Constrained X-ray tensor tomography reconstruction.

Quite recently, a method has been presented to reconstruct X-ray scattering tensors from projections obtained in a grating interferometry setup. The original publications present a rather specialised approach, for instance by suggesting a single SART-based solver. In this work, we propose a novel approach to solving the inverse problem, allowing the use of other algorithms than SART (like conjugate gradient), a faster tensor recovery, and an intuitive visualisation. Furthermore, we introduce constraint enforcement for X-ray tensor tomography (cXTT) and demonstrate that this yields visually smoother results in comparison to the state-of-art approach, similar to regularisation.

An automated optimization pipeline for clinical-grade computer-assisted planning of high tibial osteotomies under consideration of weight-bearing.

3D preoperative planning for high tibial osteotomies (HTO) has increasingly replaced 2D planning but is complex, time-consuming and therefore expensive. Several interdependent clinical objectives and constraints have to be considered, which often requires multiple rounds of revisions between surgeons and biomedical engineers. We therefore developed an automated preoperative planning pipeline, which takes imaging data as an input to generate a ready-to-use, patient-specific planning solution. Deep-learning based segmentation and landmark localization was used to enable the fully automated 3D lower limb deformity assessment. A 2D-3D registration algorithm allowed the transformation of the 3D bone models into the weight-bearing state. Finally, an optimization framework was implemented to generate ready-to use preoperative plannings in a fully automated fashion, using a genetic algorithm to solve the multi-objective optimization (MOO) problem based on several clinical requirements and constraints. The entire pipeline was evaluated on a large clinical dataset of 53 patient cases who previously underwent a medial opening-wedge HTO. The pipeline was used to automatically generate preoperative solutions for these patients. Five experts blindly compared the automatically generated solutions to the previously generated manual plannings. The overall mean rating for the algorithm-generated solutions was better than for the manual solutions. In 90% of all comparisons, they were considered to be equally good or better than the manual solution. The combined use of deep learning approaches, registration methods and MOO can reliably produce ready-to-use preoperative solutions that significantly reduce human workload and related health costs.

Three-dimensional preoperative planning in the weight-bearing state: validation and clinical evaluation.

OBJECTIVES: 3D preoperative planning of lower limb osteotomies has become increasingly important in light of modern surgical technologies. However, 3D models are usually reconstructed from Computed Tomography data acquired in a non-weight-bearing posture and thus neglecting the positional variations introduced by weight-bearing. We developed a registration and planning pipeline that allows for 3D preoperative planning and subsequent 3D assessment of anatomical deformities in weight-bearing conditions. METHODS: An intensity-based algorithm was used to register CT scans with long-leg standing radiographs and subsequently transform patient-specific 3D models into a weight-bearing state. 3D measurement methods for the mechanical axis as well as the joint line convergence angle were developed. The pipeline was validated using a leg phantom. Furthermore, we evaluated our methods clinically by applying it to the radiological data from 59 patients. RESULTS: The registration accuracy was evaluated in 3D and showed a maximum translational and rotational error of 1.1 mm (mediolateral direction) and 1.2° (superior-inferior axis). Clinical evaluation proved feasibility on real patient data and resulted in significant differences for 3D measurements when the effects of weight-bearing were considered. Mean differences were 2.1 ± 1.7° and 2.0 ± 1.6° for the mechanical axis and the joint line convergence angle, respectively. 37.3 and 40.7% of the patients had differences of 2° or more in the mechanical axis or joint line convergence angle between weight-bearing and non-weight-bearing states. CONCLUSIONS: Our presented approach provides a clinically feasible approach to preoperatively fuse 2D weight-bearing and 3D non-weight-bearing data in order to optimize the surgical correction.

The role of organic matrices in the fate of hydrophobic pesticides: An outdoor stream mesocosm study.

To assess potential aquatic pesticide risks, environmental monitoring strategies often focus on water and sediment. However, knowledge gaps with regard to the pollution status of organic matrices important for the structure and functioning of aquatic ecosystems do exist. The present study assessed the dissipation of the triazole fungicide tebuconazole (TEB; KOW = 5.01 × 103) and the pyrethroid insecticide etofenprox (ETO; KOW = 7.94 × 106) as model hydrophobic pesticide compounds among aquatic plants, vertical layers of allochthonous leaf litter, and detritus within flow-through outdoor stream mesocosms. During a 3-h pesticide exposure and a subsequent 24-h post-exposure period, retention was higher for ETO (max concentration: Myriophyllum spicatum > Elodea nuttallii > Ranunculus fluitans > Potamogeton perfoliatus â‰« leaf litter > detritus) and depended amongst other factors on surface area, while in the water compartment the pesticides reached concentration levels < LOQ 2 h after exposure. Desorption was observed for both pesticides in plants, and for TEB in detritus, while in leaves the ETO levels even increased over time, suggesting leaf litter to be a suitable additional sampling matrix for transient hydrophobic pesticide peaks, yet also a potential source of contamination for invertebrate shredders. The upper layer of leaf material contained higher ETO levels than those situated further in the sediment, which implies short-term positive effects for species inhabiting the deeper leaf layers, yet again pinpoints to a potential pesticide exposure pathway via organic matter in aquatic systems.

