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1.
J Psychiatry Neurosci ; 49(3): E157-E171, 2024.
Article in English | MEDLINE | ID: mdl-38692693

ABSTRACT

BACKGROUND: Critical adolescent neural refinement is controlled by the DCC (deleted in colorectal cancer) protein, a receptor for the netrin-1 guidance cue. We sought to describe the effects of reduced DCC on neuroanatomy in the adolescent and adult mouse brain. METHODS: We examined neuronal connectivity, structural covariance, and molecular processes in a DCC-haploinsufficient mouse model, compared with wild-type mice, using new, custom analytical tools designed to leverage publicly available databases from the Allen Institute. RESULTS: We included 11 DCC-haploinsufficient mice and 16 wild-type littermates. Neuroanatomical effects of DCC haploinsufficiency were more severe in adolescence than adulthood and were largely restricted to the mesocorticolimbic dopamine system. The latter finding was consistent whether we identified the regions of the mesocorticolimbic dopamine system a priori or used connectivity data from the Allen Brain Atlas to determine de novo where these dopamine axons terminated. Covariance analyses found that DCC haploinsufficiency disrupted the coordinated development of the brain regions that make up the mesocorticolimbic dopamine system. Gene expression maps pointed to molecular processes involving the expression of DCC, UNC5C (encoding DCC's co-receptor), and NTN1 (encoding its ligand, netrin-1) as underlying our structural findings. LIMITATIONS: Our study involved a single sex (males) at only 2 ages. CONCLUSION: The neuroanatomical phenotype of DCC haploinsufficiency described in mice parallels that observed in DCC-haploinsufficient humans. It is critical to understand the DCC-haploinsufficient mouse as a clinically relevant model system.


Subject(s)
Brain , DCC Receptor , Dopamine , Haploinsufficiency , Animals , DCC Receptor/genetics , Brain/metabolism , Brain/growth & development , Brain/anatomy & histology , Dopamine/metabolism , Mice , Male , Gene Expression , Neural Pathways , Age Factors , Female , Mice, Inbred C57BL , Aging/genetics , Aging/physiology
2.
J Morphol ; 285(6): e21710, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38760949

ABSTRACT

Lithornithidae, an assemblage of volant Palaeogene fossil birds, provide our clearest insights into the early evolutionary history of Palaeognathae, the clade that today includes the flightless ratites and volant tinamous. The neotype specimen of Lithornis vulturinus, from the early Eocene (approximately 53 million years ago) of Europe, includes a partial neurocranium that has never been thoroughly investigated. Here, we describe these cranial remains including the nearly complete digital endocasts of the brain and bony labyrinth. The telencephalon of Lithornis is expanded and its optic lobes are ventrally shifted, as is typical for crown birds. The foramen magnum is positioned caudally, rather than flexed ventrally as in some crown birds, with the optic lobes, cerebellum, and foramen magnum shifted further ventrally. The overall brain shape is similar to that of tinamous, the only extant clade of flying palaeognaths, suggesting that several aspects of tinamou neuroanatomy may have been evolutionarily conserved since at least the early Cenozoic. The estimated ratio of the optic lobe's surface area relative to the total brain suggests a diurnal ecology. Lithornis may provide the clearest insights to date into the neuroanatomy of the ancestral crown bird, combining an ancestrally unflexed brain with a caudally oriented connection with the spinal cord, a moderately enlarged telencephalon, and ventrally shifted, enlarged optic lobes.


