MethodsX最新文献

英文中文

ViT-HHO: Optimized vision transformer for diabetic retinopathy detection using Harris Hawk optimization ViT-HHO：利用哈里斯-霍克优化技术检测糖尿病视网膜病变的优化视觉转换器

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-23 DOI: 10.1016/j.mex.2024.103018

Diabetic retinopathy (DR) is a significant cause of vision impairment globally, emphasizing the importance of timely and precise detection to prevent severe consequences. This study presents an optimized Vision Transformer (ViT) model that incorporates Harris Hawk Optimization (HHO) to improve the automated detection of diabetic retinopathy (DR). The ViT architecture utilizes self-attention mechanisms to capture local and global features in retinal images. Additionally, HHO optimizes key hyperparameters to maximize the performance of the model. The proposed ViT-HHO model achieved exceptional performance on the APTOS-2019 and IDRiD datasets. Specifically, it achieved 99.83 % accuracy, 99.78 % sensitivity, 99.85 % specificity, and 99.80 % AUC-ROC on the APTOS-2019 dataset, surpassing traditional CNNs and alternative optimization techniques. The model exhibited strong generalization on the IDRiID dataset, achieving an accuracy of 99.11 % and an AUC-ROC of 99.12 %. The ViT-HHO model demonstrates the potential for enhancing the clinical detection of diabetic retinopathy (DR), providing high precision and reliability.

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An optimized Vision Transformer (ViT) model was developed using HHO for improved detection of Diabetic Retinopathy (DR).
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The model was validated on the APTOS-2019 and IDRiID datasets, demonstrating superior accuracy and AUC-ROC metrics.
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The model's generalization and robustness were demonstrated through comprehensive performance evaluations.

糖尿病视网膜病变（DR）是全球视力受损的重要原因之一，因此必须及时、精确地检测以防止严重后果的发生。本研究提出了一种优化的视觉转换器（ViT）模型，该模型结合了哈里斯鹰优化（HHO）技术，以改进糖尿病视网膜病变（DR）的自动检测。ViT 架构利用自我注意机制捕捉视网膜图像中的局部和全局特征。此外，HHO 还优化了关键超参数，以最大限度地提高模型的性能。所提出的 ViT-HHO 模型在 APTOS-2019 和 IDRiD 数据集上取得了优异的性能。具体来说，它在 APTOS-2019 数据集上实现了 99.83 % 的准确率、99.78 % 的灵敏度、99.85 % 的特异性和 99.80 % 的 AUC-ROC，超越了传统的 CNN 和其他优化技术。该模型在 IDRiID 数据集上表现出很强的泛化能力，准确率达到 99.11%，AUC-ROC 达到 99.12%。该模型在 APTOS-2019 和 IDRiID 数据集上进行了验证，显示出卓越的准确性和 AUC-ROC 指标。

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引用次数: 0

The TOPSIS method: Figuring the landslide susceptibility using Excel and GIS TOPSIS 方法：使用 Excel 和 GIS 计算滑坡易发性

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-17 DOI: 10.1016/j.mex.2024.103005

The current study introduced Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) to enhance landslide susceptibility. It determines the relative distance of each alternative from the ideal best and ideal worst value. The ArcGIS environment was used to prepare eleven landslide conditioning factors, while raster values were extracted for the decision matrix preparation. We utilized subjective expert judgment to create a weighted matrix that considers the roles of each conditioning component. In addition, a Euclidean distance was measured from each alternative to the ideal best and worst values. The relative closeness value (R_i) has been used to prepare the landslide susceptibility index by the inverse distance weighting (IDW) interpolation. Furthermore, the precision of the landslide susceptibility was justified by area under curve-receiver operating characteristic (AUC-ROC) which was 0.987. Hence, multi-criteria decision-making (MCDM) techniques like the TOPSIS method are very useful for natural hazard mapping.

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The simplified TOPSIS approach described by Hwang and Yoon (1981) is applied in this study. The criteria have been categorized and assigned weights based on expert judgment and previously published material.
•
The TOPSIS approach and GIS integration has significantly enhanced the creation of a landslide susceptibility map for a sensitive area.
•
The method is easiest and suitable for short term operation research.

