Showing papers by "University of Fribourg published in 2014"

Nonequilibrium dynamical mean-field theory and its applications

Abstract: The study of nonequilibrium phenomena in correlated lattice systems has developed into one of the most active and exciting branches of condensed matter physics. This research field provides rich new insights that could not be obtained from the study of equilibrium situations, and the theoretical understanding of the physics often requires the development of new concepts and methods. On the experimental side, ultrafast pump-probe spectroscopies enable studies of excitation and relaxation phenomena in correlated electron systems, while ultracold atoms in optical lattices provide a new way to control and measure the time evolution of interacting lattice systems with a vastly different characteristic time scale compared to electron systems. A theoretical description of these phenomena is challenging because, first, the quantum-mechanical time evolution of many-body systems out of equilibrium must be computed and second, strong-correlation effects which can be of a nonperturbative nature must be addressed. This review discusses the nonequilibrium extension of the dynamical mean field theory (DMFT), which treats quantum fluctuations in the time domain and works directly in the thermodynamic limit. The method reduces the complexity of the calculation via a mapping to a self-consistent impurity problem, which becomes exact in infinite dimensions. Particular emphasis is placed on a detailed derivation of the formalism, and on a discussion of numerical techniques, which enable solutions of the effective nonequilibrium DMFT impurity problem. Insights gained into the properties of the infinite-dimensional Hubbard model under strong nonequilibrium conditions are summarized. These examples illustrate the current ability of the theoretical framework to reproduce and understand fundamental nonequilibrium phenomena, such as the dielectric breakdown of Mott insulators, photodoping, and collapse-and-revival oscillations in quenched systems. Furthermore, remarkable novel phenomena have been predicted by the nonequilibrium DMFT simulations of correlated lattice systems, including dynamical phase transitions and field-induced repulsion-to-attraction conversions.

A Unified Classification of Alien Species Based on the Magnitude of their Environmental Impacts

Abstract: Species moved by human activities beyond the limits of their native geographic ranges into areas in which they do not naturally occur (termed aliens) can cause a broad range of significant changes to recipient ecosystems; however, their impacts vary greatly across species and the ecosystems into which they are introduced. There is therefore a critical need for a standardised method to evaluate, compare, and eventually predict the magnitudes of these different impacts. Here, we propose a straightforward system for classifying alien species according to the magnitude of their environmental impacts, based on the mechanisms of impact used to code species in the International Union for Conservation of Nature (IUCN) Global Invasive Species Database, which are presented here for the first time. The classification system uses five semi-quantitative scenarios describing impacts under each mechanism to assign species to different levels of impact-ranging from Minimal to Massive-with assignment corresponding to the highest level of deleterious impact associated with any of the mechanisms. The scheme also includes categories for species that are Not Evaluated, have No Alien Population, or are Data Deficient, and a method for assigning uncertainty to all the classifications. We show how this classification system is applicable at different levels of ecological complexity and different spatial and temporal scales, and embraces existing impact metrics. In fact, the scheme is analogous to the already widely adopted and accepted Red List approach to categorising extinction risk, and so could conceivably be readily integrated with existing practices and policies in many regions.

Comparison of the properties of cellulose nanocrystals and cellulose nanofibrils isolated from bacteria, tunicate, and wood processed using acid, enzymatic, mechanical, and oxidative methods

Abstract: This work describes the measurement and comparison of several important properties of native cellulose nanocrystals (CNCs) and cellulose nanofibrils (CNFs), such as crystallinity, morphology, aspect ratio, and surface chemistry. Measurement of the fundamental properties of seven different CNCs/CNFs, from raw material sources (bacterial, tunicate, and wood) using typical hydrolysis conditions (acid, enzymatic, mechanical, and 2,2,6,6-tetramethylpiperidinyl-1-oxyl (TEMPO)-mediated oxidation), was accomplished using a variety of measurement methods. Atomic force microscopy (AFM), transmission electron microscopy (TEM), and 13C cross-polarization magic angle spinning (CPMAS) nuclear magnetic resonance (NMR) spectroscopy were used to conclude that CNCs, which are rodlike in appearance, have a higher crystallinity than CNFs, which are fibrillar in appearance. CNC aspect ratio distributions were measured and ranged from 148 ± 147 for tunicate-CNCs to 23 ± 12 for wood-CNCs. Hydrophobic interactions, measured usin...

