Genetic diversity of Swiss sheep breeds in the focus of conservation research

There is constant pressure to improve evaluation of animal genetic resources in order to prevent their erosion. Maintaining the integrity of livestock species as well as their genetic diversity is of paramount interest for long-term agricultural policies. One major use of DNA techniques in conservation is to reveal genetic diversity within and between populations. Forty-one microsatellites were analysed to assess genetic diversity in nine Swiss sheep breeds and to measure the loss of the overall diversity when one breed would become extinct. The expected heterozygosities varied from 0.65 to 0.74 and 10.8% of the total genetic diversity can be explained by the variation among breeds. Based on the proportion of shared alleles, each of the nine breeds were clearly defined in their own cluster in the neighbour-joining tree describing the relationships among the breeds. Bayesian clustering methods assign individuals to groups based on their genetic similarity and infer the number of populations. In STRUCTURE, this approach pooled the Valais Blacknose and the Valais Red. With BAPS method the two Valais sheep breeds could be separated. Caballero & Toro approach (2002) was used to calculate the loss or gain of genetic diversity when each of the breeds would be removed from the set. The changes in diversity based on between-breed variation ranged from -12.2% (Valais Blacknose) to 0% (Swiss Black Brown Mountain and Mirror Sheep); based on within-breed diversity the removal of a breed could also produce an increase in diversity (-0.6% to + 0.6%). Allelic richness ranged from 4.9 (Valais Red) to 6.7 (Brown Headed Meat sheep and Red Engadine Sheep). Breed conservation decisions cannot be limited to genetic diversity alone. In Switzerland, conservation goals are embedded in the desire to carry the cultural legacy over to future generations.

Nicoletella semolina gen. nov., sp. nov., a new member of Pasteurellaceae isolated from horses with airway disease

Gram-negative, nonmotile bacteria that are catalase, oxidase, and urease positive are regularly isolated from the airways of horses with clinical signs of respiratory disease. On the basis of the findings by a polyphasic approach, we propose that these strains be classified as Nicoletella semolina gen. nov, sp. nov., a new member of the family Pasteurellaceae. N. semolina reduces nitrate to nitrite but is otherwise biochemically inert; this includes the lack of an ability to ferment glucose and other sugars. Growth is fastidious, and the isolates have a distinctive colony morphology, with the colonies being dry and waxy and looking like a semolina particle that can be moved around on an agar plate without losing their shape. DNA-DNA hybridization data and multilocus phylogenetic analysis, including 16S rRNA gene (rDNA), rpoB, and infB sequencing, clearly placed N. semolina as a new genus in the family Pasteurellaceae. In all the phylogenetic trees constructed, N. semolina is on a distinct branch displaying approximately 5% 16S rDNA, approximately 16% rpoB, and approximately 20% infB sequence divergence from its nearest relative within the family Pasteurellaceae. High degrees of conservation of the 16S rDNA (99.8%), rpoB (99.6%), and infB (99.7%) sequences exist within the species, indicating that N. semolina isolates not only are phenotypically homogeneous but also are genetically homogeneous. The type strain of N. semolina is CCUG43639(T) (DSM16380(T)).

Strong Down-Valley Low-Level Jets over the Atacama Desert: Observational Characterization

The near-surface wind and temperature regime at three points in the Atacama Desert of northern Chile is described using two-year multi-level measurements from 80-m towers located in an altitude range between 2100 and 2700 m ASL. The data reveal the frequent development of strong nocturnal drainage flows at all sites. Down-valley nose-shaped wind speed profiles are observed with maximum values occurring at heights between 20 m and 60 m AGL. The flow intensity shows considerable inter-daily variability and a seasonal modulation of maximum speeds, which in the cold season can attain hourly average values larger than 20 m s−1. Turbulent mixing appears significant over the full tower layer, affecting the curvature of the nighttime temperature profile and possibly explaining the observed increase of surface temperatures in the down-valley direction. Nocturnal valley winds and temperatures are weakly controlled by upper-air conditions observed at the nearest aerological station. Estimates of terms in the momentum budget for the development and the quasi-stationary phases of the down-valley flows suggest that the pressure gradient force due to the near-surface cooling along the sloping valley axes plays an important role in these drainage flows. A scale for the jet nose height of equilibrium turbulent down-slope jets is proposed, based on surface friction velocity and surface inversion intensity. At one of the sites this scale explains about 70% of the case-to-case observed variance of jet nose heights. Further modeling and observational work is needed, however, in order to better define the dynamics, extent and turbulence structure of this flow system, which has significant wind-energy, climatic and environmental implications.

