Center for Neuroscience and Cognitive Systems

Abstract Over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight 1 . Here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of MRI data ( http://www.brainchart.io/ ). With the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of MRI studies relative to the diversity of the global population, we aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. MRI metrics were quantified by centile scores, relative to non-linear trajectories 2 of brain structural changes, and rates of change, over the lifespan. Brain charts identified previously unreported neurodevelopmental milestones 3 , showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. Centile scores showed increased heritability compared with non-centiled MRI phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. In summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.

Cortical oscillations are likely candidates for segmentation and coding of continuous speech. Here, we monitored continuous speech processing with magnetoencephalography (MEG) to unravel the principles of speech segmentation and coding. We demonstrate that speech entrains the phase of low-frequency (delta, theta) and the amplitude of high-frequency (gamma) oscillations in the auditory cortex. Phase entrainment is stronger in the right and amplitude entrainment is stronger in the left auditory cortex. Furthermore, edges in the speech envelope phase reset auditory cortex oscillations thereby enhancing their entrainment to speech. This mechanism adapts to the changing physical features of the speech envelope and enables efficient, stimulus-specific speech sampling. Finally, we show that within the auditory cortex, coupling between delta, theta, and gamma oscillations increases following speech edges. Importantly, all couplings (i.e., brain-speech and also within the cortex) attenuate for backward-presented speech, suggesting top-down control. We conclude that segmentation and coding of speech relies on a nested hierarchy of entrained cortical oscillations.

BACKGROUND: The available classifications of gastritis are inconsistently used, possibly because none provides immediate prognostic/therapeutic information to clinicians. As histology reporting of hepatitis in terms of stage is clinically useful and widely accepted, an international group (Operative Link on Gastritis Assessment (OLGA)) proposed an equivalent staging system for reporting gastric histology. Gastritis staging integrates the atrophy score (obtained by biopsy) and the atrophy topography (achieved through directed biopsy mapping). AIM: To test in a prospective cross-sectional study whether OLGA staging consistently stratified patients according to their cancer risk and provided clear prognostic/therapeutic information. METHODS: OLGA staging for gastric cancer risk (0-IV) and gastritis grading (overall score of the inflammatory infiltrate, grade 1-4) were applied in 439 prospectively enrolled, consecutive, dyspeptic outpatients who underwent endoscopy with standardised biopsy sampling. Incidental neoplastic lesions and coexisting peptic ulcers were recorded. Results were presented as stage (including antral (A) and corpus (C) atrophy scores) and H pylori status (eg, A = 3; C = 2: stage IV; Hp+ve). RESULTS: Benign conditions (including duodenal ulcers; p<0.001) consistently clustered in stages 0-II, whereas all neoplastic (invasive and non-invasive) lesions clustered in stages III-IV (p<0.001). CONCLUSIONS: Gastritis staging, combined with H pylori status, provided clinically relevant information on the overall status of the gastric mucosa with implications for prognosis, therapy and management.

Leaky integrate-and-fire (LIF) network models are commonly used to study how the spiking dynamics of neural networks changes with stimuli, tasks or dynamic network states. However, neurophysiological studies in vivo often rather measure the mass activity of neuronal microcircuits with the local field potential (LFP). Given that LFPs are generated by spatially separated currents across the neuronal membrane, they cannot be computed directly from quantities defined in models of point-like LIF neurons. Here, we explore the best approximation for predicting the LFP based on standard output from point-neuron LIF networks. To search for this best "LFP proxy", we compared LFP predictions from candidate proxies based on LIF network output (e.g, firing rates, membrane potentials, synaptic currents) with "ground-truth" LFP obtained when the LIF network synaptic input currents were injected into an analogous three-dimensional (3D) network model of multi-compartmental neurons with realistic morphology, spatial distributions of somata and synapses. We found that a specific fixed linear combination of the LIF synaptic currents provided an accurate LFP proxy, accounting for most of the variance of the LFP time course observed in the 3D network for all recording locations. This proxy performed well over a broad set of conditions, including substantial variations of the neuronal morphologies. Our results provide a simple formula for estimating the time course of the LFP from LIF network simulations in cases where a single pyramidal population dominates the LFP generation, and thereby facilitate quantitative comparison between computational models and experimental LFP recordings in vivo.

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

Why are some visual stimuli consciously detected, whereas others remain subliminal? We investigated the fate of weak visual stimuli in the visual and frontal cortex of awake monkeys trained to report stimulus presence. Reported stimuli were associated with strong sustained activity in the frontal cortex, and frontal activity was weaker and quickly decayed for unreported stimuli. Information about weak stimuli could be lost at successive stages en route from the visual to the frontal cortex, and these propagation failures were confirmed through microstimulation of area V1. Fluctuations in response bias and sensitivity during perception of identical stimuli were traced back to prestimulus brain-state markers. A model in which stimuli become consciously reportable when they elicit a nonlinear ignition process in higher cortical areas explained our results.

