A new framework for the integrative analytics of intravascular ultrasound and optical coherence tomography images

Abstract:The integrative analysis of multimodal medical images plays an important role in the diagnosis of coronary artery disease by providing additional comprehensive information that cannot be found in an individual source image. Intravascular ultrasound (IVUS) and optical coherence tomography (IV-OCT) are two imaging modalities that have been widely used in the medical practice for the assessment of arterial health and the detection of vascular lumen lesions. IV-OCT has a high resolution and poor penetration, while IVUS has a low resolution and high detection depth. This paper proposes a new approach for the fusion of intravascular ultrasound and optical coherence tomography pullbacks to significantly improve the use of those two types of medical images. It also presents a new two-phase multimodal fusion framework using a coarse-to-fine registration and a wavelet fusion method. In the coarse-registration process, we define a set of new feature points to match the IVUS image and IV-OCT image. Then, the improved quality image is obtained based on the integration of the mutual information of two types of images. Finally, the matched registered images are fused with an approach based on the new proposed wavelet algorithm. The experimental results demonstrate the performance of the proposed new approach for significantly enhancing both the precision and computational stability. The proposed approach is shown to be promising for providing additional information to enhance the diagnosis and enable a deeper understanding of atherosclerosis

A novel WebVR-Based lightweight framework for virtual visualization of blood vasculum

With the arrival of the Web 2.0 era and the rapid development of virtual reality (VR) technology in recent years, WebVR technology has emerged as the combination of Web 2.0 and VR. Moreover, the concept of “WebVR + medical science”is also proposed to advance medical applications. However, due to the limited storage space and low computing capability of Web browsers, it is difficult to achieve real-time rendering of large-scale medical vascular models on the Web, let alone large-scale vascular animation simulations. The framework proposed in this paper can achieve virtual display of the medical blood vasculum, including lightweight processing of the vasculum and virtual realization of blood flow. This innovative framework presents a simulation algorithm for the virtual blood path based on the Catmull-Rom spline. The mechanisms of progressive compression and online recovery of the lightweight vascular structure are further proposed. The experimental results show that our framework has a shorter browser-side response time than existing methods and achieves efficient real-time simulation

Lumen contour segmentation in ivoct based on n-type cnn

Automatic segmentation of lumen contour plays an important role in medical imaging and diagnosis, which is the first step towards the evaluation of morphology of vessels under analysis and the identification of possible atherosclerotic lesions. Meanwhile, quantitative information can only be obtained with segmentation, contributing to the appearance of novel methods which can be successfully applied to intravascular optical coherence tomography (IVOCT) images. This paper proposed a new end-to-end neural network (N-Net) for the automatic lumen segmentation, using multi-scale features based deep neural network, for IVOCT images. The architecture of the N-Net contains a multi-scale input layer, a N-type convolution network layer and a cross-entropy loss function. The multi-scale input layer in the proposed N-Net is designed to avoid the loss of information caused by pooling in traditional U-Net and also enriches the detailed information in each layer. The N-type convolutional network is proposed as the framework in the whole deep architecture. Finally, the loss function guarantees the degree of fidelity between the output of proposed method and the manually labeled output. In order to enlarge the training set, data augmentation is also introduced. We evaluated our method against loss, accuracy, recall, dice similarity coefficient, jaccard similarity coefficient and specificity. The experimental results presented in this paper demonstrate the superior performance of the proposed N-Net architecture, comparing to some existing networks, for enhancing the precision of automatic lumen segmentation and increasing the detailed information of edges of the vascular lumen

A nine months follow-up study of hemodynamic effect on bioabsorbable coronary stent implantation

