bluuebunny/crossref_metadata_2025 huggingface dataset:
SHINE: Protein Language Model based Pathogenicity Prediction for Inframe Insertion and Deletion Variants
Authors: Fan Xiao , Pan Hongbing , Tian Alan , Chung Wendy K. , Shen Yufeng
Published: September 2022

Inframe insertion and deletion variants (indels) alter protein sequence and length. Accurate pathogenicity predictions are important in genetic studies of human diseases. Indel Interpretation is challenging due to limitations in the available number of known pathogenic variants for training. Existing methods largely use manually encoded features including conservation, protein structure and function, and allele frequency. Recent advances in deep learning modeling of protein sequences and structures provide an opportunity to improve the representation of salient features based on large numbers of protein sequences. We developed a new pathogenicity predictor for SHort Inframe iNsertion and dEletion (SHINE). SHINE uses pre-trained protein language models to construct a latent representation of an indel and its protein context from protein sequences and multiple protein sequence alignments, and feeds the latent representation into supervised machine learning models for pathogenicity prediction. We curated training data from ClinVar and gnomAD, and created two test datasets from different sources. SHINE achieved better prediction performance than existing methods for both deletion and insertion variants in these two test datasets. Our work suggests that unsupervised protein language models can provide valuable information about proteins, and new methods based on these models can improve variant interpretation in genetic analyses.
Forward genetic screen of homeostatic antibody levels in the Collaborative Cross identifies MBD1 as a novel regulator of B cell homeostasis
Authors: Hampton Brea K. , Plante Kenneth S. , Whitmore Alan C. , Linnertz Colton L. , Madden Emily A. , Noll Kelsey E. , Boyson Samuel P. , Parotti Breantie , Bell Timothy A. , Hock Pablo , Shaw Ginger D. , de Villena Fernando Pardo-Manuel , Ferris Martin T. , Heise Mark T.
Published: September 2022

Variation in immune homeostasis, the state in which the immune system is maintained in the absence of stimulation, is highly variable across populations. This variation is attributed to both genetic and environmental factors. However, the identity and function of specific regulators have been difficult to identify in humans. We evaluated homeostatic antibody levels in the serum of the Collaborative Cross (CC) mouse genetic reference population. We found heritable variation in all antibody isotypes and subtypes measured. We identified 4 quantitative trait loci (QTL) associated with 3 IgG subtypes: IgG1, IgG2b, and IgG2c. While 3 of these QTL maps to known immunologically important regions of the genomes,Qih1(associated with variation in IgG1) mapped to a novel locus on Chromosome 18. We further associated this locus with B cell proportions in the spleen and show that Methyl-CpG binding domain protein 1 is a novel regulator of homeostatic IgG1 levels in the serum and marginal zone B cells (MZB) in the spleen, consistent with a role in MZB differentiation to antibody secreting cells.

Homeostatic antibody levels are highly variable between Collaborative Cross (CC) mouse strains. This forward genetic screen in the CC identifies Methyl-CpG binding domain protein 1 (MBD1) as a regulator of homeostatic IgG1 levels and marginal zone B cell differentiation.
Mathematical Modeling of Bottleneck Transmissions of RNA Virus Infecting a Homogeneous Host Population
Authors: Naomi Furuyama Taimá , Ramos Janini Luiz Mario , Guedes de Carvalho Isabel Maria Vicente , Antoneli Fernando Martins
Published: September 2022

There is no consensus about when a potential viral infection event presents greater risk of a successful transmission. Some authors suggest that late infection stages present higher risk of transmission. Others suggest that the early infection stages play a most relevant role in transmission events. However, studies considering the fitness or mutational effects on the viral particles over transmission events are lacking. We propose to approach this question through a two-level mathematical model based on RNA viral population dynamics. The first level of the model represents the intra-host viral population dynamics and the second level of the model represents the host-to-host dynamics of transmission events. The intra-host dynamics model uses the fitness of viral particles as means to track the presence of ‘highly infective’ particles during transmission bottlenecks. More specifically, the intra-host dynamics is described by a stochastic quasispecies, based on a multivariate branching process. The host-to-host dynamics of transmission events is emulated by a ‘putative’ transmission tree with ‘host zero’ at the root and a fixed number of branches emanating from each internal node. A ‘Monte Carlo’ strategy was adopted to explore the tree by sampling random walks along transmission chains along the tree. Viral infections of a single host and several transmission events among hosts were simulated in early and late infection stages scenarios. The results show that the early infection stages may represent a key factor in the viral pandemic. Over the evolution of the viral population within each host the mean fitness decreases due to occurrence of mutations (most of them causing deleterious effects). Despite the small opportunity interval, transmissions that occur in early stages could probably infect new hosts at a higher rate than in late stages. It was observed that a very early transmission scenario could reach a transmission chain 20 times longer than a very late transmission scenario. This indicates that the quality of the viral particles is a relevant factor for transmission events.
Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation
Authors: Breusing Corinna , Xiao Yao , Russell Shelbi L. , Corbett-Detig Russell B. , Li Sixuan , Sun Jin , Chen Chong , Lan Yi , Qian Pei-Yuan , Beinart Roxanne A.
Published: September 2022

