Effect of sparsity and exposure on total variation regularized X-ray tomography from few projections

We address effects of exposure and image gradient sparsity for total variation-regularized reconstruction: is it better to collect many low-quality or few high-quality projections, and can gradient sparsity predict how many projections are necessary? Preliminary results suggest collecting many low-quality projections is favorable, and that a link may exist between gradient sparsity level and successful reconstruction

2DeteCT -- A large 2D expandable, trainable, experimental Computed Tomography dataset for machine learning

Recent research in computational imaging largely focuses on developing machine learning (ML) techniques for image reconstruction, which requires large-scale training datasets consisting of measurement data and ground-truth images. However, suitable experimental datasets for X-ray Computed Tomography (CT) are scarce, and methods are often developed and evaluated only on simulated data. We fill this gap by providing the community with a versatile, open 2D fan-beam CT dataset suitable for developing ML techniques for a range of image reconstruction tasks. To acquire it, we designed a sophisticated, semi-automatic scan procedure that utilizes a highly-flexible laboratory X-ray CT setup. A diverse mix of samples with high natural variability in shape and density was scanned slice-by-slice (5000 slices in total) with high angular and spatial resolution and three different beam characteristics: A high-fidelity, a low-dose and a beam-hardening-inflicted mode. In addition, 750 out-of-distribution slices were scanned with sample and beam variations to accommodate robustness and segmentation tasks. We provide raw projection data, reference reconstructions and segmentations based on an open-source data processing pipeline

Inhibition of Triggering Receptor Expressed on Myeloid Cells 1 Ameliorates Inflammation and Macrophage and Neutrophil Activation in Alcoholic Liver Disease in Mice

Alcoholic liver disease (ALD) is characterized by macrophage and neutrophil leukocyte recruitment and activation in the liver. Damage- and pathogen-associated molecular patterns contribute to a self-perpetuating proinflammatory state in ALD. Triggering receptor expressed on myeloid cells 1 (TREM-1) is a surface receptor that amplifies inflammation induced by toll-like receptors (TLRs) and is expressed on neutrophils and monocytes/macrophages. We hypothesized that TREM-1 signaling contributes to proinflammatory pathway activation in ALD. Using an in vivo ALD model in mice, we tested the effects of ligand-independent TREM-1 inhibitory peptides that were formulated into human high-density lipoprotein (HDL)-mimicking complexes GF9-HDL and GA/E31-HDL. As revealed in vitro, macrophages endocytosed these rationally designed complexes through scavenger receptors. A 5-week alcohol feeding with the Lieber-DeCarli diet in mice resulted in increased serum alanine aminotransferase (ALT), liver steatosis, and increased proinflammatory cytokines in the liver. TREM-1 messenger RNA (mRNA) expression was significantly increased in alcohol-fed mice, and TREM-1 inhibitors significantly reduced this increase. TREM-1 inhibition significantly attenuated alcohol-induced spleen tyrosine kinase (SYK) activation, an early event in both TLR4 and TREM-1 signaling. The TREM-1 inhibitors significantly inhibited macrophage (epidermal growth factor-like module-containing mucin-like hormone receptor-like 1 [F4/80], clusters of differentiation [CD]68) and neutrophil (lymphocyte antigen 6 complex, locus G [Ly6G] and myeloperoxidase [MPO]) markers and proinflammatory cytokines (monocyte chemoattractant protein 1 [MCP-1], tumor necrosis factor alpha [TNF-alpha], interleukin-1beta [IL-1beta], macrophage inflammatory protein 1alpha [MIP-1alpha]) at the mRNA level compared to the HDL vehicle. Administration of TREM-1 inhibitors ameliorated liver steatosis and early fibrosis markers (alpha-smooth muscle actin [alphaSMA] and procollagen1alpha [Pro-Col1alpha]) at the mRNA level in alcohol-fed mice. However, the HDL vehicle also reduced serum ALT and some cytokine protein levels in alcohol-fed mice, indicating HDL-related effects. Conclusion: HDL-delivered novel TREM-1 peptide inhibitors ameliorate early phases of inflammation and neutrophil and macrophage recruitment and activation in the liver and attenuate hepatocyte damage and liver steatosis. TREM-1 inhibition represents a promising therapeutic approach for further investigations in ALD

AMPK Is the Crucial Target for the CDK4/6 Inhibitors Mediated Therapeutic Responses in PANC-1 and MIA PaCa-2 Pancreatic Cancer Cell Lines

The survival rate of pancreatic ductal adenocarcinoma (PDAC) patients is short, and PDAC is a cancer type that ranks fourth in the statistics regarding death due to cancer. Mutation in the KRAS gene, which plays a role in pancreatic cancer development, activates the PI3K/AKT/mTOR signaling pathway. The activity of the AMPK as a cellular energy sensor is one of the fundamental mechanisms that can induce effective therapeutic responses against CDK4/6 inhibitors via adjusting the cellular and tumor microenvironment stress management. The phosphorylation of AMPKα at the different phosphorylation residues such as Thr172 and Ser 377 causes metabolic differentiation in the cells following CDK4/6 inhibitor treatment in accordance with an increased cell cycle arrest and senescence under the control of different cellular players. In this study, we examined the competencies of the CDK4/6 inhibitors LY2835219 and PD-0332991 on the mechanism of cell survival and death based on AMPK signaling. Both CDK4/6 inhibitors LY2835219 and PD-0332991 modulated different molecular players on the PI3K/AKT/mTOR and AMPK signaling axis in different ways to reduce cell survival in a cell type dependent manner. These drugs are potential inducers of apoptosis and senescence that can alter the therapeutic efficacy cells

Ancient manuring of Amazonian Dark Earths as assessed by molecular markers.

