Journal Description
Methods and Protocols
Methods and Protocols
is an international, peer-reviewed, open access journal aiming to establish and describe new experimental techniques in the fields of Life Sciences, Chemistry, and Biomedical Sciences, published bimonthly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), PubMed, PMC, CAPlus / SciFinder, and other databases.
- Journal Rank: CiteScore - Q2 (Biochemistry, Genetics and Molecular Biology (miscellaneous))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 27.9 days after submission; acceptance to publication is undertaken in 3.9 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
2.4 (2022);
5-Year Impact Factor:
2.4 (2022)
Latest Articles
A Comprehensive Methodology for Microbial Strain Typing Using Fourier-Transform Infrared Spectroscopy
Methods Protoc. 2024, 7(3), 48; https://doi.org/10.3390/mps7030048 - 11 Jun 2024
Abstract
Timely and accurate detection and characterization of microbial threats is crucial for effective infection and outbreak management. Additionally, in food production, rapid microbe identification is indispensable for maintaining quality control and hygiene standards. Current methods for typing microbial strains often rely on labor-intensive,
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Timely and accurate detection and characterization of microbial threats is crucial for effective infection and outbreak management. Additionally, in food production, rapid microbe identification is indispensable for maintaining quality control and hygiene standards. Current methods for typing microbial strains often rely on labor-intensive, time-consuming, and expensive DNA- and sera-serotyping techniques, limiting their applicability in rapid-response scenarios. In this context, the IR Biotyper®, utilizing Fourier-transform infrared (FTIR) spectroscopy, offers a novel approach, providing specific spectra for fast strain typing within 3 h. This methodology article serves as a comprehensive resource for researchers and technicians aiming to utilize FTIR spectroscopy for microbial strain typing. It encompasses detailed guidelines on sample preparation, data acquisition, and analysis techniques, ensuring the generation of reliable and reproducible results. We highlight the IR Biotyper®’s rapid and accurate discrimination capabilities, showcasing its potential for real-time pathogen monitoring and source-tracking to enhance public health and food safety. We propose its integration as an early screening method, followed by more detailed analysis with whole-genome sequencing, to optimize detection accuracy and response efficiency in microbial surveillance systems.
Full article
(This article belongs to the Section Molecular and Cellular Biology)
Open AccessStudy Protocol
Evaluation of the Sexually Transmitted Infections Programme among Key and Priority Populations in Primary Healthcare Facilities to Inform a Targeted Response: A Protocol Paper
by
Mohlago Ablonia Seloka, Edith Phalane and Refilwe Nancy Phaswana-Mafuya
Methods Protoc. 2024, 7(3), 47; https://doi.org/10.3390/mps7030047 - 5 Jun 2024
Abstract
Primary healthcare facilities lack routine diagnostic screening due to resource limitations and dependence on syndromic management, resulting in an unprecedented prevalence and incidence of sexually transmitted infections (STIs), particularly among key and priority populations. Specific focuses are essential to strengthen current STI control
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Primary healthcare facilities lack routine diagnostic screening due to resource limitations and dependence on syndromic management, resulting in an unprecedented prevalence and incidence of sexually transmitted infections (STIs), particularly among key and priority populations. Specific focuses are essential to strengthen current STI control measures. Therefore, this article describes the protocol for evaluating STI programme among key and priority populations in selected primary healthcare facilities in South Africa. We will employ an exploratory, descriptive research design to assess the STI programme in terms of its facility operations, functions, scope, gaps, delivery services, STI surveillance methods, and indicators in the selected primary healthcare facilities. A purposive sample of 15–20 STI programme stakeholders will be selected from five primary healthcare facilities in Limpopo Province, South Africa. The programme evaluation will use the World Health Organization assessment checklist tool, a globally recognised and validated instrument comprising open- and closed-ended questions to assess the STI programme. This tool, known for its credibility and reliability, ensures the study’s validity. Quantitative data will be captured on STATA software (College Station, TX, USA) version 18 for descriptive analysis and presented as the mean and standard deviation for continuous variables, proportions and percentages for categorical variables. A p ≤ 0.05 will demonstrate a statistically significant level. Thematic content analysis will be conducted for the qualitative data using Atlas. ti software (Technical University, Berlin, Germany) version 23.1. The study’s results will inform new approaches to strengthen STI coverage, service delivery, and linkage to care.