Subject(s)
Biological Evolution , Fossils , Palaeognathae , Skull , Animals , Fossils/anatomy & histology , Palaeognathae/anatomy & histology , Skull/anatomy & histology , Central Nervous System/anatomy & histology , Brain/anatomy & histology , Birds/anatomy & histology , Paleontology , Phylogeny
3.
Sci Rep ; 14(1): 9835, 2024 05 14.
Article in English | MEDLINE | ID: mdl-38744901

ABSTRACT

Biological sex is a crucial variable in neuroscience studies where sex differences have been documented across cognitive functions and neuropsychiatric disorders. While gross statistical differences have been previously documented in macroscopic brain structure such as cortical thickness or region size, less is understood about sex-related cellular-level microstructural differences which could provide insight into brain health and disease. Studying these microstructural differences between men and women paves the way for understanding brain disorders and diseases that manifest differently in different sexes. Diffusion MRI is an important in vivo, non-invasive methodology that provides a window into brain tissue microstructure. Our study develops multiple end-to-end classification models that accurately estimates the sex of a subject using volumetric diffusion MRI data and uses these models to identify white matter regions that differ the most between men and women. 471 male and 560 female healthy subjects (age range, 22-37 years) from the Human Connectome Project are included. Fractional anisotropy, mean diffusivity and mean kurtosis are used to capture brain tissue microstructure characteristics. Diffusion parametric maps are registered to a standard template to reduce bias that can arise from macroscopic anatomical differences like brain size and contour. This study employ three major model architectures: 2D convolutional neural networks, 3D convolutional neural networks and Vision Transformer (with self-supervised pretraining). Our results show that all 3 models achieve high sex classification performance (test AUC 0.92-0.98) across all diffusion metrics indicating definitive differences in white matter tissue microstructure between males and females. We further use complementary model architectures to inform about the pattern of detected microstructural differences and the influence of short-range versus long-range interactions. Occlusion analysis together with Wilcoxon signed-rank test is used to determine which white matter regions contribute most to sex classification. The results indicate that sex-related differences manifest in both local features as well as global features / longer-distance interactions of tissue microstructure. Our highly consistent findings across models provides new insight supporting differences between male and female brain cellular-level tissue organization particularly in the central white matter.


Subject(s)
Deep Learning , Diffusion Magnetic Resonance Imaging , Sex Characteristics , White Matter , Humans , White Matter/diagnostic imaging , Male , Female , Adult , Diffusion Magnetic Resonance Imaging/methods , Young Adult , Brain/diagnostic imaging , Brain/anatomy & histology , Connectome , Image Processing, Computer-Assisted/methods
4.
Hum Brain Mapp ; 45(7): e26705, 2024 May.
Article in English | MEDLINE | ID: mdl-38716698

ABSTRACT

The global ageing of populations calls for effective, ecologically valid methods to support brain health across adult life. Previous evidence suggests that music can promote white matter (WM) microstructure and grey matter (GM) volume while supporting auditory and cognitive functioning and emotional well-being as well as counteracting age-related cognitive decline. Adding a social component to music training, choir singing is a popular leisure activity among older adults, but a systematic account of its potential to support healthy brain structure, especially with regard to ageing, is currently missing. The present study used quantitative anisotropy (QA)-based diffusion MRI connectometry and voxel-based morphometry to explore the relationship of lifetime choir singing experience and brain structure at the whole-brain level. Cross-sectional multiple regression analyses were carried out in a large, balanced sample (N = 95; age range 21-88) of healthy adults with varying levels of choir singing experience across the whole age range and within subgroups defined by age (young, middle-aged, and older adults). Independent of age, choir singing experience was associated with extensive increases in WM QA in commissural, association, and projection tracts across the brain. Corroborating previous work, these overlapped with language and limbic networks. Enhanced corpus callosum microstructure was associated with choir singing experience across all subgroups. In addition, choir singing experience was selectively associated with enhanced QA in the fornix in older participants. No associations between GM volume and choir singing were found. The present study offers the first systematic account of amateur-level choir singing on brain structure. While no evidence for counteracting GM atrophy was found, the present evidence of enhanced structural connectivity coheres well with age-typical structural changes. Corroborating previous behavioural studies, the present results suggest that regular choir singing holds great promise for supporting brain health across the adult life span.


