Biology subjects

Song, H.

Publications and source records attributed to Song, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

The ZmHEAT1/ZmKAKU42-ZmNCH1 module regulates heat stress tolerance by modulating nuclear envelope structure in maize

Heat stress threatens maize production. Through a genome-wide association study using pollen viability decline rate as a phenotype, we identified ZmHEAT1, encoding the nuclear envelope protein ZmKAKU41, as a key regulator of thermotolerance. ZmHEAT1 positively regulates heat tolerance at seedling and reproductive stages, with its overexpression improving thermotolerance and its knockout reducing pollen viability and yield under high temperatures. ZmHEAT1 interacts with its homolog ZmKAKU42 and the nucleoskeleton protein ZmNCH1 to form a complex at the nuclear envelope. Mutants lacking ZmHEAT1 or ZmKAKU42 exhibit increased nuclear envelope damage under heat stress, along with repressed expression of key heat shock protein genes (e.g., HSP90-2, HSP17.4). This work establishes the ZmHEAT1/ZmKAKU42-ZmNCH1 complex as a critical guardian of nuclear integrity and heat response, providing a valuable genetic resource for breeding heat-tolerant maize varieties. One-sentence summaryModulation of the nuclear envelope structure in maize is involved in heat stress tolerance.

molecular biology↗

bioRxiv2026

Triatomine host preference in an experimental cafeteria: the impact of Trypanosoma cruzi infections

BackgroundHematophagous triatomine vectors of the Chagas disease parasite, Trypanosoma cruzi, have a wide bloodmeal host breadth yet mammals are the primary competent reservoirs for T. cruzi. Accordingly, the transmission of T. cruzi is dependent on triatomines encountering mammalian hosts. We hypothesized T. cruzi-infected triatomines exhibit a preference for mammalian versus non-mammalian hosts, as compared to uninfected triatomines. Methodology/Principal FindingsWe used a dual-choice olfactometer to present individual T. cruzi-infected and uninfected Triatoma gerstaeckeri- an important North American triatomine species- to pairwise combinations of no host, dog, human, or chicken. We found that uninfected T. gerstaeckeri preferred dogs over chickens and humans, but T. cruzi-infected T. gerstaeckeri had no host preference. Additionally, T. cruzi-infected T. gerstaeckeri took less time to begin advancing towards hosts (average of 522 s {+/-} 577 s vs 801 s {+/-} 704 s) and spent more time on both sides of the olfactometer compared to uninfected insects As a comparative group,we tested Rhodnius prolixus- a potent South American vector- and found no statistical preference among hosts, yet they advanced towards hosts more often (63.2% vs 47.1%) and faster compared to T. gerstaeckeri. Conclusions/SignificanceThe increased locomotion of R. prolixus and T. cruzi-infected T. gerstaeckeri toward hosts may promote increased transmission of T. cruzi. Dogs are a preferred host for T. gerstaeckeri and may be considered in future host-targeted interventions for triatomine control. Author SummaryVectors are often generalists or opportunists with a wide range of available hosts, yet the parasites they transmit may have a narrower host range. It is in the parasites best interest for the vectors they infect to interact with competent hosts, thereby introducing the setting for parasite manipulation of vectors. We aimed to understand the foraging behaviors of vectors and how those behaviors may be different when the vector is infected with a parasite. We studied the triatomine ( kissing bug) insect vectors of the Chagas disease parasite, Trypanosoma cruzi, using one of North Americas most important vector species in comparison to a potent South American vector species. We tested if parasite-infected triatomines exhibited a preference toward vertebrate hosts that are also competent reservoirs for the T. cruzi (i.e., mammals). We used an experimental cafeteria, in which individual vectors were introduced to a dual-choice olfactometer and allowed to walk toward hosts including restrained humans, dogs, or chickens. We found differences in apparent host preference between species of vectors and between infected vs. uninfected vectors. Uninfected vectors displayed a host preference toward dogs, yet this preference was not significant among infected vectors. Uninfected vectors had higher frequency of locomotion in the arena, suggesting the opportunity for more vector-host contact.

