Reversed-phase ultrahigh-performance liquid chromatography-mass spectrometry (RP-UHPLC/MS) method is optimized for the quantitation of a large number of lipid species in biological samples, primarily in human plasma and serum. The method uses a C18 bridged ethylene hybrid (BEH) column (150 × 2.1 mm; 1.7 μm) for the separation of lipids from 23 subclasses with a total run time of 25 min. Lipid species separation allows the resolution of isobaric and isomeric lipid forms. A triple quadrupole mass spectrometer is used for targeted lipidomic analysis using multiple reaction monitoring (MRM) in the positive ion mode. Data are evaluated by Skyline software, and the concentrations of analytes are determined using internal standards per each individual lipid class.

• Keywords
• High-throughput lipidomics, Mass spectrometry, Plasma, Quantitation, Reversed-phase, Serum, Ultrahigh-performance liquid chromatography,
• MeSH
• Chromatography, Reverse-Phase * methods   MeSH
• Mass Spectrometry methods   MeSH
• Liquid Chromatography-Mass Spectrometry MeSH
• Humans MeSH
• Lipidomics * methods   MeSH
• Lipids * analysis   MeSH
• High-Throughput Screening Assays methods   MeSH
• Software MeSH
• Tandem Mass Spectrometry methods   MeSH
• Chromatography, High Pressure Liquid methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Lipids * MeSH

The prevalence of dementia is increasing every year, with one person developing dementia every 3 s. Therefore, this study proposes a novel multi-sensory rehabilitation interactive game system (MRIGS), which uses grip assistive devices combined with different colors and tactile stimulation to achieve multi-sensory training effects of vision, hearing, and touch. This study involved 17 older adults (72.2 years) with mild dementia (the MMSE between 17 and 23 points). To explore how the MRIGS affects their willingness to continue rehabilitation training, the system usability scale (SUS) with ten items was adopted to compare the differences between traditional multi-sensory rehabilitation (TMR) and MRIGS regarding gender, rehabilitation experience, and age. The novel MRIGS interested older adults and improved their willingness for continuous rehabilitation. According to the overall SUS score, the MRIGS had better overall usability performance (86.18, being "Good+") than the TMR (66.62, only being "Average-") (t = -4.44, p = 0.00 < 0.05). In addition, the result shows that the MRIGS was a promising way to improve seven (out of 10) usability items (Willingness, Convenience, Stress, etc.) compared to TMR. For males, the MRIGS had better usability in "Willingness," "Convenience," and "Difficulty," while "Consistency" was better for females. We also found a significant difference in "Willingness" for those with previous rehabilitation experience because they had experienced the difficulties and boring feelings encountered in TMR in medical institutions. On the contrary, the MRIGS could make rehabilitation more exciting and motivating. For those over 70, the MRIGS performed better in "Convenience" and "Consistency," indicating that improving the overall convenience of training operations had become more important along with their natural decline of physical functions by aging. In addition, among older adults with weak grip strength in their dominant hand, the hand grip strength significantly influences their willingness to use the novel MRIGS. The MRIGS developed in this study could integrate multi-sensory training to help older adults with mild dementia improve their motivation and willingness to continue rehabilitation training.

• Keywords
• Dementia, Interactive game, Multi-sensory, Older adults, Rehabilitation, Usability,
• MeSH
• Dementia * rehabilitation   physiopathology   MeSH
• Humans MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Video Games * MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH

BACKGROUND: The optimal moment to deliver digital prompts for reducing sedentary behavior (SB) is when individuals are susceptible to prolonged SB (vulnerability) and open to behavior change (opportunity). This study aims to examine both vulnerability and opportunity. METHODS: A 14-day ecological momentary assessment study was conducted with 105 older adults. Participants wore a Fitbit activity tracker and an ActivPAL accelerometer and used a smartphone-based ecological momentary assessment app. Sensor-triggered questionnaires were delivered via the app after 30 minutes of SB to capture participants' activity, physical, social, and temporal contexts; feelings of pain and fatigue; and willingness to interrupt SB. Descriptive statistics identified states of vulnerability, whereas linear mixed models examined when participants are willing to interrupt prolonged SB, shedding light on states of opportunity. RESULTS: Ecological momentary assessment data (n = 2580) showed that older adults were most vulnerable to prolonged SB while watching TV (36.3%) and using digital devices (14.7%). Prolonged SB predominantly occurred at home (91.2%), in the evening (46.4%), when feeling fatigue (52.2%), and when experiencing mild pain (21.1%). The willingness to interrupt SB varied by activity, physical and social context, perceived pain, and level of fatigue, but not by time of day. Specifically, participants were more willing to interrupt their SB when engaging in mentally active SB and when indoors, alone, or with close relatives. CONCLUSIONS: Contextual factors significantly influence older adults' vulnerability to prolonged SB and their willingness to interrupt it. This empirical information can guide the design of just-in-time adaptive interventions that deliver strategically timed prompts to reduce prolonged SB in older adults.

