scholarly journals Raman Spectral Signatures of Serum-Derived Extracellular Vesicle-Enriched Isolates May Support the Diagnosis of CNS Tumors

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1407
Author(s):  
Matyas Bukva ◽  
Gabriella Dobra ◽  
Juan Gomez-Perez ◽  
Krisztian Koos ◽  
Maria Harmati ◽  
...  
Keyword(s):  
Lumbar Disc ◽  
Area Under The Curve ◽  
Principal Component ◽  
Extracellular Vesicle ◽  
Classification Performance ◽  
Cns Tumors ◽  
Clinical Samples ◽  
Support Vector ◽  
Serum Samples ◽  
Raman Spectroscopic

Investigating the molecular composition of small extracellular vesicles (sEVs) for tumor diagnostic purposes is becoming increasingly popular, especially for diseases for which diagnosis is challenging, such as central nervous system (CNS) malignancies. Thorough examination of the molecular content of sEVs by Raman spectroscopy is a promising but hitherto barely explored approach for these tumor types. We attempt to reveal the potential role of serum-derived sEVs in diagnosing CNS tumors through Raman spectroscopic analyses using a relevant number of clinical samples. A total of 138 serum samples were obtained from four patient groups (glioblastoma multiforme, non-small-cell lung cancer brain metastasis, meningioma and lumbar disc herniation as control). After isolation, characterization and Raman spectroscopic assessment of sEVs, the Principal Component Analysis–Support Vector Machine (PCA–SVM) algorithm was performed on the Raman spectra for pairwise classifications. Classification accuracy (CA), sensitivity, specificity and the Area Under the Curve (AUC) value derived from Receiver Operating Characteristic (ROC) analyses were used to evaluate the performance of classification. The groups compared were distinguishable with 82.9–92.5% CA, 80–95% sensitivity and 80–90% specificity. AUC scores in the range of 0.82–0.9 suggest excellent and outstanding classification performance. Our results support that Raman spectroscopic analysis of sEV-enriched isolates from serum is a promising method that could be further developed in order to be applicable in the diagnosis of CNS tumors.

scholarly journals Small Extracellular Vesicles Isolated from Serum May Serve as Signal-Enhancers for the Monitoring of CNS Tumors

2020 ◽  
Vol 21 (15) ◽  
pp. 5359 ◽  
Author(s):  
Gabriella Dobra ◽  
Matyas Bukva ◽  
Zoltan Szabo ◽  
Bella Bruszel ◽  
Maria Harmati ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Serum Proteins ◽  
Lumbar Disc ◽  
Principal Component ◽  
Cns Tumors ◽  
Serum Samples ◽  
Force Microscopy ◽  
Isolation And Characterization ◽  
Atomic Force ◽  
Patient Groups

Liquid biopsy-based methods to test biomarkers (e.g., serum proteins and extracellular vesicles) may help to monitor brain tumors. In this proteomics-based study, we aimed to identify a characteristic protein fingerprint associated with central nervous system (CNS) tumors. Overall, 96 human serum samples were obtained from four patient groups, namely glioblastoma multiforme (GBM), non-small-cell lung cancer brain metastasis (BM), meningioma (M) and lumbar disc hernia patients (CTRL). After the isolation and characterization of small extracellular vesicles (sEVs) by nanoparticle tracking analysis (NTA) and atomic force microscopy (AFM), liquid chromatography -mass spectrometry (LC-MS) was performed on two different sample types (whole serum and serum sEVs). Statistical analyses (ratio, Cohen’s d, receiver operating characteristic; ROC) were carried out to compare patient groups. To recognize differences between the two sample types, pairwise comparisons (Welch’s test) and ingenuity pathway analysis (IPA) were performed. According to our knowledge, this is the first study that compares the proteome of whole serum and serum-derived sEVs. From the 311 proteins identified, 10 whole serum proteins and 17 sEV proteins showed the highest intergroup differences. Sixty-five proteins were significantly enriched in sEV samples, while 129 proteins were significantly depleted compared to whole serum. Based on principal component analysis (PCA) analyses, sEVs are more suitable to discriminate between the patient groups. Our results support that sEVs have greater potential to monitor CNS tumors, than whole serum.

