Imaging extended single crystal lattice distortion fields with multi-peak Bragg ptychography.

Recent advances in phase-retrieval-based x-ray imaging methods have demonstrated the ability to reconstruct 3D distortion vector fields within a nanocrystal by using coherent diffraction information from multiple crystal Bragg reflections. However, these works do not provide a solution to the challenges encountered in imaging lattice distortions in crystals with significant defect content that result in phase wrapping. Moreover, these methods only apply to isolated crystals smaller than the x-ray illumination, and therefore cannot be used for imaging of distortions in extended crystals. We introduce multi-peak Bragg ptychography which addresses both challenges via an optimization framework that combines stochastic gradient descent and phase unwrapping methods for robust image reconstruction of lattice distortions and defects in extended crystals. Our work uses modern automatic differentiation toolsets so that the method is easy to extend to other settings and easy to implement in high-performance computers. This work is particularly timely given the broad interest in using the increased coherent flux in fourth-generation synchrotrons for innovative material research.

Operando Nanoscale Imaging of Electrochemically Induced Strain in a Locally Polarized Pt Grain.

Developing new methods that reveal the structure of electrode materials under polarization is key to constructing robust structure-property relationships. However, many existing methods lack the spatial resolution in structural changes and fidelity to electrochemical operating conditions that are needed to probe catalytically relevant structures. Here, we combine a nanopipette electrochemical cell with three-dimensional X-ray Bragg coherent diffractive imaging to study how strain in a single Pt grain evolves in response to applied potential. During polarization, marked changes in surface strain arise from the Coulombic attraction between the surface charge on the electrode and the electrolyte ions in the electrochemical double layers, while the strain in the bulk of the crystal remains unchanged. The concurrent surface redox reactions have a strong influence on the magnitude and nature of the strain changes under polarization. Our studies provide a powerful blueprint to understand how structural evolution influences electrochemical performance at the nanoscale.

Limitation of sucrose biosynthesis shapes carbon partitioning during plant cold acclimation.

Cold acclimation is a multigenic process by which many plant species increase their freezing tolerance. Stabilization of photosynthesis and carbohydrate metabolism plays a crucial role in cold acclimation. To study regulation of primary and secondary metabolism during cold acclimation of Arabidopsis thaliana, metabolic mutants with deficiencies in either starch or flavonoid metabolism were exposed to 4°C. