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Specification Clones: An Empirical Study of the Structure of Event-B Specifications [chapter]

Marie Farrell, Rosemary Monahan, James F. Power
2017 Lecture Notes in Computer Science  
In this paper we present an empirical study of formal specifications written in the Event-B language.  ...  We describe our algorithm used to identify clones at the machine, context and event level, and present results from an analysis of a large corpus of Event-B specifications.  ...  Our empirical study supports this claim by evaluating code clones at the specification level.  ... 
doi:10.1007/978-3-319-66197-1_10 fatcat:ojhfctizhrakrhfvnzu24fnj34

Molecular Cloning and Characterization of Pregnancy Specific Protein Uteroglobin can Lead to Pregnancy Detection in Cattle- A Review

Er. Nazakat Ali
2017 Journal of Medical Science And clinical Research  
Uteroglobin is a small progesterone-binding protein expressed in various organs of the cattle. Uteroglobin (UG) is an anti-inflammatory protein secreted by the airway epithelia of all mammals.  ...  Several methods of pregnancy diagnosis are being practiced in bovine species, yet none qualifies as the ideal pregnancy diagnosis method due to the inherent limitations of sensitivity, accuracy, specificity  ...  The former showed an immune reaction similar to that of -fetoprotein, while the latter showed no reactivity with known proteins and it was given the name "protein B" or the "pregnancy-specific protein  ... 
doi:10.18535/jmscr/v5i12.05 fatcat:pq4yyfttcvacdm6ggjvkbakm6m

Cloned Defective Interfering Influenza RNA and a Possible Pan-Specific Treatment of Respiratory Virus Diseases

Nigel Dimmock, Andrew Easton
2015 Viruses  
2015) Cloned defective interfering influenza RNA and a 7 possible pan-specific treatment of respiratory virus 8 diseases. Viruses , 7 (7). pp. 3768-3788.  ...  This review describes the application of DI virus to protect from virus-associated diseases in vivo using as an example a highly active cloned influenza A DI genome and virus that protects broadly in preclinical  ...  Conflicts of Interest Both authors hold patents on the use of DI influenza viruses as antivirals.  ... 
doi:10.3390/v7072796 pmid:26184282 pmcid:PMC4517125 fatcat:6rwit6b7njhbdkka7hkr7vdxge

Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

J. L. Nielsen, A. Schramm, A. E. Bernhard, G. J. van den Engh, D. A. Stahl
2004 Applied and Environmental Microbiology  
This approach, termed fluorescence-activated cell sorting-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental  ...  A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs.  ...  The validation of probes designed for FISH generally includes an empirical demonstration of discrimination between target and nontarget mismatch variants.  ... 
doi:10.1128/aem.70.12.7550-7554.2004 pmid:15574959 pmcid:PMC535210 fatcat:pqre2g6zrnfule4dtce2ev3egi

A highly accurate platform for clone-specific mutation discovery enables the study of active mutational processes

Mohammad KaramiNejadRanjbar, Sahand Sharifzadeh, Nina C Wietek, Mara Artibani, Salma El-Sahhar, Tatjana Sauka-Spengler, Christopher Yau, Volker Tresp, Ahmed A Ahmed
2020 eLife  
This was unidentifiable from the bulk WGS data. Overall, we propose DigiPico/MutLX method as a powerful framework for the identification of clone-specific variants at an unprecedented accuracy.  ...  Such studies, however, are inherently problematic because of the discovery of excessive false positive mutations when sequencing picogram quantities of DNA.  ...  (B) This active mutational process is 431 highlighted by the presence of a strong clone-specific kataegis event on chromosome 17 in run 432 D1111.  ... 
doi:10.7554/elife.55207 pmid:32255426 pmcid:PMC7228773 fatcat:dqookwnm6veihiy3w46vycuzz4

Cloning, Expression, and Substrate Specificity of MeCPA, a Zinc Carboxypeptidase That Is Secreted into Infected Tissues by the Fungal EntomopathogenMetarhizium anisopliae

