Cell line name recognition in support of the identification of synthetic lethality in cancer from text

Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus. Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers

Cell Line Monolayer Tissue Culture FKDL dan Cell Line OL sebagai Media Penumbuh Virus pada Pengembangan Bioteknologi Biomolekuler (Penelitian Eksperimental Laboratoris)

Cell line sangatlah penting dalam dunia medis, khususnya dibidang diagnosis, produksi vaksin maupun dibidang bioteknologi serta biomolekuler. Berbagai penelitian telah dilakukan untuk tehnik pembuatan Cell Line Monolayer Tissue Culture. Namun selama ini kita dapat membeli cell line di ITCC Canada; dengan harga yang cukup tinggi dan memerlukan waktu yang cukup lama untuk tibanya seed cell line ini ke Indonesia. Bertitik tolak dari permasalahan diatas, pada ini penelitian dikembangkan biakan jaringan dari FKDL (Foetal Kidney Lamb) dan OL (Ovine Lung). Biakan jaringan dapat digunakan untuk kepentingan pengembangan Bioteknologi, Bio Molekuer, Identifikasi Virus, diagnosis ,maupun Rekayasa Genetik, Stem Cell. Bahan yang digunakan pada penelitian ini adalah Foetus Domba Muda yang diambil ginjal (Kidney Lamb) dan paru-paru domba muda (Ovine Lung), eagle medium, versen tripsin, phosphate buffer saline yang manganding Ca++ dan Mg++ serta yang Ca dan Mg Free, serta Foetal Calf Serum dan Serum sapi (semua bahan dan alat haruslah steril). Pembuatan vaksin sub unit molekuler dengan menggunakan cell line (OL). Cell OL ditanami virus EBL, terbentuk CPE, dititrasi dengan menemukan titer virus EBL yang sesuai standar 105,5 TCD50. suspensi virus dikumpulkan kemudian disonikasi untuk mendapatkan envelope virus, selanjutnya dilihat berat molekul antigen melalui SDS page, ditemukan 51 Kda. Kemudian diadakan uji postulat koch, dengan menggunakan cell line (OL), dilanjutkan dengan PCR, setelah itu diadakan uji serum netralisasi untuk melihat titer antibody serta diadakan uji immunoblotting ditemukan satu band envelope protein Egp51, yang berarti protein Egp51 adalah murni dan dapat digunakan sebagai kandidat vaksin sub unit molekuler. Dari hasil penelitian dapat disimpulkan Virus EBL isolat lokal mengandung sub unit protein envelope gp 51 yang merupakan protein hemaglutinin. Protein hemaglutinin envelope gp 51 virus EBL isolat lokal bersifat imunogenik dan protektif

Development and characterization of a new human hepatic cell line

The increasing demand and hampered use of primary human hepatocytes for research purposes have urged scientists to search for alternative cell sources, such as immortalized hepatic cell lines. The aim of this study was to develop a human hepatic cell line using the combined overexpression of TERT and the cell cycle regulators cyclin D1 and mutant isoform CDK4R24C. Following transduction of adult human primary hepatocytes with the selected immortalization genes, cell growth was triggered and a cell line was established. When cultured under appropriate conditions, the cell line expressed several hepatocytic markers and liver-enriched transcription factors at the transcriptional and/or translational level, secreted liver-specific proteins and showed glycogen deposition. These results suggest that the immortalization strategy applied to primary human hepatocytes could generate a novel hepatic cell line that seems to retain some key hepatic characteristics

Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types.

Cancer cell lines are a cornerstone of cancer research but previous studies have shown that not all cell lines are equal in their ability to model primary tumors. Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia to evaluate cell lines as models of primary tumors across 22 tumor types. We perform correlation analysis and gene set enrichment analysis to understand the differences between cell lines and primary tumors. Additionally, we classify cell lines into tumor subtypes in 9 tumor types. We present our pancreatic cancer results as a case study and find that the commonly used cell line MIA PaCa-2 is transcriptionally unrepresentative of primary pancreatic adenocarcinomas. Lastly, we propose a new cell line panel, the TCGA-110-CL, for pan-cancer studies. This study provides a resource to help researchers select more representative cell line models

An Empirical-Mathematical Approach for Calibration and Fitting Cell-Electrode Electrical Models in Bioimpedance Tests

This paper proposes a new yet efficient method allowing a significant improvement in the on-line analysis of biological cell growing and evolution. The procedure is based on an empirical-mathematical approach for calibration and fitting of any cell-electrode electrical model. It is valid and can be extrapolated for any type of cellular line used in electrical cell-substrate impedance spectroscopy (ECIS) tests. Parameters of the bioimpedance model, acquired from ECIS experiments, vary for each cell line, which makes obtaining results difficult and—to some extent-renders them inaccurate. We propose a fitting method based on the cell line initial characterization,and carry out subsequent experiments with the same line to approach the percentage of well filling and the cell density (or cell number in the well). To perform our calibration technique, the so-called oscillation-based test (OBT) approach is employed for each cell density. Calibration results are validated by performing other experiments with different concentrations on the same cell line with the same measurement technique. Accordingly, a bioimpedance electrical model of each cell line is determined, which is valid for any further experiment and leading to a more precise electrical model of the electrode-cell system. Furthermore, the model parameters calculated can be also used by any other measurement techniques. Promising experimental outcomes for three different cell-lines have been achieved, supporting the usefulness of this technique

UVB radiation induced effects on cells studied by FTIR spectroscopy

We have made a preliminary analysis of the results about the eVects on tumoral cell line (lymphoid T cell line Jurkat) induced by UVB radiation (dose of 310 mJ/cm^2) with and without a vegetable mixture. In the present study, we have used two techniques: Fourier transform infrared spectroscopy (FTIR) and flow cytometry. FTIR spectroscopy has the potential to provide the identiWcation of the vibrational modes of some of the major compounds (lipid, proteins and nucleic acids) without being invasive in the biomaterials. The second technique has allowed us to perform measurements of cytotoxicity and to assess the percentage of apoptosis. We already studied the induction of apoptotic process in the same cell line by UVB radiation; in particular, we looked for correspondences and correlations between FTIR spetroscopy and flow cytometry data finding three highly probable spectroscopic markers of apoptosis (Pozzi et al. in Radiat Res 168:698-705, 2007). In the present work, the results have shown significant changes in the absorbance and spectral pattern in the wavenumber protein and nucleic acids regions after the treatments