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1.  Vobi One: a data processing software package for functional optical imaging 
Optical imaging is the only technique that allows to record the activity of a neuronal population at the mesoscopic scale. A large region of the cortex (10–20 mm diameter) is directly imaged with a CCD camera while the animal performs a behavioral task, producing spatio-temporal data with an unprecedented combination of spatial and temporal resolutions (respectively, tens of micrometers and milliseconds). However, researchers who have developed and used this technique have relied on heterogeneous software and methods to analyze their data. In this paper, we introduce Vobi One, a software package entirely dedicated to the processing of functional optical imaging data. It has been designed to facilitate the processing of data and the comparison of different analysis methods. Moreover, it should help bring good analysis practices to the community because it relies on a database and a standard format for data handling and it provides tools that allow producing reproducible research. Vobi One is an extension of the BrainVISA software platform, entirely written with the Python programming language, open source and freely available for download at https://trac.int.univ-amu.fr/vobi_one.
doi:10.3389/fnins.2014.00002
PMCID: PMC3901006  PMID: 24478623
python; neuroscience; optical imaging; linear model; signal processing
2.  BMP7 Expression Correlates with Secondary Drug Resistance in Mantle Cell Lymphoma 
PLoS ONE  2013;8(9):e73993.
Purpose
We designed a gene profiling experiment to identify genes involved in secondary drug resistance in mantle cell lymphomas (MCL).
Experimental Design
We obtained paired tissue samples collected from the same patients before treatment and after relapse or progression. Variations in gene expression between the 2 samples were estimated for 5 patients. For each gene, the mean variation was estimated for patients with a refractory primary tumor and for responders who developed secondary drug resistance. Nine genes of interest were selected on the basis of the magnitude and statistical significance of the variation of expression in responders and non-responders.
Results
BMP7 was the only one with significantly increased expression at relapse in patients who developed secondary resistance. Validation of BMP7 as a key gene involved in secondary resistance was performed using cultures of cell line. Incubation of BMP7 with MCL cell lines increased their resistance to bortezomib and cytarabine, while inhibition of BMP7 expression by siRNA correlated with increased cell death linked to drug application.
Conclusion
Variations in gene expression after treatment point out BMP7 as a key gene involved in secondary resistance in mantle cell lymphoma.
doi:10.1371/journal.pone.0073993
PMCID: PMC3771972  PMID: 24069261
3.  The Local Field Potential Reflects Surplus Spike Synchrony 
Cerebral Cortex (New York, NY)  2011;21(12):2681-2695.
While oscillations of the local field potential (LFP) are commonly attributed to the synchronization of neuronal firing rate on the same time scale, their relationship to coincident spiking in the millisecond range is unknown. Here, we present experimental evidence to reconcile the notions of synchrony at the level of spiking and at the mesoscopic scale. We demonstrate that only in time intervals of significant spike synchrony that cannot be explained on the basis of firing rates, coincident spikes are better phase locked to the LFP than predicted by the locking of the individual spikes. This effect is enhanced in periods of large LFP amplitudes. A quantitative model explains the LFP dynamics by the orchestrated spiking activity in neuronal groups that contribute the observed surplus synchrony. From the correlation analysis, we infer that neurons participate in different constellations but contribute only a fraction of their spikes to temporally precise spike configurations. This finding provides direct evidence for the hypothesized relation that precise spike synchrony constitutes a major temporally and spatially organized component of the LFP.
doi:10.1093/cercor/bhr040
PMCID: PMC3209854  PMID: 21508303
motor cortex; oscillation; population signals; synchrony
4.  Impact of bosentan on health-related quality of life and dyspnoea in idiopathic pulmonary fibrosis: the BUILD-1 trial 
Objective:
No therapy is known to improve health-related quality of life (HRQL) or dyspnoea in patients with idiopathic pulmonary fibrosis (IPF). This study investigated longitudinal changes in HRQL and dyspnoea and explored the effects of bosentan on these endpoints during the BUILD-1 trial.
Methods:
In total 154 subjects received oral bosentan (n=71) or placebo (n=83). Changes in HRQL and dyspnoea from baseline to month 6 (M6) and up to month 12 (M12) were measured using the St George's Respiratory Questionnaire (SGRQ), Short-Form 36-item instrument (SF-36), Transition Dyspnoea Index, and Borg Dyspnoea Index.
Results:
Overall, minimal changes occurred in measures of HRQL and dyspnoea among placebo-treated subjects during the study. Effects of bosentan treatment on HRQL and dyspnoea in the all-treated population were minimal. However, in the subset of subjects who underwent surgical lung biopsy (SLB) for diagnosis of IPF, treatment effects were observed up to M12 in the Impacts domain of the SGRQ and the Physical functioning, General health and Role emotional domains of the SF-36.
Conclusions:
HRQL and dyspnoea changed minimally during the course of the study. Observations from exploratory analyses suggest benefits of bosentan on HRQL among patients who underwent SLB for diagnosis and merit further investigation.
doi:10.1183/09031936.00188108
PMCID: PMC2848824  PMID: 19679600
bosentan; dyspnoea; idiopathic pulmonary fibrosis; health-related quality of life

Results 1-4 (4)