bluuebunny/crossref_metadata_2025 huggingface dataset:
Disrupted spatial and contextual memory encoding in the hippocampus of 5xFAD mice precedes cognitive impairment
Authors: Li Yimei , Go Mary Ann , Zhang Hualong , Schultz Simon R
Published: February 2025

Alzheimer’s disease (AD) is marked by progressive cognitive decline, yet the underlying neural mechanisms are not fully understood. To address this, we investigated hippocampal activity in 5xFAD model mice performing a continuous spatial alternation task, combining behavioural assessment within vivotwo-photon calcium imaging. Young 5xFAD mice exhibited mild performance deficits, which worsened with age. Older 5xFAD mice showed significant impairments in task acquisition and alternation accuracy, with significant behavioural hyperactivity. Hippocampal CA1 neurons in 5xFAD mice showed early impairments in spatial representation, prior to showing behavioural deficits. Both young and old 5xFAD mice exhibited reduced spatial tuning, fewer place cells, and decreased trial-to-trial reliability in comparison to wildtype sibling controls. Additionally, 5xFAD mice demonstrated disrupted spatial encoding of reward locations, with reduced spatial correlation between correct and error trials. Analysis of hippocampal “splitter” cells revealed reduced splitting activity in 5xFAD mice, with reduced discriminability and reliability of trajectory-dependent activity. These deficits correlated with poorer task performance, suggesting that disrupted contextual encoding contributes to cognitive decline in AD. Our findings highlight early disruptions in hippocampal spatial and contextual encoding in 5xFAD mice, which precede behavioural impairments and provide insights into AD pathophysiology.

Teaser

Two-photon imaging in behaving AD mice reveals impairments in spatial and contextual memory circuits prior to cognitive deficits.
Cerebral blood perfusion across biological systems and the human lifespan
Authors: Farahani Asa , Liu Zhen-Qi , Ceballos Eric G. , Hansen Justine Y , Wennberg Karl , Zeighami Yashar , Dadar Mahsa , Gauthier Claudine J , Dagher Alain , Misic Bratislav
Published: February 2025

Blood perfusion delivers oxygen and nutrients to all cells, making it a fundamental feature of brain organization. How cerebral blood perfusion maps onto micro-, meso- and macro-scale brain structure and function is therefore a key question in neuroscience. Here we analyze pseudo-continuous arterial spin labeling (ASL) data from 1,305 healthy individuals in the HCP Lifespan studies (5-100 years) to reconstruct a high-resolution normative cerebral blood perfusion map. At the cellular and molecular level, cerebral blood perfusion co-localizes with granular layer IV, biological pathways for maintenance of cellular relaxation potential and mitochondrial organization, and with neurotransmitter and neuropeptide receptors involved in vasomodulation. At the regional level, blood perfusion aligns with cortical arealization and is greatest in regions with high metabolic demand and resting-state functional hubs. Looking across individuals, blood perfusion is dynamic throughout the lifespan, follows micro-architectural changes in development, and maps onto individual differences in physiological changes in aging. In addition, we find that cortical atrophy in multiple neurodegenerative diseases (late-onset Alzheimer's disease, TDP-43C, and dementia with Lewy bodies) is most pronounced in regions with lower perfusion, highlighting the utility of perfusion topography as an indicator of transdiagnostic vulnerability. Finally, we show that ASL-derived perfusion can be used to delineate arterial territories in a data-driven manner, providing insights into how the vascular system is linked to human brain function. Collectively, this work highlights how cerebral blood perfusion is central to, and interlinked with, multiple structural and functional systems in the brain.
Bat things come in threes: within-host dynamics of herpesvirus triple infection in bats
Authors: Aguillon Samantha , Turpin Magali , Le Minter Gildas , Lebarbenchon Camille , Hoarau Axel O. G. , Mavingui Patrick , Dietrich Muriel
Published: February 2025

Understanding viral community ecology in bats is essential for elucidating shedding patterns and the drivers of co-infections. In this study, we explore the genetic diversity and within-host dynamics of herpesviruses (HSV) in Mormopterus francoismoutoui, a tropical insectivorous bat endemic to Reunion Island. Over three consecutive years, we collected saliva samples from seven roosts, including repeated samples from recaptured individuals. Illumina sequencing of HSV PCR-positive samples revealed a high diversity of strains (n = 20), belonging to alpha, beta and gamma-HSV subfamilies. Co-infection was frequent, with 44% of bats shedding strains from all three subfamilies. While most shedding patterns with different subfamilies appeared random, our results suggested a negative influence of gamma-HSV occurrence of the probability of co-shedding alpha-HSV. We also demonstrated a lower HSV diversity in juveniles as compared to adult bats, while pregnancy appeared to increase viral diversity-although this requires further confirmation. Longitudinal recaptures of bats revealed an accumulation of multiple HSV latent-infections over life, as the probability to be infected with a new subfamily increased with time interval between recaptures. Within-host strain dynamics were highly variable, with 79% of bats showing fluctuations in strain diversity over time-either gaining or losing strains-consistent with latency and reactivation mechanisms. These findings provide new insights into the ecological and evolutionary dynamics of herpesviruses in wild bat populations.
Evolutionary trends inBombellaapis CRISPR-Cas systems
Authors: Ganote Carrie L , Caesar Lílian , Rice Danny W , Whitaker Rachel J , Newton Irene LG
Published: February 2025

Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found in Bombella apis, a microbe associated with honey bee queens, brood, and royal jelly. Unlike other honey bee microbiome members, B. apis does not colonize the worker bee midgut or hindgut and has therefore been understudied with regards to its importance in the honey bee colony. However, B. apis appears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously we identified CRISPR-Cas systems as being acquired by B. apis in its transition to bee association, as they are absent in a sister clade. Here we assess the variation and distribution of CRISPR-Cas types across B. apis strains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the same B. apis genomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for each B. apis strain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that the B. apis CRISPR-Cas systems are dynamic, that microbes in the same niche have unique spacers which supports the functionality of these CRISPR-Cas systems, and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe.

IMPORTANCE

Honey bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host a different group of microbes, including the acetic acid bacteriumBombella apis. B. apisis found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen digestive tract. The roles thatB. apismay serve in these environments are just beginning to be discovered and include production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bol-stering their nutrition. Niche specificity inB. apismay be affected by the pressures of bacteriophage and other mobile elements which may target different strains in each specific bee environment. Studying the interplay betweenB. apisand its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host.
The impact of perturbation intensity schedule on improvements in reactive balance control in young adults: an experimental study
Authors: Wong Piufat , Yeh Isabel , Mansfield Avril , McCrum Christopher
Published: February 2025

Background

Reactive balance training (RBT) uses unanticipated perturbations to improve balance reactions and prevent falls. Intensity and predictability of perturbations may affect the generalizability of RBT, but their relative contributions remain unclear. This study aimed to compare the effects of three RBT schedules with differing intensity and predictability on participants’ balance recovery following untrained perturbations, and to determine perceived difficulty and challenge of the training schedules.

Methods

Participants were 36 healthy young adults (20-35 years). Participants were randomly assigned to one of three RBT intensity schedules (fixed high intensity, low-to-high intensity, and variable intensity). Training took place on a motion platform that delivered perturbations in varying directions (forward, backward, left, and right) and intensities across five trial blocks. Balance reactions (number of recovery steps) pre- and post-training, and electrodermal responses, and perceived difficulty during training were collected. Statistical analyses compared post-training outcomes between training groups, controlling for the baseline value.

Results

Participants took fewer steps and decreased the proportion of multi-step reactions pre- to post-training (p<0.0001), with no significant between-group differences. Perceived exertion decreased significantly across training blocks in the fixed-high group and increased significantly in the low-to-high group. Electrodermal responses declined across all groups between training blocks 1 and 3 (p=0.017).

Conclusions

Improvements in step reactions to untrained perturbations did not differ between training groups, highlighting the importance of multi-directional variability over specific intensity schedules for enhancing balance recovery.
Avid lysosomal acidification in fibroblasts of the Mediterranean mouse Mus spretus
Authors: Sui Melissa , Teh Joanne , Fort Kayleigh Annette , Shaw Daniel E , Sudmant Peter H , Koide Tsuyoshi , Good Jeffrey , Vazquez Juan Manuel , Brem Rachel B
Published: February 2025

Failures of the lysosome-autophagy system are a hallmark of aging and many disease states. As a consequence, interventions that enhance lysosome function are of keen interest in the context of drug development. Throughout the biomedical literature, evolutionary biologists have discovered that challenges faced by humans in clinical settings have been resolved by non-model organisms adapting to wild environments. Here, we used a primary cell culture approach to survey lysosomal characteristics in selected species of the genus Mus. We found that cells from M. musculus, mice adapted to human environments, had weak lysosomal acidification and high expression and activity of the lysosomal enzyme β-galactosidase, a classic marker of cellular senescence. Cells of wild relatives, especially the Mediterranean mouse M. spretus, had more robustly performing lysosomes and dampened β-galactosidase levels. We propose that classic laboratory models of lysosome function and senescence may reflect characters that diverge from the phenotypes of wild mice. The M. spretus phenotype may ultimately provide a blueprint for interventions that ameliorate lysosome breakdown in stress and disease.
Dietary quorum quenching AHL lactonase impairs the adaptation of commensal bacterium to host innate immunity
Authors: Xia Rui , Yao Yuanyuan , Meng Delong , Zhao Yajie , Xu Shichang , Jin Ya , Zhang Zhen , Yang Yalin , Ran Chao , Zhou Zhigang
Published: February 2025