On the structural stability of mutualistic systems

Abstract: In theoretical ecology, traditional studies based on dynamical stability and numerical simulations have not found a unified answer to the effect of network architecture on community persistence. Here, we introduce a mathematical framework based on the concept of structural stability to explain such a disparity of results. We investigated the range of conditions necessary for the stable coexistence of all species in mutualistic systems. We show that the apparently contradictory conclusions reached by previous studies arise as a consequence of overseeing either the necessary conditions for persistence or its dependence on model parameterization. We show that observed network architectures maximize the range of conditions for species coexistence. We discuss the applicability of structural stability to study other types of interspecific interactions.

Worldwide dissemination of the NDM-type carbapenemases in Gram-negative bacteria.

Abstract: The emergence of one of the most recently described carbapenemases, namely, the New Delhi metallo-lactamase (NDM-1), constitutes a critical and growingly important medical issue. This resistance trait compromises the efficacy of almost all lactams (except aztreonam), including the last resort carbapenems. Therapeutical options may remain limited mostly to colistin, tigecycline, and fosfomycin. The main known reservoir of NDM producers is the Indian subcontinent whereas a secondary reservoir seems to have established the Balkans regions and the Middle East. Although the spread of bla NDM-like genes (several variants) is derived mostly by conjugative plasmids in Enterobacteriaceae, this carbapenemase has also been identified in P. aeruginosa and Acinetobacter spp. Acinetobacter sp. may play a pivotal role for spreading bla NDM genes for its natural reservoir to Enterobacteriaceae. Rapid diagnostic techniques (Carba NP test) and screening of carriers are the cornerstone to try to contain this outbreak which threatens the efficacy of the modern medicine.

Different endocytotic uptake mechanisms for nanoparticles in epithelial cells and macrophages

Abstract: Precise knowledge regarding cellular uptake of nanoparticles is of great importance for future biomedical applications. Four different endocytotic uptake mechanisms, that is, phagocytosis, macropinocytosis, clathrin- and caveolin-mediated endocytosis, were investigated using a mouse macrophage (J774A.1) and a human alveolar epithelial type II cell line (A549). In order to deduce the involved pathway in nanoparticle uptake, selected inhibitors specific for one of the endocytotic pathways were optimized regarding concentration and incubation time in combination with fluorescently tagged marker proteins. Qualitative immunolocalization showed that J774A.1 cells highly expressed the lipid raft-related protein flotillin-1 and clathrin heavy chain, however, no caveolin-1. A549 cells expressed clathrin heavy chain and caveolin-1, but no flotillin-1 uptake-related proteins. Our data revealed an impeded uptake of 40 nm polystyrene nanoparticles by J774A.1 macrophages when actin polymerization and clathrin-coated pit formation was blocked. From this result, it is suggested that macropinocytosis and phagocytosis, as well as clathrin-mediated endocytosis, play a crucial role. The uptake of 40 nm nanoparticles in alveolar epithelial A549 cells was inhibited after depletion of cholesterol in the plasma membrane (preventing caveolin-mediated endocytosis) and inhibition of clathrin-coated vesicles (preventing clathrin-mediated endocytosis). Our data showed that a combination of several distinguishable endocytotic uptake mechanisms are involved in the uptake of 40 nm polystyrene nanoparticles in both the macrophage and epithelial cell line.

