Biology subjects

Alexander, A.

Publications and source records attributed to Alexander, A..

18 recordsLinked to original sources

bioRxiv2026

Genomic indicators of risk and resilience in global leatherback turtle populations

Understanding the drivers of genomic health and their consequences for population viability is often overlooked but potentially important to effective conservation amidst the biodiversity crisis of the Anthropocene. Leatherback turtle (Dermochelys coriacea) populations have declined globally due to anthropogenic factors, with some populations losing over 90% of their abundance over the past 30-50 years. While conservation efforts have been successful in stabilizing some populations, others continue to decline, and the reasons for these differential trajectories remain unclear. To assess how recent demographic factors, such as population size and decline, influence population genomic health, we combined population monitoring information with medium depth whole-genome and reduced representation resequencing data from globally representative populations. We found that small-stable populations have lower genomic diversity and higher inbreeding than large declining populations, reflecting prolonged small population sizes and limited gene flow. Yet, small-stable populations also show evidence of deleterious allele purging, suggesting genetic resilience. This, combined with lack of detectable genomic erosion over the study period, provides hope for potential recovery of healthy leatherback populations provided that anthropogenic threats are effectively mitigated. However, potential time lags and possible recent increases in inbreeding among close relatives in recently declined populations warrant continued monitoring and assessment. Genomic and abundance-based metrics were less aligned following rapid population declines, emphasizing the different timescales of the evolutionary and demographic processes they reflect, respectively, and the strength in their complementary, integrative use for extinction risk assessments. This also supports that it is not too late to turn the tide for recently declined leatherback populations and that continued investment in conservation efforts and threat reductions are warranted. Collectively, our results highlight how recent and historical demography shapes current genomic health and recovery potential in leatherback turtles, aids understanding of current risks and informs future conservation and management strategies.

ecology↗

bioRxiv2025

MosaicSim: A Novel Mosaic Variant Simulator Reveals Diminishing Returns of Ultra-High Coverage for Mosaic Variant Detection

Genetic mutations within select cells of a tissue, termed mosaic variants (MV), are being increasingly recognized for their role in human disease. This growing interest underscores the need for specialized tools to detect and analyze MVs. However, such detection methods still lack thorough evaluation, largely due to missing benchmarking datasets that are large, reliable, and reflective of the complexity of biological samples. To address this gap, we developed MosaicSim, a tool for simulating variants in realistic sequencing data. The TweakVar workflow is at the tools core and represents a unique simulation pipeline that layers simulated MVs onto empirical whole genome sequencing data, generating a large, realistic ground truth dataset that combines the strengths of both simulation and biological data. To demonstrate the functionality of the workflow, we simulated 1,000 mosaic single nucleotide polymorphisms using TweakVar within whole genome sequencing files of different coverages. MVs were called with Illuminas DRAGEN and compared to the ground truth. Our results show 150x-445x coverage performed comparably, with a true-positive rate between 50.4% (300x) and 54.9% (150x) and no false-positives detected. Across all samples, increasing variant allele frequency had a significant positive effect on call success. Additionally, we observed that call rates for variants in lower complexity regions improved with increasing read depth. We did not find significant effects attributable to specific mutation patterns or mean read map quality. MosaicSim fills a critical unmet need by providing representative, customizable ground truth datasets for MV benchmarking, enabling systematic evaluation and optimization of variant calling methods.

genomics↗

bioRxiv2025

Chromosomal Fusions and Evolutionary Forces: Exploring theNeo-Sex Chromosome System of Anolis distichus

