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De Vos, M.

Publications and source records attributed to De Vos, M..

6 recordsLinked to original sources

Brain age as an estimator of neurodevelopmental outcome: A deep learning approach for neonatal cot-side monitoring

The preterm neonate can experience stressors that affect the rate of brain maturation and lead to long-term neurodevelopmental deficits. However, some neonates who are born early follow normal developmental trajectories. Extraction of data from electroencephalography (EEG) signals can be used to calculate the neonates brain age which can be compared to their true age. Discrepancies between true age and brain age (the brain age delta) can then be used to quantify maturational deviation, which has been shown to correlate with long-term abnormal neurodevelopmental outcomes. Nevertheless, current brain age models that are based on traditional analytical techniques are less suited to clinical cot-side monitoring due to their dependency on long-duration EEG recordings, the need to record activity across multiple EEG channels, and the manual calculation of predefined EEG features which is time-consuming and may not fully capture the wealth of information in the EEG signal. In this study, we propose an alternative deep-learning approach to determine brain age, which operates directly on the EEG, using a Convolutional Neural Network (CNN) block based on the Inception architecture (called Sinc). Using this deep-learning approach on a dataset of preterm infants with normal neurodevelopmental outcomes (where we assume brain age = postmenstrual age), we can calculate infant brain age with a Mean Absolute Error (MAE) of 0.78 weeks (equivalent to a brain age estimation error for the infant within +/- 5.5 days of their true age). Importantly, this level of accuracy can be achieved by recording only 20 minutes of EEG activity from a single channel. This compares favourably to the degree of accuracy that can be achieved using traditional methods that require long duration recordings (typically >2 hours of EEG activity) recorded from a higher density 8-electrode montage (MAE = 0.73 weeks). Importantly, the deep learning models brain age deltas also distinguish between neonates with normal and severely abnormal outcomes (Normal MAE = 0.71 weeks, severely abnormal MAE = 1.27 weeks, p=0.02, one-way ANOVA), making it highly suited for potential clinical applications. Lastly, in an independent dataset collected at an independent site, we demonstrate the models generalisability in age prediction, as accurate age predictions were also observed (MAE of 0.97 weeks). HighlightsO_LIPreterm stress exposure leads to long-term neurodevelopmental deficits C_LIO_LIDeficits are quantifiable using EEG-based brain age prediction errors C_LIO_LIOur deep-learning solution for brain age prediction outperforms previous approaches C_LIO_LIPredictions are achieved with only 20 mins EEG and a single bipolar channel C_LIO_LIPrediction errors correlate with long-term Bayley scale neurodevelopmental outcomes C_LI

neuroscience↗

The role of copper resistance in Mycobacterium tuberculosis pathogenesis

Despite the development of new drugs and social interventions, tuberculosis remains a leading cause of mortality. This burden falls disproportionately on developing countries, particularly those where the incidence of HIV is high. In the Western Cape, South Africa, we have identified and isolated two Beijing family strains of Mycobacterium tuberculosis that, despite few differences at a genomic level, differ greatly in their severity of disease caused, providing an opportunity to study virulence in this organism. The aim of this study was to identify differences at a genomic and transcriptomic level that may identify the cause of the different virulence levels observed in the two isolates. The isolates were compared at the transcriptome level under four different growth conditions including oxidative stress. In comparing the transcriptome of the two isolates, an operon containing genes involved in the production of molybdenum cofactor that showed consistently lower levels of expression in the hypervirulent isolate was identified. A copper sensing transcriptional regulator was identified as the most probable regulator, and we found that the Cso operon which it is known to regulate was similarly differentially expressed in the strains. The production of molybdenum cofactor is effected in two ways by copper levels. Through the independent insertion of copper into molybdopterin (MPT), and destabilisation of Fe-S clusters. As MoaA3 contains a Fe-S cluster that is known to be destabilised by copper, and a number of copper sensitive genes are likewise found differentially expressed, it is likely that the strains differ in terms of their levels of resistance to copper. It is therefore hypothesised that the differences in virulence are as a result of different levels of resistance to phagosome copper overload, and the mechanism by which copper levels are linked to the production of molybdenum cofactor is described. Author summaryIn this article, we describe the differences in gene expression of two closely related strains of Mycobacterium tuberculosis isolated in the Western Cape of South Africa that differ in the severity of disease that they cause. We compared the strains at a genomic and transcriptomic level, and in doing so, we discovered a set of molybdenum cofactor genes regulated by a copper sensing transcription factor that came up in all datasets. Further genes linked to copper response were identified, providing greater evidence that the difference between the two strains was the manner in which they responded to copper stress. Phagocytes are known to exploit high levels of copper to kill intracellular bacteria, suggesting an important link between copper and disease. We conclude that resistance to copper toxicity is the most probable reason for the relative increase in virulence, and describe the regulatory relationship between copper levels and molybdenum cofactor synthesis.

microbiology↗

Reduced interhemispheric and increased intrahemispheric connectivity in schizophrenia brain networks

