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Article ; Online: A transformer-based deep-learning approach for classifying brain metastases into primary organ sites using clinical whole-brain MRI images.

Patterns (New York, N.Y.)

2022 Volume 3, Issue 11, Page(s) 100613

Abstract: ... enhanced T1-weighted and fast spoiled gradient echo brain MRI exams (n = 1,582) were preprocessed and input ...

Abstract	Treatment decisions for brain metastatic disease rely on knowledge of the primary organ site and are currently made with biopsy and histology. Here, we develop a deep-learning approach for accurate non-invasive digital histology with whole-brain magnetic resonance imaging (MRI) data. Contrast-enhanced T1-weighted and fast spoiled gradient echo brain MRI exams (n = 1,582) were preprocessed and input to the proposed deep-learning workflow for tumor segmentation, modality transfer, and primary site classification into one of five classes. Tenfold cross-validation generated an overall area under the receiver operating characteristic curve (AUC) of 0.878 (95% confidence interval [CI]: 0.873,0.883). These data establish that whole-brain imaging features are discriminative enough to allow accurate diagnosis of the primary organ site of malignancy. Our end-to-end deep radiomic approach has great potential for classifying metastatic tumor types from whole-brain MRI images. Further refinement may offer an invaluable clinical tool to expedite primary cancer site identification for precision treatment and improved outcomes.
Language	English
Publishing date	2022-10-27
Publishing country	United States
Document type	Journal Article
ISSN	2666-3899
ISSN (online)	2666-3899
DOI	10.1016/j.patter.2022.100613
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mitochondrial concept of leukemogenesis: key role of oxygen-peroxide effects.

Lyu, Boris N / Ismailov, Sanzhar B / Ismailov, Bolat / Lyu, Marina B

Theoretical biology & medical modelling

2008 Volume 5, Page(s) 23

Abstract: Background and hypothesis: The high sensitivity of hematopoietic cells, especially stem cells, to radiation and to pro-oxidative and other leukemogenic agents is related to certain of their morphological and metabolic features. It is attributable to the ...

Abstract	Background and hypothesis: The high sensitivity of hematopoietic cells, especially stem cells, to radiation and to pro-oxidative and other leukemogenic agents is related to certain of their morphological and metabolic features. It is attributable to the low (minimal) number of active mitochondria and the consequently slow utilization of O2 entering the cell. This results in an increased intracellular partial pressure of O2 (pO2) and increased levels of reactive oxygen (ROS) and nitrogen (RNS) species, and a Delta(PO - AO) imbalance between the pro-oxidative (PO) and antioxidative (AO) constituents. Proposed mechanism: Because excessive O2 is toxic, we suggest that hematopoietic cells exist in a kind of unstable dynamic balance. This suggestion is based on the idea that mitochondria not only consume O2 in the process of ATP production but also constitute the main anti-oxygenic stage in the cell's protective antioxidative system. Variations in the mitochondrial base capacity (quantity and quality of mitochondria) constitute an important and highly efficient channel for regulating the oxidative stress level within a cell.The primary target for leukemogenic agents is the few mitochondria within the hematopoietic stem cell. Disturbance and weakening of their respiratory function further enhances the initial pro-oxidative state of the cell. This readily results in peroxygenation stress, creating the necessary condition for inducing leukemogenesis. We propose that this is the main cause of all related genetic and other disorders in the cell. ROS, RNS and peroxides act as signal molecules affecting redox-sensitive transcription factors, enzymes, oncogenes and other effectors. Thereby, they influence the expression and suppression of many genes, as well as the course and direction of proliferation, differentiation, leukemogenesis and apoptosis.Differentiation of leukemic cells is blocked at the precursor stage. While the transformation of non-hematopoietic cells into tumor cells starts during proliferation, hematopoietic cells become leukemic at one of the interim stages in differentiation, and differentiation does not continue beyond that point. Proliferation is switched to differentiation and back according to a trigger principle, again involving ROS and RNS. When the leukemogenic DeltaL(PO - AO) imbalance decreases in an under-differentiated leukemia cell to the differentiation level DeltaD(PO - AO), the cell may continue to differentiate to the terminal stage. Conclusion: The argument described in this article is used to explain the causes of congenital and children's leukemia, and the induction of leukemia by certain agents (vitamin K3, benzene, etc.). Specific research is required to validate the proposals made in this article. This will require accurate and accessible methods for measuring and assessing oxidative stress in different types of cells in general, and in hematopoietic cells in particular, in their different functional states.
MeSH term(s)	Apoptosis ; Cell Differentiation ; Cell Line, Tumor ; Cell Proliferation ; Humans ; Leukemia/metabolism ; Leukemia/physiopathology ; Mitochondria/metabolism ; Mitochondria/physiology ; Models, Biological ; Oxidative Stress ; Oxygen/chemistry ; Oxygen Consumption ; Peroxides/chemistry ; Reactive Nitrogen Species ; Reactive Oxygen Species
Chemical Substances	Peroxides ; Reactive Nitrogen Species ; Reactive Oxygen Species ; Oxygen (S88TT14065)
Language	English
Publishing date	2008-11-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2156462-0
ISSN	1742-4682 ; 1742-4682
ISSN (online)	1742-4682
ISSN	1742-4682
DOI	10.1186/1742-4682-5-23
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Article ; Online: USC-087 protects Syrian hamsters against lethal challenge with human species C adenoviruses.

