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Radiology Radiology

Potential use of deep learning techniques for postmortem imaging.

In Forensic science, medicine, and pathology

The use of postmortem computed tomography in forensic medicine, in addition to conventional autopsy, is now a standard procedure in several countries. However, the large number of cases, the large amount of data, and the lack of postmortem radiology experts have pushed researchers to develop solutions that are able to automate diagnosis by applying deep learning techniques to postmortem computed tomography images. While deep learning techniques require a good understanding of image analysis and mathematical optimization, the goal of this review was to provide to the community of postmortem radiology experts the key concepts needed to assess the potential of such techniques and how they could impact their work.

Dobay Akos, Ford Jonathan, Decker Summer, Ampanozi Garyfalia, Franckenberg Sabine, Affolter Raffael, Sieberth Till, Ebert Lars C

2020-Sep-29

Computed tomography, Convolutional neural networks, Deep learning, Forensic sciences, PMCT

General General

A novel semi-supervised multi-view clustering framework for screening Parkinson's disease.

In Mathematical biosciences and engineering : MBE

In recent years, there are many research cases for the diagnosis of Parkinson's disease (PD) with the brain magnetic resonance imaging (MRI) by utilizing the traditional unsupervised machine learning methods and the supervised deep learning models. However, unsupervised learning methods are not good at extracting accurate features among MRIs and it is difficult to collect enough data in the field of PD to satisfy the need of training deep learning models. Moreover, most of the existing studies are based on single-view MRI data, of which data characteristics are not sufficient enough. In this paper, therefore, in order to tackle the drawbacks mentioned above, we propose a novel semi-supervised learning framework called Semi-supervised Multi-view learning Clustering architecture technology (SMC). The model firstly introduces the sliding window method to grasp different features, and then uses the dimensionality reduction algorithms of Linear Discriminant Analysis (LDA) to process the data with different features. Finally, the traditional single-view clustering and multi-view clustering methods are employed on multiple feature views to obtain the results. Experiments show that our proposed method is superior to the state-of-art unsupervised learning models on the clustering effect. As a result, it may be noted that, our work could contribute to improving the effectiveness of identifying PD by previous labeled and subsequent unlabeled medical MRI data in the realistic medical environment.

Zhang Xiao Bo, Zhai Dong Hai, Yang Yan, Zhang Yi Ling, Wang Chun Lin

2020-Apr-30

** Parkinson’s disease (PD) , clustering , dimensionality reduction , feature extraction , semi-supervised learning **

General General

Visual interpretation of [18F]Florbetaben PET supported by deep learning-based estimation of amyloid burden.

In European journal of nuclear medicine and molecular imaging ; h5-index 66.0

PURPOSE : Amyloid PET which has been widely used for noninvasive assessment of cortical amyloid burden is visually interpreted in the clinical setting. As a fast and easy-to-use visual interpretation support system, we analyze whether the deep learning-based end-to-end estimation of amyloid burden improves inter-reader agreement as well as the confidence of the visual reading.

METHODS : A total of 121 clinical routines [18F]Florbetaben PET images were collected for the randomized blind-reader study. The amyloid PET images were visually interpreted by three experts independently blind to other information. The readers qualitatively interpreted images without quantification at the first reading session. After more than 2-week interval, the readers additionally interpreted images with the quantification results provided by the deep learning system. The qualitative assessment was based on a 3-point BAPL score (1: no amyloid load, 2: minor amyloid load, and 3: significant amyloid load). The confidence score for each session was evaluated by a 3-point score (0: ambiguous, 1: probably, and 2: definite to decide).

RESULTS : Inter-reader agreements for the visual reading based on a 3-point scale (BAPL score) calculated by Fleiss kappa coefficients were 0.46 and 0.76 for the visual reading without and with the deep learning system, respectively. For the two reading sessions, the confidence score of visual reading was improved at the visual reading session with the output (1.27 ± 0.078 for visual reading-only session vs. 1.66 ± 0.63 for a visual reading session with the deep learning system).

CONCLUSION : Our results highlight the impact of deep learning-based one-step amyloid burden estimation system on inter-reader agreement and confidence of reading when applied to clinical routine amyloid PET reading.

Kim Ji-Young, Oh Dongkyu, Sung Kiyoung, Choi Hongyoon, Paeng Jin Chul, Cheon Gi Jeong, Kang Keon Wook, Lee Dong Young, Lee Dong Soo

2020-Sep-29

Alzheimer’s disease, Amyloid PET, Deep learning, PET, Visual quantification, [18F]Florbetaben

General General

Beyond abstinence and relapse: cluster analysis of drug-use patterns during treatment as an outcome measure for clinical trials.