Quorum sensing (QS) is the communication system of bacteria that depends on QS signals. Quorum quenching (QQ) enzymes degrade QS signals and are promising alternatives of antibiotics to treat bacterial infections. Here, we found that dietary QQN-acyl homoserine (AHL) lactonase led to microbiota dysbiosis in zebrafish, with reduction ofAeromonasand enrichment ofPlesiomonas. Through gnotobiotic zebrafish colonized with a minimal microbiota, we found that QQ-mediated microbial alteration relies on host Myd88 signaling and neutrophil elastase. Mechanistically, quorum quenching increased the susceptibility of commensalAeromonasto host neutrophil elastase by impairing bacterial lateral flagellar system, leading to reduced colonization ofAeromonasand subsequent enrichment ofPlesiomonasdue to ecological competition of the two species. Together, we found that dietary QQ lactonase led to microbiota alteration by impairing the adaptation of commensalAeromonasto host innate immunity, which provided novel insight in the role of quorum sensing in host-microbiota interaction.
Single-nucleus analysis reveals dysregulated oxidative phosphorylation in Down syndrome basal forebrain at birth
Authors: West Nicole R. , Arachchilage Kalpana Hanthanan , Knaack Sara , Hosseini Masoumeh , Risgaard Ryan D. , MacGregor Shawn , Kumarage Pubudu , Martinez Jose L. , Wang Daifeng , Sousa Andre M.M. , Bhattacharyya Anita
Published: February 2025

INTRODUCTION

Basal forebrain cholinergic neurons (BFCNs) are integral to learning, attention, and memory, and are prone to degeneration in Down syndrome (DS), Alzheimer’s disease, and other neurodegenerative diseases. However, the mechanisms that lead to degeneration of these neurons are not known.

METHODS

Single-nuclei gene expression and ATAC sequencing were performed on postmortem human basal forebrain from unaffected control and DS tissue samples at 0-2 years of age (n=4 each).

RESULTS

Sequencing analysis of postmortem human basal forebrain identifies gene expression differences in early postnatal DS early in life. Genes encoding proteins associated with energy metabolism pathways, specifically oxidative phosphorylation and glycolysis, and genes encoding antioxidant enzymes are upregulated in DS BFCNs.

DISCUSSION

Multiomic analyses reveal that energy metabolism may be disrupted in DS BFCNs by birth. Increased oxidative phosphorylation and the accumulation of reactive oxygen species byproducts may be early contributors to DS BFCN neurodegeneration.
Functional Impact of Glycosylation and Splicing Variants of LRIG1 on EGFR Proteostasis in Cancer
Authors: Kondo Jumpei , Nagao Himari , Oyama Koki , Sakon Daisuke , Nakayama Honoka , Takamatsu Shinji , Miyoshi Eiji
Published: February 2025

LRIG1, a membrane glycoprotein, has emerged as a significant stem cell marker and negative regulator of receptor tyrosine kinases (RTKs), including EGFR. Glycosylation is a major post-translational modification, which plays a crucial role in protein function and stability. In cancer biology, abnormal glycosylation can serve as a biomarker and contribute to pathogenesis. We aimed to investigate the effects of glycosylation on LRIG1 functions. Through database analysis and experimental approaches, we focused on evolutionarily conserved glycosylation sites of LRIG1, particularly N74 in humans. We found that a mutation of the N74 glycosylation site (N74Q) enhances LRIG1’s binding to EGFR and promotes EGFR degradation. Furthermore, we identified a naturally occurring splice variant of LRIG1 lacking exon 2, which includes the N74 site, that shows similar enhanced EGFR binding and degradation. Analysis of TCGA data revealed that exon 2 skipping in LRIG1 occurs in various cancers, with higher levels correlating with poorer survival in breast and ovarian cancers. Our findings suggest that the absence of glycosylation at N74 enhances LRIG1-EGFR binding, providing an example of glycosylation negatively regulating protein-protein interaction. This mechanism, achieved through alternative splicing, provides insights into the importance of glycosylation deficiency in cancer biology.
Heterogeneity ofCandidabloodstream isolates in an academic medical center and affiliated hospitals
Authors: Scott Nancy E. , Wash Elizabeth , Zajac Christopher , Erayil Serin E. , Kline Susan E. , Selmecki Anna
Published: February 2025

InvasiveCandidabloodstream infections (candidemia) are a deadly global health threat. RareCandidaspecies are increasingly important causes of candidemia and phenotypic data, including patterns of antifungal drug resistance, is limited. There is geographic variation in the distribution ofCandidaspecies and frequency of antifungal drug resistance, which means that collecting and reporting regional data can have significant clinical value. Here, we report the first survey of species distribution, frequency of antifungal drug resistance, and phenotypic variability ofCandidabloodstream isolates from an academic medical center and 5 affiliated hospitals in the Minneapolis-Saint Paul region of Minnesota, collected during an 18-month period from 2019 to 2021. We collected 288 isolates spanning 11 species from 119 patients.C. albicanswas the most frequently recovered species, followed byC. glabrataandC. parapsilosis, with 10% of cases representing additional, rare species. We performed antifungal drug susceptibility for the three major drug classes and, concerningly, we identified fluconazole, micafungin and multidrug resistance rates inC. glabratathat were ∼ 2 times higher than that reported in other regions of the United States. We report some of the first phenotypic data in rare non-albicans Candidaspecies. Through analysis of serial isolates from individual patients, we identified clinically relevant within-patient differences of MIC values in multiple drug classes. Our results provide valuable clinical data relevant to antifungal stewardship efforts and highlight important areas of future research, including within-patient dynamics of infection and the mechanisms of drug resistance in rareCandidaspecies.
PET imaging of an antisense oligonucleotide in the living non-human primate brain using click chemistry
Authors: Cook Brendon E. , Pickel Thomas C. , Nag Sangram , Bolduc Philippe N. , Beshr Rouaa , Morén Anton Forsberg , Muste Cathy , Boscutti Giulia , Jiang Di , Yuan Long , Datta Prodip , Ochniewicz Piotr , Meynaq Yasir Khani , Tang Sac-Pham , Plisson Christophe , Amatruda Mario , Zhang Qize , DuBois Jonathan M. , Delavari Armin , Klein Stephanie K. , Polyak Ildiko , Shoroye Adebowale , Girmay Sara , Halldin Christer , Martarello Laurent , Peterson Emily A. , Kaliszczak Maciej
Published: February 2025

