Ab initio modeling and molecular dynamics simulation of the alpha 1b-adrenergic receptor activation.

This work describes the ab initio procedure employed to build an activation model for the alpha 1b-adrenergic receptor (alpha 1b-AR). The first version of the model was progressively modified and complicated by means of a many-step iterative procedure characterized by the employment of experimental validations of the model in each upgrading step. A combined simulated (molecular dynamics) and experimental mutagenesis approach was used to determine the structural and dynamic features characterizing the inactive and active states of alpha 1b-AR. The latest version of the model has been successfully challenged with respect to its ability to interpret and predict the functional properties of a large number of mutants. The iterative approach employed to describe alpha 1b-AR activation in terms of molecular structure and dynamics allows further complications of the model to allow prediction and interpretation of an ever-increasing number of experimental data.

Molecular estimation of dispersal for ecology and population genetics

The dispersal process, by which individuals or other dispersing agents such as gametes or seeds move from birthplace to a new settlement locality, has important consequences for the dynamics of genes, individuals, and species. Many of the questions addressed by ecology and evolutionary biology require a good understanding of species' dispersal patterns. Much effort has thus been devoted to overcoming the difficulties associated with dispersal measurement. In this context, genetic tools have long been the focus of intensive research, providing a great variety of potential solutions to measuring dispersal. This methodological diversity is reviewed here to help (molecular) ecologists find their way toward dispersal inference and interpretation and to stimulate further developments.

Family relationships and learning experiences in anxious vs. non-anxious families: Are there differences ?

L'objectif principal de ce travail était d'explorer les relations parent-enfant et les processus d'apprentissage familiaux associés aux troubles anxieux. A cet effet, des familles ayant un membre anxieux (la mère ou l'enfant) ont été comparées avec des familles n'ayant aucun membre anxieux. Dans une première étude, l'observation de l'interaction mère-enfant, pendant une situation standardisée de jeu, a révélé que les mères présentant un trouble panique étaient plus susceptibles de se montrer verbalement contrôlantes, critiques et moins sensibles aux besoins de l'enfant, que les mères qui ne présentaient pas de trouble panique. Une deuxième étude a examiné les perceptions des différents membres de la famille quant aux relations au sein de la famille et a indiqué que, par comparaison aux adolescents non-anxieux, les adolescents anxieux étaient plus enclins à éprouver un sentiment d'autonomie individuelle diminué par rapport à leurs parents. Finalement, une troisième étude s'est intéressée à déterminer l'impact d'expériences d'apprentissage moins directes dans l'étiologie de l'anxiété. Les résultats ont indiqué que les mères présentant un trouble panique étaient plus enclines à s'engager dans des comportements qui maintiennent la panique et à impliquer leurs enfants dans ces comportements, que les mères ne présentant pas de trouble panique. En se basant sur des recherches antérieures qui ont établi une relation entre le contrôle parental, la perception de contrôle chez l'enfant et les troubles anxieux, le présent travail non seulement confirme ce lien mais propose également un modèle pour résumer l'état actuel des connaissances concernant les processus familiaux et le développement des troubles anxieux. Deux routes ont été suggérées par lesquelles l'anxiété pourrait être transmise de manière intergénérationnelle. Chacune de ces routes attribue un rôle important à la perception de contrôle chez l'enfant. L'idée est que lorsque les enfants présentent une prédisposition à interpréter le comportement de leurs parents comme hors de leur contrôle, ils seraient plus enclins à développer de l'anxiété. A ce titre, la perception du contrôle représenterait un tampon entre le comportement de contrôle/surprotection des parents et le trouble anxieux chez l'enfant. - The principal objective of the present work was to explore parent-child relationships and family learning processes associated with anxiety disorders. To this purpose, families with and without an anxious family member (mother or child) were compared. In a first study, observation of mother-child interaction, during a standard play situation, revealed that mothers with panic disorder were more likely to display verbal control and criticism, and less likely to display sensitivity toward their children than mothers without panic disorder. A second study examined family members' perceptions of family relationships and indicated that compared to non-anxious adolescents, anxious adolescents were more prone to experience a diminished sense of individual autonomy in relation to their parents. Finally a third study was interested in determining the effect of less direct learning experiences in the aetiology of anxiety. Results indicated that mothers with panic disorder were more likely to engage in panic-maintaining behaviour and to involve their children in this behaviour than mothers without panic disorder. Based on previous research showing a relationship between parental control, children's perception of control, and anxiety disorders, the present work not only further adds evidence to support this link but also proposes a model summarizing the current knowledge concerning family processes and the development of anxiety disorders. Two pathways have been suggested through which anxiety may be intergenerationally transmitted. Both pathways assign an important role to children's perception of control. The idea is that whenever children have a predisposition towards interpreting their parents' behaviour as beyond of their control, they may be more prone to develop anxiety. As such, perceived control may represent a buffer between parental overcontrolling/overprotective behaviours and childhood anxiety disorder.