Full article
(This article belongs to the Section Public Health Research)
Open AccessReview
Advances in 3D Inner Ear Reconstruction Software for Cochlear Implants: A Comprehensive Review
by
Michail Athanasopoulos, Pinelopi Samara and Ioannis Athanasopoulos
Methods Protoc. 2024, 7(3), 46; https://doi.org/10.3390/mps7030046 - 23 May 2024
Abstract
Auditory impairment stands as a pervasive global issue, exerting significant effects on individuals’ daily functioning and interpersonal engagements. Cochlear implants (CIs) have risen as a cutting-edge solution for severe to profound hearing loss, directly stimulating the auditory nerve with electrical signals. The success
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Auditory impairment stands as a pervasive global issue, exerting significant effects on individuals’ daily functioning and interpersonal engagements. Cochlear implants (CIs) have risen as a cutting-edge solution for severe to profound hearing loss, directly stimulating the auditory nerve with electrical signals. The success of CI procedures hinges on precise pre-operative planning and post-operative evaluation, highlighting the significance of advanced three-dimensional (3D) inner ear reconstruction software. Accurate pre-operative imaging is vital for identifying anatomical landmarks and assessing cochlear deformities. Tools like 3D Slicer, Amira and OTOPLAN provide detailed depictions of cochlear anatomy, aiding surgeons in simulating implantation scenarios and refining surgical approaches. Post-operative scans play a crucial role in detecting complications and ensuring CI longevity. Despite technological advancements, challenges such as standardization and optimization persist. This review explores the role of 3D inner ear reconstruction software in patient selection, surgical planning, and post-operative assessment, tracing its evolution and emphasizing features like image segmentation and virtual simulation. It addresses software limitations and proposes solutions, advocating for their integration into clinical practice. Ultimately, this review underscores the impact of 3D inner ear reconstruction software on cochlear implantation, connecting innovation with precision medicine.
Full article
(This article belongs to the Section Biomedical Sciences and Physiology)
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Open AccessStudy Protocol
MUltiparametric Score for Ventilation Discontinuation in Intensive Care Patients: A Protocol for an Observational Study
by
Iacopo Cappellini, Andrea Cardoni, Lorenzo Campagnola and Guglielmo Consales
Methods Protoc. 2024, 7(3), 45; https://doi.org/10.3390/mps7030045 - 20 May 2024
Abstract
Background: Mechanical ventilation significantly improves patient survival but is associated with complications, increasing healthcare costs and morbidity. Identifying optimal weaning times is paramount to minimize these risks, yet current methods rely heavily on clinical judgment, lacking specificity. Methods: This study introduces a novel
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Background: Mechanical ventilation significantly improves patient survival but is associated with complications, increasing healthcare costs and morbidity. Identifying optimal weaning times is paramount to minimize these risks, yet current methods rely heavily on clinical judgment, lacking specificity. Methods: This study introduces a novel multiparametric predictive score, the MUSVIP (MUltiparametric Score for Ventilation discontinuation in Intensive care Patients), aimed at accurately predicting successful extubation. Conducted at Santo Stefano Hospital’s ICU, this single-center, observational, prospective cohort study will span over 12 months, enrolling adult patients undergoing invasive mechanical ventilation. The MUSVIP integrates variables measured before and during a spontaneous breathing trial (SBT) to formulate a predictive score. Results: Preliminary analyses suggest an Area Under the Curve (AUC) of 0.815 for the MUSVIP, indicating high predictive capacity. By systematically applying this score, we anticipate identifying patients likely to succeed in weaning earlier, potentially reducing ICU length of stay and associated healthcare costs. Conclusion: This study’s findings could significantly influence clinical practices, offering a robust, easy-to-use tool for optimizing weaning processes in ICUs.
Full article
(This article belongs to the Section Biomedical Sciences and Physiology)
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Open AccessArticle
Pole Dancing-Specific Muscle Strength: Development and Reliability of a Novel Assessment Protocol
by
Despoina Ignatoglou, Achilleas Paliouras, Eleftherios Paraskevopoulos, Nikolaos Strimpakos, Paraskevi Bilika, Maria Papandreou and Eleni Kapreli
Methods Protoc. 2024, 7(3), 44; https://doi.org/10.3390/mps7030044 - 18 May 2024
Abstract
Background: Pole dancing is a physically demanding sport that combines dance and acrobatic movements on a vertical pole. Despite its highly growing popularity, there is currently limited research in the field. The aim of this study was to create and evaluate a strength
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Background: Pole dancing is a physically demanding sport that combines dance and acrobatic movements on a vertical pole. Despite its highly growing popularity, there is currently limited research in the field. The aim of this study was to create and evaluate a strength assessment protocol for athletes in pole dancing, with a specific focus on functional positions on the pole. Methods: Thirty-two female pole dancing athletes participated in this study. Maximal voluntary isometric contractions (MVIC) were measured at three different sport-specific positions on the pole (shoulder abduction and adduction, and hip adduction), on two separate days (test and re-test) with a five to seven day interval between them. A hand-held dynamometer (Activ5- Activbody) stabilized on the pole was used for this study. Results: The intra-session reliability was good to excellent for all sports-specific positions and for both sides of the body, across all different movements (ICC = 0.837–0.960, SEM = 5.02 Kg–2.24 Kg, and SDD = 27.46%–14.92%). Slightly better results were found regarding inter-session reliability (ICC = 0.927–0.970, SEM = 3.72 Kg–1.97 Kg, and SDD = 22.86%–15.19%). There was not a statistically significant difference between the MVICs between the left and right or dominant and non-dominant side in shoulder abduction (p = 0.105) and hip adduction (p = 0.282), in contrast to shoulder adduction (p = 0.00). Conclusion: The strength assessment protocol developed in the current study has proven to be a reliable and functional tool, with the potential for utilization in clinical practice as part of objective strength testing. Further studies are needed in order to expand the protocol to other muscle groups and positions and to generalize the results in all pole dancing populations such as male athletes.
