Clone Detection

Over the last decade many techniques and tools for software clone detection have been proposed. In this paper, we provide a qualitative comparison and evaluation of the current state-of-the-art in clone detection techniques and tools, and organize the large amount of information into a coherent conceptual framework. We begin with background concepts, a generic clone detection process and an overall taxonomy of current techniques and tools. We then classify, compare and evaluate the techniques and tools in two different dimensions. First, we classify and compare approaches based on a number of facets, each of which has a set of (possibly overlapping) attributes. Second, we qualitatively evaluate the classified techniques and tools with respect to a taxonomy of editing scenarios designed to model the creation of Type-1, Type-2, Type-3 and Type-4 clones. Finally, we provide examples of how one might use the results of this study to choose the most appropriate clone detection tool or technique in the context of a particular set of goals and constraints. The primary contributions of this paper are: (1) a schema for classifying clone detection techniques and tools and a classification of current clone detectors based on this schema, and (2) a taxonomy of editing scenarios that produce different clone types and a qualitative evaluation of current clone detectors based on this taxonomy.

Although Streptococcus mutans has been implicated as a major etiological agent of dental caries, our cross-sectional preliminary study indicated that 10% of subjects with rampant caries in permanent teeth do not have detectable levels of S. mutans . Our aims were to use molecular methods to detect all bacterial species associated with caries in primary and permanent teeth and to determine the bacterial profiles associated with different disease states. Plaque was collected from 39 healthy controls and from intact enamel and white-spot lesions, dentin lesions, and deep-dentin lesions in each of 51 subjects with severe caries. 16S rRNA genes were PCR amplified, cloned, and sequenced to determine species identities. In a reverse-capture checkerboard assay, 243 samples were analyzed for 110 prevalent bacterial species. A sequencing analysis of 1,285 16S rRNA clones detected 197 bacterial species/phylotypes, of which 50% were not cultivable. Twenty-two new phylotypes were identified. PRO...

Lymphomas express a tumor-specific antigen which can be targeted by cancer vaccination. We evaluated the ability of a new idiotype protein vaccine formulation to eradicate residual t(14;18)+ lymphoma cells in 20 patients in a homogeneous, chemotherapy-induced first clinical complete remission. All 11 patients with detectable translocations in their primary tumors had cells from the malignant clone detectable in their blood by PCR both at diagnosis and after chemotherapy, despite being in complete remission. However, 8 of 11 patients converted to lacking cells in their blood from the malignant clone detectable by PCR after vaccination and sustained their molecular remissions. Tumor-specific cytotoxic CD8+ and CD4+ T cells were uniformly found (19 of 20 patients), whereas antibodies were detected, but apparently were not required for molecular remission. Vaccination was thus associated with clearance of residual tumor cells from blood and long-term disease-free survival. The demonstra...

Molecular approaches aimed at detection of a broadrange of prokaryotes in the environment routinely rely on classifying heterogeneous 16S rRNA genes amplified by polymerase chain reaction (PCR) using primers with broad specificity. The general method of sampling and categorizing DNA has been to clone then sequence the PCR products. However, the number of clones required to adequately catalog the majority of taxa in a sample is unwieldy. Alternatively, hybridizing target sequences to a universal 16S rRNA gene microarray may provide a more rapid and comprehensive view of prokaryotic community composition. This study investigated the breadth and accuracy of a microarray in detecting diverse 16S rRNA gene sequence types compared to clone-and-sequencing using three environmental samples: urban aerosol, subsurface soil, and subsurface water. PCR products generated from universal 16S rRNA gene-targeted primers were classified by using either the clone-and-sequence method or by hybridization to a novel high-density microarray of 297,851 probes complementary to 842 prokaryotic subfamilies. The three clone libraries comprised 1391 highquality sequences. Approximately 8% of the clones could not be placed into a known subfamily and were considered novel. The microarray results confirmed the majority of clone-detected subfamilies and additionally demonstrated greater amplicon diversity extending into phyla not observed by the cloning method. Sequences matching operational taxonomic units within the phyla Nitrospira, Planctomycetes, and TM7, which were uniquely detected by the array, were verified with specific primers and subsequent amplicon sequencing. Subfamily richness detected by the array corresponded well with nonparametric richness predictions extrapolated from clone libraries except in the water community where clone-based richness predictions were greatly exceeded. It was concluded that although the microarray is unreliable in identifying novel prokaryotic taxa, it reveals greater diversity in environmental samples than sequencing a typically sized clone library. Furthermore, the microarray allowed samples to be rapidly evaluated with replication, a significant advantage in studies of microbial ecology.

