<p>Functional validation of TAGLN-KO cells</p>
BACKGROUND: Spatial transcriptomics (ST) technologies are reshaping our understanding of tissue organization and cellular context in health and disease. However, technical benchmarking across platforms remains limited, particularly in formalin-fixed, paraffin-embedded (FFPE) clinical samples, which represent the most common tissue format in oncology. RESULTS: Here, we systematically benchmark five commercial ST platforms (Visium v1, Visium v2/CytAssist, Visium HD, Xenium, and CosMx) using matched FFPE human tumor sections from six cancer types. Uniquely, our study includes both sequencing-based and imaging-based platforms profiled on the same samples, enabling direct technical comparisons across spatial capture modalities. We evaluate platform performance across multiple dimensions, including transcript and UMI detection, gene-histology concordance, cell type recovery, and integration with a targeted protein panel (Visium v2, 30 proteins), enabling spatial multi-omics. We also quantify the impact of sampling strategies and area coverage on cell type estimation, revealing trade-offs in spatial resolution versus tissue context. Notably, we present the first same-sample comparison of Xenium Multi-Tissue (377 genes) and Xenium Prime (5,000 genes), highlighting key differences in transcript recovery and spatial signal despite shared chemistry and imaging infrastructure. Finally, we integrate Visium targeted protein data with matched RNA profiles, uncovering widespread RNA-protein decoupling and spatial heterogeneity in concordance. CONCLUSIONS: Collectively, this work provides a harmonized dataset and technical reference for the spatial transcriptomics community, offering insight into the relative strengths, limitations, and design considerations associated with high-throughput spatial profiling of FFPE tumors.
<p>Identification of BaC identity markers expressed in the basal compartment of healthy human breast. <b>A,</b> Schematic representation of a mammary gland duct cross-section, showing BaCs (blue) and LCs cells (red). ERα<sup>pos</sup> and ERα<sup>neg</sup> statuses are indicated by nuclear color. <b>B,</b> Integrated UMAP plot showing epithelial cell clustering from three murine scRNA-seq datasets. Color coding differentiates between BaCs (blue), ERα<sup>pos</sup> LC (red), and ERα<sup>neg</sup> LCs (green). <b>C,</b> UMAP plots showing the signature score of the top 20 DEGs associated with each epithelial compartment. Signature scores are color-coded from low (gray) to high (blue). <b>D,</b> UMAP plots showing expression levels of the top 10 BaC-associated genes across the integrated human dataset. Color gradient indicates expression levels from low (blue) to high (red). <b>E,</b> Representative IHC staining of breast tissue consecutive serial sections showing proteins expression of candidate BaC-associated genes. Scale bar, 50 μm. Arrows in the APOE panel highlight expression restricted to stromal cells. <b>A,</b> Created in BioRender. Rodilla, V. (2026) <a href="https://BioRender.com/qpb7bux" target="_blank">https://BioRender.com/qpb7bux</a>.</p>
Abstract The direct electrochemical nitric oxide reduction reaction (NORR) is an attractive technique for converting NO into NH 3 with low power consumption under ambient conditions. Optimizing the electronic structure of the active sites can greatly improve the performance of electrocatalysts. Herein, we prepare body‐centered cubic RuGa intermetallic compounds (i.e., bcc RuGa IMCs) via a substrate‐anchored thermal annealing method. The electrocatalyst exhibits a remarkable NH 4 + yield rate of 320.6 μmol h −1 mg −1 Ru with the corresponding Faradaic efficiency of 72.3 % at very low potential of −0.2 V vs. reversible hydrogen electrode (RHE) in neutral media. Theoretical calculations reveal that the electron‐rich Ru atoms in bcc RuGa IMCs facilitate the adsorption and activation of *HNO intermediate. Hence, the energy barrier of the potential‐determining step in NORR could be greatly reduced.
