Deep Learning using K-space Based Data Augmentation for Automated Cardiac MR Motion Artefact Detection

Quality assessment of medical images is essential for complete automation of image processing pipelines. For large population studies such as the UK Biobank, artefacts such as those caused by heart motion are problematic and manual identification is tedious and time-consuming. Therefore, there is an urgent need for automatic image quality assessment techniques. In this paper, we propose a method to automatically detect the presence of motion-related artefacts in cardiac magnetic resonance (CMR) images. As this is a highly imbalanced classification problem (due to the high number of good quality images compared to the low number of images with motion artefacts), we propose a novel k-space based training data augmentation approach in order to address this problem. Our method is based on 3D spatio-temporal Convolutional Neural Networks, and is able to detect 2D+time short axis images with motion artefacts in less than 1ms. We test our algorithm on a subset of the UK Biobank dataset consisting of 3465 CMR images and achieve not only high accuracy in detection of motion artefacts, but also high precision and recall. We compare our approach to a range of state-of-the-art quality assessment methods.Comment: Accepted for MICCAI2018 Conferenc

Changes in the use of coronary artery revascularization procedures in the Department of Veterans Affairs, the National Hospital Discharge Survey, and the Nationwide Inpatient Sample, 1991–1999

BACKGROUND: There have been dramatic increases in the number of coronary artery bypass surgeries (CABS) and percutaneous coronary interventions (PCI) performed during the last decade. Whether this finding is true for revascularization procedures performed in Department of Veterans Affairs (VA) medical centers is the subject of this paper. METHODS: This study compared the number of revascularization procedures and rates of use in the VA, the National Hospital Discharge Survey, and the Nationwide Inpatient Sample. Included were men who underwent isolated CABS and/or PCI, including stenting, between 1991 and 1999, although data for the Nationwide Inpatient Sample were available only between 1993 and 1997. Age adjusted use rates were calculated with the direct method of standardization. RESULTS: The percent of users of VA healthcare 75 years and older increased from 10% in 1991 to 20% in 1999. In the VA, the number of isolated CABS declined from 6227 in 1991 to 6147 in 1999, whereas age adjusted rates declined from 167.6 per 100,000 in 1991 to 107.9 per 100,000 in 1999. In the 2 national surveys, both the estimated numbers of procedures and use rates increased over time. In all 3 settings, there were increases in both numbers and rate of PCI from 1993, although in the VA, use rates decreased from 191.2 per 100,000 in 1996 to 139.7 per 100,000 in 1999. VA use rates for both CABS and PCI were lower than those in the 2 national surveys. CONCLUSION: Age adjusted rates of CABS and PCI were lower in the VA than in 2 national surveys. Since 1996, there has been a decrease in the rate of use of revascularization procedures in the VA

Epistemic and Ontic Quantum Realities

Quantum theory has provoked intense discussions about its interpretation since its pioneer days. One of the few scientists who have been continuously engaged in this development from both physical and philosophical perspectives is Carl Friedrich von Weizsaecker. The questions he posed were and are inspiring for many, including the authors of this contribution. Weizsaecker developed Bohr's view of quantum theory as a theory of knowledge. We show that such an epistemic perspective can be consistently complemented by Einstein's ontically oriented position

ACL graft re-rupture after double-bundle reconstruction: factors that influence the intra-articular pattern of injury

To determine the most common rupture patterns of previously reconstructed DB-ACL cases, seen at the time of revision surgery, and to determine the influence of age, gender, time between the initial ACL reconstruction and re-injury, tunnel angle and etiology of failure. Forty patients who presented for revision surgery after previous double-bundle ACL reconstruction were enrolled. Three orthopedic surgeons independently reviewed the arthroscopic videos and determined the rupture pattern of both the anteromedial and posterolateral grafts. The graft rupture pattern was then correlated with the previously mentioned factors. The most common injury pattern seen at the time of revision ACL surgery was mid-substance AM and PL bundle rupture. Factors that influenced the rupture pattern (proximal vs. mid-substance and distal rupture vs. elongated, but in continuity) were months between ACL reconstruction and re-injury (P = 0.002), the etiology of failure (traumatic vs. atraumatic) (P = 0.025) and the measured graft tunnel angle (P = 0.048). The most common pattern of graft re-rupture was mid-substance AM and mid-substance PL. As the length of time from the initial DB-ACL reconstruction to revision surgery increased, the pattern of injury more closely resembled that of the native ACL. Evaluation of patients who have undergone double-bundle ACL reconstruction, with a particular focus on graft maturity, mechanism of injury and femoral tunnel angles, and graft rupture pattern assists in preoperative planning for revision surger

Expression and DNA methylation of TNF, IFNG and FOXP3 in colorectal cancer and their prognostic significance.

