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openother-openNov 2022View details →

Comparing the Intensity of Variability Changes in Software Product Line Evolution - Related Research Artifacts

This archived open repository contains open science material related to the following submission to the <a href="https://www.journals.elsevier.com/journal-of-systems-and-software/call-for-papers/software-reuse-for-the-next-generation">Journal of Systems and Software (JSS) special issue Software Reuse for the Next Generation</a>: C. Kröher, L. Gerling, K. Schmid, Comparing the intensity of variability changes in software product line evolution, Journal of Systems and Software. Submitted November 2022. The paper presents the application of a fine-grained, variability-centric analysis approach to four different software product lines: <a href="https://github.com/torvalds/linux">Linux kernel</a>, <a href="https://github.com/coreboot/coreboot">coreboot firmware</a>, <a href="https://github.com/mirror/busybox">BusyBox UNIX utilities</a>, and <a href="https://sourceforge.net/projects/axtls/">axTLS embedded SSL</a>. The approach is based on the differentiation between artifact-specific and variability information in code, build, and variability model artifacts to identify the intensity (the frequency and the amount) with which developers change variability information in practice. In order to complement the results presented in the submission and support reproducibility as well as reuse, the following artifacts are available: <ul> <li>JSS-VM_2022-11-01.zip: a compressed archive containing the virtual machine in which the analysis was executed. This virtual machine was created with <a href="https://www.vmware.com/content/vmware/vmware-published-sites/us/products/workstation-player/workstation-player-evaluation.html.html">VMware Workstation 16 Player</a> based on <a href="https://ubuntu.com/download/desktop">Ubuntu Desktop 22.04.1</a> (username and password: jss). It provides all installed software, configuration files, data sets, and results as described in the submission. Download, extract, and start the virtual machine to access the detailed description of its content and usage on the desktop.</li> <li>ComAnI-Applications.zip: a compressed archive containing the technical realization of the analysis approach and the configuration files used to apply it to the individual software product lines. This includes: <ul> <li>ComAnI_Guide.pdf: the guide explaining the application and its usage in general</li> <li>ComAnI.jar: the Java executable archive file representing the main application for starting an analysis</li> <li>ComAnI-PS.jar: a modified version of the previous Java executable archive file, which provides the number of code, build, and variability model artifacts as specified by the regular expressions of a given configuration file as well as their total number of lines based on the current state of a repository only (no history)</li> <li>DeadCodeChangeAnalyzer.jar: a commit analyzer plug-in for detecting changes relevant to dead code detection (not used in the submission)</li> <li>GitCommitExtractor.jar: a commit extraction plug-in for extracting commits from Git repositories</li> <li>SvnCommitExtractor.jar: a commit extraction plug-in for extracting commits from Subversion (SVN) repositories</li> <li>VariabilityChangeAnalyzer.jar: a commit analyzer plug-in for detecting changes to artifact-specific and variability information in code, build, and variability model artifacts (realization of the commit analysis process described in the submission)</li> <li>busybox-commit-list: a plain text file containing a subset of the BusyBox commits as required by the application to extract and analyze only those parts of its entire history relevant for the submission (quote from the submission: "For BusyBox, we had to further exclude commits before the complete migration to Kbuild and after the introduction of a script for extracting variability model information from code artifacts, which initiated defining variability information of the variability model as part of comments in code artifacts. This mixing of information and artifact types is not supported by our tooling")</li> <li>axtls.properties: the configuration (file) defining the required properties for extracting and analyzing commits of the axTLS history</li> <li>busybox.properties: the configuration (file) defining the required properties for extracting and analyzing all commits of the BusyBox history</li> <li>busybox-subset.properties: the configuration (file) defining the required properties for extracting and analyzing the commits specified in the busybox-commit-list file only, resulting in the respective subset of the BusyBox history</li> <li>coreboot.properties: the configuration (file) defining the required properties for extracting and analyzing all commits of the coreboot history</li> <li>linux.properties: the configuration (file) defining the required properties for extracting and analyzing all commits of the Linux kernel history</li> <li>template.properties: the configuration (file) template including descriptions of each property and its valid values</li> </ul> </li> <li>ComAnI-Results.zip: a compressed archive containing the (raw) analysis results from applying the approach via its realization as provided by the previous archive to each of the software product lines. Hence, for each subject, a directory with the respective name exist, which in turn contains the following artifacts: <ul> <li>VariabilityChangeAnalyzer-Results_2022-09-[…]: the directory containing the respective analysis results and some automated visualizations. Please note that some files are not correctly labeled, .e.g. some files for axTLS and BusyBox are prefixed with "coreboot", while containing the correct data for the respective subjects. Further, for BusyBox, two directories exist, which the additional readme-file explains</li> <li>project-size-trace.txt: the complete trace from starting ComAnI-PS.jar (see description above) with a specific configuration file to its final output</li> </ul> </li> <li>JSS23_Extended-Evolution-Analysis_Statistics.ods: a <a href="https://www.libreoffice.org/discover/calc/">LibreOffice Calc</a> spreadsheet containing data derived from the raw ones of the ComAnI-Results.zip and the respective visualizations as presented in the submission. Further, some sheets include additional data preparations used to write certain parts of the result and discussion sections.</li> </ul> The additional LICENSE file defines <a href="https://www.apache.org/licenses/LICENSE-2.0">Apache License Version 2.0, January 2004</a> to apply for all artifacts in this repository. This work is partially supported by the Evoline project, funded by the DFG (German Research Foundation) under Priority Programme SPP 1593 and by the ITEA3 project REVaMP², funded by the BMBF (German Ministry of Research and Education) under grant 01IS16042H. Any opinions expressed herein are solely by the authors and not of the DFG or BMBF.

