Quantification of dose nonuniformities by voxel-based dosimetry in patients receiving 90Y-ibritumomab-tiuxetan.

OBJECTIVE: To assess the impact of nonuniform dose distribution within lesions and tumor-involved organs of patients receiving Zevalin, and to discuss possible implications of equivalent uniform biological effective doses (EU-BED) on treatment efficacy and toxicity. MATLAB? -based software for voxel-based dosimetry was adopted for this purpose. METHODS: Eleven lesions from seven patients with either indolent or aggressive non-Hodgkin lymphoma were analyzed, along with four organs with disease. Absorbed doses were estimated by a direct integration of single-voxel kinetic data from serial tomographic images. After proper corrections, differential BED distributions and surviving cell fractions were estimated, allowing for the calculation of EU-BED. To quantify dose uniformity in each target area, a heterogeneity index was defined. RESULTS: Average doses were below those prescribed by conventional radiotherapy to eradicate lymphoma lesions. Dose heterogeneity and effect on tumor control varied among lesions, with no apparent relation to tumor mass. Although radiation doses to involved organs were safe, unexpected liver toxicity occurred in one patient who presented with a pattern of diffuse infiltration. CONCLUSION: Voxel-based dosimetry and radiobiologic modeling can be successfully applied to lesions and tumor-involved organs, representing a methodological advance over estimation of mean absorbed doses. However, effects on tumor control and organ toxicity still cannot be easily predicted.

Synchronous versus asynchronous modeling of gene regulatory networks.

MOTIVATION: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene-gene, protein-protein and gene-protein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes. RESULTS: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks. Algorithms for synchronous and asynchronous transition models have been proposed and their corresponding computational properties have been analyzed. These algorithms allow users to compute cyclic attractors of large networks that are currently not feasible using existing software. Hereby we provide a framework to analyze the effect of multiple gene perturbation protocols, and their effect on cell differentiation processes. These algorithms were validated on the T-helper model showing the correct steady state identification and Th1-Th2 cellular differentiation process. AVAILABILITY: The software binaries for Windows and Linux platforms can be downloaded from http://si2.epfl.ch/~garg/genysis.html.

Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition.

Retroelements are important evolutionary forces but can be deleterious if left uncontrolled. Members of the human APOBEC3 family of cytidine deaminases can inhibit a wide range of endogenous, as well as exogenous, retroelements. These enzymes are structurally organized in one or two domains comprising a zinc-coordinating motif. APOBEC3G contains two such domains, only the C terminal of which is endowed with editing activity, while its N-terminal counterpart binds RNA, promotes homo-oligomerization, and is necessary for packaging into human immunodeficiency virus type 1 (HIV-1) virions. Here, we performed a large-scale mutagenesis-based analysis of the APOBEC3G N terminus, testing mutants for (i) inhibition of vif-defective HIV-1 infection and Alu retrotransposition, (ii) RNA binding, and (iii) oligomerization. Furthermore, in the absence of structural information on this domain, we used homology modeling to examine the positions of functionally important residues and of residues found to be under positive selection by phylogenetic analyses of primate APOBEC3G genes. Our results reveal the importance of a predicted RNA binding dimerization interface both for packaging into HIV-1 virions and inhibition of both HIV-1 infection and Alu transposition. We further found that the HIV-1-blocking activity of APOBEC3G N-terminal mutants defective for packaging can be almost entirely rescued if their virion incorporation is forced by fusion with Vpr, indicating that the corresponding region of APOBEC3G plays little role in other aspects of its action against this pathogen. Interestingly, residues forming the APOBEC3G dimer interface are highly conserved, contrasting with the rapid evolution of two neighboring surface-exposed amino acid patches, one targeted by the Vif protein of primate lentiviruses and the other of yet-undefined function.