Defining the Impact of Non-Native Species

Abstract: Non-native species cause changes in the ecosystems to which they are introduced. These changes, or some of them, are usually termed impacts; they can be manifold and potentially damaging to ecosystems and biodiversity. However, the impacts of most non-native species are poorly understood, and a synthesis of available information is being hindered because authors often do not clearly define impact. We argue that explicitly defining the impact of non-native species will promote progress toward a better understanding of the implications of changes to biodiversity and ecosystems caused by non-native species; help disentangle which aspects of scientific debates about non-native species are due to disparate definitions and which represent true scientific discord; and improve communication between scientists from different research disciplines and between scientists, managers, and policy makers. For these reasons and based on examples from the literature, we devised seven key questions that fall into 4 categories: directionality, classification and measurement, ecological or socio-economic changes, and scale. These questions should help in formulating clear and practical definitions of impact to suit specific scientific, stakeholder, or legislative contexts.

Hallin and Mancini Revisited: Four Empirical Types of Western Media Systems

Abstract: The analysis of media systems has become a cornerstone in the field of comparative communication research. Ten years after its publication, we revisit the landmark study in the field, Hallin and Mancini's “Comparing Media Systems”, and operationalize its framework for standardized measurement. The study at hand is, to the best of our knowledge, the first to comprehensively validate the original dimensions and models using aggregated data from the same sample of Western countries. Three out of four dimensions of media systems show relatively high levels of internal consistency, but “role of the state” should be disaggregated into 3 subdimensions. A cluster analysis reveals 4 empirical types of media systems that differentiate and extend the original typology.

Work–Family Boundary Dynamics

Abstract: Theory, constructs, and research with regard to individual work–family boundary management dynamics are reviewed with the goal of promoting a greater understanding and integration of the existing literature. The article begins by noting trends that have contributed to interest in the topic, and then outlines major theoretical perspectives on boundary management and boundary characteristics, integration/segmentation, and associated constructs. It next notes limitations of existing research and concludes with recommendations for future research.

The cuticle and plant defense to pathogens

Abstract: The cuticle provides a physical barrier against water loss and protects against irradiation, xenobiotics, and pathogens. Components of the cuticle are perceived by invading fungi and activate developmental processes during pathogenesis. In addition, cuticle alterations of various types induce a syndrome of reactions that often results in resistance to necrotrophs. This article reviews the current knowledge on the role of the cuticle in relation to the perception of pathogens and activation of defenses.

Phosphorus and nitrogen regulate arbuscular mycorrhizal symbiosis in petunia hybrida

Abstract: Phosphorus and nitrogen are essential nutrient elements that are needed by plants in large amounts. The arbuscular mycorrhizal symbiosis between plants and soil fungi improves phosphorus and nitrogen acquisition under limiting conditions. On the other hand, these nutrients influence root colonization by mycorrhizal fungi and symbiotic functioning. This represents a feedback mechanism that allows plants to control the fungal symbiont depending on nutrient requirements and supply. Elevated phosphorus supply has previously been shown to exert strong inhibition of arbuscular mycorrhizal development. Here, we address to what extent inhibition by phosphorus is influenced by other nutritional pathways in the interaction between Petunia hybrida and R. irregularis. We show that phosphorus and nitrogen are the major nutritional determinants of the interaction. Interestingly, the symbiosis-promoting effect of nitrogen starvation dominantly overruled the suppressive effect of high phosphorus nutrition onto arbuscular mycorrhiza, suggesting that plants promote the symbiosis as long as they are limited by one of the two major nutrients. Our results also show that in a given pair of symbiotic partners (Petunia hybrida and R. irregularis), the entire range from mutually symbiotic to parasitic can be observed depending on the nutritional conditions. Taken together, these results reveal complex nutritional feedback mechanisms in the control of root colonization by arbuscular mycorrhizal fungi.

Identifying influential spreaders by weighted LeaderRank

Abstract: Identifying influential spreaders is crucial for understanding and controlling spreading processes on social networks. Via assigning degree-dependent weights onto links associated with the ground node, we proposed a variant to a recent ranking algorithm named LeaderRank (Lu et al., 2011). According to the simulations on the standard SIR model, the weighted LeaderRank performs better than LeaderRank in three aspects: (i) the ability to find out more influential spreaders; (ii) the higher tolerance to noisy data; and (iii) the higher robustness to intentional attacks.