Our understanding of the degradation of organic matter will benefit from a greater appreciation for the genes encoding enzymes involved in the hydrolysis of biopolymers such as chitin, one of the most abundant polymers in nature. To isolate representative and abundant chitinase genes from uncultivated marine bacteria, we constructed libraries of genomic DNA isolated from coastal and estuarine waters. The libraries were screened for genes encoding proteins that hydrolyze a fluorogenic analogue of chitin, 4-methylumbelliferyl beta-D-N,N'-diacetylchitobioside (MUF-diNAG). The abundance of clones capable of MUF-diNAG hydrolysis was higher in the library constructed with DNA from the estuary than in that constructed with DNA from coastal waters, although the abundance of positive clones was also dependent on the method used to screen the library. Plaque assays revealed nine MUF-diNAG-positive clones of 75,000 screened for the estuarine sample and two clones of 750,000 for the coastal...

Finding, understanding and managing software clones -passages of duplicated source code -is of large interest in research and practice. There is an abundance of techniques to detect clones. However, all these techniques are limited to a single revision of a program. When the code changes, the analysis must be run again from scratch even though only small parts may have changed.

In recent years many methods and tools for software clone detection have been proposed. While some work has been done on assessing and comparing performance of these tools, very little empirical evaluation has been done. In particular, accuracy measures such as precision and recall have only been roughly estimated, due both to problems in creating a validated clone benchmark against which tools can be compared, and to the manual effort required to hand check large numbers of candidate clones. In this paper we propose an automated method for empirically evaluating clone detection tools that leverages mutation-based techniques to overcome these limitations by automatically synthesizing large numbers of known clones based on an editing theory of clone creation. Our framework is effective in measuring recall and precision of clone detection tools for various types of fine-grained clones in real systems without manual intervention.

Although numerous different clone detection approaches have been proposed to date, not a single one is both incremental and scalable to very large code bases. They thus cannot provide real-time cloning information for clone management of very large systems. We present a novel, index-based clone detection algorithm for type 1 and 2 clones that is both incremental and scalable. It enables a new generation of clone management tools that provide real-time cloning information for very large software. We report on several case studies that show both its suitability for real-time clone detection and its scalability: on 42 MLOC of Eclipse code, average time to retrieve all clones for a file was below 1 second; on 100 machines, detection of all clones in 73 MLOC was completed in 36 minutes.

Model-based development is becoming an increasingly common development methodology. In important domains like embedded systems already major parts of the code are generated from models specified with domain-specific modelling languages. Hence, such models are nowadays an integral part of the software development and maintenance process and therefore have a major economic and strategic value for the software-developing organisations. Nevertheless almost no work has been done on a quality defect that is known to seriously hamper maintenance productivity in classic codebased development: Cloning. This paper presents an approach for the automatic detection of clones in large models as they are used in model-based development of control systems. The approach is based on graph theory and hence can be applied to most graphical data-flow languages. An industrial case study demonstrates the applicability of our approach for the detection of clones in Matlab/Simulink models that are widely used in model-based development of embedded systems in the automotive domain.

Cloning in software systems is known to create problems during software maintenance. Several techniques have been proposed to detect the same or similar code fragments in software, so-called simple clones. While the knowledge of simple clones is useful, detecting design-level similarities in software could ease maintenance even further, and also help us identify reuse opportunities. We observed that recurring patterns of simple clones -so-called structural clones -often indicate the presence of interesting design-level similarities. An example would be patterns of collaborating classes or components. Finding structural clones that signify potentially useful design information requires efficient techniques to analyze the bulk of simple clone data and making non-trivial inferences based on the abstracted information.

In this study, the composition of the metabolically active fraction of the microbial community occurring in Gulf of Mexico marine sediments (water depth, 550 to 575 m) with overlying filamentous bacterial mats was determined. The mats were mainly composed of either orange-or white-pigmented Beggiatoa spp. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from three different sediment depths (0 to 2, 6 to 8, and 10 to 12 cm) that had been subjected to reverse transcription-PCR amplification. Domainspecific 16S PCR primers were used to construct 12 different 16S crDNA libraries containing 333 Archaea and 329 Bacteria clones. Analysis of the Archaea clones indicated that all sediment depths associated with overlying orange-and white-pigmented microbial mats were almost exclusively dominated by ANME-2 (95% of total Archaea clones), a lineage related to the methanogenic order Methanosarcinales. In contrast, bacterial diversity was considerably higher, with the dominant phylotype varying by sediment depth. An equivalent number of clones detected at 0 to 2 cm, representing a total of 93%, were related to the ␥ and ␦ classes of Proteobacteria, whereas clones related to ␦-Proteobacteria dominated the metabolically active fraction of the bacterial community occurring at 6 to 8 cm (79%) and 10 to 12 cm (85%). This is the first phylogenetics-based evaluation of the presumptive metabolically active fraction of the Bacteria and Archaea community structure investigated along a sediment depth profile in the northern Gulf of Mexico, a hydrocarbon-rich cold-seep region.

