738 results on '"Martin L. Yarmush,"'
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2. Partial freezing of rat livers extends preservation time by 5-fold
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Shannon N. Tessier, Reinier J. de Vries, Casie A. Pendexter, Stephanie E. J. Cronin, Sinan Ozer, Ehab O. A. Hafiz, Siavash Raigani, Joao Paulo Oliveira-Costa, Benjamin T. Wilks, Manuela Lopera Higuita, Thomas M. van Gulik, Osman Berk Usta, Shannon L. Stott, Heidi Yeh, Martin L. Yarmush, Korkut Uygun, and Mehmet Toner
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Science - Abstract
The limited preservation duration of donor organs is a big problem. Here the authors report a method for the freezing of whole rat livers at temperatures between −10 °C to −15 °C for up to 5 days, based on freeze-tolerant wood frogs, and term this partial freezing.
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- 2022
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3. Deep learning robotic guidance for autonomous vascular access.
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Alvin I. Chen, Max L. Balter, Timothy J. Maguire, and Martin L. Yarmush
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- 2020
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4. Supramolecular hybrid hydrogels as rapidly on-demand dissoluble, self-healing, and biocompatible burn dressings
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A. Aslihan Gokaltun, Letao Fan, Luca Mazzaferro, Delaney Byrne, Martin L. Yarmush, Tianhong Dai, Ayse Asatekin, and O. Berk Usta
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Biomaterials ,Biomedical Engineering ,Article ,Biotechnology - Abstract
Despite decades of efforts, state-of-the-art synthetic burn dressings to treat partial-thickness burns are still far from ideal. Current dressings adhere to the wound and necessitate debridement. This work describes the first “supramolecular hybrid hydrogel (SHH)” burn dressing that is biocompatible, self-healable, and on-demand dissoluble for easy and trauma-free removal, prepared by a simple, fast, and scalable method. These SHHs leverage the interactions of a custom-designed cationic copolymer via host-guest chemistry with cucurbit[7]uril and electrostatic interactions with clay nanosheets coated with an anionic polymer to achieve enhanced mechanical properties and fast on-demand dissolution. The SHHs show high mechanical strength (>50 kPa), self-heal rapidly in ∼1 min, and dissolve quickly (4–6 min) using an amantadine hydrochloride (AH) solution that breaks the supramolecular interactions in the SHHs. Neither the SHHs nor the AH solution has any adverse effects on human dermal fibroblasts or epidermal keratinocytes in vitro. The SHHs also do not elicit any significant cytokine response in vitro. Furthermore, in vivo murine experiments show no immune or inflammatory cell infiltration in the subcutaneous tissue and no change in circulatory cytokines compared to sham controls. Thus, these SHHs present excellent burn dressing candidates to reduce the time of pain and time associated with dressing changes.
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- 2023
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5. Multifunctional Elastin-Like Polypeptide Fusion Protein Coacervates Inhibit Receptor-Mediated Proinflammatory Signals and Promote Angiogenesis in Mouse Diabetic Wounds
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Hwan June Kang, Henry C. Hsia, Biraja C. Dash, Francois Berthiaume, Martin L. Yarmush, and Suneel Kumar
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Tube formation ,integumentary system ,biology ,business.industry ,Angiogenesis ,Pharmacology ,Critical Care and Intensive Care Medicine ,Fusion protein ,RAGE (receptor) ,Glycation ,Emergency Medicine ,biology.protein ,Medicine ,business ,Receptor ,Wound healing ,Elastin - Abstract
Objective Chronic skin wounds are one of the most devastating complications in diabetic patients due to the formation of advanced glycation end products (AGEs) resulting from non-enzymatic glycation of proteins and lipids in hyperglycemia. AGEs, upon binding their receptors (RAGEs), trigger pro-inflammatory signals that impair wound healing in diabetes and contribute to the pathology of chronic skin wounds. Approach We previously developed a recombinant fusion protein containing the binding domain of RAGE (vRAGE) linked to elastin-like polypeptides (ELPs) that acts as a competitive inhibitor of AGEs, and another ELP fusion protein containing stromal cell-derived factor 1 (SDF1) that promotes revascularization. Herein, we report the effects of protein coacervates incorporating both vRAGE-ELP and SDF1-ELP on wound healing in an in vitro diabetes-mimicking cell culture system, and in in vivo in full-thickness wounds on diabetic mice. Results The combination of vRAGE-ELP and SDF1-ELP increased cell metabolic activity in AGE-stimulated endothelial cells, promoted in vitro tube formation and accelerated healing in an in vitro cell migration assay. When used in a single topical application on full-thickness excisional skin wounds in diabetic mice, wound closure in the combination groups reached almost 100% on post-wounding day 35, compared to 62% and 85% on the same days in animals treated with fibrin gel control and vehicle control consisting of ELP alone. Innovation To our knowledge, this is the first study that attempts to reverse the AGE-RAGE-mediated signaling as well as to promote cell proliferation and vascularization in one single treatment. Conclusion The co-delivery of vRAGE-ELP and SDF1-ELP has potential for the treatment of diabetic wounds.
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- 2023
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6. Human-Origin iPSC-Based Recellularization of Decellularized Whole Rat Livers
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Aylin Acun, Ruben Oganesyan, Maria Jaramillo, Martin L. Yarmush, and Basak E. Uygun
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decellularization ,liver bioengineering ,iPSCs ,recellularization ,Technology ,Biology (General) ,QH301-705.5 - Abstract
End-stage liver diseases lead to mortality of millions of patients, as the only treatment available is liver transplantation and donor scarcity means that patients have to wait long periods before receiving a new liver. In order to minimize donor organ scarcity, a promising bioengineering approach is to decellularize livers that do not qualify for transplantation. Through decellularization, these organs can be used as scaffolds for developing new functional organs. In this process, the original cells of the organ are removed and ideally should be replaced by patient-specific cells to eliminate the risk of immune rejection. Induced pluripotent stem cells (iPSCs) are ideal candidates for developing patient-specific organs, yet the maturity and functionality of iPSC-derived cells do not match those of primary cells. In this study, we introduced iPSCs into decellularized rat liver scaffolds prior to the start of differentiation into hepatic lineages to maximize the exposure of iPSCs to native liver matrices. Through exposure to the unique composition and native 3D organization of the liver microenvironment, as well as the more efficient perfusion culture throughout the differentiation process, iPSC differentiation into hepatocyte-like cells was enhanced. The resulting cells showed significantly higher expression of mature hepatocyte markers, including important CYP450 enzymes, along with lower expression of fetal markers, such as AFP. Importantly, the gene expression profile throughout the different stages of differentiation was more similar to native development. Our study shows that the native 3D liver microenvironment has a pivotal role to play in the development of human-origin hepatocyte-like cells with more mature characteristics.
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- 2022
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7. A comparison of hepato-cellular in vitro platforms to study CYP3A4 induction.
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Beyza Bulutoglu, Camilo Rey-Bedón, Safak Mert, Lipeng Tian, Yoon-Young Jang, Martin L Yarmush, and O Berk Usta
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Medicine ,Science - Abstract
In vitro studies of drug toxicity and drug-drug interactions are crucial for drug development efforts. Currently, the utilization of primary human hepatocytes (PHHs) is the de facto standard for this purpose, due to their functional xenobiotic response and drug metabolizing CYP450 enzyme metabolism. However, PHHs are scarce, expensive, require laborious maintenance, and exhibit lot-to-lot heterogeneity. Alternative human in vitro platforms include hepatic cell lines, which are easy to access and maintain, and induced pluripotent stem cell (iPSC) derived hepatocytes. In this study, we provide a direct comparison of drug induced CYP3A4 and PXR expression levels of PHHs, hepatic cell lines Huh7 and HepG2, and iPSC derived hepatocyte like cells. Confluently cultured Huh7s exhibited an improved CYP3A4 expression and were inducible by up to 4.9-fold, and hepatocytes differentiated from human iPSCs displayed a 3.3-fold CYP3A4 induction. In addition, an increase in PXR expression levels was observed in both hepatic cell lines and iPSC derived hepatocytes upon rifampicin treatment, whereas a reproducible increase in PXR expression was not achieved in PHHs. Our results indicate that both hepatoma originated cell lines and iPSCs may provide alternative sources to primary hepatocytes, providing reliable and reproducible results for CYP3A4/PXR metabolism, upon in vitro maturation. This study may serve as a guide for the selection of suitable and feasible in vitro platforms for drug-drug interaction and toxicology studies.
