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We present a finite difference time domain (FDTD) model for computation of A line scans in time domain optical coherence tomography (OCT). The OCT output signal is created using two different simulations for the reference and sample arms, with a successive computation of the interference signal with external software. In this paper we present the model applied to two different samples: a glass rod filled with water-sucrose solution at different concentrations and a peripheral nerve. This work aims to understand to what extent time domain OCT can be used for non-invasive, direct optical monitoring of peripheral nerve activity. [ABSTRACT FROM AUTHOR]

Work spaces for assembly or maintenance operations are considered in the design stage of products. Maintenance space is a key factor in determining how well a product can be maintained. If the work space is sufficiently considered in the design stage, it will benefit both the user and the maintainer. From a maintenance perspective, this paper proposes a quantitative method to evaluate the maintenance space by virtual simulation and consideration of ergonomics. In this method, maintenance operations are concisely classified into three types. Based on the virtual simulation of the maintenance process and maintainer data, the swept volume of a hand is built using envelope theory. The operation range of the maintainer is derived by establishing a mathematical model for the upper limb. Combining the swept volume and operation range, the maintenance space can be quantitatively evaluated. A concise validation demonstrates that the proposed method is effective for evaluating the maintenance space to improve the space design. The proposed method could be applied to the space design of a complex product. [ABSTRACT FROM AUTHOR]

Neuraxial anesthesia (spinal and epidural anesthesia) procedures have significant learning curves and have been traditionally taught at the bed side, exposing patients to the increased risk associated with procedures done by novices. Simulation based medical education allows trainees to repeatedly practice and hone their skills prior to patient interaction. Wide-spread adoption of simulation-based medical education for procedural teaching has been slow due to the expense and limited variety of commercially available phantoms. Free/Libre/open-source (FLOS) software and desktop 3D printing technologies has enabled the fabrication of low-cost, patient-specific medical phantoms. However, few studies have evaluated the performance of these devices compared to commercially available phantoms. This paper describes the fabrication of a low-cost 3D printed neuraxial phantom based on computed tomorography (CT) scan data, and expert validation data comparing this phantom to a commercially available model. Methods: Anonymized CT DICOM data was segmented to create a 3D model of the lumbar spine. The 3D model was modified, placed inside a digitally designed housing unit and fabricated on a desktop 3D printer using polylactic acid (PLA) filament. The model was filled with an echogenic solution of gelatin with psyllium fiber. Twenty-two staff anesthesiologists performed a spinal and epidural on the 3D printed simulator and a commercially available Simulab phantom. Participants evaluated the tactile and ultrasound imaging fidelity of both phantoms via Likert-scale questionnaire. Results: The 3D printed neuraxial phantom cost $13 to print and required 25 hours of non-supervised printing and 2 hours of assembly time. The 3D printed phantom was found to be less realistic to surface palpation than the Simulab phantom due to fragility of the silicone but had significantly better fidelity for loss of resistance, dural puncture and ultrasound imaging than the Simulab phantom. Conclusion: Low-cost neuraxial phantoms with fidelity comparable to commercial models can be produced using CT data and low-cost infrastructure consisting of FLOS software and desktop 3D printers. [ABSTRACT FROM AUTHOR]

This paper proposes a discrete particle model based on the random-walk theory for simulating cement infiltration within open-cell structures to prevent osteoporotic proximal femur fractures. Model parameters consider the cement viscosity (high and low) and the desired direction of injection (vertical and diagonal). In vitro and in silico characterizations of augmented open-cell structures validated the computational model and quantified the improved mechanical properties (Young’s modulus) of the augmented specimens. The cement injection pattern was successfully predicted in all the simulated cases. All the augmented specimens exhibited enhanced mechanical properties computationally and experimentally (maximum improvements of 237.95 ± 12.91% and 246.85 ± 35.57%, respectively). The open-cell structures with high porosity fraction showed a considerable increase in mechanical properties. Cement augmentation in low porosity fraction specimens resulted in a lesser increase in mechanical properties. The results suggest that the proposed discrete particle model is adequate for use as a femoroplasty planning framework. [ABSTRACT FROM AUTHOR]

Next-generation sequencing technologies have made RNA sequencing (RNA-seq) a popular choice for measuring gene expression level. To reduce the noise of gene expression measures and compare them between several conditions or samples, normalization is an essential step to adjust for varying sample sequencing depths and other unwanted technical effects. In this paper, we develop a novel global scaling normalization method by employing the available knowledge of housekeeping genes. We formulate the problem from the hypothesis testing perspective and find an optimal scaling factor that minimizes the deviation between the empirical and the nominal type I error. Applying our approach to various simulation studies and real examples, we demonstrate that it is more accurate and robust than the state-of-the-art alternatives in detecting differentially expression genes. [ABSTRACT FROM AUTHOR]

Retinal microaneurysms (MAs) are the earliest clinically observable lesions of diabetic retinopathy. Reliable automated MAs detection is thus critical for early diagnosis of diabetic retinopathy. This paper proposes a novel method for the automated MAs detection in color fundus images based on gradient vector analysis and class imbalance classification, which is composed of two stages, i.e. candidate MAs extraction and classification. In the first stage, a candidate MAs extraction algorithm is devised by analyzing the gradient field of the image, in which a multi-scale log condition number map is computed based on the gradient vectors for vessel removal, and then the candidate MAs are localized according to the second order directional derivatives computed in different directions. Due to the complexity of fundus image, besides a small number of true MAs, there are also a large amount of non-MAs in the extracted candidates. Classifying the true MAs and the non-MAs is an extremely class imbalanced classification problem. Therefore, in the second stage, several types of features including geometry, contrast, intensity, edge, texture, region descriptors and other features are extracted from the candidate MAs and a class imbalance classifier, i.e., RUSBoost, is trained for the MAs classification. With the Retinopathy Online Challenge (ROC) criterion, the proposed method achieves an average sensitivity of 0.433 at 1/8, 1/4, 1/2, 1, 2, 4 and 8 false positives per image on the ROC database, which is comparable with the state-of-the-art approaches, and 0.321 on the DiaRetDB1 V2.1 database, which outperforms the state-of-the-art approaches. [ABSTRACT FROM AUTHOR]

