Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging.

Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.

Top-down and bottom-up oscillatory dynamics regulate implicit visuomotor sequence learning.

Implicit visuomotor sequence learning is crucial for acquiring skills that result in automated behaviors. The oscillatory dynamics underpinning this learning process are not well understood. To address this gap, the current study employed electroencephalography with a medium-density array (64 electrodes) to investigate oscillatory activity associated with implicit visuomotor sequence learning in the Serial Reaction Time task. In the task, participants unknowingly learn a series of finger movements. Eighty-five healthy adults participated in the study. Analyses revealed that theta activity at the vertex and alpha/beta activity over the motor areas decreased over the course of learning. No associations between alpha/beta and theta power were observed. These findings are interpreted within a dual-process framework: midline theta activity is posited to regulate top-down attentional processes, whereas beta activity from motor areas underlies the bottom-up encoding of sensory information from movement. From this model, we suggest that during implicit visuomotor sequence learning, top-down processes become disengaged (indicated by a reduction in theta activity), and modality specific bottom-up processes encode the motor sequence (indicated by a reduction in alpha/beta activity).

GABA and glutamate response to social processing: a functional MRS feasibility study.

Several studies have suggested that atypical social processing in neurodevelopmental conditions (e.g. autism) is associated with differences in excitation and inhibition, through changes in the levels of glutamate and gamma-aminobutyric acid (GABA). While associations between baseline metabolite levels and behaviours can be insightful, assessing the neurometabolic response of GABA and glutamate during social processing may explain altered neurochemical function in more depth. Thus far, there have been no attempts to determine whether changes in metabolite levels are detectable using functional MRS (fMRS) during social processing in a control population. We performed Mescher-Garwood point resolved spectroscopy edited fMRS to measure the dynamic response of GABA and glutamate in the superior temporal sulcus (STS) and visual cortex (V1) while viewing social stimuli, using a design that allows for analysis in both block and event-related approaches. Sliding window analyses were used to investigate GABA and glutamate dynamics at higher temporal resolution. The changes of GABA and glutamate levels with social stimulus were largely non-significant. A small decrease in GABA levels was observed during social stimulus presentation in V1, but no change was observed in STS. Conversely, non-social stimulus elicited changes in both GABA and glutamate levels in both regions. Our findings suggest that the current experimental design primarily captures effects of visual stimulation, not social processing. Here, we discuss the feasibility of using fMRS analysis approaches to assess changes in metabolite response.

Towards consistency in dietary pattern scoring: standardising scoring workflows for healthy dietary patterns using 24-h recall and two variations of a food frequency questionnair.

Healthy dietary patterns such as the Mediterranean diet (MeDi), Dietary Approaches to Stop Hypertension (DASH) and the Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) have been evaluated for their potential association with health outcomes. However, the lack of standardisation in scoring methodologies can hinder reproducibility and meaningful cross-study comparisons. Here we provide a reproducible workflow for generating the MeDi, DASH and MIND dietary pattern scores from frequently used dietary assessment tools including the 24-h recall tool and two variations of FFQ. Subjective aspects of the scoring process are highlighted and have led to a recommended reporting checklist. This checklist enables standardised reporting with sufficient detail to enhance the reproducibility and comparability of their outcomes. In addition to these aims, valuable insights in the strengths and limitations of each assessment tool for scoring the MeDi, DASH and MIND diet can be utilised by researchers and clinicians to determine which dietary assessment tool best meets their needs.

A neural oscillatory signature of sustained anxiety.

