Biology subjects

Clark, C. A.

Publications and source records attributed to Clark, C. A..

7 recordsLinked to original sources

bioRxiv2026

Quantitative Susceptibility Mapping for Differentiating Hydroxyapatite and Calcium Oxalate Breast Calcifications at 3T: A Phantom Study

PurposeBreast microcalcifications trigger 70-80% of unnecessary biopsies because current imaging cannot distinguish malignancy-associated hydroxyapatite (HA) from benign-associated calcium oxalate (CaOx). Quantitative susceptibility mapping (QSM) could exploit the susceptibility contrast between these minerals (HA: {Delta}{chi} {approx} -7 ppm; CaOx: {Delta}{chi} {approx} -1 ppm relative to water), but no study has demonstrated compositional differentiation at clinical field strength. This work assessed susceptibility and R2* relaxation rate maps for microcalcification differentiation at 3 T using tissue-mimicking phantoms. MethodsA phantom comprising 12 tubes, each containing co-embedded HA and CaOx particles in BaCl2-crosslinked alginate gels (pure alginate, adipose-mimicking, and fibroglandular tissue-mimicking relaxation properties; n = 4 per type), were scanned at 0.70 mm and 0.86 mm isotropic resolution using a multi-echo gradient echo sequence. A consensus-aligned QSM pipeline and mono-exponential R2* fitting was developed. A digital twin phantom simulation quantified the contributions of partial volume effects and Total Variation (TV) regularisation to susceptibility underestimation. ResultsQSM detected HA in 18/24 measurements ({Delta}{chi}peak = -0.37 {+/-} 0.07 ppm in alginate at 0.70 mm) and CaOx in 0/24. R2* mapping detected HA in 23/24 and CaOx in 22/24. The digital twin identified TV regularisation as the dominant signal loss mechanism (57.5% loss), exceeding partial volume effects (24.3% loss). Combined parameters yielded three classification categories: QSM-positive with elevated R2* (HA), QSM-negative with moderate R2* (CaOx), and neither elevated (no calcification). ConclusionQSM at 3 T enables categorical HA detection while R2* provides complementary CaOx sensitivity, together enabling two-parameter microcalcification classification from a single multi-echo acquisition.

biophysics↗

bioRxiv2026

Unexpected ribosome turnover during prolonged translation inhibition

Eukaryotes use several distinct quality control pathways to resolve aberrant ribosomes and mRNAs. For example, the no-go decay mRNA pathway is stimulated after ribosome collisions caused by stalled ribosomes translating damaged or truncated mRNAs. Separate decay pathways for non-functional 40S and 60S subunits containing rRNA mutations affecting decoding and peptidyl transferase activity, respectively, have also been elucidated. To our knowledge, whether eukaryotes have evolved a quality control pathway to sense and process globally stalled ribosomes is unclear; however, such a pathway would be advantageous to eukaryotes during exposure to natural elongation inhibitors such as ricin and diphtheria toxin. Here, we test how prolonged robust inhibition of elongation using a high dose of cycloheximide (CHX) affects ribosome turnover. Despite no decrease in cell viability and that mammalian ribosomes have been classically characterized of having a half-life of 3-5 days, a single 24 hr high dose of CHX resulted in drastically shortened half-lives (<24 hr) of 28S and 18S rRNA in A549 cells. A [~]2-fold reduction in nearly all ribosome species was observed by polysome analysis in HeLa and A549 cells after prolonged CHX treatment. Depletion of ribosomes was also evident when assessing ribosomal proteins from both the 40S and 60S subunits by Western blot. Literature supports that ribosomes can be degraded by autophagy and the ubiquitin (Ub)-proteasome system. Upon testing inhibitors of both pathways, only proteasome inhibitors (i.e., MG132 and bortezomib) rescued both rRNA and ribosomal protein levels. Proteasome inhibitors also rescued ribosome levels in polysome profiling experiments. Remarkably, rRNA levels were not rescued during CHX treatment when co-treated with the Ub activating enzyme E1 inhibitor, TAK243. Polysome analysis also showed that the high prolonged dose of CHX did not cause robust accumulation of collided ribosomes compared to control treatments. Proteasome-dependent turnover of rRNA was also observed with high doses of other elongation inhibitors, namely anisomycin, homoharringtonine, and lactimidomycin. The recognition capabilities of the pathway were further expanded as we observed that 80S ribosomes not trapped on the mRNA were also targeted for degradation by the proteasome. Together, our findings define the framework of a regulatory pathway in mammalian cells that degrades both ribosomal subunits in response to prolonged periods of robust elongation inhibition.

molecular biology↗

bioRxiv2023

Cognitive outcome and its neural correlates after cardiorespiratory arrest in childhood

Hypoxia-ischaemia (HI) can result in structural brain abnormalities, which in turn can lead to behavioural deficits in various cognitive and motor domains, in both adult and paediatric populations. Cardiorespiratory arrest (CA) is a major cause of hypoxia-ischaemia in adults, but it is relatively rare in infants and children. While the effects of adult CA on brain and cognition have been widely studied, to date, there are no studies examining the neurodevelopmental outcome of children who suffered CA early in life. Here, we studied the long-term outcome of 28 children who suffered CA during infancy or childhood (i.e., before age 16). They were compared to a group of control participants (n = 28) matched for age, gender and socio-economic status. The patient group had impairments in the domains of memory, language and academic attainment (measured using standardised tests; impairment defined as a score > 1.5 standard deviations below the control group mean). Individual scores within the impaired range were most commonly found within the memory domain (79%), followed by attainment (50%), and language (36%). The patient group also had reduced whole brain grey matter volume, and reduced volume and fractional anisotropy of the white matter. In addition, lower performance on memory tests was correlated with bilaterally reduced volume of the hippocampi, thalami, and striatum, while lower attainment scores were correlated with bilateral reduction of fractional anisotropy in the superior cerebellar peduncle, the main output tract of the cerebellum. We conclude that patients who suffered early CA are at risk of developing specific cognitive deficits associated with structural brain abnormalities.

