Methods and Protocols最新文献

{"title":"Research on the Design and Performance of Plant Volatile Organic Compounds Water Removal Device Based on Optimized Filler Ratio.","authors":"Yali Yuan, Huasen Wang, Zhihong Sun, Chao Yu","doi":"10.3390/mps7040059","DOIUrl":"10.3390/mps7040059","url":null,"abstract":"<p><p>This study focuses on the development and optimization of a water removal device for biogenic volatile organic compounds (BVOCs) from plant emissions. BVOCs play a crucial role in various ecological processes and have potential therapeutic effects on human health. However, it is challenging to accurately detect and analyze BVOCs due to their very low concentrations and interference by water vapor. This study systematically evaluates different filler materials and ratios to alleviate water vapor interference while maintaining BVOCs' integrity. The experimental results demonstrate that the combination of MgSO₄ + Na₂SO₄ mixed filling and CuSO₄ layered filling in a 3:3:1 ratio can effectively improve the collection efficiency and detection accuracy of BVOCs. Meanwhile, the effectiveness of the device in improving the detection of volatile compounds in plant samples is also confirmed by the VOC verification experiments on <i>Michelia maudiae</i> and <i>Cinnamomum camphora</i> tree species after mechanical damage. The experimental results show that the device is effective in improving the detection of volatile compounds in plant samples. The findings provide a powerful technical means for exploring the role of BVOCs in environmental monitoring and scientific research.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 4","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11357541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080918","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 Multicenter, Single-Arm, Prospective Trial to Evaluate Efficacy and Safety of Dose-Dense Methotrexate, Vinblastine, Doxorubicin, and Carboplatin (DD-MVACarbo) Chemotherapy for Cisplatin-Ineligible Patients with Advanced Urothelial Cancer: Study Protocol of the CARBUNCLE Trial.","authors":"Makito Miyake, Satoshi Anai, Yusuke Iemura, Kazuki Ichikawa, Tatsuki Miyamoto, Atsushi Tomioka, Masaomi Kuwada, Yoshitaka Itami, Yukinari Hosokawa, Yoshiaki Matsumura, Eijiro Okajima, Kazumasa Torimoto, Nobutaka Nishimura, Mitsuru Tomizawa, Takuto Shimizu, Shunta Hori, Yosuke Morizawa, Daisuke Gotoh, Yasushi Nakai, Kiyohide Fujimoto","doi":"10.3390/mps7040058","DOIUrl":"10.3390/mps7040058","url":null,"abstract":"<p><p>Unresectable, metastatic, advanced urothelial carcinoma (aUC) is an aggressive disease and is treated with platinum-containing first-line chemotherapy, followed by immune checkpoint inhibitors and antibody-drug conjugates. Response to first-line chemotherapy is a vital priority in sequential treatment strategies because a better response to first-line chemotherapy is associated with a better response to subsequent therapies. Gemcitabine plus carboplatin chemotherapy is conventionally recommended for cisplatin-ineligible patients. This multicenter, single-arm prospective trial will investigate whether dose-dense methotrexate, vinblastine, doxorubicin, and carboplatin (DD-MVACarbo) chemotherapy is superior to gemcitabine plus carboplatin chemotherapy in terms of efficacy in platinum-naïve, cisplatin-ineligible patients with aUC. After screening and registration, a total of 46 patients will be treated with this novel chemotherapy regimen. The primary endpoint is the objective response rate. The secondary endpoints include disease control rate, patient-reported outcomes, and adverse events. No evidence of this novel intervention is available as of July 2024. The results are expected to change the standard of care and improve the management of patients with aUC.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 4","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11356861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080890","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 Protocol to Extract a Specific Genomic Region from a Public Whole-Genome Database and Modify Analytical Bin Length for Population Genetic Studies.","authors":"Muhammad Shoaib Akhtar, Shoji Kawamura","doi":"10.3390/mps7040057","DOIUrl":"10.3390/mps7040057","url":null,"abstract":"<p><p>With the advent of \"next-generation\" sequencing and the continuous reduction in sequencing costs, an increasing amount of genomic data has emerged, such as whole-genome, whole-exome, and targeted sequencing data. These applications are popular not only in mega sequencing projects, such as the 1000 Genomes Project and UK BioBank, but also among individual researchers. Evolutionary genetic analyses, such as the dN/dS ratio and Tajima's <i>D</i>, are demanded more and more for whole-genome-level population data. These analyses are often carried out under a uniform custom bin size across the genome. However, these analyses require subdivision of a genomic region into functional units, such as protein-coding regions, introns, and untranslated regions, and computing these genetic measures for large-scale data remains challenging. In a recent investigation, we successfully devised a method to address this issue. This method requires a multi-sample VCF file containing population data, a reference genome, target regions in the BED file, and a list of samples to be included in the analysis. Given that the targeted regions are extracted in a new VCF file, targeted population genetic analysis can be performed. We conducted Tajima's D analysis using this approach on intact and pseudogenes, as well as non-coding regions.