MethodsX最新文献

{"title":"SCRUM: A simple model for estimating uptake of nitrogen and water by field crops","authors":"Edith N. Khaembah,&nbsp;Rogerio Cichota,&nbsp;Megan Gee,&nbsp;Hamish E. Brown","doi":"10.1016/j.mex.2026.103981","DOIUrl":"10.1016/j.mex.2026.103981","url":null,"abstract":"<div><div>This paper describes the <strong>S</strong>imple <strong>C</strong>rop Resource <strong>U</strong>ptake <strong>M</strong>odel (SCRUM), a configurable generic crop model implemented in APSIM Next Generation’s Plant Modelling Framework. SCRUM simulates crop development using a nine‑phase phenology coupled to a simplified plant module consisting of stover, product, root, and nodule (only in legumes) and a thermal‑time‑driven trajectory for daily potential growth. Water limitation is computed through APSIM’s canopy energy balance (MicroClimate). Nitrogen uptake is determined by organ growth and tissue nitrogen targets, constrained by soil mineral nitrogen supply and supplemented by biological fixation when enabled. The generic and simple nature of SCRUM makes it easy for new crops to be configured using expert knowledge, enabling rapid set‑up for species and end‑uses where comprehensive crop models are unavailable. Model evaluation using field data indicated that SCRUM, in the APSIM framework, is a promising a tool that can utilised in the analysis of nitrogen and water management practices of across a range of conditions.<ul><li><span>•</span><span><div>A generic, configurable crop model for rapid parameterization of data‑limited species and end‑uses.</div></span></li><li><span>•</span><span><div>Coupled water stress (canopy energy balance) and nitrogen dynamics (demand targets, supply constraints, optional fixation).</div></span></li><li><span>•</span><span><div>A transparent model description including structure, parameter inputs and assumptions.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103981"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148184118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Random vs. blocked perturbation training on reactive balance control in peripheral neuropathy: A protocol study for a randomized controlled trial","authors":"Razieh Javadian Kootenayi ,&nbsp;Razieh Mofateh ,&nbsp;Mehrnoosh Zakerkish ,&nbsp;Neda Orakifar ,&nbsp;Saeideh Monjezi ,&nbsp;Mohammad Mehravar ,&nbsp;Maryam Seyedtabib","doi":"10.1016/j.mex.2026.103796","DOIUrl":"10.1016/j.mex.2026.103796","url":null,"abstract":"<div><div>Diabetic peripheral neuropathy (DPN) is the leading cause of disturbances in reactive balance control. The repeated, external mechanical perturbations in perturbation-based balance training(PBBT) evoke balance recovery strategies; which subsequently improve reactive balance performance. Using the practice schedule concept of motor learning in the design of PBBT is a relatively new approach related to balance exercises. This study aims to investigate the effects of blocked and random PBBT on reactive balance control and its persistency and transfer to conditions different from those experienced during training.</div><div>Individuals with DPN will be recruited and randomly allocated to one of the three groups: random, blocked, and control group. Random and blocked PBBT groups will receive single-session balance training, including unexpected perturbations of platform during quiet standing in two directions (anterior and posterior), and three difficulty levels of platform motion (displacement, velocity, and acceleration). Each balance perturbation in blocked group will be repeated over blocks of four trials. For the random group, perturbation sequence will be unpredictable for these four trials in each block. Primary outcomes (i.e., center of pressure variables, reaction time, movement time, and total response time variables) will be assessed at baseline as well as immediately and one day after intervention.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103796"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Method development with LA-ICP-MS in U-Pb geochronology using design of experiment","authors":"Merve Caner ,&nbsp;Murat Tunç ,&nbsp;Gürsel Sunal ,&nbsp;Mehmet Akif Sarıkaya","doi":"10.1016/j.mex.2026.103795","DOIUrl":"10.1016/j.mex.2026.103795","url":null,"abstract":"<div><div>Inductively Coupled Plasma Mass Spectrometry (ICP-MS), when combined with laser ablation (LA-ICP-MS), is widely used for precise U-Pb zircon geochronology. While the technique is powerful, reliable age determinations depend on careful optimization of laser and plasma parameters of the instrument. In this study, we used a Sector Field ICP-MS (Thermo Scientific Element 2) coupled to a New Wave UP213 laser to present practical, step-by-step measurement and optimization procedures for geological U–Pb dating.