BACKGROUND: Colorectal cancer (CRC) progression is associated with suppression of host cell-mediated immunity and local immune escape mechanisms. Our aim was to assess the immune function in terms of expression of TNF, IFNG and FOXP3 in CRC. METHODS: Sixty patients with CRC and 15 matched controls were recruited. TaqMan quantitative PCR and methylation-specific PCR was performed for expression and DNA methylation analysis of TNF, IFNG and FOXP3. Survival analysis was performed over a median follow-up of 48 months. RESULTS: TNF was suppressed in tumour and IFNG was suppressed in peripheral blood mononuclear cells (PBMCs) of patients with CRC. Tumours showed enhanced expression of FOXP3 and was significantly higher when tumour size was >38 mm (median tumour size; P=0.006, Mann-Whitney U-test). Peripheral blood mononuclear cell IFNG was suppressed in recurrent CRC (P=0.01). Methylated TNFpromoter (P=0.003) and TNFexon1 (P=0.001) were associated with significant suppression of TNF in tumours. Methylated FOXP3cpg was associated with significant suppression of FOXP3 in both PBMC (P=0.018) and tumours (P=0.010). Reduced PBMC FOXP3 expression was associated with significantly worse overall survival (HR=8.319, P=0.019). CONCLUSIONS: We have detected changes in the expression of immunomodulatory genes that could act as biomarkers for prognosis and future immunotherapeutic strategies

Use of outpatient care in VA and Medicare among disability-eligible and age-eligible veteran patients

<p>Abstract</p> <p>Background</p> <p>More than half of veterans who use Veterans Health Administration (VA) care are also eligible for Medicare via disability or age, but no prior studies have examined variation in use of outpatient services by Medicare-eligible veterans across health system, type of care or time.</p> <p>Objectives</p> <p>To examine differences in use of VA and Medicare outpatient services by disability-eligible or age-eligible veterans among veterans who used VA primary care services and were also eligible for Medicare.</p> <p>Methods</p> <p>A retrospective cohort study of 4,704 disability- and 10,816 age-eligible veterans who used VA primary care services in fiscal year (FY) 2000. We tracked their outpatient utilization from FY2001 to FY2004 using VA administrative and Medicare claims data. We examined utilization differences for primary care, specialty care, and mental health outpatient visits using generalized estimating equations.</p> <p>Results</p> <p>Among Medicare-eligible veterans who used VA primary care, disability-eligible veterans had more VA primary care visits (<it>p </it>< 0.001) and more VA specialty care visits (<it>p </it>< 0.001) than age-eligible veterans. They were more likely to have mental health visits in VA (<it>p </it>< 0.01) and Medicare-reimbursed visits (<it>p </it>< 0.01). Disability-eligible veterans also had more total (VA+Medicare) visits for primary care (<it>p </it>< 0.01) and specialty care (<it>p </it>< 0.01), controlling for patient characteristics.</p> <p>Conclusions</p> <p>Greater use of primary care and specialty care visits by disability-eligible veterans is most likely related to greater health needs not captured by the patient characteristics we employed and eligibility for VA care at no cost. Outpatient care patterns of disability-eligible veterans may foreshadow care patterns of veterans returning from Afghanistan and Iraq wars, who are entering the system in growing numbers. This study provides an important baseline for future research assessing utilizations among returning veterans who use both VA and Medicare systems. Establishing effective care coordination protocols between VA and Medicare providers can help ensure efficient use of taxpayer resources and high quality care for disabled veterans.</p

Astrobiological Complexity with Probabilistic Cellular Automata

Search for extraterrestrial life and intelligence constitutes one of the major endeavors in science, but has yet been quantitatively modeled only rarely and in a cursory and superficial fashion. We argue that probabilistic cellular automata (PCA) represent the best quantitative framework for modeling astrobiological history of the Milky Way and its Galactic Habitable Zone. The relevant astrobiological parameters are to be modeled as the elements of the input probability matrix for the PCA kernel. With the underlying simplicity of the cellular automata constructs, this approach enables a quick analysis of large and ambiguous input parameters' space. We perform a simple clustering analysis of typical astrobiological histories and discuss the relevant boundary conditions of practical importance for planning and guiding actual empirical astrobiological and SETI projects. In addition to showing how the present framework is adaptable to more complex situations and updated observational databases from current and near-future space missions, we demonstrate how numerical results could offer a cautious rationale for continuation of practical SETI searches.Comment: 37 pages, 11 figures, 2 tables; added journal reference belo

The evolution of photosynthesis in chromist algae through serial endosymbioses

Chromist algae include diverse photosynthetic organisms of great ecological and social importance. Despite vigorous research efforts, a clear understanding of how various chromists acquired photosynthetic organelles has been complicated by conflicting phylogenetic results, along with an undetermined number and pattern of endosymbioses, and the horizontal movement of genes that accompany them. We apply novel statistical approaches to assess impacts of endosymbiotic gene transfer on three principal chromist groups at the heart of long-standing controversies. Our results provide robust support for acquisitions of photosynthesis through serial endosymbioses, beginning with the adoption of a red alga by cryptophytes, then a cryptophyte by the ancestor of ochrophytes, and finally an ochrophyte by the ancestor of haptophytes. Resolution of how chromist algae are related through endosymbioses provides a framework for unravelling the further reticulate history of red algal-derived plastids, and for clarifying evolutionary processes that gave rise to eukaryotic photosynthetic diversity