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- 2020
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8. Long-term deep-supercooling of large-volume water and red cell suspensions via surface sealing with immiscible liquids
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Haishui Huang, Martin L. Yarmush, and O. Berk Usta
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Science - Abstract
Supercooled water is susceptible to spontaneous freezing, and preventing this process is a challenge. Here, the authors use surface sealing with immiscible liquids to eliminate primary ice nucleation at the water/air interface, enabling deep supercooling of large volumes of water and red cell suspensions for long time periods.
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- 2018
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9. Hepatic connexin 32 associates with nonalcoholic fatty liver disease severity
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Jay Luther, Manish K. Gala, Nynke Borren, Ricard Masia, Russell P. Goodman, Ida Hatoum Moeller, Erik DiGiacomo, Alyssa Ehrlich, Andrew Warren, Martin L. Yarmush, Ashwin Ananthakrishnan, Kathleen Corey, Lee M. Kaplan, Sangeeta Bhatia, Raymond T. Chung, and Suraj J. Patel
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Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Emerging data highlight the critical role for the innate immune system in the progression of nonalcoholic fatty liver disease (NAFLD). Connexin 32 (Cx32), the primary liver gap junction protein, is capable of modulating hepatic innate immune responses and has been studied in dietary animal models of steatohepatitis. In this work, we sought to determine the association of hepatic Cx32 with the stages of human NAFLD in a histologically characterized cohort of 362 patients with NAFLD. We also studied the hepatic expression of the genes and proteins known to interact with Cx32 (known as the connexome) in patients with NAFLD. Last, we used three independent dietary mouse models of nonalcoholic steatohepatitis to investigate the role of Cx32 in the development of steatohepatitis and fibrosis. In a univariate analysis, we found that Cx32 hepatic expression associates with each component of the NAFLD activity score and fibrosis severity. Multivariate analysis revealed that Cx32 expression most closely associated with the NAFLD activity score and fibrosis compared to known risk factors for the disease. Furthermore, by analyzing the connexome, we identified novel genes related to Cx32 that associate with NAFLD progression. Finally, we demonstrated that Cx32 deficiency protects against liver injury, inflammation, and fibrosis in three murine models of nonalcoholic steatohepatitis by limiting initial diet‐induced hepatoxicity and subsequent increases in intestinal permeability. Conclusion: Hepatic expression of Cx32 strongly associates with steatohepatitis and fibrosis in patients with NAFLD. We also identify novel genes associated with NAFLD and suggest that Cx32 plays a role in promoting NAFLD development. (Hepatology Communications 2018;2:786‐797)
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- 2018
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10. Gut Microbiota-Derived Tryptophan Metabolites Modulate Inflammatory Response in Hepatocytes and Macrophages
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Smitha Krishnan, Yufang Ding, Nima Saedi, Maria Choi, Gautham V. Sridharan, David H. Sherr, Martin L. Yarmush, Robert C. Alaniz, Arul Jayaraman, and Kyongbum Lee
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Biology (General) ,QH301-705.5 - Abstract
Summary: The gut microbiota plays a significant role in the progression of fatty liver disease; however, the mediators and their mechanisms remain to be elucidated. Comparing metabolite profile differences between germ-free and conventionally raised mice against differences between mice fed a low- and high-fat diet (HFD), we identified tryptamine and indole-3-acetate (I3A) as metabolites that depend on the microbiota and are depleted under a HFD. Both metabolites reduced fatty-acid- and LPS-stimulated production of pro-inflammatory cytokines in macrophages and inhibited the migration of cells toward a chemokine, with I3A exhibiting greater potency. In hepatocytes, I3A attenuated inflammatory responses under lipid loading and reduced the expression of fatty acid synthase and sterol regulatory element-binding protein-1c. These effects were abrogated in the presence of an aryl-hydrocarbon receptor (AhR) antagonist, indicating that the effects are AhR dependent. Our results suggest that gut microbiota could influence inflammatory responses in the liver through metabolites engaging host receptors. : Dysbiosis of the intestinal microbiota is an emerging factor contributing to the progression of fatty liver disease. Krishnan et al. utilize metabolomics and biochemical assays in conjunction with animal and cell culture models to identify microbiota-dependent metabolites that engage a host receptor to affect liver inflammatory responses under lipid loading. Keywords: nonalcoholic fatty liver disease, gut microbiota, metabolomics, indole-3-acetate, inflammation, aryl hydrocarbon receptor
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- 2018
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11. System design and development of a robotic device for automated venipuncture and diagnostic blood cell analysis.
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Max L. Balter, Alvin I. Chen, Alex Fromholtz, Alex Gorshkov, Tim J. Maguire, and Martin L. Yarmush
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- 2016
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12. 3D Near Infrared and Ultrasound Imaging of Peripheral Blood Vessels for Real-Time Localization and Needle Guidance.
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Alvin I. Chen, Max L. Balter, Timothy J. Maguire, and Martin L. Yarmush
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- 2016
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13. Adaptive Kinematic Control of a Robotic Venipuncture Device Based on Stereo Vision, Ultrasound, and Force Guidance.
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Max L. Balter, Alvin I. Chen, Timothy J. Maguire, and Martin L. Yarmush
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- 2017
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14. Real-time needle steering in response to rolling vein deformation by a 9-DOF image-guided autonomous venipuncture robot.
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Alvin I. Chen, Max L. Balter, Timothy J. Maguire, and Martin L. Yarmush
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- 2015
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15. Alterations in Cytoskeleton and Mitochondria in the Development and Reversal of Steatosis in Human Hepatocytes
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Letao Fan, Aslihan Gokaltun, Sarah Maggipinto, Yoshinori Kitagawa, Jeevendra Martyn, Heidi Yeh, Basak E. Uygun, Martin L. Yarmush, and O. Berk Usta
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Hepatology ,Gastroenterology - Published
- 2023
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16. Efficient Procedure and Methods to Determine Critical Electroporation Parameters.
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Gaddi Blumrosen, Alireza Abazari, Alexander Golberg, Mehmet Tonner, and Martin L. Yarmush
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- 2014
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17. Data from Amphipathic Peptide-Based Fusion Peptides and Immunoconjugates for the Targeted Ablation of Prostate Cancer Cells
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Martin L. Yarmush, Zaki Megeed, Suraj J. Patel, and Kaushal Rege
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We describe the design, generation, and in vitro evaluation of targeted amphipathic fusion peptides and immunoconjugates for the ablation of prostate cancer cells. The overexpression of the prostate-specific membrane antigen (PSMA) was exploited as means to specifically deliver cytotoxic peptides to prostate cancer cells. Cationic amphipathic lytic peptides were chosen as cytotoxic agents due to their ability to depolarize mitochondrial membranes and induce apoptosis. Specific delivery of the lytic peptide was facilitated by PSMA-targeting peptides and antibodies. Our results indicate that although the use of PSMA-targeted peptides only modestly enhanced the cytotoxic activity of the lytic peptide, peptide-antibody conjugates were two orders of magnitude more potent than untargeted peptide. In addition to quantifying the cytotoxic activities of the individual constructs, we also investigated the mechanisms of cell death induced by the fusion peptides and immunoconjugates. Although fusion peptides induced oncotic/necrotic death in cells, treatment with immunoconjugates resulted in apoptotic death. In summary, immunoconjugates based on lytic peptides are a promising class of therapeutics for prostate cancer therapy and warrant further investigation. [Cancer Res 2007;67(13):6368–75]
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- 2023
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18. Supplementary Figures 1-2 from Amphipathic Peptide-Based Fusion Peptides and Immunoconjugates for the Targeted Ablation of Prostate Cancer Cells
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Martin L. Yarmush, Zaki Megeed, Suraj J. Patel, and Kaushal Rege
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Supplementary Figures 1-2 from Amphipathic Peptide-Based Fusion Peptides and Immunoconjugates for the Targeted Ablation of Prostate Cancer Cells
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- 2023
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19. The System Design and Evaluation of a 7-DOF Image-Guided Venipuncture Robot.
