Inferring the diet of extinct elephants: The case study of straight-tusked elephants from Neumark Nord 1 (Northeastern Germany)

Inferring the diet of fossil mammals is a major approach to mammalian palaeobiology and palaeoecology. Compared to other mammals, proboscideans pose significant problems because elephants eat different kinds of food and may change it frequently. Results obtained by analysing the last molars of Palaeoloxodon antiquus from Neumark Nord, highlight the effectiveness of a multidisciplinary approach in inferring the dietary adaptation of elephants. The microwear pattern and stable isotope data obtained for the straight-tusked elephants from Neumark Nord 1, suggest they were mainly grazers in a wooded grassland and moderately humid environment

Multi-stage prediction networks for data harmonization

In this paper, we introduce multi-task learning (MTL) to data harmonization (DH); where we aim to harmonize images across different acquisition platforms and sites. This allows us to integrate information from multiple acquisitions and improve the predictive performance and learning efficiency of the harmonization model. Specifically, we introduce the Multi Stage Prediction (MSP) Network, a MTL framework that incorporates neural networks of potentially disparate architectures, trained for different individual acquisition platforms, into a larger architecture that is refined in unison. The MSP utilizes high-level features of single networks for individual tasks, as inputs of additional neural networks to inform the final prediction, therefore exploiting redundancy across tasks to make the most of limited training data. We validate our methods on a dMRI harmonization challenge dataset, where we predict three modern platform types, from one obtained from an old scanner. We show how MTL architectures, such as the MSP, produce around 20% improvement of patch-based mean-squared error over current state-of-the-art methods and that our MSP outperforms off-the-shelf MTL networks. Our code is availabl

Single cell imaging of nuclear architecture changes

This is the final version. Available from Frontiers Media via the DOI in this record.Data and materials availability: Data obtained in this work are available upon request.The dynamic architecture of chromatin, the macromolecular complex comprised primarily of DNA and histones, is vital for eukaryotic cell growth. Chemical and conformational changes to chromatin are important markers of functional and developmental processes in cells. However, chromatin architecture regulation has not yet been fully elucidated. Therefore, novel approaches to assessing chromatin changes at the single-cell level are required. Here we report the use of FTIR imaging and microfluidic cell-stretcher chips to assess changes to chromatin architecture and its effect on the mechanical properties of the nucleus in immune cells. FTIR imaging enables label-free chemical imaging with subcellular resolution. By optimizing the FTIR methodology and couple it with cell segmentation analysis approach, we have identified key spectral changes corresponding to changes in DNA levels and chromatin conformation at the single cell level. By further manipulating live single cells using pressure-driven microfluidics, we found that chromatin decondensation – either during general transcriptional activation or during specific immune cell maturation – can ultimately lead to nuclear auxeticity which is a new biological phenomenon recently identified. Taken together our findings demonstrate the tight and, potentially bilateral, link between extra-cellular mechanotransduction and intra-cellular nuclear architecture.Engineering and Physical Sciences Research Council (EPSRC)Biotechnology and Biological Sciences Research Council (BBSRC)Academy of Medical SciencesRoyal Societ

Laboratory activity for a new procedure of MIVIS calibration and relative validation with test data

Remotely sensed data, recorded by means of the MIVIS hyperspectral scanner in the framework of the research activity of the CNR Institutes IIA-LARA and IMAA, have been calibrated to reflectance values and then quantitatively compared with ground data. A new procedure for radiometric calibration has been defined by utilizing the MIVIS test-bench and applying a wider radiance range with respect to the one provided by the manufacturing company. New calibration curves have been determined and applied in the pre-processing chain. For validation purpose ground spectra were measured during the campaign by means of a portable spectroradiometer. The atmospheric correction has been carried out by implementing an IDL procedure to manage MODTRAN4 input and output cards. MIVIS test data acquired over Passo Corese (Roma) have shown how the new calibration coefficients significantly improve the radiometric accuracy. In particular, in the VIS spectral region the percentage error, with respect to a ground truth spectrum, is about half of that occurring if the standard calibration coefficients are used

Paleopathological study of Mammuthus meridionalis of Madonna della Strada (L’Aquila)

