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.

Aversive experience drives offline ensemble reactivation to link memories across days.

Memories are encoded in neural ensembles during learning and stabilized by post-learning reactivation. Integrating recent experiences into existing memories ensures that memories contain the most recently available information, but how the brain accomplishes this critical process remains unknown. Here we show that in mice, a strong aversive experience drives the offline ensemble reactivation of not only the recent aversive memory but also a neutral memory formed two days prior, linking the fear from the recent aversive memory to the previous neutral memory.

Generalization of cognitive maps across space and time.

Prominent theories posit that associative memory structures, known as cognitive maps, support flexible generalization of knowledge across cognitive domains. Here, we evince a representational account of cognitive map flexibility by quantifying how spatial knowledge formed one day was used predictively in a temporal sequence task 24 hours later, biasing both behavior and neural response. Participants learned novel object locations in distinct virtual environments.

A hardware system for real-time decoding of in vivo calcium imaging data.

Epifluorescence miniature microscopes ('miniscopes') are widely used for in vivo calcium imaging of neural population activity. Imaging data are typically collected during a behavioral task and stored for later offline analysis, but emerging techniques for online imaging can support novel closed-loop experiments in which neural population activity is decoded in real time to trigger neurostimulation or sensory feedback. To achieve short feedback latencies, online imaging systems must be optimally designed to maximize computational speed and efficiency while minimizing errors in population decoding.

Impaired dendritic spike generation in the Fragile X prefrontal cortex is due to loss of dendritic sodium channels.

Patients with Fragile X syndrome, the leading monogenetic cause of autism, suffer from impairments related to the prefrontal cortex, including working memory and attention. Synaptic inputs to the distal dendrites of layer 5 pyramidal neurons in the prefrontal cortex have a weak influence on the somatic membrane potential. To overcome this filtering, distal inputs are transformed into local dendritic Na spikes, which propagate to the soma and trigger action potential output.

Local memory allocation recruits memory ensembles across brain regions.

Memories are thought to be stored in ensembles of neurons across multiple brain regions. However, whether and how these ensembles are coordinated at the time of learning remains largely unknown. Here, we combined CREB-mediated memory allocation with transsynaptic retrograde tracing to demonstrate that the allocation of aversive memories to a group of neurons in one brain region directly affects the allocation of interconnected neurons in upstream brain regions in a behavioral- and brain region-specific manner in mice.

Enhancing learning and retention with distinctive virtual reality environments and mental context reinstatement.

Memory is inherently context-dependent: internal and environmental cues become bound to learnt information, and the later absence of these cues can impair recall. Here, we developed an approach to leverage context-dependence to optimise learning of challenging, interference-prone material. While navigating through desktop virtual reality (VR) contexts, participants learnt 80 foreign words in two phonetically similar languages.

Feedback inhibition underlies new computational functions of cerebellar interneurons.

The function of a feedback inhibitory circuit between cerebellar Purkinje cells and molecular layer interneurons (MLIs) was defined by combining optogenetics, neuronal activity recordings both in cerebellar slices and in vivo, and computational modeling. Purkinje cells inhibit a subset of MLIs in the inner third of the molecular layer. This inhibition is non-reciprocal, short-range (less than 200 μm) and is based on convergence of one to two Purkinje cells onto MLIs.

Creation of Neuronal Ensembles and Cell-Specific Homeostatic Plasticity through Chronic Sparse Optogenetic Stimulation.

Cortical computations emerge from the dynamics of neurons embedded in complex cortical circuits. Within these circuits, neuronal ensembles, which represent subnetworks with shared functional connectivity, emerge in an experience-dependent manner. Here we induced ensembles in cortical circuits from mice of either sex by differentially activating subpopulations through chronic optogenetic stimulation.

The importance of thinking about the future in culture and cumulative cultural evolution.

Thinking about possibilities plays a critical role in the choices humans make throughout their lives. Despite this, the influence of individuals' ability to consider what is possible on culture has been largely overlooked. We propose that the ability to reason about future possibilities or prospective cognition, has consequences for cultural change, possibly facilitating the process of cumulative cultural evolution.

Pattern analysis of neuroimaging data reveals novel insights on threat learning and extinction in humans.

Several decades of rodent neurobiology research have identified a network of brain regions that support Pavlovian threat conditioning and extinction, focused predominately on the amygdala, hippocampus, and medial prefrontal cortex (mPFC). Surprisingly, functional magnetic resonance imaging (fMRI) studies have shown inconsistent evidence for these regions while humans undergo threat conditioning and extinction. In this review, we suggest that translational neuroimaging efforts have been hindered by reliance on traditional univariate analysis of fMRI.

Transgenerational effects of alcohol on behavioral sensitivity to alcohol in Caenorhabditis elegans.