Determination of a drug’s biodistribution is critical to ensure it reaches the target tissue of interest. This is particularly challenging in the brain where invasive sampling methods may not be possible. Here, a pretargeted imaging methodology is disclosed that utilizes bioorthogonal click chemistry to determine the distribution of an antisense oligonucleotide in the living brain following intrathecal dosing. A novel PET tracer, [18F]BIO-687, bearing a click-reactivetrans-cyclooctene (TCO) was discovered and tested in conjunction with a Malat1 antisense oligonucleotide (ASO) conjugated with a methyltetrazine (MeTz). PET imaging in rats demonstrated that the tracer possesses good kinetic properties for CNS imaging and can react to form a covalent linkage with high specificity to the MeTz-conjugated-ASOin vivo. Further, the amount of tracer reacted by cycloaddition with the Tz was determined to be dependent on the concentration of ASO-MeTz in tissue, as determined through comparison of the imaging signal with the LC-MS of the tissue homogenate. The system was evaluated in cynomolgus monkeys, with PET imaging showing favorable tracer kinetics and specific binding to the ASOin vivo. These results demonstrate that the tracer [18F]BIO-687 can image intrathecally-delivered ASO distribution in the brain, and future studies should leverage this technology to evaluate ASO distribution in human subjects to study distribution.

One Sentence Summary

Distribution of an intrathecally administered antisense oligonucleotide can be imaged using a pretargeted approach in the living brains of non-human primates.
Systems acclimation to osmotic stress in zygnematophyte cells
Authors: Zegers Jaccoline M.S. , Pfeifer Lukas , Darienko Tatyana , Schmitt Kerstin , Dorsch Craig A. , Kunz Cäcilia F. , Braus Gerhard H. , Classen Birgit , Valerius Oliver , de Vries Jan
Published: February 2025

Zygnematophytes are the closest algal relatives of land plants. They hold key information to infer how the earliest land plants overcame the barrage of terrestrial stressors, prime of which is osmotic stress. Here, we applied two osmotic stressors on a unicellular and a multicellular representative of zygnematophytes and studied their response over a 25-hour time course generating 130, 60, and 30 of transcriptomic, proteomic, and metabolomic samples combined with photophysiology, sugar analysis, immunocytochemical glycoprotein analysis, and microscopy. Our data highlight a shared protein chassis that shows divergent responses with the same outcome: successful acclimation to osmotic challenges. We establish a model of how the algal sisters of land plants can overcome a prime stressor in the terrestrial habitat and highlight components of the plant terrestrialization toolkit.
Noradrenaline and Acetylcholine shape Functional Connectivity organization of NREM substages: an empirical and simulation study
Authors: Lehue Fernando , Coronel-Oliveros Carlos , Medel Vicente , Liebe Thomas , Kaufmann Jörn , Orellana Sebastián , Becerra Diego , Tagliazucchi Enzo , Orio Patricio
Published: February 2025

Sleep onset is characterized by a departure from arousal, and can be separated into well-differentiated stages: NREM (which encompasses three substages: N1, N2 and N3) and REM (Rapid Eye Movement). Awake brain dynamics are maintained by various wake-promoting mechanisms, particularly the neuromodulators Acetylcholine (ACh) and Noradrenaline (NA), whose levels naturally decrease during the transition to sleep. The combined influence of these neurotransmitters on brain connectivity during sleep remains unclear, as previous models have examined them mostly in isolation or only in deep sleep. In this study, we employ a Whole Brain model to investigate how changes in brain neurochemistry during NREM sleep, specifically involving ACh and NA, affect the Functional Connectivity (FC) of the brain. Using a Wilson-Cowan whole brain model informed by an empirical connectome and a heterogeneous receptivity map of neuromodulators, we explore these dynamics. Initial FC analysis reveals distinct connectivity changes: a decrease in Locus Coeruleus (LC) connectivity with the cortex during N2 and N3, and a decrease in Basal Forebrain (BF) connectivity with the cortex during N3. Additionally, compared to Wakefulness (W), there is a transition to a more integrated state in N1 and a more segregated state in N3. We adjust the coupling and input-output slope of the Whole Brain model for ACh and NA, based on BF or LC priors, to show that region-specific neurotransmitter distribution is key to explaining their effects on FC. This work enhances our understanding of neurotransmitters’ roles in modulating sleep stages and their significant contribution to brain state transitions between different states of consciousness, both in health and disease.
Epigenome and transcriptome changes inKMT2D-related Kabuki syndrome Type 1 iPSCs, neuronal progenitors and cortical neurons
Authors: Cuvertino S. , Martirosian E. , Cheng P. , Garner T. , Donaldson I. J. , Jackson A. , Stevens A. , Sharrocks A. D. , Kimber S. J. , Banka S.
Published: February 2025