ecology↗

bioRxiv2026

Periplasmic gatekeeping of phage DNA entry by rSAM enzyme-mediated maturation of an effector with His-X-Ser repeats

In the relentless arms race between bacteria and phages, bacteria have evolved a variety of defense strategies to combat phage infection. However, no bacterial system has been identified that specifically target the phage DNA entry phase. Here, we present a novel bacterial antiphage system, termed HXS, which provides broad-spectrum and robust antiphage activity by interfering with phage DNA entry. The HXS system consists of two radical S-adenosylmethionine (rSAM) enzymes (HxsB and HxsC), a small protein (HxsD), and the effector HxsA with a peptidoglycan-binding domain and five His-Xaa-Ser (HXS) repeats. HxsB/HxsC catalyze rSAM enzyme-dependent maturation of HxsA, including N-terminal processing and a site-specific +8 Da modification, thereby producing a periplasmic effector required for HXS defense. Biochemical evidence supports a model in which the matured effector likely engages incoming DNA electrostatically to arrest entry, establishing an rSAM enzyme-modified protein effector in antiphage defense.

microbiology↗

bioRxiv2025

Urolithin A Restores Mitochondrial Function and Reverses Cardiac Remodeling in Heart Failure with Preserved Ejection Fraction

BackgroundHeart failure with preserved ejection fraction (HFpEF) accounts for nearly half of all heart failure cases; however, mechanism-based therapies targeting cellular dysfunction remain absent. Emerging evidence suggests that mitochondrial dysfunction and impaired quality control, particularly defective mitophagy, are central to the pathogenesis of HFpEF. Urolithin A (UA), a gut microbiome-derived postbiotic metabolite, has shown promise as a mitophagy activator in preclinical models; however, its therapeutic efficacy in HFpEF remains unknown. MethodsWe used a clinically relevant two-hit HFpEF mouse model (high-fat diet (HFD) plus N{omega}-nitro-L-arginine methyl ester (L-NAME)) and co-administered UA during disease progression. The cardiac structure and function were assessed using echocardiography, histology, and transmission electron microscopy. Mitochondrial bioenergetics were evaluated using Seahorse-based respirometry. Mitophagy flux was monitored using mt-Keima assays in H9c2 cells and human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Mechanistic insights were obtained using immunoblotting, integrated shotgun metagenomic and lipidomic profiling, and single-nucleus RNA sequencing (snRNA-seq). ResultsUA treatment significantly attenuated cardiac remodeling and fibrosis in HFpEF mice while improving diastolic function parameters. Transmission electron microscopy revealed restoration of the mitochondrial ultrastructure, and mitochondrial stress tests demonstrated enhanced oxidative phosphorylation capacity and glycolytic reserves. Immunoblot assays revealed that UA treatment recovered PINK1/Parkin-mediated mitophagy markers (reduced LC3-II and p62/SQSTM1). Mt-Keima assays confirmed enhanced mitophagic flux in H9c2 cells under HFpEF-like stress conditions. Integrated metagenomics and lipidomics revealed significant reductions in cardiovascular risk-associated ceramides. snRNA-seq demonstrated that HFpEF-like stress downregulated contractile, calcium-handling, and mitochondrial mitophagy gene programs. UA treatment restored the mitochondrial quality control signatures and normalized profibrotic and conduction-type cell populations. ConclusionsUrolithin A restored mitochondrial quality control through the activation of mitophagy and reversed cardiac remodeling in HFpEF. These findings establish UA as a mitochondria-targeted therapeutic candidate for HFpEF. Novelty and SignificanceO_ST_ABSWhat is known?C_ST_ABS{checkmark} Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome driven by metabolic stress and myocardial remodeling, for which effective disease-modifying therapies are lacking. {checkmark}Mitochondrial dysfunction and impaired mitophagy have been implicated in HFpEF, but their roles in cardiomyocyte state remodeling and fibrosis remain incompletely defined. {checkmark}Urolithin A, a gut microbiome-derived metabolite, enhances mitophagy in aging and metabolic tissues, but its relevance to HFpEF has not been established. What new information does this article contribute?{checkmark} Urolithin A restores mitochondrial quality control and mitophagic flux in cardiomyocytes, improving diastolic function and attenuating cardiac remodeling in a two-hit HFpEF model. {checkmark}Integrated metagenomic and lipidomic analyses identify suppression of gut microbiome-associated ceramide biosynthesis as a systemic mechanism linked to Urolithin A-mediated cardioprotection. {checkmark}Single-nucleus RNA sequencing reveals that Urolithin A reverses maladaptive cardiomyocyte transcriptional state transitions toward fibrogenic and conduction-like programs.

