gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.

Dissection of the complex phenotype in cuticular mutants of Arabidopsis reveals a role of SERRATE as a mediator.

Mutations in LACERATA (LCR), FIDDLEHEAD (FDH), and BODYGUARD (BDG) cause a complex developmental syndrome that is consistent with an important role for these Arabidopsis genes in cuticle biogenesis. The genesis of their pleiotropic phenotypes is, however, poorly understood. We provide evidence that neither distorted depositions of cutin, nor deficiencies in the chemical composition of cuticular lipids, account for these features, instead suggesting that the mutants alleviate the functional disorder of the cuticle by reinforcing their defenses. To better understand how plants adapt to these mutations, we performed a genome-wide gene expression analysis. We found that apparent compensatory transcriptional responses in these mutants involve the induction of wax, cutin, cell wall, and defense genes. To gain greater insight into the mechanism by which cuticular mutations trigger this response in the plants, we performed an overlap meta-analysis, which is termed MASTA (MicroArray overlap Search Tool and Analysis), of differentially expressed genes. This suggested that different cell integrity pathways are recruited in cesA cellulose synthase and cuticular mutants. Using MASTA for an in silico suppressor/enhancer screen, we identified SERRATE (SE), which encodes a protein of RNA-processing multi-protein complexes, as a likely enhancer. In confirmation of this notion, the se lcr and se bdg double mutants eradicate severe leaf deformations as well as the organ fusions that are typical of lcr and bdg and other cuticular mutants. Also, lcr does not confer resistance to Botrytis cinerea in a se mutant background. We propose that there is a role for SERRATE-mediated RNA signaling in the cuticle integrity pathway.

Lentiviral vectors: a powerful tool to target astrocytes in vivo.

The morphological and functional diversity of astrocytes, and their essential contribution in physiological and pathological conditions, are starting to emerge. However, experimental systems to investigate neuron-glia interactions and develop innovative approaches for the treatment of central nervous system (CNS) disorders are still very limited. Fluorescent reporter genes have been used to visualize populations of astrocytes and produce an atlas of gene expression in the brain. Knock-down or knock-out of astrocytic proteins using transgenesis have also been developed, but these techniques remain complex and time-consuming. Viral vectors have been developed to overexpress or silence genes of interest as they can be used for both in vitro and in vivo studies in adult mammalian species. In most cases, high transduction efficiency and long-term transgene expression are observed in neurons but there is limited expression in astrocytes. Several strategies have been developed to shift the tropism of lentiviral vectors (LV) and allow local and controlled gene expression in glial cells. In this review, we describe how modifications of the interaction between the LV envelope glycoprotein and the surface receptor molecules on target cells, or the integration of cell-specific promoters and miRNA post-transcriptional regulatory elements have been used to selectively express transgenes in astrocytes.

Method to assess and optimise dependability of complex macro-systems: application to a railway signalling system

Achieving a high degree of dependability in complex macro-systems is challenging. Because of the large number of components and numerous independent teams involved, an overview of the global system performance is usually lacking to support both design and operation adequately. A functional failure mode, effects and criticality analysis (FMECA) approach is proposed to address the dependability optimisation of large and complex systems. The basic inductive model FMECA has been enriched to include considerations such as operational procedures, alarm systems. environmental and human factors, as well as operation in degraded mode. Its implementation on a commercial software tool allows an active linking between the functional layers of the system and facilitates data processing and retrieval, which enables to contribute actively to the system optimisation. The proposed methodology has been applied to optimise dependability in a railway signalling system. Signalling systems are typical example of large complex systems made of multiple hierarchical layers. The proposed approach appears appropriate to assess the global risk- and availability-level of the system as well as to identify its vulnerabilities. This enriched-FMECA approach enables to overcome some of the limitations and pitfalls previously reported with classical FMECA approaches.

Calprotectine fécale: outil diagnostique dans les maladies inflammatoires chroniques de l'intestin [Fecal calprotectin: a diagnostic tool for inflammatory bowel disease].

Fecal calprotectin (FC) is a valid biomarker to discriminate with a good sensitivity and specificity the presence of mucosal lesions of the gastrointestinal tube (e.g. ulcers in the context of inflammatory bowel disease (IBD)) from functional disorders (e.g. irritable bowel syndrome). FC is not specific for IBD and can be elevated also in gastrointestinal infections, ischemic colitis or neoplasia. An elevated FC should stimulate further investigations, notably an endoscopic workup. The level of FC correlates with the endoscopic score in Crohn's disease and ulcerative colitis. The correlation of FC and the endoscopic severity is better than the one of CRP or blood leukocytes. Thus, FC can also be used in the follow-up of IBD patients.

