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Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high‐resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X‐ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab‐shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low‐cost instrument setup installed at the 2‐BM micro‐CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi‐GPU systems for processing large‐scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction. [ABSTRACT FROM AUTHOR]

To further enhance the performance of wood products, improved tools are needed to study in situ cellular scale phenomena like mechanical deformations and moisture swelling. Micro-X-ray computed tomography (μXCT) using brilliant synchrotron light sources now has the spatial and temporal resolution for real-time visualization of phenomena in three-dimensional cellular structures. However, the tradeoff for speed includes the loss of intensity contrast between different types of materials within the imaged structure, such as cell wall and air in wood. This loss of contrast prevents traditional histogram-based segmentation methods from being used effectively. A new convolutional neural network (CNN) approach was therefore developed to segment fast μXCT images of wood into cell wall and air volumes. The fast μXCT and segmentation were demonstrated in the study of moisture swelling in loblolly pine (Pinus taeda) earlywood and latewood cellular structures conditioned at 0%, 33%, 75%, and 95% relative humidity (RH). The CNN segmentation results had a mean intersection over union (IoU) metric accuracy of 96%. Initial analysis of the swelling in the latewood revealed cell walls swelled about 25% when conditioned from 0% to 95% RH. Additionally, the widths of ray cell lumina in the transverse plane of latewood could be observed to increase at higher RH. The segmentation method presented here will facilitate future quantitative analyses in in situ μXCT studies of wood and other similar cellular materials. [ABSTRACT FROM AUTHOR]

However, if acquisition is extremely fast and Graph HT ht , then the initial formula is computationally more favorable. We also added functionality for setting the rotation angle of each Graph HT ht slice to be able to follow different structures inside the sample. Implementation of this functionality is straightforward and only involves rotation of Graph HT ht planes by using a rotation matrix in 3D. [Extracted from the article]

Human mentality develops with age and is altered in psychiatric disorders, though their underlying mechanism is unknown. In this study, we analyzed nanometer-scale three-dimensional structures of brain tissues of the anterior cingulate cortex from eight schizophrenia and eight control cases. The distribution profiles of neurite curvature of the control cases showed a trend depending on their age, resulting in an age-correlated decrease in the standard deviation of neurite curvature (Pearson's r = -0.80, p = 0.018). In contrast to the control cases, the schizophrenia cases deviate upward from this correlation, exhibiting a 60% higher neurite curvature compared with the controls (p = 7.8 × 10−4). The neurite curvature also showed a correlation with a hallucination score (Pearson's r = 0.80, p = 1.8 × 10−4), indicating that neurite structure is relevant to brain function. This report is based on our 3D analysis of human brain tissues over a decade and is unprecedented in terms of the number of cases. We suggest that neurite curvature plays a pivotal role in brain aging and can be used as a hallmark to exploit a novel treatment of schizophrenia. [ABSTRACT FROM AUTHOR]

Prostate cancer is the most frequently diagnosed cancer in men in the United States. Among the different available treatment options, radiation therapy is recommended for localized or even advanced disease. Erectile dysfunction (ED) often occurs after radiation therapy due to neurological, vascular, and endocrine mechanisms resulting in arterial tone alteration, pudendal-nerve neuropraxia, and lastly fibrosis. Considering the influence of quality of life on patients' treatment choice, radiation-therapy-induced ED prevention and treatment are major issues. In this narrative review, we briefly summarize and discuss the current state of the art on radiation-therapy-induced ED in PCa patients in terms of pathophysiology and available treatment options. [ABSTRACT FROM AUTHOR]

Transperineal laser ablation (TPLA) of the prostate is a new minimally invasive treatment option in men with lower urinary tract symptoms (LUTS) due to benign prostatic enlargement (BPE). The aim of this systematic review was to investigate the efficacy and safety of TPLA in the management of BPE. The primary outcomes were the improvement in urodynamic parameters (maximum urinary flow (Qmax) and postvoiding residue (PVR)) and LUTS relief, assessed using the IPSS questionnaire. The secondary outcomes were the preservation of sexual and ejaculatory functions, assessed with the IEEF-5 and MSHQ-EjD questionnaires, respectively, and rates of postoperative complications. We reviewed the literature for prospective or retrospective studies evaluating the use of TPLA in the treatment of BPE. A comprehensive search in PubMed, Scopus, Web of Science, and ClinicalTrials.gov was performed for English language articles published between January 2000 and June 2022. Pooled analysis of the included studies with available follow-up data for the outcomes of interest was additionally performed. After screening 49 records, six full-text manuscripts were identified, including two retrospective and four prospective non-comparative studies. Overall, 297 patients were included. All the studies independently reported a statistically significant improvement, from baseline, in Qmax, PVR, and IPSS score at each timepoint. Three studies additionally demonstrated that TPLA did not affect sexual function, reporting no change in the IEEF-5 score, and a statistically significant improvement in MSHQ-EjD score at each timepoint. Low rates of complications were recorded in all the included studies. Pooled analysis showed a clinically meaningful improvement in both micturition and sexual outcomes mean values at 1, 3, 6, and 12 months of follow-up, compared with baseline. Transperineal laser ablation of the prostate for the treatment of BPE showed interesting results in pilot studies. However, higher level and comparative studies are needed to confirm its efficacy in relieving obstructive symptoms and preserving sexual function. [ABSTRACT FROM AUTHOR]

