Reconstruction and Simulation of Neocortical Microcircuitry.

We present a first-draft digital reconstruction of the microcircuitry of somatosensory cortex of juvenile rat. The reconstruction uses cellular and synaptic organizing principles to algorithmically reconstruct detailed anatomy and physiology from sparse experimental data. An objective anatomical method defines a neocortical volume of 0.29 ± 0.01 mm(3) containing ~31,000 neurons, and patch-clamp studies identify 55 layer-specific morphological and 207 morpho-electrical neuron subtypes. When digitally reconstructed neurons are positioned in the volume and synapse formation is restricted to biological bouton densities and numbers of synapses per connection, their overlapping arbors form ~8 million connections with ~37 million synapses. Simulations reproduce an array of in vitro and in vivo experiments without parameter tuning. Additionally, we find a spectrum of network states with a sharp transition from synchronous to asynchronous activity, modulated by physiological mechanisms. The spectrum of network states, dynamically reconfigured around this transition, supports diverse information processing strategies. PAPERCLIP: VIDEO ABSTRACT.

The SONATA data format for efficient description of large-scale network models.

Increasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation, as well as sharing of such large-scale models, a broadly applicable, flexible, and high-performance data format is necessary. To address this need, we have developed the Scalable Open Network Architecture TemplAte (SONATA) data format. It is designed for memory and computational efficiency and works across multiple platforms. The format represents neuronal circuits and simulation inputs and outputs via standardized files and provides much flexibility for adding new conventions or extensions. SONATA is used in multiple modeling and visualization tools, and we also provide reference Application Programming Interfaces and model examples to catalyze further adoption. SONATA format is free and open for the community to use and build upon with the goal of enabling efficient model building, sharing, and reproducibility.

NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks.

Motivation: From image stacks to computational models, processing digital representations of neuronal morphologies is essential to neuroscientific research. Workflows involve various techniques and tools, leading in certain cases to convoluted and fragmented pipelines. The existence of an integrated, extensible and free framework for processing, analysis and visualization of those morphologies is a challenge that is still largely unfulfilled. Results: We present NeuroMorphoVis, an interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks. Our framework is capable of detecting and repairing tracing artifacts, allowing the generation of high fidelity surface meshes and high resolution volumetric models for simulation and in silico imaging studies. The applicability of NeuroMorphoVis is demonstrated with two case studies. The first simulates the construction of three-dimensional profiles of neuronal somata and the other highlights how the framework is leveraged to create volumetric models of neuronal circuits for simulating different types of in vitro imaging experiments. Availability and implementation: The source code and documentation are freely available on https://github.com/BlueBrain/NeuroMorphoVis under the GNU public license. The morphological analysis, visualization and surface meshing are implemented as an extensible Python API (Application Programming Interface) based on Blender, and the volume reconstruction and analysis code is written in C++ and parallelized using OpenMP. The framework features are accessible from a user-friendly GUI (Graphical User Interface) and a rich CLI (Command Line Interface). Supplementary information: Supplementary data are available at Bioinformatics online.

Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies.

BACKGROUND: We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons. The limitations of the existing approaches for creating those models are explained, and then, a multi-stage pipeline is discussed to overcome those limitations. Starting from the neuronal morphologies, we create smooth piecewise watertight polygonal models that can be efficiently utilized to synthesize continuous and plausible volumetric models of the neurons with solid voxelization. The somata of the neurons are reconstructed on a physically-plausible basis relying on the physics engine in Blender. RESULTS: Our pipeline is applied to create 55 exemplar neurons representing the various morphological types that are reconstructed from the somatsensory cortex of a juvenile rat. The pipeline is then used to reconstruct a volumetric slice of a cortical circuit model that contains ∼210,000 neurons. The applicability of our pipeline to create highly realistic volumetric models of neocortical circuits is demonstrated with an in silico imaging experiment that simulates tissue visualization with brightfield microscopy. The results were evaluated with a group of domain experts to address their demands and also to extend the workflow based on their feedback. CONCLUSION: A systematic workflow is presented to create large scale synthetic tissue models of the neocortical circuitry. This workflow is fundamental to enlarge the scale of in silico neuroscientific optical experiments from several tens of cubic micrometers to a few cubic millimeters. AMS SUBJECT CLASSIFICATION: Modelling and Simulation.

Foxp3(+) cell infiltration and granzyme B(+)/Foxp3(+) cell ratio are associated with outcome in neoadjuvant chemotherapy-treated ovarian carcinoma.