Toth, Karoly / Spencer, Jacqueline F / Ying, Baoling / Tollefson, Ann E / Hartline, Caroll B / Richard, Eric T / Fan, Jiajun / Lyu, Jinglei / Kashemirov, Boris A / Harteg, Cheryl / Reyna, Dawn / Lipka, Elke / Prichard, Mark N / McKenna, Charles E / Wold, William S M

Antiviral research

2018 Volume 153, Page(s) 1–9

Abstract: ... drugs approved specifically to treat AdV infections. We report here that USC-087, an N-alkyl tyrosinamide ...

Abstract	Human adenoviruses (AdV) cause generally mild infections of the respiratory and GI tracts as well as some other tissues. However, AdV can cause serious infection in severely immunosuppressed individuals, especially pediatric patients undergoing allogeneic hematopoietic stem cell transplantation, where mortality rates are up to 80% with disseminated disease. Despite the seriousness of AdV disease, there are no drugs approved specifically to treat AdV infections. We report here that USC-087, an N-alkyl tyrosinamide phosphonate ester prodrug of HPMPA, the adenine analog of cidofovir, is highly effective against multiple AdV types in cell culture. USC-087 is also effective against AdV-C6 in our immunosuppressed permissive Syrian hamster model. In this model, hamsters are immunosuppressed by treatment with high dose cyclophosphamide. Injection of AdV-C6 (or AdV-C5) intravenously leads to a disseminated infection that resembles the disease seen in humans, including death. We have tested the efficacy of orally-administered USC-087 against the median lethal dose of intravenously administered AdV-C6. USC-087 completely prevented or significantly decreased mortality when administered up to 4 days post challenge. USC-087 also prevented or significantly decreased liver damage caused by AdV-C6 infection, and suppressed virus replication even when administered 4 days post challenge. These results imply that USC-087 is a promising candidate for drug development against HAdV infections.
MeSH term(s)	Adenine/administration & dosage ; Adenine/analogs & derivatives ; Adenovirus Infections, Human/drug therapy ; Adenoviruses, Human/drug effects ; Administration, Oral ; Animals ; Antiviral Agents/administration & dosage ; Disease Models, Animal ; Immunocompromised Host ; Liver/pathology ; Mesocricetus ; Organophosphonates/administration & dosage ; Prodrugs/administration & dosage ; Survival Analysis ; Treatment Outcome ; Tyrosine/administration & dosage ; Tyrosine/analogs & derivatives
Chemical Substances	Antiviral Agents ; Organophosphonates ; Prodrugs ; Tyrosine (42HK56048U) ; 9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine (92999-29-6) ; Adenine (JAC85A2161)
Language	English
Publishing date	2018-03-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2018.03.001
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Book ; Online: A transformer-based deep learning approach for classifying brain metastases into primary organ sites using clinical whole brain MRI

2021

Abstract: ... comprised of patients (n=1,399) referred for MRI treatment-planning and gamma knife radiosurgery over 21 ... n=1,582) were preprocessed and input to the proposed deep learning workflow for tumor segmentation ...

