When shared concept cells support associations: Theory of overlapping memory engrams

Assemblies of neurons, called concepts cells, encode acquired concepts in human Medial Temporal Lobe. Those concept cells that are shared between two assemblies have been hypothesized to encode associations between concepts. Here we test this hypothesis in a computational model of attractor neural networks. We find that for concepts encoded in sparse neural assemblies there is a minimal fraction cmin of neurons shared between assemblies below which associations cannot be reliably implemented; and a maximal fraction cmax of shared neurons above which single concepts can no longer be retrieved. In the presence of a periodically modulated background signal, such as hippocampal oscillations, recall takes the form of association chains reminiscent of those postulated by theories of free recall of words. Predictions of an iterative overlap-generating model match experimental data on the number of concepts to which a neuron responds.

Multi-Domain Dynamic Modelling of a Low-Cost Upper Limb Rehabilitation Robot

Tracking patient progress through a course of robotic tele-rehabilitation requires constant position data logging and comparison, alongside periodic testing with no powered assistance. The test data must be compared with previous test attempts and an ideal baseline, for which a good understanding of the dynamics of the robot is required. The traditional dynamic modelling techniques for serial chain robotics, which involve forming and solving equations of motion, do not adequately describe the multi-domain phenomena that affect the movement of the rehabilitation robot. In this study, a multi-domain dynamic model for an upper limb rehabilitation robot is described. The model, built using a combination of MATLAB, SimScape, and SimScape Multibody, comprises the mechanical electro-mechanical and control domains. The performance of the model was validated against the performance of the robot when unloaded and when loaded with a human arm proxy. It is shown that this combination of software is appropriate for building a dynamic model of the robot and provides advantages over the traditional modelling approach. It is demonstrated that the responses of the model match the responses of the robot with acceptable accuracy, though the inability to model backlash was a limitation.

Mathematical Multiobjective Optimization for Metal Hip Arthroplasty with Medical Physics Applications

Total hip metal arthroplasty (THA) model-parameters for a group of commonly used ones is optimized and numerically studied. Based on previous ceramic THA optimization software contributions, an improved multiobjective programming method/algorithm is implemented in wear modeling for THA. This computational nonlinear multifunctional optimization is performed with a number of THA metals with different hardnesses and erosion in vitro experimental rates. The new software was created/designed with two types of Sytems, Matlab and GNU Octave. Numerical results show be improved/acceptable for in vitro simulations. These findings are verified with 2D Graphical Optimization and 3D Interior Optimization methods, giving low residual-norms. The solutions for the model match mostly the literature in vitro standards for experimental simulations. Numerical figures for multifunctional optimization give acceptable model-parameter values with low residual-norms. Useful mathematical consequences/calculations are obtained for wear predictions, model advancements and simulation methodology. The wear magnitude for in vitro determinations with these model parameter data constitutes the advance of the method. In consequence, the erosion prediction for laboratory experimental testing in THA add up to the literature an efficacious usage-improvement. Results, additionally, are extrapolated to efficient Medical Physics applications and metal-THA Bioengineering designs.

The Paradox of the Plankton: Coexistence of Structured Microbial Communities

In the framework of resource-competition models, it has been argued that the number of species stably coexisting in an ecosystem cannot exceed the number of shared resources. However, plankton seems to be an exception of this so-called "competitive-exclusion principle". In planktic ecosystems, a large number of different species stably coexist in an environment with limited resources. This contradiction between theoretical expectations and empirical observations is often referred to as "The Paradox of the Plankton". This project aims to investigate biophysical models that can account for the large biodiversity observed in real ecosystems in order to resolve this paradox. A model is proposed that combines classical resource competition models, metabolic trade-offs and stochastic ecosystem assembly. Simulations of the model match empirical observations, while relaxing some unrealistic assumptions from previous models.

Collective Cell Migration in a Fibrous Environment: A Hybrid Multiscale Modelling Approach

The specific structure of the extracellular matrix (ECM), and in particular the density and orientation of collagen fibres, plays an important role in the evolution of solid cancers. While many experimental studies discussed the role of ECM in individual and collective cell migration, there are still unanswered questions about the impact of nonlocal cell sensing of other cells on the overall shape of tumour aggregation and its migration type. There are also unanswered questions about the migration and spread of tumour that arises at the boundary between different tissues with different collagen fibre orientations. To address these questions, in this study we develop a hybrid multi-scale model that considers the cells as individual entities and ECM as a continuous field. The numerical simulations obtained through this model match experimental observations, confirming that tumour aggregations are not moving if the ECM fibres are distributed randomly, and they only move when the ECM fibres are highly aligned. Moreover, the stationary tumour aggregations can have circular shapes or irregular shapes (with finger-like protrusions), while the moving tumour aggregations have elongate shapes (resembling to clusters, strands or files). We also show that the cell sensing radius impacts tumour shape only when there is a low ratio of fibre to non-fibre ECM components. Finally, we investigate the impact of different ECM fibre orientations corresponding to different tissues, on the overall tumour invasion of these neighbouring tissues.