Retention of plant protection products (PPPs) by aquatic plants in flow-through systems.

Understanding fate and transport of plant protection products (PPPs) that enter vegetated streams from agricultural fields is important for both exposure assessment and risk attenuation, yet limited knowledge is available. The present laboratory study investigated sorption processes governing mass transfer of three common PPPs between water and aquatic plant phases at flow-through exposure conditions (transient aqueous-phase PPP-peak of 4 h 25 min) using three temperature regimes. The exposure produced rapid sorption of PPPs to plants, followed by a gradual depuration from plants. Dynamic sorption kinetics depended on temperature, plant species, and physicochemical properties of the PPPs. Sorption to plants contributed to a 10% reduction of the water-phase peak concentrations of the PPPs. However, being reversible, the attenuation effect was limited to the residence time of the PPPs in the systems. Results of the present study highlight that effectivity of aquatic plants in the attenuation of PPP loads may vary greatly depending on hydrodynamic properties of aquatic systems.

Brain Connectivity Exposed by Anisotropic X-ray Dark-field Tomography.

To understand the interaction of different parts of the human brain it is essential to know how they are connected. Such connections are predominantly related to the brain's white matter, which forms the neuronal pathways, the axons. These axons, also referred to as nerve fibers, have a size on the micrometer scale and are therefore too small to be imaged by standard X-ray systems. In this paper, we use a grating interferometer and a method based on Anisotropic X-ray Dark-field Tomography (AXDT) with the goal to generate a three-dimensional tomographic reconstruction of these functional structures. A first preclinical survey shows that we successfully reconstruct the orientations of the brain fibers connectivity with our approach.

Structural and functional effects of a short-term pyrethroid pulse exposure on invertebrates in outdoor stream mesocosms.

Agricultural land-use frequently results in short pulse exposures of insecticides such as pyrethroids in river systems, adversely affecting local invertebrate communities. In order to assess insecticide-induced effects, stream mesocosms are used within higher tier aquatic risk assessment. Regulatory acceptable concentrations (RACs) derived from those studies are often higher compared with tier 1 RACs. Hence, the present mesocosm study evaluates this aspect using a pulse exposure scenario typical for streams and the pyrethroid insecticide etofenprox. A 6-h pulse exposure with measured concentrations of 0.04, 0.3 and 5.3µgL-1 etofenprox was used. We considered abundance, drift and emergence of invertebrates as structural endpoints and the in situ-measured feeding rates of the isopod Asellus aquaticus as functional endpoint. Most prominent effects were visible at 5.3µgL-1 etofenprox which caused adverse effects of up to 100% at the individual and population level, as well as community structure alterations. Transient effects were observed for invertebrate drift (effect duration ≤24h) and for the invertebrate community (9 days after exposure) at 0.3µgL-1 etofenprox. Furthermore, 0.04µgL-1 etofenprox affected the abundance of the mayfly Cloeon simile (decrease by 66%) and the feeding rate of A. aquaticus (decrease by 44%). Thus, implications for the functional endpoint leaf litter breakdown in heterotrophic ecosystems may be expected. A hypothetical RAC derived from the present mesocosm study (0.004µgL-1) is in line with the official tier 1 RAC (0.0044µgL-1) and thus shows that the present mesocosm study did not result in a higher RAC.

Response and recovery of the macrophytes Elodea canadensis and Myriophyllum spicatum following a pulse exposure to the herbicide iofensulfuron-sodium in outdoor stream mesocosms.

Interest in stream mesocosms has recently revived for higher tier aquatic macrophyte risk assessment of plant protection products mainly because 1) the highest predicted environmental concentrations for the assessment of effects are frequently derived from stream scenarios, and 2) they allow an effect assessment using stream-typical pulse exposures. Therefore, the present stream mesocosm study used an herbicide pulse exposure and evaluated the responses of Elodea canadensis and Myriophyllum spicatum. Macrophytes were exposed for 24 h to 1 µg/L, 3 µg/L, 10 µg/L, and 30 µg/L of the herbicide iofensulfuron-sodium with a subsequent recovery period of 42 d. Biological endpoints were growth rates of the main, side, and total shoot length, the shoot number, the maximum root length, and the dry weight. The total shoot length was identified as the most sensitive endpoint; the growth rate of the total shoot length was inhibited by up to 66% and 45% in M. spicatum and E. canadensis, respectively. The lowest no observed effect concentrations (NOECs) were observed at day 7 and/or day 14 after herbicide treatment and were 1 µg/L for M. spicatum and 3 µg/L for E. canadensis. The no-observed-ecologically-adverse-effect concentrations (NOEAECs) were 10 µg/L and 30 µg/L for M. spicatum and E. canadensis, respectively. Such or similar mesocosm designs are useful to simulate typical stream exposures and estimate herbicide effects on aquatic macrophytes in stream systems. Environ Toxicol Chem 2017;36:1090-1100. © 2016 SETAC.

