Specification and Verification of Declarative Open Interaction Models - A Logic-based framework

The advent of distributed and heterogeneous systems has laid the foundation for the birth of new architectural paradigms, in which many separated and autonomous entities collaborate and interact to the aim of achieving complex strategic goals, impossible to be accomplished on their own. A non exhaustive list of systems targeted by such paradigms includes Business Process Management, Clinical Guidelines and Careflow Protocols, Service-Oriented and Multi-Agent Systems. It is largely recognized that engineering these systems requires novel modeling techniques. In particular, many authors are claiming that an open, declarative perspective is needed to complement the closed, procedural nature of the state of the art specification languages. For example, the ConDec language has been recently proposed to target the declarative and open specification of Business Processes, overcoming the over-specification and over-constraining issues of classical procedural approaches. On the one hand, the success of such novel modeling languages strongly depends on their usability by non-IT savvy: they must provide an appealing, intuitive graphical front-end. On the other hand, they must be prone to verification, in order to guarantee the trustworthiness and reliability of the developed model, as well as to ensure that the actual executions of the system effectively comply with it. In this dissertation, we claim that Computational Logic is a suitable framework for dealing with the specification, verification, execution, monitoring and analysis of these systems. We propose to adopt an extended version of the ConDec language for specifying interaction models with a declarative, open flavor. We show how all the (extended) ConDec constructs can be automatically translated to the CLIMB Computational Logic-based language, and illustrate how its corresponding reasoning techniques can be successfully exploited to provide support and verification capabilities along the whole life cycle of the targeted systems.

Investigations on formation and specification of neural precursor cells in the central nervous system of the Drosophila melanogaster embryo

Investigations on formation and specification of neural precursor cells in the central nervous system of the Drosophila melanogaster embryoSpecification of a unique cell fate during development of a multicellular organism often is a function of its position. The Drosophila central nervous system (CNS) provides an ideal system to dissect signalling events during development that lead to cell specific patterns. Different cell types in the CNS are formed from a relatively few precursor cells, the neuroblasts (NBs), which delaminate from the neurogenic region of the ectoderm. The delamination occurs in five waves, S1-S5, finally leading to a subepidermal layer consisting of about 30 NBs, each with a unique identity, arranged in a stereotyped spatial pattern in each hemisegment. This information depends on several factors such as the concentrations of various morphogens, cell-cell interactions and long range signals present at the position and time of its birth. The early NBs, delaminating during S1 and S2, form an orthogonal array of four rows (2/3,4,5,6/7) and three columns (medial, intermediate, and lateral) . However, the three column and four row-arrangement pattern is only transitory during early stages of neurogenesis which is obscured by late emerging (S3-S5) neuroblasts (Doe and Goodman, 1985; Goodman and Doe, 1993). Therefore the aim of my study has been to identify novel genes which play a role in the formation or specification of late delaminating NBs.In this study the gene anterior open or yan was picked up in a genetic screen to identity novel and yet unidentified genes in the process of late neuroblast formation and specification. I have shown that the gene yan is responsible for maintaining the cells of the neuroectoderm in an undifferentiated state by interfering with the Notch signalling mechanism. Secondly, I have studied the function and interactions of segment polarity genes within a certain neuroectodermal region, namely the engrailed (en) expressing domain, with regard to the fate specification of a set of late neuroblasts, namely NB 6-4 and NB 7-3. I have dissected the regulatory interaction of the segment polarity genes wingless (wg), hedgehog (hh) and engrailed (en) as they maintain each other’s expression to show that En is a prerequisite for neurogenesis and show that the interplay of the segmentation genes naked (nkd) and gooseberry (gsb), both of which are targets of wingless (wg) activity, leads to differential commitment of NB 7-3 and NB 6-4 cell fate. I have shown that in the absence of either nkd or gsb one NB fate is replaced by the other. However, the temporal sequence of delamination is maintained, suggesting that formation and specification of these two NBs are under independent control.

