Biology subjects

Carter, A. R.

Publications and source records attributed to Carter, A. R..

10 recordsLinked to original sources

bioRxiv2025

Neural mechanisms of handedness for precision drawing: hand-dependent engagement of cortical networks for bimanual control and tool use

Neural mechanisms underlying handedness remain poorly understood. We used functional magnetic resonance imaging (fMRI) to study performance of a visually guided drawing task with each hand. We hypothesized that the left superior parietal lobule supports drawing with either hand, and individuals with chronic peripheral nerve injury (PNI) to the dominant hand use the same mechanism as healthy adults. Thirty-three right-handed adults (23 healthy, 10 patients) underwent fMRI while performing a precision drawing task, alternating between the right hand (RH) and left hand (LH). BOLD magnitude and functional connectivity (FC) modulation via generalized psychophysiological interaction were analyzed in 12 a priori regions of interest, followed by additional exploratory areas identified via whole brain magnitude analysis. During LH drawing (compared to RH drawing), contralateral primary motor cortex showed lower BOLD magnitude but greater FC with two networks: First, a left motor-premotor network with increased FC and equal-or-greater magnitude during LH drawing. Second, a right parietal network characterized by increased FC during LH drawing but increased magnitude during RH drawing. Exploratory whole-brain analyses supported and extended these motor and parietal networks, and additionally suggested that RH drawing may involve greater magnitude and FC within a bilateral parieto-premotor network centered on right paracingulate cortex. Patient group (PNI vs. control) did not interact with these effects. These results describe the first proposed mechanisms for LH precision drawing, both of which depend on differential engagement of bimanual control networks: a left hemisphere motor-premotor network for precision motor control, which engages intrahemispherically (directly) during RH drawing and interhemispherically (indirectly) during LH drawing; and a right hemisphere parietal network with greater distributed coordination during LH drawing. These mechanisms did not differ between PNI patients and healthy adults, highlighting these mechanisms potential as neuromodulatory targets to enhance LH performance after RH impairment.

neuroscience↗

bioRxiv2021

Individualized precision targeting of dorsal attention and default mode networks with rTMS in traumatic brain injury-associated depression

BackgroundAt the group level, antidepressant efficacy of rTMS targets is inversely related to their normative connectivity with subgenual anterior cingulate cortex (sgACC). Individualized connectivity may yield better targets, particularly in patients with neuropsychiatric disorders who may have aberrant connectivity. However, sgACC connectivity shows poor test-retest reliability at the individual level. Individualized resting-state network mapping (RSNM) can reliably map inter-individual variability in brain network organization. ObjectiveTo identify individualized RSNM-based rTMS targets that reliably target the sgACC connectivity profile. MethodsWe used RSNM to identify network-based rTMS targets in 10 healthy controls and 13 individuals with traumatic brain injury-associated depression (TBI-D). These "RSNM targets" were compared with consensus structural targets and targets based on individualized anti-correlation with a group-mean-derived sgACC region ("anti-group-mean sgACC targets"). The TBI-D cohort was randomized to receive active (n=9) or sham (n=4) rTMS to RSNM targets. ResultsThe group-mean sgACC connectivity profile was reliably estimated by individualized correlation with default mode network (DMN) and anti-correlation with dorsal attention network (DAN). Individualized RSNM targets were then identified based on DAN anti-correlation and DMN correlation. Counterintuitively, anti-correlation with the group-mean sgACC connectivity profile was stronger and more reliable for RSNM-derived targets than for "anti-group-mean sgACC targets". Improvement in depression after RSNM-targeted rTMS was predicted by target anti-correlation with the portions of sgACC. Active treatment led to increased connectivity within and between several relevant regions. ConclusionsRSNM may enable reliable individualized rTMS targeting, although further research is needed to determine whether this personalized approach can improve clinical outcomes.

