Do contaminants compromise the use of recycled nutrients in organic agriculture? A review and synthesis of current knowledge on contaminant concentrations, fate in the environment and risk assessment.

Use of nutrients recycled from societal waste streams in agriculture is part of the circular economy, and in line with organic farming principles. Nevertheless, diverse contaminants in waste streams create doubts among organic farmers about potential risks for soil health. Here, we gather the current knowledge on contaminant levels in waste streams and recycled nutrient sources, and discuss associated risks. For potentially toxic elements (PTEs), the input of zinc (Zn) and copper (Cu) from mineral feed supplements remains of concern, while concentrations of PTEs in many waste streams have decreased substantially in Europe. The same applies to organic contaminants, although new chemical groups such as flame retardants are of emerging concern and globally contamination levels differ strongly. Compared to inorganic fertilizers, application of organic fertilizers derived from human or animal feces is associated with an increased risk for environmental dissemination of antibiotic resistance. The risk depends on the quality of the organic fertilizers, which varies between geographical regions, but farmland application of sewage sludge appears to be a safe practice as shown by some studies (e.g. from Sweden). Microplastic concentrations in agricultural soils show a wide spread and our understanding of its toxicity is limited, hampering a sound risk assessment. Methods for assessing public health risks for organic contaminants must include emerging contaminants and potential interactions of multiple compounds. Evidence from long-term field experiments suggests that soils may be more resilient and capable to degrade or stabilize pollutants than often assumed. In view of the need to source nutrients for expanding areas under organic farming, we discuss inputs originating from conventional farms vs. non-agricultural (i.e. societal) inputs. Closing nutrient cycles between agriculture and society is feasible in many cases, without being compromised by contaminants, and should be enhanced, aided by improved source control, waste treatment and sound risk assessments.

Sparse recovery of undersampled intensity patterns for coherent diffraction imaging at high X-ray energies.

Coherent X-ray photons with energies higher than 50 keV offer new possibilities for imaging nanoscale lattice distortions in bulk crystalline materials using Bragg peak phase retrieval methods. However, the compression of reciprocal space at high energies typically results in poorly resolved fringes on an area detector, rendering the diffraction data unsuitable for the three-dimensional reconstruction of compact crystals. To address this problem, we propose a method by which to recover fine fringe detail in the scattered intensity. This recovery is achieved in two steps: multiple undersampled measurements are made by in-plane sub-pixel motion of the area detector, then this data set is passed to a sparsity-based numerical solver that recovers fringe detail suitable for standard Bragg coherent diffraction imaging (BCDI) reconstruction methods of compact single crystals. The key insight of this paper is that sparsity in a BCDI data set can be enforced by recognising that the signal in the detector, though poorly resolved, is band-limited. This requires fewer in-plane detector translations for complete signal recovery, while adhering to information theory limits. We use simulated BCDI data sets to demonstrate the approach, outline our sparse recovery strategy, and comment on future opportunities.

Bragg Coherent Diffractive Imaging of Zinc Oxide Acoustic Phonons at Picosecond Timescales.

Mesoscale thermal transport is of fundamental interest and practical importance in materials such as thermoelectrics. Coherent lattice vibrations (acoustic phonons) govern thermal transport in crystalline solids and are affected by the shape, size, and defect density in nanoscale materials. The advent of hard x-ray free electron lasers (XFELs) capable of producing ultrafast x-ray pulses has significantly impacted the understanding of acoustic phonons by enabling their direct study with x-rays. However, previous studies have reported ensemble-averaged results that cannot distinguish the impact of mesoscale heterogeneity on the phonon dynamics. Here we use Bragg coherent diffractive imaging (BCDI) to resolve the 4D evolution of the acoustic phonons in a single zinc oxide rod with a spatial resolution of 50 nm and a temporal resolution of 25 picoseconds. We observe homogeneous (lattice breathing/rotation) and inhomogeneous (shear) acoustic phonon modes, which are compared to finite element simulations. We investigate the possibility of changing phonon dynamics by altering the crystal through acid etching. We find that the acid heterogeneously dissolves the crystal volume, which will significantly impact the phonon dynamics. In general, our results represent the first step towards understanding the effect of structural properties at the individual crystal level on phonon dynamics.

