Biology subjects

Caffarra, S.

Publications and source records attributed to Caffarra, S..

14 recordsLinked to original sources

bioRxiv2026

Highly replicable multisite patterns of adolescent white matter maturation

The Adolescent Brain Cognitive Development (ABCD) Study is the largest U.S.-based neuroimaging initiative of adolescent brain maturation. Diffusion MRI (dMRI) provides unique insights into white matter organization, yet applying advanced processing pipelines and managing technical variability across scanning environments remains challenging at scale. To address these issues, we present ABCD-BIDS Community Collection (ABCC) release 3.1.0, including a curated resource of more than 24,000 fully processed ABCD dMRI datasets. ABCC provides fully processed images, nuanced image quality metrics, advanced microstructural measures, and person-specific bundle tractography. Evaluating these rich data revealed that measures of diffusion restriction and non-Gaussianity--in particular the intracellular volume fraction from NODDI and return-to-origin probability from MAP-MRI--were highly sensitive to neurodevelopment and robust to variation in image quality. Additionally, harmonization of microstructural features markedly improved the cross-vendor generalizability of developmental effects. Together, ABCC accelerates reproducible, rigorous research on adolescent white matter development.

neuroscience↗

bioRxiv2026

Alternative strategies of orthographic processing: the case of skilled deaf readers

The cognitive factors that enable us to be proficient readers can greatly vary across individuals. The case of skilled deaf readers is emblematic as it shows that high reading performances can be achieved even when lifelong acoustic experience is absent or minimal. Here we present a set of experiments investigating how alternative strategies of orthographic processing can lead to high levels of reading proficiency. Four EEG studies compared behavioral and brain correlates of orthographic processing in skilled deaf readers and matched hearing controls. Using single word recognition and priming paradigms, we investigated two pillars of orthographic processing: letter identity and letter position. Our findings show that, although both groups had similarly accurate reading performance, skilled deaf readers were faster, and they consistently differ from hearing controls in the way they process letter identity. This group difference was observed in both lexical and sublexical tasks and was specifically related to the identity of orthographic representations, regardless of the visual form of the written stimuli (such as character visual similarity and letter case). These findings uncover alternative strategies that make possible high reading performance, even in the absence of acoustic experience. Public Significance StatementThis research identifies alternative orthographic strategies that improve single-word reading efficiency and can potentially serve as effective compensatory tools when phonological processing is impaired.

neuroscience↗

bioRxiv2024

Assessing white matter plasticity in a randomized controlled trial of early literacy training in preschoolers

Reading is a cognitive skill that requires our brain to go through a myriad of changes during learning. While many studies have described how reading acquisition shapes childrens brain function, less is known about the impact of reading on brain structure. Here we examined short-term causal effects of reading training on preschoolers behavior and white matter structure. Forty-eight English-speaking preschoolers (4y10m to 6y2m) participated in a randomized controlled trial where they were randomly assigned to two training programs: the Letter training program was focused on key skills for reading (e.g., decoding and letter knowledge), while the Language training program strengthened oral language comprehension skills without exposure to text. Longitudinal behavioral data showed that only the Letter Training group increased letter knowledge and decoding skills after the two-week training. Diffusion MRI measures (FA and MD) of eighteen white matter pathways (including the left arcuate and the left inferior longitudinal fasciculus) did not reveal any statistically significant changes for either group despite high degrees of scan-rescan reliability across sessions. These findings suggest that a two- week reading training program can cause changes in preschoolers letter knowledge and decoding abilities, without being accompanied by measurable changes in the diffusion properties of the major white matter pathways of the reading network. We conclude highlighting possible constraints (i.e., age, training onset and duration, cognitive profile) to reading-related white matter plasticity.

