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Front Matter: Volume 10140

Proceedings of SPIE, Metin N. Gurcan, John E. Tomaszewski
2017 Medical Imaging 2017: Digital Pathology  
SPIEDigitalLibrary.org Paper Numbering: Proceedings of SPIE follow an e-First publication model. A unique citation identifier (CID) number is assigned to each article at the time of publication.  ...  using a Base 36 numbering system employing both numerals and letters.  ...  10140 0J A computational framework to detect normal and tuberculosis infected lung from H and E- stained whole slide images [10140-18] 10140 0K Evaluation of nucleus segmentation in digital pathology  ... 
doi:10.1117/12.2270372 dblp:conf/midp/X17 fatcat:6yeb63ix6bau7jhipthayjih24

Automatic discovery of clinically interpretable imaging biomarkers for Mycobacterium tuberculosis supersusceptibility using deep learning

Thomas E. Tavolara, M. Khalid Khan Niazi, Melanie Ginese, Cesar Piedra-Mora, Daniel M. Gatti, Gillian Beamer, Metin N. Gurcan
2020 EBioMedicine  
The proposed machine learning model diagnosed supersusceptibility with high accuracy (91.50 ± 4.68%) compared to two expert pathologists using H&E stained lung sections (94.95% and 94.58%).  ...  This led us to utilize deep learning to identify supersusceptibility from hematoxylin & eosin (H&E) lung tissue sections utilizing only clinical outcomes (supersusceptible or not-supersusceptible) as labels  ...  Acknowledgements We thank Aubrey Specht (Tufts Cummings School of Medicine) for her time and effort using the heatmaps to classify supersusceptible and not-supersusceptible mice. We thank Ms.  ... 
doi:10.1016/j.ebiom.2020.103094 pmid:33166789 pmcid:PMC7658666 fatcat:74a25dgt5fffpft2dtqd6h4yvm

X-ray-based virtual slicing of TB-infected lungs

Ana Ortega-Gil, Juan José Vaquero, Mario Gonzalez-Arjona, Joaquín Rullas, Arrate Muñoz-Barrutia
2019 Scientific Reports  
Organ samples were taken from five control and five tuberculosis-infected mice.  ...  Hollow organs such as the lungs pose a considerable challenge for post-mortem imaging in preclinical research owing to their extremely low contrast and high structural complexity.  ...  comprise funding from the European Union Seventh Framework Programme (FP7/2007-2013) and EFPIA companies in kind contribution.  ... 
doi:10.1038/s41598-019-55986-y pmid:31852973 pmcid:PMC6920455 fatcat:eksyfebxvnampm6bdmssgo7i7u

Deep learning-based six-type classifier for lung cancer and mimics from histopathological whole slide images: a retrospective study

Huan Yang, Lili Chen, Zhiqiang Cheng, Minglei Yang, Jianbo Wang, Chenghao Lin, Yuefeng Wang, Leilei Huang, Yangshan Chen, Sui Peng, Zunfu Ke, Weizhong Li
2021 BMC Medicine  
Digital whole slide images (WSIs) witnessed the transition from traditional histopathology to computational approaches, arousing a hype of deep learning methods for histopathological analysis.  ...  tuberculosis, organizing pneumonia, and normal lung.  ...  Acknowledgements We acknowledge the pathologists and assistants participating in this study for specimen collection, preparation, and quality control at the Sun Yat-sen University.  ... 
doi:10.1186/s12916-021-01953-2 pmid:33775248 fatcat:q7q7anzgcbeybmxfoz3vxt4sfm

Digital Image Analysis of Heterogeneous Tuberculosis Pulmonary Pathology in Non-Clinical Animal Models using Deep Convolutional Neural Networks

Bryce C. Asay, Blake Blue Edwards, Jenna Andrews, Michelle E. Ramey, Jameson D. Richard, Brendan K. Podell, Juan F. Muñoz Gutiérrez, Chad B. Frank, Forgivemore Magunda, Gregory T. Robertson, Michael Lyons, Asa Ben-Hur (+1 others)
2020 Scientific Reports  
Alongside efficacy testing of novel therapies, effects on pulmonary pathology and disease progression are monitored by using histopathology images from these infected animals.  ...  LIRA was developed to improve the efficiency of histopathology analysis for mouse tuberculosis infection models, this approach has also broader applications to other disease models and tissues.  ...  Acknowledgements We would like to thank the TB Drug Accelerator (BMGF) and the Global Alliance for TB Drug Development for their assistance with earlier mouse studies, which provided the necessary histopathology  ... 
doi:10.1038/s41598-020-62960-6 pmid:32269234 fatcat:5a3zg4dk7fahpfohkd5i2nk46m

