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A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field
(2019)
Ancient evaporite deposits are geological archives of depositional environments characterized by a long‐term negative precipitation balance and bear evidence for global ocean element mass balance calculations. Here, Cretaceous selenite pseudomorphs from western Anatolia (‘Rosetta Marble’) — characterized by their exceptional morphological preservation — and their ‘marine’ geochemical signatures are described and interpreted in a process‐oriented context. These rocks recorded Late Cretaceous high‐pressure/low‐temperature, subduction‐related metamorphism with peak conditions of 1·0 to 1·2 GPa and 300 to 400°C. Metre‐scale, rock‐forming radiating rods, now present as fibrous calcite marble, clearly point to selenitic gypsum as the precursor mineral. Stratigraphic successions are recorded along a reconstructed proximal to distal transect. The cyclical alternation of selenite beds and radiolarian ribbon‐bedded cherts in the distal portions are interpreted as a two type of seawater system. During arid intervals, shallow marine brines cascaded downward into basinal settings and induced precipitation. During more humid times, upwelling‐induced radiolarian blooms caused the deposition of radiolarite facies. Interestingly, there is no comparable depositional setting known from the Cenozoic world. Meta‐selenite geochemical data (δ13C, δ18O and 87Sr/86Sr) plot within the range of reconstructed middle Cretaceous seawater signatures. Possible sources for the 13C‐enriched (mean 2·2‰) values include methanogenesis, gas hydrates and cold seep fluid exhalation. Spatially resolved component‐specific analysis of a rock slab displays isotopic variances between meta‐selenite crystals (mean δ13C 2·2‰) and host matrix (mean δ13C 1·3‰). The Cretaceous evaporite‐pseudomorphs of Anatolia represent a basin wide event coeval with the Aptian evaporites of the Proto‐Atlantic and the pseudomorphs share many attributes, including lateral distribution of 600 km and stratigraphic thickness of 1·5 to 2·0 km, with the evaporites formed during the younger Messinian salinity crisis. The Rosetta Marble of Anatolia may represent the best‐preserved selenite pseudomorphs worldwide and have a clear potential to act as a template for the study of meta‐selenite in deep time.
Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming.
Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons.
Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.
Advances in the field of seismic interferometry have provided a basic theoretical interpretation to the full spectrum of the microtremor horizontal-to-vertical spectral ratio [H/V(f)]. The interpretation has been applied to ambient seismic noise data recorded both at the surface and at depth. The new algorithm, based on the diffuse wavefield assumption, has been used in inversion schemes to estimate seismic wave velocity profiles that are useful input information for engineering and exploration seismology both for earthquake hazard estimation and to characterize surficial sediments. However, until now, the developed algorithms are only suitable for on land environments with no offshore consideration. Here, the microtremor H/V(z, f) modelling is extended for applications to marine sedimentary environments for a 1-D layered medium. The layer propagator matrix formulation is used for the computation of the required Green’s functions. Therefore, in the presence of a water layer on top, the propagator matrix for the uppermost layer is defined to account for the properties of the water column. As an application example we analyse eight simple canonical layered earth models. Frequencies ranging from 0.2 to 50 Hz are considered as they cover a broad wavelength interval and aid in practice to investigate subsurface structures in the depth range from a few meters to a few hundreds of meters. Results show a marginal variation of 8 per cent at most for the fundamental frequency when a water layer is present. The water layer leads to variations in H/V peak amplitude of up to 50 per cent atop the solid layers.
A Fuzzy Rule-Based Model for Remote Monitoring of Preterm in the Intensive Care Unit of Hospitals
(2019)
The use of Remote patient monitoring (RPM) systems to monitor critically ill patients in the Intensive Care Unit (ICU) has enabled quality and real-time healthcare management. Fuzzy logic as an approach to designing RPM systems provides a means for encapsulating the subjective decision-making process of medical experts in an algorithm suitable for computer implementation. In this paper, a remote monitoring system for preterm in neonatal ICU incubators is modeled and simulated. The model was designed with 4 input variables (body temperature, heart rate, respiratory rate, and oxygen level saturation), and 1 output variable (action performed represented as ACT). ACT decides whether-an alert is generated or not and also determines the message displayed when a notification is required. ACT classifies the clinical priority of the monitored preterm into 5 different fields: code blue, code red, code yellow, code green, and-code black. The model was simulated using a fuzzy logic toolbox of MATLAB R2015A. About 216 IF_THEN rules were formulated to monitor the inputs data fed into the model. The performance of the model was evaluated using-the confusion matrix to determine the model’s accuracy, precision, sensitivity, specificity, and false alarm rate. The-experimental results obtained shows that the fuzzy-based system is capable of producing satisfactory results when used for monitoring and classifying the clinical statuses of neonates in ICU incubators.