Soluble major histocompatibility complex-peptide octamers with impaired CD8 binding selectively induce Fas-dependent apoptosis.

Fluorescence-labeled soluble major histocompatibility complex class I-peptide "tetramers" constitute a powerful tool to detect and isolate antigen-specific CD8(+) T cells by flow cytometry. Conventional "tetramers" are prepared by refolding of heavy and light chains with a specific peptide, enzymatic biotinylation at an added C-terminal biotinylation sequence, and "tetramerization" by reaction with phycoerythrin- or allophycocyanin-labeled avidin derivatives. We show here that such preparations are heterogeneous and describe a new procedure that allows the preparation of homogeneous tetra- or octameric major histocompatibility complex-peptide complexes. These compounds were tested on T1 cytotoxic T lymphocytes (CTLs), which recognize the Plasmodium berghei circumsporzoite peptide 252-260 (SYIPSAEKI) containing photoreactive 4-azidobenzoic acid on Lys(259) in the context of H-2K(d). We report that mutation of the CD8 binding site of K(d) greatly impairs the binding of tetrameric but not octameric or multimeric K(d)-PbCS(ABA) complexes to CTLs. This mutation abolishes the ability of the octamer to elicit significant phosphorylation of CD3, intracellular calcium mobilization, and CTL degranulation. Remarkably, however, this octamer efficiently activates CTLs for Fas (CD95)-dependent apoptosis.

The temporoparietal fascia flap: a versatile tool in head and neck reconstruction.

PURPOSE OF REVIEW: The article reviews recent significant advances and current applications of the temporoparietal fascia flap (TPFF) in head and neck surgery. RECENT FINDINGS: The recent literature describes a wide span of new applications of the TPFF in many areas. Significant developments and refinements in the reconstruction of orbitomaxillary composite defects and orbital exenteration cavities are reported. The TPFF combined with alloplastic framework is gaining in importance in external ear reconstruction. Innovative prefabricated skin or soft-tissue grafts based on the TPFF are used to restore facial contour or in the reconstruction of complex facial defects. The free TPFF finds a role in laryngotracheal reconstruction as a vascular carrier to support cartilage grafts. SUMMARY: Owing to its reliability and unequalled structural properties, the TPFF still plays a central role in facial reconstruction. Future investigation will likely incorporate the free TPFF as a vascular carrier of bioengineered tissues, such as cartilage and mucosa, for various head and neck indications.

Predictive analysis and mapping of indoor radon concentrations in a complex environment using kernel estimation: an application to Switzerland.

PURPOSE: The aim of this study was to develop models based on kernel regression and probability estimation in order to predict and map IRC in Switzerland by taking into account all of the following: architectural factors, spatial relationships between the measurements, as well as geological information. METHODS: We looked at about 240,000 IRC measurements carried out in about 150,000 houses. As predictor variables we included: building type, foundation type, year of construction, detector type, geographical coordinates, altitude, temperature and lithology into the kernel estimation models. We developed predictive maps as well as a map of the local probability to exceed 300 Bq/m(3). Additionally, we developed a map of a confidence index in order to estimate the reliability of the probability map. RESULTS: Our models were able to explain 28% of the variations of IRC data. All variables added information to the model. The model estimation revealed a bandwidth for each variable, making it possible to characterize the influence of each variable on the IRC estimation. Furthermore, we assessed the mapping characteristics of kernel estimation overall as well as by municipality. Overall, our model reproduces spatial IRC patterns which were already obtained earlier. On the municipal level, we could show that our model accounts well for IRC trends within municipal boundaries. Finally, we found that different building characteristics result in different IRC maps. Maps corresponding to detached houses with concrete foundations indicate systematically smaller IRC than maps corresponding to farms with earth foundation. CONCLUSIONS: IRC mapping based on kernel estimation is a powerful tool to predict and analyze IRC on a large-scale as well as on a local level. This approach enables to develop tailor-made maps for different architectural elements and measurement conditions and to account at the same time for geological information and spatial relations between IRC measurements.