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 4","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11357298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080913","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 Review of Histological Techniques for Differentiating Human Bone from Animal Bone.","authors":"Emanuela Stan, Camelia-Oana Muresan, Ecaterina Daescu, Raluca Dumache, Veronica Ciocan, Stefania Ungureanu, Dan Costachescu, Alexandra Enache","doi":"10.3390/mps7040051","DOIUrl":"10.3390/mps7040051","url":null,"abstract":"<p><p>The first step in anthropological study is the positive identification of human remains, which can be a challenging undertaking when bones are broken. When bone pieces from different species are mixed together, it can be crucial to distinguish between them in forensic and archaeological contexts. For years, anthropology and archaeology have employed the histomorphological analysis of bones to evaluate species-specific variations. Based on variations in the dimensions and configuration of Haversian systems between the two groups, these techniques have been devised to distinguish between non-human and human bones. All of those techniques concentrate on a very particular kind of bone, zone, and segment. Histomorphometric techniques make the assumption that there are size, form, and quantity variations between non-humans and humans. The structural components of Haversian bones are significant enough to use discriminant function analysis to separate one from the other. This review proposes a comprehensive literature analysis of the various strategies or techniques available for distinguishing human from non-human bones to demonstrate that histomorphological analysis is the most effective method to be used in the case of inadequate or compromised samples.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 4","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11270420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759788","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":"In Vitro Methods for Assessing the Antibacterial and Antibiofilm Properties of Essential Oils as Potential Root Canal Irrigants-A Simplified Description of the Technical Steps.","authors":"Jihad Diouchi, Jelena Marinković, Milica Nemoda, Lhoussaine El Rhaffari, Babacar Toure, Sonia Ghoul","doi":"10.3390/mps7040050","DOIUrl":"10.3390/mps7040050","url":null,"abstract":"<p><strong>Background: </strong>Essential oils have gained in significance due to their various biological activities, and there is a growing demand for them in many industries. The present article focuses on the technical steps for an in vitro evaluation of the antibacterial and antibiofilm activities of essential oils for potential use as root canal irrigant in dentistry.</p><p><strong>Methods: </strong>The bioactivities of the essential oil were investigated through in vitro assays. The gram-positive bacterium <i>Enterococcus faecalis</i> was used as a micro-organism model. The antibacterial activity of the essential oil was assessed using the microdilution method, and resazurin staining to determine the minimal inhibition concentrations (MICs) and the minimal bactericidal concentrations (MBCs). The antibiofilm effect was evaluated spectrophotometrically at 570 nm using the microplate cultivation technique and crystal violet staining.</p><p><strong>Conclusions: </strong>This article features a detailed in vitro protocol to facilitate the preparation of the essential oil samples, the bacterial suspension, and the methods used for assessment of the antibiofilm and antibacterial activities of the essential oil. The advantages of these approaches are presented in relation to the limits linked to the choice of the bacteria and the essential oil.