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General General

Classifications of Neurodegenerative Disorders Using a Multiplex Blood Biomarkers-Based Machine Learning Model.

In International journal of molecular sciences ; h5-index 102.0

Easily accessible biomarkers for Alzheimer's disease (AD), Parkinson's disease (PD), frontotemporal dementia (FTD), and related neurodegenerative disorders are urgently needed in an aging society to assist early-stage diagnoses. In this study, we aimed to develop machine learning algorithms using the multiplex blood-based biomarkers to identify patients with different neurodegenerative diseases. Plasma samples (n = 377) were obtained from healthy controls, patients with AD spectrum (including mild cognitive impairment (MCI)), PD spectrum with variable cognitive severity (including PD with dementia (PDD)), and FTD. We measured plasma levels of amyloid-beta 42 (Aβ42), Aβ40, total Tau, p-Tau181, and α-synuclein using an immunomagnetic reduction-based immunoassay. We observed increased levels of all biomarkers except Aβ40 in the AD group when compared to the MCI and controls. The plasma α-synuclein levels increased in PDD when compared to PD with normal cognition. We applied machine learning-based frameworks, including a linear discriminant analysis (LDA), for feature extraction and several classifiers, using features from these blood-based biomarkers to classify these neurodegenerative disorders. We found that the random forest (RF) was the best classifier to separate different dementia syndromes. Using RF, the established LDA model had an average accuracy of 76% when classifying AD, PD spectrum, and FTD. Moreover, we found 83% and 63% accuracies when differentiating the individual disease severity of subgroups in the AD and PD spectrum, respectively. The developed LDA model with the RF classifier can assist clinicians in distinguishing variable neurodegenerative disorders.

Lin Chin-Hsien, Chiu Shu-I, Chen Ta-Fu, Jang Jyh-Shing Roger, Chiu Ming-Jang

2020-Sep-21

Alzheimer’s disease, Parkinson’s disease, biomarkers, classification, deep learning model, frontotemporal dementia, linear discriminant analysis, multivariate imputation by chained equations, neurodegenerative disorders

General General

Pandemic number five - Latest insights into the COVID-19 crisis.

In Biomedical journal

About nine months after the emergence of SARS-CoV-2, this special issue of the Biomedical Journal takes stock of its evolution into a pandemic. We acquire an elaborate overview of the history and virology of SARS-CoV-2, the epidemiology of COVID-19, and the development of therapies and vaccines, based on useful tools such as a pseudovirus system, artificial intelligence, and repurposing of existing drugs. Moreover, we learn about a potential link between COVID-19 and oral health, and some of the strategies that allowed Taiwan to handle the outbreak exceptionally well, including a COVID-19 biobank establishment, online tools for contact tracing, and the efficient management of emergency departments.

Häfner Sophia Julia

2020-Aug-27

COVID-19, Contact tracing, Pseudovirus system, Repurposing drugs, SARS-CoV-2

Ophthalmology Ophthalmology

DPN: Detail-Preserving Network with High Resolution Representation for Efficient Segmentation of Retinal Vessels

ArXiv Preprint

Retinal vessels are important biomarkers for many ophthalmological and cardiovascular diseases. It is of great significance to develop an accurate and fast vessel segmentation model for computer-aided diagnosis. Existing methods, such as U-Net follows the encoder-decoder pipeline, where detailed information is lost in the encoder in order to achieve a large field of view. Although detailed information could be recovered in the decoder via multi-scale fusion, it still contains noise. In this paper, we propose a deep segmentation model, called detail-preserving network (DPN) for efficient vessel segmentation. To preserve detailed spatial information and learn structural information at the same time, we designed the detail-preserving block (DP-Block). Further, we stacked eight DP-Blocks together to form the DPN. More importantly, there are no down-sampling operations among these blocks. As a result, the DPN could maintain a high resolution during the processing, which is helpful to locate the boundaries of thin vessels. To illustrate the effectiveness of our method, we conducted experiments over three public datasets. Experimental results show, compared to state-of-the-art methods, our method shows competitive/better performance in terms of segmentation accuracy, segmentation speed, extensibility and the number of parameters. Specifically, 1) the AUC of our method ranks first/second/third on the STARE/CHASE_DB1/DRIVE datasets, respectively. 2) Only one forward pass is required of our method to generate a vessel segmentation map, and the segmentation speed of our method is over 20-160x faster than other methods on the DRIVE dataset. 3) We conducted cross-training experiments to demonstrate the extensibility of our method, and results revealed that our method shows superior performance. 4) The number of parameters of our method is only around 96k, less then all comparison methods.

Song Guo

2020-09-25

Cardiology Cardiology

A comparison of artificial intelligence-based algorithms for the identification of patients with depressed right ventricular function from 2-dimentional echocardiography parameters and clinical features.

In Cardiovascular diagnosis and therapy

Background : Recognizing low right ventricular (RV) function from 2-dimentiontial echocardiography (2D-ECHO) is challenging when parameters are contradictory. We aim to develop a model to predict low RV function integrating the various 2D-ECHO parameters in reference to cardiac magnetic resonance (CMR)-the gold standard.