In recent years the role of FSI (fluid-structure interaction) simulations in the analysis of the fluid-mechanics of heart valves is becoming more and more important, being able to capture the interaction between the blood and both the surrounding biological tissues and the valve itself. When setting up an FSI simulation, several choices have to be made to select the most suitable approach for the case of interest: in particular, to simulate flexible leaflet cardiac valves, the type of discretization of the fluid domain is crucial, which can be described with an ALE (Arbitrary Lagrangian-Eulerian) or an Eulerian formulation. The majority of the reported 3D heart valve FSI simulations are performed with the Eulerian formulation, allowing for large deformations of the domains without compromising the quality of the fluid grid. Nevertheless, it is known that the ALE-FSI approach guarantees more accurate results at the interface between the solid and the fluid. The goal of this paper is to describe the same aortic valve model in the two cases, comparing the performances of an ALE-based FSI solution and an Eulerian-based FSI approach. After a first simplified 2D case, the aortic geometry was considered in a full 3D set-up. The model was kept as similar as possible in the two settings, to better compare the simulations’ outcomes. Although for the 2D case the differences were unsubstantial, in our experience the performance of a full 3D ALE-FSI simulation was significantly limited by the technical problems and requirements inherent to the ALE formulation, mainly related to the mesh motion and deformation of the fluid domain. As a secondary outcome of this work, it is important to point out that the choice of the solver also influenced the reliability of the final results. [ABSTRACT FROM AUTHOR]

Refraction techniques make it possible to determine the most appropriate sphero-cylindrical lens prescription to achieve the best possible visual quality. Among these techniques, subjective refraction (i.e., patient’s response-guided refraction) is the most commonly used approach. In this context, this paper’s main goal is to present a simulation software that implements in a virtual manner various subjective-refraction techniques—including Jackson’s Cross-Cylinder test (JCC)—relying all on the observation of computer-generated retinal images. This software has also been used to evaluate visual quality when the JCC test is performed in multifocal-contact-lens wearers. The results reveal this software’s usefulness to simulate the retinal image quality that a particular visual compensation provides. Moreover, it can help to gain a deeper insight and to improve existing refraction techniques and it can be used for simulated training. [ABSTRACT FROM AUTHOR]

Diffusion Weighted (DW) MRI allows for the non-invasive study of water diffusion inside living tissues. As such, it is useful for the investigation of human brain white matter (WM) connectivity in vivo through fiber tractography (FT) algorithms. Many DW-MRI tailored restoration techniques and FT algorithms have been developed. However, it is not clear how accurately these methods reproduce the WM bundle characteristics in real-world conditions, such as in the presence of noise, partial volume effect, and a limited spatial and angular resolution. The difficulty lies in the lack of a realistic brain phantom on the one hand, and a sufficiently accurate way of modeling the acquisition-related degradation on the other. This paper proposes a software phantom that approximates a human brain to a high degree of realism and that can incorporate complex brain-like structural features. We refer to it as a Diffusion BRAIN (D-BRAIN) phantom. Also, we propose an accurate model of a (DW) MRI acquisition protocol to allow for validation of methods in realistic conditions with data imperfections. The phantom model simulates anatomical and diffusion properties for multiple brain tissue components, and can serve as a ground-truth to evaluate FT algorithms, among others. The simulation of the acquisition process allows one to include noise, partial volume effects, and limited spatial and angular resolution in the images. In this way, the effect of image artifacts on, for instance, fiber tractography can be investigated with great detail. The proposed framework enables reliable and quantitative evaluation of DW-MR image processing and FT algorithms at the level of large-scale WM structures. The effect of noise levels and other data characteristics on cortico-cortical connectivity and tractography-based grey matter parcellation can be investigated as well. [ABSTRACT FROM AUTHOR]

Drug delivery to the brain is challenging due to the presence of the blood-brain barrier. Mathematical modeling and simulation are essential tools for the deeper understanding of transport processes in the blood, across the blood-brain barrier and within the tissue. Here we present a mathematical model for drug delivery through capillary networks with increasingly complex topologies with the goal to understand the scaling behavior of model predictions on a coarse-to-fine sequence of grids. We apply our model to the delivery of L-Dopa, the primary drug used in the therapy of Parkinson’s Disease. Our model replicates observed blood flow rates and ratios between plasma and tissue concentrations. We propose an optimal network grain size for the simulation of tissue volumes of 1 cm3 that allows to make reliable predictions with reasonable computational costs. [ABSTRACT FROM AUTHOR]

Aging or cerebral diseases may induce architectural modifications in human brain microvascular networks, such as capillary rarefaction. Such modifications limit blood and oxygen supply to the cortex, possibly resulting in energy failure and neuronal death. Modelling is key in understanding how these architectural modifications affect blood flow and mass transfers in such complex networks. However, the huge number of vessels in the human brain—tens of billions—prevents any modelling approach with an explicit architectural representation down to the scale of the capillaries. Here, we introduce a hybrid approach to model blood flow at larger scale in the brain microcirculation, based on its multiscale architecture. The capillary bed, which is a space-filling network, is treated as a porous medium and modelled using a homogenized continuum approach. The larger arteriolar and venular trees, which cannot be homogenized because of their fractal-like nature, are treated as a network of interconnected tubes with a detailed representation of their spatial organization. The main contribution of this work is to devise a proper coupling model at the interface between these two components. This model is based on analytical approximations of the pressure field that capture the strong pressure gradients building up in the capillaries connected to arterioles or venules. We evaluate the accuracy of this model for both very simple architectures with one arteriole and/or one venule and for more complex ones, with anatomically realistic tree-like vessels displaying a large number of coupling sites. We show that the hybrid model is very accurate in describing blood flow at large scales and further yields a significant computational gain by comparison with a classical network approach. It is therefore an important step towards large scale simulations of cerebral blood flow and lays the groundwork for introducing additional levels of complexity in the future. [ABSTRACT FROM AUTHOR]

