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Sustainability in Scientific Software: Ecosystem complexity and Software Visibility
2020
Zenodo
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use it to
reduce recombination. ...
high user numbers -knowing how things "out there" are changing
• Adjustment
-making appropriate changes to account for
changing surroundings
• Synchronization
-ensuring that changes in multiple ...
doi:10.5281/zenodo.3885803
fatcat:hqoredvguvc4vbvtigu4k4anni
The Role of Protein Engineering in the Design and Production of Recombinant Proteins
2016
International Journal of Vaccines & Vaccination
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For this purpose, bioinformatics studies, how to predict the second and third buildings based on homology and adaptive modeling, predicting protein performance for the production of recombinant proteins ...
This study investigates the protein engineering tools in producing the recombinant and engineered proteins. ...
Protein engineering purposes, especially in enzymes, is enlarging the active position, changes activity (change specific activity, change the characteristics of the substrate), sustainability (change thermal ...
doi:10.15406/ijvv.2016.03.00067
fatcat:7rsclbgzgbe7xk3cfhtegkneo4
Polymorphisms in the S1 spike glycoprotein of Arkansas-type infectious bronchitis virus (IBV) show differential binding to host tissues and altered antigenicity
2016
Virology
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These findings are important because they propose that specific changes in S1 enhances virus fitness by more effective binding to host tissues (Y43H) and by evading a vaccine-induced antibody response ...
Protein histochemistry showed that the Y43H change allows for enhanced binding to trachea, whereas the ArkDPI S1 spike with H43 alone was able to bind CAM. ...
Acknowledgments We would like to thank Lisa Stabler and Debbie Hilt for their technical assistance. ...
doi:10.1016/j.virol.2016.08.030
pmid:27619927
pmcid:PMC7111678
fatcat:24t6xgqpgnadhhy5bmfaangz2m
Program fracture and recombination for efficient automatic code reuse
2015
2015 IEEE High Performance Extreme Computing Conference (HPEC)
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Program fracture and recombination allows developers to work with the simple implementation during development and testing, then use program fracture and recombination to automatically find and deploy ...
include automatic generation of new applications incorporating the best or most desirable functionality developed anywhere, the automatic elimination of errors and security vulnerabilities, effective software ...
Shards as Specifications and Code Search Program fracture and recombination promotes the view of shards as specifications. ...
doi:10.1109/hpec.2015.7396314
dblp:conf/hpec/AmidonDSR15
fatcat:rthwbwxmbjarzn7hatsthihy6u
Challenges and Pathways to Sustainability in Scientific Software Ecosystems
2018
Figshare
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use it to reduce
recombination complexity. ...
• Sensing work
-knowing how things "out there" are changing
• Adjustment
-making appropriate changes to account for
changing surroundings
• Synchronization
-ensuring that changes in multiple ...
@jameshowison Grant making and sustainability Grant-making • Software that reports its own use? ...
doi:10.6084/m9.figshare.7043093.v1
fatcat:ls7vm225bvdudgd75mzu2zmvzy
Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects
2016
Metabolic Engineering Communications
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multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and ...
In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface ...
Workflow design automation Existing cloning software packages cannot be used to quickly and easily implement changes in the design workflow and allow propagation of those changes throughout the downstream ...
doi:10.1016/j.meteno.2016.05.003
pmid:29468123
pmcid:PMC5779711
fatcat:wd3clkhlqnavrppkuiyrzsh66i
HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis
2021
Diversity
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By studying the phylogenetic incongruence, similarity plots and the distribution patterns of lineage-specific SNPs, we identify several potential recombination events between the two major HPV16 evolutionary ...
sequences, SNPs that have been reported in the literature to increase the risk of cancer. ...
Acknowledgments: M.N. would like to thank the Bodossakis foundation (MSc studentship: BDA-394) and the University of Thessaly Research committee (DEKA PhD studentship: DEKA-UTH-259) for financial support ...
doi:10.3390/d13100497
fatcat:tagyv4ka4fewjcihkdlrjfzpsi
Study of Specific Region of Plasmodium falciparum Nicotinamide/Nicotinate Mononucleotide Adenylyl Transferase (PfNMNAT): Characterizing a Possible Therapeutic Target
2017
Journal of Molecular and Genetic Medicine
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Citation: Nieto CA, Marín CY, Contreras LE, Ramírez MH (2017) Study of Specific Region of Plasmodium falciparum Nicotinamide/Nicotinate Mononucleotide Adenylyl Transferase (PfNMNAT): Characterizing a Possible ...
MatchMaker tool of the UCSF Chimera software was used to perform structural alignments of mutant vs. wild-type protein, identifying site-specific changes affecting NMN and ATP binding. ...