molecular biology↗

bioRxiv2025

Quantification and Localisation of New Brain Lipid Synthesis Using Deuterium Oxide and High Resolution Mass Spectrometry

Myelin is the lipid-rich membrane that surrounds neuronal axons and is essential for neurological function in vertebrates. The development of therapeutics that stimulate myelin repair to treat demyelinating disorders such as multiple sclerosis is hampered by the inability to distinguish newly-synthesised from pre-existing myelin. This study aimed to develop a method to quantify and localise new myelin lipid synthesis in vivo. Deuterium oxide was administered for two weeks in the drinking water of mice fed normal chow, chow containing the demyelinating toxin cuprizone, or during spontaneous remyelination following cuprizone withdrawal. Liquid chromatography-tandem mass spectrometry and mass spectrometry imaging were used to quantify and localise the newly synthesised, deuterated lipids. While most glycerophospholipids were constitutively deuterated, deuteration of myelin-enriched sulfatides, hexosylceramides, and phosphatidylethanolamine plasmalogens was only apparent during remyelination. Deuterated hexosylceramide and phosphatidylethanolamine plasmalogen species were localised primarily to the corpus callosum, the white matter tract that is most heavily affected by cuprizone. Most deuterium atoms were found in the fatty acyl chains, indicative of de novo lipid synthesis. These methods provide the means to quantify and spatially profile dynamic lipid synthesis across diverse biological contexts, including understanding myelin homeostasis and preclinical evaluation of remyelinating therapeutics.

biochemistry↗

bioRxiv2025

High-resolution MRI Guided Whole Mouse Brain Cell Type Atlas using Deep Learning

Cell types represent groupings of cells defined by shared anatomical and functional properties. Traditional mouse brain cell atlases rely heavily on single-cell sequencing, which provides valuable molecular detail but lacks whole-brain, isotropic resolution. Diffusion MRI (dMRI) offers a complementary approach for probing cytoarchitecture and myeloarchitecture, with quantitative metrics increasingly used as biomarkers of brain development and neurodegenerative disorders. Although prior work has linked dMRI metrics with gene expression, the capacity of dMRI to directly predict cell types remains unclear. Here, we present a deep learning framework that integrates high-resolution dMRI with three-dimensional light-sheet microscopy (LSM) registered to the Allen Mouse Brain Common Coordinate Framework (CCFv3). We investigated correlations between dMRI and spatial transcriptomics-derived cell types and generated a whole-brain cell type atlas at 10 {micro}m isotropic resolution. Together, these results establish an efficient, high-resolution strategy for brain cell atlas generation and underscore the potential of advanced imaging to illuminate cellular mechanisms of the brain.

