Topological exploration of artificial neuronal network dynamics

One of the paramount challenges in neuroscience is to understand the dynamics of individual neurons and how they give rise to network dynamics when interconnected. Historically, researchers have resorted to graph theory, statistics, and statistical mechanics to describe the spatiotemporal structure of such network dynamics. Our novel approach employs tools from algebraic topology to characterize the global properties of network structure and dynamics. We propose a method based on persistent homology to automatically classify network dynamics using topological features of spaces built from various spike-train distances. We investigate the efficacy of our method by simulating activity in three small artificial neural networks with different sets of parameters, giving rise to dynamics that can be classified into four regimes. We then compute three measures of spike train similarity and use persistent homology to extract topological features that are fundamentally different from those used in traditional methods. Our results show that a machine learning classifier trained on these features can accurately predict the regime of the network it was trained on and also generalize to other networks that were not presented during training. Moreover, we demonstrate that using features extracted from multiple spike-train distances systematically improves the performance of our method

Garba IV and the Melka Kunture Formation. A preliminary lithostratigraphic approach

autorisation des éditeurs de l'ouvrage par email du 01/07/05The lithostratigraphic analysis of the different sections at Garba and Gombore clarify the dynamics nature of the deposition processes for the lower part of the Melka Kunture Formation. Downstream transport and accumulation are prevalent during sedimentation processes. Channel lag petrographic suites reflect the basin geology and indicate a period of global dismantling of ancient volcanic relief and important lateral contributions from both banks' tributaries to alluvial processes. Volcanic activity is the main provider for fine grains sediments: pumice derived from pyroclastites of penecontemporaneous plinian eruptions contribute massively to channel lags and to major accretion events (Sl, Sp, St facies), reworked coarse tuffs form massive beds (Sm facies) while cinereous tephras are responsible for silts deposition (Fsm, Fm facies). Resistant and opaque minerals form the matrix of bed lags and most of the sandy bases of current structures. Grain-size distribution also reflects the evolution of channels. At Gombore, six channels are superposed and partly embedded. Each of them exhibits a logical facies succession leading to complete infilling and abandonment while the main stream migrates towards SE. Archaeological layers are systematically associated with the bedforms, except for the uppermost one. The volcanic input is responsible for overloading of streams and forces channel changes. Facies previously considered as lacustrine are actually fluvial facies. The “major cut-and-fill” previously considered as major erosion phases by Chavaillon (1973) are only simple channeling processes. At Garba IV, three channels are superposed and partly embedded. Each of them exhibits a logical facies succession leading to a complete infilling and eventual abandonment. Archaeological layers are associated with the bedforms, local erosional surface or temporary abandoned channel. The volcanic input is systematically responsible for over-loading and forces channeling. Here again, facies previously considered as lacustrine are actually fluvial and the “major cut-and-fill” previously considered as important erosional phases are only simple channeling processes. Considering the paleomagnetic data and especially the brief normal polarity event recognized both at Garba in the upper part of “Tuff A” and at Gombore Ig at the top of sands above the archaeological layer (Cressier 1980), the preliminary absolute dating (Schmitt et. al. 1977) and the revisited tuff correlations, it can be concluded that both series deposited between 1.77 Ma (end of Oldoway Polarity Subzone) and 0.78 Ma (Brunhes-Matuyama limit) at most. From an archaeological perspective, Oldowan and Acheulian sites are associated with bedforms and gravel bars. These layers have been affected by currents (sieve effect, re-orientation of large pieces) and repeatedly washed and covered by abrasive sands during accretion or subjected to erosional episodes which have highly disturbed the primary organisation of artefacts. The superposition of the different facies clearly indicates a tectonic control of the sedimentation for the Melka Kunture Formation (at least for its lower terms described in this paper) during the Lower Pleistocene: the recurrent faulting (moderate subsidence of the semi-graben) along the Melka scarp which borders the Garba-Gombore area is directly responsible for this architecture. A pause in subsidence combined with head erosion through the Melka Kunture raised block allowed a return to valley incision processes and installation of valley-plain and stepped terraces fossilized by the non-welded ignimbrite episode, significantly wide-spread and thus named Kella Formation.This unit belongs clearly to the Matuyama Polarity Zone with a minimum age of 0.78 Ma. The setting of this ignimbrite seems to have fit into a topography close to the present one. After the emplacement of the non-welded ignimbrites a fault reactivation takes place with an important displacement. The meandering of the palaeo-Awash was certainly determined by the obstacle of the raised block of Melka Kunture according to the Main Ethiopian Rift evolution (see Bardin et al. in this volume). Combined head erosion and subsident faulting are responsible for the successive changes in sedimentation style such as channeling, superposition or down-cutting when volcanic input increases deposition rates and forces channeling changes. The different facies identified indicate a shallow, seasonal, low-sinuosity, braided river environment. This is indicative of a well-contrasted dry-wet seasonal climate