The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown whether these patterns are universal and how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea musselBathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses.Bathymodiolus septemdierumlives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with less exposure to geochemical reductants. Our analyses indicate that symbiont populations associated withB. septemdierumshow structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurringAlviniconchaandIfremeriasymbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that vary in ecological niche and relative host dependency.
Unweighted versus weighted regression methods may be sufficient to analyze complex survey data in the Canadian Longitudinal Study on Aging
Authors: Oremus Mark , Maxwell Colleen , Tyas Suzanne L. , Griffith Lauren E. , van den Heuvel Edwin R.
Published: September 2022

Introduction

Complex surveys use stratified or cluster sampling to recruit participants. Researchers analyzing these surveys often wish to make inferences about the source populations from which the participants are drawn. In such cases, methodologists recommend employing sample weights in regression analyses; however, the utilization of weights in studies of associations are not without dispute.

Materials and methods

To help guide analyses of complex surveys, we utilized baseline data from the Comprehensive Cohort of the Canadian Longitudinal Study on Aging (CLSA) (n = 30,097) and compared unweighted and weighted regression analyses of the association between social support availability (SSA) and cognitive function. We also conducted simulation studies to validate our findings in the CLSA.

Results

The regression coefficients for SSA were similar across the unweighted and weighted regression models; the standard errors of the were lower in the unweighted models. The simulation studies mimicking CLSA confirmed these findings. Overall, our findings demonstrated a small advantage for the unweighted analysis of CLSA data due to the smaller standard errors.

Discussion

Although we cannot guarantee that this would be the case for all association analyses with CLSA data, the current study showed the use of analytical weights was not necessary for our associations of interest.
Temperature-dependent Thermodynamic and Photophysical Properties of SYTO-13 Dye Bound to DNA
Authors: DeJaco Robert F. , Majikes Jacob M. , Liddle J. Alexander , Kearsley Anthony J.
Published: September 2022

The benefits of dyes in nucleic acid assays above room temperature are limited by a nonlinear, highdimensional relationship between fluorescence and the biophysical and chemical processes occurring in solution. To overcome these limitations, we identify an experimental regime that eliminates bias and unnecessary complexities in this relationship, and develop an experimental–computational workflow to generate the property data required to describe the dependence of fluorescence on temperature and concentration. Specifically, we exploit the temperature-cycling capabilities of real-time PCR machine, as well as the utility of numerical optimization, to determine the binding strength and molar fluorescence of the SYTO-13 dye bound to double-stranded (DS) or single-stranded (SS) DNA at more than 60 temperatures. We find that the data analysis approach is robust; it can account for significant well-to-well and plate-to-plate variation. The weak binding strength of SYTO-13 relative to SYBR Green I is consistent with previous reports of its negligible influence on PCR and melting temperature. Discriminating between molar fluorescence and binding strength clarifies the mechanism for the larger fluorescence of a DS/dye solution than a SS/dye solution; in fact, the explanation is different at high temperature than at low temperature. The temperature-dependence of the binding strength allows for ascertainment of the enthalpic and entropic contributions to the free energy, as well as the sign of the differential heat capacity of binding. The temperature-dependence of the molar fluorescence allows for calculation of the brightness (quantum yield times molar extinction coefficient) of SYTO-13 bound to DS relative to SS. The more accurate and complete description of the relationship between solution behavior and fluorescence enabled by this work can lead to more accurate selection of dyes and quantification of nucleic acids.

SIGNIFICANCE

Fluorescent dyes are often used to quantify nucleic acids. The accuracy and precision of quantification, however, is limited by a complex and high-dimensional relationship between fluorescence and solution behavior. This is especially true for assays above room temperature, where empirical approximations are often required in the absence of available property data. In this work, we present an experimental and computational workflow that can more accurately describe this relationship and more efficiently generate the temperature-dependent thermodynamic and photophysical properties required. This approach can improve quantification and selection of high-performing dyes for particular assays.
Activation of ERK by altered RNA splicing in cancer
Authors: Zhang Yushan , Siraj Md Afjalus , Chakraborty Prabir , Tseng Robert , Ku Li-Ting , Das Shamik , Dey Anindya , Dhar Dwivedi Shailendra Kumar , Rao Geeta , Zhang Min , Yang Da , Hossen Md Nazir , Ding Wei-Qun , Fung Kar-Ming , Bhattacharya Resham , Escobar-Hoyos Luisa , Mukherjee Priyabrata
Published: September 2022

Many cancers carry change-of-function mutations affecting RNA splicing factors, however, less is known about the functional consequences of upregulated RNA splicing factors in cancer. Here, we demonstrate that SMNDC1, a poorly studied splicing factor, which we found to be upregulated in multiple carcinomas and associated with poor patient prognosis, promotes cell proliferation, clonal expansion, and tumor growth by promoting the retention of G-rich exons, which otherwise would be excluded or retained at a lower rate after RNA splicing in normal cells. Inclusion of exon 4 (E4) of MAPK3 (ERK1), which encodes both kinase phosphorylation sites (Thr202/Tyr204), was among the promoted exons by SMNDC1. Forced exclusion of MAPK3-E4 using anti-sense oligos inhibited the ERK1 phosphorylation, expression of target genes and decreased tumor cell growth. These data support that cancer cells exploit a “splicing switch” to promote ERK kinase activity and offer a druggable alternative to block oncogenic signaling and altered RNA splicing in cancer cells

