A population-averaged structural connectomic brain atlas dataset from 422 HCP-aging subjects

Population-averaged brain atlases, that are represented in a standard space with anatomical labels, are instrumental tools in neurosurgical planning and the study of neurodegenerative conditions. Traditional brain atlases are primarily derived from anatomical scans and contain limited information regarding the axonal organization of the white matter. With the advance of diffusion MRI that allows the modeling of fiber orientation distribution (FOD) in the brain tissue, there is an increasing interest for a population-averaged FOD template, especially based on a large healthy aging cohort, to offer structural connectivity information for connectomic surgery and analysis of neurodegeneration. The dataset described in this article contains a set of multi-contrast structural connectomic MRI atlases, including T1w, T2w, and FOD templates, along with the associated whole brain tractograms. The templates were made using multi-contrast group-wise registration based on 3T MRIs of 422 Human Connectome Project in Aging (HCP-A) subjects. To enhance the usability, probabilistic tissue maps and segmentation of 22 subcortical structures are provided. Finally, the subthalamic nucleus shown in the atlas is parcellated into sensorimotor, limbic, and associative sub-regions based on their structural connectivity to facilitate the analysis and planning of deep brain stimulation procedures. The dataset is available on the OSF Repository: https://osf.io/p7syt.

A method for chronic and semi-chronic microelectrode array implantation in deep brain structures using image guided neuronavigation

BACKGROUND

Accurate targeting of brain structures for in-vivo electrophysiological recordings is essential for basic as well as clinical neuroscience research. Although methodologies for precise targeting and recording from the cortical surface are abundant, such protocols are scarce for deep brain structures.

NEW METHOD

We have incorporated stable fiducial markers within a custom cranial cap for improved image-guided neuronavigation targeting of subcortical structures in macaque monkeys. Anchor bolt chambers allowed for a minimally invasive entrance into the brain for chronic recordings. A 3D-printed microdrive allowed for semi-chronic applications.

RESULTS

We achieved an average Euclidean targeting error of 1.6 mm and a radial error of 1.2 mm over three implantations in two animals. Chronic and semi-chronic implantations allowed for recording of extracellular neuronal activity, with single-neuron activity examples shown from one macaque monkey.

COMPARISON WITH EXISTING METHOD(S)

Traditional stereotactic methods ignore individual anatomical variability. Our targeting approach allows for a flexible, subject-specific surgical plan with targeting errors lower than what is reported in humans, and equal to or lower than animal models using similar methods. Utilizing an anchor bolt as a chamber reduced the craniotomy size needed for electrode implantation, compared to conventional large access chambers which are prone to infection. Installation of an in-house, 3D-printed, screw-to-mount mechanical microdrive is in contrast to existing semi-chronic methods requiring fabrication, assembly, and installation of complex parts.

CONCLUSIONS

Leveraging commercially available tools for implantation, our protocol decreases the risk of infection from open craniotomies, and improves the accuracy of chronic electrode implantations targeting deep brain structures in large animal models.

X-ray image decomposition for improved magnetic navigation

PURPOSE

Existing field generators (FGs) for magnetic tracking cause severe image artifacts in X-ray images. While FG with radio-lucent components significantly reduces these imaging artifacts, traces of coils and electronic components may still be visible to trained professionals. In the context of X-ray-guided interventions using magnetic tracking, we introduce a learning-based approach to further reduce traces of field-generator components from X-ray images to improve visualization and image guidance.

METHODS

An adversarial decomposition network was trained to separate the residual FG components (including fiducial points introduced for pose estimation), from the X-ray images. The main novelty of our approach lies in the proposed data synthesis method, which combines existing 2D patient chest X-ray and FG X-ray images to generate 20,000 synthetic images, along with ground truth (images without the FG) to effectively train the network.

RESULTS

For 30 real images of a torso phantom, our enhanced X-ray image after image decomposition obtained an average local PSNR of 35.04 and local SSIM of 0.97, whereas the unenhanced X-ray images averaged a local PSNR of 31.16 and local SSIM of 0.96.

CONCLUSION

In this study, we proposed an X-ray image decomposition method to enhance X-ray image for magnetic navigation by removing FG-induced artifacts, using a generative adversarial network. Experiments on both synthetic and real phantom data demonstrated the efficacy of our method.

Spatiotemporally dynamic electric fields for brain cancer treatment

OBJECTIVE

The treatment of glioblastoma (GBM) using low intensity electric fields (~1 V/cm) is being investigated using multiple implanted bioelectrodes, which was termed intratumoral modulation therapy (IMT). Previous IMT studies theoretically optimized treatment parameters to maximize coverage with rotating fields, which required experimental investigation. In this study, we employed computer simulations to generate spatiotemporally dynamic electric fields, designed and purpose-built an IMT device for in vitro experiments, and evaluated the human GBM cellular responses to these fields. &#xD;Approach: After measuring the electrical conductivity of the in vitro culturing medium, we designed experiments to evaluate the efficacy of various spatiotemporally dynamic fields: (a) different rotating field magnitudes, (b) rotating vs. non-rotating fields, (c) 200 kHz vs. 10 kHz stimulation, and (d) constructive vs. destructive interference. A custom printed circuit board (PCB) was fabricated to enable four-electrode IMT in a 24-well plate. Patient-derived GBM cells were treated and analyzed for viability using bioluminescence imaging. &#xD;Main results: The optimal PCB design had electrodes placed 6.3 mm from the center. Spatiotemporally dynamic IMT fields at magnitudes of 1, 1.5, and 2 V/cm reduced GBM cell viability to 58%, 37% and 2% of sham controls respectively. Rotating vs. non-rotating, and 200 kHz vs. 10 kHz fields showed no statistical difference. The rotating configuration yielded a significant reduction (p<0.01) in cell viability (47±4%) compared to the voltage matched (99±2%) and power matched (66±3%) destructive interference cases.&#xD;Significance: We found the most important factors in GBM cell susceptibility to IMT are electric field strength and homogeneity. Spatiotemporally dynamic electric fields have been evaluated in this study, where improvements to electric field coverage with lower power consumption and minimal field cancellations has been demonstrated. The impact of this optimized paradigm on cell susceptibility justifies its future use in preclinical and clinical trial investigations.

