In vivo neuropil density from anatomical MRI and machine learning.

Brain energy budgets specify metabolic costs emerging from underlying mechanisms of cellular and synaptic activities. While current bottom-up energy budgets use prototypical values of cellular density and synaptic density, predicting metabolism from a person's individualized neuropil density would be ideal. We hypothesize that in vivo neuropil density can be derived from magnetic resonance imaging (MRI) data, consisting of longitudinal relaxation (T1) MRI for gray/white matter distinction and diffusion MRI for tissue cellularity (apparent diffusion coefficient, ADC) and axon directionality (fractional anisotropy, FA). We present a machine learning algorithm that predicts neuropil density from in vivo MRI scans, where ex vivo Merker staining and in vivo synaptic vesicle glycoprotein 2A Positron Emission Tomography (SV2A-PET) images were reference standards for cellular and synaptic density, respectively. We used Gaussian-smoothed T1/ADC/FA data from 10 healthy subjects to train an artificial neural network, subsequently used to predict cellular and synaptic density for 54 test subjects. While excellent histogram overlaps were observed both for synaptic density (0.93) and cellular density (0.85) maps across all subjects, the lower spatial correlations both for synaptic density (0.89) and cellular density (0.58) maps are suggestive of individualized predictions. This proof-of-concept artificial neural network may pave the way for individualized energy atlas prediction, enabling microscopic interpretations of functional neuroimaging data.

Multimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization.

Large-scale functional networks have been characterized in both rodent and human brains, typically by analyzing fMRI-BOLD signals. However, the relationship between fMRI-BOLD and underlying neural activity is complex and incompletely understood, which poses challenges to interpreting network organization obtained using this technique. Additionally, most work has assumed a disjoint functional network organization (i.e., brain regions belong to one and only one network). Here, we employ wide-field Ca2+ imaging simultaneously with fMRI-BOLD in mice expressing GCaMP6f in excitatory neurons. We determine cortical networks discovered by each modality using a mixed-membership algorithm to test the hypothesis that functional networks exhibit overlapping organization. We find that there is considerable network overlap (both modalities) in addition to disjoint organization. Our results show that multiple BOLD networks are detected via Ca2+ signals, and networks determined by low-frequency Ca2+ signals are only modestly more similar to BOLD networks. In addition, the principal gradient of functional connectivity is nearly identical for BOLD and Ca2+ signals. Despite similarities, important differences are also detected across modalities, such as in measures of functional connectivity strength and diversity. In conclusion, Ca2+ imaging uncovers overlapping functional cortical organization in the mouse that reflects several, but not all, properties observed with fMRI-BOLD signals.

Estimating county-level vaccination coverage using small area estimation with the National Immunization Survey-Child.

The National Immunization Survey-Child (NIS-Child) provides annual vaccination coverage estimates in the United States for children aged 19 through 35 months, nationally, for each state, and for select local areas and territories. There is a need for vaccination coverage estimates for smaller geographic areas to support local authority planning and identify counties with potentially low vaccination coverage for possible further intervention. We describe small area estimation methods using 2008-2018 NIS-Child data to generate county-level estimates for children up to two years of age born 2007-2011 and 2012-2016. We applied an empirical best linear unbiased prediction method to combine direct estimates of vaccination coverage with model-based prediction using county-level predictors regarding health and demographic characteristics. We review the predictors commonly selected for the small area models and note multiple predictors related to barriers to vaccination.

Spatiotemporal features of neurovascular (un)coupling with stimulus-induced activity and hypercapnia challenge in cerebral cortex and olfactory bulb.