neuroscience↗

bioRxiv2025

A deep learning framework for building INDEL mutation rate maps

Germline short insertions and deletions (INDELs) are pervasive genetic variants that shape genome evolution and contribute to human disease. However, accurately quantifying fine-scale INDEL mutation rates remains challenging due to data limitations and the diversity of INDEL subtypes. Here, we present MuRaL-indel, a deep learning framework that predicts germline INDEL mutation rates by leveraging long-range sequence context through a U-Net architecture. Using extensive rare variant data from large population cohorts, MuRaL-indel generates base-resolution, length-specific mutation rate maps for the human genome and achieves superior accuracy compared with existing models across multiple genomic scales. We successfully apply MuRaL-indel to three non-human species (Macaca mulatta, Drosophila melanogaster, and Arabidopsis thaliana), demonstrating its broad applicability across taxa. Using the predicted mutation rate maps, we reveal the mutational landscape around human coding genes and show that MuRaL-indel-derived constraint scores better prioritize pathogenic INDELs than previous models. Through deep learning interpretability analyses, we uncovered sequence motifs--including both repeat and non-repeat elements--associated with elevated INDEL mutability, providing insights into underlying mutational mechanisms. Together, MuRaL-indel establishes a generalizable and scalable framework for building high-resolution INDEL mutation rate maps, offering a valuable resource for studies of genome evolution, mutational mechanism, variant interpretation, and genetic disease.

genomics↗

bioRxiv2025

Contrastive modelling of transcription and transcript abundance in legumes using PlanTT

Predicting the impacts of sequence variation on gene expression remains a challenging task. Further, in plants, we have a limited understanding of the relative contributions of different gene expression regulatory mechanisms. To address these limitations we generated a comparative multiomic dataset comprising matched 3-RNA-seq and PRO-seq data from matched tissues of reference genotypes of four legumes of the invert repeat lacking clade (Pisum sativum, Vicia faba, Lathyrus sativa and Medicago truncatula). Focused on the challenging task of predicting expression differences between ortholog pairs from unseen orthogroups, we used this dataset and a novel prediction framework to build contrastive models that predict quantitative differences (effect size differences) in transcription and transcript abundance.

bioinformatics↗

bioRxiv2025

Local and network neural activations and their associations with sleep parameters during threat conditioning and extinction in persons with Generalized Anxiety Disorder with and without Insomnia Disorder

Deficient extinction learning and memory are hypothesized mechanisms for pathological anxiety that are associated with sleep disturbance. fMRI neural activations to threat conditioning, extinction learning, and extinction recall were measured. Activations were compared, in persons with Generalized Anxiety Disorder (GAD), between those with moderate to severe Insomnia Disorder (ID) and those with absent or sub-threshold ID. Relationships of activations with measures of sleep quality and physiology were examined. Between-group comparisons and whole-sample correlation with sleep parameters were examined in relation to large-scale brain networks using a liberal cluster-determining threshold. Localized activations were then identified using family-wise error correction. Activations to the reinforced stimulus (CS+) that increased from the beginning to end ("across") threat conditioning were more extensive within the GAD+ID group. Increased activations to the CS+ across extinction learning were greater within the GAD-ID than the GAD+ID group, and delayed 24h in the latter. Greater sleep efficiency was associated with decreased activations across threat conditioning, but with increased activations across extinction learning. Better sleep quality promoted greater engagement of neural substrates of extinction learning. The GAD+ID group failed to engage brain areas supporting extinction learning immediately following threat conditioning, but did so when stimuli were again presented following a delay. HighlightsGeneralized Anxiety Disorder subjects with moderate/severe vs absent/mild insomnia compared Neural responses to threat conditioning, extinction learning/memory analyzed and sleep recorded Low and high thresholds identified large-scale networks and localized activations respectively Threat and regulatory activations at extinction learning in mild insomnia delayed when more severe Better sleep quality predicted greater activation of regulatory areas during extinction learning