Medical image analysis based on deep learning approach

Muralikrishna Puttagunta, S. Ravi
2021 Multimedia tools and applications  
It provides a systematic review of the articles for classification, detection, and segmentation of medical images based on DLA.  ...  Deep Learning Approach (DLA) in medical image analysis emerges as a fast-growing research field. DLA has been widely used in medical imaging to detect the presence or absence of the disease.  ...  Lin et al. 2019 [83] H & E Fast Scan Net: FCN based model Automatic detection of breast cancer metastases from whole-slide image 2016 Camelyon Grand Challenge (400 WSI) NODE: Neural Ordinary  ... 
doi:10.1007/s11042-021-10707-4 pmid:33841033 pmcid:PMC8023554 fatcat:cm522go4nbdbnglgzpw4nu7tbi

Systemic Mycobacterium kansasii Infection in Two Related Cats

Petra Černá, Jordan Mitchell, Joanna Lodzinska, Paola Cazzini, Katarina Varjonen, Danièlle Gunn-Moore
2020 Pathogens  
the other; interferon-gamma release assay inferred M. avium-complex and M. tuberculosis-complex infection in the two cats, respectively.  ...  This case report describes systemic M. kansasii infection in two sibling indoor-only cats that presented two and half years apart with cutaneous disease that was found to be associated with osteolytic  ...  Acknowledgments: The authors would like to thank Paul Burr (Biobest Laboratories, Edinburgh) and Deborah Gascoyne-Binzi (Leeds Teaching Hospitals NHS Trust) for providing resources for IGRA and PCR diagnostic  ... 
doi:10.3390/pathogens9110959 pmid:33218094 pmcid:PMC7698836 fatcat:47av2hbhmfb4zihjatds2xowre

A Survey of Deep Learning for Lung Disease Detection on Medical Images: State-of-the-Art, Taxonomy, Issues and Future Directions

Stefanus Tao Hwa Kieu, Abdullah Bade, Mohd Hanafi Ahmad Hijazi, Hoshang Kolivand
2020 Journal of Imaging  
Hence, numerous work on the detection of lung disease using deep learning can be found in the literature. This paper presents a survey of deep learning for lung disease detection in medical images.  ...  The objectives of this paper are to present a taxonomy of the state-of-the-art deep learning based lung disease detection systems, visualise the trends of recent work on the domain and identify the remaining  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/jimaging6120131 pmid:34460528 fatcat:jhi5r4nj5nccbklrdbtuk4qo6e

Low Levels of T Cell Exhaustion in Tuberculous Lung Granulomas

Eileen A. Wong, Louis Joslyn, Nicole L. Grant, Edwin Klein, Philana Ling Lin, Denise E. Kirschner, JoAnne L. Flynn, Andreas J. Bäumler
2018 Infection and Immunity  
We then used these experimental data to calibrate and inform an agent-based computational model that captures environmental, cellular, and bacterial dynamics within granulomas in lungs during M. tuberculosis  ...  T cell exhaustion is proposed to result from continual antigen stimulation, inducing them to enter a state characterized by low cytokine production, low proliferation, and expression of a series of inhibitory  ...  This research was supported by the following NIH grants awarded to J.L.F. and D.E.K.: R01 AI123093, U01HL131072, and R01 HL110811.  ... 
doi:10.1128/iai.00426-18 pmid:29891540 fatcat:cxt7qna5uzhpjjj6lpdxywj5i4

Cytology Image Analysis Techniques Towards Automation: Systematically Revisited [article]

Shyamali Mitra, Nibaran Das, Soumyajyoti Dey, Sukanta Chakrabarty, Mita Nasipuri, Mrinal Kanti Naskar
2020 arXiv   pre-print
We take a short tour to 17 types of cytology and explore various segmentation and/or classification techniques which evolved during last three decades boosting the concept of automation in cytology.  ...  The inflush of intelligent technological units with high computational power and improved specimen collection techniques helped to achieve its technological heights.  ...  Authors are also thankful to the members of "Theism Medical Diagnostics Centre", Kolkata, India and "Saroj Gupta Cancer Centre & Research Institute", Thakurpukur, Kolkata, India.  ... 
arXiv:2003.07529v1 fatcat:eossjujftzflbfnfhbsw55tlta

Microanatomic Distribution of Myeloid Heme Oxygenase-1 Protects against Free Radical-Mediated Immunopathology in Human Tuberculosis

Krishna C. Chinta, Md. Aejazur Rahman, Vikram Saini, Joel N. Glasgow, Vineel P. Reddy, Jeremie M. Lever, Shepherd Nhamoyebonde, Alasdair Leslie, Ryan M. Wells, Amie Traylor, Rajhmun Madansein, Gene P. Siegal (+8 others)
2018 Cell Reports  
Heme oxygenase-1 (HO-1) is a cytoprotective enzyme that controls inflammatory responses and redox homeostasis; however, its role during pulmonary tuberculosis (TB) remains unclear.  ...  Using whole-body or myeloid-specific HO-1-deficient mice, we demonstrate that HO-1 is required to control myeloid cell infiltration and inflammation to protect against TB progression.  ...  (D) H&E staining of representative lung and spleen sections from Mtb-infected HO-1 +/+ and HO-1 À/À mice at 18 weeks post-infection.  ... 
doi:10.1016/j.celrep.2018.10.073 pmid:30428359 pmcid:PMC6250977 fatcat:ytgrkl4i2nawhfve3ycbklaxju

Rapid GPR183-mediated recruitment of eosinophils to the lung after Mycobacterium tuberculosis infection [article]

Andrea C Bohrer, Ehydel Castro, Claire E Tocheny, Maike Assmann, Benjamin Schwarz, Eric Bohrnsen, Michelle A Makiya, Fanny Legrand, Kerry L Hilligan, Paul J Baker, Flor Torres-Juarez, Zhidong Hu (+19 others)
2022 bioRxiv   pre-print
Our findings show that eosinophils are among the first cells from circulation to sense and respond to Mtb infection of alveolar macrophages and reveal a novel role for GPR183 in the migration of eosinophils  ...  However, we previously reported that eosinophils accumulate in lung lesions during type-I inflammatory responses to Mycobacterium tuberculosis (Mtb) in humans, macaques, and mice where they contribute  ...  David Sacks and Yasmine Belkaid for discussion and feedback on the manuscript and Ryan Kissinger for graphical abstract assistance.  ... 
doi:10.1101/2022.02.18.480919 fatcat:73qqj66wmrb6fherlrlftotrf4

A combined method for correlative 3D imaging of biological samples from macro to nano scale

Manuela Kellner, Marko Heidrich, Raoul-Amadeus Lorbeer, Georgios C. Antonopoulos, Lars Knudsen, Christoph Wrede, Nicole Izykowski, Roman Grothausmann, Danny Jonigk, Matthias Ochs, Tammo Ripken, Mark P. Kühnel (+1 others)
2016 Scientific Reports  
In diseases like cancer, fibrosis or bacterial/parasite infection (e.g. tuberculosis) the ROI might be fairly limited in number and difficult to locate in the 3D environment of an affected organ.  ...  Here we use Scanning Laser Optical Tomography 8,11,24 (SLOT) to image the entire accessory lobe of a rat lung with a resolution reaching down to the sub-alveolar level.  ...  and Research (BMBF) via the German Center for Lung Research (DZL).  ... 
doi:10.1038/srep35606 pmid:27759114 pmcid:PMC5069670 fatcat:h7ct3fo2ivanpe2pnp64tm7mh4

Assessment of the Cytotoxic and Immunomodulatory Effects of Substances in Human Precision-cut Lung Slices

Vanessa Neuhaus, Olga Danov, Sebastian Konzok, Helena Obernolte, Susann Dehmel, Peter Braubach, Danny Jonigk, Hans-Gerd Fieguth, Patrick Zardo, Gregor Warnecke, Christian Martin, Armin Braun (+1 others)
2018 Journal of Visualized Experiments  
Pro-inflammatory cytokines, tumor necrosis factor alpha (TNF-α), and interleukin 1 alpha (IL-1α) were significantly increased in human PCLS after exposure to a sub-toxic concentration of HClPt.  ...  In view of the 3Rs principle and public skepticism against animal experiments, human alternative methods, such as precisioncut lung slices (PCLS), have been evolving.  ...  Some of the research was supported by a grant from the European Commission within the 6 th framework program SENS-IT-IV "Novel Testing Strategies for In Vitro Assessment of Allergens".  ... 
doi:10.3791/57042 pmid:29806827 pmcid:PMC6101160 fatcat:drefyw2hanc7vg5fjxk4wbno5u

7thESACP Congress in Caen April 1–5, 2001

2001 Analytical Cellular Pathology  
Conclusion: MP-FCM was in all cases sufficient, and even superior to H&E and IHC, to detect micrometastatic tumor cells in a large volume of lymph node tissue from SLN.  ...  multiple slides and stains.  ...  Aims: To develop a new type of didactic tool as a combination of computer based teaching and learning multimedia software with a knowledge based diagnostic system in cytopathology of effusions.  ... 
doi:10.1155/2001/414753 fatcat:7vxekd2dbjherbnpv5q7dshpsu
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