The human IgG anti-carbohydrate repertoire exhibits a universal architecture and contains specificity for microbial attachment sites.

Despite the paradigm that carbohydrates are T cell-independent antigens, isotype-switched glycan-specific immunoglobulin G (IgG) antibodies and polysaccharide-specific T cells are found in humans. We used a systems-level approach combined with glycan array technology to decipher the repertoire of carbohydrate-specific IgG antibodies in intravenous and subcutaneous immunoglobulin preparations. A strikingly universal architecture of this repertoire with modular organization among different donor populations revealed an association between immunogenicity or tolerance and particular structural features of glycans. Antibodies were identified with specificity not only for microbial antigens but also for a broad spectrum of host glycans that serve as attachment sites for viral and bacterial pathogens and/or exotoxins. Tumor-associated carbohydrate antigens were differentially detected by IgG antibodies, whereas non-IgG2 reactivity was predominantly absent. Our study highlights the power of systems biology approaches to analyze immune responses and reveals potential glycan antigen determinants that are relevant to vaccine design, diagnostic assays, and antibody-based therapies.

Inherited structural controls on fault geometry, architecture and hydrothermal activity: an example from Grimsel Pass, Switzerland

Exhumed faults hosting hydrothermal systems provide direct insight into relationships between faulting and fluid flow, which in turn are valuable for making hydrogeological predictions in blind settings. The Grimsel Breccia Fault (Aar massif, Central Swiss Alps) is a late Neogene, exhumed dextral strike-slip fault with a maximum displacement of 25–45 m, and is associated with both fossil and active hydrothermal circulation. We mapped the fault system and modelled it in three dimensions, using the distinctive hydrothermal mineralisation as well as active thermal fluid discharge (the highest elevation documented in the Alps) to reveal the structural controls on fluid pathway extent and morphology. With progressive uplift and cooling, brittle deformation inherited the mylonitic shear zone network at Grimsel Pass; preconditioning fault geometry into segmented brittle reactivations of ductile shear zones and brittle inter-shear zone linkages. We describe ‘pipe’-like, vertically oriented fluid pathways: (1) within brittle fault linkage zones and (2) through alongstrike- restricted segments of formerly ductile shear zones reactivated by brittle deformation. In both cases, low-permeability mylonitic shear zones that escaped brittle reactivation provide important hydraulic seals. These observations show that fluid flow along brittle fault planes is not planar, but rather highly channelised into sub-vertical flow domains, with important implications for the exploration and exploitation of geothermal energy.

Long-term trends in invertebrate–habitat relationships under protected and fished conditions

Few studies examine the long-term effects of changing predator size and abundance on the habitat associations of resident organisms despite that this knowledge is critical to understand the ecosystem effects of fishing. Marine reserves offer the opportunity to determine ecosystem-level effects of manipulated predator densities, while parallel monitoring of adjacent fished areas allows separating these effects from regional-scale change. Relationships between two measures of benthic habitat structure (reef architecture and topographic complexity) and key invertebrate species were followed over 17 years at fished and protected subtidal rocky reefs associated with two southern Australian marine reserves. Two commercially harvested species, the southern rock lobster (Jasus edwardsii) and blacklip abalone (Haliotis rubra) were initially weakly associated with habitat structure across all fished and protected sites. The strength of association with habitat for both species increased markedly at protected sites 2 years after marine reserve declaration, and then gradually weakened over subsequent years. The increasing size of rock lobster within reserves apparently reduced their dependency on reef shelters as refuges from predation. Rising predation by fish and rock lobster in the reserves corresponded with weakening invertebrate–habitat relationships for H. rubra and sea urchins (Heliocidaris erythrogramma). These results emphasise that animal–habitat relationships are not necessarily stable through time and highlight the value of marine reserves as reference sites. Our work shows that fishery closures to enhance populations of commercially important and keystone species should be in areas with a range of habitat features to accommodate shifting ecological requirements with ontogenesis.