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Max L. Balter, Alvin I. Chen, Timothy Maguire, and Martin L. Yarmush
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- 2015
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20. FOXA1/2 depletion drives global reprogramming of differentiation state and metabolism in a human liver cell line and inhibits differentiation of human stem cell-derived hepatic progenitor cells
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Iyan Warren, Michael M. Moeller, Daniel Guiggey, Alexander Chiang, Mitchell Maloy, Ogechi Ogoke, Theodore Groth, Tala Mon, Saber Meamardoost, Xiaojun Liu, Sarah Thompson, Antoni Szeglowski, Ryan Thompson, Peter Chen, Ramasamy Paulmurugan, Martin L. Yarmush, Srivatsan Kidambi, and Natesh Parashurama
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Homeobox protein NANOG ,Mesoderm ,Organogenesis ,Germ layer ,Biology ,Biochemistry ,Cell biology ,medicine.anatomical_structure ,Downregulation and upregulation ,embryonic structures ,medicine ,Genetics ,FOXA2 ,Stem cell ,Endoderm ,Molecular Biology ,Biotechnology - Abstract
FOXA factors are critical members of the developmental gene regulatory network (GRN) composed of master transcription factors (TF) which regulate murine cell fate and metabolism in the gut and liver. How FOXA dictates human liver cell fate, differentiation, and simultaneously regulate metabolic pathways is poorly understood. Here, we aimed to determine the role of FOXA2 (and FOXA1 which is believed to compensate for FOXA2) in hepatic differentiation and cell metabolism in a human hepatic cell line (HepG2). siRNA targeting of FOXA1 and FOXA2 in human hepatic (HepG2) cells and during hepatic differentiation significantly downregulated albumin (p < 0.05) and GRN TF gene expression (HNF4A, HEX, HNF1B, TBX3) (p < 0.05) and significantly upregulated endoderm/gut/hepatic endoderm markers (goosecoid (GSC), FOXA3, and GATA4), gut TF (CDX2), pluripotent TF (NANOG), and neuroectodermal TF (PAX6) (p < 0.05), all consistent with a partial/transient cell reprogramming. shFOXA1/2 targeting resulted in similar findings and demonstrated evidence of reversibility. RNA-seq followed by bioinformatic analysis of shFOXA1/2 knockdown HepG2 cells demonstrated 235 significant downregulated genes and 448 upregulated genes, including upregulation of markers for alternate germ layers lineages (cardiac, endothelial, muscle) and neurectoderm (eye, neural). We found widespread downregulation of glycolysis, citric acid cycle, mitochondrial genes, and alterations in lipid metabolism, pentose phosphate pathway, and ketogenesis. Functional metabolic analysis agreed with these findings, demonstrating significantly diminished glycolysis and mitochondrial respiration, and accumulation of lipid droplets. We hypothesized that FOXA1/2 inhibit the initiation of human liver differentiation in vitro. During hPSC-hepatic differentiation, siRNA knockdown demonstrated de-differentiation and unexpectedly, activation of pluripotency factors and neuroectoderm. shRNA knockdown demonstrated similar results and activation of SOX9 (hepatobiliary). These results demonstrate complex effects of FOXA1/2 on hepatic GRN effecting de-differentiation and metabolism with applications in studies of cancer, differentiation, and organogenesis.
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- 2022
21. Design and modeling of a protein based nanoGripper.
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Gaurav Sharma 0003, Kaushal Rege, David Budil, Martin L. Yarmush, and Constantinos Mavroidis
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- 2008
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22. Dynamics and Kinematics of Viral Protein Linear Nano-actuators for Bio-nano Robotic Systems.
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Atul Dubey, Gaurav Sharma 0003, Constantinos Mavroidis, Silvina-Maria Tomassone, K. Nikitczuk, and Martin L. Yarmush
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- 2004
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23. Nonthermal Irreversible Electroporation: Fundamentals, Applications, and Challenges.
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Alexander Golberg and Martin L. Yarmush
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- 2013
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24. Combinatorial Use of Therapeutic ELP-Based Micelle Particles in Tissue Engineering
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Beyza Bulutoglu, Aylin Acun, Sarah L. Deng, Safak Mert, Elise Lupon, Alexandre G. Lellouch, Curtis L. Cetrulo, Basak E. Uygun, and Martin L. Yarmush
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Biomaterials ,Mice ,Wound Healing ,Tissue Engineering ,Biomedical Engineering ,Pharmaceutical Science ,Animals ,Nanoparticles ,Article ,Micelles ,Diabetes Mellitus, Experimental ,Elastin - Abstract
Elastin-like peptides (ELPs) are a versatile platform for tissue engineering and drug delivery. In this study, micelle forming ELP chains are genetically fused to three therapeutic molecules, keratinocyte growth factor (KGF), stromal cell-derived growth factor 1 (SDF1), and cathelicidin (LL37), to be used in wound healing. Chronic wounds represent a growing problem worldwide. A combinatorial therapy approach targeting different aspects of wound healing would be beneficial, providing a controlled and sustained release of active molecules, while simultaneously protecting these therapeutics from the surrounding harsh wound environment. The results of this study demonstrate that the conjugation of the growth factors KGF and SDF1, and the antimicrobial peptide LL37 to ELPs does not affect the micelle structure and that all three therapeutic moieties retain their bioactivity in vitro. Importantly, when the combination of these micelle ELP nanoparticles are applied to wounds in diabetic mice, over 90% wound closure is observed, which is significantly higher than when the therapeutics are applied in their naked forms. The application of the nanoparticles designed in this study is the first report of targeting different aspect of wound healing synergistically.
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- 2022
25. An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells.
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Ipsita Banerjee, Spandan Maiti, Natesh Parashurama, and Martin L. Yarmush
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- 2010
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26. Computational Studies of a Protein-based Nanoactuator for Nanogripping Applications.
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Gaurav Sharma 0003, Constantinos Mavroidis, Kaushal Rege, Martin L. Yarmush, and David Budil
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- 2009
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27. Rat liver regeneration following ablation with irreversible electroporation
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Alexander Golberg, Bote G. Bruinsma, Maria Jaramillo, Martin L. Yarmush, and Basak E. Uygun
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Liver regeneration ,Irreversible electroporation ,Liver ablation ,Pulsed electric fields ,Scarless regeneration ,Progenitor cells ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
During the past decade, irreversible electroporation (IRE) ablation has emerged as a promising tool for the treatment of multiple diseases including hepatic cancer. However, the mechanisms behind the tissue regeneration following IRE ablation have not been investigated. Our results indicate that IRE treatment immediately kills the cells at the treatment site preserving the extracellular architecture, in effect causing in vivo decellularization. Over the course of 4 weeks, progenitor cell differentiation, through YAP and notch pathways, together with hepatocyte expansion led to almost complete regeneration of the ablated liver leading to the formation of hepatocyte like cells at the ablated zone. We did not observe significant scarring or tumor formation at the regenerated areas 6 months post IRE. Our study suggests a new model to study the regeneration of liver when the naïve extracellular matrix is decellularized in vivo with completely preserved extracellular architecture.
