Evaluating Code Duplication to Identify Rich Business Objects from Data Transfer Objects

Java Enterprise Applications (JEAs) are complex software systems written using multiple technologies. Moreover they are usually distributed systems and use a database to deal with persistence. A particular problem that appears in the design of these systems is the lack of a rich business model. In this paper we propose a technique to support the recovery of such rich business objects starting from anemic Data Transfer Objects (DTOs). Exposing the code duplications in the application's elements using the DTOs we suggest which business logic can be moved into the DTOs from the other classes.

Duplication of the sodium channel gene cluster on 2q24 in children with early onset epilepsy

Sodium channel gene aberrations are associated with a wide range of seizure disorders, particularly Dravet syndrome. They usually consist of missense or truncating gene mutations or deletions. Duplications involving multiple genes encoding for different sodium channels are not widely known. This article summarizes the clinical, radiologic, and genetic features of patients with 2q24 duplication involving the sodium channel gene cluster.

Role for tandem duplication and lon protease in AcrAB-TolC- dependent multiple antibiotic resistance (Mar) in an Escherichia coli mutant without mutations in marRAB or acrRAB

A spontaneous mutant (M113) of Escherichia coli AG100 with an unstable multiple antibiotic resistance (Mar) phenotype was isolated in the presence of tetracycline. Two mutations were found: an insertion in the promoter of lon (lon3::IS186) that occurred first and a subsequent large tandem duplication, dupIS186, bearing the genes acrAB and extending from the lon3::IS186 to another IS186 present 149 kb away from lon. The decreased amount of Lon protease increased the amount of MarA by stabilization of the basal quantities of MarA produced, which in turn increased the amount of multidrug effux pump AcrAB-TolC. However, in a mutant carrying only a lon mutation, the overproduced pump mediated little, if any, increased multidrug resistance, indicating that the Lon protease was required for the function of the pump. This requirement was only partial since resistance was mediated when amounts of AcrAB in a lon mutant were further increased by a second mutation. In M113, amplification of acrAB on the duplication led to increased amounts of AcrAB and multidrug resistance. Spontaneous gene duplication represents a new mechanism for mediating multidrug resistance in E. coli through AcrAB-TolC.

Short communication: duplication in the 5'-flanking region of the beta-lactoglobulin gene is linked to the BLG A allele

beta-Lactoglobulin (beta-LG) is the major whey protein in the milk of cows and other ruminants. It is well established that the predominant genetic variants beta-LG A and B are differentially expressed. Extensive investigation of the genetic variation in the promoter region of the BLG gene revealed the existence of specific haplotypes associated with the A and B variants. However, the genetic basis for the differentially expressed BLG A and B alleles is still elusive. In this study additional genetic variation further upstream in the 5'-flanking region of the BLG gene was identified, including 6 single nucleotide substitutions, a single nucleotide deletion, and a 7-bp duplication. Comparison of DNA sequences showed that the investigated 5'-flanking region is highly conserved between ruminants, and the duplication g.-1885_-1879dupCTCTCGC and the substitution g.-1888A>G are only found in the BLG A and D alleles in cattle. The cytosine at position g.-1957 and the thymines at positions g.-2008 and g.-2049 are only found in BLG B alleles of cattle. It is suggested that the described genetic variability contributes to the differential allelic expression of the BLG gene.

Gene duplication: a drive for phenotypic diversity and cause of human disease

Gene duplication is one of the key factors driving genetic innovation, i.e., producing novel genetic variants. Although the contribution of whole-genome and segmental duplications to phenotypic diversity across species is widely appreciated, the phenotypic spectrum and potential pathogenicity of small-scale duplications in individual genomes are less well explored. This review discusses the nature of small-scale duplications and the phenotypes produced by such duplications. Phenotypic variation and disease phenotypes induced by duplications are more diverse and widespread than previously anticipated, and duplications are a major class of disease-related genomic variation. Pathogenic duplications particularly involve dosage-sensitive genes with both similar and dissimilar over- and underexpression phenotypes, and genes encoding proteins with a propensity to aggregate. Phenotypes related to human-specific copy number variation in genes regulating environmental responses and immunity are increasingly recognized. Small genomic duplications containing defense-related genes also contribute to complex common phenotypes.

Respiratory depression with tramadol in a patient with renal impairment and CYP2D6 gene duplication

We observed opioid-related respiratory depression in a patient receiving tramadol via patient-controlled analgesia. Predisposing factors were the patient's genetic background and renal impairment. Complete recovery occurred after naloxone administration, thus confirming opioid intoxication. Analysis of the patient's genotype revealed a CYP2D6 gene duplication resulting in ultra-rapid metabolism of tramadol to its active metabolite (+)O-desmethyltramadol. Concomitant renal impairment resulting in decreased metabolite clearance enhanced opioid toxicity. This genetic CYP2D6 variant is particularly common in specific ethnic populations and should be a future diagnostic target whenever administration of tramadol or codeine is anticipated, as both drugs are subject to a comparable CYP2D6-dependent metabolism.

A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.

