Analyses of six homologous proteins of Protochlamydia amoebophila UWE25 encoded by large GC-rich genes (lgr): a model of evolution and concatenation of leucine-rich repeats.

BACKGROUND: Along the chromosome of the obligate intracellular bacteria Protochlamydia amoebophila UWE25, we recently described a genomic island Pam100G. It contains a tra unit likely involved in conjugative DNA transfer and lgrE, a 5.6-kb gene similar to five others of P. amoebophila: lgrA to lgrD, lgrF. We describe here the structure, regulation and evolution of these proteins termed LGRs since encoded by "Large G+C-Rich" genes. RESULTS: No homologs to the whole protein sequence of LGRs were found in other organisms. Phylogenetic analyses suggest that serial duplications producing the six LGRs occurred relatively recently and nucleotide usage analyses show that lgrB, lgrE and lgrF were relocated on the chromosome. The C-terminal part of LGRs is homologous to Leucine-Rich Repeats domains (LRRs). Defined by a cumulative alignment score, the 5 to 18 concatenated octacosapeptidic (28-meric) LRRs of LGRs present all a predicted alpha-helix conformation. Their closest homologs are the 28-residue RI-like LRRs of mammalian NODs and the 24-meres of some Ralstonia and Legionella proteins. Interestingly, lgrE, which is present on Pam100G like the tra operon, exhibits Pfam domains related to DNA metabolism. CONCLUSION: Comparison of the LRRs, enable us to propose a parsimonious evolutionary scenario of these domains driven by adjacent concatenations of LRRs. Our model established on bacterial LRRs can be challenged in eucaryotic proteins carrying less conserved LRRs, such as NOD proteins and Toll-like receptors.

Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses.

Nucleotide composition analyses of bacterial genomes such as cumulative GC skew highlight the atypical, strongly asymmetric architecture of the recently published chromosome of Idiomarina loihiensis L2TR, suggesting that an inversion of a 600-kb chromosomal segment occurred. The presence of 3.4-kb inverted repeated sequences at the borders of the putative rearrangement supports this hypothesis. Reverting in silico this segment restores (1) a symmetric chromosome architecture; (2) the co-orientation of transcription of all rRNA operons with DNA replication; and (3) a better conservation of gene order between this chromosome and other gamma-proteobacterial ones. Finally, long-range PCRs encompassing the ends of the 600-kb segment reveal the existence of the reverted configuration but not of the published one. This demonstrates how cumulative nucleotide-skew analyses can validate genome assemblies.

Détermination des vents extrêmes à l'aide d'analyses statistiques et de modélisations numériques dans une topographie accidentée en Suisse.

Les constructions en Suisse et en Europe doivent être dimensionnées pour subir sans dommages des vents extrêmes (rafales) avec une période de retour d'au moins 50 ans. Des analyses de Gumbel ont donc été effectuées sur des séries de mesures d'une vingtaine d'années à 67 endroits de la Suisse, afin de déterminer les vitesses extrêmes des vents pour différents courants régionaux. Elles ont abouti à de bons résultats pour la majorité des endroits. Mais ces vitesses extrêmes ne peuvent être extrapolées linéairement aux autres régions dans une topographie aussi accidentée que la Suisse. Un modèle numérique tridimensionnel des écoulements non hydrostatique a été expérimenté pour calculer les champs de vent extrêmes en Suisse avec une résolution horizontale de 2 km et une période de retour de 50 ans. Ces modélisations ont permis de reproduire de manière satisfaisante ces vents extrêmes pour l'ensemble du pays. Toutefois, elles sous-estiment leurs intensités sur les reliefs jurassiens et alpins, comparativement aux vallées alpines et au Plateau Suisse.

Whose DNA is this? How relevant a question? (a note for forensic scientists).

This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during the analysis of a stain, relevant from the point of view of a Court of Justice? This question relates to skeptical views previously voiced by commentators mainly in the judicial area, but is avoided by a large majority of forensic scientists. Notwithstanding, the pivotal role of this question has recently been evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly that a huge gap still exists between questions lawyers are actually interested in, and the answers that scientists deliver to Courts in written reports or during oral testimony. Participants in the justice system, namely lawyers and jurors on the one hand and forensic geneticists on the other, unfortunately talk considerably different languages. It thus is fundamental to address this issue of communication about results of forensic DNA analyses, and open a dialogue with practicing non-scientists at large who need to make meaningful use of scientific results to approach and help solve judicial cases. This paper intends to emphasize the actuality of this topic and suggest beneficial ways ahead towards a more reasoned use of forensic DNA in criminal proceedings.