A skeleton of a male, 50-55 years old Mammuthus meridionalis, dated to the Pleistocene and conserved at the Spanish Fort in L’Aquila (Italy), showed a broken left tusk, in association with the presence of a deep (15x20 cm) bone erosion, involving the dental alveolus and the premaxillary bone, in close proximity to the maxillary sinus and the nasal cavity. During gross examination, small samples from three representative areas of the eroded bone were obtained. Thin sections were made and the specimens were examined under plane and polarized light, using a high resolution microscope with an incorporated digital camera. Microscopical study revealed the intra vitam origin of the lesions, characterized by the presence of woven bone fibers, typical of the early phases of bone remodeling, and lamellar bone with dilated and remodeled Haversian systems. The gross and histological findings were consistent with an osteomyelitis with bone sequestration, caused by a localized blunt trauma or, more likely, resulting from an ascending, post-traumatic chronic pulpitis, due to the tusk fracture occurred during an accident or interspecies fights. The histological exam excluded the involvement of granulomatous inflammation (e.g. tuberculosis) or neoplasia. A disease process of at least several months in duration may be hypothesized, as suggested by the histologically visible bone remodeling. A long survival of the animal after tusk loss may also be supposed, since alteration of masticatory function with altered molar teeth consumption and postural changes (i.e. atlantoaxial fusion), resulting from asymmetric weight distribution, were observed. In this study, the application of (paleo)histological techniques proved to be fundamental in order to establish the nature of bone lesions detected on archeological samples, also providing a good case for studying skull trauma and shedding light on the life history of these large mammals

Inflammatory and Microbiota-Related Regulation of the Intestinal Epithelial Barrier

The intestinal epithelial barrier (IEB) is one of the largest interfaces between the environment and the internal milieu of the body. It is essential to limit the passage of harmful antigens and microorganisms and, on the other side, to assure the absorption of nutrients and water. The maintenance of this delicate equilibrium is tightly regulated as it is essential for human homeostasis. Luminal solutes and ions can pass across the IEB via two main routes: the transcellular pathway or the paracellular pathway. Tight junctions (TJs) are a multi-protein complex responsible for the regulation of paracellular permeability. TJs control the passage of antigens through the IEB and have a key role in maintaining barrier integrity. Several factors, including cytokines, gut microbiota, and dietary components are known to regulate intestinal TJs. Gut microbiota participates in several human functions including the modulation of epithelial cells and immune system through the release of several metabolites, such as short-chain fatty acids (SCFAs). Mediators released by immune cells can induce epithelial cell damage and TJs dysfunction. The subsequent disruption of the IEB allows the passage of antigens into the mucosa leading to further inflammation. Growing evidence indicates that dysbiosis, immune activation, and IEB dysfunction have a role in several diseases, including irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and gluten-related conditions. Here we summarize the interplay between the IEB and gut microbiota and mucosal immune system and their involvement in IBS, IBD, and gluten-related disorders

Impact of within-voxel heterogeneity in fibre geometry on spherical deconvolution

Axons in white matter have been shown to have varying geometries within a bundle using ex vivo imaging techniques, but what does this mean for diffusion MRI (dMRI) based spherical deconvolution (SD)? SD attempts to estimate the fibre orientation distribution function (fODF) by assuming a single dMRI fibre response function (FRF) for all white matter populations and deconvolving this FRF from the dMRI signal at each voxel to estimate the fODF. Variable fibre geometry within a bundle however suggests the FRF might not be constant even within a single voxel. We test what impact realistic fibre geometry has on SD by simulating the dMRI signal in a range of realistic white matter numerical phantoms, including synthetic phantoms and real axons segmented from electron microscopy. We demonstrate that variable fibre geometry leads to a variable FRF across axons and that in general no single FRF is effective to recover the underlying fibre orientation distribution function (fODF). This finding suggests that assuming a single FRF can lead to misestimation of the fODF, causing further downstream errors in techniques such as tractography

Reply to comment by C. Morhange, C. Flaux, P.A. Pirazzoli, M.B. Carre on \u201cHolocene Sea level Change in Malta\u201d

The pits of Birzebbugia are located near the present-day mean sea level, and some are partially submerged. They were dated using pottery discovered in an archaeological site close to the coast, dated to the Bronze Age (Zammit, 1928; Abela, 1999). As they have been interpreted as sites for the retting of flax, during their utilization they should have remained dry and the sea could not submerge them. This is the reason why these structures are not directly related to the sea level, as suggested by Biolchi et al. (2011), so they represent an upper limit.peer-reviewe