Biology subjects

Zhao, L. S.

Publications and source records attributed to Zhao, L. S..

4 recordsLinked to original sources

bioRxiv2026

MR KLEAN: a Generalized Acquisition-agnostic LLR k-Space Denoising Method for High-dimensional Imaging

PurposeHigh-dimensional and dynamic MRI are often limited by thermal noise, particularly in accelerated acquisitions. Although image-domain low-rank denoising methods (e.g., MP-PCA and NORDIC) are effective, their reliance on stationary noise distributions limits applicability to non-Cartesian sampling and advanced reconstructions. This work introduces Magnetic Resonance K-space Local low-rank Estimation for Attenuating Noise (MR KLEAN), a k-space low-rank denoising framework agnostic to acquisition trajectory and reconstruction strategy. Theory and MethodsMR KLEAN exploits local low-rank structure in multichannel, high-dimensional k-space. Data are prewhitened using a noise-only scan to enforce independent and identically distributed, zero-mean, unit-variance noise. Casorati matrices from local k-space patches are denoised by singular-value thresholding, with thresholds set via Monte-Carlo simulations under known noise statistics. MR KLEAN was evaluated in (1) a Cartesian 3D FLASH phantom study, (2) an ASL study with spiral readout and compressed sensing reconstruction to assess generalizability and preservation of temporal information via resting-state connectivity analysis, and (3) an accelerated cardiac cine study assessing performance under rapid temporal dynamics. ResultsMR KLEAN increased SNR and CNR in phantom studies. In vivo ASL showed reduced noise in perfusion images, improved relative SNR, and substantially enhanced resting-state networks detection. In cardiac imaging, noise was reduced and delineation of fine anatomical features improved while temporal fidelity was preserved across cardiac phases. ConclusionMR KLEAN provides robust, acquisition- and reconstruction-agnostic k-space denoising, improving image quality and allowing flexible spatial-temporal trade-offs. Results further support that high-dimensional k-space data retain intrinsic local low-rank structure analogous to image-space despite temporal signal variations.

bioengineering↗

bioRxiv2025

RAB18 Orchestrates Signaling Protein Ciliary Homeostasis by Facilitating BBSome Diffusion through the Transition Zone for Ciliary Entry

The BBSome acts as an intraflagellar transport (IFT) cargo adaptor that connects transmembrane and membrane-anchored signaling proteins to the process of IFT within cilia. This function is critical for ciliary homeostasis maintenance of signaling proteins, allowing for successfully sensing and transducing extracellular stimuli inside the cell. It is established that, upon reaching the proximal ciliary region just above the transition zone (TZ), a diffusion barrier, via retrograde IFT, the BBSome, carrying signaling proteins, disengages from IFT and diffuses through the TZ for ciliary retrieval. This TZ passage event is promoted by the Arf-like 3 GTPase, which utilizes the BBSome autonomously of IFT association as its major effector. While it is known that the intact BBSome is recruited to the basal bodies before entering cilia, the precise mechanism by which it crosses the TZ to access cilia remains elusive. In our study on Chlamydomonas reinhardtii, we disclose that the Ras-associated binding (Rab) GTPase RAB18 is concentrated in a basal body region that overlaps with the BBSome. Positioned at this location, RAB18 in a GTP-bound state (RAB18-GTP) is anchored to the membrane, allowing it to diffuse into cilia. Throughout this process, the BBSome functions as a RAB18 effector, binding to RAB18-GTP and subsequently being recruited to diffuse through the TZ for ciliary entry in an IFT-independent manner. This collaboration between the BBSome and RAB18 is pivotal in maintaining the signaling protein phospholipase D ciliary homeostasis, providing a precise mechanistic understanding of the inward BBSome TZ passage essential for proper ciliary signaling. Significance statementAlthough certain ciliary signaling proteins cross the transition zone (TZ) for ciliary removal via the RABL2-ARL3 module-mediated outward BBSome TZ diffusion pathway, how the BBSome passes the TZ for ciliary entry remains unclear. Here, we show that RAB18, in its GTP-bound state, anchors to the membrane at the basal bodies. As a RAB18 effector, the BBSome is recruited to cross the TZ for ciliary entry via lateral transport between plasma and ciliary membranes. Once inside cilia, the BBSome integrates into anterograde IFT trains and subsequently functions as a phospholipase D (PLD) adaptor, ensuring PLD removal from cilia. This study highlights RAB18s pivotal role in facilitating BBSome entry into cilia, unveiling a regulatory mechanism crucial for maintaining ciliary signaling protein homeostasis.

cell biology↗

bioRxiv2024

A Comprehensive Assessment of Methylation-Based Age Prediction Methods

DNA methylation (DNAm) clock is widely used to measure biological age, helping to identify key biomarkers associated with aging, infer the progression of aging, and have promise for elucidating, delaying, or even reversing aging. During the past decade, a large number of epigenetic clocks have been developed. However, they are decentralized, with applicable scopes overlapping. We benchmark 15 of these methods on 142 Illumina DNAm array datasets in five criteria and analyze the biological significance of CPGs about aging and overlapping. There are many exciting commons in models performance. We found the optimal model closely related to the numbers and characteristics of the training data. We provided a comprehensive assessment process to guide DNAm clock research at (https://dnamclock.com), the corresponding data and evaluation pipeline are freely available (https://github.comyNENUBioCompute/MethylationEvaluation), this study will aid in the development of improved tools designed to analyze increasingly large DNAm datasets.

bioinformatics↗

bioRxiv2024

Leveraging Multi-echo EPI to Enhance BOLD Sensitivity in Task-based Olfactory fMRI

Functional magnetic resonance imaging (fMRI) using blood-oxygenation-level-dependent (BOLD) contrast relies on gradient echo echo-planar imaging (GE-EPI) to quantify dynamic susceptibility changes associated with the hemodynamic response to neural activity. However, acquiring BOLD fMRI in human olfactory regions is particularly challenging due to their proximity to the sinuses where large susceptibility gradients induce magnetic field distortions. BOLD fMRI of the human olfactory system is further complicated by respiratory artifacts that are highly correlated with event onsets in olfactory tasks. Multi-echo EPI (ME-EPI) acquires gradient echo data at multiple echo times (TEs) during a single acquisition and can leverage signal evolution over the multiple echo times to enhance BOLD sensitivity and reduce artifactual signal contributions. In the current study, we developed a ME-EPI acquisition protocol for olfactory task-based fMRI and demonstrated significant improvement in BOLD signal sensitivity over conventional single-echo EPI (1E-EPI). The observed improvement arose from both an increase in BOLD signal changes through a T2*-weighted echo combination and a reduction in non-BOLD artifacts through the application of the Multi-Echo Independent Components Analysis (ME-ICA) denoising method. This study represents one of the first direct comparisons between 1E-EPI and ME-EPI in high-susceptibility regions and provides compelling evidence in favor of using ME-EPI for future task-based fMRI studies.

neuroscience↗