The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC

Positive selection is widely estimated from protein coding sequence alignments by the nonsynonymous-to-synonymous ratio omega. Increasingly elaborate codon models are used in a likelihood framework for this estimation. Although there is widespread concern about the robustness of the estimation of the omega ratio, more efforts are needed to estimate this robustness, especially in the context of complex models. Here, we focused on the branch-site codon model. We investigated its robustness on a large set of simulated data. First, we investigated the impact of sequence divergence. We found evidence of underestimation of the synonymous substitution rate for values as small as 0.5, with a slight increase in false positives for the branch-site test. When dS increases further, underestimation of dS is worse, but false positives decrease. Interestingly, the detection of true positives follows a similar distribution, with a maximum for intermediary values of dS. Thus, high dS is more of a concern for a loss of power (false negatives) than for false positives of the test. Second, we investigated the impact of GC content. We showed that there is no significant difference of false positives between high GC (up to similar to 80%) and low GC (similar to 30%) genes. Moreover, neither shifts of GC content on a specific branch nor major shifts in GC along the gene sequence generate many false positives. Our results confirm that the branch-site is a very conservative test.

Significance of an isolated new right bundle branch block in a patient with chest pain.

Chest pain is a common presenting symptom in emergency departments, and a typical manifestation of acute myocardial infarction (AMI). Recognition of ECG changes in AMI is essential for timely diagnosis and treatment. Right bundle branch block (RBBB) may be an isolated sign of AMI, and was previously considered as a criterion for fibrinolytic therapy. Since the most recent European Society of Cardiology and American Heart Association guidelines in 2013, RBBB alone is no longer considered a diagnostic criterion of AMI, even if it occurs in the context of acute chest pain, as RBBB does not usually interfere with the interpretation of ST-segment alteration. Our case illustrates an acute septal myocardial infarction with an isolated RBBB, and thus the importance of recognising this pattern in order to permit timely diagnosis and treatment.

Posterior Sub-Tenon Triamcinolone Injection for Chronic Macular Oedema Associated With Non-Ischemic Branch or Central Retinal Vein Occlusion

Aims: To evaluate the effectiveness and safety of Posterior Sub-Tenon (PST) Triamcinolone Acetonide (TA) injection for persistent macular oedema associated with non-ischemic Central Retinal Vein Occlusion (CRVO) or Branch Retinal Vein Occlusion (BRVO) in non-vitrectomized eye. Methods: Fourteen consecutive eyes of 14 patients characterized by macular oedema lasting more than 3 months and with a visual acuity of less than 20/40 were enrolled. Six eyes presented with BRVO, 8 eyes with CRVO. PST injection of 40 mg TA was performed in topical anaesthesia. All patients were phakic, and followed for at least 6 months. Snellen visual acuity converted to LogMAR units and anatomic responses were evaluated before, and at 1, 3, 6, and 12 (if required) months after injections and re-injection considered. Results: In the BRVO group, mean foveal thickness was 548.2±49.50 μm preoperatively, and 452.8±56.2 μm and 280.8±62.5 μm at 1 and 12 month follow-up, respectively. Statistical analysis showed significant differences between preoperative and postoperative measurements (P<.05, paired t test) 3 months after injections. Improvement of visual acuity by at least 0.2 LogMAR was seen in 3(50%) of the 6 eyes. No re-injection was needed. In the CRVO group, mean foveal thickness was 543.7±34.4 μm preoperatively, and 283.0±29.0 μm and 234.8±23.6 μm at 1 and 12 month follow-up, respectively. Statistical analysis showed significant differences between preoperative and postoperative measurements (P<.05, paired t test). Improvement of visual acuity by at least 0.2 LogMAR was seen in 7 eyes (88%). Mean number of re-injection was of 2.1±0.3. Intraocular pressure elevation of 22 mm Hg or higher was found in 2/14 eyes (14%). Cataract progression was noted in 5/14 eyes (36%). Conclusions: PST injection of TA appears to be as safe and effective treatment for chronic macular oedema associated due to both non-ischemic BRVO or CRVO, with a better efficacy in BRVO.

