bluuebunny/crossref_metadata_2025 huggingface dataset:
Insight into spatial intratumoral genomic evolution in glioblastoma
Authors: Anand Atul , Petersen Jeanette Krogh , Andersen Lars van Brakel , Burton Mark , Larsen Martin Jakob , Pedersen Christian Bonde , Poulsen Frantz Rom , Grupe Peter , Kruse Torben A. , Thomassen Mads , Kristensen Bjarne Winther
Published: September 2023

Glioblastoma undergoes a complex and dynamic evolution involving genetic and epigenetic changes. Understanding the mechanisms underlying this evolution is vital for the development of efficient therapeutic strategies. Although treatment resistance is associated with intratumoral heterogeneity in glioblastoma, it remains uncertain whether hypometabolic and hypermetabolic lesions observed through positron emission tomography (PET) imaging are influenced by spatial intratumoral genomic evolution. In this study, we precisely isolated autologous hypometabolic and hypermetabolic lesions from glioblastoma using advanced neurosurgical and brain tumor imaging technologies, followed by comprehensive whole-genome exome and transcriptome analyses. Our findings revealed that hypermetabolic lesions evolved from hypometabolic lesions, harbored shrewd focal amplifications and deletions, and exhibited a higher frequency of critical genomic alterations linked to increased aggressiveness, upregulated APOBEC3 and hypoxic genes, and downregulated putative tumor suppressors. This study highlights spatial genomic evolution with diagnostic implications and unveils the obstacles and possibilities that should be considered in the development of novel therapeutic strategies.

Statement of significance:

Glioblastoma is a multifaceted disease that is difficult to treat, and insights into the metabolic gradient observed in imaging and the underlying role of genomic evolution are lacking. This study is the first to investigate the molecular basis of hypermetabolic tumor lesions in glioblastoma using precise three-dimensional biopsy isolation, whole genome/exome, and mRNA sequencing. These findings have diagnostic significance, provide insights into therapeutic resistance, and shed light on the obstacles encountered by precision therapeutics for glioblastoma.
Identifying latent genetic interactions in genome-wide association studies using multiple traits
Authors: Bass Andrew J. , Bian Shijia , Wingo Aliza P. , Wingo Thomas S. , Cutler David J. , Epstein Michael P.
Published: September 2023

Genome-wide association studies of complex traits frequently find that SNP-based estimates of heritability are considerably smaller than estimates from classic family-based studies. This ‘missing’ heritability may be partly explained by genetic variants interacting with other genes or environments that are difficult to specify, observe, and detect. To circumvent these challenges, we propose a new method to detect genetic interactions that leverages pleiotropy from multiple related traits without requiring the interacting variable to be specified or observed. Our approach, Latent Interaction Testing (LIT), uses the observation that correlated traits with shared latent genetic interactions have trait variance and covariance patterns that differ by genotype. LIT examines the relationship between trait variance/covariance patterns and genotype using a flexible kernel-based framework that is computationally scalable for biobank-sized datasets with a large number of traits. We first use simulated data to demonstrate that LIT substantially increases power to detect latent genetic interactions compared to a trait-by-trait univariate method. We then apply LIT to four obesity-related traits in the UK Biobank and detect genetic variants with interactive effects near known obesity-related genes. Overall, we show that LIT, implemented in the R packagelit, uses shared information across traits to improve detection of latent genetic interactions compared to standard approaches.
Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution
Authors: Taylor Ashley L. , Starr Tyler N.
Published: September 2023

Substitutions that fix between SARS-CoV-2 variants can transform the mutational landscape of future evolution via epistasis. For example, large epistatic shifts in mutational effects caused by N501Y underlied the original emergence of Omicron variants, but whether such large epistatic saltations continue to define ongoing SARS-CoV-2 evolution remains unclear. We conducted deep mutational scans to measure the impacts of all single amino acid mutations and single-codon deletions in the spike receptor-binding domain (RBD) on ACE2-binding affinity and protein expression in the recent Omicron BQ.1.1 and XBB.1.5 variants, and we compared mutational patterns to earlier viral strains that we have previously profiled. As with previous RBD deep mutational scans, we find many mutations that are tolerated or even enhance binding to ACE2 receptor. The tolerance of sites to single-codon deletion largely conforms with tolerance to amino acid mutation. Though deletions in the RBD have not yet been seen in dominant lineages, we observe many tolerated deletions including at positions that exhibit indel variation across broader sarbecovirus evolution and in emerging SARS-CoV-2 variants of interest, most notably the well-tolerated Δ483 deletion in BA.2.86. The substitutions that distinguish recent viral variants have not induced as dramatic of epistatic perturbations as N501Y, but we identify ongoing epistatic drift in SARS-CoV-2 variants, including interaction between R493Q reversions and mutations at positions 453, 455, and 456, including mutations like F456L that define the newly emerging EG.5 lineage. Our results highlight ongoing drift in the effects of mutations due to epistasis, which may continue to direct SARS-CoV-2 evolution into new regions of sequence space.
The Effect of Mechanical Stimuli on the Phenotypic Plasticity of Induced Pluripotent Stem Cell-Derived Vascular Smooth Muscle Cells in a 3D Hydrogel
Authors: Meijer Elana M. , Giles Rachel , van Dijk Christian G.M. , Maringanti Ranganath , Wissing Tamar B. , Appels Ymke , Chrifi Ihsan , Crielaard Hanneke , Verhaar Marianne C. , Smits Anthal I.P.M. , Cheng Caroline
Published: September 2023