Bayesian Networks for Probabilistic Inference and Decision Analysis in Forensic Science

Continuing developments in science and technology mean that the amounts of information forensic scientists are able to provide for criminal investigations is ever increasing. The commensurate increase in complexity creates difficulties for scientists and lawyers with regard to evaluation and interpretation, notably with respect to issues of inference and decision. Probability theory, implemented through graphical methods, and specifically Bayesian networks, provides powerful methods to deal with this complexity. Extensions of these methods to elements of decision theory provide further support and assistance to the judicial system. Bayesian Networks for Probabilistic Inference and Decision Analysis in Forensic Science provides a unique and comprehensive introduction to the use of Bayesian decision networks for the evaluation and interpretation of scientific findings in forensic science, and for the support of decision-makers in their scientific and legal tasks. Includes self-contained introductions to probability and decision theory. Develops the characteristics of Bayesian networks, object-oriented Bayesian networks and their extension to decision models. Features implementation of the methodology with reference to commercial and academically available software. Presents standard networks and their extensions that can be easily implemented and that can assist in the reader's own analysis of real cases. Provides a technique for structuring problems and organizing data based on methods and principles of scientific reasoning. Contains a method for the construction of coherent and defensible arguments for the analysis and evaluation of scientific findings and for decisions based on them. Is written in a lucid style, suitable for forensic scientists and lawyers with minimal mathematical background. Includes a foreword by Ian Evett. The clear and accessible style of this second edition makes this book ideal for all forensic scientists, applied statisticians and graduate students wishing to evaluate forensic findings from the perspective of probability and decision analysis. It will also appeal to lawyers and other scientists and professionals interested in the evaluation and interpretation of forensic findings, including decision making based on scientific information.

New Horizons in Forensic Imaging: Post Mortem CT Angiography - Benefits and Practical Application.

Puropse/Aim: To learn about the developement of post mortem CT angiography, its indications, benefits, pitfalls and practical application. Content Organization: A. Developement of post mortem CT angiography B. Technical prerequisites C. Practical application of post mortem CT angiography (preparation of the body, injection of contrast agent, examination protocol) D. Indications and benefits (including a comparison with conventional autopsy) E. Interpretation of imaging data (with case demonstrations) F. Artifacts, pitfalls and limitations G. Current and potential future use. Summary: This exhibit demonstrates the developement, application and interpretation of post mortem CT angiography. Teaching points: 1. post mortem CT angiography is feasible and useful for identification of the cause of death 2. depending on the indication it can be superior to autopsy 3. limitations and artifacts need to be known for interpreta

Clinical and genetic findings in a large cohort of patients with congenital myopathies due to mutations in the skeletal muscle ryanodine receptor (RYR1) gene

