Extraction of Airways with Probabilistic State-space Models and Bayesian Smoothing

Segmenting tree structures is common in several image processing applications. In medical image analysis, reliable segmentations of airways, vessels, neurons and other tree structures can enable important clinical applications. We present a framework for tracking tree structures comprising of elongated branches using probabilistic state-space models and Bayesian smoothing. Unlike most existing methods that proceed with sequential tracking of branches, we present an exploratory method, that is less sensitive to local anomalies in the data due to acquisition noise and/or interfering structures. The evolution of individual branches is modelled using a process model and the observed data is incorporated into the update step of the Bayesian smoother using a measurement model that is based on a multi-scale blob detector. Bayesian smoothing is performed using the RTS (Rauch-Tung-Striebel) smoother, which provides Gaussian density estimates of branch states at each tracking step. We select likely branch seed points automatically based on the response of the blob detection and track from all such seed points using the RTS smoother. We use covariance of the marginal posterior density estimated for each branch to discriminate false positive and true positive branches. The method is evaluated on 3D chest CT scans to track airways. We show that the presented method results in additional branches compared to a baseline method based on region growing on probability images.Comment: 10 pages. Pre-print of the paper accepted at Workshop on Graphs in Biomedical Image Analysis. MICCAI 2017. Quebec Cit

Vertex-Ball Spring Smoothing: An efficient method for unstructured dynamic hybrid meshes

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Language-specific and individual variation in anticipatory nasal coarticulation: A comparative study of American English, French, and German

Anticipatory contextual nasalization, whereby an oral segment (usually a vowel) preceding a nasal consonant becomes partially or fully nasalized, has received considerable attention in research that seeks to uncover predictive factors for the temporal domain of coarticulation. Within this research, it has been claimed that the phonological status of vowel nasality in a language can determine the temporal extent of phonetic nasal coarticulation. We present a comparative study of anticipatory nasal coarticulation in American English, Northern Metropolitan French, and Standard German. These languages differ in whether nasality is contrastive (French), ostensibly phonologized but not contrastive (American English), or neither (German). We measure nasal intensity during a comparatively large temporal interval preceding a nasal or oral control consonant. In English, coarticulation has the largest temporal domain, whereas in French, anticipatory nasalization is more constrained. German differs from English, but not from French. While these results confirm some of the expected language-specific effects, they underscore that the temporal extent of anticipatory nasal coarticulation can go beyond the preceding vowel if the context does not inhibit velum lowering. For all languages, the onset of coarticulation may considerably precede the pre-nasal vowel in VN sequences, especially so for English. We propose that in English, the pre-nasal vowel has itself become a source of coarticulation, making American English pre-nasal vowel nasality uninformative about coarticulatory nasalization. Degrees of individual variation between the languages align with the phonological or phonologized role of nasalization therein. Overall, our data further add to our understanding of the non-local temporal scope of anticipatory coarticulation and its language-specific expressions

Lysosomal acidification dysfunction in microglia: an emerging pathogenic mechanism of neuroinflammation and neurodegeneration

Microglia are the resident innate immune cells in the brain with a major role in orchestrating immune responses. They also provide a frontline of host defense in the central nervous system (CNS) through their active phagocytic capability. Being a professional phagocyte, microglia participate in phagocytic and autophagic clearance of cellular waste and debris as well as toxic protein aggregates, which relies on optimal lysosomal acidification and function. Defective microglial lysosomal acidification leads to impaired phagocytic and autophagic functions which result in the perpetuation of neuroinflammation and progression of neurodegeneration. Reacidification of impaired lysosomes in microglia has been shown to reverse neurodegenerative pathology in Alzheimer's disease. In this review, we summarize key factors and mechanisms contributing to lysosomal acidification impairment and the associated phagocytic and autophagic dysfunction in microglia, and how these defects contribute to neuroinflammation and neurodegeneration. We further discuss techniques to monitor lysosomal pH and therapeutic agents that can reacidify impaired lysosomes in microglia under disease conditions. Finally, we propose future directions to investigate the role of microglial lysosomal acidification in lysosome-mitochondria crosstalk and in neuron-glia interaction for more comprehensive understanding of its broader CNS physiological and pathological implications

Overview on the phenomenon of two-qubit entanglement revivals in classical environments

