Association of global and local low endothelial shear stress with high-risk plaque using intracoronary 3D optical coherence tomography: Introduction of 'shear stress score'

Aims

The association of low endothelial shear stress (ESS) with high-risk plaque (HRP) has not been thoroughly investigated in humans. We investigated the local ESS and lumen remodelling patterns in HRPs using optical coherence tomography (OCT), developed the shear stress score, and explored its association with the prevalence of HRPs and clinical outcomes.

Methods and results

A total of 35 coronary arteries from 30 patients with stable angina or acute coronary syndrome (ACS) were reconstructed with three dimensional (3D) OCT. ESS was calculated using computational fluid dynamics and classified into low, moderate, and high in 3-mm-long subsegments. In each subsegment, (i) fibroatheromas (FAs) were classified into HRPs and non-HRPs based on fibrous cap (FC) thickness and lipid pool size, and (ii) lumen remodelling was classified into constrictive, compensatory, and expansive. In each artery the shear stress score was calculated as metric of the extent and severity of low ESS. FAs in low ESS subsegments had thinner FC compared with high ESS (89 ± 84 vs.138 ± 83 µm, P < 0.05). Low ESS subsegments predominantly co-localized with HRPs vs. non-HRPs (29 vs. 9%, P < 0.05) and high ESS subsegments predominantly with non-HRPs (9 vs. 24%, P < 0.05). Compensatory and expansive lumen remodelling were the predominant responses within subsegments with low ESS and HRPs. In non-stenotic FAs, low ESS was associated with HRPs vs. non-HRPs (29 vs. 3%, P < 0.05). Arteries with increased shear stress score had increased frequency of HRPs and were associated with ACS vs. stable angina.

Conclusion

Local low ESS and expansive lumen remodelling are associated with HRP. Arteries with increased shear stress score have increased frequency of HRPs and propensity to present with ACS.

IRProfiler - a software toolbox for high throughput immune receptor profiling

Background

The study of the huge diversity of immune receptors, often referred to as immune repertoire profiling, is a prerequisite for diagnosis, prognostication and monitoring of hematological disorders. In the era of high-throughput sequencing (HTS), the abundance of immunogenetic data has revealed unprecedented opportunities for the thorough profiling of T-cell receptors (TR) and B-cell receptors (BcR). However, the volume of the data to be analyzed mandates for efficient and ease-to-use immune repertoire profiling software applications.

Results

This work introduces Immune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. Adopting 5 alternative clonotype definitions, IRProfiler implements a series of algorithms for 1) data filtering, 2) calculation of clonotype diversity and expression, 3) calculation of gene usage for the V and J subgroups, 4) detection of shared and exclusive clonotypes among multiple repertoires, and 5) comparison of gene usage for V and J subgroups among multiple repertoires. IRProfiler has been implemented as a toolbox of the Galaxy bioinformatics platform, comprising 6 tools. Theoretical and experimental evaluation has shown that the tools of IRProfiler are able to scale well with respect to the size of input dataset(s). IRProfiler has been utilized by a number of recently published studies concerning hematological disorders.

Conclusion

IRProfiler is made freely available via 3 distribution channels, including the Galaxy Tool Shed. Despite being a new entry in a crowded ecosystem of immune repertoire profiling software, IRProfiler founds its added value on its support for alternative clonotype definitions in conjunction with a combination of properties stemming from its user-centric design, namely ease-of-use, ease-of-access, exploitability of the output data, and analysis flexibility.

Detection of wheezes using their signature in the spectrogram space and musical features

In this work thirty features were tested in order to identify the best feature set for the robust detection of wheezes. The features include the detection of the wheezes signature in the spectrogram space (WS-SS) and twenty-nine musical features usually used in the context of Music Information Retrieval. The method proposed to detect the signature of wheezes imposes a temporal Gaussian regularization and a reduction of the false positives based on the (geodesic) morphological opening by reconstruction operator. Our dataset contains wheezes, crackles and normal breath sounds. Four selection algorithms were used to rank the features. The performance of the features was asserted having into account the Matthews correlation coefficient (MCC). All the selection algorithms ranked the WS-SS feature as the most important. A significant boost in performance was obtained by using around ten features. This improvement was independent of the selection algorithm. The use of more than ten features only allows for a small increase of the MCC value.

