arXiv subjects

Jia Dong

Publications and source records attributed to Jia Dong.

6 recordsLinked to original sources

arXiv2026

Non-perturbative Bacterial Identification Directly from Solid Agar Plates Using Raman

Raman spectroscopy is a promising tool for microbial identification, yet its implementation in microbiology and clinical workflow is still restricted due to the accompanying additional preparation required to focus on microbial signals. Here, we demonstrate Raman-based bacterial identification directly from unopened, inverted agar plates, the same conditions used during incubation. Our approach enabled identification with single gene-level sensitivity using two Escherichia coli variants, differing only in green fluorescent protein (GFP) expression, across diverse media and substrate material conditions, despite the interrogation path traversing 3-4 mm thick background material. We integrated traditional density functional theory (DFT)-based material computation with machine learning analysis, achieving over 97.7% classification accuracy, surpassing the performance of standard measurements from opened plates by 10.8% higher mean accuracy and 0.76% less variance. We further demonstrated Raman mapping-based colony identification via Raman peaks characteristic to GFPmut3 chromophore structure generated by DFT. Our approach is robust to changes in algorithms or substrate materials and promises real-time, non-perturbative monitoring of bacterial growth, biofilm formation, and antimicrobial resistance development.

q-bio.QM↗

arXiv2025

Towards Breath Based Diagnostics via Water-mediated Capture of Synthetic Breath Biomarkers in SERS-active Plasmonic Nanogaps

Volatile organic compounds (VOCs) are valuable health indicators, with synthetic breath biomarkers offering rapid and disease specific diagnostics. However, their <100 ppb level exhalation requires mass spectrometry, limiting clinical integration. Surface-enhanced Raman spectroscopy (SERS) offers a portable, cost-effective alternative. Yet, detecting synthetic breath biomarkers, with inherently low Raman cross-sections, at <100 ppb remains challenging. We demonstrate SERS detection down to clinically relevant 10 ppb via water-mediated trapping in hydroxylated nanoporous silica-coated plasmonic nanogaps, using pentafluoropropylamine (PFP) as a representative synthetic breath biomarker. Uniform nanogaps, with >1000 times electric field enhancement, were generated between a gold film and gold-silica core-shell nanoparticle assemblies using electric field-driven evaporation. Oxygen plasma treatment hydroxylated the silica, enabling water-mediated hydrogen bonding that strengthened PFP adsorption, confirmed by density functional theory. This mechanism improved SERS sensitivity by 10000 fold, enabling ppb level PFP detection in mouse bronchial fluid and establishing a VOC capturing SERS platform for breath-based diagnostics.

physics.app-ph↗

arXiv2025

Interplay of Electrostatic Interaction and Steric Repulsion between Bacteria and Gold Surface Influences Raman Enhancement

Plasmonic nanostructures have wide applications in photonics including pathogen detection and diagnosis via Surface-Enhanced Raman Spectroscopy (SERS). Despite major role plasmonics play in signal enhancement, electrostatics in SERS is yet to be fully understood and harnessed. Here, we perform a systematic study of electrostatic interactions between 785 nm resonant gold nanorods designed to harbor zeta potentials of +29, +16, 0 and -9 mV spanning positive neutral and negative domains. SERS activity is tested on representative Gram-negative Escherichia coli and Gram-positive Staphylococcus epidermidis bacteria with zeta potentials of -30 and -23 mV respectively in water. Raman spectroscopy and Cryo-Electron microscopy reveal that +29, +16, 0 and -9 mV nanorods give SERS enhancement of 7.2X, 3.6X, 4.2X, 1.3X to Staphylococcus epidermidis and 3.9X, 2.8X, 2.9X, 1.1X to Escherichia coli. Theoretical results show that electrostatics play the major role among all interaction forces in determining cell-nanorod proximity and signal enhancement. We identify steric repulsion due to cell protrusions to be the critical opposing force. Finally, a design principle is proposed to estimate the electrostatic strength in SERS. Our work provides new insights into the principle of bacteria-nanorod interactions, enabling reproducible and precise biomolecular readouts, critical for next-generation point-of-care diagnostics and smart healthcare applications.