Kabuki syndrome type 1 (KS1) is a neurodevelopmental disorder caused by loss-of-function variants inKMT2Dwhich encodes a H3K4 methyltransferase. The mechanisms underlying neurodevelopmental problems in KS1 are still largely unknown. Here, we track the epigenome and transcriptome across three stages of neuronal differentiation using patient-derived induced pluripotent stem cells (iPSCs) to gain insights into the disease mechanism of KS1. In KS1 iPSCs we detected significantly lower levels of functionalKMT2Dtranscript and KMT2D protein, and lower global H3K4me1 and H3K4me2 levels. We identify loss of thousands of H3K4me1 peaks in iPSCs, neuronal progenitors (NPs) and early cortical neurons (CNs) in KS1. We show that the number of lost peaks increase as differentiation progresses. We also identify hundreds of differentially expressed genes (DEGs) in iPSCs, NPs and CNs in KS1. In contrast with the epigenomic changes, the number of DEGs decrease as differentiation progresses. Our analysis reveals significant enrichment of differentially downregulated genes in areas containing putative enhancer regions with H3K4me1 loss. We also identify a set of distinct transcription factor binding sites in differentially methylated regions and a set of DEGs related to KS1 phenotypes. We find that genes regulated by SUZ12, a subunit of Polycomb Repressive complex 2, are over-represented in KS1 DEGs at early stages of differentiation. In conclusion, we present a disease-relevant human cellular model for KS1 that provides mechanistic insights for the disorder and could be used for high throughput drug screening for KS1.
The diversity of cellular systems involved in carbonate precipitation byEscherichia coli
Authors: Jennings Matthew E. , Breley George J. , Blackwell Reilly S. , Drabik Anna , Gisser Kathleen R. , Kainrad Joe , Ligman Victoria , Proctor Jaycie , Deshler Rose , O’Hart Brian A. , Rivera Arlyn , Centrella Lorelei , Bonn Sara , Chaudhry Bisma , Barton Hazel A.
Published: February 2025

Climate change is increasing the need to limit levels of anthropogenic CO2released into the atmosphere. One approach being investigated is to generate products based on microbially induced carbonate precipitation (MICP), which can trap CO2as CaCO3. We recently identified a novel MICP pathway in bacteria that is initiated by Ca2+toxicity in cells, causing extracellular CO2to be trapped as CO2-byEscherichia coli,although the yield of precipitated CaCO remained low (in the milligram range). In this work, we used theE. coliKeio gene knock-out library to identify 54 genes involved in MICP inE. coli,which could be broadly characterized into four groups: central metabolism, iron metabolism, cell architecture, and transport. The role of central metabolism appears to be crucial in maintaining alkaline conditions surrounding the cell that promote CaCO3precipitation. The role of iron metabolism was less clear, although the results suggest that growth rate influences the initiation of MICP. While the impact of repeating polymeric structures on cell surfaces promoting MICP is well established, our results suggest that other structural features may play a role, including fimbriae and flagella. Finally, the results confirmed that Ca2+transport is central to MICP under calcium stress. The results further suggest that the ZntB efflux pump may play a previously unidentified role in Ca2+transport inE. coli.By overexpressing some of these genes, our work suggests that there are several previously unidentified cellular mechanisms that could serve as a target for enhanced MICP inE. coli.By incorporating these processes into MICP pathways inE. coli,it may be possible to increase the volume of CO2fixed using this pathway and yield potentially new products that can replace CO2intensive products, such as precipitated calcium carbonates (PCCs) for industry.
Museum genomics reveals temporal genetic stasis and global genetic diversity inArabidopsis thaliana
Authors: Lopez Lua , Lang Patricia L. M. , Marciniak Stephanie , Kistler Logan , Latorre Sergio M. , Haile Asnake , Vasquez Cerda Eleanna , Gamba Diana , Xu Yuxing , Woods Patrick , Yifru Mistire , Kerby Jeffrey , McKay John K. , Oakley Christopher G. , Ågren Jon , Wondimu Tigist , Bulafu Collins , Perry George H. , Burbano Hernán A. , Lasky Jesse R.
Published: February 2025

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, environmental change (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections ofArabidopsis thalianaand combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.
Serial Dependence Predicts Generalization in Perceptual Learning
Authors: Pinchuk-Yacobi Noga , Sagi Dov , Bonneh Yoram S.
Published: February 2025