Abstract	Treatment decisions for brain metastatic disease rely on knowledge of the primary organ site, and currently made with biopsy and histology. Here we develop a novel deep learning approach for accurate non-invasive digital histology with whole-brain MRI data. Our IRB-approved single-site retrospective study was comprised of patients (n=1,399) referred for MRI treatment-planning and gamma knife radiosurgery over 21 years. Contrast-enhanced T1-weighted and T2-weighted Fluid-Attenuated Inversion Recovery brain MRI exams (n=1,582) were preprocessed and input to the proposed deep learning workflow for tumor segmentation, modality transfer, and primary site classification into one of five classes. Ten-fold cross-validation generated overall AUC of 0.878 (95%CI:0.873,0.883), lung class AUC of 0.889 (95%CI:0.883,0.895), breast class AUC of 0.873 (95%CI:0.860,0.886), melanoma class AUC of 0.852 (95%CI:0.842,0.862), renal class AUC of 0.830 (95%CI:0.809,0.851), and other class AUC of 0.822 (95%CI:0.805,0.839). These data establish that whole-brain imaging features are discriminative to allow accurate diagnosis of the primary organ site of malignancy. Our end-to-end deep radiomic approach has great potential for classifying metastatic tumor types from whole-brain MRI images. Further refinement may offer an invaluable clinical tool to expedite primary cancer site identification for precision treatment and improved outcomes.
Keywords	Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition ; Physics - Medical Physics
Subject code	610
Publishing date	2021-10-07
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mitochondrial concept of leukemogenesis

Ismailov Bolat / Ismailov Sanzhar B / Lyu Boris N / Lyu Marina B

Theoretical Biology and Medical Modelling, Vol 5, Iss 1, p

key role of oxygen-peroxide effects

2008 Volume 23

Abstract: Abstract Background and hypothesis The high sensitivity of hematopoietic cells, especially stem cells, to radiation and to pro-oxidative and other leukemogenic agents is related to certain of their morphological and metabolic features. It is attributable ...

Abstract	Abstract Background and hypothesis The high sensitivity of hematopoietic cells, especially stem cells, to radiation and to pro-oxidative and other leukemogenic agents is related to certain of their morphological and metabolic features. It is attributable to the low (minimal) number of active mitochondria and the consequently slow utilization of O 2 entering the cell. This results in an increased intracellular partial pressure of O 2 (pO 2 ) and increased levels of reactive oxygen (ROS) and nitrogen (RNS) species, and a Δ(PO – AO) imbalance between the pro-oxidative (PO) and antioxidative (AO) constituents. Proposed mechanism Because excessive O 2 is toxic, we suggest that hematopoietic cells exist in a kind of unstable dynamic balance. This suggestion is based on the idea that mitochondria not only consume O 2 in the process of ATP production but also constitute the main anti-oxygenic stage in the cell's protective antioxidative system. Variations in the mitochondrial base capacity (quantity and quality of mitochondria) constitute an important and highly efficient channel for regulating the oxidative stress level within a cell. The primary target for leukemogenic agents is the few mitochondria within the hematopoietic stem cell. Disturbance and weakening of their respiratory function further enhances the initial pro-oxidative state of the cell. This readily results in peroxygenation stress, creating the necessary condition for inducing leukemogenesis. We propose that this is the main cause of all related genetic and other disorders in the cell. ROS, RNS and peroxides act as signal molecules affecting redox-sensitive transcription factors, enzymes, oncogenes and other effectors. Thereby, they influence the expression and suppression of many genes, as well as the course and direction of proliferation, differentiation, leukemogenesis and apoptosis. Differentiation of leukemic cells is blocked at the precursor stage. While the transformation of non-hematopoietic cells into tumor cells starts during proliferation, hematopoietic cells become leukemic at one of the interim stages in differentiation, and differentiation does not continue beyond that point. Proliferation is switched to differentiation and back according to a trigger principle, again involving ROS and RNS. When the leukemogenic Δ L (PO – AO) imbalance decreases in an under-differentiated leukemia cell to the differentiation level Δ D (PO – AO), the cell may continue to differentiate to the terminal stage. Conclusion The argument described in this article is used to explain the causes of congenital and children's leukemia, and the induction of leukemia by certain agents (vitamin K3, benzene, etc.). Specific research is required to validate the proposals made in this article. This will require accurate and accessible methods for measuring and assessing oxidative stress in different types of cells in general, and in hematopoietic cells in particular, in their different functional states.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2008-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes.

Zaitsev, Aleksandr / Chelushkin, Maksim / Dyikanov, Daniiar / Cheremushkin, Ilya / Shpak, Boris / Nomie, Krystle / Zyrin, Vladimir / Nuzhdina, Ekaterina / Lozinsky, Yaroslav / Zotova, Anastasia / Degryse, Sandrine / Kotlov, Nikita / Baisangurov, Artur / Shatsky, Vladimir / Afenteva, Daria / Kuznetsov, Alexander / Paul, Susan Raju / Davies, Diane L / Reeves, Patrick M /

Lanuti, Michael / Goldberg, Michael F / Tazearslan, Cagdas / Chasse, Madison / Wang, Iris / Abdou, Mary / Aslanian, Sharon M / Andrewes, Samuel / Hsieh, James J / Ramachandran, Akshaya / Lyu, Yang / Galkin, Ilia / Svekolkin, Viktor / Cerchietti, Leandro / Poznansky, Mark C / Ataullakhanov, Ravshan / Fowler, Nathan / Bagaev, Alexander

Cancer cell

2022 Volume 40, Issue 8, Page(s) 879–894.e16

Abstract: Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. We present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of >9,400 tissue and blood ... ...