neuroscience↗

bioRxiv2025

Harnessing artificial intelligence to automate environmental predictions

Predicting heterogeneous and non-linear processes remains a fundamental challenge in Earth sciences. Here, we present an artificial intelligence (AI)-guided framework that iteratively combines predictive modeling with targeted field sampling to rapidly improve environmental predictions. We demonstrate our workflow by predicting oxygen consumption, a key process of stream metabolism, across the contiguous United States (CONUS). Our approach consisted of 18 iterative loops of measurements and models, combining distributed participatory field sampling, lab analysis, automated machine learning (ML) predictions, and error and distinctiveness analyses to autonomously guide the next sampling at optimal site locations. Through our approach, we increased the predictive power of sediment oxygen consumption across CONUS by over fifteenfold between the first and last iteration. Relative to our last sampling iteration, our first sampling missed sites with high rates and underestimated median oxygen consumption rates by 68%. In addition to identifying areas of high oxygen consumption rates, iterations enabled refinement of laboratory and data handling methods, and engagement with a broad community of field researchers. We conclude that AI-guided iterative loops between targeted sampling and predictive modeling are a powerful and efficient approach for improving predictions of heterogeneous environmental processes.

ecology↗

bioRxiv2025

Oncogenic EGFR rewires STING-TBK1 immune machinery to license DNA damage tolerance

EGFR hotspot mutations (mEGFR), including primary L858R, exon 19 deletion, and secondary T790M, are pivotal oncogenic drivers in human non-small cell lung cancer (NSCLC). Meanwhile, NSCLC resistance to third-generation tyrosine kinase inhibitors (TKIs) is a major clinical challenge and remains mechanistically unresolved. Here, we uncover a previously unrecognized immunological mechanism whereby mEGFR exploits cGAS-STING innate immune signaling, conventionally regarded as tumor-suppressive, to sustain oncogenic signaling and therapeutic resistance. Mechanistically, mutant EGFR kinase aberrantly incorporates into STING signalosomes, directly phosphorylating STING (Y245/Y314) and TBK1 (Y577/Y677), stabilizing and hyperactivating TBK1 proteins, and establishing an unexpected and kinase loop critical for DNA damage repair. Disruption of this mEGFR-STING-TBK1 axis, genetically or pharmacologically, profoundly sensitized resistant patient-derived NSCLC organoids to chemotherapy. Combining TBK1 inhibition with cisplatin notably eradicated mEGFR-driven tumors in spontaneous and immunocompetent NSCLC murine models and patient-derived organoids. Our findings suggest a new function of cGAS-STING in the DNA damage repair program, its paradoxical exploitation by oncogenic driver mutations, and an innate immune therapeutic vulnerability in NSCLC.

cancer biology↗

bioRxiv2025

Ca2+ signature-dependent control of auxin sensitivity in Arabidopsis

Plants must continually balance growth with arrest, especially under stress. Auxin signaling acts as a central regulatory hub in this process, yet the mechanisms that dynamically tune early auxin signalling in real time remain unknown. Here, we used the light-gated, Ca2+-permeable Channelrhodopsin 2 variant XXM2.0 to optogenetically impose defined Ca2+ signatures on Arabidopsis root cells. Repetitive light activation triggered cytosolic Ca2+ signals that in turn suppressed auxin-induced membrane depolarization and Ca2+ transients. Moreover, prolonged optogenetic Ca2+ stimulation affects auxin-responsive transcriptional reprogramming. As phenotypic output, reversible inhibition of root growth by suppressing cell division and elongation was observed. We further identify a candidate CaM7-CNGC14 module that likely mediates Ca2+-dependent gating of early auxin signalling. Our study thus introduces a synthetic biology approach to decompose calcium-auxin crosstalk in plant cells, and demonstrates that optogenetically imposed cytosolic Ca2+ signals act as dynamic regulators of auxin susceptibility in roots.

plant biology↗

bioRxiv2025

A widespread protein misfolding mechanism is differentially rescued by chaperones based on gene essentiality

