Danyal Akarca

University of Cambridge | Cam · MRC Cognition and Brain Sciences Unit

Organisational gradients refer to a continuous low-dimensional embedding of brain regions and can quantify core organisational principles of complex systems like the human brain. Mapping how these organisational principles are altered or refined across development and phenotypes is essential to understanding the relationship between brain and behav...

Organisational gradients refer to a continuous low-dimensional embedding of brain regions and can quantify core organisational principles of complex systems like the human brain. Mapping how these organisational principles are altered or refined across development and phenotypes is essential to understanding the relationship between brain and behav...

Structural brain organization in infancy is associated with later cognitive, behavioral, and educational outcomes. Due to practical limitations, such as technological advancements and data availability of fetal MRI, there is still much we do not know about the early emergence of topological organization. We combine the developing Human Connectome P...

Connectome generative models, otherwise known as generative network models, provide insight into the wiring principles underpinning brain network organization. While these models can approximate numerous statistical properties of empirical networks, they typically fail to explicitly characterize an important contributor to brain organization—axonal...

Understanding how biological constraints shape neural computation is a central goal of computational neuroscience. Spatially embedded recurrent neural networks provide a promising avenue to study how modelled constraints shape the combined structural and functional organisation of networks over learning. Prior work has shown that spatially embedded...

As deep learning systems are scaled up to many billions of parameters, relating their internal structure to external behaviors becomes very challenging. Although daunting, this problem is not new: Neuroscientists and cognitive scientists have accumulated decades of experience analyzing a particularly complex system - the brain. In this work, we arg...

Organisational gradients refer to a continuous low-dimensional embedding of brain regions and can quantify core organisational principles of complex systems like the human brain. Mapping how these organisational principles are altered or refined across development and phenotypes is essential to understanding the relationship between brain and behav...

Key principles of structural brain organization are established very early in fetal development. The frontal cortex is an important hub for integration and control of information, and its integrity and connectivity within the wider neural system are linked to individual differences across multiple cognitive domains and neurodevelopmental conditions...

Loss-of-function ZDHHC9 variants are associated with X-linked intellectual disability (XLID), rolandic epilepsy (RE) and developmental language difficulties. This study integrates human neurophysiological data with a computational model to identify a potential neural mechanism explaining ZDHHC9 -associated differences in cortical function and cogni...

Connectome generative models, otherwise known as generative network models, provide insight into the wiring principles underpinning brain network organization. While these models can approximate numerous statistical properties of empirical networks, they typically fail to explicitly characterize an important contributor to brain organization – axon...

Brain networks exist within the confines of resource limitations. As a result, a brain network must overcome the metabolic costs of growing and sustaining the network within its physical space, while simultaneously implementing its required information processing. Here, to observe the effect of these processes, we introduce the spatially embedded r...

Neural phenotypes are the result of probabilistic developmental processes. This means that stochasticity is an intrinsic aspect of the brain as it self-organizes over a protracted period. In other words, while both genomic and environmental factors shape the developing nervous system, another significant—though often neglected—contributor is the ra...

The structural organisation of the human brain emerges probabilistically as we develop. Due to the inherent complexity of the human brain, understanding the forces that shape this probabilistic emergence remains one of the central challenges of systems theory and neuroscience. Across 2153 children (9-11 years old) we used a computational model to s...

Resting-state network activity has been associated with the emergence of individual differences across childhood development. However, due to the limitations of time-averaged representations of neural activity, little is known about how cognitive and behavioural variability relates to the rapid spatiotemporal dynamics of these networks. Magnetoence...

Probabilistic generative network models have offered an exciting window into the constraints governing the human connectome's organization. In particular, they have highlighted the economic context of network formation and the special roles that physical geometry and self-similarity likely play in determining the connectome's topology. However, a c...

Early adversity can change educational, cognitive, and mental health outcomes. However, the neural processes through which early adversity exerts these effects remain largely unknown. We used generative network modeling of the mouse connectome to test whether unpredictable postnatal stress shifts the constraints that govern the organization of the...