目前的研究引入了 "与理想方案相似度排序偏好技术"（TOPSIS），以提高滑坡的易发性。它确定了每个备选方案与理想最佳值和理想最坏值的相对距离。我们使用 ArcGIS 环境编制了 11 个滑坡条件因子，并提取了栅格值用于编制决策矩阵。我们利用专家的主观判断创建了一个加权矩阵，该矩阵考虑了每个调节因素的作用。此外，我们还测量了每个备选方案与理想的最佳值和最坏值之间的欧氏距离。通过反距离加权（IDW）插值法，利用相对接近值（Ri）来编制滑坡易感性指数。此外，曲线下面积-接收器工作特征（AUC-ROC）为 0.987，证明了滑坡易感性的精确性。因此，像 TOPSIS 方法这样的多标准决策（MCDM）技术对于绘制自然灾害地图非常有用。本研究采用了 Hwang 和 Yoon（1981 年）描述的简化 TOPSIS 方法，并根据专家判断和以前发表的资料对标准进行了分类和权重分配。

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引用次数: 0

Standardized lab-scale production of the recombinant fusion protein HUG for the nanoscale analysis of bilirubin 用于胆红素纳米级分析的重组融合蛋白 HUG 的标准化实验室规模生产

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-17 DOI: 10.1016/j.mex.2024.103001

The recombinant bifunctional protein HELP-UnaG (HUG) is a fusion product of the Human Elastin-like Polypeptide (HELP) with the bilirubin-binding fluorescent protein UnaG. HUG is used for the fluorometric detection of bilirubin in serum and a variety of biological fluids and extracts. Here we describe a detailed method for the standardized production and purification of HUG from E. coli extracts on a laboratory scale. This method takes advantage of the HELP-specific thermoreactive behavior that enables the separation of HUG from complex E. coli extracts by repeated precipitation/re-dissolution steps at near physiological temperature.

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The method is based on the inverse thermal transition process.
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The “green” method is affordable for basic laboratories and can be easily transferred to new users.

重组双功能蛋白 HELP-UnaG (HUG) 是人弹性蛋白样多肽 (HELP) 与胆红素结合荧光蛋白 UnaG 的融合产物。HUG 可用于血清、各种生物液体和提取物中胆红素的荧光检测。在此，我们介绍了一种在实验室规模上从大肠杆菌提取物中标准化生产和纯化 HUG 的详细方法。这种方法利用了 HELP 特有的热反应行为，在接近生理温度的条件下，通过重复沉淀/再溶解步骤，从复杂的大肠杆菌提取物中分离出 HUG。

引用次数: 0

Automated prediction of phosphorus concentration in soils using reflectance spectroscopy and machine learning algorithms 利用反射光谱学和机器学习算法自动预测土壤中的磷浓度

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-15 DOI: 10.1016/j.mex.2024.102996

A method is presented for predicting total phosphorus concentration in soils from Santander de Quilichao, Colombia, using a UV-VIS V-750 Spectrophotometer and machine learning techniques. A total of 152 soil samples, prepared with varying proportions of P₂O₅ fertilizer and soil, were analyzed, obtaining reflectance spectra in the 200 to 900 nm range with 3501 wavelengths. Additionally, 152 laboratory results of total phosphorus concentration were used to train the prediction model. The spectra were filtered using a Savitzky-Golay filter. Key wavelengths were identified using Variable Importance in Projection - Partial Least Squares (VIP-PLS) and Random Forest (RF), reducing the spectral bands to 1085. Principal Component Analysis (PCA) further reduced data dimensionality. A feedforward artificial neural network was then trained to predict phosphorus concentration. This method is faster than traditional lab tests by leveraging advanced data analysis and machine learning, offering results in less time. While sample preparation remains consistent with standard spectroscopic analysis, the value added by the proposed method lies in its data processing and interpretation. Currently applied to a single soil type, future improvements will include more soil types and other macronutrients, enhancing nutrient management in agriculture. Accurate macronutrient measurements aid in better fertilizer uses planning.

• Filtering spectra and determining relevant wavelengths using VIP-PLS and RF.

• Dimensionality reduction with PCA.

• Training feedforward artificial neural networks.