Subject(s)
Singing , White Matter , Humans , Adult , Male , Middle Aged , Aged , Female , Young Adult , Singing/physiology , Aged, 80 and over , White Matter/diagnostic imaging , White Matter/physiology , White Matter/anatomy & histology , Aging/physiology , Cross-Sectional Studies , Brain/diagnostic imaging , Brain/physiology , Brain/anatomy & histology , Gray Matter/diagnostic imaging , Gray Matter/anatomy & histology , Gray Matter/physiology , Diffusion Magnetic Resonance Imaging , Diffusion Tensor Imaging
5.
Hum Brain Mapp ; 45(7): e26695, 2024 May.
Article in English | MEDLINE | ID: mdl-38727010

ABSTRACT

Human infancy is marked by fastest postnatal brain structural changes. It also coincides with the onset of many neurodevelopmental disorders. Atlas-based automated structure labeling has been widely used for analyzing various neuroimaging data. However, the relatively large and nonlinear neuroanatomical differences between infant and adult brains can lead to significant offsets of the labeled structures in infant brains when adult brain atlas is used. Age-specific 1- and 2-year-old brain atlases covering all major gray and white matter (GM and WM) structures with diffusion tensor imaging (DTI) and structural MRI are critical for precision medicine for infant population yet have not been established. In this study, high-quality DTI and structural MRI data were obtained from 50 healthy children to build up three-dimensional age-specific 1- and 2-year-old brain templates and atlases. Age-specific templates include a single-subject template as well as two population-averaged templates from linear and nonlinear transformation, respectively. Each age-specific atlas consists of 124 comprehensively labeled major GM and WM structures, including 52 cerebral cortical, 10 deep GM, 40 WM, and 22 brainstem and cerebellar structures. When combined with appropriate registration methods, the established atlases can be used for highly accurate automatic labeling of any given infant brain MRI. We demonstrated that one can automatically and effectively delineate deep WM microstructural development from 3 to 38 months by using these age-specific atlases. These established 1- and 2-year-old infant brain DTI atlases can advance our understanding of typical brain development and serve as clinical anatomical references for brain disorders during infancy.


Subject(s)
Atlases as Topic , Brain , Diffusion Tensor Imaging , Gray Matter , White Matter , Humans , Infant , Child, Preschool , Male , White Matter/diagnostic imaging , White Matter/anatomy & histology , White Matter/growth & development , Female , Gray Matter/diagnostic imaging , Gray Matter/growth & development , Gray Matter/anatomy & histology , Diffusion Tensor Imaging/methods , Brain/diagnostic imaging , Brain/growth & development , Brain/anatomy & histology , Image Processing, Computer-Assisted/methods
6.
7.
Cereb Cortex ; 34(4)2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38647221

ABSTRACT

A comprehensive three-dimensional digital brain atlas of cortical and subcortical regions based on MRI and histology has a broad array of applications in anatomical, functional, and clinical studies. We first generated a Subcortical Atlas of the Marmoset, called the "SAM," from 251 delineated subcortical regions (e.g. thalamic subregions, etc.) derived from high-resolution Mean Apparent Propagator-MRI, T2W, and magnetization transfer ratio images ex vivo. We then confirmed the location and borders of these segmented regions in the MRI data using matched histological sections with multiple stains obtained from the same specimen. Finally, we estimated and confirmed the atlas-based areal boundaries of subcortical regions by registering this ex vivo atlas template to in vivo T1- or T2W MRI datasets of different age groups (single vs. multisubject population-based marmoset control adults) using a novel pipeline developed within Analysis of Functional NeuroImages software. Tracing and validating these important deep brain structures in 3D will improve neurosurgical planning, anatomical tract tracer injections, navigation of deep brain stimulation probes, functional MRI and brain connectivity studies, and our understanding of brain structure-function relationships. This new ex vivo template and atlas are available as volumes in standard NIFTI and GIFTI file formats and are intended for use as a reference standard for marmoset brain research.


