The amphioxus genome and the evolution of the chordate karyotype.

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

Use of phylogeny to resolve the taxonomy of the widespread and highly polymorphic African giant shrews (Crocidura olivieri group, Crocidurinae, Mammalia).

The aim of this study is to provide a better understanding of the genetic relationships within the widespread and highly polymorphic group of African giant shrews (Crocidura olivieri group). We sequenced 769 base pairs (bp) of the mitochondrial cytochrome b gene and 472 bp of the mitochondrial control region over the entire geographic range from South Africa to Morocco. The analyses reveal four main clades associated with different biomes. The largest clade occurs over a range covering Northwest and Central Africa and includes samples of C. fulvastra, C. olivieri, and C. viaria. The second clade is composed of C. goliath from Gabon, while South African C. flavescens, and C. hirta form two additional clades. On the basis of these results, the validity of some taxa in the C. olivieri group should be re-evaluated.

How to govern the urban hydrosocial cycle : archaeo-genealogy of hydromentalities in the Swiss urban water sector between 1850 and 1950

Switzerland appears to be a privileged place to investigate the urban political ecology of tap water because of the specificities of its political culture and organization and the relative abundance of drinking water in the country. In this paper, we refer to a Foucauldian theorization of power that is increasingly employed in the social sciences, including in human geography and political ecology. We also implement a Foucauldian methodology. In particular, we propose an archaeo-genealogical analysis of discourse to apprehend the links between urban water and the forms of governmentality in Switzerland between 1850 and 1950. Results show that two forms of governmentality, namely biopower and neoliberal governmentality, were present in the water sector in the selected period. Nonetheless, they deviate from the models proposed by Foucault, as their periodization and the classification of the technologies of power related to them prove to be much more blurred than Foucault's work, mainly based on France, might have suggested.

Cluster kernels for semisupervised classification of VHR urban images

In this paper, we present and apply a semisupervised support vector machine based on cluster kernels for the problem of very high resolution image classification. In the proposed setting, a base kernel working with labeled samples only is deformed by a likelihood kernel encoding similarities between unlabeled examples. The resulting kernel is used to train a standard support vector machine (SVM) classifier. Experiments carried out on very high resolution (VHR) multispectral and hyperspectral images using very few labeled examples show the relevancy of the method in the context of urban image classification. Its simplicity and the small number of parameters involved make it versatile and workable by unexperimented users.

Metastatic primary adenocarcinoma of the bladder in a twenty-five years old woman.

Primary adenocarcinoma of the bladder is a rare tumor. The classification between primary vesical and urachal is debated. We present the case of a young female who presented clinicopathological features of a metastatic urachal adenocarcinoma, but the histological result revealed primary adenocarcinoma of the bladder contrary to expectancy. To the best of our knowledge this is the first reported case of a metastatic adenocarcinoma of the bladder in a 25 years old female. This case emphasizes the challenge for urologists to recognize and manage this aggressive tumor in the setting described.

Alveolar echinococcosis of the liver: diffusionweighted MR imaging findings

Purpose: To report the diffusion-weighted MR imaging (DWI) findings in hepatic alveolar echinococcosis (AE). To evaluate the usefulness of apparent diffusion coefficients (ADCs) for differentiating the 5 types of AE lesions (as reported by Kodama, Radiology, 2003).Methods and Materials: We retrospectively included 17 patients (10 women, mean age 64.3years) with 48 AE liver lesions (>1cm2) that had been investigated by 3-Tesla MR imaging between March 2008 and August 2011 performing our standard protocol including DWI (b-values: 0, 300 and 600s/mm2). In consensus, two radiologists assessed lesion characteristics such as diameter, cystic and/or fibrotic components including Kodama classification, signal intensity, contrast enhancement, calcifications (on CT), and measured the ADC of each lesion. AE was confirmed by serology, biopsy and/or surgery in all patients.Results: Seventeen lesions of Kodama type 1, 10 of type 2, 19 of type 3, 1 of type 4 and 1 of type 5 were found. Mean(±SD) ADC of all AE lesions was 1.75±0.45 ×10-3mm2/s. Mean(±SD) ADCs of Kodama type 1, 2, 3, 4 and 5 lesions were 1.74±0.55, 1.71±0.49, 1.82±0.36, 1.46±0 and 1.43±0 ×10-3mm2/s, respectively. No significant difference was noted between the different Kodama types (p=0.89). Presence of fibrotic (p=0.24) and/or calcified (p=0.90) components, or contrast enhancement (p=0.84) of AE lesions were not correlated with significant differences in ADCs.Conclusion: ADCs of AE lesions are relatively low compared to other cystic liver lesions, which is helpful in suggesting the diagnosis. However, ADCs were not found to be useful for differentiating Kodama types of AE lesions.