Protein misfolding involving changes in non-covalent lasso entanglement (NCLE) status has been proposed based on simulations and biochemical assays of a small number of proteins. Here, we detect hallmarks of these misfolded states across hundreds of proteins by integrating E. coli proteome-wide limited-proteolysis mass spectrometry with structural datasets of protein native structures. Proteins containing native NCLEs are twice as likely to misfold, predominantly in regions where these NCLEs naturally occur. Surprisingly, the chaperones DnaK and GroEL do not typically correct this misfolding, except in the case of essential proteins. Statistical analysis links this differential rescue activity to weaker loop-closing contacts in the NCLEs of essential proteins, suggesting misfolding involving these loops is easier to rectify by chaperones. Molecular simulations indicate a mechanism where premature NCLE loop closure, prior to proper placement of the threading segment, leads to persistent misfolded states. This mechanism explains why, in the mass spectrometry data, proteins with NCLEs are more likely to misfold and misfold in NCLE regions. These results suggest widespread NCLE misfolding, that such misfolded states in non-essential proteins can bypass the refolding action of chaperones, and that some protein sequences may have evolved to allow chaperone rescue from this class of misfolding.

biophysics↗

bioRxiv2025

Dual-LLM Adversarial Framework for Information Extraction from Research Literature

Information Extraction (IE) is a fundamental task in Natural Language Processing (NLP) that aims to automatically identify relevant information from unstructured or semi-structured data. Information extraction from lengthy research literature, particularly in multi-omics studies, faces significant challenges due to their complex narratives and extensive context. To address this, we present a novel dual-LLM adversarial framework in which one large language model (LLM) performs the extraction and another provides iterative feedback to refine the results. This process systematically reduces errors, enhances consistency across heterogeneous data sources, and converges toward more accurate outputs. We evaluated our approach against manual and single-LLM extraction, using LLMs as evaluators. Experimental results show that our adversarial framework outperforms these baselines, highlighting its effectiveness for extracting structured information from lengthy scientific texts.

bioinformatics↗

bioRxiv2025

A neural network with episodic memory learns causal relationships between narrative events

Humans reflect on memories to make sense of ongoing events. Past work has shown that people retrieve causally related memories during comprehension, but the mechanisms underlying this process remain unclear. Here, we used a recurrent neural network augmented with a key-value episodic memory buffer and trained it to predict upcoming scenes while watching a television episode. At each time step, the model transformed the current scene into a value representing memory content and a key representing memory address, both stored as episodic memory. The model retrieved selective past values by applying self-attention over stored keys and integrated these memories with the current scene representation to generate predictions. The model retrieved memories similar to those retrieved by human participants watching the same episode during fMRI. Importantly, this similarity disappeared when causal relationships between events were controlled for. The model also represented causally related events with similar patterns, similar to how the human brain represents these events. These findings suggest that using two distinct memory representations allows the model to retrieve memories and organize events based on causal relationships, beyond semantic or perceptual similarities. Together, this work proposes a key-value episodic memory system as a candidate computational mechanism for how humans retrieve causally related memories to comprehend naturalistic events.

neuroscience↗

bioRxiv2025

To jump or not to jump: Comparing effects of phenotypic plasticity on the visual responses and escape behavior of locusts and grasshoppers