Preoperative neoadjuvant chemotherapy (NAC) can significantly reduce tumour burden in patients with primarily unresectable chemosensitive tumours, allowing a more complete cytoreduction during debulking surgery and facilitating evaluation of tumour chemosensitivity, identification of appropriate treatment options and improvement of intervention protocols. In this study, we investigate, using immunohistochemistry, the impact of platinum/taxane-based NAC (NAC) on tumour-infiltrating lymphocytes (TILs) in advanced epithelial ovarian cancer (EOC) and their relationship with clinical outcome. All patients had clinical response, as shown by ascites volume and CA125 levels compared to pre-treatment findings. NAC intervention significantly increased CD4(+), CD8(+) and granzyme B(+) infiltration while Foxp3(+) accumulation remained unaffected. TILs were prognostically neutral for both progression-free survival (PFS) and overall survival (OS) before NAC. In contrast, after NAC, elevated granzyme B(+) infiltration displayed a tendency for improved PFS (log-rank 0.064). Further, low Foxp3(+) cell density was associated with longer PFS, as compared with strong Foxp3(+) infiltration (median 20.94 vs. 11.24 months; log-rank 0.0001) and with improved OS (median 30.75 vs. 16.04 months, respectively; log-rank 0.056), demonstrating clear prognostic significance for PFS. In addition, high granzyme B(+)/Foxp3(+) ratio post-NAC strongly correlated with improved PFS compared to low granzyme B(+)/Foxp3(+) cell ratio (median 17.88 vs. 11.24 months, respectively), and showed to be a favourable prognostic factor for PFS (log-rank 0.014). Our findings indicate that NAC elicited an immunologic profile in which low immunosuppressive Foxp3(+) infiltration and elevated numbers of activated granzyme B(+) cells were significantly associated with EOC-specific PFS, suggesting a contribution of immunologic effects to improved clinical outcome.

[Relationship between C-reactive protein level and early recurrence of atrial fibrillation after electrical cardioversion]. / Relación entre concentraciones de proteína C reactiva y recurrencia precoz de la fibrilación auricular tras cardioversión eléctrica.

INTRODUCTION AND OBJECTIVES: Atrial remodeling is responsible for the early recurrence of atrial fibrillation (AF) after cardioversion. Recently, it has been shown that the C-reactive protein (CRP) level is elevated in patients with AF, indicating that inflammation may play a role in the pathogenesis of this arrhythmia. We postulated that a high CRP level would predict early recurrence of AF after electrical cardioversion. PATIENTS AND METHOD: Forty-two patients with persistent AF, but without known heart disease, who underwent elective electrical cardioversion were investigated. The CRP level was measured immediately before cardioversion. The study population comprised the 37 patients in whom sinus rhythm was restored. RESULTS: After a follow-up period of 30 days, 16 patients (43%) had recurrence of AF; the other 21 (57%) remained in sinus rhythm. The mean CRP level was significantly higher in patients with AF recurrence (6.3 [3.3] mg/L vs 2.4 [2.1] mg/L, P=.0001). On dividing patients according to whether their CRP level was < or =3 mg/L or >3 mg/L, it was observed that only 33% of those in sinus rhythm had a level >3 mg/L compared with 81% of those with AF recurrence (P=.004). Patients with a CRP level >3 mg/L had a significant increase in the 1-month risk of AF recurrence (RR=3.7; 95% CI, 1.3-10.8). There was no association between CRP level and left atrial diameter (P =.50) or AF duration (P=.458). CONCLUSIONS: A high CRP level is associated with early recurrence of AF after electrical cardioversion, suggesting that inflammation could play a role in atrial remodeling.

The diagnostic utility of human papillomavirus-testing in combination with immunohistochemistry in advanced gynaecologic pelvic tumours: a new diagnostic approach.

