Supervised Methods for Biomarker Detection from Microarray Experiments

Author(s):  
Angela Serra ◽  
Luca Cattelani ◽  
Michele Fratello ◽  
Vittorio Fortino ◽  
Pia Anneli Sofia Kinaret ◽  
...  
2021 ◽  
Vol 10 (2) ◽  
pp. 319
Author(s):  
Hee Cheol Yang ◽  
Won Jong Rhee

Because cancers are heterogeneous, it is evident that multiplexed detection is required to achieve disease diagnosis with high accuracy and specificity. Extracellular vesicles (EVs) have been a subject of great interest as sources of novel biomarkers for cancer liquid biopsy. However, EVs are nano-sized particles that are difficult to handle; thus, it is necessary to develop a method that enables efficient and straightforward EV biomarker detection. In the present study, we developed a method for single step in situ detection of EV surface proteins and inner miRNAs simultaneously using a flow cytometer. CD63 antibody and molecular beacon-21 were investigated for multiplexed biomarker detection in normal and cancer EVs. A phospholipid-polymer-phospholipid conjugate was introduced to induce clustering of the EVs analyzed using nanoparticle tracking analysis, which enhanced the detection signals. As a result, the method could detect and distinguish cancer cell-derived EVs using a flow cytometer. Thus, single step in situ detection of multiple EV biomarkers using a flow cytometer can be applied as a simple, labor- and time-saving, non-invasive liquid biopsy for the diagnosis of various diseases, including cancer.


2021 ◽  
Vol 14 (2) ◽  
pp. 201-214
Author(s):  
Danilo Croce ◽  
Giuseppe Castellucci ◽  
Roberto Basili

In recent years, Deep Learning methods have become very popular in classification tasks for Natural Language Processing (NLP); this is mainly due to their ability to reach high performances by relying on very simple input representations, i.e., raw tokens. One of the drawbacks of deep architectures is the large amount of annotated data required for an effective training. Usually, in Machine Learning this problem is mitigated by the usage of semi-supervised methods or, more recently, by using Transfer Learning, in the context of deep architectures. One recent promising method to enable semi-supervised learning in deep architectures has been formalized within Semi-Supervised Generative Adversarial Networks (SS-GANs) in the context of Computer Vision. In this paper, we adopt the SS-GAN framework to enable semi-supervised learning in the context of NLP. We demonstrate how an SS-GAN can boost the performances of simple architectures when operating in expressive low-dimensional embeddings; these are derived by combining the unsupervised approximation of linguistic Reproducing Kernel Hilbert Spaces and the so-called Universal Sentence Encoders. We experimentally evaluate the proposed approach over a semantic classification task, i.e., Question Classification, by considering different sizes of training material and different numbers of target classes. By applying such adversarial schema to a simple Multi-Layer Perceptron, a classifier trained over a subset derived from 1% of the original training material achieves 92% of accuracy. Moreover, when considering a complex classification schema, e.g., involving 50 classes, the proposed method outperforms state-of-the-art alternatives such as BERT.


Cancers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 3827
Author(s):  
Jae Young Hur ◽  
Kye Young Lee

Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.


IEEE Access ◽  
2021 ◽  
Vol 9 ◽  
pp. 35834-35845
Author(s):  
Limin Xia ◽  
Jiahui Zhu ◽  
Zhimin Yu

Technologies ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 2
Author(s):  
Ashish Jaiswal ◽  
Ashwin Ramesh Babu ◽  
Mohammad Zaki Zadeh ◽  
Debapriya Banerjee ◽  
Fillia Makedon

Self-supervised learning has gained popularity because of its ability to avoid the cost of annotating large-scale datasets. It is capable of adopting self-defined pseudolabels as supervision and use the learned representations for several downstream tasks. Specifically, contrastive learning has recently become a dominant component in self-supervised learning for computer vision, natural language processing (NLP), and other domains. It aims at embedding augmented versions of the same sample close to each other while trying to push away embeddings from different samples. This paper provides an extensive review of self-supervised methods that follow the contrastive approach. The work explains commonly used pretext tasks in a contrastive learning setup, followed by different architectures that have been proposed so far. Next, we present a performance comparison of different methods for multiple downstream tasks such as image classification, object detection, and action recognition. Finally, we conclude with the limitations of the current methods and the need for further techniques and future directions to make meaningful progress.


Nanoscale ◽  
2021 ◽  
Author(s):  
Yang Xiong ◽  
Tong Fu ◽  
Daxiao Zhang ◽  
Shunping Zhang ◽  
Hongxing Xu

Easy-to-use and sensitive quantification of biomarkers has great significance in disease prediction, diagnosis, and monitoring. Here, we report a biosensor for simple and sensitive biomarker detection based on the strong...


The Analyst ◽  
2021 ◽  
Author(s):  
Man Tang ◽  
Jinyao Chen ◽  
Jia Lei ◽  
Zhao Ai ◽  
Feng Liu ◽  
...  

The existed multiplex biomarker detections are limited by the high demand for coding material and expensive detection equipment. This paper has proposed a convenient and precise coding method based on...


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