opencc-zeroNov 2022View details →

Comparative analysis of health authorities spokesperson and health influencer during the COVID-19 pandemic: A case in Indonesia

Background: Concerns over an infodemic following a surge in health misinformation circulating on social media sets out the government's priority for Indonesia. Given the urgent work on the coronavirus disease 2019 (COVID-19) response, the government collaborated with health-related spokespersons and influencers with a medical background by starting a COVID-19 public education campaign on social media. A collaborative initiative involved health spokespersons from government and non-government to clarify misinformation about COVID-19. Methods: The primary purpose of this research is to compare government and non-government spokespersons by examining their role in educating about the COVID-19 vaccine and health services. This study employed comparative factor analysis and non-participatory observation toward the media activity of spokespersons in Indonesia. Using a questionnaire, this study examines the dimensions of public campaigns, risk communication, health and emergency, leadership, and communication from Indonesian spokespersons. The data collection was conducted in two stages. The first stage was a pilot study that collected data from 102 respondents, the second stage collected data from 276 respondents. Results: Findings show that utilizing the spokesperson is important due to its capabilities of reaching diverse audiences, and improving public engagement, trustworthiness, and credibility. Conclusions: With the combination of health authorities spokespersons and health influencers in Indonesia, this study provides valuable insights for communication management in developing and supporting the role of health authorities from the government, non-government as well as medical sectors.

opencc-zeroDec 2022View details →

Supplementary files for: Why should we compare morphological and molecular disparity?

1. Indices of morphological disparity seek to summarise the highly multivariate morphological variation across groups of species within clades, time bins or other groups. Morphological variation can be quantified using geometric morphometric, outline or surface-based methods. These are most effective when morphological differences are relatively modest and there are numerous ubiquitous landmarks and phase-aligned features of shape variation. The most disparate samples, such as those across classes and phyla, typically necessitate the use of discrete characters. Unfortunately, such characters are often compiled subjectively in a manner reflecting the level of morphological and taxonomic focus and the intensity of taxon sampling. 2. Sampling intensity is often highly variable within a single data set, especially in repurposed and amalgamated cladistic matrices. Here we propose indices of molecular disparity analogous to those of morphological disparity. Molecular sequence data can be obtained in a more objective, automated and scaleable manner than morphological data. 3. Comparisons of the morphological and molecular disparity of subclades in sixteen large data sets suggest that molecular disparity is less susceptible to sampling biases than morphological disparity. Moreover, distance matrices inferred from individual genes tend to correlate strongly with each other and with distances from all concatenated genes. By contrast, morphological and molecular disparity are typically not significantly correlated across subclades, such that comparisons for groups can help to give a fuller picture of their evolution. Within mammals, Afrotheria have conspicuously high morphological disparity but modest molecular disparity, suggesting unusually high morphological plasticity. Even more strikingly, the molecular disparity of rodents is over five times that for Artiodactyla, despite having only half of their morphological disparity. These contrasts suggest the differential operation of geometric, biomechanical, ontogenetic and environmental constraints on form. 4. Given the increasing abundance of total evidence data sets in the literature and the widespread and sometimes uncritical repurposing of discrete morphological characters, we propose the comparison of morphological and molecular disparity as a useful tool to understand subclade evolution more fully.