Methods : We retrospectively identified patients who underwent a 2D-ECHO and a CMR within 3 months of each other at our institution (American University of Beirut Medical Center). We extracted three parameters (TAPSE, S' and FACRV) that are classically used to assess RV function. We have assessed the ability of 2D-ECHO derived parameters and clinical features to predict RV function measured by the gold standard CMR. We compared outcomes from four machine learning algorithms, widely used in the biomedical community to solve classification problems.

Results : One hundred fifty-five patients were identified and included in our study. Average age was 43±17.1 years old and 52/156 (33.3%) were females. According to CMR, 21 patients were identified to have RV dysfunction, with an RVEF of 34.7%±6.4%, as opposed to 54.7%±6.7% in the normal RV population (P<0.0001). The Random Forest model was able to detect low RV function with an AUC =0.80, while general linear regression performed poorly in our population with an AUC of 0.62.

Conclusions : In this study, we trained and validated an ML-based algorithm that could detect low RV function from clinical and 2D-ECHO parameters. The algorithm has two advantages: first, it performed better than general linear regression, and second, it integrated the various 2D-ECHO parameters.

Ahmad Ali, Ibrahim Zahi, Sakr Georges, El-Bizri Abdallah, Masri Lara, Elhajj Imad H, El-Hachem Nehme, Isma’eel Hussain

2020-Aug

2D-ECHO, CMR, RV function, machine learning

Radiology Radiology

Machine learning-based CT fractional flow reserve assessment in acute chest pain: first experience.

In Cardiovascular diagnosis and therapy

Background : Computed tomography (CT)-derived fractional flow reserve (FFRCT) enables the non-invasive functional assessment of coronary artery stenosis. We evaluated the feasibility and potential clinical role of FFRCT in patients presenting to the emergency department with acute chest pain who underwent chest-pain CT (CPCT).

Methods : For this retrospective IRB-approved study, we included 56 patients (median age: 62 years, 14 females) with acute chest pain who underwent CPCT and who had at least a mild (≥25% diameter) coronary artery stenosis. CPCT was evaluated for the presence of acute plaque rupture and vulnerable plaque features. FFRCT measurements were performed using a machine learning-based software. We assessed the agreement between the results from FFRCT and patient outcome (including results from invasive catheter angiography and from any non-invasive cardiac imaging test, final clinical diagnosis and revascularization) for a follow-up of 3 months.

Results : FFRCT was technically feasible in 38/56 patients (68%). Eleven of the 38 patients (29%) showed acute plaque rupture in CPCT; all of them underwent immediate coronary revascularization. Of the remaining 27 patients (71%), 16 patients showed vulnerable plaque features (59%), of whom 11 (69%) were diagnosed with acute coronary syndrome (ACS) and 10 (63%) underwent coronary revascularization. In patients with vulnerable plaque features in CPCT, FFRCT had an agreement with outcome in 12/16 patients (75%). In patients without vulnerable plaque features (n=11), one patient showed myocardial ischemia (9%). In these patients, FFRCT and patient outcome showed an agreement in 10/11 patients (91%).

Conclusions : Our preliminary data show that FFRCT is feasible in patients with acute chest pain who undergo CPCT provided that image quality is sufficient. FFRCT has the potential to improve patient triage by reducing further downstream testing but appears of limited value in patients with CT signs of acute plaque rupture.

Eberhard Matthias, Nadarevic Tin, Cousin Andrej, von Spiczak Jochen, Hinzpeter Ricarda, Euler Andre, Morsbach Fabian, Manka Robert, Keller Dagmar I, Alkadhi Hatem

2020-Aug

Acute coronary syndrome (ACS), computed tomography angiography, fractional flow reserve, machine learning, myocardial

General General

Insight into glycogen synthase kinase-3β inhibitory activity of phyto-constituents from Melissa officinalis: in silico studies.

In In silico pharmacology

Over activity of Glycogen synthase kinase-3β (GSK-3β), a serine/threonine-protein kinase has been implicated in a number of diseases including stroke, type II diabetes and Alzheimer disease (AD). This study aimed to find novel inhibitors of GSK-3β from phyto-constituents of Melissa officinalis with the aid of computational analysis. Molecular docking, induced-fit docking (IFD), calculation of binding free energy via the MM-GBSA approach and Lipinski's rule of five (RO5) were employed to filter the compounds and determine their druggability. Most importantly, the compounds pIC50 were predicted by machine learning-based model generated by AutoQSAR algorithm. The generated model was validated to affirm its predictive model. The best model obtained was Model kpls_desc_38 (R2 = 0.8467 and Q2 = 0.8069), and this external validated model was utilized to predict the bioactivities of the lead compounds. While a number of characterized compounds from Melissa officinalis showed better docking score, binding free energy alongside adherence to RO5 than co-cystallized ligand, only three compounds (salvianolic acid C, ellagic acid and naringenin) showed more satisfactory pIC50. The results obtained in this study can be useful to design potent inhibitors of GSK-3β.

Iwaloye Opeyemi, Elekofehinti Olusola Olalekan, Oluwarotimi Emmanuel Ayo, Kikiowo Babatom Iwa, Fadipe Toyin Mary

2020

AutoQSAR, Glycogen synthase kinase-3β, Induced-fit docking (IFD), MM-GBSA, Melissa officinalis