Analytical procedures and the applicability of this methods to detect ancient human manuring in those soils, which were as far as we know, not used before in the humid tropics, will be discussed

A non-invasive imaging approach for improved assessments on the construction and the condition of historical knotted-pile carpets

The appraisal of the design and the weaving structure of Islamic knotted-pile carpets can tell plenty about the context in which they were produced, and the identification of signs of deterioration can help to establish their condition. These are often somewhat imprecise and laborious examinations, especially when considering carpets of large dimensions. Analytical methods that support these disciplines urge further exploration so that improved interpretations can be obtained.  An interdisciplinary combination of art history, analytical science and textile conservation aimed, on the one hand, to improve the weaving examination of these complex textile objects – by considering the spin of threads and the ply of yarns; the knot count and density; and the weaving structure of warps, wefts and piles – and on the other, to help their condition assessment – by mapping of damaged areas, old repairs and contaminations. For this purpose, the possibilities and limitations of several non-invasive imaging techniques, namely transmitted, raking or incident visible, ultraviolet (UV) and infrared (IR) illumination through Visual Spectral Comparator (VSC), as well as conventional X-radiography, mammography and (micro) CT scanning, were assessed to support the conventional visual examination of the weaving details and present condition of two 17th-century Safavid knotted-pile carpet fragments.  Observation with NUV and NIR imaging with VSC, as well as CT techniques, offered enriching overviews about weaving characteristics, damaged areas or contaminations that were not easily discernible with the naked eye, thus supporting the conventional visual examination. As a result, detailed digital mappings about the technological structure and the condition of the fragments could be obtained in a relatively efficient and accessible way. Moreover, combining art historical identification of the design with the analysis of the weaving structure confirmed that both carpet fragments are border corners that originally belonged to much larger carpets made in the so-called “Indo-Persian” style. The outcome of this interdisciplinary research brings very useful contributions for future art historical and conservation assessments of historical carpets, and it encourages further exploration of imaging techniques in the examination of other textile objects in museums and private collections

Myocardial biomechanics and the consequent differentially expressed genes of the left atrial ligation chick embryonic model of hypoplastic left heart syndrome

Left atrial ligation (LAL) of the chick embryonic heart is a model of the hypoplastic left heart syndrome (HLHS) where a purely mechanical intervention without genetic or pharmacological manipulation is employed to initiate cardiac malformation. It is thus a key model for understanding the biomechanical origins of HLHS. However, its myocardial mechanics and subsequent gene expressions are not well-understood. We performed finite element (FE) modeling and single-cell RNA sequencing to address this. 4D high-frequency ultrasound imaging of chick embryonic hearts at HH25 (ED 4.5) were obtained for both LAL and control. Motion tracking was performed to quantify strains. Image-based FE modeling was conducted, using the direction of the smallest strain eigenvector as the orientations of contractions, the Guccione active tension model and a Fung-type transversely isotropic passive stiffness model that was determined via micro-pipette aspiration. Single-cell RNA sequencing of left ventricle (LV) heart tissues was performed for normal and LAL embryos at HH30 (ED 6.5) and differentially expressed genes (DEG) were identified.After LAL, LV thickness increased by 33%, strains in the myofiber direction increased by 42%, while stresses in the myofiber direction decreased by 50%. These were likely related to the reduction in ventricular preload and underloading of the LV due to LAL. RNA-seq data revealed potentially related DEG in myocytes, including mechano-sensing genes (Cadherins, NOTCH1, etc.), myosin contractility genes (MLCK, MLCP, etc.), calcium signaling genes (PI3K, PMCA, etc.), and genes related to fibrosis and fibroelastosis (TGF-β, BMP, etc.). We elucidated the changes to the myocardial biomechanics brought by LAL and the corresponding changes to myocyte gene expressions. These data may be useful in identifying the mechanobiological pathways of HLHS

Dating and provenancing the <i>Woman with lantern</i> sculpture – A contribution towards attribution of Netherlandish art

Studying the wood of art objects such as sculptures, panel paintings and furniture can be crucial to elucidate their chronology and production centre. Here we present an approach that considers the provenance of the wood and its potential availability in different areas as a means to identify the provenance of wooden art objects. We illustrate this approach with an interdisciplinary study aimed to determine the date and provenance of the Woman with lantern, a carved altar fragment from the Rijksmuseum's collections (Amsterdam, The Netherlands). The origin of this object is undocumented, but based on stylistic and iconographic features its provenance was proposed to be the altarpiece of Rennes cathedral (France), carved in Antwerp (Belgium) around 1520 C.E. However, doubts arose when curators tested the potential fit of the sculpture in that altarpiece and could not find a neat match. Dating and provenancing the wood of the sculpture by standard dendrochronological means failed to produce a date, and comparison of the tree-ring pattern from the sculpture with those of the sculptures from Rennes altarpiece delivered no results either, supporting the suspicion that the Woman with lantern belonged elsewhere. In 2019, X-ray computed tomography (CT) provided digital cross-sections throughout the sculpture and a longer tree-ring series was obtained. This time, the outermost ring was dated to the year 1487 C.E. The tree was estimated to have been cut after 1495 C.E., indicating a likely production in the first quarter of the 16th century. The origin of the timber in the eastern Netherlands/northwest Germany, combined with empirical evidence about timber availability in various regions of the Low Countries at that time, suggests that the sculpture was made in a workshop located north of the Rhine in the (current) Netherlands, rather than Antwerp. This research has led to the hypothesis that workshops north and south of the Rhine river branches in the Low Countries were supplied by forests located in different areas. If proven correct, establishing the wood provenance will assist in determining the origin of Netherlandish works of art from the late-Gothic and Northern Renaissance periods