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Thorn forking, weak normality, and theories with selectors [article]

Daniel Max Hoffmann, Anand Pillay
2020 arXiv   pre-print
We discuss the role of weakly normal formulas in the theory of thorn forking, as part of a commentary on the paper "Thorn forking and stable forking" by Ealy and Onshuus (Rev. acad. colomb. cienc. exact  ...  We also give a counterexample to Corollary 4.2 from that paper, and in the process discuss "theories with selectors".  ...  We will be assuming a basic knowledge of notions from stability such as forking, dividing, and canonical bases of stationary types. In addition to [7] one could refer to [4] for example.  ... 
arXiv:2006.15630v1 fatcat:lskjgyprofcv7dslbrsg7xsgba

DNA Replication Origin Plasticity and Perturbed Fork Progression in Human Inverted Repeats

R. Lebofsky, A. Bensimon
2005 Molecular and Cellular Biology  
Whether origin usage and/or fork elongation can cope with the variable structure of these genes is unknown.  ...  The stability of metazoan genomes during their duplication depends on the spatiotemporal activation of origins and the progression of forks.  ...  Ronald Lebofsky is supported the Natural Sciences and Engineering Council of Canada.  ... 
doi:10.1128/mcb.25.15.6789-6797.2005 pmid:16024811 pmcid:PMC1190330 fatcat:goya77htsfgdtodjdi2jciyc7q

Page 38 of Entomological Society of America. Annals of the Entomological Society of America Vol. 17, Issue 1 [page]

1924 Entomological Society of America. Annals of the Entomological Society of America  
Cornicles .25 mm. in diameter at base. Beak attaining cornicles, ter- minal joints stout, measuring .18, .15, .07 mm., respectively. Media variable, sometimes once forked and sometimes twice forked.  ...  In 31 individuals 7 showed both wings twice forked; 11, once forked, and 13 showed one wing once forked and one twice forked. Hind wing with both cross veins present.  ... 

On Weak Elimination of Hyperimaginaries and its Consequences [article]

Donald Brower, Cameron Donnay Hill
2012 arXiv   pre-print
Generalizing results of [1] and [3], we show that in a simple theory with WEHI, forking and thorn-forking coincide.  ...  As a further application of our technology, we demonstrate stable forking for 1-based theories of finite SU-rank that have WEHI.  ...  Introduction Canonical bases were and are a key notion in geometric stability theory.  ... 
arXiv:1210.7883v1 fatcat:izgqwiwnsvayxh6c6odqup6yq4

SURFACE: A Practical Blockchain Consensus Algorithm for Real-World Networks [article]

Zhijie Ren, Ziheng Zhou
2020 arXiv   pre-print
Consequently, the blockchain can normally achieve fast probabilistic confirmation with high throughput and low latency.  ...  SURFACE, standing for Secure, Use-case adaptive, and Relatively Fork-free Approach of Chain Extension, is a consensus algorithm that is designed for real-world networks and enjoys the benefits from both  ...  Moreover, by our assumption of the normal situation, all node should have a consistent B(u, r) and canonical chain C.  ... 
arXiv:2002.07565v3 fatcat:6itmyaovsnhltlfs4rqu6r7k5e

Replication dynamics of recombination-dependent replication forks

Karel Naiman, Eduard Campillo-Funollet, Adam T. Watson, Alice Budden, Izumi Miyabe, Antony M. Carr
2021 Nature Communications  
We further demonstrate that HR-restarted forks progress uninterrupted through a fork barrier that arrests canonical forks.  ...  AbstractReplication forks restarted by homologous recombination are error prone and replicate both strands semi-conservatively using Pol δ.  ...  progress (and possibly during fork convergence and termination with the incoming canonical fork).  ... 
doi:10.1038/s41467-021-21198-0 pmid:33568651 fatcat:fbbgpi6y5fagfczxxfkhrdrl3u

Some remarks on log surfaces

Haidong Liu
2017 Proceedings of the Japan Academy. Series A Mathematical sciences  
Fujino and Tanaka established the minimal model theory for Q-factorial log surfaces in characteristic 0 and p, respectively.  ...  We prove that every intermediate surface has only log terminal singularities if we run the minimal model program starting with a pair consisting of a smooth surface and a boundary R-divisor.  ...  He would also like to thank Chen Jiang for many discussions on MR log canonical when they were attending in the conference of HDAG held in Utah.  ... 
doi:10.3792/pjaa.93.115 fatcat:bjmslzyiobfylkpdrgsld74kfu

Control of DNA Damage Bypass by Ubiquitylation of PCNA

Ripley, Gildenberg, Washington
2020 Genes  
We will focus on the structure and function of the E3 ubiquitin ligases Rad18 and Rad5 that facilitate the mono-ubiquitylation and poly-ubiquitylation of PCNA, respectively.  ...  These pathways include translesion synthesis and template switching.  ...  Acknowledgments: We thank Christine Kondratick, Justin Ling, Devin Reusch, Kyle Powers, and Elizabeth Boehm for discussions. Conflicts of Interest: The authors declare no conflicts of interest.  ... 
doi:10.3390/genes11020138 pmid:32013080 pmcid:PMC7074500 fatcat:eetf4th3arevbkbxhawgalq22a

Roles for DNA polymerase δ in initiating and terminating leading strand DNA replication

