Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals

A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically infeasible, even in simpler systems like dissociated neuronal cultures. We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct structural connectivity from network activity monitored through calcium imaging. We focus in this study on the inference of excitatory synaptic links. Based on information theory, our method requires no prior assumptions on the statistics of neuronal firing and neuronal connections. The performance of our algorithm is benchmarked on surrogate time series of calcium fluorescence generated by the simulated dynamics of a network with known ground-truth topology. We find that the functional network topology revealed by Transfer Entropy depends qualitatively on the time-dependent dynamic state of the network (bursting or non-bursting). Thus by conditioning with respect to the global mean activity, we improve the performance of our method. This allows us to focus the analysis to specific dynamical regimes of the network in which the inferred functional connectivity is shaped by monosynaptic excitatory connections, rather than by collective synchrony. Our method can discriminate between actual causal influences between neurons and spurious non-causal correlations due to light scattering artifacts, which inherently affect the quality of fluorescence imaging. Compared to other reconstruction strategies such as cross-correlation or Granger Causality methods, our method based on improved Transfer Entropy is remarkably more accurate. In particular, it provides a good estimation of the excitatory network clustering coefficient, allowing for discrimination between weakly and strongly clustered topologies. Finally, we demonstrate the applicability of our method to analyses of real recordings of in vitro disinhibited cortical cultures where we suggest that excitatory connections are characterized by an elevated level of clustering compared to a random graph (although not extreme) and can be markedly non-local.

Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data.

Microstructure imaging from diffusion magnetic resonance (MR) data represents an invaluable tool to study non-invasively the morphology of tissues and to provide a biological insight into their microstructural organization. In recent years, a variety of biophysical models have been proposed to associate particular patterns observed in the measured signal with specific microstructural properties of the neuronal tissue, such as axon diameter and fiber density. Despite very appealing results showing that the estimated microstructure indices agree very well with histological examinations, existing techniques require computationally very expensive non-linear procedures to fit the models to the data which, in practice, demand the use of powerful computer clusters for large-scale applications. In this work, we present a general framework for Accelerated Microstructure Imaging via Convex Optimization (AMICO) and show how to re-formulate this class of techniques as convenient linear systems which, then, can be efficiently solved using very fast algorithms. We demonstrate this linearization of the fitting problem for two specific models, i.e. ActiveAx and NODDI, providing a very attractive alternative for parameter estimation in those techniques; however, the AMICO framework is general and flexible enough to work also for the wider space of microstructure imaging methods. Results demonstrate that AMICO represents an effective means to accelerate the fit of existing techniques drastically (up to four orders of magnitude faster) while preserving accuracy and precision in the estimated model parameters (correlation above 0.9). We believe that the availability of such ultrafast algorithms will help to accelerate the spread of microstructure imaging to larger cohorts of patients and to study a wider spectrum of neurological disorders.

FluxEXPLORER: a new high-speed laser Doppler imaging system for the assessment of burn injuries.

BACKGROUND: Deep burn assessment made by clinical evaluation has an accuracy varying between 60% and 80% and will determine if a burn injury will need tangential excision and skin grafting or if it will be able to heal spontaneously. Laser Doppler Imaging (LDI) techniques allow an improved burn depth assessment but their use is limited by the time-consuming image acquisition which may take up to 6 min per image. METHODS: To evaluate the effectiveness and reliability of a newly developed full-field LDI technology, 15 consecutive patients presenting with intermediate depth burns were assessed both clinically and by FluxExplorer LDI technology. Comparison between the two methods of assessment was carried out. RESULTS: Image acquisition was done within 6 s. FluxEXPLORER LDI technology achieved a significantly improved accuracy of burn depth assessment compared to the clinical judgement performed by board certified plastic and reconstructive surgeons (P < 0.05, 93% of correctly assessed burns injuries vs. 80% for clinical assessment). CONCLUSION: Technological improvements of LDI technology leading to a decreased image acquisition time and reliable burn depth assessment allow the routine use of such devices in the acute setting of burn care without interfering with the patient's treatment. Rapid and reliable LDI technology may assist clinicians in burn depth assessment and may limit the morbidity of burn patients through a minimization of the area of surgical debridement. Future technological improvements allowing the miniaturization of the device will further ease its clinical application.

A multi-center study: intra-scan and inter-scan variability of diffusion spectrum imaging.

