Evidence of P3a During Sleep, a Process Associated With Intrusions Into Consciousness in the Waking State

The present study examines processes associated with intrusions into consciousness during an unconscious state, natural sleep. The definition of sleep is still much debated. Almost all researchers agree that sleep onset represents a gradual loss of consciousness of the external environment. For sleep to be beneficial, it needs to remain as undisturbed as possible. Nevertheless, unlike other unconsciousness states, sleep is reversible. For purposes of survival, it is critical that the sleeper be able to “detect” and perhaps become conscious of highly relevant biological or personal information. Therefore, even in sleep, the brain must decide whether a new incoming stimulus is relevant and if so, may require an arousal to wakefulness, or whether it is irrelevant and can be gated to prevent disruption of sleep. Event-related potentials (ERPs) were used to measure the extent processing of auditory stimuli some of which elicited an ERP component, the P3a, in the waking state. The P3a is associated with processes resulting in the interruption of frontal central executive, leading to conscious awareness. Very little research has focused on the occurrence of the P3a during sleep. A multi-feature paradigm was used to examine the processing of a frequently occurring “standard” stimulus and six rarely occurring different “deviant” stimuli during wakefulness, NREM, and REM sleep. A P3a was elicited by novel environmental sounds and white noise bursts in the waking state, replicating previous studies. Other deviant stimuli (changes in pitch, intensity, duration) failed to do so. The ERPs indicated that processing of the stimuli that did not elicit a P3a in wakefulness were much inhibited during both NREM and REM sleep. Surprisingly, those deviants that did elicit a P3a in wakefulness continued to do so in stage N2 and REM sleep. The subject did not, however, awaken. These results suggest processes leading to consciousness in wakefulness may still remain active during sleep possibly allowing subjects to act on potentially highly relevant input. This may also explain how sleep can be reversed if the stimulus input is sufficiently critical

Personal semantics: Is it distinct from episodic and semantic memory? An electrophysiological study of memory for autobiographical facts and repeated events in honor of Shlomo Bentin

Declarative memory is thought to consist of two independent systems: episodic and semantic. Episodic memory represents personal and contextually unique events, while semantic memory represents culturally-shared, acontextual factual knowledge. Personal semantics refers to aspects of declarative memory that appear to fall somewhere in between the extremes of episodic and semantic. Examples include autobiographical knowledge and memories of repeated personal events. These two aspects of personal semantics have been studied little and rarely compared to both semantic and episodic memory. We recorded the event-related potentials (ERPs) of 27 healthy participants while they verified the veracity of sentences probing four types of questions: general (i.e., semantic) facts, autobiographical facts, repeated events, and unique (i.e., episodic) events. Behavioral results showed equivalent reaction times in all 4 conditions. True sentences were verified faster than false sentences, except for unique events for which no significant difference was observed. Electrophysiological results showed that the N400 (which is classically associated with retrieval from semantic memory) was maximal for general facts and the LPC (which is classically associated with retrieval from episodic memory) was maximal for unique events. For both ERP components, the two personal semantic conditions (i.e., autobiographical facts and repeated events) systematically differed from semantic memory. In addition, N400 amplitudes also differentiated autobiographical facts from unique events. Autobiographical facts and repeated events did not differ significantly from each other but their corresponding scalp distributions differed from those associated with general facts. Our results suggest that the neural correlates of personal semantics can be distinguished from those of semantic and episodic memory, and may provide clues as to how unique events are transformed to semantic memory

Characterising the novel MYB-TYK2 fusion gene in high-risk acute lymphoblastic leukaemia: oncogenic potential, effective therapeutic strategies and in vitro modelling of drug resistance mechanisms

A growing number of TYK2 activating alterations have been detected in acute lymphoblastic leukaemia (ALL) patients, including the MYB-TYK2 fusion gene. MYB-TYK2 was identified in a high risk (HR) Ph- ALL case and is associated with poor outcome. The transforming and leukaemogenic potential of activating TYK2 alterations, including those of MYB-TYK2, requires clarification in the ALL setting. Tyk2 is a member of the JAK family of tyrosine kinases and similar to JAK fusions, may result in activation of JAK/STAT signalling, and potentially be amenable to JAK inhibitor (JAKi) therapy. In depth characterisation of the underlying mechanisms resulting in leukaemogenesis are warranted and will inform drug response and targetability potential. Moreover, since the development of clinical resistance to targeted therapies such as JAKi, broad investigation of effective small molecule inhibitors (SMIs) is essential. Exploration of the possible modes of drug resistance following long-term treatment and importantly, how to circumvent resistance development, will provide alternative therapies for JAKi resistance in TYK2-altered patients. Hence, this study aimed to 1) identify and characterise the mechanisms of oncogenicity and activated downstream signalling pathways in MYB-TYK2 harbouring cells, 2) assess the efficacy of targeted therapeutics against MYB-TYK2 altered disease and 3) determine the possible mechanisms of resistance to candidate therapy via in vitro models to inform alternative therapeutic approaches to overcome possible disease persistence and resistance. In vitro and in vivo models were used to comprehensively model MYB-TYK2-altered disease. Depending on the downstream experiments, either cytokine-dependent Ba/F3 pro-B cells, Arf-/- pre-B primary mouse cells or NIH-3T3 cells, were retrovirally transduced with the MYB-TYK2 fusion gene isolated from an ALL patient. The targetability of the MYB-TYK2 fusion gene was investigated via high throughput screen (HTS) of 3088 cytotoxic and targeted compounds with further validation of candidates in pre-clinical models. Resistance modelling of the candidate JAKi cerdulatinib was achieved by gradual exposure of cells expressing the MYB-TYK2 fusion gene to increasing concentrations of cerdulatinib over several months. This study elucidated the transformative ability and functional significance of the MYB-TYK2 fusion gene to induce B-ALL in vivo. Results demonstrated the constitutive activation of JAK/STAT signalling due to expression of the MYB-TYK2 fusion gene. HTS identified the HDACi, vorinostat and the HSP90i, tanespimycin as effective targeted therapeutics against cells harbouring the MYB-TYK2 fusion gene in vitro. In addition, the sensitivity of the MYB-TYK2 fusion gene was established to the novel JAKi, cerdulatinib. Both vorinostat and cerdulatinib demonstrated anti-leukaemic effects in pre-clinical in vivo models of the MYB-TYK2 altered disease, resulting in a significantly reduced leukaemic burden. Further investigations into resistance following long-term exposure to cerdulatinib, indicated the likelihood of resistance to cerdulatinib therapy. Results suggested a persistent JAK/STAT activation despite Tyk2 inhibition via possible heterodimer formation with Jak1 and thus, Myb-Tyk2 trans-phosphorylation. This persistent signalling, however, was successfully reversed by HDACi treatment. Overall, the findings presented in this thesis demonstrate, for the first time, the driving potential of TYK2 activating alterations. Through robust modelling and rigorous testing of effective SMIs, this study identified novel therapeutic strategies using vorinostat and cerdulatinib against MYB-TYK2-altered disease. These results provide strong evidence for re-purposing of these drugs as an addition to a chemotherapy backbone for treatment of this highly aggressive subtype of B-ALL. Further insights into the resistance profile in response to cerdulatinib, as well as incorporation of targeted therapeutics to overcome this resistance, will assist high-risk patients in a clinical setting. These findings contribute to precision medicine approaches and will ultimately improve outcome and long-term survival for patients harbouring activating TYK2 alterations.Thesis (Ph.D.) -- University of Adelaide, Adelaide Medical School, 202

