Rajkumar Arumugam Jeeva, Edward D Lemaire, Ramiro Olleac, Kevin Cheung, Albert Tu, Natalie Baddour
{"title":"Automated Video Quality Assessment for the Edinburgh Visual Gait Score (EVGS).","authors":"Rajkumar Arumugam Jeeva, Edward D Lemaire, Ramiro Olleac, Kevin Cheung, Albert Tu, Natalie Baddour","doi":"10.3390/mps8040071","DOIUrl":"10.3390/mps8040071","url":null,"abstract":"<p><p>This research addresses critical challenges in clinical gait analysis by developing an automated video quality assessment framework to support Edinburgh Visual Gait Score (EVGS) scoring. The proposed methodology uses the MoveNet Lightning pose estimation model to extract body keypoints from video frames, enabling detection of multiple persons, tracking the person of interest, assessment of plane orientation, identification of overlapping individuals, detection of zoom artifacts, and evaluation of video resolution. These components are integrated into a unified quality classification system using a random forest classifier. The framework achieved high performance across key metrics, with 96% accuracy in detecting multiple persons, 95% in assessing overlaps, and 92% in identifying zoom events, culminating in an overall video quality categorization accuracy of 95%. This performance not only facilitates the automated selection of videos suitable for analysis but also provides specific video improvement suggestions when quality standards are not met. Consequently, the proposed system has the potential to streamline gait analysis workflows, reduce reliance on manual quality checks in clinical practice, and enable automated EVGS scoring by ensuring appropriate video quality as input to the gait scoring system.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144698996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ammar D Siddiqi, Maggie Britton, Isabel Martinez Leal, Matthew Taing, Tzuan A Chen, Lisa M Lowenstein, Jennifer A Minnix, Lorraine R Reitzel
{"title":"Project SWITCH Study Protocol: A Tobacco-Free Workplace Program for Dissemination and Implementation in Lung Cancer Screening Centers.","authors":"Ammar D Siddiqi, Maggie Britton, Isabel Martinez Leal, Matthew Taing, Tzuan A Chen, Lisa M Lowenstein, Jennifer A Minnix, Lorraine R Reitzel","doi":"10.3390/mps8040070","DOIUrl":"10.3390/mps8040070","url":null,"abstract":"<p><strong>Background/objectives: </strong>Cigarette smoking has been causally linked to 90% of all cases of lung cancer, contributing to its high mortality rate. Lung cancer screening centers offer low-dose computed tomography, the only recommended diagnostic screening tool for lung cancer detection. A previous Texas-based study found that centers with lung cancer screening programs failed to consistently provide evidence-based tobacco cessation and relapse prevention interventions recommended by clinical practice guidelines to their patients, who are primarily people who currently or previously smoked. This represents a missed opportunity to assist patients by providing evidence-based tobacco use care during a particularly relevant clinical encounter.</p><p><strong>Methods: </strong>To improve cigarette smoking cessation care delivery and relapse prevention in this setting, this protocol paper seeks to provide a framework for adapting Taking Texas Tobacco Free, a comprehensive, evidence-based tobacco-free workplace program, to lung cancer screening centers. The adapted program, Project SWITCH, will be developed through a formative evaluation process with center stakeholders to identify proactive adaptations to programming based on center-specific contexts. Project SWITCH is expected to be implemented in at least nine lung cancer screening centers in Texas and will be disseminated more broadly to centers statewide.</p><p><strong>Results: </strong>Quantitative and qualitative data will be collected from multiple stakeholders throughout the intervention using a convergent parallel mixed methods design to make additional program adaptations and comprehensively evaluate the achievement of the project's implementation and dissemination goals.</p><p><strong>Conclusions: </strong>Results from this project's implementation and dissemination phases are expected to reduce lung cancer morbidity and mortality in Texas by providing an evidence-based, sustainable framework for tobacco-free workplace programs in this specific setting that improves cancer prevention and control practices.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Comparing the Impact of Pre-Operative Antibiotics on the Outcomes of Immediately Placed Dental Implants: A Retrospective Multi-Center Study.","authors":"Georgios S Chatzopoulos, Larry F Wolff","doi":"10.3390/mps8040069","DOIUrl":"10.3390/mps8040069","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to evaluate and compare the survival rates of immediate dental implants (type 1) in patients who received different types of prophylactic antibiotics.