</div><div>Here, Design of Experiments (DoE)—a statistical approach that evaluates multiple parameters simultaneously and reveals their interactions—was used to efficiently determine optimal analytical conditions with a limited number of experiments. For the first time in LA-ICP-MS research, a DoE framework was applied to systematically optimize instrumental settings. DoE is also compared with conventional manual optimization strategies, providing clear evidence that statistically guided optimization enhances accuracy, reproducibility, and robustness, while reducing operator bias and time required for method development.<ul><li><span>•</span><span><div>The outcome of our method demonstrate that DoE not only identifies the most influential parameters but also accounts for interactions often overlooked during manual refinement. Optimization of U-Pb dating using LA-ICP-MS.</div></span></li><li><span>•</span><span><div>First systematic application of DoE in LA-ICP-MS studies.</div></span></li><li><span>•</span><span><div>Comparative evaluation of manual versus DoE-based optimization.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103795"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"YOLO-AVCA-CBAMNet: Attention-driven framework for detection and classification of green pepper maturity stages","authors":"Bipin Nair B J,&nbsp;Abrav Nanda K M,&nbsp;V Raghavendra","doi":"10.1016/j.mex.2026.103784","DOIUrl":"10.1016/j.mex.2026.103784","url":null,"abstract":"<div><div>Accurate identification of pepper berry maturity is essential for ensuring optimal harvest timing and maintaining quality standards in spice production. This study proposes “<strong>YOLO-AVCA-CBAMNet”</strong> an integrated detection-and-classification framework designed to operate effectively under natural field conditions. A self-collected dataset of pepper berries, captured using a smartphone across diverse illumination settings and background complexities, forms the basis of the evaluation. The pipeline first applies YOLOv8 to detect individual berries within cluttered scenes. The extracted regions are then classified using convolutional neural networks enhanced with two complementary attention mechanisms. The <strong>Adaptive Visual Cortex Attention Module (AVCAM)</strong> strengthens global contextual weighting by adaptively recalibrating salient features, while the <strong>Convolutional Block Attention Module (CBAM)</strong> improves spatial and channel-specific discrimination through sequential attention refinement. This dual-attention design enables more reliable separation of visually similar maturity stages. Experimental results indicate accuracy gains of <strong>5–9</strong> <strong>%</strong> across all backbone architectures, with the DenseNet121-based configuration achieving a peak accuracy of <strong>96.19</strong> <strong>%</strong>. The findings demonstrate the potential of attention-driven models to support interpretable, efficient, and scalable maturity assessment solutions in precision agriculture.<ul><li><span>•</span><span><div>Developed an end-to-end framework “YOLO-AVCA-CBAMNet” integrating object detection and attention-driven classification for pepper maturity assessment in natural field conditions.</div></span></li><li><span>•</span><span><div>Employed a field-derived image dataset of pepper berries collected under naturally varying illumination and environmental conditions, thereby supporting the ecological validity and practical relevance of the proposed maturity assessment approach.</div></span></li><li><span>•</span><span><div>Incorporated complementary attention mechanisms—AVCAM to enhance global contextual representation and CBAM to refine spatial and channel-specific feature responses—thereby improving discrimination among visually similar maturity stages.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103784"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Actor-critic guided CDBN with GAN augmentation for robust facial emotion recognition","authors":"Akshay S ,&nbsp;Jnana Sai S R ,&nbsp;Sinchana B R ,&nbsp;Kannan M ,&nbsp;Adwitiya Mukhopadhyay","doi":"10.1016/j.mex.2025.103774","DOIUrl":"10.1016/j.mex.2025.103774","url":null,"abstract":"<div><div>Facial emotion recognition (FER) remains challenging under limited data, noise, and occlusion. This study introduces an <strong>Actor–Critic Convolutional Deep Belief Network (ACCDBN)</strong> that unifies Generative Adversarial Network (GAN)–based augmentation, deep probabilistic feature learning, and reinforcement-driven optimization. Conditional GANs expand minority emotion classes, enhancing data diversity, while the CDBN extracts hierarchical texture features through convolutional and restricted Boltzmann layers. An Actor–Critic module dynamically refines representations by rewarding accurate emotion classification and penalizing uncertain predictions. Trained and validated on the CK+ dataset with five-fold cross-validation, the proposed model achieves higher accuracy and stability than CNN, LSTM, and ResNet-50 baselines, maintaining strong performance under noise and occlusion. The approach demonstrates how reinforcement-guided generative learning can improve both accuracy and robustness in FER tasks.</div><div>1. To implement this, the research utilised the publicly available Cohn-Kanade+ dataset, consisting of eight classes with samples of 920 grey-scale images.