A relevant consequence of the unceasing expansion of the Web and e-commerce is the growth of the demand of new Web sites and Web applications. As a result, Web sites and applications are usually developed without a formalized process, but Web pages are directly coded in an incremental way, where new pages are obtained by duplicating existing ones. Duplicated Web pages, having the same structure and just differing for the data they include, can be considered as clones. The identification of clones may reduce the effort devoted to test, maintain and evolve Web sites and applications. Moreover, clone detection among different Web sites aims to detect cases of possible plagiarism. In this paper we propose an approach, based on similarity metrics, to detect duplicated pages in Web sites and applications, implemented with HTML language and ASP technology. The proposed approach has been assessed by analyzing several Web sites and Web applications. The obtained results are reported in the paper with respect to some case studies.

Code clones are similar program structures recurring in variant forms in software system(s). Several techniques have been proposed to detect similar code fragments in software, so-called simple clones. Identification and subsequent unification of simple clones is beneficial in software maintenance. Even further gains can be obtained by elevating the level of code clone analysis. We observed that recurring patterns of simple clones often indicate the presence of interesting higher-level similarities that we call structural clones. Structural clones show a bigger picture of similarity situation than simple clones alone. Being logical groups of simple clones, structural clones alleviate the problem of huge number of clones typically reported by simple clone detection tools, a problem that is often dealt with post-detection visualization techniques. Detection of structural clones can help in understanding the design of the system for better maintenance and in reengineering for reuse, among other uses. In this paper, we propose a technique to detect some useful types of structural clones. The novelty of our approach includes the formulation of the structural clone concept and the application of data mining techniques to detect these higherlevel similarities. We describe a tool called Clone Miner that implements our proposed technique. We assess the usefulness and scalability of the proposed techniques via several case studies. We discuss various usage scenarios to demonstrate in what ways the knowledge of structural clones adds value to the analysis based on simple clones alone.

The area of clone detection has considerably evolved over the last decade, leading to approaches with better results, but at the same time using more elaborate algorithms and tool chains. In our opinion a level has been reached, where the initial investment required to setup a clone detection tool chain and the code infrastructure required for experimenting with new heuristics and algorithms seriously hampers the exploration of novel solutions or specific case studies. As a solution, this paper presents CloneDetective, an open source framework and tool chain for clone detection, which is especially geared towards configurability and extendability and thus supports the preparation and conduction of clone detection research.

However, there has been little work on clone detection in models with the limitations on detection precision and completeness. This paper presents ModelCD, a novel clone detection tool for Matlab/Simulink models, that is able to efficiently and accurately detect both exactly matched and approximate model clones. The core of ModelCD is two novel graph-based clone detection algorithms that are able to systematically and incrementally discover clones with a high degree of completeness, accuracy, and scalability. We have conducted an empirical evaluation with various experimental studies on many real-world systems to demonstrate the usefulness of our approach and to compare the performance of ModelCD with existing tools.

Code clones are similar code fragments that occur at multiple locations in a software system. Detection of code clones provides useful information for maintenance, reengineering, program understanding and reuse. Several techniques have been proposed to detect code clones. These techniques differ in the code representation used for analysis of clones, ranging from plain text to parse trees and program dependence graphs. Clone detection based on lexical tokens involves minimal code transformation and gives good results, but is computationally expensive because of the large number of tokens that need to be compared. We explored string algorithms to find suitable data structures and algorithms for efficient token based clone detection and implemented them in our tool Repeated Tokens Finder (RTF). Instead of using suffix tree for string matching, we use more memory efficient suffix array. RTF incorporates a suffix array based linear time algorithm to detect string matches. It also provides a simple and customizable tokenization mechanism. Analysis and experiments show that our clone detection is simple, flexible, precise, scalable, and performs better than the previous well-known tools.

Microbial diversity was characterized in miningimpacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.

