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T-REx: Table Repair Explanations

Daniel Deutch, Nave Frost, Amir Gilad, Oren Sheffer
2020 Proceedings of the 2020 ACM SIGMOD International Conference on Management of Data  
T-REx then ranks the constraints and table cells according to their importance in the repair of this cell.  ...  To assist users in understanding the output of such data repair algorithms, we propose T-REx, a system for providing data repair explanations through Shapley values.  ...  T-REx 1 is a novel system for data repair explanations based on Shapley values [6] .  ... 
doi:10.1145/3318464.3384700 dblp:conf/sigmod/DeutchFGS20 fatcat:yrlczibdxzb2ffpntaf7kv2qgu

Impairment of APE1 Function Enhances Cellular Sensitivity to Clinically Relevant Alkylators and Antimetabolites

D. R. McNeill, W. Lam, T. L. DeWeese, Y.-C. Cheng, D. M. Wilson
2009 Molecular Cancer Research  
Base excision repair (BER) is the major pathway for removing mutagenic and cytotoxic oxidative and alkylation DNA modifications.  ...  Using a catalytically inactive, dominant negative protein form of human APE1, termed ED, which binds with high affinity to substrate DNA and blocks subsequent repair steps, we assessed the role of BER  ...  June 2009 Table 2 . 2 Cell Cycle Distribution of Chronic ED-Expressing CHO Cell Lines and the T-REx CHO Control Cell Cycle Distribution T-REx ED5 ED6 ED8 −Tet +Tet −Tet +Tet −Tet +Tet −Tet +Tet %G 1  ... 
doi:10.1158/1541-7786.mcr-08-0519 pmid:19470598 pmcid:PMC2745049 fatcat:ieoprlxrdralrdmof7btojsj4y

Page 43 of JAMA Internal Medicine Vol. 87, Issue 1 [page]

1951 JAMA Internal Medicine  
T.; Rex, R. O., and Williams, R. G.: Recent Modifica- tions in the Method of Studying Living Cells and Tissues in Transparent Chambers Inserted in the Rabbit’s Ear, Anat. Rec. 47:187-211 (Nov.) 1930.  ...  Compensatory processes seemed to offer an explanation for the continued good health of their patients.  ... 

Survey of Mission Planning and Management Architectures for Underwater Cooperative Robotics Operations

Lucas Martínez, Martínez-Ortega, Castillejo, Beltrán Martínez
2020 Applied Sciences  
A summary of the categorization for the measured features is included in Table 6 . Table 6 . T-REX assessment.  ...  Feature Category Explanation Plan Specification 1 Table 10 . 10 CPEF assessment. Feature Category Explanation Plan Specification 1 Table 11 . 11 TRAC assessment.  ... 
doi:10.3390/app10031086 fatcat:5nxnjqgldncdvpuhkp67ow7rfe

A human somatic cell culture system for modelling gene silencing by transcriptional interference

Theresa Kühnel, Helena Sophie Barbara Heinz, Nadja Utz, Tanja Božić, Bernhard Horsthemke, Laura Steenpass
2020 Heliyon  
Hemmo Meyer, University Duisburg-Essen, for providing Flp-In T-REx HeLa cells. We also acknowledge Dr. Jasmin Beygo for performing the PWS-SRO methylation analysis shown in Figure 1B .  ...  293) or 55 (Flp-In T-REx HeLa) cycles, 72 C for 10 min.  ...  ) or Fugene HD (Flp-In T-REx HeLa; Promega, #E2311) with 100 ng of minigene-BV-plasmids and 900 ng of plasmid pCSFLPe (Table S2) . 24 hours after transfection cells were transferred to four 10 cm cell  ... 
doi:10.1016/j.heliyon.2020.e03261 pmid:32021933 pmcid:PMC6994850 fatcat:itr6zhcyrzgmdl2uphzofqtika

From Ownership to Service-oriented Business Models: A Survey in Capital Goods Companies and a PSS Typology

Federico Adrodegari, Andrea Alghisi, Marco Ardolino, Nicola Saccani
2015 Procedia CIRP  
Acknowledgements The work described in this document has been conducted as part of the project T-REX (  ...  Given this context, the present paper, which stems from a research project (T-REX) funded by the European Commission that addresses the development of serviceoriented business models in the domains of  ...  In fact, the T-REX project aims to develop and implement a new business platform whose main elements are a new service-oriented business model, an improved design of the products and a reengineering of  ... 
doi:10.1016/j.procir.2015.02.105 fatcat:jsujp7px5jcjhb37xqhamjaiqu

