Molecular detection of CF lung pathogens:current status and future potential

Molecular diagnostic tests, based on the detection and identification of nucleic acids in human biological samples, are increasingly employed in the diagnosis of infectious diseases and may be of future benefit to CF microbiology services. Our growing understanding of the complex polymicrobial nature of CF airway infection has highlighted current and likely future shortcomings in standard diagnostic practices. Failure to detect fastidious or slow growing microbes and misidentification of newly emerging pathogens could potentially be addressed using culture-independent molecular technologies with high target specificity. This review considers existing molecular diagnostic tests in the context of the key requirements for an envisaged CF microbiology focussed assay. The issues of assay speed, throughput, detection of multiple pathogens, data interpretation and antimicrobial susceptibility testing are discussed.

Development and Validation of a Novel Lateral Flow Immunoassay (LFIA) for the Rapid Screening of Paralytic Shellfish Toxins (PSTs) from Shellfish Extracts

A single-step lateral flow immunoassay (LFIA) was developed and validated for the rapid screening of paralytic shellfish toxins (PSTs) from a variety of shellfish species, at concentrations relevant to regulatory limits of 800 μg STX-diHCl equivalents/kg shellfish meat. A simple aqueous extraction protocol was performed within several minutes from sample homogenate. The qualitative result was generated after a 5 min run time using a portable reader which removed subjectivity from data interpretation. The test was designed to generate noncompliant results with samples containing approximately 800 μg of STX-diHCl/kg. The cross-reactivities in relation to STX, expressed as mean ± SD, were as follows: NEO: 128.9% ± 29%; GTX1&4: 5.7% ± 1.5%; GTX2&3: 23.4% ± 10.4%; dcSTX: 55.6% ± 10.9%; dcNEO: 28.0% ± 8.9%; dcGTX2&3: 8.3% ± 2.7%; C1&C2: 3.1% ± 1.2%; GTX5: 23.3% ± 14.4% (n = 5 LFIA lots). There were no indications of matrix effects from the different samples evaluated (mussels, scallops, oysters, clams, cockles) nor interference from other shellfish toxins (domoic acid, okadaic acid group). Naturally contaminated sample evaluations showed no false negative results were generated from a variety of different samples and profiles (n = 23), in comparison to reference methods (MBA method 959.08, LC-FD method 2005.06). External laboratory evaluations of naturally contaminated samples (n = 39) indicated good correlation with reference methods (MBA, LC-FD). This is the first LFIA which has been shown, through rigorous validation, to have the ability to detect most major PSTs in a reliable manner and will be a huge benefit to both industry and regulators, who need to perform rapid and reliable testing to ensure shellfish are safe to eat.

Patience, Persistence and Pragmatism: Experiences and Lessons Learnt from the Implementation of Clinically Integrated Teaching and Learning of Evidence-Based Health Care - A Qualitative Study

Background

Clinically integrated teaching and learning are regarded as the best options for improving evidence-based healthcare (EBHC) knowledge, skills and attitudes. To inform implementation of such strategies, we assessed experiences and opinions on lessons learnt of those involved in such programmes.

Methods and Findings

We conducted semi-structured interviews with 24 EBHC programme coordinators from around the world, selected through purposive sampling. Following data transcription, a multidisciplinary group of investigators carried out analysis and data interpretation, using thematic content analysis. Successful implementation of clinically integrated teaching and learning of EBHC takes much time. Student learning needs to start in pre-clinical years with consolidation, application and assessment following in clinical years. Learning is supported through partnerships between various types of staff including the core EBHC team, clinical lecturers and clinicians working in the clinical setting. While full integration of EBHC learning into all clinical rotations is considered necessary, this was not always achieved. Critical success factors were pragmatism and readiness to use opportunities for engagement and including EBHC learning in the curriculum; patience; and a critical mass of the right teachers who have EBHC knowledge and skills and are confident in facilitating learning. Role modelling of EBHC within the clinical setting emerged as an important facilitator. The institutional context exerts an important influence; with faculty buy-in, endorsement by institutional leaders, and an EBHC-friendly culture, together with a supportive community of practice, all acting as key enablers. The most common challenges identified were lack of teaching time within the clinical curriculum, misconceptions about EBHC, resistance of staff, lack of confidence of tutors, lack of time, and negative role modelling.