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- 2016
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28. Development of liver microtissues with functional biliary ductular network
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Basak E. Uygun, Hoda Abu-Taleb, Martin L. Yarmush, Ali El-Hindawi, Yibin Chen, Ehab O A Hafiz, Somia A. M. Soliman, Beyza Bulutoglu, and Soheir S. Mansy
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Biliary drainage ,Stromal cell ,Tissue Engineering ,Tight junction ,Chemistry ,Spheroid ,Bioengineering ,Bone canaliculus ,digestive system ,Applied Microbiology and Biotechnology ,Article ,Rats ,Cell biology ,medicine.anatomical_structure ,Liver ,Spheroids, Cellular ,Liver tissue ,Hepatocytes ,Duodenum ,medicine ,Animals ,Lobules of liver ,Bile Ducts ,Cells, Cultured ,Biotechnology - Abstract
Liver tissue engineering aims to create transplantable liver grafts that can serve as substitutes for donor's livers. One major challenge in creating a fully functional liver tissue has been to recreate the biliary drainage in an engineered liver construct through integration of bile canaliculi (BC) with the biliary ductular network that would enable the clearance of bile from the hepatocytes to the host duodenum. In this study, we show the formation of such a hepatic microtissue by coculturing rat primary hepatocytes with cholangiocytes and stromal cells. Our results indicate that within the spheroids, hepatocytes maintained viability and function for up to 7 days. Viable hepatocytes became polarized by forming BC with the presence of tight junctions. Morphologically, hepatocytes formed the core of the spheroids, while cholangiocytes resided at the periphery forming a monolayer microcysts and tubular structures extending outward. The spheroids were subsequently cultured in clusters to create a higher order ductular network resembling hepatic lobule. The cholangiocytes formed functional biliary ductular channels in between hepatic spheroids that were able to collect, transport, and secrete bile. Our results constitute the first step to recreate hepatic building blocks with biliary drainage for repopulating the whole liver scaffolds to be used as transplantable liver grafts.
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- 2020
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29. Differential Cell Death and Regrowth of Dermal Fibroblasts and Keratinocytes After Application of Pulsed Electric Fields
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Martin L. Yarmush, Francois Berthiaume, Alexander Golberg, Anil B. Shrirao, Rene S. Schloss, and Bodhisatwa Das
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Transplantation ,Programmed cell death ,Pathology ,medicine.medical_specialty ,Debridement ,business.industry ,medicine.medical_treatment ,Biomedical Engineering ,Medicine (miscellaneous) ,respiratory system ,respiratory tract diseases ,immune system diseases ,Electric field ,Medicine ,Electrical and Electronic Engineering ,Wound healing ,business ,Original Research ,circulatory and respiratory physiology - Abstract
Background: High-powered pulsed electric fields (PEF) may be used for tissue debridement and disinfection, while lower PEF intensities may stimulate beneficial cellular responses for wound healing. We investigated the dual effects of nonuniform PEF on cellular death and stimulation. Methods: Dermal fibroblast or keratinocyte monolayers were exposed to PEF induced by two needle electrodes (2 mm apart). Voltages (100–600 V; 1 Hz; 70 micros pulse width; 90 pulses/cycle) were applied between the two electrodes. Controls consisted of similar monolayers subjected to a scratch mechanical injury. Results: Cell growth and closure of the cell-free gap was faster in PEF-treated cell monolayers versus scratched ones. Media conditioned from cells pre-exposed to PEF, when applied to responder cells, stimulated greater proliferation than media from scratched monolayers. Conclusions: PEF treatment causes the release of soluble factors that promote cell growth, and thus may play a role in the accelerated healing of wounds post PEF.
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- 2020
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30. Anti‐inflammatory effects of haptoglobin on <scp>LPS</scp> ‐stimulated macrophages: Role of <scp>HMGB1</scp> signaling and implications in chronic wound healing
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Rene S. Schloss, Yixin Meng, Andre F. Palmer, Kishan Patel, Ivan S. Pires, Martin L. Yarmush, Suneel Kumar, Maurice D. O'Reggio, Hwan June Kang, Francois Berthiaume, and Paulina Krzyszczyk
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Lipopolysaccharides ,Chronic wound ,Lipopolysaccharide ,medicine.drug_class ,Antigens, Differentiation, Myelomonocytic ,Mice, Obese ,Receptors, Cell Surface ,Inflammation ,Dermatology ,Pharmacology ,HMGB1 ,Anti-inflammatory ,Hemoglobins ,Mice ,030207 dermatology & venereal diseases ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Antigens, CD ,In vivo ,Diabetes Mellitus ,Animals ,Humans ,Medicine ,Macrophage ,HMGB1 Protein ,Wound Healing ,Haptoglobins ,biology ,business.industry ,Macrophages ,Haptoglobin ,chemistry ,biology.protein ,Surgery ,medicine.symptom ,business ,Heme Oxygenase-1 ,Signal Transduction - Abstract
Nonhealing wounds possess elevated numbers of pro-inflammatory M1 macrophages, which fail to transition to anti-inflammatory M2 phenotypes that promote healing. Hemoglobin (Hb) and haptoglobin (Hp) proteins, when complexed (Hb-Hp), can elicit M2-like macrophages through the heme oxygenase-1 (HO-1) pathway. Despite the fact that nonhealing wounds are chronically inflamed, previous studies have focused on non-inflammatory systems, and do not thoroughly compare the effects of complexed vs individual proteins. We aimed to investigate the effect of Hb/Hp treatments on macrophage phenotype in an inflammatory, lipopolysaccharide (LPS)-stimulated environment, similar to chronic wounds. Human M1 macrophages were cultured in vitro and stimulated with LPS. Concurrently, Hp, Hb, or Hb-Hp complexes were delivered. The next day, 27 proteins related to inflammation were measured in the supernatants. Hp treatment decreased a majority of inflammatory factors, Hb increased many, and Hb-Hp had intermediate trends, indicating that Hp attenuated overall inflammation to the greatest extent. From this data, Ingenuity Pathway Analysis software identified high motility group box 1 (HMGB1) as a key canonical pathway-strongly down-regulated from Hp, strongly up-regulated from Hb, and slightly activated from Hb-Hp. HMGB1 measurements in macrophage supernatants confirmed this trend. In vivo results in diabetic mice with biopsy punch wounds demonstrated accelerated wound closure with Hp treatment, and delayed wound closure with Hb treatment. This work specifically studied Hb/Hp effects on macrophages in a highly inflammatory environment relevant to chronic wound healing. Results show that Hp-and not Hb-Hp, which is known to be superior in noninflammatory conditions-reduces inflammation in LPS-stimulated macrophages, and HMGB1 signaling is also implicated. Overall, Hp treatment on M1 macrophages in vitro reduced the inflammatory secretion profile, and also exhibited benefits in in silico and in vivo wound-healing models.
