Top 3 Biorxiv Papers Today in Pathology


2.007 Mikeys
#1. A precision medicine approach uncovers a unique signature of neutrophils in patients with brushite kidney stones
Mohammad Shahidul Makki, Seth Winfree, James E Lingeman, Frank A Witzmann, Elaine M Worcester, Amy Krambeck, Fred Coe, Andrew P Evan, Sharon Bledsoe, Kristin Bergsland, Suraj Khochare, Daria Barwinska, James C Willliams, Tarek M El-Achkar
Background: We have previously found that papillary histopathology differs greatly between calcium oxalate and brushite stone formers (SF); the latter have much more papillary mineral deposition and tissue fibrosis. Methods: In this study, we applied unbiased orthogonal omics approaches on biopsied renal papillae and extracted stones from patients with brushite or calcium oxalate (CaOx) stones. Our goal was to discover stone type-specific molecular signatures to advance our understanding of the underlying pathogenesis. Results: Brushite SF did not differ from CaOx SF with respect to metabolic risk factors for stones, but did exhibit increased tubule plugging in their papillae. Brushite SF had upregulation of inflammatory pathways in papillary tissue, and increased neutrophil markers in stone matrix compared to those with CaOx stones. Large-scale 3D tissue cytometry on renal papillary biopsies showed an increase in the number and density of neutrophils in the papillae of brushite vs. CaOx patients, thereby linking the observed...
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2.007 Mikeys
#2. Proteomic analysis of Caenorhabditis elegans against S. Typhi toxic proteins
K. Balamurugan, Dilawar Ahmad Mir
Background & Aims: Bacterial effector molecules are the crucial infectious agents and are sufficient to cause pathogenesis. In the present study, pathogenesis of S. Typhi toxic proteins on the model host Caenorhabditis elegans was investigated by exploring the host regulatory proteins during infection through quantitative proteomics approach. Methods: In this regard, the host proteome was analysed using two-dimensional gel electrophoresis (2D-GE) and differentially regulated proteins were identified using MALDI TOF/TOF/MS analysis. Out of the 150 regulated proteins identified, 95 proteins were appeared to be downregulated while 55 were upregulated. Interaction network for regulated proteins was predicted using STRING tool. Results: Most of the downregulated proteins were found to be involved in muscle contraction, locomotion, energy hydrolysis, lipid synthesis, serine/threonine kinase activity, oxidoreductase activity and protein unfolding and upregulated proteins were found to be involved in oxidative stress pathways. Hence,...
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biorxivpreprint: Proteomic analysis of Caenorhabditis elegans against S. Typhi toxic proteins https://t.co/WpdIp9XT9f #bioRxiv
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1.992 Mikeys
#3. A deep learning-based model of normal histology
Tobias Sing, Holger Hoefling, Imtiaz Hossain, Julie Boisclair, Arno Doelemeyer, Thierry Flandre, Alessandro Piaia, Vincent Romanet, Gianluca Santarossa, Chandrassegar Saravanan, Esther Sutter, Oliver Turner, Kuno Wuersch, Pierre Moulin
Deep learning models have been applied on various tissues in order to recognize malignancies. However, these models focus on relatively narrow tissue context or well-defined pathologies. Here, instead of focusing on pathologies, we introduce models characterizing the diversity of normal tissues. We obtained 1,690 slides with rat tissue samples from the control groups of six preclinical toxicology studies, on which tissue regions were outlined and annotated by pathologists into 46 different tissue classes. From these annotated regions, we sampled small patches of 224 x 224 pixels at six different levels of magnification. Using four studies as training set and two studies as test set, we trained VGG-16, ResNet-50, and Inception-v3 networks separately at each of these magnification levels. Among these models, Inception-v3 consistently outperformed the other networks and attained accuracies up to 83.4% (top-3 accuracy: 96.3%). Further analysis showed that most tissue confusions occurred within clusters of histologically similar...
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