Conclusions

Implementing clinically integrated EBHC curricula requires institutional support, a critical mass of the right teachers and role models in the clinical setting combined with patience, persistence and pragmatism on the part of teachers.

Autosomal dominant retinitis pigmentosa:linkage to rhodopsin and evidence for genetic heterogeneity

Retinitis pigmentosa (RP) is the most prevalent human retinopathy of genetic origin. Chromosomal locations for X-linked RP and autosomal dominant RP genes have recently been established. Multipoint analyses with ADRP and seven markers on the long arm of chromosome 3 demonstrate that the gene for rhodopsin, the pigment of the rod photoreceptors, cosegregates with the disease locus with a maximum lod score of approximately 19, implicating rhodopsin as a causative gene. Recent studies have indicated the presence of a point mutation at codon 23 in exon 1 of rhodopsin which results in the substitution of histidine for the highly conserved amino acid proline, suggesting that this mutation is a cause of rhodopsin-linked ADRP. This mutation is not present in the Irish pedigree in which ADRP has been mapped close to rhodopsin. Another mutation in the rhodopsin gene or in a gene closely linked to rhodopsin may be involved. Moreover, the gene in a second ADRP pedigree, with Type II late onset ADRP, does not segregate with chromosome 3q markers, indicating that nonallelic as well as perhaps allelic genetic heterogeneity exists in the autosomal dominant form of this disease.

EFFECTS OF ENVIRONMENTAL ANTIOXIDANTS ON PRO-ANGIOGENIC ROS SIGNALLING IN ENDOTHELIAL COLONY FORMING CELLS IN VITRO

Introduction. Endothelial colony-forming cells (ECFCs) hold great cytotherapeutic potential for ischaemic disease. Whilst increasing evidence supports a key role for reactive oxygen species (ROS), specifically those derived from Nox NADPH oxidases, in the underlying angiogenic processes of these and other endothelial cells, such studies investigating the role of redox signalling may be hampered by the standard inclusion of antioxidant agents in endothelial cell media, such as phenol red. Aims. To study the effects of antioxidants present in culture media on pro-angiogenic function of ECFCs in vitro. Methods. Human ECFCs isolated from umbilical cord blood were maintained in media with and without antioxidant components (EGM2 and phenol red-free DMEM, respectively) prior to treatment with pro-oxidant PMA and assessment of their in vitro migratory capacity using a scratch-wound assay to measure pro-angiogenic activity. Results. Our previous work in our group indicated that PMA (500nM) increased ECFC migration in a both a superoxide and NADPH oxidase-dependent manner (control 18.6±2.8, PMA 32.7±6.6% wound closure; n=6, P<0.05), as indicated by attenuation with PEG-SOD and VAS2870. However, inconsistencies in the data generated under varying experimental conditions led us to hypothesise that antioxidant agents in the standard ECFC media may be influencing these effects. Indeed, a direct comparison of cell migration between ECFCs incubated in EGM2 DMEM demonstrated a clear trend towards higher migration in the latter (EGM2 9.0±4.5, DMEM 22.7±6.4%; n=3, P=NS). Similar to our previous EGM2 studies, cell migration was potentiated by PMA (control 11.6±1.6, PMA 25.1±2.8%; n=3, P<0.05), but at a lower dose (100nM), which is consistent with a reduction in media antioxidants. Notably, this response was attenuated by VAS2870 (PMA 37.6±7.3, PMA+VAS2870 10.3±2.9%; n=6, P<0.05), underlining a likely role for Nox NADPH oxidases. Conclusion. Taken together, these data indicate that ECFC migration is sensitive to different endothelial cell growth media, which appears to be dependent upon their antioxidant content. Although further experiments, such as quantification of cellular superoxide generation by dihydroethidium fluorescence may be required to confirm a specific role for antioxidants, such blunting of ROS signalling in vitro is clearly an important consideration which may significantly impact upon data interpretation.

