater Dice coefficients for VTAs were 0.78 and 0.75, respectively. Since the median distances are close to the size of the target nucleus, any clinical use should be preceded by careful review of the outputs.
- MeSH
- Deep Brain Stimulation * methods instrumentation MeSH
- Electrodes, Implanted * MeSH
- Middle Aged MeSH
- Humans MeSH
- Magnetic Resonance Imaging MeSH
- Subthalamic Nucleus surgery MeSH
- Parkinson Disease * therapy MeSH
- Aged MeSH
- Software MeSH
- Check Tag
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
Mixed reality technology and three-dimensional (3D) printing are becoming more and morecommon in the field of medicine. During the COVID-19 pandemic and immediately after the restrictions had beeneased, many innovations were implemented in the teaching of future doctors. There was also interest in immersive techniques and 3D printing technology in anatomy teaching. However, these are not common implementations. In 2023, 3D prints and holograms in mixed reality technology were prepared for classes focused on the structure of the heart. They were used to teach students, who, with the support of engineers, could learn about the detailed structure of the heart and familiarize themselves with the new technologies that support the traditional model of learning on human cadavers. Students findthis possibility to be highly valuable. The article presents the process of preparing materials for classes and further implementation possibilities. The authors see an opportunity for the development of the presented technologies in students'teaching at various levels of education and the justification for increasingly widespread implementation.
- MeSH
- Printing, Three-Dimensional * MeSH
- Anatomy * education MeSH
- Augmented Reality * MeSH
- COVID-19 MeSH
- Humans MeSH
- Heart * anatomy & histology MeSH
- Teaching MeSH
- Check Tag
- Humans MeSH
- Publication type
- Video-Audio Media MeSH
- Journal Article MeSH
Pulmonary artery banding is a surgical procedure performed when there is a shunt between the left and right ventricle. Its aim is to constrict the lumen of the pulmonary artery by using a band to reduce blood flow to the lungs. In this study, we report the results of investigating the mechanical properties of a composite composed of poly(L-lactide-co-ε-caprolactone) layers and a collagen matrix (PLCL-COLL). PLCL layers were obtained by electrospinning, impregnated with collagen solution, and finally cross-linked to increase the stiffness of the material. Bands of PLCL-COLL were implanted into a rat peritoneum and explanted after 1, 3, and 6 months in vivo. The mechanical properties of the material before and after implantation were determined using uniaxial tensile tests. The same was done with samples of strips prepared from GORE-TEX material. By comparing the results of tensile tests before implantation and after explantation, it was found that PLCL-COLL degrades in the rat's body and that it exhibits a mechanical response showing of elastic modulus values that correspond well to arterial biomechanics (elastic modulus measured in the initial linear region of the deformation was found to be: 4.14 MPa ± 1.11 MPa, 2.34 MPa ± 1.02 MPa, 1.11 MPa ± 0.77 MPa, and 0.88 MPa ± 0.60 MPa before implantation, and 1, 3, and 6 months after implantation respectively). Similar to the elastic modulus, the strength of the PLCL-COLL composite decreased during in vivo exposure (1.32 ± 0.32 MPa, 0.60 ± 0.26 MPa, 0.44 ± 0.11 MPa, and 0.46 ± 0.28 MPa before implantation, and 1, 3, and 6 months after implantation respectively). In our experiments, PLCL-COLL material was always more compliant than GORE-TEX (elastic modulus 34.7 MPa ± 2.06 MPa before implantation, and 9.35 MPa ± 6.80 MPa after implantation). The results suggest that PLCL-COLL could be a suitable candidate for the development of artery banding tapes, and also for further use in cardiovascular surgery.