Occipito-temporal cortex is known to house visual object representations, but the organization of the neural activation patterns along this cortex is still being discovered. Here we found a systematic, large-scale structure in the neural responses related to the interaction between two major cognitive dimensions of object representation: animacy and real-world size. Neural responses were measured with functional magnetic resonance imaging while human observers viewed images of big and small animals and big and small objects. We found that real-world size drives differential responses only in the object domain, not the animate domain, yielding a tripartite distinction in the space of object representation. Specifically, cortical zones with distinct response preferences for big objects, all animals, and small objects, are arranged in a spoked organization around the occipital pole, along a single ventromedial, to lateral, to dorsomedial axis. The preference zones are duplicated on the ventral and lateral surface of the brain. Such a duplication indicates that a yet unknown higher-order division of labor separates object processing into two substreams of the ventral visual pathway. Broadly, we suggest that these large-scale neural divisions reflect the major joints in the representational structure of objects and thus place informative constraints on the nature of the underlying cognitive architecture.

Abstract Focusing on the dehumanization of sexually objectified targets, study 1 tested the extent to which objectified and non‐objectified male and female publicity photos were associated with human compared to animal concepts. Results confirmed the hypothesis that, among all targets, only objectified women were associated with less human concepts. This pattern of results emerged for both male and female participants but likely for different reasons. Study 2 directly looked at female and male participants' affinity with sexually objectified women. Results indicated that the more women distanced themselves from sexually objectified women the more they dehumanized them, whereas men's sexual attraction moderated their tendency to dehumanize female targets. In study 3, this latter motivation was operationalized as the activation of a sex goal and showed to trigger man's but not woman's dehumanization of female targets. Overall, the present set of studies show that only sexually objectified women are dehumanized by both men and women but for different reasons. Whereas sexual attraction shifts a men's focus of a female target away from her personality onto her body triggering a dehumanization process, women are more inclined to dehumanize their sexually objectified counterparts the more they distance themselves from these sexualized representations of their gender category. Copyright © 2011 John Wiley &amp; Sons, Ltd.

Parkinson's disease is associated with gastrointestinal motility abnormalities favoring the occurrence of local infections. The aim of this study was to investigate whether small intestinal bacterial overgrowth contributes to the pathophysiology of motor fluctuations. Thirty-three patients and 30 controls underwent glucose, lactulose, and urea breath tests to detect small intestinal bacterial overgrowth and Helicobacter pylori infection. Patients also underwent ultrasonography to evaluate gastric emptying. The clinical status and plasma concentration of levodopa were assessed after an acute drug challenge with a standard dose of levodopa, and motor complications were assessed by Unified Parkinson's Disease Rating Scale-IV and by 1-week diaries of motor conditions. Patients with small intestinal bacterial overgrowth were treated with rifaximin and were clinically and instrumentally reevaluated 1 and 6 months later. The prevalence of small intestinal bacterial overgrowth was significantly higher in patients than in controls (54.5% vs. 20.0%; P = .01), whereas the prevalence of Helicobacter pylori infection was not (33.3% vs. 26.7%). Compared with patients without any infection, the prevalence of unpredictable fluctuations was significantly higher in patients with both infections (8.3% vs. 87.5%; P = .008). Gastric half-emptying time was significantly longer in patients than in healthy controls but did not differ in patients based on their infective status. Compared with patients without isolated small intestinal bacterial overgrowth, patients with isolated small intestinal bacterial overgrowth had longer off time daily and more episodes of delayed-on and no-on. The eradication of small intestinal bacterial overgrowth resulted in improvement in motor fluctuations without affecting the pharmacokinetics of levodopa. The relapse rate of small intestinal bacterial overgrowth at 6 months was 43%. © 2013 Movement Disorder Society.

Anxiety is a mental state characterized by an intense sense of tension, worry or apprehension, relative to something adverse that might happen in the future. Researchers differentiate aspects of anxiety into state and trait, respectively defined as a more transient reaction to an adverse situation, and as a more stable personality attribute in experiencing events. It is yet unclear whether brain structural and functional features may distinguish these aspects of anxiety. To study this, we assessed 42 healthy participants with the State-Trait Anxiety Inventory and then investigated with MRI to characterize structural grey matter covariance and resting-state functional connectivity (rs-FC). We found several differences in the structural-functional patterns across anxiety types: (1) trait anxiety was associated to both structural covariance of Default Mode Network (DMN), with an increase in dorsal nodes and a decrease in its ventral part, and to rs-FC of DMN within frontal regions; (2) state anxiety, instead, was widely related to rs-FC of Salience Network and of DMN, specifically in its ventral nodes, but not associated with any structural pattern. In conclusion, our study provides evidence of a neuroanatomical and functional distinction between state and trait anxiety. These neural features may be additional markers in future studies evaluating early diagnosis or treatment effects.