Analyse der temporären Neuroblastenbildung und der segmentalen Spezifizierung des Neuroblasten 6-4 im embryonalen zentralen Nervensystem von Drosophila melanogaster

Die vorliegende Arbeit gewährte neue Einblicke in zwei fundamentale Vorgänge der frühen Neurogenese von Drosophila melanogaster. Der erste Teil untersuchte die zeitliche Spezifizierung der Neuroblastenidentitäten. Durch die Expression verschiedener Gene entlang der Dorsoventral- und der Anterioposteriorachse wird ein kartesisches Koordinatensystem aufgebaut, indem ein Neuroblast (NB), der in einem bestimmten Quadranten entsteht, eine spezifische Identität erhält. Die Delamination der NBs erfolgt in fünf Segregationswellen, wobei in jeder Welle die gleiche Population NBs gebildet wird. In dieser Arbeit konnte nun gezeigt werden, dass es nicht nur einen räumlichen, sondern auch einen zeitlichen Aspekt bei der Entstehung der NBs gibt: So zeigten Transplantationsexperimente, dass sowohl im frühen als auch im späten Neuroektoderm extrinsische induktive Signale an der Spezifizierung der Neuroblastenidentität beteiligt sind. Die Natur dieser Signale bleibt noch unklar. Allerdings stellen die Segmentpolaritätsgene aufgrund ihrer dynamischen Expression eine potenzielle Kandidatengruppe dar. Der zweite Teil beschäftigte sich mit der segmentalen Spezifizierung der Neuroblasten. Für diesen Prozess zeigten frühere Genexpressionsstudien, dass NBs, die zwar an korrespondierenden Positionen innerhalb des kartesischen Systems, aber in unterschiedlichen Segmenten gebildet werden, die gleichen Genexpressionsmuster aufweisen und fast identische Zellstammbäume hervorbringen. Einige dieser seriell homologen NBs generieren jedoch segmentspezifische Zellstammbäume – ein solches Beispiel ist der NB6-4, der als Modellsystem benutzt wurde. Für die thorakale Variante dieses NBs konnte ich zeigen, dass die Homöotischen Gene zur Spezifizierung nicht notwendig sind – thorakales Schicksal ist eine Grundidentität. Diese wird in abdominalen Segmenten jedoch durch die Funktion der Homöotischen Gene abdominal-A (abd-A) und Abdominal-B (Abd-B) in abdominales Schicksal transformiert. Dieser segmentale Unterschied wird durch die Regulation des Zellzyklusgens CycE bewerkstelligen. Genauer: CycE ist notwendig, um neurogliales Schicksal in thorakalen Segmenten zu generieren und ausreichend, dieses Schicksal ebenfalls in abdominalen Segmenten zu erzeugen. Eine direkte Inhibierung der Expression von CycE durch Abd-A in abdominalen Segmenten führt dagegen zu einer differenziellen Expression von CycE im neuronalen thorakalen Anteil des Zellstammbaums. Weiterhin konnten in einem Enhancerelement, das für die Expression von CycE im Nervensystem verantwortlich ist, mehrere Bindestellen für Abd-A und Abd-B gefunden werden. Die gewonnen Daten legen – in Verbindung mit bereits bekannten Ergebnissen – den Schluss nahe, dass diese neuronspezifizierende Funktion von CycE unabhängig von seiner Rolle im Zellzyklus ist.

