Showing papers by "University of Bremen published in 2012"
TL;DR: The aim of the new guidelines for coeliac disease was to achieve a high diagnostic accuracy and to reduce the burden for patients and their families.
Abstract: Objective: Diagnostic criteria for coeliac disease (CD) from the European Society for Paediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN) were published in 1990. Since then, the autoantigen in CD, tissue transglutaminase, has been identified; the perception of CD has changed from that of a rather uncommon enteropathy to a common multiorgan disease strongly dependent on the haplotypes human leukocyte antigen (HLA)-DQ2 and HLA-DQ8; and CD-specific antibody tests have improved. Methods: A panel of 17 experts defined CD and developed new diagnostic criteria based on the Delphi process. Two groups of patients were defined with different diagnostic approaches to diagnose CD: children with symptoms suggestive of CD (group 1) and asymptomatic children at increased risk for CD (group 2). The 2004 National Institutes of Health/ Agency for Healthcare Research and Quality report and a systematic literature search on antibody tests for CD in paediatric patients covering the years 2004 to 2009 was the basis for the evidence-based recommendations on CD-specific antibody testing. Results: In group 1, the diagnosis of CD is based on symptoms, positive serology, and histology that is consistent with CD. If immunoglobulin A anti-tissue transglutaminase type 2 antibody titers are high (>10 times the upper limit of normal), then the option is to diagnose CD without duodenal biopsies by applying a strict protocol with further laboratory tests. In group 2, the diagnosis of CD is based on positive serology and histology. HLADQ2 and HLA-DQ8 testing is valuable because CD is unlikely if both haplotypes are negative. Conclusions: The aim of the new guidelines was to achieve a high diagnostic accuracy and to reduce the burden for patients and their families. The performance of these guidelines in clinical practice should be evaluated prospectively. (JPGN 2012;54: 136–160)
2,242 citations
TL;DR: The pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants is reported to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages.
Abstract: Sequencing of the Arabidopsis thaliana root microbiome shows that its composition is strongly influenced by location, inside or outside the root, and by soil type. The association between a land plant and the soil microbes of the root microbiome is important for the plant's well-being. A deeper understanding of these microbial communities will offer opportunities to control plant growth and susceptibility to pathogens, particularly in sustainable agricultural regimes. Two groups, working separately but developing best-practice protocols in parallel, have characterized the root microbiota of the model plant Arabidopis thaliana. Working on two continents and with five different soil types, they reach similar general conclusions. The bacterial communities in each root compartment — the rhizosphere immediately surrounding the root and the endophytic compartment within the root — are most strongly influenced by soil type, and to a lesser degree by host genotype. In natural soils, Arabidopsis plants are preferentially colonized by Actinobacteria, Proteobacteria, Bacteroidetes and Chloroflexi species. And — an important point for future work — Arabidopsis root selectivity for soil bacteria under controlled environmental conditions mimics that of plants grown in a natural environment. Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation1,2,3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant–microbe interactions derived from complex soil communities.
2,097 citations
TL;DR: Methodology is described to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization.
Abstract: The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication. Several studies attempted to describe the structure of bacterial root endophytes; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.
1,787 citations
TL;DR: The platform presented here provides a significant advancement in the ability to understand the spatiotemporal dynamics of metabolite production in live microbial colonies and communities.
Abstract: Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of live microbial colonies directly from a Petri dish without any sample preparation. Nanospray desorption electrospray ionization mass spectrometry (MS), combined with alignment of MS data and molecular networking, enabled monitoring of metabolite production from live microbial colonies from diverse bacterial genera, including Bacillus subtilis, Streptomyces coelicolor, Mycobacterium smegmatis, and Pseudomonas aeruginosa. This work demonstrates that, by using these tools to visualize small molecular changes within bacterial interactions, insights can be gained into bacterial developmental processes as a result of the improved organization of MS/MS data. To validate this experimental platform, metabolic profiling was performed on Pseudomonas sp. SH-C52, which protects sugar beet plants from infections by specific soil-borne fungi [R. Mendes et al. (2011) Science 332:1097–1100]. The antifungal effect of strain SH-C52 was attributed to thanamycin, a predicted lipopeptide encoded by a nonribosomal peptide synthetase gene cluster. Our technology, in combination with our recently developed peptidogenomics strategy, enabled the detection and partial characterization of thanamycin and showed that it is a monochlorinated lipopeptide that belongs to the syringomycin family of antifungal agents. In conclusion, the platform presented here provides a significant advancement in our ability to understand the spatiotemporal dynamics of metabolite production in live microbial colonies and communities.
723 citations
TL;DR: It is demonstrated that it is possible to predict the toxicity of a large series of MOx nanoparticles in the lung premised on semiconductor properties and an integrated in vitro/in vivo hazard ranking model premisedon oxidative stress.