The objective of this study was to investigate whether it is possible to pool together diffusion spectrum imaging data from four different scanners, located at three different sites. Two of the scanners had identical configuration whereas two did not. To measure the variability, we extracted three scalar maps (ADC, FA and GFA) from the DSI and utilized a region and a tract-based analysis. Additionally, a phantom study was performed to rule out some potential factors arising from the scanner performance in case some systematic bias occurred in the subject study. This work was split into three experiments: intra-scanner reproducibility, reproducibility with twin-scanner settings and reproducibility with other configurations. Overall for the intra-scanner and twin-scanner experiments, the region-based analysis coefficient of variation (CV) was in a range of 1%-4.2% and below 3% for almost every bundle for the tract-based analysis. The uncinate fasciculus showed the worst reproducibility, especially for FA and GFA values (CV 3.7-6%). For the GFA and FA maps, an ICC value of 0.7 and above is observed in almost all the regions/tracts. Looking at the last experiment, it was found that there is a very high similarity of the outcomes from the two scanners with identical setting. However, this was not the case for the two other imagers. Given the fact that the overall variation in our study is low for the imagers with identical settings, our findings support the feasibility of cross-site pooling of DSI data from identical scanners.

Characterization of hydroxyapatite laser ablation plumes by fast intensified CCD-imaging

ArF excimer laser pulses (193 nm, 20 ns, 150 mJ) have been focused on a hydroxyapatite (HA) target in similar conditions to those normally used for thin film deposition. Fast intensified CCD images of HA laser ablation plumes have been taken in vacuum and under different water vapor pressures ranging from 0.01 mbar to 1 mbar. Images of HA ablation in vacuum have shown a plume freely expanding at a constant velocity of 2.3 106 cm/s. HA ablation under a water vapor pressure of 0.01 mbar has revealed an expansion behavior very similar to that of ablation in vacuum. Images taken under a water vapor pressure of 0.1 mbar have shown the formation of a shock structure in the plume. Finally, HA ablation under a water vapor pressure of 1 mbar has revealed the development of some irregularities in the shape of the plume.

Time-resolved imaging of the laser forward transfer of liquids

Time-resolved imaging is carried out to study the dynamics of the laser-induced forward transfer of an aqueous solution at different laser fluences. The transfer mechanisms are elucidated, and directly correlated with the material deposited at the analyzed irradiation conditions. It is found that there exists a fluence range in which regular and well-defined droplets are deposited. In this case, laser pulse energy absorption results in the formation of a plasma, which expansion originates a cavitation bubble in the liquid. After the further expansion and collapse of the bubble, a long and uniform jet is developed, which advances at a constant velocity until it reaches the receptor substrate. On the other hand, for lower fluences no material is deposited. In this case, although a jet can be also generated, it recoils before reaching the substrate. For higher fluences, splashing is observed on the receptor substrate due to the bursting of the cavitation bubble. Finally, a discussion of the possible mechanisms which lead to such singular dynamics is also provided.

La fibrose rétropéritonéale, une maladie inflammatoire méconnue. Observations cliniques et revue de la littérature [Retroperitoneal fibrosis, an unrecognized inflammatory disease. Clinical observations and review of the literature]

Retroperitoneal fibrosis (RF) is a rare disease, typically with an insidious clinical course. The peak incidence is seen in patients 40 to 60 years of age and mostly in man. The characteristic finding in this disease is a periaortic fibrous mass that often surrounds the ureters. Although usually regarded as an obstructive uropathy, there has been growing recognition of the condition as a generalized disease. It may have a wide variety of manifestations including mediastinitis, thyroiditis and sclerosing cholangitis. The most common mode of presentation remains abdominal or flank pain with uremia, anemia and a high sedimentation rate. Although ultrasound and renal scintigraphy may contribute to the general evaluation of patients with RF, CT-scanner is the preferred imaging method. The multiplanar imaging capability of magnetic resonance may facilitate assessment of disease extent. The pathogenesis of the disease remains unknown. Steroids and, more recently tamoxifen, appear to be effective in the treatment of the RF. In most instances, RF does not lead to long-term morbidity or affect survival. The three cases of RF reported herein illustrate the varied mode of presentation and the response to the treatment.

