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Parasites of the nematode genus Anisakis are associated with aquatic organisms. They can be found in a variety of marine hosts including whales, crustaceans, fish and cephalopods and are known to be the cause of the zoonotic disease anisakiasis, a painful inflammation of the gastro-intestinal tract caused by the accidental consumptions of infectious larvae raw or semi-raw fishery products. Since the demand on fish as dietary protein source and the export rates of seafood products in general is rapidly increasing worldwide, the knowledge about the distribution of potential foodborne human pathogens in seafood is of major significance for human health. Studies have provided evidence that a few Anisakis species can cause clinical symptoms in humans. The aim of our study was to interpolate the species range for every described Anisakis species on the basis of the existing occurrence data. We used sequence data of 373 Anisakis larvae from 30 different hosts worldwide and previously published molecular data (n = 584) from 53 field-specific publications to model the species range of Anisakis spp., using a interpolation method that combines aspects of the alpha hull interpolation algorithm as well as the conditional interpolation approach. The results of our approach strongly indicate the existence of species-specific distribution patterns of Anisakis spp. within different climate zones and oceans that are in principle congruent with those of their respective final hosts. Our results support preceding studies that propose anisakid nematodes as useful biological indicators for their final host distribution and abundance as they closely follow the trophic relationships among their successive hosts. The modeling might although be helpful for predicting the likelihood of infection in order to reduce the risk of anisakiasis cases in a given area.
Acanthocephalans are attractive candidates as model organisms for studying the ecology and co-evolutionary history of parasitic life cycles in the marine ecosystem. Adding to earlier molecular analyses of this taxon, a total of 36 acanthocephalans belonging to the classes Archiacanthocephala (3 species), Eoacanthocephala (3 species), Palaeacanthocephala (29 species), Polyacanthocephala (1 species) and Rotifera as outgroup (3 species) were analyzed by using Bayesian Inference and Maximum Likelihood analyses of nuclear 18S rDNA sequence. This data set included three re-collected and six newly collected taxa, Bolbosoma vasculosum from Lepturacanthus savala, Filisoma rizalinum from Scatophagus argus, Rhadinorhynchus pristis from Gempylus serpens, R. lintoni from Selar crumenophthalmus, Serrasentis sagittifer from Johnius coitor, and Southwellina hispida from Epinephelus coioides, representing 5 new host and 3 new locality records. The resulting trees suggest a paraphyletic arrangement of the Echinorhynchida and Polymorphida inside the Palaeacanthocephala. This questions the placement of the genera Serrasentis and Gorgorhynchoides within the Echinorhynchida and not the Polymorphida, necessitating further insights into the systematic position of these taxa based on morphology.
Recent phylogenomic studies have failed to conclusively resolve certain branches of the placental mammalian tree, despite the evolutionary analysis of genomic data from 32 species. Previous analyses of single genes and retroposon insertion data yielded support for different phylogenetic scenarios for the most basal divergences. The results indicated that some mammalian divergences were best interpreted not as a single bifurcating tree, but as an evolutionary network. In these studies the relationships among some orders of the super-clade Laurasiatheria were poorly supported, albeit not studied in detail. Therefore, 4775 protein-coding genes (6,196,263 nucleotides) were collected and aligned in order to analyze the evolution of this clade. Additionally, over 200,000 introns were screened in silico, resulting in 32 phylogenetically informative long interspersed nuclear elements (LINE) insertion events.
The present study shows that the genome evolution of Laurasiatheria may best be understood as an evolutionary network. Thus, contrary to the common expectation to resolve major evolutionary events as a bifurcating tree, genome analyses unveil complex speciation processes even in deep mammalian divergences. We exemplify this on a subset of 1159 suitable genes that have individual histories, most likely due to incomplete lineage sorting or introgression, processes that can make the genealogy of mammalian genomes complex.
These unexpected results have major implications for the understanding of evolution in general, because the evolution of even some higher level taxa such as mammalian orders may sometimes not be interpreted as a simple bifurcating pattern.
