Biology subjects

Bennett, M.

Publications and source records attributed to Bennett, M..

32 records · Page 2Linked to original sources

bioRxiv2021

Computer-Assisted Mitotic Count Using a Deep Learning-based Algorithm Improves Inter-Observer Reproducibility and Accuracy in canine cutaneous mast cell tumors

The mitotic count (MC) is an important histological parameter for prognostication of malignant neoplasms. However, it has inter- and intra-observer discrepancies due to difficulties in selecting the region of interest (MC-ROI) and in identifying/classifying mitotic figures (MFs). Recent progress in the field of artificial intelligence has allowed the development of high-performance algorithms that may improve standardization of the MC. As algorithmic predictions are not flawless, the computer-assisted review by pathologists may ensure reliability. In the present study we have compared partial (MC-ROI preselection) and full (additional visualization of MF candidate proposal and display of algorithmic confidence values) computer-assisted MC analysis to the routine (unaided) MC analysis by 23 pathologists for whole slide images of 50 canine cutaneous mast cell tumors (ccMCTs). Algorithmic predictions aimed to assist pathologists in detecting mitotic hotspot locations, reducing omission of MF and improving classification against imposters. The inter-observer consistency for the MC significantly increased with computer assistance (interobserver correlation coefficient, ICC = 0.92) compared to the unaided approach (ICC = 0.70). Classification into prognostic stratifications had a higher accuracy with computer assistance. The algorithmically preselected MC-ROIs had a consistently higher MCs than the manually selected MC-ROIs. Compared to a ground truth (developed with immunohistochemistry for phosphohistone H3), pathologist performance in detecting individual MF was augmented when using computer assistance (F1-score of 0.68 increased to 0.79) with a reduction in false negatives by 38%. The results of this study prove that computer assistance may lead to a more reproducible and accurate MCs in ccMCTs.

pathology↗

bioRxiv2021

Resource Profile and User Guide of the Polygenic Index Repository

Polygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is rapidly growing. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs prediction accuracies, we constructed them using genome-wide association studies--some of which are novel--from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the "additive SNP factor." Regressions in which the true regressor is the additive SNP factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available.

genomics↗

bioRxiv2021

Unravelling the Physiological Correlates of Mental Workload Variations in Tracking and Collision Prediction Tasks: Implications for Air Traffic Controllers

ObjectiveWe have designed tracking and collision prediction tasks to elucidate the differences in the physiological response to the workload variations in basic ATC tasks to untangle the impact of workload variations experienced by operators working in a complex ATC environment. BackgroundEven though several factors influence the complexity of ATC tasks, keeping track of the aircraft and preventing collision are the most crucial. MethodsPhysiological measures, such as electroencephalogram (EEG), eye activity, and heart rate variability (HRV) data, were recorded from 24 participants performing tracking and collision prediction tasks with three levels of difficulty. ResultsThe neurometrics of workload variations in the tracking and collision prediction tasks were markedly distinct, indicating that neurometrics can provide insights on the type of mental workload. The pupil size, number of blinks and HRV metric, root mean square of successive difference (RMSSD), varied significantly with the mental workload in both these tasks in a similar manner. ConclusionOur findings indicate that variations in task load are sensitively reflected in physiological signals, such as EEG, eye activity and HRV, in these basic ATC-related tasks. ApplicationThese findings have applicability to the design of future mental workload adaptive systems that integrate neurometrics in deciding not just when but also what to adapt. Our study provides compelling evidence in the viability of developing intelligent closed-loop mental workload adaptive systems that ensure efficiency and safety in ATC and beyond. PrecisThis article identifies the physiological correlates of mental workload variation in basic ATC tasks. The findings assert that neurometrics can provide more information on the task that contributes to the workload, which can aid in the design of intelligent mental workload adaptive system.

neuroscience↗

bioRxiv2021

Genome-scale metabolic modelling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism.