SIGNIFICANCE

ERK signaling promotes tumor growth and survival. Exon 4 of MAPK3 (ERK1) encodes the activation phosphorylation sites of ERK1 kinase. Aberrant RNA splicing induced by SMNDC1 in cancer cells increases the retention of exon 4 during mRNA splicing, unleashes the kinase activity. SMNDC1 potentializes as a cancer therapeutic target.
Brain-wide transcriptome-based metabolic alterations in Parkinson’s disease: human inter-region and human-experimental model correlations
Authors: Odongo Regan , Bellur Orhan , Abdik Ecehan , Çakır Tunahan
Published: September 2022

Alterations in brain metabolism are closely associated with the molecular hallmarks of Parkinson’s disease (PD). A clear understanding of the main metabolic perturbations in PD is therefore important. Here, we retrospectively analysed the expression of metabolic genes from 34 PD-control post-mortem human brain transcriptome data from literature, spanning multiple brain regions, and found significant metabolic correlations between the Substantia nigra (SN) and cerebral cortical tissues with high perturbations in protein modification, transport, nucleotide and inositol phosphate metabolic pathways. Moreover, three main metabolic clusters of SN tissues were identified from patient cohort studies, each characterised by perturbations in (a) pyruvate, amino acid, neurotransmitter, and complex lipid metabolisms (b) inflammation-related metabolism, and (c) lipid breakdown for energy metabolism. Finally, we analysed 58 PD-control transcriptome data from in vivo/in vitro disease models and identified experimental PD models with significant correlations to matched human brain regions. Collectively, our findings are based on 47 PD transcriptome datasets covering 92 PD-control comparisons spanning more than 1000 samples in total, and they suggest metabolic alterations in several brain regions, heterogeneity in metabolic alterations between study cohorts for the SN tissues and suggest the need to optimize current experimental models to advance research on metabolic aspects of PD.
The RhoGEF protein Plekhg5 regulates medioapical actomyosin dynamics of apical constriction during Xenopus gastrulation
Authors: Baldwin Austin T. , Popov Ivan K. , Keller Ray , Wallingford John B. , Chang Chenbei
Published: September 2022

Apical constriction results in apical surface reduction in epithelial cells and is a widely used mechanism for epithelial morphogenesis during embryo development. Both medioapical and junctional actomyosin remodeling are involved in apical constriction, but the deployment of medial versus junctional actomyosin in specific developmental processes has not been fully described. Additionally, genetic regulation of actomyosin dynamics during apical constriction is poorly understood in vertebrate systems. In this study, we investigate actomyosin dynamics and their regulation by the RhoGEF protein Plekhg5 in Xenopus bottle cells. Using live imaging and quantitative image analysis, we show that bottle cells assume different shapes, with rounding bottle cells constricting earlier in small clusters followed by fusiform bottle cells forming between the clusters. Though both medioapical and junctional actomyosin accumulate as surface area decreases, apical constriction is better correlated with medioapical actomyosin localization, which may promote formation of microvilli in the apical membrane. Knockdown of plekhg5 disrupts both medioapical actomyosin activity and apical constriction but does not affect initial F-actin dynamics. Taken together, our study reveals distinct cell morphologies, uncovers actomyosin behaviors, and demonstrates the crucial role of a RhoGEF protein in controlling actomyosin dynamics during apical constriction of bottle cells in Xenopus gastrulation.
Effect of genomic and cellular environments on gene expression noise
Authors: Hong Clarice KY , Ramu Avinash , Zhao Siqi , Cohen Barak A
Published: September 2022

Individual cells from isogenic populations often display large cell-to-cell differences in gene expression. This “noise” in expression derives from several sources, including the genomic and cellular environment in which a gene resides. Large-scale maps of genomic environments have revealed the effects of epigenetic modifications and transcription factor occupancy on mean expression levels, but leveraging such maps to explain expression noise will require new methods to assay how expression noise changes at locations across the genome. To address this gap, we present Single-cell Analysis of Reporter Gene Expression Noise and Transcriptome (SARGENT), a method that simultaneously measures the noisiness of reporter genes integrated throughout the genome and the global mRNA profiles of individual reporter-gene-containing cells. Using SARGENT, we performed the first comprehensive genome-wide survey of how genomic locations impact gene expression noise. We found that the mean and noise of expression correlate with different histone modifications. We quantified the intrinsic and extrinsic components of reporter gene noise and, using the associated mRNA profiles, assigned the extrinsic component to differences between the CD24+ “stem-like” sub-state and the more “differentiated” sub-state. SARGENT also reveals the effects of transgene integrations on endogenous gene expression, which will help guide the search for “safe-harbor” loci. Taken together, we show that SARGENT is a powerful tool to measure both the mean and noise of gene expression at locations across the genome, and that the data generated by SARGENT reveals important insights into the regulation of gene expression noise genome-wide.
Novel eDNA approaches to monitor Western honey bee (Apis mellifera) microbial and arthropod communities
Authors: Boardman Leigh , Marcelino Jose A.P. , Valentin Rafael E. , Boncristiani Humberto , Standley Jennifer , Ellis James D.
Published: September 2022