The role of the temporal pole in temporal lobe epilepsy: A diffusion kurtosis imaging study

This study aimed to evaluate the use of diffusion kurtosis imaging (DKI) to detect microstructural abnormalities within the temporal pole (TP) and its temporopolar cortex in temporal lobe epilepsy (TLE) patients. DKI quantitative maps were obtained from fourteen lesional TLE and ten non-lesional TLE patients, along with twenty-three healthy controls. Data collected included mean (MK); radial (RK) and axial kurtosis (AK); mean diffusivity (MD) and axonal water fraction (AWF). Automated fiber quantification (AFQ) was used to quantify DKI measurements along the inferior longitudinal (ILF) and uncinate fasciculus (Unc). ILF and Unc tract profiles were compared between groups and tested for correlation with disease duration. To characterize temporopolar cortex microstructure, DKI maps were sampled at varying depths from superficial white matter (WM) towards the pial surface. Patients were separated according to the temporal lobe ipsilateral to seizure onset and their AFQ results were used as input for statistical analyses. Significant differences were observed between lesional TLE and controls, towards the most temporopolar segment of ILF and Unc proximal to the TP within the ipsilateral temporal lobe in left TLE patients for MK, RK, AWF and MD. No significant changes were observed with DKI maps in the non-lesional TLE group. DKI measurements correlated with disease duration, mostly towards the temporopolar segments of the WM bundles. Stronger differences in MK, RK and AWF within the temporopolar cortex were observed in the lesional TLE and noticeable differences (except for MD) in non-lesional TLE groups compared to controls. This study demonstrates that DKI has potential to detect subtle microstructural alterations within the temporopolar segments of the ILF and Unc and the connected temporopolar cortex in TLE patients including non-lesional TLE subjects. This could aid our understanding of the extrahippocampal areas, more specifically the temporal pole role in seizure generation in TLE and might inform surgical planning, leading to better seizure outcomes.

Affinity purification of in vivo assembled whirlin-associated protein complexes from the zebrafish retina

Mutations in WHRN lead to Usher syndrome type 2d or to non-syndromic hearing impairment. The WHRN-encoded gene product whirlin directly interacts with the intracellular regions of the other two Usher syndrome type 2-associated proteins, usherin and ADGRV1. In photoreceptor cells, this protein complex constitutes fibrous links between the periciliary membrane and the connecting cilium. However, the molecular mechanism(s) of retinal degeneration due to compromised formation and function of the USH2-associated protein complex remains elusive. To unravel this pathogenic mechanism, we isolated and characterized whirlin-associated protein complexes from zebrafish photoreceptor cells. We generated transgenic zebrafish that express Strep/FLAG-tagged Whrna, a zebrafish ortholog of human whirlin, under the control of a photoreceptor-specific promoter. Affinity purification of Strep/FLAG-tagged Whrna and associated proteins from adult transgenic zebrafish retinas followed by mass spectrometry identified 19 novel candidate associated proteins. Pull down experiments and dedicated yeast two-hybrid assays confirmed the association of Whrna with 7 of the co-purified proteins. Several of the co-purified proteins are part of the synaptic proteome, which indicates a role for whirlin in the photoreceptor synapse. Future studies will elucidate which of the newly identified protein-protein interactions contribute to the development of the retinal phenotype observed in USH2d patients. SIGNIFICANCE: Since protein-protein interactions identified using targeted in vitro studies do not always recapitulate interactions that are functionally relevant in vivo, we established a transgenic zebrafish line that stably expresses a Strep/FLAG-tagged ortholog of human whirlin (SF-Whrna) in photoreceptor cells. Affinity purification of in vivo-assembled SF-Whrna-associated protein complexes from retinal lysates followed by mass spectrometry, identified 19 novel candidate interaction partners, many of which are enriched in the synaptic proteome. Two human orthologs of the identified candidate interaction partners, FRMPD4 and Kir2.3, were validated as direct interaction partners of human whirlin using a yeast two-hybrid assay. The strong connection of whirlin with postsynaptic density proteins was not identified in previous in vitro protein-protein interaction assays, presumably due to the absence of a biologically relevant context. Isolation and identification of in vivo-assembled whirlin-associated protein complexes from the tissue of interest is therefore a powerful methodology to obtain novel insight into tissue specific protein-protein interactions and has the potential to improve significantly our understanding of the function of whirlin and the molecular pathogenesis underlying Usher syndrome type 2.

3D localization of vena contracta using Doppler ICE imaging in tricuspid valve interventions

Purpose

Tricuspid valve (TV) interventions face the challenge of imaging the anatomy and tools because of the ‘TEE-unfriendly’ nature of the TV. In edge-to-edge TV repair, a core step is to position the clip perpendicular to the coaptation gap. In this study, we provide a semi-automated method to localize the VC from Doppler intracardiac echo (ICE) imaging in a tracked 3D space, thus providing a pre-mapped location of the coaptation gap to assist device positioning.

Methods

A magnetically tracked ICE probe with Doppler imaging capabilities is employed in this study for imaging three patient-specific TVs placed in a pulsatile heart phantom. For each of the valves, the ICE probe is positioned to image the maximum regurgitant flow for five cardiac cycles. An algorithm then extracts the regurgitation imaging and computes the exact location of the vena contracta on the image.