</div><div>2. An improved ACCDBN model outperformed with 90.4% accuracy and 0.69 MCC (Mathew’s Correlation Coefficient) in 5-fold cross-validation using the cGAN-generated dataset and 87% on the CK+ dataset</div><div>3. The main objective is to present an advanced facial emotion recognition (FER) system that combines a Convolution Deep Belief Network (CDBN) with a model-free reinforcement learning technique, namely the actor-critic approach.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103774"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145926349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Method for estimating discharge, hydraulic depth, and mean velocity in rivers through spatial interpolation of at-a-station hydraulic geometry in data- scarce regions","authors":"Eduardo Zamudio-Huertas ,&nbsp;César Augusto García-Ubaque ,&nbsp;Nelson Obregón-Neira","doi":"10.1016/j.mex.2026.103804","DOIUrl":"10.1016/j.mex.2026.103804","url":null,"abstract":"<div><div>Reliable discharge estimation is essential for water resource management, yet many regions lack sufficient hydrological stations. To address this limitation, we propose the Spatial Hydraulic Geometry Interpolation (SHGI) method, which estimates discharge (Q), hydraulic depth (D), and mean velocity (V) from river width (W) obtained via surveys or satellite imagery. SHGI integrates hydraulic geometry theory with multiquadric radial basis interpolation, applied to the Meta and Atrato river basins in Colombia. Parameters of at‑station hydraulic geometry (coefficients <span><math><mi>a</mi></math></span>, <em>c, k</em> and exponents <em>b, f, m</em>) were derived using least squares and transformed into log‑ratio space to preserve their compositional constraints. Interpolation along upstream distance ensures spatial continuity, and closure operations guarantee internal consistency. Validation against observed data in basins with contrasting geomorphology and data density confirmed the method’s robustness.</div><div>The principal contributions of SHGI are:<ul><li><span>•</span><span><div>Longitudinal continuity: explicit incorporation of upstream distance to interpolate parameters consistently along channels and tributaries.</div></span></li><li><span>•</span><span><div>Compositional integrity: preservation of the multiplicative and additive constraints of hydraulic geometry parameters during interpolation.</div></span></li><li><span>•</span><span><div>Estimation under data scarcity: enabling calculation of Q, D, and V at ungauged sites using only river width.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103804"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146077547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Method for determining residual total suspended solids retained in pressurized sand filter media","authors":"Juliana S. Benítez ,&nbsp;Gustavo L. Muniz ,&nbsp;Jhonnatan A.Y. Guarnizo ,&nbsp;Nicolás D. Cano ,&nbsp;Antonio P. Camargo","doi":"10.1016/j.mex.2026.103980","DOIUrl":"10.1016/j.mex.2026.103980","url":null,"abstract":"<div><div>Residual solids retained in the sand bed after backwashing are commonly used to assess the cleaning efficiency of pressurized sand filters employed in irrigation systems. However, procedures originally proposed for slow sand filters are not fully suitable for pressurized filters because these systems differ in operating conditions and bed configuration. In this study, an adapted procedure was developed to determine residual total suspended solids (TSSf) retained in pressurized sand filter media after backwashing. The method involves collecting the upper 0–100 mm layer of the sand bed, followed by drying, homogenization, controlled subsampling, sequential washing cycles under rotational agitation, and determination of suspended solids by vacuum filtration with 0.45 μm glass microfiber filters. Method validation included analysis of grain-size representativeness and reproducibility. The grain-size distribution curves obtained from different subsample masses showed Pearson correlation coefficients higher than 0.99 (p &lt; 0.01), while coefficients of variation for TSSf determination remained below 20% for all evaluated samples. The procedure allows direct evaluation of residual solids retained in pressurized sand filters after backwashing and may be useful for comparing backwashing conditions and assessing filter cleaning performance in irrigation systems.</div><div>The main features and applications of this method are as follows:<ul><li><span>•</span><span><div>Quantification of residual solids retained in pressurized sand filter media after backwashing.</div></span></li><li><span>•</span><span><div>Representative sand subsampling and extraction of retained solids using sequential washing cycles.</div></span></li><li><span>•</span><span><div>Evaluation of backwashing performance in irrigation sand filters.