Mutations inducing resistance to anti-epidermal growth factor receptor (EGFR) therapy may have a clinical impact even if present in minor cell clones which could expand during treatment. We tested this hypothesis in lung cancer patients treated with tyrosine kinase inhibitors (TKIs). Eighty-three patients with lung adenocarcinoma treated with erlotinib or gefitinib were included in this study. The mutational status of KRAS and EGFR was investigated by direct sequencing (DS). KRAS mutations were also assessed by mutant-enriched sequencing (ME-sequencing). DS detected KRAS mutations in 16 (19%) of 83 tumors; ME-sequencing identified all the mutations detected by DS but also mutations in minor clones of 14 additional tumors, for a total of 30 (36%) of 83. KRAS mutations assessed by DS and ME-sequencing significantly correlated with resistance to TKIs (P = .04 and P = .004, respectively) and significantly affected progression-free survival (PFS) and overall survival (OS). However, the predictive power of mutations assessed by ME-sequencing was higher than that obtained by DS (hazard ratio [HR] = 2.82, P = .0001 vs HR = 1.98, P = .04, respectively, for OS; HR = 2.52, P = .0005 vs HR = 2.21, P = .007, respectively, for PFS). Survival outcome of patients harboring KRAS mutations in minor clones, detected only by ME-sequencing, did not differ from that of patients with KRAS mutations detected by DS. Only KRAS mutations assessed by ME-sequencing remained an independent predictive factor at multivariate analysis. KRAS mutations in minor clones have an important impact on response and survival of patients with lung adenocarcinoma treated with EGFR-TKI. The use of sensitive detection methods could allow to more effectively identify treatment-resistant patients.

In this paper we describe a new approach for the detection of clones in source code, which is inspired by the concept of frequent itemsets from data mining. The source code is represented as an abstract syntax tree in XML; we can use different kinds of XML-languages for different programming languages, such as Java, C++, or PROLOG. Our approach is very flexible; it can be configured easily to work with multiple languages.

Over the last decade many techniques for software clone detection have been proposed. In this paper, we provide a comprehensive survey of the capabilities of currently available clone detection techniques. We begin with an overall survey based on criteria that capture the main features of detection techniques. We then propose a set of hypothetical editing scenarios for different clone types, and evaluate the techniques based on their estimated potential to accurately detect clones that may be created by those scenarios.

Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/ 1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms.

This paper describes the design, implementation, and application of a new algorithm to detect cloned code. It operates on the abstract syntax trees formed by many compilers as an intermediate representation. It extends prior work by identifying clones even when arbitrary subtrees have been changed. On a 16,000-line code corpus, 20-50% of its clones eluded previous methods. The method also identifies cloning in declarations, so it is somewhat more general than conventional procedural abstraction.

Due to their pivotal role in software engineering, considerable effort is spent on the quality assurance of software requirements specifications. As they are mainly described in natural language, relatively few means of automated quality assessment exist. However, we found that clone detection, a technique widely applied to source code, is promising to assess one important quality aspect in an automated way, namely redundancy that stems from copy&paste operations. This paper describes a large-scale case study that applied clone detection to 28 requirements specifications with a total of 8,667 pages. We report on the amount of redundancy found in real-world specifications, discuss its nature as well as its consequences and evaluate in how far existing code clone detection approaches can be applied to assess the quality of requirements specifications in practice.

biologic features of 9 cases Spontaneous regression of chronic lymphocytic leukemia: clinical and http://bloodjournal.hematologylibrary.org/content/114/3/638.full.html Updated information and services can be found at: (896 articles) Lymphoid Neoplasia (1258 articles) Free Research Articles (3309 articles) Clinical Trials and Observations Articles on similar topics can be found in the following Blood collections http://bloodjournal.hematologylibrary.org/site/misc/rights.xhtml#repub_requests Information about reproducing this article in parts or in its entirety may be found online at: http://bloodjournal.hematologylibrary.org/site/misc/rights.xhtml#reprints Information about ordering reprints may be found online at: http://bloodjournal.hematologylibrary.org/site/subscriptions/index.xhtml Information about subscriptions and ASH membership may be found online at: In chronic lymphocytic leukemia (CLL), spontaneous regressions are an exceptional phenomenon, whose biologic features are unknown. We describe 9 CLL patients who underwent a spontaneous clinical regression over an 11-year followup, despite a residual neoplastic clone detected by flow cytometry. CD38 and ZAP-70 were negative in all cases. Immunoglobulin heavy chain variable region (IgVH) genes, mutated in all 7 evaluable patients, were restricted to the VH3 family in 6, with the usage of V H 3-30 gene in 2. The light chain variable region genes were mutated in 6 of 8 cases, with the use of V 4-1 gene in 3. Microarray analysis of CLL cells showed a distinctive genomic profile with an overrepresentation of BCRrelated and ribosomal genes, regulators of signal transduction and transcription. The number of activated T lymphocytes expressing IFN-␥, TNF-␣, and IL-4 was similar between CLL in spontaneous regression and healthy persons. In conclu-sion, spontaneous clinical regressions can occur in CLL despite the persistence of the neoplastic clone, and the biologic features include negative CD38 and ZAP-70, mutated V H 3-30 and V 4-1 genes. The peculiar gene profile suggests that BCR signaling may play an important role in this scenario as the most significant feature of the leukemic clone in regression. (Blood. 2009;114:638-646)