Information Technology Can Enhance Quality in Regional Health Delivery

Objectives: a) The use of information technology (IT) based solutions for quality health delivery in regional health information networks and the study of the enabling factors for their use in a regional health care network from key classes of users such as the medical personnel and the citizens. b) Identification of potential technologies for usage from all citizens and health providers in a regional environment, in all aspects of everyday life. c) Presentation of a generic user model for reference when developing and assessing IT based health delivery solutions.

Methods: After defining the major questions to be addressed, an overview of tele-health and tele-medicine technologies and solutions currently available shall be presented. Further, a generic user model applied to the use of IT based regional health delivery solutions both for the daily life and home care, and for research and clinical routine purposes are presented. Enabling technologies for integration of different IT modules, medical data processing and management procedures and the wireless application protocol (WAP) technology is discussed.

Results: Different levels of user applications are presented such as mobile telephony driven health information monitoring and systems integrating electronic health care records with multimedia medical information management and processing modules.

Conclusions: Although IT solutions are advanced and continue to evolve, still the user acceptance and user friendliness issues are unresolved. Mobile telecommunication solutions however may hold the key for wide scale implementation of IT solutions in regional health information networks and increased quality of health services.

Linear and nonlinear features of fetal heart rate on the assessment of fetal development in the course of pregnancy and the impact of fetal gender

OBJECTIVE

This work aims to investigate the impact of gestational age and fetal gender on fetal heart rate (FHR) tracings.

APPROACH

Different linear and nonlinear parameters indicating correlation or complexity were used to study the influence of fetal age and gender on FHR tracings. The signals were recorded from 99 normal pregnant women in a singleton pregnancy at gestational ages from 28 to 40 weeks, before the onset of labor. There were 56 female fetuses and 43 male.

MAIN RESULTS

Analysis of FHR shows that the means as well as measures of irregularity of FHR, such as approximate entropy and algorithmic complexity, decrease as gestation progresses. There were also indications that mutual information and multiscale entropy were lower in male fetuses in early pregnancy.

SIGNIFICANCE

Fetal age and gender seem to influence FHR tracings. Taking this into consideration would improve the interpretation of FHR monitoring.

An Open and Reconfigurable Wireless Sensor Network for Pervasive Health Monitoring

Objectives: Sensor networks constitute the backbone for the construction of personalized monitoring systems. Up to now, several sensor networks have been proposed for diverse pervasive healthcare applications, which are however characterized by a significant lack of open architectures, resulting in closed, non-interoperable and difficult to extend solutions. In this context, we propose an open and reconfigurable wireless sensor network (WSN) for pervasive health monitoring, with particular emphasis in its easy extension with additional sensors and functionality by incorporating embedded intelligence mechanisms.

Methods: We consider a generic WSN architecture comprised of diverse sensor nodes (with communication and processing capabilities) and a mobile base unit (MBU) operating as the gateway between the sensors and the medical personnel, formulating this way a body area network (BAN). The primary focus of this work is on the intra-BAN data communication issues, adopting SensorML as the data representation mean, including the encoding of the monitoring patterns and the functionality of the sensor network.

Results: In our prototype implementation two sensor nodes are emulated; one for heart rate monitoring and the other for blood glucose observations, while the MBU corresponds to a personal digital assistant (PDA) device. Java 2 Micro Edition (J2ME) is used to implement both the sensor nodes and the MBU components. Intra-BAN wireless communication relies on the Bluetooth protocol. Via an adaptive user interface in the MBU, health professionals may specify the monitoring parameters of the WSN and define the monitoring patterns of interest in terms of rules.

Conclusions: This work constitutes an essential step towards the construction of open, extensible, inter - operable and intelligent WSNs for pervasive health monitoring.

Gamifying Motion Control Assessments Using Leap Motion Controller

In rehabilitation, exergames and serious games are widely usedin order to motivate patients in the therapeutic procedure. Patients are asked to modify their incorrect motor patterns or reinforce the proper ones through activity rather than exercise. Interactive applications as such, can have a huge impact on a patient's motivation making repetitive physical exercises into pleasant experiences, thus maximizing the gains of therapy. In this paper we present the design and implementation of a serious game platform based on virtual 3D game environment and leap motion controller for interaction. For each session, achieved goals and response to stimuli is recorded and analyzed. Preliminary analysis results from evaluating the game with healthy subjects are encouraging.