Introduction

Vascular smooth muscle cells (VSMCs) play a pivotal role in vascular homeostasis, with dysregulation leading to vascular complications. Human induced pluripotent stem cell (hiPSC)-derived VSMCs offer prospects for personalized disease modeling and regenerative strategies. Current research lacks comparative studies on the impact of 3D substrate properties under cyclic strain on phenotype adaptation in hiPSC-derived VSMCs. Here we investigated the potential of human mural cells derived from hiPSC-derived organoids (ODMCs) to undergo phenotypical adaptation under various biological and 3D mechanical stimuli.

Methods and results

ODMCs were cultured in 2D conditions with synthetic or contractile differentiation medium, or 3D Gelatin Methacryloyl (GelMa) substrates with varying degrees of functionalization and percentages to modulate material stiffness, elasticity, and crosslink density. Cells in 3D substrates were exposed to cyclic unidirectional strain. Phenotype characterization was conducted using specific markers through immunofluorescence and gene expression analysis. Under static 2D culture, ODMCs derived from hiPSCs exhibited a VSMC phenotype, expressing key mural markers, and demonstrated a level of phenotypic plasticity like primary human vSMCs. In static 3D culture, higher substrate stiffness, lower elasticity and higher crosslink density promoted a contractile phenotype in ODMCs and vSMCs. Dynamic stimulation in 3D substrate promoted a switch towards a contractile phenotype in both cell types.

Conclusion

Our study demonstrates a phenotypic plasticity of human ODMCs in response to 2D biological and 3D mechanical stimuli that equals that of primary human vSMCs. These findings may contribute to the advancement of tailored approaches for vascular disease modelling and regenerative strategies
Position-independent functional refinement within the vagus motor topographic map
Authors: Kaneko Takuya , Boulanger-Weill Jonathan , Isabella Adam J , Moens Cecilia B
Published: September 2023

Motor neurons in the central nervous system often lie in a continuous topographic map, where neurons that innervate different body parts are spatially intermingled. This is the case for the efferent neurons of the vagus nerve, which innervate diverse muscle and organ targets in the head and viscera for brain-body communication. It remains elusive how neighboring motor neurons with different fixed peripheral axon targets develop the separate somatodendritic (input) connectivity they need to generate spatially precise body control. Here we show that vagus motor neurons in the zebrafish indeed generate spatially appropriate peripheral responses to focal sensory stimulation even when they are transplanted into ectopic positions within the topographic map, indicating that circuit refinement occurs after the establishment of coarse topography. Refinement depends on motor neuron synaptic transmission, suggesting that an experience-dependent periphery-to-brain feedback mechanism establishes specific input connectivity amongst intermingled motor populations.
Determination of glomerular filtration rate, a spin off after contrast-enhanced computed tomography among critically ill patients – proof of concept
Authors: Kågedal Bertil , Helldén Anders , Dernroth Dženeta Nezirevic , Andersen Anders , Ekman Andreas , Haglund Mats , Kataria Bharti , Oskarsson Frida , Tobieson Lovisa , Östholm Balkhed Åse , Hanberger Håkan
Published: September 2023

Background

Recently, Gong et al. (Gong et al. 2022) showed, in nine heathy subjects, that plasma clearance of high doses of iohexol given as contrast enhanced computed tomography (CT) could be used for determination of glomerular filtration rate (GFR). We utilized high doses of iohexol from angiographic or other contrast enhanced CT given to critical ill patients for calculation of GFRiohexoland compared these data with standard low dose iohexol GFR determinations.

Method

Patients at intensive care units (ICUs) in Southeast Sweden intended for radiographic investigations that included injection of 45-120 ml of iohexol (Omnipaque) were included, and the concentration of iohexol in plasma was measured by HPLC. Iohexol clearance was calculated by the method of Bröchner-Mortensen. The following days was iohexol clearance determined using the standard low dose of 5 mL of iohexol. Sixteen patients admitted to ICUs were included in this pilot study.

Results

GFR after high dosing of iohexol at contrast enhanced CT could be measured for all sixteen critically ill patients. Patients with normal or increased renal function had neglectable iohexol concentrations the day following the CT scan. There was excellent correlation between GFR determination with high and standard low iohexol dosing among these 6 patients. Ten patients had decreased renal function and delayed elimination of iohexol, thus was not GFR measurement with low dose iohexol possible to analyse the day after CT scan with high dose iohexol.