Results

Across the three pathological, patient-specific valves, the average distance error between the detected VC and the ground truth model is \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$({1.22 \pm 2.00})$$\end{document}(1.22±2.00)mm. For each of the valves, one case represented the outlier where the algorithm misidentified the vena contracta to be near the annulus. In such cases, it is recommended to retake the five-second imaging data.

Conclusion

This study presented a method for ultrasound-based localization of vena contracta in 3D space. Mapping such anatomical landmarks has the potential to assist with device positioning and to simplify tricuspid valve interventions by providing more contextual information to the interventionalists, thus enhancing their spatial awareness. Additionally, ICE can be used to provide live US and Doppler imaging of the complex TV anatomy throughout the procedure.

Long-term effects of laparoscopic sleeve gastrectomy and Roux-Y-gastric bypass on body composition and bone mass density

Objective

Currently, the two most common bariatric procedures are laparoscopic sleeve gastrectomy (LSG) and laparoscopic gastric bypass (LRYGB). Long-term data comparing the two interventions in terms of their effect on body composition and bone mass density (BMD) is scarce. The aim of this study was to assess body composition and BMD at least five years after sleeve gastrectomy (LSG) and gastric bypass (LRYGB).

Methods

Bariatric patients at least five years post-surgery (LSG or LRYGB) were recruited and body composition and BMD was measured by means of DEXA. Data from body composition before surgery was included in the analysis. Blood samples were taken for determination of plasma calcium, parathyroid hormone (PTH), Vitamin D3, alkaline phosphatase and C-terminal telopeptide (CTX), and individual risk for osteoporotic fracture assessed by The Fracture Risk Assessment Tool (FRAX) score was calculated. After surgery, all patients received multivitamins, vitamin D3, and zinc. In addition, LRYGB-patients were prescribed calcium.

Results

A total of 142 patients were included, 72 LSG and 70 LRYGB, before surgery: median BMI 43.1 kg/m2, median age 45.5 years, 62.7% females. Follow-up after a median of 6.7 years. For LRYGB, percentage total weight loss (%TWL) at follow up was 26.3%, and for LSG 24.1%, (p = 0.243). LRYGB lead to a slightly lower fat percentage in body composition. At follow-up, 45% of both groups had a T-score at the femoral neck below -1, indicating osteopenia. No clinically relevant difference between the groups in BMD was found.

Conclusion

At 6.7 years post-surgery, no difference in body composition and BMD between LRYGB and LSG was found. Deficiencies and bone loss remain an issue after both interventions and should be monitored.

Long-term effects of laparoscopic sleeve gastrectomy: What are the results beyond 10 years?

Objective

Sleeve gastrectomy (SG) has become the most commonly performed bariatric procedure worldwide. Newer studies providing long-term follow-up are showing high incidence of weight regain and high incidence of de novo reflux or worsening of preexisting GERD leading to conversion to different bariatric procedure. The objective of our study was to present 5 to 15-year follow-up results in terms of weight loss, remission of comorbidities and reoperation rate.

Methods

This is a retrospective analysis of prospectively collected data. The minimal follow-up time was 5 years. Patients who underwent SG between August 2004 and December 2014 were included. In case of reoperation patients were converted to Roux-en-Y gastric bypass or biliopancreatic diversion type duodenal-switch with or without hiatal hernia repair.

Results

A total of 307 patients underwent SG either as primary bariatric procedure (n = 262) or as redo operation after failed laparoscopic gastric banding (n = 45). Mean body mass index at time of primary SG was 46.4 ± 8.0 kg/m2. Mean age at operation was 43.7 ± 12.4 years with 68% females. Follow-up was 84% and 70% at 5 and 10 years respectively. The mean EBMIL for primary SG was 62.8 ± 23.1% after 5 years, 53.6 ± 24.6% after 10 years and 51.2 ± 20.3% after 13 years. Reoperation after SG was necessary in almost every fifth SG patient: 24 patients (7.8%) were reoperated due to insufficient weight loss, 12 patients (3.9 %) due to reflux, while 23 patients (7.5%) needed conversion due to both, insufficient weight loss and reflux. Comorbidities improved considerably while the incidence of new onset reflux was 29.7%.

Conclusion

SG provides a long-term EBMIL from 51 to 54% beyond 10 years and a significant improvement of comorbidities. On the other hand, a high incidence of both weight loss failure and de novo reflux was observed leading to conversion.

Does the non-absorbable suture closure of the jejunal mesenteric defect reduce the incidence and severity of internal hernias after laparoscopic Roux-en-Y gastric bypass?

Objective

Internal hernias (IH) are frequent complications after laparoscopic Roux-en-Y gastric bypass (LRYGB). Closure of the jejunal mesenteric and the Petersen defect reduces IH incidence in prospective and retrospective trials. This study investigates whether closing the jejunal mesenteric space alone by non-absorbable suture and splitting the omentum can be beneficial to prevent IH after LRYGB.

Methods

Observational cohort study of 785 patients undergoing linear LRYGB including omental split at a single institution, 493 without jejunal mesenteric defect closure, 292 with closure by non-absorbable suture with a minimal follow-up of 2 years. Patients were assessed for appearance and severity of IH. Additionally, open mesenteric gaps without herniated bowel, as well as early obstructions due to kinking of the entero-enterostomy (EE) were explored.

Results

By primary mesenteric defect closure, the rate of manifest jejunal mesenteric and Petersen IH could be reduced from 6.5% to 3.8%, but without reaching statistical significance. The most common location for an IH was the jejunal mesenteric space, where defect closure during primary surgery could reduce the rate of IH from 5.3% to 2.4%. Higher weight loss seemed to increase the risk of developing an IH.