The evolutionary dynamics of sex chromosomes differ from autosomes due to their unique pattern of in-heritance and regions of hemizygosity in non-recombining areas. However, the study of sex chromosomes and sex-linked gene evolution has been limited by the rarity of truly novel sex chromosome complements in model systems. Recent advances in next-generation sequencing have enabled the identification of neo-sex chromosomes, created by the fission or fusion of autosomes with sex chromosomes, providing a new avenue to investigate the dynamics of sex chromosome evolution. Squamate reptiles, particularly Anolis lizards, are an excellent system for studying the consequences of sex-linkage due to their frequent sex chromosome-autosome fusions. The Hispaniolan Bark Anole, Anolis distichus, has experienced two sex chromosome and autosome fusions that led to a multiple sex chromosome system (X1X2Y). We present a high-quality whole-genome assembly and annotation of a male A. distichus (X1X2Y), enabling a detailed analysis of all three of its neo-sex chromosomes. We identify scaffolds associated with X1, X2, and Y chromosomes using an integra-tive approach and estimate degeneration and selection strength. Our results support long-held theories of differential evolutionary pressures in sex chromosomes, such as the Fast X effect and Y degeneration. Additionally, we find that chromosome 12 has become sex-linked independently in two different Anolis species, suggesting that some autosomes may be more likely to become sex-linked. Altogether, our genome adds to the diversity of available taxa sequenced and enables novel comparative analyses in a variety of fields, including speciation, chromosomal synteny, and sex chromosome evolution.

genomics↗

bioRxiv2024

Dynamic imbalances in cell-type specific striatal ensemble activity during visually guided locomotion.

Basal ganglia models commonly propose that relative imbalances between direct and indirect pathway output shapes movement, but how such imbalances are expressed during behavior remains unclear. We simultaneously imaged identified direct-pathway and indirect-pathway spiny projection neurons (dSPNs and iSPNs) in dorsal striatum as mice locomoted through virtual visual environments for reward. Individual dSPNs and iSPNs encoded discrete locations within specific visual environments and, in a distance-based task, encoded distance traveled or elapsed time, revealing structured representations of goal-directed trajectories. At the population level, both pathways were broadly co-active and similarly correlated with locomotor speed, but their relative activity shifted systematically across learned trajectories: dSPNs dominated during early accelerating segments, and iSPNs dominated during later slowing segments. These imbalances were selectively expressed within ensembles tuned to spatial location or distance/time, depending on task structure, but were absent during comparable spontaneous locomotion outside the task context and during initial exposure to a novel environment. A computational model demonstrated that opponent plasticity driven by kinematics-linked teaching signals can reproduce the observed task-dependent imbalances through cell-type-specific plasticity of discrete trajectory-related inputs and can progressively organize locomotor kinematics over learning. Our findings indicate that direct/indirect pathway imbalances are not a general reflection of motor output, but are dynamic, state-dependent features of striatal activity that link structured trajectory representations to associated changes in behavioral vigor along repeated, goal-directed locomotor paths through learning.

neuroscience↗

bioRxiv2024

A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Sagmatias cruciger) Genome

The hourglass dolphin (Lagenorhynchus cruciger) is a small cetacean species of the Southern Ocean, with significance to iwi M[a]ori (M[a]ori tribes) of Aotearoa New Zealand as taonga (treasured/valued). Due to the remoteness and difficulty of surveying Antarctic waters, it remains one of the least-studied dolphin species. A recent stranding of an hourglass dolphin represented a rare opportunity to generate a genome assembly as a resource for future study into the conservation and evolutionary biology of this species. In this study, we present a high-quality genome assembly of an hourglass dolphin individual using a single sequencing platform, Oxford Nanopore Technologies, coupled with computationally efficient assembly methods. Our assembly strategy yielded a genome of high contiguity (N50 of 8.07 Mbp) and quality (98.3% BUSCO completeness). Compared to other Delphinoidea reference genomes, this assembly has fewer missing BUSCOs than any except Orcinus orca, more single-copy complete BUSCOs than any except Phocoena sinus, and 20% fewer duplicated BUSCOs than the average Delphinoidea reference genome. This suggests that it is one of the most complete and accurate marine mammal genomes to date. This study showcases the feasibility of a cost-effective mammalian genome assembly method, allowing for genomic data generation outside the traditional confines of academia and/or resource-rich genome assembly hubs, and facilitating the ability to uphold Indigenous data sovereignty. In the future the genome assembly presented here will allow valuable insights into the past population size changes, adaptation, vulnerability to future climate change of the hourglass dolphin and related species.