Probing functional groups at the gas-aerosol interface using heterogeneous titration reactions: a tool for predicting aerosol health effects?

The complex chemical and physical nature of combustion and secondary organic aerosols (SOAs) in general precludes the complete characterization of both bulk and interfacial components. The bulk composition reveals the history of the growth process and therefore the source region, whereas the interface controls--to a large extent--the interaction with gases, biological membranes, and solid supports. We summarize the development of a soft interrogation technique, using heterogeneous chemistry, for the interfacial functional groups of selected probe gases [N(CH(3))(3), NH(2)OH, CF(3)COOH, HCl, O(3), NO(2)] of different reactivity. The technique reveals the identity and density of surface functional groups. Examples include acidic and basic sites, olefinic and polycyclic aromatic hydrocarbon (PAH) sites, and partially and completely oxidized surface sites. We report on the surface composition and oxidation states of laboratory-generated aerosols and of aerosols sampled in several bus depots. In the latter case, the biomarker 8-hydroxy-2'-deoxyguanosine, signaling oxidative stress caused by aerosol exposure, was isolated. The increase in biomarker levels over a working day is correlated with the surface density N(i)(O3) of olefinic and/or PAH sites obtained from O(3) uptakes as well as with the initial uptake coefficient, γ(0), of five probe gases used in the field. This correlation with γ(0) suggests the idea of competing pathways occurring at the interface of the aerosol particles between the generation of reactive oxygen species (ROS) responsible for oxidative stress and cellular antioxidants.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

Enterprise Portal as a Knowledge Management Tool in a Global Forest Products Company

Tietojohtaminen on osoittautunut nykypäivänä organisaatioiden yhdeksi suurimmaksi haasteeksi. Haasteena ei vain ole se tiedon määrä mitä tulisi hallita, vaan pikemminkin tiedonhallinta toimii yritykselle kilpailuetuna globaalissa yritysmaailmassa. Tämän työn tavoitteena on tutkia yritysportaalin soveltuvuutta tiedonhallintaan globaalissa metsäteollisuusyrityksessä. Lisäksi tavoitteena on selvittää portaalin sovittamista kullekin käyttäjäryhmälle case yrityksessä. Työn teoriaosassa on käsitelty tiedonhallinnan monimuotoisuutta ja vaikeutta kuvata sitä yksiselitteisesti. Lisäksi käyttäjäryhmien ja käyttäjäprofiilien määrittämiseen vaikuttavia seikkoja on selvitetty tässä osassa. Empiirinen osa käsittelee case-yritystä ja sen suhdetta tiedonhallintaan sekä tämän kaltaisen tiedonhallinnan työvälineen käyttöön. Työstä saatujen tulosten perusteella voidaan todeta yritysportaalin soveltuvan hyvin tiedonhallintaan monimutkaisessakin yrityksessä. Portaali muuttaa yrityksen liiketoimintaprosesseja läpinäkyvämmiksi, kun bisneskriittistä tietoa tarjotaan yhdessä paikassa.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