opencc-by-4.0Dec 2022View details →

Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family.Supplementary_data

This is Supplementary files for the paper "Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family". The description for each dataset is located inside files.

opencc-zeroDec 2022View details →

Higher spring phenological sensitivity to forcing temperatures of Asian compared to European tree species under low and high pre-chilling conditions Datasets

Winter chilling, spring forcing temperature and photoperiod are the most important drivers explaining the spatial and temporal variability of spring phenology in temperate trees. However, how these factors interact with each other on dormancy release and spring budburst date remains unclear and varies greatly depending on species. Our knowledge is also limited as to whether heat accumulation of forcing temperatures that trigger bud break in spring is a linear or non-linear process. Here, we aimed at experimentally quantifying the effect of chilling, forcing, photoperiod and their interactions on the budburst dates of nine different temperate tree species from East Asia (near Beijing, China) and Central Europe (near Zurich, Switzerland), including six phylogenetically related species (same genus). We conducted a full factorial experiment in climate chambers using two chilling (low and high, i.e., 0 vs. 56 days at 2C after sampling at the end of December), four forcing (5, 10, 15, and 20C), and two photoperiod (8 vs. 16 h) treatments simultaneously in Beijing and Zurich. We found that species growing near Beijing responded more readily to forcing conditions than species of the same genus growing near Zurich regardless of chilling treatment. Budburst timing of most species but European beech was marginally, if at all, affected by photoperiod. Furthermore, our results suggest that linear heat accumulation, as commonly used with the growing degree hours (GDH) model, could result in accurate prediction of budburst date depending on the temperature threshold used as a basis for heat accumulation. Our results also demonstrate the important role of chilling in shaping the sensitivity and rate of forcing accumulation to trigger budburst and suggest that species-specific sigmoid relationship for accumulating heat that accounts for prior chilling exposure may yield better predictions of budburst dates. Our results suggest that deciduous trees may have adapted their chilling and forcing requirements in regards to the predictability of winter-spring transition and late spring frosts. A less predictable winter-spring transition, as observed in Central Europe, could have driven species evolution towards higher chilling and forcing requirements compared to species growing in a more predictable climate of Northeastern Asia. Our cross-continental experiment therefore suggests that the spring phenology of East Asian species is tighter coupled to spring forcing temperature than Central European forests.

opencc-by-4.0Dec 2022View details →

A comparative assessment of different adaptive spatial refinement strategies in phase-field fracture models for brittle fracture

