[Medical biology in the face of the evolution of health care needs]. / Rapport des Académies nationales de médecine et de pharmacie sur la biologie médicale La biologie médicale face aux défis de l'évolution des besoins de santé.

Since the publication of the ordinance of January 13th 2010, ratified by the law of May 30th 2013, medical biology in France has undergone a massive restructuration with the emergence of groups of several hundred laboratories. This evolution, which leads to a considerable reduction in the number of structures, causes numerous problems related to increased industrialization and financialization, difficulties of accreditation and disappearance of the proximity link between the biologist and the prescriber or the patient. It also leads to a clear disaffection of students, especially medical students, for this specialty whose medical character has been clearly affirmed by the law. This report takes stock of the current situation of medical biology and makes recommendations to strengthen the role of the medical biologist in the health system and patients' care.

Cephalopod biology and care, a COST FA1301 (CephsInAction) training school: anaesthesia and scientific procedures.

Cephalopods are the sole invertebrates included in the list of regulated species following the Directive 2010/63/EU. According to the Directive, achieving competence through adequate training is a requisite for people having a role in the different functions (article 23) as such carrying out procedures on animals, designing procedures and projects, taking care of animals, killing animals. Cephalopod Biology and Care Training Program is specifically designed to comply with the requirements of the "working document on the development of a common education and training framework to fulfil the requirements under the Directive 2010/63/EU". The training event occurred at the ICM-CSIC in Barcelona (Spain) where people coming from Europe, America and Asia were instructed on how to cope with regulations for the use of cephalopod molluscs for scientific purposes. The training encompasses discussion on the guidelines for the use and care of animals and their welfare with particular reference to procedures that may be of interest for neuroscience. Intensive discussion has been carried out during the training sessions with focus on behavioural studies and paradigms, welfare assessment, levels of severity of scientific procedures, animal care, handling, transport, individual identification and marking, substance administration, anaesthesia, analgesia and humane killing.

Robin Hood: A cost-efficient two-stage approach to large-scale simultaneous inference with non-homogeneous sparse effects.

A classical approach to experimental design in many scientific fields is to first gather all of the data and then analyze it in a single analysis. It has been recognized that in many areas such practice leaves substantial room for improvement in terms of the researcher's ability to identify relevant effects, in terms of cost efficiency, or both. Considerable attention has been paid in recent years to multi-stage designs, in which the user alternates between data collection and analysis and thereby sequentially reduces the size of the problem. However, the focus has generally been towards designs that require a hypothesis be tested in every single stage before it can be declared as rejected by the procedure. Such procedures are well-suited for homogeneous effects, i.e. effects of (almost) equal sizes, however, with effects of varying size a procedure that permits rejection at interim stages is much more suitable. Here we present precisely such multi-stage testing procedure called Robin Hood. We show that with heterogeneous effects our method substantially improves on the existing multi-stage procedures with an essentially zero efficiency trade-off in the homogeneous effect realm, which makes it especially useful in areas such as genetics, where heterogeneous effects are common. Our method improves on existing approaches in a number of ways including a novel way of performing two-sided testing in a multi-stage procedure with increased power for detecting small effects.

Caveat on the Boltzmann distribution function use in biology.

Sigmoid semilogarithmic functions with shape of Boltzmann equations, have become extremely popular to describe diverse biological situations. Part of the popularity is due to the easy availability of software which fits Boltzmann functions to data, without much knowledge of the fitting procedure or the statistical properties of the parameters derived from the procedure. The purpose of this paper is to explore the plasticity of the Boltzmann function to fit data, some aspects of the optimization procedure to fit the function to data and how to use this plastic function to differentiate the effect of treatment on data and to attest the statistical significance of treatment effect on the data.

Quasielastic neutron scattering in biology: Theory and applications.

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

Integration of specialties: An institutional and organizational view.