Une approche psychanalytique de la notion de dangerosité. Violence et subjectivation : le risque de la rencontre

Après avoir situé la question de la dangerosité dans les perspectives psychiatriques actuelles, l'auteur propose de penser cette notion complexe dans un renversement du paradigme couramment admis : ainsi la référence à la dangerosité témoignerait-elle, au premier plan, de la part non symbolisée de la rencontre de la violence. Cette proposition prend appui dans un premier temps sur les propositions esquissées par M. Foucault dans sa compréhension du rapport à la violence et à la dangerosité. Puis, le recours au concept psychanalytique d'identification projective permet de proposer une modélisation clinique de la dangerosité, qui sera discutée à partir de deux observatoires dans le champ des violences sexuelles : celui d'une recherche menée auprès d'adolescents engagés dans des agirs sexuels violents et celui d'une pratique d'expertise judiciaire. First the author proposes to situate dangerousness's question in actual psychiatric field. Then, he proposes to think this complex notion into a reversal of dangerousness's paradigm: the reference to dangerousness will be thought as the expression of non-symbolized part through violence's meeting. This proposition relies in a first time on M. Foucault's propositions about a comprehension of the relation with violence and dangerousness. In a second time, the psychoanalytic concept of projective identification allows to propose clinical comprehension of dangerousness's notion. Two clinical situations about sexual violences will be asked in this plan: a research with Young sexual offenders and practice of judiciary evaluation.

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.

A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.

Directed integration of new insulated lentiviral vectors to heterochromatin towards safer gene transfer to stem cells

The need for better gene transfer systems towards improved risk=benefit balance for patients remains a major challenge in the clinical translation of gene therapy (GT). We have investigated the improvement of integrating vectors safety in combining (i) new short synthetic genetic insulator elements (GIE) and (ii) directing genetic integration to heterochromatin. We have designed SIN-insulated retrovectors with two candidate GIEs and could identify a specific combination of insulator 2 repeats which translates into best functional activity, high titers and boundary effect in both gammaretro (p20) and lentivectors (DCaro4) (see Duros et al, abstract ibid). Since GIEs are believed to shield the transgenic cassette from inhibitory effects and silencing, DCaro4 has been further tested with chimeric HIV-1 derived integrases which comprise C-ter chromodomains targeting heterochromatin through either histone H3 (ML6chimera) or methylatedCpGislands (ML10). With DCaro4 only and both chimeras, a homogeneous expression is evidenced in over 20% of the cells which is sustained over time. With control lentivectors, less than 2% of cells express GFP as compared to background using a control double-mutant in both catalytic and ledgf binding-sites; in addition, a two-times increase of expression can be induced with histone deacetylase inhibitors. Our approach could significantly reduce integration into open chromatin sensitive sites in stem cells at the time of transduction, a feature which might significantly decrease subsequent genotoxicity, according to X-SCIDs patients data.Work performed with the support of EC-DG research within the FP6-Network of Excellence, CLINIGENE: LSHB-CT-2006-018933

Epidémiologie clinique: définitions, utilités et raisons pour un développement en Suisse. [Clinical epidemiology: definitions, uses and reasons for development in Switzerland].

Clinical epidemiology is the most currently used name for a comparatively new branch of medicine covering a certain number of activities related to the practice of clinical medicine, but using epidemiological techniques and methods. Clinical epidemiology has only just begun to be known in Europe, whereas units are being increasingly developed and expanded in North America, particularly within the clinical departments of hospitals. The methods it offers are valid for both practicing physicians and hospital doctors (or those being trained in hospitals) and serve the purpose of promoting a better quality medical service, especially where a more adequate evaluation of the effectiveness of diagnostic methods, therapy and prognosis in medicine is concerned. Clinical epidemiology proposes a methodology of medical reasoning and of decision-making, as well as techniques intended to facilitate the indispensable task of keeping up with advances in medical knowledge.

