Faculty Bibliography

Diverse environmental and biological systems interact to influence individual differences in response to environmental stress. Understanding the nature of these complex relationships can enhance the development of methods to: (1) identify risk, (2) classify individuals as healthy or ill, (3) understand mechanisms of change, and (4) develop effective treatments. The Research Domain Criteria (RDoC) initiative provides a theoretical framework to understand health and illness as the product of multiple inter-related systems but does not provide a framework to characterize or statistically evaluate such complex relationships. Characterizing and statistically evaluating models that integrate multiple levels (e.g. synapses, genes, environmental factors) as they relate to outcomes that a free from prior diagnostic benchmarks represents a challenge requiring new computational tools that are capable to capture complex relationships and identify clinically relevant populations. In the current review, we will summarize machine learning methods that can achieve these goals.

We have developed a unique delivery system of growth factors using collagen membranes (CMs) to induce bone regeneration. We hypothesized that fibroblast growth factor18 (FGF-18), a pleiotropic protein that stimulates proliferation in several tissues, can be a good candidate to use our delivery system for bone regeneration. Cell viability, cell proliferation, alkaline phosphatase activity, mineralization, and marker gene expression of osteoblastic differentiation were evaluated after mouse preosteoblasts were cultured with a CM containing FGF-18, a CM containing platelet-derived growth factor, or a CM alone. Furthermore, expression of microRNA, especially miR-133a and miR-135a involving inhibition of osteogenic factors, was measured in preosteoblasts with CM/FGF-18 or CM alone. A sustained release of FGF-18 from the CM was observed over 21 days. CM/FGF-18 significantly promoted cell proliferation, alkaline phosphatase activity, and mineralization compared to CM alone. Gene expression of type I collagen, runt-related transcription factor 2, osteocalcin, Smad5, and osteopontin was significantly upregulated in CM/FGF-18 compared to CM alone, and similar to CM/platelet-derived growth factor. Additionally, CM/FGF-18 downregulated expression of miR-133a and miR-135a. These results suggested that released FGF-18 from a CM promotes osteoblastic activity involved with downregulation of miR-133a and miR-135a.

The main cell of origin of the Sonic hedgehog (SHH) subgroup of medulloblastoma (MB) is granule cell precursors (GCPs), a SHH-dependent transient amplifying population in the developing cerebellum. SHH-MBs can be further subdivided based on molecular and clinical parameters, as well as location because SHH-MBs occur preferentially in the lateral cerebellum (hemispheres). Our analysis of adult patient data suggests that tumors with Smoothened (SMO) mutations form more specifically in the hemispheres than those with Patched 1 (PTCH1) mutations. Using sporadic mouse models of SHH-MB with the two mutations commonly seen in adult MB, constitutive activation ofSmo(SmoM2) or loss-of-Ptch1, we found that regardless of timing of induction or type of mutation, tumors developed primarily in the hemispheres, withSmoM2-mutants indeed showing a stronger specificity. We further uncovered that GCPs in the hemispheres are more susceptible to high-level SHH signaling compared with GCPs in the medial cerebellum (vermis), as moreSmoM2orPtch1-mutant hemisphere cells remain undifferentiated and show increased tumorigenicity when transplanted. Finally, we identified location-specific GCP gene-expression profiles, and found that deletion of the genes most highly expressed in the hemispheres (Nr2f2) or vermis (Engrailed1) showed opposing effects on GCP differentiation. Our studies thus provide insights into intrinsic differences within GCPs that impact on SHH-MB progression.

Genetic engineering by viral infection of single cells is useful to study complex systems such as the brain. However, available methods for infecting single cells have drawbacks that limit their applications. Here we describe 'virus stamping', in which viruses are reversibly bound to a delivery vehicle-a functionalized glass pipette tip or magnetic nanoparticles in a pipette-that is brought into physical contact with the target cell on a surface or in tissue, using mechanical or magnetic forces. Different single cells in the same tissue can be infected with different viruses and an individual cell can be simultaneously infected with different viruses. We use rabies, lenti, herpes simplex, and adeno-associated viruses to drive expression of fluorescent markers or a calcium indicator in target cells in cell culture, mouse retina, human brain organoid, and the brains of live mice. Virus stamping provides a versatile solution for targeted single-cell infection of diverse cell types, both in vitro and in vivo.

PURPOSE/OBJECTIVE:To compare estimates for the diffusional kurtosis in brain as obtained from a cumulant expansion (CE) of the diffusion MRI (dMRI) signal and from q-space (QS) imaging. THEORY AND METHODS/UNASSIGNED:were used to determine the diffusion displacement probability density function (dPDF) via Stejskal's formula. The kurtosis was then calculated directly from the second and fourth order moments of the dPDF. These two approximations were studied for in vivo human data obtained on a 3T MRI scanner using three orthogonal diffusion encoding directions. RESULTS:The whole brain mean values for the CE and QS kurtosis estimates differed by 16% or less in each of the considered diffusion encoding directions, and the Pearson correlation coefficients all exceeded 0.85. Nonetheless, there were large discrepancies in many voxels, particularly those with either very high or very low kurtoses relative to the mean values. CONCLUSION/CONCLUSIONS:Estimates of the diffusional kurtosis in brain obtained using CE and QS approximations are strongly correlated, suggesting that they encode similar information. However, for the choice of b-values employed here, there may be substantial differences, depending on the properties of the diffusion microenvironment in each voxel.