Pests and pathogens are a continuous threat to the health of Western honey bees Apis mellifera L. Monitoring honey bee colonies for arthropod pests, disease-causing bacteria and fungi, and early detection of new invasions is essential to maintain the pollination services provided by honey bees. Here, we investigated the feasibility of using eDNA metabarcoding to detect honey bee pests and pathogens in their hives and across their foraging environment. We sampled 13 different surfaces within and outside hives from our test apiary to determine where the most informative eDNA could be obtained. Furthermore, we compared two main eDNA collection techniques – wiping surfaces with moistened forensic swabs and using a spray/wash technique that washed surface DNA into a bucket, before collecting the DNA on a filter. We used DNA metabarcoding with universal primer sets to target arthropod, bacterial and fungal communities. Our results showed that most surfaces yielded usable DNA, and that results of the swabs and spray/wash methods were similar when they could be applied to the same surface. We were able to detect DNA from the small hive beetle (Aethina tumida), Varroa destructor mites and European foulbrood (Melissococcus plutonius), all of which matched our visual observations of clinical signs of these pests and pathogens in the hives we tested. DNA from some species was location specific, which has implications for using eDNA as a monitoring tool. Collectively, our data show that eDNA metabarcoding can accurately detect DNA from arthropods and microbes honey bees contact and has the potential to provide information on disease and pest incidence, Apis species identity, and A. mellifera subspecies identity of the colony and/or apiary. In sum, eDNA metabarcoding can be used as a comprehensive molecular predictor tool for colony health surveys.
Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity
Authors: Kim Dongjoo , Biancon Giulia , Bai Zhiliang , VanOudenhove Jennifer , Liu Yuxin , Kothari Shalin , Gowda Lohith , Kwan Jennifer M. , Buitrago-Pocasangre Nicholas Carlos , Lele Nikhil , Asashima Hiromitsu , Racke Michael K. , Wilson JoDell E. , Givens Tara S. , Tomayko Mary M. , Schulz Wade L. , Longbrake Erin E. , Hafler David A. , Halene Stephanie , Fan Rong
Published: September 2022

The immune response to SARS-CoV-2 for patients with altered immunity such as hematologic malignancies and autoimmune disease may differ substantially from that in general population. These patients remain at high risk despite wide-spread adoption of vaccination. It is critical to examine the differences at the systems level between the general population and the patients with altered immunity in terms of immunologic and serological responses to COVID-19 infection and vaccination. Here, we developed a novel microfluidic chip for high-plex immuno-serological assay to simultaneously measure up to 50 plasma or serum samples for up to 50 soluble markers including 35 plasma proteins, 11 anti-spike/RBD IgG antibodies spanning all major variants, and controls. Our assay demonstrated the quintuplicate test in a single run with high throughput, low sample volume input, high reproducibility and high accuracy. It was applied to the measurement of 1,012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein association matrix analysis revealed distinct immune mediator protein modules that exhibited a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies and patients with autoimmune disorders receiving B cell depletion therapy. Serological analysis identified that COVID infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which could be associated with limited clonotype diversity and functional deficiency in B cells and was further confirmed by single-cell BCR and transcriptome sequencing. These findings underscore the importance to individualize immunization strategy for these high-risk patients and provide an informative tool to monitor their responses at the systems level.
Altered correlation of concurrently recorded EEG-fMRI connectomes in temporal lobe epilepsy
Authors: Wirsich Jonathan , Iannotti Giannina Rita , Ridley Ben , Shamshiri Elhum A , Sheybani Laurent , Grouiller Frédéric , Bartolomei Fabrice , Seeck Margitta , Lazeyras François , Ranjeva Jean-Philippe , Guye Maxime , Vulliemoz Serge
Published: September 2022

Whole brain, large-scale functional connectivity networks or connectomes have been characterized on different temporal and spatial scales in humans using EEG and fMRI. Whole brain epileptic networks have been investigated with both EEG and fMRI, but due to the different acquisition approaches it is unclear to what extent those results can be related. In consequence clinical research in epilepsy would profit from a unified multimodal functional connectome description as a linking framework to better map underlying brain function and pathological functional networks. In this study we aim to characterize the spatial correlation between EEG and fMRI connectivity in temporal lobe epilepsy.

From two independent centers, we acquired resting-state concurrent EEG-fMRI from a total of 35 healthy controls and 34 TLE patients (18 right TLE and 16 left TLE). Data was projected into the Desikan brain atlas (mean BOLD activity for fMRI and source reconstruction for EEG). Whole brain functional connectivity from fMRI (Pearson correlation) and EEG (corrected imaginary part of the coherency) were correlated for all subjects.

In healthy controls, average EEG and fMRI whole-brain connectivity was moderately correlated (r∼0.3). For both imaging centers, correlation between EEG and fMRI whole brain connectivity was increased in rTLE when compared to controls for lower frequency bands (EEG-delta, theta and alpha). Conversely correlation between EEG and fMRI connectivity of lTLE patients was decreased in respect to healthy subjects (EEG-beta vs. fMRI connectivity only). While the alteration of the EEG-fMRI correlation in rTLE patients could not be related to a local effect, in lTLE patients it was locally linked to the Default Mode Network.