Subject(s)
Atlases as Topic , Brain , Callithrix , Magnetic Resonance Imaging , Callithrix/anatomy & histology , Animals , Magnetic Resonance Imaging/methods , Brain/diagnostic imaging , Brain/anatomy & histology , Male , Female , Imaging, Three-Dimensional/methods , Image Processing, Computer-Assisted/methods
9.
Hum Brain Mapp ; 45(5): e26671, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38590252

ABSTRACT

There remains little consensus about the relationship between sex and brain structure, particularly in early adolescence. Moreover, few pediatric neuroimaging studies have analyzed both sex and gender as variables of interest-many of which included small sample sizes and relied on binary definitions of gender. The current study examined gender diversity with a continuous felt-gender score and categorized sex based on X and Y allele frequency in a large sample of children ages 9-11 years old (N = 7195). Then, a statistical model-building approach was employed to determine whether gender diversity and sex independently or jointly relate to brain morphology, including subcortical volume, cortical thickness, gyrification, and white matter microstructure. Additional sensitivity analyses found that male versus female differences in gyrification and white matter were largely accounted for by total brain volume, rather than sex per se. The model with sex, but not gender diversity, was the best-fitting model in 60.1% of gray matter regions and 61.9% of white matter regions after adjusting for brain volume. The proportion of variance accounted for by sex was negligible to small in all cases. While models including felt-gender explained a greater amount of variance in a few regions, the felt-gender score alone was not a significant predictor on its own for any white or gray matter regions examined. Overall, these findings demonstrate that at ages 9-11 years old, sex accounts for a small proportion of variance in brain structure, while gender diversity is not directly associated with neurostructural diversity.


Subject(s)
Magnetic Resonance Imaging , White Matter , Humans , Male , Female , Adolescent , Child , Magnetic Resonance Imaging/methods , Brain/diagnostic imaging , Brain/anatomy & histology , Gray Matter/diagnostic imaging , Gray Matter/anatomy & histology , White Matter/diagnostic imaging , Neuroimaging
10.
Anat Histol Embryol ; 53(3): e13043, 2024 May.
Article in English | MEDLINE | ID: mdl-38666620

ABSTRACT

Capybara is considered the largest living rodent and is widespread distributed in the South America and in the Brazilian territory. The purpose of this study was to provide the anatomical description of the brain in the capybara (Hydrochoerus hydrochaeris) using magnetic resonance imaging (MRI). Brains of ten normal capybaras were imaged and sectioned in the anatomical studies. MRI was acquired on 0.25 Tesla equipment, promoting good-quality images capable to identify and classify the main anatomical structures of clinical interest. MRI reference images were validated by comparing them with gross anatomical sections. The capybara sulci and gyri were named for its similar location and orientation to those described in the previous descriptions in the capybara and in the domestic dog. Capybaras presented prominent cerebral sulcus and gyrus in relation to other caviomorph rodents, but in reduced number when compared to domestic animals and other wild mammals such as elephants and giraffes. The findings of this study indicate that the shape of the capybara brain is remarkably similar to that of the caviomorph rodents with a higher neocortilization. The capybara rhinencephalon was well-developed implying a good sense of smell. Due to this development of the rhinencephalon, we can suggest that capybara brain is a macrosmatic brain. The MRI and gross anatomical sections of capybara brain may help veterinary researchers and clinicians increase the accuracy of brain MRI scans interpretation in these animals.


Subject(s)
Brain , Magnetic Resonance Imaging , Rodentia , Animals , Rodentia/anatomy & histology , Magnetic Resonance Imaging/veterinary , Brain/anatomy & histology , Brain/diagnostic imaging , Male , Female
11.
J Comp Neurol ; 532(4): e25617, 2024 04.
Article in English | MEDLINE | ID: mdl-38629472