Redundant source code hinders software maintenance, since updates have to be performed in multiple places. This holds independent of whether redundancy was created by copy&paste or by independent development of behaviorally similar code. Existing clone detection tools successfully discover syntactically similar redundant code. They thus work well for redundancy that has been created by copy&paste. But: how syntactically similar is behaviorally similar code of independent origin? This paper presents the results of a controlled experiment that demonstrates that behaviorally similar code of independent origin is highly unlikely to be syntactically similar. In fact, it is so syntactically different, that existing clone detection approaches cannot identify more than 1% of such redundancy. This is unfortunate, as manual inspections of open source software indicate that behaviorally similar code of independent origin does exist in practice and does present problems to maintenance.

Genetic diversity at variable-number-tandem-repeat (VNTR) loci was examined in the common cattail, Typha latifolia (Typhaceae), using three synthetic DNA probes composed of tandemly repeated ''core'' sequences (GACA, GATA, and GCAC). The principal objectives of this investigation were to determine whether: (1) the previously reported almost complete lack of polymorphism at allozyme loci in this species was indicative of a reduced amount of genetic diversity at VNTR loci as well; (2) VNTR markers were informative about possible clonal propagation; and (3) significant differences in genetic structure of sampling sites were associated with differences in environmental levels of pollutants at those sites. Previously, widespread sampling across the eastern United States, surveying across ten allozyme loci, has detected only two genotypes, involving a difference at a single locus, among 104 populations. In this study, the amount of genetic diversity detected at VNTR loci: (1) among ramets (N ϭ 40; 40 genotypes detected) collected at ϳ8-km intervals along a 320-km transect; (2) among ramets (N ϭ 220; 117 genotypes detected) from five study sites separated by 50-3000 m; and (3) even among ramets within each study site [N ϭ 44 per site; from 13 to 34 genotypes detected per site (270 m 2 )] exceeds that previously found in those more geographically widespread allozyme surveys. Among the 260 ramets analyzed here, the mean number of bands scored per individual was 48.61 (SD ϭ 2.80). Mean genetic similarity among ramets collected along the 320-km transect was 0.91, which was within the range of mean genetic similarity within the five study sites (range: 0.89-0.95). Among the five study sites, 61% of the samples analyzed appeared to be clonal ramets, with up to 12 clones detected for 44 ramets sampled within a site. Clones grew intermingled and ranged up to 39 m in extent. Permutation tests of genetic similarity revealed significant genetic differentiation between each of the five study sites. Consistent with the previous allozyme studies, T. latifolia was characterized by extremely low genetic variation relative to levels of polymorphism detected at VNTR loci in other plant species. Estimated heterozygosity among ramets along the 320-km transect ranged from 0.11 to 0.13, while that within the five study sites ranged from 0.05 to 0.12. Estimates of F st (0.32-0.41) also indicated considerable genetic subdivision among these stands. Significantly higher genetic diversity was detected at the two study sites that chemistry and toxicity data indicate to be the most severely impacted by pollutants. Although this correlation does not establish cause and effect, the results of this study indicate that the analysis of genetic diversity at VNTR loci may be a useful tool for monitoring anthropogenic-induced changes in the genetic structure of natural populations of plants.

Recent research results show several benefits of the management of code clones. In this paper, we introduce Clever, a novel clone-aware software configuration management (SCM) system. In addition to traditional SCM functionality, Clever provides clone management support, including clone detection and update, clone change management, clone consistency validating, clone synchronizing, and clone merging. Clever represents source code and clones as (sub)trees in Abstract Syntax Trees (ASTs), measures code similarity based on structural characteristic vectors, and describes code changes as tree editing scripts. The key techniques of Clever include the algorithms to compute tree editing scripts; to detect and update code clones and their groups; and to analyze the changes of cloned code to validate their consistency and recommend the relevant synchronization. Our empirical study on many real-world programs shows that Clever is highly efficient and accurate in clone detection and updating, and provides useful analysis of clone changes. : First of all, a developer could use Eclipse to work on a software project. At any time, (s)he can start code clone detection on any version of the project. When (s)he checks in the code, if clone detection has never been initiated, Clever will perform the detection. It reads source files and extracts important features. The initial detection is launched using our algorithm on those fragments (Section 5). In addition to the normal check-in data, clonerelated information is also stored for future updating.