Background: Fishes show an amazing diversity in hearing abilities, inner ear structures, and otolith morphology. Inner ear morphology, however, has not yet been investigated in detail in any member of the diverse order Cyprinodontiformes. We, therefore, studied the inner ear of the cyprinodontiform freshwater fish Poecilia mexicana by analyzing the position of otoliths in situ, investigating the 3D structure of sensory epithelia, and examining the orientation patterns of ciliary bundles of the sensory hair cells, while combining μ-CT analyses, scanning electron microscopy, and immunocytochemical methods. P. mexicana occurs in different ecotypes, enabling us to study the intra-specific variability (on a qualitative basis) of fish from regular surface streams, and the Cueva del Azufre, a sulfidic cave in southern Mexico.
Results: The inner ear of Poecilia mexicana displays a combination of several remarkable features. The utricle is connected rostrally instead of dorso-rostrally to the saccule, and the macula sacculi, therefore, is very close to the utricle. Moreover, the macula sacculi possesses dorsal and ventral bulges. The two studied ecotypes of P. mexicana showed variation mainly in the shape and curvature of the macula lagenae, in the curvature of the macula sacculi, and in the thickness of the otolithic membrane.
Conclusions: Our study for the first time provides detailed insights into the auditory periphery of a cyprinodontiform inner ear and thus serves a basis—especially with regard to the application of 3D techniques—for further research on structure-function relationships of inner ears within the species-rich order Cyprinodontiformes. We suggest that other poeciliid taxa, or even other non-poeciliid cyprinodontiforms, may display similar inner ear morphologies as described here.
The duration of use is usually significantly longer for marine vessels than for roadside vehicles. Therefore, these vessels are often powered by relatively old engines which may propagate air pollution. Also, the quality of fuel used for marine vessels is usually not comparable to the quality of fuels used in the automotive sector and therefore, port areas may exhibit a high degree of air pollution. In contrast to the multitude of studies that addressed outdoor air pollution due to road traffic, only little is known about ship-related air pollution. Therefore the present article aims to summarize recent studies that address air pollution, i.e. particulate matter exposure, due to marine vessels. It can be stated that the data in this area of research is still largely limited. Especially, knowledge on the different air pollutions in different sea areas is needed.
Background: Drowning is a constant global problem which claims proximately half a million victims worldwide each year, whereas the number of near-drowning victims is considerably higher. Public health strategies to reduce the burden of death are still limited. While research activities in the subject drowning grow constantly, yet there is no scientometric evaluation of the existing literature at the present time.
Methods: The current study uses classical bibliometric tools and visualizing techniques such as density equalizing mapping to analyse and evaluate the scientific research in the field of drowning. The interpretation of the achieved results is also implemented in the context of the data collection of the WHO.
Results: All studies related to drowning and listed in the ISI-Web of Science database since 1900 were identified using the search term "drowning". Implementing bibliometric methods, a constant increase in quantitative markers such as number of publications per state, publication language or collaborations as well as qualitative markers such as citations were observed for research in the field of drowning. The combination with density equalizing mapping exposed different global patterns for research productivity and the total number of drowning deaths and drowning rates respectively. Chart techniques were used to illustrate bi- and multilateral research cooperation.
Conclusions: The present study provides the first scientometric approach that visualizes research activity on the subject of drowning. It can be assumed that the scientific approach to this topic will achieve even greater dimensions because of its continuing actuality.
Background: Closely related lineages of livebearing fishes have independently adapted to two extreme environmental factors: toxic hydrogen sulphide (H2S) and perpetual darkness. Previous work has demonstrated in adult specimens that fish from these extreme habitats convergently evolved drastically increased head and offspring size, while cave fish are further characterized by reduced pigmentation and eye size. Here, we traced the development of these (and other) divergent traits in embryos of Poecilia mexicana from benign surface habitats (“surface mollies”) and a sulphidic cave (“cave mollies”), as well as in embryos of the sister taxon, Poecilia sulphuraria from a sulphidic surface spring (“sulphur mollies”). We asked at which points during development changes in the timing of the involved processes (i.e., heterochrony) would be detectible.
Methods and Results: Data were extracted from digital photographs taken of representative embryos for each stage of development and each type of molly. Embryo mass decreased in convergent fashion, but we found patterns of embryonic fat content and ovum/embryo diameter to be divergent among all three types of mollies. The intensity of yellow colouration of the yolk (a proxy for carotenoid content) was significantly lower in cave mollies throughout development. Moreover, while relative head size decreased through development in surface mollies, it increased in both types of extremophile mollies, and eye growth was arrested in mid-stage embryos of cave mollies but not in surface or sulphur mollies.