genomics↗

bioRxiv2023

A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

The Notomicrus traili species group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed to N. traili and the closely related N. gracilipes recovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within the N. traili group. First, we use short-read whole genome sequencing of four noterid genera to design a noterid-specific UCE probe set (Noteridae 3.4Kv1) targeting over 3,400 unique loci. Using this probe set, we capture UCE data from population-level sampling of 44 traili group specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putative N. traili group populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within the traili group that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co-ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of the traili group in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow-scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography.

evolutionary biology↗

bioRxiv2023

The ghost of selection past: evolution and conservation relevance of the kakapo color polymorphism

The information contained in population genomic data can tell us much about the past ecology and evolution of species. We leveraged detailed phenotypic and genomic data of nearly all living k[a]k[a]p[o] to understand the evolution of its remarkable feather color polymorphism. The k[a]k[a]p[o] is an endangered and culturally significant parrot endemic to Aotearoa New Zealand, and the green and olive feather colorations are present at similar frequencies in the population. The presence of such a neatly balanced color polymorphism is remarkable because the entire population currently numbers less than 250 birds, which means it has been exposed to severe genetic drift. We dissected the color phenotype, demonstrating that the two colors differ in their light reflectance patterns due to differential feather structure. We used quantitative genomics methods to identify two genetic variants whose epistatic interaction can fully explain the species color phenotype. Our genomic forward simulations show that balancing selection might have been pivotal to establish the polymorphism in the ancestrally large population, and to maintain it during population declines that involved a severe bottleneck. We hypothesize that an extinct apex predator was the likely agent of balancing selection, making the color polymorphism in the k[a]k[a]p[o] a "ghost of selection past".

genomics↗

bioRxiv2023

A framework for identifying fertility gene targets for mammalian pest control

O_LIFertility-targeted gene drives have been proposed as an ethical genetic approach for managing wild populations of vertebrate pests for public health and conservation benefit. C_LIO_LIThis manuscript introduces a framework to identify and evaluate target gene suitability based on biological gene function, gene expression, and results from mouse knockout models. C_LIO_LIThis framework identified 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other non-drive genetic pest control technology. Further, a comparative genomics analysis demonstrates the conservation of the identified genes across several globally significant invasive mammals. C_LIO_LIIn addition to providing important considerations for identifying candidate genes, our framework and the genes identified in this study may have utility in developing additional pest control tools such as wildlife contraceptives. C_LI

genetics↗

bioRxiv2022

Diminished distractor filtering with increased perceptual load and sustained effort explains attention deficit in post-stroke fatigue

ObjectivesPost-stroke fatigue (PSF) is a prevalent symptom associated with attention deficits. However, it is currently unclear what drives these. Here we applied Load Theory of Attention to investigate the role of perceptual load in the relationship between attention, distraction, and fatigue levels in PSF. MethodsThirty-two chronic stroke survivors performed a selective attention task under different perceptual load levels. Neural responses to targets and distractors were measured with frequency-tagged EEG responses. ResultsWe showed that Fatigue Severity Scale-7 (FSS-7) scores are predictive of slower responses, irrespective of the task level of perceptual load. Although average distractor frequency (10Hz) power was reduced with higher perceptual load, the reduction in 10Hz power with increasing task load, was smaller in those with higher FSS-7 scores. Higher FSS-7 scores were also associated with increased 10Hz distractor response as time progressed, both within task-trials and across the experiment duration. ConclusionThe results are consistent with previous reports of slower processing speed and sustained selective attention deficits. Importantly they demonstrate that higher fatigue severity is associated with a reduced ability to suppress neural response to irrelevant distractors stimuli when the task demands more attention due to its increased perceptual load. An account for attention deficit in PSF based on a distractor filtering deficit that emerges with increased perceptual load and sustained effort can explain a myriad of PSF symptoms (e.g. sensory perceptual overload, and difficulties to concentrate). Key messagesO_LIWhat is already known on this topic [tpltrtarr]Post-stroke fatigue involves mental fatigue which is exacerbated in cognitively demanding task, as well as difficulties in concentrating and sustaining attention on a task. [tpltrtarr]However previous research has not converged on a clear account of the nature of attention deficits in post-stroke fatigue, as well as on how these relate to the level of perceptual demand in a cognitive task C_LIO_LIWhat this study adds [tpltrtarr]The study suggests that attention deficits in post-stroke fatigue are attributed to a failure to attenuate neural responses to distractors with increased perceptual load in the task, as well as with increased demands on sustained attention with a longer task engagement [tpltrtarr]This pattern points to a distractor filtering deficit that is magnified by perceptual load and sustained mental effort as main drivers of attention deficits in post-stroke fatigue How this study might affect research, practice or policy [tpltrtarr]This study enhances our understanding of attentional deficit in post-stroke fatigue, within an integrative account that explains mental fatigue symptomology C_LI