ABSTRACT

The New World suboscines (Passeriformes and Tyrannides) are one of the biggest endemic vertebrate radiations in South America, including the families Furnariidae and Tyrannidae. Avian brain morphology is a reliable proxy to study their evolution. The aim of this work is to elucidate whether the brains of these families reflect the ecological differences (e.g., feeding behavior) and to clarify macroevolutionary aspects of their neuroanatomy. Our hypotheses are as follows: Brain size is similar between both families and with other Passeriformes; brain morphology in Tyrannides is the result of the pressure of ecological factors; and brain disparity is low since they share ecological traits. Skulls of Furnariidae and Tyrannidae were micro-computed tomography-scanned, and three-dimensional models of the endocast were generated. Regression analyses were performed between brain volume and body mass. Linear and surface measurements were used to build phylomorphospaces and to calculate the amount of phylogenetic signal. Tyrannidae showed a larger brain disparity than Furnariidae, although it is not shaped by phylogeny in the Tyrannides. Furnariidae present enlarged Wulsts (eminentiae sagittales) but smaller optic lobes, while in Tyrannidae, it is the opposite. This could indicate that in Tyrannides there is a trade-off between the size of these two visual-related brain structures.


Subject(s)
Passeriformes , Animals , Humans , Passeriformes/anatomy & histology , Phylogeny , X-Ray Microtomography , Brain/anatomy & histology
12.
Cereb Cortex ; 34(4)2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38679479

ABSTRACT

Normative ferret brain development was characterized using magnetic resonance imaging. Brain growth was longitudinally monitored in 10 ferrets (equal numbers of males and females) from postnatal day 8 (P8) through P38 in 6-d increments. Template T2-weighted images were constructed at each age, and these were manually segmented into 12 to 14 brain regions. A logistic growth model was used to fit data from whole brain volumes and 8 of the individual regions in both males and females. More protracted growth was found in males, which results in larger brains; however, sex differences were not apparent when results were corrected for body weight. Additionally, surface models of the developing cortical plate were registered to one another using the anatomically-constrained Multimodal Surface Matching algorithm. This, in turn, enabled local logistic growth parameters to be mapped across the cortical surface. A close similarity was observed between surface area expansion timing and previous reports of the transverse neurogenic gradient in ferrets. Regional variation in the extent of surface area expansion and the maximum expansion rate was also revealed. This characterization of normative brain growth over the period of cerebral cortex folding may serve as a reference for ferret studies of brain development.


Subject(s)
Brain , Ferrets , Magnetic Resonance Imaging , Animals , Ferrets/growth & development , Magnetic Resonance Imaging/methods , Male , Female , Brain/growth & development , Brain/diagnostic imaging , Brain/anatomy & histology , Longitudinal Studies , Sex Characteristics
13.
Brain Behav ; 14(5): e3484, 2024 May.
Article in English | MEDLINE | ID: mdl-38680075

ABSTRACT

BACKGROUND: Living in a social dominance hierarchy presents different benefits and challenges for dominant and subordinate males and females, which might in turn affect their cognitive needs. Despite the extensive research on social dominance in group-living species, there is still a knowledge gap regarding how social status impacts brain morphology and cognitive abilities. METHODS: Here, we tested male and female dominants and subordinates of Neolamprologus pulcher, a social cichlid fish species with size-based hierarchy. We ran three executive cognitive function tests for cognitive flexibility (reversal learning test), self-control (detour test), and working memory (object permanence test), followed by brain and brain region size measurements. RESULTS: Performance was not influenced by social status or sex. However, dominants exhibited a brain-body slope that was relatively steeper than that of subordinates. Furthermore, individual performance in reversal learning and detour tests correlated with brain morphology, with some trade-offs among major brain regions like telencephalon, cerebellum, and optic tectum. CONCLUSION: As individuals' brain growth strategies varied depending on social status without affecting executive functions, the different associated challenges might yield a potential effect on social cognition instead. Overall, the findings highlight the importance of studying the individual and not just species to understand better how the individual's ecology might shape its brain and cognition.


