Search bioRxiv⌕ Search

Biology subjects

Jia, G.

Publications and source records attributed to Jia, G..

At least 19 recordsLinked to original sources

A Unified Form of Batch Harmonization Equation for Normative Modeling: A Location Scale Framework

Normative modeling quantifies individual deviation from population norms by estimating the conditional mean and variance of brain-derived measures as functions of clinically relevant parameters such as age. The rapid growth of multi-center consortia has created an urgent need for normative models that incorporate batch harmonization. Several harmonization methods based on linear mixed models--ComBat, GAMLSS, HBR, and Generalized Normative Modeling (GNM)--offer explicit formulations of the mean and variance, making them natural candidates for batch-harmonized normative modeling; yet the absence of a unified theoretical framework leaves it unclear whether and how these methods support the computation of batch-harmonized z-scores. We bridge this gap by writing existing harmonization methods as special cases of a single location-scale equation, y = m(x, {Theta})+{sigma}(x, {Theta}){varepsilon} , which we term the unified form of batch harmonization equation for normative modeling. The methods differ only in the functional forms of m and{sigma} , how batch parameters enter{Theta} , and how{Theta} is estimated. This unified form yields both harmonized data y* and site-invariant z-scores from the same model, providing a common theoretical language for harmonized normative modeling. Building on this framework, we evaluate the underlying regression engines (parametric, spline, Gaussian process, kernel, deep learning), sensitivity to outliers, computational scalability, and federated decomposability for privacy-preserving multi-center computation. By clarifying what each method assumes, what it delivers, and where the boundaries of current methodology lie, the unified equation establishes a principled foundation for method selection and charts a path toward reliable, scalable, and privacy-aware normative modeling across multi-center neuroimaging.

bioengineering↗

Generalized Normative Modeling: A One-Step Hierarchical Kernel Framework for Multi-Site Brain Charts with Self-Correcting Z-Scores

Normative modeling expresses individual brain phenotypes as z-scores relative to a population norm, but in multi-site studies batch effects contaminate these z-scores and undermine their biomarker value. Existing approaches either harmonize data before fitting a normative model (ComBat+Normative), letting residual site effects leak into z-scores, or use parametric one-step methods (GAMLSS, HBR) that cannot flexibly model multivariate covariate interactions. We propose Generalized Normative Modeling (GNM), a onestep hierarchical framework that jointly estimates the global trajectory and site-specific effects via NUFFT-accelerated kernel regression with GCV bandwidth selection. Because the z-score is the ratio of batch-corrected residual to batch-corrected scale, residual site variance cancels algebraically -- a property we term self-correction. On ABIDE I cortical thickness (387 HC, 11 sites, 68 ROIs) and HarMNqEEG log-power spectra (1,564 subjects, 14 sites, 18 channels x 235 frequency bins), GNM produced the most site-invariant z-scores and best age-signal preservation among four methods. This work provides an open-source MATLAB toolbox with a declarative formula interface (https://github.com/LMNonlinear/Generalized-Normative-Modeling), enabling reliable individual-level inference in pooled multi-site cohorts and advancing the use of normative deviations as clinical biomarkers in precision psychiatry and neurology.

bioengineering↗

OpenAc4C: A gateway to decode the landscape, regulation and pathogenesis of N4-acetylcytidine (ac4C) epitranscriptome