We demonstrated, using two independent datasets, that EEG and fMRI connectivity is correlated for both healthy subjects and patients. The increased correlation of EEG and fMRI connectivity in rTLE patients vs. controls and decreased correlation in lTLE patients vs. controls suggests a differential organization of mono-lateral focal epilepsy of the same type, which needs to be considered when comparing fMRI to EEG connectivity. It also demonstrates that each modality provides distinct information, highlighting the benefit of multimodal assessment in epilepsy. The observed property of distinct topological patterns depending on the lateralization of the epilepsy could be taken into account when clinically defining the epileptic focus of patients.
Rebound in asthma exacerbations following relaxation of COVID-19 restrictions: a longitudinal population-based study (COVIDENCE UK)
Authors: Tydeman Florence , Pfeffer Paul E , Vivaldi Giulia , Holt Hayley , Talaei Mohammad , Jolliffe David A , Davies Gwyneth A , Lyons Ronan A , Griffiths Christopher J , Kee Frank , Sheikh Aziz , Shaheen Seif O , Martineau Adrian R
Published: September 2022

Background

The imposition of restrictions on social mixing early in the COVID-19 pandemic was followed by a reduction in asthma exacerbations in multiple settings internationally. Temporal trends in social mixing, incident acute respiratory infections (ARI) and asthma exacerbations following relaxation of COVID-19 restrictions have not yet been described.

Methods

We conducted a population-based longitudinal study in 2,312 UK adults with asthma between November 2020 and April 2022. Details of face covering use, social mixing, incident ARI and moderate/severe asthma exacerbations were collected via monthly on-line questionnaires. Temporal changes in these parameters were visualised using Poisson generalised additive models. Multilevel logistic regression was used to test for associations between incident ARI and risk of asthma exacerbations, adjusting for potential confounders.

Results

Relaxation of COVID-19 restrictions from April 2021 coincided with reduced face covering use (p<0.001), increased frequency of indoor visits to public places and other households (p<0.001) and rising incidence of COVID-19 (p<0.001), non-COVID-19 ARI (p<0.001) and moderate/severe asthma exacerbations (p=0.007). Incident non-COVID-19 ARI associated independently with increased risk of asthma exacerbation (adjusted odds ratio 5.75, 95% CI 4.75 to 6.97) as did incident COVID-19, both prior to emergence of the omicron variant of SARS-CoV-2 (5.89, 3.45 to 10.04) and subsequently (5.69, 3.89 to 8.31).

Conclusions

Relaxation of COVID-19 restrictions coincided with decreased face covering use, increased social mixing and a rebound in ARI and asthma exacerbations. Associations between incident ARI and risk of moderate/severe asthma exacerbation were similar for non-COVID-19 ARI and COVID-19, both before and after emergence of the SARS-CoV-2 omicron variant.

Funding

Barts Charity, UKRI
An automated EEG algorithm detect polymorphic delta activity in acute encephalopathy presenting as postoperative delirium
Authors: Ditzel Fienke L , Hut Suzanne CA , Dijkstra-Kersten Sandra MA , Numan Tianne , Leijten Frans SS , van den Boogaard Mark , Slooter Arjen JC
Published: September 2022

Aim

Delirium, a clinical manifestation of acute encephalopathy, is often unrecognised. An important electroencephalography (EEG) characteristic of acute encephalopathy is polymorphic delta activity (PDA), which can be detected automatically. We aimed to study whether automated assessment of PDA in unselected EEG could detect acute encephalopathy that presents clinically as delirium.

Methods

We assessed PDA in 145 elderly patients using the first 96 seconds of unselected single-channel EEG (Fp2-Pz). We compared fully automated PDA detection with visual inspection by EEG experts. Additionally, we tested its performance as a delirium monitor by comparing PDA detection with a standardized delirium assessment by a clinical expert panel.

Results

PDA detection showed an area under the receiver operating characteristic (AUC) of 0.86 (95%CI 0.81–0.90) compared to EEG experts. When compared with the delirium classification of clinical experts, PDA detection achieved an AUC of 0.78 (95%CI 0.71–0.85). PDA detection correlated with the likelihood of delirium, its severity and the levels of attention and consciousness (all p<0.001).

Conclusion

Automated PDA detection in unselected, single-channel EEG can classify acute encephalopathy clinically presenting as delirium.

Significance

A fully automated EEG algorithm can assist in the recognition of delirium.
High-pass filter settings and possible mechanism of discrete electrograms in left bundle branch pacing
Authors: Shen Jiabo , Jiang Longfu , Wu Hao , Li Hengdong , Zhang Lu , Zhong Jinyan , Zhuo Shanshan , Pan Lifang
Published: September 2022

Objective

The characteristics of discrete intracardiac electrograms in selective left bundle branch (SLBB) pacing (SLBBP) have not been described in detail previously. This study aimed to examine the effect of different high-pass filter (HPF) settings on discrete ventricular components in an intracardiac electrogram (EGM) and to analyze its possible mechanisms.

