Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics

2019 ◽  
pp. 191-217 ◽  
Author(s):  
Biswapriya B. Misra
Keyword(s):  
Single Cell ◽  
Open Source ◽  
Open Source Software ◽  
Software Tools ◽  
Cell Type ◽  
Single Cell Type

scholarly journals Open-source software tools for measuring resources consumption and DASH metrics

2020 ◽  
Author(s):  
Mario Montagud ◽  
Juan Antonio De Rus ◽  
Rafael Fayos-Jordan ◽  
Miguel Garcia-Pineda ◽  
Jaume Segura-Garcia
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Tools

scholarly journals Author Correction: iLoF: An intelligent Lab on Fiber Approach for Human Cancer Single-Cell Type Identification

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Joana S. Paiva ◽  
Pedro A. S. Jorge ◽  
Rita S. R. Ribeiro ◽  
Meritxell Balmaña ◽  
Diana Campos ◽  
...  
Keyword(s):  
Single Cell ◽  
Human Cancer ◽  
Cell Type ◽  
Single Cell Type

Differential calcium signalling by m2 and m3 muscarinic acetylcholine receptors in a single cell type

1995 ◽  
Vol 352 (5) ◽  
pp. 469-476 ◽  
Author(s):  
Martina Schmidt ◽  
Christine Bienek ◽  
Chris J. van Koppen ◽  
Martin C. Michel ◽  
Karl H. Jakobs
Keyword(s):  
Single Cell ◽  
Acetylcholine Receptors ◽  
Calcium Signalling ◽  
Muscarinic Acetylcholine Receptors ◽  
Cell Type ◽  
Muscarinic Acetylcholine ◽  
Single Cell Type

scholarly journals Practical application of open source software tools in cryptography

2014 ◽  
pp. 115-135 ◽  
Author(s):  
Dragan Ranđelović ◽  
Miloš Ranđelović ◽  
Željko Kuzmanović
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Tools ◽  
Practical Application

The Immunohistochemical Characterisation of an SV40-immortalised Human Corneal Epithelial Cell Line

2003 ◽  
Vol 31 (4) ◽  
pp. 409-417 ◽  
Author(s):  
Anne Huhtala ◽  
Sami K. Nurmi ◽  
Hanna Tähti ◽  
Lotta Salminen ◽  
Päivi Alajuuma ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Cell Line ◽  
Cell Cultures ◽  
Corneal Epithelium ◽  
Culture Medium ◽  
Corneal Epithelial Cell ◽  
Cell Type ◽  
Corneal Epithelial ◽  
Single Cell Type

Alternatives to the Draize rabbit eye irritation test are currently being investigated. Because of morphological and biochemical differences between the rabbit and the human eye, continuous human cell lines have been proposed for use in ocular toxicology studies. Single cell-type monolayer cultures in culture medium have been used extensively in ocular toxicology. In the present study, an SV40-immortalised human corneal epithelial (HCE) cell line was characterised immunohistochemically, by using 13 different monoclonal antibodies to cytokeratins (CKs), ranging from CK3 to CK20. The results from the monolayer HCE cell cultures were compared with those from the corneal epithelium of human corneal cryostat sections. Previous studies have shown that the morphology of the HCE cell is similar to that of primary cultured human corneal epithelial cells, and that the cells express the cornea-specific CK3. In the study reported here, we show that the cell line also expresses CKs 7, 8, 18 and 19. These CKs are typically expressed by simple epithelial cells, and are not found in the human cornea in vivo. Therefore, the monolayer HCE cell line grown in culture medium does not express the CK pattern that is typical of human corneal epithelium. This should be taken into consideration when using HCE cell cultures in similar single cell-type experiments for ocular toxicology.

scholarly journals An Online Dynamic Examination System (ODES) based on open source software tools

2021 ◽  
Vol 7 ◽  
pp. 100046
Author(s):  
George F. Fragulis ◽  
Maria Papatsimouli ◽  
Lazaros Lazaridis ◽  
Ioannis A. Skordas
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Tools ◽  
Examination System ◽  
Dynamic Examination

scholarly journals Species Having C4 Single-Cell-Type Photosynthesis in the Chenopodiaceae Family Evolved a Photosynthetic Phosphoenolpyruvate Carboxylase Like That of Kranz-Type C4 Species

2006 ◽  
Vol 142 (2) ◽  
pp. 673-684 ◽  
Author(s):  
María Valeria Lara ◽  
Simon D.X. Chuong ◽  
Hossein Akhani ◽  
Carlos Santiago Andreo ◽  
Gerald E. Edwards
Keyword(s):  
Single Cell ◽  
Phosphoenolpyruvate Carboxylase ◽  
Cell Type ◽  
C4 Species ◽  
Single Cell Type

A Single-Cell-Type Real-Time PCR Method Based on a Modified Patch-Pipette Cell Harvesting System

2016 ◽  
Vol 58 (8-9) ◽  
pp. 558-565 ◽  
Author(s):  
Yuanlong Song ◽  
Miaomiao Zhang ◽  
Xiaoqing Tao ◽  
Zifen Xu ◽  
Liangpin Zhang ◽  
...  
Keyword(s):  
Single Cell ◽  
Real Time ◽  
Real Time Pcr ◽  
Cell Type ◽  
Cell Harvesting ◽  
Patch Pipette ◽  
Pcr Method ◽  
Single Cell Type

A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type

2017 ◽  
Vol 16 (5-6) ◽  
Author(s):  
Lajmi Lakhal-Chaieb ◽  
Celia M.T. Greenwood ◽  
Mohamed Ouhourane ◽  
Kaiqiong Zhao ◽  
Belkacem Abdous ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Em Algorithm ◽  
Single Cell ◽  
Cell Lines ◽  
Methylation Status ◽  
Embryonic Stem ◽  
Cell Type ◽  
Data Set ◽  
Cpg Sites ◽  
Single Cell Type

AbstractWe consider the assessment of DNA methylation profiles for sequencing-derived data from a single cell type or from cell lines. We derive a kernel smoothed EM-algorithm, capable of analyzing an entire chromosome at once, and to simultaneously correct for experimental errors arising from either the pre-treatment steps or from the sequencing stage and to take into account spatial correlations between DNA methylation profiles at neighbouring CpG sites. The outcomes of our algorithm are then used to (i) call the true methylation status at each CpG site, (ii) provide accurate smoothed estimates of DNA methylation levels, and (iii) detect differentially methylated regions. Simulations show that the proposed methodology outperforms existing analysis methods that either ignore the correlation between DNA methylation profiles at neighbouring CpG sites or do not correct for errors. The use of the proposed inference procedure is illustrated through the analysis of a publicly available data set from a cell line of induced pluripotent H9 human embryonic stem cells and also a data set where methylation measures were obtained for a small genomic region in three different immune cell types separated from whole blood.

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