BACKGROUND: Anxiety is a sustained response to uncertain threats; yet few studies have explored sustained neurobiological activities underlying anxious states, particularly spontaneous neural oscillations. To address this gap, we reanalysed magnetoencephalographic (MEG) data recorded during induced anxiety to identify differences in sustained oscillatory activity between high- and low-anxiety states. METHODS: We combined data from three previous MEG studies in which healthy adults (total N = 51) were exposed to alternating periods of threat of unpredictable shock and safety while performing a range of cognitive tasks (passive oddball, mixed-saccade or stop-signal tasks). Spontaneous, band-limited, oscillatory activity was extracted from middle and late intervals of the threat and safe periods, and regional power distributions were reconstructed with adaptive beamforming. Conjunction analyses were used to identify regions showing overlapping spectral power differences between threat and safe periods across the three task paradigms. RESULTS: MEG source analyses revealed a robust and widespread reduction in beta (14-30 Hz) power during threat periods in bilateral sensorimotor cortices extending into right prefrontal regions. Alpha (8-13 Hz) power reductions during threat were more circumscribed, with notable peaks in left intraparietal sulcus and thalamus. CONCLUSIONS: Threat-induced anxiety is underpinned by a sustained reduction in spontaneous beta- and alpha-band activity in sensorimotor and parietal cortical regions. This general oscillatory pattern likely reflects a state of heightened action readiness and vigilance to cope with uncertain threats. Our findings provide a critical reference for which to identify abnormalities in cortical oscillatory activities in clinically anxious patients as well as evaluating the efficacy of anxiolytic treatments.

Anxious arousal alters prefrontal cortical control of stopping.

Anxiety heightens vigilance and stimulus-driven attention to the environment, which may in turn disrupt cognitive control processes such as response inhibition. How this unfolds at the neural level is unclear. Previous evidence implicates the right inferior frontal gyrus (IFG) as an important cortical node in both stimulus-driven attention and inhibitory control. Here we used magnetoencephalography (MEG) to investigate the neural mechanisms involved in the relationship between threat-induced anxiety and stopping during a stop-signal task, where a visual go signal was occasionally followed by an auditory stop signal. Healthy individuals (N = 18) performed the task during the threat of unpredictable shocks and safety to modulate anxious arousal. Behaviorally, we observed that stopping was impaired during threat (i.e. slower estimated stop-signal reaction times), indicating that anxious arousal weakens inhibitory control. MEG source analyses revealed that bilateral IFG and right dorsal prefrontal cortex showed increased beta-band activity (14-30 Hz) to the stop signal that varied as a function of successful stopping during nonanxious (safe) conditions only. Moreover, peak beta-band responses from right IFG were inversely correlated with stopping efficiency during nonanxious conditions. These findings support theoretical claims that beta oscillations function to maintain the current sensorimotor state, and that the lack of differential beta-band activity in prefrontal cortices underlies anxiety-related deficits in inhibitory control. We specifically argue that altered right IFG functioning might directly link impaired cognitive control to heightened stimulus-driven responding in anxiety states.

Cognition and reproductive success in cowbirds.

Understanding the relationships between cognitive abilities and fitness is integral to an evolutionary study of brain and behavior. However, these relationships are often difficult to measure and detect. Here we draw upon an opportunistic sample of brown-headed cowbird (Molothrus ater) subjects that had two separate research experiences: First, they engaged in a large series of cognitive tests in David Sherry's Lab in the Advanced Facility for Avian Research (AFAR) at Western University, then subsequently moved to the Field Avian Research Megalab (FARM) at Wilfrid Laurier University where they lived in large breeding flocks in aviaries with other wild-caught cowbirds. Thus, we had extensive measures of cognitive abilities, breeding behavior, and reproductive success for these birds. We report here, for the fist time, the surprisingly strong connections we found among these different measures. Female cowbirds' spatial cognitive abilities correlated positively with how intensely they were courted by males, and with their overall egg production. Males' spatial cognition correlated positively with their ability to engage in singing contests ("countersinging") with other males. In addition, a separate non-spatial cognitive ability correlated positively with the attractiveness of the songs they sung. In sum, these results suggest the cognitive skills assessed in the lab were strongly connected to breeding behavior and reproductive success. Moreover, since certain cognitive abilities related to different aspects of breeding success, it suggests that cognitive modules may have specialized adaptive value, but also that these specialized skills may interact and influence fitness in surprising ways.

Effects of Panax quinquefolius (American ginseng) on the steady state visually evoked potential during cognitive performance.

OBJECTIVE: To investigate the effects of acute Panax quinquefolius (American ginseng) administration on steady state visually evoked potentials (SSVEPs) during completion of working memory and continuous performance tasks. METHODS: A randomised, double-blind, placebo controlled, balanced, cross-over trial was conducted in middle-aged volunteers aged between 40 and 60 years. Participants were administered 200 mg P. quinquefolius and placebo on two separate testing sessions. Six-h post-dose participants completed spatial working memory (SWM) and continuous performance (CP) tasks while SSVEP from a diffuse task-irrelevant 13 Hz flicker was recorded. RESULTS: During SWM retrieval, P. quinquefolius was associated with significantly reduced prefrontal SSVEP latency. There were no significant treatment effects on CP nor behavioural performance of either task. CONCLUSIONS: These findings provide preliminary evidence of increased recruitment of prefrontal brain regions during working memory processing following a single acute dose of P. quinquefolius.