Volcanic markers in coarse alluvium at Melka Kunture (Upper Awash, Ethiopia)

autorisation des éditeurs de l'ouvrage par email du 01/07/05The knowledge we have today of the different volcanic episodes which occurred over the last several million years in the environment of the Melka Kunture prehistoric sites allows a new appraisal of the nature and abundance of emitted lavas that are represented in the alluviums of the Awash River and its tributaries. Moreover, the most compact facies can also be seen in the different archaeological sites. Several alluvial units and some archaeological layers have been sampled and petrographic counts performed on the basis of mainly macroscopic and some microscopic determinations of the lavas. They allow comparisons between samples and offer a better understanding of local available raw materials for use by hominids

Antinuclear Antibodies in Patients with Psoriatic Arthritis Treated or Not with Biologics

International audienceBackground:With the emergence of biotherapies, accurate diagnosis in early arthritis is needed. At this time, there is no biological marker of psoriatic arthritis.Objective:To test whether antinuclear antibodies (ANA) can be used as a diagnostic tool in psoriatic arthritis (PsA), we evaluated the prevalence of ANA in biologic-naïve PsA patients and in healthy blood donors.Methods:232 patients from the Rheumatology department, St Marguerite's Hospital, Marseilles, who fulfilled the CASPAR criteria for PsA, underwent clinical and laboratory investigations. Antinuclear antibodies (ANA), anti-extractable nuclear antigen antibodies (ENA), rheumatoid factor (RF), anti-citrullinated protein antibodies (ACPA) were assayed. Ninety-one healthy blood donors were also tested.Results:Detection of ANA by indirect immunofluorescence was significantly more frequent in sera from PsA patients than those from controls at serum dilution of 1:100 (57% compared with 40%, Odds Ratio (OR) 1.98 (1.2-3.4) p<0.02) and 1:160 (52% compared with 24%, OR 3,7 (1.9-7.2) p<0.001). No patients had lupus specific autoantibodies, 15 % had RF (34/232), and 1.7 % had ACPA (4/232).Conclusions:Detection of ANA was more frequent in sera from PsA patients than in those from healthy controls. This suggests that ANA could be a diagnosis orientation tool in PsA. Nevertheless, the specificity of these antibodies still remains to be investigated

3-Amino­carbonyl­pyridinium difluoro­acetate at 123 K

In the crystal of the title compound, C6H7N2O+·C2HF2O2 −, the cation adopts a catemeric N—H⋯O hydrogen-bonded chain motif involving the carboxamide group, with two further N—H⋯O hydrogen bonds connecting the cations to adjacent difluoro­acetate anions via the carboxamide and pyridinium N atoms. The carboxamide group of the nicotinamidium ion is twisted by 32.3 (6)° from the pyridine ring plane. A number of C—H⋯O and C—H⋯F interactions consolidate the packing

Ptk7-Deficient Mice Have Decreased Hematopoietic Stem Cell Pools as a Result of Deregulated Proliferation and Migration

International audienceHematopoietic stem cells (HSCs) located in adult bone marrow or fetal liver in mammals produce all cells from the blood system. Atthe top of the hierarchy are long-term HSCs endowed with lifelong self-renewal and differentiation properties. These features arecontrolled through key microenvironmental cues and regulatory pathways, such as Wnt signaling.We showed previously that PTK7,a tyrosine kinase receptor involved in planar cell polarity, plays a role in epithelial Wnt signaling; however, its function in hematopoiesishas remained unexplored. In this article, we show that PTK7 is expressed by hematopoietic stem and progenitor cells, withthe highest level of protein expression found on HSCs. Taking advantage of a Ptk7-deficient mouse strain, we demonstrate that loss ofPtk7 leads to a diminished pool of HSCs but does not affect in vitro or in vivo hematopoietic cell differentiation. This is correlatedwith increased quiescence and reduced homing abilities of Ptk7-deficient hematopoietic stem and progenitor cells, unraveling noveland unexpected functions for planar cell polarity pathways in HSC fate

Patch-Based Markov Models for Event Detection in Fluorescence Bioimaging

International audienceThe study of protein dynamics is essential for understanding the multi-molecular complexes at subcellular levels. Fluorescent Protein (XFP)-tagging and time-lapse fluorescence microscopy enable to observe molecular dynamics and interactions in live cells, unraveling the live states of the matter. Original image analysis methods are then required to process challenging 2D or 3D image sequences. Recently, tracking methods that estimate the whole trajectories of moving objects have been successfully developed. In this paper, we address rather the detection of meaningful events in spatio-temporal fluorescence image sequences, such as apparent stable "stocking areas" involved in membrane transport. We propose an original patch-based Markov modeling to detect spatial irregularities in fluorescence images with low false alarm rates. This approach has been developed for real image sequences of cells expressing XFP-tagged Rab proteins, known to regulate membrane trafficking