Restriction fragment length polymorphism (RFLP) markers linked to genes controlling Hessian fly resistance from Triticum tauschii (Coss.) Schmal. were identified for two wheat (Triticum aestivum L.) germ plasm lines KS89WGRC3 (C3) and KS89WGRC6 (C6). Forty-six clones with loci on chromosomes of homoeologous group 3 and 28 clones on those of group 6 were surveyed for polymorphisms. Eleven and 12 clones detected T. tauschii loci in the two lines, respectively. Analysis of F 2 progenies indicated that the Hessian fly resistance gene H23 identified in C3 is linked to XksuH4 (6.9 cM) and XksuG48(A) (15.6 cM), located on 6D. The resistance gene H24 in C6 is linked to XcnlBCD451 (5.9 cM), XcnlCD0482 (5.9 cM) and XksuG48(B) (12.9 cM), located on 3DL.

To facilitate biochemical studies of protective filarial antigens, a Agtl1 cDNA library was constructed from Brugia malayi adult mRNA and screened with rabbit sera that recognizes a limited set of filarial antigens of approximately 25, 42, 60, and 112 kDa. Antigens of z25 and ==60 kDa have been shown previously to induce enhanced clearance of microrflaremia in mice. A 154-base pair clone detected by immunological reactivity was used to isolate by hybridization a nearly fulllength cDNA clone of 1.8 kilobases. Nucleotide-sequence analysis indicated that this clone was derived from a mRNA encoding a 63-kDa antigen. A fusion polypeptide containing 37 kDa of the Escherichia coli TrpE protein (anthranilate synthase) and 55 kDa of the cloned protein was recognized in immunoblot experiments with antisera raised against a partially purified preparation of the 460-kDa protective filarial antigen. These data relate the cloned antigen to a potentially protective antigen in lymphatic fiariasis.

We present the R 2 D 2 redundancy detector. R 2 D 2 identifies redundant code fragments in large software systems written in Lisp. For each pair of code fragments, R 2 D 2 uses a combination of techniques ranging from syntaxbased analysis to semantics-based analysis, that detects positive and negative evidences regarding the redundancy of the analyzed code fragments. These evidences are combined according to a well-defined model and sufficiently redundant fragments are reported to the user. R 2 D 2 explores several techniques and heuristics to operate within reasonable time and space bounds and is designed to be extensible.

It has long been recognized that spinal meningiomas show particular clinical and histological features. Here, we compare the clinico-biological characteristics as well as the genetic abnormalities and patterns of gene expression of spinal and intracranial meningiomas. Fourteen spinal and 141 intracranial meningioma patients were analyzed at diagnosis. In all tumors, interphase fluorescence in situ hybridization (iFISH) studies were performed for the detection of quantitative abnormalities for 11 different chromosomes. Additionally, microarray analyses were performed on a subgroup of 18 histologically benign meningiomas (7 spinal and 11 intracranial). Upon comparison with intracranial tumors, spinal meningiomas showed a marked predominance of psammomatous and transitional tumors (p = 0.001), together with a higher proportion of cases displaying a single tumor cell clone by iFISH (p = 0.004). In 86% of the spinal versus 56% of the intracranial tumors (p = 0.01), the ancestral tumor cell clone detected showed either absence of any chromosomal abnormality or monosomy 22/22q j alone. Analysis of gene expression profiles showed differential expression between spinal and intracranial meningiomas for a total of 1555 genes, 35 of which allowed a clear distinction between both tumor types. Most of these 35 genes (n = 30) showed significantly higher expression among spinal tumors and corresponded to genes involved in signal transduction pathways, which did not show a significantly different expression according to tumor histopathology. In summary, we show the occurrence of unique patterns of genetic abnormalities and gene expression profiles in spinal as compared to intracranial meningiomas that provide new insights into the molecular pathways involved in the tumorigenesis and progression of spinal meningiomas, and could help explain their particular clinical and histological features.

Programmers copy and paste code for many reasons. Regardless of the specific reasons, similar code fragments (clones) are introduced into software systems. Like other software artifacts, clones may require attention and effort from programmers so that they can be understood, and correctly adapted and evolved. More specifically, when understanding and maintaining clones, programmers need to know where the clones are. Programmers also need to compare and contrast code clones in order to figure out how they correspond and differ. Finally, they also need to edit or remove clones. In addition to what clone detection-based tools can offer, more automated support is needed to better assist programmers in these activities. In this paper, we introduce a toolkit CnP that is aimed to support and manage clones proactively as they are created and evolved. We describe the initial features and the design decisions taken in CnP. We also discuss possible future design extensions.

In-network data aggregation is favorable for wireless sensor networks (WSNs): It allows in-network data processing while reducing the network traffic and hence saving the sensors energy. However, due to the distributed and unattended nature of WSNs, several attacks aiming at compromising the authenticity of the collected data could be perpetrated. For example, an adversary could capture a node to create clones of the captured one. These clones disseminated through the network could provide malicious data to the aggregating node, thus poisoning/disrupting the aggregation process. In this paper we address the problem of detecting cloned nodes; a requirement to be fulfilled to provide authenticity of the data fusion process.