Abstract: We demonstrate for 24 metal oxide (MOx) nanoparticles that it is possible to use conduction band energy levels to delineate their toxicological potential at cellular and whole animal levels. Among the materials, the overlap of conduction band energy (Ec) levels with the cellular redox potential (−4.12 to −4.84 eV) was strongly correlated to the ability of Co3O4, Cr2O3, Ni2O3, Mn2O3, and CoO nanoparticles to induce oxygen radicals, oxidative stress, and inflammation. This outcome is premised on permissible electron transfers from the biological redox couples that maintain the cellular redox equilibrium to the conduction band of the semiconductor particles. Both single-parameter cytotoxic as well as multi-parameter oxidative stress assays in cells showed excellent correlation to the generation of acute neutrophilic inflammation and cytokine responses in the lungs of C57 BL/6 mice. Co3O4, Ni2O3, Mn2O3, and CoO nanoparticles could also oxidize cytochrome c as a representative redox couple involved in redox ho...
702 citations
TL;DR: The Constrained Application Protocol (CoAP) is a transfer protocol for constrained nodes and networks, such as those that will form the Internet of Things, which uses the REST architectural style.
Abstract: The Constrained Application Protocol (CoAP) is a transfer protocol for constrained nodes and networks, such as those that will form the Internet of Things. Much like its older and heavier cousin HTTP, CoAP uses the REST architectural style. Based on UDP and unencumbered by historical baggage, however, CoAP aims to achieve its modest goals with considerably less complexity.
603 citations
TL;DR: The first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods, suggests a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.
Abstract: Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere...
597 citations
TL;DR: An archaeal amoA consensus phylogeny is presented based on all publicly available sequences and evidence for the diversification of AOA into four previously recognized clusters and one newly identified major cluster is provided.
Abstract: Ammonia-oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their amoA genes as marker for their diversity and abundance. We present an archaeal amoA consensus phylogeny based on all publicly available sequences (status June 2010) and provide evidence for the diversification of AOA into four previously recognized clusters and one newly identified major cluster. These clusters, for which we suggest a new nomenclature, harboured 83 AOA species-level OTU (using an inferred species threshold of 85% amoA identity). 454 pyrosequencing of amoA amplicons from 16 soils sampled in Austria, Costa Rica, Greenland and Namibia revealed that only 2% of retrieved sequences had no database representative on the species-level and represented 30–37 additional species-level OTUs. With the exception of an acidic soil from which mostly amoA amplicons of the Nitrosotalea cluster were retrieved, all soils were dominated by amoA amplicons from the Nitrososphaera cluster (also called group I.1b), indicating that the previously reported AOA from the Nitrosopumilus cluster (also called group I.1a) are absent or represent minor populations in soils. AOA richness estimates on the species level ranged from 8–83 co-existing AOAs per soil. Presence/absence of amoA OTUs (97% identity level) correlated with geographic location, indicating that besides contemporary environmental conditions also dispersal limitation across different continents and/or historical environmental conditions might influence AOA biogeography in soils.
439 citations
Ruhr University Bochum1, Karolinska Institutet2, University of Duisburg-Essen3, University of Bremen4, International Agency for Research on Cancer5, University of Turin6, University of Padua7, Université de Montréal8, Institut national de la recherche scientifique9, University of Milan10, National Institutes of Health11, Russian Academy12, University of Liverpool13, Nofer Institute of Occupational Medicine14, Curie Institute15, French Institute of Health and Medical Research16, Charles University in Prague17, Johns Hopkins University18
TL;DR: The major result that smoking exerted a steeper risk gradient on SqCC and SCLC than on AdCa is in line with previous population data and biological understanding of lung cancer development.
Abstract: Lung cancer is mainly caused by smoking, but the quantitative relations between smoking and histologic subtypes of lung cancer remain inconclusive. By using one of the largest lung cancer datasets ever assembled, we explored the impact of smoking on risks of the major cell types of lung cancer. This pooled analysis included 13,169 cases and 16,010 controls from Europe and Canada. Studies with population controls comprised 66.5% of the subjects. Adenocarcinoma (AdCa) was the most prevalent subtype in never smokers and in women. Squamous cell carcinoma (SqCC) predominated in male smokers. Age-adjusted odds ratios (ORs) were estimated with logistic regression. ORs were elevated for all metrics of exposure to cigarette smoke and were higher for SqCC and small cell lung cancer (SCLC) than for AdCa. Current male smokers with an average daily dose of >30 cigarettes had ORs of 103.5 (95% confidence interval (CI): 74.8-143.2) for SqCC, 111.3 (95% CI: 69.8-177.5) for SCLC and 21.9 (95% CI: 16.6-29.0) for AdCa. In women, the corresponding ORs were 62.7 (95% CI: 31.5-124.6), 108.6 (95% CI: 50.7-232.8) and 16.8 (95% CI: 9.2-30.6), respectively. Although ORs started to decline soon after quitting, they did not fully return to the baseline risk of never smokers even 35 years after cessation. The major result that smoking exerted a steeper risk gradient on SqCC and SCLC than on AdCa is in line with previous population data and biological understanding of lung cancer development.
