Lateral flow immunoassays (LFIA) are widely used worldwide for the detection of different analytes because they combine multiple advantages such as low production cost, simplicity, and portability, which allows biomarkers detection without requiring infrastructure or highly trained personnel. Here we propose to provide solutions to the manufacturing process of LFIA at laboratory-scale, particularly to the controlled and active dispensing of the reagents in the form the Test Lines (TL) and the Control Lines (CL). To accomplish this task, we adapted a 3D printer to also control Syringe Pumps (SP), since the proposed adaptation of a 3D printer is easy, free and many laboratories already have it in their infrastructure. In turn, the standard function of the 3D printer can be easily restored by disconnecting the SPs and reconnecting the extruder. Additionally, the unified control of the 3D printer enables dual, active, regulable and simultaneous dispensing, four features that are typically found only in certain high-cost commercial equipment. With the proposed setup, the challenge of dispensing simultaneously at least 2 lines (CL and TL) with SPs controlled by a 3D printer was addressed, including regulation in the width of dispensed lines within experimental limits. Also, the construction of a LFIA for the detection of leptospirosis is shown as a practical example of automatized reagent dispensing.
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Accurate identification and quantification of unruptured intracranial aneurysms (UIAs) is crucial for the risk assessment and treatment of this cerebrovascular disorder. Current 2D manual assessment on 3D magnetic resonance angiography (MRA) is suboptimal and time-consuming. In addition, one major issue in medical image segmentation is the need for large well-annotated data, which can be expensive to obtain. Techniques that mitigate this requirement, such as weakly supervised learning with coarse labels are highly desirable. In the paper, we propose FocalSegNet, a novel 3D focal modulation UNet, to detect an aneurysm and offer an initial, coarse segmentation of it from time-of-flight MRA image patches, which is further refined with a dense conditional random field (CRF) post-processing layer to produce a final segmentation map. We trained and evaluated our model on a public dataset, and in terms of UIA detection, our model showed a low false-positive rate of 0.21 and a high sensitivity of 0.80. For voxel-wise aneurysm segmentation, we achieved a Dice score of 0.68 and a 95% Hausdorff distance of ~0.95 mm, demonstrating its strong performance. We evaluated our algorithms against the state-of-the-art 3D Residual-UNet and Swin-UNETR, and illustrated the superior performance of our proposed FocalSegNet, highlighting the advantages of employing focal modulation for this task.
Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.
It has been shown that unclocked, recurrent networks of Boolean gates in FPGAs can be used for low-SWaP reservoir computing. In such systems, topology and node functionality of the network are randomly initialized. To create a network that solves a task, weights are applied to output nodes and learning is achieved by adjusting those weights with conventional machine learning methods. However, performance is often limited compared to networks where all parameters are learned. Herein, we explore an alternative learning approach for unclocked, recurrent networks in FPGAs. We use evolutionary computation to evolve the Boolean functions of network nodes. In one type of implementation the output nodes are used directly to perform a task and all learning is via evolution of the network's node functions. In a second type of implementation a back-end classifier is used as in traditional reservoir computing. In that case, both evolution of node functions and adjustment of output node weights contribute to learning. We demonstrate the practicality of node function evolution, obtaining an accuracy improvement of ~30% on an image classification task while processing at a rate of over three million samples per second. We additionally demonstrate evolvability of network memory and dynamic output signals.
Accelerated failure time (AFT) models are frequently used for modelling survival data. This approach is attractive as it quantifies the direct relationship between the time until an event occurs and various covariates. It asserts that the failure times experience either acceleration or deceleration through a multiplicative factor when these covariates are present. While existing literature provides numerous methods for fitting AFT models with time-fixed covariates, adapting these approaches to scenarios involving both time-varying covariates and partly interval-censored data remains challenging. In this paper, we introduce a maximum penalised likelihood approach to fit a semiparametric AFT model. This method, designed for survival data with partly interval-censored failure times, accommodates both time-fixed and time-varying covariates. We utilise Gaussian basis functions to construct a smooth approximation of the nonparametric baseline hazard and fit the model via a constrained optimisation approach. To illustrate the effectiveness of our proposed method, we conduct a comprehensive simulation study. We also present an implementation of our approach on a randomised clinical trial dataset on advanced melanoma patients.
