Literature DB >> 31814616

Databases to Efficiently Manage Medium Sized, Low Velocity, Multidimensional Data in Tissue Engineering.

Alexander R Ochs1, Mehrsa Mehrabi1, Danielle Becker1, Mira N Asad1, Jing Zhao1, Michael V Zaragoza2, Anna Grosberg3.   

Abstract

Science relies on increasingly complex data sets for progress, but common data management methods such as spreadsheet programs are inadequate for the growing scale and complexity of this information. While database management systems have the potential to rectify these issues, they are not commonly utilized outside of business and informatics fields. Yet, many research labs already generate "medium sized", low velocity, multi-dimensional data that could greatly benefit from implementing similar systems. In this article, we provide a conceptual overview explaining how databases function and the advantages they provide in tissue engineering applications. Structural fibroblast data from individuals with a lamin A/C mutation was used to illustrate examples within a specific experimental context. Examples include visualizing multidimensional data, linking tables in a relational database structure, mapping a semi-automated data pipeline to convert raw data into structured formats, and explaining the underlying syntax of a query. Outcomes from analyzing the data were used to create plots of various arrangements and significance was demonstrated in cell organization in aligned environments between the positive control of Hutchinson-Gilford progeria, a well-known laminopathy, and all other experimental groups. In comparison to spreadsheets, database methods were enormously time efficient, simple to use once set up, allowed for immediate access of original file locations, and increased data rigor. In response to the National Institutes of Health (NIH) emphasis on experimental rigor, it is likely that many scientific fields will eventually adopt databases as common practice due to their strong capability to effectively organize complex data.

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Year:  2019        PMID: 31814616      PMCID: PMC7156791          DOI: 10.3791/60038

Source DB:  PubMed          Journal:  J Vis Exp        ISSN: 1940-087X            Impact factor:   1.355


  20 in total

1.  Ensembles of engineered cardiac tissues for physiological and pharmacological study: heart on a chip.

Authors:  Anna Grosberg; Patrick W Alford; Megan L McCain; Kevin Kit Parker
Journal:  Lab Chip       Date:  2011-11-10       Impact factor: 6.799

2.  Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome.

Authors:  Maria Eriksson; W Ted Brown; Leslie B Gordon; Michael W Glynn; Joel Singer; Laura Scott; Michael R Erdos; Christiane M Robbins; Tracy Y Moses; Peter Berglund; Amalia Dutra; Evgenia Pak; Sandra Durkin; Antonei B Csoka; Michael Boehnke; Thomas W Glover; Francis S Collins
Journal:  Nature       Date:  2003-04-25       Impact factor: 49.962

Review 3.  Systems cell biology.

Authors:  Fred D Mast; Alexander V Ratushny; John D Aitchison
Journal:  J Cell Biol       Date:  2014-09-15       Impact factor: 10.539

4.  Age of heart disease presentation and dysmorphic nuclei in patients with LMNA mutations.

Authors:  Jason Q Core; Mehrsa Mehrabi; Zachery R Robinson; Alexander R Ochs; Linda A McCarthy; Michael V Zaragoza; Anna Grosberg
Journal:  PLoS One       Date:  2017-11-17       Impact factor: 3.240

5.  Heart-hand syndrome IV: a second family with LMNA-related cardiomyopathy and brachydactyly.

Authors:  M V Zaragoza; S A Hakim; V Hoang; A M Elliott
Journal:  Clin Genet       Date:  2016-10-10       Impact factor: 4.438

Review 6.  Questionnaires in clinical trials: guidelines for optimal design and administration.

Authors:  Phil Edwards
Journal:  Trials       Date:  2010-01-11       Impact factor: 2.279

7.  MediaDB: a database of microbial growth conditions in defined media.

Authors:  Matthew A Richards; Victor Cassen; Benjamin D Heavner; Nassim E Ajami; Andrea Herrmann; Evangelos Simeonidis; Nathan D Price
Journal:  PLoS One       Date:  2014-08-06       Impact factor: 3.240

8.  Exome Sequencing Identifies a Novel LMNA Splice-Site Mutation and Multigenic Heterozygosity of Potential Modifiers in a Family with Sick Sinus Syndrome, Dilated Cardiomyopathy, and Sudden Cardiac Death.

Authors:  Michael V Zaragoza; Lianna Fung; Ember Jensen; Frances Oh; Katherine Cung; Linda A McCarthy; Christine K Tran; Van Hoang; Simin A Hakim; Anna Grosberg
Journal:  PLoS One       Date:  2016-05-16       Impact factor: 3.240

9.  Dupuytren's and Ledderhose Diseases in a Family with LMNA-Related Cardiomyopathy and a Novel Variant in the ASTE1 Gene.

Authors:  Michael V Zaragoza; Cecilia H H Nguyen; Halida P Widyastuti; Linda A McCarthy; Anna Grosberg
Journal:  Cells       Date:  2017-11-01       Impact factor: 6.600

10.  Getting rigorous with scientific rigor.

Authors:  Lorne J Hofseth
Journal:  Carcinogenesis       Date:  2018-01-12       Impact factor: 4.944

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  1 in total

1.  Data Block and Tuple Identification Using Master Index.

Authors:  Michal Kvet; Karol Matiasko
Journal:  Sensors (Basel)       Date:  2020-03-26       Impact factor: 3.576

  1 in total

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