Gynaecologic pelvic tumours comprise a range of histological entities that are highly variable with respect to their clinical behaviour. The distinction of these tumours can be extremely difficult. Accurate identification of the primary tumour site has significant impact on the treatment strategy and prognosis. In this study we investigated the diagnostic and clinical utility of HPV (Human Papillomavirus)-testing in combination with selected immunohistochemical markers in advanced pelvic tumours of unknown primary origin. Specimens of eight patients who presented with advanced gynaecologic pelvic tumour of unknown primary origin, 10 unequivocal cervical carcinomas with 10 corresponding metastases and 10 unequivocal endometrial carcinomas with 4 corresponding metastases were studied. All cases were analysed for HPV-infection by PCR. The expression of CEA, vimentin (VIM), estrogen receptor (ER) and progesterone receptor (PR) was studied by immunohistochemistry. HPV-DNA was exclusively detected in cervical carcinomas and their corresponding metastases but in none of the endometrial carcinomas (Fisher's exact test p<0.001). Endometrial carcinomas and their metastases were generally positive for ER (86%), PR (93%) and VIM (100%) but rarely positive for CEA (14%) and HPV (0%). Most cervical carcinomas and their corresponding metastases were positive for CEA (79%) and HPV (89%). They rarely expressed ER (5%), PR (5%) and VIM (10%). Among the eight patients with unknown primary tumour four patients were diagnosed with a cervical carcinoma and four with an endometrial carcinoma. In one case we could exclude an ovarian carcinoma. Immunohistochemical analysis of selected markers in combination with HPV-testing is simple and inexpensive. The detection of HPV-DNA seems to provide the most compelling evidence for the primary tumour site, when immunohistochemical analysis is less definitive. The proposed diagnostic approach is helpful in the identification and management of pelvic tumours of unknown primary origin.

Dendritic cell-based vaccines in breast and gynaecologic cancer.

Major advances in understanding the functional interactions between tumour cells and the host immune system, in particular the generation and regulation of T cell immunity, have revived interest in cancer vaccination strategies. A crucial step for mounting an anti-tumour response is the capture, processing and presentation of tumour antigens (TA) to cognate T cells by professional antigen-presenting cells (APC), followed by their activation and clonal proliferation. Dendritic cells (DC) are potent APC with the unique ability to stimulate primary immune responses. Animal models have demonstrated that TA-charged DC can activate specific cytotoxic T cells (CTL) and even regression of established tumours in cancer-bearing hosts. These findings, as well as the elaboration of methods for generating large numbers of DC ex vivo, have provided a compelling rationale for using DC as potent adjuvants to deliver TA to the immune system in order to trigger or amplify an inadequate response. The capacity of TA-pulsed DC to induce significant CTL immunity translating into occasional therapeutic benefit has been documented in several clinical settings including B cell lymphoma, myeloma, melanoma, prostate, colon, ovarian and renal cell carcinoma. In this review, we summarize key biological functions of DC and focus on recent DC-based vaccination trials of breast, ovarian and cervical cancer.

A neuron membrane mesh representation for visualization of electrophysiological simulations.

We present a process to automatically generate three-dimensional mesh representations of the complex, arborized cell membrane surface of cortical neurons (the principal information processing cells of the brain) from nonuniform morphological measurements. Starting from manually sampled morphological points (3D points and diameters) from neurons in a brain slice preparation, we construct a polygonal mesh representation that realistically represents the continuous membrane surface, closely matching the original experimental data. A mapping between the original morphological points and the newly generated mesh enables simulations of electrophysiolgical activity to be visualized on this new membrane representation. We compare the new mesh representation with the state of the art and present a series of use cases and applications of this technique to visualize simulations of single neurons and networks of multiple neurons.

Vaccination with autologous tumour antigen-pulsed dendritic cells in advanced gynaecological malignancies: clinical and immunological evaluation of a phase I trial.

Dendritic cell (DC)-based therapy has proven to be effective in patients with malignant lymphoma, melanoma, and renal and prostate carcinoma. In this phase I clinical trial, we have shown that patients with advanced gynaecological malignancies can be effectively vaccinated with DC pulsed with keyhole limpet haemocyanin (KLH) and autologous tumour antigens. Two patients with uterine sarcoma and six subjects with ovarian carcinoma received three to 23 intracutaneous injections of antigen-pulsed DC at 10-day or 4-week intervals. Three patients showed stable disease lasting 25 to 45 weeks, and five experienced tumour progression within the first 14 weeks. KLH- and tumour lysate-specific delayed-type hypersensitivity (DTH) reactions were observed in six and one patient, respectively. Lymphoproliferative responses to KLH and to tumour lysate stimulation were recorded in six patients and in two patients respectively. Tumour antigen-stimulated interferon-gamma (IFN-gamma) secretion by peripheral blood mononuclear cells (PBMC) in one patient was consistent with a T(H) type 1 cytokine bias. The treatment was safe, well tolerated, immunologically active and except for local cutaneous hypersensitivity devoid of significant adverse effects.