neuroscience↗

bioRxiv2021

DNA looping by protamine follows a nonuniform spatialdistribution

DNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors like lac repressor or by structural maintenance of chromosomes (SMC) proteins such as condensin. Here, however, we are interested in a different looping method whereby multivalent cations (charge[≥]+3), such as protamine proteins, neutralize the DNA, causing it to form loops and toroids. We considered two previously proposed mechanisms for DNA looping by protamine. In the first mechanism, protamine stabilizes spontaneous DNA fluctuations, forming randomly distributed loops along the DNA. In the second mechanism, protamine binds and bends the DNA to form a loop, creating a distribution of loops that is biased by protamine binding. To differentiate between these mechanisms, we imaged both spontaneous and protamine-induced loops on short-length ([≤] 1 m) DNA fragments using atomic force microscopy (AFM). We then compared the spatial distribution of the loops to several model distributions. A random looping model, which describes the mechanism of spontaneous DNA folding, fit the distribution of spontaneous loops, but it did not fit the distribution of protamine-induced loops. Specifically, it overestimated the number of loops that form at the ends of the molecule and failed to predict a peak in the spatial distribution of loops at an intermediate location along the DNA. An electrostatic multibinding model, which was created to mimic the bind-and-bend mechanism of protamine, was a better fit of the distribution of protamine-induced loops. In this model, multiple protamines bind to the DNA electrostatically within a particular region along the DNA to coordinate the formation of a loop. We speculate that these findings will impact our understanding of protamines in vivo role for looping DNA into toroids and the mechanism of DNA condensation by multivalent cations more broadly. SIGNIFICANCEDNA looping is important in a variety of both in vivo functions (e.g. gene regulation) and in vitro applications (e.g. DNA origami). Here, we sought a mechanistic understanding of DNA looping by multivalent cations ([≥]+3), which condense DNA into loops and toroids. One such multivalent cation is the protein protamine, which condenses DNA in sperm. We investigated the mechanism for loop formation by protamine and found that the experimental data was consistent with an electrostatic multibinding model in which two protamines bind electrostatically to the DNA within a 50-nm region to form a loop. This model is likely general to all multivalent cations and may be helpful in applications involving toroid formation or DNA nanoengineering.

biophysics↗

bioRxiv2020

Cingulo-Opercular Control Network Supports Disused Motor Circuits in Standby Mode

Whole-brain resting-state functional MRI (rs-fMRI) during two weeks of limb constraint revealed that disused motor regions became more strongly connected to the cingulo-opercular network (CON), an executive control network that includes regions of the dorsal anterior cingulate cortex (dACC) and insula (1). Disuse-driven increases in functional connectivity (FC) were specific to the CON and somatomotor networks and did not involve any other networks, such as the salience, frontoparietal, or default mode networks. Censoring and modeling analyses showed that FC increases during casting were mediated by large, spontaneous activity pulses that appeared in the disused motor regions and CON control regions. During limb constraint, disused motor circuits appear to enter a standby mode characterized by spontaneous activity pulses and strengthened connectivity to CON executive control regions. SignificanceMany studies have examined plasticity in the primary somatosensory and motor cortex during disuse, but little is known about how disuse impacts the brain outside of primary cortical areas. We leveraged the whole-brain coverage of resting-state functional MRI (rs-fMRI) to discover that disuse drives plasticity of distant executive control regions in the cingulo-opercular network (CON). Two complementary analyses, pulse censoring and pulse addition, demonstrated that increased functional connectivity between the CON and disused motor regions was driven by large, spontaneous pulses of activity in the CON and disused motor regions. These results point to a previously unknown role for the CON in supporting motor plasticity and reveal spontaneous activity pulses as a novel mechanism for reorganizing the brains functional connections.

neuroscience↗

bioRxiv2019

Mendelian randomisation for mediation analysis: current methods and challenges for implementation

Mediation analysis seeks to explain the pathway(s) through which an exposure affects an outcome. Mediation analysis experiences a number of methodological difficulties, including bias due to confounding and measurement error. Mendelian randomisation (MR) can be used to improve causal inference for mediation analysis. We describe two approaches that can be used for estimating mediation analysis with MR: multivariable Mendelian randomisation (MVMR) and two-step Mendelian randomisation. We outline the approaches and provide code to demonstrate how they can be used in mediation analysis. We review issues that can affect analyses, including confounding, measurement error, weak instrument bias, and analysis of multiple mediators. Description of the methods is supplemented by simulated and real data examples. Although Mendelian randomisation relies on large sample sizes and strong assumptions, such as having strong instruments and no horizontally pleiotropic pathways, our examples demonstrate that it is unlikely to be affected by confounders of the exposure or mediator and the outcome, reverse causality and non-differential measurement error of the exposure or mediator. Both MVMR and two-step MR can be implemented in both individual-level MR and summary data MR, and can improve causal inference in mediation analysis.

genetics↗

bioRxiv2019

Using genetic instruments to estimate interactions in Mendelian Randomization studies