Truncated recombinant human SP-D attenuates emphysema and type II cell changes in SP-D deficient mice

BACKGROUND: Surfactant protein D (SP-D) deficient mice develop emphysema-like pathology associated with focal accumulations of foamy alveolar macrophages, an excess of surfactant phospholipids in the alveolar space and both hypertrophy and hyperplasia of alveolar type II cells. These findings are associated with a chronic inflammatory state. Treatment of SP-D deficient mice with a truncated recombinant fragment of human SP-D (rfhSP-D) has been shown to decrease the lipidosis and alveolar macrophage accumulation as well as production of proinflammatory chemokines. The aim of this study was to investigate if rfhSP-D treatment reduces the structural abnormalities in parenchymal architecture and type II cells characteristic of SP-D deficiency. METHODS: SP-D knock-out mice, aged 3 weeks, 6 weeks and 9 weeks were treated with rfhSP-D for 9, 6 and 3 weeks, respectively. All mice were sacrificed at age 12 weeks and compared to both PBS treated SP-D deficient and wild-type groups. Lung structure was quantified by design-based stereology at the light and electron microscopic level. Emphasis was put on quantification of emphysema, type II cell changes and intracellular surfactant. Data were analysed with two sided non-parametric Mann-Whitney U-test. MAIN RESULTS: After 3 weeks of treatment, alveolar number was higher and mean alveolar size was smaller compared to saline-treated SP-D knock-out controls. There was no significant difference concerning these indices of pulmonary emphysema within rfhSP-D treated groups. Type II cell number and size were smaller as a consequence of treatment. The total volume of lamellar bodies per type II cell and per lung was smaller after 6 weeks of treatment. CONCLUSION: Treatment of SP-D deficient mice with rfhSP-D leads to a reduction in the degree of emphysema and a correction of type II cell hyperplasia and hypertrophy. This supports the concept that rfhSP-D might become a therapeutic option in diseases that are characterized by decreased SP-D levels in the lung.

Inhibition of integrin alphavbeta6 on cholangiocytes blocks transforming growth factor-beta activation and retards biliary fibrosis progression

BACKGROUND ; AIMS: Integrin alphavbeta6 is highly expressed on certain activated epithelia, where it mediates attachment to fibronectin and serves as coreceptor for the activation of latent transforming growth factor (TGF)-beta1. Because its role in liver fibrosis is unknown, we studied alphavbeta6 function in vitro and explored the antifibrotic potential of the specific alphavbeta6 antagonist EMD527040. METHODS: Experimental liver fibrosis was studied in rats after bile duct ligation (BDL) and in Mdr2(abcb4)(-/-) mice. Different doses of EMD527040 were given to rats from week 2 to 6 after BDL and to Mdr2(-/-) mice from week 4 to 8. Liver collagen was quantified, and expression of alphavbeta6 and fibrosis-related transcripts was determined by quantitative reverse-transcription polymerase chain reaction. alphavbeta6-expressing cells, bile duct proliferation, and apoptosis were assessed histologically. The effect of EMD527040 on cholangiocyte adhesion, proliferation, apoptosis, and TGF-beta1 activation was studied in vitro. RESULTS: alphavbeta6 was highly expressed on proliferating bile duct epithelia in fibrosis, with 100-fold increased transcript levels in advanced fibrosis. EMD527040 attenuated bile ductular proliferation and peribiliary collagen deposition by 40%-50%, induced down-regulation of fibrogenic and up-regulation of fibrolytic genes, and improved liver architecture and function. In vitro alphavbeta6 inhibition reduced activated cholangiocyte proliferation, their adhesion to fibronectin, and endogenous activation of TGF-beta1 by 50% but did not affect bile duct apoptosis. CONCLUSIONS: Integrin alphavbeta6 is strongly up-regulated in proliferating bile duct epithelia and drives fibrogenesis via adhesion to fibronectin and auto/paracrine TGF-beta1 activation. Pharmacologic inhibition of alphavbeta6 potently inhibits the progression of primary and secondary biliary fibrosis.

