Notes

A new mechanistic along with data-driven reconstruction with the time-varying imitation amount: Software towards the COVID-19 pandemic.
We propose a procedure for modeling a phenotype using QTLs which estimate the additive and dominance effects of genotypes and epistasis. The estimation of the model is implemented through a Bayesian approach which uses the data-driven reversible jump (DDRJ) for multiple QTL mapping and model selection. We compare the DDRJ's performance with the usual reversible jump (RJ), QTLBim, multiple interval mapping (MIM) and LASSO using real and simulated data sets. The DDRJ outperforms the available methods to estimate the number of QTLs in epistatic models and it identifies their locations in the genome, without increasing the number of false-positive QTLs in the considered data. Since QTL mapping is a regression model involving complex non-observable variables and their interactions, the model selection procedure proposed here is also useful in other areas of research. The application for identifying main and epistatic relevant QTLs to systolic blood pressure after salt intervention is our main motivation.Deterministic asynchronous Boolean networks play a crucial role in modeling and analysis of gene regulatory networks. In this paper, we focus on a typical type of deterministic asynchronous Boolean networks called deterministic generalized asynchronous random Boolean networks (DGARBNs). We first formulate the extended state transition graph, which captures the whole dynamics of a DGARBN and paves potential ways to analyze this DGARBN. We then propose two SMT-based methods for attractor detection and optimal control of DGARBNs. These methods are implemented in a JAVA tool called DABoolNet. Two experiments are designed to highlight the scalability of the proposed methods. We also formally state and prove several relations between DGARBNs and other models including deterministic asynchronous models, block-sequential Boolean networks, generalized asynchronous random Boolean networks, and mixed-context random Boolean networks. Several case studies are presented to show the applications of our methods.
To clarify whether there are any muscle synergy changes in individuals with knee osteoarthritis, and to determine whether muscle synergy analysis could be applied to other musculoskeletal diseases.

Subjects in this study included 11 young controls (YC), 10 elderly controls (EC), and 10 knee osteoarthritis patients (KOA). Gait was assessed on a split-belt treadmill at 3 km/h. A non-negative matrix factorization (NNMF) was applied to the electromyogram data matrix to extract muscle synergies. To assess the similarity of each module, we performed the NNMF analysis assuming four modules for all of the participants. Further, we calculated joint angles to compare the kinematic data between the module groups.

The number of muscle modules was significantly lower in the EC (2-3) and KOA (2-3) groups than in the YC group (3-4), which reflects the merging of late swing and early stance modules. The EC and KOA groups also showed greater knee flexion angles in the early stance phase. Contrarily, by focusing on the module structure, we found that the merging of early and late stance modules is characteristic in KOA.

The lower number of modules in the EC and KOA groups was due to the muscle co-contraction with increased knee flexion angle. Contrarily, the merging of early and late stance modules are modular structures specific to KOA and may be biomarkers for detecting KOA.

