Contrasting dedicated model transformation languages versus general purpose languages: a historical perspective on ATL versus Java based on complexity and size

Model transformations are among the key concepts of model-driven engineering (MDE), and dedicated model transformation languages (MTLs) emerged with the popularity of the MDE pssaradigm about 15 to 20 years ago. MTLs claim to increase the ease of development of model transformations by abstracting from recurring transformation aspects and hiding complex semantics behind a simple and intuitive syntax. Nonetheless, MTLs are rarely adopted in practice, there is still no empirical evidence for the claim of easier development, and the argument of abstraction deserves a fresh look in the light of modern general purpose languages (GPLs) which have undergone a significant evolution in the last two decades. In this paper, we report about a study in which we compare the complexity and size of model transformations written in three different languages, namely (i) the Atlas Transformation Language (ATL), (ii) Java SE5 (2004–2009), and (iii) Java SE14 (2020); the Java transformations are derived from an ATL specification using a translation schema we developed for our study. In a nutshell, we found that some of the new features in Java SE14 compared to Java SE5 help to significantly reduce the complexity of transformations written in Java by as much as 45%. At the same time, however, the relative amount of complexity that stems from aspects that ATL can hide from the developer, which is about 40% of the total complexity, stays about the same. Furthermore we discovered that while transformation code in Java SE14 requires up to 25% less lines of code, the number of words written in both versions stays about the same. And while the written number of words stays about the same their distribution throughout the code changes significantly. Based on these results, we discuss the concrete advancements in newer Java versions. We also discuss to which extent new language advancements justify writing transformations in a general purpose language rather than a dedicated transformation language. We further indicate potential avenues for future research on the comparison of MTLs and GPLs in a model transformation context.Universität Ulm (1055)Peer Reviewe

Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution

<p>Abstract</p> <p>Background</p> <p>Genome comparisons have made possible the reconstruction of the eutherian ancestral karyotype but also have the potential to provide new insights into the evolutionary inter-relationship of the different eutherian orders within the mammalian phylogenetic tree. Such comparisons can additionally reveal (i) the nature of the DNA sequences present within the evolutionary breakpoint regions and (ii) whether or not the evolutionary breakpoints occur randomly across the genome. Gene synteny analysis (E-painting) not only greatly reduces the complexity of comparative genome sequence analysis but also extends its evolutionary reach.</p> <p>Results</p> <p>E-painting was used to compare the genome sequences of six different mammalian species and chicken. A total of 526 evolutionary breakpoint intervals were identified and these were mapped to a median resolution of 120 kb, the highest level of resolution so far obtained. A marked correlation was noted between evolutionary breakpoint frequency and gene density. This correlation was significant not only at the chromosomal level but also sub-chromosomally when comparing genome intervals of lengths as short as 40 kb. Contrary to previous findings, a comparison of evolutionary breakpoint locations with the chromosomal positions of well mapped common fragile sites and cancer-associated breakpoints failed to reveal any evidence for significant co-location. Primate-specific chromosomal rearrangements were however found to occur preferentially in regions containing segmental duplications and copy number variants.</p> <p>Conclusion</p> <p>Specific chromosomal regions appear to be prone to recurring rearrangement in different mammalian lineages ('breakpoint reuse') even if the breakpoints themselves are likely to be non-identical. The putative ancestral eutherian genome, reconstructed on the basis of the synteny analysis of 7 vertebrate genome sequences, not only confirmed the results of previous molecular cytogenetic studies but also increased the definition of the inferred structure of ancestral eutherian chromosomes. For the first time in such an analysis, the opossum was included as an outgroup species. This served to confirm our previous model of the ancestral eutherian genome since all ancestral syntenic segment associations were also noted in this marsupial.</p

Revised diagnostic criteria for neurofibromatosis type 1 and Legius syndrome: an international consensus recommendation

Purpose By incorporating major developments in genetics, ophthalmology, dermatology, and neuroimaging, to revise the diagnostic criteria for neurofibromatosis type 1 (NF1) and to establish diagnostic criteria for Legius syndrome (LGSS). Methods We used a multistep process, beginning with a Delphi method involving global experts and subsequently involving non-NF experts, patients, and foundations/patient advocacy groups. Results We reached consensus on the minimal clinical and genetic criteria for diagnosing and differentiating NF1 and LGSS, which have phenotypic overlap in young patients with pigmentary findings. Criteria for the mosaic forms of these conditions are also recommended. Conclusion The revised criteria for NF1 incorporate new clinical features and genetic testing, whereas the criteria for LGSS were created to differentiate the two conditions. It is likely that continued refinement of these new criteria will be necessary as investigators (1) study the diagnostic properties of the revised criteria, (2) reconsider criteria not included in this process, and (3) identify new clinical and other features of these conditions. For this reason, we propose an initiative to update periodically the diagnostic criteria for NF1 and LGSS

Flüssigphasen-Dehydratisierung von Milchsäure zur Produktion von biobasierter Acrylsäure Entwicklung eines mehrstufigen Prozesses