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 4","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11270344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759789","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":"The Frailty Reduction via Implementation of Exercise, Nutrition, and Deprescribing (FRIEND) Trial: Study Protocol and Recruitment Results.","authors":"Michael Inskip, Carolina Almendrales Rangel, Chidiamara Maria Njoku, Fiona Barnett, Isabel Shih, Leonie O'Neill, Maria A Fiatarone Singh, Trinidad Valenzuela","doi":"10.3390/mps7020026","DOIUrl":"10.3390/mps7020026","url":null,"abstract":"<p><strong>Introduction: </strong>Virtually all adults in aged care facilities are frail, a condition which contributes to falls, cognitive decline, hospitalisation, and mortality. Polypharmacy, malnutrition, sedentariness, and sarcopenia are risk factors amenable to intervention. The Asia-Pacific Frailty Management Guidelines recommend anabolic exercise and the optimisation of medications and nutrition. However, no study has evaluated this best practice intervention triad in aged care.</p><p><strong>Methods: </strong>The Frailty Reduction via the Implementation of Exercise, Nutrition, and Deprescribing (FRIEND) Trial (ANZCTR No.ACTRN12622000926730p) is a staged 6-month translational trial evaluating resident outcomes, staff/caregiver knowledge, and institutional implementation in a Townsville aged care facility. Residents received high-intensity resistance exercise and balance training and medication and nutrition optimisation co-implemented by investigators (exercise physiologist, geriatrician, pharmacist, and nutritionist) and facility staff. Staff and caregivers completed comprehensive education modules and training. We report the trial protocol and recruitment results.</p><p><strong>Results: </strong>29 residents (21 female, age: 88.6 ± 6.3 years) were recruited. At baseline, the residents were frail (frailty scale nursing home (FRAIL-NH); 6.3 ± 2.4/14), cognitively impaired (Montreal Cognitive Assessment; 13.8 ± 6.8/30), functionally impaired (Short Physical Performance Battery; 4.9 ± 3.1/12, 6 min walk distance; 222.2 ± 104.4 m), and were prescribed numerous medications (15.5 ± 5.9). Two residents died and one withdrew before the intervention's commencement. Thirty family members and 19 staff (carers, allied health assistants, nurse managers, registered nurses, lifestyle-leisure officers, kitchen/hospitality staff, and senior leadership) were recruited to receive frailty education modules.</p><p><strong>Conclusions: </strong>The FRIEND trial is currently being implemented with results expected in mid-2024. This is the first trial to evaluate the implementation of the best practice frailty guidelines including anabolic exercise and medication/nutritional optimisation in residential aged care.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10961770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140207210","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":"Development and Validation of Micro-Azocasein Assay for Quantifying Bromelain.","authors":"Krishna Pillai, Javed Akhter, Ahmed H Mekkawy, Sarah J Valle, David L Morris","doi":"10.3390/mps7020025","DOIUrl":"10.3390/mps7020025","url":null,"abstract":"<p><p>The proteolytic activity of enzymes may be evaluated by a colorimetric method with azocasein. Hence, we developed a micro-assay to quantify bromelain using azocasein. A total of 250 µL of 1.0% azocasein in dH₂O was added to 250 µL of test solution, vortexed and incubated at ambient room temperature/30 min. The reaction was terminated with 1500 µL of 5% trichloroacetic acid, vortexed and centrifuged. A total of 150 µL of 0.5M NaOH was added to 150 µL of supernatant in triplicates, and absorbance was recorded at 410 nm. The linearity of the calibration curve was tested with 200-800 µg/mL serial dilutions. The detection limit, precision, accuracy, and robustness were tested along with the substrate enzyme reaction time and solvent matrix effect. Good linearity was seen with serially diluted 200 µg/mL bromelain. The limit of quantification and limit of detection were 5.412 and 16.4 µg/mL, respectively. Intra-day and inter-day analyses showed a relative standard deviation below 2.0%. The assay was robust when tested over 400-450 nm wavelengths. The assays performed using dH₂O or PBS diluents indicated a higher sensitivity in dH₂O. The proteolytic activity of bromelain was enhanced with L-cysteine or N-acetylcysteine. Hence, this micro-azocasein assay is reliable for quantifying bromelain.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10961761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140207250","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":"Effects on Quality of Life of a Telemonitoring Platform amongst Patients with Cancer (EQUALITE): A Randomized Trial Protocol.","authors":"Felipe Martínez, Carla Taramasco, Manuel Espinoza, Johanna Acevedo, Carolina Goic, Bruno Nervi","doi":"10.3390/mps7020024","DOIUrl":"10.3390/mps7020024","url":null,"abstract":"<p><p>Cancer, a pervasive global health challenge, necessitates chemotherapy or radiotherapy treatments for many prevalent forms. However, traditional follow-up approaches encounter limitations, exacerbated by the recent COVID-19 pandemic. Consequently, telemonitoring has emerged as a promising solution, although its clinical implementation lacks comprehensive evidence. This report depicts the methodology of a randomized trial which aims