Lokesh Joshi, Raymond J. St. Leger
1999 Journal of Biological Chemistry  
Thus, in evolutionary terms the fungal enzyme is an intermediate between the divergence of A and B forms and the differentiation of the A form into A1 and A2 isoforms.  ...  We report here the cDNA cloning of a carboxypeptidase A (MeCPA) that is secreted by an insect pathogenic fungus Metarhizium anisopliae into infected tissues.  ...  One aim of our study was the development of an efficient recombinant expression system for MeCPA.  ... 
doi:10.1074/jbc.274.14.9803 pmid:10092670 fatcat:6i7exd67snct5ouxiwk7a3eiae

Cloning of an inflammation-specific phosphatidyl inositol-linked form of murine vascular cell adhesion molecule-1

P Moy, R Lobb, R Tizard, D Olson, C Hession
1993 Journal of Biological Chemistry  
Thus in rodents alternate splicing of the VCAM1 gene generates a unique truncated inflammation-specific phosphatidylinositol-linked form of VCAM1.  ...  We have cloned a novel cDNA encoding only the three N-terminal domains of murine VCAM1 followed by a unique C-terminal tail generated by alternate splicing of a previously undescribed exon.  ...  human VCAMl genomic fragments, Linda Burkly for murine VCAMl genomic fragments, Janice DeMarinis and Lars Tragethon for DNA sequencing, Blake Pepinsky for PI-PLC, Barbara Wallner and Glenn Miller for the  ... 
pmid:7682556 fatcat:6vu2i5gjtrhgtc4k3ak673yw6q

Clonal Relationships between Invasive and CarriageStreptococcus pneumoniaeand Serotype‐ and Clone‐Specific Differences in Invasive Disease Potential

Angela B. Brueggemann, David T. Griffiths, Emma Meats, Timothy Peto, Derrick W. Crook, Brian G. Spratt
2003 Journal of Infectious Diseases  
The prevalence n p 351 of individual clones (sequence types) and serotypes among isolates from invasive disease was related to their prevalence in carriage, and an odds ratio (OR) for invasive disease  ...  The lack of heterogeneity between the ORs of different clones of the same serotype, and analysis of isolates of the same genotype, but different serotype, suggested that capsular serotype may be more important  ...  Acknowledgments We thank Karen Sleeman and Kyle Knox for selecting a random sample of pneumococcal carriage isolates from the Oxford carriage studies for use in this study.  ... 
doi:10.1086/374624 pmid:12717624 fatcat:ggcohq6pmvab3jeqpwhb6i3fbe

Cloning parallel simulations

Maria Hybinette, Richard M. Fujimoto
2001 ACM Transactions on Modeling and Computer Simulation  
NOTE: This is a preliminary release of an article accepted by the ACM Transactions on Modeling and Computer Simulation.  ...  The definitive version is currently in production at ACM and, when released, will supersede this version.  ...  ACKNOWLEDGMENTS The D-PAT application was written by Frederick Wieland of the MITRE Corporation and we are also grateful for his helpful comments on this work. This work was supported in part by U.S.  ... 
doi:10.1145/508366.508370 fatcat:7gaye7i4zjcevp7gfjm27vobaa

Things structural clones tell that simple clones don't

Hamid Abdul Basit, Usman Ali, Sidra Haque, Stan Jarzabek
2012 2012 28th IEEE International Conference on Software Maintenance (ICSM)  
We also discuss the contribution of structural clone detection towards program understanding, design recovery, maintenance, and refactoring using examples from the case study systems.  ...  Our case study of 11 open source systems revealed that over 50% of simple clones are captured by structural clones that often correspond to meaningful design or application domain concepts.  ...  ACKNOWLEDGMENT The authors are thankful to Arif Zaman for providing help in the data analysis.  ... 
doi:10.1109/icsm.2012.6405283 dblp:conf/icsm/BasitAHJ12 fatcat:kuvdmn25qbgt3fthv7yqthovua