The occurrence of revivals of quantum entanglement between separated open quantum systems has been shown not only for dissipative non-Markovian quantum environments but also for classical environments in absence of back-action. While the phenomenon is well understood in the first case, the possibility to retrieve entanglement when the composite quantum system is subject to local classical noise has generated a debate regarding its interpretation. This dynamical property of open quantum systems assumes an important role in quantum information theory from both fundamental and practical perspectives. Hybrid quantum-classical systems are in fact promising candidates to investigate the interplay among quantum and classical features and to look for possible control strategies of a quantum system by means of a classical device. Here we present an overview on this topic, reporting the most recent theoretical and experimental results about the revivals of entanglement between two qubits locally interacting with classical environments. We also review and discuss the interpretations provided so far to explain this phenomenon, suggesting that they can be cast under a unified viewpoint.Comment: 16 pages, 9 figures. Chapter written for the upcoming book "Lectures on general quantum correlations and their applications

Carbon and nitrogen isotopic ratios of urine and faeces as novel nutritional biomarkers of meat and fish intake

Purpose Meat and fish consumption are associated with changes in the risk of chronic diseases. Intake is mainly assessed using self-reporting, as no true quantitative nutritional biomarker is available. The measurement of plasma fatty acids, often used as an alternative, is expensive and time-consuming. As meat and fish differ in their stable isotope ratios, δ13C and δ15N have been proposed as biomarkers. However, they have never been investigated in controlled human dietary intervention studies. Objective In a short-term feeding study, we investigated the suitability of δ13C and δ15N in blood, urine and faeces as biomarkers of meat and fish intake. Methods The dietary intervention study (n = 14) followed a randomised cross-over design with three eight-day dietary periods (meat, fish and half-meat–half-fish). In addition, 4 participants completed a vegetarian control period. At the end of each period, 24-h urine, fasting venous blood and faeces were collected and their δ13C and δ15N analysed. Results There was a significant difference between diets in isotope ratios in faeces and urine samples, but not in blood samples (Kruskal–Wallis test, p < 0.0001). In pairwise comparisons, δ13C and δ15N were significantly higher in urine and faecal samples following a fish diet when compared with all other diets, and significantly lower following a vegetarian diet. There was no significant difference in isotope ratio between meat and half-meat–half-fish diets for blood, urine or faecal samples. Conclusions The results of this study show that urinary and faecal δ13C and δ15N are suitable candidate biomarkers for short-term meat and fish intake

Oldest known pantherine skull and evolution of the tiger

The tiger is one of the most iconic extant animals, and its origin and evolution have been intensely debated. Fossils attributable to extant pantherine species-lineages are less than 2 MYA and the earliest tiger fossils are from the Calabrian, Lower Pleistocene. Molecular studies predict a much younger age for the divergence of modern tiger subspecies at <100 KYA, although their cranial morphology is readily distinguishable, indicating that early Pleistocene tigers would likely have differed markedly anatomically from extant tigers. Such inferences are hampered by the fact that well-known fossil tiger material is middle to late Pleistocene in age. Here we describe a new species of pantherine cat from Longdan, Gansu Province, China, Panthera zdanskyi sp. nov. With an estimated age of 2.55–2.16 MYA it represents the oldest complete skull of a pantherine cat hitherto found. Although smaller, it appears morphologically to be surprisingly similar to modern tigers considering its age. Morphological, morphometric, and cladistic analyses are congruent in confirming its very close affinity to the tiger, and it may be regarded as the most primitive species of the tiger lineage, demonstrating the first unequivocal presence of a modern pantherine species-lineage in the basal stage of the Pleistocene (Gelasian; traditionally considered to be Late Pliocene). This find supports a north-central Chinese origin of the tiger lineage, and demonstrates that various parts of the cranium, mandible, and dentition evolved at different rates. An increase in size and a reduction in the relative size of parts of the dentition appear to have been prominent features of tiger evolution, whereas the distinctive cranial morphology of modern tigers was established very early in their evolutionary history. The evolutionary trend of increasing size in the tiger lineage is likely coupled to the evolution of its primary prey species

Kidney tissue proteome profiles in short versus long duration of delayed graft function – a pilot study in donation after circulatory death donors