Methods

This study included 95 patients with indications of permanent cardiac pacing. EGMs were collected at four different HPF settings (30, 60, 100, and 200 Hz) with a low-pass filter at 500 Hz, and their possible mechanisms were analyzed.

Results

LBBP was successfully achieved in 92.6% (88/95) of patients. SLBBP was achieved in 80 patients. The occurrence rates of discrete EGM were 18.9%, 40.0%, 74.7%, and 84.2% for HPF settings of 30 Hz, 60 Hz, 100 Hz, and 200 Hz, respectively. The analysis of discrete ECG detection showed significant differences between the different HPF settings. By using the discrete EGM as the SLBB capture golden standard, the results of EGMs revealed that the 30 Hz HPF has a sensitivity of 23% and specificity of 100%. The 60 Hz HPF had a sensitivity of 48% and a specificity of 100%. The 100 Hz HPF had a sensitivity of 89% and a specificity of 100%. The 200 Hz HPF had a sensitivity of 100% and specificity of 100%.

Conclusions

An optimal HPF setting of 200 Hz is recommended for discrete electrogram detection. A discrete EGM should exhibit an isoelectric interval. A steep deflection and spinous ventricular EGM morphology nearly identify an intrinsic EGM morphology.
The impact and progression of the COVID-19 pandemic in Bulgaria in its first two years
Authors: Rangachev Antoni , Marinov Georgi K. , Mladenov Mladen
Published: September 2022

After initially having low levels of SARS-CoV-2 infections for much of the year, at the end of 2020 Bulgaria experienced a major epidemic surge, which caused the highest recorded excess mortality in Europe and among the highest in the word (Excess Mortality Rate, or EMR ∼ 0.25%). Two more major waves followed in 2021, followed by another one in early 2022. In this study we analyze the temporal and spatial patterns of excess mortality at the national and local levels and across different demographic groups in Bulgaria, and compare those at the European level. The country has continued to exhibit the previous pattern of extremely high excess mortality as measured both by crude mortality metrics (EMR ∼ 1.05% up to the end of March 2022) and by standardized ones – Potential Years of Life Lost (PYLL) and Aged-Standardized Years of life lost Rate (ASYR). Unlike Western Europe, the bulk of excess mortality in Bulgaria, as well as in several other countries in Eastern Europe, occurred in the second year of the pandemic, likely related to the differences in the levels of vaccination coverage between these regions. We also observe even more extreme levels of excess mortality at the regional level and in some subpopulations (e.g. total EMR values for males ≥ 2% and EMR values for males aged 40-64 ≥ 1% in certain areas). We discuss these observations in light of the estimates of infection fatality rate (IFR) and eventual population fatality rate (PFR) made early in the course of the pandemic.
Mitochondrial dysfunction underlies cortical atrophy in prodromal synucleinopathies
Authors: Rahayel Shady , Tremblay Christina , Vo Andrew , Mišić Bratislav , Lehéricy Stéphane , Arnulf Isabelle , Vidailhet Marie , Corvol Jean-Christophe ,   the ICEBERG Study Group, Gagnon Jean-François , Postuma Ronald B. , Montplaisir Jacques , Lewis Simon , Matar Elie , Martens Kaylena Ehgoetz , Borghammer Per , Knudsen Karoline , Hansen Allan K. , Monchi Oury , Gan-Or Ziv , Dagher Alain
Published: September 2022

Isolated rapid eye movement sleep behavior disorder (iRBD) is a prodromal synucleinopathy characterized by several changes including brain atrophy. The mechanisms underlying atrophy in iRBD are poorly understood. Here, we performed imaging transcriptomics and comprehensive spatial mapping in a multicentric cohort of 171 polysomnography-confirmed iRBD patients and 238 controls with T1-weighted MRI to investigate the gene expression patterns and the specific neurotransmitter, functional, cytoarchitectonic, and cognitive brain systems associated with cortical thinning in iRBD. We found that genes involved in mitochondrial function and macroautophagy were the strongest contributors to the thinning occurring in iRBD. Moreover, we demonstrated that thinning was constrained by the brain’s connectome and that it mapped onto specific networks involved in motor and planning functions. In contrast with thickness, changes in cortical surface area related to distinct gene and spatial mapping patterns. This study demonstrates that the development of atrophy in synucleinopathies is constrained by specific genes and networks.
Revisiting deficits in threat and safety appraisal in obsessive-compulsive disorder
Authors: Hearne Luke J. , Breakspear Michael , Harrison Ben J. , Hall Caitlin V. , Savage Hannah S. , Robinson Conor , Sonkusare Saurabh , Savage Emma , Nott Zoie , Marcus Leo , Naze Sebastien , Burgher Bjorn , Zalesky Andrew , Cocchi Luca
Published: September 2022