Deep Learning Associated with Laser-Induced Breakdown Spectroscopy (LIBS) for the Prediction of Lead in Soil

2019 ◽  
Vol 73 (5) ◽  
pp. 565-573 ◽  
Author(s):  
Yun Zhao ◽  
Mahamed Lamine Guindo ◽  
Xing Xu ◽  
Miao Sun ◽  
Jiyu Peng ◽  
...  
Keyword(s):  
Deep Learning ◽  
Confusion Matrix ◽  
Principal Component ◽  
Classification Performance ◽  
Soil Samples ◽  
Laser Induced Breakdown Spectroscopy ◽  
Support Vector ◽  
Breakdown Spectroscopy ◽  
Laser Induced Breakdown ◽  
Different Levels

In this study, a method based on laser-induced breakdown spectroscopy (LIBS) was developed to detect soil contaminated with Pb. Different levels of Pb were added to soil samples in which tobacco was planted over a period of two to four weeks. Principal component analysis and deep learning with a deep belief network (DBN) were implemented to classify the LIBS data. The robustness of the method was verified through a comparison with the results of a support vector machine and partial least squares discriminant analysis. A confusion matrix of the different algorithms shows that the DBN achieved satisfactory classification performance on all samples of contaminated soil. In terms of classification, the proposed method performed better on samples contaminated for four weeks than on those contaminated for two weeks. The results show that LIBS can be used with deep learning for the detection of heavy metals in soil.

scholarly journals An Electronic Component Recognition Algorithm Based on Deep Learning with a Faster SqueezeNet

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Yuanyuan Xu ◽  
Genke Yang ◽  
Jiliang Luo ◽  
Jianan He
Keyword(s):  
Deep Learning ◽  
Characteristic Curve ◽  
Area Under The Curve ◽  
Principal Component ◽  
Recognition Algorithm ◽  
Electronic Component ◽  
Support Vector ◽  
Learning Networks ◽  
Component Recognition ◽  
And Performance

Electronic component recognition plays an important role in industrial production, electronic manufacturing, and testing. In order to address the problem of the low recognition recall and accuracy of traditional image recognition technologies (such as principal component analysis (PCA) and support vector machine (SVM)), this paper selects multiple deep learning networks for testing and optimizes the SqueezeNet network. The paper then presents an electronic component recognition algorithm based on the Faster SqueezeNet network. This structure can reduce the size of network parameters and computational complexity without deteriorating the performance of the network. The results show that the proposed algorithm performs well, where the Receiver Operating Characteristic Curve (ROC) and Area Under the Curve (AUC), capacitor and inductor, reach 1.0. When the FPR is less than or equal 10 − 6   level, the TPR is greater than or equal to 0.99; its reasoning time is about 2.67 ms, achieving the industrial application level in terms of time consumption and performance.

Variability in Muscle Recruitment Strategy Between Operators During Assisted Assembly Tasks

2018 ◽  
Author(s):  
Yingxin Qiu ◽  
Keerthana Murali ◽  
Jun Ueda ◽  
Atsushi Okabe ◽  
Dalong Gao
Keyword(s):  
Upper Limb ◽  
Lower Limb ◽  
Wrist Joint ◽  
Principal Component ◽  
Classification Performance ◽  
Body Motion ◽  
Recruitment Strategy ◽  
Support Vector ◽  
Recruitment Strategies ◽  
Muscle Recruitment

This paper reports the variability in muscle recruitment strategies among individuals who operate a non-powered lifting device for general assembly (GA) tasks. Support vector machine (SVM) was applied to the classification of motion states of operators using electromyography (EMG) signals collected from a total of 15 upper limb, lower limb, shoulder, and torso muscles. By comparing the classification performance and muscle activity features, variability in muscle recruitment strategy was observed from lower limb and torso muscles, while the recruitment strategies of upper limb and shoulder muscles were relatively consistent across subjects. Principal component analysis (PCA) was applied to identify key muscles that are highly correlated with body movements. Selected muscles at the wrist joint, ankle joint and scapula are considered to have greater significance in characterizing the muscle recruitment strategies than other investigated muscles. PCA loading factors also indicate the existence of body motion redundancy during typical pick-and-place tasks.

scholarly journals To Explore the Predictive Power of Visuomotor Network Dysfunctions in Mild Cognitive Impairment and Alzheimer’s Disease

2021 ◽  
Vol 15 ◽  
Author(s):  
Justine Staal ◽  
Francesco Mattace-Raso ◽  
Hennie A. M. Daniels ◽  
Johannes van der Steen ◽  
Johan J. M. Pel
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Support Vector Machine ◽  
Cognitive Impairment ◽  
Mild Cognitive Impairment ◽  
Predictive Power ◽  
Area Under The Curve ◽  
Classification Performance ◽  
Support Vector ◽  
Potential Biomarker

