Continuum microhaemodynamics modelling using inverse rheology

Modelling blood flow in microvascular networks is challenging due to the complex nature of haemorheology. Zero- and one-dimensional approaches cannot reproduce local haemodynamics, and models that consider individual red blood cells (RBCs) are prohibitively computationally expensive. Continuum approaches could provide an efficient solution, but dependence on a large parameter space and scarcity of experimental data for validation has limited their application. We describe a method to assimilate experimental RBC velocity and concentration data into a continuum numerical modelling framework. Imaging data of RBCs were acquired in a sequentially bifurcating microchannel for various flow conditions. RBC concentration distributions were evaluated and mapped into computational fluid dynamics simulations with rheology prescribed by the Quemada model. Predicted velocities were compared to particle image velocimetry data. A subset of cases was used for parameter optimisation, and the resulting model was applied to a wider data set to evaluate model efficacy. The pre-optimised model reduced errors in predicted velocity by 60% compared to assuming a Newtonian fluid, and optimisation further reduced errors by 40%. Asymmetry of RBC velocity and concentration profiles was demonstrated to play a critical role. Excluding asymmetry in the RBC concentration doubled the error, but excluding spatial distributions of shear rate had little effect. This study demonstrates that a continuum model with optimised rheological parameters can reproduce measured velocity if RBC concentration distributions are known a priori. Developing this approach for RBC transport with more network configurations has the potential to provide an efficient approach for modelling network-scale haemodynamics

Contribution of orbital forcing and Deccan volcanism to global climatic and biotic changes across the Cretaceous-Paleogene boundary at Zumaia, Spain

Untangling the timing of the environmental effects of Deccan volcanism with respect to the Chicxulub impact is instrumental to fully assessing the contributions of both to climate change over the Cretaceous-Paleogene boundary (KPB) interval. Despite recent improvements in radiometric age calibrations, the accuracy of age constraints and correlations is insufficient to resolve the exact mechanisms leading to environmental and climate change in the 1 m.y. across the KPB. We present new high-resolution planktic foraminiferal, geochemical, and geophysical data from the Zumaia section (Spain), calibrated to an updated orbitally tuned age model. We provide a revised chronology for the major carbon isotope excursions (CIEs) and planktic foraminiferal events and test temporal relationships with different models of the eruptive phases of the Deccan Traps. Our data show that the major CIEs near the KPB, i.e., the late Maastrichtian warming event (66.25–66.10 Ma) and the Dan-C2 event (65.8–65.7 Ma), are synchronous with the last and the first 405 k.y. eccentricity maximum of the Maastrichtian and the Danian, respectively, and that the minor Lower C29n event (65.48–65.41 Ma) is well constrained to a short eccentricity maximum. Conversely, we obtained evidence of abrupt environmental change likely related to Deccan volcanism at ca. 65.9 Ma, based on a bloom of opportunistic triserial guembelitriids (Chiloguembelitria). The orbital, isotopic, and paleobiological temporal relationships with Deccan volcanism established here provide new insights into the role of Deccan volcanism in climate and environmental change in the 1 m.y. across the KPB. © 2021. The Authors. Gold Open Access: This paper is published under the terms of the CC-BY license

Geometric reconstruction methods for electron tomography

Electron tomography is becoming an increasingly important tool in materials science for studying the three-dimensional morphologies and chemical compositions of nanostructures. The image quality obtained by many current algorithms is seriously affected by the problems of missing wedge artefacts and nonlinear projection intensities due to diffraction effects. The former refers to the fact that data cannot be acquired over the full $180^\circ$ tilt range; the latter implies that for some orientations, crystalline structures can show strong contrast changes. To overcome these problems we introduce and discuss several algorithms from the mathematical fields of geometric and discrete tomography. The algorithms incorporate geometric prior knowledge (mainly convexity and homogeneity), which also in principle considerably reduces the number of tilt angles required. Results are discussed for the reconstruction of an InAs nanowire

A re‐evaluation of the Plenus Cold Event, and the links between CO2, temperature, and seawater chemistry during OAE 2

International audienceThe greenhouse world of the mid‐Cretaceous (~94 Ma) was punctuated by an episode of abrupt climatic upheaval: Oceanic Anoxic Event 2 (OAE 2). High‐resolution climate records reveal considerable changes in temperature, carbon cycling, and ocean chemistry during this climatic perturbation. In particular, an interval of cooling has been detected in the English Chalk on the basis of an invasive boreal fauna and bulk oxygen‐isotope excursions registered during the early stages of OAE 2—a phenomenon known as the Plenus Cold Event (PCE), which has tentatively been correlated with climatic shifts worldwide.Here we present new high‐resolution neodymium‐, carbon‐, and oxygen‐isotope data, as well as elemental chromium concentrations and cerium anomalies, from the English Chalk exposed at Dover, UK, which we evaluate in the context of >400 records from across the globe. A negative carbon‐isotope excursion that correlates with the original ‘PCE’ is consistently expressed worldwide, and CO2 proxy records, where available, indicate a rise and subsequent fall in CO2 over the Plenus interval. However, variability in the timing and expression of cooling at different sites suggests that, although sea‐surface paleo‐temperatures may reflect a response to global CO2 change, local processes likely played a dominant role at many sites. Variability in the timing and expression of changes in water‐mass character, and problems in determining the driver of observed proxy changes, suggest that no single simple mechanism can link the carbon cycle to oceanography during the Plenus interval and other factors including upwelling and circulation patterns were locally important. As such, it is proposed that the Plenus carbon‐isotope event is a more reliable stratigraphic marker to identify the Plenus interval, rather than any climatic shifts that may have been overprinted by local effects

