MethodsX最新文献

{"title":"Integrating musealized archaeological sediment collections into current geoarchaeological analytical frameworks for sustainable research practices","authors":"","doi":"10.1016/j.mex.2024.102897","DOIUrl":"10.1016/j.mex.2024.102897","url":null,"abstract":"<div><p>We present a review of the latest framework achievements in geoarchaeological sciences applied to microstratigraphic and biomolecular studies of prehistoric archaeological contexts, highlighting the importance of musealized archaeological stratigraphies. We assess how today's scientific and technological accomplishments can be tailored for archaeological human ecology studies with analytical ensembles that provide unprecedented results. Sampling and processing workflows originating from resin consolidation and thin section micromorphology of undisturbed blocks of archaeological soils and sediments, guarantee subsampling accuracy at the micrometre scale granting access to individual components otherwise impossible to target: the achievable information yield makes even the smallest soil samples potential sources of pioneering discoveries. Yet, archaeological excavations are still the primary mode of retrieving new soil samples. We argue that, when dealing with archaeological sites that were excavated and partially musealised in the past, the exploration of related museum collections should be prioritized as perspective source of new study samples. Analysing old and potentially very informative samples, with an approach that we define as “Green Archaeology”, may represent a source of well-structured primary data as well as a means for planning new excavations, delivering novel discoveries while safeguarding site integrity and promoting Third Mission valorisation of sites and heritage dormant collections.</p></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003492/pdfft?md5=4ecee528752df05f61f1c3d5a57313fb&pid=1-s2.0-S2215016124003492-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141979390","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":"Mindfulness and compassion-based programs on eating behavior of post-bariatric surgery patients: A two phased clinical trial protocol","authors":"","doi":"10.1016/j.mex.2024.102885","DOIUrl":"10.1016/j.mex.2024.102885","url":null,"abstract":"<div><p>Introduction: Weight regain after bariatric surgery remains a relevant and worrisome topic, requiring greater understanding and involvement in research into new adjuvant treatments. This study aims to compare the preliminary effectiveness and feasibility of the Mindfulness-Based Health Promotion and Attachment-Based Compassion Therapy programs as opposed to usual treatments (workshops) on the eating behavior of patients with progressive weight gain after bariatric surgery in Brazilian patients at a private clinic. It was hypothesized that both interventions are feasible and that the self-compassion program may be more effective than the mindfulness program. Methods: The study will be divided into two phases: a cross-analytical study of those who underwent bariatric surgery and a randomized controlled trial only with the ones who had weight regain. Interventions will be conducted for eight weeks synchronously with three assessment points (baseline, post intervention, and 6-month follow-up), both online. The primary outcome will be a change in eating behavior. Secondary outcomes will include improved quality of life, enhanced body image satisfaction and reduced distortion (Brazilian Silhouette Scales for adults), better weight management (maintenance or weight reduction), increased frequency of activity and monitoring with the surgery team. Qualitative data will also be collected by online identification of a sub-sample of participants. Results: Improvements are expected in eating behavior, weight, reverse progressive weight gain, classification of self-image, quality of life, and levels of mindfulness, self-compassion, and anxiety. Conclusion: This study seeks to gather preliminary evidence on the effectiveness of mindfulness and compassion training for the adjunctive treatment of progressive weight gain in post-bariatric patients.</p><p><em>Clinical Trials.gov</em> Registration ID: NCT04171713.</p></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003376/pdfft?md5=897a7d4fabcc2917ee683d6d6667da22&pid=1-s2.0-S2215016124003376-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142040687","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":"Challenges in illumination analysis and design for Martian surface-level habitation","authors":"","doi":"10.1016/j.mex.2024.102898","DOIUrl":"10.1016/j.mex.2024.102898","url":null,"abstract":"<div><p>It is needless to say that travel to and settlement on Mars are associated with extreme levels of scientific and engineering issues. This will only be amplified with the long-term duration of the mission, not only due to scarcity of resources, but also as the psychological aspects of the dynamics among the crew increase drastically. It should be emphasized that this is a scientific crew, who have undergone high levels of confinement during space travel to Mars, O (10² Earth days), are living in semi-solitude and partial confinement