Correlation of pre-operative cancer imaging techniques with post-operative gross and microscopic pathology images

In this paper, different algorithms for volume reconstruction from tomographic cross-sectional pathology slices are described and tested. A tissue-mimicking phantom made with a mixture of agar and aluminium oxide was sliced at different thickness as per pathological standard guidelines. Phantom model was also virtually sliced and reconstructed in software. Results showed that shape-based spline interpolation method was the most precise, but generated a volume underestimation of 0.5%

BROOD: Bilevel and Robust Optimization and Outlier Detection for Efficient Tuning of High-Energy Physics Event Generators

The parameters in Monte Carlo (MC) event generators are tuned on experimental measurements by evaluating the goodness of fit between the data and the MC predictions. The relative importance of each measurement is adjusted manually in an often time consuming, iterative process to meet different experimental needs. In this work, we introduce several optimization formulations and algorithms with new decision criteria for streamlining and automating this process. These algorithms are designed for two formulations: bilevel optimization and robust optimization. Both formulations are applied to the datasets used in the ATLAS A14 tune and to the dedicated hadronization datasets generated by the SHERPA generator, respectively. The corresponding tuned generator parameters are compared using three metrics. We compare the quality of our automatic tunes to the published ATLAS A14 tune. Moreover, we analyze the impact of a pre-processing step that excludes data that cannot be described by the physics models used in the MC event generators

TDP-43 Phase Separation Does Not Likely Regulate LPS-Induced Neuroinflammation

Immunohistochemistry (IHC) was performed to assess whether Transactive response Deoxyribonucleic acid binding Protein 43 (TDP-43) liquid-liquid phase separation (LLPS) regulates lipopolysaccaride (LPS)-induced neuroinflammation. Quantification and intensity results of glia cells and cytokines indicate that TDP-43 LLPS does not likely regulate LPS-induced neuroinflammation.https://digitalcommons.unmc.edu/surp2021/1060/thumbnail.jp

Apprentice for Event Generator Tuning

Apprentice is a tool developed for event generator tuning. It contains a range of conceptual improvements and extensions over the tuning tool Professor. Its core functionality remains the construction of a multivariate analytic surrogate model to computationally expensive Monte-Carlo event generator predictions. The surrogate model is used for numerical optimization in chi-square minimization and likelihood evaluation. Apprentice also introduces algorithms to automate the selection of observable weights to minimize the effect of mis-modeling in the event generators. We illustrate our improvements for the task of MC-generator tuning and limit setting.Comment: 9 pages, 2 figures, submitted to the 25th International Conference on Computing in High-Energy and Nuclear Physic

Lung tumor 3D reconstruction from planar CT scans and registration to micro and macroscopic pathology imaging

The overall goal of this project is to ascertain whether a given PET radiotracer reliably and accurately identifies an active cancerous region within the gross tumour volume. The only means to assess it is to compare the PET signal with the gold standard of histopathology. To allow for this comparison both images need to be spatially aligned or registered. However, lung tissue undergoes several deformations following surgical resection and pathological processing. Therefore, these distortions need to be taken into account in order to obtain a truthful mapping. Moreover, PET signals are intrinsically 3D, whereas histopathology slices are planar images. In order to overcome this problem, 2D slices have to be stacked together to reconstruct the original volume prior to registration

Correlation of pre-operative cancer imaging techniques with post-operative macro and microscopic lung pathology images

Background: This research project aims to investigate the performance of several PET radiotracers in lung cancer by aligning PET-CT and pathology imagery acquired from the same patients at different points in time. The discrimination of tumour substructures is of great importance in therapy planning, as a given treatment may be better adapted depending on the local characteristics of the carcinoma. Method: Due to the high deformability of lung tissue, several intermediate steps must be used for merging pathology and pre-operative PET-CT in a coherent manner. Firstly, the tumour volume is reconstructed from the macroscopic images taken during dissection. For this purpose, an enhanced dissection protocol is used, where the lung specimen is placed in a bespoke slicing rig and embedded in agar to hold it in place. Using a threaded plunger, the specimen is pushed upwards in 5mm steps, sliced and photographed. This procedure allows us to obtain slices of uniform thickness. Secondly, microscopic digital slides of the cancerous tissue are merged with the macroscopic 3D model. Finally, the whole volume is fused with the preoperative PET-CT scan, using a non-linear deformable model. Result: Preliminary results obtained with a synthetic phantom allowed us to analyse the accuracy of the tumour 3D reconstruction algorithm from planar macroscopic slices. Using these findings, we could optimise the interpolation and segmentation routines for building an accurate 3D model of the tumour mass. During our first trial with lung tissue (ongoing work), each cross-sectional slice was photographed, the tumour boundary was delineated in each image by a pathologist (CD), and from these contours a high-resolution 3D tumour model was built. Next, the corresponding microscopic digitised slices were merged. To date, ten patients have been identified and consented, therefore allowing us to test our algorithm on different cases and assess its performance. Conclusion: We demonstrate a novel set of methods for co-registration of preoperative PET-CT to macro and microscopically defined lung tumours. This proof of principle now allows interrogation of the raw data from PET-CTs using a range of tracers and the development of algorithms that identify substructure detail within a tumour mass, which could lead to tailored radiotherapy for individual tumours based on tracer patterns and uptake

A Case of Amblyomma testudinarium Tick Bite in a Korean Woman

A case of tick bite was found in the inguinal region of a 74-year-old Korean woman. She was attacked by the tick while working in her vegetable garden in the vicinity of mountain located in Suncheon City, the southern coastal area of the Korean Peninsula. On admission she complained of mild discomfort and itching around the bite area. The causative tick was 23 mm long and had slender pedipalps. The scutum was quite ornate and had eyes at the edge. The genital aperture was located anterior to the level of the coxa II. The spiracular plate was comma-shaped and the anus was surrounded posteriorly by the anal groove. The coxa I had subequal 2 spurs; the external one slightly larger. The spur of coxa IV was slightly longer than those of coxae II and III. The tarsus IV had 2 distinct subapical ventral spurs. It was identified as the fully engorged adult female of Amblyomma testudinarium. This is the first human case of Amblyomma bite in Korea

Comparison of The Genome Profiles Between Head and Body Lice

The body louse (Pediculus humanus humanus) is known to have diverged from the head louse (P. humanus capitis) but genomic differences between these two subspecies still remain unexplored. To compare genomic profiles between head and body lice, whole genome sequences of head lice were determined by next generation sequencing methods based on both Illumina Genome analyzer and Roche GS FLX pyrosequencing and compared with the reference genome sequences of the body louse. Total consensuses generated by mapping to the body louse genome in conjunction with de novo assembly of head louse genome sequences revealed a head louse genome size of 110 Mbp with a 96% coverage of the body louse genome sequences. A total of 12,651 genes were predicted from the head louse genome sequences although more precise assembly and functional annotation of the genome is required for a more accurate gene count. Among the 873 genes that were putatively specific to the head louse, 15 genes were confirmed to be transcribed in both head and body lice, suggesting the previously estimated gene number of the body louse was likely underestimated. The single nucleotide polymorphism analysis showed that the nucleotide diversity of genome between head and body lice was 2.2%, which was larger than that of the transcriptome between head and body lice. An endosymbiont genome analysis showed that the composition of endosymbionts in head lice was similar to that of body lice and Candidatus Riesia pediculicola was the primary endosymbiont in both head and body lice