Aggregation and errors in management accounting

Il est important pour les entreprises de compresser les informations détaillées dans des sets d'information plus compréhensibles. Au chapitre 1, je résume et structure la littérature sur le sujet « agrégation d'informations » en contrôle de gestion. Je récapitule l'analyse coûts-bénéfices que les comptables internes doivent considérer quand ils décident des niveaux optimaux d'agrégation d'informations. Au-delà de la perspective fondamentale du contenu d'information, les entreprises doivent aussi prendre en considération des perspectives cogni- tives et comportementales. Je développe ces aspects en faisant la part entre la comptabilité analytique, les budgets et plans, et la mesure de la performance. Au chapitre 2, je focalise sur un biais spécifique qui se crée lorsque les informations incertaines sont agrégées. Pour les budgets et plans, des entreprises doivent estimer les espérances des coûts et des durées des projets, car l'espérance est la seule mesure de tendance centrale qui est linéaire. A la différence de l'espérance, des mesures comme le mode ou la médiane ne peuvent pas être simplement additionnés. En considérant la forme spécifique de distributions des coûts et des durées, l'addition des modes ou des médianes résultera en une sous-estimation. Par le biais de deux expériences, je remarque que les participants tendent à estimer le mode au lieu de l'espérance résultant en une distorsion énorme de l'estimati¬on des coûts et des durées des projets. Je présente également une stratégie afin d'atténuer partiellement ce biais. Au chapitre 3, j'effectue une étude expérimentale pour comparer deux approches d'esti¬mation du temps qui sont utilisées en comptabilité analytique, spécifiquement « coûts basés sur les activités (ABC) traditionnelles » et « time driven ABC » (TD-ABC). Au contraire des affirmations soutenues par les défenseurs de l'approche TD-ABC, je constate que cette dernière n'est pas nécessairement appropriée pour les calculs de capacité. Par contre, je démontre que le TD-ABC est plus approprié pour les allocations de coûts que l'approche ABC traditionnelle. - It is essential for organizations to compress detailed sets of information into more comprehensi¬ve sets, thereby, establishing sharp data compression and good decision-making. In chapter 1, I review and structure the literature on information aggregation in management accounting research. I outline the cost-benefit trade-off that management accountants need to consider when they decide on the optimal levels of information aggregation. Beyond the fundamental information content perspective, organizations also have to account for cognitive and behavi¬oral perspectives. I elaborate on these aspects differentiating between research in cost accounti¬ng, budgeting and planning, and performance measurement. In chapter 2, I focus on a specific bias that arises when probabilistic information is aggregated. In budgeting and planning, for example, organizations need to estimate mean costs and durations of projects, as the mean is the only measure of central tendency that is linear. Different from the mean, measures such as the mode or median cannot simply be added up. Given the specific shape of cost and duration distributions, estimating mode or median values will result in underestimations of total project costs and durations. In two experiments, I find that participants tend to estimate mode values rather than mean values resulting in large distortions of estimates for total project costs and durations. I also provide a strategy that partly mitigates this bias. In the third chapter, I conduct an experimental study to compare two approaches to time estimation for cost accounting, i.e., traditional activity-based costing (ABC) and time-driven ABC (TD-ABC). Contrary to claims made by proponents of TD-ABC, I find that TD-ABC is not necessarily suitable for capacity computations. However, I also provide evidence that TD-ABC seems better suitable for cost allocations than traditional ABC.

Ultrastructural and morphometrical analyses of the brown adipocyte nucleus in a hibernating dormouse.

The fine morphology, size, and perichromatin granule frequency were analysed in brown adipocyte nuclei from hibernating, arousing, and euthermic dormice, Muscardinus avellanarius. Unusual nuclear structural constituents such as nuclear amorphous bodies, coiled body-like constituents and bundles of nucleoplasmic filaments were described as typical of hibernating nuclei. Morphometrical findings showed significant difference in total nuclear and nucleolar size in the three physiological conditions investigated as well as decreasing frequency of perichromatin granules in nuclei of hibernating to arousing to euthermic animals. A possible involvement of these granules in the intranuclear transport or storage of pre-mRNA is discussed in the context of other experimental evidence.