Abstract	Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. We present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of >9,400 tissue and blood sorted cell RNA profiles incorporated into millions of artificial transcriptomes to accurately reconstruct the tumor microenvironment (TME). Bioinformatics correction for technical and biological variability, aberrant cancer cell expression inclusion, and accurate quantification and normalization of transcript expression increased Kassandra stability and robustness. Performance was validated on 4,000 H&E slides and 1,000 tissues by comparison with cytometric, immunohistochemical, or single-cell RNA-seq measurements. Kassandra accurately deconvolved TME elements, showing the role of these populations in tumor pathogenesis and other biological processes. Digital TME reconstruction revealed that the presence of PD-1-positive CD8
MeSH term(s)	Algorithms ; CD8-Positive T-Lymphocytes ; Humans ; Machine Learning ; Neoplasms/genetics ; RNA-Seq ; Sequence Analysis, RNA ; Transcriptome ; Tumor Microenvironment/genetics
Language	English
Publishing date	2022-07-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078448-X
ISSN	1878-3686 ; 1535-6108
ISSN (online)	1878-3686
ISSN	1535-6108
DOI	10.1016/j.ccell.2022.07.006
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Zs.MG 104: Show issues

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Article: Preservation of Tilapia (Oreochromis aureus) Fillet by Isochoric (Constant Volume) Freezing

Bilbao-Sainz, Cristina / Sinrod, Amanda J. G / Williams, Tina / Wood, Delilah / Chiou, Bor-Sen / Bridges, David F / Wu, Vivian C. H / Lyu, Chenang / Rubinsky, Boris / McHugh, Tara

Journal of aquatic food product technology. 2020 Aug. 08, v. 29, no. 7

2020

Abstract: ... frozen samples, respectively. Total volatile basic nitrogen (TVB-N) content was 1.4 times higher ... for isochoric samples than for fresh samples. For chilled, super-chilled, and frozen samples, TVB-N content was ...

Abstract	The aim of this work was to evaluate the effects of isochoric freezing on the quality of tilapia fillet. Isochoric freezing was compared to chilling, super-chilling, and freezing. Isochoric freezing showed muscle color alterations similar to the other preservation methods. All preservation methods resulted in softer fillets, with the isochoric frozen fillet having the most similar texture to that of the fresh sample. Thiobarbituric acid reactive substances (TBARS) for isochoric samples were similar to those of fresh samples. However, there was a 53%, 55%, and 34% increase in TBARS for chilled, super-chilled, and frozen samples, respectively. Total volatile basic nitrogen (TVB-N) content was 1.4 times higher for isochoric samples than for fresh samples. For chilled, super-chilled, and frozen samples, TVB-N content was 3.0, 1.9, and 1.3, respectively, times higher than for fresh samples. Microstructural analysis indicated that isochoric samples showed less cell damage compared to those using other methods. Subfreezing temperatures in conjunction with no ice formation during isochoric freezing contributed to improved quality of tilapia fillet. This study may find application in the commercial preservation of fish to increase shelf life and allow for expanded distribution of raw fish. This study might also be a potential solution to “food desert” areas, where residents have low access to fresh healthy foods.
Keywords	Oreochromis aureus ; color ; fish ; ice ; muscles ; raw fish ; shelf life ; supercooling ; texture ; total volatile basic nitrogen
Language	English
Dates of publication	2020-0808
Size	p. 629-640.
Publishing place	Taylor & Francis
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1150134-0
ISSN	1547-0636 ; 1049-8850
ISSN (online)	1547-0636
ISSN	1049-8850
DOI	10.1080/10498850.2020.1785602
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A transformer-based deep-learning approach for classifying brain metastases into primary organ sites using clinical whole-brain MRI images.

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Article ; Online: Mitochondrial concept of leukemogenesis: key role of oxygen-peroxide effects.

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Article ; Online: USC-087 protects Syrian hamsters against lethal challenge with human species C adenoviruses.

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Book ; Online: A transformer-based deep learning approach for classifying brain metastases into primary organ sites using clinical whole brain MRI

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Article ; Online: Mitochondrial concept of leukemogenesis

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Article ; Online: Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes.

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Article: Preservation of Tilapia (Oreochromis aureus) Fillet by Isochoric (Constant Volume) Freezing

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In stock of ZB MED Bonn / Germany

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