</p><p><strong>Methods: </strong>This retrospective analysis examined data from 3351 immediate implants placed in 2391 patients (mean age 59.56 ± 13.42 years, 75.9% white, 53.6% female, 7.8% smokers, 6.7% with diabetes) within the BigMouth network between 2011 and 2022. Patient demographics, medical history, and the type of prophylactic antibiotic administered (amoxicillin, amoxicillin and clavulanic acid (Augmentin), clindamycin, azithromycin, ciprofloxacin, doxycycline, metronidazole) were analyzed in relation to implant survival or failure. Statistical analyses included descriptive statistics, chi-square tests, <i>t</i>-tests, Kaplan-Meier survival analysis, and Cox regression. All statistical analyses were performed with a significance level at <i>p</i> < 0.05.</p><p><strong>Results: </strong>The overall implant failure rate was 3.2% at the patient level (77 out of 2391 patients) and 1.9% at the implant level (65 out of 3351 implants), with a mean follow-up of 77 months. No significant associations were found between patient-related characteristics or implant position and implant failure, such as age (<i>p</i> = 0.84), gender (<i>p</i> = 0.30), or tobacco use (<i>p</i> = 0.83). Amoxicillin was the most frequently prescribed antibiotic (86.4%). Kaplan-Meier survival analysis revealed significantly shorter survival times for implants in patients who received ciprofloxacin and clindamycin compared to amoxicillin (n = 2894 implants) (<i>p</i> < 0.001). Cox regression analysis indicated a significantly increased risk of implant failure with ciprofloxacin (n = 5 implants) (HR: 16.50, <i>p</i> = 0.006) and clindamycin (n = 290 implants) (HR: 3.70, <i>p</i> < 0.001) compared to amoxicillin.</p><p><strong>Conclusion: </strong>The choice of prophylactic antibiotic significantly impacted the survival of immediate dental implants. Ciprofloxacin and clindamycin were associated with higher failure rates compared to amoxicillin. These findings underscore the importance of antibiotic selection in immediate implant procedures and highlight the need for further research to establish evidence-based guidelines for antibiotic prophylaxis in this context.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144698997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Expression of Concern: König, B.; Kirchner, J.O. Methodological Considerations Regarding the Quantification of DNA Impurities in the COVID-19 mRNA Vaccine Comirnaty<sup>®</sup>. <i>Methods Protoc.</i> 2024, <i>7</i>, 41.","authors":"Methods And Protocols Editorial Office","doi":"10.3390/mps8040068","DOIUrl":"10.3390/mps8040068","url":null,"abstract":"<p><p>Following publication [...].</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Simplified Method for Extracting the Movement Trajectories of Small Aquatic Animals.","authors":"Xin Liu, Huanan Gao, Aimin Hao, Yasushi Iseri","doi":"10.3390/mps8040067","DOIUrl":"10.3390/mps8040067","url":null,"abstract":"<p><p>Understanding the motion behaviors of animals is crucial for unraveling the mechanisms underlying ethology across various domains, such as movement patterns, food detection, and defense strategies. In this study, we devised a simplified method enabling the movement of small animals to be tracked conveniently using high-resolution smartphone videos and freely available tracking software. Employing a laboratory video setup, we traced the swimming trajectory of the small copepod zooplankton <i>Eodiaptomus japonicus</i>, which has a body size of approximately 1 mm. From the tracked position data, we analyzed key motion parameters, including swimming distance, speed, and jump frequency. The results of our video analysis showed that adult female <i>E. japonicus</i> exhibited an average swimming speed of 9.8 mm s<sup>-1</sup>, displaying a predominant cruising pattern with speeds of around 5.0 mm s<sup>-1</sup>, punctuated by sporadic jumps, showcasing maximum instantaneous speeds reaching a remarkable 190.1 mm s<sup>-1</sup>. Our successful tracking of the high-speed swimming copepod not only sheds light on its locomotion dynamics but also underscores the potential to refine this method to study the motion trajectories of diverse animal species.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12388259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nataliya Slater, Anuradha Sooda, Frank L Mastaglia, Sue Fletcher, Mark Watson, Merrilee Needham, Jerome D Coudert