406 citations
University of Bristol1, University of Oregon2, Macquarie University3, Imperial College London4, University of Wyoming5, University of Exeter6, Centre national de la recherche scientifique7, Osaka City University8, University of Wisconsin-Madison9, University of New South Wales10, American Museum of Natural History11, Australian National University12, University of Bern13, Slovenian Academy of Sciences and Arts14, Sofia University15, University of Göttingen16, University of Montpellier17, Canadian Forest Service18, Geological Survey of Denmark and Greenland19, University of Newcastle20, École Polytechnique Fédérale de Lausanne21, Monash University22, Australian Nuclear Science and Technology Organisation23, University of Bremen24, UPRRP College of Natural Sciences25, University of Calgary26, University of Tennessee27, University of Cologne28, Virginia Tech29, Russian Academy of Sciences30, University of Wisconsin–Oshkosh31, Sapienza University of Rome32, Katholieke Universiteit Leuven33, University of Chile34, University of Queensland35, University of the Witwatersrand36, University of Münster37, Stockholm University38, Laval University39, Geode40, University of Franche-Comté41, University of Plymouth42, Fordham University43, University of the Free State44, Kyoto Prefectural University45, University of Orléans46, University of Kansas47, University of Geneva48, Central Washington University49, Chinese Academy of Sciences50
TL;DR: This article analyzed sedimentary charcoal records to show that the changes in fire regime over the past 21,000 yrs are predictable from changes in regional climates and showed that fire increases monotonically with changes in temperature and peaks at intermediate moisture levels.
Abstract: Climate is an important control on biomass burning, but the sensitivity of fire to changes in temperature and moisture balance has not been quantified. We analyze sedimentary charcoal records to show that the changes in fire regime over the past 21,000 yrs are predictable from changes in regional climates. Analyses of paleo- fire data show that fire increases monotonically with changes in temperature and peaks at intermediate moisture levels, and that temperature is quantitatively the most important driver of changes in biomass burning over the past 21,000 yrs. Given that a similar relationship between climate drivers and fire emerges from analyses of the interannual variability in biomass burning shown by remote-sensing observations of month-by-month burnt area between 1996 and 2008, our results signal a serious cause for concern in the face of continuing global warming.
362 citations
Alfred Wegener Institute for Polar and Marine Research1, National Institute of Oceanography, India2, Norwegian Polar Institute3, Stazione Zoologica Anton Dohrn4, Centre national de la recherche scientifique5, Vrije Universiteit Brussel6, University of Cape Town7, Spanish National Research Council8, Leibniz Institute for Baltic Sea Research9, Bjerknes Centre for Climate Research10, Norwegian Institute for Water Research11, Stanford University12, Leibniz Institute of Marine Sciences13, National University of Ireland, Galway14, University of Vienna15, University of Liverpool16, Commonwealth Scientific and Industrial Research Organisation17, University of Bremen18, Max Planck Society19, University of Plymouth20
TL;DR: Iron-fertilized diatom blooms may sequester carbon for timescales of centuries in ocean bottom water and for longer in the sediments.
Abstract: Fertilization of the ocean by adding iron compounds has induced diatom-dominated phytoplankton blooms accompanied by considerable carbon dioxide drawdown in the ocean surface layer. However, because the fate of bloom biomass could not be adequately resolved in these experiments, the timescales of carbon sequestration from the atmosphere are uncertain. Here we report the results of a five-week experiment carried out in the closed core of a vertically coherent, mesoscale eddy of the Antarctic Circumpolar Current, during which we tracked sinking particles from the surface to the deep-sea floor. A large diatom bloom peaked in the fourth week after fertilization. This was followed by mass mortality of several diatom species that formed rapidly sinking, mucilaginous aggregates of entangled cells and chains. Taken together, multiple lines of evidence—although each with important uncertainties—lead us to conclude that at least half the bloom biomass sank far below a depth of 1,000 metres and that a substantial portion is likely to have reached the sea floor. Thus, iron-fertilized diatom blooms may sequester carbon for timescales of centuries in ocean bottom water and for longer in the sediments.