Learning Healthcare Systems: Scaling-Up Integrated Care Programs

Current healthcare systems are struggling with rising costs and unbalanced quality of care. Integrated care (IC) is a worldwide trend in healthcare reforms designed to tackle these problems. ACT@Scale is a partnership of leading European regions, industry and academia which aims to identify, transfer and scale-up existing integrated healthcare practices. In this context, participating programs are applying iterative process improvement cycles using collaborative methodologies. The vision of learning health systems (LHS) is similar to IC, but it focuses on IT means as a change enabler for rapid and continuous knowledge integration into better outcomes. In this paper, we present the ACT@Scale program as an example of an LHS that monitors integrated care performance and effects of process improvement cycles.

ARCOCT: Automatic detection of lumen border in intravascular OCT images

BACKGROUND AND OBJECTIVE

Intravascular optical coherence tomography (OCT) is an invaluable tool for the detection of pathological features on the arterial wall and the investigation of post-stenting complications. Computational lumen border detection in OCT images is highly advantageous, since it may support rapid morphometric analysis. However, automatic detection is very challenging, since OCT images typically include various artifacts that impact image clarity, including features such as side branches and intraluminal blood presence. This paper presents ARCOCT, a segmentation method for fully-automatic detection of lumen border in OCT images.

METHODS

ARCOCT relies on multiple, consecutive processing steps, accounting for image preparation, contour extraction and refinement. In particular, for contour extraction ARCOCT employs the transformation of OCT images based on physical characteristics such as reflectivity and absorption of the tissue and, for contour refinement, local regression using weighted linear least squares and a 2nd degree polynomial model is employed to achieve artifact and small-branch correction as well as smoothness of the artery mesh. Our major focus was to achieve accurate contour delineation in the various types of OCT images, i.e., even in challenging cases with branches and artifacts.

RESULTS

ARCOCT has been assessed in a dataset of 1812 images (308 from stented and 1504 from native segments) obtained from 20 patients. ARCOCT was compared against ground-truth manual segmentation performed by experts on the basis of various geometric features (e.g. area, perimeter, radius, diameter, centroid, etc.) and closed contour matching indicators (the Dice index, the Hausdorff distance and the undirected average distance), using standard statistical analysis methods. The proposed method was proven very efficient and close to the ground-truth, exhibiting non statistically-significant differences for most of the examined metrics.

CONCLUSIONS

ARCOCT allows accurate and fully-automated lumen border detection in OCT images.

Beat-to-beat P-wave morphology as a predictor of paroxysmal atrial fibrillation

BACKGROUND AND OBJECTIVES

Atrial Fibrillation (AF) is the most common cardiac arrhythmia. The initiation and the perpetuation of AF is linked with phenomena of atrial remodeling, referring to the modification of the electrical and structural characteristics of the atrium. P-wave morphology analysis can reveal information regarding the propagation of the electrical activity on the atrial substrate. The purpose of this study is to investigate patterns on the P-wave morphology that may occur in patients with Paroxysmal AF (PAF) and which can be the basis for distinguishing between PAF and healthy subjects.

METHODS

Vectorcardiographic signals in the three orthogonal axes (X, Y and Z), of 3-5 min duration, were analyzed during SR. In total 29 PAF patients and 34 healthy volunteers were included in the analysis. These data were divided into two distinct datasets, one for the training and one for the testing of the proposed approach. The method is based on the identification of the dominant and the secondary P-wave morphology by combining adaptive k-means clustering of morphologies and a beat-to-beat cross correlation technique. The P-waves of the dominant morphology were further analyzed using wavelet transform whereas time domain characteristics were also extracted. Following a feature selection step, a SVM classifier was trained, for the discrimination of the PAF patients from the healthy subjects, while its accuracy was tested using the independent testing dataset.