The Long Tail of the Rainbow Serpent: New Technologies and the Protection and Promotion of Traditional Cultural Expressions

New technologies, in particular those stemming from digitisation, allow amongst other things the production of perfect copies, instantaneous and ubiquitous distribution of and easy access to information with no real location restrictions. The effects of these technological advances have largely been perceived as negative for the protection of traditional cultural expressions (TCE), both because of the peculiarities of the digital networked environment and because of the lack of appropriate intellectual property protection models for TCE. The purpose of this article is, while accounting for the diversity and complexity of issues related to TCE, to reveal a more positive side of digital technologies. It shows the potential of these to be proactively applied and the further reaching possibilities for designing an efficient multi-level and multi-faceted toolbox for the protection and promotion of TCE in the digital ecology.

The chemokine CCL20 and its receptor CCR6 in human malignancy with focus on colorectal cancer

Chemokines are a superfamily of small chemotactic cytokines, which interact with their G-protein-coupled receptors. These interactions regulate multiple physiological functions, particularly tissue architecture and compartment-specific migration of white blood cells. It has been found that the chemokine/chemokine receptor system has been utilized by cancer cells for migration and metastasis. The chemokine receptor CCR6 is expressed in colorectal cancer and several other cancer types, and stimulation by its physiological chemokine ligand CCL20 has been reported to promote cancer cell proliferation and migration in vitro. Moreover, CCR6/CCL20 interactions apparently play a role in organ selective liver metastasis of colorectal cancer. Here, we review the literature on expression patterns of CCL20 and CCR6 and their physiological interactions as well as the currently presumed role of CCR6 and CCL20 in the formation of colorectal cancer liver metastasis, providing a potential basis for novel treatment strategies.

Computer-aided diagnosis of carotid atherosclerosis based on ultrasound image statistics, laws' texture and neural networks

Quantitative characterisation of carotid atherosclerosis and classification into symptomatic or asymptomatic is crucial in planning optimal treatment of atheromatous plaque. The computer-aided diagnosis (CAD) system described in this paper can analyse ultrasound (US) images of carotid artery and classify them into symptomatic or asymptomatic based on their echogenicity characteristics. The CAD system consists of three modules: a) the feature extraction module, where first-order statistical (FOS) features and Laws' texture energy can be estimated, b) the dimensionality reduction module, where the number of features can be reduced using analysis of variance (ANOVA), and c) the classifier module consisting of a neural network (NN) trained by a novel hybrid method based on genetic algorithms (GAs) along with the back propagation algorithm. The hybrid method is able to select the most robust features, to adjust automatically the NN architecture and to optimise the classification performance. The performance is measured by the accuracy, sensitivity, specificity and the area under the receiver-operating characteristic (ROC) curve. The CAD design and development is based on images from 54 symptomatic and 54 asymptomatic plaques. This study demonstrates the ability of a CAD system based on US image analysis and a hybrid trained NN to identify atheromatous plaques at high risk of stroke.

Geometric properties of the lung parenchyma after postnatal glucocorticoid treatment in rats

While glucocorticoid (GC) administration appears to be beneficial during the acute phase of treatment of neonates at risk of developing chronic lung disease, it is still not clear whether steroid application has an adverse long-term effect on the lung maturation. Thus, the goal of the present work was to analyze GC effects on the pulmonary structure in a rat model where dosage and timing of drug administration were adapted to the therapeutic situation in human neonatology. The animals received daily a maximum of 0.1 mg dexamethasone phosphate per kilogram body weight during the first 4 postnatal days. Investigations were performed at the light microscopic level by means of a digital image analysis system. While there were no differences in the lung architecture between experimental animals and controls on day 4, the earliest time point of observation, we found a widening of airspaces with a concomitant decrease in the alveolar surface area density, representing a loss of parenchymal complexity, on days 10 and 21 in treated rats. On days 36 and 60, however, no alterations in the pulmonary parenchyma could be detected in experimental animals. We conclude from these findings that the GC-induced initial inhibition of development (days 10 and 21) was completely reversed, so that a normal parenchymal architecture and also a normal alveolar surface area density were found in adult rats (days 36 and 60). From the results obtained using the regimen of GC administration described, mimicking more closely the steroid treatment in human neonatology, we conclude that the observed short-term adverse effects on lung development can be fully compensated until adult age.