Recent visual experiences systematically bias current perceptual reports, a phenomenon known as serial dependence. This study examines how serial dependence interacts with perceptual learning, specifically focusing on its role in learning generalization. We reanalyzed data from 50 observers who practiced the texture discrimination task (TDT) under three conditions designed to modulate learning generalization: consistent target location, alternating two target locations, and mixed with targetless trials (Harris et al., 2012); over 200,000 trials. Our analysis revealed substantial report biases toward the orientation of targets from previous trials, extending up to 10 trials back, much longer than previously reported. These biases, when accumulated across consistent trial sequences, nearly overshadowed responses to the current target. Remarkably, although TDT thresholds improved by 40% over the 8 days of training, the biases persisted despite the randomization of target orientations, with trial history being irrelevant to the current trial. The effect was most pronounced when current targets had low visibility, prior targets were highly visible, and prior targets appeared at the same location as the current target. Training conditions that facilitated learning generalization exhibited stronger and longer serial dependence effects from distant trial histories compared to conditions promoting specific learning. Across observers, stronger serial dependence from distant history was associated with greater learning transfer, suggesting that distant memory traces are essential for efficient learning. We propose that these extended memory traces integrate information across multiple trials to create a generalized learning template, preventing overfitting to specific stimuli thus enhancing learning transfer. In contrast, strong adaptation in the consistent target location condition disrupts these traces, thereby limiting generalization.
Long non-coding RNA BCAR4 is required for efficient influenza A virus replication
Authors: Cao Yi , Chin Alex W.H. , Gu Haogao , Li Mengting , Poon Leo L.M.
Published: February 2025

Long non-coding RNAs (lncRNAs) regulate diverse biological processes, including influenza A virus (IAV) infection. However, the understanding of lncRNAs in IAV infection is limited. By using both bioinformatic analyses and virological assays, we showed that lncRNABCAR4expression can be highly induced by infection of multiple different IAV subtypes.BCAR4was required for the propagation of IAV infection. Genetic inactivation ofBCAR4inhibited IAV growth. Investigation of the IAV infection cycle revealed a suppressed IAV viral RNA transcription and replication, and attenuated viral protein synthesis in theBCAR4-deficient cells.BCAR4potentially interacted with cellular splicing-associated proteins and the activation ofBCAR4was associated with influenza viralNSsegment. These findings suggest the important role of lncRNABCAR4in regulation of IAV infection.

Importance

Long non-coding RNAs (lncRNAs) serve as critical regulators in the biological processes of influenza A virus (IAV) infection. However, how lncRNAs engage IAV infection remains unclear. Here we showBCAR4as highly universally induced lncRNA in infection of multiple different IAV subtypes. Deletion ofBCAR4reduced IAV multiplication. In the IAV infection cycle,BCAR4deficiency decreased IAV viral RNA transcription, replication and viral protein biosynthesis.BCAR4was potentially binding to the host RNA splicing associated protein, and the IAV viral NS segment is required for the activation ofBCAR4. Our results highlight important regulation ofBCAR4in IAV infection.
Fluctuations in arousal reflect latent state transitions that facilitate behavioral optimization
Authors: Li Tiantian , Marble Harrison , Chen Timothy , Razmi Niloufar , Nassar Matthew R
Published: February 2025

People are often faced with surprising events that defy expectations. Such events elicit transient activity in the locus coeruleus/norepinephrine system and elevation of peripheral arousal markers including pupil dilation and the EEG P300, but the function of these signals remains unclear. We propose that they reflect latent state transitions that dynamically control the mental context governing learning and perception. We tested and confirmed five preregistered predictions of this theory using EEG and pupil measurements collected from people performing a color prediction and reproduction task. Task latent state transitions elicited pupil dilation and amplified event-related potentials including the P300. These EEG and pupil measures related to behavioral signatures of latent state updating, including reduced bias and bidirectional adjustment of learning, both across trials and individuals. Our findings support the theory that LC/NE-linked arousal systems optimize behavior by signaling environmental transitions to facilitate rapid adjustments of mental context.
Implications of successive blood feeding onWolbachia-mediated dengue virus inhibition inAedes aegyptimosquitoes
Authors: Johnson Rebecca M. , Breban Mallery I. , Nolan Braiya L. , Sodeinde Afeez , Ott Isabel M. , Ross Perran A. , Gu Xinyue , Grubaugh Nathan D. , Alex Perkins T. , Brackney Doug E. , Vogels Chantal B. F.
Published: February 2025

Dengue virus (DENV) is a mosquito-borne virus that poses a continued and increasing threat to public health. A promising strategy to mitigate the burden of DENV is introgression of the virus-inhibitingWolbachia pipientisbacterium intoAedes aegyptipopulations in the field. While previous studies onWolbachia-mediated virus inhibition have typically assessed viral replication following a single bloodmeal, the main vector of DENV,Ae. aegypti, feeds frequently, often biting multiple hosts per gonotrophic cycle and promptly attempting to refeed following egg laying. Previously, we demonstrated that successive blood feeding reduces the extrinsic incubation period (EIP) and shortens the time it takes for a mosquito to be able to transmit viruses to a new host. With this in mind, we investigated the impact of successive blood meals on DENV serotype 2 (DENV-2) inAe. aegyptiin the presence or absence ofWolbachia(wAlbB andwMelM). We found that both WT andWolbachiatransinfected had increased DENV-2 dissemination 7 days post-infection as well as higher body titers of DENV-2 in the double-fed groups. Using these empirical data in a binomial regression model, we estimated that successive feeding increased the probability of WT andWolbachiatransinfected mosquitoes surviving the EIP. When we estimated the odds of surviving the EIP for mosquitoes withWolbachiarelative to WT mosquitoes, successive feeding increased the chances of WT mosquitoes surviving the EIP more than in mosquitoes withWolbachia, indicating a strong inhibitory effect ofWolbachiaeven in the context of natural frequent blood feeding behavior. Our work shows that mosquito feeding behavior should be considered when assessing the inhibitory effects ofWolbachiaon DENV.
Theory of terahertz-driven magnetic switching in rare-earth orthoferrites: The case of
TmFeO3
Authors: Vovk N. R. , Ezerskaya E. V. , Mikhaylovskiy R. V.
Published: February 2025