A form-function mismatch?
(2019)
A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A
(2019)
The genetics of many congenital heart diseases (CHDs) can only unsatisfactorily be explained by known chromosomal or Mendelian syndromes. Here, we present sequencing data of a family with a potentially multigenic origin of CHD. Twelve of nineteen family members carry a familial mutation [NM_004329.2:c.1328 G > A (p.R443H)] which encodes a predicted deleterious variant of BMPR1A. This mutation co-segregates with a linkage region on chromosome 1 that associates with the emergence of severe CHDs including Ebstein’s anomaly, atrioventricular septal defect, and others. We show that the continuous overexpression of the zebrafish homologous mutation bmpr1aap.R438H within endocardium causes a reduced AV valve area, a downregulation of Wnt/ß-catenin signalling at the AV canal, and growth of additional tissue mass in adult zebrafish hearts. This finding opens the possibility of testing genetic interactions between BMPR1A and other candidate genes within linkage region 1 which may provide a first step towards unravelling more complex genetic patterns in cardiovascular disease aetiology.
Diagnostics of Autoimmune Diseases involve screening of patient samples for containing autoantibodies against various antigens. To ensure quality of diagnostic assays a calibrator is needed in each assay system. Different calibrators as recombinant human monoclonal antibodies as well as chimeric antibodies against the autoantigens of interest are described. A less cost-intensive and also more representative possibility covering different targets on the antigens is the utilization of polyclonal sera from other species. Nevertheless, the detection of human autoantibodies as well as the calibration reagent containing antibodies from other species in one assay constitutes a challenge in terms of assay calibration. We therefore developed a cross-reactive monoclonal antibody which binds human as well as rabbit sera with similar affinities in the nanomolar range. We tested our monoclonal antibody S38CD11B12 successfully in the commercial Serazym (R) Anti-Cardiolipin-beta 2-GPI IgG/IgM assay and could thereby prove the eligibility of S38CD11B12 as detection antibody in autoimmune diagnostic assays using rabbit derived sera as reference material.
Transverse dispersion, or tracer spreading orthogonal to the mean flow direction, which is relevant e.g, for quantifying bio-degradation of contaminant plumes or mixing of reactive solutes, has been studied in the literature less than the longitudinal one. Inferring transverse dispersion coefficients from field experiments is a difficult and error-prone task, requiring a spatial resolution of solute plumes which is not easily achievable in applications. In absence of field data, it is a questionable common practice to set transverse dispersivities as a fraction of the longitudinal one, with the ratio 1/10 being the most prevalent. We collected estimates of field-scale transverse dispersivities from existing publications and explored possible scale relationships as guidance criteria for applications. Our investigation showed that a large number of estimates available in the literature are of low reliability and should be discarded from further analysis. The remaining reliable estimates are formation-specific, span three orders of magnitude and do not show any clear scale-dependence on the plume traveled distance. The ratios with the longitudinal dispersivity are also site specific and vary widely. The reliability of transverse dispersivities depends significantly on the type of field experiment and method of data analysis. In applications where transverse dispersion plays a significant role, inference of transverse dispersivities should be part of site characterization with the transverse dispersivity estimated as an independent parameter rather than related heuristically to longitudinal dispersivity.
