Biology subjects

Thomas, A. G.

Publications and source records attributed to Thomas, A. G..

12 recordsLinked to original sources

bioRxiv2026

Sex Differences in Human Subcortical Anatomy are Robust and Replicable in Adulthood, Already Evident Prepubertally, and Aligned with Sex Chromosomal and Gonadal Influences

The existence and mechanistic bases of sex effects on human subcortical anatomy remain unclear. To address these gaps, we combined structural neuroimaging of sex differences in subcortical volume and shape across three independent cohorts (combined N=2,886) with neuroimaging maps of sex chromosomal and endocrine effects from three clinical cohorts (combined N=313, including sex chromosome aneuploidies and isolated gonadotropin-releasing hormone deficiency). We found that human subcortical anatomy shows focal sex differences of moderate-strong effect size during young adulthood (male-biased surface area overlying lateral/ventral putamen and pallidum, nucleus accumbens, ventral posterior complex of thalamus, anterior hippocampus, and medial and central nuclei of amygdala; female-biased surface area overlying caudate head, posterior/dorsal pallidum, mediodorsal, lateral dorsal, lateral geniculate, and medial geniculate nuclei of thalamus, posterior hippocampus, and basolateral and lateral nuclei of amygdala). These regional sex differences show strong within-sample reproducibility at modest sample sizes (N[≥]200) and are replicable in a fully independent mid-adulthood cohort. Adult subcortical sex differences are already evident in nascent form by pre/early puberty (age 9 years), and the same holds for cortical sex differences. Comparison with neuroimaging data from rare disorder cohorts reveals a statistically significant spatial and directional congruence of subcortical sex differences with the anatomical effects of X-chromosome dosage in the striatum and effects of testicular hormones in the amygdala. Our findings provide a reference map for the fine-grained spatial patterning of sex differences in adult subcortical shape, demonstrating its replicability, establishment before pubertal progression, and spatial concordance with potentially causal sex chromosomal and gonadal effects.

neuroscience↗

bioRxiv2026

labapi: a Python object model for the LabArchives electronic lab notebook

labapi is a Python library that enables computational workflows to connect to LabArchives' electronic lab notebook (ELN). Without an Application Programming Interface (API) connection, researchers must manually add workflow outputs through the LabArchives web interface, navigating to the appropriate page and uploading each output so that it appears with the experimental notes that provide context. labapi translates the flat LabArchives API into a Python object model following the existing hierarchy of the web interface, allowing workflows to navigate and modify notebook content through familiar paths. labapi enables researchers to build interconnected workflows that both read in and write data to LabArchives' ELN automatically. Researchers can inspect those outputs in the notebook, and later analysis code can read them back for another stage of analysis.

bioinformatics↗

bioRxiv2026

Building an open ecosystem for molecular neuroimaging: standards and tools from the OpenNeuroPET initiative

Molecular neuroimaging with positron emission tomography (PET) and single-photon emission computed tomography (SPECT) enables quantification of specific molecular targets in the living brain. Despite its scientific impact, molecular neuroimaging research has historically faced challenges due to high costs, small sample sizes, laboratory-specific analysis pipelines, and limited large-scale data sharing. These factors have hindered reproducibility and the broader reuse of valuable PET datasets. The OpenNeuroPET initiative was established to address these barriers by developing standards, infrastructure, and open-source tools currently focused on PET. Through collaborations across Europe and North America, OpenNeuroPET has supported the PET extension of the Brain Imaging Data Structure (PET-BIDS), providing a standardized framework for PET datasets and metadata. Building on PET-BIDS, tools such as PET2BIDS, ezBIDS, and BIDSCoin facilitate data conversion and curation. In parallel, OpenNeuro now hosts PET-BIDS datasets for open sharing, while complementary platforms such as PublicnEUro provide controlled-access pathways designed to support compliance with the European Union General Data Protection Regulation (GDPR). Emerging open-source workflows further support automated, reproducible PET analysis, promoting harmonization across centers. Together, these developments mark an important step toward an open molecular neuroimaging community in which datasets, software, and workflows can be transparently shared, reused, and scaled for collaborative research.

