ResearchPub Date : 2025-01-17eCollection Date: 2025-01-01DOI: 10.34133/research.0568
Yongxin Ge, Jiake Leng, Ziyang Tang, Kanran Wang, Kaicheng U, Sophia Meixuan Zhang, Sen Han, Yiyan Zhang, Jinxi Xiang, Sen Yang, Xiang Liu, Yi Song, Xiyue Wang, Yuchen Li, Junhan Zhao
{"title":"Deep Learning-Enabled Integration of Histology and Transcriptomics for Tissue Spatial Profile Analysis.","authors":"Yongxin Ge, Jiake Leng, Ziyang Tang, Kanran Wang, Kaicheng U, Sophia Meixuan Zhang, Sen Han, Yiyan Zhang, Jinxi Xiang, Sen Yang, Xiang Liu, Yi Song, Xiyue Wang, Yuchen Li, Junhan Zhao","doi":"10.34133/research.0568","DOIUrl":"10.34133/research.0568","url":null,"abstract":"<p><p>Spatially resolved transcriptomics enable comprehensive measurement of gene expression at subcellular resolution while preserving the spatial context of the tissue microenvironment. While deep learning has shown promise in analyzing SCST datasets, most efforts have focused on sequence data and spatial localization, with limited emphasis on leveraging rich histopathological insights from staining images. We introduce GIST, a deep learning-enabled gene expression and histology integration for spatial cellular profiling. GIST employs histopathology foundation models pretrained on millions of histology images to enhance feature extraction and a hybrid graph transformer model to integrate them with transcriptome features. Validated with datasets from human lung, breast, and colorectal cancers, GIST effectively reveals spatial domains and substantially improves the accuracy of segmenting the microenvironment after denoising transcriptomics data. This enhancement enables more accurate gene expression analysis and aids in identifying prognostic marker genes, outperforming state-of-the-art deep learning methods with a total improvement of up to 49.72%. GIST provides a generalizable framework for integrating histology with spatial transcriptome analysis, revealing novel insights into spatial organization and functional dynamics.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0568"},"PeriodicalIF":11.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143009479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"High-Performance Edge-Contact Monolayer Molybdenum Disulfide Transistors.","authors":"Jiankun Xiao, Xiong Xiong, Xinhang Shi, Shiyuan Liu, Shenwu Zhu, Yue Zhang, Ru Huang, Yanqing Wu","doi":"10.34133/research.0593","DOIUrl":"10.34133/research.0593","url":null,"abstract":"<p><p>Edge contact is essential for achieving the ultimate device pitch scaling of stacked nanosheet transistors with monolayer 2-dimensional (2D) channels. However, due to large edge-contact resistance between 2D channels and contact metal, there is currently a lack of high-performance edge-contact device technology for 2D material channels. Here, we report high-performance edge-contact monolayer molybdenum disulfide (MoS<sub>2</sub>) field-effect transistors (FETs) utilizing well-controlled plasma etching techniques. Plasma etching with pure argon improves the edge dangling bonds and thus improves the edge-contact quality. Edge-contact monolayer MoS<sub>2</sub> FET shows good ohmic contact even at cryogenic temperatures (20 K), achieving a record-low contact resistance (<i>R</i> <sub>c</sub>) of 1.25 kΩ·μm among all edge-contact MoS<sub>2</sub> devices. The record-high on-state current of 436 μA/μm and transconductance of 123 μS/μm at <i>V</i> <sub>ds</sub> = 1 V are achieved on an edge-contact monolayer MoS<sub>2</sub> FET with <i>L</i> <sub>ch</sub> = 120 nm. This work highlights the great potential of edge contacts for high-performance monolayer transition metal dichalcogenide (TMD) material electronics.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0593"},"PeriodicalIF":11.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Recent Advances in Indocyanine Green-Based Probes for Second Near-Infrared Fluorescence Imaging and Therapy.","authors":"Dehong Hu, Menglei Zha, Hairong Zheng, Duyang Gao, Zonghai Sheng","doi":"10.34133/research.0583","DOIUrl":"10.34133/research.0583","url":null,"abstract":"<p><p>Fluorescence imaging, a highly sensitive molecular imaging modality, is being increasingly integrated into clinical practice. Imaging within the second near-infrared biological window (NIR-II; 1,000 to 1,700 nm), also referred to as shortwave infrared, has received substantial attention because of its markedly reduced autofluorescence, deeper tissue penetration, and enhanced spatiotemporal resolution