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A comparative gene-expression analysis of CD34+ hematopoietic stem and progenitor cells grown in static and stirred culture systems

Qunliang Li, Qiwei Liu, Haibo Cai, Wen-Song Tan
2006 Cellular & Molecular Biology Letters  
The results revealed that 103 and 99 genes were significantly expressed in CD34+ cells from static and stirred systems, respectively.  ...  To understand the genetic changes provoked by culture microenvironments, the gene expression profiling of CD34+ HSPCs grown in static and stirred culture systems was compared using SMART-PCR and cDNA arrays  ...  We are grateful to Yan Zhou, Xu Zhang, Minglong Zhu and Ping Hua for their help in the laboratory, and Lin Wei and Dongning Pan for their work on the cDNA array analysis.  ... 
doi:10.2478/s11658-006-0039-x pmid:16983455 fatcat:zmuidldcuzcapcr2lt52yatpwm

A comparative gene-expression analysis of CD34+ hematopoietic stem and progenitor cells grown in static and stirred culture systems

Qunliang Li, Qiwei Liu, Haibo Cai, Wen-Song Tan
2006 Cellular & Molecular Biology Letters  
Static and stirred culture systems are widely used to expand hematopoietic cells, but differential culture performances are observed between these systems.  ...  The results revealed that 103 and 99 genes were significantly expressed in CD34 + cells from static and stirred systems, respectively.  ...  We are grateful to Yan Zhou, Xu Zhang, Minglong Zhu and Ping Hua for their help in the laboratory, and Lin Wei and Dongning Pan for their work on the cDNA array analysis.  ... 
doi:10.2478/s11658-006-0051-1 fatcat:vdwuoumjanhwfiztca6m2dnbxe

Biology of biomechanics: Finite element analysis of a statically determinate system to rotate the occlusal plane for correction of a skeletal Class III open-bite malocclusion

W. Eugene Roberts, Rodrigo F. Viecilli, Chris Chang, Thomas R. Katona, Nasser H. Paydar
2015 American Journal of Orthodontics and Dentofacial Orthopedics  
Finite element analysis (FEA) is emerging as a clinical technology to assist in diagnosis, treatment planning and retrospective analysis.  ...  Methods: Seventeen published case reports were selected for patients treated with statically determinate mechanics, utilizing posterior mandible (PM) or infrazygomatic crest (IZC) bone screw anchorage,  ...  For 3D statically determinate systems, there can be 3 force components and 3 moment components.  ... 
doi:10.1016/j.ajodo.2015.10.002 pmid:26672700 fatcat:io6kuff3pzaf7o5bmgfdjrhwga

Korean Systems Biology and Biotechnology Research

Sang Yup Lee, Do Han Kim, Jin Sik Kim, Hyun Uk Kim, Hongseok Yun
2006 Asia-Pacific Biotech News  
Acknowledgements This study was supported by Korean Systems Biology Research grant from Korean Ministry of Science and Technology, and the Brain Korea 21 Project.  ...  We also like to thank the support received from the LG Chemicals Chair Professorship, Microsoft and IBM SUR program.  ...  The static model includes constraints-based fl ux analysis, topology analysis and stoichiometric analysis.  ... 
doi:10.1142/s0219030306001509 fatcat:nayftmu2ivd27exnntkqlgcibe


Nicola Cannata, Emanuela Merelli
2009 Theoretical Computer Science  
In order to better meet the modelling, simulation and analysis requirements of systems biology, molecular and cellular processes have begun inspiring the creation and evolution of novel formalisms and  ...  We propose to use the term "concurrent systems biology" for this recent research frontier of systems biology (which indeed was originally based on differential equations) stemming from the community of  ...  The analysis offers a basis for establishing static checks of biological dynamic properties.  ... 
doi:10.1016/j.tcs.2009.04.001 fatcat:koifdbhh6jhojmdo6k7brcvfc4

Static Analysis for Biological Systems (BioAmbients) [article]

A. Aziz Altowayan
2015 arXiv   pre-print
In this paper, I present a summary on some works that utilized static analysis techniques for understanding biological systems.  ...  Control flow analysis, context dependent analysis, and other techniques were employed to investigate the properties of BioAmbients.  ...  Nielson [2] is currently investigating a methodology to code biological systems in BioAmbients.  ... 
arXiv:1501.00349v1 fatcat:njnagdmzlfebfe3x2uvn5bzrna


M.J. Peffers, P.D. Clegg, S. Tew, P.I. Milne
2010 Osteoarthritis and Cartilage  
Cyp1A1 mRNA expression was synergistically stimulated by TCDD and IL-1B treatment,.  ...  Conversely, AhR ligands synergized with IL1-B and clearly increased the amount of IL-1B mRNA, but only moderately that of IL1-RA mRNA.  ...  Understanding the regulation of SOX9 could lead to novel strategies to improve techniques of cartilage repair Systems Biology Approach and High-throughput Proteomic Analysis Identifies Toll-Like-Receptor  ... 
doi:10.1016/s1063-4584(10)60306-8 fatcat:c6duw5lwhjcgvfg6hbaoa24pnm

Validation of a multicellular tumor microenvironment system for modeling patient tumor biology and drug response