Locusts exhibit remarkable phenotypic plasticity changing their appearance and behavior from solitary grasshoppers to gregarious locusts when population density increases. These changes include morphological differences in the size and shape of brain regions, but little is known about plasticity within individual neurons and alterations in behavior not directly related to aggregation or swarming. We examined looming escape behavior and the properties of a well-studied collision-detection neuron in gregarious and solitarious animals of three closely related species, the desert locust (Schistocerca gregaria), the Central American locust (S. piceifrons) and the American bird grasshopper (S. americana). For this neuron, the lobula giant movement detector (LGMD), we examined dendritic morphology, membrane properties, gene expression, and looming responses. Gregarious animals reliably jumped in response to looming stimuli, but surprisingly solitarious desert locusts did not produce escape jumps. These solitarious animals also had smaller LGMD dendrites. This is the first study done on three different species of grasshoppers to observe the effects of phenotypic plasticity on the jump escape behavior, physiology and transcriptomics of these animals. Surprisingly, there were little differences in these properties between the two phases except for behavior. For all the three species, gregarious animals jumped more than solitarious animals, but no significant differences were found between the two phases of animals in the electrophysiological and transcriptomics studies. Our results suggest that phase change impacts mainly the motor system and that the physiological properties of motor neurons need to be characterized to understand fully the variation in jump escape behavior across phases. New & Noteworthy (74 words): Swarming is observed in some grasshopper species, called locusts. We compared jump escape behavior between gregarious and solitarious grasshoppers and locusts, as well as LGMD responses to looming stimuli, and analyzed the morphological differences in this neuron. This study provides insights into the effects of phase change on the visual system of locusts and grasshoppers as it relates to looming-evoked jump escape behavior. In this context, our results suggest that phenotypic plasticity mainly impacts the motor system.

neuroscience↗

bioRxiv2025

Field evaluation of non-invasive sampling for monitoring nine swine pathogens in the Republic of Korea

BackgroundNon-invasive sampling methods, such as swine oral fluid (OF) and fecal boot (FB) sampling, have gained attention due to their animal welfare considerations, ease of collection, and cost effectiveness. However, comparative data regarding non-invasive and standard sampling methods remain limited, particularly in the Republic of Korea, where research on OF and FB sampling is sparse. Therefore, we investigated representative pig pathogens, including six porcine respiratory pathogens and three gastrointestinal pathogens, using OF and FB samples for pathogen surveillance across commercial farms in the Republic of Korea. MethodsThe results from targeted polymerase chain reaction (PCR) assays for major respiratory and gastrointestinal pathogens obtained using OF and FB samples were compared with those obtained from standard samples. Non-invasive samples included 30 OF ropes and 30 FBs collected from nine farms, and 360 standard samples (blood, fecal, oral, and nasal swabs) were also collected. PCR assays for the nine pathogens were conducted, and the results from OF, FB, and combined OF+FB were compared with those from standard samples at the pen level. ResultsOF sampling showed superior test concordance with respiratory pathogens than gastrointestinal pathogens, and FB sampling demonstrated superior detection of gastrointestinal pathogens compared with OF sampling. Additionally, the combination of OF+FB sampling improved the detection concordance for all nine target pathogens investigated. ConclusionsWe demonstrated the feasibility and potential applicability of OF and FB sampling under field conditions in Korean pig farms. Therefore, this study supports OF and FB sampling as useful tools for swine pathogen monitoring in both research and practical field applications.

microbiology↗

bioRxiv2025

Ongoing thoughts at rest reflect functional brain organization and behavior

Resting-state functional connectivity (rsFC)--brain connectivity observed when people rest with no external tasks--predicts individual differences in behavior. Yet, rest is not idle; it involves streams of thoughts. Are these ongoing thoughts reflected in FC and do they contribute to the relationship between rsFC and behavior? To test this question, we developed an annotated rest paradigm where participants rated and verbally described their thoughts after each rest period during functional MRI (N = 60). Our findings revealed rich and idiosyncratic thoughts across individuals. Similarity in thoughts was associated with more similar FC patterns within and across individuals. In addition, both thought ratings and topics could be decoded from FC. Furthermore, neuromarkers of these thoughts generalized to unseen individuals in the Human Connectome Project dataset (N = 908), where decoded thought patterns during rest predicted positive vs. negative trait-level individual differences. Together, our findings reveal that ongoing thoughts at rest are reflected in brain dynamics and these network patterns predict everyday cognition and experiences. Understanding subjective in-scanner experiences is thus crucial in characterizing the relationship between individual differences in functional brain organization and behavior.

neuroscience↗