The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

Subcortical serotonin 5HT2c receptor-containing neurons sex-specifically regulate binge-like alcohol consumption, social, and arousal behaviors in mice

Binge alcohol consumption induces discrete social and arousal disturbances in human populations that promote increased drinking and accelerate the progression of Alcohol Use Disorder. Here, we show in a mouse model that binge alcohol consumption disrupts social recognition in females and potentiates sensorimotor arousal in males. These negative behavioral outcomes were associated with sex-specific adaptations in serotonergic signaling systems within the lateral habenula (LHb) and the bed nucleus of the stria terminalis (BNST), particularly those related to the receptor 5HT2c. While both BNST and LHb neurons expressing this receptor display potentiated activation following binge alcohol consumption, the primary causal mechanism underlying the effects of alcohol on social and arousal behaviors appears to be excessive activation of LHb5HT2c neurons. These findings may have valuable implications for the development of sex-specific treatments for mood and alcohol use disorders targeting the brain's serotonin system.

Short- and long-interval intracortical inhibition in EPM1 is related to genotype

OBJECTIVE

Progressive myoclonic epilepsy type 1 (EPM1) is caused by biallelic alterations in the CSTB gene, most commonly dodecamer repeat expansions. Although transcranial magnetic stimulation (TMS)-induced long-interval intracortical inhibition (LICI) was previously reported to be normal in EPM1, short-interval intracortical inhibition (SICI) was reduced. We explored the association between these measures and the clinical and genetic features in a separate group of patients with EPM1.

METHODS

TMS combined with electromyography was performed under neuronavigation. LICI was induced with an inter-stimulus interval (ISI) of 100 ms, and SICI with ISIs of 2 and 3 ms, and their means (mSICIs) were expressed as the ratio of conditioned to unconditioned stimuli. LICI and mSICI were compared between patients and controls. Nonparametric correlation was used to study the association between inhibition and parameters of clinical severity, including the Unified Myoclonus Rating Scale (UMRS); among patients with EPM1 due to biallelic expansion repeats, also the association with the number of repeats was assessed.

RESULTS

The study protocol was completed in 19 patients (15 with biallelic expansion repeats and 4 compound heterozygotes), and 7 healthy, age- and sex-matched control participants. Compared to controls, patients demonstrated significantly less SICI (median mSICI ratio 1.18 vs 0.38; p < .001). Neither LICI nor SICI was associated with parameters of clinical severity. In participants with biallelic repeat expansions, the number of repeats in the more affected allele (greater repeat number [GRN]) correlated with LICI (rho = 0.872; p < .001) and SICI (rho = 0.689; p = .006).

SIGNIFICANCE

Our results strengthen the finding of deranged γ-aminobutyric acid (GABA)ergic inhibition in EPM1. LICI and SICI may have use as markers of GABAergic impairment in future trials of disease-modifying treatment in this condition. Whether a higher number of expansion repeats leads to greater GABAergic impairment warrants further study.

Physiological symmetry of transcranial magnetic stimulation-evoked EEG spectral features

Transcranial magnetic stimulation (TMS)-evoked EEG potentials (TEPs) have been used to study the excitability of different cortical areas (CAs) in humans. Characterising the interhemispheric symmetry of TMS-EEG may provide further understanding of structure-function association in physiological and pathological conditions. We hypothesise that, in keeping with the underlying cytoarchitectonics, TEPs in contralateral homologous CAs share similar, symmetric spectral features, whilst ipsilateral TEPs from different CAs diverge in their waveshape and frequency content. We performed single-pulse (<1 Hz) navigated monophasic TMS, combined with high-density EEG with active electrodes, in 10 healthy participants. We targeted two bilateral CAs: premotor and motor. We compared frequency power bands, computed Pearson correlation coefficient (R) and Correlated Component Analysis (CorrCA) to detect divergences, as well as common components across TEPs. The main frequency of TEPs was faster in premotor than in motor CAs (p < .05) across all participants. Frequencies were not different between contralateral homologous CAs, whilst, despite closer proximity, there was a significant difference between ipsilateral premotor and motor CAs (p > .5), with frequency decreasing from anterior to posterior CAs. Correlation was high between contralateral homologous CAs and low between ipsilateral CAs. When applying CorrCA, specific components were shared by contralateral homologous TEPs. We show physiological symmetry of TEP spectral features between contralateral homologous CAs, whilst ipsilateral premotor and motor TEPs differ despite lower geometrical distance. Our findings support the role of TEPs as biomarker of local cortical properties and provide a first reference dataset for TMS-EEG studies in asymmetric brain disorders.