bioinformatics↗

bioRxiv2023

A bipolar taxonomy of adult human brain sulcal morphology related to timing of fetalsulcation and trans-sulcal gene expression gradients

We developed a computational pipeline (now provided as a resource) for measuring morphological similarity between cortical surface sulci to construct a sulcal phenotype network (SPN) from each magnetic resonance imaging (MRI) scan in an adult cohort (N=34,725; 45-82 years). Networks estimated from pairwise similarities of 40 sulci on 5 morphological metrics comprised two clusters of sulci, represented also by the bipolar distribution of sulci on a linear-to-complex dimension. Linear sulci were more heritable and typically located in unimodal cortex; complex sulci were less heritable and typically located in heteromodal cortex. Aligning these results with an independent fetal brain MRI cohort (N=228; 21-36 gestational weeks), we found that linear sulci formed earlier, and the earliest and latest-forming sulci had the least between-adult variation. Using high-resolution maps of cortical gene expression, we found that linear sulcation is mechanistically underpinned by trans-sulcal gene expression gradients enriched for developmental processes.

neuroscience↗

bioRxiv2022

A 2D Fragment-Assisted Protein Mimetic Approach to Rescue α-Synuclein Aggregation Mediated Early and Post-Disease Parkinsons Phenotypes

We have developed a Oligopyridylamide (OP) based 2-Dimensional Fragment-Assisted Structure-based Technique (2D-FAST) to identify potent antagonists of -Synuclein (S) aggregation, a process central to Parkinsons disease (PD). The 2D-FAST utilizes a fragment-based screening of large chemical space in OPs, which led to the identification of NS132 as an antagonist of the multiple facets of S aggregation. We also identified a better cell permeability analog (NS163) without sacrificing activity. OPs rescue S aggregation mediated PD phenotypes in muscle cells and dopaminergic (DA) neurons in C. elegans models. OPs prevent the progression of PD phenotypes in a novel post-disease onset PD model. This is one of the first examples of a synthetic mimetic-based 2D-FAST to identify antagonists of toxic S self-assembly. We envision that 2D-FAST will have tremendous potential as it is expandable for other oligoamide scaffolds and for a much larger chemical space to identify lead therapeutics for various diseases.

biochemistry↗

bioRxiv2021

High-throughput Activity Assay for Screening Inhibitors of the SARS-CoV-2 Mac1 Macrodomain

Macrodomains are a class of conserved ADP-ribosylhydrolases expressed by viruses of pandemic concern, including coronaviruses and alphaviruses. Viral macrodomains are critical for replication and virus-induced pathogenesis; therefore, these enzymes are a promising target for antiviral therapy. However, no potent or selective viral macrodomain inhibitors currently exist, in part due to the lack of a high-throughput assay for this class of enzymes. Here, we developed a high-throughput ADP-ribosylhydrolase assay using the SARS-CoV-2 macrodomain Mac1. We performed a pilot screen which identified dasatinib and dihydralazine as ADP-ribosylhydrolase inhibitors. Importantly, dasatinib does not inhibit MacroD2, the closest Mac1 homolog in humans. Our study demonstrates the feasibility of identifying selective inhibitors based on ADP-ribosylhydrolase activity, paving the way for screening large compound libraries to identify improved macrodomain inhibitors and explore their potential as antiviral therapies for SARS-CoV-2 and future viral threats.

biochemistry↗

bioRxiv2021

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging datasets. It serves not only to facilitate the process of data sharing and aggregation, but also to simplify the application and development of new methods and software for working with neuroimaging data. Here, we present an extension of BIDS to include positron emission tomography (PET) data (PET-BIDS). We describe the PET-BIDS standard in detail and share several open-access datasets curated following PET-BIDS. Additionally, we highlight several tools which are already available for converting, validating and analyzing PET-BIDS datasets.

neuroscience↗

bioRxiv2021

Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits - the Hispanic/Latino Anthropometry Consortium