Mendelian randomization uses genetic variants as instrumental variables to make causal inferences about the effects of modifiable risk factors on diseases from observational data. One of the major challenges in Mendelian randomization is that many genetic variants are only modestly or even weakly associated with the risk factor of interest, a setting known as many weak instruments. Many existing methods, such as the popular inverse-variance weighted (IVW) method, could be biased when the instrument strength is weak. To address this issue, the debiased IVW (dIVW) estimator, which is shown to be robust to many weak instruments, was recently proposed. However, this estimator still has non-ignorable bias when the effective sample size is small. In this paper, we propose a modified debiased IVW (mdIVW) estimator by multiplying a modification factor to the original dIVW estimator. After this simple correction, we show that the bias of the mdIVW estimator converges to zero at a faster rate than that of the dIVW estimator under some regularity conditions. Moreover, the mdIVW estimator has smaller variance than the dIVW estimator.We further extend the proposed method to account for the presence of instrumental variable selection and balanced horizontal pleiotropy. We demonstrate the improvement of the mdIVW estimator over the dIVW estimator through extensive simulation studies and real data analysis.
Regression models that incorporate smooth functions of predictor variables to explain the relationships with a response variable have gained widespread usage and proved successful in various applications. By incorporating smooth functions of predictor variables, these models can capture complex relationships between the response and predictors while still allowing for interpretation of the results. In situations where the relationships between a response variable and predictors are explored, it is not uncommon to assume that these relationships adhere to certain shape constraints. Examples of such constraints include monotonicity and convexity. The scam package for R has become a popular package to carry out the full fitting of exponential family generalized additive modelling with shape restrictions on smooths. The paper aims to extend the existing framework of shape-constrained generalized additive models (SCAM) to accommodate smooth interactions of covariates, linear functionals of shape-constrained smooths and incorporation of residual autocorrelation. The methods described in this paper are implemented in the recent version of the package scam, available on the Comprehensive R Archive Network (CRAN).
Compared to other techniques, particle swarm optimization is more frequently utilized because of its ease of use and low variability. However, it is complicated to find the best possible solution in the search space in large-scale optimization problems. Moreover, changing algorithm variables does not influence algorithm convergence much. The PSO algorithm can be combined with other algorithms. It can use their advantages and operators to solve this problem. Therefore, this paper proposes the onlooker multi-parent crossover discrete particle swarm optimization (OMPCDPSO). To improve the efficiency of the DPSO algorithm, we utilized multi-parent crossover on the best solutions. We performed an independent and intensive neighborhood search using the onlooker bees of the bee algorithm. The algorithm uses onlooker bees and crossover. They do local search (exploitation) and global search (exploration). Each of these searches is among the best solutions (employed bees). The proposed algorithm was tested on the allocation problem, which is an NP-hard optimization problem. Also, we used two types of simulated data. They were used to test the scalability and complexity of the better algorithm. Also, fourteen 2D test functions and thirteen 30D test functions were used. They also used twenty IEEE CEC2005 benchmark functions to test the efficiency of OMPCDPSO. Also, to test OMPCDPSO's performance, we compared it to four new binary optimization algorithms and three classic ones. The results show that the OMPCDPSO version had high capability. It performed better than other algorithms. The developed algorithm in this research (OMCDPSO) in 36 test functions out of 47 (76.60%) is better than other algorithms. The Onlooker bees and multi-parent operators significantly impact the algorithm's performance.
We show that for log-concave real random variables with fixed variance the Shannon differential entropy is minimized for an exponential random variable. We apply this result to derive upper bounds on capacities of additive noise channels with log-concave noise. We also improve constants in the reverse entropy power inequalities for log-concave random variables.
Topic detection is a complex process and depends on language because it somehow needs to analyze text. There have been few studies on topic detection in Persian, and the existing algorithms are not remarkable. Therefore, we aimed to study topic detection in Persian. The objectives of this study are: 1) to conduct an extensive study on the best algorithms for topic detection, 2) to identify necessary adaptations to make these algorithms suitable for the Persian language, and 3) to evaluate their performance on Persian social network texts. To achieve these objectives, we have formulated two research questions: First, considering the lack of research in Persian, what modifications should be made to existing frameworks, especially those developed in English, to make them compatible with Persian? Second, how do these algorithms perform, and which one is superior? There are various topic detection methods that can be categorized into different categories. Frequent pattern and clustering are selected for this research, and a hybrid of both is proposed as a new category. Then, ten methods from these three categories are selected. All of them are re-implemented from scratch, changed, and adapted with Persian. These ten methods encompass different types of topic detection methods and have shown good performance in English. The text of Persian social network posts is used as the dataset. Additionally, a new multiclass evaluation criterion, called FS, is used in this paper for the first time in the field of topic detection. Approximately 1.4 billion tokens are processed during experiments. The results indicate that if we are searching for keyword-topics that are easily understandable by humans, the hybrid category is better. However, if the aim is to cluster posts for further analysis, the frequent pattern category is more suitable.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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