MethodsX最新文献

{"title":"Measurement of ethanol concentration for monitoring the solvent exchange during the alcogel preparation","authors":"","doi":"10.1016/j.mex.2024.102960","DOIUrl":"10.1016/j.mex.2024.102960","url":null,"abstract":"<div><div>A crucial and time-consuming stage in aerogel production is the solvent exchange process for alcogel formation. This process involves multiple steps, exposing the hydrogel to ethanol solutions with increasing concentration until the equilibrium in each step. Currently, the determination of contact time between phases (hydrogel and liquid solution) is either arbitrary or based on prior studies. However, considering the unique physicochemical characteristics of each system, as well as the solid-liquid interactions and the liquid diffusion within the matrix, the required time may vary. Monitoring this step can lead to a reduction in the time needed for alcogel production and the optimization of the entire process. The refractive index serves as a tool to assess ethanol concentration in the liquid solution over time, providing immediate information about the status of the solvent exchange. Alongside, differential scanning calorimetry can be employed to evaluate ethanol content in the alcogel (solid phase), confirming the attainment of equilibrium between phases.</div><div><ul><li><span>•</span><span><div>This research introduces a technique for monitoring solvent exchange.</div></span></li><li><span>•</span><span><div>Refractive index measurement of the liquid solvent offers immediate concentration information into the status of the solvent exchange.</div></span></li><li><span>•</span><span><div>Differential scanning calorimetry is applicable for measuring the ethanol content within the alcogel and validating refractive index findings.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318886","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":"Facilitating microplastic ingestion in aquatic models: A verified protocol for daphnia magna as a trojan horse vector","authors":"","doi":"10.1016/j.mex.2024.102973","DOIUrl":"10.1016/j.mex.2024.102973","url":null,"abstract":"<div><div>Microplastic pollution poses a significant environmental threat due to its persistence, widespread distribution, and inherent toxic potential. Despite the increasing number of publications in this field, a standardized protocol for the laboratory intake of microplastics by <em>Daphnia magna</em> has yet to be established. In this study, we introduce a verified protocol designed to facilitate the ingestion of microplastic particles (MPs) by <em>D. magna</em>, ranging in size from 5–55 µm. This protocol can be further applied to evaluate the toxicity of MPs on <em>D. magna</em>, a crucial organism model in ecotoxicology. Furthermore, this protocol can be used to assess toxicity of MPs in other aquatic species, such as fish, by using daphnids as a vehicle for ensuring the ingestion of these particles. Consequently, this protocol can be applied to study also one of the most pressing concerns regarding exposure to MPs, the transfer of MPs through different trophic levels, which has a great potential for ecotoxicological studies.<ul><li><span>•</span><span><div>The influence of MPs concentration, duration and exposure dynamics and <em>D. magna</em> age/size in MPs intake were tested.</div></span></li><li><span>•</span><span><div>We have determined the optimal conditions for promoting microplastic ingestion by <em>D. magna</em>.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142326447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An artificial bee colony optimization algorithms for solving fuzzy capacitated logistic distribution center problem","authors":"","doi":"10.1016/j.mex.2024.102964","DOIUrl":"10.1016/j.mex.2024.102964","url":null,"abstract":"<div><div>This paper presents a methodological approach to solving the fuzzy capacitated logistic distribution center problem, with a focus on the optimal selection of distribution centers to meet the demands of multiple plants. The distribution centers are characterized by fixed costs and capacities, while plant demands are modeled using fuzzy triangular membership functions. The problem is mathematically formulated by converting fuzzy demands into crisp values, providing a structured framework for addressing uncertainty in logistic planning. To support future research and facilitate comparative analysis, 20 benchmark problems were generated, filling a gap in the existing literature. Three distinct artificial bee colony algorithm variants were hybridized with a heuristic: one using the best solution per iteration, another incorporating chaotic mapping and adaptive procedures, and the third employing convergence and diversity archives. An experimental design based on Taguchi's orthogonal arrays was employed for optimizing the algorithm parameters, ensuring systematic exploration of the solution space. The developed methods offer a comprehensive toolkit for addressing complex, uncertain demands in logistic distribution, with code provided for reproducibility.