FastVentricle: Cardiac Segmentation with ENet

Cardiac Magnetic Resonance (CMR) imaging is commonly used to assess cardiac structure and function. One disadvantage of CMR is that post-processing of exams is tedious. Without automation, precise assessment of cardiac function via CMR typically requires an annotator to spend tens of minutes per case manually contouring ventricular structures. Automatic contouring can lower the required time per patient by generating contour suggestions that can be lightly modified by the annotator. Fully convolutional networks (FCNs), a variant of convolutional neural networks, have been used to rapidly advance the state-of-the-art in automated segmentation, which makes FCNs a natural choice for ventricular segmentation. However, FCNs are limited by their computational cost, which increases the monetary cost and degrades the user experience of production systems. To combat this shortcoming, we have developed the FastVentricle architecture, an FCN architecture for ventricular segmentation based on the recently developed ENet architecture. FastVentricle is 4x faster and runs with 6x less memory than the previous state-of-the-art ventricular segmentation architecture while still maintaining excellent clinical accuracy.Comment: 11 pages, 6 figures, Accepted to Functional Imaging and Modeling of the Heart (FIMH) 201

Craniomaxillofacial Trauma in Dogs-Part I: Fracture Location, Morphology and Etiology.

Treatment of craniomaxillofacial (CMF) trauma in dogs often requires a multidisciplinary approach and a thorough understanding of the CMF skeletal structures involved. The aim of this retrospective study was to use a large number of CT studies of dogs evaluated for CMF trauma and to describe fracture location and morphology in relation to demographic data and trauma etiology. The medical records and CT studies of 165 dogs over a 10-year period were evaluated. The skeletal location of CMF fractures as well as the severity of displacement and fragmentation of each fracture was recorded. Patient demographic data and trauma etiology were also recorded. Animal bites accounted for the majority of trauma (50%), followed by unknown trauma (15%), vehicular accidents (13%), and blunt force trauma (13%). Small dogs, <10 kg, and juveniles accounted for the majority of patients (41.8 and 25.5%, respectively). The most likely bone or region to be fractured was the maxillary bone, followed by the premolar and molar regions of the mandible. Up to 37 bones or regions were fractured in any given patient, with an average of 8.2 fractured bones or regions per dog. The most commonly fractured location varied according to trauma etiology. Specifically, vehicular accidents tended to result in more locations with a higher probability of fracture than other trauma types. A major conclusion from this study is that every bone of the CMF region was fractured in at least one case and many cases had a large number of fractured regions. Thus, the need for comprehensive assessment of the entire CMF region, preferably using CT, is underscored

Craniomaxillofacial Trauma in Dogs-Part II: Association Between Fracture Location, Morphology and Etiology.

Treatment of craniomaxillofacial (CMF) trauma in dogs requires a thorough understanding of the CMF skeletal structures involved. The human medical literature has several examples of CMF trauma and fracture classification, including the classically described Le Fort fractures. The recent classification schemes require large studies using computed tomography (CT). In the veterinary medical literature, such studies are lacking. The aims of part II of this retrospective study were to use a large number of CT studies of dogs evaluated for CMF trauma to determine whether specific fracture locations in the CMF region occur concurrently, and whether trauma etiology influences fracture morphology. This information may then be used to form a fracture classification scheme in the future. The medical records and CT studies of 165 dogs over a 10-year period were evaluated. The skeletal location of CMF fractures as well as the severity of displacement and fragmentation of each fracture was recorded. Dogs' demographic data and trauma etiology were also recorded. Fractured portions of the mandible tended to occur with fractures of adjacent bones, with the major exception of symphyseal separation, which occurred simultaneously with fractures of the cribriform plate. Fractures of the maxillary bone were accompanied by many concurrent fractures affecting the majority of the midface, skull base, and cranial vault. When the zygomatic bone was fractured, the other bones comprising the orbit also tended to fracture. Fractures of the relatively superficially located frontal and nasal bones were often accompanied by fractures of the skull base. Fracture etiology influenced fracture morphology such that vehicular trauma resulted in a relatively higher number of severely displaced and comminuted fractures than did other trauma etiologies. This study provides examples of fractures that, when found, should prompt veterinarians to look for additional injuries in specific locations. In addition, it further highlights the need for thorough CT evaluation of the entire CMF region, even when clinically apparent fractures appear relatively superficial