Treeline and climate change : analyzing and modeling patterns and shifts in the Swiss Alps

Summary: Global warming has led to an average earth surface temperature increase of about 0.7 °C in the 20th century, according to the 2007 IPCC report. In Switzerland, the temperature increase in the same period was even higher: 1.3 °C in the Northern Alps anal 1.7 °C in the Southern Alps. The impacts of this warming on ecosystems aspecially on climatically sensitive systems like the treeline ecotone -are already visible today. Alpine treeline species show increased growth rates, more establishment of young trees in forest gaps is observed in many locations and treelines are migrating upwards. With the forecasted warming, this globally visible phenomenon is expected to continue. This PhD thesis aimed to develop a set of methods and models to investigate current and future climatic treeline positions and treeline shifts in the Swiss Alps in a spatial context. The focus was therefore on: 1) the quantification of current treeline dynamics and its potential causes, 2) the evaluation and improvement of temperaturebased treeline indicators and 3) the spatial analysis and projection of past, current and future climatic treeline positions and their respective elevational shifts. The methods used involved a combination of field temperature measurements, statistical modeling and spatial modeling in a geographical information system. To determine treeline shifts and assign the respective drivers, neighborhood relationships between forest patches were analyzed using moving window algorithms. Time series regression modeling was used in the development of an air-to-soil temperature transfer model to calculate thermal treeline indicators. The indicators were then applied spatially to delineate the climatic treeline, based on interpolated temperature data. Observation of recent forest dynamics in the Swiss treeline ecotone showed that changes were mainly due to forest in-growth, but also partly to upward attitudinal shifts. The recent reduction in agricultural land-use was found to be the dominant driver of these changes. Climate-driven changes were identified only at the uppermost limits of the treeline ecotone. Seasonal mean temperature indicators were found to be the best for predicting climatic treelines. Applying dynamic seasonal delimitations and the air-to-soil temperature transfer model improved the indicators' applicability for spatial modeling. Reproducing the climatic treelines of the past 45 years revealed regionally different attitudinal shifts, the largest being located near the highest mountain mass. Modeling climatic treelines based on two IPCC climate warming scenarios predicted major shifts in treeline altitude. However, the currently-observed treeline is not expected to reach this limit easily, due to lagged reaction, possible climate feedback effects and other limiting factors. Résumé: Selon le rapport 2007 de l'IPCC, le réchauffement global a induit une augmentation de la température terrestre de 0.7 °C en moyenne au cours du 20e siècle. En Suisse, l'augmentation durant la même période a été plus importante: 1.3 °C dans les Alpes du nord et 1.7 °C dans les Alpes du sud. Les impacts de ce réchauffement sur les écosystèmes - en particuliers les systèmes sensibles comme l'écotone de la limite des arbres - sont déjà visibles aujourd'hui. Les espèces de la limite alpine des forêts ont des taux de croissance plus forts, on observe en de nombreux endroits un accroissement du nombre de jeunes arbres s'établissant dans les trouées et la limite des arbres migre vers le haut. Compte tenu du réchauffement prévu, on s'attend à ce que ce phénomène, visible globalement, persiste. Cette thèse de doctorat visait à développer un jeu de méthodes et de modèles pour étudier dans un contexte spatial la position présente et future de la limite climatique des arbres, ainsi que ses déplacements, au sein des Alpes suisses. L'étude s'est donc focalisée sur: 1) la quantification de la dynamique actuelle de la limite des arbres et ses causes potentielles, 2) l'évaluation et l'amélioration des indicateurs, basés sur la température, pour la limite des arbres et 3) l'analyse spatiale et la projection de la position climatique passée, présente et future de la limite des arbres et des déplacements altitudinaux de cette position. Les méthodes utilisées sont une combinaison de mesures de température sur le terrain, de modélisation statistique et de la modélisation spatiale à l'aide d'un système d'information géographique. Les relations de voisinage entre parcelles de forêt ont été analysées à l'aide d'algorithmes utilisant des fenêtres mobiles, afin de mesurer les déplacements de la limite des arbres et déterminer leurs causes. Un modèle de transfert de température air-sol, basé sur les modèles de régression sur séries temporelles, a été développé pour calculer des indicateurs thermiques de la limite des arbres. Les indicateurs ont ensuite été appliqués spatialement pour délimiter la limite climatique des arbres, sur la base de données de températures interpolées. L'observation de la dynamique forestière récente dans l'écotone de la limite des arbres en Suisse a montré que les changements étaient principalement dus à la fermeture des trouées, mais aussi en partie à des déplacements vers des altitudes plus élevées. Il a été montré que la récente déprise agricole était la cause principale de ces changements. Des changements dus au climat n'ont été identifiés qu'aux limites supérieures de l'écotone de la limite des arbres. Les indicateurs de température moyenne saisonnière se sont avérés le mieux convenir pour prédire la limite climatique des arbres. L'application de limites dynamiques saisonnières et du modèle de transfert de température air-sol a amélioré l'applicabilité des indicateurs pour la modélisation spatiale. La reproduction des limites climatiques des arbres durant ces 45 dernières années a mis en évidence des changements d'altitude différents selon les régions, les plus importants étant situés près du plus haut massif montagneux. La modélisation des limites climatiques des arbres d'après deux scénarios de réchauffement climatique de l'IPCC a prédit des changements majeurs de l'altitude de la limite des arbres. Toutefois, l'on ne s'attend pas à ce que la limite des arbres actuellement observée atteigne cette limite facilement, en raison du délai de réaction, d'effets rétroactifs du climat et d'autres facteurs limitants.