Mechanically-compliant intracortical implants reduce the neuroinflammatory response

Abstract: Objective. The mechanisms underlying intracortical microelectrode encapsulation and failure are not well understood. A leading hypothesis implicates the role of the mechanical mismatch between rigid implant materials and the much softer brain tissue. Previous work has established the benefits of compliant materials on reducing early neuroinflammatory events. However, recent studies established late onset of a disease-like neurodegenerative state. Approach. In this study, we implanted mechanically-adaptive materials, which are initially rigid but become compliant after implantation, to investigate the long-term chronic neuroinflammatory response to compliant intracortical microelectrodes. Main results. Three days after implantation, during the acute healing phase of the response, the tissue response to the compliant implants was statistically similar to that of chemically matched stiff implants with much higher rigidity. However, at two, eight, and sixteen weeks post-implantation in the rat cortex, the compliant implants demonstrated a significantly reduced neuroinflammatory response when compared to stiff reference materials. Chronically implanted compliant materials also exhibited a more stable blood-brain barrier than the stiff reference materials. Significance. Overall, the data show strikingly that mechanically-compliant intracortical implants can reduce the neuroinflammatory response in comparison to stiffer systems.

Estimating the volume of glaciers in the Himalayan–Karakoram region using different methods

Abstract: Ice volume estimates are crucial for assessing water reserves stored in glaciers. Due to its large glacier coverage, such estimates are of particular interest for the Himalayan-Karakoram (HK) region. In this study, different existing methodologies are used to estimate the ice reserves: three area-volume relations, one slope-dependent volume estimation method, and two ice-thickness distribution models are applied to a recent, detailed, and complete glacier inventory of the HK region, spanning over the period 2000-2010 and revealing an ice coverage of 40 775 km(2). An uncertainty and sensitivity assessment is performed to investigate the influence of the observed glacier area and important model parameters on the resulting total ice volume. Results of the two ice-thickness distribution models are validated with local ice-thickness measurements at six glaciers. The resulting ice volumes for the entire HK region range from 2955 to 4737 km(3), depending on the approach. This range is lower than most previous estimates. Results from the ice thickness distribution models and the slope-dependent thickness estimations agree well with measured local ice thicknesses. However, total volume estimates from area-related relations are larger than those from other approaches. The study provides evidence on the significant effect of the selected method on results and underlines the importance of a careful and critical evaluation.

Mechanochemistry with metallosupramolecular polymers.

Abstract: The transduction of mechanical force into useful chemical reactions is an emerging design approach to impart soft materials with new functions. Here, we report that mechanochemical transductions can be achieved in metallosupramolecular polymers. We show that both reversible and irreversible reactions are possible and useful to create mechanically responsive materials that display new functions. The metallopolymer studied was a cross-linked network assembled from a europium salt and a telechelic poly(ethylene-co-butylene) with 2,6-bis(1′-methylbenzimidazolyl)pyridine (Mebip) ligands at the termini. The Eu3+ complexes serve both as mechanically responsive binding motifs and as built-in optical probes that can monitor the extent of (dis)assembly due to their characteristic photoluminescent properties. Indeed, dose-dependent and reversible metal–ligand dissociation occurs upon exposure to ultrasound in solution. The absence of ultrasound-induced dissociation of a low-molecular weight model complex and in-dept...

Differential effects of non-REM and REM sleep on memory consolidation?

Abstract: Sleep benefits memory consolidation. Previous theoretical accounts have proposed a differential role of slow-wave sleep (SWS), rapid-eye-movement (REM) sleep, and stage N2 sleep for different types of memories. For example the dual process hypothesis proposes that SWS is beneficial for declarative memories, whereas REM sleep is important for consolidation of non-declarative, procedural and emotional memories. In fact, numerous recent studies do provide further support for the crucial role of SWS (or non-REM sleep) in declarative memory consolidation. However, recent evidence for the benefit of REM sleep for non-declarative memories is rather scarce. In contrast, several recent studies have related consolidation of procedural memories (and some also emotional memories) to SWS (or non-REM sleep)-dependent consolidation processes. We will review this recent evidence, and propose future research questions to advance our understanding of the role of different sleep stages for memory consolidation.