neuroscience↗

bioRxiv2023

The impact of speaker accent on discourse processing: a frequency investigation

Previous studies show that there are differences in native and foreign speech processing (Lev-Ari, 2018) while mixed evidence has been found regarding differences between dialectal and foreign accent processing (see: Adank et al., 2009; Floccia et al. 2006 but see also: Floccia et al., 2009; Girard et al., 2008). Within this field, two theories have been proposed. The Perceptual Distance Hypothesis states that the mechanisms underlying dialectal accent processing are attenuated versions of those of foreign (Clarke & Garrett, 2004). While, the Different Processes Hypothesis argues that the mechanisms of foreign and dialectal accent processing are qualitatively different (Floccia et al, 2009). A recent study looking at single-word EEG data, suggested that there may be flexibility in processing mechanisms (Thomas et al., 2022). The present study deepens this investigation by addressing in which frequency bands native, dialectal and foreign accent processing differ when listening to extended speech. Electroencephalographic data was recorded from 30 participants who listened to dialogues of approximately six minutes spoken in native, dialectal and foreign accents. Power spectral density estimation (1-35 hz) was performed. Linear mixed models were done in frequency windows of particular relevance to discourse processing. Frequency bands associated with phoneme [gamma], syllable [theta], and prosody [delta] were considered along with those of general cognitive mechanisms [alpha and beta]. Results show power differences in the Gamma frequency range. While in higher frequency ranges foreign accent processing is differentiated from power amplitudes of native and dialectal accent processing, in low frequencies we do not see any accent-related power amplitude modulations. This suggests that there may be a difference in phoneme processing for native accent types and foreign accent, while we speculate that top-down mechanisms during discourse processing may mitigate the effects observed with short units of speech.

neuroscience↗

bioRxiv2023

Specific and non-linear effects of glaucoma on optic radiation tissue properties

Changes in sensory input with aging and disease affect brain tissue properties. To establish the link between glaucoma, the most prevalent cause of irreversible blindness, and changes in major brain connections, we characterized white matter tissue properties in diffusion MRI measurements in a large sample of subjects with glaucoma (N=905; age 49-80) and healthy controls (N=5,292; age 45-80) from the UK Biobank. Confounds due to group differences were mitigated by matching a sub-sample of controls to glaucoma subjects. A convolutional neural network (CNN) accurately classified whether a subject has glaucoma using information from the primary visual connection to cortex (the optic radiations, OR), but not from non-visual brain connections. On the other hand, regularized linear regression could not classify glaucoma, and the CNN did not generalize to classification of age-group or of age-related macular degeneration. This suggests a unique non-linear signature of glaucoma in OR tissue properties.

neuroscience↗

bioRxiv2022

Optic radiations representing different eccentricities age differently

The white matter pathways that carry information from the foveal, macular, and peripheral visual fields have distinct biological properties. The optic radiations (OR) carry foveal and peripheral information from the thalamus to the primary visual cortex (V1) through adjacent but separate pathways in the white matter. Here, we perform white matter tractometry using pyAFQ 1 on a large sample of diffusion MRI (dMRI) data from the UK Biobank dataset (UKBB; N=6021; age 45-81). We use pyAFQ to characterize white matter tissue properties in parts of the OR that transmit information about the foveal, macular, and peripheral visual fields, and to characterize the changes in these tissue properties with age. We find that (1) independent of age there is higher fractional anisotropy, lower mean diffusivity, and higher mean kurtosis in the foveal and macular OR than in peripheral OR, consistent with denser, more organized nerve fiber populations in foveal/parafoveal pathways, and (2) age is associated with increased diffusivity and decreased anisotropy and kurtosis, consistent with decreased density and tissue organization with adulthood aging. However, anisotropy in foveal OR decreases faster with age than in peripheral OR, while diffusivity increases faster in peripheral OR, suggesting foveal/peri-foveal OR and peripheral OR differ in how they age.

neuroscience↗

bioRxiv2022

Development of the alpha rhythm is linked to visual white matter pathways and visual detection performance

Alpha is the strongest electrophysiological rhythm in awake humans at rest. Despite its predominance in the EEG signal, strong variations can be observed in alpha properties during development, with an increase of alpha frequency over childhood and adulthood. Here we tested the hypothesis that these changes of alpha rhythm are related to the maturation of visual white matter pathways. We capitalized on a large dMRI-EEG dataset (dMRI n=2,747, EEG n=2,561) of children and adolescents (age range: 5-21 years old) and showed that maturation of the optic radiation specifically accounts for developmental changes of alpha frequency. Behavioral analyses also confirmed that variations of alpha frequency are related to maturational changes in visual perception. The present findings demonstrate the close link between developmental variations in white matter tissue properties, electrophysiological responses, and behavior.