By what mechanisms of organizational and institutional change do different specialties succeed in accommodating and working with one another? How do these mechanisms function over time to support and retard the emergence and stability of new knowledge? This paper considers two such mechanisms, metawork (work that determines the organization of work) and common knowledge (knowledge that participants know is known by all participants). These mechanisms integrate specialties by making the activities of multiple specialties dependent upon one another, and by segmenting the common effort from the parent specialties. Integration of specialties can lead to the development of new specialties. Integration is facilitated and impeded by the anchoring of specialties in the system of institutions that participate in research. Host organizations, degree programs, sponsors, associations, regulators, and other organizations provide resources and impose demands that shape research. Some of these impacts are obvious and direct; others are indirect and more subtle. The research specialties form a network (not a hierarchy) in which connections constantly form and reform, and in which the influence of different anchoring institutions are constantly waxing and waning. The complexity of connections and their pattern of change are especially obvious in the life sciences, which are an especially good place to study problems of integration.

ZINC: a free tool to discover chemistry for biology.

ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site also enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Small custom subsets may be created, edited, shared, docked, downloaded, and conveyed to a vendor for purchase. The database is maintained and curated for a high purchasing success rate and is freely available at zinc.docking.org.

Elastic scattering cross section models used for Monte Carlo simulation of electron tracks in media of biological and medical interest.

PURPOSE: Elastic scattering is important for the spatial distribution of electrons penetrating matter, and thus for the distribution of deposited energy and DNA damage. Scattering media of interest are in particular liquid and gaseous water and gaseous nitrogen. The former are used as surrogates for tissue and cell environments (since more than 70% of the cell consists of water), while cross section data for nitrogen have been scaled and used as input in Monte Carlo (MC) codes simulating scattering in biologically relevant media. A short review is given of electron elastic scattering cross section models used in a biological and medical context and their experimental and theoretical background. CONCLUSIONS: Adequate theories and models exist for calculating elastic electron scattering in gaseous nitrogen and gaseous water (i.e., by free molecules) down to electron energies well below 100 eV. However, elastic electron scattering in liquid water at such low energies is apparently uncertain and not well understood. Further studies in the case of liquid water are thus motivated due to its biological importance.

Source partitioning using stable isotopes: coping with too much variation.

BACKGROUND: Stable isotope analysis is increasingly being utilised across broad areas of ecology and biology. Key to much of this work is the use of mixing models to estimate the proportion of sources contributing to a mixture such as in diet estimation. METHODOLOGY: By accurately reflecting natural variation and uncertainty to generate robust probability estimates of source proportions, the application of Bayesian methods to stable isotope mixing models promises to enable researchers to address an array of new questions, and approach current questions with greater insight and honesty. CONCLUSIONS: We outline a framework that builds on recently published Bayesian isotopic mixing models and present a new open source R package, SIAR. The formulation in R will allow for continued and rapid development of this core model into an all-encompassing single analysis suite for stable isotope research.

Staircase tableaux, the asymmetric exclusion process, and Askey-Wilson polynomials.

We introduce some combinatorial objects called staircase tableaux, which have cardinality 4(n)n!, and connect them to both the asymmetric exclusion process (ASEP) and Askey-Wilson polynomials. The ASEP is a model from statistical mechanics introduced in the late 1960s, which describes a system of interacting particles hopping left and right on a one-dimensional lattice of n sites with open boundaries. It has been cited as a model for traffic flow and translation in protein synthesis. In its most general form, particles may enter and exit at the left with probabilities alpha and gamma, and they may exit and enter at the right with probabilities beta and delta. In the bulk, the probability of hopping left is q times the probability of hopping right. Our first result is a formula for the stationary distribution of the ASEP with all parameters general, in terms of staircase tableaux. Our second result is a formula for the moments of (the weight function of) Askey-Wilson polynomials, also in terms of staircase tableaux. Since the 1980s there has been a great deal of work giving combinatorial formulas for moments of classical orthogonal polynomials (e.g. Hermite, Charlier, Laguerre); among these polynomials, the Askey-Wilson polynomials are the most important, because they are at the top of the hierarchy of classical orthogonal polynomials.

Assessment of the propensity of biofilm growth on newfloat carrier media through process and biological experiments.