Conclusion: Our results clearly demonstrate that even among sister taxa convergence in phenotypic traits is not always achieved by the same processes during embryo development. Furthermore, teleost development is crucially dependent on sufficient carotenoid stores in the yolk, and so we discuss how the apparent ability of cave mollies to overcome this carotenoid-dependency may represent another potential mechanism explaining the lack of gene flow between surface and cave mollies.
Background and Objective: The slow delayed rectifier current (IKs) is important for cardiac action potential termination. The underlying channel is composed of Kv7.1 α-subunits and KCNE1 β-subunits. While most evidence suggests a role of KCNE1 transmembrane domain and C-terminus for the interaction, the N-terminal KCNE1 polymorphism 38G is associated with reduced IKs and atrial fibrillation (a human arrhythmia). Structure-function relationship of the KCNE1 N-terminus for IKs modulation is poorly understood and was subject of this study.
Methods: We studied N-terminal KCNE1 constructs disrupting structurally important positively charged amino-acids (arginines) at positions 32, 33, 36 as well as KCNE1 constructs that modify position 38 including an N-terminal truncation mutation. Experimental procedures included molecular cloning, patch-clamp recording, protein biochemistry, real-time-PCR and confocal microscopy.
Results: All KCNE1 constructs physically interacted with Kv7.1. IKs resulting from co-expression of Kv7.1 with non-atrial fibrillation ‘38S’ was greater than with any other construct. Ionic currents resulting from co-transfection of a KCNE1 mutant with arginine substitutions (‘38G-3xA’) were comparable to currents evoked from cells transfected with an N-terminally truncated KCNE1-construct (‘Δ1-38’). Western-blots from plasma-membrane preparations and confocal images consistently showed a greater amount of Kv7.1 protein at the plasma-membrane in cells co-transfected with the non-atrial fibrillation KCNE1-38S than with any other construct.
Conclusions: The results of our study indicate that N-terminal arginines in positions 32, 33, 36 of KCNE1 are important for reconstitution of IKs. Furthermore, our results hint towards a role of these N-terminal amino-acids in membrane representation of the delayed rectifier channel complex.
Background: MicroRNA-21 (miR-21) is up-regulated in tumor tissue of patients with malignant diseases, including hepatocellular carcinoma (HCC). Elevated concentrations of miR-21 have also been found in sera or plasma from patients with malignancies, rendering it an interesting candidate as serum/plasma marker for malignancies. Here we correlated serum miR-21 levels with clinical parameters in patients with different stages of chronic hepatitis C virus infection (CHC) and CHC-associated HCC.
Methodology/Principal Findings: 62 CHC patients, 29 patients with CHC and HCC and 19 healthy controls were prospectively enrolled. RNA was extracted from the sera and miR-21 as well as miR-16 levels were analyzed by quantitative real-time PCR; miR-21 levels (normalized by miR-16) were correlated with standard liver parameters, histological grading and staging of CHC. The data show that serum levels of miR-21 were elevated in patients with CHC compared to healthy controls (P<0.001); there was no difference between serum miR-21 in patients with CHC and CHC-associated HCC. Serum miR-21 levels correlated with histological activity index (HAI) in the liver (r = −0.494, P = 0.00002), alanine aminotransferase (ALT) (r = −0.309, P = 0.007), aspartate aminotransferase (r = −0.495, P = 0.000007), bilirubin (r = −0.362, P = 0.002), international normalized ratio (r = −0.338, P = 0.034) and γ-glutamyltransferase (r = −0.244, P = 0.034). Multivariate analysis revealed that ALT and miR-21 serum levels were independently associated with HAI. At a cut-off dCT of 1.96, miR-21 discriminated between minimal and mild-severe necroinflammation (AUC = 0.758) with a sensitivity of 53.3% and a specificity of 95.2%.
Conclusions/Significance: The serum miR-21 level is a marker for necroinflammatory activity, but does not differ between patients with HCV and HCV-induced HCC.