本文介绍了一种利用 UV-VIS V-750 分光光度计和机器学习技术预测哥伦比亚桑坦德德基利乔土壤中总磷浓度的方法。共分析了 152 份土壤样本，这些样本是用不同比例的 P2O5 肥料和土壤制备的，获得了 200 到 900 纳米范围内 3501 个波长的反射光谱。此外，152 项实验室总磷浓度结果也用于训练预测模型。光谱使用 Savitzky-Golay 过滤器进行过滤。使用投影中的变量重要性--偏最小二乘法（VIP-PLS）和随机森林（RF）确定了关键波长，将光谱波段减少到 1085 个。主成分分析（PCA）进一步降低了数据维度。然后训练一个前馈人工神经网络来预测磷浓度。这种方法利用先进的数据分析和机器学习技术，比传统的实验室测试更快，能在更短的时间内得出结果。虽然样品制备与标准光谱分析保持一致，但拟议方法的附加值在于其数据处理和解释。目前，该方法只适用于单一土壤类型，未来的改进将包括更多土壤类型和其他宏量营养元素，从而加强农业养分管理。精确的宏量营养元素测量有助于更好地规划肥料使用。

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引用次数: 0

A method to improve binary forecast skill verification 改进二进制预报技能验证的方法。

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-15 DOI: 10.1016/j.mex.2024.103010

To overcome the limitations of existing deterministic binary forecast skill verification methods that award a perfect score for forecasting events considered easy to forecast, an improvement factor is introduced. It comprises two components which are 1) a measure of the ease with which an event can be accurately forecasted and 2) a measure of frequency of event. By using two hypothetical datasets, this study demonstrates that an improvement factor could enhance the performance of existing deterministic binary forecast skill verification methods by awarding score that is close to score for no-skill forecast for the perfect forecasts of events considered easy to forecast. In addition, the forecast and actual data on annual inflation rate are used to demonstrate how an improvement factor could be used together with the existing deterministic binary forecast skill verification methods in order to assess skills of the forecasters in practice.

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Existing deterministic binary forecast skill verification methods fail to award correct score for events considered easy to forecast.
•
An improvement factor is developed in order to enhance performance of existing deterministic binary forecast skill verification methods.
•
Hypothetical and empirical data are used to validate how an improvement factor works.

现有的确定性二元预报技能验证方法对容易预报的事件给予满分，为了克服这种方法的局限性，我们引入了一个改进因子。它由两部分组成：1）事件准确预报难易程度的度量；2）事件发生频率的度量。通过使用两个假设数据集，本研究证明了改进因子可以提高现有确定性二元预测技能验证方法的性能，即对被认为容易预测的事件的完美预测给予接近无技能预测的分数。现有的确定性二元预测技能验证方法无法对被认为容易预测的事件给出正确的分数。

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引用次数: 0

Determination of critical energy release rate at the EVA/Si cell interface of a flexible silicon solar cell 测定柔性硅太阳能电池 EVA/Si 电池界面的临界能量释放率。

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-11 DOI: 10.1016/j.mex.2024.103004

Recently, commercial flexible silicon(Si) solar cells have been available for charging batteries and electronic devices. In this research, we present a methodology for determining the critical energy release rate at the EVA/Si cell interface of a flexible silicon solar cell, which can also be applied to other interfaces in solar cells. The outline of procedure is as follows:

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Conduct a peeling test at the EVA/Si cell interface of the solar cell sample
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Perform a tensile test on the upper layer of the solar cell sample
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Execute IC Peel software
Inputs: Peeling force between EVA and Si layer, Young's modulus (E), Yield stress (σ_y), and Yield strain (ε_y) of the upper layer
Output: critical energy release rate (Gc) between EVA and the silicon (Si) layer

最近，商用柔性硅（Si）太阳能电池已可用于为电池和电子设备充电。在这项研究中，我们提出了一种确定柔性硅太阳能电池 EVA/Si 电池界面临界能量释放率的方法，该方法也可应用于太阳能电池的其他界面。程序概要如下：-在太阳能电池样品的 EVA/Si 电池界面上进行剥离测试-在太阳能电池样品的上层进行拉伸测试-执行 IC Peel 软件输入：输出：EVA 和硅（Si）层之间的临界能量释放率（Gc）。

引用次数: 0

Protocol to analyse the structural composition by fluorescence microscopy and different conventional and fluorescence staining methods 利用荧光显微镜和不同的传统及荧光染色方法分析结构组成的规程

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-10 DOI: 10.1016/j.mex.2024.102999

The protocol shows the effectiveness of using safranin-fast green stain for fluorescence microscopy. This staining technique has been used in conventional microscopy to perform anatomical characterizations of plants. However, this protocol describes the procedure for using samples stained with safranin-fast green in conjunction with fluorescence microscopy. The strength of the protocol lies in the fact that the samples are permanent and allows for effective differentiation of lignified and cellulosic walls unlike conventional fluorescence microscopy stains such as Congo red-acridine orange, calcofluor, and autofluorescence. The protocol for making fluorescence intensity measurements is also standardized, allowing the data to be used for statistical analysis and inference about the chemical composition of plant cell walls.