This paper presents the results of research on biomass growth on Newfloat carrier elements and the implications of this growth on the wastewater treatment process. Supervision of the experiment comprised of the analysis of treatment efficiency (dynamic experiments), the estimation of the content of nitrifying bacteria in the biofilm (batch tests) and biological investigations of the biofilm structure and composition. It has been demonstrated that the biofilm growing on the carrier elements was rich in nitrifying bacteria and that this in turn guaranteed the highly efficient oxidation of ammoniacal nitrogen. After the full growth of biofilm had been established, average removal efficiencies were as follows: organic C removal-88.8% (effluent COD below 60 mg O2 l(-1)), nitrification-97.9% (effluent ammoniacal N below 1 mg N-NH4+ l(-1)), denitrification (after the COD loading rate increased to over 0.53 kg COD m(-3) d(-1))-95.7% (total N in the effluent below 8 mg N l(-1)).

A many-body field theory approach to stochastic models in population biology.

BACKGROUND: Many models used in theoretical ecology, or mathematical epidemiology are stochastic, and may also be spatially-explicit. Techniques from quantum field theory have been used before in reaction-diffusion systems, principally to investigate their critical behavior. Here we argue that they make many calculations easier and are a possible starting point for new approximations. METHODOLOGY: We review the many-body field formalism for Markov processes and illustrate how to apply it to a 'Brownian bug' population model, and to an epidemic model. We show how the master equation and the moment hierarchy can both be written in particularly compact forms. The introduction of functional methods allows the systematic computation of the effective action, which gives the dynamics of mean quantities. We obtain the 1-loop approximation to the effective action for general (space-) translation invariant systems, and thus approximations to the non-equilibrium dynamics of the mean fields. CONCLUSIONS: The master equations for spatial stochastic systems normally take a neater form in the many-body field formalism. One can write down the dynamics for generating functional of physically-relevant moments, equivalent to the whole moment hierarchy. The 1-loop dynamics of the mean fields are the same as those of a particular moment-closure.

Ants (Formicidae): models for social complexity.

The family Formicidae (ants) is composed of more than 12,000 described species that vary greatly in size, morphology, behavior, life history, ecology, and social organization. Ants occur in most terrestrial habitats and are the dominant animals in many of them. They have been used as models to address fundamental questions in ecology, evolution, behavior, and development. The literature on ants is extensive, and the natural history of many species is known in detail. Phylogenetic relationships for the family, as well as within many subfamilies, are known, enabling comparative studies. Their ease of sampling and ecological variation makes them attractive for studying populations and questions relating to communities. Their sociality and variation in social organization have contributed greatly to an understanding of complex systems, division of labor, and chemical communication. Ants occur in colonies composed of tens to millions of individuals that vary greatly in morphology, physiology, and behavior; this variation has been used to address proximate and ultimate mechanisms generating phenotypic plasticity. Relatedness asymmetries within colonies have been fundamental to the formulation and empirical testing of kin and group selection theories. Genomic resources have been developed for some species, and a whole-genome sequence for several species is likely to follow in the near future; comparative genomics in ants should provide new insights into the evolution of complexity and sociogenomics. Future studies using ants should help establish a more comprehensive understanding of social life, from molecules to colonies.

Collecting live ant specimens (colony sampling).

Because of the great diversity of ants, it is difficult to give a single protocol for the collection of live specimens. Ant body size can be very small or extremely large; the ants can be hard or soft, sting or spray toxic chemicals, live in the open or in hard-to-reach places; and colony size can range from tens of individuals to millions. Thus, collection techniques must be tailored to each particular species. In particular, caution must always be taken when dealing with stinging species, and symptoms and basic first-aid measures, especially for the treatment of anaphylactic shock, should be reviewed before beginning fieldwork. Nonetheless, many species are collectable as whole colonies. This protocol reviews some basic techniques for collecting ground-nesting species and describes how to collect whole live colonies (with queens), which are necessary for long-term laboratory studies and addressing questions of social organization and ecology.