Although climate is known to be one of the key factors determining animal species distributions amongst others, projections of global change impacts on their distributions often rely on bioclimatic envelope models. Vegetation structure and landscape configuration are also key determinants of distributions, but they are rarely considered in such assessments. We explore the consequences of using simulated vegetation structure and composition as well as its associated landscape configuration in models projecting global change effects on Iberian bird species distributions. Both present-day and future distributions were modelled for 168 bird species using two ensemble forecasting methods: Random Forests (RF) and Boosted Regression Trees (BRT). For each species, several models were created, differing in the predictor variables used (climate, vegetation, and landscape configuration). Discrimination ability of each model in the present-day was then tested with four commonly used evaluation methods (AUC, TSS, specificity and sensitivity). The different sets of predictor variables yielded similar spatial patterns for well-modelled species, but the future projections diverged for poorly-modelled species. Models using all predictor variables were not significantly better than models fitted with climate variables alone for ca. 50% of the cases. Moreover, models fitted with climate data were always better than models fitted with landscape configuration variables, and vegetation variables were found to correlate with bird species distributions in 26–40% of the cases with BRT, and in 1–18% of the cases with RF. We conclude that improvements from including vegetation and its landscape configuration variables in comparison with climate only variables might not always be as great as expected for future projections of Iberian bird species.
Functional near-infrared spectroscopy (fNIRS) is an established optical neuroimaging method for measuring functional hemodynamic responses to infer neural activation. However, the impact of individual anatomy on the sensitivity of fNIRS measuring hemodynamics within cortical gray matter is still unknown. By means of Monte Carlo simulations and structural MRI of 23 healthy subjects (mean age: (25.0 +- 2.8 years), we characterized the individual distribution of tissue-specific NIR-light absorption underneath 24 prefrontal fNIRS channels. We, thereby, investigated the impact of scalp-cortex distance (SCD), frontal sinus volume as well as sulcal morphology on gray matter volumes (V gray) traversed by NIR-light, i.e. anatomy-dependent fNIRS sensitivity. The NIR-light absorption between optodes was distributed describing a rotational ellipsoid with a mean penetration depth of (23.6 +- 0.7 mm) considering the deepest 5% of light. Of the detected photon packages scalp and bone absorbed (96.4 +- 9.7)% and absorbed (3,1 +- 1.8)% of the energy. The mean V gray volume (1.1 +- 0.4)cm 3 was negatively correlated (r = -.76) with the SCD and frontal sinus volume (r= -.57) and was reduced by in subjects with relatively large compared to small frontal sinus. Head circumference was significantly positively correlated with the mean SCD (r= .46) and the traversed frontal sinus volume (r= .43). Sulcal morphology had no significant impact on . Our findings suggest to consider individual SCD and frontal sinus volume as anatomical factors impacting fNIRS sensitivity. Head circumference may represent a practical measure to partly control for these sources of error variance.
Various optimality principles have been proposed to explain the characteristics of coordinated eye and head movements during visual orienting behavior. At the same time, researchers have suggested several neural models to underly the generation of saccades, but these do not include online learning as a mechanism of optimization. Here, we suggest an open-loop neural controller with a local adaptation mechanism that minimizes a proposed cost function. Simulations show that the characteristics of coordinated eye and head movements generated by this model match the experimental data in many aspects, including the relationship between amplitude, duration and peak velocity in head-restrained and the relative contribution of eye and head to the total gaze shift in head-free conditions. Our model is a first step towards bringing together an optimality principle and an incremental local learning mechanism into a unified control scheme for coordinated eye and head movements.
This paper considers the logic FOcard, i.e., first-order logic with cardinality predicates that can specify the size of a structure modulo some number. We study the expressive power of FOcard on the class of languages of ranked, finite, labelled trees with successor relations. Our first main result characterises the class of FOcard-definable tree languages in terms of algebraic closure properties of the tree languages. As it can be effectively checked whether the language of a given tree automaton satisfies these closure properties, we obtain a decidable characterisation of the class of regular tree languages definable in FOcard. Our second main result considers first-order logic with unary relations, successor relations, and two additional designated symbols < and + that must be interpreted as a linear order and its associated addition. Such a formula is called addition-invariant if, for each fixed interpretation of the unary relations and successor relations, its result is independent of the particular interpretation of < and +. We show that the FOcard-definable tree languages are exactly the regular tree languages definable in addition-invariant first-order logic. Our proof techniques involve tools from algebraic automata theory, reasoning with locality arguments, and the use of logical interpretations. We combine and extend methods developed by Benedikt and Segoufin (ACM ToCL, 2009) and Schweikardt and Segoufin (LICS, 2010).