Subject(s)
Brain , Cichlids , Executive Function , Animals , Cichlids/physiology , Cichlids/anatomy & histology , Female , Male , Executive Function/physiology , Brain/anatomy & histology , Brain/physiology , Brain/growth & development , Social Dominance , Reversal Learning/physiology , Memory, Short-Term/physiology
14.
J Comp Neurol ; 532(5): e25618, 2024 May.
Article in English | MEDLINE | ID: mdl-38686628

ABSTRACT

The evolutionary history of canids and felids is marked by a deep time separation that has uniquely shaped their behavior and phenotype toward refined predatory abilities. The caudate nucleus is a subcortical brain structure associated with both motor control and cognitive, emotional, and executive functions. We used a combination of three-dimensional imaging, allometric scaling, and structural analyses to compare the size and shape characteristics of the caudate nucleus. The sample consisted of MRI scan data obtained from six canid species (Canis lupus lupus, Canis latrans, Chrysocyon brachyurus, Lycaon pictus, Vulpes vulpes, Vulpes zerda), two canid subspecies (Canis lupus familiaris, Canis lupus dingo), as well as three felids (Panthera tigris, Panthera uncia, Felis silvestris catus). Results revealed marked conservation in the scaling and shape attributes of the caudate nucleus across species, with only slight deviations. We hypothesize that observed differences in caudate nucleus size and structure for the domestic canids are reflective of enhanced cognitive and emotional pathways that possibly emerged during domestication.


Subject(s)
Canidae , Caudate Nucleus , Felidae , Magnetic Resonance Imaging , Animals , Caudate Nucleus/anatomy & histology , Caudate Nucleus/diagnostic imaging , Felidae/anatomy & histology , Felidae/physiology , Canidae/anatomy & histology , Magnetic Resonance Imaging/methods , Male , Behavior, Animal/physiology , Female , Species Specificity , Brain/anatomy & histology
15.
J Neurosci Methods ; 406: 110134, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38588923

ABSTRACT

BACKGROUND: The piglet brain has been increasingly used as an excellent surrogate for investigation of pediatric neurodevelopment, nutrition, and traumatic brain injuries. This study intends to establish a piglet brain's structural connectivity model and compare it with the adult pig, enhancing its application for structurally guided functional analysis. METHODS: In this study, diffusion-weighted (DW)-MRI data from piglets (n=11, 3-week-old) was used to establish piglet model and compare with adult pigs. We employed a data-driven independent component analysis (ICA) method to derive piglet-specific tracts. Pearson correlations and Kullback-Leibler (KL) divergences was employed to identify common tracts and unique tracts for piglet. Common tracts were then used in a blueprint connectome study to highlight differences in regions of interest (ROI). RESULTS: The data-driven approach applied to piglet brains revealed 17 common tracts, showing high similarity with adult pigs' white matter (WM) tracts, and identified 3 tracts unique to piglets and 10 negative marker tracts. Additionally, the study highlighted notable differences in 3 ROIs associated with blueprint connectome. COMPARING WITH EXISTING METHODS: This study marks a significant shift from surface-based to voxel-based methodologies in analyzing pig brain structural connectivity and generating connectome blueprints. Additionally, it sheds light on the use of the piglet model for developmental studies, offering new perspectives in this area. CONCLUSION: This study established a piglet brain tract model and conducts a comparative analysis of adult pig's and piglet's structural connectivity. These findings underscore the potential use of the piglet brain model in employing piglet model for developmental studies.


Subject(s)
Connectome , White Matter , Animals , White Matter/diagnostic imaging , White Matter/growth & development , White Matter/anatomy & histology , Swine , Connectome/methods , Diffusion Magnetic Resonance Imaging/methods , Brain/growth & development , Brain/diagnostic imaging , Brain/anatomy & histology , Animals, Newborn , Neural Pathways/growth & development , Neural Pathways/diagnostic imaging , Neural Pathways/anatomy & histology , Male , Female , Image Processing, Computer-Assisted/methods , Diffusion Tensor Imaging/methods
16.
Neuroimage ; 293: 120622, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38648869