Carbon dioxide (CO2) is traditionally considered as metabolic waste, yet its regulation is critical for brain function. It is well accepted that hypercapnia initiates vasodilation, but its effect on neuronal activity is less clear. Distinguishing how stimulus- and CO2-induced vasodilatory responses are (dis)associated with neuronal activity has profound clinical and experimental relevance. We used an optical method in mice to simultaneously image fluorescent calcium (Ca2+) transients from neurons and reflectometric hemodynamic signals during brief sensory stimuli (i.e., hindpaw, odor) and CO2 exposure (i.e., 5%). Stimuli-induced neuronal and hemodynamic responses swiftly increased within locally activated regions exhibiting robust neurovascular coupling. However, hypercapnia produced slower global vasodilation which was temporally uncoupled to neuronal deactivation. With trends consistent across cerebral cortex and olfactory bulb as well as data from GCaMP6f/jRGECO1a mice (i.e., green/red Ca2+ fluorescence), these results unequivocally reveal that stimuli and CO2 generate comparable vasodilatory responses but contrasting neuronal responses. In summary, observations of stimuli-induced regional neurovascular coupling and CO2-induced global neurovascular uncoupling call for careful appraisal when using CO2 in gas mixtures to affect vascular tone and/or neuronal excitability, because CO2 is both a potent vasomodulator and a neuromodulator.

Multimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization.

Large-scale functional networks have been characterized in both rodent and human brains, typically by analyzing fMRI-BOLD signals. However, the relationship between fMRI-BOLD and underlying neural activity is complex and incompletely understood, which poses challenges to interpreting network organization obtained using this technique. Additionally, most work has assumed a disjoint functional network organization (i.e., brain regions belong to one and only one network). Here, we employed wide-field Ca2+ imaging simultaneously with fMRI-BOLD in mice expressing GCaMP6f in excitatory neurons. We determined cortical networks discovered by each modality using a mixed-membership algorithm to test the hypothesis that functional networks are overlapping rather than disjoint. Our results show that multiple BOLD networks are detected via Ca2+ signals; there is considerable network overlap (both modalities); networks determined by low-frequency Ca2+ signals are only modestly more similar to BOLD networks; and, despite similarities, important differences are detected across modalities (e.g., brain region "network diversity"). In conclusion, Ca2+ imaging uncovered overlapping functional cortical organization in the mouse that reflected several, but not all, properties observed with fMRI-BOLD signals.

Ketamine Effects on Energy Metabolism, Functional Connectivity and Working Memory in Healthy Humans.

Working memory (WM) is a crucial resource for temporary memory storage and the guiding of ongoing behavior. N-methyl-D-aspartate glutamate receptors (NMDARs) are thought to support the neural underpinnings of WM. Ketamine is an NMDAR antagonist that has cognitive and behavioral effects at subanesthetic doses. To shed light on subanesthetic ketamine effects on brain function, we employed a multimodal imaging design, combining gas-free calibrated functional magnetic resonance imaging (fMRI) measurement of oxidative metabolism (CMRO 2 ), resting-state cortical functional connectivity assessed with fMRI, and WM-related fMRI. Healthy subjects participated in two scan sessions in a randomized, double-blind, placebo-controlled design. Ketamine increased CMRO 2 and cerebral blood flow (CBF) in prefrontal cortex (PFC) and other cortical regions. However, resting-state cortical functional connectivity was not affected. Ketamine did not alter CBF-CMRO 2 coupling brain-wide. Higher levels of basal CMRO 2 were associated with lower task-related PFC activation and WM accuracy impairment under both saline and ketamine conditions. These observations suggest that CMRO 2 and resting-state functional connectivity index distinct dimensions of neural activity. Ketamine’s impairment of WM-related neural activity and performance appears to be related to its ability to produce cortical metabolic activation. This work illustrates the utility of direct measurement of CMRO 2 via calibrated fMRI in studies of drugs that potentially affect neurovascular and neurometabolic coupling.

A consensus protocol for functional connectivity analysis in the rat brain.

Task-free functional connectivity in animal models provides an experimental framework to examine connectivity phenomena under controlled conditions and allows for comparisons with data modalities collected under invasive or terminal procedures. Currently, animal acquisitions are performed with varying protocols and analyses that hamper result comparison and integration. Here we introduce StandardRat, a consensus rat functional magnetic resonance imaging acquisition protocol tested across 20 centers. To develop this protocol with optimized acquisition and processing parameters, we initially aggregated 65 functional imaging datasets acquired from rats across 46 centers. We developed a reproducible pipeline for analyzing rat data acquired with diverse protocols and determined experimental and processing parameters associated with the robust detection of functional connectivity across centers. We show that the standardized protocol enhances biologically plausible functional connectivity patterns relative to previous acquisitions. The protocol and processing pipeline described here is openly shared with the neuroimaging community to promote interoperability and cooperation toward tackling the most important challenges in neuroscience.

