A new ambulatory system for comparative evaluation of the three-dimensional knee kinematics, applied to anterior cruciate ligament injuries

The aim of this study was to develop an ambulatory system for the three-dimensional (3D) knee kinematics evaluation, which can be used outside a laboratory during long-term monitoring. In order to show the efficacy of this ambulatory system, knee function was analysed using this system, after an anterior cruciate ligament (ACL) lesion, and after reconstructive surgery. The proposed system was composed of two 3D gyroscopes, fixed on the shank and on the thigh, and a portable data logger for signal recording. The measured parameters were the 3D mean range of motion (ROM) and the healthy knee was used as control. The precision of this system was first assessed using an ultrasound reference system. The repeatability was also estimated. A clinical study was then performed on five unilateral ACL-deficient men (range: 19-36 years) prior to, and a year after the surgery. The patients were evaluated with the IKDC score and the kinematics measurements were carried out on a 30 m walking trial. The precision in comparison with the reference system was 4.4 degrees , 2.7 degrees and 4.2 degrees for flexion-extension, internal-external rotation, and abduction-adduction, respectively. The repeatability of the results for the three directions was 0.8 degrees , 0.7 degrees and 1.8 degrees . The averaged ROM of the five patients' healthy knee were 70.1 degrees (standard deviation (SD) 5.8 degrees), 24.0 degrees (SD 3.0 degrees) and 12.0 degrees (SD 6.3 degrees for flexion-extension, internal-external rotation and abduction-adduction before surgery, and 76.5 degrees (SD 4.1 degrees), 21.7 degrees (SD 4.9 degrees) and 10.2 degrees (SD 4.6 degrees) 1 year following the reconstruction. The results for the pathologic knee were 64.5 degrees (SD 6.9 degrees), 20.6 degrees (SD 4.0 degrees) and 19.7 degrees (8.2 degrees) during the first evaluation, and 72.3 degrees (SD 2.4 degrees), 25.8 degrees (SD 6.4 degrees) and 12.4 degrees (SD 2.3 degrees) during the second one. The performance of the system enabled us to detect knee function modifications in the sagittal and transverse plane. Prior to the reconstruction, the ROM of the injured knee was lower in flexion-extension and internal-external rotation in comparison with the controlateral knee. One year after the surgery, four patients were classified normal (A) and one almost normal (B), according to the IKDC score, and changes in the kinematics of the five patients remained: lower flexion-extension ROM and higher internal-external rotation ROM in comparison with the controlateral knee. The 3D kinematics was changed after an ACL lesion and remained altered one year after the surgery

Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque.

High levels of HIV-1 replication during the chronic phase of infection usually correlate with rapid progression to severe immunodeficiency. However, a minority of highly viremic individuals remains asymptomatic and maintains high CD4+ T cell counts. This tolerant profile is poorly understood and reminiscent of the widely studied nonprogressive disease model of SIV infection in natural hosts. Here, we identify transcriptome differences between rapid progressors (RPs) and viremic nonprogressors (VNPs) and highlight several genes relevant for the understanding of HIV-1-induced immunosuppression. RPs were characterized by a specific transcriptome profile of CD4+ and CD8+ T cells similar to that observed in pathogenic SIV-infected rhesus macaques. In contrast, VNPs exhibited lower expression of interferon-stimulated genes and shared a common gene regulation profile with nonpathogenic SIV-infected sooty mangabeys. A short list of genes associated with VNP, including CASP1, CD38, LAG3, TNFSF13B, SOCS1, and EEF1D, showed significant correlation with time to disease progression when evaluated in an independent set of CD4+ T cell expression data. This work characterizes 2 minimally studied clinical patterns of progression to AIDS, whose analysis may inform our understanding of HIV pathogenesis.

Comparative phylogeography in a specific and obligate pollination antagonism.

In specific and obligate interactions the nature and abundance of a given species can have important effects on the survival and population dynamics of associated organisms. In a phylogeographic framework, we therefore expect that the fates of organisms interacting specifically are also tightly interrelated. Here we investigate such a scenario by analyzing the genetic structures of species interacting in an obligate plant-insect pollination lure-and-trap antagonism, involving Arum maculatum (Araceae) and its specific psychodid (Diptera) visitors Psychoda phalaenoides and Psycha grisescens. Because the interaction is asymmetric (i.e., only the plant depends on the insect), we expect the genetic structure of the plant to be related with the historical pollinator availability, yielding incongruent phylogeographic patterns between the interacting organisms.Using insect mtDNA sequences and plant AFLP genome fingerprinting, we inferred the large-scale phylogeographies of each species and the distribution of genetic diversities throughout the sampled range, and evaluated the congruence in their respective genetic structures using hierarchical analyses of molecular variances (AMOVA). Because the composition of pollinator species varies in Europe, we also examined its association with the spatial genetic structure of the plant.Our findings indicate that while the plant presents a spatially well-defined genetic structure, this is not the case in the insects. Patterns of genetic diversities also show dissimilar distributions among the three interacting species. Phylogeographic histories of the plant and its pollinating insects are thus not congruent, a result that would indicate that plant and insect lineages do not share the same glacial and postglacial histories. However, the genetic structure of the plant can, at least partially, be explained by the type of pollinators available at a regional scale. Differences in life-history traits of available pollinators might therefore have influenced the genetic structure of the plant, the dependent organism, in this antagonistic interaction.