Molecular Modeling Approaches for Determining Gene Function: application to a Putative Poly-A Binding Protein from Leishmania amazonensis (LaPABP)

The great expansion in the number of genome sequencing projects has revealed the importance of computational methods to speed up the characterization of unknown genes. These studies have been improved by the use of three dimensional information from the predicted proteins generated by molecular modeling techniques. In this work, we disclose the structure-function relationship of a gene product from Leishmania amazonensis by applying molecular modeling and bioinformatics techniques. The analyzed sequence encodes a 159 aminoacids polypeptide (estimated 18 kDa) and was denoted LaPABP for its high homology with poly-A binding proteins from trypanosomatids. The domain structure, clustering analysis and a three dimensional model of LaPABP, basically obtained by homology modeling on the structure of the human poly-A binding protein, are described. Based on the analysis of the electrostatic potential mapped on the model's surface and conservation of intramolecular contacts responsible for folding stabilization we hypothesize that this protein may have less avidity to RNA than it's L. major counterpart but still account for a significant functional activity in the parasite. The model obtained will help in the design of mutagenesis experiments aimed to elucidate the mechanism of gene expression in trypanosomatids and serve as a starting point for its exploration as a potential source of targets for a rational chemotherapy.

An Adenovirus Vector Containing the Suicide Gene Thymidine Kinase for a Broad Application in Cancer Gene Therapy

Treatment of cancer using gene therapy is based on adding a property to the cell leading to its elimination. One possibility is the use of suicide genes that code for enzymes that transform a pro-drug into a cytotoxic product. The most extensively used is the herpes simplex virus thymidine kinase (TK) gene, followed by administration of the antiviral drug ganciclovir (GCV). The choice of the promoter to drive the transcription of a transgene is one of the determinants of a given transfer vector usefulness, as different promoters show different efficiencies depending on the target cell type. In the experiments presented here, we report the construction of a recombinant adenovirus carrying TK gene (Ad-TK) driven by three strong promoters (P CMV IE, SV40 and EN1) and its effectiveness in two cell types. Human HeLa and mouse CCR2 tumor cells were transduced with Ad-TK and efficiently killed after addition of GCV. We could detect two sizes of transcripts of TK gene, one derived from the close together P CMV IE/SV40 promoters and the other from the 1.5 Kb downstream EN1 promoter. The relative amounts of these transcripts were different in each cell type thus indicating a higher flexibility of this system.