Scalable detection of semantic clones

Mark Gabel, Lingxiao Jiang, Zhendong Su
2008 Proceedings of the 13th international conference on Software engineering - ICSE '08  
In this paper, we present the first scalable clone detection algorithm based on this definition of semantic clones.  ...  Our insight is the reduction of the difficult graph similarity problem to a simpler tree similarity problem by mapping carefully selected PDG subgraphs to their related structured syntax.  ...  Empirical Study This section contains a brief evaluation of the occurrence of weakly connected components and semantic threads in real systems.  ... 
doi:10.1145/1368088.1368132 dblp:conf/icse/GabelJS08 fatcat:torpmu42sfa2rh545m7g5bizcu

The Identity of Clones

Kathinka Evers
1999 Journal of Medicine and Philosophy  
This paper distinguishes between numerical and qualitative; relational and intrinsic; logical and empirical identity, and discusses the empirical individuation of clones in terms of genetics, physiology  ...  I argue that the only relation of identity cloning involves is qualitative, intrinsic and empirical: genetic indiscernibility, unlikely to include identity under other aspects mentioned.  ...  Thus far, we have reached the logical conclusions that the identity of clones that P assumes is (a) qualitative and (b) intrinsic. We now add that it is (c) empirical.  ... 
doi:10.1076/jmep. pmid:10223443 fatcat:5ldzhukk3nfavnkmy4vdrrhpsu

Towards contextual and on-demand code clone management by continuous monitoring

Gang Zhang, Xin Peng, Zhenchang Xing, Shihai Jiang, Hai Wang, Wenyun Zhao
2013 2013 28th IEEE/ACM International Conference on Automated Software Engineering (ASE)  
We implemented the proposed approach and conducted an empirical study with an industrial project.  ...  It supports on-demand customization of clone monitoring strategies in specific technical, personal, and organizational contexts using a domain-specific language.  ...  EMPIRICAL STUDY To validate the requirements for contextual and on-demand code clone management and evaluate the effectiveness of our approach, we conducted an empirical study with an industrial project  ... 
doi:10.1109/ase.2013.6693107 dblp:conf/kbse/ZhangPXJWZ13 fatcat:jjbiqkuz6nenzcbc73i73xzezi

Cloned avirulence gene of Pseudomonas syringae pv. glycinea determines race-specific incompatibility on Glycine max (L.) Merr

B. J. Staskawicz, D. Dahlbeck, N. T. Keen
1984 Proceedings of the National Academy of Sciences of the United States of America  
A single clone (pPg6L3) was detected that changed the race specificity of race 5 from virulent (compatible) to avirulent (incompatible) on the appropriate soybean cultivars.  ...  Completeness of the library was estimated by assaying clones for the expression of ice-nucleating activity in E. coli. Ice-nucleation activity was represented approximately once in every 600 clones.  ...  a specific early recognition event (4) .  ... 
doi:10.1073/pnas.81.19.6024 pmid:16593517 pmcid:PMC391851 fatcat:thxcospkwbfg7aqd26tmpta5cu

Universality of clone dynamics during tissue development

Steffen Rulands, Fabienne Lescroart, Samira Chabab, Christopher J. Hindley, Nicole Prior, Magdalena K. Sznurkowska, Meritxell Huch, Anna Philpott, Cedric Blanpain, Benjamin D. Simons
2018 Nature Physics  
Our study shows the emergence of core concepts of statistical physics in an unexpected context, identifying cellular systems as a laboratory to study non-equilibrium statistical physics.  ...  of clone sizes.  ...  (b) Histogram of the relative sizes of fragments (proportion of the total clone size) in clones consisting of two fragments.  ... 
doi:10.1038/s41567-018-0055-6 pmid:29736183 pmcid:PMC5935228 fatcat:plfh7o4b5bclziyitaee5zojli
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