Geographical Dialectology

This chapter examines how linguists have investigated the very obvious fact that different places house different dialects. We will not look at the results of such work nor how they have been used to answer linguistic and sociolinguistic questions (see Britain 2009, in press). Here we simply examine the steps dialectologists take and have taken to conduct multi-locality research on language variation. In order to do so, five studies from different time periods are presented and critiqued, examining a number of key methodological elements in each: 1. The aim of geographical dialectology is to examine variation across space, in different places. How do dialectologists then decide which places in that space to analyse? Why choose one village and not its neighbour? Why avoid that city? This question goes to the very heart of the geographical motivation of the research. 2. What sorts of speakers will be sampled from these locations? 3. What type of data is to be collected from these speakers? 4. In what circumstances is that data to be recorded? Who will collect it, in what setting and how will the voices of the speakers be captured for later analysis? As we will see, dialectological methodologies always involve compromises, no approach is ever flawless. Ultimately, a good number of difficult practical decisions have to be taken – how long can this research take, and what are the financial restrictions on the project? As we will see geographical dialectology is probably the most expensive and the most time consuming of all forms of language variation research.

A reliable, traffic-adaptive and energy-efficient link layer for wireless sensor networks

The paper presents a link layer stack for wireless sensor networks, which consists of the Burst-aware Energy-efficient Adaptive Medium access control (BEAM) and the Hop-to-Hop Reliability (H2HR) protocol. BEAM can operate with short beacons to announce data transmissions or include data within the beacons. Duty cycles can be adapted by a traffic prediction mechanism indicating pending packets destined for a node and by estimating its wake-up times. H2HR takes advantage of information provided by BEAM such as neighbour information and transmission information to perform per-hop congestion control. We justify the design decisions by measurements in a real-world wireless sensor network testbed and compare the performance with other link layer protocols.

Guaranteed greedy routing in overlay networks

Greedy routing can be used in mobile ad-hoc networks as geographic routing protocol. This paper proposes to use greedy routing also in overlay networks by positioning overlay nodes into a multi-dimensional Euclidean space. Greedy routing can only be applied when a routing decision makes progress towards the final destination. Our proposed overlay network is built such that there will be always progress at each forwarding node. This is achieved by constructing at each node a so-called nearest neighbor convex set (NNCS). NNCSs can be used for various applications such as multicast routing, service discovery and Quality-of-Service routing. NNCS has been compared with Pastry, another topology-aware overlay network. NNCS has superior relative path stretches indicating the optimality of a path.

Planet formation models: the interplay with the planetesimal disc

Context. According to the sequential accretion model (or core-nucleated accretion model), giant planet formation is based first on the formation of a solid core which, when massive enough, can gravitationally bind gas from the nebula to form the envelope. The most critical part of the model is the formation time of the core: to trigger the accretion of gas, the core has to grow up to several Earth masses before the gas component of the protoplanetary disc dissipates. Aims: We calculate planetary formation models including a detailed description of the dynamics of the planetesimal disc, taking into account both gas drag and excitation of forming planets. Methods: We computed the formation of planets, considering the oligarchic regime for the growth of the solid core. Embryos growing in the disc stir their neighbour planetesimals, exciting their relative velocities, which makes accretion more difficult. Here we introduce a more realistic treatment for the evolution of planetesimals' relative velocities, which directly impact on the formation timescale. For this, we computed the excitation state of planetesimals, as a result of stirring by forming planets, and gas-solid interactions. Results: We find that the formation of giant planets is favoured by the accretion of small planetesimals, as their random velocities are more easily damped by the gas drag of the nebula. Moreover, the capture radius of a protoplanet with a (tiny) envelope is also larger for small planetesimals. However, planets migrate as a result of disc-planet angular momentum exchange, with important consequences for their survival: due to the slow growth of a protoplanet in the oligarchic regime, rapid inward type I migration has important implications on intermediate-mass planets that have not yet started their runaway accretion phase of gas. Most of these planets are lost in the central star. Surviving planets have masses either below 10 M⊕ or above several Jupiter masses. Conclusions: To form giant planets before the dissipation of the disc, small planetesimals (~0.1 km) have to be the major contributors of the solid accretion process. However, the combination of oligarchic growth and fast inward migration leads to the absence of intermediate-mass planets. Other processes must therefore be at work to explain the population of extrasolar planets that are presently known.