Full article
(This article belongs to the Special Issue Methods on Sport Biomechanics)
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Open AccessProtocol
Isolation of Intestinal Macrophage Subpopulations for High-Quality Total RNA Purification in Zebrafish
by
Yalén Del Río-Jay, Audrey Barthelaix, Cristian Reyes-Martínez, Christophe Duperray, Camila J. Solis-Cascante, Yessia Hidalgo, Patricia Luz-Crawford, Farida Djouad and Carmen G. Feijoo
Methods Protoc. 2024, 7(3), 43; https://doi.org/10.3390/mps7030043 - 17 May 2024
Abstract
Intestinal macrophages have been poorly studied in fish, mainly due to the lack of specific molecular markers for their identification and isolation. To address this gap, using the zebrafish Tg(mpeg1:EGFP) transgenic line, we developed a fluorescence-activated cell sorting strategy (FACS)
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Intestinal macrophages have been poorly studied in fish, mainly due to the lack of specific molecular markers for their identification and isolation. To address this gap, using the zebrafish Tg(mpeg1:EGFP) transgenic line, we developed a fluorescence-activated cell sorting strategy (FACS) that allows us to isolate different intestinal macrophage subpopulations, based on GFP expression and morphological differences. Also, we achieved the purification of high-quality total RNA from each population to perform transcriptomic analysis. The complete strategy comprises three steps, including intestine dissection and tissue dissociation, the isolation of each intestinal macrophage population via FACS, and the extraction of total RNA. To be able to characterize molecularly different macrophage subpopulations and link them to their functional properties will allow us to unravel intestinal macrophage biology.
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(This article belongs to the Section Molecular and Cellular Biology)
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Open AccessArticle
Syrian Hamsters Model Does Not Reflect Human-like Disease after Aerosol Exposure to Encephalitic Alphaviruses
by
Christina L. Gardner, Rebecca A. Erwin-Cohen, Bridget S. Lewis, Russell R. Bakken, Shelley P. Honnold, Pamela J. Glass and Crystal W. Burke
Methods Protoc. 2024, 7(3), 42; https://doi.org/10.3390/mps7030042 - 15 May 2024
Abstract
Venezuelan (VEE), eastern (EEE), and western (WEE) equine encephalitis viruses are encephalitic New World alphaviruses that cause periodic epizootic and epidemic outbreaks in horses and humans that may cause severe morbidity and mortality. Currently there are no FDA-licensed vaccines or effective antiviral therapies.
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Venezuelan (VEE), eastern (EEE), and western (WEE) equine encephalitis viruses are encephalitic New World alphaviruses that cause periodic epizootic and epidemic outbreaks in horses and humans that may cause severe morbidity and mortality. Currently there are no FDA-licensed vaccines or effective antiviral therapies. Each year, there are a limited number of human cases of encephalitic alphaviruses; thus, licensure of a vaccine or therapeutic would require approval under the FDA animal rule. Approval under the FDA animal rule requires the disease observed in the animal model to recapitulate what is observed in humans. Currently, initial testing of vaccines and therapeutics is performed in the mouse model. Unfortunately, alphavirus disease manifestations in a mouse do not faithfully recapitulate human disease; the VEEV mouse model is lethal whereas in humans VEEV is rarely lethal. In an effort to identify a more appropriate small animal model, we evaluated hamsters in an aerosol exposure model of encephalitic alphavirus infection. The pathology, lethality, and viremia observed in the infected hamsters was inconsistent with what is observed in NHP models and humans. These data suggest that hamsters are not an appropriate model for encephalitic alphaviruses to test vaccines or potential antiviral therapies.
