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A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself—OME-Zarr—along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain—the file format that underlies so many personal, institutional, and global data management and analysis tasks.

Objectives School-based mindfulness interventions in children have shown benefits to child well-being. Here, we investigated the effectiveness of a remote, app-based mindfulness intervention for promoting well-being in children. Method We conducted a randomized controlled trial (RCT) with two control groups to examine the effects of an 8-week mindfulness intervention in U.S. children ages 8–10. We compared pre-post effects between a mindfulness intervention using the Inner Explorer app, and two audiobook control interventions. The 279 children who participated in the interventions were assessed on self-report measures of anxiety and depression symptoms, perceived stress and trait mindfulness and we also collected parental reports. Results Over 80% of children completed the intervention in each condition. There was evidence for reduced self-perceived stress in children and reduced negative affect in children by parental reports using the mindfulness app, but no significant reduction for anxiety or depression symptoms. In general, between-group effect sizes were small (d < 0.45). Regular use, defined as at least 30 days of mindfulness practice within the study period, was associated with reduced child negative affect by parental reports, as well as reduced parental stress and child self-perceived stress. Conclusions These findings suggest that home use of a mindfulness app in young children can have a positive impact on children’s emotional well-being if the app is used regularly, specifically for at least 30 days in the 8-week study period. Strategies aimed at promoting regular use of the mindfulness app at home could lead to even better outcomes for children. Preregistration Preregistered on OSF at https://osf.io/23vax

Background Alzheimer’s disease (AD) is characterized by a progressive loss of memory that cannot be efficiently managed by currently available AD therapeutics. So far, most treatments for AD that have the potential to improve memory target neural circuits to protect their integrity. However, the vulnerable neural circuits and their dynamic remodeling during AD progression remain largely undefined. Methods Circuit-based approaches, including anterograde and retrograde tracing, slice electrophysiology, and fiber photometry, were used to investigate the dynamic structural and functional remodeling of a GABAergic circuit projected from the medial septum (MS) to the dentate gyrus (DG) in 3xTg-AD mice during AD progression. Results We identified a long-distance GABAergic circuit that couples highly connected MS and DG GABAergic neurons during spatial memory encoding. Furthermore, we found hyperactivity of DG interneurons during early AD, which persisted into late AD stages. Interestingly, MS GABAergic projections developed a series of adaptive strategies to combat DG interneuron hyperactivity. During early-stage AD, MS-DG GABAergic projections exhibit increased inhibitory synaptic strength onto DG interneurons to inhibit their activities. During late-stage AD, MS-DG GABAergic projections form higher anatomical connectivity with DG interneurons and exhibit aberrant outgrowth to increase the inhibition onto DG interneurons. Conclusion We report the structural and functional remodeling of the MS-DG GABAergic circuit during disease progression in 3xTg-AD mice. Dynamic MS-DG GABAergic circuit remodeling represents a compensatory mechanism to combat DG interneuron hyperactivity induced by reduced GABA transmission.

Quality control (QC) for functional connectivity magnetic resonance imaging (FC-MRI) is critical to ensure the validity of neuroimaging studies. Noise confounds are common in MRI data and, if not accounted for, may introduce biases in functional measures affecting the validity, replicability, and interpretation of FC-MRI study results. Although FC-MRI analysis rests on the assumption of adequate data processing, QC is underutilized and not systematically reported. Here, we describe a quality control pipeline for the visual and automated evaluation of MRI data implemented as part of the CONN toolbox. We analyzed publicly available resting state MRI data (N = 139 from 7 MRI sites) from the FMRI Open QC Project. Preprocessing steps included realignment, unwarp, normalization, segmentation, outlier identification, and smoothing. Data denoising was performed based on the combination of scrubbing, motion regression, and aCompCor – a principal component characterization of noise from minimally eroded masks of white matter and of cerebrospinal fluid tissues. Participant-level QC procedures included visual inspection of raw-level data and of representative images after each preprocessing step for each run, as well as the computation of automated descriptive QC measures such as average framewise displacement, average global signal change, prevalence of outlier scans, MNI to anatomical and functional overlap, anatomical to functional overlap, residual BOLD timeseries variability, effective degrees of freedom, and global correlation strength. Dataset-level QC procedures included the evaluation of inter-subject variability in the distributions of edge connectivity in a 1,000-node graph (FC distribution displays), and the estimation of residual associations across participants between functional connectivity strength and potential noise indicators such as participant’s head motion and prevalence of outlier scans (QC-FC analyses). QC procedures a

Aging is a progressive multifaceted functional decline of a biological system. Chronic age-related conditions such as neurodegenerative diseases are leading causes of death worldwide, and they are becoming a pressing problem for our society. To address this global challenge, there is a need for novel, safe, and effective rejuvenation therapies aimed at reversing age-related phenotypes and improving human health. With gene expression being a key determinant of cell identity and function, and in light of recent studies reporting rejuvenation effects through genetic perturbations, we propose an age reversal strategy focused on reprogramming the cell transcriptome to a youthful state. To this end, we suggest using transcriptomic data from primary human cells to predict rejuvenation targets and develop high-throughput aging assays, which can be used in large perturbation screens. We propose neural cells as particularly relevant targets for rejuvenation due to substantial impact of neurodegeneration on human frailty. Of all cell types in the brain, we argue that glutamatergic neurons, neuronal stem cells, and oligodendrocytes represent the most impactful and tractable targets. Lastly, we provide experimental designs for anti-aging reprogramming screens that will likely enable the development of neuronal age reversal therapies, which hold promise for dramatically improving human health.