Devin G. Roller, Stephen A. Hoang, Kristopher D. Rawls, Katherine A. Owen, Michael B. Simmers, Robert A. Figler, Julia D. Wulfkuhle, Emanuel F. Petricoin, Brian R. Wamhoff, Daniel Gioeli
2021 Scientific Reports  
This work further validates the TMES for modeling patient tumor biology and drug response indicating utility of the TMES as a predictive tool for drug discovery and development and potential for use as  ...  a system for patient avatars.  ...  Gioeli, Jameson, Bouton, Dudley, Kashatus, Park, Rutkowski, Smith, and Zong for helpful discussions. We thank the team at HemoShear Therapeutics and Garnett Mingledorff for technical assistance.  ... 
doi:10.1038/s41598-021-84612-z pmid:33692370 pmcid:PMC7946945 fatcat:drzsje25rzhhpdqljxypnxx5nu

Computational Modeling, Formal Analysis, and Tools for Systems Biology

Ezio Bartocci, Pietro Lió, Marta Zofia Kwiatkowska
2016 PLoS Computational Biology  
The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static  ...  As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology.  ...  , abstraction, model checking, reachability analysis, formal verification, and static analysis) that is scarcely known in other scientific communities such as systems biology.  ... 
doi:10.1371/journal.pcbi.1004591 pmid:26795950 pmcid:PMC4721667 fatcat:6fb2c7qe4fdwzbawec5qf42qga

Differential network biology

Trey Ideker, Nevan J Krogan
2012 Molecular Systems Biology  
Protein and genetic interaction maps can reveal the overall physical and functional landscape of a biological system.  ...  gene expression and protein phosphorylation studies are already pervasive in genomic and proteomic analysis.  ...  This work was supported by grants from the NIH (GM085764 and GM084279 to TI and GM084448, GM084279, GM081879 and GM098101 to NJK). TI is a David and Lucille Packard Fellow.  ... 
doi:10.1038/msb.2011.99 pmid:22252388 pmcid:PMC3296360 fatcat:dt6vdp65fngupl6wmh5jldhjqy

Network systems biology for targeted cancer therapies

Ting-Ting Zhou
2012 Chinese Journal of Cancer  
From biological network modeling to structural/dynamic network analysis, network systems biology provides unique insight into the potential mechanisms underlying the growth and progression of cancer cells  ...  However, due to the complexity of biological systems, the current progress is far from enough.  ...  systems biology.  ... 
doi:10.5732/cjc.011.10282 pmid:22176777 pmcid:PMC3777487 fatcat:hidrfb3p4bcthlrq7x2h4knpxu

On the feasibility of dynamical analysis of network models of biochemical regulation [article]

Luis M. Rocha
2021 arXiv   pre-print
Unlike what is suggested in the article, graph-based analysis of static features is not the only analytical avenue for large systems biology models of regulation and signaling dynamics because there are  ...  However, the authors claim that dynamical analysis of large automata network models is "not even feasible."  ...  Acknowledgements The author is indebted to the anonymous reviewers for their most valuable comments and references which have considerably strengthened this letter.  ... 
arXiv:2110.10821v1 fatcat:u6oiqyt7sbguhji62vulmxwftu

Does animation enhance learning? A meta-analysis

Sandra Berney, Mireille Bétrancourt
2016 Computers & Education  
This meta-analysis investigated whether animation is beneficial overall for learning compared to static graphics, while also identifying moderator factors affecting the global effect.  ...  A total of 50 papers were considered, and consecutively 61 primary studies (N ¼ 7036), yielding 140 pair-wise comparisons of animated vs. static graphic visualizations in multimedia instructional material  ...  An important but surprising finding of this meta-analysis is that the positive effect of animation over static graphics was found only for system-paced instructional material, or in other words when learners  ... 
doi:10.1016/j.compedu.2016.06.005 fatcat:sygwbtjdbffwjiufy7sm4ibdcm

Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities

C. F. Quo, C. Kaddi, J. H. Phan, A. Zollanvari, M. Xu, M. D. Wang, G. Alterovitz
2012 Briefings in Bioinformatics  
validate and analyze theoretical system models directly through experimental synthesis, i.e. analysis-by-synthesis.  ...  The ultimate goal is to address the present and future challenges in reverse engineering biomolecular systems (REBMS) using integrated workflow of data mining, systems modeling and synthetic biology.  ...  ; Georgia Cancer Coalition Distinguished Cancer Scholar Award to MD Wang, and grants 5R21DA025168-02, 1R01HG004836-01 and 4R00LM009826-03 to G.  ... 
doi:10.1093/bib/bbs026 pmid:22833495 pmcid:PMC3404400 fatcat:rctmpuedxbcbxh6ipuloiy4kji

280 Systems Biology Approach and High-throughput Proteomic Analysis Identifies Toll-Like-Receptor Activators as Major Players of Cartilage Degeneration

L. Alexopoulos, A. Chairakaki, I. Melas, C. Provatidis, P. Kolia, Z. Dailiana
2010 Osteoarthritis and Cartilage  
Statistical analysis was performed using mixed effects regression models.  ...  Osmotic load was either static or cyclical, where loads were applied by incubating cells for 5 hours in 380 and 550mOsm medium alternating every 30 or 60 minutes, containing either DMSO, or 20μM p38 MAP  ...  Association between evolution of non-EOA to EOA and baseline characteristics OR (95% CI)* OR (95% CI)** 282 Figure 2 2 Figure 2 280 Systems 280 Biology Approach and High-throughput Proteomic Analysis  ... 
doi:10.1016/s1063-4584(10)60307-x fatcat:w6a7b7lxsrakfg7qlp3lxjs5sa
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