Purpose: To point out the advantages and drawbacks of high-dose rate brachytherapy in the treatment of mobile tongue cancer and indicate the clinical importance of modular lead-lined spacers when applying this technique to patients. Methods: First, all basic steps to construct the modular spacer are shown. Second, we simulate and evaluate the dose rate reduction for a wide range of spacer configurations. Results: With increasing distance to the source absorbed doses dropped considerably. Significantly more shielding was obtained when lead was added to the spacer and this effect was most pronounced on shorter (i.e. more clinically relevant) distances to the source. Conclusions: The modular spacer represents an important addition to the planning and treatment stages of mobile tongue cancer using HDR-ISBT. [ABSTRACT FROM AUTHOR]

Honeybees construct nests that consist of regularly arrayed hexagonal cylinders. In the first stage of honeycomb construction, they build a linear sequence of tetrapod structures that form the basis of the comb. However, considering their physiological limitations, it is unknown how honeybees produce that initial pattern. Herein, in an attempt to understand the mechanisms of honeycomb construction, we propose an agent-based model, the attachment-excavation model, in which worker honeybees are classified into attachers who secrete and attach wax, and excavators who excise the attached wax. The model assumes that workers instinctively refrain from digging through the thin parts of a wax cluster. We then conduct two-dimensional (2D) simulations that show how a tripod pattern can be seen as a projection of tetrapods onto a plane. The simulation results show that the tripod pattern emerges due to competition between the attachers and excavators. As time advances, the isotropic wax growth causes the tripods to connect planarly. Because the homogeneously broadened structures do not match that of a natural comb, we employ anisotropic wax growth to obtain a linear sequence of constructed tripods, thus suggesting that anisotropy is a significant contributor to the first stage of honeycomb construction. From our simulation results, we conclude that honeybees utilize self-organization to achieve complexity during the first stage of honeycomb construction. It is anticipated that the results of our study will provide insights into how complexity can be achieved within a hierarchy. [ABSTRACT FROM AUTHOR]

Purpose: To compare aqueous humour (AH) dynamics in the presence of a precrystalline (Implantable Collamer Lens®; ICL) or iris-fixed (Artiflex®) phakic intraocular lens (PIOL). Methods: By computational fluid dynamics simulation, AH flow was modelled through a peripheral iridotomy (PI) or central lens hole (both 360 μm) in the presence of an Artiflex or ICL lens, respectively. The impacts of AH flow were then determined in terms of wall shear stress (WSS) produced on the endothelium or crystalline lens. Effects were also modelled for different scenarios of pupil diameter (PD 3.5 or 5.5 mm), ICL vault (100, 350, 800 μm) and number of Artiflex iridotomies (1 or 2) and location (12 or 6 o’clock). Results: For a PD of 3.5 mm, AH volumes flowing from the posterior to the anterior chamber were 37.6% of total flow through the lens hole (ICL) and 84.2% through PI (Artiflex). For an enlarged PD (5.5 mm), corresponding values were 10.3% and 81.9% respectively, so PI constitutes a very efficient way of evacuating AH. Central endothelial WSS in Pa was lower for the large vault ICL and the Artiflex (1−03 and 1.1−03 respectively) compared to the PIOL-free eye (1.6−03). Crystalline lens WSS was highest for the lowest vault ICL (1−04). Conclusions: AH flow varied according to the presence of a precrystalline or iris-fixed intraocular lens. Endothelial WSS was lower for an implanted ICL with large vault and Artiflex than in the PIOL-free eye, while highest crystalline WSS was recorded for the lowest vault ICL. [ABSTRACT FROM AUTHOR]

Mental fatigue is one of the main reasons for the decline of response inhibition. This study aimed to explore the impairing influence of mental fatigue on a driver’s response inhibition. The effects of mental fatigue on response inhibition were assessed by comparing brain activity and behavioral indices when performing a Go/NoGo task before and after a 90-min fatigue manipulation task. Participants in the driving group performed a simulated driving task, while individuals in the control group spent the same time watching movies. We found that participants in the driving group reported higher levels of mental fatigue and had a higher percentage of eye closure and larger lateral deviations from their lane positions, which indicated there was effective manipulation of mental fatigue through a prolonged simulated driving task. After manipulation of mental fatigue, we observed increased reaction time and miss rates, delayed NoGo-N2 latency and Go-P3 latency, and decreased NoGo-P3 amplitude, which indicated that mental fatigue may slow down the speed of the inhibition process, delay the evaluation of visual stimuli and reduce the availability of attentional resources. These findings revealed the underlying neurological mechanisms of how mental fatigue impaired response inhibition. [ABSTRACT FROM AUTHOR]

We propose a nonparametric shrinkage estimator for the median survival times from several independent samples of right-censored data, which combines the samples and hypothesis information to improve the efficiency. We compare efficiency of the proposed shrinkage estimation procedure to unrestricted estimator and combined estimator through extensive simulation studies. Our results indicate that performance of these estimators depends on the strength of homogeneity of the medians. When homogeneity holds, the combined estimator is the most efficient estimator. However, it becomes inconsistent when homogeneity fails. On the other hand, the proposed shrinkage estimator remains efficient. Its efficiency decreases as the equality of the survival medians is deviated, but is expected to be as good as or equal to the unrestricted estimator. Our simulation studies also indicate that the proposed shrinkage estimator is robust to moderate levels of censoring. We demonstrate application of these methods to estimating median time for trauma patients to receive red blood cells in the Prospective Observational Multi-center Major Trauma Transfusion (PROMMTT) study. [ABSTRACT FROM AUTHOR]

We present a general strategy for the modeling and simulation-based control of soft robots. Although the presented methodology is completely general, we restrict ourselves to the analysis of a model robot made of hyperelastic materials and actuated by cables or tendons. To comply with the stringent real-time constraints imposed by control algorithms, a reduced-order modeling strategy is proposed that allows to minimize the amount of online CPU cost. Instead, an offline training procedure is proposed that allows to determine a sort of response surface that characterizes the response of the robot. Contrarily to existing strategies, the proposed methodology allows for a fully non-linear modeling of the soft material in a hyperelastic setting as well as a fully non-linear kinematic description of the movement without any restriction nor simplifying assumption. Examples of different configurations of the robot were analyzed that show the appeal of the method. [ABSTRACT FROM AUTHOR]