National Oceanography Centre, Southampton1, Texas A&M University2, Tohoku University3, University of Bristol4, Ocean Drilling Program5, University of California, Davis6, University of Leicester7, Stockholm University8, University of Paris9, University College London10, University of New Orleans11, University of Florida12, Goethe University Frankfurt13, University of California, Santa Cruz14, National Institute of Oceanography, India15, Imperial College London16, University of Birmingham17, Cardiff University18, Lamont–Doherty Earth Observatory19, University of Münster20, Hokkaido University21, Leibniz Institute of Marine Sciences22, Shimane University23, University of Kiel24, Indiana University of Pennsylvania25, Japan Agency for Marine-Earth Science and Technology26, Ibaraki University27, Kōchi University28, Rice University29, University of Michigan30, University of Otago31, University of Louisiana at Lafayette32, University of Rhode Island33, Spanish National Research Council34, University of South Carolina35, Pennsylvania State University36, Utrecht University37, Pusan National University38, Tongji University39, University of Leeds40, University of Bremen41, University of Hawaii at Manoa42, National Institute of Advanced Industrial Science and Technology43
TL;DR: A carbonate accumulation record that covers the past 53 million years from a depth transect in the equatorial Pacific Ocean is presented and large superimposed fluctuations in carbonate compensation depth are found during the middle and late Eocene.
Abstract: Atmospheric carbon dioxide concentrations and climate are regulated on geological timescales by the balance between carbon input from volcanic and metamorphic outgassing and its removal by weathering feedbacks; these feedbacks involve the erosion of silicate rocks and organic-carbon-bearing rocks. The integrated effect of these processes is reflected in the calcium carbonate compensation depth, which is the oceanic depth at which calcium carbonate is dissolved. Here we present a carbonate accumulation record that covers the past 53 million years from a depth transect in the equatorial Pacific Ocean. The carbonate compensation depth tracks long-term ocean cooling, deepening from 3.0-3.5 kilometres during the early Cenozoic (approximately 55 million years ago) to 4.6 kilometres at present, consistent with an overall Cenozoic increase in weathering. We find large superimposed fluctuations in carbonate compensation depth during the middle and late Eocene. Using Earth system models, we identify changes in weathering and the mode of organic-carbon delivery as two key processes to explain these large-scale Eocene fluctuations of the carbonate compensation depth.
TL;DR: Increased negative surface charge correlates strongly with increased protein solubility and may be due to strong binding of water by the acidic amino acids, and the results obtained for the two different precipitants agree closely with each other, suggesting that the two precipitant probe similar properties that are relevant to solubilty in buffer alone.
Centre national de la recherche scientifique1, Cooperative Institute for Research in Environmental Sciences2, California Institute of Technology3, Karlsruhe Institute of Technology4, Spanish National Research Council5, University of Toronto6, University of York7, Agencia Estatal de Meteorología8, National Institute of Water and Atmospheric Research9, University of Bremen10, University of Wollongong11, University of Liège12, Harvard University13, University of the Ryukyus14, Stockholm University15
TL;DR: In this paper, a large number of isotopic data sets (four satellite, sixteen ground-based remote-sensing, five surface in situ and three aircraft data sets) are analyzed to determine how H2O and HDO measurements in water vapor can be used to detect and diagnose biases in the representation of processes controlling tropospheric humidity in atmospheric general circulation models (GCMs).
Abstract: The goal of this study is to determine how H2O and HDO measurements in water vapor can be used to detect and diagnose biases in the representation of processes controlling tropospheric humidity in atmospheric general circulation models (GCMs). We analyze a large number of isotopic data sets (four satellite, sixteen ground-based remote-sensing, five surface in situ and three aircraft data sets) that are sensitive to different altitudes throughout the free troposphere. Despite significant differences between data sets, we identify some observed HDO/H2O characteristics that are robust across data sets and that can be used to evaluate models. We evaluate the isotopic GCM LMDZ, accounting for the effects of spatiotemporal sampling and instrument sensitivity. We find that LMDZ reproduces the spatial patterns in the lower and mid troposphere remarkably well. However, it underestimates the amplitude of seasonal variations in isotopic composition at all levels in the subtropics and in midlatitudes, and this bias is consistent across all data sets. LMDZ also underestimates the observed meridional isotopic gradient and the contrast between dry and convective tropical regions compared to satellite data sets. Comparison with six other isotope-enabled GCMs from the SWING2 project shows that biases exhibited by LMDZ are common to all models. The SWING2 GCMs show a very large spread in isotopic behavior that is not obviously related to that of humidity, suggesting water vapor isotopic measurements could be used to expose model shortcomings. In a companion paper, the isotopic differences between models are interpreted in terms of biases in the representation of processes controlling humidity. Copyright © 2012 by the American Geophysical Union.
