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Anatomy-specific classification of medical images using deep convolutional nets

Automated classification of human anatomy is an important prerequisite for many computer-aided diagnosis systems. The spatial complexity and variability of anatomy throughout the human body makes classification difficult. "Deep learning" methods such as convolutional networks (ConvNets) outperform other state-of-the-art methods in image classification tasks. In this work, we present a method for organ- or body-part-specific anatomical classification of medical images acquired using computed tomography (CT) with ConvNets. We train a ConvNet, using 4,298 separate axial 2D key-images to learn 5 anatomical classes. Key-images were mined from a hospital PACS archive, using a set of 1,675 patients. We show that a data augmentation approach can help to enrich the data set and improve classification performance. Using ConvNets and data augmentation, we achieve anatomy-specific classification error of 5.9 % and area-under-the-curve (AUC) values of an average of 0.998 in testing. We demonstrate that deep learning can be used to train very reliable and accurate classifiers that could initialize further computer-aided diagnosis.Comment: Presented at: 2015 IEEE International Symposium on Biomedical Imaging, April 16-19, 2015, New York Marriott at Brooklyn Bridge, NY, US

Adhesion to the extracellular matrix is required for interleukin-1 beta actions leading to reactive phenotype in rat astrocytes

The extracellular matrix (ECM) of the brain is essential for homeostasis and normal functions, but is rapidly remodelled during acute brain injury alongside the development of an inflammatory response driven by the cytokine interleukin (IL)-1. Whether the ECM regulates IL-1 actions in astrocytes is completely unknown. The aim of this study was to test the hypothesis that cellular attachment to the ECM is a critical mediator of IL-1β-induced signalling pathways and development of reactive phenotype in astrocytes. Primary rat astrocytes adhered to fibronectin, laminin and fibrillin-1 in an integrin-dependent manner. Attachment to these ECM molecules significantly increased IL-1β-induced activation of extracellular signal-regulated kinase 1/2 (ERK1/2) and inhibition of RhoA and Rho kinase (ROCK), coincident with loss of focal adhesions and cellular morphological changes. Our data demonstrate that the ECM regulates IL-1 actions in astrocytes via cross-talk mechanisms between ERK1/2 and RhoA/ROCK, which could have important implications in brain inflammatory disorders

Interleaved text/image Deep Mining on a large-scale radiology database

Despite tremendous progress in computer vision, effec-tive learning on very large-scale (> 100K patients) medi-cal image databases has been vastly hindered. We present an interleaved text/image deep learning system to extract and mine the semantic interactions of radiology images and reports from a national research hospital’s picture archiv-ing and communication system. Instead of using full 3D medical volumes, we focus on a collection of representa-tive ~216K 2D key images/slices (selected by clinicians for diagnostic reference) with text-driven scalar and vector la-bels. Our system interleaves between unsupervised learn-ing (e.g., latent Dirichlet allocation, recurrent neural net language models) on document- and sentence-level texts to generate semantic labels and supervised learning via deep convolutional neural networks (CNNs) to map from images to label spaces. Disease-related key words can be predicted for radiology images in a retrieval manner. We have demon-strated promising quantitative and qualitative results. The large-scale datasets of extracted key images and their cat-egorization, embedded vector labels and sentence descrip-tions can be harnessed to alleviate the deep learning “data-hungry ” obstacle in the medical domain

The YsrS Paralog DygS Has the Capacity To Activate Expression of the Yersinia enterocolitica Ysa Type III Secretion System