The impact of Transcranial Magnetic Stimulation (TMS) on seizure course in people with and without epilepsy

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Previous evidence on risk of TMS-induced seizures is anecdotal.

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There was no evidence that TMS caused changes in epileptiform activity.

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No seizures were induced by TMS in healthy subjects.

Objective

To elucidate the effects of single and paired-pulse TMS on seizure activity at electrographic and clinical levels in people with and without epilepsy.

Methods

A cohort of 35 people with epilepsy, two people with alternating hemiplegia of childhood (AHC) with no epilepsy, and 16 healthy individuals underwent single or paired-pulse TMS combined with EEG. Clinical records and subject interviews were used to examine seizure frequency four weeks before and after TMS.

Results

There were no significant differences in seizure frequency in any subject after TMS exposure. There was no occurrence of seizures in healthy individuals, and no worsening of hemiplegic attacks in people with AHC.

Conclusions

No significant changes in seizure activity were found before or after TMS.

Significance

This study adds evidence on the safety of TMS in people with and without epilepsy with follow-up of four weeks after TMS.

Non‐Stationary Outcome of Alternating Hemiplegia of Childhood into Adulthood

Background

Objectives

Methods

Results

Conclusions

Local sleep-like cortical reactivity in the awake brain after focal injury

The functional consequences of focal brain injury are thought to be contingent on neuronal alterations extending beyond the area of structural damage. This phenomenon, also known as diaschisis, has clinical and metabolic correlates but lacks a clear electrophysiological counterpart, except for the long-standing evidence of a relative EEG slowing over the injured hemisphere. Here, we aim at testing whether this EEG slowing is linked to the pathological intrusion of sleep-like cortical dynamics within an awake brain. We used a combination of transcranial magnetic stimulation and electroencephalography (TMS/EEG) to study cortical reactivity in a cohort of 30 conscious awake patients with chronic focal and multifocal brain injuries of ischaemic, haemorrhagic and traumatic aetiology. We found that different patterns of cortical reactivity typically associated with different brain states (coma, sleep, wakefulness) can coexist within the same brain. Specifically, we detected the occurrence of prominent sleep-like TMS-evoked slow waves and off-periods—reflecting transient suppressions of neuronal activity—in the area surrounding focal cortical injuries. These perilesional sleep-like responses were associated with a local disruption of signal complexity whereas complex responses typical of the awake brain were present when stimulating the contralesional hemisphere. These results shed light on the electrophysiological properties of the tissue surrounding focal brain injuries in humans. Perilesional sleep-like off-periods can disrupt network activity but are potentially reversible, thus representing a principled read-out for the neurophysiological assessment of stroke patients, as well as an interesting target for rehabilitation.

Sleepiness as a Local Phenomenon

Sleep occupies a third of our life and is a primary need for all animal species studied so far. Nonetheless, chronic sleep restriction is a growing source of morbidity and mortality in both developed and developing countries. Sleep loss is associated with the subjective feeling of sleepiness and with decreased performance, as well as with detrimental effects on general health, cognition, and emotions. The ideas that small brain areas can be asleep while the rest of the brain is awake and that local sleep may account for at least some of the cognitive and behavioral manifestations of sleepiness are making their way into the scientific community. We herein clarify the different ways sleep can intrude into wakefulness, summarize recent scientific advances in the field, and offer some hypotheses that help framing sleepiness as a local phenomenon.

iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology

The Brain Imaging Data Structure (BIDS) is a community-driven specification for organizing neuroscience data and metadata with the aim to make datasets more transparent, reusable, and reproducible. Intracranial electroencephalography (iEEG) data offer a unique combination of high spatial and temporal resolution measurements of the living human brain. To improve internal (re)use and external sharing of these unique data, we present a specification for storing and sharing iEEG data: iEEG-BIDS.