{"title":"Expression and Site-Specific Biotinylation of Human Cytosolic 5'-Nucleotidase 1A in <i>Escherichia coli</i>.","authors":"Nataliya Slater, Anuradha Sooda, Frank L Mastaglia, Sue Fletcher, Mark Watson, Merrilee Needham, Jerome D Coudert","doi":"10.3390/mps8030066","DOIUrl":"10.3390/mps8030066","url":null,"abstract":"<p><p>Autoantibodies targeting cytosolic 5'-nucleotidase 1A (cN1A) are found in several autoimmune diseases, including inclusion body myositis (IBM), Sjögren's syndrome, and systemic lupus erythematosus. While they have diagnostic relevance for IBM, little is known about the autoreactive B cells that produce these antibodies. To address this, we developed a robust protocol for the expression and site-specific biotinylation of recombinant human cN1A in <i>Escherichia coli</i>. The resulting antigen is suitable for generating double-labelled fluorescent baits for the isolation and characterisation of cN1A-specific B cells by flow cytometry. Site-specific biotinylation was achieved using the AviTag and BirA ligase, preserving the protein's structure and immunoreactivity. Western blot analysis confirmed that the biotinylated cN1A was recognised by both human and rabbit anti-cN1A antibodies. Compared to conventional chemical biotinylation, this strategy minimises structural alterations that may affect antigen recognition. This approach provides a reliable method for producing biotinylated antigens for use in immunological assays. While demonstrated here for cN1A, the protocol can be adapted for other autoantigens to support studies of antigen-specific B cells in autoimmune diseases.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 3","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12195718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evaluating the Effectiveness of Various Small RNA Alignment Techniques in Transcriptomic Analysis by Examining Different Sources of Variability Through a Multi-Alignment Approach.","authors":"Xinwei Zhao, Eberhard Korsching","doi":"10.3390/mps8030065","DOIUrl":"10.3390/mps8030065","url":null,"abstract":"<p><p>DNA and RNA nucleotide sequences are ubiquitous in all biological cells, serving as both a comprehensive library of capabilities for the cells and as an impressive regulatory system to control cellular function. The multi-alignment framework (MAF) provided in this study offers a user-friendly platform for sequence alignment and quantification. It is adaptable to various research needs and can incorporate different tools and parameters for in-depth analysis, especially in low read rate scenarios. This framework can be used to compare results from different alignment programs and algorithms on the same dataset, allowing for a comprehensive analysis of subtle to significant differences. This concept is demonstrated in a small RNA case study. MAF is specifically designed for the Linux platform, commonly used in bioinformatics. Its script structure streamlines processing steps, saving time when repeating procedures with various datasets. While the focus is on microRNA analysis, the templates provided can be adapted for all transcriptomic and genomic analyses. The template structure allows for flexible integration of pre- and post-processing steps. MicroRNA analysis indicates that STAR and Bowtie2 alignment programs are more effective than BBMap. Combining STAR with the Salmon quantifier or, with some limitations, the Samtools quantification, appears to be the most reliable approach. This method is ideal for scientists who want to thoroughly analyze their alignment results to ensure quality. The detailed microRNA analysis demonstrates the quality of three alignment and two quantification methods, offering guidance on assessing result quality and reducing false positives.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 3","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12195907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"An Efficient Electroporation Protocol Supporting In Vitro Studies of Oligodendrocyte Biology.","authors":"Yugo Ishino, Shoko Shimizu, Shingo Miyata","doi":"10.3390/mps8030064","DOIUrl":"10.3390/mps8030064","url":null,"abstract":"<p><p>Oligodendrocytes form myelin in the central nervous system, and their dysfunction can cause severe neurological symptoms, as large-scale analyses have highlighted numerous gene expression alterations in pathological conditions. Although in vivo functional gene analyses are preferable, they have several limitations, especially in large-scale studies. Therefore, standardized in vitro systems are needed to facilitate efficient and reliable functional analyses of genes identified in such studies. Here, we describe a practical and efficient method for oligodendrocyte precursor cell (OPC) isolation from mouse brains on postnatal day 6-8 and a gene delivery method for the isolated OPCs. By modifying the magnetic-activated cell sorting (MACS) procedure with reduced processing