as compared to traditional near-infrared (NIR) imaging. Indocyanine green (ICG), a US Food and Drug Administration-approved NIR fluorophore, has long been used in clinical applications, including blood vessel angiography, vascular perfusion monitoring, and tumor detection. Recent advancements in NIR-II imaging technology have revitalized interest in ICG, revealing its extended tail fluorescence beyond 1,000 nm and reaffirming its potential as a clinically translatable NIR-II fluorophore for in vivo imaging and theranostic applications for diagnosing various diseases. This review emphasizes the notable advances in the use of ICG and its derivatives for NIR-II imaging and image-guided therapy from both fundamental and clinical perspectives. We also provide a concise conclusion and discuss the challenges and future opportunities with NIR-II imaging using clinically approved fluorophores.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0583"},"PeriodicalIF":11.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Intratonsillar Immunotherapy: A Convenient and Effective Alternative to Subcutaneous Immunotherapy for Allergic Rhinitis.","authors":"Tian Gu, Wei Zhang, Lu Tan, Rong Xiang, Peiqiang Liu, Jingyu Huang, Qin Deng, Yuqin Deng, Zezhang Tao, Shiming Chen, Yu Xu","doi":"10.34133/research.0573","DOIUrl":"10.34133/research.0573","url":null,"abstract":"<p><p>Allergen-specific immunotherapy (AIT) is the only treatment that addresses the root cause of immunoglobulin E (IgE)-mediated allergies, but conventional methods face challenges with treatment duration, patient compliance, and adverse effects. In this study, we propose intratonsillar immunotherapy (ITIT) as a new effective and safer route for AIT. Prior to clinical trials, we analyzed tonsil samples from human subjects to assess immune responses, measuring interleukin-4 (IL-4), IL-21, total IgE (tIgE), and allergen-specific IgE concentrations using ELISA and BioIC. Our results indicated that tonsils contained higher levels of allergen-specific IgE compared to peripheral blood. In the clinical phase, 120 allergic rhinitis (AR) patients were treated with either 3 intratonsillar allergen injections over 2 months or conventional subcutaneous immunotherapy (SCIT) over 1 year. ITIT demonstrated superior and faster symptom relief, especially in younger patients, while requiring markedly fewer doses and injections than SCIT. Immunological analysis revealed reduced eosinophil counts, increased regulatory T (T<sub>reg</sub>) and follicular regulatory T (T<sub>FR</sub>) cell levels, and a favorable shift in cytokine profiles. Adverse events were minimal, and the treatment showed high patient compliance. These findings suggest that ITIT could provide an effective, safer, and more convenient alternative to AIT.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0573"},"PeriodicalIF":11.0,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Comprehensive Cellular Senescence Evaluation to Aid Targeted Therapies.","authors":"Xiaolan Zhou, Xiaofeng Zhu, Weixu Wang, Jing Wang, Haimei Wen, Yuqi Zhao, Jiayu Zhang, Qiushi Xu, Zhaozhao Zhao, Ting Ni","doi":"10.34133/research.0576","DOIUrl":"10.34133/research.0576","url":null,"abstract":"<p><p>Drug resistance to a single agent is common in cancer-targeted therapies, and rational drug combinations are a promising approach to overcome this challenge. Many Food and Drug Administration-approved drugs can induce cellular senescence, which possesses unique vulnerabilities and molecular signatures. However, there is limited analysis on the effect of the combination of cellular-senescence-inducing drugs and targeted therapy drugs. Here, we conducted a comprehensive evaluation of cellular senescence using 7 senescence-associated gene sets. We quantified the cellular senescence states of ~10,000 tumor samples from The Cancer Genome Atlas and examined their associations with targeted drug responses. Our analysis revealed that tumors with higher cellular senescence scores exhibited increased sensitivity to targeted drugs. As a proof of concept, we experimentally confirmed that etoposide-induced senescence sensitized lung cancer cells to 2 widely used targeted drugs, erlotinib and dasatinib. Furthermore, we identified multiple genes whose dependencies were associated with senescence status across ~1,000 cancer cell lines, suggesting that cellular senescence generates unique vulnerabilities for therapeutic exploitation. Our study provides a comprehensive overview of drug response related to cellular senescence and highlights the potential of combining senescence-inducing agents with targeted therapies to improve treatment outcomes in lung cancer, revealing novel applications of cellular senescence in targeted cancer therapies.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0576"},"PeriodicalIF":11.0,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2025-01-14eCollection Date: 2025-01-01DOI: 10.34133/research.0579
