Towards a mathematical definition of functional connectivity

Functional connectivity is a neurobiological notion, informally stating that there would be a strong dependence between neurons and that this dependence might be useful in understanding the way the brain encodes stimuli, programs actions, etc. However, in practice such strong dependencies are often reconstructed via Hawkes processes based on an amazingly small number of neurons, because of the very scarce observation of this very complex and huge network. We derive new simple equations, which explain how the ideal Hawkes reconstruction is linked to the covariance between the observed neurons. These equations help us in particular to understand what the Hawkes reconstruction does in two settings, synchronization and classical point process asymptotics. Moreover they might help us to also understand what is qualitatively happening at the scale of the huge unobserved network, paving the path for a possible mathematical definition of functional connectivity

Towards a mathematical definition of functional connectivity

Functional connectivity is a neurobiological notion, informally stating that there would be a strong dependence between neurons and that this dependence might be useful in understanding the way the brain encodes stimuli, programs actions, etc. However, in practice such strong dependencies are often reconstructed via Hawkes processes based on an amazingly small number of neurons, because of the very scarce observation of this very complex and huge network. We derive new simple equations, which explain how the ideal Hawkes reconstruction is linked to the covariance between the observed neurons. These equations help us in particular to understand what the Hawkes reconstruction does in two settings, synchronization and classical point process asymptotics. Moreover they might help us to also understand what is qualitatively happening at the scale of the huge unobserved network, paving the path for a possible mathematical definition of functional connectivity

Interocular interaction of contrast and luminance signals in human primary visual cortex

Interocular interaction in the visual system occurs under dichoptic conditions when contrast and luminance are imbalanced between the eyes. Human psychophysical investigations suggest that interocular interaction can be explained by a contrast normalization model. However, the neural processes that underlie such interactions are still unresolved. We set out to assess, for the first time, the proposed normalization model of interocular contrast interactions using magnetoencephalography and to extend this model to incorporate interactions based on interocular luminance differences. We used magnetoencephalography to record steady-state visual evoked responses (SSVER), and functional magnetic resonance imaging (fMRI) to obtain individual retinotopic maps that we used in combination with MEG source imaging in healthy participants. Binary noise stimuli were presented in monocular or dichoptic viewing and were frequency-tagged at 4 and 6 Hz. The contrast of the stimuli was modulated in a range between 0 and 32%. Monocularly, we reduced the luminance by placing a 1.5 ND filter over one eye in the maximal contrast condition. This ND filter reduces the mean light level by a factor of 30 without any alteration to the physical contrast. We observed in visual area V1 a monotonic increase in the magnitude of SSVERs with changes in contrast from 0 to 32%. For both eyes, dichoptic masking induced a decrease in SSVER signal power. This power decrease was well explained by the normalization model. Reducing mean luminance delayed monocular processing by approximately 38 ms in V1. The reduced luminance also decreased the masking ability of the eye under the filter. Predictions based on a temporal filtering model for the interocular luminance difference prior to the model's binocular combination stage were incorporated to update the normalization model. Our results demonstrate that the signals resulting from different contrast or luminance stimulation of the two eyes are combined in a way that can be explained by an interocular normalization model

Reference gene selection for head and neck squamous cell carcinoma gene expression studies

<p>Abstract</p> <p>Background</p> <p>It is no longer adequate to choose reference genes blindly. We present the first study that defines the suitability of 12 reference genes commonly used in cancer studies (<it>ACT, ALAS, B2M, GAPDH, HMBS, HPRT, KALPHA, RPS18, RPL27, RPS29, SHAD </it>and <it>TBP</it>) for the normalization of quantitative expression data in the field of head and neck squamous cell carcinoma (HNSCC).</p> <p>Results</p> <p>Raw expression levels were measured by RT-qPCR in HNSCC and normal matched mucosa of 46 patients. We analyzed the expression stability using geNorm and NormFinder and compared the expression levels between subgroups. In HNSCC and/or normal mucosa, the four best normalization genes were <it>ALAS, GAPDH, RPS18 </it>and <it>SHAD </it>and the most stable combination of two genes was <it>GAPDH-SHAD</it>. We recommend using <it>KALPHA-TBP </it>for the study of T1-T2 tumors, <it>RPL27-SHAD </it>for T3-T4 tumors, <it>KALPHA-SHAD </it>for N0 tumors, and <it>ALAS-TBP </it>for N+ tumors. <it>ACT, B2M, GAPDH, HMBS, HPRT, KALPHA, RPS18, RPS29, SHAD </it>and <it>TBP </it>were slightly misregulated (<1.7-fold) between tumor and normal mucosa but can be used for normalization, depending on the resolution required for the assay.</p> <p>Conclusion</p> <p>In the field of HNSCC, this study will guide researchers in selecting the most appropriate reference genes from among 12 potentially suitable reference genes, depending on the specific setting of their experiments.</p

Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

Abstract Background Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands. Results The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. Conclusions Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island

Evolution of African cassava mosaic virus by recombination between bipartite and monopartite begomoviruses

<p>Abstract</p> <p>Background</p> <p>Cassava mosaic disease (CMD) is a major constraint on cassava cultivation in Africa. The disease is endemic and is caused by seven distinct cassava mosaic geminiviruses (CMGs), some of them including several variants.</p> <p>Findings</p> <p>From cassava leaf samples presenting CMD symptoms collected in Burkina Faso, four DNA-A begomovirus components were cloned and sequenced, showing 99.9% nucleotide identity among them. These isolates are most closely related to <it>African cassava mosaic virus </it>(ACMV) but share less than 89% nucleotide identity (taxonomic threshold) with any previously described begomovirus. A DNA-B genomic component, sharing 93% nucleotide identity with DNA-B of ACMV, was also characterized. Since all genomic components have a typical genome organization of Old World bipartite begomoviruses, this new species was provisionally named African cassava mosaic Burkina Faso virus (ACMBFV). Recombination analysis of the new virus demonstrated an interspecies recombinant origin, with major parents related to West African isolates of ACMV, and minor parents related to <it>Tomato leaf curl Cameroon virus </it>and <it>Cotton leaf curl Gezira virus</it>.</p> <p>Conclusion</p> <p>This is the first report of an ACMV-like recombinant begomovirus arisen by interspecific recombination between bipartite and monopartite African begomoviruses.</p

Inquilinus limosus and Cystic Fibrosis

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