Conclusion

This pilot study showed that GFR can be measured after high doses of iohexol at enhanced CT and compare well with the standard low dose of iohexol clearance determinations.
Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology
Authors: van Boven Michiel , Backer Jantien A. , Veldhuijzen Irene , Gomme Justin , van Binnendijk Rob , Kaaijk Patricia
Published: September 2023

Mumps virus is a highly transmissible pathogen that is effectively controlled in countries with high vaccination coverage. Nevertheless, outbreaks have occurred worldwide over the past decades in vaccinated populations. Here we analyse serological data from outbreaks of mumps virus genotype G among college students in the Netherlands over the period 2009-2012. To identify infections in the presence of preexisting antibodies we compared mumps specific serum IgG concentrations in two consecutive samples (n= 746), whereby the first sample was taken when students started their study prior to the outbreaks, and the second sample was taken 2-5 years later. We fit a binary mixture model to the data. The two mixing distributions represent uninfected and infected classes. Throughout we assume that the infection probability increases with the ratio of antibody concentrations of the second to first sample. The estimated infection attack rate is higher than reported earlier (0.095 versus 0.042). The analyses yield probabilistic classifications of participants, which are mostly quite precise owing to the high intraclass correlation in uninfected participants (0.85, 95%CrI: 0.82 − 0.87). The estimated probability of infection increases with decreasing antibody concentration in the pre-outbreak sample, such that the probability of infection is 0.12 (95%CrI: 0.10 − 0.13) for the lowest quartile of the pre-outbreak samples and 0.056 (95%CrI: 0.044 − 0.068) for the highest quartile. We discuss the implications of these insights for the design of booster vaccination strategies.

Highlights

We use paired pre- and post-outbreak serological data to estimate mumps infection rates in college students.

We use a two-component mixture model to provide individual estimates of infection for each participant.

The estimated population infection attack rate is higher than reported earlier (9.5% vs 4.2%).

The estimated individual probability of infection increases with decreasing pre-outbreak antibody concentrations, from 12% in the lowest to 5.6% in the highest quartile.
Social Determinants of Genetics Referral and Completion Rates Among Child Neurology Patients
Authors: Cole Jordan J. , Sellitto Angela D. , Baratta Laura Rosa , Huecker Julia B. , Balls-Berry Joyce E. , Gurnett Christina A.
Published: September 2023

Objective

To investigate clinical, social, and systems-level determinants predictive of genetics clinic referral and completion of genetics clinic visits among child neurology patients.

Methods

Electronic health record data were extracted from patients 0-18 years old who were evaluated in child neurology clinics at a single tertiary care institution between July 2018 to January 2020. Variables aligned with the Health Equity Implementation Framework. Referral and referral completion rates to genetics and cardiology clinics were compared among Black vs White patients using bivariate analysis. Demographic variables associated with genetics clinic referral and visit completion were identified using logistic regressions.

Results

In a cohort of 11,371 child neurology patients, 304 genetics clinic referrals and 82 cardiology clinic referrals were placed. In multivariate analysis of patients with Black or White ethnoracial identity (n=10,601), genetics clinic referral rates did not differ by race, but were significantly associated with younger age, rural address, neurodevelopmental disorder diagnosis, number of neurology clinic visits, and provider type. The only predictors of genetics clinic visit completion number of neurology clinic visits and race/ethnicity, with White patients being twice as likely as Black patients to complete the visit. Cardiology clinic referrals and visit completion did not differ by race/ethnicity.

Interpretation

Although race/ethnicity was not associated with differences in genetics clinic referral rates, White patients were twice as likely as Black patients to complete a genetics clinic visit after referral. Further work is needed to determine whether this is due to systemic/structural racism, differences in attitudes toward genetic testing, or other factors.
Do dietary habits, dietary patterns, and macronutrient intakes affect aging? Multi-dimensional evidence from UK Biobank
Authors: Zhu Chen , Wang Youfa , Yang Xiaosong , Zhao Qiran , Xu Wenyan , Wang Xiaolu , Liang Yanjun , Chen Qihui , Fan Shenggen
Published: September 2023

The role of diet in aging is pivotal, yet existing research offers inconsistent findings regarding the impact of specific diets on human aging. We conducted a systematic investigation into the relationship between dietary factors and aging, exploring potential causal links between macronutrient intake and aging. Utilizing data from the UK Biobank baseline survey and a 24-hour dietary assessment survey, we employed a High-dimensional Fixed Effects (HDFE) model to examine dietary factors’ association with aging. Multivariable Mendelian Randomization (MVMR) and Semiparametric Nonlinear Mendelian Randomization (NLMR) techniques assessed causal links between macronutrient consumption and aging. HDFE analysis indicated that a healthier diet was generally linked to better aging outcomes, with various dietary components correlating with aging. For instance, plant-based food intake was associated with increased telomere length and/or reduced phenotypic age, while animal-based food consumption correlated with adverse aging effects. MVMR revealed the benefits of carbohydrate intake on aging, reducing phenotypic age (βC=C-0.0025; 95% CI=[-0.0047, -0.0003];p= 0.026) and increasing whole-brain grey matter volume (βC=C0.0262; 95% CI=[0.007, 0.046];p= 0.008). Overall, our study underscores diet’s significant role in biological aging, highlighting the potential advantages of a carbohydrate-rich diet in promoting healthy aging.
Dissociable contributions of the medial parietal cortex to recognition memory
Authors: Koslov Seth R. , Kable Joseph W. , Foster Brett L.
Published: September 2023