Goethe University Frankfurt1, Utrecht University2, Brandon University3, National Oceanography Centre, Southampton4, University of Glasgow5, University of Bremen6, University of California, San Diego7, GNS Science8, Imperial College London9, Durham University10, University of Tromsø11, Spanish National Research Council12
TL;DR: It is shown that the climate in lowland settings along the Wilkes Land coast (at a palaeolatitude of about 70° south) supported the growth of highly diverse, near-tropical forests characterized by mesothermal to megathermal floral elements including palms and Bombacoideae.
Abstract: The warmest global climates of the past 65 million years occurred during the early Eocene epoch (about 55 to 48 million years ago), when the Equator-to-pole temperature gradients were much smaller than today1, 2 and atmospheric carbon dioxide levels were in excess of one thousand parts per million by volume3, 4. Recently the early Eocene has received considerable interest because it may provide insight into the response of Earth’s climate and biosphere to the high atmospheric carbon dioxide levels that are expected in the near future5 as a consequence of unabated anthropogenic carbon emissions4, 6. Climatic conditions of the early Eocene ‘greenhouse world’, however, are poorly constrained in critical regions, particularly Antarctica. Here we present a well-dated record of early Eocene climate on Antarctica from an ocean sediment core recovered off the Wilkes Land coast of East Antarctica. The information from biotic climate proxies (pollen and spores) and independent organic geochemical climate proxies (indices based on branched tetraether lipids) yields quantitative, seasonal temperature reconstructions for the early Eocene greenhouse world on Antarctica. We show that the climate in lowland settings along the Wilkes Land coast (at a palaeolatitude of about 70° south) supported the growth of highly diverse, near-tropical forests characterized by mesothermal to megathermal floral elements including palms and Bombacoideae. Notably, winters were extremely mild (warmer than 10 °C) and essentially frost-free despite polar darkness, which provides a critical new constraint for the validation of climate models and for understanding the response of high-latitude terrestrial ecosystems to increased carbon dioxide forcing.
University of Bremen1, Max Planck Society2, Leibniz Institute for Neurobiology3, Ludwig Maximilian University of Munich4, University of Cologne5, University of Tübingen6, University of Göttingen7, University of Ulm8, University of Würzburg9, University of Potsdam10, Technische Universität München11, University of Bern12, Braunschweig University of Technology13
TL;DR: Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting, but interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T- RFs correlated positively or negatively with nitrogen content.
Abstract: In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n = 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered.
TL;DR: IgA-EmA and IgA-anti-TG2/EmA tests appear highly accurate to diagnose coeliac disease in children and may help in excluding CD, while POC tests show inferior accuracy.
Abstract: Objective The aim of this study was to summarise the evidence from 2004 to September 2009 on the performance of laboratory-based serological and point of care (POC) tests for diagnosing coeliac disease (CD) in children using histology as reference standard. Patients and methods We searched MEDLINE and EMBASE for studies reporting on children for tests based on IgA and IgG anti-gliadin (AGA), endomysial (EmA), anti-transglutaminase-2 (TG2), and anti-deamidated gliadin peptides (DGP) antibodies or POC tests. For inclusion, histological analysis of duodenal biopsies and sensitivity and specificity for index tests had to be reported. Data were pooled and summary measures calculated for sensitivity, specificity, positive and negative likelihood ratios ("LR+", "LR-"), and diagnostic odds ratios (DOR). In case of elevated statistical heterogeneity, studies reaching 90% sensitivity or specificity were reported. Results A total of 2510 articles were reviewed; 16 entered meta-analysis, reporting on 3110 patients (1876 with CD, 1234 without CD). For IgA-EmA, sensitivity was ≥90% in 7/11 studies and pooled specificity 98.2%. For IgA-anti-TG2, 11/15 studies yielded sensitivities ≥90% and 13/15 specificities ≥90%. For IgA-DGP, sensitivity ranged between 80.7% and 95.1% (specificity 86.3%-93.1%); for IgG-DGP between 80.1% and 98.6% (specificity 86.0-96.9%). IgA-EmA had the highest pooled DOR (554) and LR+ (31.8) for a laboratory test, followed by IgA-anti-TG2, IgG-DGP, IgA-DGP and IgA-AGA. POC tests showed a pooled sensitivity of 96.4% for IgA-TG2 (specificity 97.7%). Conclusions IgA-EmA and IgA-anti-TG2 tests appear highly accurate to diagnose CD. IgG-anti-DGP tests may help in excluding CD. IgA-AGA and IgA-DGP tests show inferior accuracy. POC tests may achieve high accuracy in the hands of experienced readers, but IgA-anti-TG2/EmA were superior.
TL;DR: The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change.