The Upper Cretaceous (Campanian-Maastrichtian) bioclastic wedge of the Orfento Formation in the Montagna della Maiella, Italy, is compared to newly discovered contourite drifts in the Maldives. Like the drift deposits in the Maldives, the Orfento Formation fills a channel and builds a Miocene delta-shaped and mounded sedimentary body in the basin that is similar in size to the approximately 350 km(2) large coarse-grained bioclastic Miocene delta drifts in the Maldives. The composition of the bioclastic wedge of the Orfento Formation is also exclusively bioclastic debris sourced from the shallow-water areas and reworked clasts of the Orfento Formation itself. In the near mud-free succession, age-diagnostic fossils are sparse. The depositional textures vary from wackestone to float-rudstone and breccia/conglomerates, but rocks with grainstone and rudstone textures are the most common facies. In the channel, lensoid convex-upward breccias, cross-cutting channelized beds and thick grainstone lobes with abundant scours indicate alternating erosion and deposition from a high-energy current. In the basin, the mounded sedimentary body contains lobes with a divergent progradational geometry. The lobes are built by decametre thick composite megabeds consisting of sigmoidal clinoforms that typically have a channelized topset, a grainy foreset and a fine-grained bottomset with abundant irregular angular clasts. Up to 30 m thick channels filled with intraformational breccias and coarse grainstones pinch out downslope between the megabeds. In the distal portion of the wedge, stacked grainstone beds with foresets and reworked intraclasts document continuous sediment reworking and migration. The bioclastic wedge of the Orfento Formation has been variously interpreted as a succession of sea-level controlled slope deposits, a shoaling shoreface complex, or a carbonate tidal delta. Current-controlled delta drifts in the Maldives, however, offer a new interpretation because of their similarity in architecture and composition. These similarities include: (i) a feeder channel opening into the basin; (ii) an excavation moat at the exit of the channel; (iii) an overall mounded geometry with an apex that is in shallower water depth than the source channel; (iv) progradation of stacked lobes; (v) channels that pinch out in a basinward direction; and (vi) smaller channelized intervals that are arranged in a radial pattern. As a result, the Upper Cretaceous (Campanian-Maastrichtian) bioclastic wedge of the Orfento Formation in the Montagna della Maiella, Italy, is here interpreted as a carbonate delta drift.
Design flood estimation is an essential part of flood risk assessment. Commonly applied are flood frequency analyses and design storm approaches, while the derived flood frequency using continuous simulation has been getting more attention recently. In this study, a continuous hydrological modelling approach on an hourly time scale, driven by a multi-site weather generator in combination with a -nearest neighbour resampling procedure, based on the method of fragments, is applied. The derived 100-year flood estimates in 16 catchments in Vorarlberg (Austria) are compared to (a) the flood frequency analysis based on observed discharges, and (b) a design storm approach. Besides the peak flows, the corresponding runoff volumes are analysed. The spatial dependence structure of the synthetically generated flood peaks is validated against observations. It can be demonstrated that the continuous modelling approach can achieve plausible results and shows a large variability in runoff volume across the flood events.
Apoptotic death of cells damaged by genotoxic stress requires regulatory input from surrounding tissues. The C. elegans scaffold protein KRI-1, ortholog of mammalian KRIT1/CCM1, permits DNA damage-induced apoptosis of cells in the germline by an unknown cell non-autonomous mechanism. We reveal that KRI-1 exists in a complex with CCM-2 in the intestine to negatively regulate the ERK-5/MAPK pathway. This allows the KLF-3 transcription factor to facilitate expression of the SLC39 zinc transporter gene zipt-2.3, which functions to sequester zinc in the intestine. Ablation of KRI-1 results in reduced zinc sequestration in the intestine, inhibition of IR-induced MPK-1/ERK1 activation, and apoptosis in the germline. Zinc localization is also perturbed in the vasculature of krit1(-/-) zebrafish, and SLC39 zinc transporters are mis-expressed in Cerebral Cavernous Malformations (CCM) patient tissues. This study provides new insights into the regulation of apoptosis by cross-tissue communication, and suggests a link between zinc localization and CCM disease.
The improvement of process representations in hydrological models is often only driven by the modelers' knowledge and data availability. We present a comprehensive comparison between two hydrological models of different complexity that is developed to support (1) the understanding of the differences between model structures and (2) the identification of the observations needed for model assessment and improvement. The comparison is conducted on both space and time and by aggregating the outputs at different spatiotemporal scales. In the present study, mHM, a process‐based hydrological model, and ParFlow‐CLM, an integrated subsurface‐surface hydrological model, are used. The models are applied in a mesoscale catchment in Germany. Both models agree in the simulated river discharge at the outlet and the surface soil moisture dynamics, lending their supports for some model applications (drought monitoring). Different model sensitivities are, however, found when comparing evapotranspiration and soil moisture at different soil depths. The analysis supports the need of observations within the catchment for model assessment, but it indicates that different strategies should be considered for the different variables. Evapotranspiration measurements are needed at daily resolution across several locations, while highly resolved spatially distributed observations with lower temporal frequency are required for soil moisture. Finally, the results show the impact of the shallow groundwater system simulated by ParFlow‐CLM and the need to account for the related soil moisture redistribution. Our comparison strategy can be applied to other models types and environmental conditions to strengthen the dialog between modelers and experimentalists for improving process representations in Earth system models.