Human neuroimaging studies of episodic memory retrieval routinely observe the engagement of specific cortical regions beyond the medial temporal lobe. Of these, medial parietal cortex (MPC) is of particular interest given its ubiquitous, and yet distinct, functional characteristics during different types of retrieval tasks. Specifically, while recognition memory and autobiographical recall tasks are both used to probe episodic retrieval, these paradigms consistently drive distinct patterns of response within MPC. This dissociation adds to growing evidence suggesting a common principle of functional organization across memory related brain structures, specifically regarding the control or content demands of memory-based decisions. To carefully examine this putative organization, we used a high-resolution fMRI dataset collected at ultra-high field (7T) while subjects performed thousands of recognition-memory trials to identify MPC regions responsive to recognition-decisions or semantic content of stimuli within and across individuals. We observed interleaving, though distinct, functional subregions of MPC where responses were sensitive to either recognition decisions or the semantic representation of stimuli, but rarely both. In addition, this functional dissociation within MPC was further accentuated by distinct profiles of connectivity bias with the hippocampus during task and rest. Finally, we show that recent observations of person and place selectivity within MPC reflect category specific responses from within identified semantic regions that are sensitive to mnemonic demands. Together, these data better account for how distinct patterns of MPC responses can occur as a result of task demands during episodic retrieval and may reflect a common principle of organization throughout hippocampal-neocortical memory systems.

Significance statement

Medial parietal cortex (MPC) plays a growing role in contemporary theories of episodic memory, as it is reliably observed in human neuroimaging to be engaged during tasks of recognition and retrieval. However, the spatial pattern of MPC engagement consistently differs across these putatively similar episodic memory tasks. Despite a large literature indicating that the MPC is important for episodic memory, there is little consensus about its specific role. Here, we employed ‘precision-neuroimaging’ to identify dissociable interleaving MPC subregions, where activity reflected either memory-based decision-making or stimulus content. This dissociation within MPC provides a better understanding for how retrieval demands shape response patterns and speaks to growing evidence for a common principle of organization across memory structures of the human brain.
Digital holo-tomographic 3D maps of COVID-19 microclots in blood to assess disease severity
Authors: Bergaglio Talia , Synhaivska Olena , Nirmalraj Peter Niraj
Published: September 2023

The coronavirus disease 2019 (COVID-19) has impacted health globally. Cumulative evidence points to long-term effects of COVID-19 such as cardiovascular and cognitive disorders diagnosed in patients even after the recovery period. In particular, micrometer-sized blood clots and hyperactivated platelets have been identified as potential indicators of long COVID. Here we resolve individual microclot structures in platelet-rich plasma of donors with different subphenotypes of COVID-19 in a label-free manner, using 3D digital holo-tomographic microscopy (DHTM). Based on 3D refractive index (RI) tomograms, the size, dry mass, and prevalence of microclot composites were quantified and then parametrically differentiated from fibrin-rich microclots and platelet aggregates in the plasma of COVID-19 donors. Importantly, fewer microclots and platelet aggregates were detected in the plasma of healthy controls when compared to COVID-19 donors. Our work highlights the utility of integrating DHTM in clinical settings that may allow the detection of individuals at risk of developing microvascular thrombotic disorders and for monitoring the efficiency of prescribed treatments by screening plasma samples.
Single-cell epigenomic reconstruction of developmental trajectories in human neural organoid systems from pluripotency
Authors: Zenk Fides , Fleck Jonas Simon , Jansen Sophie Martina Johanna , Kashanian Bijan , Eisinger Benedikt , Santel Małgorzata , Dupre Jean , Camp J. Gray , Treutlein Barbara
Published: September 2023

Human cell type diversity emerges through a highly regulated series of fate restrictions from pluripotent progenitors. Fate restriction is orchestrated in part through epigenetic modifications at genes and regulatory elements, however it has been difficult to study these mechanisms in humans. Here, we use organoid models of the human central nervous system and establish single-cell profiling of histone modifications (H3K27ac, H3K27me3, H3K4me3) in organoid cells over a time course to reconstruct epigenomic trajectories governing cell identity acquisition from human pluripotency. We capture transitions from pluripotency through neuroepithelium, to retinal and brain region specification, as well as differentiation from progenitors to neuronal and glial terminal states. We find that switching of repressive and activating epigenetic modifications can precede and predict decisions at each stage, providing a temporal census of gene regulatory elements and transcription factors that we characterize in a gene regulatory network underlying human cerebral fate acquisition. We use transcriptome and chromatin accessibility measurements in the same cell from a human developing brain to validate this regulatory mode in a primary tissue. We show that abolishing histone 3 lysine 27 trimethylation (H3K27me3) through inhibition of the polycomb group protein Embryonic Ectoderm Development (EED) at the neuroectoderm stage disrupts fate restriction and leads to aberrant cell fate acquisition, ultimately influencing cell type composition in brain organoids. Altogether, our single-cell genome wide map of histone modifications during human neural organoid development serves as a blueprint (https://episcape.ethz.ch) to explore human cell fate decisions in normal physiology and in neurodevelopmental disorders. More broadly, this approach can be used to study human epigenomic trajectory mechanisms in any human organoid system.