Complex dynamic tomographic experiments at brilliant X-ray light sources require real-time feedback on the sample changes with respect to environmental conditions, selecting representative regions of interest for high-resolution scanning, and on-demand data saving mechanisms for storing only relevant projections acquired by fast area detectors and reducing data volumes. Here the implementation details of a 3D real-time imaging monitoring instrument, with zooming to a volume of interest with easy-to-use visualization via ImageJ, a tool familiar to most beamline users, is presented. The instrument relies on optimized data flow between the detector and processing machines and is implemented on commodity computers. The instrument has been developed at beamline 2-BM of the Advanced Photon Source, where the automatic lens changing mechanism for zooming is implemented with an Optique Peter microscope. Performance tests demonstrate the ability to process more than 3 GB of projection data per second and generate real-time 3D zooming with different magnification. These new capabilities are essential for new APS Upgrade instruments such as the projection microscope under development at beamline 32-ID. The efficacy of the proposed instrument was demonstrated during an in situ tomographic experiment on ice and gas hydrate formation in porous samples. [ABSTRACT FROM AUTHOR]

A chaotic map algorithm is proposed to study similarity-based knowledge of temporal patterns. Several information sources can be regarded as time series, both in scientific and technological fields such as nuclear physics, computer network, biomedical signals, and many others. The application of an automatic knowledge discovery mechanism has a strong impact on system science and engineering. The advantage of the proposed algorithm is due to its capability to extract meaningful features from complex data sets, as temporal patterns, without teacher. A case study has been carried on biomedical signals, such as electroencephalographic records, to recognize patterns affected by the Huntington's disease, one of the most dangerous pathology of the central nervous system. The chaotic map algorithm succeeds in distinguishing between pathological and normal patterns, with high values of both sensitivity and specificity. Index Terms--Chaotic maps, clustering algorithms, EEG, Huntington's disease, knowledge discovery.

For reconstructing large tomographic datasets fast, filtered backprojection‐type or Fourier‐based algorithms are still the method of choice, as they have been for decades. These robust and computationally efficient algorithms have been integrated in a broad range of software packages. The continuous mathematical formulas used for image reconstruction in such algorithms are unambiguous. However, variations in discretization and interpolation result in quantitative differences between reconstructed images, and corresponding segmentations, obtained from different software. This hinders reproducibility of experimental results, making it difficult to ensure that results and conclusions from experiments can be reproduced at different facilities or using different software. In this paper, a way to reduce such differences by optimizing the filter used in analytical algorithms is proposed. These filters can be computed using a wrapper routine around a black‐box implementation of a reconstruction algorithm, and lead to quantitatively similar reconstructions. Use cases for this approach are demonstrated by computing implementation‐adapted filters for several open‐source implementations and applying them to simulated phantoms and real‐world data acquired at the synchrotron. Our contribution to a reproducible reconstruction step forms a building block towards a fully reproducible synchrotron tomography data processing pipeline. [ABSTRACT FROM AUTHOR]

Abstract Background Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. With this in mind, the perception of the intimate relationships among diverse MMPs could be a solid basis for accelerated learning in designing new selective MMP inhibitors. In this regard, decrypting the latent molecular reasons in order to elucidate similarity among MMPs is a key challenge. Results We describe a pairwise variant of the non-parametric chaotic map clustering (CMC) algorithm and its application to 104 X-ray MMP structures. In this analysis electrostatic potentials are computed and used as input for the CMC algorithm. It was shown that differences between proteins reflect genuine variation of their electrostatic potentials. In addition, the analysis has been also extended to analyze the protein primary structures and the molecular shapes of the MMP co-crystallised ligands. Conclusions The CMC algorithm was shown to be a valuable tool in knowledge acquisition and transfer from MMP structures. Based on the variation of electrostatic potentials, CMC was successful in analysing the MMP target family landscape and different subsites. The first investigation resulted in rational figure interpretation of both domain organization as well as of substrate specificity classifications. The second made it possible to distinguish the MMP classes, demonstrating the high specificity of the S1' pocket, to detect both the occurrence of punctual mutations of ionisable residues and different side-chain conformations that likely account for induced-fit phenomena. In addition, CMC demonstrated a potential comparable to the most popular UPGMA (Unweighted Pair Group Method with Arithmetic mean) method that, at present, represents a standard clustering bioinformatics approach. Interestingly, CMC and UPGMA resulted in closely comparable outcomes, but often CMC produced more informative and more easy interpretable dendrograms. Finally, CMC was successful for standard pairwise analysis (i.e., Smith-Waterman algorithm) of protein sequences and was used to convincingly explain the complementarity existing between the molecular shapes of the co-crystallised ligand molecules and the accessible MMP void volumes.

The dynamic information of lithium‐ion battery active materials obtained from coin cell‐based in‐situ characterizations might not represent the properties of the active material itself because many other factors in the cell could have impacts on the cell performance. To address this problem, a single particle cell was developed to perform the in‐situ characterization without the interference of inactive materials in the battery electrode as well as the X‐ray‐induced damage. In this study, the dynamic morphological and phase changes of selenium‐doped germanium (Ge0.9Se0.1) at the single particle level were investigated via synchrotron‐based in‐situ transmission X‐ray microscopy. The results demonstrate the good reversibility of Ge0.9Se0.1 at high cycling rate that helps understand its good cycling performance and rate capability. This in‐situ and operando technique based on a single particle battery cell provides an approach to understanding the dynamic electrochemical processes of battery materials during charging and discharging at the particle level. [ABSTRACT FROM AUTHOR]