Abstract: (from [1]) <blockquote> For the smeared approximation of a discrete crack, phase-field fracture simulations of brittle materials require suitable finite element meshes in regions where crack propagation is expected to get an accurate resolution of the phase-field function. The intuitive option is to pre-refine the mesh in regions of the expected crack paths. However, this could lead to very computationally intensive simulations due to the high number of elements. Alternatively, adaptive spatial refinement of the finite element mesh is utilized based on appropriate error indicators to obtain the required accuracy in the areas of crack propagation. Different error indicators can be used: the most common one for phase-field fracture simulations is the threshold-based approach, in which elements are refined depending on the value of the phase-field function. Alternatively, the Kelly error indicator can be used as a criterion for spatial adaptivity. It considers the jumps in the gradients of the phase-field function between the elements. We additionally introduce here an error indicator based on configurational forces, that depend on the Eshelby stress tensor. For mode I loading in linear elastic fracture mechanics, the configurational forces have a close connection to the \(\mathscr{J}\)-Integral and the critical fracture energy \(\mathrm{G}_\mathrm{c}\) , respectively. Therefore, a suitable norm of the configurational forces is introduced as an error indicator here. These three error indicators are introduced and compared to each other in terms of accuracy and efficiency by means of numerical examples for crack growth in the single edge notched shear test. </blockquote> Contact: Maurice Rohracker Institute of Applied Mechanics Friedrich-Alexander-Universität Erlangen-Nürnberg Egerlandstr. 5 91058 Erlangen Software: All phase-field fracture simulations were performed with deal.II [2], version 9.2.0, on the HPC cluster Meggie of NHR@FAU. The authors gratefully acknowledge the scientific support and HPC resources provided by the Erlangen National High Performance Computing Center (NHR@FAU) of the Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU). The hardware is funded by the German Research Foundation (DFG). License: Creative Commons Attribution 4.0 International Context: Dataset supplementing preprint: [1] M.Rohracker, P.Kumar, J.Mergheim, "A comparative assessment of different adaptive spatial refinement strategies in phase-field fracture models for brittle fracture", Forces in Mechanics, 2022, <a href="https://doi.org/10.1016/j.finmec.2022.100157">10.1016/j.finmec.2022.100157</a>. This dataset contains the complete results presented in [1], which include global variables, field variables, and meshes. File structure: The file structure is explained in more detail in the shipped README.md in the dataset folder. References: [1] M.Rohracker, P.Kumar, J.Mergheim, "A comparative assessment of different adaptive spatial refinement strategies in phase-field fracture models for brittle fracture", Forces in Mechanics, 2022, <a href="https://doi.org/10.1016/j.finmec.2022.100157">10.1016/j.finmec.2022.100157</a>. [2] D. Arndt, W. Bangerth, B. Blais, T. C. Clevenger, M. Fehling, A. V. Grayver, T. Heister, L. Heltai, M. Kronbichler, M. Maier, P. Munch, J.-P. Pelteret, R. Rastak, I. Thomas, B. Turcksin, Z. Wang, D. Wells, The deal.II Library, Version 9.2 Journal of Numerical Mathematics, vol. 28, p. 131-146, 2020.

opencc-zeroDec 2022View details →

Comparative molecular and morphological species delineation of Halammohydra Remane, 1927 (Hydrozoa) – with description of four new species

Whereas most cnidarians are macrofaunal, a few microscopic lineages have evolved and some of them inhabit marine sediments. The meiofaunal genus with the most species is Halammohydra, comprising nine nominal species. Species are described with high intraspecific variability in e.g., number of tentacles and statocysts and the shape and length of tentacles and body, complicating morphological identification to species level. Additionally, there is not much molecular data available. This study aims to revise already described species with morphological and molecular methods, as well as, to delineate potential new species answering questions about their geographical distribution. For this, specimens were sampled at 16 locations in the Northwest Atlantic and two localities in the East Atlantic, documented with light microscopy and fixed individually for sequencing (16S, 18S and CO1). Herewith morphological characters were linked to a specific sequence, enabling testing of character variation within one molecular phylogenetic group. Phylogenetic analyses were conducted (Bayesian Interference and Maximum Likelihood) in combination with species delimitation tests (ABGD, GMYC and bPTP). Four already described species were identified in the data sets, and all of these were found at multiple localities. Four new species are described. Overall, the combined molecular and morphological data acquisition revealed multiple new species and a high degree of sympatry in Halammohydra. This, together with the confirmed excessive intraspecific variation in morphological traits, underlines the necessity of molecular sequencing for taxonomy and species identification of Halammohydra.

opencc-by-4.0Dec 2022View details →

Dataset for Comparing Three Generations of D-Wave Quantum Annealers for Minor Embedded Combinatorial Optimization Problems

