Dynamics on the manifold: Identifying computational dynamical activity from neural population recordings

The question of how the collective activity of neural populations gives rise to complex behaviour is fundamental to neuroscience. At the core of this question lie considerations about how neural circuits can perform computations that enable sensory perception, decision making, and motor control. It is thought that such computations are implemented through the dynamical evolution of distributed activity in recurrent circuits. Thus, identifying dynamical structure in neural population activity is a key challenge towards a better understanding of neural computation. At the same time, interpreting this structure in light of the computation of interest is essential for linking the time-varying activity patterns of the neural population to ongoing computational processes. Here, we review methods that aim to quantify structure in neural population recordings through a dynamical system defined in a low-dimensional latent variable space. We discuss advantages and limitations of different modelling approaches and address future challenges for the field

Cube law, condition factor and weight-length relationships: history, meta-analysis and recommendations

This study presents a historical review, a meta-analysis, and recommendations for users about weight–length relationships, condition factors and relative weight equations. The historical review traces the developments of the respective concepts. The meta-analysis explores 3929 weight–length relationships of the type W = aLb for 1773 species of fishes. It shows that 82% of the variance in a plot of log a over b can be explained by allometric versus isometric growth patterns and by different body shapes of the respective species. Across species median b = 3.03 is significantly larger than 3.0, thus indicating a tendency towards slightly positive-allometric growth (increase in relative body thickness or plumpness) in most fishes. The expected range of 2.5 < b < 3.5 is confirmed. Mean estimates of b outside this range are often based on only one or two weight–length relationships per species. However, true cases of strong allometric growth do exist and three examples are given. Within species, a plot of log a vs b can be used to detect outliers in weight–length relationships. An equation to calculate mean condition factors from weight–length relationships is given as Kmean = 100aLb−3. Relative weight Wrm = 100W/(amLbm) can be used for comparing the condition of individuals across populations, where am is the geometric mean of a and bm is the mean of b across all available weight–length relationships for a given species. Twelve recommendations for proper use and presentation of weight–length relationships, condition factors and relative weight are given

Endothelial loss of Fzd5 stimulates PKC/Ets1-mediated transcription of Angpt2 and Flt1

Aims: Formation of a functional vascular system is essential and its formation is a highly regulated process initiated during embryogenesis, which continues to play important roles throughout life in both health and disease. In previous studies, Fzd5 was shown to be critically involved in this process and here we investigated the molecular mechanism by which endothelial loss of this receptor attenuates angiogenesis. Methods and results: Using short interference RNA-mediated loss-of-function assays, the function and mechanism of signaling via Fzd5 was studied in human endothelial cells (ECs). Our findings indicate that Fzd5 signaling promotes neovessel formation in vitro in a collagen matrix-based 3D co-culture of primary vascular cells. Silencing of Fzd5 reduced EC proliferation, as a result of G0/G1 cell cycle arrest, and decreased cell migration. Furthermore, Fzd5 knockdown resulted in enhanced expression of the factors Angpt2 and Flt1, which are mainly known for their destabilizing effects on the vasculature. In Fzd5-silenced ECs, Angpt2 and Flt1 upregulation was induced by enhanced PKC signaling, without the involvement of canonical Wnt signaling, non-canonical Wnt/Ca2+-mediated activation of NFAT, and non-canonical Wnt/PCP-mediated activation of JNK. We demonstrated that PKC-induced transcription of Angpt2 and Flt1 involved the transcription factor Ets1. Conclusions: The current study demonstrates a pro-angiogenic role of Fzd5, which was shown to be involved in endothelial tubule formation, cell cycle progression and migration, and partly does so by repression of PKC/Ets1-mediated transcription of Flt1 and Angpt2

The BAH domain of Rsc2 is a histone H3 binding domain

Bromo-adjacent homology (BAH) domains are commonly found in chromatin-associated proteins and fall into two classes; Remodels the Structure of Chromatin (RSC)-like or Sir3-like. Although Sir3-like BAH domains bind nucleosomes, the binding partners of RSC-like BAH domains are currently unknown. The Rsc2 subunit of the RSC chromatin remodeling complex contains an RSC-like BAH domain and, like the Sir3-like BAH domains, we find Rsc2 BAH also interacts with nucleosomes. However, unlike Sir3-like BAH domains, we find that Rsc2 BAH can bind to recombinant purified H3 in vitro, suggesting that the mechanism of nucleosome binding is not conserved. To gain insight into the Rsc2 BAH domain, we determined its crystal structure at 2.4 Å resolution. We find that it differs substantially from Sir3-like BAH domains and lacks the motifs in these domains known to be critical for making contacts with histones. We then go on to identify a novel motif in Rsc2 BAH that is critical for efficient H3 binding in vitro and show that mutation of this motif results in defective Rsc2 function in vivo. Moreover, we find this interaction is conserved across Rsc2-related proteins. These data uncover a binding target of the Rsc2 family of BAH domains and identify a novel motif that mediates this interaction

Organizing recurrent network dynamics by task-computation to enable continual learning