Contribuição dos métodos geofísicos para o modelo evolutivo da região de Santo André desde o último máximo glaciário

Tese de doutoramento, Geologia (Geologia Económica e do Ambiente), Universidade de Lisboa, Faculdade de Ciências, 2014

Modeling sequencing errors by combining Hidden Markov models.

Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.

Management of fragility fractures in Switzerland: results of a nationwide survey.

A nationwide survey was conducted in Switzerland to assess the quality level of osteoporosis management in patients aged 50 years or older presenting with a fragility fracture to the emergency ward of the participating hospitals. Eight centres recruited 4966 consecutive patients who presented with one or more fractures between 2004 and 2006. Of these, 3667 (2797 women, 73.8 years old and 870 men, 73.0 years old in average) were considered as having a fragility fracture and included in the survey. Included patients presented with a fracture of the upper limbs (30.7%), lower limbs (26.4%), axial skeleton (19.5%) or another localisation, including malleolar fractures (23.4%). Thirty-two percent reported one or more previous fractures during adulthood. Of the 2941 (80.2%) hospitalised women and men, only half returned home after discharge. During diagnostic workup, dual x-ray absorptiometry (DXA) measurement was performed in 31.4% of the patients only. Of those 46.0% had a T-score < or =-2.5 SD and 81.1% < or =-1.0 SD. Osteoporosis treatment rate increased from 26.3% before fracture to 46.9% after fracture in women and from 13.0% to 30.3% in men. However, only 24.0% of the women and 13.8% of the men were finally adequately treated with a bone active substance, generally an oral bisphosphonate, with or without calcium / vitamin D supplements. A positive history of previous fracture vs none increased the likelihood of getting treatment with a bone active substance (36.6 vs 17.9%, ? 18.7%, 95% CI 15.1 to 22.3, and 22.6 vs 9.9%, ? 12.7%, CI 7.3 to 18.5, in women and men, respectively). In Switzerland, osteoporosis remains underdiagnosed and undertreated in patients aged 50 years and older presenting with a fragility fracture.

Problems of allometric scaling analysis: examples from mammalian reproductive biology.

Biological scaling analyses employing the widely used bivariate allometric model are beset by at least four interacting problems: (1) choice of an appropriate best-fit line with due attention to the influence of outliers; (2) objective recognition of divergent subsets in the data (allometric grades); (3) potential restrictions on statistical independence resulting from phylogenetic inertia; and (4) the need for extreme caution in inferring causation from correlation. A new non-parametric line-fitting technique has been developed that eliminates requirements for normality of distribution, greatly reduces the influence of outliers and permits objective recognition of grade shifts in substantial datasets. This technique is applied in scaling analyses of mammalian gestation periods and of neonatal body mass in primates. These analyses feed into a re-examination, conducted with partial correlation analysis, of the maternal energy hypothesis relating to mammalian brain evolution, which suggests links between body size and brain size in neonates and adults, gestation period and basal metabolic rate. Much has been made of the potential problem of phylogenetic inertia as a confounding factor in scaling analyses. However, this problem may be less severe than suspected earlier because nested analyses of variance conducted on residual variation (rather than on raw values) reveals that there is considerable variance at low taxonomic levels. In fact, limited divergence in body size between closely related species is one of the prime examples of phylogenetic inertia. One common approach to eliminating perceived problems of phylogenetic inertia in allometric analyses has been calculation of 'independent contrast values'. It is demonstrated that the reasoning behind this approach is flawed in several ways. Calculation of contrast values for closely related species of similar body size is, in fact, highly questionable, particularly when there are major deviations from the best-fit line for the scaling relationship under scrutiny.