Full article
(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2024)
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Open AccessCommentary
Methodological Considerations Regarding the Quantification of DNA Impurities in the COVID-19 mRNA Vaccine Comirnaty®
by
Brigitte König and Jürgen O. Kirchner
Methods Protoc. 2024, 7(3), 41; https://doi.org/10.3390/mps7030041 - 8 May 2024
Abstract
DNA impurities can impact the safety of genetically engineered pharmaceuticals; thus, a specific limit value must be set for them during marketing authorisation. This particularly applies to mRNA vaccines, as large quantities of DNA templates are used for their production. Furthermore, when quantifying
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DNA impurities can impact the safety of genetically engineered pharmaceuticals; thus, a specific limit value must be set for them during marketing authorisation. This particularly applies to mRNA vaccines, as large quantities of DNA templates are used for their production. Furthermore, when quantifying the total DNA content in the final product, we must observe that, in addition to the mRNA active ingredient, DNA impurities are also encased in lipid nanoparticles and are therefore difficult to quantify. In fact, the manufacturer of the mRNA vaccine Comirnaty (BioNTech/Pfizer) only measures DNA impurities in the active substance by means of a quantitative polymerase chain reaction (qPCR), whose DNA target sequence is less than just 1% of the originally added DNA template. This means that no direct DNA quantification takes place, and compliance with the limit value for DNA contamination is only estimated from the qPCR data using mathematical extrapolation methods. However, it is also possible to dissolve the lipid nanoparticles with a detergent to directly measure DNA contamination in the final product by using fluorescence spectroscopic methods. Experimental testing of this approach confirms that reliable values can be obtained in this way.
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(This article belongs to the Section Biomedical Sciences and Physiology)
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Open AccessArticle
Quantifying mRNA in Highly Degraded Fixed Tissues by Nanostring Technology: A Comparative Study
by
Eros Azzalini, Barbara Di Stefano, Vincenzo Canzonieri, Tiziana Venesio, Umberto Miglio, Caterina Marchiò, Anna Sapino, Carlo Previderè, Paolo Fattorini and Serena Bonin
Methods Protoc. 2024, 7(3), 40; https://doi.org/10.3390/mps7030040 - 7 May 2024
Abstract
Archive tissues are the most available source of human tissues useful for molecular analysis in translational research. The main issues for those specimens are the modification and degradation of biomolecules, namely proteins, DNA, and RNA. In the last decade, several high-throughput analytical methods
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Archive tissues are the most available source of human tissues useful for molecular analysis in translational research. The main issues for those specimens are the modification and degradation of biomolecules, namely proteins, DNA, and RNA. In the last decade, several high-throughput analytical methods have been applied to archive tissues. Although histological tissues are fixed in neutral-buffered formalin nowadays, in the recent past, Bouin’s solution was also used in tissue processing. The present study aims to investigate the feasibility of nCounter Nanostring hybridization in quantifying mRNA in highly degraded samples, such as Bouin’s fixed and paraffin-embedded (BFPE) tissues, in comparison to the standard formalin-fixed and paraffin-embedded (FFPE) tissues as a source of RNA. A total of 16 paraffin-embedded tissue blocks from eight patients were analyzed (8 were FFPE and 8 were BEPE). Nanostring technology was applied to 300 ng of each RNA sample, whereas 360 ng of the same templates were retrotranscribed and submitted to qPCR and ddPCR. Our results show that the Nanostring technology outperforms the reference methods (ddPCR and qPCR) in detecting target mRNA in FFPE and BFPE samples. However, even Nanostring technology does not escape the limitation imposed by the degradation of the RNA templates, which could lead to misleading conclusions on the gene expression level.
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(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
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Open AccessProtocol
A Protocol for Comprehensive Analysis of Gait in Individuals with Incomplete Spinal Cord Injury
by
Emelie Butler Forslund, Minh Tat Nhat Truong, Ruoli Wang, Åke Seiger and Elena M. Gutierrez-Farewik
Methods Protoc. 2024, 7(3), 39; https://doi.org/10.3390/mps7030039 - 4 May 2024
Abstract
This is a protocol for comprehensive analysis of gait and affecting factors in individuals with incomplete paraplegia due to spinal cord injury (SCI). A SCI is a devastating event affecting both sensory and motor functions. Due to better care, the SCI population is
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This is a protocol for comprehensive analysis of gait and affecting factors in individuals with incomplete paraplegia due to spinal cord injury (SCI). A SCI is a devastating event affecting both sensory and motor functions. Due to better care, the SCI population is changing, with a greater proportion retaining impaired ambulatory function. Optimizing ambulatory function after SCI remains challenging. To investigate factors influencing optimal ambulation, a multi-professional research project was grounded with expertise from clinical rehabilitation, neurophysiology, and biomechanical engineering from Karolinska Institutet, the Spinalis Unit at Aleris Rehab Station (Sweden’s largest center for specialized neurorehabilitation), and the Promobilia MoveAbility Lab at KTH Royal Institute of Technology. Ambulatory adults with paraplegia will be consecutively invited to participate. Muscle strength, sensitivity, and spasticity will be assessed, and energy expenditure, 3D movements, and muscle function (EMG) during gait and submaximal contractions will be analyzed. Innovative computational modeling and data-driven analyses will be performed, including the identification of clusters of similar movement patterns among the heterogeneous population and analyses that study the link between complex sensorimotor function and movement performance. These results may help optimize ambulatory function for persons with SCI and decrease the risk of secondary conditions during gait with a life-long perspective.