RYR1 mutations are the most common cause of structural congenital myopathies and may exhibit both dominant and recessive inheritance. Histopathological findings are variable and include central cores, multi-minicores, type 1 predominance/ uniformity, fibre type disproportion, increased internal nucleation and fatty and connective tissue. Until recently, diagnostic RYR1 sequencing was limited to mutational hotspots due to the large size of the gene. Since the introduction of full RYR1 sequencing in 2007 we have detected pathogenic mutations in 77 families: 39 had dominant inheritance and 38 recessive inheritance. In some cases with presumably recessive inheritance, only one heterozygous mutation inherited from an asymptomatic parent was identified. Of 28 dominant mutations, 6 were novel; 37 of the 59 recessive mutations were also novel. Dominant mutations were more frequently in recognized hotspot regions, while recessive mutations were distributed throughout the coding sequence. Dominant mutations were predominantly missense, whereas recessive mutations included many nonsense and splice mutations expected to result in reduced RyR1 protein. There was wide clinical variability in patients with both dominant and recessive inheritance. As a group, those with dominant mutations were generally more mildly affected than those with recessive inheritance, who had earlier onset and were weaker with more functional limitations. Extraocular muscle involvement was almost exclusively observed in the recessive group. Bulbar involvement was also more prominent in this group, resulting in a larger number requiring gastrostomy insertion. In conclusion, genomic sequencing of the entire RYR1 leads to the detection of many novel mutations, but may miss large genetic rearrangements in some cases. Assigning pathogenicity to novel mutations is often difficult and interpretation of genetic results in the context of clinical, histological and, increasingly, muscle MRI findings is essential.

Ra isotopes and Rn as a tool for the water management resources: the Alberquillas aquifer (Málaga-Granada)

The aim of this project is to evaluate the importance of submarine groundwater discharge sector in order to improve the water balance in Málaga-Granada region. The approach of this study arose from the the geology and the aquifers that indicate that there could be some discharge to the sea between Maro (Málaga) and Almuñécar (Granada) and the Andalusian’s Government and its Water Agence were really interested in evaluating it because there is a lot of population and few water available and the magnitude of groundwater discharge has generated controversy. Is well known that water is a scarce resource in this area and it’s very important for the society and for the environment. The legislation, the water policies, the knowledge of the aquifer and the geology, the water dynamics, the land use and the water perception in the society might help the management of this resource not just in Andalusia but in all the Mediterranean basin. The main objective is to evaluate the submarine groundwater discharge from the Alberquillas Aqufier to the sea by measuring 222Rn and Ra isotopes. Specific objectives have been established to achieve the main objective: A) Reveal the importance of water resources in the Mediterranean basin; B) Learn radiometric techniques for the study of groundwater discharge to the sea; C) Learn of sampling techniques of water samples for the measurement of Ra and Rn; D) Learn the techniques for measuring Ra (RaDeCC) and Rn (RAD7); E) Interpretation and discussion of results. During this semester, and in addition of the present study in Málaga- Granada region, the author has participated in the initial phase (sampling, analysis and interpretation of preliminary results) of other research projects focused on the study of submarine groundwater discharges through the use of Ra isotopes and 222Rn. These studies have been developed in different areas, including Alt Empordà (Roses and Sant Pere Pescador), Maresme with CMIMA’s group (Mediterranean Center for Marine and Environmental Research), Delta de l’Ebre, Peñíscola and Mallorca with the IMEDEA’s group (Mediterranean Institute for Advanced Studies).

Structural characterization of Turtle Mountain anticline (Alberta, Canada) and impact on rock slope failure

his paper proposes a structural investigation of the Turtle Mountain anticline (Alberta, Canada) to better understand the role of the different tectonic features on the development of both local and large scale rock slope instabilities occurring in Turtle Mountain. The study area is investigated by combining remote methods with detailed field surveys. In particular, the benefit of Terrestrial Laser Scanning for ductile and brittle tectonic structure interpretations is illustrated. The proposed tectonic interpretation allows the characterization of the fracturing pattern, the fold geometry and the role of these tectonic features in rock slope instability development. Ten discontinuity sets are identified in the study area, their local variations permitting the differentiation of the study zone into 20 homogenous structural domains. The anticline is described as an eastern verging fold that displays considerable geometry differences along its axis and developed by both flexural slip and tangential longitudinal strain folding mechanisms. Moreover, the origins of the discontinuity sets are determined according to the tectonic phases affecting the region (pre-folding, folding, post-folding). The localization and interpretation of kinematics of the different instabilities revealed the importance of considering the discrete brittle planes of weakness, which largely control the kinematic release of the local instabilities, and also the rock mass damage induced by large tectonic structures (fold hinge, thrust).