A catalog of genetic loci associated with kidney function from analyses of a million individuals
(2019)
Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through transancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these,147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
Aldol reactions play an important role in organic synthesis, as they belong to the class of highly beneficial C-C-linking reactions. Aldol-type reactions can be efficiently and stereoselectively catalyzed by the enzyme 2-deoxy-D-ribose-5-phosphate aldolase (DERA) to gain key intermediates for pharmaceuticals such as atorvastatin. The immobilization of DERA would open the opportunity for a continuous operation mode which gives access to an efficient, large-scale production of respective organic intermediates. In this contribution, we synthesize and utilize DERA/polymer conjugates for the generation and fixation of a DERA bearing thin film on a polymeric membrane support. The conjugation strongly increases the tolerance of the enzyme toward the industrial relevant substrate acetaldehyde while UV-cross-linkable groups along the conjugated polymer chains provide the opportunity for covalent binding to the support. First, we provide a thorough characterization of the conjugates followed by immobilization tests on representative, nonporous cycloolefinic copolymer supports. Finally, immobilization on the target supports constituted of polyacrylonitrile (PAN) membranes is performed, and the resulting enzymatically active membranes are implemented in a simple membrane module setup for the first assessment of biocatalytic performance in the continuous operation mode using the combination hexanal/acetaldehyde as the substrate.
Remote Sensing technologies allow to map biophysical, biochemical, and earth surface parameters of the land surface. Of especial interest for various applications in environmental and urban sciences is the combination of spectral and 3D elevation information. However, those two data streams are provided separately by different instruments, namely airborne laser scanner (ALS) for elevation and a hyperspectral imager (HSI) for high spectral resolution data. The fusion of ALS and HSI data can thus lead to a single data entity consistently featuring rich structural and spectral information. In this study, we present the application of fusing the first pulse return information from ALS data at a sub-decimeter spatial resolution with the lower-spatial resolution hyperspectral information available from the HSI into a hyperspectral point cloud (HSPC). During the processing, a plausible hyperspectral spectrum is assigned to every first-return ALS point. We show that the complementary implementation of spectral and 3D information at the point-cloud scale improves object-based classification and information extraction schemes. This improvements have great potential for numerous land cover mapping and environmental applications.
We present a new three-dimensional density model of the Central Andes characterizing the structure and composition of the lithosphere together with a geodynamic simulation subjected to continental intraplate shortening. The principal aim of this study is to assess the link between heterogeneities in the lithosphere and different deformation patterns and styles along the orogen-foreland system of the Central Andes. First, we performed a 3D integration of new geological and geophysical data with previous models through forward modelling of Bouguer anomalies. Subsequently, a geodynamic model was set-up and parametrized from the previously obtained 3D structure and composition. We do not find a unambigous correlation between the resulting density configuration and terrane boundaries proposed by other authors. Our models reproduce the observed Bouguer anomaly and deformation patterns in the foreland. We find that thin-skinned deformation in the Subandean fold-and thrust belt is controlled by a thick sedimentary layer and coeval underthrusting of thin crust of the foreland beneath the thick crust of the Andean Plateau. In the adjacent thick-skinned deformation province of the inverted Cretaceous extensional Santa Barbara System sedimentary strata are much thinner and crustal thickness transitions from greater values in the Andean to a more reduced thickness in the foreland. Our results show that deformation processes occur where the highest gradients of lithospheric strength are present between the orogen and the foreland, thus suggesting a spatial correlation between deformation and lithospheric strength.