Parageobacillus thermoglucosidasius represents a thermophilic, facultative anaerobic bacterial chassis, with several desirable traits for metabolic engineering and industrial production. To further optimize strain productivity, a systems level understanding of its metabolism is needed, which can be facilitated by a genome-scale metabolic model. Here, we present p-thermo, the most complete, curated and validated genome-scale model (to date) of Parageobacillus thermoglucosidasius NCIMB 11955. It spans a total of 890 metabolites, 1175 reactions and 917 metabolic genes, forming an extensive knowledge base for P. thermoglucosidasius NCIMB 11955 metabolism. The model accurately predicts aerobic utilization of 22 carbon sources, and the predictive quality of internal fluxes was validated with previously published 13C-fluxomics data. In an application case, p-thermo was used to facilitate more in-depth analysis of reported metabolic engineering efforts, giving additional insight into fermentative metabolism. Finally, p-thermo was used to resolve a previously uncharacterised bottleneck in anaerobic metabolism, by identifying the minimal required supplemented nutrients (thiamin, biotin and iron(III)) needed to sustain anaerobic growth. This highlights the usefulness of p-thermo for guiding the generation of experimental hypotheses and for facilitating data-driven metabolic engineering, expanding the use of P. thermoglucosidasius as a high yield production platform.

microbiology↗

bioRxiv2020

A multiplexed work-flow for absolute quantification of Klebsiella oxytoca Nif proteins

Global imbalances of the nitrogen cycle are increasingly recognized as a major challenge to human development, and are exacerbated by the use of synthetic inorganic fertilizers. Biotechnology alternatives to inorganic fertilizers include biofertilisation from nitrogen fixing bacteria (diazotrophs), expressing nitrogenase and auxiliary genes (nif genes). In order to directly quantify all twenty Nif proteins through multiple reaction monitoring (MRM) MS, we established a high throughput pipeline to generate a set of Klebsiella oxytoca Nif protein QconCATs as quantotypic standards. A stringent validation of the pipeline and QconCATs application with regards to isotopic labelling efficiency (100%), limits of detection and quantification, analyte to internal standard concentration boundaries was used for optimisation. Using three QconCATs for the measurement of 20 likely low, middle and high Nif protein abundances enabled detection of all Nif proteins, 19 of which could be accurately quantified and their variation over time monitored. Stoichiometries between Klebsiella oxytoca Nif proteins and changes between early and late transition into diazotrophy suggest i) a temporal regulation of nif gene cluster expression that may be linked to nitrogenase expression and maturation; ii) vast disparities in Nif protein abundances and iii) high dependency on the nifLA master regulator pair for nif gene expression.

biochemistry↗

bioRxiv2019

Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports its Classification as a Novel Species

Hantaviruses are a diverse group of single-stranded, negative-sensed RNA viruses, known to cause sporadic outbreaks of potentially fatal human disease. To date, only two Orthohantavirus species have been detected in the UK - Seoul virus and Tatenale. Whilst Seoul is known to be pathogenic in humans, only partial fragments of Tatenale have been recovered, precluding any accurate analysis of its phylogeny or potential pathogenicity. To overcome this shortfall we used a degenerate primer PCR method to identify Tatenale-infection in rodents living in two separate locations in the UK. PCR positive samples were then subjected to either unbiased high-throughput sequencing or overlapping PCR product sequencing to recover the complete coding sequence of the Tatenale virus. This analysis provided in-depth insight into the evolutionary origins of this recently identified UK Orthohantavirus and unequivocally showed that Tatenale virus meets the established criteria for classification as a novel species. Crucially, our data will facilitate in vitro investigation into the zoonotic potential of Tatenale virus.

microbiology↗

bioRxiv2019

Hyperactive/impulsive and inattention symptoms are associated with reduced ERP activity during different reward processing stages: Evidence from the electrophysiological Monetary Incentive Delay Task in adult ADHD