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- 2020
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31. Deep learning robotic guidance for autonomous vascular access
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Max L. Balter, Alvin I. Chen, Tim Maguire, and Martin L. Yarmush
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0301 basic medicine ,Computer Networks and Communications ,Computer science ,business.industry ,Deep learning ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Vascular access ,Difficult Vascular Access ,Convolutional neural network ,Imaging phantom ,Human-Computer Interaction ,03 medical and health sciences ,Task (computing) ,030104 developmental biology ,0302 clinical medicine ,Artificial Intelligence ,Multimodal image ,Robot ,Computer vision ,Computer Vision and Pattern Recognition ,Artificial intelligence ,business ,030217 neurology & neurosurgery ,Software - Abstract
Medical robots have demonstrated the ability to manipulate percutaneous instruments into soft tissue anatomy while working beyond the limits of human perception and dexterity. Robotic technologies further offer the promise of autonomy in carrying out critical tasks with minimal supervision when resources are limited. Here, we present a portable robotic device capable of introducing needles and catheters into deformable tissues such as blood vessels to draw blood or deliver fluids autonomously. Robotic cannulation is driven by predictions from a series of deep convolutional neural networks that encode spatiotemporal information from multimodal image sequences to guide real-time servoing. We demonstrate, through imaging and robotic tracking studies in volunteers, the ability of the device to segment, classify, localize and track peripheral vessels in the presence of anatomical variability and motion. We then evaluate robotic performance in phantom and animal models of difficult vascular access and show that the device can improve success rates and procedure times compared to manual cannulations by trained operators, particularly in challenging physiological conditions. These results suggest the potential for autonomous systems to outperform humans on complex visuomotor tasks, and demonstrate a step in the translation of such capabilities into clinical use. Getting safe and fast access to blood vessels is vital to many methods of treatment and diagnosis in medicine. Robot-assisted or even fully autonomous methods can potentially do the task more reliably than humans, especially when veins are hard to detect. In this work, a method is tested that uses deep learning to find blood vessels and track the movement of a patient’s arm.
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- 2020
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32. Tissue scaffolds functionalized with therapeutic elastin‐like biopolymer particles
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Sarah L. Deng, Aylin Acun, Sarah S. Kelangi, Julie Devalliere, Beyza Bulutoglu, Basak E. Uygun, and Martin L. Yarmush
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Scaffold ,Fibroblast Growth Factor 7 ,Neovascularization, Physiologic ,Bioengineering ,Applied Microbiology and Biotechnology ,Article ,Mice ,chemistry.chemical_compound ,Biopolymers ,Tissue engineering ,In vivo ,Cell Line, Tumor ,medicine ,Animals ,Humans ,Cell Proliferation ,Tissue Engineering ,Tissue Scaffolds ,biology ,medicine.disease ,Elastin ,Cell biology ,Cellular infiltration ,chemistry ,Drug delivery ,biology.protein ,Collagen ,Keratinocyte growth factor ,Wound healing ,Biotechnology - Abstract
Tissue engineering scaffolds are intended to provide mechanical and biological support for cells to migrate, engraft and ultimately regenerate the tissue. Development of scaffolds with sustained delivery of growth factors and chemokines would enhance the therapeutic benefits, especially in wound healing. In this study, we incorporated our previously designed therapeutic particles, composed of fusion of elastin-like peptides (ELPs) as the drug delivery platform to keratinocyte growth factor (KGF), into a tissue scaffold, alloderm. The results demonstrated that sustained KGF-ELP release was achieved and the bioactivity of the released therapeutic particles was shown via cell proliferation assay, as well as a mouse pouch model in vivo, where higher cellular infiltration and vascularization were observed in scaffolds functionalized with KGF-ELPs.
- Published
- 2020
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33. Development of Metabolic Indicators of Burn Injury: Very Low Density Lipoprotein (VLDL) and Acetoacetate Are Highly Correlated to Severity of Burn Injury in Rats
- Author
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Maria-Louisa Izamis, Korkut Uygun, Nripen S. Sharma, Basak Uygun, Martin L. Yarmush, and Francois Berthiaume
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hypermetabolism ,metabonomics ,flux analysis ,cluster analysis ,regression ,variable selection ,burn injury ,Microbiology ,QR1-502 - Abstract
Hypermetabolism is a significant sequela to severe trauma such as burns, as well as critical illnesses such as cancer. It persists in parallel to, or beyond, the original pathology for many months as an often-fatal comorbidity. Currently, diagnosis is based solely on clinical observations of increased energy expenditure, severe muscle wasting and progressive organ dysfunction. In order to identify the minimum number of necessary variables, and to develop a rat model of burn injury-induced hypermetabolism, we utilized data mining approaches to identify the metabolic variables that strongly correlate to the severity of injury. A clustering-based algorithm was introduced into a regression model of the extent of burn injury. As a result, a neural network model which employs VLDL and acetoacetate levels was demonstrated to predict the extent of burn injury with 88% accuracy in the rat model. The physiological importance of the identified variables in the context of hypermetabolism, and necessary steps in extension of this preliminary model to a clinically utilizable index of severity of burn injury are outlined.
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- 2012
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34. Informative gene selection and design of regulatory networks using integer optimization.
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Eric Yang, Timothy Maguire, Martin L. Yarmush, and Ioannis P. Androulakis
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- 2008
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35. Identification of regulatory mechanisms of the hepatic response to thermal injury.
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Eric Yang, Timothy Maguire, Martin L. Yarmush, Francois Berthiaume, and Francois P. Androulakis
- Published
- 2008
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36. A novel non-overlapping bi-clustering algorithm for network generation using living cell array data.
- Author
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Eric Yang, Panagiota T. Foteinou, K. R. King, Martin L. Yarmush, and Ioannis P. Androulakis
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- 2007
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37. Layered patterning of hepatocytes in co-culture systems using microfabricated stencils
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Cheul H. Cho, Jaesung Park, Arno W. Tilles, François Berthiaume, Mehmet Toner, and Martin L. Yarmush
- Subjects
hepatocytes ,co-culture ,layered cell patterning ,cellular interactions ,fibroblasts ,Biology (General) ,QH301-705.5 - Abstract
Microfabrication and micropatterning techniques in tissue engineering offer great potential for creating and controlling microenvironments in which cell behavior can be observed. Here we present a novel approach to generate layered patterning of hepatocytes on micropatterned fibroblast feeder layers using microfabricated polydimethylsiloxane (PDMS) stencils. We fabricated PDMS stencils to pattern circular holes with diameters of 500 µm. Hepatocytes were co-cultured with 3T3-J2 fibroblasts in two types of patterns to evaluate and characterize the cellular interactions in the co-culture systems. Results of this study demonstrated uniform intracellular albumin staining and E-cadherin expression, increased liver-specific functions, and active glycogen synthesis in the hepatocytes when the heterotypic interface between hepatocytes and fibroblasts was increased by the layered patterning technique. This patterning technique can be a useful experimental tool for applications in basic science, drug screening, and tissue engineering, as well as in the design of bioartificial liver devices.
- Published
- 2010
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38. Reversible pH-controlled DNA-binding peptide nanotweezers: An in-silico study
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Gaurav Sharma, Kaushal Rege, David E Budil, Martin L Yarmush, and Constantinos Mavroidis
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Medicine (General) ,R5-920 - Abstract
Gaurav Sharma1, Kaushal Rege2,3, David E Budil4, Martin L Yarmush2,5, Constantinos Mavroidis11Department of Mechanical and Industrial Engineering; 4Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA; 2The Center for Engineering in Medicine (CEM), Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; 3Department of Chemical Engineering, Arizona State University, Tempe, AZ, USA; 5Department of Biomedical Engineering, Rutgers University, NJ, USAAbstract: We describe the molecular dynamics (MD)-aided engineering design of mutant peptides based on the α-helical coiled-coil GCN4 leucine zipper peptide (GCN4-p1) in order to obtain environmentally-responsive nanotweezers. The actuation mechanism of the nanotweezers depends on the modification of electrostatic charges on the residues along the length of the coiled coil. Modulating the solution pH between neutral and acidic values results in the reversible movement of helices toward and away from each other and creates a complete closed-open-closed transition cycle between the helices. Our results indicate that the mutants show a reversible opening of up to 15 Å (1.5 nm; approximately 150% of the initial separation) upon pH actuation. Investigation on the physicochemical phenomena that influence conformational properties, structural stability, and reversibility of the coiled-coil peptide-based nanotweezers revealed that a rationale- and design-based approach is needed to engineer stable peptide or macromolecules into stimuli-responsive devices. The efficacy of the mutant that demonstrated the most significant reversible actuation for environmentally responsive modulation of DNA-binding activity was also demonstrated. Our results have significant implications in bioseparations and in the engineering of novel transcription factors.Keywords: bionanotechnology, nanotweezers, coiled-coil, GCN4, leucine zipper, molecular dynamics, environmentally responsive peptides, transcription factor engineering
- Published
- 2008
39. Identification of optimal classification functions for biological sample and state discrimination from metabolic profiling data.