Three-dimensional imaging of vortex structure in a ferroelectric nanoparticle driven by an electric field.

Topological defects of spontaneous polarization are extensively studied as templates for unique physical phenomena and in the design of reconfigurable electronic devices. Experimental investigations of the complex topologies of polarization have been limited to surface phenomena, which has restricted the probing of the dynamic volumetric domain morphology in operando. Here, we utilize Bragg coherent diffractive imaging of a single BaTiO3 nanoparticle in a composite polymer/ferroelectric capacitor to study the behavior of a three-dimensional vortex formed due to competing interactions involving ferroelectric domains. Our investigation of the structural phase transitions under the influence of an external electric field shows a mobile vortex core exhibiting a reversible hysteretic transformation path. We also study the toroidal moment of the vortex under the action of the field. Our results open avenues for the study of the structure and evolution of polar vortices and other topological structures in operando in functional materials under cross field configurations.Imaging of topological states of matter such as vortex configurations has generally been limited to 2D surface effects. Here Karpov et al. study the volumetric structure and dynamics of a vortex core mediated by electric-field induced structural phase transition in a ferroelectric BaTiO3 nanoparticle.

Life cycle assessment of sludge management with phosphorus utilisation and improved hygienisation in Sweden.

To provide input to sewage sludge management strategies that address expected new regulations in terms of hygienisation and phosphorus recovery in Sweden, an environmental life cycle assessment (LCA) was made. The LCA identified environmental hot spots for methods that may permit sludge or phosphorus from sludge to be applied on agricultural land. In particular, thermophilic digestion, pasteurisation, thermal hydrolysis, urea treatment and mono-incineration with phosphorus recovery were compared. In addition, a sludge management system involving drying of sludge before use in forestry was investigated. The results showed that some major impacts are related to large uncertainties, such as those related to emissions from sludge storage. It also showed that large gains can be achieved when products from the systems replace other products, in particular when biogas is used to replace natural gas in vehicles, but also when sludge is used in agriculture and forestry. In general, there are small differences between the sludge management methods. Retaining the sludge matrix to allow for its utilisation in agriculture may conflict with keeping emissions to air and water from the sludge matrix low. It is recommended that any sludge management option minimises emissions from sludge to air and water and that resources are recovered and used, in line with the principles of a circular economy.

Stability Limits and Defect Dynamics in Ag Nanoparticles Probed by Bragg Coherent Diffractive Imaging.

Dissolution is critical to nanomaterial stability, especially for partially dealloyed nanoparticle catalysts. Unfortunately, highly active catalysts are often not stable in their reactive environments, preventing widespread application. Thus, focusing on the structure-stability relationship at the nanoscale is crucial and will likely play an important role in meeting grand challenges. Recent advances in imaging capability have come from electron, X-ray, and other techniques but tend to be limited to specific sample environments and/or two-dimensional images. Here, we report investigations into the defect-stability relationship of silver nanoparticles to voltage-induced electrochemical dissolution imaged in situ in three-dimensional detail by Bragg coherent diffractive imaging. We first determine the average dissolution kinetics by stationary probe rotating disk electrode in combination with inductively coupled plasma mass spectrometry, which allows in situ measurement of Ag+ ion formation. We then observe the dissolution and redeposition processes in single nanocrystals, providing unique insight about the role of surface strain, defects, and their coupling to the dissolution chemistry. The methods developed and the knowledge gained go well beyond a "simple" silver electrochemistry and are applicable to all electrocatalytic reactions where functional links between activity and stability are controlled by structure and defect dynamics.

Three-dimensional imaging of dislocation dynamics during the hydriding phase transformation.

Crystallographic imperfections significantly alter material properties and their response to external stimuli, including solute-induced phase transformations. Despite recent progress in imaging defects using electron and X-ray techniques, in situ three-dimensional imaging of defect dynamics remains challenging. Here, we use Bragg coherent diffractive imaging to image defects during the hydriding phase transformation of palladium nanocrystals. During constant-pressure experiments we observe that the phase transformation begins after dislocation nucleation close to the phase boundary in particles larger than 300 nm. The three-dimensional phase morphology suggests that the hydrogen-rich phase is more similar to a spherical cap on the hydrogen-poor phase than to the core-shell model commonly assumed. We substantiate this using three-dimensional phase field modelling, demonstrating how phase morphology affects the critical size for dislocation nucleation. Our results reveal how particle size and phase morphology affects transformations in the PdH system.

Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography.

The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to the diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. A possible mechanism to account for these observations is proposed.

Three Dimensional Variable-Wavelength X-Ray Bragg Coherent Diffraction Imaging.

We present and demonstrate a formalism by which three-dimensional (3D) Bragg x-ray coherent diffraction imaging (BCDI) can be implemented without moving the sample by scanning the energy of the incident x-ray beam. This capability is made possible by introducing a 3D Fourier transform that accounts for x-ray wavelength variability. We demonstrate the approach by inverting coherent Bragg diffraction patterns from a gold nanocrystal measured with an x-ray energy scan. Variable-wavelength BCDI will expand the breadth of feasible in situ 3D strain imaging experiments towards more diverse materials environments, especially where sample manipulation is difficult.

Probe-diverse ptychography.

We propose an extension of ptychography where the target sample is scanned separately through several probes with distinct amplitude and phase profiles and a diffraction image is recorded for each probe and each sample translation. The resulting probe-diverse dataset is used to iteratively retrieve high-resolution images of the sample and all probes simultaneously. The method is shown to yield significant improvement in the reconstructed sample image compared to the image obtained using the standard single-probe ptychographic phase-retrieval scheme.

Avalanching strain dynamics during the hydriding phase transformation in individual palladium nanoparticles.

Phase transitions in reactive environments are crucially important in energy and information storage, catalysis and sensors. Nanostructuring active particles can yield faster charging/discharging kinetics, increased lifespan and record catalytic activities. However, establishing the causal link between structure and function is challenging for nanoparticles, as ensemble measurements convolve intrinsic single-particle properties with sample diversity. Here we study the hydriding phase transformation in individual palladium nanocubes in situ using coherent X-ray diffractive imaging. The phase transformation dynamics, which involve the nucleation and propagation of a hydrogen-rich region, are dependent on absolute time (aging) and involve intermittent dynamics (avalanching). A hydrogen-rich surface layer dominates the crystal strain in the hydrogen-poor phase, while strain inversion occurs at the cube corners in the hydrogen-rich phase. A three-dimensional phase-field model is used to interpret the experimental results. Our experimental and theoretical approach provides a general framework for designing and optimizing phase transformations for single nanocrystals in reactive environments.

BATTERIES. Topological defect dynamics in operando battery nanoparticles.

Topological defects can markedly alter nanomaterial properties. This presents opportunities for "defect engineering," where desired functionalities are generated through defect manipulation. However, imaging defects in working devices with nanoscale resolution remains elusive. We report three-dimensional imaging of dislocation dynamics in individual battery cathode nanoparticles under operando conditions using Bragg coherent diffractive imaging. Dislocations are static at room temperature and mobile during charge transport. During the structural phase transformation, the lithium-rich phase nucleates near the dislocation and spreads inhomogeneously. The dislocation field is a local probe of elastic properties, and we find that a region of the material exhibits a negative Poisson's ratio at high voltage. Operando dislocation imaging thus opens a powerful avenue for facilitating improvement and rational design of nanostructured materials.

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging.

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Design and performance of a scanning ptychography microscope.

We have designed and constructed a dedicated instrument to perform ptychography measurements and characterization of multilayer Laue lenses nanofocusing optics. The design of the scanning microscope provides stability of components and minimal thermal drifts, requirements for nanometer scale spatial resolution measurements. We performed thorough laboratory characterization of the instrument in terms of resolution and thermal drifts with subsequent measurements at a synchrotron. We have successfully acquired and reconstructed ptychography data yielding 11 nm line focus.

Ultrafast three-dimensional imaging of lattice dynamics in individual gold nanocrystals.

Key insights into the behavior of materials can be gained by observing their structure as they undergo lattice distortion. Laser pulses on the femtosecond time scale can be used to induce disorder in a "pump-probe" experiment with the ensuing transients being probed stroboscopically with femtosecond pulses of visible light, x-rays, or electrons. Here we report three-dimensional imaging of the generation and subsequent evolution of coherent acoustic phonons on the picosecond time scale within a single gold nanocrystal by means of an x-ray free-electron laser, providing insights into the physics of this phenomenon. Our results allow comparison and confirmation of predictive models based on continuum elasticity theory and molecular dynamics simulations.