Transient effects following peak exposures towards pesticides - An explanation for the unresponsiveness of in situ measured functional variables.

Invertebrate-mediated leaf litter decomposition is frequently used to assess stress-related implications in stream ecosystem integrity. In situ measures such as the mass loss from leaf bags or the feeding of caged invertebrates deployed for days or weeks may, however, fail to detect transient effects due to recovery or compensatory mechanisms. We assessed the relevance of transient effects using the peak exposure towards an insecticide (i.e., etofenprox) as a model scenario at three levels of complexity. These were 1) the assessment of the decomposition realised by invertebrate communities in stream mesocosms over 21 days via leaf bags, 2) 7-days lasting in situ bioassays quantifying the leaf consumption of Gammarus fossarum, and 3) a laboratory experiment determining the daily feeding rate of the same species over 7 days. Etofenprox did not trigger a significantly altered decomposition by invertebrate communities during the leaf bag assay, while in situ bioassays detected a significant reduction in gammarids' feeding rate at the highest tested concentration. The laboratory bioassay suggests that observed mismatches might be explained by recovery and post-exposure compensation. As leaf-shredding invertebrates are likely in a vulnerable state following transient effects, biomonitoring for implications of peak exposures and other pulsed stress events must happen at an adequate temporal resolution.

Combined Tensor Fitting and TV Regularization in Diffusion Tensor Imaging Based on a Riemannian Manifold Approach.

In this paper, we consider combined TV denoising and diffusion tensor fitting in DTI using the affine-invariant Riemannian metric on the space of diffusion tensors. Instead of first fitting the diffusion tensors, and then denoising them, we define a suitable TV type energy functional which incorporates the measured DWIs (using an inverse problem setup) and which measures the nearness of neighboring tensors in the manifold. To approach this functional, we propose generalized forward- backward splitting algorithms which combine an explicit and several implicit steps performed on a decomposition of the functional. We validate the performance of the derived algorithms on synthetic and real DTI data. In particular, we work on real 3D data. To our knowledge, the present paper describes the first approach to TV regularization in a combined manifold and inverse problem setup.

Reference scenarios for exposure to plant protection products and invertebrate communities in stream mesocosms.

Higher tier aquatic risk assessment for plant protection products (PPPs) is often based on pond-like mesocosm studies in which transient and dynamic PPP exposure scenarios as observed in lotic systems are hardly achievable. Thus, the present study presents dynamic PPP exposure scenarios at different time scales under flow-through conditions as typical for streams in agricultural landscapes. The stream mesocosm setup allows testing the influence of spatial gradients of exposure over the length of themesocosms. The use of the fluorescent tracer uranine revealed the hydraulic processes generally underlying peak- and hour-scale exposure scenarios and demonstrated an optimized application technique to achieve stable day-scale exposures. Furthermore, to account for potential reactions of invertebrates to PPP exposures in streams (e.g. avoidance behavior and drift), the present study thus aimed at a comprehensive evaluation on how PPP exposure and the establishment of invertebrates can be advanced within streammesocosm testing. For both, peak- and hour-scale exposure as well as the experiments considering the establishment of invertebrates, the presented compilation of experiments was able to highlight the influence of aquatic macrophyteswithin streammesocosms. Since the field relevance of the higher tier aquatic risk assessment for PPPs relies qualitatively on the presence of potentially sensitive or vulnerable species, those species were especially considered. Thus, the establishment of aquatic invertebrates in nondosed streams was evaluated with respect to (i) the presence of different aquatic macrophytes and (ii) the duration of the pre-experimental period. The present study highlights the beneficial influence of complex-structured macrophytes and prolonged pre-experimental periods on the abundance of invertebrate taxa. Furthermore, population dynamics were evaluated statistically by simulating PPP-related declines of 30, 50 and 70%. Thereby,

Using stable isotope analysis in stream mesocosms to study potential effects of environmental chemicals on aquatic-terrestrial subsidies.