ABSTRACT The Yersinia enterocolitica Ysa type III secretion system (T3SS) is associated with intracellular survival, and, like other characterized T3SSs, it is tightly controlled. Expression of the ysa genes is only detected following growth at low temperatures (26°C) and in high concentrations of sodium chloride (290 mM) in the medium. The YsrSTR phosphorelay (PR) system is required for ysa expression and likely responds to NaCl. During our investigations into the Ysr PR system, we discovered that genes YE3578 and YE3579 are remarkably similar to ysrR and ysrS , respectively, and are probably a consequence of a gene duplication event. The amino acid differences between YE3578 and ysrR are primarily clustered into two short regions. The differences between YE3579 and ysrS are nearly all located in the periplasmic sensing domain; the cytoplasmic domains are 98% identical. We investigated whether these paralogs were capable of activating ysa gene expression. We found that the sensor paralog, named DygS, is capable of compensating for loss of ysrS , but the response regulator paralog, DygR, cannot complement a ysrR gene deletion. In addition, YsrR, but not DygR, interacts with the histidine phosphorelay protein YsrT. Thus, DygS likely activates ysa gene expression in response to a signal other than NaCl and provides an example of a phosphorelay system in which two sensor kinases feed into the same regulatory pathway. IMPORTANCE All organisms need mechanisms to promote survival in changing environments. Prokaryotic phosphorelay systems are minimally comprised of a histidine kinase (HK) that senses an extracellular stimulus and a response regulator (RR) but can contain three or more proteins. Through gene duplication, a unique hybrid HK was created. We show that, while the hybrid appears to retain all of the phosphorelay functions, it responds to a different signal than the original. Both HKs transmit the signal to the same RR, which activates a promoter that transcribes a set of genes encoding a type III secretion system (T3SS) whose function is not yet evident. The significance of this work lies in finding that two HKs regulate this T3SS, highlighting its importance

The Coagulation and Immune Systems are Directly Linked through the Activation of Interleukin-1α by Thrombin

Ancient organisms have a combined coagulation and immune system, and although links between inflammation and haemostasis exist in mammals, they are indirect and slower to act. Here we investigated direct links between mammalian immune and coagulation systems by examining cytokine proproteins for potential thrombin protease consensus sites. We found that interleukin (IL)-1α is directly activated by thrombin. Thrombin cleaved pro-IL-1α at a site perfectly conserved across disparate species, indicating functional importance. Surface pro-IL-1α on macrophages and activated platelets was cleaved and activated by thrombin, while tissue factor, a potent thrombin activator, colocalised with pro-IL-1α in the epidermis. Mice bearing a mutation in the IL-1α thrombin cleavage site (R114Q) exhibited defects in efficient wound healing and rapid thrombopoiesis after acute platelet loss. Thrombin-cleaved IL-1α was detected in humans during sepsis, pointing to the relevance of this pathway for normal physiology and the pathogenesis of inflammatory and thrombotic diseases.This work was funded by British Heart Foundation Grants FS/09/005/26845, FS/13/3/30038, FS/18/19/33371 and RG/16/8/32388 to MC, RG/13/14/30314 to MB, the BHF Cambridge Centre for Research Excellence RE/13/6/30180, the Oxbridge BHF Regenerative Medicine Centre RM/13/3/30159, and the Cambridge NIHR Biomedical Research Centre

The Grizzly, February 9, 2012

Fong Anticipates Strategic Plan Draft • Crigler Institute Seeks to Foster Community • Job and Internship Fair Returns • Relay for Life to be Held at UC in April • Fighting for Ophelia Combats Bullying • Kathleen Bogle Visits Campus for Hooking Up Lectures • Senior Sullivan Spends Summer Transcribing • Opinion: Sexual Assault a Problem on Campus • Club Sports Gaining Campus\u27 Attention • Eachus Sounds Off: Fans Need to Get Real • Coach Profile: Katie Hagan, Women\u27s Lacrossehttps://digitalcommons.ursinus.edu/grizzlynews/1851/thumbnail.jp

Concert recording 2022-11-17

[Track 1]. Viking Horn Trio, No. 8, “The Sacred Oak Tree” / Robert Martin -- [Track 2]. Dorn Horn Trio. 1. Maestoso ; 3. Moving right along / Fred W. Teuber -- [Track 3]. Concerto in C minor, op. 8. Allegro molto / Franz Strauss -- [Track 4]. Selected duets for horn. Moderato ; Cantabile / Voxman -- [Track 5]. Romance, op. 67 / Camille Saint-Saëns -- [Track 6]. Four Duets for Horn. 1. Introduction ; 2. Watlz ; 4. Intermezzo / Kerry Turner -- [Track 7]. Three for Five. 1-3 / James Naigus -- [Track 8]. Benedixti / Giovanni Gabrielli -- [Track 9]. Let Me Fly / arr. Robert Cormier ; Chris Dorner