Purpose: To develop a generative mathematical model of wet age-related macular degeneration (AMD) and model the impact of injections of anti-vascular endothelial growth factor to virtual patients with the condition. Methods: We isolated key pathophysiological components of macular degeneration in terms of macular edema development and response to anti-vascular endothelial growth factor (VEGF) agents. We developed mathematical models for each of these components using constants determined from published biological experimentation. Consequently, we combined the mathematical models of the separate components to arrive at an end-to-end model of the evolution of macular edema size and its response to treatment. Results: We present a series of simulations based upon our idealised model. Initially, we demonstrate the theoretical change in macular edema height in wet macular degeneration over time without and with anti-VEGF interventions. In our final simulation, we demonstrate the powerful possibilities of virtual clinical trials by simulating a virtual model of a landmark study using our existing mathematical AMD model. Conclusions: Using our mathematical modelling based upon known pathological and pharmacological processes we have been able to model the effect of intravitreal injection of an anti-VEGF agent on macular edema from age related macular degeneration. We were subsequently able to mathematically simulate a major clinical trial with results that mirror many key features of the clinical established study. We anticipate that the generative model presented here can evolve to be a useful supportive tool in the challenge to deliver optimal therapy for patients with wet macular degeneration. [ABSTRACT FROM AUTHOR]

Aims: (1) To model the process of use and usability of pH strips (2) to identify, through simulation studies, the likelihood of misreading pH strips, and to assess professional’s acceptance, trust and perceived usability of pH strips. Methods: This study was undertaken in four phases and used a mixed method approach (an audit, a semi-structured interview, a survey and simulation study). The three months audit was of 24 patients, the semi-structured interview was performed with 19 health professionals and informed the process of use of pH strips. A survey of 134 professionals and novices explored the likelihood of misinterpreting pH strips. Standardised questionnaires were used to assess professionals perceived usability, trust and acceptance of pH strip use in a simulated study. Results: The audit found that in 45.7% of the cases aspiration could not be achieved, and that 54% of the NG-tube insertions required x-ray confirmation. None of those interviewed had received formal training on pH strips use. In the simulated study, participants made up to 11.15% errors in reading the strips with important implications for decision making regarding NG tube placement. No difference was identified between professionals and novices in their likelihood of misinterpreting the pH value of the strips. Whilst the overall experience of usage is poor (47.3%), health professionals gave a positive level of trust in both the interview (62.6%) and the survey (68.7%) and acceptance (interview group 65.1%, survey group 74.7%). They also reported anxiety in the use of strips (interview group 29.7%, survey group 49.7%). Conclusions: Significant errors occur when using pH strips in a simulated study. Manufacturers should consider developing new pH strips, specifically designed for bedside use, that are more usable and less likely to be misread. [ABSTRACT FROM AUTHOR]

The core principles of the evolutionary theories of emotions declare that affective states represent crucial drives for action selection in the environment and regulated the behavior and adaptation of natural agents in ancestrally recurrent situations. While many different studies used autonomous artificial agents to simulate emotional responses and the way these patterns can affect decision-making, few are the approaches that tried to analyze the evolutionary emergence of affective behaviors directly from the specific adaptive problems posed by the ancestral environment. A model of the evolution of affective behaviors is presented using simulated artificial agents equipped with neural networks and physically inspired on the architecture of the iCub humanoid robot. We use genetic algorithms to train populations of virtual robots across generations, and investigate the spontaneous emergence of basic emotional behaviors in different experimental conditions. In particular, we focus on studying the emotion of fear, therefore the environment explored by the artificial agents can contain stimuli that are safe or dangerous to pick. The simulated task is based on classical conditioning and the agents are asked to learn a strategy to recognize whether the environment is safe or represents a threat to their lives and select the correct action to perform in absence of any visual cues. The simulated agents have special input units in their neural structure whose activation keep track of their actual “sensations” based on the outcome of past behavior. We train five different neural network architectures and then test the best ranked individuals comparing their performances and analyzing the unit activations in each individual’s life cycle. We show that the agents, regardless of the presence of recurrent connections, spontaneously evolved the ability to cope with potentially dangerous environment by collecting information about the environment and then switching their behavior to a genetically selected pattern in order to maximize the possible reward. We also prove the determinant presence of an internal time perception unit for the robots to achieve the highest performance and survivability across all conditions. [ABSTRACT FROM AUTHOR]

Chaotic itinerancy is a phenomenon in which the state of a nonlinear dynamical system spontaneously explores and attracts certain states in a state space. From this perspective, the diverse behavior of animals and its spontaneous transitions lead to a complex coupled dynamical system, including a physical body and a brain. Herein, a series of simulations using different types of non-linear oscillator networks (i.e., regular, small-world, scale-free, random) with a musculoskeletal model (i.e., a snake-like robot) as a physical body are conducted to understand how the chaotic itinerancy of bodily behavior emerges from the coupled dynamics between the body and the brain. A behavior analysis (behavior clustering) and network analysis for the classified behavior are then applied. The former consists of feature vector extraction from the motions and classification of the movement patterns that emerged from the coupled dynamics. The network structures behind the classified movement patterns are revealed by estimating the “information networks” different from the given non-linear oscillator networks based on the transfer entropy which finds the information flow among neurons. The experimental results show that: (1) the number of movement patterns and their duration depend on the sensor ratio to control the balance of strength between the body and the brain dynamics and on the type of the given non-linear oscillator networks; and (2) two kinds of information networks are found behind two kinds movement patterns with different durations by utilizing the complex network measures, clustering coefficient and the shortest path length with a negative and a positive relationship with the duration periods of movement patterns. The current results seem promising for a future extension of the method to a more complicated body and environment. Several requirements are also discussed. [ABSTRACT FROM AUTHOR]