Hillslope Processes in Temperate Environments

In this chapter, we discuss the factors controlling the mechanisms and rates of hillslope failure in temperate environments with a major focus on the Swiss Alps. We frame this presentation by defining Alpine hillslopes as either strength- or transport-limited hillslopes. We organize this discussion into individual sections that outline how hillslope processes are related to (1) the mechanical strength and bedding orientation of bedrock, (2) the competition between channelized and hillslope processes, (3) hillslope–channel coupling relationships, and (4) fluvial erosion rates. We find that hillslope angles depend on bedrock strength along nonincised channels, but are not related to this parameter in inner gorges. We also find that valley flanks host deep-seated landslides where the bedrock dips parallel to the topographic slope. In the opposite case, the valley sides are dissected by a network of bedrock channels bordered by strength-limited hillslopes. In this chapter, we illustrate that a high ratio between sediment discharge on hillslopes and in channels explains the formation of smooth landscapes with low channel densities and long response times. This chapter considers the formation of strength-limited hillslopes as a consequence of an upslope-directed coupling between channels and hillslopes. The chapter also discusses that soil-mantled hillslopes occur where fluvial incision rates are less than weathering rates of bedrock, which are limited to 0.1–0.3 mm yr−1. We finally present evidence for a decreasing trend of hillslope-derived sediment discharge during the Holocene, but predict an opposite trend in the nearest future as winters are warmer and wetter.

Information-Centric Networking in Mobile and Opportunistic Networks

Information Centric Networking (ICN) as an emerging paradigm for the Future Internet has initially been rather focusing on bandwidth savings in wired networks, but there might also be some significant potential to support communication in mobile wireless networks as well as opportunistic network scenarios, where end systems have spontaneous but time-limited contact to exchange data. This chapter addresses the reasoning why ICN has an important role in mobile and opportunistic networks by identifying several challenges in mobile and opportunistic Information-Centric Networks and discussing appropriate solutions for them. In particular, it discusses the issues of receiver and source mobility. Source mobility needs special attention. Solutions based on routing protocol extensions, indirection, and separation of name resolution and data transfer are discussed. Moreover, the chapter presents solutions for problems in opportunistic Information-Centric Networks. Among those are mechanisms for efficient content discovery in neighbour nodes, resume mechanisms to recover from intermittent connectivity disruptions, a novel agent delegation mechanisms to offload content discovery and delivery to mobile agent nodes, and the exploitation of overhearing to populate routing tables of mobile nodes. Some preliminary performance evaluation results of these developed mechanisms are provided.

The importance of biotic interactions and local adaptation for plant response to environmental changes: field evidence along an elevational gradient

Predicting the response of species to environmental changes is a great and on-going challenge for ecologists, and this requires a more in-depth understanding of the importance of biotic interactions and the population structuration in the landscape. Using a reciprocal transplantation experiment, we tested the response of five species to an elevational gradient. This was combined to a neighbour removal treatment to test the importance of local adaptation and biotic interactions. The trait studied was performance measured as survival and biomass. Species response varied along the elevational gradient, but with no consistent pattern. Performance of species was influenced by environmental conditions occurring locally at each site, as well as by positive or negative effects of the surrounding vegetation. Indeed, we observed a shift from competition for biomass to facilitation for survival as a response to the increase in environmental stress occurring in the different sites. Unlike previous studies pointing out an increase of stress along the elevation gradient, our results supported a stress gradient related to water availability, which was not strictly parallel to the elevational gradient. For three of our species, we observed a greater biomass production for the population coming from the site where the species was dominant (central population) compared to population sampled at the limit of the distribution (marginal population). Nevertheless, we did not observe any pattern of local adaptation that could indicate adaptation of populations to a particular habitat. Altogether, our results highlighted the great ability of plant species to cope with environmental changes, with no local adaptation and great variability in response to local conditions. Our study confirms the importance of taking into account biotic interactions and population structure occurring at local scale in the prediction of communities’ responses to global environmental changes.