</div><div>Key contributions include:<ul><li><span>•</span><span><div>Development of a fuzzy model for the selection of distribution centers with fixed costs and capacities under uncertain plant demands.</div></span></li><li><span>•</span><span><div>Generation of 20 benchmark problems to advance research in the fuzzy capacitated logistic distribution center problem domain.</div></span></li><li><span>•</span><span><div>Integration of a heuristic approach with three distinct ABC algorithm variants, each contributing unique methodological insights.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318887","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":"Developing a new tool to capture the nature dose to reduce loneliness and improve quality of life","authors":"","doi":"10.1016/j.mex.2024.102969","DOIUrl":"10.1016/j.mex.2024.102969","url":null,"abstract":"<div><div>Recognition of the health benefits of nature contact has increased. Simultaneously, growing numbers of people worldwide experience loneliness. There is a movement towards prescribing nature-based activities to improve/promote social connections, health, and quality of life. Yet, what constitutes a therapeutic nature dose is not well understood, due in part, to the lack of instruments that capture the characteristics of nature-based activities and measure ‘nature dose.’ We created a nature dose measurement tool to fill this gap by capturing various aspects of contact with nature and perceptions regarding park access, quality, naturalness, psychological distance to nature, and biodiversity. This tool will facilitate greater understanding of how natural areas, nature-based activities, and nature exposure reduce loneliness and promote health-related quality of life. Measuring nature dose with standardized tools and documenting benefits will generate</div><div>the evidence base needed to design, implement and evaluate nature-based social interventions for improving health and quality of life.<ul><li><span>•</span><span><div>This tool captures the nature dose to reduce loneliness and promote quality of life.</div></span></li><li><span>•</span><span><div>Constructs range from park quality and access, to mood, to biodiversity perceptions.</div></span></li><li><span>•</span><span><div>The standardized nature dose tool will help design nature-based social interventions.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124004205/pdfft?md5=aea2a32aba116c5d19435dc3ef5793bb&pid=1-s2.0-S2215016124004205-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142314780","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":"Explainable rotation-invariant self-supervised representation learning","authors":"","doi":"10.1016/j.mex.2024.102959","DOIUrl":"10.1016/j.mex.2024.102959","url":null,"abstract":"<div><p>This paper describes a method that can perform robust detection and classification in out-of-distribution rotated images in the medical domain. In real-world medical imaging tools, noise due to the rotation of the body part is frequently observed. This noise reduces the accuracy of AI-based classification and prediction models. Hence, it is important to develop models which are rotation invariant. To that end, the proposed method - RISC (rotation invariant self-supervised vision framework) addresses this issue of rotational corruption. We present state-of-the-art rotation-invariant classification results and provide explainability for the performance in the domain. The evaluation of the proposed method is carried out on real-world adversarial examples in Medical Imagery-OrganAMNIST, RetinaMNIST and PneumoniaMNIST. It is observed that RISC outperforms the rotation-affected benchmark methods by obtaining 22%, 17% and 2% accuracy boost on OrganAMNIST, PneumoniaMNIST and RetinaMNIST rotated baselines respectively. Further, explainability results are demonstrated.</p><p>This methods paper describes:</p><ul><li><span>•</span><span><p>a representation learning approach that can perform robust detection and classification in out-of-distribution rotated images in the medical domain.</p></span></li><li><span>•</span><span><p>It presents a method that incorporates self-supervised rotation invariance for correcting rotational corruptions.