Taxon-specific δ13C analysis of chitinous invertebrate remains in sediments from Strandsjön, Sweden

Taxon-specific stable carbon isotope (δ13C) analysis of chitinous remains of invertebrates can provide valuable information about the carbon sources used by invertebrates living in specific habitats of lake ecosystems (for example, sediments, water column, or aquatic vegetation). This is complementary to δ13C of sedimentary organic matter (SOM), which provides an integrated signal of organic matter produced in a lake and its catchment, and of diagenetic processes within sediments. In a sediment record from Strandsjön (Sweden) covering the past circa 140years, we analyzed SOM geochemistry (δ13C, C:Natomic, organic carbon content) and δ13C of chitinous invertebrate remains in order to examine whether taxon-specific δ13C records could be developed for different invertebrate groups and whether these analyses provide insights into past changes of organic carbon sources for lacustrine invertebrates available in benthic and planktonic compartments of the lake. Invertebrate taxa included benthic chironomids (Chironomus, Chironomini excluding Chironomus, Tanytarsini, and Tanypodinae), filter-feeders on suspended particulate organic matter (Daphnia, Plumatella and Cristatella mucedo), and Rhabdocoela. δ13C of chironomid remains indicated periodic availability of 13C-depleted carbon sources in the benthic environment of the lake as δ13C values of the different chironomid taxa fluctuated simultaneously between −34.7 and −30.5‰ (VPDB). Daphnia and Bryozoa showed parallel changes in their δ13C values which did not coincide with variations in δ13C of chironomids, though, and a 2-3‰ decrease since circa AD 1960. The decrease in δ13C of Daphnia and Bryozoa could indicate a decrease in phytoplankton δ13C as a result of lower lake productivity, which is in accordance with historical information about the lake that suggests a shift to less eutrophic conditions after AD 1960. In contrast, Rhabdocoela cocoons were characterized by relatively high δ13C values (−30.4 to −28.2‰) that did not show a strong temporal trend, which could be related to the predatory feeding mode and wide prey spectrum of this organism group. The taxon-specific δ13C analyses of invertebrate remains indicated that different carbon sources were available for the benthic chironomid larvae than for the filter-feeding Daphnia and bryozoans. Our results therefore demonstrate that taxon-specific analysis of δ13C of organic invertebrate remains can provide complementary information to measurements on bulk SOM and that δ13C of invertebrate remains may allow the reconstruction of past changes in carbon sources and their δ13C in different habitats of lake ecosystems

Multi Scale Curriculum CNN for Context-Aware Breast MRI Malignancy Classification

Classification of malignancy for breast cancer and other cancer types is usually tackled as an object detection problem: Individual lesions are first localized and then classified with respect to malignancy. However, the drawback of this approach is that abstract features incorporating several lesions and areas that are not labelled as a lesion but contain global medically relevant information are thus disregarded: especially for dynamic contrast-enhanced breast MRI, criteria such as background parenchymal enhancement and location within the breast are important for diagnosis and cannot be captured by object detection approaches properly. In this work, we propose a 3D CNN and a multi scale curriculum learning strategy to classify malignancy globally based on an MRI of the whole breast. Thus, the global context of the whole breast rather than individual lesions is taken into account. Our proposed approach does not rely on lesion segmentations, which renders the annotation of training data much more effective than in current object detection approaches. Achieving an AUROC of 0.89, we compare the performance of our approach to Mask R-CNN and Retina U-Net as well as a radiologist. Our performance is on par with approaches that, in contrast to our method, rely on pixelwise segmentations of lesions.Comment: Accepted to MICCAI 201

Compound-specific carbon and nitrogen isotopic compositions of chlorophyll a and its derivatives reveal the eutrophication history of Lake Zurich (Switzerland)

© 2016 Elsevier B.V. To reconstruct the impact of eutrophication on phototrophic communities and the biogeochemical cycling of carbon and nitrogen in the surface water, we investigated the distributions and carbon and nitrogen isotopic compositions (d13C and d15N values) of chlorins in the sediments of Lake Zurich. The chlorin distributions were dominated by chlorophyll a (Chl a) and its derivatives, which reflect rapid degradation to the pheopigments in the water column and sediments of the lake. The d13C values of these sedimentary chlorins followed the historical trends of eutrophication and reoligotrophication, except in the surface sediments, which were characterised by higher relative contributions of aged, redeposited organic matter (OM). The d13C values of the sedimentary chlorins together with bulk sediment d13C values and C/N ratios indicate that the phototrophic communities in the lake used a 13C-depleted carbon source, which is mainly of aquatic origin. The d15N values of chlorins reflect the predominance of nitrate assimilating phototrophs, especially the non-N2-fixing cyanobacterium Planktothrix rubescens prevalent during sediment deposition. Shifts in d15N values of Chl a followed mostly the trends in eutrophication and reoligotrophication, but were also affected by community assemblage shifts to diatoms and/or other cyanobacteria at the end of the 19th century and during the eutrophication maximum in the 1970s.The lower d15NChl-a values in the surface sediments coincide with increasing nitrogen to phosphorus ratios and reduced water column mixing that characterise the recent reoligotrophication period and may explain the predominance of P. rubescens in Lake Zurich. In contrast, the higher contributions of laterally transported OM explains the large offset of d15N values of the pheopigments relative to Chl a, which is supported by the high radiocarbon age of the surface sediments

The Swiss Multiple Sclerosis Cohort-Study (SMSC): A Prospective Swiss Wide Investigation of Key Phases in Disease Evolution and New Treatment Options.