Hispanic/Latinos have been underrepresented in genome-wide association studies (GWAS) for anthropometric traits despite notable anthropometric variability with ancestry proportions, and a high burden of growth stunting and overweight/obesity in Hispanic/Latino populations. This address this knowledge gap, we analyzed densely-imputed genetic data in a sample of Hispanic/Latino adults, to identify and fine-map common genetic variants associated with body mass index (BMI), height, and BMI-adjusted waist-to-hip ratio (WHRadjBMI). We conducted a GWAS of 18 studies/consortia as part of the Hispanic/Latino Anthropometry (HISLA) Consortium (Stage 1, n=59,769) and validated our findings in 9 additional studies (HISLA Stage 2, n=9,336). We conducted a trans-ethnic GWAS with summary statistics from HISLA Stage 1 and existing consortia of European and African ancestries. In our HISLA Stage 1+2 analyses, we discovered one novel BMI locus, as well two novel BMI signals and another novel height signal, each within established anthropometric loci. In our trans-ethnic meta- analysis, we identified three additional novel BMI loci, one novel height locus, and one novel WHRadjBMI locus. We also identified three secondary signals for BMI, 28 for height, and two for WHRadjBMI. We replicated >60 established anthropometric loci in Hispanic/Latino populations at genome-wide significance--representing up to 30% of previously-reported index SNP anthropometric associations. Trans-ethnic meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our novel findings demonstrate that future studies may also benefit from leveraging differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification.

genetics↗

bioRxiv2020

Computationally replicating the Smith et al. (2015) positive-negative mode linking functional connectivity and subject measures

Understanding brain functionality and predicting human behavior based on functional brain activity is a major goal of neuroscience. Numerous studies have been conducted to investigate the relationship between functional brain activity and attention, subject characteristics, autism, psychiatric disorders, and more. By modeling brain activity data as networks, researchers can leverage the mathematical tools of graph and network theory to probe these relationships. In their landmark study, Smith et al. (2015) analyzed the relationship of young adult connectomes and subject measures, using data from the Human Connectome Project (HCP). Using canonical correlation analysis (CCA), Smith et al. found that there was a single prominent CCA mode which explained a statistically significant percentage of the observed variance in connectomes and subject measures. They also found a strong positive correlation of 0.87 between the primary CCA mode connectome and subject measure weights. In this study, we computationally replicate the findings of the original study in both the HCP 500 and HCP 1200 subject releases. The exact computational replication in the HCP 500 dataset was a success, validating our analysis pipeline for extension studies. The extended replication in the larger HCP 1200 dataset was partially successful and demonstrated a dominant primary mode.

neuroscience↗

bioRxiv2020

Microglia-targeted dendrimer-2PMPA therapy robustly inhibits GCPII and improves cognition in a mouse model of multiple sclerosis

Roughly half of all individuals with multiple sclerosis (MS) experience cognitive impairment, but there are no approved treatments that target this aspect of the disease. Recent studies link reduced brain N-acetylaspartylglutamate (NAAG) levels to impaired cognition in various neurological diseases, including MS. NAAG levels are regulated by glutamate carboxypeptidase II (GCPII), which hydrolyzes the neuropeptide to N-acetyl-aspartate (NAA) and glutamate. Although several GCPII inhibitors, such as 2-(phosphonomethyl)-pentanedioic acid (2-PMPA), elevate brain NAAG levels and restore cognitive function in preclinical studies when given at high systemic doses or via direct brain injection, no GCPII inhibitors are clinically available due to poor bioavailability and limited brain penetration. Systemic hydroxyl dendrimers (~4 nm) have been successfully used to enhance brain delivery of drugs selectively to activated glia. We recently discovered that GCPII is highly upregulated in activated microglia after brain injury. To determine if dendrimer conjugation could enhance the brain delivery of GCPII inhibitors, specifically in the context of MS, we attached 2-PMPA to hydroxyl polyamidoamicne (PAMAM) dendrimers (D-2PMPA) using a highly efficient click chemistry approach. Targeted uptake of D-2PMPA into activated glia was subsequently confirmed in glial cultures where it showed robust anti-inflammatory activity, including an elevation in TGF{beta} and a reduction in TNF. Given these positive effects, D-2PMPA (20mg/kg) or vehicle dendrimer were dosed twice weekly to experimental autoimmune encephalomyelitis (EAE)-immunized mice starting at disease onset (therapeutic paradigm). D-2PMPA significantly improved cognition in EAE as assessed by Barnes maze performance, even though physical severity was not impacted. Glial target engagement was confirmed, as CD11b+ enriched cells isolated from hippocampi in D-2PMPA-treated mice exhibited almost complete loss of GCPII activity. These data demonstrate the utility of hydroxyl dendrimers to enhance brain penetration and support the development of D-2PMPA to treat cognitive impairment in MS. FundingThis work was funded by the National Multiple Sclerosis Society (RG-1507-05403 to BSS), the National Institute of Health NINDS (R01NS093416 to SK, RM and BSS), and Ashvattha Therapeutics. We would also like to acknowledge support for the statistical analysis from the National Center for Research Resources and NIH NCATS (1UL1TR001079). HighlightsO_LIThe GCPII inhibitor 2-PMPA was conjugated to hydroxyl PAMAM dendrimers (D-2PMPA) C_LIO_LID-2PMPA targeted activated glia in culture and displayed anti-inflammatory activity C_LIO_LIWhen dosed systemically to EAE mice, D-2PMPA inhibited CD11b+ cell GCPII activity C_LIO_LIWhen dosed systemically to EAE mice, D-2PMPA improved cognitive function C_LI