Alcohol abuse and dependence have a substantial heritable component. Although the genome has been considered the sole vehicle of heritable phenotypes, recent studies suggest that drug or alcohol exposure may induce alterations in gene expression that are transmitted across generations. Still, the transgenerational impact of alcohol use (and abuse) remains largely unexplored in part because multigenerational studies using rodent models present challenges for time, sample size, and genetic heterogeneity.

Know thy SEFL: Fear sensitization and its relevance to stressor-related disorders.

Extreme stress can cause long-lasting changes in affective behavior manifesting in conditions such as post-traumatic stress disorder (PTSD). Understanding the biological mechanisms that govern trauma-induced behavioral dysregulation requires reliable and rigorous pre-clinical models that recapitulate multiple facets of this complex disease. For decades, Pavlovian fear conditioning has been a dominant paradigm for studying the effects of trauma through an associative learning framework.

Ionic and morphological contributions to the variable gain of membrane responses in layer 2/3 pyramidal neurons of mouse primary visual cortex.

Many neuronal cell types exhibit a sliding scale of neuronal excitability in the subthreshold voltage range. This is due to a variable contribution of different voltage-gated ion channels, leading to scaling of input resistance (R) as a function of membrane potential (Vm) and a voltage-dependent dynamic gain of neuronal responsiveness. In layer 2/3 pyramidal neurons within the primary visual cortex (V1), this response influences sensory processing by tightening neuronal tuning to preferred orientations, but the identity of the ionic conductances involved remains unknown.

New research tools suggest a "levels-less" image of the behaving organism and dissolution of the reduction vs. anti-reduction dispute.

A kind of "ruthless reductionism" characterized the experimental practices of the first two decades of molecular and cellular cognition (MCC). More recently, new research tools have expanded experimental practices in this field, enabling researchers to image and manipulate individual molecular mechanisms in behaving organisms with an unprecedented temporal, sub-cellular, cellular, and even circuit-wide specificity. These tools dramatically expand the range and reach of experiments in MCC, and in doing so they may help us transcend the worn-out and counterproductive debates about "reductionism" and "emergence" that divide neuroscientists and philosophers alike.

Amygdala-cortical collaboration in reward learning and decision making.

Adaptive reward-related decision making requires accurate prospective consideration of the specific outcome of each option and its current desirability. These mental simulations are informed by stored memories of the associative relationships that exist within an environment. In this review, I discuss recent investigations of the function of circuitry between the basolateral amygdala (BLA) and lateral (lOFC) and medial (mOFC) orbitofrontal cortex in the learning and use of associative reward memories.

A locus coeruleus-dorsal CA1 dopaminergic circuit modulates memory linking.

Individual memories are often linked so that the recall of one triggers the recall of another. For example, contextual memories acquired close in time can be linked, and this is known to depend on a temporary increase in excitability that drives the overlap between dorsal CA1 (dCA1) hippocampal ensembles that encode the linked memories. Here, we show that locus coeruleus (LC) cells projecting to dCA1 have a key permissive role in contextual memory linking, without affecting contextual memory formation, and that this effect is mediated by dopamine.

The role of CCR5 in HIV-associated neurocognitive disorders.

While combination antiretroviral therapy (cART) has successfully increased the lifespan of individuals infected with HIV, a significant portion of this population remains affected by HIV-associated neurocognitive disorder (HAND). C-C chemokine receptor 5 (CCR5) has been well studied in immune response and as a co-receptor for HIV infection. HIV-infected (HIV) patients experienced mild to significant amelioration of cognitive function when treated with different CCR5 antagonists, including maraviroc and cenicriviroc.

Interpersonal Family Dynamics Relate to Hippocampal CA Subfield Structure.

Social environments that are extremely enriched or adverse can influence hippocampal volume. Though most individuals experience social environments that fall somewhere in between these extremes, substantially less is known about the influence of normative variation in social environments on hippocampal structure. Here, we examined whether hippocampal volume tracks normative variation in interpersonal family dynamics in 7- to 12-year-olds and adults recruited from the general population.

Rewarded Extinction Increases Amygdalar Connectivity and Stabilizes Long-Term Memory Traces in the vmPFC.

Neurobiological evidence in rodents indicates that threat extinction incorporates reward neurocircuitry. Consequently, incorporating reward associations with an extinction memory may be an effective strategy to persistently attenuate threat responses. Moreover, while there is considerable research on the short-term effects of extinction strategies in humans, the long-term effects of extinction are rarely considered.

The surprising difficulty of "simple" equilibrium binding measurements on ligand-gated ion channels.

Godellas and Grosman revisit equilibrium binding assays to shed new light on pentameric ligand-gated ion channels.