Conclusion

The closure of the jejunal mesenteric defect by non-absorbable suture can reduce the rate of IH at the jejunal mesenteric space after LRYGB. However, the beneficial effect in our collective is smaller than expected, especially in patients with excellent weight loss. Petersen IH rate remained low by consequent T-shape split of the omentum without suturing of the defect.

Evaluating High Spatial Resolution Diffusion Kurtosis Imaging at 3T: Reproducibility and Quality of Fit

BACKGROUND

Diffusion kurtosis imaging (DKI) quantifies the non-Gaussian diffusion of water within tissue microstructure. However, it has increased fitting parameters and requires higher b-values. Evaluation of DKI reproducibility is important for clinical purposes.

PURPOSE

To assess the reproducibility in whole-brain high-resolution DKI at varying b-values.

STUDY TYPE

Retrospective.

SUBJECTS AND PHANTOMS

In all, 44 individuals from the test-retest Human Connectome Project (HCP) database and 12 3D-printed phantoms.

FIELD STRENGTH/SEQUENCE

Diffusion-weighted multiband echo-planar imaging sequence at 3T and 9.4T. magnetization-prepared rapid acquisition gradient echo at 3T for in vivo structural data only.

ASSESSMENT

From HCP data with b-values = 1000, 2000, 3000 s/mm² (dataset A), two additional datasets with b-values = 1000, 3000 s/mm² (dataset B) and b-values = 1000, 2000 s/mm² (dataset C) were extracted. Estimated DKI metrics from each dataset were used for evaluating reproducibility and fitting quality in white matter (WM) and gray matter (GM) based on whole-brain and regions of interest (ROIs).

STATISTICAL TESTS

DKI reproducibility was assessed using the within-subject coefficient of variation (CoV), fitting residuals to evaluate DKI fitting accuracy and Pearson's correlation to investigate the presence of systematic biases. Repeated measures analysis of variance was used for statistical comparison.

RESULTS

Datasets A and B exhibited lower DKI CoVs (<20%) compared to C (<50%) in both WM and GM ROIs (all P < 0.05). This effect varies between DKI and DTI parameters (P < 0.005). Whole-brain fitting residuals were consistent across datasets (P > 0.05), but lower residuals in dataset B were detected for the WM ROIs (P < 0.001). A similar trend was observed for the phantom data CoVs (<7.5%) at varying fiber orientations for datasets A and B. Finally, dataset C was characterized by higher residuals across the different fiber crossings (P < 0.05).

DATA CONCLUSION

The study demonstrates that high reproducibility can still be achieved within a reasonable scan time, specifically dataset B, supporting the potential of DKI for aiding clinical tools in detecting microstructural changes.

0529 Behavioral Therapy Components for Insomnia and Fatigue in COPD

Introduction

Insomnia contributes to fatigue, a common symptom in COPD. Our study aims were: (1) to determine the efficacy of a) cognitive behavioral therapy for insomnia (CBT-I) and b) COPD education (COPD-ED) on insomnia and fatigue, and (2) to define potential mechanistic contributors to pre/post intervention change in insomnia and fatigue in patients with COPD and insomnia.

Methods

A randomized 2x2 factorial design was used with factors representing CBT-I (yes/no) and COPD-ED (yes/no). Attention control (health videos) were used in the absence of CBT-I or COPD-ED. All patients received 6, 75-minute weekly sessions. Dependent variables included insomnia severity (Sleep Impairment Index (SII), range 0-28) and fatigue (Chronic Respiratory Disease Questionnaire (CRQ) range 1-7) measured at baseline, just post-intervention, and at 3-months post-intervention.

Results

One hundred nine patients (FEV1% predicted 67 ± 24% (mean ± SD), age 65 ± 8 years, SII 15.9 ± 8, CRQ 3.7 ± 1.1) participated in the study. After 6 sessions, insomnia decreased more in patients who received CBT-I (-5.8) than those who did not (-2.2; p=0.0002). This effect was sustained at the 3-month follow-up (p=0.0003). Fatigue showed no significant differences for CBT-I at 6-weeks (p=.27) but at 3-months patients receiving CBT-I showed marginally better improvement (.75, a clinically important difference) compared to those who did not receive CBT-I (.43; p=.09). COPD-ED showed no effect on insomnia or fatigue. Two main effects suggest mechanisms for the pre-post efficacy of CBT-I: improved sleep beliefs (p=0.0257) and self-efficacy for sleep (p=0.0619) after 6 sessions which were sustained at 3 months (p=0.0184 and p=0.0431 respectively).

Conclusion

CBT-I produced sustained decreases in insomnia in patients with COPD. Results suggest that changes in beliefs about sleep and improved self-efficacy for managing sleep may mediate CBT-I associated decreases in insomnia.

Support

This research was supported by the National Institute of Nursing Research of the National Institutes of Health R01NR013937.

Determining blood flow direction from short neurovascular surgical microscope videos

Neurovascular surgery aims to repair diseased or damaged blood vessels in the brain or spine. There are numerous procedures that fall under this category, and in all of them, the direction of blood flow through these vessels is crucial information. Current methods to determine this information intraoperatively include static pre-operative images combined with augmented reality, Doppler ultrasound, and injectable fluorescent dyes. Each of these systems has inherent limitations. This study includes the proposal and preliminary validation of a technique to identify the direction of blood flow through vessels using only video segments of a few seconds acquired from routinely used surgical microscopes. The video is enhanced to reveal subtle colour fluctuations related to blood pulsation, and these rhythmic signals are further analysed in Fourier space to reveal the direction of blood flow. The proposed method was validated using a novel physical phantom and retrospective analysis of surgical videos and demonstrated high accuracy in identifying the direction of blood flow.

