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HALO AI Publications

Indica Labs / HALO AI Publications

Two distinct immunopathological profiles in autopsy lungs of COVID-19

Nienhold, R., Ciani, Y., Koelzer, V.H. et al. Two distinct immunopathological profiles in autopsy lungs of COVID-19. Nat Commun 11, 5086 (2020). Coronavirus Disease 19 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has grown to a worldwide pandemic with substantial mortality. Immune mediated damage has been proposed as a pathogenic factor, but immune responses in lungs of COVID-19 patients remain poorly characterized. Here we show transcriptomic, histologic and cellular profiles of post mortem...

Pulmonary Mycobacterium tuberculosis control associates with CXCR3- and CCR6-expressing antigen-specific Th1 and Th17 cell recruitment

Uma Shanmugasundaram, Allison N. Bucsan, Shashank R. Ganatra, Chris Ibegbu, Melanie Quezada, Robert V. Blair, Xavier Alvarez, Vijayakumar Velu, Deepak Kaushal, and Jyothi Rengarajan JCI Insight | Volume 5, Issue 14, July 23, 2020| https://doi.org/10.1172/jci.insight.137858 Mycobacterium tuberculosis–specific (M. tuberculosis–specific) T cell responses associated with immune control during asymptomatic latent tuberculosis infection (LTBI) remain poorly understood. Using a nonhuman primate aerosol model, we studied the kinetics, phenotypes, and functions of M. tuberculosis antigen-specific T cells in peripheral and lung compartments of M. tuberculosis–infected...

Artificial Intelligence-Based Quantification of Epithelial Proliferation in Mammary Glands of Rats and Oviducts of Göttingen Minipigs

Henning Hvid, Mikala Skydsgaard, Nikolai K. Jensen, Birgitte M. Viuff, Henrik E. Jensen, Martin B. Oleksiewicz, Peter H. Kvist Toxicologic Pathology | First Published August 25, 2020 | Research Article | https://doi.org/10.1177/0192623320950633 Quantitative assessment of proliferation can be an important endpoint in toxicologic pathology. Traditionally, cell proliferation is quantified by labor-intensive manual counting of positive and negative cells after immunohistochemical staining for proliferation markers (eg, Ki67, bromo-2′-deoxyuridine, or proliferating cell nuclear antigen). Currently, there is a lot of interest in replacing manual...

Immunogradient Indicators for Antitumor Response Assessment by Automated Tumor-Stroma Interface Zone Detection

Allan Rasmusson, Dovile Zilenaite, Ausrine Nestarenkaite, Renaldas Augulis, Aida Laurinaviciene, Valerijus Ostapenko, Tomas Poskus, and Arvydas Laurinavicius The American Journal of Pathology, Vol. 190, No. 6, June 2020 | DOI: doi.org/10.1016/j.ajpath.2020.01.018 The distribution of tumor-infiltrating lymphocytes (TILs) within the tumor microenvironment provides strong prognostic value, which is increasingly important with the arrival of new immunotherapy modalities. Both visual and image analysisebased assays are developed to assess the immune contextureof the tumors. We propose an automated method based on grid subsampling of microscopy...

Prognostic significance of mesothelin expression in colorectal cancer disclosed by area-specific four-point tissue microarrays

Takehiro Shiraishi, Eiji Shinto, Ines P. Nearchou, Hitoshi Tsuda, Yoshiki Kajiwara, Takahiro Einama, Peter D. Caie, Yoji Kishi & Hideki Ueno Virchows Archiv | February 2020 | DOI: 10.1007/s00428-020-02775-y Mesothelin (MSLN) is a cell surface glycoprotein present in many cancer types. Its expression is generally associated with an unfavorable prognosis. This study examined the prognostic significance of MSLN expression in different areas of individual colorectal cancers (CRCs) using tissue microarrays (TMAs) by enrolling 314 patients with stage II (T3–T4, N0, M0) CRCs....

Detection of Lung Cancer Lymph Node Metastases from Whole-Slide Histopathologic Images Using a Two-Step Deep Learning Approach

Hoa Hoang Ngoc Pham, Mitsuru Futakuchi, Andrey Bychkov, Tomoi Furukawa, Kishio Kuroda, Junya Fukuoka The American Journal of Pathology | Volume 189, Issue 12, December 2019 | DOI: 10.5858/arpa.2019-0004-OA The application of deep learning for the detection of lymph node metastases on histologic slides has attracted worldwide attention due to its potentially important role in patient treatment and prognosis. Despite this attention, false-positive predictions remain problematic, particularly in the case of reactive lymphoid follicles. In this study, a novel two-step deep learning algorithm...

A Deep Learning Convolutional Neural Network Can Recognize Common Patterns of Injury in Gastric Pathology

Martin, D.R., Hanson, J.A., Gullapalli, R.R., Schultz, F.A., Sethi, A. and Clark, D.P. Archives of Pathology & Laboratory Medicine In-Press | Published April 5, 2019 | DOI: 10.5858/arpa.2019-0004-OA Context.— Most deep learning (DL) studies have focused on neoplastic pathology, with the realm of inflammatory pathology remaining largely untouched. Objective.— To investigate the use of DL for nonneoplastic gastric biopsies. Design.— Gold standard diagnoses were blindly established by 2 gastrointestinal pathologists. For phase 1, 300 classic cases (100 normal, 100 Helicobacter pylori, 100 reactive gastropathy)...