N4-acetylcytidine (ac4C) is an ancient and highly conserved chemical marker found in all domains of life. Recent advancements in sequencing techniques have enabled the functional analysis of ac4C occurrence by accurately capturing its locations and levels, shedding light on its significant regulatory potential and emerging role in diseases. The OpenAc4C, the first comprehensive knowledgebase exclusively designed for unraveling the ac4C epitranscriptome across diverse species, spanning vertebrates, mammals, insects, fungi, plants, bacteria, archaea, and viruses. By mining a large array of ac4C epitranscriptome datasets with deep learning-based pipelines, OpenAc4C features a collection of 536,745 ac4C sites identified from four distinct next-generation sequencing (NGS)-based techniques, alongside novel insights from Oxford Nanopore direct RNA sequencing (ONT)-based samples, encompassing a total of 33 species. Beyond the ac4C landscape, a total of 536,986 ac4C-affecting variants were identified in seven species. Among them, 4,766 pathogenic ac4C-SNPs may drive ac4C dysregulation with implications for disease pathogenesis. In addition, OpenAc4C offers a user-friendly graphical interface and a web-based analysis platform for comprehensive querying and interactive exploration of the database collections. Together, OpenAc4C will serve as a valuable integrated resource to facilitate studies of ac4C modification. It is freely accessible at: www.rnamd.org/ac4cportal.

bioinformatics↗

Aperiodic and Periodic EEG Component Lifespan Trajectories: Monotonic Decrease versus Growth-then-Decline

1.1Unraveling the lifespan trajectories of human brain development is critical for understanding brain health and disease. Recent research demonstrates that electroencephalography signals are composed of periodic and aperiodic components reflecting distinct physiological substrates. This dissociation raises the possibility that they follow different developmental tendencies. Here, we delineate the lifespan trajectories of aperiodic and periodic neural oscillations using a large international cohort (N=1,563, ages 5-95, resting state, eyes closed). We reveal two fundamental developmental patterns: a Monotonic decrease in aperiodic activity and a Growth-and-Decline pattern for periodic activity. Both components have inflections around age 20 and transition to a stable senescent phase around age 40. Spatially, anterior regions mainly exhibit aperiodic activity, while periodic activity concentrate on posterior regions and these patterns remain stable throughout life. Crucially, multimodal analysis shows these trajectories map onto distinct biological substrates. The periodic components Growth and Decline trajectory aligns with GABAergic function and myelination. In contrast, the monotonically decreasing trajectory of aperiodic activity mirrors fundamental biomarkers of biological aging, such as DNA methylation and telomere length. Transforming age to a logarithmic scale simplifies these nonlinear trajectories into a linear decreasing and a piecewise concave linear model for aperiodic and periodic components. This form provides a robust and parsimonious framework for quantifying maturation and identifying neurological deviations. HighlightsO_LIWe delineate distinct lifespan trajectories of aperiodic and periodic neural activity in a large-scale international cohort (N=1,563, ages 5-95). Aperiodic activity undergoes a Monotonic Decrease with age. In contrast, periodic activity follows a Growth-then-Decline trajectory, peaking in early adulthood. C_LIO_LIBoth trajectories feature a critical transition around age 20 and stabilize into a protracted senescent phase from approximately 40 onward. C_LIO_LIThese neural trajectories map onto distinct biological substrates: periodic activity tracks integrative functions (myelination, GABAergic, and aperiodic decline mirrors fundamental aging processes (DNA methylation). C_LIO_LIA stable pattern observed throughout the lifespan is the spatial segregation of neural activity, where aperiodic signals are dominant in anterior regions and periodic signals are concentrated in posterior ones. C_LIO_LILogarithmically transforming age linearized the developmental trajectories, yielding a monotonic decline for the aperiodic component and a concave piecewise for the periodic one. This process establishes robust linear norms for the personalized assessment of brain dysfunction. C_LI

neuroscience↗

Structural innovations and neurogenic continuity define avian brain development and evolution

Understanding how neurogenic diversity and brain architecture emerge is crucial for deciphering the mechanisms of brain plasticity and cognitive evolution. Here, we present a comprehensive single-cell and spatial transcriptomic atlas of the budgerigar brain, a highly cognitive avian species. We uncover a striking dorsoventral symmetry in excitatory neuron distribution, precisely organized along the lamina mesopallialis intermedia (LMI), a key boundary structure. Cross-species comparisons further reveal the origins of this unique avian pallial organization, offering new insight into avian brain evolution. Our study also highlights distinct developmental trajectories and asynchronous maturation patterns between telencephalic and optic tectum excitatory neurons, underscoring their contribution to innate circuit assembly. Furthermore, we identify adult neural stem cells (NSCs) with evolutionarily conserved transcriptomic signatures across avian species, emphasizing their role in brain plasticity and adaptation. These findings refine fundamental models of avian brain development and elucidate conserved principles of cognitive plasticity.