• Keywords
• elderly, experience sampling, just-in-time adaptive intervention, sitting,
• MeSH
• Accelerometry MeSH
• Smartphone MeSH
• Exercise MeSH
• Fitness Trackers MeSH
• Middle Aged MeSH
• Humans MeSH
• Longitudinal Studies MeSH
• Mobile Applications MeSH
• Ecological Momentary Assessment * MeSH
• Surveys and Questionnaires MeSH
• Sedentary Behavior * MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH

Mass spectrometry-based lipidomics and metabolomics generate extensive data sets that, along with metadata such as clinical parameters, require specific data exploration skills to identify and visualize statistically significant trends and biologically relevant differences. Besides tailored methods developed by individual labs, a solid core of freely accessible tools exists for exploratory data analysis and visualization, which we have compiled here, including preparation of descriptive statistics, annotated box plots, hypothesis testing, volcano plots, lipid maps and fatty acyl chain plots, unsupervised and supervised dimensionality reduction, dendrograms, and heat maps. This review is intended for those who would like to develop their skills in data analysis and visualization using freely available R or Python solutions. Beginners are guided through a selection of R and Python libraries for producing publication-ready graphics without being overwhelmed by the code complexity. This manuscript, along with associated GitBook code repository containing step-by-step instructions, offers readers a comprehensive guide, encouraging the application of R and Python for robust and reproducible chemometric analysis of omics data.

• MeSH
• Mass Spectrometry MeSH
• Humans MeSH
• Lipidomics * methods   MeSH
• Metabolomics * methods   MeSH
• Programming Languages MeSH
• Software * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Review MeSH

Light simulations hold great potential for advancing optical techniques in neuroscience. They facilitate the in-silico refinement of optical stimulator designs and enable simulations of optical recordings from computational brain models, aiding neuroscience in forming a mechanistic understanding of brain circuitry. However, many published light models are inaccessible due to unavailable source code and documentation or are impractical due to excessive computational demands. To address these challenges, we replicate and enhance the efficient and accurate light simulation model by Yona et al. [1], which was previously available only in compiled form accompanied by sparse documentation. In this work, we resolve ambiguities in the original model, correct errors that caused discrepancies between simulations and published results, improve computational efficiency by an order of magnitude, and open-source all the resulting code and detailed documentation. These enhancements enable simulations of cortical volumes exceeding [Formula: see text] to run in seconds on standard laptop hardware. Our model software provides an accessible, adaptable, and rapid light simulation tool, which adheres to FAIR principles to ensure future-proof and broad utility for the neuroscience community.

• MeSH
• Humans MeSH
• Models, Neurological * MeSH
• Brain * physiology   MeSH
• Computer Simulation MeSH
• Software * MeSH
• Light * MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH

SUMMARY: MOLEonline is an interactive, web-based tool designed to detect and analyse channels (pores and tunnels) within protein structures. The latest version of MOLEonline addresses the limitations of its predecessor by integrating the Mol* viewer for visualization and offering a streamlined, fully interactive user experience. The new features include colouring tunnels in the 3D viewer based on their physicochemical properties. A 2D representation of the protein structure and calculated tunnels is generated using 2DProts. Users can now store tunnels directly in the mmCIF file format, facilitating sharing via the community-standard FAIR format for structural data. In addition, the ability to store and load computation settings ensures the reproducibility of tunnel computation results. Integration with the ChannelsDB 2.0 database allows users to access precomputed tunnels. AVAILABILITY AND IMPLEMENTATION: The MOLEonline application is freely available at https://moleonline.cz with no login requirement, its source code is stored at GitHub under the MIT licence at https://github.com/sb-ncbr/moleonline-web, and archived at Figshare at https://doi.org/10.6084/m9.figshare.29816174.