Mutation Processes in 293-Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B

Monica K. Akre, Gabriel J. Starrett, Jelmar S. Quist, Nuri A. Temiz, Michael A. Carpenter, Andrew N. J. Tutt, Anita Grigoriadis, Reuben S. Harris, Javier Marcelo Di Noia
2016 PLoS ONE  
Surprisingly, both control and A3B-eGFP clones also elicited strong mutator phenotypes characteristic of defective mismatch repair.  ...  (B) Anti-GFP immunoblot of T-REx-293 A3B-eGFP and eGFP daughter cultures 24 hrs after Dox treatment.  ...  T-REx-293 cells were cultured in high glucose DMEM (Hyclone) supplemented with 10% FBS and 0.5% Pen/Strep.  ... 
doi:10.1371/journal.pone.0155391 pmid:27163364 pmcid:PMC4862684 fatcat:joktfrmbbrhjzdcox76tbcwq3y

ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells

Dongsung Kim, Yi Liu, Susannah Oberly, Raimundo Freire, Marcus B Smolka
2018 Nucleic Acids Research  
The ATR kinase is crucial for genome maintenance, but the mechanisms by which ATR controls the DNA repair machinery are not fully understood.  ...  Here, we find that long-term chronic inhibition of ATR signaling severely impairs the ability of cells to utilize homologous recombination (HR)-mediated DNA repair.  ...  We thank Robertus A. de Bruin for generously providing the 293-T-REX-E2F6 cells.  ... 
doi:10.1093/nar/gky625 pmid:30010936 fatcat:6irsyp3njrft7ipk3qhs44cf7i

RNAi Screening Uncovers a Synthetic Sick Interaction between CtIP and the BARD1 Tumor Suppressor

Hella A. Bolck, Sara Przetocka, Roger Meier, Christine von Aesch, Christina Zurfluh, Kay Hänggi, Vincent Spegg, Matthias Altmeyer, Michael Stebler, Simon F. Nørrelykke, Peter Horvath, Alessandro A. Sartori (+1 others)
2022 Cells  
Human CtIP is best known for its role in DNA end resection to initiate DNA double-strand break repair by homologous recombination.  ...  In brief, U2OS and U2OS Flp-In T-REx cells transfected with indicated siRNAs were grown on glass coverslips.  ...  U2OS Flp-In T-REx cell lines inducibly expressing siRNA-resistant RFP-FLAG-BARDwt and the L44R mutant variant were a kind gift from Jo Morris (University of Birmingham, U.K.) [20] .  ... 
doi:10.3390/cells11040643 pmid:35203293 pmcid:PMC8870135 fatcat:3nmc5fxeyzfurlecpsqd5xvdqa

Regulation of the RNAPII Pool Is Integral to the DNA Damage Response

Ana Tufegdžić Vidaković, Richard Mitter, Gavin P. Kelly, Michelle Neumann, Michelle Harreman, Marta Rodríguez-Martínez, Anna Herlihy, Juston C. Weems, Stefan Boeing, Vesela Encheva, Liam Gaul, Laura Milligan (+6 others)
2020 Cell  
K1268 ubiquitylation affects DNA repair and signals RNAPII degradation, essential for surviving genotoxic insult.  ...  In response to transcription-blocking DNA damage, cells orchestrate a multi-pronged reaction, involving transcription-coupled DNA repair, degradation of RNA polymerase II (RNAPII), and genome-wide transcription  ...  9 (in Flp-In T-Rex HEK293) This manuscript N/A Switchover RPB1-His WT clone 10 (in Flp-In T-Rex HEK293) This manuscript N/A Switchover RPB1-His K1268R clone 3 (in Flp-In T-Rex HEK293) This  ... 
doi:10.1016/j.cell.2020.02.009 pmid:32142654 pmcid:PMC7103762 fatcat:s6sl6qfmjjf55jzlxydt7s55hu

Loss of ZBTB24 impairs nonhomologous end-joining and class-switch recombination in patients with ICF syndrome