Role of the Transcription Factor Sox2 in the Osteogenic Lineage

The Sox2 transcription factor is modified by sumoylation at the K247 position although the addition of SUMO1 and Pias1 promotes the sumoylation of Sox2 at the additional K123 site. The role of sumoylation on Sox2 biological functions was analyzed by comparing the activity of WT and sumoylation mutants on the transcription of the FGF4 gene in HeLa cells and on the downregulation of the Wnt pathwayvin 293T cells. When SUMO1 and PIAS1 promote the sumoylation of WT Sox2, the transcriptional activity of the FGF4 promoter is inhibited showing that Sox2 sumoylation is necessary for the repression function. However, there is no effect of Sox2 sumoylation on β-Catenin activity. Since we were interested in osteoblast differentiation we set up an inducible system for Sox2 in primary osteoblasts. Following Sox2 doxycycline induction, 158 genes were differentially expressed: 120 up-regulated and 38 down-regulated. We annotated as direct Sox2 targets a number of genes involved in osteoblast biology and we further analyzed 3 of them involved in the BMP pathway. The results show that Sox2 regulates the BMP pathway without affecting SMAD phosphorylation, and that Sox2 sumoylation is not necessary for this function. We also found that genes involved in the Hippo pathway were direct Sox2 targets. As the Hippo pathway is activated by Sox2 and Sox2 interacts with the NF2 promoter, we checked the effect of Sox2 on the expression of NF2. We showed that Sox2 down-regulates the transcriptional activity of the NF2 promoter, allowing the transcription of the YAP/TEAD genes in osteoblasts, thus acting as an upstream regulator of the Hippo pathway. We conclude that Sox2 induction in osteoblasts triggers FGF dependent inhibition of the BMP, Wnt and Hippo pathways.

Klonale Analysen im embryonalen Gehirn von Drosophila mit besonderem Fokus auf die Entwicklung der Pilzkörper

Eine wichtige Voraussetzung für das Verständnis der Spezifizierungsmechanismen unterschiedlicher Zelltypen im embryonalen Gehirn ist die detaillierte Kenntnis des neuroektodermalen Ursprungs seiner neuralen Stammzellen (Neuroblasten, NB), sowie der Morphologie und zellulären Komposition der daraus hervorgehenden Zellstammbäume (ZSBe). In der vorliegenden Arbeit wurde die Entstehung und Topologie von 21 embryonalen ZSBen im anteriorsten Gehirnteil, dem Protocerebrum, charakterisiert, mit besonderem Fokus auf solche ZSBe, die den Pilzkörper konstituieren. Pilzkörper sind prominente, paarige Neuropilzentren, die eine wichtige Rolle bei der Verarbeitung olfaktorischer Informationen, beim Lernen und bei der Gedächtnisbildung spielen. In dieser Arbeit konnte erstmalig die Embryonalentwicklung der Pilzkörper ab dem Zeitpunkt der Entstehung ihrer NBen im procephalen Neuroektoderm (pNE), bis hin zum funktionellen Gehirnzentrum in der frühen Larve auf Ebene individueller ZSBe bzw. einzelner Neurone beschrieben werden. Mittels der klonalen Di-Markierungstechnik konnte ich zeigen, dass die vier NBen der Pilzkörper (PKNBen) jeder Gehirnhemisphäre innerhalb des NE aus dem ventralen Bereich der mitotischen Domäne B (δB) hervorgehen. Ein in diesem Bereich liegendes proneurales Feld beherbergt etwa 10-12 Zellen, die alle das Potential haben sich zu PKNBen zu entwickeln. Des Weiteren zeigen diese Untersuchungen, dass die PKNBen (und weitere NBen der δB) aus benachbarten NE-Zellen hervorgehen. Dieser Befund impliziert, dass der Mechanismus der lateralen Inhibition in diesem Bereich des NE keine Rolle spielt. Weiterhin stellte sich heraus, dass jeder PKNB eine ihm eigene Position im sich entwickelnden Pilzkörperkortex besetzt und eine spezifische Kombination der Transkriptionsfaktoren Dachshund, Eyeless und Retinal homeobox exprimiert. Dadurch konnte jeder der vier PKNBen in den betreffenden frühembryonalen NB-Karten einem der ca. 105 NBen pro Gehirnhemisphäre zugeordnet werden. Die PKNBen bringen individuelle ZSBe hervor, die Pilzkörper-intrinsische γ-Neurone beinhalten, aber auch jeweils charakteristische Sets an Interneuronen, die nicht am Aufbau des Pilzkörpers beteiligt sind. Diese verschiedenen Neuronentypen entstehen in einer zeitlichen Abfolge, die für jeden PKNBen spezifisch ist. Ihre embryonalen ZSBe sind aber nicht nur durch individuelle Sets an frühgeborenen ni-Neuronen charakterisiert, sondern auch durch spezifische Unterschiede in der Anzahl ihrer γ-Neurone, welche jedoch, wie ich zeigen konnte, nicht durch Apoptose reguliert wird. Weiterhin konnte ich zeigen, dass γ-Neurone, in einer PKNB Klon-abhängigen Weise, spezifische Unterschiede in der räumlich-zeitlichen Innervation des Pedunkels, der Calyx und der Loben aufweisen. Im Weiteren wurde die Expression verschiedener molekularer Marker in diesen ZSBen charakterisiert, u.a. die Expression verschiedener Gal4-Fliegenstämme, und solcher Transkriptionsfaktoren, die eine wichtige Rolle bei der temporären Spezifizierung im VNS spielen. So werden hb, Kr, pdm1 auch in Nachkommenzellen der PKNBen exprimiert und haben möglicherweise eine Funktion bei ihrer temporären Spezifizierung. Diese Arbeit gibt auch erstmalig Einblick in die vollständige spätembryonale/frühlarvale Morphologie anderer protocerebraler Gehirnzellstammbäume aus δB und δ1. Die Beschreibungen dieser ZSBe beinhalten Angaben zu deren Zellzahl, Zelltypen, der Lage der ZSBe im Gehirn, axonalen/dendritischen Projektionsmustern sowie dem Entstehungsort des NBen.