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Kyongbum Lee, Daehee Hwang, Tadaaki Yokoyama, George Stephanopoulos, Gregory Stephanopoulos, and Martin L. Yarmush
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- 2004
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40. Hepatic Injury in Nonalcoholic Steatohepatitis Contributes to Altered Intestinal PermeabilitySummary
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Jay Luther, John J. Garber, Hamed Khalili, Maneesh Dave, Shyam Sundhar Bale, Rohit Jindal, Daniel L. Motola, Sanjana Luther, Stefan Bohr, Soung Won Jeoung, Vikram Deshpande, Gurminder Singh, Jerrold R. Turner, Martin L. Yarmush, Raymond T. Chung, and Suraj J. Patel
- Subjects
Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Background & Aims: Emerging data suggest that changes in intestinal permeability and increased gut microbial translocation contribute to the inflammatory pathway involved in nonalcoholic steatohepatitis (NASH) development. Numerous studies have investigated the association between increased intestinal permeability and NASH. Our meta-analysis of this association investigates the underlying mechanism. Methods: A meta-analysis was performed to compare the rates of increased intestinal permeability in patients with NASH and healthy controls. To further address the underlying mechanism of action, we studied changes in intestinal permeability in a diet-induced (methionine-and-choline-deficient; MCD) murine model of NASH. In vitro studies were also performed to investigate the effect of MCD culture medium at the cellular level on hepatocytes, Kupffer cells, and intestinal epithelial cells. Results: Nonalcoholic fatty liver disease (NAFLD) patients, and in particular those with NASH, are more likely to have increased intestinal permeability compared with healthy controls. We correlate this clinical observation with in vivo data showing mice fed an MCD diet develop intestinal permeability changes after an initial phase of liver injury and tumor necrosis factor-α (TNFα) induction. In vitro studies reveal that MCD medium induces hepatic injury and TNFα production yet has no direct effect on intestinal epithelial cells. Although these data suggest a role for hepatic TNFα in altering intestinal permeability, we found that mice genetically resistant to TNFα-myosin light chain kinase (MLCK)âinduced intestinal permeability changes fed an MCD diet still develop increased permeability and liver injury. Conclusions: Our clinical and experimental results strengthen the association between intestinal permeability increases and NASH and also suggest that an early phase of hepatic injury and inflammation contributes to altered intestinal permeability in a fashion independent of TNFα and MLCK. Keywords: Meta-Analysis, Myosin Light Chain Kinase, Steatosis, Tight Junctions
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- 2015
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41. The Role of CHI3L1 (Chitinase-3-Like-1) in the Pathogenesis of Infections in Burns in a Mouse Model.
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Stefan Bohr, Suraj J Patel, Radovan Vasko, Keyue Shen, Alexander Golberg, Francois Berthiaume, and Martin L Yarmush
- Subjects
Medicine ,Science - Abstract
In severe burn injury the unique setting of a depleted, dysfunctional immune system along with a loss of barrier function commonly results in opportunistic infections that eventually proof fatal. Unfortunately, the dynamic sequence of bacterial contamination, colonization and eventually septic invasion with bacteria such as Pseudomonas species is still poorly understood although a limiting factor in clinical decision making. Increasing evidence supports the notion that inhibition of bacterial translocation into the wound site may be an effective alternative to prevent infection. In this context we investigated the role of the mammalian Chitinase-3-Like-1 (CHI3L1) non-enyzmatic protein predominately expressed on epithelial as well as innate immune cells as a potential bacterial-translocation-mediating factor. We show a strong trend that a modulation of chitinase expression is likely to be effective in reducing mortality rates in a mouse model of burn injury with superinfection with the opportunistic PA14 Pseudomonas strain, thus demonstrating possible clinical leverage.
- Published
- 2015
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- View/download PDF
42. Autofluorescence of blood and its application in biomedical and clinical research
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Mayur V. Shrirao, Robert T. Rosen, Anil B. Shrirao, Martin L. Yarmush, Zachary Fritz, and Rene S. Schloss
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Pathology ,medicine.medical_specialty ,Biomedical Research ,business.industry ,Spectroscopy methods ,Optical Imaging ,Diagnostic test ,Bioengineering ,Cancer detection ,Blood Physiological Phenomena ,Applied Microbiology and Biotechnology ,Autofluorescence ,Mice ,Clinical research ,Risk groups ,Blood ,Clinical diagnosis ,Medicine ,Animals ,Humans ,business ,Biotechnology ,Label free ,Fluorescent Dyes - Abstract
Autofluorescence of blood has been explored as a label free approach for detection of cell types, as well as for diagnosis and detection of infection, cancer, and other diseases. Although blood autofluorescence is used to indicate the presence of several physiological abnormalities with high sensitivity, it often lacks disease specificity due to use of a limited number of fluorophores in the detection of several abnormal conditions. In addition, the measurement of autofluorescence is sensitive to the type of sample, sample preparation, and spectroscopy method used for the measurement. Therefore, while current blood autofluorescence detection approaches may not be suitable for primary clinical diagnosis, it certainly has tremendous potential in developing methods for large scale screening that can identify high risk groups for further diagnosis using highly specific diagnostic tests. This review discusses the source of blood autofluorescence, the role of spectroscopy methods, and various applications that have used autofluorescence of blood, to explore the potential of blood autofluorescence in biomedical research and clinical applications.
- Published
- 2021
43. High-Voltage, Pulsed Electric Fields Eliminate Pseudomonas aeruginosa Stable Infection in a Mouse Burn Model
- Author
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Andrey Ethan Rubin, Martin L. Yarmush, Mengjie Wu, Osman Berk Usta, Tianhong Dai, Alexander Golberg, and Rene S. Schloss
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0301 basic medicine ,Vascular Endothelial Growth Factor A ,Burn injury ,Electric Stimulation Therapy ,Critical Care and Intensive Care Medicine ,medicine.disease_cause ,030207 dermatology & venereal diseases ,03 medical and health sciences ,0302 clinical medicine ,Sepsis ,Tachycardia ,Medicine ,Animals ,Pseudomonas Infections ,Forum Technology Advances ,Inflammation ,business.industry ,Pseudomonas aeruginosa ,Incidence (epidemiology) ,Electrophoresis, Gel, Pulsed-Field ,Disinfection ,Disease Models, Animal ,030104 developmental biology ,Anesthesia ,Emergency Medicine ,Wound Infection ,business ,Burns ,Burn infections - Abstract
Objective: The incidence of severe infectious complications after burn injury increases mortality by 40%. However, traditional approaches for managing burn infections are not always effective. High-voltage, pulsed electric field (PEF) treatment shortly after a burn injury has demonstrated an antimicrobial effect in vivo; however, the working parameters and long-term effects of PEF treatment have not yet been investigated. Approach: Nine sets of PEF parameters were investigated to optimize the applied voltage, pulse duration, and frequency or pulse repetition for disinfection of Pseudomonas aeruginosa infection in a stable mouse burn wound model. The bacterial load after PEF administration was monitored for 3 days through bioluminescence imaging. Histological assessments and inflammation response analyses were performed at 1 and 24 h after the therapy. Results: Among all tested PEF parameters, the best disinfection efficacy of P. aeruginosa infection was achieved with a combination of 500 V, 100 μs, and 200 pulses delivered at 3 Hz through two plate electrodes positioned 1 mm apart for up to 3 days after the injury. Histological examinations revealed fewer inflammatory signs in PEF-treated wounds compared with untreated infected burns. Moreover, the expression levels of multiple inflammatory-related cytokines (interleukin [IL]-1α/β, IL-6, IL-10, leukemia inhibitory factor [LIF], and tumor necrosis factor-alpha [TNF-α]), chemokines (macrophage inflammatory protein [MIP]-1α/β and monocyte chemoattractant protein-1 [MCP-1]), and inflammation-related factors (vascular endothelial growth factor [VEGF], macrophage colony-stimulating factor [M-CSF], and granulocyte–macrophage colony-stimulating factor [G-CSF]) were significantly decreased in the infected burn wound after PEF treatment. Innovation: We showed that PEF treatment on infected wounds reduces the P. aeruginosa load and modulates inflammatory responses. Conclusion: The data presented in this study suggest that PEF treatment is a potent candidate for antimicrobial therapy for P. aeruginosa burn infections.