neuroscience↗

bioRxiv2022

An ERP investigation of accented isolated single word processing

Previous studies show that there are differences in native and non-native speech processing (Lev-Ari, 2018). However, less is known about the differences between processing native and dialectal accents. Is dialectal processing more similar to foreign or native speech? To address this, two theories have been proposed. The Perceptual Distance Hypothesis states that the mechanisms underlying dialectal accent processing are attenuated versions of those of foreign (Clarke & Garrett, 2004). Conversely, the Different Processes Hypothesis argues that the mechanisms of foreign and dialectal accent processing are qualitatively different (Floccia et al, 2009). The present study addresses these hypotheses. Electroencephalographic data was recorded from 25 participants who listened to 40 isolated words in different accents. Event-Related Potential mean amplitudes were extracted: P2 [150-250 ms], PMN [250-400 ms] and N400 [400-600 ms]. Support for the Different Processes Hypothesis was found in different time windows. Results show that early processing mechanisms distinguish only between native and non-native speech, with a reduced P2 amplitude for foreign accent processing, supporting the Different Processes Hypothesis. Furthermore, later processing mechanisms show a similar binary difference in the processing of the accents, with a larger PMN negativity elicited in the foreign accent than the others, further supporting the Different Processes Hypothesis. Results contribute to the understanding of single word processing, in which it is uniquely difficult to extract acoustic characteristics from foreign accent, and in which foreign accented speech is associated with the largest cost, as compared to native and dialectal speech, of phonological matching between representations and acoustic input. HighlightsO_LIAccent affects early speech processing mechanisms at the level of the isolated word C_LIO_LIAcoustic characteristic extraction is more difficult for foreign-accented speech C_LIO_LIPhonological normalization of foreign-accented speech is uniquely difficult C_LIO_LIAccent no longer affects later speech processing mechanisms at the isolated word C_LI

neuroscience↗

bioRxiv2022

An open, analysis-ready, and quality controlled resource for pediatric brain white-matter research

We created resources to facilitate research on the role of human brain microstructure in the development of mental health disorders, based on openly-available diffusion MRI (dMRI) data from the Healthy Brain Network (HBN) study. First, we curated the HBN dMRI data (N=2747) into the Brain Imaging Data Structure and preprocessed it according to best-practices, including denoising and correcting for motion effects, susceptibility-related distortions, and eddy currents. Preprocessed, analysis-ready data was made openly available. Data quality plays a key role in the analysis of dMRI, and we provide automated quality control (QC) scores for every scan, as part of the data release. To scale QC to this large dataset, we trained a neural network through the combination of a small data subset scored by experts and a larger set scored by community scientists. The network performs QC highly concordant with that of experts on a held out set (ROC-AUC = 0.947). A further analysis of the neural network demonstrates that it relies on image features with relevance to QC. Altogether, this work both delivers a resource for transdiagnostic research in brain connectivity and pediatric mental health and serves as a novel tool for automated QC of large datasets.

neuroscience↗

bioRxiv2022

Reading instruction causes changes in category-selective visual cortex

Education sculpts specialized neural circuits for skills like reading that are critical to success in modern society but were not anticipated by the selective pressures of evolution. Does the emergence of brain regions that selectively process novel visual stimuli like words occur at the expense of cortical representations of other stimuli like faces and objects? To answer this question we conducted a randomized controlled trial with pre-school children (five years of age). We found that being taught reading versus oral language skills induced different patterns of change in category-selective regions of visual cortex. Reading instruction enhanced the response to text but did not diminish the response to other categories. How these changes play out over a longer timescale is still unknown but, based on these data, we can surmise that high-level visual cortex undergoes rapid changes as children enter school and begin establishing new skills like literacy.

neuroscience↗

bioRxiv2021

Development of the visual white matter pathways mediates development of electrophysiological responses in visual cortex