Huang Lin, Cong Luo, Fangyuan Cheng, Kui Xie
{"title":"Engineering Active Interfaces on the Surface of Porous Single-Crystalline TiO<sub>2</sub> Monoliths for Enhanced Catalytic Activity and Stability.","authors":"Huang Lin, Cong Luo, Fangyuan Cheng, Kui Xie","doi":"10.34133/research.0579","DOIUrl":"10.34133/research.0579","url":null,"abstract":"<p><p>The engineering design and construction of active interfaces represents a promising approach amidst numerous initiatives aimed at augmenting catalytic activity. Herein, we present a novel approach to incorporate interconnected pores within bulk single crystals for the synthesis of macroscopic porous single-crystalline rutile titanium oxide (R-TiO<sub>2</sub>). The porous single crystal (PSC) R-TiO<sub>2</sub> couples a nanocrystalline framework as the solid phase with pores as the fluid phase within its structure, providing unique advantages in localized structure construction and in the field of catalysis. We successfully construct well-defined Ni cluster/TiO<sub>2</sub> active interfaces by directly confining Ni clusters on the continuous lattice surface of PSC R-TiO<sub>2</sub>. We confirm that the lattice oxygen connected to the Ni clusters exhibits exceptional activation capability at temperatures close to room temperature compared to the pure phase PSC R-TiO<sub>2</sub> monoliths. The PSC Ni/TiO<sub>2</sub> catalyst demonstrates complete CO oxidation and stable catalytic performance during continuous operation in air at ~80 °C for 200 h.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0579"},"PeriodicalIF":11.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Recent Advances in Self-Powered Sensors Based on Ionic Hydrogels.","authors":"Jianyu Yin, Peixue Jia, Ziqi Ren, Qixiang Zhang, Wenzhong Lu, Qianqian Yao, Mingfang Deng, Xubin Zhou, Yihua Gao, Nishuang Liu","doi":"10.34133/research.0571","DOIUrl":"10.34133/research.0571","url":null,"abstract":"<p><p>After years of research and development, flexible sensors are gradually evolving from the traditional \"electronic\" paradigm to the \"ionic\" dimension. Smart flexible sensors derived from the concept of ion transport are gradually emerging in the flexible electronics. In particular, ionic hydrogels have increasingly become the focus of research on flexible sensors as a result of their tunable conductivity, flexibility, biocompatibility, and self-healable capabilities. Nevertheless, the majority of existing sensors based on ionic hydrogels still mainly rely on external power sources, which greatly restrict the dexterity and convenience of their applications. Advances in energy harvesting technologies offer substantial potential toward engineering self-powered sensors. This article reviews in detail the self-powered mechanisms of ionic hydrogel self-powered sensors (IHSSs), including piezoelectric, triboelectric, ionic diode, moist-electric, thermoelectric, potentiometric transduction, and hybrid modes. At the same time, structural engineering related to device and material characteristics is discussed. Additionally, the relevant applications of IHSS toward wearable electronics, human-machine interaction, environmental monitoring, and medical diagnostics are further reviewed. Lastly, the challenges and prospective advancement of IHSS are outlined.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0571"},"PeriodicalIF":11.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Recent Advances in Asymmetric Wettability Dressings for Wound Exudate Management.","authors":"Fang Wang, Wenqing He, Bing Dai, Xueji Zhang, Yongqiang Wen","doi":"10.34133/research.0591","DOIUrl":"10.34133/research.0591","url":null,"abstract":"<p><p>The management of wound exudate is of vital importance for wound healing. Exudate accumulation around wound prolongs inflammation and hinders healing. Although traditional dressings can absorb wound exudate, they are unable to drain exudate in time, often resulting in a poor feature with wound healing. In recent years, the appearance of asymmetric wettability dressings has shown great potential in exudate management. Here, we summarize the latest progress of 3 kinds of asymmetric wettability wound dressings in exudate management, including Janus structure, sandwich structure, and gradient structure. The most common Janus structural dressing among asymmetric wettability dressings is highlighted from 2 aspects: single-layer modified Janus structure and double-layer Janus structure. The challenges faced by asymmetric wettability wound dressings are discussed, and the developing trends of smart wound dressings in this field are prospected.