该方案显示了在荧光显微镜下使用黄绿素-快绿染色剂的有效性。这种染色技术已在传统显微镜中用于植物的解剖特征描述。不过，本方案介绍的是将使用快绿素染色的样本与荧光显微镜结合使用的程序。与刚果红-吖啶橙、钙荧光和自发荧光等传统荧光显微染色法不同，本方案的优势在于样品是永久性的，可有效区分木质化壁和纤维素壁。荧光强度测量的规程也是标准化的，可将数据用于统计分析和推断植物细胞壁的化学成分。

引用次数: 0

A new methodology for evaluating the neighbor discovery time in schedule-based asynchronous duty-cycling wireless sensor networks 评估基于计划的异步占空比无线传感器网络中邻居发现时间的新方法

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-10 DOI: 10.1016/j.mex.2024.102967

Duty cycling is a fundamental mechanism for battery-operated wireless networks, such as wireless sensor networks. Due to its importance, it is an integral part of several Medium Access Protocols and related wireless technologies. In Schedule-based Asynchronous Duty Cycle, nodes activate and deactivate their radio interfaces according to a pre-designed schedule of slots, which guarantees overlapping uptime between two neighbors, independent of the offset between their internal clocks, making communication between them possible. This paper presents a new methodology for evaluating the Neighbor Discovery Time (NDT) of Schedule-based Asynchronous Duty Cycle. Differently from previous methodologies, it accounts for the possibility of the slots in the schedules of the two neighbors not being perfectly border-aligned — an unrealistic assumption in practice. By means of simulation, we show that not taking this under consideration can lead to an overestimate of the NDT by a factor of 2 depending on the particular scenario, thus justifying the importance of our work.

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We propose a new subslot-based methodology for computing the NDT of a wakeup schedule used for asynchronous duty cycling.
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It replaces the traditional slot-based methodology, by dividing slots into subslots, allowing for the analysis of non-integer clock offsets between nodes, and further allowing mathematical models to consider the more realistic continuous-time case.
•
Our validation data shows that the slot-based methodology may overestimate NDT by a factor of up to 2, making the proposed subslot-based methodology much more precise.

占空比是电池供电的无线网络（如无线传感器网络）的基本机制。由于其重要性，它已成为若干介质访问协议和相关无线技术的组成部分。在基于时间表的异步占空比中，节点根据预先设计的时隙时间表激活和停用其无线电接口，从而保证两个相邻节点之间的正常运行时间重叠，不受其内部时钟偏移的影响，使它们之间的通信成为可能。本文提出了一种评估基于时间表的异步占空比的邻居发现时间（NDT）的新方法。与以往的方法不同，它考虑到了两个邻居时间表中的时隙不完全边界对齐的可能性--这在实践中是不现实的假设。通过仿真，我们证明了不考虑这种情况会导致 NDT 被高估 2 倍，具体取决于特定场景，从而证明了我们工作的重要性。-它取代了传统的基于插槽的方法，将插槽划分为子插槽，允许分析节点之间的非整数时钟偏移，并进一步允许数学模型考虑更现实的连续时间情况。

{"title":"A new methodology for evaluating the neighbor discovery time in schedule-based asynchronous duty-cycling wireless sensor networks","authors":"","doi":"10.1016/j.mex.2024.102967","DOIUrl":"10.1016/j.mex.2024.102967","url":null,"abstract":"<div><div>Duty cycling is a fundamental mechanism for battery-operated wireless networks, such as wireless sensor networks. Due to its importance, it is an integral part of several Medium Access Protocols and related wireless technologies. In Schedule-based Asynchronous Duty Cycle, nodes activate and deactivate their radio interfaces according to a pre-designed schedule of slots, which guarantees overlapping uptime between two neighbors, independent of the offset between their internal clocks, making communication between them possible. This paper presents a new methodology for evaluating the Neighbor Discovery Time (NDT) of Schedule-based Asynchronous Duty Cycle. Differently from previous methodologies, it accounts for the possibility of the slots in the schedules of the two neighbors not being perfectly border-aligned — an unrealistic assumption in practice. By means of simulation, we show that not taking this under consideration can lead to an overestimate of the NDT by a factor of 2 depending on the particular scenario, thus justifying the importance of our work.<ul><li><span>•</span><span><div>We propose a new subslot-based methodology for computing the NDT of a wakeup schedule used for asynchronous duty cycling.</div></span></li><li><span>•</span><span><div>It replaces the traditional slot-based methodology, by dividing slots into subslots, allowing for the analysis of non-integer clock offsets between nodes, and further allowing mathematical models to consider the more realistic continuous-time case.</div></span></li><li><span>•</span><span><div>Our validation data shows that the slot-based methodology may overestimate NDT by a factor of up to 2, making the proposed subslot-based methodology much more precise.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142432863","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}