The latency of neural responses in the visual cortex changes systematically across the lifespan. Here we test the hypothesis that development of visual white matter pathways mediates maturational changes in the latency of visual signals. Thirty-eight children participated in a cross-sectional study including diffusion MRI and MEG sessions. During the MEG acquisition, participants performed a lexical decision and a fixation task on words presented at varying levels of contrast and noise. For all stimuli and tasks, early evoked fields were observed around 100 ms after stimulus onset (M100), with slower and lower amplitude responses for low as compared to high contrast stimuli. The optic radiations and optic tracts were identified in each individuals brain based on diffusion MRI tractography. The diffusion properties of the optic radiations predicted M100 responses, especially for high contrast stimuli. Higher optic radiation fractional anisotropy (FA) values were associated with faster and larger M100 responses. Over this developmental window, the M100 responses to high contrast stimuli became faster with age and the optic radiation FA mediated this effect. These findings suggest that the maturation of the optic radiations over childhood accounts for individual variations observed in the developmental trajectory of visual cortex responses.

neuroscience↗

bioRxiv2021

Reading-related brain changes in audiovisual processing: cross-sectional and longitudinal MEG evidence

The ability to establish associations between visual objects and speech sounds is essential for human reading. Understanding the neural adjustments required for acquisition of these arbitrary audiovisual associations can shed light on fundamental reading mechanisms and help reveal how literacy builds on pre-existing brain circuits. To address these questions, the present longitudinal and cross-sectional MEG studies characterize the temporal and spatial neural correlates of audiovisual syllable congruency in children (4-9 years old, 22 males and 20 females) learning to read. Both studies showed that during the first years of reading instruction children gradually set up audiovisual correspondences between letters and speech sounds, which can be detected within the first 400 ms of a bimodal presentation and recruit the superior portions of the left temporal cortex. These findings suggest that children progressively change the way they treat audiovisual syllables as a function of their reading experience. This reading-specific brain plasticity implies (partial) recruitment of pre-existing brain circuits for audiovisual analysis. Significance StatementLinking visual and auditory linguistic representations is the basis for the development of efficient reading, while dysfunctional audiovisual letter processing predicts future reading disorders. Our developmental MEG project included a longitudinal and a cross-sectional study; both studies showed that childrens audiovisual brain circuits progressively change as a function of reading experience. They also revealed an exceptional degree of neuroplasticity in audiovisual neural networks, showing that as children develop literacy, the brain progressively adapts so as to better detect new correspondences between letters and speech sounds.

neuroscience↗

bioRxiv2021

Evaluating the reliability of human brain white matter tractometry

The validity of research results depends on the reliability of analysis methods. In recent years, there have been concerns about the validity of research that uses diffusion-weighted MRI (dMRI) to understand human brain white matter connections in vivo, in part based on reliability of the analysis methods used in this field. We defined and assessed three dimensions of reliability in dMRI-based tractometry, an analysis technique that assesses the physical properties of white matter pathways: (1) reproducibility, (2) test-retest reliability and (3) robustness. To facilitate reproducibility, we provide software that automates tractometry (https://yeatmanlab.github.io/pyAFQ). In measurements from the Human Connectome Project, as well as clinical-grade measurements, we find that tractometry has high test-retest reliability that is comparable to most standardized clinical assessment tools. We find that tractometry is also robust: showing high reliability with different choices of analysis algorithms. Taken together, our results suggest that tractometry is a reliable approach to analysis of white matter connections. The overall approach taken here both demonstrates the specific trustworthiness of tractometry analysis and outlines what researchers can do to demonstrate the reliability of computational analysis pipelines in neuroimaging.

neuroscience↗

bioRxiv2017

Is the LAN effect in morphosyntactic processing an ERP artifact?

The left anterior negativity (LAN) is an ERP component that has been often associated with morphosyntactic processing, but recent reports have questioned whether the LAN effect, in fact, exists. The present project examined whether the LAN effect, observed in the grand average response to local agreement violations, is the result of the overlap between two different ERP effects (N400, P600) at the level of subjects (n=80), items (n=120), or trials (n=6160). By-subject, by-item, and by-trial analyses of the ERP effect between 300 and 500 ms showed a LAN for 55% of the participants, 46% of the items, and 49% of the trials. Many examples of the biphasic LAN-P600 response were observed. Mixed-linear models showed that the LAN effect size was not reduced after accounting for subject variability. The present results suggest that there are cases where the grand average LAN effect represents the brain responses of individual participants, items, and trials.

neuroscience↗