Structural brain organization in infancy is associated with later cognitive, behavioral, and educational outcomes. Due to practical limitations, such as poor in-utero imaging, there is a lack of understanding of the early emergence of topological organization. We combine the developing Human Connectome Project’s large infant dataset with generative...

Neural phenotypes are the result of probabilistic developmental processes. This means that stochasticity is an intrinsic aspect of the brain as it self-organizes over a protracted period. In other words, while both genomic and environmental factors shape the developing nervous system, another significant - though often neglected - contributor is th...

Brain development is underpinned by complex interactions between neural assemblies, driving structural and functional change. This neuroconstructivism (the notion that neural functions are shaped by these interactions) is core to some developmental theories. However, due to their complexity, understanding underlying developmental mechanisms is chal...

Inattention and hyperactivity are cardinal symptoms of Attention Deficit Hyperactivity Disorder (ADHD). These characteristics have also been observed across a range of other neurodevelopmental conditions, such as autism and dyspraxia, suggesting that they might best be studied across diagnostic categories. Here, we evaluated the associations betwee...

There is a concerted effort to build domain-general artificial intelligence in the form of universal neural network models with sufficient computational flexibility to solve a wide variety of cognitive tasks but without requiring fine-tuning on individual problem spaces and domains. To do this, models need appropriate priors and inductive biases, s...

In an attempt to better characterise the complexity of difficulties observed within developing populations, numerous data-driven techniques have been applied to large, mixed datasets. However, many have failed to incorporate the core role of developmental time in these approaches. That is, the typical course of change in behavioural features that o...

Brain networks exist within the confines of resource limitations. As a result, a brain network must overcome metabolic costs of growing and sustaining the network within its physical space, while simultaneously implementing its required information processing. To observe the effect of these processes, we introduce the spatially-embedded recurrent n...

Brain development can be viewed through many lenses and studied at many scales. However, multiple theoretical perspectives have argued that brain organisation develops via competitive interactions between its constituent units, dynamically over time. In this thesis, I focus on modelling these interactions. In Chapter 1, after providing an historica...

Background Behavioural and language difficulties co‐occur in multiple neurodevelopmental conditions. Our understanding of these problems has arguably been slowed by an overreliance on study designs that compare diagnostic groups and fail to capture the overlap across different neurodevelopmental disorders and the heterogeneity within them. Methods...

Inattention and hyperactivity are cardinal symptoms of Attention Deficit Hyperactivity Disorder (ADHD). These characteristics have also been observed across a range of other neurodevelopmental conditions, such as autism and dyspraxia, suggesting that they might best be studied across diagnostic categories. Here, we evaluated the associations betwee...

Early adversity can change educational, cognitive, and mental health outcomes. However, the neural processes through which early adversity exerts these effects remain largely unknown. We used generative network modelling of the mouse connectome to test whether unpredictable postnatal stress shifts the constraints that govern the formation of the st...

The quality of a child’s social and physical environment is a key influence on brain development, educational attainment and mental wellbeing. However, there still remains a mechanistic gap in our understanding of how environmental influences converge on changes in the brain’s developmental trajectory. In a sample of 145 children with structural di...

BACKGROUND Cranial dural arteriovenous fistulas with cortical venous drainage are rare lesions that can present with hemorrhage. A high rate of rebleeding in the early period following hemorrhage has been reported, but published long-term rates are much lower. No study has examined how risk of rebleeding changes over time. Our objective was to quan...

Economical efficiency has been a popular explanation for how networks organize themselves within the developing nervous system. However, the precise nature of the economic negotiations governing this self- organization remain unclear. We approach this problem by combining high-density microelectrode array (HD-MEA) recordings, which allow for detail...

Background Behavioural and language difficulties co-occur in multiple neurodevelopmental conditions. Our understanding of these problems has arguably been slowed by an overreliance on study designs that compare deficit/diagnostic groups and fail to capture the overlap across different neurodevelopmental disorders and the heterogeneity within them....

