Modeled larval fish prey fields and growth rates help predict recruitment success of cod and anchovy in the North Sea

Abstract. We introduce a new, coupled modeling approach for simulating ecosystem-wide patterns in larval fish foraging and growth. An application of the method reveals how interplay between temperature and plankton dynamics during 1970-2009 impacted a cold-water species (Atlantic cod Gadus morhua) and a warm-water species (European anchovy Engraulis encrasicolus) in the North Sea. Larval fish growth rates were estimated by coupling models depicting traitbased foraging and bioenergetics of individuals, spatiotemporal changes in their prey field, and the biogeochemistry and hydrodynamics of the region. The biomass composition of modeled prey fields varied from 89% nano-, 10% micro-, and 1% mesoplankton to 15% nano-, 20% micro-, and 65% mesoplankton. The mean slope of the normalized biomass size spectrum was near -1.2, consistent with theoretical and empirical estimates. Median larval fish growth rates peaked in June for cod (24% d(-1)) and in July for anchovy (17% d(-1)). Insufficient prey resources played a substantial role in limiting the growth rates of cod larvae. Anchovy were consistently limited by cold temperatures. Faster median larval growth during specific months was significantly (p < 0.05) positively associated with detrended (i.e. higher than expected) juvenile recruitment indices in cod (rank correlation Kendall's tau = 22%) and anchovy (tau = 42%). For cod, the most predictive month was February, which was also when food limitation was most prevalent. The continued development of modeling tools based on first principles can help further a mechanistic understanding of how changes in the environment affect the productivity of living marine resources

Prevention of Birch Pollen-Related Food Allergy by Mucosal Treatment with Multi-Allergen-Chimers in Mice

Among birch pollen allergic patients up to 70% develop allergic reactions to Bet v 1-homologue food allergens such as Api g 1 (celery) or Dau c 1 (carrot), termed as birch pollen-related food allergy. In most cases, specific immunotherapy with birch pollen extracts does not reduce allergic symptoms to the homologue food allergens. We therefore genetically engineered a multi-allergen chimer and tested if mucosal treatment with this construct could represent a novel approach for prevention of birch pollen-related food allergy.BALB/c mice were poly-sensitized with a mixture of Bet v 1, Api g 1 and Dau c 1 followed by a sublingual challenge with carrot, celery and birch pollen extracts. For prevention of allergy sensitization an allergen chimer composed of immunodominant T cell epitopes of Api g 1 and Dau c 1 linked to the whole Bet v 1 allergen, was intranasally applied prior to sensitization.Intranasal pretreatment with the allergen chimer led to significantly decreased antigen-specific IgE-dependent β-hexosaminidase release, but enhanced allergen-specific IgG2a and IgA antibodies. Accordingly, IL-4 levels in spleen cell cultures and IL-5 levels in restimulated spleen and cervical lymph node cell cultures were markedly reduced, while IFN-γ levels were increased. Immunomodulation was associated with increased IL-10, TGF-β and Foxp3 mRNA levels in NALT and Foxp3 in oral mucosal tissues. Treatment with anti-TGF-β, anti-IL10R or anti-CD25 antibodies abrogated the suppression of allergic responses induced by the chimer.Our results indicate that mucosal application of the allergen chimer led to decreased Th2 immune responses against Bet v 1 and its homologue food allergens Api g 1 and Dau c 1 by regulatory and Th1-biased immune responses. These data suggest that mucosal treatment with a multi-allergen vaccine could be a promising treatment strategy to prevent birch pollen-related food allergy

Block-Centric Visualization Of Histological Whole Slide Images With Application To Revealing Growth-Patterns Of Early Colorectal Adenomas And Aberrant Crypt Foci