evolutionary biology↗

ARBUR: a Machine Learning-based Analysis System for Relating Behaviors and Ultrasonic Vocalizations of Rats

Deciphering how different types of behavior and ultrasonic vocalizations (USVs) of rats interact can yield insights into the neural basis of social interaction. However, the behavior-vocalization interplay of rats remains elusive because of the challenges of relating the two communication media in complex social contexts. Here, we propose a machine learning-based analysis system (ARBUR) that can cluster without bias both non-step (continuous) and step USVs, hierarchically detect eight types of behavior of two freely behaving rats with high accuracy, and locate the vocal rat in 3-D space. By simultaneously recording the video and ultrasonic streams of two freely behaving rats, ARBUR reveals that rats communicate via distinct USVs when engaging in different types of social behavior. Moreover, we show that ARBUR can not only automatically reveal the well-understood behavior-associated vocalizations that were carefully concluded by other behavioral researchers, but also hold the promise to indicate novel findings that can be hardly found by manual analysis, especially regarding step USVs and the active/passive rat-associated USVs during easy-to-confuse social behaviors. This work highlights the potential of machine learning algorithms in automatic animal behavioral and acoustic analysis and could help mechanistically understand the interactive influence between the behaviors and USVs of rats.

animal behavior and cognition↗

Endothelial Cell Serum and Glucocorticoid Regulated Kinase 1 (SGK1) Mediates Vascular Stiffening

BackgroundExcess dietary salt increases vascular stiffness in humans, especially in salt- sensitive populations. While we recently suggested that the endothelial sodium channel (EnNaC) contributes to salt-sensitivity related endothelial cell (EC) and arterial stiffening, mechanistic understanding is incomplete. This study thus aimed to explore the role of EC-serum and glucocorticoid regulated kinase 1 (SGK1), as a regulator of sodium channels, in EC and arterial stiffening. Methods and ResultsA mouse model of salt sensitivity-associated vascular stiffening was produced by subcutaneous implantation of slow-release deoxycorticosterone acetate (DOCA) pellets, with salt (1% NaCl, 0.2% KCl) administered via drinking water. Preliminary data showed that global SGK1 deletion caused significantly decreased blood pressure, EnNaC activity and aortic endothelium stiffness as compared to control mice following DOCA-salt treatment. To probe EC signaling pathways, selective deletion of EC-SGK1 was performed by cross-breeding cadherin 5-Cre mice with sgk1flox/flox mice. DOCA-salt treated control mice had significantly increased blood pressure, EC and aortic stiffness in vivo and ex vivo, which were attenuated by EC-SGK1 deficiency. To demonstrate relevance to humans, human aortic ECs were cultured in the absence or presence of aldosterone and high salt with or without the SGK1 inhibitor, EMD638683 (10uM or 25uM). Treatment with aldosterone and high salt increased intrinsic stiffness of ECs, which was prevented by SGK1 inhibition. Further, the SGK1 inhibitor prevented aldosterone and high salt induced actin polymerization, a key mechanism in cellular stiffening. ConclusionEC-SGK1 mediates salt-sensitivity related EC and aortic stiffening by mechanisms appearing to involve regulation actin polymerization. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/563167v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@74497forg.highwire.dtl.DTLVardef@855709org.highwire.dtl.DTLVardef@151c72org.highwire.dtl.DTLVardef@1feae92_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

SeMOE allows for quantitative glycan perception and exhibits anti-cancer potentiality

Metabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and background signal readout makes it challenging to achieve absolute glycan quantification. Here we develop SeMOE, a selenosugar-based metabolic oligosaccharide engineering strategy that combines elemental analysis and MOE to enable the absolute quantification and mass spectrometric imaging of glycome in a concise procedure. We demonstrate that SeMOE probes allow for perception, absolute quantification and visualization of glycans in diverse biological contexts. We demonstrate that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. We further show the anti-cancer potentiality of SeMOE probes. SeMOE thus provides a convenient and simplified method to "see more" of the glyco-world.

bioengineering↗

Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence

Pseudomonas aeruginosa is an opportunistic human pathogen that poses threats to hospitalized immunocompromised patients 1. A non-coding small RNA (sRNA) from the repressor of secondary metabolites (Rsm) system, RsmZ, sequesters the global repressor protein RsmA to regulate downstream gene expressions that reprogram virulence repertoires associated with acute and chronic P. aeruginosa infections 2,3. Molecular insights into the full-length RsmZ architecture remain elusive, leading to the lack of understanding of RsmZ binding to RsmA and subsequent modulations of gene expressions. Here we use cryo-electron microscopy (cryo-EM) to resolve structures of the full-length RsmZ in complexes with RsmA, in which five stem-loops (SLs) and one single-stranded junction carrying the GGA binding sites in RsmZ form three pairs of clamps, each binding to a RsmA homodimer. Disruptions of the base-pairings in all stems of RsmZ significantly reduced the binding affinity to RsmA by 17-fold, which resulted in enhanced RsmA downregulation of gene expressions and phenotypes associated to both acute and chronic virulence of P. aeruginosa. Double mutations that rescued these stems of RsmZ restored the binding to RsmA by more than 5-fold, and recovered the corresponding phenotypes. Our results reveal the molecular mechanism of RsmZ regulation of P. aeruginosa virulence and suggest RsmZ as a potential target for the development of new antimicrobial agents.

microbiology↗

HybAVPnet: a novel hybrid network architecture for antiviral peptides identification

MotivationThe virus poses a great threat to human production and life, thus the research and development of antiviral drugs is urgently needed. Antiviral peptides play an important role in drug design and development. Compared with the time-consuming and laborious wet chemical experiment methods, accurate and rapid identification of antiviral peptides using computational methods is critical. However, it is still challenging to extract effective feature representations from the sequences for the accurate identification of antiviral peptides. ResultsThis study introduces a novel two-step approach, named HybAVPnet, with a hybrid network architecture to identify antiviral peptides based on neural networks and traditional machine learning methods. Firstly, eighteen kinds of features are extracted to predict labels and probabilities by the neural network classifier and LightGBM classifier, respectively. Secondly, the support vector machine classifier is carried out using the predicted probability of the first step to make the final prediction. The experimental result shows HybAVPnet can achieve better and more robust performance compared with the state-of-the-art methods, especially on independent datasets, which makes it useful for the research and development of antiviral drugs. Meanwhile, it can also be extended to other peptide recognition problems because of its generalization ability. Availability and implementationThe predicted model could be downloaded from: https://github.com/greyspring/HybAVPnet Contactgespring@hdu.edu.cn; yp.cai@siat.ac.cn Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

Induction of Anxiety-Like Phenotypes by Knockout of Cannabinoid Type-1 Receptor in Amygdala of Marmosets

The amygdala is an important hub for the regulation of emotions, which is crucial for elucidating cellular and molecular mechanisms of many mental diseases. In the central nervous system, the endocannabinoid system plays a key role in the regulation of emotions and mainly functions through the cannabinoid type-1 receptor (CB1R), which is encoded by the Cnr1 gene. Although CB1R is highly expressed in the amygdala of non-human primates, little is known about its function. Here, we investigated the function of CB1R by knocking out the CB1R in the amygdala of adult marmosets through regional delivery of AAV-SaCas9-gRNA. We found that CB1R knockout in the amygdala of marmosets induced anxiety-like behaviors, including disrupted night sleep, agitated psychomotor activity in new environments, and reduced social desire, but had no effect on hedonic state and fear response. Moreover, CB1R-knockout marmosets exhibited up-regulated plasma cortisol levels, suggesting increased stress. These results showed that knockout of CB1R in the amygdala induced anxiety-like phenotypes in marmosets and shed new light on the mechanisms underlying the regulation of anxiety by CB1R in the amygdala of non-human primates.

