Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.

Spatial transcriptomics methods provide insight into the cellular heterogeneity and spatial architecture of complex, multicellular systems. Combining molecular and spatial information provides important clues to study tissue architecture in development and disease. Here, we present a comprehensive do-it-yourself (DIY) guide to perform such experiments at reduced costs leveraging open-source approaches.

3D in-system calibration method for PET detectors.

Background: Light-sharing detector designs for positron emission tomography (PET) systems have sparked interest in the scientific community. Particularly, (semi-)monoliths show generally good performance characteristics regarding 2D positioning, energy-, and timing resolution, as well as readout area. This is combined with intrinsic depth-of-interaction (DOI) capability to ensure a homogeneous spatial resolution across the entire field of view (FoV).

Holistic evaluation of a machine learning-based timing calibration for PET detectors under varying data sparsity.

Modern PET scanners offer precise TOF information, improving the SNR of the reconstructed images. Timing calibrations are performed to reduce the worsening effects of the system components and provide valuable TOF information. Traditional calibration procedures often provide static or linear corrections, with the drawback that higher-order skews or event-to-event corrections are not addressed.

A 5:2 intermittent fasting regimen ameliorates NASH and fibrosis and blunts HCC development via hepatic PPARα and PCK1.

The role and molecular mechanisms of intermittent fasting (IF) in non-alcoholic steatohepatitis (NASH) and its transition to hepatocellular carcinoma (HCC) are unknown. Here, we identified that an IF 5:2 regimen prevents NASH development as well as ameliorates established NASH and fibrosis without affecting total calorie intake. Furthermore, the IF 5:2 regimen blunted NASH-HCC transition when applied therapeutically.

Histopathological biomarkers for predicting the tumour accumulation of nanomedicines.

The clinical prospects of cancer nanomedicines depend on effective patient stratification. Here we report the identification of predictive biomarkers of the accumulation of nanomedicines in tumour tissue. By using supervised machine learning on data of the accumulation of nanomedicines in tumour models in mice, we identified the densities of blood vessels and of tumour-associated macrophages as key predictive features.

pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging.

Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these limitations, new imaging-based methods have emerged, giving rise to the field of spatial genomics. Here, we present pyHiM, a user-friendly python toolbox specifically designed for the analysis of multiplexed DNA-FISH data and the reconstruction of chromatin traces in individual cells.

A finely segmented semi-monolithic detector tailored for high-resolution PET.

Background: Preclinical research and organ-dedicated applications use and require high (spatial-)resolution positron emission tomography (PET) detectors to visualize small structures (early) and understand biological processes at a finer level of detail. Researchers seeking to improve detector and image spatial resolution have explored various detector designs. Current commercial high-resolution systems often employ finely pixelated or monolithic scintillators, each with its limitations.

Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells.

Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate reactivation after mitotic gene silencing. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the biological significance and importance of their bookmarking function. Here we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover a large redundancy in mitotic binding among members of the protein super-family of nuclear receptors.

Near-field coded-mask technique and its potential for proton therapy monitoring.

Prompt-gamma imaging encompasses several approaches to the online monitoring of the beam range or deposited dose distribution in proton therapy. We test one of the imaging techniques - a coded mask approach - both experimentally and via simulations.Two imaging setups have been investigated experimentally.

Improving the Timing Resolution of Positron Emission Tomography Detectors Using Boosted Learning-A Residual Physics Approach.

Artificial intelligence (AI) is entering medical imaging, mainly enhancing image reconstruction. Nevertheless, improvements throughout the entire processing, from signal detection to computation, potentially offer significant benefits. This work presents a novel and versatile approach to detector optimization using machine learning (ML) and residual physics.

Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer.

Background & Aims: As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions, including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. We aimed to unveil a detailed view of the immune micromilieu in PDAC using a spatially resolved multimodal single-cell approach.

Methods: We applied single-cell RNA sequencing, spatial transcriptomics, multiplex immunohistochemistry, and mass cytometry to profile the immune compartment in treatment-naïve PDAC tumors and matched adjacent normal pancreatic tissue, as well as in the systemic circulation.

An interactive murine single-cell atlas of the lung responses to radiation injury.

Radiation Induced Lung Injury (RILI) is one of the main limiting factors of thorax irradiation, which can induce acute pneumonitis as well as pulmonary fibrosis, the latter being a life-threatening condition. The order of cellular and molecular events in the progression towards fibrosis is key to the physiopathogenesis of the disease, yet their coordination in space and time remains largely unexplored. Here, we present an interactive murine single cell atlas of the lung response to irradiation, generated from C57BL6/J female mice.