An accurate registration of the BigBrain dataset with the MNI PD25 and ICBM152 atlases

Brain atlases that encompass detailed anatomical or physiological features are instrumental in the research and surgical planning of various neurological conditions. Magnetic resonance imaging (MRI) has played important roles in neuro-image analysis while histological data remain crucial as a gold standard to guide and validate such analyses. With cellular-scale resolution, the BigBrain atlas offers 3D histology of a complete human brain, and is highly valuable to the research and clinical community. To bridge the insights at macro- and micro-levels, accurate mapping of BigBrain and established MRI brain atlases is necessary, but the existing registration is unsatisfactory. The described dataset includes co-registration of the BigBrain atlas to the MNI PD25 atlas and the ICBM152 2009b atlases (symmetric and asymmetric versions) in addition to manual segmentation of the basal ganglia, red nucleus, amygdala, and hippocampus for all mentioned atlases. The dataset intends to provide a bridge between insights from histological data and MRI studies in research and neurosurgical planning. The registered atlases, anatomical segmentations, and deformation matrices are available at: https://osf.io/xkqb3/ .

Layer-based visualization and biomedical information exploration of multi-channel large histological data

BACKGROUND AND OBJECTIVE

Modern microscopes can acquire multi-channel large histological data from tissues of human beings or animals, which contain rich biomedical information for disease diagnosis and biological feature analysis. However, due to the large size, fuzzy tissue structure, and complicated multiple elements integrated in the image color space, it is still a challenge for current software systems to effectively calculate histological data, show the inner tissue structures and unveil hidden biomedical information. Therefore, we developed new algorithms and a software platform to address this issue.

METHODS

This paper presents a multi-channel biomedical data computing and visualization system that can efficiently process large 3D histological images acquired from high-resolution microscopes. A novelty of our system is that it can dynamically display a volume of interest and extract tissue information using a layer-based data navigation scheme. During the data exploring process, the actual resolution of the loaded data can be dynamically determined and updated, and data rendering is synchronized in four display windows at each data layer, where 2D textures are extracted from the imaging volume and mapped onto the displayed clipping planes in 3D space.

RESULTS

To test the efficiency and scalability of this system, we performed extensive evaluations using several different hardware systems and large histological color datasets acquired from a CryoViz 3D digital system. The experimental results demonstrated that our system can deliver interactive data navigation speed and display detailed imaging information in real time, which is beyond the capability of commonly available biomedical data exploration software platforms.

CONCLUSION

Taking advantage of both CPU (central processing unit) main memory and GPU (graphics processing unit) graphics memory, the presented software platform can efficiently compute, process and visualize very large biomedical data and enhance data information. The performance of this system can satisfactorily address the challenges of navigating and interrogating volumetric multi-spectral large histological image at multiple resolution levels.

Augmented reality guidance in cerebrovascular surgery using microscopic video enhancement

Cerebrovascular surgery treats vessel abnormalities in the brain and spinal cord, including arteriovenous malformations (AVMs) and aneurysms. These procedures often involve clipping the vessels feeding blood to these abnormalities, making accurate classification of blood vessel types (feeding versus draining) important during surgery. Previous work to guide the intraoperative identification of the vessels included augmented reality (AR) using pre-operative images, injected dyes, and Doppler ultrasound, but each with their drawbacks. The authors propose and demonstrate a novel technique to help differentiate vessels by enhancing short videos of a few seconds from the surgical microscope using motion magnification and spectral analysis, and constructing AR views that fuse the analysis results as intuitive colourmaps and the surgical microscopic view. They demonstrated the proposed technique retrospectively with two real cerebrovascular surgical cases: one AVM and one aneurysm. The results showed that the proposed technique can help characterise different vessel types (feeding and draining the abnormality), which agree with those identified by the operating surgeon.

Endoscopic image enhancement with noise suppression

Stereoscopic endoscopes have been used increasingly in minimally invasive surgery to visualise the organ surface and manipulate various surgical tools. However, insufficient and irregular light sources become major challenges for endoscopic surgery. Not only do these conditions hinder image processing algorithms, sometimes surgical tools are barely visible when operating within low-light regions. In addition, low-light regions have low signal-to-noise ratio and metrication artefacts due to quantisation errors. As a result, present image enhancement methods usually suffer from heavy noise amplification in low-light regions. In this Letter, the authors propose an effective method for endoscopic image enhancement by identifying different illumination regions and designing the enhancement design criteria for desired image quality. Compared with existing image enhancement methods, the proposed method is able to enhance the low-light region while preventing noise amplification during image enhancement process. The proposed method is tested with 200 images acquired by endoscopic surgeries. Computed results show that the proposed algorithm can outperform state-of-the-art algorithms for image enhancement, in terms of naturalness image quality evaluator and illumination index.

Patient-specific cardiac phantom for clinical training and preprocedure surgical planning

Minimally invasive mitral valve repair procedures including MitraClip^® are becoming increasingly common. For cases of complex or diseased anatomy, clinicians may benefit from using a patient-specific cardiac phantom for training, surgical planning, and the validation of devices or techniques. An imaging compatible cardiac phantom was developed to simulate a MitraClip^® procedure. The phantom contained a patient-specific cardiac model manufactured using tissue mimicking materials. To evaluate accuracy, the patient-specific model was imaged using computed tomography (CT), segmented, and the resulting point cloud dataset was compared using absolute distance to the original patient data. The result, when comparing the molded model point cloud to the original dataset, resulted in a maximum Euclidean distance error of 7.7 mm, an average error of 0.98 mm, and a standard deviation of 0.91 mm. The phantom was validated using a MitraClip^® device to ensure anatomical features and tools are identifiable under image guidance. Patient-specific cardiac phantoms may allow for surgical complications to be accounted for preoperative planning. The information gained by clinicians involved in planning and performing the procedure should lead to shorter procedural times and better outcomes for patients.