Many crowded biomolecular structures in cells and tissues are inaccessible to labelling antibodies. To understand how proteins within these structures are arranged with nanoscale precision therefore requires that these structures be decrowded before labelling. Here we show that an iterative variant of expansion microscopy (the permeation of cells and tissues by a swellable hydrogel followed by isotropic hydrogel expansion, to allow for enhanced imaging resolution with ordinary microscopes) enables the imaging of nanostructures in expanded yet otherwise intact tissues at a resolution of about 20 nm. The method, which we named 'expansion revealing' and validated with DNA-probe-based super-resolution microscopy, involves gel-anchoring reagents and the embedding, expansion and re-embedding of the sample in homogeneous swellable hydrogels. Expansion revealing enabled us to use confocal microscopy to image the alignment of pre-synaptic calcium channels with post-synaptic scaffolding proteins in intact brain circuits, and to uncover periodic amyloid nanoclusters containing ion-channel proteins in brain tissue from a mouse model of Alzheimer's disease. Expansion revealing will enable the further discovery of previously unseen nanostructures within cells and tissues.

Children who speak one language at home and a different language at school may be at higher risk of falling behind in their academic achievement when schooling is disrupted. The present study examined the effects of COVID-19-related school disruptions on English language and literacy development among monolingual and bilingual children in the US. All children attended English-only schools that implemented varied forms of virtual and hybrid schooling during the pandemic. Pre-COVID-19 and during-COVID-19 examinations were conducted with 237 children (M(SD)age = 7.78 (1.54) at Time 1) from relatively high SES homes, including 95 monolinguals, 75 Spanish–English and 67 Chinese–English bilinguals. The findings revealed different impacts of COVID-19 school disruptions on the present bilingual and monolingual participants. Specifically, between Time 1 and Time 2, monolingual children made age-appropriate improvements in all literacy measurements. Relative to monolinguals, both bilingual groups showed greater gains in vocabulary but lower gains in reading comprehension. Moreover, across groups, children’s independent reading practices during COVID-19 were positively associated with children’s literacy growth during the pandemic-related schooling disruptions. Taken together, these findings inform theoretical perspectives on learning to read in linguistically diverse children experiencing COVID-19-related schooling disruptions.

Autism spectrum disorder (ASD) is characterized by challenges in social communication and the presence of repetitive behaviors or restricted interests. Notably, males are four times as likely as females to be diagnosed with autism. Despite efforts to increase representation and characterization of autistic females, research studies consistently enroll small samples of females, or exclude females altogether. Importantly, researchers often rely on standardized measures to confirm diagnosis prior to enrollment in research studies. We retrospectively analyzed the effects of one such measure (Autism Diagnostic Observation Schedule, ADOS) on research inclusion/exclusion rates by sex in autistic adults, all of whom had a preexisting community diagnosis of autism (n = 145, 95 male, 50 female). Using the ADOS as a confirmatory diagnostic measure resulted in the exclusion of autistic females at a rate over 2.5 times higher than that of autistic males. We compared sex ratios in our sample to those in other large, publically available datasets that rely either on community diagnosis (6 datasets, total n = 42,209) or standardized assessments (2 datasets, total n = 214) to determine eligibility of participants for research. Reliance on community diagnosis rather than confirmatory diagnostic assessments resulted in significantly more equal sex ratios. These results provide evidence for a "leaky" recruitment-to-research pipeline for females in autism research. LAY SUMMARY: Despite efforts to increase the representation of autistic females in research, studies consistently enroll small samples of females or exclude females altogether. We find that despite making up almost 50% of the initially recruited sample based upon self-report of community diagnosis, autistic females are disproportonately excluded from research participation as a result of commonly used autism diagnostic measures. In our sample, and several other publically available datasets, reliance on community diagnosis re

Broad adoption of magnetic soft robotics is hampered by the sophisticated field paradigms for their manipulation and the complexities in controlling multiple devices. Furthermore, high‐throughput fabrication of such devices across spatial scales remains challenging. Here, advances in fiber‐based actuators and magnetic elastomer composites are leveraged to create 3D magnetic soft robots controlled by unidirectional fields. Thermally drawn elastomeric fibers are instrumented with a magnetic composite synthesized to withstand strains exceeding 600%. A combination of strain and magnetization engineering in these fibers enables programming of 3D robots capable of crawling or walking in magnetic fields orthogonal to the plane of motion. Magnetic robots act as cargo carriers, and multiple robots can be controlled simultaneously and in opposing directions using a single stationary electromagnet. The scalable approach to fabrication and control of magnetic soft robots invites their future applications in constrained environments where complex fields cannot be readily deployed.