• MeSH
• Databases, Protein MeSH
• Internet MeSH
• Protein Conformation MeSH
• Proteins * chemistry   MeSH
• Software * MeSH
• User-Computer Interface MeSH
• Computational Biology * methods   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Proteins * MeSH

Stereotactic arrhythmia radioablation (STAR) for ventricular tachycardia (VT) is a non-invasive treatment modality to reduce the VT burden by delivering a single high radiation dose to the arrhythmogenic substrate. Identification and delineation of the arrhythmogenic substrate, definition of the radiation target, and transfer of this target across different imaging modalities from the invasive electroanatomic map (EAM) to the planning computed tomography (CT) scan are key to the success of therapeutic radiation. The VT substrate is identified using EAM data and co-localized with radiological correlates of the ventricular scar. Precise transfer to the non-ECG-gated treatment planning CT is essential for safe and effective STAR delivery. Current challenges include translating the endocardial or epicardial EAM surface target into a 3D cardiac target volume (CTV), reconciling different acquisition methods (e.g., (exhale-gated) EAM, contrast-enhanced ECG-gated CT angiography, and non-gated non-contrast planning CT), and achieving accurate CTV transfer using multi-modal image integration. Early approaches relied on manual delineation using side-by-side EAM and CT rendering, leading to poor reproducibility and potential treatment failure. Emerging (semi)auto-segmentation software based on the American Heart Association (AHA) 17-segment left ventricular model offers promise but lacks standardized weighing of identified segments and methods for handling partially involved segments. More recently, 2D-to-3D and 3D-to-3D target transfer methods, including commercial and in-house computer-aided tools, have been developed to address these difficulties. Currently, a standardized workflow has not been established. This review addresses the need to standardize CTV definitions and transfer workflows, assessing available tools and proposing quality assurance measures based on recommendations of the STOPSTORM.eu consortium.

• Keywords
• Catheter ablation, Stereotactic arrhythmia radioablation, Target volume transfer, Ventricular tachycardia,
• MeSH
• Tachycardia, Ventricular * diagnostic imaging   radiotherapy   surgery   MeSH
• Humans MeSH
• Radiotherapy Planning, Computer-Assisted * methods   MeSH
• Tomography, X-Ray Computed * methods   MeSH
• Radiosurgery * methods   MeSH
• Software * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Review MeSH

BACKGROUND: Palliative care is crucial for patients with life-threatening and serious diseases such as cancer, as it addresses their physical, psychosocial, and spiritual needs. Hematological malignancies significantly contribute to global cancer cases, impacting both older adults and children. To meet the increasing demand for palliative care, electronic patient-reported outcome (ePRO) interventions offer valuable insights into patient monitoring and treatment decision-making. The MyPal project developed a digital ePRO solution to improve palliative care by enabling structured symptom reporting and promoting physician-patient communication. OBJECTIVE: This study aims to explore the perceptions, opinions, and needs of adult and pediatric patients with cancer, caregivers, and health care professionals (HCPs) regarding low-fidelity versions of the MyPal project's digital solution, which is designed to improve palliative cancer care. METHODS: A qualitative, cross-sectional study was conducted using 12 prepilot focus groups (FGs) across 4 European countries (Greece, Italy, Germany, and the Czech Republic) at participating hospitals and research centers. The FGs, held in person, included 61 participants, including 27 (44%) adult patients with chronic lymphocytic leukemia or myelodysplastic syndromes, 19 (31%) children with hematological malignancies or solid tumors and their parents, and 15 (25%) HCPs specializing in oncology and palliative care. A semistructured discussion guide, informed by vignettes and user personas, was used to facilitate discussions. Sessions were audio recorded, transcribed, and analyzed using thematic analysis to identify and extract themes and subthemes from the FG discussions. RESULTS: Three main themes emerged from the FG discussions. The first theme, improved care, showcased the project's potential to enhance health care through patient-reported measures by improving symptom monitoring, streamlining decision-making, and strengthening physician-patient communication. Patients and caregivers valued the ability to report symptoms remotely, reducing unnecessary hospital visits, while HCPs appreciated having structured patient data to guide treatment. The second theme, digital communication framework, revealed that while participants recognized the benefits of digital tools, they had concerns about data security, privacy, and clarity regarding communication protocols. Questions emerged about how and when HCPs would review and respond to patient-reported data. In the third theme, applicability for use in health care, participants emphasized the importance of the system's ease of use, particularly for older patients and young children. Concerns were raised about the potential intrusiveness of the system, particularly regarding notification frequency and the impact on daily life. HCPs highlighted workload challenges, suggesting the need for a structured alert system to prioritize urgent cases. CONCLUSIONS: Our findings indicate that ePRO-based interventions such as MyPal can improve palliative care by facilitating communication and patient monitoring. However, addressing privacy concerns, optimizing usability for diverse populations, and ensuring seamless integration into clinical workflows are critical for successful adoption. Insights from this study will inform future development and optimization of eHealth interventions in palliative care.