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(This article belongs to the Section Biomedical Sciences and Physiology)
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Open AccessReview
Chromatographic Methods for the Determination of Glyphosate in Cereals Together with a Discussion of Its Occurrence, Accumulation, Fate, Degradation, and Regulatory Status
by
Maurizio Masci, Roberto Caproni and Teresina Nevigato
Methods Protoc. 2024, 7(3), 38; https://doi.org/10.3390/mps7030038 - 2 May 2024
Abstract
The European Union’s recent decision to renew the authorization for the use of glyphosate until 15 December 2033 has stimulated scientific discussion all around the world regarding its toxicity or otherwise for humans. Glyphosate is a chemical of which millions of tons have
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The European Union’s recent decision to renew the authorization for the use of glyphosate until 15 December 2033 has stimulated scientific discussion all around the world regarding its toxicity or otherwise for humans. Glyphosate is a chemical of which millions of tons have been used in the last 50 years worldwide to dry out weeds in cultivated fields and greenhouses and on roadsides. Concern has been raised in many areas about its possible presence in the food chain and its consequent adverse effects on health. Both aspects that argue in favor of toxicity and those that instead may indicate limited toxicity of glyphosate are discussed here. The widespread debate that has been generated requires further investigations and field measurements to understand glyphosate’s fate once dispersed in the environment and its concentration in the food chain. Hence, there is a need for validated analytical methods that are available to analysts in the field. In the present review, methods for the analytical determination of glyphosate and its main metabolite, AMPA, are discussed, with a specific focus on chromatographic techniques applied to cereal products. The experimental procedures are explained in detail, including the cleanup, derivatization, and instrumental conditions, to give the laboratories involved enough information to proceed with the implementation of this line of analysis. The prevalent chromatographic methods used are LC-MS/MS, GC-MS/SIM, and GC-MS/MS, but sufficient indications are also given to those laboratories that wish to use the better performing high-resolution MS or the simpler HPLC-FLD, HPLC-UV, GC-NPD, and GC-FPD techniques for screening purposes. The concentrations of glyphosate from the literature measured in wheat, corn, barley, rye, oats, soybean, and cereal-based foods are reported, together with its regulatory status in various parts of the world and its accumulation mechanism. As for its accumulation in cereals, the available data show that glyphosate tends to accumulate more in wholemeal flours than in refined ones, that its concentration in the product strictly depends on the treatment period (the closer it is to the time of harvesting, the higher the concentration), and that in cold climates, the herbicide tends to persist in the soil for a long time.
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(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
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Open AccessProtocol
Dedicated Protocol for Ultrastructural Analysis of Farmed Rainbow Trout (Oncorhynchus mykiss) Tissues with Red Mark Syndrome: The Skin—Part One
by
Diana Torge, Sara Bernardi, Giulia Ciciarelli, Guido Macchiarelli and Serena Bianchi
Methods Protoc. 2024, 7(3), 37; https://doi.org/10.3390/mps7030037 - 24 Apr 2024
Abstract
The present study aims to provide a specific protocol for transmission electron microscopy of a sample of skin of rainbow trout affected by red mark syndrome (RMS). The red mark syndrome is a skin disease that affects the rainbow trout (Oncorhynchus mykiss
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The present study aims to provide a specific protocol for transmission electron microscopy of a sample of skin of rainbow trout affected by red mark syndrome (RMS). The red mark syndrome is a skin disease that affects the rainbow trout (Oncorhynchus mykiss). The disease, probably due to the Midichloria-like organism infection, is not lethal, but morbidity can reach up to 60%, leading to significant economic impact associated with the downgrading of the commercial product, increased labor, and susceptibility to secondary infections. The ultrastructure analyses allowed an earlier study to identify the presence of scattered microorganisms characterized by an oval shape, mainly in the cytoplasm of the cells. The protocol developed in this study will be instrumental in visualizing the ultrastructure of the microorganism, which is probably responsible for red mark syndrome infection.