With a steep rise in the urban population requiring an increased number of buildings, public and private transport systems, urban noise is posing a serious environmental problem affecting health. To attenuate the effect on the well-being of human health, a variety of conventional sound-absorbing materials suitable at mid and higher-frequency noise absorption are commonly being used but low and mid-frequency noise remains a challenge. These applications are further limited by the acoustic performance and ventilation efficiency in conventional noise barrier limits of their fields. Acoustic metamaterial presents a unique solution as an artificially designed material showing low-frequency noise mitigation. A novel subwavelength device having thickness of 15mm (<2 cm) ,with potential application in noise mitigation and air ventilation solution is presented herein. In this study, the design and fabrication of a small prototype based on a Fresnel-spiral shape composed of several arms are performed. Numerical and experimental investigations were carried out to determine the acoustical properties of the proposed ventilated metamaterial in terms of sound absorption and sound transmission loss. The experimental investigation shows significant sound absorption with a high bandwidth (more than one octave in the range of > 900 Hz ), acoustic properties leading to potential applications in urban noise control for low and mid-frequency ranges.
Design of high-efficiency, low frequency (&lt;1000Hz) soundproof window or wall absorber which is transparent to airflow is presented. Due to the massive rise in human population and modernization, environmental noise has significantly risen globally. Prolonged noise exposure can cause severe physiological and psychological symptoms like nausea, headaches, fatigue, and insomnia. There has been continuous growth in building construction and infrastructure like offices, bus stops, and airports due to urban population. Generally, a ventilated window is used for getting fresh air into the room, but at the same time, unwanted noise comes along. Researchers used traditional approaches like noise barrier mats in front of the window or designed the entire window using sound-absorbing materials. However, this solution is not aesthetically pleasing, and at the same time, it is heavy and not adequate for low-frequency noise shielding. To address this challenge, we design a transparent hexagonal panel based on Sierpiński fractal triangle which is aesthetically pleasing, demonstrates normal incident sound absorption coefficient more than 0.96 around 700 Hz and transmission loss around 23 dB, while maintaining air circulation through triangular cutout. Next, we present a concept of fabrication of large acoustic panel for large-scale applications which lead to suppressing the urban noise pollution
Programmable acoustic metamaterials allow to manipulate sound waves at desirable frequency ranges intelligently, which makes it a viable and practical alternative to many noise cancellation applications. These kinds of metamaterials are amenable to intelligent programming and find place in a variety of real-life applications such as acoustic cloaking, noise cancellation, stealth applications, noise focusing, etc., simply with intelligent programming of the microstructure and the control of micro-movement of the various control boundaries instead of rebuilding new structures every time. Metamaterials are artificially designed materials that possess unique, unusual physical and mechanical properties, making them good lightweight candidates for various noise-shielding applications. However, many papers have been published on studying passive kinds of metamaterial structures whose material properties are fixed in space and time once designed and fabricated. This article is about a different class of metamaterials which are programmable and changeable through various control boundaries forming the structures for the applications pertaining to acoustic isolation (vibro-acoustics) and acoustic mitigation. The incorporation of shape memory polymers or smart polymers into the metamaterial structures enables fine and coarse tuning of these structures to the incoming noise frequency spectrum on a real-time basis. This article reviews some recent trends in progress made with smart materials and programmable metamaterials, their various programming techniques, the fundamental concept involved, various design strategies of such materials and their emergent applications in various fields of technology. The current fabrication challenges and future outlook in this promising field are also discussed.