The limitations of using the NTP chronic bioassay on vanadium pentoxide in risk assessments.

Regulatory interest in assessing the health effects of vanadium compounds is hindered by the limited chronic toxicity data available. The National Toxicology Program (NTP) conducted a robust chronic inhalation bioassay of crystalline vanadium pentoxide (V2O5), but this study has noteworthy limitations. Multiple dose range-finding studies were conducted at two separate laboratories that showed cross-laboratory differences in lung pathology (inflammation) in both species and likely complicated dose-selection. In mice, the only tissue pathology (inflammation and tumors) was at the site of entry, the respiratory system. Although significantly different from control, because lung tumor incidences were at a maximal level across all concentrations tested, the ability to extrapolate risks to the public is problematic. In rats, lung inflammation and vanadium lung burdens were comparable to those of mice, but lung tumorigenicity was not substantiated, further raising questions about appropriate species extrapolation. Open questions also exist regarding test material chemical characterization, as the laboratory relied on vanadium measurement in test chambers as a surrogate for V2O5. In sum, the NTP V2O5 study does not provide an appropriate dataset for purposes of classification and risk assessment. Additional repeat exposure studies of vanadium compounds are needed and recommendations for future studies are provided.

Nest prospecting brown-headed cowbirds 'parasitize' social information when the value of personal information is lacking.

Brood parasites face considerable cognitive challenges in locating and selecting host nests for their young. Here, we test whether female brown-headed cowbirds, Molothrus ater, could use information acquired from observing the nest prospecting patterns of conspecifics to influence their own patterns of nest selection. In laboratory-based experiments, we created a disparity in the amount of personal information females had about the quality of nests. Females with less personal information about the quality of two nests spent more time investigating the nest that more knowledgeable females investigated. Furthermore, there was a strong negative relationship between individual's ability to track nest quality using personal information and their tendency to copy others. These two contrasting strategies for selecting nests are equally effective, but lead to different patterns of parasitism.

Are There Place Cells in the Avian Hippocampus?

Birds possess a hippocampus that serves many of the same spatial and mnemonic functions as the mammalian hippocampus but achieves these outcomes with a dramatically different neuroanatomical organization. The properties of spatially responsive neurons in birds and mammals are also different. Much of the contemporary interest in the role of the mammalian hippocampus in spatial representation dates to the discovery of place cells in the rat hippocampus. Since that time, cells that respond to head direction and cells that encode a grid-like representation of space have been described in the rat brain. Research with homing pigeons has discovered hippocampal cells, including location cells, path cells, and pattern cells, that share some but not all properties of spatially responsive neurons in the rodent brain. We have recently used patterns of immediate-early gene expression, visualized by the catFISH method, to investigate how neurons in the hippocampus of brood-parasitic brown-headed cowbirds respond to spatial context. We have found cells that discriminate between different spatial environments and are re-activated when the same spatial environment is re-experienced. Given the differences in habitat and behaviour between birds and rodents, it is not surprising that spatially responsive cells in their hippocampus and other brain regions differ. The enormous diversity of avian habitats and behaviour offers the potential for understanding the general principles of neuronal representation of space.

The effect of a single dose of multivitamin and mineral combinations with and without guaraná on functional brain activity during a continuous performance task.