Single-hole GPR reflection imaging of solute transport in a granitic aquifer

Identifying transport pathways in fractured rock is extremely challenging as flow is often organized in a few fractures that occupy a very small portion of the rock volume. We demonstrate that saline tracer experiments combined with single-hole ground penetrating radar (GPR) reflection imaging can be used to monitor saline tracer movement within mm-aperture fractures. A dipole tracer test was performed in a granitic aquifer by injecting a saline solution in a known fracture, while repeatedly acquiring single-hole GPR sections in the pumping borehole located 6 m away. The final depth-migrated difference sections make it possible to identify consistent temporal changes over a 30 m depth interval at locations corresponding to fractures previously imaged in GPR sections acquired under natural flow and tracer-free conditions. The experiment allows determining the dominant flow paths of the injected tracer and the velocity (0.4-0.7 m/min) of the tracer front. Citation: Dorn, C., N. Linde, T. Le Borgne, O. Bour, and L. Baron (2011), Single-hole GPR reflection imaging of solute transport in a granitic aquifer, Geophys. Res. Lett., 38, L08401, doi: 10.1029/2011GL047152.

The phagocytosis of gas-filled microbubbles by human and murine antigen-presenting cells.

This study was designed to evaluate the potential of gas-filled microbubbles (MB) to be internalized by antigen-presenting cells (APC). Fluorescently labeled MB were prepared, thus permitting to track binding to, and internalization in, APC. Both human and mouse cells, including monocytes and dendritic cells (DC), prove capable to phagocyte MB in vitro. Observation by confocal laser scanning microscopy showed that interaction between MB and target cells resulted in a rapid internalization in cellular compartments and to a lesser extent in the cytoplasm. Capture of MB by APC resulted in phagolysosomal targeting as verified by double staining with anti-lysosome-associated membrane protein-1 monoclonal antibody and decrease of internalization by phagocytosis inhibitors. Fluorescent MB injected subcutaneously (s.c.) in mice were found to be associated with CD11c(+)DC in lymph nodes draining the injection sites 24 h after administration. Altogether, our study demonstrates that MB can successfully target APC both in vitro and in vivo, and thus may serve as a potent Ag delivery system without requirement for ultrasound-based sonoporation. This adds to the potential of applications of MB already extensively used for diagnostic imaging in humans.

Breast cancer and melanoma cell line identification by FTIR imaging after formalin-fixation and paraffin-embedding.

Over the past few decades, Fourier transform infrared (FTIR) spectroscopy coupled to microscopy has been recognized as an emerging and potentially powerful tool in cancer research and diagnosis. For this purpose, histological analyses performed by pathologists are mostly carried out on biopsied tissue that undergoes the formalin-fixation and paraffin-embedding (FFPE) procedure. This processing method ensures an optimal and permanent preservation of the samples, making FFPE-archived tissue an extremely valuable source for retrospective studies. Nevertheless, as highlighted by previous studies, this fixation procedure significantly changes the principal constituents of cells, resulting in important effects on their infrared (IR) spectrum. Despite the chemical and spectral influence of FFPE processing, some studies demonstrate that FTIR imaging allows precise identification of the different cell types present in biopsied tissue, indicating that the FFPE process preserves spectral differences between distinct cell types. In this study, we investigated whether this is also the case for closely related cell lines. We analyzed spectra from 8 cancerous epithelial cell lines: 4 breast cancer cell lines and 4 melanoma cell lines. For each cell line, we harvested cells at subconfluence and divided them into two sets. We first tested the "original" capability of FTIR imaging to identify these closely related cell lines on cells just dried on BaF2 slides. We then repeated the test after submitting the cells to the FFPE procedure. Our results show that the IR spectra of FFPE processed cancerous cell lines undergo small but significant changes due to the treatment. The spectral modifications were interpreted as a potential decrease in the phospholipid content and protein denaturation, in line with the scientific literature on the topic. Nevertheless, unsupervised analyses showed that spectral proximities and distances between closely related cell lines were mostly, but not entirely, conserved after FFPE processing. Finally, PLS-DA statistical analyses highlighted that closely related cell lines are still successfully identified and efficiently distinguished by FTIR spectroscopy after FFPE treatment. This last result paves the way towards identification and characterization of cellular subtypes on FFPE tissue sections by FTIR imaging, indicating that this analysis technique could become a potential useful tool in cancer research.