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Joseph P. Bidwell - One of the best experts on this subject based on the ideXlab platform.

  • Multilevel text mining for Bone Biology
    Concurrency and Computation: Practice and Experience, 2011
    Co-Authors: Omkar Tilak, Andrew Hoblitzell, Snehasis Mukhopadhyay, Qian You, Shiaofen Fang, Yuni Xia, Joseph P. Bidwell
    Abstract:

    Osteoporosis is characterized by reduced Bone mass and debilitating fractures and is likely to reach epidemic proportions. Because of the vigorous research taking place in fields related to osteoporosis, Bone biologists are overwhelmed by the amount of literature being generated on a regular basis. This problem can be alleviated by inferring and extracting novel relationships among biological entities appearing in the biological literature. With the development of large online publicly available databases of biological literature, such an approach becomes even more appealing. The novel relationships between biological terms thus discovered constitute new hypotheses that can be verified using experiments. This paper presents a novel method called multilevel text mining for the extraction of potentially meaningful biological relationships. Multilevel mining uses transitive maximum flow graph analysis coupled with set combination operations of union and intersection. Set operators are applied along and across the paths of a transitive flow graph to combine the data. In the first level of the multilevel mining process, protein domain names are used. Novel relationships between domains are extracted by the transitive text mining analysis. In the second level, these newly discovered relationships are used to extract relevant protein names. Set operators are used in various combinations to obtain different sets of results. Copyright © 2011 John Wiley & Sons, Ltd.

  • HPDC - Text mining for Bone Biology
    Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10, 2010
    Co-Authors: Andrew Hoblitzell, Snehasis Mukhopadhyay, Qian You, Shiaofen Fang, Yuni Xia, Joseph P. Bidwell
    Abstract:

    Osteoporosis, which is characterized by reduced Bone mass and debilitating fractures, may reach epidemic proportions with the aging of the US population. The intensity of research in this field of study is reflected by the facts that The American Society of Bone and Mineral Research has a membership of nearly 4,000 physicians, clinical investigators, and basic research scientists from over fifty countries and that NIH is expected to spend over 200 million dollars on osteoporosis research alone in 2010. Bone biologists may be overwhelmed by the amount of literature constantly being generated, thus the identification and extraction of existing and novel relationships among biological entities or terms appearing in the biological literature is an ongoing problem. The problem has become more pressing with the development of large online publicly available databases of biological literature. Extraction and visualization of relationships between biological entities appearing in these databases offers the opportunity of keeping researchers up-to-date in their research domain. This may be achieved through helping them visualize possible biological pathways and by generating likely new hypotheses concerning novel interactions through methods such as transitive closure network flow. All generated predictions can be verified against already existing data, and possible new relationships can be verified against experiment. This paper presents a method for the extraction and visualization of potentially meaningful relationships.

Wei Yao - One of the best experts on this subject based on the ideXlab platform.

Anne George - One of the best experts on this subject based on the ideXlab platform.

  • Exosomes in Extracellular Matrix Bone Biology
    Current Osteoporosis Reports, 2018
    Co-Authors: Adrienn Pethő, Yinghua Chen, Anne George
    Abstract:

    Purpose of Review Exosomes are membrane vesicles that are released by most cell types into the extracellular environment. The purpose of this article is to discuss the main morphological features and contents of Bone-derived exosomes, as well as their major isolation and physical characterization techniques. Furthermore, we present various scenarios and discuss potential clinical applications of Bone-derived exosomes in Bone repair and regeneration. Recent Findings Exosomes were believed to be nanosized vesicles derived from the multivesicular body. Reports now suggest that nanovesicles could bud directly from the plasma membrane. However, the exosome cargo is cell-type specific and is derived from the parent cell. In the Bone matrix, several intracellular proteins lacking a signal peptide are transported to the ECM by exosomes. Besides proteins, several mRNA, miRNA, and lipids are exported to the ECM by Bone cells and Bone marrow stromal cells. Recent evidence suggests that several of the functional components in the cargo could regulate processes of Bone formation, inhibit osteoclast activity, and promote fracture repair. Summary Exosomes are powerful cellular molecular machines produced without human intervention and packaged with physiological cargo that could be utilized for molecular therapy in several skeletal disorders such as osteoporosis, osteogenesis imperfecta, and fracture healing. Although much work has been done, there is a lot of information that is still unknown, as exosomes contain a multitude of molecules whose identity and function have yet to be identified.

  • Exosomes in Extracellular Matrix Bone Biology.
    Current osteoporosis reports, 2018
    Co-Authors: Adrienn Pethő, Yinghua Chen, Anne George
    Abstract:

    Purpose of Review Exosomes are membrane vesicles that are released by most cell types into the extracellular environment. The purpose of this article is to discuss the main morphological features and contents of Bone-derived exosomes, as well as their major isolation and physical characterization techniques. Furthermore, we present various scenarios and discuss potential clinical applications of Bone-derived exosomes in Bone repair and regeneration.