Chirurgie de l'incontinence urinaire a l'effort féminine par voie transobturatrice: dehors-dedans ou dedans-dehors? Etude anatomique comparative

OBJECTIVE: Transobturator route is now largely used for the positioning of the supporting sub uretral tape in the surgical treatment of female urinary incontinence. This operation can be done using the original technique from the outside to the inside or by inside to outside. Our anatomic study evaluates the specific dangers of each MATERIAL AND METHODS: Our study is based on the dissection of seven fresh bodies, therefore 14 obturator regions. The dissections were done after the positioning of the tape from outside to inside on one side and inside to outside on the other side. We particularly studied the distances separating the tape from the inferior pudendal vascular bundle and the posterior branch of the obturator nerve. RESULTS: With the inside - outside technique there is a greater proximity between the path of the tape and the studied structures, therefore the risk of damage is greater. CONCLUSIONS: The two techniques are not equivalent. There are less vascular and neurological risk using the original outside to inside technique.

Three Essays on the Formation and Impact of Economic Policy

Introduction In my thesis I argue that economic policy is all about economics and politics. Consequently, analysing and understanding economic policy ideally has at least two parts. The economics part, which is centered around the expected impact of a specific policy on the real economy both in terms of efficiency and equity. The insights of this part point into which direction the fine-tuning of economic policies should go. However, fine-tuning of economic policies will be most likely subject to political constraints. That is why, in the politics part, a much better understanding can be gained by taking into account how the incentives of politicians and special interest groups as well as the role played by different institutional features affect the formation of economic policies. The first part and chapter of my thesis concentrates on the efficiency-related impact of economic policies: how does corporate income taxation in general, and corporate income tax progressivity in specific, affect the creation of new firms? Reduced progressivity and flat-rate taxes are in vogue. By 2009, 22 countries are operating flat-rate income tax systems, as do 7 US states and 14 Swiss cantons (for corporate income only). Tax reform proposals in the spirit of the "flat tax" model typically aim to reduce three parameters: the average tax burden, the progressivity of the tax schedule, and the complexity of the tax code. In joint work, Marius Brülhart and I explore the implications of changes in these three parameters on entrepreneurial activity, measured by counts of firm births in a panel of Swiss municipalities. Our results show that lower average tax rates and reduced complexity of the tax code promote firm births. Controlling for these effects, reduced progressivity inhibits firm births. Our reading of these results is that tax progressivity has an insurance effect that facilitates entrepreneurial risk taking. The positive effects of lower tax levels and reduced complexity are estimated to be significantly stronger than the negative effect of reduced progressivity. To the extent that firm births reflect desirable entrepreneurial dynamism, it is not the flattening of tax schedules that is key to successful tax reforms, but the lowering of average tax burdens and the simplification of tax codes. Flatness per se is of secondary importance and even appears to be detrimental to firm births. The second part of my thesis, which corresponds to the second and third chapter, concentrates on how economic policies are formed. By the nature of the analysis, these two chapters draw on a broader literature than the first chapter. Both economists and political scientists have done extensive research on how economic policies are formed. Thereby, researchers in both disciplines have recognised the importance of special interest groups trying to influence policy-making through various channels. In general, economists base their analysis on a formal and microeconomically founded approach, while abstracting from institutional details. In contrast, political scientists' frameworks are generally richer in terms of institutional features but lack the theoretical rigour of economists' approaches. I start from the economist's point of view. However, I try to borrow as much as possible from the findings of political science to gain a better understanding of how economic policies are formed in reality. In the second chapter, I take a theoretical approach and focus on the institutional policy framework to explore how interactions between different political institutions affect the outcome of trade policy in presence of special interest groups' lobbying. Standard political economy theory treats the government as a single institutional actor which sets tariffs by trading off social welfare against contributions from special interest groups seeking industry-specific protection from imports. However, these models lack important (institutional) features of reality. That is why, in my model, I split up the government into a legislative and executive branch which can both be lobbied by special interest groups. Furthermore, the legislative has the option to delegate its trade policy authority to the executive. I allow the executive to compensate the legislative in exchange for delegation. Despite ample anecdotal evidence, bargaining over delegation of trade policy authority has not yet been formally modelled in the literature. I show that delegation has an impact on policy formation in that it leads to lower equilibrium tariffs compared to a standard model without delegation. I also show that delegation will only take place if the lobby is not strong enough to prevent it. Furthermore, the option to delegate increases the bargaining power of the legislative at the expense of the lobbies. Therefore, the findings of this model can shed a light on why the U.S. Congress often practices delegation to the executive. In the final chapter of my thesis, my coauthor, Antonio Fidalgo, and I take a narrower approach and focus on the individual politician level of policy-making to explore how connections to private firms and networks within parliament affect individual politicians' decision-making. Theories in the spirit of the model of the second chapter show how campaign contributions from lobbies to politicians can influence economic policies. There exists an abundant empirical literature that analyses ties between firms and politicians based on campaign contributions. However, the evidence on the impact of campaign contributions is mixed, at best. In our paper, we analyse an alternative channel of influence in the shape of personal connections between politicians and firms through board membership. We identify a direct effect of board membership on individual politicians' voting behaviour and an indirect leverage effect when politicians with board connections influence non-connected peers. We assess the importance of these two effects using a vote in the Swiss parliament on a government bailout of the national airline, Swissair, in 2001, which serves as a natural experiment. We find that both the direct effect of connections to firms and the indirect leverage effect had a strong and positive impact on the probability that a politician supported the government bailout.