Susceptibility of Colombian Plasmodium falciparum isolates to 4-aminoquinolines and the definition of amodiaquine resistance in vitro

There are wide variations in the threshold used to define in vitro resistance of Plasmodium falciparum to amodiaquine (AQ), probably due to differences in methodology and interpretation. In vitro susceptibility data of Colombian P. falciparum strains to AQ and N-desethylamodiaquine is used to illustrate the need to standardized methodologies and compare inhibitory concentrations, instead of resistant/susceptible phenotypes, when studying the mechanisms of resistance to AQ and monitoring drug susceptibility trends in the field.

Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell.

Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G envelope protein (VSV-G)-pseudotyped HIV vector. At 24 h postinfection, both cellular and viral transcriptomes were analyzed by serial analysis of gene expression followed by high-throughput sequencing (SAGE-Seq). Read mapping resulted in 33 to 44 million tags aligning with the human transcriptome and 0.23 to 0.25 million tags aligning with the genome of the HIV-1 vector. Thus, at peak infection, 1 transcript in 143 is of viral origin (0.7%), including a small component of antisense viral transcription. Of the detected cellular transcripts, 826 (2.3%) were differentially expressed between mock- and HIV-infected samples. The approach also assessed whether HIV-1 infection modulates the expression of repetitive elements or endogenous retroviruses. We observed very active transcription of these elements, with 1 transcript in 237 being of such origin, corresponding on average to 123,123 reads in mock-infected samples (0.40%) and 129,149 reads in HIV-1-infected samples (0.45%) mapping to the genomic Repbase repository. This analysis highlights key details in the generation and interpretation of high-throughput data in the setting of HIV-1 cellular infection.

Obesity and survival in operable breast cancer patients treated with adjuvant anthracyclines and taxanes according to pathological subtypes: a pooled analysis.

INTRODUCTION Obesity is an unfavorable prognostic factor in breast cancer (BC) patients regardless of menopausal status and treatment received. However, the association between obesity and survival outcome by pathological subtype requires further clarification. METHODS We performed a retrospective analysis including 5,683 operable BC patients enrolled in four randomized clinical trials (GEICAM/9906, GEICAM/9805, GEICAM/2003-02, and BCIRG 001) evaluating anthracyclines and taxanes as adjuvant treatments. Our primary aim was to assess the prognostic effect of body mass index (BMI) on disease recurrence, breast cancer mortality (BCM), and overall mortality (OM). A secondary aim was to detect differences of such prognostic effects by subtype. RESULTS Multivariate survival analyses adjusting for age, tumor size, nodal status, menopausal status, surgery type, histological grade, hormone receptor status, human epidermal growth factor receptor 2 (HER2) status, chemotherapy regimen, and under-treatment showed that obese patients (BMI 30.0 to 34.9) had similar prognoses to that of patients with a BMI < 25 (reference group) in terms of recurrence (Hazard Ratio [HR] = 1.08, 95% Confidence Interval [CI] = 0.90 to 1.30), BCM (HR = 1.02, 0.81 to 1.29), and OM (HR = 0.97, 0.78 to 1.19). Patients with severe obesity (BMI ≥ 35) had a significantly increased risk of recurrence (HR = 1.26, 1.00 to 1.59, P = 0.048), BCM (HR = 1.32, 1.00 to 1.74, P = 0.050), and OM (HR = 1.35, 1.06 to 1.71, P = 0.016) compared to our reference group. The prognostic effect of severe obesity did not vary by subtype. CONCLUSIONS Severely obese patients treated with anthracyclines and taxanes present a worse prognosis regarding recurrence, BCM, and OM than patients with BMI < 25. The magnitude of the harmful effect of BMI on survival-related outcomes was similar across subtypes.

Clinical and genetic findings in a large cohort of patients with ryanodine receptor 1 gene-associated myopathies.