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(This article belongs to the Section Tissue Engineering and Organoids)
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Open AccessArticle
Simplifying Data Analysis in Biomedical Research: An Automated, User-Friendly Tool
by
Rúben Araújo, Luís Ramalhete, Ana Viegas, Cristiana P. Von Rekowski, Tiago A. H. Fonseca, Cecília R. C. Calado and Luís Bento
Methods Protoc. 2024, 7(3), 36; https://doi.org/10.3390/mps7030036 - 24 Apr 2024
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Robust data normalization and analysis are pivotal in biomedical research to ensure that observed differences in populations are directly attributable to the target variable, rather than disparities between control and study groups. ArsHive addresses this challenge using advanced algorithms to normalize populations (e.g.,
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Robust data normalization and analysis are pivotal in biomedical research to ensure that observed differences in populations are directly attributable to the target variable, rather than disparities between control and study groups. ArsHive addresses this challenge using advanced algorithms to normalize populations (e.g., control and study groups) and perform statistical evaluations between demographic, clinical, and other variables within biomedical datasets, resulting in more balanced and unbiased analyses. The tool’s functionality extends to comprehensive data reporting, which elucidates the effects of data processing, while maintaining dataset integrity. Additionally, ArsHive is complemented by A.D.A. (Autonomous Digital Assistant), which employs OpenAI’s GPT-4 model to assist researchers with inquiries, enhancing the decision-making process. In this proof-of-concept study, we tested ArsHive on three different datasets derived from proprietary data, demonstrating its effectiveness in managing complex clinical and therapeutic information and highlighting its versatility for diverse research fields.
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Open AccessStudy Protocol
Effects of a WhatsApp-Assisted Health Educational Intervention for Cardiac Rehabilitation: A Randomized Controlled Clinical Trial Protocol
by
Adriana Marcela Jacome-Hortua, Zully Rocio Rincon-Rueda, Diana C. Sanchez-Ramirez and Adriana Angarita-Fonseca
Methods Protoc. 2024, 7(2), 35; https://doi.org/10.3390/mps7020035 - 19 Apr 2024
Abstract
Although the effectiveness of cardiac rehabilitation (CR) programs in secondary prevention is well-recognized, there is a lack of studies exploring the potential of mobile health to enhance educational interventions within CR. The objective is to assess the impact of a structured WhatsApp-assisted health
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Although the effectiveness of cardiac rehabilitation (CR) programs in secondary prevention is well-recognized, there is a lack of studies exploring the potential of mobile health to enhance educational interventions within CR. The objective is to assess the impact of a structured WhatsApp-assisted health educational intervention, in conjunction with the usual care, compared to the usual care alone among participants enrolled in a CR program. The trial will recruit 32 participants enrolled in a CR program, who will be randomly assigned to a structured WhatsApp-assisted health educational intervention plus usual care or usual care alone group. The intervention will span 4 weeks, with assessments at baseline, 4 weeks, and 3, 6, and 12 months. The primary outcome measure is the cardiovascular risk factors knowledge score. Secondary outcomes include physical activity levels, anxiety and depression, and quality of life. Expected results include improved knowledge of cardiovascular risk factors, increased physical activity levels, and better mental health outcomes in the intervention group. Additionally, an enhancement in the overall quality of life is anticipated. These findings are expected to underscore the value of integrating mHealth with traditional CR methods, potentially shaping future approaches in chronic disease management and prevention.
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(This article belongs to the Section Public Health Research)
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Open AccessStudy Protocol
Financial Toxicity in Renal Patients (FINTORE) Study: A Cross-Sectional Italian Study on Financial Burden in Kidney Disease—A Project Protocol
by
Rossella Siligato, Guido Gembillo, Emanuele Di Simone, Alessio Di Maria, Simone Nicoletti, Laura Maria Scichilone, Matteo Capone, Francesca Maria Vinci, Marta Bondanelli, Cristina Malaventura, Alda Storari, Domenico Santoro, Marco Di Muzio, Sara Dionisi and Fabio Fabbian
Methods Protoc. 2024, 7(2), 34; https://doi.org/10.3390/mps7020034 - 14 Apr 2024
Abstract
Financial toxicity (FT) refers to the negative impact of health-care costs on clinical conditions. In general, social determinants of health, especially poverty, socioenvironmental stressors, and psychological factors, are increasingly recognized as important determinants of non-communicable diseases, such as chronic kidney disease (CKD), and
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Financial toxicity (FT) refers to the negative impact of health-care costs on clinical conditions. In general, social determinants of health, especially poverty, socioenvironmental stressors, and psychological factors, are increasingly recognized as important determinants of non-communicable diseases, such as chronic kidney disease (CKD), and their consequences. We aim to investigate the prevalence of FT in patients at different stages of CKD treated in our universal health-care system and from pediatric nephrology, hemodialysis, peritoneal dialysis and renal transplantation clinics. FT will be assessed with the Patient-Reported Outcome for Fighting Financial Toxicity (PROFFIT) score, which was first developed by Italian oncologists. Our local ethics committee has approved the study. Our population sample will answer the sixteen questions of the PROFFIT questionnaire, seven of which are related to the outcome and nine the determinants of FT. Data will be analyzed in the pediatric and adult populations and by group stratification. We are confident that this study will raise awareness among health-care professionals of the high risk of adverse health outcomes in patients who have both kidney disease and high levels of FT. Strategies to reduce FT should be implemented to improve the standard of care for people with kidney disease and lead to truly patient-centered care.
