Validation study of small-angle X-ray scattering tensor tomography

Small-angle scattering tensor tomography (SASTT) is a recently developed technique able to tomographically reconstruct the 3D reciprocal space from voxels within a bulk volume. SASTT extends the concept of X-ray computed tomography, which typically reconstructs scalar values, by reconstructing a tensor per voxel, which represents the local nanostructure 3D organization. In this study, the nanostructure orientation in a human trabecular-bone sample obtained by SASTT was validated by sectioning the sample and using 3D scanning small-angle X-ray scattering (3D sSAXS) to measure and analyze the orientation from single voxels within each thin section. Besides the presence of cutting artefacts from the slicing process, the nanostructure orientations obtained with the two independent methods were in good agreement, as quantified with the absolute value of the dot product calculated between the nanostructure main orientations obtained in each voxel. The average dot product per voxel over the full sample containing over 10 000 voxels was 0.84, and in six slices, in which fewer cutting artefacts were observed, the dot product increased to 0.91. In addition, SAXS tensor tomography not only yields orientation information but can also reconstruct the full 3D reciprocal-space map. It is shown that the measured anisotropic scattering for individual voxels was reproduced from the SASTT reconstruction in each voxel of the 3D sample. The scattering curves along different 3D directions are validated with data from single voxels, demonstrating SASTT\u27s potential for a separate analysis of nanostructure orientation and structural information from the angle-dependent intensity distribution

Ultrastructure organization of human trabeculae assessed by 3D sSAXS and relation to bone microarchitecture

Although the organization of bone ultrastructure, i.e. the orientation and arrangement of the mineralized collagen fibrils, has been in the focus of research for many years for cortical bone, and many models on the osteonal arrangement have been proposed, limited attention has been paid to trabecular bone ultrastructure. This is surprising because trabeculae play a crucial role for the mechanical strength of several bone sites, including the vertebrae and the femoral head. On this account, we first validated a recently developed method (3D sSAXS or 3D scanning small-angle X-ray scattering) for investigating bone ultrastructure in a quantitative and spatially resolved way, using conventional linearly polarized light microscopy as a gold standard. While both methods are used to analyze thin tissue sections, in contrast to polarized light microscopy, 3D sSAXS has the important advantage that it provides 3D information on the orientation and arrangement of bone ultrastructure. In this first study of its kind, we used 3D sSAXS to investigate the ultrastructural organization of 22 vertebral trabeculae of different alignment, types and sizes, obtained from 4 subjects of different ages. Maps of ultrastructure orientation and arrangement of the trabeculae were retrieved by stacking information from consecutive 20-?m-thick bone sections. The organization of the ultrastructure was analyzed in relation to trabecular microarchitecture obtained from computed tomography and to relevant parameters such as distance to trabecular surface, local curvature or local bone mineralization. We found that (i) ultrastructure organization is similar for all investigated trabeculae independent of their particular characteristics, (ii) bone ultrastructure exhibiting a high degree of orientation was arranged in domains, (iii) highly oriented ultrastructural areas were located closer to the bone surface, (iv) the ultrastructure of the human trabecular bone specimens followed the microarchitecture, being oriented mostly parallel to bone surface, and (v) local surface curvature seems to have an effect on the ultrastructure organization. Further studies that investigate bone ultrastructure orientation and arrangement are needed in order to understand its organization and consequently its relation to bone biology and mechanics

High-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithm

The recent advent of tensor tomography techniques has enabled tomographic investigations of the 3D nanostructure organization of biological and material science samples. These techniques extended the concept of conventional X-ray tomography by reconstructing not only a scalar value such as the attenuation coefficient per voxel, but also a set of parameters that capture the local anisotropy of nanostructures within every voxel of the sample. Tensor tomography data sets are intrinsically large as each pixel of a conventional X-ray projection is substituted by a scattering pattern, and projections have to be recorded at different sample angular orientations with several tilts of the rotation axis with respect to the X-ray propagation direction. Currently available reconstruction approaches for such large data sets are computationally expensive. Here, a novel, fast reconstruction algorithm, named iterative reconstruction tensor tomography (IRTT), is presented to simplify and accelerate tensor tomography reconstructions. IRTT is based on a second-rank tensor model to describe the anisotropy of the nanostructure in every voxel and on an iterative error backpropagation reconstruction algorithm to achieve high convergence speed. The feasibility and accuracy of IRTT are demonstrated by reconstructing the nanostructure anisotropy of three samples: a carbon fiber knot, a human bone trabecula specimen and a fixed mouse brain. Results and reconstruction speed were compared with those obtained by the small-angle scattering tensor tomography (SASTT) reconstruction method introduced by Liebi et al. [Nature (2015), 527, 349–352]. The principal orientation of the nanostructure within each voxel revealed a high level of agreement between the two methods. Yet, for identical data sets and computer hardware used, IRTT was shown to be more than an order of magnitude faster. IRTT was found to yield robust results, it does not require prior knowledge of the sample for initializing parameters, and can be used in cases where simple anisotropy metrics are sufficient, i.e. the tensor approximation adequately captures the level of anisotropy and the dominant orientation within a voxel. In addition, by greatly accelerating the reconstruction, IRTT is particularly suitable for handling large tomographic data sets of samples with internal structure or as a real-time analysis tool during the experiment for online feedback during data acquisition. Alternatively, the IRTT results might be used as an initial guess for models capturing a higher complexity of structural anisotropy such as spherical harmonics based SASTT in Liebi et al. (2015), improving both overall convergence speed and robustness of the reconstruction