Valuation of ecosystem goods and services. Part 2: Implications of unpredictable novel change

This is the second part of a two-part paper which offers a new approach to the valuation of ecosystem goods and services. In the first part a simple pre-industrial model was introduced to show how the interdependencies between the three subsystems, society, economy and nature, influence values, and how values change over time. In this second part the assumption of perfect foresight is dropped. I argue that due to novelty and complexity ex ante unpredictable change occurs within the three subsystems society, economy and nature. Again the simple pre-industrial model, which was introduced in part 1, serves as a simple paradigm to show how unpredictable novel change limits the possibility to derive accurate estimates of values.

New Technologies and the Protection and Promotion of Traditional Cultural Expressions

New technologies, in particular those stemming from digitization, allow amongst other things the production of perfect copies, instantaneous and ubiquitous distribution of and easy access to information with no real location restrictions. The effects of these technological advances have largely been perceived as negative for the protection of Traditional Cultural Expressions (TCE), both because of the peculiarities of the digital networked environment and because of the lack of appropriate intellectual property protection models for TCE. The purpose of this article is, while accounting for the diversity and complexity of issues related to TCE, to reveal a more positive side of digital technologies. It shows the potential of these to be proactively applied and the further reaching possibilities for designing an efficient multi-level and multi-faceted toolbox for the protection and promotion of TCE in the digital ecology.

A hybrid method for large-scale short-term scheduling of make-and-pack production processes

Due to the ongoing trend towards increased product variety, fast-moving consumer goods such as food and beverages, pharmaceuticals, and chemicals are typically manufactured through so-called make-and-pack processes. These processes consist of a make stage, a pack stage, and intermediate storage facilities that decouple these two stages. In operations scheduling, complex technological constraints must be considered, e.g., non-identical parallel processing units, sequence-dependent changeovers, batch splitting, no-wait restrictions, material transfer times, minimum storage times, and finite storage capacity. The short-term scheduling problem is to compute a production schedule such that a given demand for products is fulfilled, all technological constraints are met, and the production makespan is minimised. A production schedule typically comprises 500–1500 operations. Due to the problem size and complexity of the technological constraints, the performance of known mixed-integer linear programming (MILP) formulations and heuristic approaches is often insufficient. We present a hybrid method consisting of three phases. First, the set of operations is divided into several subsets. Second, these subsets are iteratively scheduled using a generic and flexible MILP formulation. Third, a novel critical path-based improvement procedure is applied to the resulting schedule. We develop several strategies for the integration of the MILP model into this heuristic framework. Using these strategies, high-quality feasible solutions to large-scale instances can be obtained within reasonable CPU times using standard optimisation software. We have applied the proposed hybrid method to a set of industrial problem instances and found that the method outperforms state-of-the-art methods.

Plant architecture

Plant architecture is species specific, indicating that it is under strict genetic control. Although it is also influenced by environmental conditions such as light, temperature, humidity and nutrient status, here we wish to focus only on the endogenous regulatory principles that control plant architecture. We summarise recent progress in the understanding of the basic patterning mechanisms involved in the regulation of leaf arrangement, the genetic regulation of meristem determinacy, i.e. the decision to stop or continue growth, and the control of branching during vegetative and generative development. Finally, we discuss the basis of leaf architecture and the role of cell division and cell growth in morphogenesis.