Decreased but diverse activity of cortical and thalamic neurons in consciousness-impairing rodent absence seizures.

Absence seizures are brief episodes of impaired consciousness, behavioral arrest, and unresponsiveness, with yet-unknown neuronal mechanisms. Here we report that an awake female rat model recapitulates the behavioral, electroencephalographic, and cortical functional magnetic resonance imaging characteristics of human absence seizures. Neuronally, seizures feature overall decreased but rhythmic firing of neurons in cortex and thalamus. Individual cortical and thalamic neurons express one of four distinct patterns of seizure-associated activity, one of which causes a transient initial peak in overall firing at seizure onset, and another which drives sustained decreases in overall firing. 40-60 s before seizure onset there begins a decline in low frequency electroencephalographic activity, neuronal firing, and behavior, but an increase in higher frequency electroencephalography and rhythmicity of neuronal firing. Our findings demonstrate that prolonged brain state changes precede consciousness-impairing seizures, and that during seizures distinct functional groups of cortical and thalamic neurons produce an overall transient firing increase followed by a sustained firing decrease, and increased rhythmicity.

Habitat suitability modelling to improve understanding of seagrass loss and recovery and to guide decisions in relation to coastal discharge.

Habitat suitability modelling was used to test the relationship between coastal discharges and seagrass occurrence based on data from Adelaide (South Australia). Seven variables (benthic light including epiphyte shading, temperature, salinity, substrate, wave exposure, currents and tidal exposure) were simulated using a coupled hydrodynamic-biogeochemical model and interrogated against literature-derived thresholds for nine local seagrass species. Light availability was the most critical driver across the study area but wave exposure played a key role in shallow nearshore areas. Model validation against seagrass mapping data showed 86 % goodness-of-fit. Comparison against later mapping data suggested that modelling could predict ~745 ha of seagrass recovery in areas previously classified as 'false positives'. These results suggest that habitat suitability modelling is reliable to test scenarios and predict seagrass response to reduction of land-based loads, providing a useful tool to guide (investment) decisions to prevent loss and promote recovery of seagrasses.

A 3D atlas of functional human brain energetic connectome based on neuropil distribution.

The human brain is energetically expensive, yet the key factors governing its heterogeneous energy distributions across cortical regions to support its diversity of functions remain unexplored. Here, we built up a 3D digital cortical energy atlas based on the energetic costs of all neuropil activities into a high-resolution stereological map of the human cortex with cellular and synaptic densities derived, respectively, from ex vivo histological staining and in vivo PET imaging. The atlas was validated with PET-measured glucose oxidation at the voxel level. A 3D cortical activity map was calculated to predict the heterogeneous activity rates across all cortical regions, which revealed that resting brain is indeed active with heterogeneous neuronal activity rates averaging around 1.2 Hz, comprising around 70% of the glucose oxidation of the cortex. Additionally, synaptic density dominates spatial patterns of energetics, suggesting that the cortical energetics rely heavily on the distribution of synaptic connections. Recent evidence from functional imaging studies suggests that some cortical areas act as hubs (i.e., interconnecting distinct and functionally active regions). An inverse allometric relationship was observed between hub metabolic rates versus hub volumes. Hubs with smaller volumes have higher synapse density, metabolic rate, and activity rates compared to nonhubs. The open-source BrainEnergyAtlas provides a granular framework for exploring revealing design principles in energy-constrained human cortical circuits across multiple spatial scales.

Fluorescently-tagged magnetic protein nanoparticles for high-resolution optical and ultra-high field magnetic resonance dual-modal cerebral angiography.