Excessive self-grooming, gene dysregulation and imbalance between the striosome and matrix compartments in the striatum of mutant mice.

Autism is characterized by atypical social communication and stereotyped behaviors. Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are detected in 1-2% of patients with autism and intellectual disability, but the mechanisms underpinning the symptoms remain largely unknown. Here, we characterized the behavior of mice from 3 to 12 months of age.

A specific molecular signature in SARS-CoV-2-infected kidney biopsies.

Acute kidney injury is one of the most important complications in patients with COVID-19 and is considered a negative prognostic factor with respect to patient survival. The occurrence of direct infection of the kidney by SARS-CoV-2, and its contribution to the renal deterioration process, remain controversial issues. By studying 32 renal biopsies from patients with COVID-19, we verified that the major pathological feature of COVID-19 is acute tubular injury (ATI).

Analysis of a convex time skew calibration for light sharing-based PET detectors.

Positron emission tomography (PET) detectors providing attractive coincidence time resolutions (CTRs) offer time-of-flight information, resulting in an improved signal-to-noise ratio of the PET image. In applications with photosensor arrays that employ timestampers for individual channels, timestamps typically are not time synchronized, introducing time skews due to different signal pathways. The scintillator topology and transportation of the scintillation light might provoke further skews.

Digitalization impacts the COVID-19 pandemic and the stringency of government measures.

COVID-19 poses a significant burden to populations worldwide. Although the pandemic has accelerated digital transformation, little is known about the influence of digitalization on pandemic developments. Therefore, this country-level study aims to explore the impact of pre-pandemic digital adoption on COVID-19 outcomes and government measures.

New Wound Management of Driveline Infections with Cold Atmospheric Plasma.

The use of ventricular assist devices as a bridge to transplant or as destination therapy has increased. Wound complications increase morbidity in this cohort. Cold atmospheric plasma is a source of reactive oxygen and nitrogen species and can reduce the microbial load in skin wounds without negative effects on the surrounding tissue.

HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging.

The ability to visualize RNA in its native subcellular environment by using single-molecule fluorescence in situ hybridization (smFISH) has reshaped our understanding of gene expression and cellular functions. A major hindrance of smFISH is the difficulty to perform systematic experiments in medium- or high-throughput formats, principally because of the high cost of generating the individual fluorescent probe sets. Here, we present high-throughput smFISH (HT-smFISH), a simple and cost-efficient method for imaging hundreds to thousands of single endogenous RNA molecules in 96-well plates.

A semi-monolithic detector providing intrinsic DOI-encoding and sub-200 ps CRT TOF-capabilities for clinical PET applications.

Background: Current clinical positron emission tomography (PET) systems utilize detectors where the scintillator typically contains single elements of 3-6-mm width and about 20-mm height. While providing good time-of-flight performance, this design limits the spatial resolution and causes radial astigmatism as the depth-of-interaction (DOI) remains unknown.

Purpose: We propose an alternative, aiming to combine the advantages of current detectors with the DOI capabilities shown for monolithic concepts, based on semi-monolithic scintillators (slabs).

Frequency-selective signal enhancement by a passive dual coil resonator for magnetic particle imaging.

Magnetic particle imaging (MPI) visualizes the spatial distribution of magnetic nanoparticles. MPI already provides excellent temporal and good spatial resolution, however, to achieve translation into clinics, further advances in the fields of sensitivity, image reconstruction and tracer performance are needed. In this work, we propose a novel concept to enhance the MPI signal and image resolution by a purely passive receive coil insert for a preclinical MPI system.

FISH-quant v2: a scalable and modular tool for smFISH image analysis.

Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling quantitative studies of gene expression and its regulatory mechanisms. Today, these methods are applicable at a large scale, which in turn come with a need for adequate tools for data analysis and exploration.

Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH.

The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The positive-sense single-stranded RNA virus contains a single linear RNA segment that serves as a template for transcription and replication, leading to the synthesis of positive and negative-stranded viral RNA (vRNA) in infected cells. Tools to visualize vRNA directly in infected cells are critical to analyze the viral replication cycle, screen for therapeutic molecules, or study infections in human tissue.

piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development.

Eukaryotic genomes harbor invading transposable elements that are silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C.

The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions.

RNA localization and local translation are important for numerous cellular functions. In mammals, a class of mRNAs localize to cytoplasmic protrusions in an APC-dependent manner, with roles during cell migration. Here, we investigated this localization mechanism.