We report a theoretical formalism that describes a dynamic magnetic response of rare-earth orthoferrites, particularly those with non-Kramers rare-earth () ions, when driven by strong terahertz fields. We derive a total thermodynamic potential for the exchange coupled -Fe system by constructing an effective Hamiltonian and employing a mean-field theory approximation. We investigate static properties of the and Fe subsystems across the spin-reorientation phase transitions and obtain resonance frequencies for Fe and magnetic sublattices as a function of temperature. Taking an example of the archetypical orthoferrite TmFeO3, we perform numerical modeling to accurately describe the behavior of its anisotropy functions vs temperature. Finally, we analyze switching dynamics of Fe spins and nonlinear effects in the subsystem of TmFeO3 driven by strong terahertz radiation.

Published by the American Physical Society
2025
Unoccupied electronic states of
Fe3O4
(100): An angle-resolved inverse-photoemission study
Authors: Bieling Jan , Donath Markus
Published: February 2025

We present an experimental study that offers first insights into the unoccupied electronic states of a pristine (2×2)R45∘ reconstructed Fe3O4(100) surface. We initially demonstrate the successful sample preparation by analyzing the surface periodicity and chemical composition by low-energy electron diffraction and Auger electron spectroscopy, respectively. Using angle-resolved inverse photoemission, we study the unoccupied electronic states. We observe three nondispersive emissions, one dominant feature around 2eV above the Fermi level and two additional ones at higher energies. For the low-lying triple-split feature, we propose two possible interpretations based on former theoretical studies. We either ascribe it to 3d-related bandgroups originating from tetrahedrally and octahedrally coordinated bulk iron atoms or attribute it to a mixture of 3d states originating from octahedrally coordinated iron atoms within the bulk and the reconstructed surface layer. The high-lying features are ascribed to bulk bands based on the experimentally observed characteristics.

Published by the American Physical Society
2025
Chiral phase transition and spin alignment of vector mesons with chiral imbalance in a rotating QCD medium
Authors: Hua Yang , Feng Sheng-Qin
Published: February 2025

We study the two-flavor Nambu-Jona-Lasinio model under the rotation and chiral chemical potential μ5. First, the influence of chiral imbalance on the chiral phase transition in the Tpc−ω plane is investigated. Research manifests that, as μ5 increases, the critical point of the Tpc−ω plane chiral phase transition will move closer to the T axis. This means that the chiral chemical potential μ5 can significantly affect the Tpc−ω phase diagram and phase transition behavior. While discussing the Tpc−ω phase diagram, we also study the spin alignment of the ρ vector meson under rotation. In the study of the spin alignment of the vector meson ρ, ρ00 is the 00 element of the spin density matrix of vector mesons. At high temperatures, ρ00 is close to 1/3, which indicates that the spin alignment of the vector meson ρ is isotropic. The study found that, under finite rotation, increasing the chiral chemical potential μ5 can significantly enhance ρ00 around the phase transition temperature. When rotational angular velocity is zero, ρ00 is close to 1/3, but as ω increases, ρ00 significantly decreases and deviates 1/3, indicating that rotation can significantly cause polarization characteristics. The ρ00−r relationship near the phase transition temperature is studied. It is found that the farther away from the center of rotation, the lower the degree of spin polarization of the system. It is also found that the influence of chiral imbalance on the ρ00−r relationship is also significant.

Published by the American Physical Society
2025
Representing spatial futures in the age of social media: unpacking the case of The Line
Authors: Alaily-Mattar Nadia , Jones Paul
Published: February 2025

Purpose

This paper is concerned with materials developed to represent and communicate state-commissioned spatial experiments on social media. Our objective is to reveal what such materials can do, even before – or whether–the projects they represent are built. Such materials can constitute an intervention in the way political territory is created, shared and made sense of.

Design/methodology/approach

We use empirical research of The Line, a new city set to be built in the Kingdom of Saudi Arabia (KSA), to explore this contention. Our research data is the publicly available visual, textual and audio-visual materials commissioned by The Line’s delivery company to be disseminated on digital platforms. Our methodological approach to these materials is a qualitative content analysis.