Background Copy number variations, and particularly duplications of genomic regions, have been strongly associated with various neurodegenerative conditions including autism spectrum disorder (ASD). These genetic variations have been found to have a significant impact on brain development and function, which can lead to the emergence of neurological and behavioral symptoms. Developing strategies to target these genomic duplications has been challenging, as the presence of endogenous copies of the duplicate genes often complicates the editing strategies. Results Using the ASD and anxiety mouse model Flailer, which contains a partial genomic duplication working as a dominant negative for MyoVa, we demonstrate the use of DN-CRISPRs to remove a 700 bp genomic region in vitro and in vivo. Importantly, DN-CRISPRs have not been used to remove genomic regions using sgRNA with an offset greater than 300 bp. We found that editing the flailer gene in primary cortical neurons reverts synaptic transport and transmission defects. Moreover, long-term depression (LTD), disrupted in Flailer animals, is recovered after gene editing. Delivery of DN-CRISPRs in vivo shows that local delivery to the ventral hippocampus can rescue some of the mutant behaviors, while intracerebroventricular delivery, completely recovers the Flailer animal phenotype associated to anxiety and ASD. Conclusions Our results demonstrate the potential of DN-CRISPR to efficiently remove larger genomic duplications, working as a new gene therapy approach for treating neurodegenerative diseases.

Non-invasive Gamma ENtrainment Using Sensory stimulation (GENUS) at 40Hz reduces Alzheimer’s disease (AD) pathology such as amyloid and tau levels, prevents cerebral atrophy, and improves behavioral testing performance in mouse models of AD. Here, we report data from (1) a Phase 1 feasibility study (NCT04042922, ClinicalTrials.gov) in cognitively normal volunteers (n = 25), patients with mild AD dementia (n = 16), and patients with epilepsy who underwent intracranial electrode monitoring (n = 2) to assess safety and feasibility of a single brief GENUS session to induce entrainment and (2) a single-blinded, randomized, placebo-controlled Phase 2A pilot study (NCT04055376) in patients with mild probable AD dementia (n = 15) to assess safety, compliance, entrainment, and exploratory clinical outcomes after chronic daily 40Hz sensory stimulation for 3 months. Our Phase 1 study showed that 40Hz GENUS was safe and effectively induced entrainment in both cortical regions and other cortical and subcortical structures such as the hippocampus, amygdala, insula, and gyrus rectus. Our Phase 2A study demonstrated that chronic daily 40Hz light and sound GENUS was well-tolerated and that compliance was equally high in both the control and active groups, with participants equally inaccurate in guessing their group assignments prior to unblinding. Electroencephalography recordings show that our 40Hz GENUS device safely and effectively induced 40Hz entrainment in participants with mild AD dementia. After 3 months of daily stimulation, the group receiving 40Hz stimulation showed (i) lesser ventricular dilation and hippocampal atrophy, (ii) increased functional connectivity in the default mode network as well as with the medial visual network, (iii) better performance on the face-name association delayed recall test, and (iv) improved measures of d

© 2018, The Author(s), under exclusive licence to Springer Nature America, Inc. Animals strategically scan the environment to form an accurate perception of their surroundings. Here we investigated the neuronal representations that mediate this behavior. Ca2+ imaging and selective optogenetic manipulation during an active sensing task reveals that layer 5 pyramidal neurons in the vibrissae cortex produce a diverse and distributed representation that is required for mice to adapt their whisking motor strategy to changing sensory cues. The optogenetic perturbation degraded single-neuron selectivity and network population encoding through a selective inhibition of active dendritic integration. Together the data indicate that active dendritic integration in pyramidal neurons produces a nonlinearly mixed network representation of joint sensorimotor parameters that is used to transform sensory information into motor commands during adaptive behavior. The prevalence of the layer 5 cortical circuit motif suggests that this is a general circuit computation.

CRISPR-Cas13 systems have been developed for precise RNA editing, and can potentially be used therapeutically when temporary changes are desirable or when DNA editing is challenging. We have identified and characterized an ultrasmall family of Cas13b proteins-Cas13bt-that can mediate mammalian transcript knockdown. We have engineered compact variants of REPAIR and RESCUE RNA editors by functionalizing Cas13bt with adenosine and cytosine deaminase domains, and demonstrated packaging of the editors within a single adeno-associated virus.

Searching for factors to improve knockin efficiency for therapeutic applications, biotechnology, and generation of non-human primate models of disease, we found that the strand exchange protein RAD51 can significantly increase Cas9-mediated homozygous knockin in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is a hallmark of meiosis but only occurs at low frequencies in somatic cells, and its occurrence in zygotes is controversial. Using multiple approaches, we provide evidence for an endogenous IHR mechanism in the early embryo that can be enhanced by RAD51. This process can be harnessed to generate homozygotes from wild-type zygotes using exogenous donors and to convert heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we identify additional IHR-promoting factors and describe features of IHR events. Together, our findings show conclusive evidence for IHR in mouse embryos and describe an efficient method for enhanced gene conversion.

Significance Bioelectronic medicine relies on electrical stimulation for most applications in the peripheral nervous system. It faces persistent challenges in selectively activating bundled nerve fibers. Here, we investigated ion-concentration modulation with ion-selective membranes and whether this modality may enhance the functional selectivity of peripheral nerve stimulation. We designed a multimodal stimulator that could control Ca 2+ concentrations within a focused volume. Acutely implanting it on the sciatic nerve of a rat, we demonstrated that Ca 2+ depletion could increase the sensitivity of the nerve to electrical stimulation in vivo. We provided evidence that it selectively influenced individual fascicles of the nerve, allowing selective activation by electrical current. Improved functional selectivity may improve outcomes for important therapeutic modalities.