The Recording and Quantification of Event-Related Potentials: I. Stimulus Presentation and Data Acquisition

Event-related potentials (ERPs) are the changes in the ongoing electrical activity of the brain (the EEG) that are elicited by either an external physical stimulus or an internal psychological “event”. This article provides a tutorial review of the methods used for the collection of ERP data. Because ERPs are influenced by both stimulus parameters and the mental state of the subject (what the subject is “doing”), precise control over how the stimulus is presented and how the subject’s response is monitored must be described. ERPs are generally recorded from electrodes placed on the scalp. How the electrodes are placed (the montage) and the choice of the reference to which the electrical activity of the scalp are compared will have a large influence on the results. Electrodes will also pick up extraneous artifact or “noise”. Methods to reduce this noise are described. ERPs provide high temporal resolution of the extent of information processing allowing researchers to access to both sensory and cognitive processes involved in complex decision-making

The Recording and Quantification of Event-Related Potentials: I. Stimulus Presentation and Data Acquisition

Event-related potentials (ERPs) are the changes in the ongoing electrical activity of the brain (the EEG) that are elicited by either an external physical stimulus or an internal psychological “event”. This article provides a tutorial review of the methods used for the collection of ERP data. Because ERPs are influenced by both stimulus parameters and the mental state of the subject (what the subject is “doing”), precise control over how the stimulus is presented and how the subject’s response is monitored must be described. ERPs are generally recorded from electrodes placed on the scalp. How the electrodes are placed (the montage) and the choice of the reference to which the electrical activity of the scalp are compared will have a large influence on the results. Electrodes will also pick up extraneous artifact or “noise”. Methods to reduce this noise are described. ERPs provide high temporal resolution of the extent of information processing allowing researchers to access to both sensory and cognitive processes involved in complex decision-making

The Recording and Quantification of Event-Related Potentials: II. Signal Processing and Analysis

Event-related potentials are an informative method for measuring the extent of information processing in the brain. The voltage deflections in an ERP waveform reflect the processing of sensory information as well as higher-level processing that involves selective attention, memory, semantic comprehension, and other types of cognitive activity. ERPs provide a non-invasive method of studying, with exceptional temporal resolution, cognitive processes in the human brain. ERPs are extracted from scalp-recorded electroencephalography by a series of signal processing steps. The present tutorial will highlight several of the analysis techniques required to obtain event-related potentials. Some methodological issues that may be encountered will also be discussed

The Recording and Quantification of Event-Related Potentials: II. Signal Processing and Analysis

Event-related potentials are an informative method for measuring the extent of information processing in the brain. The voltage deflections in an ERP waveform reflect the processing of sensory information as well as higher-level processing that involves selective attention, memory, semantic comprehension, and other types of cognitive activity. ERPs provide a non-invasive method of studying, with exceptional temporal resolution, cognitive processes in the human brain. ERPs are extracted from scalp-recorded electroencephalography by a series of signal processing steps. The present tutorial will highlight several of the analysis techniques required to obtain event-related potentials. Some methodological issues that may be encountered will also be discussed

On Computing Average Common Substring Over Run Length Encoded Sequences

The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS of a sequence X[1, x] w.r.t. another sequence Y[1, y] is ACS(X, Y) = 1 x Σ i=1 x max j lcp(X[i, x], Y[j, y]) The lcp(·, ·) of two input sequences is the length of their longest common prefix. The ACS can be computed in O(n) space and time, where n = x + y is the input size. The compressed string matching is the study of string matching problems with the following twist: the input data is in a compressed format and the underling task must be performed with little or no decompression. In this paper, we revisit the ACS problem under this paradigm where the input sequences are given in their run-length encoded format. We present an algorithm to compute ACS(X, Y) in O(N logN) time using O(N) space, where N is the total length of sequences after run-length encoding