Large multi-platform software systems are likely to encompass hardware-dependent code or sub-systems. However, analyzing multi-platform source code poses several challenges, intrinsically due to the variety of supported configurations. Often, the system was originally developed for a single platform, and then new target platforms were added.This practice promotes the presence of duplicated code, also said "cloned" code.

Clones are code segments that have been created by copying-and-pasting from other code segments. Clones occur often in large software systems. It is reported that 5 to 50% of the source code of a large software system is cloned. A major challenge when studying code cloning in large software systems is handling the large amount of clone candidates produced by leading edge clone detection tools. For example, the CCFinder, clone detection tool, produces over 7 million pairs of clone candidates for the Linux kernel (which consists of over 4 MLOC). Moreover, the output of clone detection tools grows rapidly as a software system evolves. Researchers and developers need tools to help them study the large amount of clone data in order to better understand the clone phenomena in large systems. In this paper, we propose a data mining framework to help researchers cope with the large amount of data produced by clone detection tools. We propose techniques to reduce, abstract and highlight the most interesting data produced by clone detection tools. Our framework also introduces a visualization tool which allows users to query and explore clone data at various abstraction levels. We demonstrate our framework on a case study of the clone phenomena in the Linux kernel.

Code clone management has been shown to have several benefits for software developers. When source code evolves, clone management requires a mechanism to efficiently and incrementally detect code clones in the new revision. This paper introduces an incremental clone detection tool, called ClemanX. Our tool represents code fragments as subtrees of Abstract Syntax Trees (ASTs), measures their similarity levels based on their characteristic vectors of structural features, and solves the task of incrementally detecting similar code as an incremental distance-based clustering problem. Our empirical evaluation on large-scale software projects shows the usefulness and good performance of ClemanX.

The chromosomal region 3p21.2-p22 has been shown to be involved in the development of several forms of solid tumors. Such deletions, translocations, and rearrangements presumably result in the disturbance or loss of a critical gene function. Pulsed-field gel electrophoresis (PFGE), using Not/ linking clones as a probe represent a powerful tool for analyzing such rearrangements. A Not/linking clone, AP20 (D3S1641), was localized by in situ hybridization to 3p21.3-p22. Two NoU jumping clones adjacent to this clone were isolated, clone J32-612 covering 0.5 Mb and clone ]31-611 covering approximately I Mb. Clone ]31-611 crosses the border of the deletion present in hybrid cell line MCH939. 2, which contains a deleted 3p21 region. For these jumping clones, corresponding NoU linking clones, NLJ3 (D3S1642) and NL3-O03, were isolated. Altogether, linking and jumping clones from the AP20 locus hybridize to Not/fragments totaling 2.5 Mb in length. These NoU-containing clones detect expressed sequences in several human tissues. Clone NLJ3 possesses homology to the human platelet-derived endothelial cell growth factor gene and may represent a new member of this gene family. Another clone (AP20) revealed 66% sequence similarity to rat skeletal muscle voltage-sensitive sodium channel subtype 2. Therefore, this group of clones will be useful not only for analyzing rearrangements in tumors, but also for the isolation of new genes from the 3p21.3-p22 region.

a b s t r a c t PCR and Southern blot hybridization were used to determine the distribution of Trypanosoma cruzi clones in 37 chronic chagasic cardiopathic and non-cardiopathic patients. Parasite DNA amplified from peripheral blood or dejections of Triatoma infestans fed on patient blood was hybridized with probes containing hypervariable minicircle nucleotide sequences capable of detecting three sublineages of T. cruzi. Probes Z-I and Z-IIb detect unique sequences in lineages TcI and TcIIb, respectively. Probe Z-hybrid detects sequences of lineages TcIId and TcIIe. T. cruzi clones of the Z-I sublineage were detected in 62.2% of T. infestans dejections and 5.4% of peripheral blood samples. Clones of Z-IIb and Z-hybrid sublineages had similar distribution in blood and dejection samples. Interestingly, clones of the Z-IIb sublineage were significantly lower in cardiopathic than in non-cardiopathic patients (23.5% versus 75%; P = 0.0006). Clones of the Zhybrid sublineage were found in 29.4% of cardiopathic and 75% of non-cardiopathic patients, respectively (P = 0.0051). By contrast, clones of sublineage Z-I were similarly distributed in both groups of patients. The low frequency of Z-IIb and Z-hybrid sublineage clones detected in cardiopathic patients suggests that the immunological mechanisms involved in controlling and eliminating these T. cruzi parasites may be detrimental to the host, leading to the development of chagasic cardiomyopathy.