q-bio.CB↗

arXiv2024

F3T: A soft tactile unit with 3D force and temperature mathematical decoupling ability for robots

The human skin exhibits remarkable capability to perceive contact forces and environmental temperatures, providing intricate information essential for nuanced manipulation. Despite recent advancements in soft tactile sensors, a significant challenge remains in accurately decoupling signals - specifically, separating force from directional orientation and temperature - resulting in fail to meet the advanced application requirements of robots. This research proposes a multi-layered soft sensor unit (F3T) designed to achieve isolated measurements and mathematical decoupling of normal pressure, omnidirectional tangential forces, and temperature. We developed a circular coaxial magnetic film featuring a floating-mountain multi-layer capacitor, facilitating the physical decoupling of normal and tangential forces in all directions. Additionally, we incorporated an ion gel-based temperature sensing film atop the tactile sensor. This sensor is resilient to external pressure and deformation, enabling it to measure temperature and, crucially, eliminate capacitor errors induced by environmental temperature changes. This innovative design allows for the decoupled measurement of multiple signals, paving the way for advancements in higher-level robot motion control, autonomous decision-making, and task planning.

cs.RO↗

arXiv2024

From Pixel to Slide image: Polarization Modality-based Pathological Diagnosis Using Representation Learning

Thyroid cancer is the most common endocrine malignancy, and accurately distinguishing between benign and malignant thyroid tumors is crucial for developing effective treatment plans in clinical practice. Pathologically, thyroid tumors pose diagnostic challenges due to improper specimen sampling. In this study, we have designed a three-stage model using representation learning to integrate pixel-level and slice-level annotations for distinguishing thyroid tumors. This structure includes a pathology structure recognition method to predict structures related to thyroid tumors, an encoder-decoder network to extract pixel-level annotation information by learning the feature representations of image blocks, and an attention-based learning mechanism for the final classification task. This mechanism learns the importance of different image blocks in a pathological region, globally considering the information from each block. In the third stage, all information from the image blocks in a region is aggregated using attention mechanisms, followed by classification to determine the category of the region. Experimental results demonstrate that our proposed method can predict microscopic structures more accurately. After color-coding, the method achieves results on unstained pathology slides that approximate the quality of Hematoxylin and eosin staining, reducing the need for stained pathology slides. Furthermore, by leveraging the concept of indirect measurement and extracting polarized features from structures correlated with lesions, the proposed method can also classify samples where membrane structures cannot be obtained through sampling, providing a potential objective and highly accurate indirect diagnostic technique for thyroid tumors.

eess.IV↗

arXiv2023

A Polarization and Radiomics Feature Fusion Network for the Classification of Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma

Classifying hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) is a critical step in treatment selection and prognosis evaluation for patients with liver diseases. Traditional histopathological diagnosis poses challenges in this context. In this study, we introduce a novel polarization and radiomics feature fusion network, which combines polarization features obtained from Mueller matrix images of liver pathological samples with radiomics features derived from corresponding pathological images to classify HCC and ICC. Our fusion network integrates a two-tier fusion approach, comprising early feature-level fusion and late classification-level fusion. By harnessing the strengths of polarization imaging techniques and image feature-based machine learning, our proposed fusion network significantly enhances classification accuracy. Notably, even at reduced imaging resolutions, the fusion network maintains robust performance due to the additional information provided by polarization features, which may not align with human visual perception. Our experimental results underscore the potential of this fusion network as a powerful tool for computer-aided diagnosis of HCC and ICC, showcasing the benefits and prospects of integrating polarization imaging techniques into the current image-intensive digital pathological diagnosis. We aim to contribute this innovative approach to top-tier journals, offering fresh insights and valuable tools in the fields of medical imaging and cancer diagnosis. By introducing polarization imaging into liver cancer classification, we demonstrate its interdisciplinary potential in addressing challenges in medical image analysis, promising advancements in medical imaging and cancer diagnosis.

eess.IV↗