Analyzing complex rock slope deformation at Stampa, western Norway, by integrating geomorphology, kinematics and numerical modeling

The unstable rock slope, Stampa, above the village of Flåm, Norway, shows signs of both active and postglacial gravitational deformation over an area of 11 km2. Detailed structural field mapping, annual differential Global Navigation Satellite System (GNSS) surveys, as well as geomorphic analysis of high-resolution digital elevation models based on airborne and terrestrial laser scanning indicate that slope deformation is complex and spatially variable. Numerical modeling was used to investigate the influence of former rockslide activity and to better understand the failure mechanism. Field observations, kinematic analysis and numerical modeling indicate a strong structural control of the unstable area. Based on the integration of the above analyses, we propose that the failure mechanism is dominated by (1) a toppling component, (2) subsiding bilinear wedge failure and (3) planar sliding along the foliation at the toe of the unstable slope. Using differential GNSS, 18 points were measured annually over a period of up to 6 years. Two of these points have an average yearly movement of around 10 mm/year. They are located at the frontal cliff on almost completely detached blocks with volumes smaller than 300,000 m3. Large fractures indicate deep-seated gravitational deformation of volumes reaching several 100 million m3, but the movement rates in these areas are below 2 mm/year. Two different lobes of prehistoric rock slope failures were dated with terrestrial cosmogenic nuclides. While the northern lobe gave an average age of 4,300 years BP, the southern one resulted in two different ages (2,400 and 12,000 years BP), which represent most likely multiple rockfall events. This reflects the currently observable deformation style with unstable blocks in the northern part in between Joasete and Furekamben and no distinct blocks but a high rockfall activity around Ramnanosi in the south. With a relative susceptibility analysis it is concluded that small collapses of blocks along the frontal cliff will be more frequent. Larger collapses of free-standing blocks along the cliff with volumes > 100,000 m3, thus large enough to reach the fjord, cannot be ruled out. A larger collapse involving several million m3 is presently considered of very low likelihood.

SwissDock, a protein-small molecule docking web service based on EADock DSS.

Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

Reverse transcription-polymerase chain reaction construction of plasmid-based, full-length cDNA libraries from Leishmania infantum for in vitro expression screening

We describe a streamlined reverse transcription-polymerase chain reaction methodology for constructing full-length cDNA libraries of trypanosomatids on the basis of conserved sequences located at the 5' and 3'ends of trans-spliced mRNAs. The amplified cDNA corresponded to full-length messengers and was amenable to in vitro expression. Fractionated libraries could be rapidly constructed in a plasmid vector by the TA cloning method (Invitrogen). We believe this is useful when there are concerns over the use of restriction enzymes and phage technology as well as in cases where expression of proteins in their native conformation is desired.

Uncertainties regarding dengue modeling in Rio de Janeiro, Brazil

Dengue fever is currently the most important arthropod-borne viral disease in Brazil. Mathematical modeling of disease dynamics is a very useful tool for the evaluation of control measures. To be used in decision-making, however, a mathematical model must be carefully parameterized and validated with epidemiological and entomological data. In this work, we developed a simple dengue model to answer three questions: (i) which parameters are worth pursuing in the field in order to develop a dengue transmission model for Brazilian cities; (ii) how vector density spatial heterogeneity influences control efforts; (iii) with a degree of uncertainty, what is the invasion potential of dengue virus type 4 (DEN-4) in Rio de Janeiro city. Our model consists of an expression for the basic reproductive number (R0) that incorporates vector density spatial heterogeneity. To deal with the uncertainty regarding parameter values, we parameterized the model using a priori probability density functions covering a range of plausible values for each parameter. Using the Latin Hypercube Sampling procedure, values for the parameters were generated. We conclude that, even in the presence of vector spatial heterogeneity, the two most important entomological parameters to be estimated in the field are the mortality rate and the extrinsic incubation period. The spatial heterogeneity of the vector population increases the risk of epidemics and makes the control strategies more complex. At last, we conclude that Rio de Janeiro is at risk of a DEN-4 invasion. Finally, we stress the point that epidemiologists, mathematicians, and entomologists need to interact more to find better approaches to the measuring and interpretation of the transmission dynamics of arthropod-borne diseases.

