Why Medical Informatics (still) Needs Cognitive and Social Sciences.

International audienceOBJECTIVES: To summarize current excellent medical informatics research in the field of human factors and organizational issues. METHODS: Using PubMed, a total of 3,024 papers were selected from 17 journals. The papers were evaluated on the basis of their title, keywords, and abstract, using several exclusion and inclusion criteria. 15 preselected papers were carefully evaluated by six referees using a standard evaluation grid. RESULTS: Six best papers were selected exemplifying the central role cognitive and social sciences can play in medical informatics research. Among other contributions, those studies: (i) make use of the distributed cognition paradigm to model and understand clinical care situations; (ii) take into account organizational issues to analyse the impact of HIT on information exchange and coordination processes; (iii) illustrate how models and empirical data from cognitive psychology can be used in medical informatics; and (iv) highlight the need of qualitative studies to analyze the unexpected side effects of HIT on cognitive and work processes. CONCLUSION: The selected papers demonstrate that paradigms, methodologies, models, and results from cognitive and social sciences can help to bridge the gap between HIT and end users, and contribute to limit adoption failures that are reported regularly

Transport properties of 2D graphene containing structural defects

We propose an extensive report on the simulation of electronic transport in 2D graphene in presence of structural defects. Amongst the large variety of such defects in sp$^2$ carbon-based materials, we focus on the Stone-Wales defect and on two divacancy-type reconstructed defects. First, based on ab initio calculations, a tight-binding model is derived to describe the electronic structure of these defects. Then, semiclassical transport properties including the elastic mean free paths, mobilities and conductivities are computed using an order-N real-space Kubo-Greenwood method. A plateau of minimum conductivity ($\sigma^{min}_{sc}= 4e^2/\pi h$) is progressively observed as the density of defects increases. This saturation of the decay of conductivity to $\sigma^{min}_{sc}$ is associated with defect-dependent resonant energies. Finally, localization phenomena are captured beyond the semiclassical regime. An Anderson transition is predicted with localization lengths of the order of tens of nanometers for defect densities around 1%.Comment: 17 pages, 17 figures, submitted to Phys. Rev.

Two-Dimensional Graphene with Structural Defects: Elastic Mean Free Path, Minimum Conductivity, and Anderson Transition

4 páginas, 4 figuras.-- PACS numbers: 73.23. b, 72.15.Rn, 73.43.Qt.-- et al.Quantum transport properties of disordered graphene with structural defects (Stone-Wales and divacancies) are investigated using a realistic π-π* tight-binding model elaborated from ab initio calculations. Mean free paths and semiclassical conductivities are then computed as a function of the nature and density of defects (using an order-N real-space Kubo-Greenwood method). By increasing the defect density, the decay of the semiclassical conductivities is predicted to saturate to a minimum value of 4e2/πh over a large range (plateau) of carrier density (>0.5×1014  cm-2). Additionally, strong contributions of quantum interferences suggest that the Anderson localization regime could be experimentally measurable for a defect density as low as 1%.J.-C. C. and A. L. acknowledge financial support from the FNRS of Belgium. Parts of this work are connected to the Belgian Program on Interuniversity Attraction Poles (PAI6), to the NanoHymo ARC, to the ETSF e-I3 project (Grant No. 211956), and to the NANOSIM-GRAPHENE Project No. ANR-09-NANO-016-01.Peer reviewe

Does root plasticity contribute to crop tolerance to abiotic stresses?