High-resolution three-dimensional partially coherent diffraction imaging.

The wave properties of light, particularly its coherence, are responsible for interference effects, which can be exploited in powerful imaging applications. Coherent diffractive imaging relies heavily on coherence and has recently experienced rapid growth. Coherent diffractive imaging recovers an object from its diffraction pattern by computational phasing with the potential of wavelength-limited resolution. Diminished coherence results in reconstructions that suffer from artefacts or fail completely. Here we demonstrate ab initio phasing of partially coherent diffraction patterns in three dimensions, while simultaneously determining the coherence properties of the illuminating wavefield. Both the dramatic improvements in image interpretability and the three-dimensional evaluation of the coherence will have broad implications for quantitative imaging of nanostructures and wavefield characterization with X-rays and electrons.

The effect of exit beam phase aberrations on parallel beam coherent x-ray reconstructions.

Diffraction artifacts from imperfect x-ray windows near the sample are an important consideration in the design of coherent x-ray diffraction measurements. In this study, we used simulated and experimental diffraction patterns in two and three dimensions to explore the effect of phase imperfections in a beryllium window (such as a void or inclusion) on the convergence behavior of phasing algorithms and on the ultimate reconstruction. A predictive relationship between beam wavelength, sample size, and window position was derived to explain the dependence of reconstruction quality on beryllium defect size. Defects corresponding to this prediction cause the most damage to the sample exit wave and induce signature error oscillations during phasing that can be used as a fingerprint of experimental x-ray window artifacts. The relationship between x-ray window imperfection size and coherent x-ray diffractive imaging reconstruction quality explored in this work can play an important role in designing high-resolution in situ coherent imaging instrumentation and will help interpret the phasing behavior of coherent diffraction measured in these in situ environments.

Growth of testes and testicular morphology after eight generations of selection for increased predicted weight of testes at 150 days of age in boars.

Weights of testes and epididymides, body weight, and morphometric measurements of testicular tissue of 75 boars of a line selected for eight generations for predicted weight of testes at 150 d of age and 75 boars of a randomly selected control line were used to evaluate the effects of selection on testicular development at 70, 100, 130, 160, and 450 d of age (n = 15 boars per line per age). Body weights for boars of the select and control line did not differ (P < .05) and the shape of the body growth curve was similar for both lines. Boars of the select line had larger testes than control boars at each age (P < .05), but there was a significant line x age interaction. The percentage increase of the select line mean over the control mean for weight of testes was 37% at 70 d, a maximum of 120% at 100 d, and 25% at 450 d. The percentage of the testes made up of seminiferous tubules differed between lines (P < .01). Lines had similar means of approximately 28% at 70 d and 71% at 450 d, but the mean for the select line was larger between 100 and 160 d of age; the greatest difference was 11.6% (control = 43.7, select = 55.3%) at 100 d. After 70 d of age, select-line boars had a greater percentage of seminiferous tubules with lumens that contained elongated spermatids (P < .10).(ABSTRACT TRUNCATED AT 250 WORDS)

Detection of the anti-p53 antibody response in malignant and benign pancreatic disease.

Genomic alterations in the p53 tumour-suppressor gene and overexpression of p53 protein, resulting from gene mutations, are frequently found in pancreatic cancer. In this study we analysed the sera of 160 patients with malignant and benign pancreatic diseases for the presence of circulating antibodies to the p53 protein. The analysis of the sera was performed using two different enzyme-linked immunosorbent assay (ELISA) systems. To further substantiate the results, all sera were analysed by the Western blot technique using a cell lysate of PancTu-1 cells (p53 mutation at codon 176) as antigen source. Additionally, all positive sera were analysed by the Western blot technique using recombinant p53 as the antigen source. Although the rate of p53 mutations in pancreatic tumours is of the same order as in other adenocarcinomas (> or = 50%), an antibody response was found in only 5/78 (6.4%) sera from patients with pancreatic cancer. Two out of 82 (2.4%) sera of patients with benign pancreatic diseases were clearly positive for p53 antibodies. One additional specimen was weakly positive, i.e. only in one ELISA and Western blot system.