Membrane proteins (MPs) constitute about 30% of the genome and are essential in many cellular processes. In particular structural characterisation of MPs is challenged by their hydrophobic nature resulting in expression difficulties and structural instability upon extraction from the membrane. Despite these challenges, progress in sample preparation and the techniques to solve MP structures has led to 281 unique MP structures as of January 2011. Through the combination of a cell-free expression system and selective labelling strategies, this thesis aimed to advance the structure determination of α-helical MPs by NMR spectroscopy and resulted in the structure determination of a seven-ransmembrane-helix protein. Results were obtained for the 5-lipoxygenase-activating protein (FLAP) and proteorhodopsin (PR). The detergent-based cell-free expression mode proved most efficient for production of both targets, but optimisation of FLAP and PR followed different routes. The presence of a retinal cofactor in PR greatly facilitated the search for an appropriate hydrophobic environment. For structural studies, NMR spectra of FLAP indicated favourable properties of the lysolipid LPPG. In contrast, PR was stable and homogenous in the short-chain lipid diC7PC. As NMR spectra of α-helical MPs are generally characterised by broad lines and signal overlap, selective labelling strategies were essential in the assignment process of both targets. For the backbone assignment of FLAP the transmembrane segment-enhanced (TMS) labelling was developed, employing the six amino acids AFGILV. These residues cluster predominantly in transmembrane helices and form long stretches allowing a large extent of backbone assignment. Besides that, the combinatorial labelling enables identification of unique pairs in the sequence based on a mixture of 15N and 1-13C-labelled amino acids. To find the optimal labelling pattern for a given primary structure, the UPLABEL algorithm has been made available and successfully applied in the backbone assignment of PR. Both selective labelling approaches greatly benefitted from the use of a cell-free expression system to reduce isotope scrambling. Additionally, the de novo structure of PR was determined with an average backbone rmsd of 1.2 Å based on TALOS-derived backbone torsion angles, intrahelical hydrogen bond restraints and distance restraints from the NOE and paramagnetic relaxation enhancement (PRE). A major bottleneck in the NMR structure determination of MPs concerns the number of long-range distances which are often limited. In PR, side chain assignment was enabled by stereo-array isotope labelling as well as selective labelling which provided 33 long-range NOEs. These NOEs stabilised the symmetry of the seven helix bundle. With a total number of 1031, the majority of long-range distances were derived from PREs. The structure of PR reveals differences to its homologues such as the absence of an anti-parallel β-sheet between helices B and C and allows conclusions towards the mechanism of colour tuning.
The role of small leucine-rich proteoglycans, biglycan and decorin, in podocytopathy and albuminuria
(2011)
Biglycan is a member of the small leucine-rich proteoglycan (SLRP) family and is involved in the assembly of extracellular matrix components. In macrophages soluble biglycan acts as an endogenous ligand of the innate immunity receptors TLR2 and TLR4. Data addressing the role of biglycan in renal pathology are surprisingly limited. In a normal kidney, biglycan is expressed mainly in the tubulointerstitium; however, in the course of various renal diseases its expression may be altered. The biological role and mechanisms of biglycan action in the pathology of renal diseases, especially those affecting glomeruli, remain poorly understood.
Albuminuria is the first detectable clinical abnormality in diabetic nephropathy. In this study we detected increased biglycan mRNA expression in glomeruli of renal biopsies of patients with incipient diabetic nephropathy, with predominant localization in podocytes. This novel finding raised the question about the role and mechanisms of biglycan action in diabetic podocyte injury and whether the mechanisms of biglycan signaling causing podocyte injury and albuminuria could be extrapolated to other glomerular diseases.
To investigate the role of biglycan in the cause of diabetic podocyte injury and albuminuria we used the murine model of STZ-induced diabetic nephropathy and wild type (Bgn+/0) and biglycan deficient (Bgn-/0) mice. We observed that biglycan was expressed on mRNA and protein levels in podocytes of diabetic Bgn+/0 mice and that diabetic Bgn+/0 mice also had significantly higher albuminuria compared to non-diabetic mice 6 and 12 weeks after disease induction. Biglycan deficiency was shown to be an important factor in albuminuria development. Namely, we observed that diabetic Bgn-/0 mice had significantly lower levels of urinary albumin compared to diabetic Bgn+/0 mice. We showed that less severe podocyte loss in the urine of diabetic Bgn-/0 mice was associated with significantly higher nephrin and podocin glomerular expression compared to diabetic Bgn+/0 mice. Our data suggested that biglycan deficiency was protective against podocyte loss into urine and might be beneficial against development of albuminuria in diabetes.