to investigate whether leveraging a smartphone app called <i>Contigo</i> for disease monitoring enhances self-reported quality of life among patients with various solid cancers compared to standard care. Secondary objectives encompass evaluating the app's impact on depressive symptoms and assessing adherence to in-person appointments. Randomization will be performed independently using an allocation sequence that will be kept concealed from clinical investigators. Contigo offers two primary functions: monitoring cancer patients' progress and providing educational content to assist patients in managing common clinical situations related to their disease. The study will assess outcomes such as quality of life changes and depressive symptom development using validated scales, and adherence to in-person appointments. Specific scales include the EuroQol Group's EQ-5D questionnaire and the Patient Health Questionnaire (PHQ-9). We hypothesize that the use of Contigo will assist and empower patients receiving cancer treatment, which will translate to better quality of life scores and a reduced incidence of depressive symptoms. All analyses will be undertaken with the intention-to-treat principle by a statistician unaware of treatment allocation. This trial is registered in ClinicalTrials under the registration number NCT06086990.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10961787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140207251","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 Virtual Case Presentation Platform: Protocol Study.","authors":"Imad Alex Awada, Adina Magda Florea, Alexandru Scafa-Udriște","doi":"10.3390/mps7020023","DOIUrl":"10.3390/mps7020023","url":null,"abstract":"<p><p>Gaining practical experience is indispensable for medical students. Therefore, when medical students were prevented access to hospitals during the COVID-19 pandemic in Romania, there was an urgent need to find a solution that would allow medical students to develop the skills they would usually develop in hospitals but without the need to be physically present in a hospital. This was the reason behind the idea of developing a Virtual Case Presentation Platform. The platform offers the possibility for medical students to reproduce virtually, in clinically valid scenarios, the diagnostic process and treatment recommendation, as well as the interactions with patients that usually take place in hospitals using natural language through speech and text. On the platform, the students receive valuable feedback from the professors about their performance. In order to reproduce the whole targeted experience for students, without missing anything, before starting the development of the platform, it was mandatory to identify and understand all the aspects that should be covered by the platform. The proposed platform covers the different aspects that have been identified for the diagnostic process and treatment recommendation. It enables medical students to develop essential skills for their future careers as doctors.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10961792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140207249","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 Simple and Rapid Protocol for the Isolation of Murine Bone Marrow Suitable for the Differentiation of Dendritic Cells.","authors":"Runqiu Song, Mariam Bafit, Kirsteen M Tullett, Peck Szee Tan, Mireille H Lahoud, Meredith O'Keeffe, Anthony W Purcell, Asolina Braun","doi":"10.3390/mps7020020","DOIUrl":"10.3390/mps7020020","url":null,"abstract":"<p><p>The generation of bone-marrow-derived dendritic cells is a widely used approach in immunological research to study antigen processing and presentation, as well as T-cell activation responses. However, the initial step of isolating the bone marrow can be time-consuming, especially when larger numbers of precursor cells are required. Here, we assessed whether an accelerated bone marrow isolation method using centrifugation is suitable for the differentiation of FMS-like tyrosine kinase 3 ligand-driven dendritic cells. Compared to the conventional flushing method, the centrifugation-based isolation method resulted in a similar bone marrow cell yield on Day 0, increased cell numbers by Day 8, similar proportions of dendritic cell subsets, and consequently a higher number of type 1 conventional dendritic cells (cDC1) from the culture. Although the primary purpose of this method of optimization was to improve experimental efficiency and increase the output of cDC1s, the protocol is also compatible with the differentiation of other dendritic cell subsets such as cDC2 and plasmacytoid dendritic cells, with an improved output cell count and a consistent phenotype.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":"7 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10961764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140207248","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}