Abstract: Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink. Their response to global warming and environmental pollution is one of the largest unknowns in the upcoming decades to centuries. In this review, we highlight the role of sulfate-reducing microorganisms (SRM) in the intertwined element cycles of wetlands. Although regarded primarily as methanogenic environments, biogeochemical studies have revealed a previously hidden sulfur cycle in wetlands that can sustain rapid renewal of the small standing pools of sulfate. Thus, dissimilatory sulfate reduction, which frequently occurs at rates comparable to marine surface sediments, can contribute up to 36–50% to anaerobic carbon mineralization in these ecosystems. Since sulfate reduction is thermodynamically favored relative to fermentative processes and methanogenesis, it effectively decreases gross methane production thereby mitigating the flux of methane to the atmosphere. However, very little is known about wetland SRM. Molecular analyses using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] as marker genes demonstrated that members of novel phylogenetic lineages, which are unrelated to recognized SRM, dominate dsrAB richness and, if tested, are also abundant among the dsrAB-containing wetland microbiota. These discoveries point towards the existence of so far unknown SRM that are an important part of the autochthonous wetland microbiota. In addition to these numerically dominant microorganisms, a recent stable isotope probing study of SRM in a German peatland indicated that rare biosphere members might be highly active in situ and have a considerable stake in wetland sulfate reduction. The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change.
TL;DR: There are considerable differences in the prevalence of chronic diseases between German health insurance funds that remained after controlling for age and sex, and even after adjustment for further health-related variables.
Abstract: Aim Claims data of health insurance companies are an important database for health services research. We investigated if there are differences in baseline characteristics and prevalence of chronic diseases between members of several health insurance funds in Germany, and if so, whether adjusting for age and sex could explain these differences. Methods 10 representative surveys (conducted between 2004 and 2008) of the 'Bertelsmann Health-Care Monitor' comprising 15 089 participants aged 18 to 79 years were analysed. Our main independent variable was membership in one of 8 health insurance funds. The prevalence of self-reported hypertension, diabetes, atopic diseases, coronary heart disease and heart failure was studied. We first estimated the crude prevalence of chronic diseases stratified by these funds. We further fitted logistic regression models and adjusted for age and sex as well as for further comorbidities and health related factors. Results Most respondents were insured in the BKK (Betriebskrankenkassen; 20.1%), the AOK (Allgemeinen Ortskrankenkassen; 19.2%) and private health insurances (15.3%). Substantial differences were found according to age, sex, educational level and prevalences of chronic diseases. Stratified by health insurance funds, prevalences ranged between 17.1-29.6% for hypertension, between 3.9-11.4% for diabetes, between 4.3-6.7% for atopic diseases, between 3.4-6.7% for coronary heart disease and between 2.6-5.7% for heart failure. When adjusting for sex and age, estimates for all 5 diseases were significant higher in AOK members compared to privately insured persons (3 diseases within the BAMER and the DAK, accordingly). In total, this was the case for 17 out of 35 comparisons. Even after adjusting for further comorbidities and health related factors 6 out of 35 comparisons showed significant increased estimates compared to privately insured persons. Conclusion We found considerable differences in the prevalence of chronic diseases between German health insurance funds that remained after controlling for age and sex, and even after adjustment for further health-related variables. Further methodological studies are urgently needed to assess strengths and weaknesses of German claim data.
California Institute of Technology1, Colorado State University2, University of Leicester3, University of Bremen4, University of Wollongong5, Japan Aerospace Exploration Agency6, National Institute for Environmental Studies7, National Institute of Water and Atmospheric Research8, University of Maryland, College Park9
TL;DR: This article reported preliminary estimates of column averaged carbon dioxide (CO2) dry air mole fraction, XCO2, retrieved from spectra recorded over land by the Greenhouse gases Observing Satellite, GOSAT (nicknamed "Ibuki"), using retrieval methods originally developed for the NASA Orbiting Carbon Observatory (OCO) mission.
Abstract: . Here, we report preliminary estimates of the column averaged carbon dioxide (CO2) dry air mole fraction, XCO2, retrieved from spectra recorded over land by the Greenhouse gases Observing Satellite, GOSAT (nicknamed "Ibuki"), using retrieval methods originally developed for the NASA Orbiting Carbon Observatory (OCO) mission. After screening for clouds and other known error sources, these retrievals reproduce much of the expected structure in the global XCO2 field, including its variation with latitude and season. However, low yields of retrieved XCO2 over persistently cloudy areas and ice covered surfaces at high latitudes limit the coverage of some geographic regions, even on seasonal time scales. Comparisons of early GOSAT XCO2 retrievals with XCO2 estimates from the Total Carbon Column Observing Network (TCCON) revealed a global, −2% (7–8 parts per million, ppm, with respect to dry air) XCO2 bias and 2 to 3 times more variance in the GOSAT retrievals. About half of the global XCO2 bias is associated with a systematic, 1% overestimate in the retrieved air mass, first identified as a global +10 hPa bias in the retrieved surface pressure. This error has been attributed to errors in the O2 A-band absorption cross sections. Much of the remaining bias and spurious variance in the GOSAT XCO2 retrievals has been traced to uncertainties in the instrument's calibration, oversimplified methods for generating O2 and CO2 absorption cross sections, and other subtle errors in the implementation of the retrieval algorithm. Many of these deficiencies have been addressed in the most recent version (Build 2.9) of the retrieval algorithm, which produces negligible bias in XCO2 on global scales as well as a ~30% reduction in variance. Comparisons with TCCON measurements indicate that regional scale biases remain, but these could be reduced by applying empirical corrections like those described by Wunch et al. (2011b). We recommend that such corrections be applied before these data are used in source sink inversion studies to minimize spurious fluxes associated with known biases. These and other lessons learned from the analysis of GOSAT data are expected to accelerate the delivery of high quality data products from the Orbiting Carbon Observatory-2 (OCO-2), once that satellite is successfully launched and inserted into orbit.