Ryanodine receptor 1 (RYR1) mutations are a common cause of congenital myopathies associated with both dominant and recessive inheritance. Histopathological findings frequently feature central cores or multi-minicores, more rarely, type 1 predominance/uniformity, fiber-type disproportion, increased internal nucleation, and fatty and connective tissue. We describe 71 families, 35 associated with dominant RYR1 mutations and 36 with recessive inheritance. Five of the dominant mutations and 35 of the 55 recessive mutations have not been previously reported. Dominant mutations, typically missense, were frequently located in recognized mutational hotspot regions, while recessive mutations were distributed throughout the entire coding sequence. Recessive mutations included nonsense and splice mutations expected to result in reduced RyR1 protein. There was wide clinical variability. As a group, dominant mutations were associated with milder phenotypes; patients with recessive inheritance had earlier onset, more weakness, and functional limitations. Extraocular and bulbar muscle involvement was almost exclusively observed in the recessive group. In conclusion, our study reports a large number of novel RYR1 mutations and indicates that recessive variants are at least as frequent as the dominant ones. Assigning pathogenicity to novel mutations is often difficult, and interpretation of genetic results in the context of clinical, histological, and muscle magnetic resonance imaging findings is essential.

Colorectal Cancer Classification and Cell Heterogeneity: A Systems Oncology Approach.

Colorectal cancer is a heterogeneous disease that manifests through diverse clinical scenarios. During many years, our knowledge about the variability of colorectal tumors was limited to the histopathological analysis from which generic classifications associated with different clinical expectations are derived. However, currently we are beginning to understand that under the intense pathological and clinical variability of these tumors there underlies strong genetic and biological heterogeneity. Thus, with the increasing available information of inter-tumor and intra-tumor heterogeneity, the classical pathological approach is being displaced in favor of novel molecular classifications. In the present article, we summarize the most relevant proposals of molecular classifications obtained from the analysis of colorectal tumors using powerful high throughput techniques and devices. We also discuss the role that cancer systems biology may play in the integration and interpretation of the high amount of data generated and the challenges to be addressed in the future development of precision oncology. In addition, we review the current state of implementation of these novel tools in the pathological laboratory and in clinical practice.

Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): explanation and elaboration.

Much medical research is observational. The reporting of observational studies is often of insufficient quality. Poor reporting hampers the assessment of the strengths and weaknesses of a study and the generalisability of its results. Taking into account empirical evidence and theoretical considerations, a group of methodologists, researchers, and editors developed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) recommendations to improve the quality of reporting of observational studies. The STROBE Statement consists of a checklist of 22 items, which relate to the title, abstract, introduction, methods, results and discussion sections of articles. Eighteen items are common to cohort studies, case-control studies and cross-sectional studies and four are specific to each of the three study designs. The STROBE Statement provides guidance to authors about how to improve the reporting of observational studies and facilitates critical appraisal and interpretation of studies by reviewers, journal editors and readers. This explanatory and elaboration document is intended to enhance the use, understanding, and dissemination of the STROBE Statement. The meaning and rationale for each checklist item are presented. For each item, one or several published examples and, where possible, references to relevant empirical studies and methodological literature are provided. Examples of useful flow diagrams are also included. The STROBE Statement, this document, and the associated Web site (http://www.strobe-statement.org/) should be helpful resources to improve reporting of observational research.

Interpretation of plasma amino acids in the follow-up of patients: the impact of compartmentation

Results of plasma or urinary amino acids are used for suspicion, confirmation or exclusion of diagnosis, monitoring of treatment, prevention and prognosis in inborn errors of amino acid metabolism. The concentrations in plasma or whole blood do not necessarily reflect the relevant metabolite concentrations in organs such as the brain or in cell compartments; this is especially the case in disorders that are not solely expressed in liver and/or in those which also affect nonessential amino acids. Basic biochemical knowledge has added much to the understanding of zonation and compartmentation of expressed proteins and metabolites in organs, cells and cell organelles. In this paper, selected old and new biochemical findings in PKU, urea cycle disorders and nonketotic hyperglycinaemia are reviewed; the aim is to show that integrating the knowledge gained in the last decades on enzymes and transporters related to amino acid metabolism allows a more extensive interpretation of biochemical results obtained for diagnosis and follow-up of patients and may help to pose new questions and to avoid pitfalls. The analysis and interpretation of amino acid measurements in physiological fluids should not be restricted to a few amino acids but should encompass the whole quantitative profile and include other pathophysiological markers. This is important if the patient appears not to respond as expected to treatment and is needed when investigating new therapies. We suggest that amino acid imbalance in the relevant compartments caused by over-zealous or protocol-driven treatment that is not adjusted to the individual patient's needs may prolong catabolism and must be corrected