Biology subjects

Barone, P.

Publications and source records attributed to Barone, P..

5 recordsLinked to original sources

bioRxiv2025

Optimizing short-channel regression in fNIRS: an empirical evaluation in a naturalistic multimodal paradigm

SignificanceFunctional Near-Infrared Spectroscopy (fNIRS) is increasingly favored for its portability and suitability for ecological paradigms, yet methodological standardization remains a challenge regarding the optimal use of short-separation channels (SC) to remove systemic physiological noise. AimWe aim to evaluate and compare methods of SC regression as implemented in the most widely used fNIRS analysis toolboxes, with the goal of reaching a consensus on best practices for incorporating SC into generalized linear model (GLM)-based analyses. Specifically, we compared ten SC regression strategies addressing SC selectivity, dimensionality reduction strategies, and SC availability. Approach16 healthy adults passively listened and watched ecological auditory, visual, and audiovisual stimuli while occipital and bilateral auditory cortices were recorded. ResultsOxygenated hemoglobin signals (HbO) processed without SC regression produced uninterpretable results in the context of the present study. Non-selective SC regression methods that pooled all available SC signals consistently outperformed anatomically or functionally restricted approaches. Orthogonalization further enhanced performance by reducing redundancy and capturing shared systemic variance, improving detection of stimulus-specific cortical responses and contrast sensitivity. Deoxygenated hemoglobin signals (HbR), while less sensitive to systemic artifacts than HbO, benefited most, similarly to HbO, from the pooled, orthogonalized SC signal approach. ConclusionOverall, our findings highlight the essential role of SC regression in recovering physiologically meaningful signals in fNIRS and recommend including all available SC channels within the GLM, coupled with orthogonalization techniques, as a generalizable best practice for denoising across hardware configurations.

neuroscience↗

bioRxiv2020

Efficient Gene Targeting in Maize using Inducible CRISPR-Cas9 and Marker-Free Donor Template

CRISPR-Cas9 is a powerful tool for generating targeted mutations and genomic deletions. However, precise gene insertion or sequence replacement remains a major hurdle before application of CRISPR-Cas9 technology is fully realized in plant breeding. Here we report high frequency, selectable marker-free intra-genomic gene targeting (GT) in maize. Heat shock-inducible Cas9 was used for generating targeted double-strand breaks (DSBs) and simultaneous mobilization of the donor template from pre-integrated T-DNA. The construct was designed such that release of the donor template and subsequent DNA repair activated expression of the selectable marker gene within the donor locus. This approach generated up to 4.7% targeted insertion of the donor sequence into the target locus in T0 plants, with up to 86% detected donor template release and 99% mutation rate were observed at the donor loci and the genomic target site, respectively. Unlike previous in planta or intra-genomic homologous recombination reports, that required multiple generations and extensive screening, our method provides non-chimeric, heritable GT in the T0 generation.

plant biology↗

bioRxiv2019

Stimulation-specific information is represented as local activity patterns across the brain

Modern neuroimaging represents three-dimensional brain activity, which varies across brain regions. It remains unknown whether activity within brain regions is organized in spatial configurations to reflect perceptual and cognitive processes. We developed a rotational cross-correlation method allowing a straightforward analysis of spatial activity patterns for the precise detection of the spatially correlated distributions of brain activity. Using several statistical approaches, we found that the seed patterns in the fusiform face area were robustly correlated to brain regions involved in face-specific representations. These regions differed from the non-specific visual network meaning that activity structure in the brain is locally preserved in stimulation-specific regions. Our findings indicate spatially correlated perceptual representations in cerebral activity and suggest that the 3D coding of the processed information is organized in locally preserved activity patterns. More generally, our results provide the first demonstration that information is represented and transmitted as local spatial configurations of brain activity.

neuroscience↗

bioRxiv2019

Unique Features of Sub-Cortical Circuits in A Macaque Model of Congenital Blindness

There is extensive modification of the functional organization of the brain in the congenital blind human, although there is little understanding of the structural underpinnings of these changes. The visual system of macaque has been extensively characterized both anatomically and functionally. We have taken advantage of this to examine the influence of the congenital blindness in macaque resulting from the removal of the retina during in utero development. Developmental anophthalmia in macaque effectively removes the normal influence of the thalamus on cortical development leading to an induced hybrid cortex (HC) combining features of primary visual and extrastriate cortex. Here we show that retrograde tracers injected in early visual areas including hybrid cortex reveals a drastic reduction of cortical projections of the reduced lateral geniculate nucleus. In addition, there is an important expansion of projections from the pulvinar complex to the hybrid cortex, compared to the controls. These findings show that the functional consequences of congenital blindness need to be considered in terms of both modifications of the inter-areal cortical network and the ascending visual pathways.

neuroscience↗

bioRxiv2017

Cortical Connectivity In A Macaque Model Of Congenital Blindness

AbstractBrain-mapping of the congenitally blind human reveals extensive plasticity(1). The visual cortex of the blind has been observed to support higher cognitive functions including language and numerical processing(2, 3). This functional shift is hypothesized to reflect a metamodal cortical function, where computations are defined by the local network. In the case of developmental deafferentation, local circuits are considered to implement higher cognitive functions by accommodating diverse long-distance inputs(4-7). However, the extent to which visual deprivation triggers a reorganization of the large-scale network in the cortex is still controversial(8). Here we show that early prenatal ablation of the retina, an experimental model of anophthalmia in macaque, leads to a major reduction of area V1 and the creation of a default extrastriate cortex (DEC)(9, 10). Anophthalmic and normal macaques received retrograde tracer injections in DEC, as well as areas V2 and V4 post-natally. This revealed a six-fold expansion of the spatial extent of local connectivity in the DEC and a surprisingly high location of the DEC derived from a computational model of the cortical hierarchy(11). In the anophthalmic the set of areas projecting to the DEC, area V2 and V4 does not differ from that of normal adult controls, but there is a highly significant increase in the relative cumulative weight of the ventral stream areas input to the early visual areas. These findings show that although occupying the territory that would have become primary visual cortex the DEC exhibits features of a higher order area, thus reflecting a combination of intrinsic and extrinsic factors on cortical specification. Understanding the interaction of these contributing factors will shed light on cortical plasticity during primate development and the neurobiology of blindness.

neuroscience↗