Eye movements provide insights into what people pay attention to, and therefore are commonly included in a variety of human-computer interaction studies. Eye movement recording devices (eye trackers) produce gaze trajectories, that is, sequences of gaze location on the screen. Despite recent technological developments that enabled more affordable hardware, gaze data are still costly and time consuming to collect, therefore some propose using mouse movements instead. These are easy to collect automatically and on a large scale. If and how these two movement types are linked, however, is less clear and highly debated. We address this problem in two ways. First, we introduce a new movement analytics methodology to quantify the level of dynamic interaction between the gaze and the mouse pointer on the screen. Our method uses volumetric representation of movement, the space-time densities, which allows us to calculate interaction levels between two physically different types of movement. We describe the method and compare the results with existing dynamic interaction methods from movement ecology. The sensitivity to method parameters is evaluated on simulated trajectories where we can control interaction levels. Second, we perform an experiment with eye and mouse tracking to generate real data with real levels of interaction, to apply and test our new methodology on a real case. Further, as our experiment tasks mimics route-tracing when using a map, it is more than a data collection exercise and it simultaneously allows us to investigate the actual connection between the eye and the mouse. We find that there seem to be natural coupling when eyes are not under conscious control, but that this coupling breaks down when instructed to move them intentionally. Based on these observations, we tentatively suggest that for natural tracing tasks, mouse tracking could potentially provide similar information as eye-tracking and therefore be used as a proxy for attention. However, more research is needed to confirm this. [ABSTRACT FROM AUTHOR]

High-frequency oscillations (HFO) have been suggested as biomarkers of epileptic tissues. While visual marking of these short and small oscillations is tedious and time-consuming, automatic HFO detectors have not yet met a large consensus. Even though detectors have been shown to perform well when validated against visual marking, the large number of false detections due to their lack of robustness hinder their clinical application. In this study, we developed a validation framework based on realistic and controlled simulations to quantify precisely the assets and weaknesses of current detectors. We constructed a dictionary of synthesized elements—HFOs and epileptic spikes—from different patients and brain areas by extracting these elements from the original data using discrete wavelet transform coefficients. These elements were then added to their corresponding simulated background activity (preserving patient- and region- specific spectra). We tested five existing detectors against this benchmark. Compared to other studies confronting detectors, we did not only ranked them according their performance but we investigated the reasons leading to these results. Our simulations, thanks to their realism and their variability, enabled us to highlight unreported issues of current detectors: (1) the lack of robust estimation of the background activity, (2) the underestimated impact of the 1/f spectrum, and (3) the inadequate criteria defining an HFO. We believe that our benchmark framework could be a valuable tool to translate HFOs into a clinical environment. [ABSTRACT FROM AUTHOR]

Background: Although some studies have suggested that transfusion recipients may have better medical outcomes if transfused with red blood cell units stored for a short time, the overall body of evidence shows mixed results. It is important to understand how using fresher stored red blood cell units for certain patient groups may affect blood availability. Methods: Based on the Stock-and-Flow simulation model of the US blood supply developed by Simonetti et al. 2014, we evaluated a newly implemented allocation method of preferentially transfusing fresher stored red blood cell units to a subset of high-risk group of critically ill patients and its potential impact on supply. Results: Simulation results showed that, depending on the scenario, the US blood total supply might be reduced between 2-42%, when compared to the standard of care in transfusion medicine practice. Among our simulated scenarios, we observed that the number of expired red blood cell units modulated the supply levels. The age threshold of the required red blood cell units was inversely correlated with both the supply levels and the number of transfused units that failed to meet that age threshold. Conclusion: To our knowledge, this study represents the first attempt to develop a comprehensive framework to evaluate the impact of preferentially transfusing fresher stored red blood cells to the higher-risk critically ill patients on supply. Model results show the difficulties to identify an optimal scenario. [ABSTRACT FROM AUTHOR]

Random Positioning Machines (RPMs) are widely used as tools to simulate microgravity on ground. They consist of two gimbal mounted frames, which constantly rotate biological samples around two perpendicular axes and thus distribute the Earth’s gravity vector in all directions over time. In recent years, the RPM is increasingly becoming appreciated as a laboratory instrument also in non-space-related research. For instance, it can be applied for the formation of scaffold-free spheroid cell clusters. The kinematic rotation of the RPM, however, does not only distribute the gravity vector in such a way that it averages to zero, but it also introduces local forces to the cell culture. These forces can be described by rigid body analysis. Although RPMs are commonly used in laboratories, the fluid motion in the cell culture flasks on the RPM and the possible effects of such on cells have not been examined until today; thus, such aspects have been widely neglected. In this study, we used a numerical approach to describe the fluid dynamic characteristic occurring inside a cell culture flask turning on an operating RPM. The simulations showed that the fluid motion within the cell culture flask never reached a steady state or neared a steady state condition. The fluid velocity depends on the rotational velocity of the RPM and is in the order of a few centimeters per second. The highest shear stresses are found along the flask walls; depending of the rotational velocity, they can reach up to a few 100 mPa. The shear stresses in the “bulk volume,” however, are always smaller, and their magnitude is in the order of 10 mPa. In conclusion, RPMs are highly appreciated as reliable tools in microgravity research. They have even started to become useful instruments in new research fields of mechanobiology. Depending on the experiment, the fluid dynamic on the RPM cannot be neglected and needs to be taken into consideration. The results presented in this study elucidate the fluid motion and provide insight into the convection and shear stresses that occur inside a cell culture flask during RPM experiments. [ABSTRACT FROM AUTHOR]

Supervised machine learning methods typically require splitting data into multiple chunks for training, validating, and finally testing classifiers. For finding the best parameters of a classifier, training and validation are usually carried out with cross-validation. This is followed by application of the classifier with optimized parameters to a separate test set for estimating the classifier’s generalization performance. With limited data, this separation of test data creates a difficult trade-off between having more statistical power in estimating generalization performance versus choosing better parameters and fitting a better model. We propose a novel approach that we term “Cross-validation and cross-testing” improving this trade-off by re-using test data without biasing classifier performance. The novel approach is validated using simulated data and electrophysiological recordings in humans and rodents. The results demonstrate that the approach has a higher probability of discovering significant results than the standard approach of cross-validation and testing, while maintaining the nominal alpha level. In contrast to nested cross-validation, which is maximally efficient in re-using data, the proposed approach additionally maintains the interpretability of individual parameters. Taken together, we suggest an addition to currently used machine learning approaches which may be particularly useful in cases where model weights do not require interpretation, but parameters do. [ABSTRACT FROM AUTHOR]