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(This article belongs to the Section Public Health Research)
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Open AccessArticle
Research and Simulation on the Development of a Hydraulic Prop Support System of Powered Roof Support to Increase Work Safety
by
Beata Borska and Dawid Szurgacz
Methods Protoc. 2024, 7(2), 33; https://doi.org/10.3390/mps7020033 - 11 Apr 2024
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The underground mining environment is currently based on technology that uses mainly analogue sensors in machine and equipment control systems. The primary machine performing the most important functions in a mining system is the powered roof support. In order for it to work
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The underground mining environment is currently based on technology that uses mainly analogue sensors in machine and equipment control systems. The primary machine performing the most important functions in a mining system is the powered roof support. In order for it to work properly, it is important that it achieves the required power. To ensure this, it is necessary to continuously and precisely monitor the pressure in the under-piston space of the prop. Due to the extreme environmental conditions, pressure sensors should have high sensitivity, large transmission capacity, small size and light weight. To achieve these requirements, the authors of the article propose to implement a monitoring system based on photonics technology. To achieve this goal, several studies were carried out. The range of these studies included simulations, bench tests and tests under real conditions. The obtained test results showed the possibility of developing the control system for the powered roof support, the additional function to supercharge power. Based on the analysis of the obtained test results, assumptions were developed for the development of a power charging system with monitoring sensors. Based on the guidelines obtained from the research results, thedevelopment of the above prototype based on photonics technology is proposed.
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Open AccessCommunication
Optimization of the Amplification of Equine Muscle-Derived Mesenchymal Stromal Cells in a Hollow-Fiber Bioreactor
by
Julien Duysens, Hélène Graide, Ariane Niesten, Ange Mouithys-Mickalad, Justine Ceusters and Didier Serteyn
Methods Protoc. 2024, 7(2), 32; https://doi.org/10.3390/mps7020032 - 2 Apr 2024
Abstract
The main causes of mortality in horses are the gastrointestinal pathologies associated with septic shock. Stem cells have shown, through systemic injection, a capacity to decrease inflammation and to regenerate injured tissue faster. Nevertheless, to achieve this rapid and total regeneration, systemic injections
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The main causes of mortality in horses are the gastrointestinal pathologies associated with septic shock. Stem cells have shown, through systemic injection, a capacity to decrease inflammation and to regenerate injured tissue faster. Nevertheless, to achieve this rapid and total regeneration, systemic injections of 1 to 2 million cells per kilogram of body weight must be considered. Here, we demonstrate for the first time the feasibility and expansion capacity of equine muscle-derived mesenchymal stromal cells (mdMSCs) in a functionally closed, automated, perfusion-based, hollow-fiber bioreactor (HFBR) called the Quantum™ Cell Expansion System (Terumo Blood and Cell Technologies). This feature greatly increases the number of generated cells with a surface area of 1.7 m2. The expansion of mdMSCs is very efficient in this bioreactor. The maximum expansion generated twenty times more cells than the initial seeding in nine days. The best returns were observed with an optimal seeding between 10 and 25 million mdMSCs, using the Bull’s eye loading method and with a run duration between 7 and 10 days. Moreover, all the generated cells kept their stem properties: the ability to adhere to plastic and to differentiate into chondroblasts, osteoblasts and adipocytes. They also showed the expression of CD-44 and CD-90 markers, with a positive rate above 93%, while CD-45 and MHCII were non-expressed, with a positive rate below 0.5%. By capitalizing on the scalability, automation and 3D culture capabilities of the Quantum™, it is possible to generate large quantities of high-quality equine mdMSCs for gastrointestinal disorders and other clinical applications.