- MeSH
- Pulmonary Artery * surgery MeSH
- Biocompatible Materials chemistry MeSH
- Biomechanical Phenomena MeSH
- Collagen * chemistry metabolism MeSH
- Rats MeSH
- Mechanical Phenomena * MeSH
- Peritoneum * surgery MeSH
- Tensile Strength MeSH
- Polyesters * chemistry metabolism MeSH
- Materials Testing MeSH
- Animals MeSH
- Check Tag
- Rats MeSH
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
Perflorochemicals (PFCs), among which are the most commonly detected perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), are persistent emergent contaminants of concern in recent times. These compounds have been reported for their cytotoxicity, genotoxicity, carcinogenicity, immunotoxicity, and developmental toxicities. Meanwhile, they have been detected in diverse matrices such as soil, sediment, and, surprisingly, in serum and even breastmilk. Worrisomely, these compounds are detected in drinking water across the globe, aquaculture water, and other surface waters. Thus, it was important to appraise the studies conducted on PFOS and PFOA to provide an overview of the environmental status of contamination regarding them. The present review article sought to provide insights into the occurrence patterns and ecotoxic effects of both pollutants in the water ecosystems within five continents of the world. Based on the information gathered in this article, the ∑PFOS concentration (ng/L) within the five continents is in the order Europe > Asia > Africa > North America > South America, while the ∑PFOA level (ng/L) is in the order Europe > Asia > South America > Africa > North America. The study also investigated the previous works that have been conducted regarding the diverse elimination technologies employed for the removal of these pollutants from the aqueous environments, with plasma combined with surfactant process being the most efficient. Generally, studies on PFOS/PFOA are still scanty when compared to those on pharmaceuticals and personal care products (PPCPs), especially in North America. The information gathered in this study could be useful in establishing thresholds of PFOA and PFOS environmental levels and be adopted by appropriate authorities as safety guidelines.
- Publication type
- Journal Article MeSH
- Review MeSH
BACKGROUND AND OBJECTIVE: Metabolomic interaction networks provide critical insights into the dynamic relationships between metabolites and their regulatory mechanisms. This study introduces MInfer, a novel computational framework that integrates outputs from MetaboAnalyst, a widely used metabolomic analysis tool, with Jacobian analysis to enhance the derivation and interpretation of these networks. METHODS: MInfer combines the comprehensive data processing capabilities of MetaboAnalyst with the mathematical modeling power of Jacobian analysis. This framework was applied to various metabolomic datasets, employing advanced statistical tests to construct interaction networks and identify key metabolic pathways. RESULTS: The application of MInfer revealed significant metabolic pathways and potential regulatory mechanisms across multiple datasets. The framework demonstrated high precision, sensitivity, and specificity in identifying interactions, enabling robust network interpretations. CONCLUSIONS: MInfer enhances the interpretation of metabolomic data by providing detailed interaction networks and uncovering key regulatory insights. This tool holds significant potential for advancing the study of complex biological systems.
- MeSH
- Algorithms MeSH
- Humans MeSH
- Metabolic Networks and Pathways * MeSH
- Metabolomics * MeSH
- Software MeSH
- Computational Biology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750×, uses 33× less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/.
The evaluation of large experimental datasets is a fundamental aspect of research in every scientific field. Streamlining this process can improve the reliability of results while making data analysis more efficient and faster to execute. In biomedical research it is often very important to determine the type of cell death after various treatments. Thus, differentiating between viable, apoptotic, and necrotic cells provide critical insights into the treatment efficacy, a key aspect in the field of drug development. Fluorescent microscopy is perceived as a widely used technique for cell metabolism assessment and can therefore be used to investigate treatment outcomes after staining samples with cell death detection kit. However, accurate evaluation of therapeutic results requires quantitative analysis, often necessitating extensive postprocessing of imaging data. In this study, we introduce a complementary tool designed as a macro for the Fiji platform, enabling the automated postprocessing of fluorescent microscopy images to accurately distinguish and quantify viable, apoptotic, and necrotic cells.