Functional traits determine plant co-occurrence more than environment or evolutionary relatedness in global drylands

Plant-plant interactions are driven by environmental conditions, evolutionary relationships (ER) and the functional traits of the plants involved. However, studies addressing the relative importance of these drivers are rare, but crucial to improve our predictions of the effects of plant-plant interactions on plant communities and of how they respond to differing environmental conditions. To analyze the relative importance of - and interrelationships among - these factors as drivers of plant-plant interactions, we analyzed perennial plant co-occurrence at 106 dryland plant communities established across rainfall gradients in nine countries. We used structural equation modelling to disentangle the relationships between environmental conditions (aridity and soil fertility), functional traits extracted from the literature, and ER, and to assess their relative importance as drivers of the 929 pairwise plant-plant co-occurrence levels measured. Functional traits, specifically facilitated plants' height and nurse growth form, were of primary importance, and modulated the effect of the environment and ER on plant-plant interactions. Environmental conditions and ER were important mainly for those interactions involving woody and graminoid nurses, respectively. The relative importance of different plant-plant interaction drivers (ER, functional traits, and the environment) varied depending on the region considered, illustrating the difficulty of predicting the outcome of plant-plant interactions at broader spatial scales. In our global-scale study on drylands, plant-plant interactions were more strongly related to functional traits of the species involved than to the environmental variables considered. Thus, moving to a trait-based facilitation/competition approach help to predict that: (1) positive plant-plant interactions are more likely to occur for taller facilitated species in drylands, and (2) plant-plant interactions within woody-dominated ecosystems might be more sensitive to changing environmental conditions than those within grasslands. By providing insights on which species are likely to better perform beneath a given neighbour, our results will also help to succeed in restoration practices involving the use of nurse plants. (C) 2014 Geobotanisches Institut ETH, Stiftung Ruebel. Published by Elsevier GmbH. All rights reserved.

Negative density dependence of seed dispersal and seedling recruitment in a Neotropical palm

Negative density dependence (NDD) of recruitment is pervasive in tropical tree species. We tested the hypotheses that seed dispersal is NDD, due to intraspecific competition for dispersers, and that this contributes to NDD of recruitment. We compared dispersal in the palm Attalea butyracea across a wide range of population density on Barro Colorado Island in Panama and assessed its consequences for seed distributions. We found that frugivore visitation, seed removal and dispersal distance all declined with population density of A. butyracea, demonstrating NDD of seed dispersal due to competition for dispersers. Furthermore, as population density increased, the distances of seeds from the nearest adult decreased, conspecific seed crowding increased and seedling recruitment success decreased, all patterns expected under poorer dispersal. Unexpectedly, however, our analyses showed that NDD of dispersal did not contribute substantially to these changes in the quality of the seed distribution; patterns with population density were dominated by effects due solely to increasing adult and seed density.

AIDS defining opportunistic infections in patients with high CD4 counts in the combination antiretroviral therapy (cART) era: things ain't what they used to be.