The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series

Pore REconstruction and Segmentation (PORES) method for improved porosity quantification of nanoporous materials

Electron tomography is currently a versatile tool to investigate the connection between the structure and properties of nanomaterials. However, a quantitative interpretation of electron tomography results is still far from straightforward. Especially accurate quantification of pore-space is hampered by artifacts introduced in all steps of the processing chain, i.e., acquisition, reconstruction, segmentation and quantification. Furthermore, most common approaches require subjective manual user input. In this paper, the PORES algorithm “POre REconstruction and Segmentation” is introduced; it is a tailor-made, integral approach, for the reconstruction, segmentation, and quantification of porous nanomaterials. The PORES processing chain starts by calculating a reconstruction with a nanoporous-specific reconstruction algorithm: the Simultaneous Update of Pore Pixels by iterative REconstruction and Simple Segmentation algorithm (SUPPRESS). It classifies the interior region to the pores during reconstruction, while reconstructing the remaining region by reducing the error with respect to the acquired electron microscopy data. The SUPPRESS reconstruction can be directly plugged into the remaining processing chain of the PORES algorithm, resulting in accurate individual pore quantification and full sample pore statistics. The proposed approach was extensively validated on both simulated and experimental data, indicating its ability to generate accurate statistics of nanoporous materials

Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene

Abstract Glucocorticoids act in part via glucocortocoid receptor binding to hormone response elements (HREs), but their direct target genes in vivo are still largely unknown. We developed the criterion that genomic occurrence of paired HREs at an inter-HRE distance less than 200 bp predicts hormone responsiveness, based on synergy of multiple HREs, and HRE information from known target genes. This criterion predicts a substantial number of novel responsive genes, when applied to genomic regions 10 kb upstream of genes. Multiple-tissue in situ hybridization showed that mRNA expression of 6 out of 10 selected genes was induced in a tissue-specific manner in mice treated with a single dose of corticosterone, with the spleen being the most responsive organ. Caveolin-1 was strongly responsive in several organs, and the HRE pair in its upstream region showed increased occupancy by glucocorticoid receptor in response to corticosterone. Our approach allowed for discovery of novel tissue specific glucocorticoid target genes, which may exemplify responses underlying the permissive actions of glucocorticoids

Late Maastrichtian carbon isotope stratigraphy and cyclostratigraphy of the Newfoundland Margin (Site U1403, IODP Expedition 342)

Earth’s climate during the Maastrichtian (latest Cretaceous) was punctuated by brief warming and cooling episodes, accompanied by perturbations of the global carbon cycle. Superimposed on a long-term cooling trend, the middle Maastrichtian is characterized by deep-sea warming and relatively high values of stable carbon-isotope ratios, followed by strong climatic variability towards the end of the Cretaceous. A lack of knowledge on the timing of climatic change inhibits our understanding of underlying causal mechanisms. We present an integrated stratigraphy from Integrated Ocean Drilling Program (IODP) Site U1403, providing an expanded deep ocean record from the North Atlantic (Expedition 342, Newfoundland Margin). Distinct sedimentary cyclicity suggests that orbital forcing played a major role in depositional processes, which is confirmed by statistical analyses of high resolution elemental data obtained by X-ray fluorescence (XRF) core scanning. Astronomical calibration reveals that the investigated interval encompasses seven 405-kyr cycles (Ma4051 to Ma4057) and spans the 2.8 Myr directly preceding the Cretaceous/Paleocene (K/Pg) boundary. A high-resolution carbon-isotope record from bulk carbonates allows us to identify global trends in the late Maastrichtian carbon cycle. Low-amplitude variations (up to 0.4‰) in carbon isotopes at Site U1403 match similar scale variability in records from Tethyan and Pacific open-ocean sites. Comparison between Site U1403 and the hemipelagic restricted basin of the Zumaia section (northern Spain), with its own well-established independent cyclostratigraphic framework, is more complex. Whereas the pre-K/Pg oscillations and the negative values of the Mid-Maastrichtian Event (MME) can be readily discerned in both the Zumaia and U1403 records, patterns diverge during a ~ 1 Myr period in the late Maastrichtian (67.8–66.8 Ma), with Site U1403 more reliably reflecting global carbon cycling. Our new carbon isotope record and cyclostratigraphy offer promise for Site U1403 to serve as a future reference section for high-resolution studies of late Maastrichtian paleoclimatic change

Measuring Lattice Strain in Three Dimensions through Electron Microscopy

The three-dimensional (3D) atomic structure of nanomaterials, including strain, is crucial to understand their properties. Here, we investigate lattice strain in Au nanodecahedra using electron tomography. Although different electron tomography techniques enabled 3D characterizations of nanostructures at the atomic level, a reliable determination of lattice strain is not straightforward. We therefore propose a novel model-based approach from which atomic coordinates are