- MeSH
- Apoptosis MeSH
- Cell Death MeSH
- Microscopy, Fluorescence * methods MeSH
- Humans MeSH
- Necrosis MeSH
- Image Processing, Computer-Assisted * methods MeSH
- Software MeSH
- Cell Survival MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
The visual evaluation of data derived from screening and optimization experiments in the development of new analytical methods poses a considerable time investment and introduces the risk of subjectivity. This study presents a novel approach to processing such data, based on factor analysis of mixed data and hierarchical clustering - multivariate techniques implemented in the R programming language. The methodology is demonstrated in the early-stage screening and optimization of the chromatographic separation of 15 structurally diverse drugs that affect the central nervous system, using a custom R Language script. The presented explorative approach enabled the identification of key parameters affecting the separation and significantly reduced the time required to evaluate the comprehensive dataset from the screening experiments. Based on the data analysis results, the optimal combination of stationary phase and mobile phase composition was selected, considering retention, overall resolution, and peak shape of compounds. Additionally, compounds vulnerable to changes in selected chromatographic conditions were identified. As a complement to the presented R Language script, a web-based application ChromaFAMDeX has been developed to offer an intuitive interface that enhances the accessibility of the used statistical methods. Accompanying the publication, the R script and the link to the standalone application are provided, enabling replication and adaptation of the methodology.
- MeSH
- Chromatography, Liquid methods MeSH
- Multivariate Analysis MeSH
- Programming Languages * MeSH
- Cluster Analysis MeSH
- Software MeSH
- Publication type
- Journal Article MeSH
INTRODUCTION: Stem cells derived from adipose tissue are gaining popularity in the field of regenerative medicine due to their adaptability and clinical potential. Their rapid growth, ability to differentiate, and easy extraction with minimal complications make adipose-derived stem cells (ADSCs) a promising option for many treatments, particularly those targeting bone-related diseases. This study analyzed gene expression in canine ADSCs subjected to long-term culture and osteogenic differentiation. METHODS: ADSCs were isolated from discarded surgical waste and cultured for 14 days with and without differentiation media to assess osteogenic changes. RNA sequencing (RNA-seq) and bioinformatical analysis were performed to obtain comprehensive transcriptomic data. A total of 17793 genes were detected and GO enrichment analysis was performed on the differentially expressed genes to identify significantly up- and downregulated Biological Process (BP) GO terms across each comparison. RESULTS: The upregulation of apoptosis-regulating genes and genes related to circulatory system development suggest an induction of these processes, while the downregulation of neurogenesis and gliogenesis genes points to reciprocal regulation during osteogenic differentiation of canine ADSCs. DISCUSSION: These findings underscore the potential of ADSCs in bone regeneration and offer valuable insights for advancing tissue engineering, however further studies, including proteomic analyses, are needed to confirm these patterns and their biological significance.
- Publication type
- Journal Article MeSH
Fast Photochemical Oxidation of Proteins (FPOP) is a promising technique for studying protein structure and dynamics. The quality of insight provided by FPOP depends on the reliability of the determination of the modification site. This study investigates the performance of two search engines, Mascot and PEAKS, for the data processing of FPOP analyses. Comparison of Mascot and PEAKS of the hemoglobin--haptoglobin Bruker timsTOF data set (PXD021621) revealed greater consistency in the Mascot identification of modified peptides, with around 26% of the IDs being mutual for all three replicates, compared to approximately 22% for PEAKS. The intersection between Mascot and PEAKS results revealed a limited number (31%) of shared modified peptides. Principal Component Analysis (PCA) using the peptide-spectrum match (PSM) score, site probability, and peptide intensity was applied to evaluate the results, and the analyses revealed distinct clusters of modified peptides. Mascot showed the ability to assess confident site determination, even with lower PSM scores. However, high PSM scores from PEAKS did not guarantee a reliable determination of the modification site. Fragmentation coverage of the modification position played a crucial role in Mascot assignments, while the AScore localizations from PEAKS often become ambiguous because the software employs MS/MS merging.