Minimum Information Required to Annotate Food Safety Risk Assessment Models (MIRARAM)

Abstract In the last decades, mathematical models and model-based simulations became important elements not only in the area of risk assessment concerning microbiological and chemical hazards but also in modelling biological phenomena in general. Unfortunately, many of the developed models are published in non-standardized ways, which hinders efficient exchange, re-use and continuous improvement of models within the risk assessment domain. The establishment of guidelines for model annotation is an important pre-condition to overcome these obstacles. Additionally, implementation of annotation guidelines can improve transparency, quality control and even aid the clarification of intellectual property rights. Here, we address the question of "What is the minimum set of metadata that should be provided for a model in the risk assessment domain?". The proposed guideline focuses on food safety risk assessment models and is called "Minimum Information Required to Annotate food safety Risk Assessment Models (MIRARAM)". MIRARAM supports the model creator during the model documentation step and could also be used as a checklist by scientific journal editors or database curators. Software developers could take up MIRARAM and develop easy-to-use software tools or new features in existing programs that can help model creators to provide proposed model annotations in harmonized file formats. Based on experiences from similar guidelines in related scientific disciplines (like systems biology), it is expected that MIRARAM could contribute to the promotion of application and re-use of models as well as to implementing more standardized quality control in the food safety modelling domain

The public health risk posed by Listeria monocytogenes in frozen fruit and vegetables including herbs, blanched during processing

A multi-country outbreak ofListeria monocytogenesST6 linked to blanched frozen vegetables (bfV)took place in the EU (2015–2018). Evidence of food-borne outbreaks shows thatL. monocytogenesisthe most relevant pathogen associated with bfV. The probability of illness per serving of uncooked bfV,for the elderly (65–74 years old) population, is up to 3,600 times greater than cooked bfV and verylikely lower than any of the evaluated ready-to-eat food categories. The main factors affectingcontamination and growth ofL. monocytogenesin bfV during processing are the hygiene of the rawmaterials and process water; the hygienic conditions of the food processing environment (FPE); andthe time/Temperature (t/T) combinations used for storage and processing (e.g. blanching, cooling).Relevant factors after processing are the intrinsic characteristics of the bfV, the t/T combinations usedfor thawing and storage and subsequent cooking conditions, unless eaten uncooked. Analysis of thepossible control options suggests that application of a complete HACCP plan is either not possible orwould not further enhance food safety. Instead, specific prerequisite programmes (PRP) andoperational PRP activities should be applied such as cleaning and disinfection of the FPE, water control,t/T control and product information and consumer awareness. The occurrence of low levels ofL. monocytogenesat the end of the production process (e.g.<10 CFU/g) would be compatible with thelimit of 100 CFU/g at the moment of consumption if any labelling recommendations are strictly followed(i.e. 24 h at 5°C). Under reasonably foreseeable conditions of use (i.e. 48 h at 12°C),L. monocytogeneslevels need to be considerably lower (not detected in 25 g). Routine monitoring programmes forL. monocytogenesshould be designed following a risk-based approach and regularly revised based ontrend analysis, being FPE monitoring a key activity in the frozen vegetable industry

SAXS imaging reveals optimized osseointegration properties of bioengineered oriented 3D-PLGA/aCaP scaffolds in a critical size bone defect model

Healing large bone defects remains challenging in orthopedic surgery and is often associated with poor outcomes and complications. A major issue with bioengineered constructs is achieving a continuous interface between host bone and graft to enhance biological processes and mechanical stability. In this study, we have developed a new bioengineering strategy to produce oriented biocompatible 3D PLGA/aCaP nanocomposites with enhanced osseointegration. Decellularized scaffolds -containing only extracellular matrix- or scaffolds seeded with adipose-derived mesenchymal stromal cells were tested in a mouse model for critical size bone defects. In parallel to micro-CT analysis, SAXS tensor tomography and 2D scanning SAXS were employed to determine the 3D arrangement and nanostructure within the critical-sized bone. Both newly developed scaffold types, seeded with cells or decellularized, showed high osseointegration, higher bone quality, increased alignment of collagen fibers and optimal alignment and size of hydroxyapatite minerals

Draft for internal testing Scientific Committee guidance on appraising and integrating evidence from epidemiological studies for use in EFSA's scientific assessments.

EFSA requested its Scientific Committee to prepare a guidance document on appraising and integrating evidence from epidemiological studies for use in EFSA's scientific assessments. The guidance document provides an introduction to epidemiological studies and illustrates the typical biases of the different epidemiological study designs. It describes key epidemiological concepts relevant for evidence appraisal. Regarding study reliability, measures of association, exposure assessment, statistical inferences, systematic error and effect modification are explained. Regarding study relevance, the guidance describes the concept of external validity. The principles of appraising epidemiological studies are illustrated, and an overview of Risk of Bias (RoB) tools is given. A decision tree is developed to assist in the selection of the appropriate Risk of Bias tool, depending on study question, population and design. The customisation of the study appraisal process is explained, detailing the use of RoB tools and assessing the risk of bias in the body of evidence. Several examples of appraising experimental and observational studies using a Risk of Bias tool are annexed to the document to illustrate the application of the approach. This document constitutes a draft that will be applied in EFSA's assessments during a 1-year pilot phase and be revised and complemented as necessary. Before finalisation of the document, a public consultation will be launched