Unguided neural organoids reveal widespread and dynamic switching of epigenetic modifications during development and recapitulate fate restriction from pluripotency to terminally differentiated cells of the human central nervous system.
A pipeline for constructing reference genomes for large cohort-specific metagenome compression
Authors: Wang Linqi , Ding Renpeng , He Shixu , Wang Qinyu , Zhou Yan
Published: September 2023

Metagenomic data compression is very important as metagenomic projects are facing the challenges of larger data volumes per sample and more samples nowadays. The reference-based compression is a promising method to obtain a high compression ratio. However, existing microbial reference genome databases are not suitable to be directly used as references for compression due to their large size and redundancy, and different metagenomic cohorts often have various microbial compositions. We presented a novel pipeline that generated simplified and tailored reference genomes for large metagenomic cohorts, enabling reference-based compression for metagenomic data. We constructed customized reference genomes, ranging from 2.4 to 3.9GB, for 29 real metagenomic datasets, and evaluated their compression performance. Reference-based compression achieved an impressive compression ratio of over 20 for human whole-genome data and up to 33.8 for all samples, demonstrating a remarkably 4.5 times improvement than the standard Gzip compression. Our method provides new insights into reference-based metagenomic data compression and has a broad application potential for faster and cheaper data transfer, storage, and analysis.
Toolkits for detailed and high-throughput interrogation of synapses inC. elegans
Authors: Majeed Maryam , Han Haejun , Zhang Keren , Cao Wen Xi , Liao Chien-Po , Hobert Oliver , Lu Hang
Published: September 2023

Visualizing synaptic connectivity has traditionally relied on time-consuming electron microscopy-based imaging approaches. To scale the analysis of synaptic connectivity, fluorescent protein-based techniques have been established, ranging from the labeling of specific pre- or postsynaptic components of chemical or electrical synapses to transsynaptic proximity labeling technology such as GRASP and iBLINC. In this paper, we describe WormPsyQi, a generalizable image analysis pipeline that automatically quantifies synaptically localized fluorescent signals in a high-throughput and robust manner, with reduced human bias. We also present a resource of 30 transgenic strains that label chemical or electrical synapses throughout the nervous system of the nematodeC. elegans, using CLA-1, RAB-3, GRASP (chemical synapses), or innexin (electrical synapse) reporters. We show that WormPsyQi captures synaptic structures in spite of substantial heterogeneity in neurite morphology, fluorescence signal, and imaging parameters. We use these toolkits to quantify multiple obvious and subtle features of synapses - such as number, size, intensity, and spatial distribution of synapses - in datasets spanning various regions of the nervous system, developmental stages, and sexes. Although the pipeline is described in the context of synapses, it may be utilized for other ‘punctate’ signals, such as fluorescently-tagged neurotransmitter receptors and cell adhesion molecules, as well as proteins in other subcellular contexts. By overcoming constraints on time, sample size, cell morphology, and phenotypic space, this work represents a powerful resource for further analysis of synapse biology inC. elegans.
Inference of multiple mergers while dating a pathogen phylogeny
Authors: Helekal David , Koskela Jere , Didelot Xavier
Published: September 2023

The vast majority of pathogen phylogenetic studies do not consider the possibility of multiple merger events being present, where a single node of the tree leads to more than two descendent branches. These events are however likely to occur when studying a relatively small population or if there is high variability in the reproductive chances. Here we consider the problem of detecting the presence of multiple mergers in the context of dating a phylogeny, that is determining the date of each of the nodes. We use the Lambda-coalescent theory as a modelling framework and show how Bayesian inference can be efficiently performed using a Billera-Holmes-Vogtmann space embedding and a customised Markov Chain Monte Carlo sampling scheme. We applied this new analysis methodology to a large number of simulated datasets to show that it is possible to infer if and when multiple merger events occurred, and that the phylogenetic dating is improved as a result of taking this information into account. We also analysed real datasets ofVibrio choleraeandMycobacterium tuberculosisto demonstrate the relevance of our approach to real pathogen evolutionary epidemiology. We have implemented our new methodology in a R package which is freely available athttps://github.com/dhelekal/MMCTime.
Inferring viral transmission time from phylogenies for known transmission pairs
Authors: Goldberg Emma E. , Lundgren Erik J. , Romero-Severson Ethan O. , Leitner Thomas
Published: September 2023

When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously-described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the source’s infection, and different sampling times relative to transmission, we found that overall our time-slice model provided accurate and narrower estimates of the time of transmission. We also identified situations when transmission time or direction was difficult to estimate by any method, particularly when transmission occurred long after the source was infected and when sampling occurred long after transmission. Applying our model to real HIV transmission pairs showed some agreement with facts known from the case investigations. We also found, however, that uncertainty on the inferred transmission time was driven more by uncertainty from time-calibration of the phylogeny than from the model inference itself. Encouragingly, comparable performance of the Markov time-slice model and the coalescent model—which make use of different information within a tree—suggests that a new method remains to be described that will make full use of the topology and node times for improved transmission time inference.
A Meta-Atlas of the Developing Human Cortex Identifies Modules Driving Cell Subtype Specification
Authors: Nano Patricia R. , Fazzari Elisa , Azizad Daria , Nguyen Claudia V. , Wang Sean , Kan Ryan L. , Wick Brittney , Haeussler Maximilian , Bhaduri Aparna
Published: September 2023