Dataset for the paper titled "Comparing Three Generations of D-Wave Quantum Annealers for Minor Embedded Combinatorial Optimization Problems" LA-UR-23-20367

opencc-by-4.0Jan 2023View details →

Comparative performance of coarse-grained IDP models at different resolutions

Files for simulations. Molsim start scripts and final outputs, MARTINI Stark start scripts (including force field files, and some intermediate data). Not all intermediate data available, but all data necessary to reproduce simulations should be included. MARTINI simulations follow the procedure "Dry energy minimization" -> "Solvation" -> "Salting" -> "Energy minimization" -> "NVT equilibration" -> "NPT equilibration" -> "Production Run", where the output from the previous step is the input into the next step. For some folders, the output from previous step has been copied, but not always. In case of another simulation, but using a bigger box, some files from the simulation with smaller box were re-used. Thus, if a file seems to be missing, check the folder with corresponding simulation using a smaller box. Some "analysis files" are included, e.g. the radius of gyration for each time step, in order to allow for the reproduction of graphs in upcoming publication, and further exploration.

opencc-zeroFeb 2023View details →

Data and code for: Feeding, mating, and animal wellbeing: New insights from Phylogenetic Comparative Methods

Some species tend to thrive in captivity, while others risk health and reproductive problems. This enables the use of Phylogenetic Comparative Methods (PCMs) to identify aspects of natural biology that predispose species to faring poorly or well. Risk factors can then suggest new ways to improve animal care. A steady trickle of studies has applied PCMs to animal welfare over the last two decades, Lewis et al. (1) providing the latest. Here we contextualise this new work and suggest further research it might inspire. Provided here are the data and R code for Figure 1 provided in a commentary on: (1) Lewis, K., M.O. Parker, L. Proops, and S.D. McBride, Risk factors for stereotypic behaviour in captive ungulates. Proceedings of the Royal Society B: Biological Sciences, 2022. 289(1983): p. 20221311.

Records used to compare duplicate detection of three systematic review screener tools

This upload contains records obtained from PubMed, Scopus and Web of Science that were used to compare the sensitivity of the duplicate detection systems of three systematic review screening tools, as well as a custom-made dataset to evaluate the detection of duplicates under various scenarios.

Comparative Mitochondrial Genomics of selected Noctuoid Moths (Lepidoptera: Noctuoidea) with implications for their Phylogeny

In this study, I sequenced and annotated the complete mitochondrial genome sequences of 19 species that belong to the superfamily Noctuoidea viz. Actinotia polyodon, Episparis tortuosalis, Ercheia cyllaria, Eudocima salaminia, Hulodes caranea, Hypospila bolinoides, Ischyja manlia, Lygephila dorsigera, Mecodina praecipua, Mocis undata, Odontodes seranensis, Ophiusa tirhaca, Oraesia emarginata, Pandesma quenavadi, Polydesma boarmoides, Psimada quadripennis, Rusicada privata, Trigonodes hyppasia and Xanthodes albago. In addition to this, I performed the analysis of their genetic compositions as well as their molecular characterization in order to provide molecular insights into their taxonomic and phylogenetic implications. Based on the data and those obtained from the NCBI database, I examined the phylogenetic relationships among the species of the superfamily Noctuoidea.

opencc-zeroFeb 2023View details →

Reconstructing locomotor ecology of extinct avialans: a case study of Ichthyornis comparing sternum morphology and skeletal proportions

Avian skeletal morphology is associated with locomotor function, including flight style, swimming and terrestrial locomotion, and permits informed inferences on locomotion in extinct taxa. The fossil taxon Ichthyornis (Avialae: Ornithurae) has long been regarded as highly aerial, with flight similar to terns or gulls (Laridae), and skeletal features resembling foot-propelled diving adaptations. However, rigorous testing of locomotor hypotheses has yet to be performed on Ichthyornis, despite its notable phylogenetic position as one of the most crownward stem birds. We analysed separate datasets of 3D sternal shape (geometric morphometrics) and skeletal proportions (linear measurements across the skeleton), to examine how well these data types predict locomotor traits in Neornithes. We then used this information to infer locomotor capabilities of Ichthyornis. We find strong support for both soaring and foot-propelled swimming capabilities in Ichthyornis. Further, sternal shape and skeletal proportions provide complementary information on avian locomotion: skeletal proportions allow better predictions of the capacity for flight, whereas sternal shape predicts variation in more specific locomotor abilities such as soaring, foot-propelled swimming, and escape burst flight. These results have important implications for future studies of extinct avialan ecology, and underscore the importance of closely considering sternum morphology in investigations of fossil bird locomotion.