Coronary artery disease has emerged as one of the major diseases causing death worldwide. Coronary stent has great effect to improve blood flow to the myocardium subtended by that artery, in which bioresorbable vascular scaffolds are new-generation stents used by people. However, Coronary stents implantation has a risk of restenosis, which is relative to hemodynamic parameters. Most of existing literatures studied in this issue have not taken into account such important factors as the strut thickness and lumen profile, and has yet to analyze the time effects among hemodynamic parameters over a certain period of time based on individual models. In this research, we proposed a framework to assess the chronic impact of hemodynamic on coronary stent implantation. In the framework, the optical coherence tomography (OCT) is combined with angiography to reconstruct patient-specific models of bioresorbable vascular scaffolds. Then, the hemodynamics parameters are extracted through the simulated 3D models, obtaining the distribution of wall shear stress (WSS), relative residence time (RRT) and oscillatory shear index (OSI). Finally, the changes of these parameters representing the effectiveness of hemodynamics exerted on the implanted stent can be assessed to estimate the chronic impacts. By a 9-month follow-up case study, it is observed that the difference of hemodynamic parameters are not significance. Both at baseline and 9-month follow-up experiments show that the hemodynamic parameters remain normal and similar, proving that the coronary stent implantation nowadays appears to have a robust and everlasting curative effect

Patient-Specific Coronary Artery 3D Printing Based on Intravascular Optical Coherence Tomography and Coronary Angiography

Despite the new ideas were inspired in medical treatment by the rapid advancement of three-dimensional (3D) printing technology, there is still rare research work reported on 3D printing of coronary arteries being documented in the literature. In this work, the application value of 3D printing technology in the treatment of cardiovascular diseases has been explored via comparison study between the 3D printed vascular solid model and the computer aided design (CAD) model. In this paper, a new framework is proposed to achieve a 3D printing vascular model with high simulation. The patient-specific 3D reconstruction of the coronary arteries is performed by the detailed morphological information abstracted from the contour of the vessel lumen. In the process of reconstruction which has 5 steps, the morphological details of the contour view of the vessel lumen are merged along with the curvature and length information provided by the coronary angiography. After comparing with the diameter of the narrow section and the diameter of the normal section in CAD models and 3D printing model, it can be concluded that there is a high correlation between the diameter of vascular stenosis measured in 3D printing models and computer aided design models. The 3D printing model has high-modeling ability and high precision, which can represent the original coronary artery appearance accurately. It can be adapted for prevascularization planning to support doctors in determining the surgical procedures

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome

INTRODUCTION Although much effort has been devoted to studying yeast in the past few decades, our understanding of this model organism is still limited. Rapidly developing DNA synthesis techniques have made a “build-to-understand” approach feasible to reengineer on the genome scale. Here, we report on the completion of a 770-kilobase synthetic yeast chromosome II (synII). SynII was characterized using extensive Trans-Omics tests. Despite considerable sequence alterations, synII is virtually indistinguishable from wild type. However, an up-regulation of translational machinery was observed and can be reversed by restoring the transfer RNA (tRNA) gene copy number. RATIONALE Following the “design-build-test-debug” working loop, synII was successfully designed and constructed in vivo. Extensive Trans-Omics tests were conducted, including phenomics, transcriptomics, proteomics, metabolomics, chromosome segregation, and replication analyses. By both complementation assays and SCRaMbLE (synthetic chromosome rearrangement and modification by loxP -mediated evolution), we targeted and debugged the origin of a growth defect at 37°C in glycerol medium. RESULTS To efficiently construct megabase-long chromosomes, we developed an I- Sce I–mediated strategy, which enables parallel integration of synthetic chromosome arms and reduced the overall integration time by 50% for synII. An I- Sce I site is introduced for generating a double-strand break to promote targeted homologous recombination during mitotic growth. Despite hundreds of modifications introduced, there are still regions sharing substantial sequence similarity that might lead to undesirable meiotic recombinations when intercrossing the two semisynthetic chromosome arm strains. Induction of the I- Sce I–mediated double-strand break is otherwise lethal and thus introduced a strong selective pressure for targeted homologous recombination. Since our strategy is designed to generate a markerless synII and leave the URA3 marker on the wild-type chromosome, we observed a tenfold increase in URA3 -deficient colonies upon I- Sce I induction, meaning that our strategy can greatly bias the crossover events toward the designated regions. By incorporating comprehensive phenotyping approaches at multiple levels, we demonstrated that synII was capable of powering the growth of yeast indistinguishably from wild-type cells (see the figure), showing highly consistent biological processes comparable to the native strain. Meanwhile, we also noticed modest but potentially significant up-regulation of the translational machinery. The main alteration underlying this change in expression is the deletion of 13 tRNA genes. A growth defect was observed in one very specific condition—high temperature (37°C) in medium with glycerol as a carbon source—where colony size was reduced significantly. We targeted and debugged this defect by two distinct approaches. The first approach involved phenotype screening of all intermediate strains followed by a complementation assay with wild-type sequences in the synthetic strain. By doing so, we identified a modification resulting from PCRTag recoding in TSC10 , which is involved in regulation of the yeast high-osmolarity glycerol (HOG) response pathway. After replacement with wild-type TSC10 , the defect was greatly mitigated. The other approach, debugging by SCRaMbLE, showed rearrangements in regions containing HOG regulation genes. Both approaches indicated that the defect is related to HOG response dysregulation. Thus, the phenotypic defect can be pinpointed and debugged through multiple alternative routes in the complex cellular interactome network. CONCLUSION We have demonstrated that synII segregates, replicates, and functions in a highly similar fashion compared with its wild-type counterpart. Furthermore, we believe that the iterative “design-build-test-debug” cycle methodology, established here, will facilitate progression of the Sc2.0 project in the face of the increasing synthetic genome complexity. SynII characterization. ( A ) Cell cycle comparison between synII and BY4741 revealed by the percentage of cells with separated CEN2-GFP dots, metaphase spindles, and anaphase spindles. ( B ) Replication profiling of synII (red) and BY4741 (black) expressed as relative copy number by deep sequencing. ( C ) RNA sequencing analysis revealed that the significant up-regulation of translational machinery in synII is induced by the deletion of tRNA genes in synII. </jats:sec