Hyper-reactivity to sensory input is a common and debilitating symptom in individuals with autism spectrum disorders (ASD), but the neural basis underlying sensory abnormality is not completely understood. Here we examined the neural representations of sensory perception in the neocortex of a Shank3B−/− mouse model of ASD. Male and female Shank3B−/− mice were more sensitive to relatively weak tactile stimulation in a vibrissa motion detection task. In vivo population calcium imaging in vibrissa primary somatosensory cortex (vS1) revealed increased spontaneous and stimulus-evoked firing in pyramidal neurons but reduced activity in interneurons. Preferential deletion of Shank3 in vS1 inhibitory interneurons led to pyramidal neuron hyperactivity and increased stimulus sensitivity in the vibrissa motion detection task. These findings provide evidence that cortical GABAergic interneuron dysfunction plays a key role in sensory hyper-reactivity in a Shank3 mouse model of ASD and identify a potential cellular target for exploring therapeutic interventions., National Institutes of Health (Grant R01MH097104), NIMH (Grants P50MH094271, F32MH100749 and R01NS045130)

© 2019 by The Keio Journal of Medicine. The class 2 CRISPR-Cas endonuclease Cas12a (previously known as Cpf1) offers several advantages over Cas9, including the ability to process its own array and the requirement for just a single RNA guide. These attributes make Cas12a promising for many genome engineering applications. To further expand the suite of Cas12a tools available, we tested 16 Cas12a orthologs for activity in eukaryotic cells. Four of these new enzymes demonstrated targeted activity, one of which, from Moraxella bovoculi AAX11_00205 (Mb3Cas12a), exhibited robust indel formation. We also showed that Mb3Cas12a displays some tolerance for a shortened PAM (TTN versus the canonical Cas12a PAM TTTV). The addition of these enzymes to the genome editing toolbox will further expand the utility of this powerful technology., National Institutes of Health (Grants 1R01-HG009761, 1R01-MH110049 and 1DP1-HL141201)

Thermal drawing has been recently leveraged to yield multifunctional, fiber-based neural probes at near kilometer length scales. Despite its promise, the widespread adoption of this approach has been impeded by (1) material compatibility requirements and (2) labor-intensive interfacing of functional features to external hardware. Furthermore, in multifunctional fibers, significant volume is occupied by passive polymer cladding that so far has only served structural or electrical insulation purposes. In this article, we report a rapid, robust, and modular approach to creating multifunctional fiber-based neural interfaces using a solvent evaporation or entrapment-driven (SEED) integration process. This process brings together electrical, optical, and microfluidic modalities all encased within a copolymer comprised of water-soluble poly(ethylene glycol) tethered to water-insoluble poly(urethane) (PU-PEG). We employ these devices for simultaneous optogenetics and electrophysiology and demonstrate that multifunctional neural probes can be used to deliver cellular cargo with high viability. Upon exposure to water, PU-PEG cladding spontaneously forms a hydrogel, which in addition to enabling integration of modalities, can harbor small molecules and nanomaterials that can be released into local tissue following implantation. We also synthesized a custom nanodroplet forming block polymer and demonstrated that embedding such materials within the hydrogel cladding of our probes enables delivery of hydrophobic small molecules in vitro and in vivo. Our approach widens the chemical toolbox and expands the capabilities of multifunctional neural interfaces.

Hitching a ride with a retroelement Retroviruses and retroelements have inserted their genetic code into mammalian genomes throughout evolution. Although many of these integrated virus-like sequences pose a threat to genomic integrity, some have been retooled by mammalian cells to perform essential roles in development. Segel et al . found that one of these retroviral-like proteins, PEG10, directly binds to and secretes its own mRNA in extracellular virus–like capsids. These virus-like particles were then pseudotyped with fusogens to deliver functional mRNA cargos to mammalian cells. This potentially provides an endogenous vector for RNA-based gene therapy. —DJ

The onset of the 2020 global COVID-19 pandemic led to a marked increase in positive discussion of Universal Basic Income (UBI) in political and media circles. However, we do not know whether there was a corresponding increase in support for the policy in the public at large, or why. Here, we present three studies carried out during 2020 in UK and US samples. In study 1 (n = 802, April 2020), people expressed much stronger support for a UBI policy for the times of the pandemic and its aftermath than for normal times. This was largely explained by the increased importance they attached, in the pandemic context, to a system that is simple and efficient to administer, and that reduces stress and anxiety in society. In study 2 (n = 400, May 2020), we pitted UBI against a conditional targeted social transfer system. Preferences for UBI were stronger for pandemic times than for normal times. This was partially explained by a number of perceived advantages, such as simplicity of administration and suitability for a changing world. In study 3 (n = 397, September 2020), we found that the headline results of studies 1 and 2 persisted six months after the onset of the pandemic, albeit with attenuated effect sizes. Our results illustrate how a changing social and economic situation can bring about markedly different policy preferences, through changes in citizens’ perceptions of what is currently important.

Fiber drawing enables scalable fabrication of multifunctional flexible fibers that integrate electrical, optical and microfluidic modalities to record and modulate neural activity. Constraints on thermomechanical properties of materials, however, have prevented integrated drawing of metal electrodes with low-loss polymer waveguides for concurrent electrical recording and optical neuromodulation. Here we introduce two fabrication approaches: (1) an iterative thermal drawing with a soft, low melting temperature (Tm) metal indium, and (2) a metal convergence drawing with traditionally non-drawable high Tm metal tungsten. Both approaches deliver multifunctional flexible neural interfaces with low-impedance metallic electrodes and low-loss waveguides, capable of recording optically-evoked and spontaneous neural activity in mice over several weeks. We couple these fibers with a light-weight mechanical microdrive (1g) that enables depth-specific interrogation of neural circuits in mice following chronic implantation. Finally, we demonstrate the compatibility of these fibers with magnetic resonance imaging (MRI) and apply them to visualize the delivery of chemical payloads through the integrated channels in real time. Together, these advances expand the domains of application of the fiber-based neural probes in neuroscience and neuroengineering.

Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.

© 2019 Many studies have investigated the development of face-, scene-, and body-selective regions in the ventral visual pathway. This work has primarily focused on comparing the size and univariate selectivity of these neural regions in children versus adults. In contrast, very few studies have investigated the developmental trajectory of more distributed activation patterns within and across neural regions. Here, we scanned both children (ages 5–7) and adults to test the hypothesis that distributed representational patterns arise before category selectivity (for faces, bodies, or scenes) in the ventral pathway. Consistent with this hypothesis, we found mature representational patterns in several ventral pathway regions (e.g., FFA, PPA, etc.), even in children who showed no hint of univariate selectivity. These results suggest that representational patterns emerge first in each region, perhaps forming a scaffold upon which univariate category selectivity can subsequently develop. More generally, our findings demonstrate an important dissociation between category selectivity and distributed response patterns, and raise questions about the relative roles of each in development and adult cognition.

Nucleic acid detection is vital for agricultural applications including trait detection during breeding, pest surveillance, and pathogen identification. Here, we use a modified version of the CRISPR-based nucleic acid detection platform SHERLOCK to quantify levels of a glyphosate resistance gene in a mixture of soybeans and to detect multiple plant genes in a single reaction. SHERLOCK is rapid (∼15 min), quantitative, and portable, and can process crude soybean extracts as input material for minimal nucleic acid sample preparation. This field-ready SHERLOCK platform with color-based lateral flow readout can be applied for detection and quantitation of genes in a range of agricultural applications.

Negative symptoms in the motivational domain are strongly correlated with deficits in social and occupational functioning in schizophrenia. However, the neural substrates underlying these symptoms remain largely unknown. Twenty-eight adults with schizophrenia and twenty healthy volunteers underwent functional magnetic resonance while completing a lottery game designed to capture reward-related cognitive processes. Each trial demanded an initial investment of effort in form of key presses to increase the odds of winning. Brain activity in response to different reward cues (1 euro versus 1 cent) was compared between groups. Whereas controls invested more effort in improving their chances to win 1 euro compared to 1 cent in the lottery game, patients invested similarly high amounts of effort in both reward conditions. The neuroimaging analysis revealed lower neural activity in the bilateral caudate and cingulo-opercular circuits and decreased effective connectivity between reward-associated areas and neural nodes in the frontoparietal and salience network in response to high- versus low-reward conditions in schizophrenia patients compared to controls. Effective connectivity differences across conditions were associated with amotivation symptoms in patients. Overall, our data provide the evidence of alterations in neural activity in the caudate and cingulo-opercular “task maintenance” circuits and frontoparietal effective connectivity with reward-associated nodes as possible underlying mechanisms of reward value discrimination deficits affecting effort computation in schizophrenia.

In the last three decades, functional magnetic resonance imaging (fMRI) has transformed the field of cognitive neuroscience. A standard analytic approach entails aligning a set of individual activation maps in a common brain space, performing a statistical test in each voxel, and interpreting significant activation clusters with respect to macroanatomic landmarks. In the last several years, however, this group-analytic approach is being increasingly replaced by analyses where neural responses are examined within each brain individually. In this opinion piece, I trace the origins of individual-subject analyses in human neuroscience and speculate on why group analyses had risen vastly in popularity during the 2000s. I then discuss a core problem with group analyses — their limited utility in informing the human cognitive architecture — and talk about how the individual-subject functional localization approach solves this problem. Finally, I discuss other reasons for why researchers have been turning to individual-subject analyses, and argue that such approaches are likely to be the future of human neuroscience.

© 2020, The Author(s). Music perception is plausibly constrained by universal perceptual mechanisms adapted to natural sounds. Such constraints could arise from our dependence on harmonic frequency spectra for segregating concurrent sounds, but evidence has been circumstantial. We measured the extent to which concurrent musical notes are misperceived as a single sound, testing Westerners as well as native Amazonians with limited exposure to Western music. Both groups were more likely to mistake note combinations related by simple integer ratios as single sounds (‘fusion’). Thus, even with little exposure to Western harmony, acoustic constraints on sound segregation appear to induce perceptual structure on note combinations. However, fusion did not predict aesthetic judgments of intervals in Westerners, or in Amazonians, who were indifferent to consonance/dissonance. The results suggest universal perceptual mechanisms that could help explain cross-cultural regularities in musical systems, but indicate that these mechanisms interact with culture-specific influences to produce musical phenomena such as consonance.