PfNMNAT mutants were designed using bioinformatics software to obtain 2 mutants in order to evaluate the specific sequences of the P. falciparum enzyme. ...
doi:10.4172/1747-0862.1000311
fatcat:whi7w5rkzfeujaytw6d7dngsye
Chemical complementarity between immune receptors and cancer mutants, independent of antigen presentation protein binding, is associated with increased survival rates
2021
Translational Oncology
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Therefore, we used several bioinformatics approaches to explore specific interactions between T-cell receptor (TCR) and tumor mutant peptide sequences. ...
Uterine cancer has been associated with a T-cell immune response that leads to increased survival. ...
for that change to occur at a specific AA position in the proteins. ...
doi:10.1016/j.tranon.2021.101069
pmid:33780706
fatcat:tgcgdsdkqfghpbzw67ngk2fcqq
Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing
2016
PLoS ONE
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A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. ...
With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia ...
Acknowledgments We are very grateful to Martin Figeac, Claude Preudhomme and the people in the hematology laboratory of the Lille hospital. ...
doi:10.1371/journal.pone.0166126
pmid:27835690
pmcid:PMC5106020
fatcat:uf2nddfb5zellcusi7yae6tvr4
Development and evaluation of loop-mediated isothermal amplification assay for rapid detection of Capripoxvirus
2015
Veterinary World
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Serial tenfold dilution of SPPV recombinant plasmid DNA was used for a calculating limit of detection. Analytical sensitivity and specificity were performed. ...
LAMP assay results were monitored by color change method using picogreen dye and agarose gel electrophoresis. ...
Acknowledgments The authors are thankful to Dr. Ravindra Sharma, Director of Research for providing required facilities and Mr. Chandan Singh and Kul Bahadur for all help. ...
doi:10.14202/vetworld.2015.1286-1292
pmid:27047031
pmcid:PMC4774739
fatcat:wywn3vy3qjaa3carm2h7n7rvcq
LDJump : Estimating variable recombination rates from population genetic data
2019
Molecular Ecology Resources
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We propose a novel approach for estimating population recombination rates based on genotyping or sequence data that involves a sequential multiscale change point estimator. ...
Our proposed method is accurate, computationally fast, and provides a parsimonious solution by ensuring a type I error control against too many changes in the recombination rate. ...
ACK N OWLED G EM ENTS The authors are very grateful to the editor and the reviewers for their valuable comments. We thank Kerstin Spitzer, Renato Pereira ...
doi:10.1111/1755-0998.12994
pmid:30666785
pmcid:PMC6519033
fatcat:m277ya45qnetvdxp3gqet3tmcy
Recombination shapes African swine fever virus serotype-specific locus evolution
2020
Scientific Reports
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Here, we analyzed ASFV serotype-specific locus (C-type lectin (EP153R) and CD2v (EP402R)) in order to allocate the recombination breakpoints in these immunologically important proteins and reveal driving ...
The phylogenetic analysis demonstrated the lack of clonal evolution for African strains which conclusively support the significance of recombinations in the serotype-specific locus. ...
Taking together, we hypothesize that serotype-specific locus consist of C-type lectin and CD2v, might be a hot-spot for drastic evolutionary changes due to: (i) unprecedented selective pressure during ...
doi:10.1038/s41598-020-75377-y
pmid:33116230
fatcat:ninaefb7wjfhtoxmglhfjmimam
A new metric for predicting software change using gene expression programming
2014
Proceedings of the 5th International Workshop on Emerging Trends in Software Metrics - WETSoM 2014
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. ¡ Specificity (Spec.) ...
develop quality models which predict
attributes like fault proneness and
CHANGE PRONENESS
¡ It is the probability of a class of a software
to change in the forthcoming release
software i.e. after ...
CHANGE INDEX METRIC ¡ Change Index (CI) -A new metric for ¡ Based on the results of the Simutrans metric was proposed as follows: ¡ For a given class C j , the CI for the following equation: CI = ((((0.24 ...
doi:10.1145/2593868.2593870
dblp:conf/icse/MalhotraK14
fatcat:mshwpx2zczdrhhsre4edjq2e64
Complete Genome Sequence of Potato leafroll virus Isolates Infecting Potato in the Different Geographical Areas of India Shows Low Level Genetic Diversity
2013
Indian Journal of Virology
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Amino acid changes specific to Indian isolates were observed and it was more in ORF 2 than in ORF 0, ORF 3 and ORF 4. ...
Out of five isolates, the isolate PBI-6 was recombinant one as detected by RDP3 software. ...
Amino acid changes specific to Indian isolates were observed ( Table 2 ). More number of amino acid changes was observed in ORF 2 than in ORF 3, ORF 4 and ORF 0. ...
doi:10.1007/s13337-013-0138-z
pmid:24426276
pmcid:PMC3784903
fatcat:4u65ltmojffizdp3pqsxlm6sti
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