Functions of Arginase Isoforms in Macrophage Inflammatory Responses: Impact on Cardiovascular Diseases and Metabolic Disorders

Abstract: Macrophages play a paramount role in immunity and inflammation-associated diseases, including infections, cardiovascular diseases, obesity‐associated metabolic imbalances and cancer Compelling evidence from studies of recent years demonstrates that macrophages are heterogeneous and undergo heterogeneous phenotypic changes in response to microenvironmental stimuli The M1 Killer type response and the M2 Repair type response are best known, and are two extreme examples Among other markers, inducible nitric oxide synthase (iNOS) and type-I arginase (Arg-I), the enzymes that are involved in L-arginine/nitric oxide (NO) metabolism, are associated with the M1 and M2 phenotype, respectively, and therefore widely used as the markers for characterization of the two macrophage phenotypes There is also a type-II arginase (Arg-II) which is expressed in macrophages and prevalently viewed as having the same function as Arg-I in the cells In contrast to Arg-I, little information on the role of Arg‐II in macrophage inflammatory responses is available Emerging evidence, however, suggests differential roles of Arg-I and Arg-II in regulating macrophage functions In this article, we will review recent developments on the functional roles of the two arginase isoforms in regulation of macrophage inflammatory responses by focusing on their impact on the pathogenesis of cardiovascular diseases and metabolic disorders

Resistance to Colistin Associated with a Single Amino Acid Change in Protein PmrB among Klebsiella pneumoniae Isolates of Worldwide Origin

Abstract: A series of colistin-resistant Klebsiella pneumoniae isolates recovered from different countries was investigated in order to evaluate the involvement of the PmrA/PmrB two-component system in this resistance. Six isolates possessed a mutated PmrB protein, which is encoded by the pmrBgene, part of thepmrCABoperon involved in lipopolysaccharide modification. The same amino acid substitution (Thr157Pro) in PmrB was identified in the six isolates. The six isolates belonged to four distinct clonal groups, recovered in South Africa (sequence type 14 [ST14]), Turkey (ST101), and Colombia (ST258 and ST15). Three out of the four clones produced a carbapenemase, OXA-181, OXA-48, or KPC-3, while a single isolate did not produce any carbapenemase. Expression assays revealed an overexpression of the pmrA(70-fold),pmrB(70-fold),pmrC(170-fold), and pmrK(40-fold) genes in the pmrB-mutated isolate compared to expression of the pmrB wild-type isogenic K. pneumoniae isolate, confirming that the PmrB substitution was responsible for increased expression levels of those genes. Complementation assays leading to the expression of a wild-type PmrB protein restored the susceptibility to colistin in all isolates, confirming that the substitution in PmrB was responsible for the resistance phenotype. This study identified a key amino acid located in the PmrB protein as being responsible for the overexpression of pmrCABandpmrHFIJKLMoperons, leading to resistance to colistin.

Glaciers and Climate Change

Abstract: Concurrent with atmospheric warming glaciers around the world are rapidly retreating, thinning, and losing mass. While total volume compared with the ice sheets in Greenland and Antarctica is small, glaciers outside the ice sheets have contributed significantly to recent global sea level rise. On average, these glaciers experienced only slightly negative mass budgets in the 1960s–80s, but mass loss has increased considerably since. While air temperature is the primary driver of global glacier mass loss, many feedback mechanisms, for example, due to changing glacier geometry, as well as ice–water interactions at marine- or lake-terminating glacier fronts, complicate the glacier response. Advances of individual glaciers are rare and often linked to dynamical processes largely unrelated to climate. Globally, glaciers have been projected to lose approximately 18%–36% of their 2015 ice volume by the end of the 21st century depending on the emission pathways. Continued monitoring of the world's glaciers using in situ and satellite observations and further studies to advance process understanding and model development are needed to reduce the uncertainties in glacier mass–change assessments and projections.

