EDEN: A high-performance, general-purpose, NeuroML-based neural simulator

Modern neuroscience employs in silico experimentation on ever-increasing and more detailed neural networks. The high modelling detail goes hand in hand with the need for high model reproducibility, reusability and transparency. Besides, the size of the models and the long timescales under study mandate the use of a simulation system with high computational performance, so as to provide an acceptable time to result. In this work, we present EDEN (Extensible Dynamics Engine for Networks), a new general-purpose, NeuroML-based neural simulator that achieves both high model flexibility and high computational performance, through an innovative model-analysis and code-generation technique. The simulator runs NeuroML v2 models directly, eliminating the need for users to learn yet another simulator-specific, model-specification language. EDEN's functional correctness and computational performance were assessed through NeuroML models available on the NeuroML-DB and Open Source Brain model repositories. In qualitative experiments, the results produced by EDEN were verified against the established NEURON simulator, for a wide range of models. At the same time, computational-performance benchmarks reveal that EDEN runs up to 2 orders-of-magnitude faster than NEURON on a typical desktop computer, and does so without additional effort from the user. Finally, and without added user effort, EDEN has been built from scratch to scale seamlessly over multiple CPUs and across computer clusters, when available.Comment: 29 pages, 9 figure

Mediastinal debulking for a T-cell leukaemia/lymphoma presenting with cardiac tamponade

Anterior mediastinal masses are relatively uncommon and include a wide variety of lesions. Lymphomas account for 25% of anterior mediastinal masses. Lymphomas and other haematological malignancies are associated with pericardial effusion. There are also cases where a cardiac tamponade occurred. The aim of the case reported herein is to discuss the surgical approach and particularly the mediastinal debulking as an adjunct to systematic treatment for haematological diseases presenting as an anterior mediastinal mass responsible for a cardiac tamponade

A novel simulator for extended Hodgkin-Huxley neural networks

Computational neuroscience aims to investigate and explain the behaviour and functions of neural structures, through mathematical models. Due to the models' complexity, they can only be explored through computer simulation. Modern research in this field is increasingly adopting large networks of neurons, and diverse, physiologically-detailed neuron models, based on the extended Hodgkin-Huxley (eHH) formalism. However, existing eHH simulators either support highly specific neuron models, or they provide low computational performance, making model exploration costly in time and effort. This work introduces a simulator for extended Hodgkin-Huxley neural networks, on multiprocessing platforms. This simulator supports a broad range of neuron models, while still providing high performance. Simulator performance is evaluated against varying neuron complexity parameters, network size and density, and thread-level parallelism. Results indicate performance is within existing literature for single-model eHH codes, and scales well for large CPU core counts. Ultimately, this application combines model flexibility with high performance, and can serve as a new tool in computational neuroscience.</p

Dual Emission in the Near-Infrared and Visible Regions from a Mixed Cyanido-Bridged Eu^III/Nd^III(4-OHpy)-Co^III Layered Material

Coordination polymers (CPs) with a dual emission spanning from the visible (vis) to near-infrared (NIR) regions of the electromagnetic spectrum are used for optical sensors, medical diagnostics, and telecommunication technologies. We herein report the synthesis, structural characterization, and optical response of heterometallic cyanido-bridged layered {[EuxNdy(4-OHpy)2(H2O)3][Co(CN)6]} CPs, where 4-OHpy = 4-hydroxypyridine, with a multicolor emission profile across the vis and NIR regions. The crystals show an efficient energy transfer (ET) from the 4-OHpy ligand and the [Co(CN)6] ions to the Eu3+ and Nd3+ ions, resulting in an enhanced photoluminescence (PL) efficiency. We study the ET with steady-state and time-resolved PL, reporting an ET between the Ln3+ centers. The excitation-dependent emission of the mixed Ln3+ CPs and the control over the PL lifetime yield new insights into the optoelectronic properties of these materials

Red Blood Cell Abnormalities as the Mirror of SARS-CoV-2 Disease Severity: A Pilot Study

PurposeUnraveling the pathophysiology of COVID-19 disease is of crucial importance for designing treatment. The purpose of this study is to investigate the effects of the disease on erythrocytes (RBCs) and to correlate the findings with disease severity. Materials and MethodsHospitalized patients (n = 36) with COVID-19 and control group of healthy volunteers (n = 18) were included in the study. Demographic data, clinical, laboratory and chest Computed Tomography (CT) findings at time of admission were recorded. Laboratory measurements included: Hemoglobin (H b), indirect billirubin, LDH, D-Dimers, and plasma free hemoglobin (plasma free-Hb). On RBCs were performed: osmotic fragility (MCF), Free-Hb after mechanical stress (Free-Hb-MECH), intracellular RBC concentration of calcium ions (iCa(2+)), intracellular ROS (iROS), G6PD, intracellular active caspase-3 (RBC-caspase-3), IgG immunoglobulins (RBC-IgGs), which are bound on RBCs’ senescent neo-antigen proteins and RBC surface phosphatidylserine (RBC-PS). ResultsThe percentage of males was 50 and 66% and the mean age was 65.16 +/- 14.24 and 66.33 +/- 13.48 years among patients and controls respectively (mean +/- SD, p = 0.78). Upon admission patients’ PO2/FiO(2) ratio was 305.92 +/- 76.75 and distribution of infiltration extend on chest CT was: 0-25% (N = 19), 25-50%: (N = 7), and 50-75% (N = 9). Elevated hemolysis markers (LDH and plasma free-Hb) were observed in patients compared to the control group. Patients’ RBCs were more sensitive to mechanical stress, and exhibited significantly elevated apoptotic markers (iCa(2+), RBC-PS). Plasma free Hb levels correlated with the extend of pulmonary infiltrates on chest CT in COVID-19 patients. Surprisingly, patients’ RBC-iROS were decreased, a finding possibly related with the increased G6PDH levels in this group, suggesting a possible compensatory mechanism against the virus. This compensatory mechanism seemed to be attenuated as pulmonary infiltrates on chest CT deteriorated. Furthermore, RBC-IgGs correlated with the severity of pulmonary CT imaging features as well as the abnormality of lung function, which are both associated with increased disease severity. Lastly, patients’ D-Dimers correlated with RBC surface phosphatidylserine, implying a possible contribution of the red blood cells in the thrombotic diathesis associated with the SARS-CoV-2 disease. ConclusionThis pilot study suggests that SARS-CoV-2 infection has an effect on red blood cells and there seems to be an association between RBC markers and disease severity in these patients