Myocardium Segmentation From DE MRI Using Multicomponent Gaussian Mixture Model and Coupled Level Set

Objective: In this paper, we propose a fully automatic framework for myocardium segmentation of delayed-enhancement (DE) MRI images without relying on prior patient-specific information. Methods: We employ a multicomponent Gaussian mixture model to deal with the intensity heterogeneity of myocardium caused by the infarcts. To differentiate the myocardium from other tissues with similar intensities, while at the same time maintain spatial continuity, we introduce a coupled level set (CLS) to regularize the posterior probability. The CLS, as a spatial regularization, can be adapted to the image characteristics dynamically. We also introduce an image intensity gradient based term into the CLS, adding an extra force to the posterior probability based framework, to improve the accuracy of myocardium boundary delineation. The prebuilt atlases are propagated to the target image to initialize the framework. Results: The proposed method was tested on datasets of 22 clinical cases, and achieved Dice similarity coefficients of 87.43 ± 5.62% (endocardium), 90.53 ± 3.20% (epicardium) and 73.58 ± 5.58% (myocardium), which have outperformed three variants of the classic segmentation methods. Conclusion: The results can provide a benchmark for the myocardial segmentation in the literature. Significance: DE MRI provides an important tool to assess the viability of myocardium. The accurate segmentation of myocardium, which is a prerequisite for further quantitative analysis of myocardial infarction (MI) region, can provide important support for the diagnosis and treatment management for MI patients.Objective: In this paper, we propose a fully automatic framework for myocardium segmentation of delayed-enhancement (DE) MRI images without relying on prior patient-specific information. Methods: We employ a multicomponent Gaussian mixture model to deal with the intensity heterogeneity of myocardium caused by the infarcts. To differentiate the myocardium from other tissues with similar intensities, while at the same time maintain spatial continuity, we introduce a coupled level set (CLS) to regularize the posterior probability. The CLS, as a spatial regularization, can be adapted to the image characteristics dynamically. We also introduce an image intensity gradient based term into the CLS, adding an extra force to the posterior probability based framework, to improve the accuracy of myocardium boundary delineation. The prebuilt atlases are propagated to the target image to initialize the framework. Results: The proposed method was tested on datasets of 22 clinical cases, and achieved Dice similarity coefficients of 87.43 ± 5.62% (endocardium), 90.53 ± 3.20% (epicardium) and 73.58 ± 5.58% (myocardium), which have outperformed three variants of the classic segmentation methods. Conclusion: The results can provide a benchmark for the myocardial segmentation in the literature. Significance: DE MRI provides an important tool to assess the viability of myocardium. The accurate segmentation of myocardium, which is a prerequisite for further quantitative analysis of myocardial infarction (MI) region, can provide important support for the diagnosis and treatment management for MI patients.

Modeling Patient-Specific Deformable Mitral Valves

Medical imaging has advanced enormously over the last few decades, revolutionizing patient diagnostics and care. At the same time, additive manufacturing has emerged as a means of reproducing physical shapes and models previously not possible. In combination, they have given rise to 3-dimensional (3D) modeling, an entirely new technology for physicians. In an era in which 3D imaging has become a standard for aiding in the diagnosis and treatment of cardiac disease, this visualization now can be taken further by bringing the patient's anatomy into physical reality as a model. The authors describe the generalized process of creating a model of cardiac anatomy from patient images and their experience creating patient-specific dynamic mitral valve models. This involves a combination of image processing software and 3D printing technology. In this article, the complexity of 3D modeling is described and the decision-making process for cardiac anesthesiologists is summarized. The management of cardiac disease has been altered with the emergence of 3D echocardiography, and 3D modeling represents the next paradigm shift.

The role of visual and direct force feedback in robotics-assisted mitral valve annuloplasty

BACKGROUND

The objective of this work was to determine the effect of both direct force feedback and visual force feedback on the amount of force applied to mitral valve tissue during ex vivo robotics-assisted mitral valve annuloplasty.

METHODS

A force feedback-enabled master-slave surgical system was developed to provide both visual and direct force feedback during robotics-assisted cardiac surgery. This system measured the amount of force applied by novice and expert surgeons to cardiac tissue during ex vivo mitral valve annuloplasty repair.

RESULTS

The addition of visual (2.16 ± 1.67), direct (1.62 ± 0.86), or both visual and direct force feedback (2.15 ± 1.08) resulted in lower mean maximum force applied to mitral valve tissue while suturing compared with no force feedback (3.34 ± 1.93 N; P < 0.05).

CONCLUSIONS

To achieve better control of interaction forces on cardiac tissue during robotics-assisted mitral valve annuloplasty suturing, force feedback may be required.

Comparative study of all Salmonella enterica serovar Enteritidis strains isolated from food and food animals in Greece from 2008 to 2010 with clinical isolates

The aim of the present work was to study the epidemiology of Salmonella enterica serovar Enteritidis (S. Enteritidis) in Greece, comparing all the food and food animal isolates during a 3-year period with clinical isolates. Submission of the generated data to the PulseNet Europe database was carried out in order to study the population structure of this particular serovar and indicate possible connections with European strains. One hundred and sixty-eight (168) S. Enteritidis strains of human, animal, and food origin, isolated during the period 2008-2010 in Greece, were studied. Strains were characterized by phenotypic (antibiotic resistance) and molecular [pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST)] methods. PFGE revealed 39 XbaI, 48 BlnI, and 80 XbaI-BlnI distinct pulsotypes, suggesting several clones circulating through the food chain and multiple sources of transmission. Submission to the PulseNet Europe database indicated that PFGE profile SENTXB.0001, the most common PFGE profile in Europe, was also predominant in Greece (33.3 %). MLST showed that all the strains studied shared the same sequence type (ST11), representing the most common ST in Europe. High rates of resistance to nalidixic acid were observed among human and poultry isolates (~25 %), indicating the potential fluoroquinolone treatment failure. Our data suggest that strains originating from multiple reservoirs circulated in Greece through the food chain during the study period. Predominant profiles in Greece were common to PulseNet Europe profiles, indicating similarities between the S. Enteritidis populations in Greece and Europe.