The interaction of human pathogenic arena viruses with the host cell

SummaryResearch projects presented in this thesis aimed to investigate two major aspects of the arenaviruses life cycle in the host cell: viral entry and the biosynthesis of the viral envelope glycoprotein.Old World arenaviruses (OWAV), such as Lassa virus (LASV) and lymphocytic choriomeningitis virus (LCMV), attach to the cell by binding to their receptor, alpha-dystroglycan. Virions are then internalized by a largely unknown pathway of endocytosis and delivered to the late endosome/lysosome where fusion occurs at low pH. In the major project of my thesis, we sought to identify cellular factors involved in OWAV cell entry. Our work indicates that OWAV cell entry requires microtubular transport and a functional multivesicular body (MVB) compartment. Infection indeed depends on phosphatidyl inositol 3-kinase (PI3K) activity and lysobisphosphatidic acid (LBPA), a lipid found in membranes of intraluminal vesicles (ILVs) of the MVB. We further found a requirement of factors that are part of the endosomal sorting complex required for transport (ESCRT), involved in the formation of ILVs. This suggests an ESCRT-mediated sorting of virus- receptor complex during the entry process.During viral replication, biosynthesis of viral glycoprotein takes place in the endoplasmic reticulum (ER) of the host cell. When protein load exceeds the folding capacity of the ER, the accumulation of unfolded proteins is sensed by three ER resident proteins, activating transcription factor 6 (ATF6), inositol-requiring enzyme 1 (IRE1) and PKR-like ER kinase (PERK), whose signaling induces the cellular unfolded protein response (UPR). Our results indicate that acute LCMV infection transiently induces the activation of the ATF6 branch of the UPR, whereas the PERK, and IRE1 axis of UPR are neither triggered nor blocked during infection. Our data also demonstrate that activation of ATF6 pathway is required for optimal viral replication during acute infection.The formation of the mature, fusion-active form of arenaviruses glycoproteins requires proteolytic cleavage mediated by the cellular protease subtilisin kexin isozyme-1 (SKI-l)/site-l protease (SIP). We show that targeting the SKI-1/S1P enzymatic activity with specific inhibitors is a powerful strategy to block arenaviruses productive infection. Moreover, characterization of protease function highlights differences in processing between cellular and viral substrates, opening new possibilities in term of drug development against human pathogenic arenaviruses.RésuméLes projets de recherche présentés dans cette thèse visaient à étudier deux aspects du cycle de vie des arenavirus: l'entrée du virus dans la cellule hôte et la biosynthèse de la glycoprotéine durant la réplication virale.Les arenavirus du vieux monde (OWAV), tels que le virus de Lassa (LASV) et le virus de la chorioméningite lymphocytaire (LCMV) s'attachent à la cellule hôte en se liant à leur récepteur, l'alpha-dystroglycane. Les virions sont ensuite intemalisés par une voie d'endocytose inconnue et livrés à l'endosome tardif/lysosome, où le pH acide permet la fusion entre l'enveloppe virale et la membrane du compartiment. Le projet principal de ma thèse consistait à identifier les facteurs cellulaires impliqués dans l'entrée des OWAV dans la cellule hôte. Nos résultats indiquent que l'entrée des OWAV nécessite le transport microtubulaire et la présence d'un corps multivésiculaire (MVB) fonctionnel. L'infection dépend en effet de l'activité de phosphatidyl inositol 3-kinase (PI3K) et de lysobisphosphatidic acid (LBPA), un lipide présent dans les membranes des vésicules intraluminales (ILVs) du MVB. Nous avons également trouvé l'implication de facteurs constituant l'endosomal sorting complex required for sorting (ESCRT) qui joue un rôle dans la formation des ILVs. Ces donnés suggèrent l'incorporation du complexe virus-récepteur dans des ILVs durant le processus d'entrée.Lors de la réplication virale, la biosynthèse de la glycoprotéine virale a lieu dans le réticulum endoplasmique (ER) de la cellule hôte. Lorsque la charge de protéines nouvellement synthétisées excède la capacité de pliage des protéines dans le ER, l'accumulation de protéines mal pliées est détectée par trois facteurs: activating transcription factor 6 (ATF6), inositol-requiring enzyme 1 (IRE1) et PKR-like ER kinase (PERK). Leur signalisation constitue la réponse cellulaire face aux protéines mal pliées (UPR). Nos résultats montrent que l'infection aiguë avec LCMV induit transitoirement l'activation de la voie de signalisation ATF6 alors que les axes PERK et IRE1 de l'UPR ne sont ni induits ni bloqués pendant l'infection. Nos données prouvent également que l'activation de la voie ATF6 est nécessaire à une réplication virale optimale lors de l'infection aiguë avec LCMV.La maturation des glycoprotéines des arenavirus nécessite un clivage protéolytique par la protéase cellulaire subtilisin kexin isozyme-1 (SKI-l)/site-l protease (SIP). Nous avons démontré que le ciblage de l'activité enzymatique de SKI-1/SIΡ avec des inhibiteurs spécifiques est une stratégie prometteuse pour bloquer l'infection par les arenavirus. La caractérisation du mécanisme d'action de la protéase a, par ailleurs, révélé des différences au niveau du clivage entre les substrats cellulaires et viraux, ce qui ouvre de nouvelles perspectives en terme de développement de médicaments contre les arenavirus pathogènes pour l'homme.