neuroscience↗

bioRxiv2022

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 MYA, yet the genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of non-collinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared to other reptiles, and harbor a higher genetic load compared to green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage. Statement of significanceSea turtle populations have undergone recent global declines. We analyzed de novo assembled genomes for both extant sea turtle families through the Vertebrate Genomes Project to inform their conservation and evolutionary biology. These highly conserved genomes were differentiated by localized gene-rich regions of divergence, particularly within microchromosomes, suggesting that these genomic elements play key functional roles in the evolution of sea turtles and possibly other vertebrates. We further demonstrate that dissimilar evolutionary histories impact standing genomic diversity and genetic load, and are critical to consider when using these metrics to assess adaptive potential and extinction risk. Our results also demonstrate how reference genome quality impacts inferences of comparative and conservation genomics analyses that need to be considered in their application.

genomics↗

bioRxiv2021

Insights from the IronTract challenge: optimal methods for mapping brain pathways from multi-shell diffusion MRI

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accuracy. Over a period of two years, we have engaged the dMRI community in the IronTract Challenge, which aims to answer this question by leveraging a unique dataset. Macaque brains that have received both tracer injections and ex vivo dMRI at high spatial and angular resolution allow a comprehensive, quantitative assessment of tractography accuracy on state-of-the-art dMRI acquisition schemes. We find that, when analysis methods are carefully optimized, the HCP scheme can achieve similar accuracy as a more time-consuming, Cartesian-grid scheme. Importantly, we show that simple pre- and post-processing strategies can improve the accuracy and robustness of many tractography methods. Finally, we find that fiber configurations that go beyond crossing (e.g., fanning, branching) are the most challenging for tractography. The IronTract Challenge remains open and we hope that it can serve as a valuable validation tool for both users and developers of dMRI analysis methods.

neuroscience↗

bioRxiv2021

A NET4-RabG3 couple mediate the link between actin and the tonoplast and is essential for normal actin cytoskeletal remodelling in stomatal closure to flg22

Members of the NETWORKED (NET) family are involved in actin-membrane interactions. They tether the cells plasma membrane (PM) to the actin network. Moreover, in a similar manner, they are also involved in the tethering of membrane bound organelles to the actin cytoskeleton; the endoplasmic reticulum (ER) and the ER to the PM. This raises the question as to whether NET proteins are involved in actin cytoskeletal remodelling. Here we show that two members of the NET family, NET4A and NET4B, are essential for normal guard cell actin reorganization, which is a process critical for stomatal closure in plant immunity. NET4 proteins interact with F-actin and with members of the Rab7 GTPase RABG3 family through two distinct domains, allowing for simultaneous localization to actin filaments and the tonoplast. NET4 proteins interact with GTP-bound, active RABG3 members, suggesting their function as downstream effectors. We also show that RABG3b is critical for stomatal closure induced by microbial patterns. Taken together, we conclude that the actin cytoskeletal remodelling during stomatal closure depends on a molecular link between actin filaments and the tonoplast, which is mediated by the NET4-RABG3b interaction. We propose that stomatal closure to microbial patterns involves the coordinated action of immune signalling events and proper actin cytoskeletal remodelling.