Policy Diffusion: An Agent-Based Approach

Methods like Event History Analysis can show the existence of diffusion and part of its nature, but do not study the process itself. Nowadays, thanks to the increasing performance of computers, processes can be studied using computational modeling. This thesis presents an agent-based model of policy diffusion mainly inspired from the model developed by Braun and Gilardi (2006). I first start by developing a theoretical framework of policy diffusion that presents the main internal drivers of policy diffusion - such as the preference for the policy, the effectiveness of the policy, the institutional constraints, and the ideology - and its main mechanisms, namely learning, competition, emulation, and coercion. Therefore diffusion, expressed by these interdependencies, is a complex process that needs to be studied with computational agent-based modeling. In a second step, computational agent-based modeling is defined along with its most significant concepts: complexity and emergence. Using computational agent-based modeling implies the development of an algorithm and its programming. When this latter has been developed, we let the different agents interact. Consequently, a phenomenon of diffusion, derived from learning, emerges, meaning that the choice made by an agent is conditional to that made by its neighbors. As a result, learning follows an inverted S-curve, which leads to partial convergence - global divergence and local convergence - that triggers the emergence of political clusters; i.e. the creation of regions with the same policy. Furthermore, the average effectiveness in this computational world tends to follow a J-shaped curve, meaning that not only time is needed for a policy to deploy its effects, but that it also takes time for a country to find the best-suited policy. To conclude, diffusion is an emergent phenomenon from complex interactions and its outcomes as ensued from my model are in line with the theoretical expectations and the empirical evidence.Les méthodes d'analyse de biographie (event history analysis) permettent de mettre en évidence l'existence de phénomènes de diffusion et de les décrire, mais ne permettent pas d'en étudier le processus. Les simulations informatiques, grâce aux performances croissantes des ordinateurs, rendent possible l'étude des processus en tant que tels. Cette thèse, basée sur le modèle théorique développé par Braun et Gilardi (2006), présente une simulation centrée sur les agents des phénomènes de diffusion des politiques. Le point de départ de ce travail met en lumière, au niveau théorique, les principaux facteurs de changement internes à un pays : la préférence pour une politique donnée, l'efficacité de cette dernière, les contraintes institutionnelles, l'idéologie, et les principaux mécanismes de diffusion que sont l'apprentissage, la compétition, l'émulation et la coercition. La diffusion, définie par l'interdépendance des différents acteurs, est un système complexe dont l'étude est rendue possible par les simulations centrées sur les agents. Au niveau méthodologique, nous présenterons également les principaux concepts sous-jacents aux simulations, notamment la complexité et l'émergence. De plus, l'utilisation de simulations informatiques implique le développement d'un algorithme et sa programmation. Cette dernière réalisée, les agents peuvent interagir, avec comme résultat l'émergence d'un phénomène de diffusion, dérivé de l'apprentissage, où le choix d'un agent dépend en grande partie de ceux faits par ses voisins. De plus, ce phénomène suit une courbe en S caractéristique, poussant à la création de régions politiquement identiques, mais divergentes au niveau globale. Enfin, l'efficacité moyenne, dans ce monde simulé, suit une courbe en J, ce qui signifie qu'il faut du temps, non seulement pour que la politique montre ses effets, mais également pour qu'un pays introduise la politique la plus efficace. En conclusion, la diffusion est un phénomène émergent résultant d'interactions complexes dont les résultats du processus tel que développé dans ce modèle correspondent tant aux attentes théoriques qu'aux résultats pratiques.

Meta-analysis based SVM classification enables accurate detection of Alzheimer's disease across different clinical centers using FDG-PET and MRI.