conditions for durations of O (10³ Earth days), and even at the nominal termination of the mission, foresee a high-risk and arduous travel time of O (10² Earth days) back to the Earth. The mental weight of the described mission with its slow pace and tardy episodes, puts the crew under severe psychological issues. Minimal and conservative design of spaces, lack of constant access to the exterior, and social solitude are among major factors contributing to the psychological well-being of the crew. Furthermore, the overall lower levels of natural light, accompanied by the minimum possible area of transparent facades, protecting the crew from harmful radiations and cold exterior, burden the mental conditions of the crew even more. Given the limited availability of data from the surface of Mars, study of the effects linked to the lighting and illumination design of the habitats is challenging. The current manuscript hopes to shed light on the illumination and lighting design and simulation procedure, required data, assumptions, and final results for the surface-level habitats on Mars.</p><ul><li><span>•</span><span><p>Mars / Sub orbital configuration allows for limited natural lighting, however, upon site-specific analysis, it might be considerable as a base passive source.</p></span></li><li><span>•</span><span><p>Current simulation tools are design based on Earth-bound design requirements. These need to be re-oriented to match available planetary data.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003509/pdfft?md5=a6cb63e79b90ced700f91396a46b6861&pid=1-s2.0-S2215016124003509-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991110","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":"Real-time sign language detection: Empowering the disabled community","authors":"","doi":"10.1016/j.mex.2024.102901","DOIUrl":"10.1016/j.mex.2024.102901","url":null,"abstract":"<div><p>Interaction and communication for normal human beings are easier than for a person with disabilities like speaking and hearing who may face communication problems with other people. Sign Language helps reduce this communication gap between a normal and disabled person. The prior solutions proposed using several deep learning techniques, such as Convolutional Neural Networks, Support Vector Machines, and K-Nearest Neighbors, have either demonstrated low accuracy or have not been implemented as real-time working systems. This system addresses both issues effectively. This work extends the difficulties faced while classifying the characters in Indian Sign Language(ISL). It can identify a total of 23 hand poses of the ISL. The system uses a pre-trained VGG16 Convolution Neural Network(CNN) with an attention mechanism. The model's training uses the Adam optimizer and cross-entropy loss function. The results demonstrate the effectiveness of transfer learning for ISL classification, achieving an accuracy of 97.5 % with VGG16 and 99.8 % with VGG16 plus attention mechanism.</p><ul><li><span>•</span><span><p>Enabling quick and accurate sign language recognition with the help of trained model VGG16 with an attention mechanism.</p></span></li><li><span>•</span><span><p>The system does not require any external gloves or sensors, which helps to eliminate the need for physical sensors while simplifying the process with reduced costs.</p></span></li><li><span>•</span><span><p>Real-time processing makes the system more helpful for people with speaking and hearing disabilities, making it easier for them to communicate with other humans.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003534/pdfft?md5=f4ed0ed2c2e051e0fcb53b858a504e61&pid=1-s2.0-S2215016124003534-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141993833","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 reliable method to prepare milligram size environmental samples to quantify metal(loid)s by high-resolution graphite furnace atomic absorption spectrometry","authors":"","doi":"10.1016/j.mex.2024.102896","DOIUrl":"10.1016/j.mex.2024.102896","url":null,"abstract":"<div><p>We searched for an extraction method that would allow a precise quantification of metal(loid)s in milligram-size samples using high-resolution graphite furnace atomic absorption spectrometry (HR-GFAAS). We digested biological (DORM-4, DOLT-5 and TORT-3) and sediment (MESS-4) certified reference materials (CRMs) using nitric acid in a drying oven, aqua regia in a drying oven, or nitric acid in a microwave. In addition, we digested MESS-4 using a mixture of nitric and hydrofluoric acids in a drying oven. We also evaluated the effect of sample size (100 and 200 mg) on the extraction efficiency. Nitric acid extraction in a drying oven yielded the greatest recovery rates for all metal(loid)s in all tested CRMs (80.0 %–100.0 %) compared with the other extraction methods tested (67.3 %–99.2 %). In most cases, the sample size did not have a significant effect on the extraction efficiency. Therefore, we conclude that nitric acid digestion in a drying oven is a reliable extraction method for milligram-size samples to quantify metal(loid)s with HR-GFAAS. This validated method could provide substantial benefits to environmental quality monitoring programs by significantly reducing the time and costs required for sample collection, storage, transport and preparation, as well as the amount of hazardous chemicals used during sample extraction and analysis.