Biological systems face dynamic environments that require continual learning. It is not well understood how these systems balance the tension between flexibility for learning and robustness for memory of previous behaviors. Continual learning without catastrophic interference also remains a challenging problem in machine learning. Here, we develop a novel learning rule designed to minimize interference between sequentially learned tasks in recurrent networks. Our learning rule preserves network dynamics within activity-defined subspaces used for previously learned tasks. It encourages dynamics associated with new tasks that might otherwise interfere to instead explore orthogonal subspaces, and it allows for reuse of previously established dynamical motifs where possible. Employing a set of tasks used in neuroscience, we demonstrate that our approach successfully eliminates catastrophic interference and offers a substantial improvement over previous continual learning algorithms. Using dynamical systems analysis, we show that networks trained using our approach can reuse similar dynamical structures across similar tasks. This possibility for shared computation allows for faster learning during sequential training. Finally, we identify organizational differences that emerge when training tasks sequentially versus simultaneously

Temporal alignment and latent Gaussian process factor inference in population spike trains

We introduce a novel scalable approach to identifying common latent structure in neural population spike-trains, which allows for variability both in the trajectory and in the rate of progression of the underlying computation. Our approach is based on shared latent Gaussian processes (GPs) which are combined linearly, as in the Gaussian Process Factor Analysis (GPFA) algorithm. We extend GPFA to handle unbinned spike-train data by incorporating a continuous time point-process likelihood model, achieving scalability with a sparse variational approximation. Shared variability is separated into terms that express condition dependence, as well as trial-to-trial variation in trajectories. Finally, we introduce a nested GP formulation to capture variability in the rate of evolution along the trajectory. We show that the new method learns to recover latent trajectories in synthetic data, and can accurately identify the trial-to-trial timing of movement-related parameters from motor cortical data without any supervision

Learning interpretable continuous-time models of latent stochastic dynamical systems

We develop an approach to learn an interpretable semi-parametric model of a latent continuoustime stochastic dynamical system, assuming noisy high-dimensional outputs sampled at uneven times. The dynamics are described by a nonlinear stochastic differential equation (SDE) driven by a Wiener process, with a drift evolution function drawn from a Gaussian process (GP) conditioned on a set of learnt fixed points and corresponding local Jacobian matrices. This form yields a flexible nonparametric model of the dynamics, with a representation corresponding directly to the interpretable portraits routinely employed in the study of nonlinear dynamical systems. The learning algorithm combines inference of continuous latent paths underlying observed data with a sparse variational description of the dynamical process. We demonstrate our approach on simulated data from different nonlinear dynamical systems

A Smart Computational Tool for Personalized Coronary Blood Flow Settings During Normothermic &lt;i&gt;Ex Situ&lt;/i&gt; Heart Perfusion

Myocardial edema significantly develops during current subnormothermic ex situ heart perfusion (ESHP) procedures, resulting in myocardial function decline during prolonged perfusion. A relatively high coronary blood flow (CBF) during ESHP is thought to be responsible for this high degree of myocardial edema formation. In this study, we present a novel tool to calculate CBF based on individual donor (sex and body weight) and perfusate (hemoglobin concentration, oxygen saturation, partial pressure of oxygen [PO2]) characteristics. The tool continuously evaluates the balance between myocardial oxygen consumption (MVO2) and delivery to facilitate adequate and preventing excess perfusion. Taking this personalized approach, the CBF can potentially be lowered while still providing sufficient oxygen to the donor heart. Furthermore, the tool automatically calculates MVO2, ΔPO2, and coronary vascular resistance during ESHP, which aids in the qualitative assessment of the heart before transplantation.</p

Fluoroscopy usage in contemporary interventional electrophysiology: Insights from a European registry

Background: Fluoroscopy has been an essential part of every electrophysiological procedure since its inception. However, till now no clear standards regarding acceptable x-ray exposure nor recommendation how to achieve them have been proposed. Hypothesis: Current norms and quality markers required for optimal clinical routine can be identified. Methods: Centers participating in this Europe-wide multicenter, prospective registry were requested to provide characteristics of the center, operators, technical equipment as well as procedural settings of consecutive cases. Results: Twenty-five centers (72% university clinics, with a mean volume of 526 ± 348 procedures yearly) from 14 European countries provided data on 1788 cases [9% diagnostic procedures (DP), 38% atrial fibrillation (AF) ablations, 44% other supraventricular (SVT) ablations, and 9% ventricular ablations (VT)] conducted by 95 operators (89% male, 41 ± 7 years old). Mean dose area product (DAP) and time was 304 ± 608 cGy*cm2, 3.6 ± 4.8 minutes, 1937 ± 608 cGy*cm2, 15.3 ± 15.5 minutes, 805 ± 1442 cGy*cm2, 10.6 ± 10.7 minutes, and 1277 ± 1931 cGy*cm2, 10.4 ± 12.3 minutes for DP, AF, SVT, and VT ablations, respectively. Seven percent of all procedures were conducted without any use of fluoroscopy. Procedures in the lower quartile of DAP were performed more frequently by female operators (OR 1.707, 95%CI 1.257-2.318, P =.001), in higher-volume center (OR 1.001 per one additional procedure, 95%CI 1.000-1.001, P =.002), with the use of 3D-mapping system (OR 2.622, 95%CI 2.053-3.347, P &lt;.001) and monoplane x-ray system (OR 2.945, 95%CI 2.149-4.037, P &lt;.001). Conclusion: Exposure to ionizing radiation varies widely in daily practice for all procedure. Significant opportunities for harmonization of exposure toward the lower range has been identified