IntroductionBrain connectivity is disturbed in schizophrenia, both during resting state and during active tasks. Schizophrenia is characterised by a corpus callosum pathology and an inability to suppress overstimulation, both of which relate to this disturbed connectivity. We wanted to verify whether network analysis on EEG sensor level can reveal the corpus callosum pathology in schizophrenia.\n\nMethodsWe measured 62-channel EEG on 46 schizophrenia patients and 43 healthy controls during eyes-closed and eyes-open resting-state, mismatch negativity and visual and auditory oddball. We assessed connectivity through correlation, coherence and directed transfer function (DTF) in the delta, theta, alpha, low- and high beta bands.\n\nResultsThe coherence and the DTF picked up a consistent pattern of reduced interhemispheric and enhanced intrahemispheric connectivity strength in schizophrenia in the alpha and beta band. This disturbance pattern appeared across all paradigms in the parietal and the occipital region and was generally more pronounced in the right hemisphere.\n\nConclusionsThis is the first study to use multiple similarity measures and different tasks to confirm disturbed brain connectivity on EEG sensor level. We hypothesise that the interhemispheric reductions reflect transcallosal disconnection, while the intrahemispheric increases indicate the inability to suppress the response to stimuli.

neuroscience↗

Impact of Different Acoustic Components on EEG-based Auditory Attention Decoding in Noisy and Reverberant Conditions

Recently, a least-squares-based method has been proposed to decode auditory attention from single-trial EEG recordings for an acoustic scenario with two competing speakers. This method aims at reconstructing the attended speech envelope from the EEG recordings using a trained spatio-temporal filter. While the performance of this method has been mainly studied for noiseless and anechoic acoustic conditions, it is important to fully understand its performance in realistic noisy and reverberant acoustic conditions. In this paper, we investigate auditory attention decoding (AAD) using EEG recordings for different acoustic conditions (anechoic, reverberant, noisy, and reverberant-noisy). In particular, we investigate the impact of different acoustic conditions for AAD filter training and for decoding. In addition, we investigate the influence on the decoding performance of the different acoustic components (i.e. reverberation, background noise and interfering speaker) in the reference signals used for decoding and the training signals used for computing the filters. First, we found that for all considered acoustic conditions it is possible to decode auditory attention with a decoding performance larger than 90%, even when the acoustic conditions for AAD filter training and for decoding are different. Second, when using reference signals affected by reverberation and/or background noise, a comparable decoding performance as when using clean reference signals can be obtained. In contrast, when using reference signals affected by the interfering speaker, the decoding performance significantly decreases. Third, the experimental results indicate that it is even feasible to use training signals affected by reverberation, background noise and/or the interfering speaker for computing the filters.

neuroscience↗

Online detection of auditory attention with mobile EEG: closing the loop with neurofeedback

Auditory attention detection (AAD) is promising for use in auditory-assistive devices to detect to which sound the user is attending. Being able to train subjects in achieving high AAD performance would greatly increase its application potential. In order to do so an acceptable temporal resolution and online implementation are essential prerequisites. Consequently, users of an online AAD can be presented with feedback about their performance. Here we describe two studies that investigate the effects of online AAD with feedback. In the first study, we implemented a fully automated closed-loop system that allows for user-friendly recording environments. Subjects were presented online with visual feedback on their ongoing AAD performance. Following these results we implemented a longitudinal case study in which two subjects were presented with AAD sessions during four weeks. The results prove the feasibility of a fully working online (neuro)feedback system for AAD decoding. The detected changes in AAD for the feedback subject during and after training suggest that changes in AAD may be achieved via training. This is early evidence of such training effects and needs to be confirmed in future studies to evaluate training of AAD in more detail. Finally, the large number of sessions allowed to examine the correlation between the stimuli (i.e. acoustic stories) and AAD performance which was found to be significant. Future studies are suggested to evaluate their acoustic stimuli with care to prevent spurious associations.

neuroscience↗

The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only.

The ability to quickly obtain accurate genome sequences of eukaryotic pathogens at low costs provides a tremendous opportunity to identify novel targets for therapeutics, develop pesticides with increased target specificity and breed for resistance in food crops. Here, we present the first report of the ~54 MB eukaryotic genome sequence of Rhizoctonia solani, an important pathogenic fungal species of maize, using nanopore technology. Moreover, we show that optimizing the strategy for wet-lab procedures aimed to isolate high quality and ultra-pure high molecular weight (HMW) DNA results in increased read length distribution and thereby allowing generation of the most contiguous genome assembly for R. solani to date. We further determined sequencing accuracy and compared the assembly to short-read technologies. With the current sequencing technology and bioinformatics tool set, we are able to deliver an eukaryotic fungal genome at low cost within a week. With further improvements of the sequencing technology and increased throughput of the PromethION sequencer we aim to generate near-finished assemblies of large and repetitive plant genomes and cost-efficiently perform de novo sequencing of large collections of microbial pathogens and the microbial communities that surround our crops.

genomics↗