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103980"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148184117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of a thermoelectric cooling approach for localized hypothermia in a murine model","authors":"Kosala D. Waduthanthri ,&nbsp;Gregory S. Korbutt ,&nbsp;Andrew R. Pepper ,&nbsp;Larry D. Unsworth","doi":"10.1016/j.mex.2025.103754","DOIUrl":"10.1016/j.mex.2025.103754","url":null,"abstract":"<div><div>Achieving localized and adjustable hypothermia is critical for various clinical and experimental applications, including reducing oxidative stress, modulating inflammatory responses, and enabling temperature-triggered drug delivery. However, existing cooling techniques such as ice packs, and cryogenic sprays limitations in precision, efficiency, duration, and cooling capacity. In this study, we used a commercially available thermoelectric cooling module to construct a simple and low-cost cooling system, and applied it in a preclinical mouse model to achieve focal hypothermia at a subcutaneous transplant site.<ul><li><span>•</span><span><div>The system, assembled using a TES1–4903 thermoelectric module, a heat sink, and a power supply, achieved rapid temperature reduction rates. At 5 V, the subcutaneous temperature decreased at an average rate of ∼1.5 °C/s during the first 10 s, reaching a stable temperature of ∼8 °C within 120 s. At 2 V, the average rate was ∼0.4 °C/s, stabilizing at ∼17 °C over the same period.</div></span></li><li><span>•</span><span><div>The system demonstrated precise temperature control with minimal variability, maintaining temperature steps of &lt;2 °C and ensuring a stable temperature range.</div></span></li><li><span>•</span><span><div>Compared to literature, our system highlights the utility of thermoelectric modules for biomedical cooling applications, demonstrating faster and safer subcutaneous hypothermia with more precise temperature control than other approaches.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103754"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A method for reconstituting the motility of membrane-bound myosin on the surface of the cell-sized W/O droplet","authors":"Yusei Sato ,&nbsp;Rieko Sumiyoshi ,&nbsp;Masahito Hayashi ,&nbsp;Masahiko Yamagishi ,&nbsp;Junichiro Yajima","doi":"10.1016/j.mex.2025.103755","DOIUrl":"10.1016/j.mex.2025.103755","url":null,"abstract":"<div><div>Membrane-bound myosin generates force through interactions with the cytoskeletal actin filament beneath the cell membrane and constitutes the mechanical basis for living cells. Myosin ID, a membrane-bound myosin, drives the gliding motion of actin filaments and binds to phospholipids in the lipid membrane of a living cell. Here, we describe the <em>in-droplet</em> actin filament gliding assay, a method that reconstitutes the motility of actomyosin that dynamically interacts with lipid membranes within water-in-oil (W/O) droplets, which mimic the confined geometry of the intracellular environment. Our method enables quantification of the gliding velocity of actin filaments driven by myosin ID on the inner surface of W/O droplets surrounded by a phospholipid membrane. The <em>in-droplet</em> actin filament gliding assay provides a valuable platform for reconstituting the motile properties of other membrane-bound myosins on membrane surfaces in confined spaces and for analyzing the dynamics of actomyosin networks. The main features and applications of this method are as follows:<ul><li><span>•</span><span><div>Reconstitution of actin filament gliding driven by membrane-bound myosin ID within confined water-in-oil droplets.</div></span></li><li><span>•</span><span><div>Quantitative evaluation of actomyosin dynamics on the inner surface of the lipid membrane within water-in-oil-droplets.</div></span></li><li><span>•</span><span><div>Broadly applicable assay platform for studying the motile properties of membrane-associated myosin families.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103755"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A protocol for assessing smallholder farmers’ climate resilience: A guidance for researchers to construct a robust multidimensional domain","authors":"Imade Yoga Prasada ,&nbsp;Jangkung Handoyo Mulyo ,&nbsp;Hani Perwitasari ,&nbsp;Agus Dwi Nugroho","doi":"10.1016/j.mex.2025.103763","DOIUrl":"10.1016/j.mex.2025.103763","url":null,"abstract":"<div><div>In recent years, the theoretical frameworks on climate resilience of smallholder farmers have continued to develop. This has encouraged the emergence of a variety of domains, indicators, and items. Meanwhile, inappropriate construct domains, indicators, and items can lead to biased research findings. Therefore, developing a robust construct domain, indicators, and items requires a clear, easily understood, and statistically accountable protocol. This protocol emphasizes the formation of a framework for conducting a statistical approach to assess smallholder farmers’ climate resilience.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103763"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}