TL;DR: Nutrition habits of university students differed across countries and by sex, and students living at parental home displayed more healthy nutrition habits, with some exceptions.
Abstract: The transition of young people from school to university has many health implications. Food choice at the university can differ because of childhood food consumption patterns, sex and the living arrangements. Food consumption may change especially if students are living away from home. We aimed to assess food consumption patterns among university students from four European countries and how they differ by their living arrangements. We analysed data from a cross-country survey assessing health and health behaviours of students. The sample comprised a total of 2402 first year undergraduate students from one university in each of the countries of Germany, Denmark, Poland and Bulgaria. Food consumption was assessed by means of a food frequency questionnaire with 9 food groups (indicators). Students’ food consumption patterns differed across the countries. Frequent consumption of unhealthy items was common. Bulgarian students reported most often frequent consumption of sweets and cakes and snacks (e.g. chips and fast food). Polish students reported the least frequent consumption of vegetables and a low consumption of fruits. Across all countries except Bulgaria, men reported substantially more often frequent consumption of snacks than women. Students living at parental home consumed more fruit, vegetables, and meat than those who resided outside of their family home in all studied countries. There was more variation with regard to cakes and salads with more frequent consumption of cakes among Bulgarian female students and Danish male students and more frequent consumption of salads among Danish female students not living at parental home, compared to students from other countries. Nutrition habits of university students differed across countries and by sex. Students living at parental home displayed more healthy nutrition habits, with some exceptions.
02 Jun 2012
TL;DR: An observational study of 28 professional developers from seven companies, investigating how developers comprehend software finds that developers put themselves in the role of end users by inspecting user interfaces and that face-to-face communication is preferred to documentation.
Abstract: Research in program comprehension has considerably evolved over the past two decades. However, only little is known about how developers practice program comprehension under time and project pressure, and which methods and tools proposed by researchers are used in industry. This paper reports on an observational study of 28 professional developers from seven companies, investigating how developers comprehend software. In particular we focus on the strategies followed, information needed, and tools used. We found that developers put themselves in the role of end users by inspecting user interfaces. They try to avoid program comprehension, and employ recurring, structured comprehension strategies depending on work context. Further, we found that standards and experience facilitate comprehension. Program comprehension was considered a subtask of other maintenance tasks rather than a task by itself. We also found that face-to-face communication is preferred to documentation. Overall, our results show a gap between program comprehension research and practice as we did not observe any use of state of the art comprehension tools and developers seem to be unaware of them. Our findings call for further careful analysis and for reconsidering research agendas.
TL;DR: It is hypothesized that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen in the ocean.
Abstract: . The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA) over their bacterial counterparts (AOB) in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O) that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O. Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA) were detectable throughout the water column of the eastern tropical North Atlantic (ETNA) and eastern tropical South Pacific (ETSP) Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen in the ocean.
TL;DR: The years between 2005 and 2014 have been declared as a worldwide Decade of Education for Sustainable Development (DESD) by the United Nations as discussed by the authors, and all educational levels and domains are to be involved in contributing to ESD, including chemistry.
Abstract: The years between 2005 and 2014 have been declared as a worldwide Decade of Education for Sustainable Development (DESD) by the United Nations. DESD's intended purpose is to promote and more thoroughly focus education as a crucial tool preparing young people to be responsible future citizens, so that our future generations can shape society in a sustainable manner. All educational levels and domains are to be involved in contributing to ESD, including chemistry. This paper reflects upon the meaning of the UN's challenge and on what ESD pedagogy will mean for chemistry education. Additionally, it provides an overview of different models suggesting how such integration of sustainability issues can be compatible with chemistry education. Various consequences and implications arising from this approach will also be discussed.
TL;DR: It is shown by first-principles calculations that the magnetic and electronic properties of zigzag MoS2NRs exhibit sensitive response to applied strain and electric field, suggesting a robust and efficient approach to modulating the properties of MoS 2NRs by a combination of strain engineering andElectric field tuning.