Diagnostic quality assessment of compressed sensing accelerated magnetic resonance neuroimaging

PURPOSE

To determine the efficacy of compressed sensing (CS) reconstructions for specific clinical magnetic resonance neuroimaging applications beyond more conventional acceleration techniques such as parallel imaging (PI) and low-resolution acquisitions.

MATERIALS AND METHODS

Raw k-space data were acquired from five healthy volunteers on a 3T scanner using a 32-channel head coil using T2 -FLAIR, FIESTA-C, time of flight (TOF), and spoiled gradient echo (SPGR) sequences. In a series of blinded studies, three radiologists independently evaluated CS, PI (GRAPPA), and low-resolution images at up to 5× accelerations. Synthetic T2 -FLAIR images with artificial lesions were used to assess diagnostic accuracy for CS reconstructions.

RESULTS

CS reconstructions were of diagnostically acceptable quality at up to 4× acceleration for T2 -FLAIR and FIESTA-C (average qualitative scores 3.7 and 4.3, respectively, on a 5-point scale at 4× acceleration), and at up to 3× acceleration for TOF and SPGR (average scores 4.0 and 3.7, respectively, at 3× acceleration). The qualitative scores for CS reconstructions were significantly better than low-resolution images for T2 -FLAIR, FIESTA-C, and TOF and significantly better than GRAPPA for TOF and SPGR (Wilcoxon signed rank test, P < 0.05) with no significant difference found otherwise. Diagnostic accuracy was acceptable for both CS and low-resolution images at up to 3× acceleration (area under the ROC curve 0.97 and 0.96, respectively.)

CONCLUSION

Mild to moderate accelerations are possible for those sequences by a combined CS and PI reconstruction. Nevertheless, for certain sequences/applications one might mildly reduce the acquisition time by appropriately reducing the imaging resolution rather than the more complicated CS reconstruction. J. Magn. Reson. Imaging 2016;44:433-444.

The DTI Challenge: Toward Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery

BACKGROUND AND PURPOSE

Diffusion tensor imaging (DTI) tractography reconstruction of white matter pathways can help guide brain tumor resection. However, DTI tracts are complex mathematical objects and the validity of tractography-derived information in clinical settings has yet to be fully established. To address this issue, we initiated the DTI Challenge, an international working group of clinicians and scientists whose goal was to provide standardized evaluation of tractography methods for neurosurgery. The purpose of this empirical study was to evaluate different tractography techniques in the first DTI Challenge workshop.

METHODS

Eight international teams from leading institutions reconstructed the pyramidal tract in four neurosurgical cases presenting with a glioma near the motor cortex. Tractography methods included deterministic, probabilistic, filtered, and global approaches. Standardized evaluation of the tracts consisted in the qualitative review of the pyramidal pathways by a panel of neurosurgeons and DTI experts and the quantitative evaluation of the degree of agreement among methods.

RESULTS

The evaluation of tractography reconstructions showed a great interalgorithm variability. Although most methods found projections of the pyramidal tract from the medial portion of the motor strip, only a few algorithms could trace the lateral projections from the hand, face, and tongue area. In addition, the structure of disagreement among methods was similar across hemispheres despite the anatomical distortions caused by pathological tissues.

CONCLUSIONS

The DTI Challenge provides a benchmark for the standardized evaluation of tractography methods on neurosurgical data. This study suggests that there are still limitations to the clinical use of tractography for neurosurgical decision making.

Vertebroplasty Performance on Simulator for 19 Surgeons Using Hierarchical Task Analysis

We present a unique simulator-based methodology for assessing both technical and nontechnical (cognitive) skills for surgical trainees while immersed in a complete medical simulation environment. Further, we have included two crisis scenarios which allow for the evaluation of the effect of cognitive strategy selection on the low-level surgical skills. Training these mixed-mode scenarios can thereby be evaluated on our platform, allowing for improved assessment and a stronger foundation for credentialing, with the potential to reduce the occurrence of adverse events in the operating room. Scientific evaluation and validation of our work is conducted together with 19 junior surgeons in order to achieve the following goals: 1) to provide a qualitative measure of usability, 2) to assess vertebroplasty technical performance of the surgeon, and 3) to explore the relationship between mental workload and surgical performance during crisis. Our results indicate that: 1) the surgeons scored the face validity of our modeled simulation environment very highly ( 4.68 ±0.48, using a 5-point Likert scale), 2) surgeon training enabled completion of tasks more quickly, and 3) the introduction of crisis scenarios negatively affected the surgeons' objective performance. Taken together, our results underscore the need to develop realistic simulation environments that prepare young residents to respond to emergent events in the operating room.