Systematic review of population pharmacokinetic analyses of imatinib and relationships with treatment outcomes

Several population pharmacokinetic (PPK) analyses of the anticancer drug imatinib have been performed to investigate different patient populations and covariate effects. The present analysis offers a systematic qualitative and quantitative summary and comparison of those. Its primary objective was to provide useful information for evaluating the expectedness of imatinib plasma concentration measurements in the frame of therapeutic drug monitoring. The secondary objective was to review clinically important concentration-effect relationships to provide help in evaluating the potential suitability of plasma concentration values. Nine PPK models describing total imatinib plasma concentration were identified. Parameter estimates were standardized to common covariate values whenever possible. Predicted median exposure (Cmin) was derived by simulations and ranged between models from 555 to 1388 ng/mL (grand median: 870 ng/mL and interquartile "reference" range: 520-1390 ng/mL). Covariates of potential clinical importance (up to 30% change in pharmacokinetic predicted by at least 1 model) included body weight, albumin, α1 acid glycoprotein, and white blood cell count. Various other covariates were included but were statistically not significant or seemed clinically less important or physiologically controversial. Concentration-response relationships had more importance below the average reference range and concentration-toxicity relationships above. Therapeutic drug monitoring-guided dosage adjustment seems justified for imatinib, but a formal predictive therapeutic range remains difficult to propose in the absence of prospective target concentration intervention trials. To evaluate the expectedness of a drug concentration measurement in practice, this review allows comparison of the measurement either to the average reference range or to a specific range accounting for individual patient characteristics. For future research, external PPK model validation or meta-model development should be considered.

Expression analyses of three members of the AtPHO1 family reveal differential interactions between signaling pathways involved in phosphate deficiency and the responses to auxin, cytokinin, and abscisic acid.

The PHO1 protein is involved in loading inorganic phosphate (Pi) to the root xylem. Ten genes homologous to AtPHO1 are present in the Arabidopsis thaliana (L.) Heyn genome. From this gene family, transcript levels of only AtPHO1, AtPHO1;H1 and AtPHO1;H10 were increased by Pi-deficiency. While the up-regulation of AtPHO1;H1 and AtPHO1;H10 by Pi deficiency followed the same rapid kinetics and was dependent on the PHR1 transcription factor, phosphite only strongly suppressed the expression of AtPHO1;H1 and had a minor effect on AtPHO1;H10. Addition of sucrose was found to increase transcript levels of both AtPHO1 and AtPHO1;H1 in Pi-sufficient or Pi-deficient plants, but to suppress AtPHO1:H10 under the same conditions. Treatments of plants with auxin or cytokinin had contrasting effect depending on the gene and on the Pi status of the plants. Thus, while both hormones down-regulated expression of AtPHO1 independently of the plant Pi status, auxin and cytokinin up-regulated AtPHO1;H1 and AtPHO1;H10 expression in Pi-sufficient plants and down-regulated expression in Pi-deficient plants. Treatments with abscisic acid inhibited AtPHO1 and AtPHO1;H1 expression in both Pi-sufficient and Pi-deficient plants, but increased AtPHO1;H10 expression under the same conditions. The inhibition of expression by abscisic acid of AtPHO1 and AtPHO1;H1, and of the Pi-starvation responsive genes AtPHT1;1 and AtIPS1, was dependant on the ABI1 type 2C protein phosphatase. These results reveal that various levels of cross talk between the signal transduction pathways to Pi, sucrose and phytohormones are involved in the regulation of expression of the three AtPHO1 homologues.

There and back again? Combining habitat suitability modelling and connectivity analyses to assess a potential return of the otter to Switzerland

After a steady decline in the early 20th century, several terrestrial carnivore species have recently recovered in Western Europe, either through reintroductions or natural recolonization. Because of the large space requirements of these species and potential conflicts with human activities, ensuring their recovery requires the implementation of conservation and management measures that address the environmental, landscape and social dimensions of the problem. Few examples exist of such integrated management. Taking the case of the otter (Lutra lutra) in Switzerland, we propose a multi-step approach that allows to (1) identify areas with potentially suitable habitat, (2) evaluate their connectivity, (3) verify the potentiality of the species recolonization from populations in neighbouring countries. We showed that even though suitable habitat is available for the species and the level of structural connectivity within Switzerland is satisfactory, the level of connectivity with neighbouring populations is crucial to prioritize strategies that favour the species recovery in the field. This research is the first example integrating habitat suitability and connectivity assessment at different scales with other factors in a multi-step assessment for species recovery.

Errors in palliative care: kinds, causes, and consequences: a pilot survey of experiences and attitudes of palliative care professionals.