Human brain development requires the generation of hundreds of diverse cell types, a process targeted by recent single-cell transcriptomic profiling efforts. Through a meta-analysis of seven of these published datasets, we have generated 225 meta-modules – gene co-expression networks that can describe mechanisms underlying cortical development. Several meta-modules have potential roles in both establishing and refining cortical cell type identities, and we validated their spatiotemporal expression in primary human cortical tissues. These include meta-module 20, associated with FEZF2+ deep layer neurons. Half of meta-module 20 genes are putative FEZF2 targets, including TSHZ3, a transcription factor associated with neurodevelopmental disorders. Human cortical organoid experiments validated that both factors are necessary for deep layer neuron specification. Importantly, subtle manipulations of these factors drive slight changes in meta-module activity that cascade into strong differences in cell fate – demonstrating how of our meta-atlas can engender further mechanistic analyses of cortical fate specification.
SKIN REINNERVATION BY COLLATERAL SPROUTING FOLLOWING SPARED NERVE INJURY IN MICE
Authors: Jeon S.M. , Pradeep A. , Chang D. , McDonough L. , Chen Y. , Latremoliere A. , Crawford L.K. , Caterina M.J.
Published: September 2023

Following peripheral nerve injury, denervated tissues can be reinnervated via regeneration of injured neurons or via collateral sprouting of neighboring uninjured afferents into the denervated territory. While there has been substantial focus on mechanisms underlying regeneration, collateral sprouting has received relatively less attention. In this study, we used immunohistochemistry and genetic neuronal labeling to define the subtype specificity of sprouting-mediated reinnervation of plantar hind paw skin in the mouse spared nerve injury (SNI) model, in which productive regeneration cannot occur. Following an initial loss of cutaneous afferents in the tibial nerve territory, we observed progressive centripetal reinnervation by multiple subtypes of neighboring uninjured fibers into denervated glabrous and hairy plantar skin. In addition to dermal reinnervation, CGRP-expressing peptidergic fibers slowly but continuously repopulated the denervated epidermis, Interestingly, GFRα2-expressing nonpeptidergic fibers exhibited a transient burst of epidermal reinnervation, followed by trend towards regression. Presumptive sympathetic nerve fibers also sprouted into the denervated territory, as did a population of myelinated TrkC lineage fibers, though the latter did so less efficiently. Conversely, rapidly adapting Aβ fiber and C fiber low threshold mechanoreceptor (LTMR) subtypes failed to exhibit convincing collateral sprouting up to 8 weeks after nerve injury. Optogenetics and behavioral assays further demonstrated the functionality of collaterally sprouted fibers in hairy plantar skin with restoration of punctate mechanosensation without hypersensitivity. Our findings advance understanding of differential collateral sprouting among sensory neuron subpopulations and may guide strategies to promote the progression of sensory recovery or limit maladaptive sensory phenomena after peripheral nerve injury.

Significance Statement

Following nerve injury, whereas one mechanism for tissue reinnervation is regeneration of injured neurons, another, less well studied mechanism is collateral sprouting of nearby uninjured neurons. In this study, we examined collateral sprouting in denervated mouse skin and showed that it involves some, but not all neuronal subtypes. Despite such heterogeneity, a significant degree of restoration of punctate mechanical sensitivity is achieved. These findings highlight the diversity of collateral sprouting among peripheral neuron subtypes and reveal important differences between pre- and post-denervation skin that might be appealing targets for therapeutic correction to enhance functional recovery from denervation and prevent unwanted sensory phenomena such as pain or numbness.
ATLAS: A rationally designed anterograde transsynaptic tracer
Authors: Rivera Jacqueline F. , Weng Weiguang , Huang Haoyang , Rao Sadhna , Herring Bruce E. , Arnold Don B.
Published: September 2023

Neural circuits, which constitute the substrate for brain processing, can be traced in the retrograde direction, from postsynaptic to presynaptic cells, using methods based on introducing modified rabies virus into genetically marked cell types. These methods have revolutionized the field of neuroscience. However, similarly reliable, transsynaptic, and non-toxic methods to trace circuits in the anterograde direction are not available. Here, we describe such a method based on an antibody-like protein selected against the extracellular N-terminus of the AMPA receptor subunit GluA1 (AMPA.FingR). ATLAS (AnterogradeTranssynapticLabel based onAntibody-likeSensors) is engineered to release the AMPA.FingR and its payload, which can include Cre recombinase, from presynaptic sites into the synaptic cleft, after which it binds to GluA1, enters postsynaptic cells through endocytosis and subsequently carries its payload to the nucleus. Testing in vivo and in dissociated cultures shows that ATLAS mediates monosynaptic tracing from genetically determined cells that is strictly anterograde, synaptic, and non-toxic. Moreover, ATLAS shows activity dependence, which may make tracing active circuits that underlie specific behaviors possible.
Reduced cerebellar Gq-protein signaling elicits early onset spatial navigation deficits in a SCA6 mouse model
Authors: Grömmke Michelle , Schulte Hannah , Theis Candy D. C. , Nonnweiler Lena , Mark Melanie D.
Published: September 2023