Sleep as a model to understand neuroplasticity and recovery after stroke: Observational, perturbational and interventional approaches

Our own experiences with disturbances to sleep demonstrate its crucial role in the recovery of cognitive functions. This importance is likely enhanced in the recovery from stroke; both in terms of its physiology and cognitive abilities. Decades of experimental research have highlighted which aspects and mechanisms of sleep are likely to underlie these forms of recovery. Conversely, damage to certain areas of the brain, as well as the indirect effects of stroke, may disrupt sleep. However, only limited research has been conducted which seeks to directly explore this bidirectional link between both the macro and micro-architecture of sleep and stroke. Here we describe a series of semi-independent approaches that aim to establish this link through observational, perturbational, and interventional experiments. Our primary aim is to describe the methodology for future clinical and translational research needed to delineate competing accounts of the current data. At the observational level we suggest the use of high-density EEG recording, combined analysis of macro and micro-architecture of sleep, detailed analysis of the stroke lesion, and sensitive measures of functional recovery. The perturbational approach attempts to find the causal links between sleep and stroke. We promote the use of transcranial magnetic stimulation combined with EEG to examine the cortical dynamics of the peri-infarct stroke area. Translational research should take this a step further using optogenetic techniques targeting more specific cell populations. The interventional approach focuses on how the same clinical and translational perturbational techniques can be adapted to influence long-term recovery of function.

The ω-SQUIPT as a tool to phase-engineer Josephson topological materials

Multi-terminal superconducting Josephson junctions based on the proximity effect offer the opportunity to tailor non-trivial quantum states in nanoscale weak links. These structures can realize exotic topologies in several dimensions, for example, artificial topological superconductors that are able to support Majorana bound states, and pave the way to emerging quantum technologies and future quantum information schemes. Here we report the realization of a three-terminal Josephson interferometer based on a proximized nanosized weak link. Our tunnelling spectroscopy measurements reveal transitions between gapped (that is, insulating) and gapless (conducting) states that are controlled by the phase configuration of the three superconducting leads connected to the junction. We demonstrate the topological nature of these transitions: a gapless state necessarily occurs between two gapped states of different topological indices, in much the same way that the interface between two insulators of different topologies is necessarily conducting. The topological numbers that characterize such gapped states are given by superconducting phase windings over the two loops that form the Josephson interferometer. As these gapped states cannot be transformed to one another continuously without passing through a gapless condition, they are topologically protected. The same behaviour is found for all of the points of the weak link, confirming that this topology is a non-local property. Our observation of the gapless state is pivotal for enabling phase engineering of different and more sophisticated artificial topological materials.

Benzamide prevention of ultraviolet radiation-induced transformation as measured by anchorage-independent growth and the absence of correlation with thymidine dimer formation and DNA repair

Synchronized human fibroblasts were exposed in early S phase to increasing doses of ultraviolet (UV) irradiation in the presence and absence of an antitransforming drug, benzamide. Cellular survival, initial thymidine dimer formation and its repair, and cellular phenotypic transformation were simultaneously monitored in the presence and absence of 1 mM externally added benzamide that reaches 8 to 15 microM intracellular levels. Cellular transformation as measured by an expression of anchorage-independent growth was inhibited by nontoxic doses of benzamide. Antitransforming action of benzamide is confined to low intracellular drug concentrations, which in the case of benzamide is in the 4-9 microM range. Because of the lack of effect of benzamide on the formation of UV-induced thymidine dimers and the specific repair of these dimers, these results suggest that the processes of thymidine dimer formation and its repair are not involved in the mode of action of benzamide that influences the expression of a transformed phenotype with low malignant vigor.