</p><p></p><ul><li><span>•</span><span><p>Sample digestion with nitric acid in a drying oven yielded the greatest recovery rates of metal(loid)s from biological and sediment certified reference materials.</p></span></li><li><span>•</span><span><p>The recovery rates of metal(loid)s from biological and sediment certified reference materials using nitric acid digestion in a drying oven ranged from 73 % to 100 %.</p></span></li><li><span>•</span><span><p>Digestion with nitric acid in a drying oven is a simple and reliable method to extract small size environmental samples for metal(loid)s quantification by high-resolution graphite furnace atomic absorption spectrometry.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003480/pdfft?md5=b76f6c496dae42d2cf20a4edf24a4e9e&pid=1-s2.0-S2215016124003480-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141964337","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":"Methods to quantify gait rehabilitation following lower limb fractures","authors":"","doi":"10.1016/j.mex.2024.102894","DOIUrl":"10.1016/j.mex.2024.102894","url":null,"abstract":"<div><p>Lower limb fragility fractures require long-term rehabilitation and are also very expensive to treat. Clinically, early weight bearing and walking stability were reported as key measures of fracture restoration. This study introduces methods to numerically quantify these performance indices for a range of ankle and knee joint fractures. As a follow-up of initial treatment, experimental data was collected using force plates from 367 subjects divided into seven groups: ankle fracture (AF), lower leg ankle fracture (AL), calcaneus foot fracture (CF), knee tibia fracture (KF), knee patella fracture (KP), kneecap rupture (KR), and normal limb (NL). For each joint, data was analysed to evaluate intralimb and interlimb weight-bearing and walking stability for all fracture conditions. These thresholds were statistically compared with normal subjects. Some advantages of evaluating fracture restoration indices over the others include:</p><ul><li><span>•</span><span><p>to quantify fracture restoration (weight-bearing, walking stability, and gait symmetry) using minimum setup and signal requirements.</p></span></li><li><span>•</span><span><p>to provide comprehensive tools to assess and overcome fracture-associated complications through a detailed preview of fractured limb functionality during subphases of a gait cycle.</p></span></li><li><span>•</span><span><p>in clinical research, such assessments are important as a reference to evaluate existing or new rehabilitative interventions.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003467/pdfft?md5=173a41de64e273203b892357ae3cba17&pid=1-s2.0-S2215016124003467-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141978040","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":"Improving the measurement of nitrogen stable isotopes in organic materials containing high C:N ratios using a 5A molecular sieve column","authors":"","doi":"10.1016/j.mex.2024.102889","DOIUrl":"10.1016/j.mex.2024.102889","url":null,"abstract":"<div><p>The nitrogen stable isotope composition (δ¹⁵N) of plant materials has numerous applications. Plant materials like bark can have a very high C:N ratio. Incomplete C combustion in such samples interferes with the δ¹⁵N measurement due to CO production. We modified the standard setup for δ¹⁵N measurement using an elemental analyzer (EA) coupled to an isotope ratio mass spectrometer (IRMS) by incorporating a 5A molecular sieve column, which better separates N₂ from CO. We compared this new modified setup and the standard one for the measurement of bark samples. Precision and accuracy for δ¹⁵N in standards with low C:N ratio were equivalent for the two methods. However, for bark the results obtained with the new method had better precision and accuracy than the standard method. <strong>Replicates are nevertheless recommended with the new method to ensure confidence in the results.</strong></p><ul><li><span>•</span><span><p>During elemental analysis, incomplete combustion of material with high C:N ratio can lead to CO formation, which interferes with δ¹⁵N IRMS measurements.</p></span></li><li><span>•</span><span><p>Here we use a 5A molsieve column to remove the CO interference in δ¹⁵N measurements Precision and accuracy on δ¹⁵N measurements of samples with high C content are significantly improved</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003418/pdfft?md5=b26da25765ee88c19104b645709e0b9f&pid=1-s2.0-S2215016124003418-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141978096","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 unified purification method for actin-binding proteins using a TEV-cleavable His-Strep-tag","authors":"","doi":"10.1016/j.mex.2024.102884","DOIUrl":"10.1016/j.mex.2024.102884","url":null,"abstract":"<div><p>The actin cytoskeleton governs the dynamic functions of cells, ranging from motility to phagocytosis and cell division. To elucidate the molecular mechanism, <em>in