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In silico analysis of nuclei in glioblastoma using large-scale microscopy images improves prediction of treatment response

Jun Kong, Lee Cooper, Carlos Moreno, Fusheng Wang, Tahsin Kurc, Joel Saltz, Daniel Brat
2011 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
In this paper, we present a complete and novel workflow for quantitative nuclear feature analysis of glioblastoma using high-throughput whole-slide microscopy image processing as it relates to treatment  ...  With a complete suite of computer algorithms, large numbers of micro-anatomical structures, in this case nuclei, are analyzed and represented efficiently from whole-slide digitized images with numerical  ...  In an effort to address these issues, we initiated an integrated exploration of the complementary, multi-modal data on glioblastomas (GBMs) from cohorts of patients collected in large-scale efforts by  ... 
doi:10.1109/iembs.2011.6089903 pmid:22254257 pmcid:PMC3292262 dblp:conf/embc/KongCMWKSB11 fatcat:7exrpb4slzdshdps4inb5w2rla

Integrative, Multimodal Analysis of Glioblastoma Using TCGA Molecular Data, Pathology Images, and Clinical Outcomes

Jun Kong, L. A. D. Cooper, Fusheng Wang, D. A. Gutman, Jingjing Gao, C. Chisolm, A. Sharma, T. Pan, E. G. Van Meir, T. M. Kurc, C. S. Moreno, J. H. Saltz (+1 others)
2011 IEEE Transactions on Biomedical Engineering  
Multi-modal, multi-scale data synthesis is becoming increasingly critical for successful translational biomedical research. In this paper, we present a large-scale investigative initiative on  ...  Microscopy Imaging Analysis We developed a suite of image analysis tools for segmenting and characterizing nuclei.  ...  glioblastoma, a high-grade brain tumor, with complementary data types using in silico approaches.  ... 
doi:10.1109/tbme.2011.2169256 pmid:21947516 pmcid:PMC3292263 fatcat:orjha4fr6fe75f5sdr2ojviwsi

High-performance computational analysis of glioblastoma pathology images with database support identifies molecular and survival correlates

Jun Kong, Fusheng Wang, George Teodoro, Lee Cooper, Carlos S. Moreno, Tahsin Kurc, Tony Pan, Joel Saltz, Daniel Brat
2013 2013 IEEE International Conference on Bioinformatics and Biomedicine  
In this paper, we present a novel framework for microscopic image analysis of nuclei, data management, and high performance computation to support translational research involving nuclear morphometry features  ...  Our image analysis pipeline consists of nuclei segmentation and feature computation facilitated by high performance computing with coordinated execution in multi-core CPUs and Graphical Processor Units  ...  To strengthen our ability to extract such phenotypic information embedded in tissue, we have made significant advances in large-scale pathology image analysis within the In Silico Brain Tumor Research  ... 
doi:10.1109/bibm.2013.6732495 pmid:25098236 pmcid:PMC4120024 dblp:conf/bibm/KongWTCMKPSB13 fatcat:bavl4tbe6jgz5fcuvufcg4cxrq

AI and Medical Imaging Informatics: Current Challenges and Future Directions

Andreas S. Panayides, Amir Amini, Nenad Filipovic, Ashish Sharma, Sotirios Tsaftaris, Alistair Young, David J. Foran, Nhan Do, Spyretta Golemati, Tahsin Kurc, Kun Huang, Konstantina S. Nikita (+4 others)
2020 IEEE journal of biomedical and health informatics  
The clinical benefits of in-silico modelling advances linked with evolving 3D reconstruction and visualization applications are further documented.  ...  of AI in big healthcare data analytics.  ...  There is a large body of image analysis research that targets H&E stained tissue as covered in this paper.  ... 
doi:10.1109/jbhi.2020.2991043 pmid:32609615 pmcid:PMC8580417 fatcat:dcaefxwwqjfwla5asin34x2hxm

Digital Pathology: Data-Intensive Frontier in Medical Imaging

Lee A. D. Cooper, Alexis B. Carter, Alton B. Farris, Fusheng Wang, Jun Kong, David A. Gutman, Patrick Widener, Tony C. Pan, Sharath R. Cholleti, Ashish Sharma, Tahsin M. Kurc, Daniel J. Brat (+1 others)
2012 Proceedings of the IEEE  
Computer-based image analysis is already available in commercial diagnostic systems, but further advances in image analysis algorithms are warranted in order to fully realize the benefits of digital pathology  ...  therapeutic targets, and predict patient outcomes and therapeutic responses.  ...  His research is in imaging and translational informatics, specifically the issues stemming from supported federation of distributed data sources, integration of imaging with nonimaging modalities, high-performance  ... 
doi:10.1109/jproc.2011.2182074 pmid:25328166 pmcid:PMC4197933 fatcat:gqg4whf3bzbu3ay27j452g2esy