Magnetoencephalography (MEG) is a sophisticated tool which yields rich information on the spatial, spectral and temporal signatures of human brain function. Despite unique potential, MEG is limited by a low signal-to-noise ratio (SNR) which is caused by both the inherently small magnetic fields generated by the brain, and the scalp-to-sensor distance. The latter is limited in current systems due to a requirement for pickup coils to be cryogenically cooled. Recent work suggests that optically-pumped magnetometers (OPMs) might be a viable alternative to superconducting detectors for MEG measurement. They have the advantage that sensors can be brought to within ~4 mm of the scalp, thus offering increased sensitivity. Here, using simulations, we quantify the advantages of hypothetical OPM systems in terms of sensitivity, reconstruction accuracy and spatial resolution. Our results show that a multi-channel whole-head OPM system offers (on average) a fivefold improvement in sensitivity for an adult brain, as well as clear improvements in reconstruction accuracy and spatial resolution. However, we also show that such improvements depend critically on accurate forward models; indeed, the reconstruction accuracy of our simulated OPM system only outperformed that of a simulated superconducting system in cases where forward field error was less than 5%. Overall, our results imply that the realisation of a viable whole-head multi-channel OPM system could generate a step change in the utility of MEG as a means to assess brain electrophysiological activity in health and disease. However in practice, this will require both improved hardware and modelling algorithms. [ABSTRACT FROM AUTHOR]

We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as “sepsis”. Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-α ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies. [ABSTRACT FROM AUTHOR]

Electrical stimulation of the lateral hypothalamus can motivate feeding or can serve as a reward in its own right. It remains unclear whether the same or independent but anatomically overlapping circuitries mediate the two effects. Electrical stimulation findings implicate medial forebrain bundle (MFB) fibers of passage in both effects, and optogenetic studies confirm a contribution from fibers originating in the lateral hypothalamic area and projecting to or through the ventral tegmental area. Here we report that optogenetic activation of ventral tegmental fibers from cells of origin in more anterior or posterior portions of the MFB failed to induce either reward or feeding. The feeding and reward induced by optogenetic activation of fibers from the lateral hypothalamic cells of origin were influenced similarly by variations in stimulation pulse width and pulse frequency, consistent with the hypothesis of a common substrate for the two effects. There were, however, several cases where feeding but not self-stimulation or self-stimulation but not feeding were induced, consistent with the hypothesis that distinct but anatomically overlapping systems mediate the two effects. Thus while optogenetic stimulation provides a more selective tool for characterizing the mechanisms of stimulation-induced feeding and reward, it does not yet resolve the question of common or independent substrates. [ABSTRACT FROM AUTHOR]

During aging, systolic blood pressure continuously increases over time, whereas diastolic pressure first increases and then slightly decreases after middle age. These pressure changes are usually explained by changes of the arterial system alone (increase in arterial stiffness and vascular resistance). However, we hypothesise that the heart contributes to the age-related blood pressure progression as well. In the present study we quantified the blood pressure changes in normal aging by using a Windkessel model for the arterial system and the time-varying elastance model for the heart, and compared the simulation results with data from the Framingham Heart Study. Parameters representing arterial changes (resistance and stiffness) during aging were based on literature values, whereas parameters representing cardiac changes were computed through physiological rules (compensated hypertrophy and preservation of end-diastolic volume). When taking into account arterial changes only, the systolic and diastolic pressure did not agree well with the population data. Between 20 and 80 years, systolic pressure increased from 100 to 122 mmHg, and diastolic pressure decreased from 76 to 55 mmHg. When taking cardiac adaptations into account as well, systolic and diastolic pressure increased from 100 to 151 mmHg and decreased from 76 to 69 mmHg, respectively. Our results show that not only the arterial system, but also the heart, contributes to the changes in blood pressure during aging. The changes in arterial properties initiate a systolic pressure increase, which in turn initiates a cardiac remodelling process that further augments systolic pressure and mitigates the decrease in diastolic pressure. [ABSTRACT FROM AUTHOR]

Branch roads, which are densely distributed in cities, allow for the flow of local traffic and provide connections between the city and outlying areas. Branch roads are typically narrow, and two-way traffic flows on branch roads are thus affected when vehicles traveling in opposite directions meet. This study investigates the changes in the velocities of vehicles when they meet on two-way branch roads. Various widths of branch roads were selected, and their influence on traffic flows was investigated via a video survey. The results show that, depending on the average vehicle velocity, branch roads require different widths to prevent a large decrease in velocity when vehicles meet. When the velocity on a branch road is not high (e.g., the average velocity without meeting is approximately 6 m/s), appropriately increasing the road width will notably increase the meeting velocity. However, when the velocity is high (e.g., the average velocity without meeting is greater than 10 m/s), there is a large decrease in velocity when meeting even if the road surface is wide (6.5 m). This study provides a basis for selecting the width of urban branch roads and the simulation of bidirectional traffic on such roads. [ABSTRACT FROM AUTHOR]

Introduction: In the human placenta the maternal blood circulates in the intervillous space (IVS). The syncytiotrophoblast (STB) is in direct contact with maternal blood. The wall shear stress (WSS) exerted by the maternal blood flow on the STB has not been evaluated. Our objective was to determine the physiological WSS exerted on the surface of the STB during the third trimester of pregnancy. Material and Methods: To gain insight into the shear stress levels that the STB is expected to experience in vivo, we have formulated three different computational models of varying levels of complexity that reflect different physical representations of the IVS. Computations of the flow fields in all models were performed using the CFD module of the finite element code COMSOL Multiphysics 4.4. The mean velocity of maternal blood in the IVS during the third trimester was measured in vivo with dynamic MRI (0.94±0.14 mm.s-1). To investigate if the in silico results are consistent with physiological observations, we studied the cytoadhesion of human parasitized (Plasmodium falciparum) erythrocytes to primary human STB cultures, in flow conditions with different WSS values. Results: The WSS applied to the STB is highly heterogeneous in the IVS. The estimated average values are relatively low (0.5±0.2 to 2.3±1.1 dyn.cm-2). The increase of WSS from 0.15 to 5 dyn.cm-2 was associated with a significant decrease of infected erythrocyte cytoadhesion. No cytoadhesion of infected erythrocytes was observed above 5 dyn.cm-2 applied for one hour. Conclusion: Our study provides for the first time a WSS estimation in the maternal placental circulation. In spite of high maternal blood flow rates, the average WSS applied at the surface of the chorionic villi is low (<5 dyn.cm-2). These results provide the basis for future physiologically-relevant in vitro studies of the biological effects of WSS on the STB. [ABSTRACT FROM AUTHOR]