A combinatorial phage display library expressing human immunoglobulin heavy and light chain variable regions was used to identify phage clones capable of binding to the surface of Candida albicans blastoconidia. Single chain antibody Ž . variable fragments scFv derived from three clones detected C. albicans antigens by indirect immunofluorescence assay Ž . Ž . IFA , enzyme-linked immunosorbent assay ELISA , and Western blotting. The antigens detected were conserved among different strains of C. albicans and several other Candida species. Two scFv clones detected antigens specifically expressed by C. albicans blastoconidia; the third detected antigens in both blastoconidia and filamentous forms of C. albicans. The antigens containing the epitopes recognized by all three scFv could be extracted from blastoconidia by dithiothreitol, suggesting attachment to the cell wall via sulfhydryl bonds. Epitope detection by the scFv was sensitive to treatment of C. albicans blastoconidia with sodium periodate, but not proteinase K, indicating the cognate epitopes were composed of carbohydrate. Antigenic determinants for each of the three scFv were detected by immunohistochemical staining of skin sections from a model of cutaneous candidiasis, demonstrating expression in vivo. Through selection for the ability to bind intact organisms, the phage display system provides a means to rapidly identify monoclonal binding ligands to Candida AbbreÕiations: scFv, single chain variable fragments; Mab, monoclonal antibodyrantibodies; VH, immunoglobulin heavy chain variable region; VL, immunoglobulin light chain variable region; YEPD, yeast extract-peptone-dextrose; YNB, yeast nitrogen base; BSA, bovine serum albumin; DTT, dithiothreitol; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; IFA, indirect immunofluorescence assay; RT, room temperature.

Background: Individuals living in areas of high malaria transmission often have different Plasmodium falciparum clones detected in the peripheral blood over time. The aim of this study was to assess the dynamics of asymptomatic P. falciparum infections in a few hours intervals.

Technical documentation is now fully taking the step from stale printed booklets (or electronic versions of these) to interactive and online versions. This provides opportunities to reconsider how we define and assess the quality of technical documentation. This paper suggests an approach based on the Goal-Question-Metric paradigm: predefined quality goals are continuously assessed and visualized by the use of metrics. To test this approach, we perform two experiments. We adopt well known software analysis techniques, e.g., clone detection and test coverage analysis, and assess the quality of two real world documentations, that of a mobile phone and of (parts of) a warship. The experiments show that quality issues can be identified and that the approach is promising.

The successful generation of human antibodies from large naïve antibody libraries requires iterative selection steps. Here, we describe a new and fast method for the isolation of high affinity antibodies directly from human single chain Fv antibody (scFv) expression libraries. Escherichia coli scFv expression libraries were made from peripheral blood lymphocytes from four individuals vaccinated with group B Neisseria meningitidis outer membrane vesicle (OMV) vaccine. Forty thousand clones were directly screened for antibodies binding N. meningitidis strain 44/76 (B:15:P1.7,16). Of 430 specific clones detected, 225 candidates were isolated and re-screened against the N. meningitidis strains NZ-98/254 (B:4:P1.7b,4) giving 4% cross-reactive clones. Antibodies were further characterized by DNA sequencing, ELISA and surface plasmon resonance (SPR) analysis, showing broad V-gene diversity and nanomolar scFv affinities. Antibodies derived by this method may assist in the discovery and development of new vaccine antigens as well as therapeutic antibody agents for the treatment of meningococcal diseases. D

In order to find new antigens from Plasmodium falciparum, a complementary DNA (cDNA) library was constructed and screened. The study of expression library of P. falciparum was performed in an attempt to identify new antigens that could have potential relevance for the falciparum-malaria diagnosis and/or protection. Between the positive clones detected (ring erythrocyte surface antigen, merozoite erythrocyte surface antigen, RHOP H3, CSP, LSA), a new gene that correspond to a new protein (Pf62) was isolated and characterized. This antigen was useful for the diagnosis of malaria in enzyme-linked immunosorbent assay tests. The cDNA corresponding to this antigen and structure of the gene were characterized. Pf62 is a single copy gene that contains one exon. The Pf62 cDNA has an open reading frame of 1,599 nucleotides that code for a putative protein of 532 amino acids with a predicted molecular mass of 62 kDa. The polypeptide contains in the central section two regions of repeats of 21 and 19 amino acids, respectively. The localization of the Pf62 protein was performed by immunoblot, indirect immunofluorescence assay and immunoelectron microscopy. Pf62 is localized in the cytoplasm of the parasite and also on the surface of the infected erythrocyte. Serologic assays by using synthetic peptides designed from different antigenic regions of the Pf62 protein resulted in acceptable data of sensitivity and specificity in symptomatic malaria patients.