volumes, we simplified OPC isolation, allowing simultaneous handling of multiple samples and improving workflow efficiency. We also optimized electroporation parameters to achieve robust transfection efficiency with minimal cell death. Transfected OPCs are suitable for both monoculture-based differentiation assays and co-culture with dorsal root ganglion (DRG) explants, in which they reliably differentiate into mature oligodendrocytes and myelinate along the axons. This system enables stable and reproducible in vitro analysis of oligodendrocyte function, supports investigations into both intrinsic differentiation and neuron-glia interactions, and provides a powerful platform for oligodendrocyte research with efficient and timely gene manipulation.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 3","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12195875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shefra Shah, Farah Hussaini, Dumitru Mazilu, Eric E Bennett, Han Wen
{"title":"Cystic Lung Phantom to Validate Clinical CT Protocols.","authors":"Shefra Shah, Farah Hussaini, Dumitru Mazilu, Eric E Bennett, Han Wen","doi":"10.3390/mps8030063","DOIUrl":"10.3390/mps8030063","url":null,"abstract":"<p><p>In computed tomography (CT)-based evaluation of the extent of cystic changes in the lungs of patients with cystic lung diseases, such as Lymphangioleiomyomatosis (LAM), there is a lack of a lung phantom containing air-filled cavities that mimic pulmonary cysts to calibrate the measurement of cystic volumes from CT scans. We describe an easy-to-replicate cystic lung phantom consisting of basic lung structures of a trachea and two lung compartments. The lung compartments contain air cavities of varying sizes to mimic cystic lesions. The lung compartments are made of a foam material recommended by NIST to simulate the radiodensity of human lung parenchyma. In tests performed on a clinical scanner, various structures in the lung phantom were correctly recognized by two types of lung analysis software. The resulting cystic volume measurements revealed the relationship between the size of the cysts and the accuracy of the measurement. The significant finding was that the volumes of individual cysts were underestimated for small cysts. The error increased with decreasing cyst sizes. Such underestimation has not been mentioned previously and deserves the attention of clinicians using CT scans to assess the cyst burden in the lungs, particularly in patients presenting with numerous small pulmonary cysts.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 3","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yannik Schürch, Anneke Hertig-Godeschalk, Inge Eriks-Hoogland, Anke Scheel-Sailer, Martin W G Brinkhof, Ursina Arnet
{"title":"Investigating the Impact of Pressure Relief Performance on the Occurrence of Pressure Injuries and Shoulder Pain in Wheelchair Users with Spinal Cord Injury (PRperf Study): Study Protocol for a Prospective Observational Study.","authors":"Yannik Schürch, Anneke Hertig-Godeschalk, Inge Eriks-Hoogland, Anke Scheel-Sailer, Martin W G Brinkhof, Ursina Arnet","doi":"10.3390/mps8030062","DOIUrl":"10.3390/mps8030062","url":null,"abstract":"<p><strong>Background: </strong>Pressure injuries (PIs) and shoulder pain (SP) are frequent problems in individuals with spinal cord injury (SCI), affecting both quality of life and healthcare use. Although pressure relief (PR) is recommended to prevent PIs, it is often not performed regularly, and its long-term benefits remain unclear. Furthermore, some PR methods may contribute to SP, resulting in conflicting clinical guidelines. This study aims to objectively measure PR performance and investigate its long-term relationship with PI and SP.</p><p><strong>Methods: </strong>This study is a longitudinal observational study involving 70 manual wheelchair users with complete SCI. Over one year, participants attend five study visits to assess confounding factors such as comorbidities and shoulder range of motion. PR performance (technique, frequency, duration) is continuously monitored for three weeks after each of the first four visits using textile measurement mats, while SP is assessed weekly with a questionnaire. Causal associations with PI and SP will be examined using directed acyclic graphs and multivariable regression modelling.</p><p><strong>Results: </strong>The study is ongoing. Long-term objective data on PR performance will provide insights into its relationship with PI and SP.</p><p><strong>Conclusions: </strong>Findings will inform clinical practice and contribute to improved evidence-based PR guidelines for individuals with SCI.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"8 3","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}