Spinocerebellar ataxia type 6 (SCA6) is a hereditary neurodegenerative disease that manifests in a late onset and progressive impairment of motor coordination, balance and speech as well as cerebellar and brainstem atrophy. It is caused by a polyglutamine expansion in theCACNA1Agene which bicistronically encodes the α1A-subunit of the P/Q-type voltage-gated calcium channel and the transcription factor α1ACT. To date, no effective treatment exists and the exact pathobiology is controversially discussed; especially the impact on cognition is poorly understood. Here, we demonstrate that SCA6 84Q mice exhibit cognitive deficits in their spatial navigation abilities. Surprisingly, spatial memory impairments develop prior to motor impairments at 5 months of age. By expressing and stimulating a Gq-protein coupled designer receptor exclusively activated by a designer drug (Gq-DREADD) in the cerebellum, we were able to counteract these spatial navigation deficits indicating that a reduced Gq-protein signaling is part of the SCA6 phenotype. Electrophysiological recordings in anaesthetized mice further revealed that Purkinje cells (PCs) of SCA6 84Q mice exhibit a disrupted spontaneous simple spike activity that precedes the development of both cognitive and motor deficits. Concurrently, PC dysfunction was further confirmed by elevated numbers of torpedoes found in the proximal axon of PCs throughout the cerebellum. Overall, our study raises awareness to survey cognitive abnormalities more carefully during clinical examination to detect the disease earlier and potentially optimize the individual treatment by enhancing PC signaling.

Significance statement

SCA6 is a hereditary neurological disease that is mainly characterized by the late-onset development of progressive motor deficits. Here we show, using a SCA6 mouse model, that cognitive impairments in spatial navigation are also a non-negligible feature of the disease which manifests earlier than the motor deficits. Moreover, we demonstrate that these spatial navigation deficits are caused by a reduced Gq-protein signaling in the cerebellum. Electrophysiological and histological analysis further confirmed dysfunctional PC signaling even before the onset of first symptoms. Since no effective treatment is available for SCA6 patients, early onset stimulation of PC signaling may be a new therapeutic approach.
Unraveling Neural Complexity: Exploring Brain Entropy to Yield Mechanistic Insight in Neuromodulation Therapies for Tobacco Use Disorder
Authors: Jordan Timothy , Apostol Michael R. , Nomi Jason , Petersen Nicole
Published: September 2023

Neuromodulation therapies, such as repetitive transcranial magnetic stimulation (rTMS), have shown promise as treatments for tobacco use disorder (TUD). However, the underlying mechanisms of these therapies remain unclear, which may hamper optimization and personalization efforts. In this study, we investigated alteration of brain entropy as a potential mechanism underlying the neural effects of noninvasive brain stimulation by rTMS in people with TUD. We employed sample entropy (SampEn) to quantify the complexity and predictability of brain activity measured using resting-state fMRI data. Our study design included a randomized single-blind study with 42 participants who underwent 2 data collection sessions. During each session, participants received high-frequency (10Hz) stimulation to the dorsolateral prefrontal cortex (dlPFC) or a control region (visual cortex), and resting-state fMRI scans were acquired before and after rTMS. Our findings revealed that individuals who smoke exhibited higher baseline SampEn throughout the brain as compared to previously-published SampEn measurements in control participants. Furthermore, high-frequency rTMS to the dlPFC but not the control region reduced SampEn in the insula and dlPFC, regions implicated in TUD, and also reduced self-reported cigarette craving. These results suggest that brain entropy may serve as a potential biomarker for effects of rTMS, and provide insight into the neural mechanisms underlying rTMS effects on smoking cessation. Our study contributes to the growing understanding of brain-based interventions for TUD by highlighting the relevance of brain entropy in characterizing neural activity patterns associated with smoking. The observed reductions in entropy following dlPFC-targeted rTMS suggest a potential mechanism for the therapeutic effects of this intervention. These findings support the use of neuroimaging techniques to investigate the use of neuromodulation therapies for TUD.
Smooth Pursuit Inhibition Reveals Audiovisual Enhancement of Fast Movement Control
Authors: Kreyenmeier Philipp , Bhuiyan Ishmam , Gian Mathew , Chow Hiu Mei , Spering Miriam
Published: September 2023