© 2018 Elsevier Ltd Understanding neural representations of behavioral routines is critical for understanding complex behavior in health and disease. We demonstrate here that accentuated activity of striatal projection neurons (SPNs) at the beginning and end of such behavioral repertoires is a supraordinate representation specifically marking previously rewarded behavioral sequences independent of the individual movements making up the behavior. We recorded spike activity in the striatum and primary motor cortex as individual rats learned specific rewarded lever-press sequences, each one unique to a given rat. Motor cortical neurons mainly responded in relation to specific movements regardless of their sequence of occurrence. By contrast, striatal SPN populations in each rat fired preferentially at the initiation and termination of its acquired sequence. Critically, the SPNs did not exhibit this bracketing signal when the same rats performed unreinforced sequences containing the same sub-movements that were present in their acquired sequence. Thus, the SPN activity was specifically related to a given repetitively reinforced movement sequence. This striatal beginning-and-end activity did not appear to be dependent on motor cortical inputs. However, strikingly, simultaneously recorded fast-spiking striatal interneurons (FSIs) showed equally selective but inverse firing patterns: they fired in between the initiation and termination of the acquired sequences. These findings suggest that the striatum contains networks of neurons representing acquired sequences of behavior at a level of abstraction higher than that of the individual movements making up the sequence. We propose that such SPN-FSI networks of the striatum could underlie the acquisition of chunked behavioral units. Habitual behavioral routines acquired by repetition are ubiquitous in daily life. Martiros et al. demonstrate that such learned habits and skills become marked as behavioral units, regardless of th

© 2019 IOP Publishing Ltd. Objective. Intracellular patch-clamp electrophysiology, one of the most ubiquitous, high-fidelity techniques in biophysics, remains laborious and low-throughput. While previous efforts have succeeded at automating some steps of the technique, here we demonstrate a robotic 'PatcherBot' system that can perform many patch-clamp recordings sequentially, fully unattended. Approach. Comprehensive automation is accomplished by outfitting the robot with machine vision, and cleaning pipettes instead of manually exchanging them. Main results. the PatcherBot can obtain data at a rate of 16 cells per hour and work with no human intervention for up to 3 h. We demonstrate the broad applicability and scalability of this system by performing hundreds of recordings in tissue culture cells and mouse brain slices with no human supervision. Using the PatcherBot, we also discovered that pipette cleaning can be improved by a factor of three. Significance. The system is potentially transformative for applications that depend on many high-quality measurements of single cells, such as drug screening, protein functional characterization, and multimodal cell type investigations.

© 2017 Elsevier Inc. Targeted patch-clamp recording is a powerful method for characterizing visually identified cells in intact neural circuits, but it requires skill to perform. We previously developed an algorithm that automates “blind” patching in vivo, but full automation of visually guided, targeted in vivo patching has not been demonstrated, with currently available approaches requiring human intervention to compensate for cell movement as a patch pipette approaches a targeted neuron. Here we present a closed-loop real-time imaging strategy that automatically compensates for cell movement by tracking cell position and adjusting pipette motion while approaching a target. We demonstrate our system's ability to adaptively patch, under continuous two-photon imaging and real-time analysis, fluorophore-expressing neurons of multiple types in the living mouse cortex, without human intervention, with yields comparable to skilled human experimenters. Our “imagepatching” robot is easy to implement and will help enable scalable characterization of identified cell types in intact neural circuits.

The bilingual experience may place special cognitive demands on speakers and has been argued to lead to improvements in domain-general executive abilities, like cognitive control and working memory. Such improvements have been argued for based on both behavioral and brain imaging evidence. However, the empirical landscape is complex and ridden with controversy. Here we attempt to shed light on this question through an fMRI investigation of relatively large, relatively homogeneous, and carefully matched samples of early balanced bilinguals (n = 55) and monolinguals (n = 54), using robust, previously validated individual-level markers of neural activity in the domain-general multiple demand (MD) network, which supports executive functions. We find that the bilinguals, compared to the monolinguals, show significantly stronger neural responses to an executive (spatial working memory) task, and a larger difference between a harder and an easier condition of the task, across the MD network. These stronger neural responses are accompanied by better behavioral performance on the working memory task. We further show that the bilingual-vs.-monolingual difference in neural responses is not ubiquitous across the brain as no group difference in magnitude is observed in primary visual areas, which also respond to the task. Although the neural group difference in the MD network appears robust, it remains difficult to causally link it to bilingual experience specifically.

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Current approaches to single-cell RNA sequencing (RNA-seq) provide only limited information about the dynamics of gene expression. Here we present RNA timestamps, a method for inferring the age of individual RNAs in RNA-seq data by exploiting RNA editing. To introduce timestamps, we tag RNA with a reporter motif consisting of multiple MS2 binding sites that recruit the adenosine deaminase ADAR2 fused to an MS2 capsid protein. ADAR2 binding to tagged RNA causes A-to-I edits to accumulate over time, allowing the age of the RNA to be inferred with hour-scale accuracy. By combining observations of multiple timestamped RNAs driven by the same promoter, we can determine when the promoter was active. We demonstrate that the system can infer the presence and timing of multiple past transcriptional events. Finally, we apply the method to cluster single cells according to the timing of past transcriptional activity. RNA timestamps will allow the incorporation of temporal information into RNA-seq workflows.

Tn7-like transposons have co-opted CRISPR systems, including class 1 type I-F, I-B, and class 2 type V-K. Intriguingly, although these CRISPR-associated transposases (CASTs) undergo robust CRISPR RNA (crRNA)-guided transposition, they are almost never found in sites targeted by the crRNAs encoded by the cognate CRISPR array. To understand this paradox, we investigated CAST V-K and I-B systems and found two distinct modes of transposition: (1) crRNA-guided transposition and (2) CRISPR array-independent homing. We show distinct CAST systems utilize different molecular mechanisms to target their homing site. Type V-K CAST systems use a short, delocalized crRNA for RNA-guided homing, whereas type I-B CAST systems, which contain two distinct target selector proteins, use TniQ for RNA-guided DNA transposition and TnsD for homing to an attachment site. These observations illuminate a key step in the life cycle of CAST systems and highlight the diversity of molecular mechanisms mediating transposon homing.