Abstract: Effective modulation of physical properties via external control may open various potential nanoelectronic applications of single-layer MoS2 nanoribbons (MoS2NRs). We show by first-principles calculations that the magnetic and electronic properties of zigzag MoS2NRs exhibit sensitive response to applied strain and electric field. Tensile strain in the zigzag direction produces reversible modulation of magnetic moments and electronic phase transitions among metallic, half-metallic, and semiconducting states, which stem from the energy-level shifts induced by an internal electric polarization and the competing covalent/ionic interactions. A simultaneously applied electric field further enhances or suppresses the strain-induced modulations depending on the direction of the electric field relative to the internal polarization. These findings suggest a robust and efficient approach to modulating the properties of MoS2NRs by a combination of strain engineering and electric field tuning.
18 Jun 2012
TL;DR: This chapter pretends to provide a comprehensive view of this language, its many applications and available tool support as well as the latest research developments and open challenges around it.
Abstract: The Object Constraint Language (OCL) started as a complement of the UML notation with the goal to overcome the limitations of UML (and in general, any graphical notation) in terms of precisely specifying detailed aspects of a system design. Since then, OCL has become a key component of any model-driven engineering (MDE) technique as the default language for expressing all kinds of (meta)model query, manipulation and specification requirements. Among many other applications, OCL is frequently used to express model transformations (as part of the source and target patterns of transformation rules), well-formedness rules (as part of the definition of new domain-specific languages), or code-generation templates (as a way to express the generation patterns and rules).
This chapter pretends to provide a comprehensive view of this language, its many applications and available tool support as well as the latest research developments and open challenges around it.
TL;DR: In this article, the impact of particle precipitation on the chemical composition of the atmosphere has been studied, and there are a number of observations as well as model studies concerning especially the auroral impact and large solar particle events.
Abstract: Precipitation of energetic particles into the atmosphere greatly disturbs the chemical composition from the upper stratosphere to the lower thermosphere. Most important are changes to the budget of atmospheric nitric oxides (NOx = N, NO, NO2) and to atmospheric reactive hydrogen oxides (HOx = H, OH, HO2), which both contribute to ozone loss in the stratosphere and mesosphere. The impact of energetic particle precipitation on the chemical composition of the atmosphere has been studied since the 1960s, and there are a number of observations as well as model studies concerning especially the auroral impact and large solar particle events. Changes to the NOx budget due to energetic particle precipitation can be quite long-lived during polar winter and can then be transported down into the lower mesosphere and stratosphere, where NOx is one of the main participants in catalytic ozone destruction. Energetic particle precipitation can also affect temperatures and dynamics of the atmosphere from the source region down to the stratosphere and possibly even down to the surface, due to a coupling of chemical composition changes affecting atmospheric heating and cooling rates, the mean circulation, and wave propagation and breaking. Thus, energetic particle precipitation impacts have been implemented in chemistry-climate models reaching from the surface up to the mesosphere or lower thermosphere. However, there are still a number of open questions in the theoretical description of the energetic particle precipitation impact; the most important are uncertainties in the formation rate of different NOx species due to energetic particle precipitation, and the complex coupling between chemical changes, atmospheric heating and cooling rates, and atmospheric dynamics.
TL;DR: In this article, the authors constructed a varve data base (VDB) to study the worldwide distribution of varved sediment records and the fidelity of their varve chronologies.
TL;DR: Computational methods for analyzing MALDI-imaging data with the emphasis on multivariate statistical methods are outlined, their pros and cons are discussed, and their recommendations on their application are given.
Abstract: Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) imaging mass spectrometry, also called MALDI-imaging, is a label-free bioanalytical technique used for spatially-resolved chemical analysis of a sample. Usually, MALDI-imaging is exploited for analysis of a specially prepared tissue section thaw mounted onto glass slide. A tremendous development of the MALDI-imaging technique has been observed during the last decade. Currently, it is one of the most promising innovative measurement techniques in biochemistry and a powerful and versatile tool for spatially-resolved chemical analysis of diverse sample types ranging from biological and plant tissues to bio and polymer thin films. In this paper, we outline computational methods for analyzing MALDI-imaging data with the emphasis on multivariate statistical methods, discuss their pros and cons, and give recommendations on their application. The methods of unsupervised data mining as well as supervised classification methods for biomarker discovery are elucidated. We also present a high-throughput computational pipeline for interpretation of MALDI-imaging data using spatial segmentation. Finally, we discuss current challenges associated with the statistical analysis of MALDI-imaging data.
TL;DR: Empirical evidence is provided for the utility of the FRIENDS program in reducing anxiety and depressive symptoms among German children and perfectionism and avoidant coping acted as mediators of pre- to postintervention changes in anxiety scores.