YeastFab:the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae

It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae. We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using β-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts

Système portable pour évaluer rapidement les propriétés mécaniques de la peau

Pressure ulcers are localized damage to the skin and/or underlying tissue. It's expensive to treat pressure ulcers at advanced stages. Moreover, They lower the patients' quality of life, being painful and life-threatening. Early detection is one of the solutions to prevent pressure ulcers. The objective of this thesis is to develop a handheld probe to measure skin biomechanics in vivo and to aid in the early diagnosis of skin at risk. This probe is composed of two piezoelectric bending actuators that stretch the skin surface and control the tip displacement. Simultaneous force and displacement sensing is achieved by integrating two pairs of resistive strain gauge sensors. The basic functions of the probe, simultaneous sensing and displacement control, are experimentally validated. Hysteresis compensation strategies are presented to improve force sensing. The discrimination capability of the probe is first justified with tests on phantom skins. Then, we apply this probe to measure skin properties in vivo. The anatomical-site-related differences are characterized by the probe. The reliability and sensitivity of the parameters derived from the probe are studied in a collaboration with the University of Southampton. Preliminary results show that the probe can detect skin damage caused by mechanical insult (tape strapping) with a reduced dynamic modulus. This research can contribute to not only the early detection of skin issues, but also provide valuable experimental data that can be used, for example, in the development of computational models.Les escarres sont des maladies de la peau ou des tissus internes. Il est très couteux de traiter des escarres à des stades avancés. De plus, ce sont des pathologies très douloureuses, qui altèrent fortement la qualité de vie des patients atteints et peuvent même être fatals à un stade étendu. La détection précoce de ces escarres est donc primordial pour pallier leurs effets. L'objectif de cette thèse est de développer une sonde portable pour mesurer les caractéristiques biomécaniques de la peau à risque « in vivo » et ainsi aider à prévoir l'apparition d'escarres.Cette sonde est composée de deux benders piézo-électriques qui vont étendre la surface de la peau de manière contrôlée. La mesure simultanée de la force de réaction de la peau et de son déplacement est réalisée grâce à l'intégration de deux jauges de contrainte résistives. Les fonctions essentielles de la sonde, à savoir le contrôle du déplacement et l'acquisition des mesures mécaniques sont validées expérimentalement. Pour améliorer la mesure de la force, deux stratégies de compensation de l'effet d'hystérésis sont présentées.Les capacités de distinction de la sonde entre différentes surfaces sont tout d'abord testées sur des peaux artificielles dites « fantômes ». Ensuite, la sonde est appliquée pour mesurer les caractéristiques de peaux saines « in vivo », ceci sur différentes localisations. Il est montré que la sonde est capable de différencier ces localisations. La sensibilité et la fiabilité des paramètres mesurés par la sonde sont analysées en collaboration avec l'Université de Southampton. Des premiers résultats montrent que la sonde est capable de détecter des dommages de la peau dues à des dégradations mécaniques (arrachage d'un ruban adhésif par exemple).Cette recherche peut donc contribuer à la détection précoce d'escarres mais également fournir des données sur la mécanique de la peau pour renseigner le développement de modèles