Zhi-Xiong Zhou, Scott A. Lujan, Adam B. Burkholder, Marta A. Garbacz, Thomas A. Kunkel
2019 Nature Communications  
Given that ribonucleotide and mismatch incorporation rates by these replicases influence somatic and germline patterns of variation, it is important to understand the details and exceptions to this overall  ...  Most current evidence indicates that DNA polymerases ε and δ, respectively, perform the bulk of leading and lagging strand replication of the eukaryotic nuclear genome.  ...  Degtyareva, and K. Bebenek for critical reading and thoughtful comments on the manuscript. We thank T. Carr for the S. pombe strains.  ... 
doi:10.1038/s41467-019-11995-z pmid:31488849 pmcid:PMC6728351 fatcat:jvpwnsmhhbfxhnuuzqffmgmdw4

Forkable Regular Expressions [chapter]

Martin Sulzmann, Peter Thiemann
2016 Lecture Notes in Computer Science  
By IH, r φ and therefore r · s φ. The other case is similar. Case r + s: Similar to the above. Case Fork (r ): L(Fork (r )) = {} implies L(r) = {}.  ...  We consider forkable regular expressions, which enrich regular expressions with a fork operator, to establish a formal basis for static and dynamic analysis of the communication behavior of concurrent  ...  Based on the above results we obtain a decidable method to test for similarity for some behaviors r and s. We build the canonical normal forms of r and s.  ... 
doi:10.1007/978-3-319-30000-9_15 fatcat:utpe2z54svayvhrmhy7zbdnd6u

Canonical DNA Repair Pathways Influence R-Loop-Driven Genome Instability

Peter C. Stirling, Philip Hieter
2017 Journal of Molecular Biology  
In order to suppress the accumulation of mutations and maintain the genome, organisms have evolved a robust replication and mitotic apparatus and a semi-redundant network of DNA repair machinery and cell  ...  Mutations in homologous recombination, nucleotide excision repair, crosslink repair and DNA damage checkpoints have all now been linked to formation and function of transcription-coupled R-loops.  ...  Acknowledgments We thank members of the Hieter and Stirling labs for helpful comments on this manuscript. This research is funded by the Canadian Cancer Society (grant 703263 to P.C.S.). P.C.S. and P.  ... 
doi:10.1016/j.jmb.2016.07.014 pmid:27452366 pmcid:PMC5253333 fatcat:gnvlzlrzo5fzhghw4r6y4f6phi

Forkable Regular Expressions [article]

Martin Sulzmann, Peter Thiemann
2015 arXiv   pre-print
We consider forkable regular expressions, which enrich regular expressions with a fork operator, to establish a formal basis for static and dynamic analysis of the communication behavior of concurrent  ...  We define a novel compositional semantics for forkable expressions, establish their fundamental properties, and define derivatives for them as a basis for the generation of automata, for matching, and  ...  We build the canonical normal forms of r and s. If the canonical normal forms are syntactically equivalent, we find that that r and s are similar. Otherwise, r and s are dissimilar.  ... 
arXiv:1510.07293v2 fatcat:7jmvuvw3i5dedpndnxyr4heurq

The FANC/BRCA Pathway Releases Replication Blockades by Eliminating DNA Interstrand Cross-Links

Xavier Renaudin, Filippo Rosselli
2020 Genes  
Understanding how cells cope with ICLs is mandatory to ameliorate ICL-based anticancer therapies and provide the molecular basis to prevent or bypass cancer drug resistance.  ...  However, ICLs are also generated in cells as byproducts of normal metabolic activities.  ...  (A) base excision repair (BER), nucleotide excision repair (NER) and mismatch repair (MMR) repair damaged or mismatched bases.  ... 
doi:10.3390/genes11050585 pmid:32466131 fatcat:pnk2yzppxjexxml6lyxenrjtby

A new, rare and distinctive species of Panorthoptera (Insecta, Archaeorthoptera) from the Upper Carboniferous of Xiaheyan (Ningxia, China)

Jun-Jie Gu, Olivier Béthoux, Dong Ren
2017 Fossil Record  
The most common species are comparatively remote relatives of Orthoptera (grasshoppers, crickets and katydids), belonging to the Archaeorthoptera nec Panorthoptera (the latter including crown Orthoptera  ...  This research is supported by the National Natural Science Foundation of China (nos. 31360525, 31730087, 41688103), Program for Changjiang Scholars and Innovative Research Team in University (IRT17R75  ...  The photograph was taken using a digital camera Canon 5D Mark III (Canon, Tokyo, Japan), coupled to a Canon MP-E 65 mm macro lens equipped with a polarizing filter.  ... 
doi:10.5194/fr-20-253-2017 fatcat:h7dxdzpq6nea7bcq7sj4r6iihi

S. pombe Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1 [article]

Alice Budden, Murat Eravci, Eduard Campillo-Funollet, Karel Naiman, Anthony Carr
2022 bioRxiv   pre-print
Arrested replication forks, when restarted by homologous recombination, result in error-prone DNA syntheses and non-allelic homologous recombination.  ...  However, we identified Rtf2 to be physically associated with mRNA processing and splicing factors and rtf2 deletion to cause increased intron retention.  ...  forks arresting and restarting using non-canonical (ẟ/ẟ) replication.  ... 
doi:10.1101/2022.03.10.483798 fatcat:p6dy7rspvjartcq54dvuztttkm
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