The mechanisms leading to disability and the long-term efficacy and safety of disease modifying drugs (DMDs) in multiple sclerosis (MS) are unclear. We aimed at building a prospective cohort of MS patients with standardized collection of demographic, clinical, MRI data and body fluids that can be used to develop prognostic indicators and biomarkers of disease evolution and therapeutic response. The Swiss MS Cohort (SMSC) is a prospective observational study performed across seven Swiss MS centers including patients with MS, clinically isolated syndrome (CIS), radiologically isolated syndrome or neuromyelitis optica. Neurological and radiological assessments and biological samples are collected every 6-12 months. We recruited 872 patients (clinically isolated syndrome [CIS] 5.5%, relapsing-remitting MS [RRMS] 85.8%, primary progressive MS [PPMS] 3.5%, secondary progressive MS [SPMS] 5.2%) between June 2012 and July 2015. We performed 2,286 visits (median follow-up 398 days) and collected 2,274 serum, plasma and blood samples, 152 cerebrospinal fluid samples and 1,276 brain MRI scans. 158 relapses occurred and expanded disability status scale (EDSS) scores increased in PPMS, SPMS and RRMS patients experiencing relapses. Most RRMS patients were treated with fingolimod (33.4%), natalizumab (24.5%) or injectable DMDs (13.6%). The SMSC will provide relevant information regarding DMDs efficacy and safety and will serve as a comprehensive infrastructure available for nested research projects

Intraregional variability in chironomid-inferred temperature estimates and the influence of river inundations on lacustrine chironomid assemblages.

Floodplain lakes are rarely analysed for fossil chironomids and usually not incorporated in modern chironomid-climate calibration datasets because of the potential complex hydrological processes that could result from flooding of the lakes. In order to investigate this potential influence of river inundations on fossil chironomid assemblages, 13 regularly inundated lakes and 20 lakes isolated from riverine influence were sampled and their surface sediments analysed for subfossil chironomid assemblages. The physical and chemical settings of all lakes were similar, although the variation in the environmental variables was higher in the lakes isolated from riverine influence. Chironomid concentration and taxon richness show significant differences between the two classes of lakes, and the variation in these variables is best explained by loss-on-ignition of the sediments (LOI). Relative chironomid abundances show some differences between the two groups of lakes, with several chironomid taxa occurring preferentially in one of the two lake-types. The variability in chironomid assemblages is also best explained by LOI. Application of a chironomid-temperature inference model shows that both types of lakes reconstruct July air temperatures that are equal to, or slightly underestimating, the measured temperature of the region. We conclude that, although there are some differences between the chironomid assemblages of floodplain lakes and of isolated lakes, these differences do not have a major effect on chironomid-based temperature reconstruction. © 2007 Springer Science+Business Media B.V

Natural Killer T Cells Activated by a Lipopeptidophosphoglycan from Entamoeba histolytica Are Critically Important To Control Amebic Liver Abscess

The innate immune response is supposed to play an essential role in the control of amebic liver abscess (ALA), a severe form of invasive amoebiasis due to infection with the protozoan parasite Entamoeba histolytica. In a mouse model for the disease, we previously demonstrated that Jα18-/- mice, lacking invariant natural killer T (iNKT) cells, suffer from more severe abscess development. Here we show that the specific activation of iNKT cells using α-galactosylceramide (α-GalCer) induces a significant reduction in the sizes of ALA lesions, whereas CD1d−/− mice develop more severe abscesses. We identified a lipopeptidophosphoglycan from E. histolytica membranes (EhLPPG) as a possible natural NKT cell ligand and show that the purified phosphoinositol (PI) moiety of this molecule induces protective IFN-γ but not IL-4 production in NKT cells. The main component of EhLPPG responsible for NKT cell activation is a diacylated PI, (1-O-[(28∶0)-lyso-glycero-3-phosphatidyl-]2-O-(C16:0)-Ins). IFN-γ production by NKT cells requires the presence of CD1d and simultaneously TLR receptor signalling through MyD88 and secretion of IL-12. Similar to α-GalCer application, EhLPPG treatment significantly reduces the severity of ALA in ameba-infected mice. Our results suggest that EhLPPG is an amebic molecule that is important for the limitation of ALA development and may explain why the majority of E. histolytica-infected individuals do not develop amebic liver abscess

Measurement of the open-charm contribution to the diffractive proton structure function

Production of D*+/-(2010) mesons in diffractive deep inelastic scattering has been measured with the ZEUS detector at HERA using an integrated luminosity of 82 pb^{-1}. Diffractive events were identified by the presence of a large rapidity gap in the final state. Differential cross sections have been measured in the kinematic region 1.5 < Q^2 < 200 GeV^2, 0.02 < y < 0.7, x_{IP} < 0.035, beta 1.5 GeV and |\eta(D*+/-)| < 1.5. The measured cross sections are compared to theoretical predictions. The results are presented in terms of the open-charm contribution to the diffractive proton structure function. The data demonstrate a strong sensitivity to the diffractive parton densities.Comment: 35 pages, 11 figures, 6 table