Genetic analysis of phenoxyalkanoic acid degradation in Sphingomonas herbicidovorans MH.

Phenoxyalkanoic acid degradation is well studied in Beta- and Gammaproteobacteria, but the genetic background has not been elucidated so far in Alphaproteobacteria. We report the isolation of several genes involved in dichlor- and mecoprop degradation from the alphaproteobacterium Sphingomonas herbicidovorans MH and propose that the degradation proceeds analogously to that previously reported for 2,4-dichlorophenoxyacetic acid (2,4-D). Two genes for alpha-ketoglutarate-dependent dioxygenases, sdpA(MH) and rdpA(MH), were found, both of which were adjacent to sequences with potential insertion elements. Furthermore, a gene for a dichlorophenol hydroxylase (tfdB), a putative regulatory gene (cadR), two genes for dichlorocatechol 1,2-dioxygenases (dccA(I/II)), two for dienelactone hydrolases (dccD(I/II)), part of a gene for maleylacetate reductase (dccE), and one gene for a potential phenoxyalkanoic acid permease were isolated. In contrast to other 2,4-D degraders, the sdp, rdp, and dcc genes were scattered over the genome and their expression was not tightly regulated. No coherent pattern was derived on the possible origin of the sdp, rdp, and dcc pathway genes. rdpA(MH) was 99% identical to rdpA(MC1), an (R)-dichlorprop/alpha-ketoglutarate dioxygenase from Delftia acidovorans MC1, which is evidence for a recent gene exchange between Alpha- and Betaproteobacteria. Conversely, DccA(I) and DccA(II) did not group within the known chlorocatechol 1,2-dioxygenases, but formed a separate branch in clustering analysis. This suggests a different reservoir and reduced transfer for the genes of the modified ortho-cleavage pathway in Alphaproteobacteria compared with the ones in Beta- and Gammaproteobacteria.