plant biology↗

bioRxiv2021

Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data

Reduced representation sequencing (RRS) is a widely used method to assay the diversity of genetic loci across the genome of an organism. The dominant class of RRS approaches assay loci associated with restriction sites within the genome (restriction site associated DNA sequencing, or RADseq). RADseq is frequently applied to non-model organisms since it enables population genetic studies without relying on well-characterized reference genomes. However, RADseq requires the use of many bioinformatic filters to ensure the quality of genotyping calls. These filters can have direct impacts on population genetic inference, and therefore require careful consideration. One widely used filtering approach is the removal of loci which do not conform to expectations of Hardy-Weinberg equilibrium (HWE). Despite being widely used, we show that this filtering approach is rarely described in sufficient detail to enable replication. Furthermore, through analyses of in silico and empirical datasets we show that some of the most widely used HWE filtering approaches dramatically impact inference of population structure. In particular, the removal of loci exhibiting departures from HWE after pooling across samples significantly reduces the degree of inferred population structure within a dataset (despite this approach being widely used). Based on these results, we provide recommendations for best practice regarding the implementation of HWE filtering for RADseq datasets.

evolutionary biology↗

bioRxiv2021

Long distance runners in the marine realm: New insights into genetic diversity, kin relationships and social fidelity of Indian Ocean male sperm whales

BackgroundAdult male sperm whales (Physeter macrocephalus) are long distance runners of the marine realm, feeding in high latitudes and mating in tropical and subtropical waters where stable social groups of females and immatures live. Several areas of uncertainty still limit our understanding of their social and breeding behaviour, in particular concerning the potential existence of geographical and/or social fidelities. In this study, using underwater observation and sloughed-skin sampling, we looked for male social fidelity to a specific matrilineal sperm whale group near Mauritius. In addition, we captured a wider picture of kin relationships and genetic diversity of male sperm whales in the Indian Ocean thanks to biopsies of eight unique individuals taken in a feeding ground near the Kerguelen and Crozet Archipelagos (Southern Indian Ocean). ResultsTwenty-six adult male sperm whales, of which 13 were sampled, were identified when socializing with adult females and immatures off Mauritius. Long-term underwater observation recorded several noteworthy social interactions between adult males and adult females and/or immatures. We identified seven possible male recaptures over different years (three by direct observation, and four at the gametic level), which supports a certain level of male social fidelity. Several first- and second-degree kin relationships were highlighted between members of the social unit and adult males, confirming that some of the adult males observed in Mauritian waters are reproductive. Male social philopatry to their natal group can be excluded, as none of the males sampled shared the haplotype characteristic of the matrilineal social group. Mitochondrial DNA control region haplotype and nucleotide diversities calculated over the 21 total male sperm whales sampled were similar to values found by others in the Indian Ocean. ConclusionsOur study strongly supports the existence of some levels of male sperm whale social fidelity, not directed to their social group of birth, in the Indian Ocean. Males sampled in breeding and feeding grounds are linked by kin relationships. Our results support a model of male mediated gene flow occurring at the level of the whole Indian Ocean, likely interconnected with large-scale geographical fidelity to ocean basin, and a small-scale social fidelity to matrilineal social groups.

ecology↗

bioRxiv2019

Egocentric boundary vector tuning of the retrosplenial cortex

The retrosplenial cortex is reciprocally connected with a majority of structures implicated in spatial cognition and damage to the region itself produces numerous spatial impairments. However, in many ways the retrosplenial cortex remains understudied. Here, we sought to characterize spatial correlates of neurons within the region during free exploration in two-dimensional environments. We report that a large percentage of retrosplenial cortex neurons have spatial receptive fields that are active when environmental boundaries are positioned at a specific orientation and distance relative to the animal itself. We demonstrate that this vector-based location signal is encoded in egocentric coordinates, localized to the dysgranular retrosplenial sub-region, independent of self-motion, and context invariant. Further, we identify a sub-population of neurons with this response property that are synchronized with the hippocampal theta oscillation. Accordingly, the current work identifies a robust egocentric spatial code in retrosplenial cortex that can facilitate spatial coordinate system transformations and support the anchoring, generation, and utilization of allocentric representations.