BACKGROUNDThe interactive effect of two exposures on an outcome can be confounded. We demonstrate the use of Mendelian Randomization (MR) to estimate unconfounded additive interactions. METHODSUsing simulation, we test an extension to multivariable MR using two-stage least squares to estimate the additive interaction between two continuous exposures on a continuous outcome, including scenarios where one exposure has a causal effect on the other (mediation). The interaction parameters were set to be one third of the main effects parameters to impose a limit on the variance explained by interaction terms. We compare the performance of the two-stage least squares estimator to a Factorial MR design, in which genetic risk scores for each exposure are dichotomised to create four groups, akin to a factorial randomized controlled trial. As an illustrative example, we apply factorial MR and the 2SLS estimator to the interactive effect of education and BMI on systolic blood pressure in UK Biobank. RESULTSOur simulations demonstrate that factorial MR has very low statistical power; 5-7% at N=50,000 and 8-23% at N=500,000 across the range of parameters tested. The two-stage least squares estimator had higher power to detect interactions than factorial MR and a lower type I error. For N=500,000, the two-stage least squares estimator had a power ranging from 29.7-92.9% and a type I error ranging from 4-6%. 95% Monte Carlo confidence intervals suggested that the estimator was unbiased to a reasonable degree of accuracy at this sample size. In comparison, the power at N=50,000 was 7-55%. CONCLUSIONSA two-stage least squares estimator using genetic risk scores for each exposure is a more powerful alternative for detecting an unconfounded additive interaction of two exposures on an outcome than existing approaches that rely on dichotomising genetic risk scores, but it requires a large sample size and instruments of adequate strength.

epidemiology↗

bioRxiv2018

What explains the effect of education on cardiovascular disease? Applying Mendelian randomization to identify the consequences of education inequality

Key PointsO_ST_ABSQuestionC_ST_ABSWhat is the role of body mass index, systolic blood pressure and smoking in mediating the effect of education on cardiovascular disease risk?\n\nFindingWe find consistent evidence that body mass index, systolic blood pressure and smoking mediate the effect of education, explaining up to 18%, 27% and 33% respectively. Including all three risk factors in a model together explains around 40% of the effect of education.\n\nMeaningIntervening on body mass index, systolic blood pressure and smoking would lead to reductions in cases of CVD attributable to lower levels of education. Over half of the effect of education on risk of cardiovascular disease is not mediated through these risk factors.\n\nImportanceLower levels of education are causally related to higher cardiovascular risk, but the extent to which this is driven by modifiable risk factors also associated with education is unknown.\n\nObjectiveTo investigate the role of body mass index, systolic blood pressure and smoking in explaining the effect of education on risk of cardiovascular disease outcomes.\n\nDesignMultivariable regression analysis of observational data and Mendelian randomization (MR) analysis of genetic data.\n\nSettingUK Biobank and international genome-wide association study consortia.\n\nParticipantsPredominantly individuals of European ancestry.\n\nMain outcomes and measuresThe effects of education (per 1-standard deviation increase, equivalent to 3.6 years) on coronary heart disease, cardiovascular disease (all subtypes), myocardial infarction and stroke risk (all measured in odds ratio, OR), and the degree to which this is mediated through body mass index, systolic blood pressure and smoking.\n\nResultsEach additional standard deviation of education associated with 13% lower risk of coronary heart disease (OR 0.87, 95% confidence interval [CI] 0.84 to 0.89) in observational analysis and 37% lower risk (OR 0.63, 95% CI 0.60 to 0.67) in Mendelian randomization analysis. As a proportion of the total risk reduction, body mass index mediated 15% (95% CI 13% to 17%) and 18% (95% CI 14% to 23%) in the observational and Mendelian randomization estimates, respectively. Corresponding estimates for systolic blood pressure were 11% (95% CI 9% to 13%) and 21% (95% CI 15% to 27%), and for smoking, 19% (15% to 22%) and 33% (95% CI 17% to 49%). All three risk factors combined mediated 42% (95% CI 36% to 48%) and 36% (95 % CI 16% to 63%) of the effect of education on coronary heart disease in observational and Mendelian randomization respectively. Similar results were obtained when investigating risk of stroke, myocardial infarction and all-cause cardiovascular disease.\n\nConclusions and relevanceBMI, SBP and smoking mediate a substantial proportion of the protective effect of education on risk of cardiovascular outcomes and intervening on these would lead to reductions in cases of CVD attributable to lower levels of education. However, more than half of the protective effect of education remains unexplained and requires further investigation.