Angela Helfricht, Peter E Thijssen, Magdalena B Rother, Rashmi G Shah, Likun Du, Sanami Takada, Mélanie Rogier, Jacques Moritz, Hanna IJspeert, Chantal Stoepker, Monique M van Ostaijen-Ten Dam, Vincent Heyer (+14 others)
2020 Journal of Experimental Medicine  
Stoepker performed FokI assays and generated ZBTB24 KO U2OS cells and HeLa Flp-In/T-REx cells expressing inducible and siRNA-resistant GFP-ZBTB24 and GFP-ZBTB24 ΔZNF. M.S.  ...  HeLa Flp-In/T-REx cells, which were generated using the Flp-In/T-REx system (Thermo Fisher Scientific), were a gift of Geert Kops (University Medical Centre Utrecht, Utrecht, Netherlands) and Stephen Taylor  ...  S5 Analysis of HeLa Flp-In/T-REx cells expressing GFP-ZBTB24 or GFP-ZBTB24 ΔZNF. Related to Fig. 6.  ... 
doi:10.1084/jem.20191688 pmid:32865561 pmcid:PMC7526497 fatcat:edoovhaw3ncijpsvaoqmz44mtq

TOPBP1Dpb11plays a conserved role in homologous recombination DNA repair through the coordinated recruitment of 53BP1Rad9

Yi Liu, José Renato Cussiol, Diego Dibitetto, Jennie Rae Sims, Shyam Twayana, Robert Samuel Weiss, Raimundo Freire, Federica Marini, Achille Pellicioli, Marcus Bustamante Smolka
2017 Journal of Cell Biology  
Genome maintenance and cancer suppression require homologous recombination (HR) DNA repair.  ...  Our results support a model in which TOPBP1Dpb11plays a conserved role in mediating a phosphoregulated circuitry for the control of recombinational DNA repair.  ...  CTR-53BP1 is stably integrated in HEK293 cells using a Flp-In T-REx system.  ... 
doi:10.1083/jcb.201607031 pmid:28228534 pmcid:PMC5350513 fatcat:53qfpjskfvflnhasjck72jkqpq

Altering TET dioxygenase levels within physiological range affects DNA methylation dynamics of HEK293 cells

Christian Grosser, Nicholas Wagner, Katrin Grothaus, Bernhard Horsthemke
2015 Epigenetics  
carboxylcytosine; 5fC, 5-formylcytosine; 5hmC, 5-hydroxymethylcytosine; 5mC, 5-methylcytosine; CGI, CpG island; DNMT, DNA methyltransferase; FDR, false discovery rate; FLAG-tag, a polypeptide protein tag; Flp-In TM T-REx  ...  Funding This project is supported by the Deutsche Forschungsgemeinschaft (DFG) graduate research training program no. 1431: "Transcription, Chromatin Structure and DNA Repair in Development and Differentiation  ...  TET1 #1-3: single-cell derived T-REx-293-TET1 cell lines; GFP #1-3: single-cell derived T-REx-293-GFP cell lines; Cdox: doxycyclineinduced transgene expression; -dox: uninduced control.  ... 
doi:10.1080/15592294.2015.1073879 pmid:26186463 pmcid:PMC4622922 fatcat:w5imwz5nazebrb7rgkcl5mdrlm

The Role of adaptive mission planning and control in persistent autonomous underwater vehicles presence

M. P. Brito, N. Bose, Ron Lewis, Polly Alexander, Gwyn Griffiths, James Ferguson
2012 2012 IEEE/OES Autonomous Underwater Vehicles (AUV)  
In [23] Rajan et al. present the results of two experiments using T-REX. Both were volume surveys.  ...  T-REX is an instance of a Model-Based architecture, meaning that the knowledge about what is possible is held in a model.  ... 
doi:10.1109/auv.2012.6380748 fatcat:44p2ns6vlfex7jfq2r7yj3g5wq

Mitochondrial protein-linked DNA breaks perturb mitochondrial gene transcription and trigger free radical–induced DNA damage

Shih-Chieh Chiang, Martin Meagher, Nick Kassouf, Majid Hafezparast, Peter J. McKinnon, Rachel Haywood, Sherif F. El-Khamisy
2017 Science Advances  
Although much is known about the repair of PDBs in the nucleus, little is known about this process in the mitochondria.  ...  (A) Immunoblotting of Flp-In T-Rex 293 cell lines after doxycycline induction using antibodies against TDP1, GFP, and b tubulin.  ...  The resulting pcDNA5-FRT construct was used together with the Flp recombinase-expressing plasmid pPGKFLP to cotransfect the Flp-In T-Rex 293 cells.  ... 
doi:10.1126/sciadv.1602506 pmid:28508041 pmcid:PMC5409496 fatcat:7s3xw7v7vjb2nctw2flwr57sby
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