Biology subjects

Parish, G.

Publications and source records attributed to Parish, G..

4 recordsLinked to original sources

bioRxiv2026

Comparing re-referencing methods for human intracranial EEG

Stereo-electroencephalography (SEEG) involves the implantation of depth electrodes in the brain to monitor epileptic seizures for surgical feasibility. As the electrodes advance into deeper limbic structures, the macro contacts distributed along the shaft record electrical activity from more lateral sites, while a bundled array of microwires simultaneously captures highly localised signals from the tip of the electrode. In a clinical setting these electrical signals are recorded relative to a reference signal, which may be sub-optimal for subsequent analyses that are unrelated to clinical objectives. Therefore, a secondary re-referencing operation is often undertaken to transform the signal in relation to a specific hypothesis. Despite a recent surge in SEEG studies, comparative studies on the much-understudied issue of re-referencing are sparse. Here, we analyse data collected from 16 human patients during an episodic memory task and comparatively apply a range of re-referencing methods to both macro contact and micro-wire data. We find that the choice of method changes the proportion of trials that survive artefact rejection, low frequency power, and the aperiodic background against which that power is read. In the hippocampal recordings, however, no method differed from any other in the size of a memory effect in power or spike-field coherence. This early transformative decision therefore bears on how the signal is described. We found no evidence that it changes the detectability of the behavioural effects tested here, and no method reversed the direction of a memory effect.

neuroscience↗

bioRxiv2026

Exploring the antibiotic-producing capabilities of Canadian High Arctic bacteria

Microbial communities in harsh environments such as the Canadian high Arctic, remain a relatively unexplored source of antimicrobial natural products. In this study, we developed a pipeline for screening and evaluating bacterial isolates cultured from 23 Canadian high Arctic soil, sediment, and active-layer permafrost samples to discover antibacterial compounds. The pipeline incorporated an undergraduate studentsourcing program and produced created a collection of over 350 bacterial isolates with preliminary antibacterial activity. Following dereplication, whole genome sequencing and secondary screening by co-culture assays, five isolates were prioritized to test crude extracts for antibacterial activity. Among bioactive crude extracts from these isolates, the Pseudomonas isolate with the most potent activity against S. aureus was analyzed. Using liquid chromatography bioactivity guided fractionation, we identified a potential bioactive compound known as koreenceine A, a compound previously only isolated from a Pseudomonas from temperate soil and involved in gene expression of other their microbial community. Here we expanded the known antibiotic activity of koreenceine A and confirmed that a {triangleup}kecBCD genetic knockout of the putative biosynthetic gene cluster significantly abrogated the antibacterial activity.

microbiology↗

bioRxiv2020

Modelling the Replay of Dynamic Memories from Cortical Alpha Oscillations with the Sync-Fire / deSync Model.

We here propose a neural network model to explore how neural oscillations might regulate the replay of memory traces. We simulate the encoding and retrieval of a series of events, where temporal sequences are uniquely identifiable by analysing population activity, as several recent EEG/MEG studies have shown. Our model comprises three parts, each considering distinct hypotheses. A cortical region actively represents sequences through the disruption of an intrinsically generated alpha rhythm, where a desynchronisation marks information-rich operations as the literature predicts. A binding region converts each event into a discrete index, enabling repetitions through a sparse encoding of events. We also instantiate a temporal region, where an oscillatory "ticking-clock" made up of hierarchical synfire chains discretely indexes a moment in time. By encoding the absolute timing between events, we show how one can use cortical desynchronisations to dynamically detect unique temporal signatures as they are replayed in the brain.

neuroscience↗

bioRxiv2017

The Sync/deSync model: How a synchronized hippocampus and a de-synchronized neocortex code memories

Neural oscillations are important for memory formation in the brain. The de-synchronisation of Alpha (10Hz) oscillations in the neo-cortex has been shown to predict successful memory encoding and retrieval. However, when engaging in learning, it has been found that the hippocampus synchronises in Theta (4Hz) oscillations, and that learning is dependent on the phase of Theta. This inconsistency as to whether synchronisation is good for memory formation leads to confusion over which oscillations we should expect to see and where during learning paradigm experiments. This paper seeks to respond to this inconsistency by presenting a neural network model of how a well-functioning learning system could exhibit both of these phenomena, i.e. desynchronization of alpha and synchronisation of theta during successful memory encoding.\n\nWe present a spiking neural network (the Sync/deSync model) of the neo-cortical and hippocampal system. The simulated hippocampus learns through an adapted spike-time dependent plasticity rule, in which weight change is modulated by the phase of an extrinsically generated theta oscillation. Additionally, a global passive weight decay is incorporated, which is also modulated by theta phase. In this way, the Sync/deSync model exhibits theta phase-dependent long-term potentiation and long-term depression. We simulated a learning paradigm experiment and compared the oscillatory dynamics of our model with those observed in single-cell and scalp-EEG studies of the medial temporal lobe. Our Sync/deSync model suggests that both the de-synchronisation of neo-cortical Alpha and the synchronisation of hippocampal Theta are necessary for successful memory encoding and retrieval.\n\nSignificance statementA fundamental question is the role of rhythmic activation of neurons, i.e. how their firing oscillates between high and low rates. A particularly important question is how oscillatory dynamics between the neo-cortex and hippocampus contribute to memory formation. We present a spiking neural-network model of such memory formation, with the central ideas that 1) in neo-cortex, neurons need to break-out of an alpha oscillation in order to represent a stimulus (i.e. alpha desynchronises), while 2) in hippocampus, the firing of neurons at theta facilitates formation of memories (i.e. theta synchronises). Accordingly, successful memory formation is marked by reduced neo-cortical alpha and increased hippocampal theta. This pattern has been observed experimentally and gives our model its name - the Synch/deSynch model.

neuroscience↗