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Sustainability in Scientific Software: Ecosystem complexity and Software Visibility

James Howison
2020 Zenodo  
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

Hossein Shahcheraghi
2016 International Journal of Vaccines & Vaccination  
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

Christina Leyson, Monique França, Mark Jackwood, Brian Jordan
2016 Virology  
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

Peter Amidon, Eli Davis, Stelios Sidiroglou-Douskos, Martin Rinard
2015 2015 IEEE High Performance Extreme Computing Conference (HPEC)  
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

James Howison
2018 Figshare  
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

Zhenyu Shi, Claudia E. Vickers
2016 Metabolic Engineering Communications  
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

Marios Nikolaidis, Dimitris Tsakogiannis, Garyfalia Bletsa, Dimitris Mossialos, Christine Kottaridi, Ioannis Iliopoulos, Panayotis Markoulatos, Grigoris D. Amoutzias
2021 Diversity  
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

Nieto CA, Marín CY, Contreras LE, Ramirez MH
2017 Journal of Molecular and Genetic Medicine  
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

Monica Hsiang, Boris I. Chobrutskiy, Michael Diaz, Taha I. Huda, Stefan Creadore, Saif Zaman, Konrad J. Cios, Etienne C. Gozlan, George Blanck
2021 Translational Oncology  
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

Marc Duez, Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mikaël Salson, Florian Thonier, Art F. Y. Poon
2016 PLoS ONE  
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

Kanisht Batra, Aman Kumar, Vinay Kumar, Trilok Nanda, Narender S. Maan, Sushila Maan
2015 Veterinary World  
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

Philipp Hermann, Angelika Heissl, Irene Tiemann‐Boege, Andreas Futschik
2019 Molecular Ecology Resources  
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

Mariia Nefedeva, Ilya Titov, Sodnom Tsybanov, Alexander Malogolovkin
2020 Scientific Reports  
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

Ruchika Malhotra, Megha Khanna
2014 Proceedings of the 5th International Workshop on Emerging Trends in Software Metrics - WETSoM 2014  
. ¡ 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

A. Jeevalatha, Priyanka Kaundal, R. K. Shandil, N. N. Sharma, S. K. Chakrabarti, B. P. Singh
2013 Indian Journal of Virology  
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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