Findings

The materials do not provide a clear sense of fundamental elements of what The Line as an architectural project actually is. Rather the materials foreground three main tropes that disrupt existing notions of nature, space and temporality. Such disruptions propagate KSA’s official story of transformation as drafted in its Vision 2030. They lead us to understand The Line as a radical experiment to rework the Saudi territory and therefore reflecting the power of the state.

Originality/value

Exploring critically the ways in which material projects are embedded in predominantly visual digital cultural forms that imply architecture – and are compounded by affordances of social media – can illuminate much about how designed environments can be mobilized vis-a-vis political imaginaries.
Analysis of air-gap field modulation effect on torque contribution of 6-slot 4-pole high-speed permanent magnet machine
Authors: Li Kai , Wang Chen
Published: February 2025

Purpose

This paper aims to investigate and analyze the air-gap field modulation (AGFM) effect on torque contribution in a 6-slot/4-pole high-speed permanent magnet (HSPM) machine. To further illustrate the torque generation mechanism, the torque contribution is quantified using the Maxwell stress tensor (MST) method.

Design/methodology/approach

First, a simplified permanent magnet (PM) magnetomotive force model is established to identify the effective main-order working field harmonics. Then, the MST method is used to determine the average torque contributions of the effective main-order working field harmonics. Finally, the influences of various stator and rotor parameters on the AGFM effect are analyzed and optimized to enhance the torque density.

Findings

Apart from the fundamental harmonics, the AGFM harmonics contribute non-negligible average torque on the HSPM machine, and the optimized machine has higher torque density. Finally, a prototype of the 10 kW HSPM machine is manufactured and experimented with to validate the effectiveness of the theoretical analysis.

Originality/value

In this paper, the torque generation mechanism of the HSPM machine is investigated and analyzed. Meanwhile, the AGFM effect of the HSPM machine with different design parameters is analyzed and optimized to enhance the torque density.
Is reactive corporate social responsibility such a bad idea? It depends on your positioning
Authors: Baghi Ilaria , Antonetti Paolo
Published: February 2025

Purpose

Following a crisis, stakeholders tend to appreciate costly organizational responses that attempt to reverse the harm caused by the organization. The deployment of reactive corporate social responsibility (CSR), defined as a CSR initiative explicitly promoted to make amends for a negative event, can thus be an effective crisis response strategy. However, existing studies suggest that this strategy could backfire, as it increases stakeholders’ skepticism regarding an organization’s motives to engage in CSR when this is only done under external pressure. Applying attribution theory, the purpose of this paper is to demonstrate that the effectiveness of reactive CSR as a crisis response strategy depends on the positioning of the brand promoting it.

Design/methodology/approach

The authors use three between-subject experiments to test our hypotheses. In Studies 1 and 3, they consider a fictitious crisis scenario with a fictitious brand, and in Study 2, they test their hypotheses using existing brands involved in a fictitious crisis.

Findings

Compared to a purely verbal response (an apology), reactive CSR improves consumers’ responses when implemented by a brand positioned to focus on CSR rather than on performance. This effect is mediated by perceived brand benevolence: a brand focused on CSR is seen as more benevolent when proposing reactive CSR initiatives than a brand with a performance positioning. The effect holds even when the CSR positioning is not aligned with the reactive CSR domain. For a brand with a performance positioning, a costlier reactive CSR strategy is no more effective than an apology.

Originality/value

The study extends their understanding of how information on brand positioning influences reactive CSR in response to a crisis. Their analysis clarifies the circumstances under which reactive CSR can be an effective crisis response.
Simulation of generalized saturated thermo-elastic media in axisymmetric cylindrical coordinate by cell-adaptive central high-resolution schemes with compression-adaptive UNO slope limiters
Authors: Yousefi Hassan , Mahmoudzadeh Kani Iradj
Published: February 2025

Purpose

The purpose of this study is to (1) improve the spectral features of the second-order uniformly non-oscillatory (UNO) slope limiters, and (2) numerical simulation of the unified-form of generalized fully-coupled saturated thermo-poro-elastic systems in the axisymmetric cylindrical coordinate via cell-adaptive Kurganov-Tadmor (KT) central high-resolution scheme using the UNO limiters.

Design/methodology/approach

(1) The spectral features of the UNO limiter are improved by compression-adaptive MINMOD (MM) limiters, achieved by blending different types of MM limiters to achieve less numerical dissipation and dispersion. These blended MM limiters preserve the total variation diminishing (TVD) feature over non-uniform non-centered cells. Also, the spectral features of the central schemes using the UNO limiters are investigated. (2) For the thermo-poro-elastic problem, corresponding first-order hyperbolic system is provided, including flux, source, diffusion and nonlinear terms. Where, there are different interacting components in the source and flux terms. The nonlinear terms are also considered by the Picard-like linearization concept.

Findings

Compression-adaptive UNO limiters would be stable over adapted cells with centered and non-centered cells. The benchmarks confirm that both spectral features and numerical accuracy are improved. For the generalized thermo-poro-elastic problem, corresponding responses including the shock waves can properly be captured.

Originality/value

Studying heat effects (e.g. hot fluid or freezing) and explosions on tunnels. Also, the UNO limiters could be used for simulations of various systems of conservation laws.