Light-Induced Bonding and Debonding with Supramolecular Adhesives

Abstract: Light-responsive supramolecular polymers were applied as reversible adhesives that permit bonding and debonding on demand features. A telechelic poly(ethylene-co-butylene) (PEB) was functionalized with either self-complementary hydrogen-bonding ureidopyrimidinone (UPy) motifs (UPy-PEB-UPy) or 2,6-bis(1′-methylbenzimidazolyl)-pyridine (Mebip) ligands (Mebip-PEB-Mebip), which can coordinate to metal ions (Zn(NTf2)2) and form a metallosupramolecular polymer with the sum formula [Znx(Mebip-PEB-Mebip)](NTf2)2x, with x ≈ 1. In the latter case, light-heat conversion is facilitated by the ultraviolet (UV) light-absorbing metal-ligand motifs, while in the case of UPy-PEB-UPy a UV absorber was added for this purpose. Single lap joints were prepared by sandwiching films of the supramolecular polymers of a thickness of 80–100 μm between two glass, quartz, or stainless steel substrates and bonded by exposure to either UV light (320–390 nm, 900 mW/cm2) or heat (80 or 200 °C for UPy-PEB-UPy and the metallopolymer, respe...

Aging causes a reorganization of cortical and spinal control of posture

Abstract: Classical studies in animal preparations suggest a strong role for spinal control of posture. In humans it is now established that the cerebral cortex contributes to postural control of unperturbed and perturbed standing. The age-related degeneration and accompanying functional changes in the brain, reported so far mainly in conjunction with simple manual motor tasks, may also affect the mechanisms that control complex motor tasks involving posture. This review outlines the age-related structural and functional changes at spinal and cortical levels and provides a mechanistic analysis of how such changes may be linked to the behaviorally manifest postural deficits in old adults. The emerging picture is that the age-related reorganization in motor control during voluntary tasks, characterized by differential modulation of spinal reflexes, greater cortical activation and cortical disinhibition, is also present during postural tasks. We discuss the possibility that this reorganization underlies the increased coactivation and dual task interference reported in elderly. Finally, we propose a model for future studies to unravel the structure-function-behavior relations in postural control and aging.

Genetic diversity in caribou linked to past and future climate change

Abstract: Caribou populations that have experienced a relatively stable climatic history have high genetic diversity and occur in regions where climate stability is expected to continue. These findings, based on analyses of molecular data, predicted species distributions and a diffusion model, provide insight into the role of past and future climate change in controlling species’ genetic structure and evolutionary potential.

The inter‐kingdom volatile signal indole promotes root development by interfering with auxin signalling

Abstract: Recently, emission of volatile organic compounds (VOCs) has emerged as a mode of communication between bacteria and plants. Although some bacterial VOCs that promote plant growth have been identified, their underlying mechanism of action is unknown. Here we demonstrate that indole, which was identified using a screen for Arabidopsis growth promotion by VOCs from soil-borne bacteria, is a potent plant-growth modulator. Its prominent role in increasing the plant secondary root network is mediated by interfering with the auxin-signalling machinery. Using auxin reporter lines and classic auxin physiological and transport assays we show that the indole signal invades the plant body, reaches zones of auxin activity and acts in a polar auxin transport-dependent bimodal mechanism to trigger differential cellular auxin responses. Our results suggest that indole, beyond its importance as a bacterial signal molecule, can serve as a remote messenger to manipulate plant growth and development.

Quaternary coral reef refugia preserved fish diversity

Abstract: The most prominent pattern in global marine biogeography is the biodiversity peak in the Indo-Australian Archipelago. Yet the processes that underpin this pattern are still actively debated. By reconstructing global marine paleoenvironments over the past 3 million years on the basis of sediment cores, we assessed the extent to which Quaternary climate fluctuations can explain global variation in current reef fish richness. Comparing global historical coral reef habitat availability with the present-day distribution of 6316 reef fish species, we find that distance from stable coral reef habitats during historical periods of habitat loss explains 62% of the variation in fish richness, outweighing present-day environmental factors. Our results highlight the importance of habitat persistence during periods of climate change for preserving marine biodiversity.