This thesis deals with the development of a novel liquid-phase dehydration process of lactic acid (LA) for the production of bio-acrylic acid (AA). The approach of dehy- drating LA in the liquid phase is expected to offer advantages over so far existing gas-phase dehydration processes and may therefore provide a technical as well eco- nomically feasible and sustainable alternative to the incumbent petro-based route. The first part of this work provides a general introduction of the developed “NADA” technology, enabling the production of AA in a liquid phase process. The one-step and HBr-triggered dehydration of LA was realized in acidic bromide ionic liquids. Subsequently, current limitations of the process using LA as substrate were ad- dressed and a multi-step processing of the technology was conceptualized, based on the postulated reaction mechanism of the liquid-phase dehydration system. In the main part of this work, a multi-step liquid-phase dehydration process for the production of bio-AA from LA, proceeding via brominated LA-species, was devel- oped. The feasibility of splitting the “NADA” process into a spatially separated reac- tion sequence of the postulated mechanism was proven. Three individual reactions, namely bromination of LA, isomerization of 2- to 3-bromopropionic acid and dehy- drobromination of 3-bromopropionic acid to AA were developed and largely opti- mized, respectively. In this context, bromide ionic liquids played a crucial role as re- action medium and/or reactant. After evaluation of the multi-step approach from LA towards bio-AA via brominated LA-species, possibilities for potential process shortcuts were finally addressed. The presented results in this thesis contribute to the understanding of AA production from LA via brominated LA-species using (acidic) bromide ILs. The developed “NADA” technology is a novel, selective and sustainable way for the production of AA from LA, contributing to a future economic production of bio-AA.Diese Arbeit befasst sich mit der Flüssigphasen-Dehydratisierung von Milchsäure (LA) zur Produktion von biobasierter Acrylsäure (AA). Ein solcher und neuartiger Ansatz der Flüssigphasen-Reaktion bietet Vorteile gegenüber bestehender Gaspha- sen-Dehydratisierungsprozesse und kann damit als eine sowohl technisch wie auch ökonomisch attraktive und nachhaltige Alternative zum bestehenden und auf fossi- len Rohstoffen basierten Produktionsprozess von AA angesehen werden. Der erste Teil dieser Arbeit stellt eine allgemeine Einführung in die entwickelte “NADA”-Technologie dar, welche eine Produktion von AA aus LA in der Flüssig- phase ermöglicht. Die einstufige und durch HBr ausgelöste Dehydratisierung von LA wurde in sauren Bromid-Ionischen Flüssigkeiten (ILs) realisiert. Anschließend wur- den die aktuellen Limitierungen des Prozesses basierend auf dem Substrat LA her- ausgearbeitet und ein mehrstufiges Verfahren entworfen, wofür v.a. der postulierte Reaktionsmechanismus des Dehydratisierungssystems herangezogen wurde. Im Hauptteil dieser Doktorarbeit wurde die mehrstufige Flüssigphasen-Dehydrati- sierung von LA zu bio-AA entwickelt, welche über bromierte LA-Derivate verläuft. Innerhalb dieser Studie konnte die Machbarkeit der Auftrennung des „NADA“-Pro- zesses in eine räumlich getrennte Reaktionssequenz demonstriert werden. Genauer gesagt wurden die Bromierung von LA, die Isomerisierung von 2- zu 3-Brompropi- onsäure, sowie die Dehydrobromierung von 3-Brompropionsäure zu Acrylsäure, ent- wickelt und größtenteils optimiert. Im Zusammenhang mit der Entwicklung der ein- zelnen Reaktionsschritte spielten Bromid-ILs eine besonders wichtige Rolle. Sie wur- den sowohl als Reaktionsmittel als auch als Reaktionspartner eingesetzt. Nach einer Beurteilung der entwickelten und mehrstufigen Prozessführung der “NADA”-Tech- nologie wurden abschließend mögliche Optimierungen hinsichtlich einer zweistufi- gen Prozessführung untersucht. Kurzzusammenfassung vii Die vorliegende Arbeit trägt entscheidend zum Verständnis der Dehydratisierung von LA zu AA in (sauren) Bromid-ILs mithilfe von bromierten LA-Spezies bei. Die entwickelte „NADA“-Technologie stellt eine neuartige, selektive und nachhaltige Möglichkeit zur Dehydratisierung von LA dar und liefert damit einen wichtigen Bei- trag zu einer künftigen ökonomischen Herstellung von bio-AA

Recruitment of old genes to new functions: evidences obtained by comparing the orthologues of human XLMR genes in mouse and chicken

Gene mapping data indicate that the human X chromosome is enriched in genes that affect both, higher cognitive efficiency and reproductive success. This raises the question whether these functions are ancient, or whether conserved X-linked genes were recruited to new functions. We have studied three X-linked mental retardation (XLMR) genes by RNA in situ hybridization in mouse and in chicken, in which these genes are autosomal: Rho guanine nucleotide exchange factor 6 (ARHGEF6), oligophrenin (OPHN1), and p21 activated kinase 3 (PAK3). In the mouse these genes are specifically expressed in telencephalic regions. Their orthologues in the chicken gave patterns of similar specificity in ancient parts of the brain, i.e. cerebellum and mesencephalon, but were not expressed in the telencephalon. Also in the testes, specific expression was only found in mouse, not in chicken. These data are interpreted such that certain genes on the X chromosome gained novel functions during evolution