In this work, we introduce fractal acoustic metamaterials (FAMs), in thicknesses ranging from 5 (λ/69) to 25 mm (λ/18), which are observed to provide multiple narrow-band low-frequency absorptions of acoustic signals. The fractal structures used in this work are carefully designed and fabricated using a side branch Helmholtz resonator design, making these structures easily tunable to multiple frequencies. Using different sizes of the side branches distributed in a fractally oriented configuration onto a plane rigid baseplate, the propagation velocity of acoustic waves is slowed down considerably. There is also a shifting resonating response of the structures toward lower frequencies (&lt;1600 Hz). These FAM structures exhibit no dependence on the acoustic traverse length, as is otherwise commonly seen in coiled meta-structures and others. In order to achieve a near-perfect sound absorption behavior, the geometry of the structure is theoretically ascertained and validated numerically and experimentally. Significant emphasis has been placed on the associated physical mechanism modulating the loss of intensity of the incident acoustic signals. Moreover, with regression analysis performed on a response surface-based optimization scheme (using Design Expert 11 software), the geometric parameters are determined in a way that the absorption demonstrates a narrow-band characteristic at a frequency of 1 K Hz. We have shown in this work the tunability aspect of the various absorption frequency bands through appropriate designs of the FAM. It opens up wide application possibilities of multiple frequency sound absorptions (acoustic cloaking).
<div>Abstract<p>Triple-negative breast cancer (TNBC) is the most heterogeneous and aggressive subtype of breast carcinoma, characterized by the absence of clinical biomarkers and the lack of targeted therapies. Despite numerous clinical trials, patient stratification remains suboptimal, limiting the identification of effective treatment strategies. In this study, we aimed to identify biomarkers exclusively expressed in the basal mammary epithelial compartment to refine TNBC subclassification. Computational analysis of single-cell RNA sequencing data defined a set of basal identity genes, which were subsequently validated by immunohistochemistry in two independent TNBC cohorts. This approach enabled the identification of a TNBC subgroup, termed true basal TNBC (tB-TNBC), which was associated with poorer prognosis. High-throughput screening of 3,200 FDA-approved compounds in breast cancer cell lines classified according to basal marker expression identified dasatinib as a promising candidate with selective activity against tB-TNBC models. In tB-TNBC patient-derived xenograft models, dasatinib treatment effectively suppressed tumor growth. Furthermore, <i>TAGLN</i> emerged as a strong predictive biomarker of dasatinib response, with functional studies confirming its role in modulating drug sensitivity. Altogether, these findings support the clinical utility of basal markers for TNBC stratification and highlight a targeted treatment opportunity for patients with tB-TNBC.</p>Significance:<p>Basal biomarkers enable subclassification of triple-negative breast cancer and reveal a specific tumor subgroup sensitive to dasatinib, providing an effective stratification and treatment strategy for patients.</p></div>
Read moreThe recent emergence of acoustic metamaterials presents unparalleled possibilities for sound control across diverse scenarios. However, achieving both sound absorption and unrestricted airflow concurrently in a one-dimensional scenario poses a challenge. Most available acoustic metamaterials are designed in 2D or 3D, and in these configurations, a large portion of noise is reflected back. The key challenge, therefore, is how to allow maximum air to pass through the structure, make it tunable and noise be effectively damped within it. To address this, we propose four different types of configurations as KF (Kink Fiber), YAM (“Y” Type kink Fiber), CDAM (Converging Diverging Kink Fiber), and IRAM (Internal Resonator Kink Fiber, a unique one-dimensional design that simultaneously overcomes both challenges. The design subwavelength (7 cm) one-dimensional acoustic meta-structured blanket, demonstrating broadband sound absorption bandwidth of one octave with 0.5–0.9 absorption within the 500–1600 Hz range. In this study, we theoretically (through transfer matrix method), numerically (through FEM), and experimentally (through Impedance tube method) have showcased that this challenge can be surmounted by employing various configurations of kink fiber-based metamaterials. Following the concept developed in this article there have been efforts to develop blankets using hand lay-up method which can be deployed in real-world setup based on one-dimensional acoustic damping concept introduced in this work.