Highland cattle with congenital crop ears have notches of variable size on the tips of both ears. In some cases, cartilage deformation can be seen and occasionally the external ears are shortened. We collected 40 cases and 80 controls across Switzerland. Pedigree data analysis confirmed a monogenic autosomal dominant mode of inheritance with variable expressivity. All affected animals could be traced back to a single common ancestor. A genome-wide association study was performed and the causative mutation was mapped to a 4 Mb interval on bovine chromosome 6. The H6 family homeobox 1 (HMX1) gene was selected as a positional and functional candidate gene. By whole genome re-sequencing of an affected Highland cattle, we detected 6 non-synonymous coding sequence variants and two variants in an ultra-conserved element at the HMX1 locus with respect to the reference genome. Of these 8 variants, only a non-coding 76 bp genomic duplication (g.106720058_106720133dup) located in the conserved region was perfectly associated with crop ears. The identified copy number variation probably results in HMX1 misregulation and possible gain-of-function. Our findings confirm the role of HMX1 during the development of the external ear. As it is sometimes difficult to phenotypically diagnose Highland cattle with slight ear notches, genetic testing can now be used to improve selection against this undesired trait.

A duplication in the canine beta-galactosidase gene GLB1 causes exon skipping and GM1-gangliosidosis in Alaskan huskies

GM(1)-gangliosidosis is a lysosomal storage disease that is inherited as an autosomal recessive disorder, predominantly caused by structural defects in the beta-galactosidase gene (GLB1). The molecular cause of GM(1)-gangliosidosis in Alaskan huskies was investigated and a novel 19-bp duplication in exon 15 of the GLB1 gene was identified. The duplication comprised positions +1688-+1706 of the GLB1 cDNA. It partially disrupted a potential exon splicing enhancer (ESE), leading to exon skipping in a fraction of the transcripts. Thus, the mutation caused the expression of two different mRNAs from the mutant allele. One transcript contained the complete exon 15 with the 19-bp duplication, while the other transcript lacked exon 15. In the transcript containing exon 15 with the 19-bp duplication a premature termination codon (PTC) appeared, but due to its localization in the last exon of canine GLB1, nonsense-mediated RNA decay (NMD) did not occur. As a consequence of these molecular events two different truncated GLB1 proteins are predicted to be expressed from the mutant GLB1 allele. In heterozygous carrier animals the wild-type allele produces sufficient amounts of the active enzyme to prevent clinical signs of disease. In affected homozygous dogs no functional GLB1 is synthesized and G(M1)-gangliosidosis occurs.

Hot Clones, Maintaining a Link Between Software Clones Across Repositories

Code duplication is common in current programming-practice: programmers search for snippets of code, incorporate them into their projects and then modify them to their needs. In today's practice, no automated scheme is in place to inform both parties of any distant changes of the code. As code snippets continues to evolve both on the side of the user and on the side of the author, both may wish to benefit from remote bug fixes or refinements --- authors may be interested in the actual usage of their code snippets, and researchers could gather information on clone usage. We propose maintaining a link between software clones across repositories and outline how the links can be created and maintained.

Dégradation des forêts et stock de carbone dans la biomasse épigée de la forêt dense humide de Manompana - Nord Est de Madagascar

L’estimation du stock de carbone contenu dans les forêts peut être effectuée de plusieurs manières. Les méthodes les plus connues sont destructives et nécessitent l’abattage d’un grand nombre représentatif d’arbres. Cette représentativité est difficilement atteinte dans les forêts tropicales, présentant une diversité d’espèces exceptionnelles, comme à Madagascar. Afin d’évaluer le niveau de dégradation des forêts, une étude d'images par télédétection est effectuée au moyen de l’analyse du signal radiométrique, combinée à un inventaire non destructif de biomasse. L’étude de la dynamique du paysage proposé est alors basée sur une correction atmosphérique d’une image SPOT 5, de l’année 2009, et sur une classification semi supervisée de l’occupation des sols, combinant une classification préliminaire non supervisée, un échantillonnage aléatoire des classes et une classification supervisée avec un maximum de vraisemblance. La validation est effectuée à l’aide de points indépendants relevés lors des inventaires de biomasse avec des valeurs du stock de carbone bien précises. La classification non supervisée a permis de ressortir deux classes de forêt dénommées « peu dégradée » et « dégradée ». La première désigne l’état climax (le stock de carbone a atteint une valeur qui varie peu) alors que la seconde est caractérisée par un taux de carbone plus faible que le niveau climax, mais qui peut être atteint sans perturbation. Cette première classification permet alors de répartir les placettes d’inventaire dans chaque classe. La méthode d’inventaire recueille à la fois des données dendrométriques classiques (espèce, densité, hauteur totale, hauteur fût, diamètre) et des échantillons représentatifs de branches et de feuilles sur un arbre. Ces différents paramètres avec la densité de bois permettent d’établir une équation allométrique de laquelle est estimée la biomasse totale d’un arbre et conséquemment de la formation forestière. Par la suite, la classification supervisée a été effectuée à partir d’échantillons aléatoires donnant la valeur de séparabilité des classes, de la classification finale. De plus, les valeurs de stocks de carbone à l’hectare, estimées de chaque placette, ont permis de valider cette classification et d’avoir une évaluation de la précision. La connaissance de ce niveau de dégradation issue de données satellitaires à haute résolution spatiale, combinées à des données d’inventaire, ouvre le champ du suivi interannuel du stock de carbone et subséquemment de la modélisation de la situation future du stock de carbone dans différents types de forêts.