Wide genome comparisons reveal the origins of the human X chromosome

The eutherian X chromosome has one of the most conserved gene arrangements in mammals. Although earlier comparisons with distantly related mammalian groups pointed towards separate origins for the short and long arms, much deeper comparisons are now possible using draft sequences of the chicken genome, in combination with genome sequences from pufferfish and zebrafish. This enables surprising new insights into the origins of the mammalian X chromosome

Integration of Inkjet Printed Graphene as a Hole Transport Layer in Organic Solar Cells

Peer reviewed: TrueAcknowledgements: Thanks to Assoz. Univ. Markus Clark Scharber for fruitful discussions and helpful advice.This work demonstrates the green production of a graphene ink for inkjet printing and its use as a hole transport layer (HTL) in an organic solar cell. Graphene as an HTL improves the selective hole extraction at the anode and prevents charge recombination at the electronic interface and metal diffusion into the photoactive layer. Graphite was exfoliated in water, concentrated by iterative centrifugation, and characterized by Raman. The concentrated graphene ink was incorporated into inverted organic solar cells by inkjet printing on the active polymer in an ambient atmosphere. Argon plasma was used to enhance wetting of the polymer with the graphene ink during printing. The argon plasma treatment of the active polymer P3HT:PCBM was investigated by XPS, AFM and contact angle measurements. Efficiency and lifetime studies undertaken show that the device with graphene as HTL is fully functional and has good potential for an inkjet printable and flexible alternative to PEDOT:PSS

The Impact of Immersion on Cluster Identification Tasks

Recent developments in technology encourage the use of head-mounted displays (HMDs) as a medium to explore visualizations in virtual realities (VRs). VR environments (VREs) enable new, more immersive visualization design spaces compared to traditional computer screens. Previous studies in different domains, such as medicine, psychology, and geology, report a positive effect of immersion, e.g., on learning performance or phobia treatment effectiveness. Our work presented in this paper assesses the applicability of those findings to a common task from the information visualization (InfoVis) domain. We conducted a quantitative user study to investigate the impact of immersion on cluster identification tasks in scatterplot visualizations. The main experiment was carried out with 18 participants in a within-subjects setting using four different visualizations, (1) a 2D scatterplot matrix on a screen, (2) a 3D scatterplot on a screen, (3) a 3D scatterplot miniature in a VRE and (4) a fully immersive 3D scatterplot in a VRE. The four visualization design spaces vary in their level of immersion, as shown in a supplementary study. The results of our main study indicate that task performance differs between the investigated visualization design spaces in terms of accuracy, efficiency, memorability, sense of orientation, and user preference. In particular, the 2D visualization on the screen performed worse compared to the 3D visualizations with regard to the measured variables. The study shows that an increased level of immersion can be a substantial benefit in the context of 3D data and cluster detection.publishe

Molecular Characterization of the Pericentric Inversion That Causes Differences Between Chimpanzee Chromosome 19 and Human Chromosome 17

A comparison of the human genome with that of the chimpanzee is an attractive approach to attempts to understand the specificity of a certain phenotype's development. The two karyotypes differ by one chromosome fusion, nine pericentric inversions, and various additions of heterochromatin to chromosomal telomeres. Only the fusion, which gave rise to human chromosome 2, has been characterized at the sequence level. During the present study, we investigated the pericentric inversion by which chimpanzee chromosome 19 differs from human chromosome 17. Fluorescence in situ hybridization was used to identify breakpoint-spanning bacterial artificial chromosomes (BACs) and plasmid artificial chromosomes (PACs). By sequencing the junction fragments, we localized breakpoints in intergenic regions rich in repetitive elements. Our findings suggest that repeat-mediated nonhomologous recombination has facilitated inversion formation. No addition or deletion of any sequence element was detected at the breakpoints or in the surrounding sequences. Next to the break, at a distance of 10.2–39.1 kb, the following genes were found: NGFR and NXPH3 (on human chromosome 17q21.3) and GUC2D and ALOX15B (on human chromosome 17p13). The inversion affects neither the genomic structure nor the gene-activity state with regard to replication timing of these genes

Reconstruction of a 450-My-old ancestral vertebrate protokaryotype

From recent work the putative eutherian karyotype from 100 Mya has been derived. Here, we have applied a new in silico technique, electronic chromosome painting (E-painting), on a large data set of genes whose positions are known in human, chicken, zebrafish and pufferfish. E-painting identifies conserved syntenies in the data set, and it enables a stepwise reconstruction of the ancestral vertebrate protokaryotype comprising 11 protochromosomes. During karyotype evolution in land vertebrates interchromosomal rearrangements by translocation are relatively frequent, whereas the karyotypes of birds and fish are much more conserved. Although the human karyotype is one of the most conserved in eutherians, it can no longer be considered highly conserved from a vertebrate-wide perspective