| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 3. |
- Mathaikutty, Deepak A., et al.
(författare)
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SML-Sys : a functional framework with multiple models of computation for modeling heterogeneous system
- 2008
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Ingår i: Design automation for embedded systems. - : Springer Science and Business Media LLC. - 0929-5585 .- 1572-8080. ; 12:1-2, s. 1-30
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Tidskriftsartikel (refereegranskat)abstract
- System-on-Chip and other complex distributed hardware/software systems contain heterogeneous components. High-level modeling of such systems require frameworks that provide designers with the ability to express concepts of models of computation (MoC)s as modeling constructs. Many system-level modeling frameworks and corresponding modeling notations such as Ptolemy II and SystemC-H facilitate multi-MoC modeling but are based on imperative programming languages (C++, Java, etc). In such frameworks, the computation and communication aspects between the components of models get intertwined thereby hindering its amenability to formal analysis. In this work, we illustrate function-based semantic definitions of MoCs, which are formulated in a functional framework called SML-Sys. We illustrate through a number of examples how to create system models using this functional programming paradigm.
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| 4. |
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| 5. |
- Mathaikutty, Deepak Abraham, et al.
(författare)
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UMoC++ : A C++-Based Multi-MoC Modeling Environment
- 2006
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Ingår i: Advances in Design and Specification Languages for SoCs. - : Springer Publishing Company. ; , s. 115-130
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Konferensbidrag (refereegranskat)abstract
- System-on-chip (SoC) and other complex distributed hardware/software systemscontain heterogeneous components that necessitate frameworks capable of expressingheterogeneous models of computation (MoCs) for modeling their functionalities.System-level design languages (SLDLs) that facilitate multi-MoCmodeling should have well-defined semantics and should be readily subjectedto formal analysis to handle the design complexity. As a result, we follow themulti-MoC paradigm based on timing abstraction and functional parameterizationsthat have rigorous denotational semantics, which are compliant to functionalidioms as shown in functional frameworks such as ForSyDe and SML-Sys.However, functional frameworks are not widely used in the industry due toissues related to efficiency and interoperability with other widely used SLDLs.This imposes a requirement for an imperative language-based implementationof these generic MoCs that offers all the advantages of the underlying formalsemantics. In this chapter, we formulate the basis for having generic MoCs in animperative language and describe the implementation of an untimed modelingframework called UMoC++.
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| 6. |
- Mathaikutty, Deepak A., et al.
(författare)
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UMoC plus plus : A C plus plus -based Multi-MoC modeling environment
- 2006
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Ingår i: APPLICATIONS OF SPECIFICATION AND DESIGN LANGUAGES FOR SOCS. - Dordrecht : SPRINGER. ; , s. 115-130
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Konferensbidrag (refereegranskat)abstract
- System-on-chip (SoC) and other complex distributed hardware/software systems contain heterogeneous components that necessitate frameworks capable of expressing heterogeneous models of computation (MoCs) for modeling their functionalities. System-level design languages (SLDLs) that facilitate multi-MoC modeling should have well-defined semantics and should be readily subjected to formal analysis to handle the design complexity. As a result, we follow the multi-MoC paradigm based on timing abstraction and functional parameterizations that have rigorous denotational semantics, which are compliant to functional idioms as shown in functional frameworks such as ForSyDe and SML-Sys. However, functional frameworks are not widely used in the industry due to issues related to efficiency and interoperability with other widely used SLDLs. This imposes a requirement for an imperative language-based implementation of these generic MoCs that offers all the advantages of the underlying formal semantics. In this chapter, we formulate the basis for having generic MoCs in an imperative language and describe the implementation of an untimed modeling framework called UMoC++.
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| 7. |
- Mathaikutty, Deepak, et al.
(författare)
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EWD : A metamodeling driven customizable multi-MoC system modeling framework
- 2007
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Ingår i: ACM Transactions on Design Automation of Electronic Systems. - : Association for Computing Machinery (ACM). - 1084-4309 .- 1557-7309. ; 12:3, s. 1255470-
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Tidskriftsartikel (refereegranskat)abstract
- We present the EWD design environment and methodology, a modeling and simulation framework suited for complex and heterogeneous embedded systems with varying degrees of expressibility and modeling fidelity. This environment promotes the use of multiple models of computation (MoCs) to support heterogeneity and metamodeling for conformance tests of syntactic and static semantics during the process of modeling. Therefore, EWD is a multiple MoC rnodeling and simulation framework that ensures conformance of the MoC formalisms during model construction using a metamodeling approach. In addition, EWD provides a suite of translation tools that generate executable models for two simulation frameworks to demonstrate its language-independent modeling framework. The EWD methodology uses the Generic Modeling Environment for customization of the MoC-specific modeling syntax into a visual representation. To embed the execution semantics of the MoCs into the models, we have built parsing and translation tools that leverage an XML-based interoperability language. This interoperability language is then translated into executable Standard ML or Haskell models that can also be analyzed by existing simulation frameworks such as SML-Sys or ForSyDe. In summary, EWD is a metamodeling driven multitarget design environment with multi-MoC modeling capability.
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| 8. |
- Srivastava, Manu, et al.
(författare)
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A review of various materials for additive manufacturing : Recent trends and processing issues
- 2022
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Ingår i: Journal of materials research and technology. - : Elsevier. - 2238-7854. ; 21, s. 2612-2641
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Tidskriftsartikel (refereegranskat)abstract
- Tremendous growth has been witnessed in the field of additive manufacturing (AM) technology over the last few decades. It offers a plethora of applications and is already being utilized in almost every sphere of life. Owing to inherent differences between each AM technique, newer fields of research consistently emerge and demand attention. Also, the innovative applications of AM open up newer challenges and thus avenues for focused attention. One such avenue is AM materials. Raw material plays an important role in determining the properties of fabricated part. The type and form of raw material largely depend on the type of AM fabricators. There is a restriction on material compatibility with most of the established AM techniques. This review aims to provide an overview of various aspects of AM materials highlighting the progress made especially over the past two decades.
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