A QoS Controller Framework Compliant with the ETSI Network Function Virtualization Specification

The 5th generation of mobile networking introduces the concept of “Network slicing”, the network will be “sliced” horizontally, each slice will be compliant with different requirements in terms of network parameters such as bandwidth, latency. This technology is built on logical instead of physical resources, relies on virtual network as main concept to retrieve a logical resource. The Network Function Virtualisation provides the concept of logical resources for a virtual network function, enabling the concept virtual network; it relies on the Software Defined Networking as main technology to realize the virtual network as resource, it also define the concept of virtual network infrastructure with all components needed to enable the network slicing requirements. SDN itself uses cloud computing technology to realize the virtual network infrastructure, NFV uses also the virtual computing resources to enable the deployment of virtual network function instead of having custom hardware and software for each network function. The key of network slicing is the differentiation of slice in terms of Quality of Services parameters, which relies on the possibility to enable QoS management in cloud computing environment. The QoS in cloud computing denotes level of performances, reliability and availability offered. QoS is fundamental for cloud users, who expect providers to deliver the advertised quality characteristics, and for cloud providers, who need to find the right tradeoff between QoS levels that has possible to offer and operational costs. While QoS properties has received constant attention before the advent of cloud computing, performance heterogeneity and resource isolation mechanisms of cloud platforms have significantly complicated QoS analysis and deploying, prediction, and assurance. This is prompting several researchers to investigate automated QoS management methods that can leverage the high programmability of hardware and software resources in the cloud.

Lineage-specific transcription factor aberrations in AML

Transcription factors play a key role in the commitment of hematopoietic stem cells to differentiate into specific lineages [78]. This is particularly important in that a block in terminal differentiation is the key contributing factor in acute leukemias. This general theme of the role of transcription factors in differentiation may also extend to other tissues, both in terms of normal development and cancer. Consistent with the role of transcription factors in hematopoietic lineage commitment is the frequent finding of aberrations in transcription factors in AML patients. Here, we intend to review recent findings on aberrations in lineage-restricted transcription factors as observed in patients with acute myeloid leukemia (AML).