INTRODUCTION According to reports from observational databases, classic AIDS-defining opportunistic infections (ADOIs) occur in patients with CD4 counts above 500/µL on and off cART. Adjudication of these events is usually not performed. However, ADOIs are often used as endpoints, for example, in analyses on when to start cART. MATERIALS AND METHODS In the database, Swiss HIV Cohort Study (SHCS) database, we identified 91 cases of ADOIs that occurred from 1996 onwards in patients with the nearest CD4 count >500/µL. Cases of tuberculosis and recurrent bacterial pneumonia were excluded as they also occur in non-immunocompromised patients. Chart review was performed in 82 cases, and in 50 cases we identified CD4 counts within six months before until one month after ADOI and had chart review material to allow an in-depth review. In these 50 cases, we assessed whether (1) the ADOI fulfilled the SHCS diagnostic criteria (www.shcs.ch), and (2) HIV infection with CD4 >500/µL was the main immune-compromising condition to cause the ADOI. Adjudication of cases was done by two experienced clinicians who had to agree on the interpretation. RESULTS More than 13,000 participants were followed in SHCS in the period of interest. Twenty-four (48%) of the chart-reviewed 50 patients with ADOI and CD4 >500/µL had an HIV RNA <400 copies/mL at the time of ADOI. In the 50 cases, candida oesophagitis was the most frequent ADOI in 30 patients (60%) followed by pneumocystis pneumonia and chronic ulcerative HSV disease (Table 1). Overall chronic HIV infection with a CD4 count >500/µL was the likely explanation for the ADOI in only seven cases (14%). Other reasons (Table 1) were ADOIs occurring during primary HIV infection in 5 (10%) cases, unmasking IRIS in 1 (2%) case, chronic HIV infection with CD4 counts <500/µL near the ADOI in 13 (26%) cases, diagnosis not according to SHCS diagnostic criteria in 7 (14%) cases and most importantly other additional immune-compromising conditions such as immunosuppressive drugs in 14 (34%). CONCLUSIONS In patients with CD4 counts >500/ µL, chronic HIV infection is the cause of ADOIs in only a minority of cases. Other immuno-compromising conditions are more likely explanations in one-third of the patients, especially in cases of candida oesophagitis. ADOIs in HIV patients with high CD4 counts should be used as endpoints only with much caution in studies based on observational databases.

Neighbourhood socio-economic position, late presentation and outcomes in people living with HIV in Switzerland.

OBJECTIVES: Inequalities and inequities in health are an important public health concern. In Switzerland, mortality in the general population varies according to the socio-economic position (SEP) of neighbourhoods. We examined the influence of neighbourhood SEP on presentation and outcomes in HIV-positive individuals in the era of combination antiretroviral therapy (cART). METHODS: The neighbourhood SEP of patients followed in the Swiss HIV Cohort Study (SHCS) 2000-2013 was obtained on the basis of 2000 census data on the 50 nearest households (education and occupation of household head, rent, mean number of persons per room). We used Cox and logistic regression models to examine the probability of late presentation, virologic response to cART, loss to follow-up and death across quintiles of neighbourhood SEP. RESULTS: A total of 4489 SHCS participants were included. Presentation with advanced disease [CD4 cell count <200 cells/μl or AIDS] and with AIDS was less common in neighbourhoods of higher SEP: the age and sex-adjusted odds ratio (OR) comparing the highest with the lowest quintile of SEP was 0.71 [95% confidence interval (95% CI) 0.58-0.87] and 0.59 (95% CI 0.45-0.77), respectively. An undetectable viral load at 6 months of cART was more common in the highest than in the lowest quintile (OR 1.52; 95% CI 1.14-2.04). Loss to follow-up, mortality and causes of death were not associated with neighbourhood SEP. CONCLUSION: Late presentation was more common and virologic response to cART less common in HIV-positive individuals living in neighbourhoods of lower SEP, but in contrast to the general population, there was no clear trend for mortality.

Microscopic theory of cooperative spin crossover: Interaction of molecular modes with phonons

In this article, we present a new microscopic theoretical approach to the description of spin crossover in molecular crystals. The spin crossover crystals under consideration are composed of molecular fragments formed by the spin-crossover metal ion and its nearest ligand surrounding and exhibiting well defined localized (molecular) vibrations. As distinguished from the previous models of this phenomenon, the developed approach takes into account the interaction of spin-crossover ions not only with the phonons but also a strong coupling of the electronic shells with molecular modes. This leads to an effective coupling of the local modes with phonons which is shown to be responsible for the cooperative spin transition accompanied by the structural reorganization. The transition is characterized by the two order parameters representing the mean values of the products of electronic diagonal matrices and the coordinates of the local modes for the high- and low-spin states of the spin crossover complex. Finally, we demonstrate that the approach provides a reasonable explanation of the observed spin transition in the [Fe(ptz)6](BF4)2 crystal. The theory well reproduces the observed abrupt low-spin → high-spin transition and the temperature dependence of the high-spin fraction in a wide temperature range as well as the pronounced hysteresis loop. At the same time within the limiting approximations adopted in the developed model, the evaluated high-spin fraction vs. T shows that the cooperative spin-lattice transition proves to be incomplete in the sense that the high-spin fraction does not reach its maximum value at high temperature.