neuroscience↗

bioRxiv2021

Training Data Distribution Significantly Impacts the Estimation of Tissue Microstructure with Machine Learning

PurposeSupervised machine learning (ML) provides a compelling alternative to traditional model fitting for parameter mapping in quantitative MRI. The aim of this work is to demonstrate and quantify the effect of different training strategies on the accuracy and precision of parameter estimates when supervised ML is used for fitting. MethodsWe fit a two-compartment biophysical model to diffusion measurements from in-vivo human brain, as well as simulated diffusion data, using both traditional model fitting and supervised ML. For supervised ML, we train several artificial neural networks, as well as random forest regressors, on different distributions of ground truth parameters. We compare the accuracy and precision of parameter estimates obtained from the different estimation approaches using synthetic test data. ResultsWhen the distribution of parameter combinations in the training set matches those observed in similar data sets, we observe high precision, but inaccurate estimates for atypical parameter combinations. In contrast, when training data is sampled uniformly from the entire plausible parameter space, estimates tend to be more accurate for atypical parameter combinations but may have lower precision for typical parameter combinations. ConclusionThis work highlights the need to consider the choice of training data when deploying supervised ML for estimating microstructural metrics, as performance depends strongly on the training-set distribution. We show that high precision obtained using ML may mask strong bias, and visual assessment of the parameter maps is not sufficient for evaluating the quality of the estimates.

neuroscience↗

bioRxiv2020

Structure-function analysis of interallelic complementation in ROOTY transheterozygotes

Auxin is a crucial plant growth regulator. Forward genetic screens for auxin-related mutants have led to the identification of key genes involved in auxin biosynthesis, transport, and signaling. Loss-of-function mutations in the genes involved in indole glucosinolate biosynthesis, a metabolically-related route that produces defense compounds from indolic precursors shared with the auxin pathway, result in auxin overproduction. We identified an allelic series of fertile, hypomorphic mutants for an essential indole glucosinolate route gene ROOTY (RTY) that show a range of high-auxin defects. Genetic characterization of these lines uncovered phenotypic suppression by cyp79b2 b3, wei2, and wei7 mutants and revealed the phenomenon of interallelic complementation in several RTY transheterozygotes. Structural modeling of RTY shed light on the structure-to-function relations in the RTY homo- and heterodimers and unveiled the likely structural basis of interallelic complementation. This work underscores the importance of employing true null mutants in genetic complementation studies.

genetics↗

bioRxiv2019

Altered visual population receptive fields in human albinism

1Albinism is a congenital disorder where misrouting of the optic nerves at the chiasm gives rise to abnormal visual field representations in occipital cortex. In typical human development, the left occipital cortex receives retinal input predominantly from the right visual field, and vice-versa. In albinism, there is a more complete decussation of optic nerve fibers at the chiasm, resulting in partial representation of the temporal hemiretina (ipsilateral visual field) in the contralateral hemisphere. In this study, we characterize the receptive field properties for these abnormal representations by conducting detailed fMRI population receptive field mapping in a rare subset of participants with albinism and no ocular nystagmus. We find a nasal bias for receptive field positions in the abnormal temporal hemiretina representation. In addition, by modelling responses to bilateral visual field stimulation in the overlap zone, we found evidence in favor of discrete unilateral receptive fields, suggesting a conservative pattern of spatial selectivity in the presence of abnormal retinal input. HighlightsO_LIWe characterized population receptive fields in albinotic participants with no ocular nystagmus C_LIO_LIConfirmed overlapping representations of left and right visual fields in cortex C_LIO_LIDetected nasal bias in receptive field location for temporal hemiretina representation C_LIO_LIEvidence in favor of discrete unilateral receptive fields and against double coding C_LI

neuroscience↗

bioRxiv2018

Dopamine signaling modulates the stability and integration of intrinsic brain networks

Dopaminergic projections are hypothesized to stabilize neural signaling and neural representations, but how they shape regional information processing and large-scale network interactions remains unclear. Here we investigated effects of lowered dopamine levels on within-region temporal signal variability (measured by sample entropy) and between-region functional connectivity (measured by pairwise temporal correlations) in the healthy brain at rest. The acute phenylalanine and tyrosine depletion (APTD) method was used to decrease dopamine synthesis in 51 healthy participants who underwent resting-state functional MRI (fMRI) scanning. Functional connectivity and regional signal variability were estimated for each participant. Multivariate partial least squares (PLS) analysis was used to statistically assess changes in signal variability following APTD as compared to the balanced control treatment. The analysis captured a pattern of increased regional signal variability following dopamine depletion. Changes in hemodynamic signal variability were concomitant with changes in functional connectivity, such that nodes with greatest increase in signal variability following dopamine depletion also experienced greatest decrease in functional connectivity. Our results suggest that dopamine may act to stabilize neural signaling, particularly in networks related to motor function and orienting attention towards behaviorally-relevant stimuli. Moreover, dopaminedependent signal variability is critically associated with functional embedding of individual areas in large-scale networks.

neuroscience↗