vitro</em> reconstructions of the actin cytoskeleton and its force generation process have played essential roles, highlighting the importance of efficient purification methods for actin-binding proteins. In this study, we introduce a unified purification method for actin-binding proteins, including capping protein (CP), cofilin, ADF, profilin, fascin, and VASP, key regulators in force generation of the actin cytoskeleton. Exploiting a His-Strep-tag combined with a TEV protease cleavage site, we purified these diverse actin-binding proteins through a simple two-column purification process: initial purification through a Strep-Tactin column and subsequent tag removal through the reverse purification by a Ni-NTA column. Biochemical and microscopic assays validated the functionality of the purified proteins, demonstrating the versatility of the approach. Our methods not only delineate critical steps for the efficient preparation of actin-binding proteins but also hold the potential to advance investigations of mutants, isoforms, various source species, and engineered proteins involved in actin cytoskeletal dynamics.</p><ul><li><span>•</span><span><p>Unified purification method for various actin-binding proteins.</p></span></li><li><span>•</span><span><p>His-Strep-tag and TEV protease cleavage for efficient purification.</p></span></li><li><span>•</span><span><p>Functional validation through biochemical and microscopic assays.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003364/pdfft?md5=297b77b7062c95cd4a0559dd1a6cb502&pid=1-s2.0-S2215016124003364-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141964310","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":"Determination of toxicological relevant arsenic species in urine by hydride generation microwave-induced plasma optical emission spectrometry","authors":"","doi":"10.1016/j.mex.2024.102893","DOIUrl":"10.1016/j.mex.2024.102893","url":null,"abstract":"<div><p>An analytical method for the determination of toxicological relevant species of arsenic in urine was developed and validated using hydride generation microwave-induced emission spectrometry (HG-MP-AES). This strategy can be used as an alternative to HG-HPLC-ICP-MS considered as a reference technique for arsenic speciation. This procedure is notably less expensive than other techniques and sample preparation and requires only a few steps.</p><ul><li><span>•</span><span><p>Hydride generation with MP-AES detection has proven to be an effective technique for measuring arsenic metabolites in urine, which is relevant for occupational monitoring and health risk assessment purposes.</p></span></li><li><span>•</span><span><p>This method offers simplicity and cost-effectiveness, serving as an alternative to classical analytical procedures typically used for arsenic analysis in urine.</p></span></li><li><span>•</span><span><p>The methodology has been successfully applied for the purpose of workers' health surveillance.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003455/pdfft?md5=f59eef942f17c251157e6eb1ce5c7092&pid=1-s2.0-S2215016124003455-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141978097","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":"Constant head-transient method using pressure and flow data for determining permeability and specific storage of tight rocks","authors":"","doi":"10.1016/j.mex.2024.102899","DOIUrl":"10.1016/j.mex.2024.102899","url":null,"abstract":"<div><p>This paper describes a ‘constant head-transient method’ for estimating permeability and specific storage of tight rock samples, such as shale and crystalline rocks. Experimental tests are conducted using a cylindrical rock sample subjected to confining pressure, through which pressure diffusion occurs from a constant upstream pressure (or constant head) to a finite downstream storage. Unlike the pulse-transient method, the upstream fluid flow into the sample can be measured using a syringe pump because of no change in upstream pressure. By minimizing the downstream storage, the test time can be significantly reduced, but only the downstream pressure transient data do not yield accurate results on permeability and specific storage estimations. By combining the flow data with the pressure data, the proposed method aims at saving the test time and improving the accuracy of their estimations in extremely low permeability rock samples.</p><ul><li><span>•</span><span><p>A constant head-transient method for measuring the hydraulic properties of tight rocks was developed with a boundary condition of constant upstream pressure and finite downstream storage.</p></span></li><li><span>•</span><span><p>The test time can be saved by minimizing the downstream storage, and the upstream flow can be measured to improve the accuracy in measuring the hydraulic properties.</p></span></li><li><span>•</span><span><p>Combining the flow and pressure objective functions yields the best curve fitting for both pressure and flow curves.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124003510/pdfft?md5=abb0ffe6280da0e090c741642769fb6c&pid=1-s2.0-S2215016124003510-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141978098","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}