Extremely small paramagnetic iron oxide nanoparticles (FeMNPs) (<5 nm) can enhance positive magnetic resonance imaging (MRI) contrast by shortening the longitudinal relaxation time of water (T1), but these nanoparticles experience rapid renal clearance. Here, magnetic protein nanoparticles (MPNPs) are synthesized from protein-conjugated citric acid coated FeMNPs (c-FeMNPs) without loss of the T1 MRI properties and tagged with fluorescent dye (f-MPNPs) for optical cerebrovascular imaging. The c-FeMNPs shows average size 3.8 ± 0.7 nm with T1 relaxivity (r1) of 1.86 mM-1 s-1 and transverse/longitudinal relaxivity ratio (r2/r1) of 2.53 at 11.7 T. The f-MPNPs show a higher r1 value of 2.18 mM-1 s-1 and r2/r1 ratio of 2.88 at 11.7 T, which generates excellent positive MRI contrast. In vivo cerebral angiography with f-MPNPs enables detailed microvascular contrast enhancement for differentiation of major blood vessels of murine brain, which corresponds well with whole brain three-dimensional time-of-flight MRI angiograms (17 min imaging time with 60 ms repetition time and 40 µm isotropic voxels). The real-time fluorescence angiography enables unambiguous detection of brain capillaries with diameter < 40 µm. Biodistribution examination revealed that f-MPNPs were safely cleared by the organs like the liver, spleen, and kidneys within a day after injection. Blood biochemical assays demonstrated no risk of iron overload in both rats and mice. With hybrid neuroimaging technologies (e.g., MRI-optical) on the rise, f-MPNPs built on this platform can generate exciting neuroscience applications.

Lateralized Supraspinal Functional Connectivity Correlate with Pain and Motor Dysfunction in Rat Hemicontusion Cervical Spinal Cord Injury.

Afferent nociceptive activity in the reorganizing spinal cord after SCI influences supraspinal regions to establish pain. Clinical evidence of poor motor functional recovery in SCI patients with pain, led us to hypothesize that sensory-motor integration transforms into sensory-motor interference to manifest pain. This was tested by investigating supraspinal changes in a rat model of hemicontusion cervical SCI. Animals displayed ipsilateral forelimb motor dysfunction and pain, which persisted at 6 weeks after SCI. Using resting state fMRI at 8 weeks after SCI, RSFC across 14 ROIs involved in nociception, indicated lateral differences with a relatively weaker right-right connectivity (deafferented-contralateral) compared to left-left (unaffected-ipsilateral). However, the sensory (S1) and motor (M1/M2) networks showed greater RSFC using right hemisphere ROI seeds when compared to left. Voxel seeds from the somatosensory forelimb (S1FL) and M1/M2 representations reproduced the SCI-induced sensory and motor RSFC enhancements observed using the ROI seeds. Larger local connectivity occurred in the right sensory and motor networks amidst a decreasing overall local connectivity. This maladaptive reorganization of the right (deafferented) hemisphere localized the sensory component of pain emerging from the ipsilateral forepaw. A significant expansion of the sensory and motor network s overlap occurred globally after SCI when compared to sham, supporting the hypothesis that sensory and motor interference manifests pain. Voxel-seed based analysis revealed greater sensory and motor network overlap in the left hemisphere when compared to the right. This left predominance of the overlap suggested relatively larger pain processing in the unaffected hemisphere, when compared to the deafferented side.

High Throughput Omnidirectional Printing of Tubular Microstructures from Elastomeric Polymers.

Bioelastomers are extensively used in biomedical applications due to their desirable mechanical strength, tunable properties, and chemical versatility; however, three-dimensional (3D) printing bioelastomers into microscale structures has proven elusive. Herein, a high throughput omnidirectional printing approach via coaxial extrusion is described that fabricates perfusable elastomeric microtubes of unprecedently small inner diameter (350-550 µm) and wall thickness (40-60 µm). The versatility of this approach is shown through the printing of two different polymeric elastomers, followed by photocrosslinking and removal of the fugitive inner phase. Designed experiments are used to tune the microtube dimensions and stiffness to match that of native ex vivo rat vasculature. This approach affords the fabrication of multiple biomimetic shapes resembling cochlea and kidney glomerulus and affords facile, high-throughput generation of perfusable structures that can be seeded with endothelial cells for biomedical applications. Post-printing laser micromachining is performed to generate micro-sized holes (520 µm) in the tube wall to tune microstructure permeability. Importantly, for organ-on-a-chip applications, the described approach takes only 3.6 min to print microtubes (without microholes) over an entire 96-well plate device, in contrast to comparable hole-free structures that take between 1.5 and 6.5 days to fabricate using a manual 3D stamping approach.