Current behavioural treatment of obsessive-compulsive disorder (OCD) is informed by fear conditioning and involves iteratively re-evaluating previously threatening stimuli as safe. However, there is limited research investigating the neurobiological response to conditioning and reversal of threatening stimuli in individuals with OCD. A clinical sample of individuals with OCD (N=45) and matched healthy controls (N=45) underwent functional Magnetic Resonance Imaging (fMRI). While in the scanner, participants completed a well-validated fear reversal task and a resting-state scan. We found no evidence for group differences in task-evoked brain activation or functional connectivity in OCD. Multivariate analyses encompassing all participants in the clinical and control groups suggested that subjective appraisal of threatening and safe stimuli were associated with a larger difference in brain activity than the contribution of OCD symptoms. In particular, we observed a brain-behaviour continuum whereby heightened affective appraisal was related to increased bilateral insula activation during the task (r= 0.39,pFWE= 0.001). These findings suggest that changes in conditioned threat-related processes may not be a core neurobiological feature of OCD and encourage further research on the role of subjective experience in fear conditioning.
Zinc supplementation induced transcriptional changes in primary human retinal pigment epithelium: a single-cell RNA sequencing study to understand age-related macular degeneration
Authors: Emri Eszter , Cappa Oisin , Kelly Caoimhe , Kortvely Elod , SanGiovanni John Paul , McKay Brian , Bergen Arthur A , Simpson David A , Lengyel Imre
Published: September 2022

Zinc supplementation had been shown to be beneficial to slow the progression of age-related macular degeneration (AMD). However, the molecular mechanism underpinning this benefit is not well understood. In this study, we used single-cell RNA sequencing to identify transcriptomic changes induced by zinc supplementation in human primary retinal pigment epithelial (RPE) cells in culture. The RPE cells were allowed to mature for up to 19 weeks. After one or 18 weeks in culture, we supplemented the culture medium with 125 μM added zinc for one week. During maturation RPE cells developed high transepithelial electrical resistance, extensive, but variable, pigmentation and deposited sub-RPE material similar to the hallmark lesions of AMD. Unsupervised cluster analysis of the combined transcriptome of the cells isolated after two-, nine- and 19 weeks in culture, showed a significant degree of heterogeneity. Clustering based on 234 pre-selected RPE specific genes, identified from the literature, divided the cells into two distinct clusters we defined as more- and less-differentiated cells. The proportion of more differentiated cells increased with time in culture, but appreciable numbers of cells remained less differentiated even at 19 weeks. Pseudotemporal ordering identified 537 genes that could be implicated in the dynamics of RPE cell differentiation (FDR< 0.05). Zinc treatment resulted in the differential expression of 281 of these genes (FDR< 0.05). These genes were associated with several biological pathways including extracellular remodelling, retinoid metabolism and modulation ofID1/ID3transcriptional regulation, to name a few. Overall, zinc had a multitude of effects on the RPE transcriptome including a number of genes that are involved in pigmentation, complement regulation, mineralisation and cholesterol metabolism processes associated with AMD.
MMD scaffolds ACSL4 and MBOAT7 to promote polyunsaturated phospholipid synthesis and susceptibility to ferroptosis
Authors: Phadnis Vaishnavi V. , Snider Jamie , Wong Victoria , Vaccaro Kyle D. , Kunchok Tenzin , Allen Juliet , Yao Zhong , Geng Betty , Weiskopf Kipp , Stagljar Igor , Henry Whitney S. , Weinberg Robert A.
Published: September 2022

Ferroptosis is a form of regulated cell death with roles in degenerative diseases and cancer. Ferroptosis is driven by excessive iron-dependent peroxidation of membrane phospholipids, especially those containing the polyunsaturated fatty acid arachidonic acid. Here, we reveal that an understudied Golgi membrane scaffold protein, MMD, promotes susceptibility to ferroptosis in ovarian and renal carcinoma cells. Upregulation of MMD correlates with sensitization to ferroptosis upon monocyte-to-macrophage differentiation. Mechanistically, MMD interacts with ACSL4 and MBOAT7, two enzymes that catalyze consecutive reactions in the biosynthesis of phosphatidylinositol (PI) containing arachidonic acid. MMD increases cellular levels of arachidonoyl-phospholipids and heightens susceptibility to ferroptosis in an ACSL4- and MBOAT7-dependent manner. We propose that MMD potentiates the synthesis of arachidonoyl-PI by bridging ACSL4 with MBOAT7. This molecular mechanism not only clarifies the biochemical underpinnings of ferroptosis susceptibility, with potential therapeutic implications, but also contributes to our understanding of the regulation of cellular lipid metabolism.

Graphical Abstract
The Arthropoda-specific Tramtrack group BTB protein domains use previously unknown interface to form hexamers
Authors: Bonchuk Artem N. , Balagurov Konstantin I. , Baradaran Rozbeh , Boyko Konstantin M. , Sluchanko Nikolai N. , Khrustaleva Anastasia M. , Burtseva Anna D. , Arkova Olga V. , Khalisova Karina K. , Popov Vladimir O. , Naschberger Andreas , Georgiev Pavel G.
Published: September 2022