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0591"},"PeriodicalIF":11.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2025-01-13eCollection Date: 2025-01-01DOI: 10.34133/research.0578
Ruomei Cheng, Xiaopeng Tang, Qiyu Zhao, Yuming Wang, Wenlin Chen, Gan Wang, Chenxi Wang, James Mwangi, Qiumin Lu, Dawit Adisu Tadese, Xudong Zhao, Caiwen Ou, Ren Lai
{"title":"Transferrin Disassociates TCR from CD3 Signaling Apparatus to Promote Metastasis.","authors":"Ruomei Cheng, Xiaopeng Tang, Qiyu Zhao, Yuming Wang, Wenlin Chen, Gan Wang, Chenxi Wang, James Mwangi, Qiumin Lu, Dawit Adisu Tadese, Xudong Zhao, Caiwen Ou, Ren Lai","doi":"10.34133/research.0578","DOIUrl":"10.34133/research.0578","url":null,"abstract":"<p><p>Immune recognition and activation by the peptide-laden major histocompatibility complex-T cell receptor (TCR)-CD3 complex is essential for anti-tumor immunity. Tumors may escape immune surveillance by dissembling the complex. Here, we report that transferrin, which is overexpressed in patients with liver metastasis, disassociates TCR from the CD3 signaling apparatus by targeting the constant domain (CD) of T cell receptor α (TCRα), consequently suppresses T cell activation, and inhibits anti-metastatic and anti-tumor immunity. In mouse models of melanoma and lymphoma, transferrin overexpression exacerbates liver metastasis, while its knockdown, antibody, designed peptides, and CD mutation interfering with transferrin-TCRα interaction inhibit metastasis. This work reveals a novel strategy of tumor evasion of immune surveillance by blocking the coupling between TCRs and the CD3 signaling apparatus to suppress TCR activation. Given the conservation of CD and transferrin up-regulation in metastatic tumors, the strategy might be a common metastatic mechanism. Targeting transferrin-TCRα holds promise for anti-metastatic treatment.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0578"},"PeriodicalIF":11.0,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11731779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Advances in Nanoengineered Terahertz Technology: Generation, Modulation, and Bio-Applications.","authors":"Zhongwei Jin, Jing Lou, Fangzhou Shu, Zhi Hong, Cheng-Wei Qiu","doi":"10.34133/research.0562","DOIUrl":"10.34133/research.0562","url":null,"abstract":"<p><p>Recent advancements in nanotechnology have revolutionized terahertz (THz) technology. By enabling the creation of compact, efficient devices through nanoscale structures, such as nano-thick heterostructures, metasurfaces, and hybrid systems, these innovations offer unprecedented control over THz wave generation and modulation. This has led to substantial enhancements in THz spectroscopy, imaging, and especially bio-applications, providing higher resolution and sensitivity. This review comprehensively examines the latest advancements in nanoengineered THz technology, beginning with state-of-the-art THz generation methods based on heterostructures, metasurfaces, and hybrid systems, followed by THz modulation techniques, including both homogeneous and individual modulation. Subsequently, it explores bio-applications such as novel biosensing and biofunction techniques. Finally, it summarizes findings and reflects on future trends and challenges in the field. Each section focuses on the physical mechanisms, structural designs, and performances, aiming to provide a thorough understanding of the advancements and potential of this rapidly evolving technology domain. This review aims to provide insights into the creation of next-generation nanoscale THz devices and applications while establishing a comprehensive foundation for addressing key issues that limit the full implementation of these promising technologies in real-world scenarios.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"8 ","pages":"0562"},"PeriodicalIF":11.0,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}