Design and analysis of a novel AFPM with counter-rotation dual rotors based on non-linear magnetic circuit model

This paper presents a nonlinear iterative magnetic equivalent circuit (MEC) model for a novel counter-rotation dual-rotor axial flux permanent magnet synchronous machine (CRDR-AFPMSM). The proposed machine mainly consists of two rotors with opposite rotation directions, two sets of concentrated windings and a stator core sandwiched in between the two rotors. The model takes into account of the nonlinear characteristics of the saturable permeance in the stator core, and the permeance matrix is updated by an iterative procedure to accurately illustrate its nonlinear feature. The air gap flux density, back electromotive force (EMF) and torque are predicted by the model. Based on the nonlinear model, the thickness of the stator yoke is determined. All of the results obtained by the proposed model match with finite element analysis (FEA) results closely, thus the validity of the proposed MEC model is verified.

Evaluation of aerosol optical depths and clear-sky radiative fluxes of the CERES Edition 4.1 SYN1deg data product

Aerosol optical depths (AOD) used for the Edition 4.1 Clouds and the Earth’s Radiant Energy System (CERES) Synoptic (SYN1deg) are evaluated. AODs are derived from Moderate Resolution Imaging Spectroradiometer (MODIS) observations and assimilated by an aerosol transport model (MATCH). As a consequence, clear-sky AODs closely match with those derived from MODIS instruments. AODs under all-sky conditions are larger than AODs under clear-sky conditions, which is supported by ground-based AERONET observations. When all-sky MATCH AODs are compared with Modern-Era Retrospective Analysis for Research and Applications (MERRA2) AODs, MATCH AODs are generally larger than MERRA2 AODS especially over convective regions (e.g. Amazon, central Africa, and eastern Asia). The difference is largely caused by MODIS AODs used for assimilation. Including AODs with larger retrieval uncertainty makes AODs over the convective regions larger. When AODs are used for clear-sky irradiance computations and computed downward shortwave irradiances are compared with ground- based observations, the computed instantaneous irradiances are 1 % to 2 % larger than observed irradiances. The comparison of top-of-atmosphere clear-sky irradiances with those derived from CERES observations suggests that AODs used for surface radiation observation sites are larger by 0.01 to 0.03, which is within the uncertainty of instantaneous MODIS AODs. However, the comparison with AERONET AOD suggests AODs used for computations over desert sites are 0.08 larger. The cause of positive biases of downward shortwave irradiance and AODs for the desert sites are unknown.

A marker registration method to improve joint angles computed by constrained inverse kinematics

Accurate computation of joint angles from optical marker data using inverse kinematics methods requires that the locations of markers on a model match the locations of experimental markers on participants. Marker registration is the process of positioning the model markers so that they match the locations of the experimental markers. Markers are typically registered using a graphical user interface (GUI), but this method is subjective and may introduce errors and uncertainty to the calculated joint angles and moments. In this investigation, we use OpenSim to isolate and quantify marker registration–based error from other sources of error by analyzing the gait of a bipedal humanoid robot for which segment geometry, mass properties, and joint angles are known. We then propose a marker registration method that is informed by the orientation of anatomical reference frames derived from surface-mounted optical markers as an alternative to user registration using a GUI. The proposed orientation registration method reduced the average root-mean-square error in both joint angles and joint moments by 67% compared to the user registration method, and eliminated variability among users. Our results show that a systematic method for marker registration that reduces subjective user input can make marker registration more accurate and repeatable.

When shared concept cells support associations: theory of overlapping memory engrams

Assemblies of neurons, called concepts cells, encode acquired concepts in human Medial Temporal Lobe. Those concept cells that are shared between two assemblies have been hypothesized to encode associations between concepts. Here we test this hypothesis in a computational model of attractor neural networks. We find that for concepts encoded in sparse neural assemblies there is a minimal fraction cmin of neurons shared between assemblies below which associations cannot be reliably implemented; and a maximal fraction cmax of shared neurons above which single concepts can no longer be retrieved. In the presence of a periodically modulated background signal, such as hippocampal oscillations, recall takes the form of association chains reminiscent of those postulated by theories of free recall of words. Predictions of an iterative overlap-generating model match experimental data on the number of concepts to which a neuron responds.Authors contributionsAll authors contributed to conception of the study and writing of the manuscript. CG and TS developed the theory. CG wrote the code for all figures. EDF and RQQ provided the experimental data. EDF and CG analyzed the data. WG and CG developed algorithms to fit the experimental data.

Mako: a graph-based pattern growth approach to detect complex structural variants

Complex structural variants (CSVs) are genomic alterations that have more than two breakpoints and are considered as simultaneous occurrence of simple structural variants. However, detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy. As a result, there has been limited progress for CSV discovery compared with simple structural variants. We systematically analyzed the multi-breakpoint connection feature of CSVs, and proposed Mako, utilizing a bottom-up guided model-free strategy, to detect CSVs from paired-end short-read sequencing. Specifically, we implemented a graph-based pattern growth approach, where the graph depicts potential breakpoint connections and pattern growth enables CSV detection without predefined models. Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms. Notably, validation rates of CSV on real data based on experimental and computational validations as well as manual inspections are around 70%, where the medians of experimental and computational breakpoint shift are 13bp and 26bp, respectively. Moreover, Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types, including two novel types of adjacent segments swap and tandem dispersed duplication. Further analysis of these CSVs also revealed impact of sequence homology in the formation of CSVs. Mako is publicly available at https://github.com/jiadong324/Mako.