neuroscience↗

The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica

C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from rubisco. The specialized leaf anatomy required for this separation evolved independently many times. C4 root systems are highly branched, an adaptation thought to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture (RSA). Using a mutant screen in the C4 model plant Setaria italica, we identify siaux1-1 and siaux1-2 as RSA mutants, and use CRISPR/cas9-mediated genome editing and overexpression to confirm the importance of the locus. As AUX1 is not necessary for lateral root emergence in S. viridis, the species from which S. italica was domesticated, we conducted an analysis of auxin responsive elements in the promoters of auxin-responsive gene families in S. italica, and explore the molecular basis of SiAUX1s role in seedling development using an RNAseq analysis of wild type and siaux1-1 plants. Finally, we use a root coordinate system to compare cell-by-cell meristem structures in siaux1-1 and wild type Setaria plants, observing changes in the distribution of cell volumes in all cell layers and a dependence in the frequency of protophloem and protoxylem strands on siAUX1.

plant biology↗

Selective Corticofugal Modulation on Sound Processing in Auditory Thalamus of Awake Marmosets

Cortical feedback has long been considered crucial for modulation of sensory processing. In the mammalian auditory system, studies have suggested that corticofugal feedback can have excitatory, inhibitory, or both effects on the response of subcortical neurons, leading to controversies regarding the role of corticothalamic influence. This has been further complicated by studies conducted under different brain states. In the current study, we used cryo-inactivation in the primary auditory cortex (A1) to examine the role of corticothalamic feedback on medial geniculate body (MGB) neurons in awake marmosets. The primary effects of A1 inactivation were a frequency-specific decrease in the auditory response of MGB neurons coupled with an increased spontaneous firing rate, which together resulted in a decrease in the signal-to-noise ratio. In addition, we report for the first-time that A1 robustly modulated the long-lasting sustained response of MGB neurons which changed the frequency tuning after A1 inactivation, e.g., neurons with sharp tuning increased tuning bandwidth whereas those with broad tuning decreased tuning bandwidth. Taken together, our results demonstrate that corticothalamic modulation in awake marmosets serves to enhance sensory processing in a way similar to center-surround models proposed in visual and somatosensory systems, a finding which supports common principles of corticothalamic processing across sensory systems.

neuroscience↗

Relationship Between Neuroendocrine and Immune Gene Expression in Small Cell Lung Cancer

Small cell lung cancer (SCLC) is classified as a high-grade neuroendocrine (NE) tumor, but a subset of SCLC has been termed "variant" due to the loss of NE characteristics. In this study, we computed NE scores for patient-derived SCLC cell lines and xenografts, as well as human tumors. We aligned NE properties with transcription factor-defined molecular subtypes. Then we investigated the different immune phenotypes associated with high and low NE scores. We found repression of immune response genes as a shared feature between classic SCLC and pulmonary neuroendocrine cells of the healthy lung. With loss of NE fate, variant SCLC tumors regain cell-autonomous immune gene expression and exhibit higher tumor-immune interactions. Pan-cancer analysis revealed this NE lineage-specific immune phenotype in other cancers. Additionally, we observed MHC I re-expression in SCLC upon development of chemoresistance. These findings provide a new framework to guide design of treatment regimens in SCLC.

cancer biology↗

Antibody-free enzyme-assisted chemical labeling for detection of transcriptome-wide N6-methyladenosine