A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: ‘near real-time’ application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014

Binary file ES_Abstracts_Final_ECDC.txt matches

Phenotypic and molecular characterization of multidrug-resistant Salmonella enterica serovar Hadar in Greece, from 2007 to 2010

All 120 strains of Salmonella enterica serovar Hadar isolated during 2007-2010 in Greece were characterized by phenotypic and molecular methods. High rates of resistance to nalidixic acid (92%) and low levels of ciprofloxacin resistance (88%) were observed. Pulsenet-pulsed field gel electrophoresis profile SHADXB.0001 was predominant in Greece (58%) as in Europe but PT1, a rare phage type in Europe, was frequent in Greece (56%). The SHADXB.0001 and PT1 clone (38%) were found in humans, animals and food of animal origin with R-type ApSpTNxpCp being predominant (25%). The data indicate that this clone (possibly endemic) was circulating through the food chain in Greece during the study period.

High-resolution 3-dimensional late gadolinium enhancement scar imaging in surgically corrected Tetralogy of Fallot: clinical feasibility of volumetric quantification and visualization

BACKGROUND

The extent of surgical scarring in Tetralogy of Fallot (TOF) may be a marker of adverse outcomes and provide substrate for ventricular arrhythmia. In this study we evaluate the feasibility of high resolution three dimensional (3D) late gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) for volumetric scar quantification in patients with surgically corrected TOF.

METHODS

Fifteen consecutive patients underwent 3D LGE imaging with 3 Tesla CMR using a whole-heart, respiratory-navigated technique. A novel, signal-histogram based segmentation technique was tested for the quantification and modeling of surgical scar. Total scar volume was compared to the gold standard manual expert segmentation. The feasibility of segmented scar fusion to matched coronary CMR data for volumetric display was explored.

RESULTS

Image quality sufficient for 3D scar segmentation was acquired in fourteen patients. Mean patient age was 32.2 ± 11.9 years (range 21 to 57 years) with mean right ventricle (RV) ejection fraction (EF) of 53.9 ± 9.2% and mean RV end diastolic volume of 117.0 ± 41.5 mL/m². The mean total scar volume was 11.1 ± 8.2 mL using semi-automated 3D segmentation with excellent correlation to manual expert segmentation (r = 0.99, bias = 0.89 mL, 95% CI -1.66 to 3.44). The mean segmentation time was significantly reduced using the novel semi-automated segmentation technique (10.1 ± 2.6 versus 45.8 ± 12.6 minutes). Excellent intra-observer and good inter-observer reproducibility was observed.

CONCLUSION

3D high resolution LGE imaging with semi-automated scar segmentation is clinically feasible among patients with surgically corrected TOF and shows excellent accuracy and reproducibility. This approach may offer a valuable clinical tool for risk prediction and procedural planning among this growing population.

A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012

In November 2011, the presence of Salmonella Newport in a ready-to-eat watermelon slice was confirmed as part of a local food survey in England. In late December 2011, cases of S. Newport were reported in England, Wales, Northern Ireland, Scotland, Ireland and Germany. During the outbreak, 63 confirmed cases of S. Newport were reported across all six countries with isolates indistinguishable by pulsed-field gel electrophoresis from the watermelon isolate.A subset of outbreak isolates were whole-genome sequenced and were identical to, or one single nucleotide polymorphism different from the watermelon isolate.In total, 46 confirmed cases were interviewed of which 27 reported watermelon consumption. Further investigations confirmed the outbreak was linked to the consumption of watermelon imported from Brazil.Although numerous Salmonella outbreaks associated with melons have been reported in the United States and elsewhere, this is the first of its kind in Europe.Expansion of the melon import market from Brazil represents a potential threat for future outbreaks. Whole genome sequencing is rapidly becoming more accessible and can provide a compelling level of evidence of linkage between human cases and sources of infection,to support public health interventions in global food markets.

Sirolimus: a therapeutic advance for dermatologic disease

Sirolimus, also known as rapamycin (SRL, Rapamune®), was approved in 1999 by the US Food and Drug Administration to prevent graft rejection in renal transplantation. As a member of the mammalian target of rapamycin (mTOR) inhibitor class, its potent immunosuppressant, anti-angiogenic and anti-proliferative properties are well recognized. When compared to other immunosuppressants, SRL has a lower risk of renal, neurologic and lymphoproliferative complications. It has become a promising treatment modality for angiofibromas, Kaposi's sarcoma and other inflammatory and malignant disorders of the skin. With the recent discovery that mTOR inhibitors extend the lifespan of mice, sirolimus and other rapamycin analogs (rapalogs) are emerging as therapeutic targets for the treatment and prevention of age-related diseases.

Regional assessment of cardiac left ventricular myocardial function via MRI statistical features

Automating the detection and localization of segmental (regional) left ventricle (LV) abnormalities in magnetic resonance imaging (MRI) has recently sparked an impressive research effort, with promising performances and a breadth of techniques. However, despite such an effort, the problem is still acknowledged to be challenging, with much room for improvements in regard to accuracy. Furthermore, most of the existing techniques are labor intensive, requiring delineations of the endo- and/or epi-cardial boundaries in all frames of a cardiac sequence. The purpose of this study is to investigate a real-time machine-learning approach which uses some image features that can be easily computed, but that nevertheless correlate well with the segmental cardiac function. Starting from a minimum user input in only one frame in a subject dataset, we build for all the regional segments and all subsequent frames a set of statistical MRI features based on a measure of similarity between distributions. We demonstrate that, over a cardiac cycle, the statistical features are related to the proportion of blood within each segment. Therefore, they can characterize segmental contraction without the need for delineating the LV boundaries in all the frames. We first seek the optimal direction along which the proposed image features are most descriptive via a linear discriminant analysis. Then, using the results as inputs to a linear support vector machine classifier, we obtain an abnormality assessment of each of the standard cardiac segments in real-time. We report a comprehensive experimental evaluation of the proposed algorithm over 928 cardiac segments obtained from 58 subjects. Compared against ground-truth evaluations by experienced radiologists, the proposed algorithm performed competitively, with an overall classification accuracy of 86.09% and a kappa measure of 0.73.