BackgroundResearch into Alzheimer’s disease has shifted toward the identification of minimally invasive and less time-consuming modalities to define preclinical stages of Alzheimer’s disease.MethodHere, we propose visuomotor network dysfunctions as a potential biomarker in AD and its prodromal stage, mild cognitive impairment with underlying the Alzheimer’s disease pathology. The functionality of this network was tested in terms of timing, accuracy, and speed with goal-directed eye-hand tasks. The predictive power was determined by comparing the classification performance of a zero-rule algorithm (baseline), a decision tree, a support vector machine, and a neural network using functional parameters to classify controls without cognitive disorders, mild cognitive impaired patients, and Alzheimer’s disease patients.ResultsFair to good classification was achieved between controls and patients, controls and mild cognitive impaired patients, and between controls and Alzheimer’s disease patients with the support vector machine (77–82% accuracy, 57–93% sensitivity, 63–90% specificity, 0.74–0.78 area under the curve). Classification between mild cognitive impaired patients and Alzheimer’s disease patients was poor, as no algorithm outperformed the baseline (63% accuracy, 0% sensitivity, 100% specificity, 0.50 area under the curve).Comparison with Existing Method(s)The classification performance found in the present study is comparable to that of the existing CSF and MRI biomarkers.ConclusionThe data suggest that visuomotor network dysfunctions have potential in biomarker research and the proposed eye-hand tasks could add to existing tests to form a clear definition of the preclinical phenotype of AD.

scholarly journals Can Pre-Trained Convolutional Neural Networks be directly used as a Feature Extractor for Video-based Neonatal Sleep and Wake Classification?

2020 ◽  
Author(s):  
Muhammad Awais ◽  
Xi Long ◽  
Bin Yin ◽  
Chen chen ◽  
Saeed Akbarzadeh ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Video Recording ◽  
Principal Component ◽  
Classification Performance ◽  
Support Vector ◽  
Video Frames ◽  
Feature Extractor ◽  
Fully Connected

Abstract Objective: In this paper, we propose to evaluate the use of a pre-trained convolutional neural networks (CNNs) as a features extractor followed by the Principal Component Analysis (PCA) to find the best discriminant features to perform classification using support vector machine (SVM) algorithm for neonatal sleep and wake states using Fluke® facial video frames. Using pre-trained CNNs as feature extractor would hugely reduce the effort of collecting new neonatal data for training a neural network which could be computationally very expensive. The features are extracted after fully connected layers (FCL’s), where we compare several pre-trained CNNs, e.g., VGG16, VGG19, InceptionV3, GoogLeNet, ResNet, and AlexNet. Results: From around 2-h Fluke® video recording of seven neonate, we achieved a modest classification performance with an accuracy, sensitivity, and specificity of 65.3%, 69.8%, 61.0%, respectively with AlexNet using Fluke® (RGB) video frames. This indicates that using a pre-trained model as a feature extractor could not fully suffice for highly reliable sleep and wake classification in neonates. Therefore, in future a dedicated neural network trained on neonatal data or a transfer learning approach is required.

The recognition of plastic bottle using linear multi hierarchical SVM classifier

2021 ◽  
pp. 1-14
Author(s):  
LiHua Cai ◽  
Jin Cao ◽  
MingQiang Wang ◽  
Ta Zhou ◽  
HaiFeng Fang
Keyword(s):  
Loss Function ◽  
Deep Structure ◽  
Principal Component ◽  
Classification Performance ◽  
Support Vector ◽  
Svm Classifier ◽  
Input Matrix ◽  
Classification Rate ◽  
Pet Bottles ◽  
Combination Methods

Both classification rate and accuracy are crucial for the recyclable PET bottles, and the existing combination methods of SVM all simply use SVM as the unit classifier, ignoring the improvement of SVM’s classification performance in the training process of deep learning. A linear multi hierarchical deep structure based on Support Vector Machine (SVM) is proposed to cover this problem. A novel definition of the input matrix in each layer enhances the optimization of Lagrange multipliers in Sequential Minimal Optimization (SMO) algorithm, thus the datapoint in maximum interval of SVM hyperplane could be recognized, improving the classification performance of SVM classifier in this layer. The loss function defined in this paper could control the depth of Linear Multi Hierarchical SVM (LMHSVM), the generalization parameters are added in the loss function and the input matrix to enhance the generalization performance of LMHSVM. The process of creating Bottle dataset by Histogram of Oriented Gradient (HOG) and Principal Component Analysis (PCA) is introduced meanwhile, reducing the data size of bottles. Experiments are conducted on LMHSVM and multiple typical classification algorithms with Bottle dataset and UCI datasets, the results indicated that LMHSVM has excellent classification performances than FNN classifier, LIBSVM (Gaussian) and GFS-AdaBoost-C in KEEL.

scholarly journals Can pre-trained convolutional neural networks be directly used as a feature extractor for video-based neonatal sleep and wake classification?