The inert chemical property of RNA modification N6-methyladenosine (m6A) makes it very challenging to detect, and all of the transcriptome-wide m6A detection methods rely on m6A-antibody immunoprecipitation. However, their results are dependent on the quality and specificity of antibodies. Although the endoribonuclease-based single-base m6A sequencing is antibody-free, it maps only 16~25% sites. Here, we present an antibody-free, FTO-assisted chemical labeling method termed m6A-SEAL for m6A detection. We applied m6A-SEAL to profile m6A landscapes in human and plant, which had good overlaps with antibody-based results and displayed the known m6A distribution features in transcriptome. Comparison with all available m6A sequencing methods and specific m6A sites validation by SELECT, we demonstrated that m6A-SEAL has good sensitivity, specificity, and reliability for transcriptome-wide detection of m6A. Given its tagging ability and FTOs oxidation property, m6A-SEAL enables many applications like enrichment, imaging, and sequencing techniques to drive future functional studies of m6A and other modifications.

biochemistry↗

Multiple isotopic models using various kinetic fractionation coefficients to estimate δ18O of leaf water

Investigation of{delta} 18O of leaf water may improve our understanding of the evapotranspiration partitioning and material exchange between the inside and outside of leaves. In this study,{delta} 18O of bulk leaf water ({delta}L,b) was estimated by both isotopic-steady-state (ISS) and non-steady-state (NSS) assumptions considering the Peclet effect. Specifically, we carefully modified kinetic fractionation coefficients (k). The results showed that the Peclet effect is required to predict{delta} L,b. On the diel time scale, both NSS assumption + Peclet effect (NSS + P) and ISS assumption + Peclet effect (ISS + P) using modified k (k-modified) for{delta} L,b showed a good agreement with observed{delta} L,b (p > 0.05). When using previously proposed k, however, both NSS + P and ISS + P were not reliable estimators of{delta} L,b (p < 0.05). On a longer time scale (days), estimates of daily mean{delta} L,b from ISS + P outperformed the estimates from NSS + P when using the same k values. Also, the employment of k-modified improved model performance in predicting daily mean{delta} L,b compared to the use of previously proposed k. Clearly, special care must be taken concerning k when using isotopic models to estimate{delta} L,b.\n\nHighlightFor hourly and daily mean data sets, the employment of modified kinetic fractionation coefficients significantly improved model performance for{delta} 18O of bulk leaf water.

ecology↗

Water stress and CO2 concentration interactions affect carbon isotope signatures of leaf and phloem organic matter

Investigation of {delta}13C of leaf and twig phloem water-soluble organic material (WSOM) is a promising approach for analysis of the effects of environmental factors on plant performance. In this study, orthogonal treatments of three CO2 concentrations (Ca) x five soil water contents (SWC) were conducted using Platycladus orientalis saplings to investigate the interaction of water stress and CO2 concentration on {delta}13C of leaf and twig phloem WSOM. Under the lowest SWC, the {delta}13C of leaf and twig phloem WSOM had the most positive values at any Ca and their values decreased as Ca increased. However, at improved soil water conditions, the greatest values of {delta}13C of leaf and twig phloem WSOM were mostly observed at C600. In addition, a more significant relationship between SWC and {delta}13C of twig phloem WSOM than that between SWC and {delta}13C of leaf WSOM demonstrated that {delta}13C of twig phloem WSOM is a more sensitive indicator of SWC. Twig phloem WSOM was generally 13C-depleted compared with leaf WSOM for potential post-photosynthetic fractionation, and the 13C discrimination from leaves to twig phloem was insensitive to the interaction between SWC and Ca. Clearly, interacting effects play a more important role in photosynthetic fractionation than in post-photosynthetic fractionation.\n\nHighlightThe {delta}13C of leaf and twig phloem WSOM exhibited the most positive values at C400x35%-45% FC.\n\nPost-photosynthetic fractionation from leaf to twig was not be impacted by the interacting effects.

ecology↗