OBJECTIVES: Relatively few studies have explored the possibility of acute cognitive effects of multivitamin ingestion. This report explores the acute brain electrophysiological changes associated with multivitamin and mineral supplementation, with and without guaraná, using the steady-state visually evoked potential (SSVEP). METHODS: Based on the known SSVEP correlates of A-X continuous performance task (CPT) performance, and sensitivity to acute psychopharmacological manipulations, the A-X CPT was adopted as a task paradigm to explore treatment-related neurophysiological changes in attentional processing. Twenty healthy non-smoking adults aged 21-39 years (mean age = 28.35 years, SD = 5.52) took part in this double-blind, placebo-controlled, randomized, balanced crossover design study. RESULTS: The study demonstrated both transient and tonic changes in the SSVEP response during completion of the A-X CPT following multivitamin and mineral treatment both with and without guaraná. Transient changes in SSVEP response in prefrontal regions were observed after a single dose of a multivitamin and mineral preparation indicative of enhanced activity within brain regions engaged by the attentional demands of the task. This pattern of change in frontal regions was correlated with improved behavioural performance after treatment with the multivitamin and mineral combination. Where tonic shifts in SSVEP response were investigated, multivitamin and mineral treatment was associated with a pattern of increased inhibition across posterior regions, with enhanced excitatory processing in prefrontal regions. In contrast, multivitamin and mineral treatment with additional guaraná showed a tonic shift towards greater excitatory processes after a single treatment, consistent with the caffeine content of this treatment. DISCUSSION: While preliminary in nature, these findings suggest a single multivitamin/mineral dose is sufficient to impact on functional brain activity in task-related brain regions.

Stability of subsea pipelines during large storms.

On-bottom stability design of subsea pipelines transporting hydrocarbons is important to ensure safety and reliability but is challenging to achieve in the onerous metocean (meteorological and oceanographic) conditions typical of large storms (such as tropical cyclones, hurricanes or typhoons). This challenge is increased by the fact that industry design guidelines presently give no guidance on how to incorporate the potential benefits of seabed mobility, which can lead to lowering and self-burial of the pipeline on a sandy seabed. In this paper, we demonstrate recent advances in experimental modelling of pipeline scour and present results investigating how pipeline stability can change in a large storm. An emphasis is placed on the initial development of the storm, where scour is inevitable on an erodible bed as the storm velocities build up to peak conditions. During this initial development, we compare the rate at which peak near-bed velocities increase in a large storm (typically less than 10(-3) m s(-2)) to the rate at which a pipeline scours and subsequently lowers (which is dependent not only on the storm velocities, but also on the mechanism of lowering and the pipeline properties). We show that the relative magnitude of these rates influences pipeline embedment during a storm and the stability of the pipeline.

The association of dietary and nutrient patterns on neurocognitive decline: A systematic review of MRI and PET studies.

BACKGROUND: As the global population ages, there has been a growing incidence of neurodegenerative diseases such as Alzheimer's. More recently, studies exploring the relationship between dietary patterns and neuroimaging outcomes have received particular attention. This systematic literature review provides a structured overview of the association between dietary and nutrient patterns on neuroimaging outcomes and cognitive markers in middle-aged to older adults. A comprehensive literature search was conducted to find relevant articles published from 1999 to date using the following databases Ovid MEDLINE, Embase, PubMed, Scopus and Web of Science. The inclusion criteria for the articles comprised studies reporting on the association between dietary patterns and neuroimaging outcomes, which includes both specific pathological hallmarks of neurodegenerative diseases such as Aß and tau and nonspecific markers such as structural MRI and glucose metabolism. The risk of bias was evaluated using the Quality Assessment tool from the National Heart, Lung, and Blood Institute of the National Institutes of Health. The results were then organized into a summary of results table, collated based on synthesis without meta-analysis. After conducting the search, 6050 records were extracted and screened for eligibility, with 107 eligible for full-text screening and 42 articles ultimately being included in this review. The results of the systematic review indicate that there is some evidence suggesting that healthy dietary and nutrient patterns were associated with neuroimaging measures, indicative of a protective influence on neurodegeneration and brain ageing. Conversely, unhealthy dietary and nutrient patterns showed evidence pointing to decreased brain volumes, poorer cognition and increased Aß deposition. Future research should focus on sensitive neuroimaging acquisition and analysis methods, to study early neurodegenerative changes and identify critical periods for interventions and prevention. SYSTEMATIC REVIEW REGISTRATION: PROSPERO registration no, CRD42020194444).

Corrigendum: The association between diet and cardio-metabolic risk on cognitive performance: A cross-sectional study of middle-aged Australian adults.

[This corrects the article DOI: 10.3389/fnut.2022.862475.].

A combined DHA-rich fish oil and cocoa flavanols intervention does not improve cognition or brain structure in older adults with memory complaints: results from the CANN randomized, controlled parallel-design study.