Introduction: Delayed graft function (DGF) is often defined as the need for dialysis treatment in the first week after a kidney transplantation. This definition, though readily applicable, is generic and unable to distinguish between “types” of DGF or time needed to recover function that may also significantly affect longer-term outcomes. We aimed to profile biological pathways in donation after circulatory death (DCD) kidney donors that correlate with DGF and different DGF durations. Methods: A total of N = 30 DCD kidney biopsies were selected from the UK Quality in Organ Donation (QUOD) biobank and stratified according to DGF duration (immediate function, IF n = 10; “short-DGF” (1–6 days), SDGF n = 10; “long-DGF” (7–22 days), LDGF n = 10). Samples were matched for donor and recipient demographics and analyzed by label-free quantitative (LFQ) proteomics, yielding identification of N = 3378 proteins. Results: Ingenuity pathway analysis (IPA) on differentially abundant proteins showed that SDGF kidneys presented upregulation of stress response pathways, whereas LDGF presented impaired response to stress, compared to IF. LDGF showed extensive metabolic deficits compared to IF and SDGF. Conclusion: DCD kidneys requiring dialysis only in the first week posttransplant present acute cellular injury at donation, alongside repair pathways upregulation. In contrast, DCD kidneys requiring prolonged dialysis beyond 7 days present minimal metabolic and antioxidant responses, suggesting that current DGF definitions might not be adequate in distinguishing different patterns of injury in donor kidneys contributing to DGF

Effect of Intensive Patient Education vs Placebo Patient Education on Outcomes in Patients with Acute Low Back Pain: A Randomized Clinical Trial

© 2018 2018 American Medical Association. All rights reserved. Importance: Many patients with acute low back pain do not recover with basic first-line care (advice, reassurance, and simple analgesia, if necessary). It is unclear whether intensive patient education improves clinical outcomes for those patients already receiving first-line care. Objective: To determine the effectiveness of intensive patient education for patients with acute low back pain. Design, Setting, and Participants: This randomized, placebo-controlled clinical trial recruited patients from general practices, physiotherapy clinics, and a research center in Sydney, Australia, between September 10, 2013, and December 2, 2015. Trial follow-up was completed in December 17, 2016. Primary care practitioners invited 618 patients presenting with acute low back pain to participate. Researchers excluded 416 potential participants. All of the 202 eligible participants had low back pain of fewer than 6 weeks' duration and a high risk of developing chronic low back pain according to Predicting the Inception of Chronic Pain (PICKUP) Tool, a validated prognostic model. Participants were randomized in a 1:1 ratio to either patient education or placebo patient education. Interventions: All participants received recommended first-line care for acute low back pain from their usual practitioner. Participants received additional 2 × 1-hour sessions of patient education (information on pain and biopsychosocial contributors plus self-management techniques, such as remaining active and pacing) or placebo patient education (active listening, without information or advice). Main Outcomes and Measures: The primary outcome was pain intensity (11-point numeric rating scale) at 3 months. Secondary outcomes included disability (24-point Roland Morris Disability Questionnaire) at 1 week, and at 3, 6, and 12 months. Results: Of 202 participants randomized for the trial, the mean (SD) age of participants was 45 (14.5) years and 103 (51.0%) were female. Retention rates were greater than 90% at all time points. Intensive patient education was not more effective than placebo patient education at reducing pain intensity (3-month mean [SD] pain intensity: 2.1 [2.4] vs 2.4 [2.2]; mean difference at 3 months, -0.3 [95% CI, -1.0 to 0.3]). There was a small effect of intensive patient education on the secondary outcome of disability at 1 week (mean difference, -1.6 points on a 24-point scale [95% CI, -3.1 to -0.1]) and 3 months (mean difference, -1.7 points, [95% CI, -3.2 to -0.2]) but not at 6 or 12 months. Conclusions and Relevance: Adding 2 hours of patient education to recommended first-line care for patients with acute low back pain did not improve pain outcomes. Clinical guideline recommendations to provide complex and intensive support to high-risk patients with acute low back pain may have been premature. Trial Registration: Australian Clinical Trial Registration Number: 12612001180808

Longitudinal evaluation, acceptability and long-term retention of knowledge on a horizontally integrated organic and functional systems course

Undergraduate medical education is moving from traditional disciplinary basic science courses into more integrated curricula. Integration models based on organ systems originated in the 1950s, but few longitudinal studies have evaluated their effectiveness. This article outlines the development and implementation of the Organic and Functional Systems (OFS) courses at the University of Minho in Portugal, using evidence collected over 10 years. It describes the organization of content, student academic performance and acceptability of the courses, the evaluation of preparedness for future courses and the retention of knowledge on basic sciences. Students consistently rated the OFS courses highly. Physician tutors in subsequent clinical attachments considered that students were appropriately prepared. Performance in the International Foundations of Medicine examination of a self-selected sample of students revealed similar performances in basic science items after the last OFS course and 4 years later, at the moment of graduation. In conclusion, the organizational and pedagogical approaches of the OFS courses achieve high acceptability by students and result in positive outcomes in terms of preparedness for subsequent training and long-term retention of basic science knowledge