Comparison of scientometric achievements at PhD and scientific output ten years later for 4,790 academic researchers.

INTRODUCTION: PhD is the highest awarded degree offered by universities in different disciplines. Owners of a PhD can teach at universities, start independent research and receive a higher salary while further building a scientific career. We examined whether the publication output before the PhD degree has a correlation with subsequent research activities. METHODS: We downloaded publication and citation data from the Hungarian Scientific Bibliography for Hungarian researchers who obtained PhD between the ages of 24 and 45. The researchers were grouped into eleven scientific sections. We examined the number of Q1 publications published in the previous 5 years, the H-index, the total number of citations for the last complete year, and the biological age of the researcher. Each parameter was computed for the year at which the PhD was obtained and ten years later. Pre-PhD publications (and citations for these) were excluded when assessing post-PhD track records. Spearman rank correlation and Kruskal-Wallis test were computed. RESULTS: We analyzed all together 4,790 researchers. We obtained a positive correlation between the number of Q1 publications before and after PhD (corr. coeff. = 0.21-0.54, p<0.01 in all sections), between the H-index before and after PhD (corr. coeff. = 0.32-0.56, p<0.01 in all sections), and between the citations received before and after PhD (corr. coeff. = 0.34-0.51, p<0.01 in all sections). All three metrics measured ten years after the PhD were negatively correlated with the age of the researcher at the time of obtaining the PhD (number of publications corr. coeff. = -0.09-0.22, p<0.05; H-index corr. coeff. = -0.09-0.29, p<0.08; number of citations corr. coeff. = -0.14-0.30, p<0.01). Among all disciplines, Philosophy and History and Engineering sciences show the strongest correlation between pre- and post-PhD output. When running multiple regression analysis for all three metrics as dependent variables and the number of articles, the H-index, the number of citations in the year of the PhD, the calendar year of PhD, and the gender of the researcher as independent variables, the number of articles and the H-index in the year of PhD reached the strongest positive correlations while gender had a negative correlation. CONCLUSIONS: We independently evaluated pre- and post-PhD publication performance. In connection with age, the discipline-specific reference values of scientometric parameters at the time of obtaining the PhD can help to select candidates for postdoctoral grants and positions.

Thalamic activations in rat brain by fMRI during tactile (forepaw, whisker) and non-tactile (visual, olfactory) sensory stimulations.

The thalamus is a crucial subcortical hub that impacts cortical activity. Tracing experiments in animals and post-mortem humans suggest rich morphological specificity of the thalamus. Very few studies reported rodent thalamic activations by functional MRI (fMRI) as compared to cortical activations for different sensory stimuli. Here, we show different portions of the rat thalamus in response to tactile (forepaw, whisker) and non-tactile (visual, olfactory) sensory stimuli with high field fMRI (11.7T) using a custom-build quadrature surface coil to capture high sensitivity signals from superficial and deep brain regions simultaneously. Results demonstrate reproducible thalamic activations during both tactile and non-tactile stimuli. Forepaw and whisker stimuli activated broader regions within the thalamus: ventral posterior lateral (VPL), ventral posterior medial (VPM), lateral posterior mediorostral (LPMR) and posterior medial (POm) thalamic nuclei. Visual stimuli activated dorsal lateral geniculate nucleus (DLG) of the thalamus but also parts of the superior/inferior colliculus, whereas olfactory stimuli activated specifically the mediodorsal nucleus of the thalamus (MDT). BOLD activations in LGN and MDT were much stronger than in VPL, VPM, LPMR and POm. These fMRI-based thalamic activations suggest that forepaw and whisker (i.e., tactile) stimuli engage VPL, VPM, LPMR and POm whereas visual and olfactory (i.e., non-tactile) stimuli, respectively, recruit DLG and MDT exclusively.

A probabilistic framework for windows of opportunity: the role of temporal variability in critical transitions.