neuroscience↗

bioRxiv2019

Fitness and productivity increase with ecotypic diversity among E. coli evolved in a simple, constant environment

Community productivity often correlates with diversity. In the microbial world this phenomenon can sometimes be explained by highly-specific metabolic interactions that include cross-feeding and syntrophy. Such interactions help account for the astonishing variety of microbial life, and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new species. We have previously shown that in a simple, constant environment a single clone of E. coli can give rise to a consortium of genetically-and physiologically-differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes. We then used flow cytometry to show that each strain by itself is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts resources to offspring than its ancestor or any member acting in isolation.\n\nImportanceIn the microbial world, diversity and productivity of communities and consortia often correlate positively. However, it is challenging to tease apart a consortium whose members have co-evolved, and connect estimates of their fitness and the fitness of their ancestor(s) with estimates of productivity. Such analyses are prerequisite to understanding the evolutionary origins of all biological communities. Here we dissect an E. coli consortium that evolved in the laboratory and show that cooperative interactions are favored under continuous glucose limitation because a partnership of ecotypes is better able to scavenge all available resources and more efficiently convert those resources to offspring than any single individual. Such interactions may be a prelude to a special form of syntrophy, and are likely to be key determinants of microbial community structure in nature, including those having clinical significance, such as chronic infections.

microbiology↗

bioRxiv2017

The Healthy Brain Network Biobank: An open resource for transdiagnostic research in pediatric mental health and learning disorders

Technological and methodological innovations are equipping researchers with unprecedented capabilities for detecting and characterizing pathologic processes in the developing human brain. As a result, ambitions to achieve clinically useful tools to assist in the diagnosis and management of mental health and learning disorders are gaining momentum. To this end, it is critical to accrue large-scale multimodal datasets that capture a broad range of commonly encountered clinical psychopathology. The Child Mind Institute has launched the Healthy Brain Network (HBN), an ongoing initiative focused on creating and sharing a biobank of data from 10,000 New York area participants (ages 5-21). The HBN Biobank houses data about psychiatric, behavioral, cognitive, and lifestyle phenotypes, as well as multimodal brain imaging (resting and naturalistic viewing fMRI, diffusion MRI, morphometric MRI), electroencephalography, eye-tracking, voice and video recordings, genetics, and actigraphy. Here, we present the rationale, design and implementation of HBN protocols. We describe the first data release (n = 664) and the potential of the biobank to advance related areas (e.g., biophysical modeling, voice analysis).

neuroscience↗

bioRxiv2017

Local Low Frequency fMRI Synchrony Is A Proxy For The Spatial Extent Of Functional Connectivity

Functional connectivity Magnetic Resonance Imaging (fcMRI) has assumed a central role in neuroimaging efforts to understand the changes underlying brain disorders. Current models of the spatial and temporal structure of fcMRI based connectivity contain strong a priori assumptions. We report that low temporal frequency fMRI signal synchrony within the local (3 mm radius) neighborhood of a location on the cortical surface strongly predicts the scale of its global functional connectivity. This relationship is tested vertex-wise across the cortex using Spearmans rank order correlation on an individual subject basis. Furthermore, this relationship is shown to be dynamically preserved across repeated within session scans. These results provide a model free data driven method to visualize and quantitatively analyze patterns of connectivity at the imaging voxel resolution across the entire cortex on an individual subject basis. The procedure thus provides a tool to check directly the validity of spatial and temporal prior assumptions incorporated in the analysis of fcMRI data.

neuroscience↗