PML Differentially Regulates Growth and Invasion in Brain Cancer

Maria Tampakaki, Mariam-Eleni Oraiopoulou, Eleftheria Tzamali, Giorgos Tzedakis, Takis Makatounakis, Giannis Zacharakis, Joseph Papamatheakis, Vangelis Sakkalis
2021 International Journal of Molecular Sciences  
In this work, we studied the role of PML in Glioblastoma pathophysiology using the U87MG cell line.  ...  We present a combined in vitro–in silico approach, that utilizes both 2D and 3D cultures and cancer-predictive computational algorithms, in order to differentiate and interpret the observed biological  ...  Acknowledgments: Authors would like to thank Giorgos Vrentzos and Angela Pasparaki for excellent cell culture and in vitro imaging assistance, respectively.  ... 
doi:10.3390/ijms22126289 fatcat:qs5bum5wkncenmsgmxpc6amhda

Mitochondrial NIX Promotes Tumor Survival in the Hypoxic Niche of Glioblastoma

Jinkyu Jung, Ying Zhang, Orieta Celiku, Wei Zhang, Hua Song, Brian J Williams, Amber J Giles, Jeremy N. Rich, Roger Abounader, Mark R. Gilbert, Deric M Park
2019 Cancer Research  
Here, we elucidate a key survival mechanism of mitochondrial NIX-mediated mitophagy within the hypoxic region of glioblastoma, the most malignant brain tumor.  ...  Silencing NIX impaired mitochondrial reactive oxygen species clearance, cancer stem cell maintenance, and HIF/mTOR/RHEB signaling pathways under hypoxia, resulting in suppression of glioblastoma survival  ...  Zhen Yan (University of Virginia, VA, US) for kind donation of plasmid for pMitoTimer. We would like to thank the University of Virginia imaging core and animal core service teams.  ... 
doi:10.1158/0008-5472.can-19-0198 pmid:31488423 pmcid:PMC6801103 fatcat:5gvyay6fengxvl2p3frkfaorh4

Tissue Architecture Influences the Biological Effectiveness of Boron Neutron Capture Therapy in In Vitro/In Silico Three-Dimensional Self-Assembly Cell Models of Pancreatic Cancers

Lin-Sheng Yu, Megha Jhunjhunwala, Shiao-Ya Hong, Lin-Yen Yu, Wey-Ran Lin, Chi-Shuo Chen
2021 Cancers  
In this study, we evaluated the biological effectiveness of BNCT at multicellular levels using in vitro and in silico models.  ...  Intracellular boron distribution in the multicellular structure and related treatment resistance were reconstructed in silico.  ...  In addition to using molecular and cellular tools to study the radiation responses of pancreatic cancer in vitro, we adopted cellular Potts model (CPM) to simulate biological responses in silico with different  ... 
doi:10.3390/cancers13164058 fatcat:pmfc562tqvenhobjheob4ya42u

Autophagic Inhibition via Lysosomal Integrity Dysfunction Leads to Antitumor Activity in Glioma Treatment

Hui-Yun Hwang, Yoon Sun Cho, Jin Young Kim, Ki Na Yun, Jong Shin Yoo, Eunhyeong Lee, Injune Kim, Ho Jeong Kwon
2020 Cancers  
Either APZ treatment or Hsp70 inhibition attenuates integrity of lysosomes, which leads to autophagic cell death exhibiting an excellent synergism with a clinical drug, temozolomide, in vitro, in vivo,  ...  To identify APZ targets, we used a label-free drug affinity responsive target stability (DARTS) approach with a liquid chromatography/tandem mass spectrometry (LC–MS/MS) readout.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cancers12030543 pmid:32120820 pmcid:PMC7139627 fatcat:rbzpatuzfbbbvhsx5yyfmh3tfe

Oncolytic Virus Therapy Alters the Secretome of Targeted Glioblastoma Cells

Jakub Godlewski, Mohamed Farhath, Franz L. Ricklefs, Carmela Passaro, Klaudia Kiel, Hiroshi Nakashima, E. Antonio Chiocca, Agnieszka Bronisz
2021 Cancers  
Data validation and in silico analysis measured and correlated the secretome content with the response to infection and patient survival.  ...  Therefore, the upregulation of transcripts encoding for secreted proteins implies a common thread in the response of cancer cells to infection.  ...  There have been several clinical studies using oncolytic viruses against glioblastoma [82, 83] . Yet, none of these studies have shown the importance of GSC secretome in response to the treatment.  ... 
doi:10.3390/cancers13061287 pmid:33799381 fatcat:3dwwvml7e5dotjqkc6ukk2bfam

Multi-Targeting Approach in Glioblastoma Using Computer-Assisted Drug Discovery Tools to Overcome the Blood–Brain Barrier and Target EGFR/PI3Kp110β Signaling

Catarina Franco, Samina Kausar, Margarida F. B. Silva, Rita C. Guedes, Andre O. Falcao, Maria Alexandra Brito
2022 Cancers  
Predictions were validated in in vitro models of the human BBB and BBB-glioma co-cultures.  ...  These molecules crossed the endothelial monolayer in the BBB in vitro model and in the BBB-glioblastoma co-culture system. These results revealed novel drug candidates for glioblastoma treatment.  ...  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/cancers14143506 pmid:35884571 pmcid:PMC9317902 fatcat:jajczwqrdfckpepztjkmc4ecf4

The biology and mathematical modelling of glioma invasion: a review

J. C. L. Alfonso, K. Talkenberger, M. Seifert, B. Klink, A. Hawkins-Daarud, K. R. Swanson, H. Hatzikirou, A. Deutsch
2017 Journal of the Royal Society Interface  
Indeed, the widespread infiltration of healthy brain tissue by glioma cells is largely responsible for poor prognosis and the difficulty of finding curative therapies.  ...  In this review, we start with a brief introduction to current biological knowledge about glioma invasion, and then critically review and highlight future challenges for mathematical models of glioma invasion  ...  A further challenge concerns the improvement of glioma treatments.  ... 
doi:10.1098/rsif.2017.0490 pmid:29118112 pmcid:PMC5721156 fatcat:etlbfsh5p5cxxk2pkhb3xzospe

An innovative mathematical analysis of routine MRI scans in patients with glioblastoma using DoctorEye

Jonathan Zepp, Norbert Graf, Holger Stenzhorn, Wolfgang Reith, Ioannis Karatzanis, Georgios C. Manikis, Vangelis Sakkalis, Konstantinos Marias, Georgios Stamatakos
2012 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)  
genetic markers may be valuable both, in assessing prognosis and response to treatment and to predict individual courses of disease [63, 67] .  ...  Another topical approach was published by Najafi et al., trying to predict the response to bevacizumab treatment in patients with GBM [103] .  ... 
doi:10.1109/bibe.2012.6399773 dblp:conf/bibe/ZeppGSRKMSMS12 fatcat:zesgn7ywybh5zhspz4oq5xowg4

Artificial intelligence (AI) and big data in cancer and precision oncology

Zodwa Dlamini, Flavia Zita Francies, Rodney Hull, Rahaba Marima
2020 Computational and Structural Biotechnology Journal  
Advancement in technology has paved the way for analysis of big datasets in a cost- and time-effective manner. Clinical oncology and research are reaping the benefits of AI.  ...  Through these applications of AI, cancer diagnostics and prognostic prediction are enhanced with NGS and medical imaging that delivers high resolution images.  ...  Diagnostic images and genetic analysis data are obtained from complex neural networks and can predict probability of disease and treatment outcomes [2, 5] .  ... 
doi:10.1016/j.csbj.2020.08.019 pmid:32994889 pmcid:PMC7490765 fatcat:ocli2vys3zfw7mbqeuio3foipq

A patient-designed tissue-engineered model of the infiltrative glioblastoma microenvironment [article]

R Chase Cornelison, Jessica X Yuan, Kinsley M Tate, Alexis Petrosky, Garrett F Beeghly, Mathew Bloomfield, Samantha R Schwager, Alexandra L Berr, Daniela Cimini, Fahad F Bafakih, James W Mandell, Benjamin W Purow (+2 others)
2020 bioRxiv   pre-print
We conducted a six-drug screen using four outcomes and find expression of putative stemness marker CD71, opposed to viability IC50, significantly predicts murine xenograft survival.  ...  Our results dispute the paradigm of viability as predictive of drug efficacy. We posit this patient-centric, infiltrative tumor model is a novel advance towards translational personalized medicine.  ...  Therefore, glioma stemness in response to drug treatment in our TME model both correlates with and predicts xenograft drug response for two distinct patient-derived cell lines.  ... 
doi:10.1101/2020.10.02.322735 fatcat:btuy63lojjh4dg3eqpq35ylldq
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