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(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2024)
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Assessing Stress Induced by Fluid Shifts and Reduced Cerebral Clearance during Robotic-Assisted Laparoscopic Radical Prostatectomy under Trendelenburg Positioning (UroTreND Study)
by
Tobias Peschke, Matthias Feuerecker, Daniel Siegl, Nathalie Schicktanz, Christian Stief, Peter Zu Eulenburg, Alexander Choukér and Judith-Irina Buchheim
Methods Protoc. 2024, 7(2), 31; https://doi.org/10.3390/mps7020031 - 1 Apr 2024
Abstract
In addition to general anesthesia and mechanical ventilation, robotic-assisted laparoscopic radical prostatectomy (RALP) necessitates maintaining a capnoperitoneum and placing the patient in a pronounced downward tilt (Trendelenburg position). While the effects of the resulting fluid shift on the cardiovascular system seem to be
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In addition to general anesthesia and mechanical ventilation, robotic-assisted laparoscopic radical prostatectomy (RALP) necessitates maintaining a capnoperitoneum and placing the patient in a pronounced downward tilt (Trendelenburg position). While the effects of the resulting fluid shift on the cardiovascular system seem to be modest and well tolerated, the effects on the brain and the blood–brain barrier have not been thoroughly investigated. Previous studies indicated that select patients showed an increase in the optic nerve sheath diameter (ONSD), detected by ultrasound during RALP, which suggests an elevation in intracranial pressure. We hypothesize that the intraoperative fluid shift results in endothelial dysfunction and reduced cerebral clearance, potentially leading to transient neuronal damage. This prospective, monocentric, non-randomized, controlled clinical trial will compare RALP to conventional open radical prostatectomy (control group) in a total of 50 subjects. The primary endpoint will be the perioperative concentration of neurofilament light chain (NfL) in blood using single-molecule array (SiMoA) as a measure for neuronal damage. As secondary endpoints, various other markers for endothelial function, inflammation, and neuronal damage as well as the ONSD will be assessed. Perioperative stress will be evaluated by questionnaires and stress hormone levels in saliva samples. Furthermore, the subjects will participate in functional tests to evaluate neurocognitive function. Each subject will be followed up until discharge. Conclusion: This trial aims to expand current knowledge as well as to develop strategies for improved monitoring and higher safety of patients undergoing RALP. The trial was registered with the German Clinical Trials Register DRKS00031041 on 11 January 2023.
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(This article belongs to the Section Biomedical Sciences and Physiology)
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Diverting the Use of Hand-Operated Tablet Press Machines to Bioassays: A Novel Protocol to Test ‘Waste’ Insoluble Shell Matrices
by
Camille Lutet-Toti, Marie Da Silva Feliciano, Nelly Debrosse, Jérôme Thomas, Laurent Plasseraud and Frédéric Marin
Methods Protoc. 2024, 7(2), 30; https://doi.org/10.3390/mps7020030 - 1 Apr 2024
Abstract
To mineralize their shells, molluscs secrete a complex cocktail of proteins—collectively defined as the calcifying shell matrix—that remains occluded in the exoskeleton. Nowadays, protein extracts from shells are recognized as a potential source of bioactive substances, among which signalling molecules, bactericides or protease
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To mineralize their shells, molluscs secrete a complex cocktail of proteins—collectively defined as the calcifying shell matrix—that remains occluded in the exoskeleton. Nowadays, protein extracts from shells are recognized as a potential source of bioactive substances, among which signalling molecules, bactericides or protease inhibitors offer the most tangible perspectives in applied sciences, health, and aquaculture. However, one technical obstacle in testing the activity of shell extracts lies in their high insolubility. In this paper, we present a protocol that circumvents this impediment. After an adapted shell protein extraction and the production of two organic fractions—one soluble, one insoluble—we employ a hand-operated tablet press machine to generate well-calibrated tablets composed of 100% insoluble shell matrix. FT-IR monitoring of the quality of the tablets shows that the pressure used in the press machine does not impair the molecular properties of the insoluble extracts. The produced tablets can be directly tested in different biological assays, such as the bactericidal inhibition zone assay in Petri dish, as illustrated here. Diverting the use of the hand-operated tablet press opens new perspectives in the analysis of insoluble shell matrices, for discovering novel bioactive components.
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(This article belongs to the Section Synthetic and Systems Biology)
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Open AccessCorrection
Correction: Kharb et al. A Genotype-Independent, Simple, Effective and Efficient in Planta Agrobacterium-Mediated Genetic Transformation Protocol. Methods Protoc. 2022, 5, 69
by
Pushpa Kharb, Rinku Chaudhary, Narendra Tuteja and Prashant Kaushik
Methods Protoc. 2024, 7(2), 29; https://doi.org/10.3390/mps7020029 - 27 Mar 2024
Abstract
Additional Affiliation(s): Updated Affiliation [...]
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