</p></span></li><li><span>•</span><span><p>GradCAM-based explainability for the rotational SSL pretext task and the downstream classification outcomes for the three benchmark datasets are presented</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124004102/pdfft?md5=960ede7733b4b76435ee298fd9a1d9b1&pid=1-s2.0-S2215016124004102-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142242325","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":"Maximizing single cell dissociation protocol for individual zebrafish embryo","authors":"","doi":"10.1016/j.mex.2024.102958","DOIUrl":"10.1016/j.mex.2024.102958","url":null,"abstract":"<div><p>Single-cell sequencing has revolutionized our understanding of cellular heterogeneity and cell state, enabling investigations across diverse fields such as developmental biology, immunology, and cancer biology. However, obtaining a high-quality single-cell suspension is still challenging, particularly when starting with limited materials like Zebrafish embryos, a powerful animal model for studying developmental processes and human diseases. Here, we present an optimized protocol for isolating single cells from individual zebrafish embryos, offering a valuable resource for researchers interested in working with limited starting material. The protocol facilitates unique investigations utilizing individual embryos, such as inter-individual genetic differences and embryo-specific lineage tracing analysis. Using a refined single-cell isolation protocol alongside zebrafish as a model organism, researchers can access a resource for exploring the emergence of all types and states of cells, advancing our understanding of cellular processes and disease mechanisms.</p></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124004096/pdfft?md5=7985c5550bbcb1998dc3eb96d4d77256&pid=1-s2.0-S2215016124004096-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142243119","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":"Step-by-step synthetic route to access eugenol-1,2,3-triazole-chalcone hybrid","authors":"","doi":"10.1016/j.mex.2024.102956","DOIUrl":"10.1016/j.mex.2024.102956","url":null,"abstract":"<div><p>Molecular hybridization represents a strategic approach in drug design, where two or more pharmacophoric elements from distinct bioactive molecules are integrated into a single hybrid compound. In this study, we synthesized hybrid compounds of chalcone, triazole, and eugenol through straightforward reactions using 4-hydroxyacetophenone as the starting material. Initially, 4-hydroxyacetophenone (<strong>1</strong>) underwent alkylation with 1,4-dibromobutane to produce compound <strong>2</strong> with an 84 % yield. Compound <strong>2</strong> was then subjected to azidation, resulting in azidobutoxyacetophenone <strong>3</strong> with a 71 % yield. Subsequently, compound <strong>3</strong> was reacted with either benzaldehyde or 4-methoxybenzaldehyde via base-catalyzed aldol condensation, yielding azidobutoxychalcones <strong>4a</strong> (69 %) and <strong>4b</strong> (84 %). Finally, azide-alkyne [3+2] cycloaddition between <strong>4a/4b</strong> and propargylated eugenol afforded chalcone derivatives bearing eugenol-1,2,3-triazole hybrids 5a and 5b, each with a 90 % yield.</p><ul><li><span>•</span><span><p>Synthesized chalcones featuring an eugenol-1,2,3-triazole scaffold using 4-hydroxyacetophenone as the starting material.</p></span></li><li><span>•</span><span><p>Synthesis was accomplished through a four-step reaction sequence.</p></span></li><li><span>•</span><span><p>Products were obtained in good yield.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124004072/pdfft?md5=4b5eedfc3f250a812c08b771d37641eb&pid=1-s2.0-S2215016124004072-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142242324","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":"GAM4water: An R-based method for extracting wetted areas from remotely-sensed images","authors":"","doi":"10.1016/j.mex.2024.102955","DOIUrl":"10.1016/j.mex.2024.102955","url":null,"abstract":"<div><div>We present ‘GAM4water,’ a R-based method to classify wetted and non-wetted (dry) areas using remotely sensed image indices derived from such images. The GAM4water classification algorithm is built around a Generalized Additive Model (GAM) capable of accounting for non-linear responses. GAM4water can use any type of radiometric data, whether from drones, satellites or other platforms, and can be used with data of different spatial resolutions, geographic extents and spatial reference systems. It is a supervised tool that uses pixel information to distinguish between wetted and dry areas within an image set, extract them and produce a rich output that includes a binary raster, polygons of wetted areas, and a classification performance report. We tested the method in two case-studies, one using high resolution drone images and another using satellite images. The tests show that GAM4water can produce highly accurate classifications of wetted and non-wetted areas, and has the additional benefit of being easily customizable and not requiring complex implementation procedures.<ul><li><span>•</span><span><div>This paper introduces the first R based method of wetted area extraction for remotely-sensed images.</div></span></li><li><span>•</span><span><div>The method is based on Generalized Additive Models and is applicable to any remotely-sensed data.