ABSTRACT

Correlating transcriptional profiles with imaging-derived phenotypes has the potential to reveal possible molecular architectures associated with cognitive functions, brain development and disorders. Competitive null models built by resampling genes and self-contained null models built by spinning brain regions, along with varying test statistics, have been used to determine the significance of transcriptional associations. However, there has been no systematic evaluation of their performance in imaging transcriptomics analyses. Here, we evaluated the performance of eight different test statistics (mean, mean absolute value, mean squared value, max mean, median, Kolmogorov-Smirnov (KS), Weighted KS and the number of significant correlations) in both competitive null models and self-contained null models. Simulated brain maps (n = 1,000) and gene sets (n = 500) were used to calculate the probability of significance (Psig) for each statistical test. Our results suggested that competitive null models may result in false positive results driven by co-expression within gene sets. Furthermore, we demonstrated that the self-contained null models may fail to account for distribution characteristics (e.g., bimodality) of correlations between all available genes and brain phenotypes, leading to false positives. These two confounding factors interacted differently with test statistics, resulting in varying outcomes. Specifically, the sign-sensitive test statistics (i.e., mean, median, KS, Weighted KS) were influenced by co-expression bias in the competitive null models, while median and sign-insensitive test statistics were sensitive to the bimodality bias in the self-contained null models. Additionally, KS-based statistics produced conservative results in the self-contained null models, which increased the risk of false negatives. Comprehensive supplementary analyses with various configurations, including realistic scenarios, supported the results. These findings suggest utilizing sign-insensitive test statistics such as mean absolute value, max mean in the competitive null models and the mean as the test statistic for the self-contained null models. Additionally, adopting the confounder-matched (e.g., coexpression-matched) null models as an alternative to standard null models can be a viable strategy. Overall, the present study offers insights into the selection of statistical tests for imaging transcriptomics studies, highlighting areas for further investigation and refinement in the evaluation of novel and commonly used tests.


Subject(s)
Brain , Phenotype , Brain/diagnostic imaging , Brain/anatomy & histology , Humans , Transcriptome , Models, Statistical , Gene Expression Profiling/methods
17.
Nature ; 629(8013): 851-860, 2024 May.
Article in English | MEDLINE | ID: mdl-38560995

ABSTRACT

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.


Subject(s)
Birds , Evolution, Molecular , Genome , Phylogeny , Animals , Birds/genetics , Birds/classification , Birds/anatomy & histology , Brain/anatomy & histology , Extinction, Biological , Genome/genetics , Genomics , Population Density , Male , Female
18.
J Neurosci Methods ; 407: 110133, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38588922

ABSTRACT

BACKGROUND: High-precision neurosurgical targeting in nonhuman primates (NHPs) often requires presurgical anatomical mapping with noninvasive neuroimaging techniques (MRI, CT, PET), allowing for translation of individual anatomical coordinates to surgical stereotaxic apparatus. Given the varied tissue contrasts that these imaging techniques produce, precise alignment of imaging-based coordinates to surgical apparatus can be cumbersome. MRI-compatible stereotaxis with radiopaque fiducial markers offer a straight-forward and reliable solution, but existing commercial options do not fit in conformal head coils that maximize imaging quality. NEW METHOD: We developed a compact MRI-compatible stereotaxis suitable for a variety of NHP species (Macaca mulatta, Macaca fascicularis, and Cebus apella) that allows multimodal alignment through technique-specific fiducial markers. COMPARISON WITH EXISTING METHODS: With the express purpose of compatibility with clinically available MRI, CT, and PET systems, the frame is no larger than a human head, while allowing for imaging NHPs in the supinated position. This design requires no marker implantation, special software, or additional knowledge other than the operation of a common large animal stereotaxis. RESULTS: We demonstrated the applicability of this 3D-printable apparatus across a diverse set of experiments requiring presurgical planning: 1) We demonstrate the accuracy of the fiducial system through a within-MRI cannula insertion and subcortical injection of a viral vector. 2) We also demonstrated accuracy of multimodal (MRI and CT) alignment and coordinate transfer to guide a surgical robot electrode implantation for deep-brain electrophysiology. CONCLUSIONS: The computer-aided design files and engineering drawings are publicly available, with the modular design allowing for low cost and manageable manufacturing.