Abstract Background: Medical errors have recently been recognized as a relevant concern in public health, and increasing research efforts have been made to find ways of improving patient safety. In palliative care, however, studies on errors are scant. Objective: Our aim was to gather pilot data concerning experiences and attitudes of palliative care professionals on this topic. Methods: We developed a questionnaire, which consists of questions on relevance, estimated frequency, kinds and severity of errors, their causes and consequences, and the way palliative care professionals handle them. The questionnaire was sent to all specialist palliative care institutions in the region of Bavaria, Germany (n=168; inhabitants 12.5 million) reaching a response rate of 42% (n=70). Results: Errors in palliative care were regarded as a highly relevant problem (median 8 on a 10-point numeric rating scale). Most respondents experienced a moderate frequency of errors (1-10 per 100 patients). Errors in communication were estimated to be more common than those in symptom control. The causes most often mentioned were deficits in communication or organization. Moral and psychological problems for the person committing the error were seen as more frequent than consequences for the patient. Ninety percent of respondents declared that they disclose errors to the harmed patient. For 78% of the professionals, the issue was not a part of their professional training. Conclusion: Professionals acknowledge errors-in particular errors in communication-to be a common and relevant problem in palliative care, one that has, however, been neglected in training and research.

Cognitive errors assessed by observer ratings in bipolar affective disorder: relationship with symptoms and therapeutic alliance

The construct of cognitive errors is clinically relevant for cognitive therapy of mood disorders. Beck's universality hypothesis postulates the relevance of negative cognitions in all subtypes of mood disorders, as well as positive cognitions for manic states. This hypothesis has rarely been empirically addressed for patients presenting bipolar affective disorder (BD). In-patients (n = 30) presenting with BD were interviewed, as were 30 participants of a matched control group. Valid and reliable observer-rater methodology for cognitive errors was applied to the session transcripts. Overall, patients make more cognitive errors than controls. When manic and depressive patients were compared, parts of the universality hypothesis were confirmed. Manic symptoms are related to positive and negative cognitive errors. These results are discussed with regard to the main assumptions of the cognitive model for depression; thus adding an argument for extending it to the BD diagnostic group, taking into consideration specificities in terms of cognitive errors. Clinical implications for cognitive therapy of BD are suggested.

Etudes Coût-efficacité: ce que devraient retenir les médecins [Cost-effectiveness analyses: what doctors should know]

The resources of our heath care system are limited. Choices in the attribution of resources are necessary to ensure its stability. A cost-effectiveness analysis compares the effects of one health intervention to another, taking into account the costs (including the saved costs) and the saved life years, adjusted for the quality of life (cost-utility). Cost-effectiveness analyses should take the societal perspective and the studied intervention should be compared to a relevant intervention actually in use. Physicians, at the interface between patients and payers, are in an ideal position to interpret, or even perform cost-effectiveness analysis, and to promote the interventions that are most effective and that have a reasonable cost.

Do habitat suitability models reliably predict the recovery areas of threatened species?

1. Identifying those areas suitable for recolonization by threatened species is essential to support efficient conservation policies. Habitat suitability models (HSM) predict species' potential distributions, but the quality of their predictions should be carefully assessed when the species-environment equilibrium assumption is violated.2. We studied the Eurasian otter Lutra lutra, whose numbers are recovering in southern Italy. To produce widely applicable results, we chose standard HSM procedures and looked for the models' capacities in predicting the suitability of a recolonization area. We used two fieldwork datasets: presence-only data, used in the Ecological Niche Factor Analyses (ENFA), and presence-absence data, used in a Generalized Linear Model (GLM). In addition to cross-validation, we independently evaluated the models with data from a recolonization event, providing presences on a previously unoccupied river.3. Three of the models successfully predicted the suitability of the recolonization area, but the GLM built with data before the recolonization disagreed with these predictions, missing the recolonized river's suitability and badly describing the otter's niche. Our results highlighted three points of relevance to modelling practices: (1) absences may prevent the models from correctly identifying areas suitable for a species spread; (2) the selection of variables may lead to randomness in the predictions; and (3) the Area Under Curve (AUC), a commonly used validation index, was not well suited to the evaluation of model quality, whereas the Boyce Index (CBI), based on presence data only, better highlighted the models' fit to the recolonization observations.4. For species with unstable spatial distributions, presence-only models may work better than presence-absence methods in making reliable predictions of suitable areas for expansion. An iterative modelling process, using new occurrences from each step of the species spread, may also help in progressively reducing errors.5. Synthesis and applications. Conservation plans depend on reliable models of the species' suitable habitats. In non-equilibrium situations, such as the case for threatened or invasive species, models could be affected negatively by the inclusion of absence data when predicting the areas of potential expansion. Presence-only methods will here provide a better basis for productive conservation management practices.