BACKGROUND: There is evidence that both omega-3 long-chain polyunsaturated fatty acids (PUFAs) (eicosapentaenoic acid [EPA] and docosahexaenoic acid [DHA]) and cocoa flavanols can improve cognitive performance in both healthy individuals and in those with memory complaints. However, their combined effect is unknown. OBJECTIVES: To investigate the combined effect of EPA/DHA and cocoa flavanols (OM3FLAV) on cognitive performance and brain structures in older adults with memory complaints. METHODS: A randomized placebo-controlled trial of DHA-rich fish oil (providing 1.1 g/d DHA and 0.4 g/d EPA) and a flavanol-rich dark chocolate (providing 500 mg/d flavan-3-ols) was conducted in 259 older adults with either subjective cognitive impairment or mild cognitive impairment. Participants underwent assessment at baseline, 3 mo, and 12 mo. The primary outcome was the number of false-positives on a picture recognition task from the Cognitive Drug Research computerized assessment battery. Secondary outcomes included other cognition and mood outcomes, plasma lipids, brain-derived neurotrophic factor (BDNF), and glucose levels. A subset of 110 participants underwent structural neuroimaging at baseline and at 12 mo. RESULTS: 197 participants completed the study. The combined intervention had no significant effect on any cognitive outcomes, with the exception of reaction time variability (P = 0.007), alertness (P < 0.001), and executive function (P < 0.001), with a decline in function observed in the OM3FLAV group (118.6 [SD 25.3] at baseline versus 113.3 [SD 25.4] at 12 mo for executive function) relative to the control, and an associated decrease in cortical volume (P = 0.039). Compared with the control group, OM3FLAV increased plasma HDL, total cholesterol ratio (P < 0.001), and glucose (P = 0.008) and reduced TG concentrations (P < 0.001) by 3 mo, which were sustained to 12 mo, with no effect on BDNF. Changes in plasma EPA and DHA and urinary flavonoid metabolite concentrations confirmed compliance to the intervention. CONCLUSIONS: These results suggest that cosupplementation with ω-3 PUFAs and cocoa flavanols for 12 mo does not improve cognitive outcomes in those with cognitive impairment. This trial was registered at clinicaltrials.gov as NCT02525198.

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging.

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

Brain oscillatory activity during spatial navigation: theta and gamma activity link medial temporal and parietal regions.

Brain oscillatory correlates of spatial navigation were investigated using blind source separation (BSS) and standardized low resolution electromagnetic tomography (sLORETA) analyses of 62-channel EEG recordings. Twenty-five participants were instructed to navigate to distinct landmark buildings in a previously learned virtual reality town environment. Data from periods of navigation between landmarks were subject to BSS analyses to obtain source components. Two of these cortical sources were found to exhibit significant spectral power differences during navigation with respect to a resting eyes open condition and were subject to source localization using sLORETA. These two sources were localized as a right parietal component with gamma activation and a right medial-temporal-parietal component with activation in theta and gamma bandwidths. The parietal gamma activity was thought to reflect visuospatial processing associated with the task. The medial-temporal-parietal activity was thought to be more specific to the navigational processing, representing the integration of ego- and allo-centric representations of space required for successful navigation, suggesting theta and gamma oscillations may have a role in integrating information from parietal and medial-temporal regions. Theta activity on this medial-temporal-parietal source was positively correlated with more efficient navigation performance. Results are discussed in light of the depth and proposed closed field structure of the hippocampus and potential implications for scalp EEG data. The findings of the present study suggest that appropriate BSS methods are ideally suited to minimizing the effects of volume conduction in noninvasive recordings, allowing more accurate exploration of deep brain processes.

Acute rejection is associated with antibodies to non-Gal antigens in baboons using Gal-knockout pig kidneys.

We transplanted kidneys from alpha1,3-galactosyltransferase knockout (GalT-KO) pigs into six baboons using two different immunosuppressive regimens, but most of the baboons died from severe acute humoral xenograft rejection. Circulating induced antibodies to non-Gal antigens were markedly elevated at rejection, which mediated strong complement-dependent cytotoxicity against GalT-KO porcine target cells. These data suggest that antibodies to non-Gal antigens will present an additional barrier to transplantation of organs from GalT-KO pigs to humans.