IscB proteins are putative nucleases encoded in a distinct family of IS200/IS605 transposons and are likely ancestors of the RNA-guided endonuclease Cas9, but the functions of IscB and its interactions with any RNA remain uncharacterized. Using evolutionary analysis, RNA sequencing, and biochemical experiments, we reconstructed the evolution of CRISPR-Cas9 systems from IS200/IS605 transposons. We found that IscB uses a single noncoding RNA for RNA-guided cleavage of double-stranded DNA and can be harnessed for genome editing in human cells. We also demonstrate the RNA-guided nuclease activity of TnpB, another IS200/IS605 transposon-encoded protein and the likely ancestor of Cas12 endonucleases. This work reveals a widespread class of transposon-encoded RNA-guided nucleases, which we name OMEGA (obligate mobile element–guided activity), with strong potential for developing as biotechnologies.

© Cadena-Valencia et al. To prepare timely motor actions, we constantly predict future events. Regularly repeating events are often perceived as a rhythm to which we can readily synchronize our movements, just as in dancing to music. However, the neuronal mechanisms underlying the capacity to encode and maintain rhythms are not understood. We trained nonhuman primates to maintain the rhythm of a visual metronome of diverse tempos and recorded neural activity in the supplementary motor area (SMA). SMA exhibited rhythmic bursts of gamma band (30–40 Hz) reflecting an internal tempo that matched the extinguished visual metronome. Moreover, gamma amplitude increased throughout the trial, providing an estimate of total elapsed time. Notably, the timing of gamma bursts and firing rate modulations allowed predicting whether monkeys were ahead or behind the correct tempo. Our results indicate that SMA uses dynamic motor plans to encode a metronome for rhythms and a stopwatch for total elapsed time.

© 2017 The Author(s). Optogenetic control of individual neurons with high temporal precision within intact mammalian brain circuitry would enable powerful explorations of how neural circuits operate. Two-photon computer-generated holography enables precise sculpting of light and could in principle enable simultaneous illumination of many neurons in a network, with the requisite temporal precision to simulate accurate neural codes. We designed a high-efficacy soma-targeted opsin, finding that fusing the N-terminal 150 residues of kainate receptor subunit 2 (KA2) to the recently discovered high-photocurrent channelrhodopsin CoChR restricted expression of this opsin primarily to the cell body of mammalian cortical neurons. In combination with two-photon holographic stimulation, we found that this somatic CoChR (soCoChR) enabled photostimulation of individual cells in mouse cortical brain slices with single-cell resolution and <1-ms temporal precision. We used soCoChR to perform connectivity mapping on intact cortical circuits.

In the world, there is a growing need for lower limb prostheses due to a rising number of amputations caused primarily, by diabetic foot. Researchers enable functional and comfortable prostheses through prosthetic design by integrating new technologies applied to the traditional handcrafted method for prosthesis fabrication that is still current. That is why computer vision shows to be a promising tool for the integration of 3D reconstruction that may be useful for prosthetic design. This work has the objective to design, prototype, and test a functional system to scan plaster cast molds, which may serve as a platform for future technologies for lower limb reconstruction applications. The image capture system comprises 5 stereoscopic color and depth cameras, each with 4 DOF mountings on an enveloping frame, as well as algorithms for calibration, segmentation, registration, and surface reconstruction. The segmentation metrics of dice coefficient and Hausdorff distance (HD) show strong visual similarity with an average similarity of 87% and average error of 6.40 mm, respectively. Moving forward, the system was tested on a known 3D printed model obtained from a computer tomography scan to which comparison results via HD show an average error of ≤1.93 mm thereby making the system competitive against the systems reviewed from the state-of-the-art.

De novo and inherited rare genetic disorders (RGDs) are a major cause of human morbidity, frequently involving neuropsychiatric symptoms. Recent advances in genomic technologies and data sharing have revolutionized the identification and diagnosis of RGDs, presenting an opportunity to elucidate the mechanisms underlying neuropsychiatric disorders by investigating the pathophysiology of high-penetrance genetic risk factors. Here we seek out the best path forward for achieving these goals. We think future research will require consistent approaches across multiple RGDs and developmental stages, involving both the characterization of shared neuropsychiatric dimensions in humans and the identification of neurobiological commonalities in model systems. A coordinated and concerted effort across patients, families, researchers, clinicians and institutions, including rapid and broad sharing of data, is now needed to translate these discoveries into urgently needed therapies.

The atomic structure at the interface between two-dimensional (2D) and three-dimensional (3D) materials influences properties such as contact resistance, photo-response, and high-frequency electrical performance. Moiré engineering is yet to be utilized for tailoring this 2D/3D interface, despite its success in enabling correlated physics at 2D/2D interfaces. Using epitaxially aligned MoS /Au{111} as a model system, we demonstrate the use of advanced scanning transmission electron microscopy (STEM) combined with a geometric convolution technique in imaging the crystallographic 32 Å moiré pattern at the 2D/3D interface. This moiré period is often hidden in conventional electron microscopy, where the Au structure is seen in projection. We show, via ab initio electronic structure calculations, that charge density is modulated according to the moiré period, illustrating the potential for (opto-)electronic moiré engineering at the 2D/3D interface. Our work presents a general pathway to directly image periodic modulation at interfaces using this combination of emerging microscopy techniques. 2