Bayesian Variable Selection to identify QTL affecting a simulated quantitative trait

Background Recent developments in genetic technology and methodology enable accurate detection of QTL and estimation of breeding values, even in individuals without phenotypes. The QTL-MAS workshop offers the opportunity to test different methods to perform a genome-wide association study on simulated data with a QTL structure that is unknown beforehand. The simulated data contained 3,220 individuals: 20 sires and 200 dams with 3,000 offspring. All individuals were genotyped, though only 2,000 offspring were phenotyped for a quantitative trait. QTL affecting the simulated quantitative trait were identified and breeding values of individuals without phenotypes were estimated using Bayesian Variable Selection, a multi-locus SNP model in association studies. Results Estimated heritability of the simulated quantitative trait was 0.30 (SD = 0.02). Mean posterior probability of SNP modelled having a large effect ( pˆi) was 0.0066 (95%HPDR: 0.0014-0.0132). Mean posterior probability of variance of second distribution was 0.409 (95%HPDR: 0.286-0.589). The genome-wide association analysis resulted in 14 significant and 43 putative SNP, comprising 7 significant QTL on chromosome 1, 2 and 3 and putative QTL on all chromosomes. Assigning single or multiple QTL to significant SNP was not obvious, especially for SNP in the same region that were more or less in LD. Correlation between the simulated and estimated breeding values of 1,000 offspring without phenotypes was 0.91. Conclusions Bayesian Variable Selection using thousands of SNP was successfully applied to genome-wide association analysis of a simulated dataset with unknown QTL structure. Simulated QTL with Mendelian inheritance were accurately identified, while imprinted and epistatic QTL were only putatively detected. The correlation between simulated and estimated breeding values of offspring without phenotypes was high

Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings

Recently, evidence has emerged that humans approach learning using Bayesian updating rather than (model-free) reinforcement algorithms in a six-arm restless bandit problem. Here, we investigate what this implies for human appreciation of uncertainty. In our task, a Bayesian learner distinguishes three equally salient levels of uncertainty. First, the Bayesian perceives irreducible uncertainty or risk: even knowing the payoff probabilities of a given arm, the outcome remains uncertain. Second, there is (parameter) estimation uncertainty or ambiguity: payoff probabilities are unknown and need to be estimated. Third, the outcome probabilities of the arms change: the sudden jumps are referred to as unexpected uncertainty. We document how the three levels of uncertainty evolved during the course of our experiment and how it affected the learning rate. We then zoom in on estimation uncertainty, which has been suggested to be a driving force in exploration, in spite of evidence of widespread aversion to ambiguity. Our data corroborate the latter. We discuss neural evidence that foreshadowed the ability of humans to distinguish between the three levels of uncertainty. Finally, we investigate the boundaries of human capacity to implement Bayesian learning. We repeat the experiment with different instructions, reflecting varying levels of structural uncertainty. Under this fourth notion of uncertainty, choices were no better explained by Bayesian updating than by (model-free) reinforcement learning. Exit questionnaires revealed that participants remained unaware of the presence of unexpected uncertainty and failed to acquire the right model with which to implement Bayesian updating

The effect of acute vs chronic magnesium supplementation on exercise and recovery on resistance exercise, blood pressure and total peripheral resistance on normotensive adults