Improving ERP change tool processes to align business processes and ERP system

Nopea teknologian kehitys sekä kansainvälistymisen mukana tuoma kilpailupaine pakottavat yritykset jatkuvaan liiketoimintaprosessien kehittämiseen. Muutoksista organisaation rakenteissa sekä yrityksen prosesseissa on tullut yleisiä toimenpiteitä. Yksi näkyvimmistä toiminnallisista uudistuksesta on ollut toiminnanohjausjärjestelmän käyttöönotto. Toiminnanohjausjärjestelmän rakenne ja kehitys aiheuttaa yleensä suurimmat vaikeudet pyrittäessä rakentamaan liiketoimintaprosessien läpinäkyvyyttä esittävä tietojärjestelmäympäristö. Tässä tutkimuksessa liiketoiminnan sekä toiminnanohjausjärjestelmän prosessien yhdistäminen on tehty ns. toiminnanohjausjärjestelmä muutostyökaluilla. Kyseiset muutostyökalut on järjestetty yrityksissä tietojärjestelmä ympäristöön ja niiden avulla voidaan korjata teknisiä ongelmia sekä muuttaa itse prosesseja. Tutkimuksen empiria osuudessa on käytetty case-tutkimusmenetelmää Kone Oyj:n prosessien kehittämisosastolla. Tutkimuksen tavoitteena oli parantaa toiminnanohjausjärjestelmän muutostyökalujen prosesseja, liiketoimintaprosessien sekä toiminnanohjausjärjestelmän yhdistämiseksi ja harmonisoimiseksi. Tutkimuksen tavoitteiden täyttämiseksi, prosessijohtamisen käsitteitä käytettiin muutostyökaluprosessien parannusehdotusten löytymiseksi. Prosessijohtamisen käsitteet tarkoittavat prosessikartan, prosessin toimintojen, sekä prosessin kustannusten tutkimista ja hyväksikäyttöä. Prosessijohtamisen käsitteeseen kuuluu myös liiketoimintaprosessien jatkuvan parantamisen sekä uudelleenjärjestämisen mallien kuvaus. Toiminnanohjausjärjestelmäympäristön kuvaus teorian toisena osuutena antaa pohjaa muutostyökalujen prosessien käytölle. Tutkimuksen tuloksina voidaan todeta että tutkimusalue on hyvin monimutkainen ja vaikea. Toimintajärjestelmistä ei ole kirjoitettu teoriaa kovinkaan runsaasti, lukuunottamatta yritysten itse tekemiä tutkimuksia. Tutkimuksessa tarkasteltaville prosesseille löytyi kuitenkin parannusehdotuksia sekä ns. optimaalisen prosessimallin ominaisuuksia.

Accessory phases as a tool to investigate magmatic underplating in polymetamorphic metasediments : an example from a fossil lower crust : Ivrea Verbano zne, NW Italy