Behavior relies on the distributed and coordinated activity of neural populations. Population activity can be measured using multi-neuron recordings and neuroimaging. Neural recordings reveal how the heterogeneity, sparseness, timing, and correlation of population activity shape information processing in local networks, whereas neuroimaging shows how long-range coupling and brain states impact on local activity and perception. To obtain an integrated perspective on neural information processing we need to combine knowledge from both levels of investigation. We review recent progress of how neural recordings, neuroimaging, and computational approaches begin to elucidate how interactions between local neural population activity and large-scale dynamics shape the structure and coding capacity of local information representations, make them state-dependent, and control distributed populations that collectively shape behavior.

Ischemic damage to the brain triggers substantial reorganization of spared areas and pathways, which is associated with limited, spontaneous restoration of function. A better understanding of this plastic remodeling is crucial to develop more effective strategies for stroke rehabilitation. In this review article, we discuss advances in the comprehension of post-stroke network reorganization in patients and animal models. We first focus on rodent studies that have shed light on the mechanisms underlying neuronal remodeling in the perilesional area and contralesional hemisphere after motor cortex infarcts. Analysis of electrophysiological data has demonstrated brain-wide alterations in functional connectivity in both hemispheres, well beyond the infarcted area. We then illustrate the potential use of non-invasive brain stimulation (NIBS) techniques to boost recovery. We finally discuss rehabilitative protocols based on robotic devices as a tool to promote endogenous plasticity and functional restoration.

Preclinical applications of resting-state functional magnetic resonance imaging (rsfMRI) offer the possibility to non-invasively probe whole-brain network dynamics and to investigate the determinants of altered network signatures observed in human studies. Mouse rsfMRI has been increasingly adopted by numerous laboratories worldwide. Here we describe a multi-centre comparison of 17 mouse rsfMRI datasets via a common image processing and analysis pipeline. Despite prominent cross-laboratory differences in equipment and imaging procedures, we report the reproducible identification of several large-scale resting-state networks (RSN), including a mouse default-mode network, in the majority of datasets. A combination of factors was associated with enhanced reproducibility in functional connectivity parameter estimation, including animal handling procedures and equipment performance. RSN spatial specificity was enhanced in datasets acquired at higher field strength, with cryoprobes, in ventilated animals, and under medetomidine-isoflurane combination sedation. Our work describes a set of representative RSNs in the mouse brain and highlights key experimental parameters that can critically guide the design and analysis of future rodent rsfMRI investigations.

Transcranial direct current stimulation (tDCS), a non-invasive neuromodulation technique inducing prolonged brain excitability changes and promoting cerebral plasticity, is a promising option for neurorehabilitation. Here, we review progress in research on tDCS and language functions and on the potential role of tDCS in the treatment of post-stroke aphasia. Currently available data suggest that tDCS over language-related brain areas can modulate linguistic abilities in healthy individuals and can improve language performance in patients with aphasia. Whether the results obtained in experimental conditions are functionally important for the quality of life of patients and their caregivers remains unclear. Despite the fact that important variables are yet to be determined, tDCS combined with rehabilitation techniques seems a promising therapeutic option for aphasia.

Synchrony refers to the coordinated interplay of behavioural and physiological signals that reflect the bi-directional attunement of one partner to the other's psychophysiological, cognitive, emotional, and behavioral state. In mother-child relationships, a synchronous pattern of interaction indicates parental sensitivity. Parenting stress has been shown to undermine mother-child behavioural synchrony. However, it has yet to be discerned whether parenting stress affects brain-to-brain synchrony during everyday joint activities. Here, we show that greater parenting stress is associated with less brain-to-brain synchrony in the medial left cluster of the prefrontal cortex when mother and child engage in a typical dyadic task of watching animation videos together. This brain region overlaps with the inferior frontal gyrus, the frontal eye field, and the dorsolateral prefrontal cortex, which are implicated in inference of mental states and social cognition. Our result demonstrates the adverse effect of parenting stress on mother-child attunement that is evident at a brain-to-brain level. Mother-child brain-to-brain asynchrony may underlie the robust association between parenting stress and poor dyadic co-regulation. We anticipate our study to form the foundation for future investigations into mechanisms by which parenting stress impairs the mother-child relationship.

