Definition of a family of tissue-protective cytokines using functional cluster analysis: a proof-of-concept study

The discovery of the tissue-protective activities of erythropoietin (EPO) has underlined the importance of some cytokines in tissue-protection, repair, and remodeling. As such activities have been reported for other cytokines, we asked whether we could define a class of tissue-protective cytokines. We therefore explored a novel approach based on functional clustering. In this pilot study, we started by analyzing a small number of cytokines (30). We functionally classified the 30 cytokines according to their interactions by using the bioinformatics tool STRING (Search Tool for the Retrieval of Interacting Genes), followed by hierarchical cluster analysis. The results of this functional clustering were different from those obtained by clustering cytokines simply according to their sequence. We previously reported that the protective activity of EPO in a model of cerebral ischemia was paralleled by an upregulation of synaptic plasticity genes, particularly early growth response 2 (EGR2). To assess the predictivity of functional clustering, we tested some of the cytokines clustering close to EPO (interleukin-11, IL-11; kit ligand, KITLG; leukemia inhibitory factor, LIF; thrombopoietin, THPO) in an in vitro model of human neuronal cells for their ability to induce EGR2. Two of these, LIF and IL-11, induced EGR2 expression. Although these data would need to be extended to a larger number of cytokines and the biological validation should be done using more robust in vivo models, rather then just one cell line, this study shows the feasibility of this approach. This type of functional cluster analysis could be extended to other fields of cytokine research and help design biological experiments

Whole-body three-dimensional optoacoustic tomography system for small animals

We develop a system for three-dimensional whole-body optoacoustic tomography of small animals for applications in preclinical research. The tomographic images are obtained while the objects of study (phantoms or mice) are rotated within a sphere outlined by a concave arc-shaped array of 64 piezocomposite transducers. Two pulsed lasers operating in the near-IR spectral range (755 and 1064 nm) with an average pulsed energy of about 100 mJ, a repetition rate of 10 Hz, and a pulse duration of 15 to 75 ns are used as optical illumination sources. During the scan, the mouse is illuminated orthogonally to the array with two wide beams of light from a bifurcated fiber bundle. The system is capable of generating images of individual organs and blood vessels through the entire body of a mouse with spatial resolution of ∼0.5 mm

Empowering Renal Cancer Management with AI and Digital Pathology: Pathology, Diagnostics and Prognosis

Renal cell carcinoma is a significant health burden worldwide, necessitating accurate and efficient diagnostic methods to guide treatment decisions. Traditional pathology practices have limitations, including interobserver variability and time-consuming evaluations. In recent years, digital pathology tools emerged as a promising solution to enhance the diagnosis and management of renal cancer. This review aims to provide a comprehensive overview of the current state and potential of digital pathology in the context of renal cell carcinoma. Through advanced image analysis algorithms, artificial intelligence (AI) technologies facilitate quantification of cellular and molecular markers, leading to improved accuracy and reproducibility in renal cancer diagnosis. Digital pathology platforms empower remote collaboration between pathologists and help with the creation of comprehensive databases for further research and machine learning applications. The integration of digital pathology tools with other diagnostic modalities, such as radiology and genomics, enables a novel multimodal characterization of different types of renal cell carcinoma. With continuous advancements and refinement, AI technologies are expected to play an integral role in diagnostics and clinical decision-making, improving patient outcomes. In this article, we explored the digital pathology instruments available for clear cell, papillary and chromophobe renal cancers from pathologist and data analyst perspectives

Real-time optoacoustic monitoring and three-dimensional mapping of a human arm vasculature

We present our findings from a real-time laser optoacoustic imaging system (LOIS). The system utilizes a Q-switched Nd:YAG laser; a standard 128-channel ultrasonic linear array probe; custom electronics and custom software to collect, process, and display optoacoustic (OA) images at 10 Hz. We propose that this system be used during preoperative mapping of forearm vessels for hemodialysis treatment. To demonstrate the real-time imaging capabilities of the system, we show OA images of forearm vessels in a volunteer and compare our results to ultrasound images of the same region. Our OA images show blood vessels in high contrast. Manipulations with the probe enable us to locate and track arteries and veins of a forearm in real time. We also demonstrate the ability to combine a series of OA image slices into a volume for spatial representation of the vascular network. Finally, we use frame-by-frame analysis of the recorded OA video to measure dynamic changes of the crossection of the ulnar artery

Optoacoustic imaging of the prostate: development toward image-guided biopsy

Optoacoustic (OA) tomography has demonstrated utility in identifying blood-rich malignancies in breast tissue. We describe the development and characterization of a laser OA imaging system for the prostate (LOIS-P). The system consists of a fiber-coupled Q-switched laser operating at 757 nm, a commercial 128-channel ultrasonic probe, a digital signal processor, and software that uses the filtered radial back-projection algorithm for image reconstruction. The system is used to reconstruct OA images of a blood-rich lesion induced in vivo in a canine prostate. OA images obtained in vivo are compared to images acquired using ultrasound, the current gold standard for guiding biopsy of the prostate. Although key structural features such as the urethra could be identified with both imaging techniques, a bloody lesion representing a highly vascularized tumor could only be clearly identified in OA images. The advantages and limitations of both forward and backward illumination modes are also evaluated by collecting OA images of phantoms simulating blood vessels within tissue. System resolution is estimated to be 0.2 mm in the radial direction of the acoustic array. The minimum detectable pressure signal is 1.83 Pa. Our results encourage further development toward a dual-modality OA∕ultrasonic system for prostate imaging and image-guided biopsy

Measurement of the spectral directivity of optoacoustic and ultrasonic transducers with a laser ultrasonic source

Comprehensive characterization of wideband ultrasonic transducers and specifically optoacoustic detectors is achieved through the analysis of their frequency response as a function of the incident angle. The tests are performed under well-defined, repeatable operating conditions. Backillumination of a blackened, acoustically matched planar surface with a short laser pulse creates an acoustic impulse which is used as a wideband ultrasonic source. Upon illumination with a short laser pulse, the bandwidth of our source shows a −6 dB point of 12 MHz and a low-frequency roll-off around 300 kHz. Using proprietary software, we examine thoroughly the planarity of the emitted wave front within a specified amplitude cutoff and phase incoherence. Analysis of the angular dependence of the frequency response yields invaluable directivity information about the detector under study: a necessary component toward accurate optoacoustic image reconstruction and quantitative tomography. The laser ultrasonic source we developed is the main feature of our directivity measurement setup. Due to its simplicity, it can easily be adapted to various calibration devices. This paper focuses on the development and characterization of the flatness and the bandwidth of our wideband ultrasonic source

Introduction to Linked Data and Its Lifecycle on the Web

With linked data, a very pragmatic approach towards achieving the vision of the semantic web has gained some traction in the last years. The term linked data refers to a set of best practices for publishing and interlinking structured data on the web. While many standards, methods and technologies developed within by the semantic web community are applicable for linked data, there are also a number of specific characteristics of linked data, which have to be considered. In this article we introduce the main concepts of linked data. We present an overview of the linked data lifecycle and discuss individual approaches as well as the state-of-the-art with regard to extraction, authoring, linking, enrichment as well as quality of linked data. We conclude the chapter with a discussion of issues, limitations and further research and development challenges of linked data. This article is an updated version of a similar lecture given at reasoning web summer school 2011