neuroscience↗

bioRxiv2019

Understanding the basis of CYP26 mediated regulation of lens regeneration using ex vivo eye cultures and 4-oxo-RA

PURPOSEXenopus has the remarkable ability to regenerate a lens from the basal cornea epithelial cells in response to signals from the retina. Previous work demonstrated that the Retinoic Acid (RA) metabolizing enzyme CYP26 is expressed in the cornea, and that its activity is required for lens regeneration. Gaps remain in our knowledge as to whether CYP26 is needed only to attenuate RA signaling via RA elimination, or whether it also acts to generate retinoid metabolites, such as 4-oxo-RA, to act as signaling ligands. Other key questions are why CYP26 antagonism, but not exogenous retinoids, can reduce cell division in the cornea, and when during regeneration CYP26 is important.\n\nMATERIALS AND METHODSEx vivo cultures supplemented with RA, 4-oxo-RA, or the CYP26 inhibitor Liarozole were used to assay the effects of these compounds on lens regeneration. Similarly, corneas were explanted, cultured in the presence of these compounds, and assayed for mitotic changes by counting anti-Histone H3 positive nuclei. qPCRs validated responsiveness to these compounds.\n\nRESULTSEx vivo cultures showed that when the media was supplemented with the RA metabolite 4-oxo-RA in addition to Liarozole, lens regeneration was still inhibited. 4-oxo-RA also does not rescue the loss of cell division in the cornea that is observed upon CYP26 antagonism. Liarozole inhibited regeneration when added 12 hours after lentectomy, but not when added 48 hours after.\n\nCONCLUSIONSThese data show that the necessity of CYP26 is not explained as a generator of 4-oxo-RA for regeneration. Moreover, Liarozole-induced mitotic reduction is not explained by 4-oxo-RA deficiency. These results support a model of RA-independent mitotic regulation by CYP26, though other retinoid metabolites may be active. Finally, CYP26 activity is only needed between 12 and 48 hours post-surgery, showing that its action is required only during the earliest stages of lens regeneration.\n\nFinancial interestsThe authors declare no competing financial interests.

developmental biology↗

bioRxiv2018

Detecting and harmonizing scanner differences in the ABCD study - annual release 1.0

In order to obtain the sample sizes needed for robustly reproducible effects, it is often necessary to acquire data at multiple sites using different MRI scanners. This poses a challenge for investigators to account for the variance due to scanner, as balanced sampling is often not an option. Similarly, longitudinal studies must deal with known and unknown changes to scanner hardware and software over time. In this manuscript, we have explored scanner-related differences in the dataset recently released by the Adolescent Brain Cognitive Development (ABCD) project, a multi-site, longitudinal study of children age 9-10. We demonstrate that scanner manufacturer, model, as well as the individual scanner itself, are detectable in the resting and task-based fMRI results of the ABCD dataset. We further demonstrate that these differences can be harmonized using an empirical Bayes approach known as ComBat. We argue that accounting for scanner variance, including even minor differences in scanner hardware or software, is crucial for any analysis.

neuroscience↗