The person inside the nurse : the professional socialization of baccalaureate nursing students

The goal ofthis research was to gain an understanding ofthe process ofprofessional socialization by accessing role meaning ofstudents engaged in a BScN program. Students from each ofthe four years and faculty members from the school ofnursing volunteered as participants. G. Kelly's (1955) Personal Construct Theory provided the framework to determine awareness and constructed meanings. A reflective tool, called LifeMapping, was adapted and utilized to relate student experiences within education that have attributed to nurse role meaning. Focus group interviews verified data interpretation. Students are informed oftheir choice to study nursing through part-time and volunteer work, secondary school cooperative placements. Descriptions reveal that choices are tested and both positive and negative aspects ofthe role observed. Bipolar images of good and bad nurses seem to be context-related. These images may establish biases in choices related to learning experiences. The person inside ofeach aspiring nurse interprets, revises and understands experiences to incorporate individual meaning into their value and belief structures. Students are aware ofchanges and descnbe them as developments that occur personally up to Year ill and role-image changes that begin in Year II. The major difficulty that students encountered was descnbed as negative attitudes towards their anticipated role. Humanistic-interactionist philosophies are echoed in student accounts of learning experiences. Growth and role development corresponds to process factors of small group, problem-base learning.

Identification de nouveaux substrats des kinases Erk1/2 par une approche bio-informatique, pharmacologique et phosphoprotéomique

La phosphorylation est une modification post-traductionnelle omniprésente des protéines Cette modification est ajoutée et enlevée par l’activité enzymatique respective des protéines kinases et phosphatases. Les kinases Erk1/2 sont au cœur d’une voie de signalisation importante qui régule l’activité de protéines impliquées dans la traduction, le cycle cellulaire, le réarrangement du cytosquelette et la transcription. Ces kinases sont aussi impliquées dans le développement de l’organisme, le métabolisme du glucose, la réponse immunitaire et la mémoire. Différentes pathologies humaines comme le diabète, les maladies cardiovasculaires et principalement le cancer, sont associées à une perturbation de la phosphorylation sur les différents acteurs de cette voie. Considérant l’importance biologique et clinique de ces deux kinases, connaître l’étendue de leur activité enzymatique pourrait mener au développement de nouvelles thérapies pharmacologiques. Dans ce contexte, l’objectif principal de cette thèse était de mesurer l’influence de cette voie sur le phosphoprotéome et de découvrir de nouveaux substrats des kinases Erk1/2. Une étude phosphoprotéomique de cinétique d’inhibition pharmacologique de la voie de signalisation Erk1/2 a alors été entreprise. Le succès de cette étude était basé sur trois technologies clés, soit l’enrichissement des phosphopeptides avec le dioxyde de titane, la spectrométrie de masse haut débit et haute résolution, et le développement d’une plateforme bio-informatique nommée ProteoConnections. Cette plateforme permet d’organiser les données de protéomique, évaluer leur qualité, indiquer les changements d’abondance et accélérer l’interprétation des données. Une fonctionnalité distinctive de ProteoConnections est l’annotation des sites phosphorylés identifiés (kinases, domaines, structures, conservation, interactions protéiques phospho-dépendantes). Ces informations ont été essentielles à l’analyse des 9615 sites phosphorylés sur les 2108 protéines identifiées dans cette étude, soit le plus large ensemble rapporté chez le rat jusqu’à ce jour. L’analyse des domaines protéiques a révélé que les domaines impliqués dans les interactions avec les protéines, les acides nucléiques et les autres molécules sont les plus fréquemment phosphorylés et que les sites sont stratégiquement localisés pour affecter les interactions. Un algorithme a été implémenté pour trouver les substrats potentiels des kinases Erk1/2 à partir des sites identifiés selon leur motif de phosphorylation, leur cinétique de stimulation au sérum et l’inhibition pharmacologique de Mek1/2. Une liste de 157 substrats potentiels des kinases Erk1/2 a ainsi été obtenue. Parmi les substrats identifiés, douze ont déjà été rapportés et plusieurs autres ont des fonctions associées aux substrats déjà connus. Six substrats (Ddx47, Hmg20a, Junb, Map2k2, Numa1, Rras2) ont été confirmés par un essai kinase in vitro avec Erk1. Nos expériences d’immunofluorescence ont démontré que la phosphorylation de Hmg20a sur la sérine 105 par Erk1/2 affecte la localisation nucléocytoplasmique de cette protéine. Finalement, les phosphopeptides isomériques positionnels, soit des peptides avec la même séquence d’acides aminés mais phosphorylés à différentes positions, ont été étudiés avec deux nouveaux algorithmes. Cette étude a permis de déterminer leur fréquence dans un extrait enrichi en phosphopeptides et d’évaluer leur séparation par chromatographie liquide en phase inverse. Une stratégie analytique employant un des algorithmes a été développée pour réaliser une analyse de spectrométrie de masse ciblée afin de découvrir les isomères ayant été manqués par la méthode d’analyse conventionnelle.