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Objective Operative link on gastritis assessment (OLGA) staging for gastritis ranks the risk for gastric cancer (GC) in progressive stages (0–IV). This prospective study aimed at quantifying the cancer risk associated with each gastritis stage. Design A cohort of 1755 consecutive patients with dyspepsia underwent initial (T-0) oesophagogastroduodenoscopy with mapped gastric biopsies, OLGA staging and assessment of Helicobacter pylori infection. Patients were followed for 55 months (median); patients with stages II III and IV underwent a second endoscopy/restaging (T-1), and those with stages 0 and I were followed clinically and through in-depth clinical and record checking. Endpoints were OLGA stage at T-1 and development of gastric epithelial neoplasia. Results At T-0, 77.6% of patients had stage 0, 14.4% stage I, 5.1% stage II, 2.1% stage III and 0.85% stage IV. H. pylori infection was detected in 603 patients at T-0 and successfully eradicated in 602 of them; 220 had a documented history of H. pylori eradication; and 932 were H. pylori naïve-negative. Incident neoplastic lesions (prevalence=0.4%; low-grade intraepithelial neoplasia (IEN)=4; high-grade IEN=1; GC=2) developed exclusively in patients with stages III–IV. The risk for epithelial neoplasia was null in patients at stages 0, I and II (95% CI 0 to 0.4), 36.5 per 1000 person-years in patients at stage III (95% CI 13.7 to 97.4) and 63.1 per 1000 person-years in patients at stage IV (95% CI 20.3 to 195.6). Conclusions This prospective study confirms that OLGA staging reliably predicts the risk for development of gastric epithelial neoplasia. Although no neoplastic lesions arose in H. pylori- naïve patients, the H. pylori eradication in subjects with advanced stages (III–IV) did not abolish the risk for neoplastic progression.

Visual object recognition is subserved by ventral temporal and occipital regions of the brain. Regions comprising the dorsal visual pathway have not been considered relevant for object recognition, despite strong categorical biases for tool-related information in those regions. Here, we show that dorsal stream processes influence object categorization. We used two techniques to render prime pictures invisible: continuous flash suppression (CFS), which obliterates input into ventral temporal regions, but leaves dorsal stream processes largely unaffected, and backward masking (BM), which allows suppressed information to reach both ventral and dorsal stream structures. Categorically congruent primes suppressed under CFS facilitate categorization of tools but have no effect on nonmanipulable objects; in contrast, primes rendered invisible through BM facilitate target categorization for both tools and nonmanipulable things. Our findings demonstrate that information computed by the dorsal stream is used in object categorization, but only for a category of manipulable objects.

This study investigated the development of language and communication in children with Down syndrome (DS). More specifically, the aim was to examine the relations among verbal comprehension, verbal production, and gesture production in the very early stages of development. Forty children (age range: 10-49 months) with DS and 40 children with normal development (age range: 8-17 months) participated in this study. Children with DS came from two Italian health centers. The communicative and linguistic development of children with DS was measured by administering the Italian version of the MacArthur Communicative Development Inventory. The children with DS were severely delayed when compared with normally developing children in reaching the developmental stages. In such children a dissociation emerged between verbal comprehension and production, in favor of comprehension, whereas a synchronous development was found between vocal lexical comprehension and gestural production. The individual differences previously reported in these children are also evident in all domains examined. There were no significant differences between children with DS and typically developing controls matched for lexical comprehension on verbal production. However the two groups differed significantly in gestural development, suggesting a "gesture advantage" in children with DS compared with controls matched for word comprehension. Some possible reasons for this dissociative profile are discussed.

Deriving disease subtypes from electronic health records (EHRs) can guide next-generation personalized medicine. However, challenges in summarizing and representing patient data prevent widespread practice of scalable EHR-based stratification analysis. Here we present an unsupervised framework based on deep learning to process heterogeneous EHRs and derive patient representations that can efficiently and effectively enable patient stratification at scale. We considered EHRs of 1,608,741 patients from a diverse hospital cohort comprising a total of 57,464 clinical concepts. We introduce a representation learning model based on word embeddings, convolutional neural networks, and autoencoders (i.e., ConvAE) to transform patient trajectories into low-dimensional latent vectors. We evaluated these representations as broadly enabling patient stratification by applying hierarchical clustering to different multi-disease and disease-specific patient cohorts. ConvAE significantly outperformed several baselines in a clustering task to identify patients with different complex conditions, with 2.61 entropy and 0.31 purity average scores. When applied to stratify patients within a certain condition, ConvAE led to various clinically relevant subtypes for different disorders, including type 2 diabetes, Parkinson's disease, and Alzheimer's disease, largely related to comorbidities, disease progression, and symptom severity. With these results, we demonstrate that ConvAE can generate patient representations that lead to clinically meaningful insights. This scalable framework can help better understand varying etiologies in heterogeneous sub-populations and unlock patterns for EHR-based research in the realm of personalized medicine.