Background: The cam deformity causes the anterosuperior femoral head to obstruct with the acetabulum, resulting in femoroacetabular impingement (FAI) and elevated risks of early osteoarthritis. Several finite element models have simulated adverse loading conditions due to cam FAI, to better understand the relationship between mechanical stresses and cartilage degeneration. Our purpose was to conduct a systematic review and examine the previous finite element models and simulations that examined hip joint stresses due to cam FAI. Methods: The systematic review was conducted to identify those finite element studies of cam-type FAI. The review conformed to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and studies that reported hip joint contact pressures or stresses were included in the quantitative synthesis. Results: Nine articles studied FAI morphologies using finite element methods and were included in the qualitative synthesis. Four articles specifically examined contact pressures and stresses due to cam FAI and were included in the quantitative synthesis. The studies demonstrated that cam FAI resulted in substantially elevated contact pressures (median = 10.4 MPa, range = 8.5–12.2 MPa) and von Mises stresses (median 15.5 MPa, range = 15.0–16.0 MPa) at the acetabular cartilage; and elevated maximum-shear stress on the bone (median = 15.2 MPa, range = 14.3–16.0 MPa), in comparison with control hips, during large amplitudes of hip motions. Many studies implemented or adapted idealized, ball-and-cup, parametric models to predict stresses, along with homogeneous bone material properties and in vivo instrumented prostheses loading data. Conclusion: The formulation of a robust subject-specific FE model, to delineate the pathomechanisms of FAI, remains an ongoing challenge. The available literature provides clear insight into the estimated stresses due to the cam deformity and provides an assessment of its risks leading to early joint degeneration. [ABSTRACT FROM AUTHOR]

Aim: We studied various hemodialysis strategies for the removal of protein-bound solutes, which are associated with cardiovascular damage. Methods: This study included 10 patients on standard (3x4h/week) high-flux hemodialysis. Blood was collected at the dialyzer inlet and outlet at several time points during a midweek session. Total and free concentration of several protein-bound solutes was determined as well as urea concentration. Per solute, a two-compartment kinetic model was fitted to the measured concentrations, estimating plasmatic volume (V1), total distribution volume (Vtot) and intercompartment clearance (K21). This calibrated model was then used to calculate which hemodialysis strategy offers optimal removal. Our own in vivo data, with the strategy variables entered into the mathematical simulations, was then validated against independent data from two other clinical studies. Results: Dialyzer clearance K, V1 and Vtot correlated inversely with percentage of protein binding. All Ks were different from each other. Of all protein-bound solutes, K21was 2.7–5.3 times lower than that of urea. Longer and/or more frequent dialysis that processed the same amount of blood per week as standard 3x4h dialysis at 300mL/min blood flow showed no difference in removal of strongly bound solutes. However, longer and/or more frequent dialysis strategies that processed more blood per week than standard dialysis were markedly more adequate. These conclusions were successfully validated. Conclusion: When blood and dialysate flow per unit of time and type of hemodialyzer are kept the same, increasing the amount of processed blood per week by increasing frequency and/or duration of the sessions distinctly increases removal. [ABSTRACT FROM AUTHOR]

Background: Recent clinical studies have shown that recanalization rates are lower in stent-assisted coil embolization than in coiling alone in the treatment of cerebral aneurysms. Objective: This study aimed to assess and compare the hemodynamic effect of stent struts and straightening of vessels by stent placement on reducing flow velocity in sidewall aneurysms, with the goal of reducing recanalization rates. Methods: We evaluated 16 sidewall aneurysms treated with Enterprise stents. We performed computational fluid dynamics simulations using patient-specific geometries before and after treatment, with or without stent struts. Results: Stent placement straightened vessels by a mean (±standard deviation) of 12.9°±13.1° 6 months after treatment. Placement of stent struts in the initial vessel geometries reduced flow velocity in aneurysms by 23.1%±6.3%. Straightening of vessels without stent struts reduced flow velocity by 9.6%±12.6%. Stent struts had significantly stronger effects on reducing flow velocity than straightening (P = 0.004, Wilcoxon test). Deviation of the effects was larger by straightening than by stent struts (P = 0.01, F-test). The combination of stent struts and straightening reduced flow velocity by 32.6%±12.2%. There was a trend that larger inflow angles produced a larger reduction in flow velocity by straightening of vessels (P = 0.16). Conclusion: In sidewall aneurysms, stent struts have stronger effects (approximately 2 times) on reduction in flow velocity than straightening of vessels. Hemodynamic effects by straightening vary in each case and can be predicted by inflow angles of pre-operative vessel geometry. These results may be useful to design a treatment strategy for reducing recanalization rates. [ABSTRACT FROM AUTHOR]

Background: Heart failure is operationally defined as the inability of the heart to maintain blood flow to meet the needs of the body and it is the final common pathway of various cardiac pathologies. Electrophysiological remodeling, intercellular uncoupling and a pro-fibrotic response have been identified as major arrhythmogenic factors in heart failure. Objective: In this study we investigate vulnerability to reentry under heart failure conditions by incorporating established electrophysiological and anatomical remodeling using computer simulations. Methods: The electrical activity of human transmural ventricular tissue (5 cm×5 cm) was simulated using the human ventricular action potential model Grandi et al. under control and heart failure conditions. The MacCannell et al. model was used to model fibroblast electrical activity, and their electrotonic interactions with myocytes. Selected degrees of diffuse fibrosis and variations in intercellular coupling were considered and the vulnerable window (VW) for reentry was evaluated following cross-field stimulation. Results: No reentry was observed in normal conditions or in the presence of HF ionic remodeling. However, defined amount of fibrosis and/or cellular uncoupling were sufficient to elicit reentrant activity. Under conditions where reentry was generated, HF electrophysiological remodeling did not alter the width of the VW. However, intermediate fibrosis and cellular uncoupling significantly widened the VW. In addition, biphasic behavior was observed, as very high fibrotic content or very low tissue conductivity hampered the development of reentry. Detailed phase analysis of reentry dynamics revealed an increase of phase singularities with progressive fibrotic components. Conclusion: Structural remodeling is a key factor in the genesis of vulnerability to reentry. A range of intermediate levels of fibrosis and intercellular uncoupling can combine to favor reentrant activity. [ABSTRACT FROM AUTHOR]