Poster that presents the experiments, the main results and take home messages

α-Hydroxyketone Synthesis and Sensing by Legionella and Vibrio

Bacteria synthesize and sense low molecular weight signaling molecules, termed autoinducers, to measure their population density and community complexity. One class of autoinducers, the α-hydroxyketones (AHKs), is produced and detected by the water-borne opportunistic pathogens Legionella pneumophila and Vibrio cholerae, which cause Legionnaires’ disease and cholera, respectively. The “Legionella quorum sensing” (lqs) or “cholera quorum sensing” (cqs) genes encode enzymes that produce and sense the AHK molecules “Legionella autoinducer-1” (LAI-1; 3-hydroxypentadecane-4-one) or cholera autoinducer-1 (CAI-1; 3-hydroxytridecane-4-one). AHK signaling regulates the virulence of L. pneumophila and V. cholerae, pathogen-host cell interactions, formation of biofilms or extracellular filaments, expression of a genomic “fitness island” and competence. Here, we outline the processes, wherein AHK signaling plays a role, and review recent insights into the function of proteins encoded by the lqs and cqs gene clusters. To this end, we will focus on the autoinducer synthases catalysing the biosynthesis of AHKs, on the cognate trans-membrane sensor kinases detecting the signals, and on components of the down-stream phosphorelay cascade that promote the transmission and integration of signaling events regulating gene expression

The vital roles of blue foods in the global food system

Blue foods play a central role in food and nutrition security for billions of people and are a cornerstone of the livelihoods, economies, and cultures of many coastal and riparian communities. Blue foods are extraordinarily diverse, are often rich in essential micronutrients and fatty acids, and can often be produced in ways that are more environmentally sustainable than terrestrial animal-source foods. Capture fisheries constitute the largest wild-food resource for human extraction that would be challenging to replace. Yet, despite their unique value, blue foods have often been left out of food system analyses, policies, and investments. Here, we focus on three imperatives for realizing the potential of blue foods: (1) Bring blue foods into the heart of food system decision-making; (2) Protect and develop the potential of blue foods to help end malnutrition; and (3) Support the central role of small-scale actors in fisheries and aquaculture. Recognition of the importance of blue foods for food and nutrition security constitutes a critical justification to preserve the integrity and diversity of aquatic species and ecosystems.Additional co-authors: Christopher D. Golden. Benjamin S. Halpern, Christina C. Hicks, Malin Jonell, Avinash Kishore, J. Zachary Koehn, Rosamond L. Naylor, Michael J. Phillips, Elizabeth R. Selig, Rebecca E. Short, Rashid Sumaila, Shakuntala H. Thilsted, Max Troell, Colette C. C. Wabnit

The vital roles of blue foods in the global food system

Blue foods play a central role in food and nutrition security for billions of people and are a cornerstone of the livelihoods, economies, and cultures of many coastal and riparian communities. Blue foods are extraordinarily diverse, are often rich in essential micronutrients and fatty acids, and can often be produced in ways that are more environmentally sustainable than terrestrial animal-source foods. Capture fisheries constitute the largest wild-food resource for human extraction that would be challenging to replace. Yet, despite their unique value, blue foods have often been left out of food system analyses, policies, and investments. Here, we focus on three imperatives for realizing the potential of blue foods: (1) Bring blue foods into the heart of food system decision-making; (2) Protect and develop the potential of blue foods to help end malnutrition; and (3) Support the central role of small-scale actors in fisheries and aquaculture. Recognition of the importance of blue foods for food and nutrition security constitutes a critical justification to preserve the integrity and diversity of aquatic species and ecosystems

Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies

Electronic and transport properties of boron nitride and graphene-based nanostructures