Hyperactivity/impulsivity and inattention are core symptoms dimensions in attention-deficit/hyperactivity disorder. Some approaches suggest that these symptoms arise from deficits in the ability to anticipate and process rewards. However, evidence is equivocal with regard to ADHD-related differences in brain activity during reward processing. The aim of this study was to investigate when, and how, reward-related ERP activity was associated with hyperactive/impulsive symptoms and inattention symptoms. Adults with ADHD (n=34) and matched comparison participants (n=36) completed an electrophysiological version of the Monetary Incentive Delay task. This task separates reward processing into two stages-namely, an anticipation stage and a delivery stage. During the anticipation stage, visual cues signalled a possible monetary incentive (i.e. a reward or loss). After a brief delay, the delivery stage began, and incentives were delivered contingent on a speeded button-press. Electroencephalogram activity was simultaneously sampled and incentive-related event relate potentials (ERPs) calculated. These data were then analysed by calculating multiple regression models, at each sample point, wherein the correlation between incentive-related ERPs and ADHD symptoms was estimated. Linear and curvilinear associations between ERP activity and ADHD symptoms were tested in each regression mode. Findings suggest that ADHD symptoms were associated ERP activity at different reward processing stages. Hyperactive/impulsive symptoms were associated with reduced ERP activity during the initial anticipation of rewards from 224-329 ms post-reward cue. Inattention symptoms were associated with reduced ERP activity during the initial delivery of rewards from 251-280 ms post-reward onset. Finally, extreme ends of hyperactive/impulsive and inattention symptoms were associated with reduced ERP activity towards the end of the anticipation stage from 500 ms post-reward cue onwards. These results support the idea that reward processing is disrupted in ADHD while also shedding new light on the dynamic relationship between ADHD symptom dimensions and the neurological mechanisms of reward processing.

neuroscience↗

bioRxiv2019

Contralateral Delay Activity is not sensitive to cognitive decline in older adults at risk of Mild Cognitive Impairment.

Contralateral delay activity (CDA) has been proposed as a pre-clinical marker for Mild Cognitive Impairment (MCI). However, existing evidence is limited to one study with a small sample size (n=12 per group). Our aim was to compare CDA amplitudes in a larger sample of low- and high-risk older adult groups (n=35 per group). As expected, behavioural performance decreased as the number of memory items increased, and the low-risk group out-performed the high-risk group. However, we found no differences in CDA amplitudes across groups, indicating that WM capacity increased irrespective of risk-level. These findings suggest that the CDA is not a sensitive marker of MCI risk. More broadly, our results highlight the difficulty in identifying at-risk individuals, particularly as MCI is a heterogeneous, unstable condition. Future research should prioritise longitudinal approaches in order to track the progression of the CDA and its association with cognitive decline in later life.

neuroscience↗

bioRxiv2019

EEG spectral power, but not theta/beta ratio, is a neuromarker for adult ADHD

BackgroundAdults with attention-deficit/hyperactivity disorder (ADHD) have been described as having altered resting-state electroencephalographic (EEG) spectral power and theta/beta ratio (TBR). However, a recent review (Pulini et al. 2018) identified methodological errors in neuroimaging, including EEG, ADHD classification studies. Therefore, the specific EEG neuromarkers of adult ADHD remain to be identified, as do the EEG characteristics that mediate between genes and behavior (mediational endophenotypes).\n\nMethodsResting-state eyes-open and eyes-closed EEG were measured from 38 adults with ADHD, 45 first-degree relatives of people with ADHD and 51 unrelated controls. A machine learning classification analysis using penalized logistic regression (Elastic Net) examined if EEG spectral power (1-45 Hz) and TBR could classify participants into ADHD, first-degree relatives and/or control groups. Random-label permutation was used to quantify any bias in the analysis.\n\nResultsEyes-open absolute and relative EEG power distinguished ADHD from control participants (area under receiver operating characteristic = .71-.77). The best predictors of ADHD status were increased power in delta, theta and low-alpha over centro-parietal regions, and in frontal low-beta and parietal mid-beta. TBR did not classify ADHD status. Elevated eyes-open power in delta, theta, low-alpha and low-beta distinguished first-degree relatives from controls (area under receiver operating characteristic = .68-.72), suggesting that these features may be a mediational endophenotype for adult ADHD.\n\nConclusionsResting-state EEG spectral power may be a neuromarker and mediational endophenotype of adult ADHD. These results did not support TBR as a diagnostic neuromarker for ADHD. It is possible that TBR is a characteristic of childhood ADHD.

neuroscience↗

bioRxiv2019

Validation of new tools to identify expanded repeats: an intronic pentamer expansion in RFC1 causes CANVAS

Genomic technologies such as Next Generation Sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)11 short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS families and identified a core ancestral haplotype, estimated to have arisen in Europe over twenty-five thousand years ago. WGS of the four RFC1 negative CANVAS families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders.