Relations entre la mobilité, la condition physique et les fonctions cognitives dans une perspective de vieillissement sain

Thèse effectuée en cotutelle (Université de Poitiers, France)

The effectiveness of scoliosis screening programs: methods for systematic review and expert panel recommendations formulation

Background: Literature on scoliosis screening is vast, however because of the observational nature of available data and methodological flaws, data interpretation is often complex, leading to incomplete and sometimes, somewhat misleading conclusions. The need to propose a set of methods for critical appraisal of the literature about scoliosis screening, a comprehensive summary and rating of the available evidence appeared essential. METHODS: To address these gaps, the study aims were: i) To propose a framework for the assessment of published studies on scoliosis screening effectiveness; ii) To suggest specific questions to be answered on screening effectiveness instead of trying to reach a global position for or against the programs; iii) To contextualize the knowledge through expert panel consultation and meaningful recommendations. The general methodological approach proceeds through the following steps: Elaboration of the conceptual framework; Formulation of the review questions; Identification of the criteria for the review; Selection of the studies; Critical assessment of the studies; Results synthesis; Formulation and grading of recommendations in response to the questions. This plan follows at best GRADE Group (Grades of Recommendation, Assessment, Development and Evaluation) requirements for systematic reviews, assessing quality of evidence and grading the strength of recommendations. CONCLUSIONS: In this article, the methods developed in support of this work are presented since they may be of some interest for similar reviews in scoliosis and orthopaedic fields.

Environmental impact of sand mining

This thesis Entitled Environmental impact of Sand Mining :A case Study in the river catchments of vembanad lake southwest india.The entire study is addressed in nine chapters. Chapter l deals with the general introduction about rivers, problems of river sand mining, objectives, location of the study area and scope of the study. A detailed review on river classification, classic concepts in riverine studies, geological work of rivers and channel processes, importance of river ecosystems and its need for management are dealt in Chapter 2. Chapter 3 gives a comprehensive account of the study area - its location, administrative divisions, physiography, soil, geology, land use and living and non-living resources. The various methods adopted in the study are dealt in Chapter 4. Chapter 5 contains river characteristics like drainage, environmental and geologic setting, channel characteristics, river discharge and water quality of the study area. Chapter 6 gives an account of river sand mining (instream and floodplain mining) from the study area. The various environmental problems of river sand mining on the land adjoining the river banks, river channel, water, biotic and social / human environments of the area and data interpretation are presented in Chapter 7. Chapter 8 deals with the Environmental Impact Assessment (EIA) and Environmental Management Plan (EMP) of sand mining from the river catchments of Vembanad lake.