Stimulation pulse rate affects current amplitude discrimination by cochlear implant (CI) users, indicated by the evidence that the JND (just noticeable difference) in current amplitude delivered by a CI electrode becomes larger at higher pulse rates. However, it is not clearly understood whether pulse rate would affect discrimination of speech intensities presented acoustically to CI processors, or what the size of this effect might be. Intensity discrimination depends on two factors: the growth of loudness with increasing sound intensity and the loudness JND (or the just noticeable loudness increment). This study evaluated the hypothesis that stimulation pulse rate affects loudness JND. This was done by measuring current amplitude JNDs in an experiment design based on signal detection theory according to which loudness discrimination is related to internal noise (which is manifested by variability in loudness percept in response to repetitions of the same physical stimulus). Current amplitude JNDs were measured for equally loud pulse trains of 500 and 3000 pps (pulses per second) by increasing the current amplitude of the target pulse train until it was perceived just louder than a same-rate or different-rate reference pulse train. The JND measures were obtained at two presentation levels. At the louder level, the current amplitude JNDs were affected by the rate of the reference pulse train in a way that was consistent with greater noise or variability in loudness perception for the higher pulse rate. The results suggest that increasing pulse rate from 500 to 3000 pps can increase loudness JND by 60 % at the upper portion of the dynamic range. This is equivalent to a 38 % reduction in the number of discriminable steps for acoustic and speech intensities.

The overall goal of this study was to identify an objective physiological correlate of electric-acoustic pitch matching in unilaterally implanted cochlear implant (CI) participants with residual hearing in the non-implanted ear. Electrical and acoustic stimuli were presented in a continuously alternating fashion across ears. The acoustic stimulus and the electrical stimulus were either matched or mismatched in pitch. Auditory evoked potentials were obtained from nine CI users. Results indicated that N1 latency was stimulus-dependent, decreasing when the acoustic frequency of the tone presented to the non-implanted ear was increased. More importantly, there was an additional decrease in N1 latency in the pitch-matched condition. These results indicate the potential utility of N1 latency as an index of pitch matching in CI users.

Adaptive and non-adaptive beamformers have become a prominent neuroimaging tool for localizing neural sources of electroencephalographic (EEG) and magnetoencephalographic (MEG) data. In this study, we investigated single-source and multi-source scalar beamformers with respect to their performances in localizing and reconstructing source activity for simulated and real EEG data. We compared a new multi-source search approach (multi-step iterative approach; MIA) to our previous multi-source search approach (single-step iterative approach; SIA) and a single-source search approach (single-step peak approach; SPA). In order to compare performances across these beamformer approaches, we manipulated various simulated source parameters, such as the amount of signal-to-noise ratio (0.1-0.9), inter-source correlations (0.3-0.9), number of simultaneously active sources (2-8), and source locations. Results showed that localization performance followed the order of MIA > SIA > SPA regardless of the number of sources, source correlations, and single-to-noise ratios. In addition, SIA and MIA were significantly better than SPA at localizing four or more sources. Moreover, MIA was better than SIA and SPA at identifying the true source locations when signal characteristics were at their poorest. Source waveform reconstructions were similar between MIA and SIA but were significantly better than that for SPA. A similar trend was also found when applying these beamformer approaches to a real EEG dataset. Based on our findings, we conclude that multi-source beamformers (MIA and SIA) are an improvement over single-source beamformers for localizing EEG. Importantly, our new search method, MIA, had better localization performance, localization precision, and source waveform reconstruction as compared to SIA or SPA. We therefore recommend its use for improved source localization and waveform reconstruction of event-related potentials.

BACKGROUND:Oxytocin is a peptide hormone that influences the integration of social cognition with behavior and affect regulation. Oxytocin also prominently directs the transition of neuronal GABA neurotransmission from excitatory to inhibitory after birth. The oxytocin receptor (OXTR) is linked to schizophrenia, a heterogeneous syndrome. Relationships of OXTR polymorphisms with specific clinical features could aid in evaluating any role of oxytocin in the pathogenesis of schizophrenia. METHOD/METHODS:Schizophrenia cases with rare missense coding OXTR single nucleotide variants (SNVs) were identified from a well-characterized sample of cases and controls who were assessed for symptoms, cognition and early life trauma. RESULTS:Five of 48 cases showed rare OXTR variants. Compared to the other cases they had less severe negative symptoms (deficits in emotional expression and motivation) and less severe general psychopathology scores (depression and anxiety). They demonstrated lower nonverbal (performance) than verbal intelligence due to deficient perceptual organization and slow processing speed. They also reported greater early trauma exposure (physical and sexual abuse and emotional trauma). CONCLUSION/CONCLUSIONS:Cases carrying rare OXTR SNVs had less negative and affective symptoms than other cases, but similar psychotic symptoms, along with specific cognitive deficits. The clinical characterization of these cases occurred in association with environmental exposure to early trauma, especially sexual abuse, which may have influenced the expression of schizophrenia in subjects harboring specific SNVs in the OXTR.

Diverse subsets of cortical interneurons have vital roles in higher-order brain functions. To investigate how this diversity is generated, here we used single-cell RNA sequencing to profile the transcriptomes of mouse cells collected along a developmental time course. Heterogeneity within mitotic progenitors in the ganglionic eminences is driven by a highly conserved maturation trajectory, alongside eminence-specific transcription factor expression that seeds the emergence of later diversity. Upon becoming postmitotic, progenitors diverge and differentiate into transcriptionally distinct states, including an interneuron precursor state. By integrating datasets across developmental time points, we identified shared sources of transcriptomic heterogeneity between adult interneurons and their precursors, and uncovered the embryonic emergence of cardinal interneuron subtypes. Our analysis revealed that the transcription factor Mef2c, which is linked to various neuropsychiatric and neurodevelopmental disorders, delineates early precursors of parvalbumin-expressing neurons, and is essential for their development. These findings shed new light on the molecular diversification of early inhibitory precursors, and identify gene modules that may influence the specification of human interneuron subtypes.