epidemiology↗

bioRxiv2018

Investigating the combined association of BMI and alcohol consumption on liver disease and biomarkers: a Mendelian randomization study of over 90 000 adults from the Copenhagen General Population Study

BackgroundBody mass index (BMI) and alcohol consumption are suggested to independently and interactively increase the risk of liver disease. We assessed this combined effect using factorial Mendelian randomization (MR).\n\nMethodsWe used multivariable adjusted regression and MR to estimate individual and joint associations of BMI and alcohol consumption and liver disease biomarkers (alanine aminotransferase (ALT) y-glutamyltransferase (GGT)) and incident liver disease. We undertook a factorial MR study splitting participants by median of measured BMI or BMI allele score then by median of reported alcohol consumption or ADH1B genotype (AA/AG and GG), giving four groups; low BMI/low alcohol (-BMI/-alc), low BMI/high alcohol (-BMI/+alc), high BMI/low alcohol (+BMI/-alc) and high BMI/high alcohol (+BMI/+alc).\n\nResultsIndividual positive associations of BMI and alcohol with ALT, GGT and incident liver disease were found. In the factorial MR analyses, considering the +BMI/+alc group as the reference, mean circulating ALT and GGT levels were lowest in the -BMI/-alc group (2.32% (95% CI: -4.29, -0.35) and -3.56% (95% CI: -5.88; -1.24) for ALT and GGT respectively). Individuals with -BMI/+alc and +BMI/-alc had lower mean circulating ALT and GGT compared to the reference group (+BMI/+alc). For incident liver disease multivariable factorial analyses followed a similar pattern to those seen for the biomarkers, but little evidence of differences between MR factorial categories for odds of liver disease.\n\nConclusionsConsistent results from multivariable regression and MR analysis, provides compelling evidence for the individual adverse effects of BMI and alcohol consumption on liver disease. Intervening on both BMI and alcohol may improve the profiles of circulating liver biomarkers. However, this may not reduce clinical liver disease risk.

epidemiology↗

bioRxiv2017

A systematic review of sample size and power in leading neuroscience journals

Adequate sample size is key to reproducible research findings: low statistical power can increase the probability that a statistically significant result is a false positive. Journals are increasingly adopting methods to tackle issues of reproducibility, such as by introducing reporting checklists. We conducted a systematic review comparing articles submitted to Nature Neuroscience in the 3 months prior to checklists (n=36) that were subsequently published with articles submitted to Nature Neuroscience in the 3 months immediately after checklists (n=45), along with a comparison journal Neuroscience in this same 3-month period (n=123). We found that although the proportion of studies commenting on sample sizes increased after checklists (22% vs 53%), the proportion reporting formal power calculations decreased (14% vs 9%). Using sample size calculations for 80% power and a significance level of 5%, we found little evidence that sample sizes were adequate to achieve this level of statistical power, even for large effect sizes. Our analysis suggests that reporting checklists may not improve the use and reporting of formal power calculations.

scientific communication and education↗

bioRxiv2017

rTMS with individualized resting-state network mapping for neuropsychiatric sequelae of repetitive traumatic brain injury in a retired NFL player

The recent advent of individualized resting-state network mapping (RSNM) has revealed substantial inter-individual variability in anatomical localization of brain networks identified using resting-state functional MRI (rsfMRI). Such variability may be particularly important after repetitive traumatic brain injury (TBI), which is associated with treatment-resistant depression. RSNM enables personalized targeting of repetitive transcranial magnetic stimulation (rTMS), a focal brain stimulation technique that relieves depression when administered over dorsolateral prefrontal cortex.\n\nRSNM was used to identify left/right dorsolateral prefrontal rTMS targets with maximal difference between dorsal attention network and default mode network (DMN) correlations. These targets were spatially distinct from those identified by prior methods. The method was evaluated by administering twenty sessions of left-sided excitatory and right-sided inhibitory rTMS to a retired NFL defensive lineman with progressive treatment-resistant neuropsychiatric disturbances. Treatment led to improvement in Montgomery-Asberg Depression Rating Scale (72%), cognitive testing, and headache scales. In comparison with healthy individuals and subjects with TBI-associated depression, baseline rsfMRI revealed substantially elevated DMN connectivity with medial temporal lobe (MTL). Serial rsfMRI scans showed gradual improvement in MTL-DMN connectivity and stimulation site connectivity with subgenual anterior cingulate cortex. This highlights the possibility of individualized neuromodulation and biomarker-based monitoring for neuropsychiatric sequelae of repetitive TBI.

neuroscience↗