Describing the changes in multiple muscle control associated with musculoskeletal degeneration can serve as a fundamental biomarker in joint disease.
Describing the changes in multiple muscle control associated with musculoskeletal degeneration can serve as a fundamental biomarker in joint disease.The thermal effect of a novel effective electrical stimulation mapping (ESM) technique using an Ojemann's stimulation electrode in open craniotomy areas causes a nondestructive local increase in temperature. Another type of stimulating electrode is a subdural strip, routinely used in intraoperative electrocorticography (ECoG), which applies ESM in a covered subdural area over the motor cortex. ECoG electrode geometry produces a different electrical field, causing a different Joule heat distribution in tissue, one that is impossible to measure in subdural space. Therefore, the previous safety control study of the novel ESM technique needed to be extended to include an assessment of the thermal effect of ECoG strip electrodes. C75 manufacturer We adapted a previously well-validated numerical model and performed coupled complex electro-thermal transient simulations for short-time (28.4 ms) high-frequency (500 Hz) and hyperintense (peak 100 mA) ESM paradigm. The risk of heat-induced cellular damage was assessed by applying the Arrhenius equation integral on the computed time-dependent spatial distribution of temperature in the brain tissue during ESM stimulation and during the cooldown period. The results showed increases in temperature in the proximity around ECoG electrode discs in a safe range without destructive effects. As opposed to open craniotomy, subdural space is not cooled by the air; hence a higher - but still safe - induced temperature was observed. The presented simulation agrees with the previously published histopathological examination of the stimulated brain tissue, and confirms the safety of the novel ESM technique when applied using ECoG strip electrodes.Node-link diagrams are widely used to visualise networks. However, even the best network layout algorithms ultimately result in 'hairball' visualisations when the graph reaches a certain degree of complexity, requiring simplification through aggregation or interaction (such as filtering) to remain usable. Until now, there has been little data to indicate at what level of complexity node-link diagrams become ineffective or how visual complexity affects cognitive load. To this end, we conducted a controlled study to understand workload limits for a task that requires a detailed understanding of the network topology-finding the shortest path between two nodes. We tested performance on graphs with 25 to 175 nodes with varying density. We collected performance measures (accuracy and response time), subjective feedback, and physiological measures (EEG, pupil dilation, and heart rate variability). To the best of our knowledge this is the first network visualisation study to include physiological measures. Our results show that people have significant difficulty finding the shortest path in high density node-link diagrams with more than 50 nodes and even low density graphs with more than 100 nodes. From our collected EEG data we observe functional differences in brain activity between hard and easy tasks. We found that cognitive load increased up to certain level of difficulty after which it decreased, likely because participants had given up. We also explored the effects of global network layout features such as size or number of crossings, and features of the shortest path such as length or straightness on task difficulty. We found that global features generally had a greater impact than those of the shortest path.Plane-wave compounding is an active topic of research in ultrasound imaging because it is a promising technique for ultrafast ultrasound imaging. Unfortunately, due to the data-independent nature of the traditional compounding method, it imposes a fundamental limit on image quality. To address this issue, adaptive beamformers have been implemented in the compounding procedure. In this article, a new adaptive beamformer for the 2-D data set obtained from multiple plane-wave transmissions is investigated. In the proposed scheme, the minimum variance (MV) weights are applied to the backscattered echoes. Then, the final image is obtained by employing a modified version of the delay multiply-and-sum (DMAS) beamformer in the coherent compounding. The results demonstrate that the presented MV-DMAS scheme outperforms the conventional coherent compounding in both terms of resolution and contrast. It also offers improvements over the 2-D-DMAS and some MV-based methods presented in the literature, such that it achieves at least 20.9% enhancement in sidelobe reduction compared with the best result of MV-based methods. Also, by the proposed method, the in vivo study shows an improved generalized contrast-to-noise ratio (GCNR) that implies a higher probability of lesion detection.Multi-scale representations deeply learned via convolutional neural networks have shown tremendous importance for various pixel-level prediction problems. In this paper we present a novel approach that advances the state of the art on pixel-level prediction in a fundamental aspect,i.e.structured multi-scale features learning and fusion. In contrast to previous works directly considering multi-scale feature maps obtained from the inner layers of a primary CNN architecture, and simply fusing the features with weighted averaging or concatenation, we propose a probabilistic graph attention network structure based on a novel Attention-Gated Conditional Random Fields(AG-CRFs) model for learning and fusing multi-scale representations in a principled manner. In order to further improve the learning capacity of the network structure, we propose to exploit feature dependant conditional kernels within the deep probabilistic framework. Extensive experiments are conducted on four publicly available datasets (i.e.BSDS500, NYUD-V2, KITTI and Pascal-Context) and on three challenging pixel-wise prediction problems involving both discrete and continuous labels (i.e.monocular depth estimation, object contour prediction and semantic segmentation). Quantitative and qualitative results demonstrate the effectiveness of the proposed latentAG-CRF model and the overall probabilistic graph attention network with feature conditional kernels for structured feature learning and pixel-wise prediction.Non-rigid point set registration is the process of transforming a shape represented as a point set into a shape matching another shape. In this paper, we propose an acceleration method for solving non-rigid point set registration problems. We accelerate non-rigid registration by dividing it into three steps i) downsampling of point sets, ii) non-rigid registration of downsampled point sets, and iii) interpolation of shape deformation vectors corresponding to points removed during downsampling. To register downsampled point sets, we use a registration algorithm based on a prior distribution, called motion coherence prior. Using the same prior, we derive an interpolation method interpreted as Gaussian process regression. Through numerical experiments, we demonstrate that our algorithm registers point sets containing over ten million points. We also show that our algorithm reduces computing time more radically than a state-of-the-art acceleration algorithm.The generator in Generative Adversarial Networks (GANs) is driven by a discriminator to produce high-quality images through an adversarial game. At the same time, the difficulty of reaching a stable generator has been increased. This paper focuses on non-adversarial generative networks that are trained in a plain manner without adversarial loss. The given limited number of real images could be insufficient to fully represent the real data distribution. We therefore investigate a set of distributions in a Wasserstein ball centred on the distribution induced by the training data and propose to optimize the generator over this Wasserstein ball. We theoretically discuss the solvability of the newly defined objective function and develop a tractable reformulation to learn the generator. The connections and differences between the proposed non-adversarial generative networks and GANs are analyzed. Experimental results on real-world datasets demonstrate that the proposed algorithm can effectively learn image generators in a non-adversarial approach, and the generated images are of comparable quality with those from GANs.
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