BTB (Bric-a-brack, Tramtrack and Broad Complex) is a diverse group of protein-protein interaction domains found within metazoan proteins. Transcription factors contain a dimerizing BTB subtype with a characteristic N-terminal extension. The Tramtrack group (TTK) is a distinct type of BTB domain, which can multimerize. Single-particle cryo-EM microscopy revealed that the TTK-type BTB domains assemble into a hexameric structure consisting of three canonical BTB dimers connected through a previously uncharacterized interface. We demonstrated that the TTK-type BTB domains are found only in Arthropods and have undergone lineage-specific expansion in modern insects. TheDrosophilagenome encodes 24 transcription factors with TTK-type BTB domains, whereas only four have non-TTK-type BTB domains. Yeast two-hybrid analysis revealed that the TTK-type BTB domains have an unusually broad potential for heteromeric associations presumably through dimer-dimer interaction interface. Thus, the TTK-type BTB domains are a structurally and functionally distinct group of protein domains specific to Arthropodan transcription factors.
Senescent cells enhance newt limb regeneration by promoting muscle dedifferentiation
Authors: Walters Hannah E. , Troyanovskiy Konstantin , Yun Maximina H.
Published: September 2022

Salamanders are able to regenerate their entire limbs throughout lifespan, through a process that involves significant modulation of cellular plasticity. Limb regeneration is accompanied by the induction of cellular senescence, a state of irreversible cell cycle arrest associated with profound non-cell-autonomous consequences. While traditionally associated with detrimental physiological effects, here we show that senescent cells enhance newt limb regeneration. Through a lineage tracing approach, we demonstrate that senescent cells promote dedifferentiation of mature muscle tissue to generate regenerative progenitors. In a paradigm of newt myotube dedifferentiation, we uncover that senescent cells promote myotube cell cycle re-entry and reversal of muscle identity via secreted factors. Transcriptomic profiling and loss of function approaches identify the FGF-ERK signalling axis as a critical mediator of senescence-induced muscle plasticity. While chronic senescence constrains muscle regeneration in physiological mammalian contexts, we thus highlight a beneficial role for cellular senescence as an important modulator of dedifferentiation, a key mechanism for regeneration of complex structures.
Cancer-Associated Mutations Enhance The Sensitivity Of The Trupath GαQ/11 System
Authors: Safitri Dewi , Harris Matthew , Pearce Abigail , Huang Xianglin , Rosa Matthew , Barkan Kerry , Wills Edward , Marti-Solano Maria , Falk Matthew D. , Ladds Graham
Published: September 2022

G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and are a common drug target. They can be stabilised in different conformational states by ligands to activate multiple transducers and effectors leading to a variety of cellular responses. The potential of agonists to activate select pathways has important implications for drug discovery. Thus, there is a clear need to profile the initial GPCR signal transduction event, activation of G proteins, to enhance understanding of receptor coupling and guide drug design. The BRET-based biosensor suite, TRUPATH, was recently developed to enable quantification of the activation profiles of all non-visual G proteins (excluding Golf and G14) and has since been utilised in numerous studies. However, it fails to detect Gq/11 activation for a number of GPCRs previously reported to display promiscuous secondary coupling to Gq/11. Here we report modifications to the Gαq and Gα11 biosensors in the switch I region that prevent intrinsic GTPase activity (R183C/Q). Except for the PAC1R, substitution with cancer-associated mutations, Cys or Gln, significantly increased sensitivity to allow detection of robust, reliable, and representative Gq/11 responses to Class B1 GPCRs. We also demonstrate the utility of these modified biosensors for promiscuously coupled class A GPCR that have primary Gs-coupling. Thus, we propose that modification to Gαq/11 may also be necessary in other biosensor systems to enable detection of Gq/11 activation.
Small molecule G-quadruplex ligands are antibacterial candidates for Gram-negative bacteria
Authors: Takebayashi Yuiko , Ramos-Soriano Javier , Jiang Y. Jennifer , Samphire Jennifer , Belmonte-Reche Efres , O’Hagan Michael P. , Gurr Catherine , Heesom Kate J. , Lewis Philip A. , Samernate Thanadon , Nonejuie Poochit , Spencer James , Galan M. Carmen
Published: September 2022

There is great need for novel strategies to tackle antimicrobial resistance, in particular in Gram-negative species such asEscherichia colithat cause opportunistic infections of already compromised patients. Here we demonstrate, following a screen of G-quadruplex (G4) ligand candidates, that a novel pyridinium-functionalized azobenzeneL9shows promising antibacterial activity (MIC values ≤ 4 μg/mL) against multi-drug resistantE. coli. Tandem Mass Tag (TMT) proteomics ofE. colitreated with sub-lethal concentrations ofL9, identified that, consistent with its superior antibacterial activity,L9treatment influences expression levels of more G4-associated proteins than the analogous ligandsL5(stiff-stilbene) or pyridostatin (PDS), and upregulates multiple essential proteins involved in translation. Biophysical analysis showedL9binds potential target G4-containing sequences, identified from proteomic experiments and by bioinformatics, with variable affinity, in contrast to the two comparator G4 ligands (L5, PDS) that better stabilize G4 structures but have lower antimicrobial activity. Fluorescence microscopy-based Bacterial Cytological Profiling (BCP) suggests that theL9mechanism of action is distinct from other antibiotic classes. These findings support strategies discovering potential G4 ligands as antibacterial candidates for priority targets such as multi-drug resistantE. coli, warranting their further exploration as potential novel therapeutic leads with G4-mediated modes of action.

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