- Published
- 2021
44. Progressive hypoxia‐on‐a‐chip: An in vitro oxygen gradient model for capturing the effects of hypoxia on primary hepatocytes in health and disease
- Author
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Jinsu Eo, O. Berk Usta, Martin L. Yarmush, Beyza Bulutoglu, and Young Bok Abraham Kang
- Subjects
0106 biological sciences ,0301 basic medicine ,Ischemia ,chemistry.chemical_element ,Bioengineering ,01 natural sciences ,Applied Microbiology and Biotechnology ,Oxygen ,Article ,03 medical and health sciences ,In vivo ,Lab-On-A-Chip Devices ,010608 biotechnology ,medicine ,Animals ,Hypoxia ,Cells, Cultured ,Liver sinusoid ,chemistry.chemical_classification ,Reactive oxygen species ,Chemistry ,Liver Diseases ,Hypoxia (medical) ,medicine.disease ,Rats ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,Liver ,Hepatocyte ,Hepatocytes ,medicine.symptom ,Reactive Oxygen Species ,Ex vivo ,Biotechnology - Abstract
Oxygen is vital to the function of all tissues including the liver and lack of oxygen, i.e. hypoxia, can result in both acute and chronic injuries to the liver in vivo and ex vivo. Furthermore, a permanent oxygen gradient is naturally present along the liver sinusoid, which plays a role in the metabolic zonation and the pathophysiology of liver diseases. Accordingly, here, we introduce an in vitro microfluidic platform capable of actively creating a series of oxygen concentrations on a single continuous micro-tissue, ranging from normoxia to severe hypoxia. This range approximately captures both the physiologically relevant oxygen gradient generated from the portal vein to the central vein in the liver, and the severe hypoxia occurring in ischemia and liver diseases. Primary rat hepatocytes cultured in this microfluidic platform were exposed to an oxygen gradient of 0.3-6.9%. The establishment of an ascending hypoxia gradient in hepatocytes was confirmed in response to the decreasing oxygen supply. The hepatocyte viability, in this platform, decreased to approximately 80% along the hypoxia gradient. Simultaneously, a progressive increase in reactive oxygen species (ROS) accumulation and hypoxiainducible factor-1α (HIF1α) expression was observed with increasing hypoxia. These results demonstrate the induction of distinct metabolic and genetic responses in hepatocytes upon exposure to an oxygen (/hypoxia) gradient. This progressive hypoxia-on-a-chip platform can be used to study the role of oxygen and hypoxia-associated molecules in modeling healthy and injured liver tissues. Its use can be further expanded to the study of other hypoxic tissues such as tumors as well as the investigation of drug toxicity and efficacy under oxygen-limited conditions.
- Published
- 2019
- Full Text
- View/download PDF
45. Supercooling extends preservation time of human livers
- Author
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Thomas M. van Gulik, Korkut Uygun, Mehmet Toner, Sonal Nagpal, Martin L. Yarmush, Heidi Yeh, James F. Markmann, Sinan Ozer, Peony D. Banik, Stephanie E.J. Cronin, Ehab O A Hafiz, Shannon N. Tessier, Reinier J. de Vries, Graduate School, Surgery, and AGEM - Amsterdam Gastroenterology Endocrinology Metabolism
- Subjects
Organ Preservation Solutions ,Biomedical Engineering ,Bioengineering ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Supercooling ,Liver preservation ,030304 developmental biology ,Tissue Survival ,0303 health sciences ,Machine perfusion ,Ice formation ,Chemistry ,Organ Preservation ,Cell biology ,Cold Temperature ,Perfusion ,Transplantation ,Liver ,Homogeneous ,Molecular Medicine ,030217 neurology & neurosurgery ,Ex vivo ,Biotechnology - Abstract
The inability to preserve vascular organs beyond several hours contributes to the scarcity of organs for transplantation1,2. Standard hypothermic preservation at +4 °C (refs. 1,3) limits liver preservation to less than 12 h. Our group previously showed that supercooled ice-free storage at –6 °C can extend viable preservation of rat livers4,5 However, scaling supercooling preservation to human organs is intrinsically limited because of volume-dependent stochastic ice formation. Here, we describe an improved supercooling protocol that averts freezing of human livers by minimizing favorable sites of ice nucleation and homogeneous preconditioning with protective agents during machine perfusion. We show that human livers can be stored at –4 °C with supercooling followed by subnormothermic machine perfusion, effectively extending the ex vivo life of the organ by 27 h. We show that viability of livers before and after supercooling is unchanged, and that after supercooling livers can withstand the stress of simulated transplantation by ex vivo normothermic reperfusion with blood. Preservation of human livers at subzero temperatures with ice-free supercooling extends ex vivo organ life.
- Published
- 2019
- Full Text
- View/download PDF
46. Macrophage modulation by polymerized hemoglobins: Potential as a wound-healing therapy
- Author
-
Rene S. Schloss, Yixin Meng, Maurice D. O'Reggio, Francois Berthiaume, Alison Acevedo, Martin L. Yarmush, Ioannis P. Androulakis, Andre F. Palmer, Kishan Patel, Kristopher Emil Richardson, and Paulina Krzyszczyk
- Subjects
0301 basic medicine ,Skin wound ,chemistry.chemical_element ,Inflammation ,Pharmacology ,Oxygen ,030207 dermatology & venereal diseases ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,chemistry ,medicine ,Oxygen delivery ,Macrophage ,Hemoglobin ,medicine.symptom ,Wound healing - Abstract
Chronic skin wounds are hypoxic and are stalled in a pro-inflammatory state. Hemoglobin (Hb)-based oxygen carriers have shown potential in increasing oxygen delivery to aid wound healing. Macrophages also take up Hb, thus altering their phenotype and the regulation of inflammation. Herein, we compared the effect of Hb and polymerized Hbs (PolyHbs) on the phenotype of human macrophages. Macrophages were incubated with Hb or different forms of PolyHbs, and the inflammatory secretion profile was analyzed. PolyHbs were produced by polymerizing Hb in the relaxed (R) or tense (T) quaternary state and by varying the molar ratio of the glutaraldehyde crosslinking agent to Hb. Hb decreased the secretion of most measured factors. PolyHb treatment led to generally similar secretion profiles; however, Hb had more similar trends to R-state PolyHb. Ingenuity pathway analysis predicted positive outcomes in wound healing and angiogenesis for T-state PolyHb prepared with a 30:1 (glutaraldehyde:Hb) polymerization ratio. When tested in diabetic mouse wounds, T-state PolyHb resulted in the greatest epidermal thickness and vascular endothelial CD31 staining. Thus, the effects of PolyHb on macrophages are affected by the polymerization ratio and the quaternary state, and T-state PolyHb yields secretion profiles that are most beneficial in wound healing.