Système portable pour évaluer rapidement les propriétés mécaniques de la peau

Les escarres sont des maladies de la peau ou des tissus internes. Il est très couteux de traiter des escarres à des stades avancés. De plus, ce sont des pathologies très douloureuses, qui altèrent fortement la qualité de vie des patients atteints et peuvent même être fatals à un stade étendu. La détection précoce de ces escarres est donc primordial pour pallier leurs effets. L'objectif de cette thèse est de développer une sonde portable pour mesurer les caractéristiques biomécaniques de la peau à risque « in vivo » et ainsi aider à prévoir l'apparition d'escarres.Cette sonde est composée de deux benders piézo-électriques qui vont étendre la surface de la peau de manière contrôlée. La mesure simultanée de la force de réaction de la peau et de son déplacement est réalisée grâce à l'intégration de deux jauges de contrainte résistives. Les fonctions essentielles de la sonde, à savoir le contrôle du déplacement et l'acquisition des mesures mécaniques sont validées expérimentalement. Pour améliorer la mesure de la force, deux stratégies de compensation de l'effet d'hystérésis sont présentées.Les capacités de distinction de la sonde entre différentes surfaces sont tout d'abord testées sur des peaux artificielles dites « fantômes ». Ensuite, la sonde est appliquée pour mesurer les caractéristiques de peaux saines « in vivo », ceci sur différentes localisations. Il est montré que la sonde est capable de différencier ces localisations. La sensibilité et la fiabilité des paramètres mesurés par la sonde sont analysées en collaboration avec l'Université de Southampton. Des premiers résultats montrent que la sonde est capable de détecter des dommages de la peau dues à des dégradations mécaniques (arrachage d'un ruban adhésif par exemple).Cette recherche peut donc contribuer à la détection précoce d'escarres mais également fournir des données sur la mécanique de la peau pour renseigner le développement de modèles.Pressure ulcers are localized damage to the skin and/or underlying tissue. It's expensive to treat pressure ulcers at advanced stages. Moreover, They lower the patients' quality of life, being painful and life-threatening. Early detection is one of the solutions to prevent pressure ulcers. The objective of this thesis is to develop a handheld probe to measure skin biomechanics in vivo and to aid in the early diagnosis of skin at risk. This probe is composed of two piezoelectric bending actuators that stretch the skin surface and control the tip displacement. Simultaneous force and displacement sensing is achieved by integrating two pairs of resistive strain gauge sensors. The basic functions of the probe, simultaneous sensing and displacement control, are experimentally validated. Hysteresis compensation strategies are presented to improve force sensing. The discrimination capability of the probe is first justified with tests on phantom skins. Then, we apply this probe to measure skin properties in vivo. The anatomical-site-related differences are characterized by the probe. The reliability and sensitivity of the parameters derived from the probe are studied in a collaboration with the University of Southampton. Preliminary results show that the probe can detect skin damage caused by mechanical insult (tape strapping) with a reduced dynamic modulus. This research can contribute to not only the early detection of skin issues, but also provide valuable experimental data that can be used, for example, in the development of computational models