Discovery of catalases in members of the Chlamydiales order.

Catalase is an important virulence factor for survival in macrophages and other phagocytic cells. In Chlamydiaceae, no catalase had been described so far. With the sequencing and annotation of the full genomes of Chlamydia-related bacteria, the presence of different catalase-encoding genes has been documented. However, their distribution in the Chlamydiales order and the functionality of these catalases remain unknown. Phylogeny of chlamydial catalases was inferred using MrBayes, maximum likelihood, and maximum parsimony algorithms, allowing the description of three clade 3 and two clade 2 catalases. Only monofunctional catalases were found (no catalase-peroxidase or Mn-catalase). All presented a conserved catalytic domain and tertiary structure. Enzymatic activity of cloned chlamydial catalases was assessed by measuring hydrogen peroxide degradation. The catalases are enzymatically active with different efficiencies. The catalase of Parachlamydia acanthamoebae is the least efficient of all (its catalytic activity was 2 logs lower than that of Pseudomonas aeruginosa). Based on the phylogenetic analysis, we hypothesize that an ancestral class 2 catalase probably was present in the common ancestor of all current Chlamydiales but was retained only in Criblamydia sequanensis and Neochlamydia hartmannellae. The catalases of class 3, present in Estrella lausannensis and Parachlamydia acanthamoebae, probably were acquired by lateral gene transfer from Rhizobiales, whereas for Waddlia chondrophila they likely originated from Legionellales or Actinomycetales. The acquisition of catalases on several occasions in the Chlamydiales suggests the importance of this enzyme for the bacteria in their host environment.

Arbuscular mycorrhizal fungi (Glomeromycota) harbour ancient fungal tubulin genes that resemble those of the chytrids (Chytridiomycota).

The genes encoding alpha- and beta-tubulins have been widely sampled in most major fungal phyla and they are useful tools for fungal phylogeny. Here, we report the first isolation of alpha-tubulin sequences from arbuscular mycorrhizal fungi (AMF). In parallel, AMF beta-tubulins were sampled and analysed to identify the presence of paralogs of this gene. The AMF alpha-tubulin amino acid phylogeny was congruent with the results previously reported for AMF beta-tubulins and showed that AMF tubulins group together at a basal position in the fungal clade and showed high sequence similarities with members of the Chytridiomycota. This is in contrast with phylogenies for other regions of the AMF genome. The amount and nature of substitutions are consistent with an ancient divergence of both orthologs and paralogs of AMF tubulins. At the amino acid level, however, AMF tubulins have hardly evolved from those of the chytrids. This is remarkable given that these two groups are ancient and the monophyletic Glomeromycota probably diverged from basal fungal ancestors at least 500 million years ago. The specific primers we designed for the AMF tubulins, together with the high molecular variation we found among the AMF species we analysed, make AMF tubulin sequences potentially useful for AMF identification purposes.

The break-up of East Gondwana along the northeast coast of Oman: evidence from the Batain basin

Recent detailed studies on the Batain nappes (northeast coast of Oman), which represent a special part of the so-called `Oman Exotics', have led to a better understanding of the Neotethyan geodynamic evolution. The Batain Exotics bear witness to volcanic activity, sea-level changes, tectonic instability, rifting and oceanization along the Eastern Oman margin during Late Palaeozoic and Mesozoic times. They allow definition of the Batain basin as an aborted Permian branch of Neotethys. This marine basin was created in Early Permian times extending southward to the East African/Madagascar region and was linked to the Karoo rift system. The presented revised classification of the Batain nappes considers the Batain basin to be no longer a part of the Hawasina basin and the Neotethyan mat-gin proper. We attribute the Batain basin to a Mozambique-Sornali-Masirah rift system (Somoma). This system started in Early Permian, times, creating a marine basin between Arabia and India/Madagascar; rifting in the Late Triassic and oceanization during Late Jurassic times led to the separation of East Gondwana.

Principaux résultats de l'étude suisse sur les DRG (étude Casemix). [Main results of the Swiss study on DRGs (Casemix Study)].

Sponsored by the Health Administrations of nine cantons, this study was conducted by the University Institute of Social and Preventive Medicine in Lausanne in order to assess how DRGs could be used within the Swiss context. A data base mainly provided by the Swiss VESKA statistics was used. The first step provided the transformation of Swiss diagnostic and intervention codes into US codes, allowing direct use of the Yale Grouper for DRG. The second step showed that the overall performance of DRG in terms of variability reduction of the length of stay was similar to the one observed in US; there are, however, problems when the homogeneity of medicotechnical procedures for DRG is considered. The third steps showed how DRG could be used as an account unit in hospital, and how costs per DRG could be estimated. Other examples of applications of DRG were examined, for example comparison of Casemix or length of stay between hospitals.