The sudden onset of a visual object or event elicits an inhibition of eye movements at latencies approaching the minimum delay of visuomotor conductance in the brain. Typically, information presented via multiple sensory modalities, such as sound and vision, evokes stronger and more robust responses than unisensory information. Whether and how multisensory information affects ultra-short latency oculomotor inhibition is unknown. In two experiments, we investigate smooth pursuit and saccadic inhibition in response to multisensory distractors. Observers tracked a horizontally moving dot and were interrupted by an unpredictable visual, auditory, or audiovisual distractor. Distractors elicited a transient inhibition of pursuit eye velocity and catch-up saccade rate within ∼100 ms of their onset. Audiovisual distractors evoked stronger oculomotor inhibition than visual-or auditory-only distractors, indicating multisensory response enhancement. Multisensory response enhancement magnitudes were equal to the linear sum of responses to component stimuli. These results demonstrate that multisensory information affects eye movements even at ultra-short latencies, establishing a lower time boundary for multisensory-guided behaviour. We conclude that oculomotor circuits must have privileged access to sensory information from multiple modalities, presumably via a fast, subcortical pathway.
Cardiac glycosides restore autophagy flux in an iPSC-derived neuronal model of WDR45 deficiency
Authors: Papandreou Apostolos , Singh Nivedita , Gianfrancesco Lorita , Budinger Dimitri , Barwick Katy , Agrotis Alexander , Luft Christin , Shao Ying , Lenaerts An-Sofie , Gregory Allison , Jeong Suh Young , Hogarth Penelope , Hayflick Susan , Barral Serena , Kriston-Vizi Janos , Gissen Paul , Kurian Manju A , Ketteler Robin
Published: September 2023

Beta-Propeller Protein-Associated Neurodegeneration (BPAN) is one of the commonest forms of Neurodegeneration with Brain Iron Accumulation, caused by mutations in the gene encoding the autophagy-related protein, WDR45. The mechanisms linking autophagy, iron overload and neurodegeneration in BPAN are poorly understood and, as a result, there are currently no disease-modifying treatments for this progressive disorder. We have developed a patient-derived, induced pluripotent stem cell (iPSC)-based midbrain dopaminergic neuronal cell model of BPAN (3 patient, 2 age-matched controls and 2 isogenic control lines) which shows defective autophagy and aberrant gene expression in key neurodegenerative, neurodevelopmental and collagen pathways. A high content imaging-based medium-throughput blinded drug screen using the FDA-approved Prestwick library identified 5 cardiac glycosides that both corrected disease-related defective autophagosome formation and restored BPAN-specific gene expression profiles. Our findings have clear translational potential and emphasise the utility of iPSC-based modelling in elucidating disease pathophysiology and identifying targeted therapeutics for early-onset monogenic disorders.
An approach to investigate the crystallographic unit cell of human tooth enamel
Authors: Reyes-Gasga Jose , Tehuacanero-Núñez Samuel , Sánchez-Ochoa Francisco
Published: September 2023

Human tooth enamel (HTE) is the hardest tissue in the human body and its structural organization shows a hierarchical composite material. At the nanometric level, HTE is composed of approximately 97% hydroxyapatite [HAP, Ca10(PO4)6(OH)2] as inorganic phase, and of 3% as organic phase and water. However, it is still controversial whether the hexagonal HAP phase crystallizes in P63/m or another space group. The observance in HTE of Ca2+, Mg2+ and Na+ ions using X-ray characteristic energy-dispersive spectroscopy in the scanning electron microscope has been explained by substitutions in the HAP unit cell. Thus, Ca2+ can be replaced by Na+ and Mg2+ ions; the PO4
3− group can be replaced by CO3
2− ions; and the OH− ions can also be replaced by CO3
2−. A unit-cell model of the hexagonal structure of HTE is not fully defined yet. In this work, density functional theory calculations are performed to study the hexagonal HAP unit cell when substitution by OH−, CO3
2−, Mg2+ and Na+ ions are carried out. An approach is presented to study the crystallographic unit cell of HTE by examining the changes resulting from the inclusion of these different ions in the unit cell of HAP. Enthalpies of formation and crystallographic characteristics of the electron diffraction patterns are analysed in each case. The results show an enhancement in structural stability of HAP with OH defects, atomic substitution of Mg2+, carbonate and interstitial Na+. Simulated electron diffraction patterns of the generated structures show similar characteristics to those of human tooth enamel. Hence, the results explain the indiscernible structural changes shown in experimental X-ray diffractograms and electron diffraction patterns.
Effect of pre-rolling aging treatment on evolutions of the microstructure and the texture of aluminium alloy 7005 subjected to heavy cold rolling
Authors: Farshidi Mohammad Hassan , Miyamoto Hiroyuki , Ito Haruka
Published: September 2023

Aluminium alloy 7005 is widely used for structural purposes because of its attractive properties such as good weldability and age-hardening capability. However, since the workability of this alloy falls after a short period of natural aging, the application of cold rolling for the production of strain-hardened sheets of this alloy is a challenge. Two solutions proposed to overcome this challenge are as follows: (a) immediate rolling of the alloy after solution treatment and (b) rolling of the alloy after artificial aging. However, there is no comprehensive study comparing the effect of pre-rolling aging treatments on the evolutions of microstructure and texture of the alloy through heavy cold rolling. This subject is the aim of the present study. For this purpose, different pieces of the alloy are subjected to three different heat treatments before rolling, and afterward, they are rolled to obtain a thickness reduction of 80%. Scanning electron microscopy with electron backscattered diffraction observations are applied to study the evolutions of the microstructure and the texture of the alloy. Results show that the progression of pre-rolling aging decreases the incidence of micro-scaled shear bands by rolling. In addition, the rolling texture intensity decreases with the advancement of pre-rolling aging. Mechanisms responsible for this effect are discussed.