Biglycan contributed to podocyte actin rearrangement due to increased phosphorylation of Rac1 in vitro. Furthermore, biglycan induced caspase-3 activity and production of reactive oxygen species (ROS), thus enhancing apoptosis in cultured podocytes. Biglycan-induced ROS generation was TLR2/TLR4-dependent. Overexpression of soluble biglycan in wild type mice induced albuminuria under normal conditions and significantly increased albuminuria under pathological conditions (murine model of LPS-induced albuminuria). Inhibition of Rac1 activity in vivo decreased the albuminuria induced by biglycan overexpression. In patients with glomerular diseases, biglycan was detected in urine and was associated with nephrin appearance in the urine of these patients and with increased albuminuria. Collectively, our results elucidate a novel mechanism for biglycan-induced TLR2- and TLR4-dependent, Rac1- and ROS-mediated podocytopathy leading to podocyturia, albuminuria development and progression of glomerular diseases. Interfering with biglycan actions and blocking its signaling via TLR2 and TLR4 might be a potential therapeutic strategy against these diseases. To achieve this goal, the specific mechanisms for binding of biglycan to TLR2 and TLR4 must be elucidated and effective ways of preventing this binding must be developed. Nevertheless, biglycan remains the “danger signal” that activates innate immune receptors in non-immune cells and triggers the deleterious mechanisms leading to aggravation of renal injury.
Soil biogenic NO emissions (SNOx) play important direct and indirect roles in chemical processes of the troposphere. The most widely applied algorithm to calculate SNOx in global models was published 15 years ago by Yienger and Levy (1995), was based on very few measurements. Since then numerous new measurements have been published, which we used to build up a atabase of field measurements conducted world wide covering the period from 1978 to 2009, including 108 publications with 560 measurements.
Recently, several satellite based top-down approaches, which recalculated the different sources of NOx (fossil fuel, biomass burning, soil and lightning), have shown an underestimation of SNOx by the algorithm of Yienger and Levy (1995). Nevertheless, to our knowledge no general improvements of this algorithm have yet been published.
Here we present major improvements to the algorithm, which should help to optimize the representation of SNOx in atmospheric-chemistry global climate models, without modifying the underlying principal or mathematical equations. The changes include: 1) Using a new up to date land cover map, with twice the number of land cover classes, and using annually varying fertilizer application rates; 2) Adopting the fraction of SNOx induced by fertilizer application based on our database; 3) Switching from soil water column to volumetric soil moisture, to distinguish between the wet and dry state; 4) Tuning the emission factors to reproduce the measured emissions in our database and calculate the emissions based on their mean value. These steps lead us to increased global yearly SNOx, and our total SNOx source ends up being close to one of the top-down approaches. In some geographical regions the new results agree better with the top-down approach, but there are also distinct differences in other regions. This suggests that a ombination of both top-down and bottom-up approaches could be combined in a future attempt to provide an even better calculation of SNOx.
Biogenic NO emissions from soils (SNOx) play important direct and indirect roles in tropospheric chemistry. The most widely applied algorithm to calculate SNOx in global models was published 15 years ago by Yienger and Levy (1995), and was based on very few measurements. Since then, numerous new measurements have been published, which we used to build up a compilation of world wide field measurements covering the period from 1978 to 2010. Recently, several satellite-based top-down approaches, which recalculated the different sources of NOx (fossil fuel, biomass burning, soil and lightning), have shown an underestimation of SNOx by the algorithm of Yienger and Levy (1995). Nevertheless, to our knowledge no general improvements of this algorithm, besides suggested scalings of the total source magnitude, have yet been published. Here we present major improvements to the algorithm, which should help to optimize the representation of SNOx in atmospheric-chemistry global climate models, without modifying the underlying principals or mathematical equations. The changes include: (1) using a new landcover map, with twice the number of landcover classes, and using annually varying fertilizer application rates; (2) adopting a fraction of 1.0 % for the applied fertilizer lost as NO, based on our compilation of measurements; (3) using the volumetric soil moisture to distinguish between the wet and dry states; and (4) adjusting the emission factors to reproduce the measured emissions in our compilation (based on either their geometric or arithmetic mean values). These steps lead to increased global annual SNOx, and our total above canopy SNOx source of 8.6 Tg yr−1 (using the geometric mean) ends up being close to one of the satellite-based top-down approaches (8.9 Tg yr−1). The above canopy SNOx source using the arithmetic mean is 27.6 Tg yr−1, which is higher than all previous estimates, but compares better with a regional top-down study in eastern China. This suggests that both top-down and bottom-up approaches will be needed in future attempts to provide a better calculation of SNOx.