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Correction chirurgicale de la tétralogie de Fallot étude comparative de deux méthodes

La survie actuelle après correction chirurgicale de la Tétralogie de Fallot (TDF) est de 97% à 12 ans. Les principaux risques à long terme sont une régurgitation pulmonaire ou une sténose récidivante de la sortie droite du coeur, une tachycardie ventriculaire pouvant entrainer une mort subite. Le but de cette étude rétrospective est de comparer la correction chirurgicale de la TDF avec patch pulmonaire versus un conduit valvé xénogreffe. Le collectif se compose de 127 patients entre 2 mois et 16 ans, opérés pour une TDF entre l'année 2000 et 2010. La correction chirurgicale était soit avec un patch, soit avec un conduit valvé à la sortie droite. Cette étude montre d'une part qu'il n'y a pas de différence de survie à un mois entre les deux méthodes opératoires. De plus, elle montre que, lors de la pose d'un patch, il y a plus de sept fois plus d'insuffisances valvulaires modérées à sévères après un mois que lors de la pose d'un conduit valvé. D'autre part, elle démontre que la différence de gradient résiduel à la sortie droite entre la correction avec patch ou conduit n'est pas significative et que la valeur du gradient résiduel à la sortie droite en postopératoire n'est pas représentative du gradient résiduel à un mois. De plus, cette étude prouve que les coronaires aberrantes ainsi qu'un shunt palliatif de Blalock-Taussig sont des facteurs de risque indépendants pour une correction avec un conduit valvé.

Determination of 241Pu in nuclear waste slurries: a comparative study using LSC and ICP-MS.

(241)Pu was determined in slurry samples from a nuclear reactor decommissioning project at the Paul Scherrer Institute (Switzerland). To validate the results, the (241)Pu activities of five samples were determined by LSC (TriCarb and Quantulus) and ICP-MS, with each instrument at a different laboratory. In lack of certified reference materials for (241)Pu, the methods were further validated using the (241)Pu information values of two reference sediments (IAEA-300 and IAEA-384). Excellent agreement with the results was found between LSC and ICP-MS in the nuclear waste slurries and the reference sediments.

Comparative population genetic structure in a plant-pollinator/seed predator system.

Comparative analyses of spatial genetic structure of populations of plants and the insects they interact with provide an indication of how gene flow, natural selection and genetic drift may jointly influence the distribution of genetic variation and potential for local co-adaptation for interacting species. Here, we analysed the spatial scale of genetic structure within and among nine populations of an interacting species pair, the white campion Silene latifolia and the moth Hadena bicruris, along a latitudinal gradient across Northern/Central Europe. This dioecious, short-lived perennial plant inhabits patchy, often disturbed environments. The moth H. bicruris acts both as its pollinator and specialist seed predator that reproduces by laying eggs in S. latifolia flowers. We used nine microsatellite markers for S. latifolia and eight newly developed markers for H. bicruris. We found high levels of inbreeding in most populations of both plant and pollinator/seed predator. Among populations, significant genetic structure was observed for S. latifolia but not for its pollinator/seed predator, suggesting that despite migration among populations of H. bicruris, pollen is not, or only rarely, carried over between populations, thus maintaining genetic structure among plant populations. There was a weak positive correlation between genetic distances of S. latifolia and H. bicruris. These results indicate that while significant structure of S. latifolia populations creates the potential for differentiation at traits relevant for the interaction with the pollinator/seed predator, substantial gene flow in H. bicruris may counteract this process in at least some populations.

Meanings and perceptions of patient-centeredness in social work, nursing and medicine: A comparative study.

Answering patients' evolving, more complex needs has been recognized as a main incentive for the development of interprofessional care. Thus, it is not surprising that patient-centered practice (PCP) has been adopted as a major outcome for interprofessional education. Nevertheless, little research has focused on how PCP is perceived across the professions. This study aimed to address this issue by adopting a phenomenological approach and interviewing three groups of professionals: social workers (n = 10), nurses (n = 10) and physicians (n = 8). All the participants worked in the same department (the General Internal Medicine department of a university affiliated hospital). Although the participants agreed on a core meaning of PCP as identifying, understanding and answering patients' needs, they used many dimensions to define PCP. Overall, the participants expressed value for PCP as a philosophy of care, but there was the sense of a hierarchy of patient-centeredness across the professions, in which both social work and nursing regarded themselves as more patient-centered than others. On their side, physicians seemed inclined to accept their lower position in this hierarchy. Gieryn's concept of boundary work is employed to help illuminate the nature of PCP within an interprofessional context.

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

BACKGROUND: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. RESULTS: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. CONCLUSIONS: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.