The establishment of young organisms in harsh environments often requires a window of opportunity (WoO). That is, a short time window in which environmental conditions drop long enough below the hostile average level, giving the organism time to develop tolerance and transition into stable existence. It has been suggested that this kind of establishment dynamics is a noise-induced transition between two alternate states. Understanding how temporal variability (i.e. noise) in environmental conditions affects establishment of organisms is therefore key, yet not well understood or included explicitly in the WoO framework. In this paper, we develop a coherent theoretical framework for understanding when the WoO open or close based on simple dichotomous environmental variation. We reveal that understanding of the intrinsic timescales of both the developing organism and the environment is fundamental to predict if organisms can or cannot establish. These insights have allowed us to develop statistical laws for predicting establishment probabilities based on the period and variance of the fluctuations in naturally variable environments. Based on this framework, we now get a clear understanding of how changes in the timing and magnitude of climate variability or management can mediate establishment chances.

Aerobic glycolysis imaging of epileptic foci during the inter-ictal period.

BACKGROUND: In drug-resistant epilepsy, surgical resection of the epileptic focus can end seizures. However, success is dependent on the ability to identify foci locations and, unfortunately, current methods like electrophysiology and positron emission tomography can give contradictory results. During seizures, glucose is metabolized at epileptic foci through aerobic glycolysis, which can be imaged through the oxygen-glucose index (OGI) biomarker. However, inter-ictal (between seizures) OGI changes have not been studied, which has limited its application. METHODS: 18 healthy controls and 24 inter-ictal, temporal lobe epilepsy patients underwent simultaneous positron emission tomography (PET) and magnetic resonance imaging (MRI) scans. We used [18F]fluorodeoxyglucose-PET (FDG-PET) to detect cerebral glucose metabolism, and calibrated functional MRI to acquire relative oxygen consumption. With these data, we calculated relative OGI maps. FINDINGS: While bilaterally symmetrical in healthy controls, we observed, in patients during the inter-ictal period, higher OGI ipsilateral to the epileptic focus than contralateral. While traditional FDG-PET results and temporal lobe OGI results usually both agreed with invasive electrophysiology, in cases where FDG-PET disagreed with electrophysiology, temporal lobe OGI agreed with electrophysiology, and vice-versa. INTERPRETATION: As either our novel epilepsy biomarker or traditional approaches located foci in every case, our work provides promising insights into metabolic changes in epilepsy. Our method allows single-session OGI measurement which can be useful in other diseases. FUNDING: This work was supported by ShanghaiTech University, the Shanghai Municipal Government, the National Natural Science Foundation of China Grant (No. 81950410637) and Shanghai Municipal Key Clinical Specialty (No. shslczdzk03403). F. H. and P. H. were supported by USA National Institute of Health grants (R01 NS-100106, R01 MH-067528).Z. W. was supported by the Key-Area Research and Development Program of Guangdong Province (2019B030335001), National Natural Science Foundation of China (No. 82151303), and National Key R&D Program of China (No. 2021ZD0204002).

Manipulating geometric and optical properties of laser-inscribed nanogratings with a conical phase front.

The formation of volumetric nanogratings in fused silica by femtosecond laser pulses are shown to afford new opportunities for manipulating the physical shape and tailoring the optical properties of the modification zone by harnessing unconventional beam shapes. The nanograting assembly was observed to rigorously follow the beam elongation effects induced with conical-shaped phase fronts, permitting a scaling up of the writing volume. Detailed optical characterization of birefringence, dichroism, and scattering loss pointed to flexible new ways to tune the macroscopic optical properties, with advantages in decoupling the induced phase retardation from the modification thickness by controlling the conical phase front angle. Further insights into an unexpected asymmetric response from Gaussian beams modified with concave and convex phase fronts have been provided by nonlinear propagation simulations of the shaped-laser light.

Filament-arrayed Bragg gratings for azimuthally resolved displacement sensing in single-mode fibers.

Filament arrays were inscribed off-axis in the core of standard single-mode telecommunication fiber, using femtosecond laser pulses. The flexible line-by-line writing formed uniform, parallel filaments, permitting Bragg grating sensing of the photoelastic response from inside of the narrow grating plane. Active monitoring of the Bragg resonance wavelength while driving a lateral fiber tip displacement directly informed on the fiber mechanics when coupled with opto-mechanical modelling. Overlaying of parallel and orthogonal gratings further provided a strongly contrasting azimuthal sensitivity, which paves the way for multi-dimensional displacement sensing with improved precision.