Introduction/ Background Comfortable navigation through diagnostic images is a prospective challenge for the acceptance of virtual microscopy applications in routine pathology [1],[2]. Tracing different regions of interest through multiple sections on one or several slides is a typical task in diagnostic slide examination. This laborious and time-consuming co-localization is currently executed by pathologists. Retaining the relative positions of tissue structures while alternating between multiple slides is still not feasible in a satisfactory manner in conventional nor virtual microscopy. Aims To address this issue we present a more comfortable and intuitive method to read slides using computer-assisted navigation. Furthermore, we demonstrate the strengths of our method by applying it to large series of serial colorectal tissue sections, creating new kinds of visualizations of different adenomatous mucosal architectures in human tissue, while looking for human correlates of lesions recently described in mice [3]. Methods Histological images contain multiple distortions from different sources in the laboratory and digitalization process. An interconnection model was created to describe distortions by several layers, providing a normalized tissue representation. Layers were associated with specific distortions with each layer serving as a new level of abstraction. The first layers enabled a coarse alignment of tissue sections. Further alignment is achieved by piecewise, multi-resolution, SIFT-based [4] correspondence extraction and refinement. Inside the convex hull of all fiducial points local affine transformations were applied whereas a global affine transformation was used on the outside. Animated stacks were generated for regions of interest using local rigid transformations to preserve exact morphological coherences. For subsequent creation of 3D models, the relevant histological objects within these images were annotated by pathologists, partly using computer assisted segmentation based on active contours [5]. These annotations were used subsequently to create simplified 3D models by applying VTK [6].  Results The presented methods provide an efficient means to retrieve correspondences and additional spatial information from serial sections of histological slides. They also show good applicability for specimen from different origin. Alignment methods can be applied to generate block-centric visualizations such as parallel and transparent viewing of multiple stains. Moreover, the generated stack videos and 3D models demonstrate the very good accuracy of section alignment even in large series. The visualizations enable pathologists and researchers to grasp the 3D structural relationships in the tissue at a glance, providing an excellent tool to communicate more complex histomorphological findings. Interestingly, we see two kinds of tubular adenomas, which could imply multiple ways to tubular adenoma formation in FAP-patients, possibly akin to the recent observations in mice [3]

A forest typology for monitoring sustainable forest management: The case of European Forest Types

Sustainable forest management (SFM) is presently widely accepted as the overriding objective for forest policy and practice. Regional processes are in progress all over the world to develop and implement criteria and indicators of SFM. In continental Europe, a set of 35 Pan-European indicators has been endorsed under the Ministerial Conference on the Protection of Forests in Europe (MCPFE) to measure progress towards SFM in the 44 countries of the region. The formulation of seven indicators (forest area, growing stock, age structure/diameter distribution, deadwood, tree species composition, damaging agents, naturalness) requires national data to be reported by forest types. Within the vast European forest area the values taken by these indicators show a considerable range of variation, due to variable natural conditions and anthropogenic influences. Given this variability, it is very difficult to grasp the meaning of these indicators when taken out of their ecological background. The paper discusses the concepts behind, and the requirements of, a classification more soundly ecologically framed and suitable for MCPFE reporting than the three (un-informative) classes adopted so far: broadleaved forest, coniferous forest, mixed broadleaved and coniferous forest. We propose a European Forest Types scheme structured into a reasonably higher number of classes, that would improve the specificity of the indicators reported under the MCPFE process and its understanding.L'articolo è disponibile sul sito dell'editore www.tandf.co.uk/journals

Condensed Matter Theory of Dipolar Quantum Gases

Recent experimental breakthroughs in trapping, cooling and controlling ultracold gases of polar molecules, magnetic and Rydberg atoms have paved the way toward the investigation of highly tunable quantum systems, where anisotropic, long-range dipolar interactions play a prominent role at the many-body level. In this article we review recent theoretical studies concerning the physics of such systems. Starting from a general discussion on interaction design techniques and microscopic Hamiltonians, we provide a summary of recent work focused on many-body properties of dipolar systems, including: weakly interacting Bose gases, weakly interacting Fermi gases, multilayer systems, strongly interacting dipolar gases and dipolar gases in 1D and quasi-1D geometries. Within each of these topics, purely dipolar effects and connections with experimental realizations are emphasized.Comment: Review article; submitted 09/06/2011. 158 pages, 52 figures. This document is the unedited author's version of a Submitted Work that was subsequently accepted for publication in Chemical Reviews, copyright American Chemical Society after peer review. To access the final edited and published work, a link will be provided soo

Sequence Capture and Next Generation Resequencing of the MHC Region Highlights Potential Transplantation Determinants in HLA Identical Haematopoietic Stem Cell Transplantation

How cells coordinate the immune system activities is important for potentially life-saving organ or stem cell transplantations. Polymorphic immunoregulatory genes, many of them located in the human major histocompatibility complex, impact the process and assure the proper execution of tolerance-versus-activity mechanisms. In haematopoietic stem cell transplantation, on the basis of fully human leukocyte antigen (HLA)-matched donor–recipient pairs, adverse effects like graft versus leukaemia and graft versus host are observed and difficult to handle. So far, high-resolution HLA typing was performed with Sanger sequencing, but for methodological reasons information on additional immunocompetent major histocompatibility complex loci has not been revealed. Now, we have used microarray sequence capture and targeted enrichment combined with next generation pyrosequencing for 3.5 million base pair human major histocompatibility complex resequencing in a clinical transplant setting and describe 3025 variant single nucleotide polymorphisms, insertions and deletions among recipient and donor in a single sequencing experiment. Taken together, the presented data show that sequence capture and massively parallel pyrosequencing can be used as a new tool for risk assessment in the setting of allogeneic stem cell transplantation