Which factors determine whether a stimulus is consciously perceived or unconsciously processed? Here, I investigate how previous experience on two different time scales – long term experience over the course of several days, and short term experience based on the previous trial – impact conscious perception. Regarding long term experience, I investigate how perceptual learning does not only change the capacity to process stimuli, but also the capacity to consciously perceive them. To this end, subjects are trained extensively to discriminate between masked stimuli, and concurrently rate their subjective experience. Both the ability to discriminate the stimuli as well as subjective awareness of the stimuli increase as a function of training. However, these two effects are not simple byproducts of each other. On the contrary, they display different time courses, with above chance discrimination performance emerging before subjective experience; importantly, the two learning effects also rely on different circuits in the brain: Moving the stimuli outside the trained receptive field size abolishes the learning effects on discrimination ability, but preserves the learning effects on subjective awareness.
This indicates that the receptive fields serving subjective experience are larger than the ones serving objective performance, and that the channels through which they receive their information are arranged in parallel. Regarding short term experience, I investigate how memory based predictions arising from information acquired on the trial before affect visibility and the neural correlates of consciousness. To this end, I vary stimulus evidence as well as predictability and acquire electroencephalographic data.
A comparison of the neural processes distinguishing consciously perceived from unperceived trials with and without predictions reveals that predictions speed up processing, thus shifting the neural correlates forward in time. Thus, the neural correlates of consciousness display a previously unappreciated flexibility in time and do not arise invariably late as had been predicted by some theorists.
Admittedly, however, previous experience does not always stabilize perception. Instead, previous experience can have the reverse effect: Seeing the opposite of what was there, as in so-called repulsive aftereffects. Here, I investigate what determines the direction of previous experience using multistable stimuli. In a functional magnetic resonance imaging experiment, I find that a widespread network of frontal, parietal, and ventral occipital brain areas is involved in perceptual stabilization, whereas the reverse effect is only evident in extrastriate cortex. This areal separation possibly endows the brain with the flexibility to switch between exploiting already available information and emphasizing the new.
Taken together, my data show that conscious perception and its neuronal correlates display a remarkable degree of flexibility and plasticity, which should be taken into account in future theories of consciousness.
Residual circulation trajectories and transit times into the extratropical lowermost stratosphere
(2011)
Transport into the extratropical lowermost stratosphere (LMS) can be divided into a slow part (time-scale of several months to years) associated with the global-scale stratospheric residual circulation and a fast part (time-scale of days to a few months) associated with (mostly quasi-horizontal) mixing (i.e. two-way irreversible transport, including extratropical stratosphere-troposphere exchange). The stratospheric residual circulation may be considered to consist of two branches: a deep branch more strongly associated with planetary waves breaking in the middle to upper stratosphere, and a shallow branch associated with synoptic and planetary scale waves breaking in the subtropical lower stratosphere. In this study the contribution due to the stratospheric residual circulation alone to transport into the LMS is quantified using residual circulation trajectories, i.e. trajectories driven by the (time-dependent) residual mean meridional and vertical velocities. This contribution represents the advective part of the overall transport into the LMS and can be viewed as providing a background onto which the effect of mixing has to be added. Residual mean velocities are obtained from a comprehensive chemistry-climate model as well as from reanalysis data. Transit times of air traveling from the tropical tropopause to the LMS along the residual circulation streamfunction are evaluated and compared to recent mean age of air estimates. A time-scale separation with much smaller transit times into the mid-latitudinal LMS than into polar LMS is found that is indicative of a separation of the shallow from the deep branch of the residual circulation. This separation between the shallow and the deep circulation branch is further manifested in a distinction in the aspect ratio of the vertical to meridional extent of the trajectories, the integrated mass flux along the residual circulation trajectories, as well as the stratospheric entry latitude of the trajectories. The residual transit time distribution reproduces qualitatively the observed seasonal cycle of youngest air in the extratropical LMS in fall and oldest air in spring.