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124004060/pdfft?md5=f3b7be30721e0a71e17718184a15d09a&pid=1-s2.0-S2215016124004060-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142312493","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":"Characterisation of growth parameters for the extremely acidophilic archaeon Ferroplasma acidiphilum DSM 12658 using a two-step turbidimetric growth measurement method","authors":"","doi":"10.1016/j.mex.2024.102953","DOIUrl":"10.1016/j.mex.2024.102953","url":null,"abstract":"<div><p>The acidophilic archaeon <em>Ferroplasma acidiphilum</em> exhibits remarkable adaptations to life in highly acidic environments. Nevertheless, the investigation of its molecular biology is challenging because of the slow growth of the organism, low biomass yield, and limitations of standard growth measurement techniques caused by iron oxidation.</p><ul><li><span>•</span><span><p>A novel two-step turbidimetric growth measurement (2TGM) method was developed to address the shortcomings associated with iron precipitation in culture media. The method comprises two distinct preparation steps.</p></span></li><li><span>•</span><span><p>The initial 2TGM step involves centrifuging culture samples at high speed to remove <em>F. acidiphilum</em> cells and iron precipitates, thus preparing a blank.</p></span></li><li><span>•</span><span><p>The second 2TGM step involves centrifuging the culture at a lower speed with the objective of selectively removing iron precipitates, thus allowing <em>F. acidiphilum</em> cells to remain suspended in the supernatant. This preparation enables subsequent measurement of cell density.</p></span></li></ul>A study on the growth of <em>F. acidiphilum</em> showed a standard logistic pattern with a 35-h lag phase, approximately 9-h doubling time, and 0.042 OD carrying capacity. A new two-step turbidimetric growth measurement (2TGM) method overcomes limitations of existing approaches, enabling further investigation of <em>F. acidiphilum</em>.</div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124004047/pdfft?md5=894524ae4f3e1a65aab174361c237f7c&pid=1-s2.0-S2215016124004047-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142172468","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":"Adsorption performance with field emission scanning electron microscopy of fruit peel induced Silver Nanoparticles in C16H18ClN3S for waste water treatment","authors":"","doi":"10.1016/j.mex.2024.102951","DOIUrl":"10.1016/j.mex.2024.102951","url":null,"abstract":"<div><p>There is a growing demand for cost-effective and sustainable technologies for treating wastewater as water consumption increases and conventional technologies become more expensive. Nanoparticles have a great deal of potential for use in the treatment of waste water. Their unique surface area allows them to effectively remove toxic metal ions, pathogenic microorganisms, organic and inorganic solutes from water. This study investigated the potential of orange and banana peels as renewable nano adsorbents for removing dyes and dissolved organic compounds from textile wastewater. Orange and banana peels are an optimal selection due to their favourable chemical characteristics, namely the presence of cellulose, pectic, hemicellulose, and lignin. Their capacity to adsorb diverse anionic and cationic compounds on their surface-active sites is attributed to their unique functional group compositions. Silver nanoparticles are able to adsorb heavy metals due to their exceptionally low electrical and thermal resistance and surface plasmon resonance. The samples were thoroughly characterised using field emission scanning electron microscopy (FESEM), UV–Visible spectrometry, Fourier transform infrared spectroscopy (FTIR) and XRD. The nanoparticles were prepared (10 gm,50 gm,100 gm) and subsequently introduced to the wastewater sample. The optical density values were recorded at various time points. The optical density values demonstrate a decline over the course of the experiment, with a notable decrease observed over time. The results of this study provide valuable insights into the efficacy of these natural adsorbents and their potential for sustainable water purification technologies. For the purpose of this research, high performance instrumentation methods were performed as follows:</p><ul><li><span>•</span><span><p>Field emission scanning electron microscopy for surface morphology studies.</p></span></li><li><span>•</span><span><p>Gas chromatography-mass spectrometry (GC–MS) for analytical technique that combines gas chromatography (GC) and mass spectrometry (MS) to identify unknown substances or contaminants.</p></span></li><li><span>•</span><span><p>Optical density values were measured for different timings of degradation.</p></span></li></ul></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2215016124004023/pdfft?md5=2108bd0864d8b2b8608f1a74705e20a9&pid=1-s2.0-S2215016124004023-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142232070","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}