• Keywords
• adult patients with cancer, eHealth systems, focus group discussions, health care professionals, palliative care,
• MeSH
• Child MeSH
• Adult MeSH
• Patient Reported Outcome Measures * MeSH
• Qualitative Research MeSH
• Middle Aged MeSH
• Humans MeSH
• Mobile Applications * MeSH
• Neoplasms * therapy   psychology   MeSH
• Caregivers psychology   MeSH
• Palliative Care * methods   MeSH
• Cross-Sectional Studies MeSH
• Aged MeSH
• Stakeholder Participation * MeSH
• Health Personnel psychology   MeSH
• Focus Groups MeSH
• Check Tag
• Child MeSH
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH

MOTIVATION: Accurately identifying and prioritizing protein binding pockets is a foundational element of small-molecule drug discovery. Defining these known pockets currently relies on a laborious manual process of extracting key residue data from selected publications, reconciling inconsistent terminology, and independently computing volumetric representations. This manual curation to ensure biological relevance is time-consuming, error-prone, and represents a major bottleneck for efficient, high-throughput drug discovery. RESULTS: We present a novel approach for the identification and prioritization of protein binding pockets for small molecules by combining geometric pocket detection with large language models (LLMs). Our method leverages Fpocket to generate candidate pockets, which are then validated against published experimental data extracted from research articles using LLM with a series of prompts fine-tuned to identify and extract residue-level information associated with experimentally confirmed binding sites. We developed a curated benchmark dataset of diverse proteins and associated literature to train and evaluate the LLM's performance in paper relevance assessment and pocket extraction. AVAILABILITY AND IMPLEMENTATION: The developed benchmark dataset and methodology are freely available at the GitHub repository (https://github.com/receptor-ai/LLM-benchmark-dataset) and Zenodo (DOI: 10.5281/zenodo.15798647).

• MeSH
• Databases, Protein MeSH
• Drug Discovery * methods   MeSH
• Proteins * chemistry   metabolism   MeSH
• Software MeSH
• Protein Binding MeSH
• Binding Sites MeSH
• Large Language Models MeSH
• Computational Biology * methods   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Proteins * MeSH

BACKGROUND AND OBJECTIVE: Digital Holographic Microscopy provides a new kind of quantitative image data about live cells' in vitro activities. Apart from non-invasive and staining-free imaging, it offers topological weighting of cell mass. This led us to develop a particular tool for assessing cell mass dynamics. METHODS: Programming language Python and a training set of time-lapse images of adherent HT-1080 cells derived from human fibrosarcoma taken with dry objective 40x/0.95 at 30-second intervals were used to create the Analytical Image Differencing (AID) method. RESULTS: The AID makes the best of these new data by evaluating the difference between the chosen two quantitative phase images from the time-lapse series. The contribution of the method is demonstrated on hiQPI (Holographic Incoherent-light-source Quantitative Phase Imaging) image data taken with a Q-phase microscope. The analysis outputs are graphical and complemented with numerical data. To underscore the significance of the Analytical Image Differencing (AID) method, an initial pilot experiment was conducted to show the available analyses of sequential overlapping images capturing the movement of cancer cells. Notably, besides defining changes in areas used by the cell (newly or steadily occupied or better abandoned) it is an introduction to the zero-line concept, which denotes spots of tranquility among continuously moving surroundings. CONCLUSIONS: The measurement of zero-line length has emerged as a novel biomarker for characterizing cell mass transfer. The sensitivity of phase change measurements is demonstrated. The noise quality of input images obtained with incoherent (hiQPI) and coherent (QPI) methods is compared. The resulting effect on the AID method output is also shown. The findings of this study introduce a novel approach to evaluating cellular behavior in vitro. The concept emerged as a particularly noteworthy outcome. Collectively, these results highlight the substantial potential of AID in advancing the field of cancer cells biology, particularly.

• Keywords
• Biophysics, Cancer cell migration, Digital holographic microscopy, Image processing, Live cell imaging, Non-invasive, Quantitative phase imaging, Staining-free imaging,
• MeSH
• Algorithms MeSH
• Time-Lapse Imaging MeSH
• Fibrosarcoma pathology   MeSH
• Holography methods   MeSH
• Humans MeSH
• Microscopy MeSH
• Cell Line, Tumor MeSH
• Image Processing, Computer-Assisted MeSH
• Cell Movement * MeSH
• Programming Languages MeSH
• Software MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH