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In silico analysis of nuclei in glioblastoma using large-scale microscopy images improves prediction of treatment response
2011
2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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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
2011
IEEE Transactions on Biomedical Engineering
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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
2013
2013 IEEE International Conference on Bioinformatics and Biomedicine
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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
2020
IEEE journal of biomedical and health informatics
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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
2012
Proceedings of the IEEE
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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
2021
International Journal of Molecular Sciences
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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
2019
Cancer Research
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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
2021
Cancers
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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
2020
Cancers
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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
2021
Cancers
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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
2022
Cancers
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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
2017
Journal of the Royal Society Interface
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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
2012
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)
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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
2020
Computational and Structural Biotechnology Journal
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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]
2020
bioRxiv
pre-print
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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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