Read more<p>Analysis of basal marker expression and immune checkpoint genes in TNBC</p>
Read more<p>Primary antibodies used in IF and WB assays</p>
Read moreThe recent emergence of acoustic metamaterials presents unparalleled possibilities for sound control across diverse scenarios. However, achieving both sound absorption and unrestricted airflow concurrently in a one-dimensional scenario poses a challenge. Most available acoustic metamaterials are designed in 2D or 3D, and in these configurations, a large portion of noise is reflected back. The key challenge, therefore, is how to allow maximum air to pass through the structure, make it tunable and noise be effectively damped within it. To address this, we propose four different types of configurations as KF (Kink Fiber), YAM (“Y” Type kink Fiber), CDAM (Converging Diverging Kink Fiber), and IRAM (Internal Resonator Kink Fiber, a unique one-dimensional design that simultaneously overcomes both challenges. The design subwavelength (7 cm) one-dimensional acoustic meta-structured blanket, demonstrating broadband sound absorption bandwidth of one octave with 0.5-0.9 absorption within the 500-1600 Hz range. In this study, we theoretically (through transfer matrix method), numerically (through FEM), and experimentally (through Impedance tube method) have showcased that this challenge can be surmounted by employing various configurations of kink fiber-based metamaterials. Following the concept developed in this article there have been efforts to develop blankets using hand lay-up method which can be deployed in real-world setup based on one-dimensional acoustic damping concept introduced in this work.
Read moreWe present thin acoustic meta-structures with subwavelength dimensions through which almost perfect sound absorption is achieved in the low-frequency domain. Our overall strategy builds on the fact that the sound absorption capabilities of the meta-structures primarily depend on the geometric dimensions and can easily be reconfigured as per requirements through a change of geometry. To analyze various possibilities, we optimize the geometric structure through hybrid regression analysis using the genetic algorithm approach and finite element-based numerical simulations so that the geometry is tuned for high attenuation of acoustic signals over a broad range of frequencies. Both theoretical and experimental data show good parity and are able to establish the meta-structure nature of the assembly with respect to different frequency bands in the low frequency domain.
Read more<p>Histologic expression of basal markers in breast tumor samples. <b>A,</b> Representative sections of tB- and nB-TNBC samples stained with the indicated BaC markers. Scale bar, 50 μm. <b>B,</b> Bar plots representing the percentage of cells expressing each marker in tB- and nB-TNBCs. *, <i>P</i> < 0.05 based on unpaired <i>t</i> test (Holm–Sidak method); ns, not significant. <b>C, </b>Left, representative images showing TAGL staining in tB- and nB-TNBC tumors. Scale bar, 200 and 50 μm in the insets.</p>
Read moreThe proposed work enumerates a hybrid thin, deep-subwavelength (2 cm) acoustic metamaterials acting as a completely new type of sound absorber, showing multiple broadband sound absorption effects. Based on the fractal distribution of Helmholtz resonator (HRs) structures, integrated with careful design and construct hybrid cross micro-perforated panel (CMPP) that demonstrate broad banding approximately one-octave low-frequency sound absorption behavior. To determine the sound absorption coefficient of this novel type of metamaterial, the equivalent impedance model for the fractal cavity and the micro-perforated Maa's model for CMPP are both used. We validate these novel material designs through numerical, theoretical, and experimental data. It is demonstrated that the material design possesses superior sound absorption which is primarily due to the frictional losses of the structure imposed on acoustic wave energy. The peaks of different sound absorption phenomena show tunability by adjusting the geometric parameters of the fractal structures like cavity thickness 't', cross perforation diameter of micro perforated panel, etc. The fractal structures and their perforation panel are optimized dimensionally for maximum broadband sound absorption which is estimated numerically. This new kind of fractals cavity integrated with CMPP acoustic metamaterial has many applications as in multiple functional materials with broad-band absorption behavior etc.
Read more<p>Histological distribution of SMA, TAGL and TPM2 in the validation cohorts of TNBC</p>
Read more<p>Distribution of clinical and pathological features in the validation cohort BR1301a</p>
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