Geophysical data acquisition in oceanic domains is challenging, implying measurements with low and/or nonhomogeneous spatial resolution. The evolution of satellite gravimetry and altimetry techniques allows testing 3-D density models of the lithosphere, taking advantage of the high spatial resolution and homogeneous coverage of satellites. However, it is not trivial to discretise the source of the gravity field at different depths. Here, we propose a new method for inferring tectonic boundaries at the crustal level. As a novelty, instead of modeling the gravity anomalies and assuming a flat Earth approximation, we model the vertical gravity gradients (VGG) in spherical coordinates, which are especially sensitive to density contrasts in the upper layers of the Earth. To validate the methodology, the complex oceanic domain of the Caribbean region is studied, which includes different crustal domains with a tectonic history since Late Jurassic time. After defining a lithospheric starting model constrained by up-to-date geophysical data sets, we tested several a-priory density distributions and selected the model with the minimum misfits with respect to the VGG calculated from the EIGEN-6C4 data set. Additionally, the density of the crystalline crust was inferred by inverting the VGG field. Our methodology enabled us not only to refine, confirm, and/or propose tectonic boundaries in the study area but also to identify a new anomalous buoyant body, located in the South Lesser Antilles subduction zone, and high-density bodies along the Greater, Lesser, and Leeward Antilles forearcs.
The in-phase response collected by portable loop-loop electromagnetic induction (EMI) sensors operating at low and moderate induction numbers (<= 1) is typically used for sensing the magnetic permeability (or susceptibility) of the subsurface. This is due to the fact that the in-phase response contains a small induction fraction and a preponderant induced magnetization fraction. The magnetization fraction follows the magneto-static equations similarly to the magnetic method but with an active magnetic source. The use of an active source offers the possibility to collect data with several loop-loop configurations, which illuminate the subsurface with different sensitivity patterns. Such multiconfiguration soundings thereby allows the imaging of subsurface magnetic permeability/susceptibility variations through an inversion procedure. This method is not affected by the remnant magnetization and theoretically overcomes the classical depth ambiguity generally encountered with passive geomagnetic data. To invert multiconfiguration in-phase data sets, we propose a novel methodology based on a full-grid 3-D multichannel deconvolution (MCD) procedure. This method allows us to invert large data sets (e.g. consisting of more than a hundred thousand of data points) for a dense voxel-based 3-D model of magnetic susceptibility subject to smoothness constraints. In this study, we first present and discuss synthetic examples of our imaging procedure, which aim at simulating realistic conditions. Finally, we demonstrate the applicability of our method to field data collected across an archaeological site in Auvergne (France) to image the foundations of a Gallo-Roman villa built with basalt rock material. Our synthetic and field data examples demonstrate the potential of the proposed inversion procedure offering new and complementary ways to interpret data sets collected with modern EMI instruments.
Abstract. The Sea of Marmara, in northwestern Turkey, is a transition zone where the dextral North Anatolian Fault zone (NAFZ) propagates westward from the Anatolian Plate to the Aegean Sea Plate. The area is of interest in the context of seismic hazard of Istanbul, a metropolitan area with about 15 million inhabitants. Geophysical observations indicate that the crust is heterogeneous beneath the Marmara basin, but a detailed characterization of the crustal heterogeneities is still missing. To assess if and how crustal heterogeneities are related to the NAFZ segmentation below the Sea of Marmara, we develop new crustal-scale 3-D density models which integrate geological and seismological data and that are additionally constrained by 3-D gravity modeling. For the latter, we use two different gravity datasets including global satellite data and local marine gravity observation. Considering the two different datasets and the general non-uniqueness in potential field modeling, we suggest three possible “end-member” solutions that are all consistent with the observed gravity field and illustrate the spectrum of possible solutions. These models indicate that the observed gravitational anomalies originate from significant density heterogeneities within the crust. Two layers of sediments, one syn-kinematic and one pre-kinematic with respect to the Sea of Marmara formation are underlain by a heterogeneous crystalline crust. A felsic upper crystalline crust (average density of 2720 kgm⁻³) and an intermediate to mafic lower crystalline crust (average density of 2890 kgm⁻³) appear to be cross-cut by two large, dome-shaped mafic highdensity bodies (density of 2890 to 3150 kgm⁻³) of considerable thickness above a rather uniform lithospheric mantle (3300 kgm⁻³). The spatial correlation between two major bends of the main Marmara fault and the location of the highdensity bodies suggests that the distribution of lithological heterogeneities within the crust controls the rheological behavior along the NAFZ and, consequently, maybe influences fault segmentation and thus the seismic hazard assessment in the region.