© 2017 The Authors. Published under the terms of the CC BY 4.0 license Paraformaldehyde (PFA) is the most commonly used fixative for immunostaining of cells, but has been associated with various problems, ranging from loss of antigenicity to changes in morphology during fixation. We show here that the small dialdehyde glyoxal can successfully replace PFA. Despite being less toxic than PFA, and, as most aldehydes, likely usable as a fixative, glyoxal has not yet been systematically tried in modern fluorescence microscopy. Here, we tested and optimized glyoxal fixation and surprisingly found it to be more efficient than PFA-based protocols. Glyoxal acted faster than PFA, cross-linked proteins more effectively, and improved the preservation of cellular morphology. We validated glyoxal fixation in multiple laboratories against different PFA-based protocols and confirmed that it enabled better immunostainings for a majority of the targets. Our data therefore support that glyoxal can be a valuable alternative to PFA for immunostaining.

© 2020 American Association for the Advancement of Science. All rights reserved. The number of disease risk genes and loci identified through human genetic studies far outstrips the capacity to systematically study their functions. We applied a scalable genetic screening approach, in vivo Perturb-Seq, to functionally evaluate 35 autism spectrum disorder/neurodevelopmental delay (ASD/ND) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing mouse brain in utero, followed by single-cell RNAsequencing of perturbed cells in the postnatal brain. We identified cell type-specific and evolutionarily conserved gene modules from both neuronal and glial cell classes. Recurrent gene modules and cell types are affected across this cohort of perturbations, representing key cellular effects across sets of ASD/ND risk genes. In vivo Perturb-Seq allows us to investigate how diverse mutations affect cell types and states in the developing organism.

JC virus (JCV) can cause a lytic infection of oligodendrocytes and astrocytes in the central nervous system (CNS) leading to progressive multifocal leukoencephalopathy (PML). JCV can also infect meningeal and choroid plexus cells causing JCV meningitis (JCVM). Whether JCV also infects meningeal and choroid plexus cells in PML patients and other immunosuppressed individuals with no overt symptoms of meningitis remains unknown. We therefore analyzed archival formalin-fixed, paraffin-embedded brain samples from PML patients, and HIV-seropositive and seronegative control subjects by immunohistochemistry for the presence of JCV early regulatory T Ag and JCV VP1 late capsid protein. In meninges, we detected JCV T Ag in 11/48 (22.9%) and JCV VP1 protein in 8/48 (16.7%) PML patients. In choroid plexi, we detected JCV T Ag in 1/7 (14.2%) and JCV VP1 protein in 1/8 (12.5%) PML patients. Neither JCV T Ag nor VP1 protein could be detected in meninges or choroid plexus of HIV-seropositive and HIV-seronegative control subjects without PML. In addition, examination of underlying cerebellar cortex of PML patients revealed JCV-infected cells in the molecular layer, including GAD 67+ interneurons, but not in HIV-seropositive and HIV-seronegative control subjects without PML. Our findings suggest that productive JCV infection of meningeal cells and choroid plexus cells also occurs in PML patients without signs or symptoms of meningitis. The phenotypic characterization of JCV-infected neurons in the molecular layer deserves further study. This data provides new insight into JCV pathogenesis in the CNS.

The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.

Hearing in noise is a core problem in audition, and a challenge for hearing-impaired listeners, yet the underlying mechanisms are poorly understood. We explored whether harmonic frequency relations, a signature property of many communication sounds, aid hearing in noise for normal hearing listeners. We measured detection thresholds in noise for tones and speech synthesized to have harmonic or inharmonic spectra. Harmonic signals were consistently easier to detect than otherwise identical inharmonic signals. Harmonicity also improved discrimination of sounds in noise. The largest benefits were observed for two-note up-down “pitch” discrimination and melodic contour discrimination, both of which could be performed equally well with harmonic and inharmonic tones in quiet, but which showed large harmonic advantages in noise. The results show that harmonicity facilitates hearing in noise, plausibly by providing a noise-robust pitch cue that aids detection and discrimination.

We show that music-selective neural populations are clearly present in people without musical training, demonstrating that they are a fundamental and widespread property of the human brain. Additionally, we show music-selective neural populations respond strongly to music from unfamiliar genres as well as music with rhythm but little pitch information, suggesting that they are broadly responsive to music as a whole. , NSF Grant (BCS-1634050), NIH grant (DP1HD09194)

This report presents an overview of how machine learning is rapidly advancing clinical translational imaging in ways that will aid in the early detection, prediction, and treatment of diseases that threaten brain health. Towards this goal, we aresharing the information presented at a symposium, “Neuroimaging Indicators of Brain Structure and Function - Closing the Gap Between Research and Clinical Application”, co-hosted by the McCance Center for Brain Health at Mass General Hospital and the MIT HST Neuroimaging Training Program on February 12, 2021. The symposium focused on the potential for machine learning approaches, applied to increasingly large-scale neuroimaging datasets, to transform healthcare delivery and change the trajectory of brain health by addressing brain care earlier in the lifespan. While not exhaustive, this overview uniquely addresses many of the technical challenges from image formation, to analysis and visualization, to synthesis and incorporation into the clinical workflow. Some of the ethical challenges inherent to this work are also explored, as are some of the regulatory requirements for implementation. We seek to educate, motivate, and inspire graduate students, postdoctoral fellows, and early career investigators to contribute to a future where neuroimaging meaningfully contributes to the maintenance of brain health.