The formation of large-scale brain networks, and their continual refinement, represent crucial developmental processes that can drive individual differences in cognition and which are associated with multiple neurodevelopmental conditions. But how does this organization arise, and what mechanisms drive diversity in organization? We use generative n...

Network analytic methods that are ubiquitous in other areas, such as systems neuroscience, have recently been used to test network theories in psychology, including intelligence research. The network or mutualism theory of intelligence proposes that the statistical associations among cognitive abilities (e.g., specific abilities such as vocabulary...

Introduction Internal neurolysis (INL) is a surgical procedure where trigeminal nerve fibres are separated between the pons and porus trigeminus to relieve trigeminal neuralgia (TN). We report pain and functional outcomes to evaluate its safety and efficacy. Materials and methods Prospective cohort of all patients undergoing retrosigmoid craniotom...

Previous studies have identified localized associations between childhood environment – namely their socio-economic status (SES) – and particular neural structures. The primary aim of the current study was to test whether associations between SES and brain structure are widespread or limited to specific neural pathways. We employed advances in whol...

The emergence of large-scale brain networks, and their continual refinement, represent crucial developmental processes that can drive individual differences in cognition and which are associated with multiple neurodevelopmental conditions. But how does this organization arise, and what mechanisms govern the diversity of these developmental processe...

Network analytic methods that are ubiquitous in other areas, such as systems neuroscience, have recently been used to test network theories in psychology, including intelligence research. The network or mutualism theory of intelligence proposes that the statistical associations among cognitive abilities (e.g. specific abilities such as vocabulary o...

Objective: Although chronic subdural hematomas (cSDH) are often treated surgically it remains plausible that invasive treatment in elderly patients may have a negative effect on survival. The aim of this study was to characterize survival following neurosurgical intervention for cSDH in a selected cohort aged >90 years and to identify prognostic fa...

The quality of the social and physical environments that children experience, and are exposed to, is a key to educational attainment. Even if parental income and education do not necessarily determine children’s educational outcomes, but they shape the environments in which children live and learn. Children from deprived areas usually perform worse...

The emergence of large-scale brain networks, and their continual refinement, represent crucial developmental processes that can drive individual differences in cognition and which are associated with multiple neurodevelopmental conditions. But how does this organization arise, and what mechanisms govern the diversity of these developmental processe...

Background: Idiopathic intracranial hypertension (IIH) is a chronic condition characterised by raised intracranial pressure (ICP) in the absence of a known aetiology. IIH typically presents in overweight females of childbearing age. Surgical intervention for IIH involves diversion of cerebrospinal fluid (CSF), often by the placement of a shunt. Ex...

Dynamic connectivity in functional brain networks is a fundamental aspect of cognitive development, but we have little understanding of the mechanisms driving variability in these networks. Genes are likely to influence the emergence of fast network connectivity via their regulation of neuronal processes, but novel methods to capture these rapid dy...

Objectives External ventricular drain (EVD) dislodgement is common and can lead to significant morbidity and mortality. UK trial data suggests dislodgement as high as 12%. This study aimed to establish the range of methods used nationally and determine the most secure method in a porcine model. Design Survey and experimental study. Subjects 23 ne...

Cognitive processing depends on the temporal co-ordination of functional brain networks. This fundamental aspect of neurophysiology potentially bridges the genetic regulation of neuronal activity and developmental cognitive impairments. We investigated brain network dynamics in a neurodevelopmental disorder of known genetic origin, by comparing ind...

Distinct changes can be observed in the odor of human excretions during health and disease. Identifying underlying volatile metabolites responsible for these odorous changes can be correlated with the pathological process within the body. Advances in the technology have enabled us to interpret the volatile signature of these changes in the odor. Th...

Background: External ventricular drain (EVD) dislodgement is common and leads to significant morbidity and mortality. Many securement techniques to prevent this are described. There are, however, no objective studies comparing them. This study aimed to determine the most secure method of securing an EVD. Methods: A survey was distributed through...