While recent research has provided evidence that the emergence of merolimnic insects (species with an aquatic larval stage) provides a considerable energy subsidy to riparian food webs, it has also shown that merolimnic insects may serve as a vector for contaminants. Therefore, riparian food webs may be at risk from either an aquatic-terrestrial transfer of contaminants or from the contaminant-driven reductions of emerging merolimnic insects. The objective of the present study was to develop an integrated stream mesocosms test design capable of identifying these inter-ecosystem boundary effects and to provide a comprehensive approach as a basis for ecotoxicological testing. We chose the widely distributed web-building spider Tetragnatha extensa as a representative species for riparian predators. Trophic aspects of riparian food webs were investigated by stable isotope analysis of carbon (δ(13)C) and nitrogen (δ(15)N). Utilization of stable isotope ratios provided detailed information on the riparian food web structure and the dietary composition of T. extensa. Merolimnic invertebrates (mainly Cloeon spp. and Chironomidae) were found to contribute up to 71 % of T. extensa's diet, demonstrating their importance in riparian food webs in ecotoxicological mesocosm testing. This study provides a conceptual and methodological basis for assessing aquatic insect emergence-related pollutant transfer or effect translation from aquatic to adjacent terrestrial systems.

X-ray computed tomography using curvelet sparse regularization.

PURPOSE: Reconstruction of x-ray computed tomography (CT) data remains a mathematically challenging problem in medical imaging. Complementing the standard analytical reconstruction methods, sparse regularization is growing in importance, as it allows inclusion of prior knowledge. The paper presents a method for sparse regularization based on the curvelet frame for the application to iterative reconstruction in x-ray computed tomography. METHODS: In this work, the authors present an iterative reconstruction approach based on the alternating direction method of multipliers using curvelet sparse regularization. RESULTS: Evaluation of the method is performed on a specifically crafted numerical phantom dataset to highlight the method's strengths. Additional evaluation is performed on two real datasets from commercial scanners with different noise characteristics, a clinical bone sample acquired in a micro-CT and a human abdomen scanned in a diagnostic CT. The results clearly illustrate that curvelet sparse regularization has characteristic strengths. In particular, it improves the restoration and resolution of highly directional, high contrast features with smooth contrast variations. The authors also compare this approach to the popular technique of total variation and to traditional filtered backprojection. CONCLUSIONS: The authors conclude that curvelet sparse regularization is able to improve reconstruction quality by reducing noise while preserving highly directional features.

Role of submerged vegetation in the retention processes of three plant protection products in flow-through stream mesocosms.

Quantitative information on the processes leading to the retention of plant protection products (PPPs) in surface waters is not available, particularly for flow-through systems. The influence of aquatic vegetation on the hydraulic- and sorption-mediated mitigation processes of three PPPs (triflumuron, pencycuron, and penflufen; logKOW 3.3-4.9) in 45-m slow-flowing stream mesocosms was investigated. Peak reductions were 35-38% in an unvegetated stream mesocosm, 60-62% in a sparsely vegetated stream mesocosm (13% coverage with Elodea nuttallii), and in a similar range of 57-69% in a densely vegetated stream mesocosm (100% coverage). Between 89% and 93% of the measured total peak reductions in the sparsely vegetated stream can be explained by an increase of vegetation-induced dispersion (estimated with the one-dimensional solute transport model OTIS), while 7-11% of the peak reduction can be attributed to sorption processes. However, dispersion contributed only 59-71% of the peak reductions in the densely vegetated stream mesocosm, where 29% to 41% of the total peak reductions can be attributed to sorption processes. In the densely vegetated stream, 8-27% of the applied PPPs, depending on the logKOW values of the compounds, were temporarily retained by macrophytes. Increasing PPP recoveries in the aqueous phase were accompanied by a decrease of PPP concentrations in macrophytes indicating kinetic desorption over time. This is the first study to provide quantitative data on how the interaction of dispersion and sorption, driven by aquatic macrophytes, influences the mitigation of PPP concentrations in flowing vegetated stream systems.

Interactive 3D visualization of a single-view X-ray image.

In this paper, we present an interactive X-Ray perceptual visualization technique (IXPV) to improve 3D perception in standard single-view X-Ray images. Based on a priori knowledge from CT data, we re-introduce lost depth information into the original single-view X-Ray image without jeopardizing information of the original X-Ray. We propose a novel approach that is suitable for correct fusion of intraoperative X-Ray and ultrasound, co-visualization of X-Ray and surgical tools, and for improving the 3D perception of standard radiographs. Phantom and animal cadaver datasets were used during experimentation to demonstrate the impact of our technique. Results from a questionnaire completed by 11 clinicians and computer scientists demonstrate the added value of introduced depth cues directly in an X-Ray image. In conclusion, we propose IXPV as a futuristic alternative to the standard radiographic image found in today's clinical setting.