RESULTS

In the cohort study, in both groups, the majority of the P-waves matched a main and a secondary morphology, while other morphologies were also present. The percentage of P-waves which simultaneously matched the main morphology in all three leads was lower in PAF patients (90.4 ± 7.8%) than in healthy subjects (95.5 ± 3.4%, p= 0.019). Three optimal scale bands were found and wavelet parameters were extracted which presented statistically significant differences between the two groups. Classification between the two groups was based on a feature selection process which highlighted 7 features, while an SVM classifier resulted a balanced accuracy equal to 93.75%. The results show the virtue of beat-to-beat analysis for PAF prediction.

CONCLUSION

The difference in the percentage of the main P-wave-morphology and in the P-wave time-frequency characteristics suggests a higher electrical instability of the atrial substrate in patients with PAF and different conduction patterns in the atria.

Detecting fetal heart sounds by means of Fractal Dimension analysis in the Wavelet domain

Phonocardiography is a low-cost technique for the detection of fetal heart sounds (FHS) that can extend clinical auscultation in mobile and home care setups. The work presented here examines the transferability of a Wavelet Transform (WT)-based method that combines also Fractal Dimension (FD) analysis, previously proposed as WT-FD for the cases of lung and bowel sound analysis [4], to the extraction of FHSs. The WT-FD method has been evaluated with 12 simulated FHS signals and has shown promising results in terms of accuracy and performance (89%) in identifying the location of heartbeat, even in cases of signals with additive noise up to (6dB). This robustness paves the way for WT-FD testing in real FHSs, recorded under clinical setting, clearly contributing to better evaluation of the fetal heart functionality.

Fetal Heart Sounds Detection Using Wavelet Transform and Fractal Dimension

Phonocardiography is a non-invasive technique for the detection of fetal heart sounds (fHSs). In this study, analysis of fetal phonocardiograph (fPCG) signals, in order to achieve fetal heartbeat segmentation, is proposed. The proposed approach (namely WT-FD) is a wavelet transform (WT)-based method that combines fractal dimension (FD) analysis in the WT domain for the extraction of fHSs from the underlying noise. Its adoption in this field stems from its successful use in the fields of lung and bowel sounds de-noising analysis. The efficiency of the WT-FD method in fHS extraction has been evaluated with 19 simulated fHS signals, created for the present study, with additive noise up to (3 dB), along with the simulated fPCGs database available at PhysioBank. Results have shown promising performance in the identification of the correct location and morphology of the fHSs, reaching an overall accuracy of 89% justifying the efficacy of the method. The WT-FD approach effectively extracts the fHS signals from the noisy background, paving the way for testing it in real fHSs and clearly contributing to better evaluation of the fetal heart functionality.

Detection of crackle events using a multi-feature approach

The automatic detection of adventitious lung sounds is a valuable tool to monitor respiratory diseases like chronic obstructive pulmonary disease. Crackles are adventitious and explosive respiratory sounds that are usually associated with the inflammation or infection of the small bronchi, bronchioles and alveoli. In this study a multi-feature approach is proposed for the detection of events, in the frame space, that contain one or more crackles. The performance of thirty-five features was tested. These features include thirty-one features usually used in the context of Music Information Retrieval, a wavelet based feature as well as the Teager energy and the entropy. The classification was done using a logistic regression classifier. Data from seventeen patients with manifestations of adventitious sounds and three healthy volunteers were used to evaluate the performance of the proposed method. The dataset includes crackles, wheezes and normal lung sounds. The optimal detection parameters, such as the number of features, were chosen based on a grid search. The performance of the detection was studied taking into account the sensitivity and the positive predictive value. For the conditions tested, the best results were obtained for the frame size equal to 128 ms and twenty-seven features.

PATHway I: design and rationale for the investigation of the feasibility, clinical effectiveness and cost-effectiveness of a technology-enabled cardiac rehabilitation platform

INTRODUCTION

Exercise-based cardiac rehabilitation (CR) independently alters the clinical course of cardiovascular diseases resulting in a significant reduction in all-cause and cardiac mortality. However, only 15%-30% of all eligible patients participate in a phase 2 ambulatory programme. The uptake rate of community-based programmes following phase 2 CR and adherence to long-term exercise is extremely poor. Newer care models, involving telerehabilitation programmes that are delivered remotely, show considerable promise for increasing adherence. In this view, the PATHway (Physical Activity Towards Health) platform was developed and now needs to be evaluated in terms of its feasibility and clinical efficacy.