Akira Kudo - One of the best experts on this subject based on the ideXlab platform.

  • Periostin in Bone Biology
    Advances in experimental medicine and biology, 2019
    Co-Authors: Akira Kudo
    Abstract:

    Periostin is specifically expressed in periosteum that functions in Bone modeling and remodeling and Bone repair, and is sensitive to mechanical stress. Thus periostin has been expected for controlling these crucial systems in Bone. The results from periostin deficient mice demonstrate that periostin acts on Bone remodeling though detailed mechanisms are unknown. Recent findings have revealed that periostin is essential for Bone repair. In this chapter, I introduce expression and function of periostin in Bone.

Stephen M. Warren - One of the best experts on this subject based on the ideXlab platform.

  • Design and validation of a dynamic cell‐culture system for Bone Biology research and exogenous tissue‐engineering applications
    Journal of tissue engineering and regenerative medicine, 2013
    Co-Authors: Alexander C. Allori, Edward H. Davidson, Derek D. Reformat, Alexander M. Sailon, James Freeman, Adam Vaughan, David M. Wootton, Elizabeth Clark, John L. Ricci, Stephen M. Warren
    Abstract:

    Bone lacunocanalicular fluid flow ensures chemotransportation and provides a mechanical stimulus to cells. Traditional static cell-culture methods are ill-suited to study the intricacies of Bone Biology because they ignore the three-dimensionality of meaningful cellular networks and the lacunocanalicular system; furthermore, reliance on diffusion alone for nutrient supply and waste product removal effectively limits scaffolds to 2-3 mm thickness. In this project, a flow-perfusion system was custom-designed to overcome these limitations: eight adaptable chambers housed cylindrical cell-seeded scaffolds measuring 12 or 24 mm in diameter and 1-10 mm in thickness. The porous scaffolds were manufactured using a three-dimensional (3D) periodic microprinting process and were composed of hydroxyapatite/tricalcium phosphate with variable thicknesses, strut sizes, pore sizes and structural configurations. A multi-channel peristaltic pump drew medium from parallel reservoirs and perfused it through each scaffold at a programmable rate. Hermetically sealed valves permitted sampling or replacement of medium. A gas-permeable membrane allowed for gas exchange. Tubing was selected to withstand continuous perfusion for > 2 months without leakage. Computational modelling was performed to assess the adequacy of oxygen supply and the range of fluid shear stress in the bioreactor-scaffold system, using 12 × 6 mm scaffolds, and these models suggested scaffold design modifications that improved oxygen delivery while enhancing physiological shear stress. This system may prove useful in studying complex 3D Bone Biology and in developing strategies for engineering thick 3D Bone constructs. Copyright © 2013 John Wiley & Sons, Ltd.

  • Flow perfusion maintains ex vivo Bone viability: A novel model for Bone Biology research
    Journal of tissue engineering and regenerative medicine, 2011
    Co-Authors: Edward H. Davidson, Derek D. Reformat, Alessandro C. Allori, Orlando Canizares, I. Janelle Wagner, Pierre B. Saadeh, Stephen M. Warren
    Abstract:

    Encased in lacunae, osteocytes receive nutrition and biomechanical signals through the lacunocanalicular system. We have developed a novel flow-perfusion bioreactor designed to support lacunocanalicular fluid flow. We hypothesize that ex vivo fluid flow can maintain endochondral Bone viability and, ultimately, serve as a novel model to study Bone Biology in vitro. Sprague-Dawley rat femurs were harvested, stripped of soft tissue, loaded into a custom-designed bioreactor and perfused with osteogenic culture medium. After 14 days of flow-perfusion or static culture, the Bones were harvested, fixed, decalcified, embedded, sectioned and stained with haematoxylin and eosin. Fresh long Bone samples were similarly processed for comparison. Osteocyte viability and function were also evaluated, using thiazolyl blue tetrazolium bromide (MTT), fluorospectrophotometric DNA quantification, alkaline phosphatase (ALP) colorimetric assay and fluorochrome labelling of mineralizing surfaces. All samples remained free of infection throughout the study period. After 14 days of flow perfusion, histological analysis showed normal-appearing bony architecture, with 72% of lacunae being osteocyte-filled compared with 93% in freshly harvested samples and only 36% in static samples. MTT staining and assay confirmed osteocyte viability in the flow-perfusion samples as well as in fresh samples. DNA quantification demonstrated DNA to be preserved in flow-perfused samples when compared with freshly harvested samples. ALP activity in flow-perfusion explants was upregulated compared with fresh and static samples. Fluorochrome-labelled mineralizing surfaces were seen throughout the explanted flow-perfused samples. This is the first demonstration that flow perfusion provides adequate chemotransportation to explanted murine endochondal Bones.