Comparing zero-parameter theories for the WCA and harmonic-repulsive melting lines (data)

This dataset contains data related to the paper titled "Comparing zero-parameter theories for the WCA and harmonic-repulsive melting lines" by Jeppe C. Dyre and Ulf R. Pedersen, with the abstract: The melting line of the Weeks-Chandler-Andersen (WCA) system was recently determined accurately and compared to the predictions of four analytical hard-sphere approximations [Attia \textit{et al.}, J. Chem. Phys. \textbf{157}, 034502 (2022)]. Here, we study an alternative zero-parameter prediction based on the isomorph theory, the input of which relate to properties at a single reference state point on the melting line. The two central assumptions made are that the harmonic-repulsive potential approximates the WCA potential and that pair collisions are uncorrelated. The new approach gives excellent predictions at high temperatures, while the hard-sphere-theory based predictions are better at lower temperatures. Supplementing the WCA investigation, the face-centered-crystal to fluid coexistence line is determined for a system of harmonic-repulsive particles and compared to the zero-parameter theories. The results indicate that the excellent isomorph-theory predictions for the WCA potential at higher temperatures may be partly due to a cancellation of errors between the two above-mentioned assumptions.

opencc-by-4.0Apr 2007View details →

Fig. 1. A in A comparative analysis of the Baltic and Rovno amber arthropod faunas: representative samples

Fig. 1. A piece of Rovno amber (UA-662) with more than 50 inclusions.

Stowaways S1. Methods & Comparative Materials

A full description of biometric methods utilized in the Stowaways manuscript, including formulae following previously published protocols and comparative material dataset.

opencc-zeroFeb 2023View details →

Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops

Vaccinium is a large genus of shrubs that includes a handful of economically important berry crops. Given the numerous hybridizations and polyploidization events, the taxonomy of this genus has remained the subject of long debate. In addition, berries and berry-based products are liable to adulteration, either fraudulent or unintentional due to misidentification of species. The availability of more genomic information could help achieve higher phylogenetic resolution for the genus, provide molecular markers for berry crop identification, and a framework for efficient genetic engineering of chloroplasts. Therefore, in this study, we assembled five Vaccinium chloroplast sequences representing the economically relevant berry types: northern highbush blueberry (V. corymbosum), southern highbush blueberry (V. corymbosum hybrids), rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium), and bilberry (V. myrtillus). Comparative analyses showed that the Vaccinium chloroplast genomes exhibited an overall highly conserved synteny and sequence identity among them. Polymorphic regions included the expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, indels, and single nucleotide polymorphisms. Based on their in silico discrimination power, we suggested variants that could be developed into molecular markers for berry crop identification. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events that occurred during northern and southern highbush blueberry domestication.

Investigation of the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients in Jordan

As the world continues to battle the COVID-19 pandemic, Jordan is no exception. In order to improve the accuracy of diagnosis, researchers in Jordan have conducted an investigation into the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients.

opencc-by-4.0Mar 2023View details →

Comparative analysis of two Candida parapsilosis isolates from the patient with a central venous catheter harbouring the Y132F and R398I mutations

This work presents a comparative analysis of 2 clinical isolates of C. parapsilosis; isolated from haemoculture (HC) and central venous catheter (CVC). Both strains harboured Y132F and R398I mutations associated with resistance to fluconazole (FLC). Differences between HC and CVC isolates in terms of virulence, resistance to FLC and lipid distribution were addressed. Expression of the ERG6 and ERG9 genes, lipid analysis, fatty acid composition and lipase activity were assessed by qPCR, thin-layer chromatography/high performance liquid chromatography, gas chromatography and spectrophotometry, respectively. A regulation of the ERG6 and ERG9 genes did not prove any impact on FLC resistance. Analysis of lipid metabolism showed a higher accumulation of lanosterol in both isolates regardless of FLC presence. Additionally, a decreased level in triacylglycerols (TAG) with impact on the composition of total FA was observed for both isolates. Direct impact of the ERG11 mutations to lipid/FA analysis has not been confirmed. The higher lipase activity observed for C. parapsilosis HC isolate could be correlated with the significantly decreased level of TAG. The very close relatedness between both isolates suggests that one isolate was derived from another after the initial infection of the host.