引用次数: 0

A secure interoperable method for electronic health records exchange on cross platform blockchain network 跨平台区块链网络电子健康记录交换的安全互操作方法

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-10 DOI: 10.1016/j.mex.2024.103002

An Electronic Health Record (EHR) store essential and sensitive patient's medical information. Since health information is highly confidential data, it should be accessible with the consent of the patient. Blockchain based EHR management system offers improvised privacy and patient-centric approach. EHR management systems are available with multiple blockchain platforms. Generally, EHRs are maintained at several independent blockchain platforms. EHR management systems should be capable of securely exchange data on cross platform blockchain network. The interoperability in such blockchain platforms should facilitate seamless cross-chain interaction and information exchange. This article proposes a method that facilitates secure EHR exchange on Ethereum and Hyperledger fabric network using hepatitis dataset. The key contributions of the proposed method include:

•
Hash lock based interoperable cross-chain method for EHR exchange across Ethereum and Hyperledger fabric.
•
Additional security to the EHR is ensured by partitioning EHR as on-chain (blockchain platform) and off-chain InterPlanetary File System (IPFS)
•
Secure Password Authentication-Based Key Exchange (SPAKE) based session management for EHR exchange across two parties.

The proposed patient centric method is validated to ensures the successful exchange of patient EHR across Ethereum and Hyperledger fabric.

电子病历（EHR）存储病人重要而敏感的医疗信息。由于健康信息是高度机密的数据，因此必须在征得患者同意后才能访问。基于区块链的电子病历管理系统提供了更好的隐私保护和以患者为中心的方法。电子健康记录管理系统有多种区块链平台。一般来说，电子健康记录维护在多个独立的区块链平台上。电子健康记录管理系统应能够在跨平台区块链网络上安全地交换数据。这些区块链平台的互操作性应有利于无缝跨链交互和信息交换。本文提出了一种方法，利用肝炎数据集促进以太坊和超级账本网络上的安全电子病历交换。通过将电子健康记录划分为链上（区块链平台）和链下专有文件系统（IPFS），确保了电子健康记录的额外安全性--基于安全密码验证的密钥交换（SPAKE）会话管理，用于双方的电子健康记录交换。

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引用次数: 0

Urban small-scale hydroponics: A compact, smart home-based hydroponics system 城市小型水栽法：紧凑型智能家庭水培系统

IF 1.6 Q2 MULTIDISCIPLINARY SCIENCES

MethodsX

Pub Date : 2024-10-05 DOI: 10.1016/j.mex.2024.102998

The increasing population and urbanization have created a massive gap in the demand-supply model of food grains. The world is facing an acute problem with global warming and EI Nino effects, which have affected the equilibrium of the food chain. It is a need of the hour to introduce new reforms in farming to reap increased yields and reduce dependency on natural resources. Hydroponics cultivation is a boon to the agricultural sector, it enhances the cultivation of plants in an organic way by enabling Internet of Things (IoT) technology and combines technology and conventional nutritional mechanisms to enable the co-plant's growth without the strain of nutrient deficiency. This research suggests a system that integrates hardware and software into the traditional hydroponics system that the users can use to have their plantation setup in an urban environment within a small and confined space at home. This system will benefit hobbyist gardeners and small-scale urban farmers seeking an efficient, compact, and smart solution for hydroponic plant cultivation.

人口增长和城市化给粮食供需模式带来了巨大缺口。全球变暖和厄尔尼诺现象影响了食物链的平衡，世界正面临着严峻的问题。当务之急是对农业进行新的改革，以提高产量，减少对自然资源的依赖。水培栽培是农业部门的福音，它通过启用物联网（IoT）技术，以有机方式加强植物栽培，并将技术与传统营养机制相结合，使共同种植的植物在生长过程中不受营养缺乏的影响。这项研究提出了一种将硬件和软件集成到传统水培系统中的系统，用户可以利用这种系统在家中狭小的空间内，在城市环境中建立自己的种植园。该系统将使业余园艺家和寻求高效、紧凑、智能的水培植物栽培解决方案的小规模城市农民受益。

引用次数: 0

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