Extremes of Lineage Plasticity in the Drosophila Brain

An often-overlooked aspect of neural plasticity is the plasticity of neuronal composition, in which the numbers of neurons of particular classes are altered in response to environment and experience. The Drosophila brain features several well-characterized lineages in which a single neuroblast gives rise to multiple neuronal classes in a stereotyped sequence during development. We find that in the intrinsic mushroom body neuron lineage, the numbers for each class are highly plastic, depending on the timing of temporal fate transitions and the rate of neuroblast proliferation. For example, mushroom body neuroblast cycling can continue under starvation conditions, uncoupled from temporal fate transitions that depend on extrinsic cues reflecting organismal growth and development. In contrast, the proliferation rates of antennal lobe lineages are closely associated with organismal development, and their temporal fate changes appear to be cell-cycle dependent, such that the same numbers and types of uniglomerular projection neurons innervate the antennal lobe following various perturbations. We propose that this surprising difference in plasticity for these brain lineages is adaptive, given their respective roles as parallel processors versus discrete carriers of olfactory information.

Extremes of Lineage Plasticity in the Drosophila Brain

An often-overlooked aspect of neural plasticity is the plasticity of neuronal composition, in which the numbers of neurons of particular classes are altered in response to environment and experience. The Drosophila brain features several well-characterized lineages in which a single neuroblast gives rise to multiple neuronal classes in a stereotyped sequence during development [1]. We find that in the intrinsic mushroom body neuron lineage, the numbers for each class are highly plastic, depending on the timing of temporal fate transitions and the rate of neuroblast proliferation. For example, mushroom body neuroblast cycling can continue under starvation conditions, uncoupled from temporal fate transitions that depend on extrinsic cues reflecting organismal growth and development. In contrast, the proliferation rates of antennal lobe lineages are closely associated with organismal development, and their temporal fate changes appear to be cell cycle-dependent, such that the same numbers and types of uniglomerular projection neurons innervate the antennal lobe following various perturbations. We propose that this surprising difference in plasticity for these brain lineages is adaptive, given their respective roles as parallel processors versus discrete carriers of olfactory information.

Identification of an African Bacillus anthracis Lineage That Lacks Expression of the Spore Surface-Associated Anthrose-Containing Oligosaccharide

The surfaces of Bacillus anthracis endospores expose a pentasaccharide containing the monosaccharide anthrose, which has been considered for use as a vaccine or target for specific detection of the spores. In this study B. anthracis strains isolated from cattle carcasses in African countries where anthrax is endemic were tested for their cross-reactivity with monoclonal antibodies (MAbs) specific for anthrose-containing oligosaccharides. Unexpectedly, none of the isolates collected in Chad, Cameroon, and Mali were recognized by the MAbs. Sequencing of the four-gene operon encoding anthrose biosynthetic enzymes revealed the presence of premature stop codons in the aminotransferase and glycosyltransferase genes in all isolates from Chad, Cameroon, and Mali. Both immunological and genetic findings suggest that the West African isolates are unable to produce anthrose. The anthrose-deficient strains from West Africa belong to a particular genetic lineage. Immunization of cattle in Chad with a locally produced vaccine based on anthrose-positive spores of the B. anthracis strain Sterne elicited an anti-carbohydrate IgG response specific for a synthetic anthrose-containing tetrasaccharide as demonstrated by glycan microarray analysis. Competition immunoblots with synthetic pentasaccharide derivatives suggested an immunodominant role of the anthrose-containing carbohydrate in cattle. In West Africa anthrax is highly endemic. Massive vaccination of livestock in this area has taken place over long periods of time using spores of the anthrose-positive vaccine strain Sterne. The spread of anthrose-deficient strains in this region may represent an escape strategy of B. anthracis.