METHODS AND ANALYSIS

In a multicentre randomised controlled pilot trial, 120 participants (m/f, age 40-80 years) completing a phase 2 ambulatory CR programme will be randomised on a 1:1 basis to PATHway or usual care. PATHway involves a comprehensive, internet-enabled, sensor-based home CR platform and provides individualised heart rate monitored exercise programmes (exerclasses and exergames) as the basis on which to provide a personalised lifestyle intervention programme. The control group will receive usual care. Study outcomes will be assessed at baseline, 3 months and 6 months after completion of phase 2 of the CR programme. The primary outcome is the change in active energy expenditure. Secondary outcomes include cardiopulmonary endurance capacity, muscle strength, body composition, cardiovascular risk factors, peripheral endothelial vascular function, patient satisfaction, health-related quality of life (HRQoL), well-being, mediators of behaviour change and safety. HRQoL and healthcare costs will be taken into account in cost-effectiveness evaluation.

ETHICS AND DISSEMINATION

The study will be conducted in accordance with the Declaration of Helsinki. This protocol has been approved by the director and clinical director of the PATHway study and by the ethical committee of each participating site. Results will be disseminated via peer-reviewed scientific journals and presentations at congresses and events.

TRIAL REGISTRATION NUMBER

NCT02717806. This trial is currently in the pre-results stage.

Evaluation of lung ventilation distribution in chronic obstructive pulmonary disease patients using the global inhomogeneity index

The global inhomogeneity (GI) index is a electrical impedance tomography (EIT) parameter that quantifies the tidal volume distribution within the lung. In this work the global inhomogeneity index was computed for twenty subjects in order to evaluate his potential use in the detection and follow up of chronic obstructive pulmonary disease (COPD) patients. EIT data of 17 subjects were acquired: 14 patients with the main diagnoses of COPD and 3 healthy subjects which served as a control group. Two or three datasets of around 30 seconds were acquired at 33 scans/s and analysed for each subject. After reconstruction, a tidal EIT image was computed for each breathing cycle and a GI index calculated from it. Results have shown significant differences in GI values between the two groups (0.745 ± 0.007 for COPD and 0.668 ± 0.006 for lung-healthy subject, p <; 0.005). The GI values obtained for each subject have shown small variance between them, which is a good indication of stability. The results suggested that the GI may be useful for the identification and follow up of ventilation problems in patients with COPD.

The effect of cigarette smoking on fetal heart rate tracing during pregnancy

OBJECTIVE

The objective of this study is to investigate the alterations caused by smoking on the features of fetal heart rate (FHR) tracings as well as to make a comparison between pregnant smokers and pregnant women with intrauterine growth restriction (IUGR).

STUDY DESIGN

A number of established features derived from linear and nonlinear fields were employed to study the possible influence of maternal smoking on FHR tracings. Moreover, correlation and measures of complexity of the FHR were explored, in order to get closer to the core of information that the signal of FHR tracings conveys. Data included FHR tracings from 61 uncomplicated singleton pregnancies, 16 pregnant smoker cases, and 15 pregnancies of women with IUGR.

RESULTS

The analysis of FHR indicated that some parameters, such as mutual information (P=0.0025), multiscale entropy (P=0.01), and algorithmic complexity (P=0.024) appeared decreased in the group of pregnant smokers, while kurtosis (P=0.0011) increased. The comparison between pregnant smokers and pregnant women with IUGR indicated a reduction in Hjorth complexity (P=0.039) for the former.

CONCLUSION

Smoking during pregnancy seems to induce differences in several linear and nonlinear indices in recordings of FHR tracings. This may be the consequence of an altered neurodevelopmental maturation possibly resulting from chronic fetal hypoxemia in cigarette-exposed fetuses.

Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes

Purpose: We sought to investigate whether B cell receptor immunoglobulin (BcR IG) stereotypy is associated with particular clinicobiological features among chronic lymphocytic leukemia (CLL) patients expressing mutated BcR IG (M-CLL) encoded by the IGHV4-34 gene, and also ascertain whether these associations could refine prognostication.Experimental Design: In a series of 19,907 CLL cases with available immunogenetic information, we identified 339 IGHV4-34-expressing cases assigned to one of the four largest stereotyped M-CLL subsets, namely subsets #4, #16, #29 and #201, and investigated in detail their clinicobiological characteristics and disease outcomes.Results: We identified shared and subset-specific patterns of somatic hypermutation (SHM) among patients assigned to these subsets. The greatest similarity was observed between subsets #4 and #16, both including IgG-switched cases (IgG-CLL). In contrast, the least similarity was detected between subsets #16 and #201, the latter concerning IgM/D-expressing CLL. Significant differences between subsets also involved disease stage at diagnosis and the presence of specific genomic aberrations. IgG subsets #4 and #16 emerged as particularly indolent with a significantly (P < 0.05) longer time-to-first-treatment (TTFT; median TTFT: not yet reached) compared with the IgM/D subsets #29 and #201 (median TTFT: 11 and 12 years, respectively).Conclusions: Our findings support the notion that BcR IG stereotypy further refines prognostication in CLL, superseding the immunogenetic distinction based solely on SHM load. In addition, the observed distinct genetic aberration landscapes and clinical heterogeneity suggest that not all M-CLL cases are equal, prompting further research into the underlying biological background with the ultimate aim of tailored patient management. Clin Cancer Res; 23(17); 5292-301. ©2017 AACR.

Machine Learning and Data Mining Methods in Diabetes Research

The remarkable advances in biotechnology and health sciences have led to a significant production of data, such as high throughput genetic data and clinical information, generated from large Electronic Health Records (EHRs). To this end, application of machine learning and data mining methods in biosciences is presently, more than ever before, vital and indispensable in efforts to transform intelligently all available information into valuable knowledge. Diabetes mellitus (DM) is defined as a group of metabolic disorders exerting significant pressure on human health worldwide. Extensive research in all aspects of diabetes (diagnosis, etiopathophysiology, therapy, etc.) has led to the generation of huge amounts of data. The aim of the present study is to conduct a systematic review of the applications of machine learning, data mining techniques and tools in the field of diabetes research with respect to a) Prediction and Diagnosis, b) Diabetic Complications, c) Genetic Background and Environment, and e) Health Care and Management with the first category appearing to be the most popular. A wide range of machine learning algorithms were employed. In general, 85% of those used were characterized by supervised learning approaches and 15% by unsupervised ones, and more specifically, association rules. Support vector machines (SVM) arise as the most successful and widely used algorithm. Concerning the type of data, clinical datasets were mainly used. The title applications in the selected articles project the usefulness of extracting valuable knowledge leading to new hypotheses targeting deeper understanding and further investigation in DM.

Restrictions in the T-cell repertoire of chronic lymphocytic leukemia: high-throughput immunoprofiling supports selection by shared antigenic elements

Immunoglobulin (IG) gene repertoire restrictions strongly support antigen selection in the pathogenesis of chronic lymphocytic leukemia (CLL). Given the emerging multifarious interactions between CLL and bystander T cells, we sought to determine whether antigen(s) are also selecting T cells in CLL. We performed a large-scale, next-generation sequencing (NGS) study of the T-cell repertoire, focusing on major stereotyped subsets representing CLL subgroups with undisputed antigenic drive, but also included patients carrying non-subset IG rearrangements to seek for T-cell immunogenetic signatures ubiquitous in CLL. Considering the inherent limitations of NGS, we deployed bioinformatics algorithms for qualitative curation of T-cell receptor rearrangements, and included multiple types of controls. Overall, we document the clonal architecture of the T-cell repertoire in CLL. These T-cell clones persist and further expand overtime, and can be shared by different patients, most especially patients belonging to the same stereotyped subset. Notably, these shared clonotypes appear to be disease-specific, as they are found in neither public databases nor healthy controls. Altogether, these findings indicate that antigen drive likely underlies T-cell expansions in CLL and may be acting in a CLL subset-specific context. Whether these are the same antigens interacting with the malignant clone or tumor-derived antigens remains to be elucidated.