The Ivrea and the Strona-Ceneri zones, NW italy and S Switzerland, offer the possibility to study the continental crust of the Southern Alps. Because of its high metamorphic degree and the abundant Permo- Carboniferous mafic intrusions, the Ivrea Zone is classically interpreted an exposed section trough the Permian lower crust. The present work is focused here on metasedimentary slices (septa) intercalated within Permian gabbro (mafic complex). In particular I studied the evolution of accessory phases such as rutile and zircon and the chemistry of the metasediments. The septa build an irregular and discontinuous band that cut obliquely the mafic complex from its deepest part (N) to its roof (S). The chemistry of the metasediments evolves along the band and the chemical evolution can be compared with that observed in the country-rock surrounding the mafic intrusion to the NE and overprinted by a main regional metamorphic event. This suggests that the degree of chemical depletion of the septa was mainly established during the same regional metamorphic event. Moreover it suggests that incorporation of the septa within the gabbro did not modify their original stratigraphie distribution within the crust. It implies that the mafic complex has been emplaced following a dynamic substantially different from the classic model of « gabbro glacier » (Quick et al., 1992; Quick et al., 1994). It is more likely that it has been emplaced by repeated injections of sills at different depths during a protracted period of time. Zircon trace elements and U-Pb ages suggest that regional metamorphism occurred 330-320Ma, the first sills in the deepest part of the Mafic Complex are injected at ~300Ma, the mafic magmas reached higher levels in the crust at 285Ma and the magmatic activity continued locally until 275Ma. The ages of detrital cores in zircons fix the maximal sedimentation age at ~370Ma, this age corresponds therefore with the maximal age of the incorporation of the Ivrea zone within the lower crust. I propose that the Ivrea zone has been accreted to the lower crust during the Hercynian orogeny sensu lato. The analysis of detrital ages suggests that the source terrains for the Ivrea zone and those for the Strona-Ceneri zone have a completely different Palaeozoic history. The systematic analysis of rutile in partially molten metasediments of the Ivrea zone reveals the occurrence of two generations. The two generations are characterized by a different chemistry and textural distribution. A first generation is formed during pro-grade metamorphism in the restitic counterpart. The second generation is formed in the melts during cooling at the same time that part of the first generation re-equilibrate. Re-equilibration of the first generation seems to be spatially controlled by the presence of fluids. Locally the second generation forms overgrowths on the first generation. Considered the different diffusivity of U and Pb in rutile, U heterogeneities have important implication for U-Pb dating of rutile. ID-TIMS and LA-ICPMS dating coupled with a careful textural investigation (SEM) suggest that rutile grains are characterized by multiple path along which Pb diffusion can occur: volume diffusion is an important process, but intragrain and subgrain boundaries provide additional high diffusivity pathways for Pb escape and reduce drastically the effective diffusion length. -- La zone d'Ivrea et la zone de Strona-Ceneri, en Italie nord-occidentale et Suisse méridionale, offrent la possibilité d'étudier la croûte continentale des Alpes du Sud. En raison du haut degré métamorphique et l'abondance d'intrusions mafiques d'âge Permo-Carbonifère [complexe mafique), la zone d'Ivrea est interprétée classiquement comme de la croûte inférieure permienne. Ce travail ce concentre sur des bandes metasédimentaires (septa) incorporées dans les magmas mafiques lors de l'intrusion. Les septa forment une bande irrégulière qui coupe obliquement le complexe mafique du bas (N) vers le haut (S). La chimie des septa évolue du bas vers le haut et l'évolution chimique se rapproche de l'évolution observé dans la roche encaissante l'intrusion affecté par un événement métamorphique régionale. Cette relation suggère que le degré d'appauvrissement chimique des septa a été établit principalement lors de l'événement métamorphique régional. De plus l'incorporation dans les gabbros n'a pas perturbée la distribution stratigraphique originelle des septa. Ces deux observations impliquent que le métamorphisme dans la roche encaissante précède la mise en place du gabbro et que cette dernière ne se fait pas selon le modèle classique (« gabbro glacier » de Quick et al., 1992, 1994), mais se fait plutôt par injections répétées de sills a différentes profondeurs. Les âges U-Pb et les éléments traces des zircons suggèrent que le métamorphisme régionale a eu lieu 330-320Ma, alors que les premiers sills dans la partie profonde du Mafic Complex s'injectent à ~300Ma, le magmatisme mafique atteigne des niveaux supérieurs à 285Ma et continue localement jusqu'à 270Ma. Les âges des coeurs détritiques des zircons permettent de fixer l'âge maximale de sédimentation à ~370Ma ce qui correspond donc à l'âge maximale de l'incorporation de la zone d'Ivrea dans la croûte inférieur. L'analyse systématique des rutiles, nous a permit de montrer l'existence de plusieurs générations qui ont une répartition texturale et une chimie différente. Une génération se forme lors de l'événement UHT dans les restites, une autre génération se forme dans les liquides lors du refroidissement, au même temps qu'une partie de la première génération se rééquilibre au niveau du Zr. Localement la deuxième génération peut former des surcroissances autour de la première génération. Dans ces cas, des fortes différences en uranium entre les deux générations ont des importantes implications pour la datation U-Pb sur rutile. Classiquement les ratios Pb/U dans le rutile sont interprétés comme indiquant l'âges du refroidissement du minéral sous une température à la quelle la diffusion du Pb dans le minéral n'est plus détectable et la diffusion à plus hautes températures est assumée se faire par «volume diffusion» dans le grain (Mezger et al., 1989). Par des datations ID-TIMS (sur grain entier) et LA-ICPMS (in-situ) et une analyse texturale (MEB) approfondie nous montrons que cette supposition est trop simpliste et que le rutile est repartie en sous-domaines. Chacun de ces domaines a ça propre longueur ou chemin de diffusion spécifique. Nous proposons donc une nouvelle approche plus cohérente pour l'interprétation des âges U-Pb sur rutile.

Multifactor Performance Study on Complex Systems for the Benefit of Management

The primary objective is to identify the critical factors that have a natural impact on the performance measurement system. It is important to make correct decisions related to measurement systems, which are based on the complex business environment. The performance measurement system is combined with a very complex non-linear factor. The Six Sigma methodology is seen as one potential approach at every organisational level. It will be linked to the performance and financial measurement as well as to the analytical thinking on which the viewpoint of management depends. The complex systems are connected to the customer relationship study. As the primary throughput can be seen in a new well-defined performance measurement structure that will also be facilitated as will an analytical multifactor system. These critical factors should also be seen as a business innovation opportunity at the same time. This master's thesis has been divided into two different theoretical parts. The empirical part consists of both action-oriented and constructive research approaches with an empirical case study. The secondary objective is to seek a competitive advantage factor with a new analytical tool and the Six Sigma thinking. Process and product capabilities will be linked to the contribution of complex system. These critical barriers will be identified by the performance measuring system. The secondary throughput can be recognised as the product and the process cost efficiencies which throughputs are achieved with an advantage of management. The performance measurement potential is related to the different productivity analysis. Productivity can be seen as one essential part of the competitive advantage factor.