Graphene has been at the center of a tremendous research effort since its clear identification in 2004 by Andre Geim and Konstantin Novoselov. As a proof of the outstanding interest in graphene, Geim and Novoselov were awarded with the Nobel Prize in Physics in 2010, six years only after their seminal work. This interest is driven by the innovative character of graphene and its extraordinary combination of properties, unmatched by any other material known so far. Graphene is a two-dimensional one-atom thick layer of carbon. In-plane, it posseses one of the largest bond-strength (stronger than diamond), while keeping a high out-of-plane flexibility. Along with its mechanical properties, graphene exhibits exceptional chemical and optical properties. However, the most fascinating properties are undoubtedly its electronic properties. Electrons in graphene behave like massless particles, leading to new behaviors in condensed matter physics. In addition, graphene is a zero band gap semiconductor, meaning the conduction and valence band meet at exactly one single point. Finally, graphene exhibits very high electron mobilities, which are of particular interest for future electronic devices. As in conventional electronics, different ways to tailor the properties of graphene are currently under investigation (i.e. by altering locally its atomic structure or by incorporating foreign atoms in the carbon network) in order to create new specific devices for a large set of various applications. The discovery of graphene initiated the research in other two-dimensional materials, among which the single sheet of boron nitride (BN). The latter shares with graphene analogous geometry but its electronic properties are drastically different. Indeed, a single layer of BN is an insulating material. More recently, interest has grown in combining graphene together with BN, using either boron nitride as a passive material (substrate, encapsulation), or as an active system to create a new range of properties, differing from the ones of the pristine components. The present thesis investigates the properties of graphene and boron nitride nanostructures within the framework of density functional theory. Firstly, point defects as well as lines of defects are introduced in graphene. Their influence on the transport properties of graphene are estimated and transport fingerprints are predicted for each specific defect. Secondly, the doping of graphene by incorporation of boron and nitrogen atoms is examined. More specifically, scanning tunneling microscopy images are simulated in order to identify specific defects in experiments. Then, the electronic transport properties of BN-graphene composites are investigated and amazing spin filtering properties are evidenced. Finally, the electronic properties of graphene misorientedly stacked on a BN substrate are presented, evidencing, as observed experimentally, little alteration of the electronic properties of suspended graphene. These calculations suggest the BN single layer to be the ideal substrate for future graphene-based electronics.(FSA 3) -- UCL, 201

Preservation at ultra-low temperature of in vitro cultured arbuscular mycorrhizal fungi via encapsulation-drying

At present, over 300 species of arbuscular mycorrhizal fungi (AMF) have been identified, most of which being stored in international collections. Their maintenance is mostly achieved in greenhouse via continuous culture on trap plants or in vitro in association with excised root organs. Both methods are work-intensive and for the former present the risk of unwanted contaminations. The in vitro root organ culture of AMF has become an alternative preventing contamination. Nevertheless, the risk for somaclonal variation during the sub-cultivation process cannot be excluded. A method for the long-term conservation that guarantees the stability of the biological material is thus highly demanded to preserve the microorganisms and their genetic stability. Here, 12 AMF isolates cultured in vitro in association with excised carrot roots were encapsulated in alginate beads and subsequently cryopreserved. Several protocols were tested taking into consideration culture age, alginate bead pre-drying, and rate of decrease in temperature. The viability of the AMF isolates was estimated by the percentage of potentially infective beads (%PIB) that measure the % of beads that contain at least one germinated propagule. Thermal behaviour of alginate beads was analysed by a differential thermal calorimeter before and after drying to estimate the frozen and unfrozen water during the cryopreservation process. It was shown that the spore damage was directly related to ice formation during cryopreservation. The encapsulation and culture age were also determinant parameters for the successful cryopreservation. Irrespective of the AMF isolate, the optimal procedure for cryopreservation comprised five steps: (1) the encapsulation of propagules (i.e. spores and mycorrhizal root pieces) isolated from 5 m old cultures, (2) the incubation overnight in trehalose (0.5 M), (3) the drying during 48 h at 27 °C, (4) the cryopreservation in the freezer at -130 °C following a two-step decrease in temperature: a fast decrease (∼12 °C min -1) from room temperature (+20 °C) to -110 °C followed by a slow decrease in temperature (∼1 °C min -1) from -110 °C to -130 °C, and (5) the direct thawing in a water bath (+35 °C). The % PIB was above 70 % for all the isolates and even above 95 % for 11 out of the 12 isolates after several months of storage at ultra-low temperature. All the isolates kept their capacity to associate to an excised carrot root in vitro and to reproduce the fungal life cycle with the production of several hundreds to thousands of spores after 2 m. This method opens the door for the long-term maintenance at ultra-low temperature of AMF isolates within international repositories. © 2012 The British Mycological Society