Advance care planning for institutionalised older people: an integrative review of the literature.

BACKGROUND: This integrative review of the literature describes the evolution in knowledge and the paradigm shift that is necessary to switch from advance directives to advance care planning. AIMS AND OBJECTIVES: It presents an analysis of concepts, trends, models and experiments that enables identification of the best treatment strategies, particularly for older people living in nursing homes. DESIGN: Based on 23 articles published between 1999 and 2012, this review distinguishes theoretical from empirical research and presents a classification of studies based on their methodological robustness (descriptive, qualitative, associative or experimental). RESULTS: It thus provides nursing professionals with evidence-based information in the form of a synthetic vision and conceptual framework to support the development of innovative care practices in the end-of-life context. While theoretical work places particular emphasis on the impact of changes in practice on the quality of care received by residents, empirical research highlights the importance of communication between the different persons involved about care preferences at the end of life and the need for agreement between them. CONCLUSIONS: The concept of quality of life and the dimensions and factors that compose it form the basis of Advance care planning (ACP) and enable the identification of the similarities and differences between various actors. They inform professionals of the need to ease off the biomedical approach to consider the attributes prioritised by those concerned, whether patients or families, so as to improve the quality of care at the end of life. IMPLICATIONS FOR PRACTICE: It is particularly recommended that all professionals involved take into account key stakeholders' expectations concerning what is essential at the end of life, to enable enhanced communication and decision-making when faced with this difficult subject.

A comprehensive analysis of gene expression profiles in distal parts of the mouse renal tubule.

The distal parts of the renal tubule play a critical role in maintaining homeostasis of extracellular fluids. In this review, we present an in-depth analysis of microarray-based gene expression profiles available for microdissected mouse distal nephron segments, i.e., the distal convoluted tubule (DCT) and the connecting tubule (CNT), and for the cortical portion of the collecting duct (CCD; Zuber et al., Proc Natl Acad Sci USA 106:16523-16528, 2009). Classification of expressed transcripts in 14 major functional gene categories demonstrated that all principal proteins involved in maintaining the salt and water balance are represented by highly abundant transcripts. However, a significant number of transcripts belonging, for instance, to categories of G-protein-coupled receptors or serine/threonine kinases exhibit high expression levels but remain unassigned to a specific renal function. We also established a list of genes differentially expressed between the DCT/CNT and the CCD. This list is enriched by genes related to segment-specific transport functions and by transcription factors directing the development of the distal nephron or collecting ducts. Collectively, this in silico analysis provides comprehensive information about relative abundance and tissue specificity of the DCT/CNT and the CCD expressed transcripts and identifies new candidate genes for renal homeostasis.

Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil.

Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64x10(7) to 1.75x10(8)/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4x10(6) (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate-carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO(2) sequestration.

Gender differences in paediatric patients of the swiss inflammatory bowel disease cohort study.

PURPOSE: Gender differences in paediatric patients with inflammatory bowel disease (IBD) are frequently reported as a secondary outcome and the results are divergent. To assess gender differences by analysing data collected within the Swiss IBD cohort study database since 2008, related to children with IBD, using the Montreal classification for a systematic approach. METHODS: Data on gender, age, anthropometrics, disease location at diagnosis, disease behaviour, and therapy of 196 patients, 105 with Crohn's disease (CD) and 91 with ulcerative or indeterminate colitis (UC/IC) were retrieved and analysed. RESULTS: THE CRUDE GENDER RATIO (MALE : female) of patients with CD diagnosed at <10 years of age was 2.57, the adjusted ratio was 2.42, and in patients with UC/IC it was 0.68 and 0.64 respectively. The non-adjusted gender ratio of patients diagnosed at ≥10 years was 1.58 for CD and 0.88 for UC/IC. Boys with UC/IC diagnosed <10 years of age had a longer diagnostic delay, and in girls diagnosed with UC/IC >10 years a more important use of azathioprine was observed. No other gender difference was found after analysis of age, disease location and behaviour at diagnosis, duration of disease, familial occurrence of IBD, prevalence of extra-intestinal manifestations, complications, and requirement for surgery. CONCLUSION: CD in children <10 years affects predominantly boys with a sex ratio of 2.57; the impact of sex-hormones on the development of CD in pre-pubertal male patients should be investigated.