Retinoic acid signaling organizes endodermal organ specification along the entire antero-posterior axis

BACKGROUND: Endoderm organ primordia become specified between gastrulation and gut tube folding in Amniotes. Although the requirement for RA signaling for the development of a few individual endoderm organs has been established a systematic assessment of its activity along the entire antero-posterior axis has not been performed in this germ layer. METHODOLOGY/PRINCIPAL FINDINGS: RA is synthesized from gastrulation to somitogenesis in the mesoderm that is close to the developing gut tube. In the branchial arch region specific levels of RA signaling control organ boundaries. The most anterior endoderm forming the thyroid gland is specified in the absence of RA signaling. Increasing RA in anterior branchial arches results in thyroid primordium repression and the induction of more posterior markers such as branchial arch Hox genes. Conversely reducing RA signaling shifts Hox genes posteriorly in endoderm. These results imply that RA acts as a caudalizing factor in a graded manner in pharyngeal endoderm. Posterior foregut and midgut organ primordia also require RA, but exposing endoderm to additional RA is not sufficient to expand these primordia anteriorly. We show that in chick, in contrast to non-Amniotes, RA signaling is not only necessary during gastrulation, but also throughout gut tube folding during somitogenesis. Our results show that the induction of CdxA, a midgut marker, and pancreas induction require direct RA signaling in endoderm. Moreover, communication between CdxA(+) cells is necessary to maintain CdxA expression, therefore synchronizing the cells of the midgut primordium. We further show that the RA pathway acts synergistically with FGF4 in endoderm patterning rather than mediating FGF4 activity. CONCLUSIONS/SIGNIFICANCE: Our work establishes that retinoic acid (RA) signaling coordinates the position of different endoderm organs along the antero-posterior axis in chick embryos and could serve as a basis for the differentiation of specific endodermal organs from ES cells.

XML for Model Specification in Neuroscience

One of the main roles of the Neural Open Markup Language, NeuroML, is to facilitate cooperation in building, simulating, testing and publishing models of channels, neurons and networks of neurons. MorphML, which was developed as a common format for exchange of neural morphology data, is distributed as part of NeuroML but can be used as a stand-alone application. In this collection of tutorials and workshop summary, we provide an overview of these XML schemas and provide examples of their use in down-stream applications. We also summarize plans for the further development of XML specifications for modeling channels, channel distributions, and network connectivity.

Dissemination of methicillin-resistant Staphylococcus aureus USA300 sequence type 8 lineage in Latin America.

BACKGROUND: Methicillin-resistant Staphylococus aureus (MRSA) is an important nosocomial and community-associated (CA) pathogen. Recently, a variant of the MRSA USA300 clone emerged and disseminated in South America, causing important clinical problems. METHODS: S. aureus isolates were prospectively collected (2006-2008) from 32 tertiary hospitals in Colombia, Ecuador, Peru, and Venezuela. MRSA isolates were subjected to antimicrobial susceptibility testing and pulsed-field gel electrophoresis and were categorized as health care-associated (HA)-like or CA-like clones on the basis of genotypic characteristics and detection of genes encoding Panton-Valentine leukocidin and staphylococcal cassette chromosome (SCC) mec IV. In addition, multilocus sequence typing of representative isolates of each major CA-MRSA pulsotype was performed, and the presence of USA300-associated toxins and the arcA gene was investigated for all isolates categorized as CA-MRSA. RESULTS: A total of 1570 S. aureus were included; 651 were MRSA (41%)--with the highest rate of MRSA isolation in Peru (62%) and the lowest in Venezuela (26%)--and 71%, 27%, and 2% were classified as HA-like, CA-like, and non-CA/HA-like clones, respectively. Only 9 MRSA isolates were confirmed to have reduced susceptibility to glycopeptides (glycopeptide-intermediate S. aureus phenotype). The most common pulsotype (designated ComA) among the CA-like MRSA strains was found in 96% of isolates, with the majority (81%) having a < or =6-band difference with the USA300-0114 strain. Representative isolates of this clone were sequence type 8; however, unlike the USA300-0114 strain, they harbored a different SCCmec IV subtype and lacked arcA (an indicator of the arginine catabolic mobile element). CONCLUSION: A variant CA-MRSA USA300 clone has become established in South America and, in some countries, is endemic in hospital settings.