The application of support vector machine classification (SVM) to combined information from magnetic resonance imaging (MRI) and [F18]fluorodeoxyglucose positron emission tomography (FDG-PET) has been shown to improve detection and differentiation of Alzheimer's disease dementia (AD) and frontotemporal lobar degeneration. To validate this approach for the most frequent dementia syndrome AD, and to test its applicability to multicenter data, we randomly extracted FDG-PET and MRI data of 28 AD patients and 28 healthy control subjects from the database provided by the Alzheimer's Disease Neuroimaging Initiative (ADNI) and compared them to data of 21 patients with AD and 13 control subjects from our own Leipzig cohort. SVM classification using combined volume-of-interest information from FDG-PET and MRI based on comprehensive quantitative meta-analyses investigating dementia syndromes revealed a higher discrimination accuracy in comparison to single modality classification. For the ADNI dataset accuracy rates of up to 88% and for the Leipzig cohort of up to 100% were obtained. Classifiers trained on the ADNI data discriminated the Leipzig cohorts with an accuracy of 91%. In conclusion, our results suggest SVM classification based on quantitative meta-analyses of multicenter data as a valid method for individual AD diagnosis. Furthermore, combining imaging information from MRI and FDG-PET might substantially improve the accuracy of AD diagnosis.

An introductory review on gravitational-deformation induced structures, fabrics and modeling

Recent studies have pointed out a similarity between tectonics and slope tectonic-induced structures. Numerous studies have demonstrated that structures and fabrics previously interpreted as of purely geodynamical origin are instead the result of large slope deformation, and this led in the past to erroneous interpretations. Nevertheless, their limit seems not clearly defined, but it is somehow transitional. Some studies point out continuity between failures developing at surface with upper crust movements. In this contribution, the main studies which examine the link between rock structures and slope movements are reviewed. The aspects regarding model and scale of observation are discussed together with the role of pre-existing weaknesses in the rock mass. As slope failures can develop through progressive failure, structures and their changes in time and space can be recognized. Furthermore, recognition of the origin of these structures can help in avoiding misinterpretations of regional geology. This also suggests the importance of integrating different slope movement classifications based on distribution and pattern of deformation and the application of structural geology techniques. A structural geology approach in the landslide community is a tool that can greatly support the hazard quantification and related risks, because most of the physical parameters, which are used for landslide modeling, are derived from geotechnical tests or the emerging geophysical approaches.

Identification of Anopheles (Nyssorhynchus) albitarsis complex species (Diptera: Culicidae) using rDNA internal transcribed spacer 2-based polymerase chain reaction primes

Anopheles (Nyssorhynchus) marajoara is a proven primary vector of malaria parasites in Northeast Brazil, and An. deaneorum is a suspected vector in Western Brazil. Both are members of the morphologically similar Albitarsis Complex, which also includes An. albitarsis and an undescribed species, An. albitarsis "B". These four species were recognized and can be identified using random amplified polymorphic DNA (RAPD) markers, but various other methodologies also point to multiple species under the name An. albitarsis. We describe here a technique for identification of these species employing polymerase chain reaction (PCR) primers based on ribosomal DNA internal transcribed spacer 2 (rDNA ITS2) sequence. Since this method is based on known sequence it is simpler than the sometimes problematical RAPD-PCR. Primers were tested on samples previously identified using RAPD markers with complete correlation.

Isolation of a fragment homologous to the rp49 constitutive gene of Drosophila in the Neotropical malaria vector Anopheles aquasalis (Diptera: Culicidae)

The constitutive ribosomal gene rp49 is frequently used as an endogenous control in Drosophila gene expression experiments. Using the degenerate primer PCR technique we have cloned a fragment homologous to this gene in Anopheles aquasalis Curry, a Neotropical vector of malaria. In addition, based on this first sequence, a new primer was designed, which allowed the isolation of fragments of rp49 in two other species, Aedes aegypti (Linnaeus) and Culex quinquefasciatus Say, suggesting that it could be used to clone fragments of this gene in a number of other mosquito species. Primers were also designed to specifically amplify rp49 cDNA fragments in An. aquasalis and Ae. aegypti, showing that rp49 could be used as a good constitutive control in gene expression studies of these and other vectorially important mosquito species.