In Psychopharmacology

RATIONALE : Many people being treated for opioid use disorder continue to use drugs during treatment. This use occurs in patterns that rarely conform to well-defined cycles of abstinence and relapse. Systematic identification and evaluation of these patterns could enhance analysis of clinical trials and provide insight into drug use.

OBJECTIVES : To evaluate such an approach, we analyzed patterns of opioid and cocaine use from three randomized clinical trials of contingency management in methadone-treated participants.

METHODS : Sequences of drug test results were analyzed with unsupervised machine-learning techniques, including hierarchical clustering of categorical results (i.e., whether any samples were positive during each week) and K-means longitudinal clustering of quantitative results (i.e., the proportion positive each week). The sensitivity of cluster membership as an experimental outcome was assessed based on the effects of contingency management. External validation of clusters was based on drug craving and other symptoms of substance use disorder.

RESULTS : In each clinical trial, we identified four clusters of use patterns, which can be described as opioid use, cocaine use, dual use (opioid and cocaine), and partial/complete abstinence. Different clustering techniques produced substantially similar classifications of individual participants, with strong above-chance agreement. Contingency management increased membership in clusters with lower levels of drug use and fewer symptoms of substance use disorder.

CONCLUSIONS : Cluster analysis provides person-level output that is more interpretable and actionable than traditional outcome measures, providing a concrete answer to the question of what clinicians can tell patients about the success rates of new treatments.

Panlilio Leigh V, Stull Samuel W, Bertz Jeremiah W, Burgess-Hull Albert J, Kowalczyk William J, Phillips Karran A, Epstein David H, Preston Kenzie L

2020-Sep-29

Cluster analysis, Cocaine, Contingency management, Methadone, Opioids, Substance use disorder, Treatment outcomes

General General

TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function.

In Nucleic acids research ; h5-index 217.0

T cells and the T-cell receptor (TCR) repertoire play pivotal roles in immune response and immunotherapy. TCR sequencing (TCR-Seq) technology has enabled accurate profiling TCR repertoire and currently a large number of TCR-Seq data are available in public. Based on the urgent need to effectively re-use these data, we developed TCRdb, a comprehensive human TCR sequences database, by a uniform pipeline to characterize TCR sequences on TCR-Seq data. TCRdb contains more than 277 million highly reliable TCR sequences from over 8265 TCR-Seq samples across hundreds of tissues/clinical conditions/cell types. The unique features of TCRdb include: (i) comprehensive and reliable sequences for TCR repertoire in different samples generated by a strict and uniform pipeline of TCRdb; (ii) powerful search function, allowing users to identify their interested TCR sequences in different conditions; (iii) categorized sample metadata, enabling comparison of TCRs in different sample types; (iv) interactive data visualization charts, describing the TCR repertoire in TCR diversity, length distribution and V-J gene utilization. The TCRdb database is freely available at http://bioinfo.life.hust.edu.cn/TCRdb/ and will be a useful resource in the research and application community of T cell immunology.

Chen Si-Yi, Yue Tao, Lei Qian, Guo An-Yuan

2020-Sep-29

General General

miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets.

In Nucleic acids research ; h5-index 217.0

MicroRNAs (miRNAs) related single-nucleotide variations (SNVs), including single-nucleotide polymorphisms (SNPs) and disease-related variations (DRVs) in miRNAs and miRNA-target binding sites, can affect miRNA functions and/or biogenesis, thus to impact on phenotypes. miRNASNP is a widely used database for miRNA-related SNPs and their effects. Here, we updated it to miRNASNP-v3 (http://bioinfo.life.hust.edu.cn/miRNASNP/) with tremendous number of SNVs and new features, especially the DRVs data. We analyzed the effects of 7 161 741 SNPs and 505 417 DRVs on 1897 pre-miRNAs (2630 mature miRNAs) and 3'UTRs of 18 152 genes. miRNASNP-v3 provides a one-stop resource for miRNA-related SNVs research with the following functions: (i) explore associations between miRNA-related SNPs/DRVs and diseases; (ii) browse the effects of SNPs/DRVs on miRNA-target binding; (iii) functional enrichment analysis of miRNA target gain/loss caused by SNPs/DRVs; (iv) investigate correlations between drug sensitivity and miRNA expression; (v) inquire expression profiles of miRNAs and their targets in cancers; (vi) browse the effects of SNPs/DRVs on pre-miRNA secondary structure changes; and (vii) predict the effects of user-defined variations on miRNA-target binding or pre-miRNA secondary structure. miRNASNP-v3 is a valuable and long-term supported resource in functional variation screening and miRNA function studies.

Liu Chun-Jie, Fu Xin, Xia Mengxuan, Zhang Qiong, Gu Zhifeng, Guo An-Yuan

2020-Sep-29