© 2015 Kass and Poeira; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Background: Magnesium supplementation has previously shown reductions in blood pressure of up to 12 mmHg. A positive relationship between magnesium supplementation and performance gains in resistance exercise has also been seen. However, no previous studies have investigated loading strategies to optimise response. The aim of this study was to assess the effect of oral magnesium supplementation on resistance exercise and vascular response after intense exercise for an acute and chronic loading strategy on a 2-day repeat protocol. Methods: The study was a randomised, double-blind, cross-over design, placebo controlled 2 day repeat measure protocol (n = 13). Intense exercise (40 km time trial) was followed by bench press at 80% 1RM to exhaustion, with blood pressure and total peripheral resistance (TPR) recorded. 300 mg/d elemental magnesium was supplemented for either a 1 (A) or 4 (Chr) week loading strategy. Food diaries were recorded. Results: Dietary magnesium intake was above the Reference Nutrient Intake (RNI) for all groups. Bench press showed a significant increase of 17.7% (p = 0.031) for A on day 1. On day 2 A showed no decrease in performance whilst Chr showed a 32.1% decrease. On day 2 post-exercise systolic blood pressure (SBP) was significantly lower in both A (p = 0.0.47) and Chr (p = 0.016) groups. Diastolic blood pressure (DBP) showed significant decreases on day 2 solely for A (p = 0.047) with no changes in the Chr. TPR reduced for A on days 1 and 2 (p = 0.031) with Chr showing an increase on day 1 (p = 0.008) and no change on day 2. Conclusion: There was no cumulative effect of Chr supplementation compared to A. A group showed improvement for bench press concurring with previous research which was not seen in Chr. On day 2 A showed a small non-significant increase but not a decrement as expected with Chr showing a decrease. DBP showed reductions in both Chr and A loading, agreeing with previous literature. This is suggestive of a different mechanism for BP reduction than for muscular strength. TPR showed greater reductions with A than Chr, which would not be expected as both interventions had reductions in BP, which is associated with TPR.Peer reviewedFinal Published versio

Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum

Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism

Working Memory Cells' Behavior May Be Explained by Cross-Regional Networks with Synaptic Facilitation

Neurons in the cortex exhibit a number of patterns that correlate with working memory. Specifically, averaged across trials of working memory tasks, neurons exhibit different firing rate patterns during the delay of those tasks. These patterns include: 1) persistent fixed-frequency elevated rates above baseline, 2) elevated rates that decay throughout the tasks memory period, 3) rates that accelerate throughout the delay, and 4) patterns of inhibited firing (below baseline) analogous to each of the preceding excitatory patterns. Persistent elevated rate patterns are believed to be the neural correlate of working memory retention and preparation for execution of behavioral/motor responses as required in working memory tasks. Models have proposed that such activity corresponds to stable attractors in cortical neural networks with fixed synaptic weights. However, the variability in patterned behavior and the firing statistics of real neurons across the entire range of those behaviors across and within trials of working memory tasks are typical not reproduced. Here we examine the effect of dynamic synapses and network architectures with multiple cortical areas on the states and dynamics of working memory networks. The analysis indicates that the multiple pattern types exhibited by cells in working memory networks are inherent in networks with dynamic synapses, and that the variability and firing statistics in such networks with distributed architectures agree with that observed in the cortex

Helium in the adult critical care setting

Helium is a low-density inert gas whose physical properties are very different from those of nitrogen and oxygen. Such properties could be clinically useful in the adult critical care setting, especially in patients with upper to more distal airway obstruction requiring moderate to intermediate levels of FiO2. However, despite decades of utilization and reporting, it is still difficult to give any firm clinical recommendation in this setting. Numerous case reports are available in the context of upper airway obstruction of different origins, but there is a lack of controlled studies for this indication. One study reported a helium-induced beneficial effect on surrogates of work of breathing after extubation in non-COPD patients, possibly in relation to laryngeal consequences of tracheal intubation. Physiological benefits of helium-oxygen breathing have been demonstrated in the context of acute severe asthma, but there is a lack of large controlled studies demonstrating an effect on pertinent clinical endpoints, except for a study reported only as an abstract, which mentioned a reduction in the intubation rate in helium-treated patients. Finally, there are a number of physiological studies in the context of COLD-COPD patients demonstrating a beneficial effect, mainly by a reduction in the resistive inspiratory work of breathing but also by a reduction in hyperinflation. Reduction of hypercapnia was mainly observed in spontaneously breathing and noninvasively ventilated helium-treated patients but not in intubated patients during controlled ventilation, suggesting that the decrease in PaCO2 was mainly in relation to a diminution in CO2 production, related to the diminution in work of breathing and not an improved alveolar ventilation. Moreover, there is little evidence that helium-oxygen could improve parameters of heterogeneity in such patients. Two RCTs were unable to demonstrate a reduction in the intubation rate in such setting, but they were likely underpowered. An adequately powered international multicentric study is ongoing and will help to determinate the exact place of the helium-oxygen mixture in the future. The place of the mixture during the weaning period will deserve further evaluation