Subject(s)
Brain Mapping , Cebus , Magnetic Resonance Imaging , Animals , Magnetic Resonance Imaging/methods , Magnetic Resonance Imaging/instrumentation , Brain Mapping/methods , Brain Mapping/instrumentation , Stereotaxic Techniques/instrumentation , Brain/diagnostic imaging , Brain/surgery , Brain/anatomy & histology , Fiducial Markers , Multimodal Imaging/methods , Multimodal Imaging/instrumentation , Macaca mulatta , Male
19.
Sci Rep ; 14(1): 7796, 2024 04 02.
Article in English | MEDLINE | ID: mdl-38565879

ABSTRACT

Chronic musculoskeletal pain including knee osteoarthritis (OA) is a leading cause of disability worldwide. Previous research indicates ethnic-race groups differ in the pain and functional limitations experienced with knee OA. However, when socioenvironmental factors are included in analyses, group differences in pain and function wane. Pain-related brain structures are another area where ethnic-race group differences have been observed. Environmental and sociocultural factors e.g., income, education, experiences of discrimination, and social support influence brain structures. We investigate if environmental and sociocultural factors reduce previously observed ethnic-race group differences in pain-related brain structures. Data were analyzed from 147 self-identified non-Hispanic black (NHB) and non-Hispanic white (NHW), middle and older aged adults with knee pain in the past month. Information collected included health and pain history, environmental and sociocultural resources, and brain imaging. The NHB adults were younger and reported lower income and education compared to their NHW peers. In hierarchical multiple regression models, sociocultural and environmental factors explained 6-37% of the variance in pain-related brain regions. Self-identified ethnicity-race provided an additional 4-13% of explanatory value in the amygdala, hippocampus, insula, bilateral primary somatosensory cortex, and thalamus. In the rostral/caudal anterior cingulate and dorsolateral prefrontal cortex, self-identified ethnicity-race was not a predictor after accounting for environmental, sociocultural, and demographic factors. Findings help to disentangle and identify some of the factors contributing to ethnic-race group disparities in pain-related brain structures. Numerous arrays of environmental and sociocultural factors remain to be investigated. Further, the differing sociodemographic representation of our NHB and NHW participants highlights the role for intersectional considerations in future research.


Subject(s)
Brain , Musculoskeletal Pain , Humans , Middle Aged , Black or African American , Brain/anatomy & histology , Ethnicity , White , Aged
20.
Brain Struct Funct ; 229(5): 1165-1177, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38625555

ABSTRACT

The morphologic properties of brain regions co-vary or correlate with each other. Here we investigated the structural covariances of cortical thickness and subcortical volumes in the ageing brain, along with their associations with age and cognition, using cross-sectional data from the UK Biobank (N = 42,075, aged 45-83 years, 53% female). As the structural covariance should be estimated in a group of participants, all participants were divided into 84 non-overlapping, equal-sized age groups ranging from the youngest to the oldest. We examined 84 cortical thickness covariances and subcortical covariances. Our findings include: (1) there were significant differences in the variability of structural covariance in the ageing process, including an increased variance, and a decreased entropy. (2) significant enrichment in pairwise correlations between brain regions within the occipital lobe was observed in all age groups; (3) structural covariance in older age, especially after the age of around 64, was significantly different from that in the youngest group (median age 48 years); (4) sixty-two of the total 528 pairs of cortical thickness correlations and 10 of the total 21 pairs of subcortical volume correlations showed significant associations with age. These trends varied, with some correlations strengthening, some weakening, and some reversing in direction with advancing age. Additionally, as ageing was associated with cognitive decline, most of the correlations with cognition displayed an opposite trend compared to age associated patterns of correlations.


Subject(s)
Aging , Biological Specimen Banks , Brain , Magnetic Resonance Imaging , Humans , Aged , Female , Middle Aged , Male , Aged, 80 and over , Aging/physiology , Brain/anatomy & histology , Brain/diagnostic imaging , United Kingdom , Cross-Sectional Studies , Cognition/physiology , Organ Size , UK Biobank
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