- Published
- 2019
- Full Text
- View/download PDF
47. A protein interaction free energy model based on amino acid residue contributions: Assessment of point mutation stability of T4 lysozyme
- Author
-
Zachary Fritz, Lawrence J. Williams, Martin L. Yarmush, Brian J Schendt, Yonatan Attali, and Robert H Lavroff
- Subjects
0301 basic medicine ,Chemistry ,Stereochemistry ,Point mutation ,A protein ,Interaction energy ,Protein engineering ,010402 general chemistry ,01 natural sciences ,Article ,0104 chemical sciences ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Amino acid residue ,Lysozyme ,Energy (signal processing) - Abstract
Here we present a model to estimate the interaction free energy contribution of each amino acid residue of a given protein. Protein interaction energy is described in terms of per-residue interaction factors, [Formula: see text]. Multibody interactions are implicitly captured in [Formula: see text] through the combination of amino acid terms ([Formula: see text]) guided by local conformation indices ([Formula: see text]). The model enables construction of an interaction factor heat map for a protein in a given fold, allows prima facie assessment of the degree of residue–residue interaction, and facilitates a qualitative and quantitative evaluation of protein association properties. The model was used to compute thermal stability of T4 bacteriophage lysozyme mutants across seven sites. Qualitative assessment of mutational effects provides a straightforward rationale regarding whether a particular site primarily perturbs native or non-native states, or both. The presented model was found to be in good agreement with experimental mutational data ([Formula: see text]) and suggests an approach by which to convert structure space into energy space.
- Published
- 2019
- Full Text
- View/download PDF
48. IGBT-Based Pulsed Electric Fields Generator for Disinfection: Design and In Vitro Studies on Pseudomonas aeruginosa
- Author
-
Klimenty Levkov, Osman Berk Usta, Andrey Ethan Rubin, Alexander Golberg, and Martin L. Yarmush
- Subjects
Materials science ,business.industry ,Pseudomonas aeruginosa ,Electroporation ,0206 medical engineering ,Biomedical Engineering ,Multidrug resistant Pseudomonas aeruginosa ,02 engineering and technology ,Insulated-gate bipolar transistor ,medicine.disease_cause ,020601 biomedical engineering ,Disinfection ,Generator (circuit theory) ,Electromagnetic Fields ,Lower threshold ,Drug Resistance, Multiple, Bacterial ,Electric field ,medicine ,Optoelectronics ,In patient ,business - Abstract
Irreversible electroporation of cell membrane with pulsed electric fields is an emerging physical method for disinfection that aims to reduce the doses and volumes of used antibiotics for wound healing. Here we report on the design of the IGBT-based pulsed electric field generator that enabled eradication of multidrug resistant Pseudomonas aeruginosa PAO1 on the gel. Using a concentric electric configuration we determined that the lower threshold of the electric field required to kill P. aeruginosa PAO1 was 89.28 ± 12.89 V mm−1, when 200 square pulses of 300 µs duration are delivered at 3 Hz. These parameters disinfected 38.14 ± 0.79 mm2 area around the single needle electrode. This study provides a step towards the design of equipment required for multidrug-resistant bacteria disinfection in patients with pulsed electric fields.
- Published
- 2019
- Full Text
- View/download PDF
49. Oxygenated UW solution decreases ATP decay and improves survival after transplantation of DCD liver grafts
- Author
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Martin L. Yarmush, Korkut Uygun, Tim A Berendsen, Bote G. Bruinsma, Heidi Yeh, Paulo N. Martins, James F. Markmann, Maria-Louisa Izamis, Sanna op den Dries, Robert J. Porte, Andrew R. Gillooly, and Groningen Institute for Organ Transplantation (GIOT)
- Subjects
Male ,medicine.medical_specialty ,Adenosine ,medicine.medical_treatment ,Allopurinol ,Organ Preservation Solutions ,030230 surgery ,Liver transplantation ,Donor age ,03 medical and health sciences ,0302 clinical medicine ,Adenosine Triphosphate ,Raffinose ,Internal medicine ,Medicine ,Animals ,Insulin ,Viaspan ,Warm Ischemia ,Cold ischemia ,Transplantation ,Fluorocarbons ,business.industry ,Cold Ischemia ,Graft Survival ,Organ Preservation ,Warm ischemia ,Circulatory death ,Glutathione ,Liver Transplantation ,Rats ,Oxygen ,surgical procedures, operative ,Rats, Inbred Lew ,Cardiology ,030211 gastroenterology & hepatology ,business - Abstract
Donation after circulatory death (DCD) liver grafts are known to be predisposed to primary nonfunction and ischemic cholangiopathy. Many DCD grafts are discarded because of older donor age or long warm ischemia times. Thus, it is critical to improve the quality of DCD liver grafts. Here, we have tested whether an enriched oxygen carrier added to the preservation solution can prolong graft survival and reduce biliary damage.We assessed the adenosine triphosphate (ATP) content decay of mouse liver grafts after cold ischemia, warm ischemia, and combined warm+cold ischemia. In addition, we used a rat model of liver transplantation to compare survival of DCD grafts preserved in high-oxygen solution (preoxygenated perfluorocarbon [PFC] + University of Wisconsin [UW] solution) versus lower oxygen solution (preoxygenated UW solution).Adenosine triphosphate levels under UW preservation fall to less than 10% after 30 minutes of warm ischemia. Preoxygenated UW solution with PFC reached a significantly higher PaO2. After 45 minutes of warm ischemia in oxygenated UW + PFC solution, grafts showed 63% higher levels of ATP (P = 0.011). In addition, this was associated with better preservation of morphology when compared to grafts stored in standard UW solution. Animals that received DCD grafts preserved in higher oxygenation solution showed improved survival: 4 out of 6 animals survived long-term whereas all control group animals died within 24 hours.The additional oxygen provided by PFC during static cold preservation of DCD livers can better sustain ATP levels, and thereby reduce the severity of ischemic tissue damage. PFC-based preservation solution extends the tolerance to warm ischemia, and may reduce the rate of ischemic cholangiopathy.
- Published
- 2019
50. Metabolomic Modularity Analysis (MMA) to Quantify Human Liver Perfusion Dynamics
- Author
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Gautham Vivek Sridharan, Bote Gosse Bruinsma, Shyam Sundhar Bale, Anandh Swaminathan, Nima Saeidi, Martin L. Yarmush, and Korkut Uygun
- Subjects
metabolic networks ,liver ,cofactors ,modularity ,Microbiology ,QR1-502 - Abstract
Large-scale -omics data are now ubiquitously utilized to capture and interpret global responses to perturbations in biological systems, such as the impact of disease states on cells, tissues, and whole organs. Metabolomics data, in particular, are difficult to interpret for providing physiological insight because predefined biochemical pathways used for analysis are inherently biased and fail to capture more complex network interactions that span multiple canonical pathways. In this study, we introduce a nov-el approach coined Metabolomic Modularity Analysis (MMA) as a graph-based algorithm to systematically identify metabolic modules of reactions enriched with metabolites flagged to be statistically significant. A defining feature of the algorithm is its ability to determine modularity that highlights interactions between reactions mediated by the production and consumption of cofactors and other hub metabolites. As a case study, we evaluated the metabolic dynamics of discarded human livers using time-course metabolomics data and MMA to identify modules that explain the observed physiological changes leading to liver recovery during subnormothermic machine perfusion (SNMP). MMA was performed on a large scale liver-specific human metabolic network that was weighted based on metabolomics data and identified cofactor-mediated modules that would not have been discovered by traditional metabolic pathway analyses.
- Published
- 2017
- Full Text
- View/download PDF
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