genetics↗

bioRxiv2018

A network of transcriptional repressors mediates auxin response specificity

INTRODUCTORY PARAGRAPHThe regulation of signalling capacity plays a pivotal role in setting developmental patterns in both plants and animals (1). The hormone auxin is a key signal for plant growth and development that acts through the AUXIN RESPONSE FACTOR (ARF) transcription factors (2). A subset of these ARFs comprises transcriptional activators of target genes in response to auxin, and are essential for regulating auxin signalling throughout the plant lifecycle (3). While ARF activators show tissue-specific expression patterns, it is unknown how their expression patterns are established. Chromatin modifications and accessibility studies revealed the chromatin of loci encoding ARF activators is constitutively open for transcription. Using a high-throughput yeast one-hybrid (Y1H) approach, we discovered a network of transcriptional regulators of ARF activator genes from Arabidopsis thaliana. Expression analyses demonstrated that the majority of these regulators act as repressors of ARF transcription in planta. Our observations support a scenario where the default configuration of open chromatin enables a network of transcriptional repressors to shape the expression pattern of ARF activators and provide specificity in auxin signalling output throughout development.

plant biology↗

bioRxiv2018

Nucleosome remodelling at origins of Global Genome-Nucleotide Excision Repair occurs at the boundaries of higher-order chromatin structure

Repair of UV-induced DNA damage requires chromatin remodeling. How repair is initiated in chromatin remains largely unknown. We recently demonstrated that Global Genome Nucleotide Excision Repair (GG-NER) in chromatin is organized into domains around open reading frames. Here, we identify these domains, and by examining DNA damage-induced changes in the linear structure of nucleosomes, we demonstrate how chromatin remodeling is initiated during repair. In undamaged cells, we show that the GG-NER complex occupies chromatin at nucleosome free regions of specific gene promoters. This establishes the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBSs). We demonstrate that these sites are frequently located at genomic boundaries that delineate chromasomally interacting domains (CIDs). These boundaries define domains of higher-order nucleosome-nucleosome interaction. We show that efficient repair of DNA damage in chromatin is initiated following disruption of H2A.Z-containing nucleosomes adjacent to GCBSs by the GG-NER complex.

genomics↗

bioRxiv2018

Wheat shovelomics II: Revealing relationships between root crown traits and crop growth

Optimization of root system architecture represents an important goal in wheat breeding. Adopting new field methods for root phenotyping is key to delivering this goal. A novel shovelomics method was applied for phenotyping root crown traits to characterize the Savannah x Rialto doubled-haploid (DH) population in two field experiments under irrigated and rain-fed conditions. Trait validation was carried out through soil coring on a subset of 14 DH lines and the two parents. We observed that drought reduced grain yield per plant by 21.0%. Under rain-fed conditions, nodal root angle and roots shoot-1 were positively associated with root length density (RLD) at 40-60 cm depth; RLD was also positively correlated with grain yield. Nodal root angle and roots shoot-1 were also positively associated with canopy stay green and grain yield under rain-fed conditions. We conclude that shovelomics is a valuable technique for quantifying genetic variation in nodal root traits in wheat, revealing nodal root angle and root number per shoot provide useful selection criteria in breeding programs aimed at improving drought tolerance in wheat.\n\nHighlightNodal root angle and number shoot-1 measured using shovelomics were positively associated with root density at depth and yield under drought in a Savanah x Rialto wheat DH population.

plant biology↗

bioRxiv2018

Cell death in cells overlying lateral root primordia contributes to organ growth in Arabidopsis

Unlike animal development, plant organ growth is widely accepted to be determined by cell division without any contribution of cell elimination. We investigated this paradigm during Arabidopsis lateral root formation when growth of the new primordia (LRP) from pericycle-derived stem cells deep inside the root is reportedly facilitated by remodeling of the walls of overlying cells without apparent cell death. However, we observed the induction of marker genes for cell types undergoing developmental cell death in several cells overlying the growing LRP. Transmission electron microscopy, time-lapse confocal and light sheet microscopy techniques were used to establish that cell death occurred at least in a subset of endodermal LRP-overlying cells during organ emergence. Significantly, organ emergence was retarded in mutants lacking a positive cell death regulator, and restored by inducing cell death in cells overlying LRP. Hence, we conclude that in the case of LRP, cell elimination contributes to organ growth.

plant biology↗