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Muhammad Awais ◽  
Xi Long ◽  
Bin Yin ◽  
Chen Chen ◽  
Saeed Akbarzadeh ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Video Recording ◽  
Principal Component ◽  
Classification Performance ◽  
Support Vector ◽  
Video Frames ◽  
Feature Extractor ◽  
Future Work

Abstract Objective In this paper, we propose to evaluate the use of pre-trained convolutional neural networks (CNNs) as a features extractor followed by the Principal Component Analysis (PCA) to find the best discriminant features to perform classification using support vector machine (SVM) algorithm for neonatal sleep and wake states using Fluke® facial video frames. Using pre-trained CNNs as a feature extractor would hugely reduce the effort of collecting new neonatal data for training a neural network which could be computationally expensive. The features are extracted after fully connected layers (FCL’s), where we compare several pre-trained CNNs, e.g., VGG16, VGG19, InceptionV3, GoogLeNet, ResNet, and AlexNet. Results From around 2-h Fluke® video recording of seven neonates, we achieved a modest classification performance with an accuracy, sensitivity, and specificity of 65.3%, 69.8%, 61.0%, respectively with AlexNet using Fluke® (RGB) video frames. This indicates that using a pre-trained model as a feature extractor could not fully suffice for highly reliable sleep and wake classification in neonates. Therefore, in future work a dedicated neural network trained on neonatal data or a transfer learning approach is required.

scholarly journals A Circulating miRNA Signature for Stratification of Breast Lesions among Women with Abnormal Screening Mammograms

Cancers ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1872
Author(s):  
Sau Yeen Loke ◽  
Prabhakaran Munusamy ◽  
Geok Ling Koh ◽  
Claire Hian Tzer Chan ◽  
Preetha Madhukumar ◽  
...  
Keyword(s):  
Multiple Testing ◽  
Area Under The Curve ◽  
Principal Component ◽  
Classification Model ◽  
Breast Lesions ◽  
Mirna Signature ◽  
Serum Samples ◽  
Roc Curve Analysis ◽  
Benign Breast Lesions ◽  
Screening Mammograms

Although mammography is the gold standard for breast cancer screening, the high rates of false-positive mammograms remain a concern. Thus, there is an unmet clinical need for a non-invasive and reliable test to differentiate between malignant and benign breast lesions in order to avoid subjecting patients with abnormal mammograms to unnecessary follow-up diagnostic procedures. Serum samples from 116 malignant breast lesions and 64 benign breast lesions were comprehensively profiled for 2,083 microRNAs (miRNAs) using next-generation sequencing. Of the 180 samples profiled, three outliers were removed based on the principal component analysis (PCA), and the remaining samples were divided into training (n = 125) and test (n = 52) sets at a 70:30 ratio for further analysis. In the training set, significantly differentially expressed miRNAs (adjusted p < 0.01) were identified after correcting for multiple testing using a false discovery rate. Subsequently, a predictive classification model using an eight-miRNA signature and a Bayesian logistic regression algorithm was developed. Based on the receiver operating characteristic (ROC) curve analysis in the test set, the model could achieve an area under the curve (AUC) of 0.9542. Together, this study demonstrates the potential use of circulating miRNAs as an adjunct test to stratify breast lesions in patients with abnormal screening mammograms.

scholarly journals Raman spectroscopy as a non-invasive diagnostic technique for endometriosis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ugur Parlatan ◽  
Medine Tuna Inanc ◽  
Bahar Yuksel Ozgor ◽  
Engin Oral ◽  
Ercan Bastu ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Diagnostic Technique ◽  
Principal Component ◽  
Classification Model ◽  
Support Vector ◽  
Serum Samples ◽  
K Nearest Neighbors ◽  
Non Invasive ◽  
Unseen Data ◽  
Invasive Method

AbstractEndometriosis is a condition in which the endometrium, the layer of tissue that usually covers the inside of the uterus, grows outside the uterus. One of its severe effects is sub-fertility. The exact reason for endometriosis is still unknown and under investigation. Tracking the symptoms is not sufficient for diagnosing the disease. A successful diagnosis can only be made using laparoscopy. During the disease, the amount of some molecules (i.e., proteins, antigens) changes in the blood. Raman spectroscopy provides information about biochemicals without using dyes or external labels. In this study, Raman spectroscopy is used as a non-invasive diagnostic method for endometriosis. The Raman spectra of 94 serum samples acquired from 49 patients and 45 healthy individuals were compared for this study. Principal Component Analysis (PCA), k- Nearest Neighbors (kNN), and Support Vector Machines (SVM) were used in the analysis. According to the results (using 80 measurements for training and 14 measurements for the test set), it was found that kNN-weighted gave the best classification model with sensitivity and specificity values of 80.5% and 89.7%, respectively. Testing the model with unseen data yielded a sensitivity value of 100% and a specificity value of 100%. To the best of our knowledge, this is the first study in which Raman spectroscopy was used in combination with PCA and classification algorithms as a non-invasive method applied on blood sera for the diagnosis of endometriosis.

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