Background: To elucidate further from the biomechanical aspect whether microgravity-induced cerebral vascular mal-adaptation might be a contributing factor to postflight orthostatic intolerance and the underlying mechanism accounting for the potential effectiveness of intermittent artificial gravity (IAG) in preventing this adverse effect. Methodology/Principal Findings: Middle cerebral arteries (MCAs) were isolated from 28-day SUS (tail-suspended, head-down tilt rats to simulate microgravity effect), S+D (SUS plus 1-h/d −Gx gravitation by normal standing to simulate IAG), and CON (control) rats. Vascular myogenic reactivity and circumferential stress-strain and axial force-pressure relationships and overall stiffness were examined using pressure arteriography and calculated. Acellular matrix components were quantified by electron microscopy. The results demonstrate that myogenic reactivity is susceptible to previous pressure-induced, serial constrictions. During the first-run of pressure increments, active MCAs from SUS rats can strongly stiffen their wall and maintain the vessels at very low strains, which can be prevented by the simulated IAG countermeasure. The strains are 0.03 and 0.14 respectively for SUS and S+D, while circumferential stress being kept at 0.5 (106 dyn/cm2). During the second-run pressure steps, both the myogenic reactivity and active stiffness of the three groups declined. The distensibility of passive MCAs from S+D is significantly higher than CON and SUS, which may help to attenuate the vasodilatation impairment at low levels of pressure. Collagen and elastin percentages were increased and decreased, respectively, in MCAs from SUS and S+D as compared with CON; however, elastin was higher in S+D than SUS rats. Conclusions: Susceptibility to previous myogenic constrictions seems to be a self-limiting protective mechanism in cerebral small resistance arteries to prevent undue cerebral vasoconstriction during orthostasis at 1-G environment. Alleviating of active stiffening and increasing of distensibility of cerebral resistance arteries may underlie the countermeasure effectiveness of IAG. [ABSTRACT FROM AUTHOR]

Motion simulators are widely employed in basic and applied research to study the neural mechanisms of perception and action during inertial stimulation. In these studies, uncontrolled simulator-introduced noise inevitably leads to a disparity between the reproduced motion and the trajectories meticulously designed by the experimenter, possibly resulting in undesired motion cues to the investigated system. Understanding actual simulator responses to different motion commands is therefore a crucial yet often underestimated step towards the interpretation of experimental results. In this work, we developed analysis methods based on signal processing techniques to quantify the noise in the actual motion, and its deterministic and stochastic components. Our methods allow comparisons between commanded and actual motion as well as between different actual motion profiles. A specific practical example from one of our studies is used to illustrate the methodologies and their relevance, but this does not detract from its general applicability. Analyses of the simulator’s inertial recordings show direction-dependent noise and nonlinearity related to the command amplitude. The Signal-to-Noise Ratio is one order of magnitude higher for the larger motion amplitudes we tested, compared to the smaller motion amplitudes. Simulator-introduced noise is found to be primarily of deterministic nature, particularly for the stronger motion intensities. The effect of simulator noise on quantification of animal/human motion sensitivity is discussed. We conclude that accurate recording and characterization of executed simulator motion are a crucial prerequisite for the investigation of uncertainty in self-motion perception. [ABSTRACT FROM AUTHOR]

Purpose: While animal models are widely used to investigate the development of restenosis in blood vessels following an intervention, computational models offer another means for investigating this phenomenon. A computational model of the response of a treated vessel would allow investigators to assess the effects of altering certain vessel- and stent-related variables. The authors aimed to develop a novel computational model of restenosis development following an angioplasty and bare-metal stent implantation in an atherosclerotic vessel using agent-based modeling techniques. The presented model is intended to demonstrate the body’s response to the intervention and to explore how different vessel geometries or stent arrangements may affect restenosis development. Methods: The model was created on a two-dimensional grid space. It utilizes the post-procedural vessel lumen diameter and stent information as its input parameters. The simulation starting point of the model is an atherosclerotic vessel after an angioplasty and stent implantation procedure. The model subsequently generates the final lumen diameter, percent change in lumen cross-sectional area, time to lumen diameter stabilization, and local concentrations of inflammatory cytokines upon simulation completion. Simulation results were directly compared with the results from serial imaging studies and cytokine levels studies in atherosclerotic patients from the relevant literature. Results: The final lumen diameter results were all within one standard deviation of the mean lumen diameters reported in the comparison studies. The overlapping-stent simulations yielded results that matched published trends. The cytokine levels remained within the range of physiological levels throughout the simulations. Conclusion: We developed a novel computational model that successfully simulated the development of restenosis in a blood vessel following an angioplasty and bare-metal stent deployment based on the characteristics of the vessel cross-section and stent. A further development of this model could ultimately be used as a predictive tool to depict patient outcomes and inform treatment options. [ABSTRACT FROM AUTHOR]

We employed a novel cuing paradigm to assess whether dynamically versus statically presented facial expressions differentially engaged predictive visual mechanisms. Participants were presented with a cueing stimulus that was either the static depiction of a low intensity expressed emotion; or a dynamic sequence evolving from a neutral expression to the low intensity expressed emotion. Following this cue and a backwards mask, participants were presented with a probe face that displayed either the same emotion (congruent) or a different emotion (incongruent) with respect to that displayed by the cue although expressed at a high intensity. The probe face had either the same or different identity from the cued face. The participants' task was to indicate whether or not the probe face showed the same emotion as the cue. Dynamic cues and same identity cues both led to a greater tendency towards congruent responding, although these factors did not interact. Facial motion also led to faster responding when the probe face was emotionally congruent to the cue. We interpret these results as indicating that dynamic facial displays preferentially invoke predictive visual mechanisms, and suggest that motoric simulation may provide an important basis for the generation of predictions in the visual system. [ABSTRACT FROM AUTHOR]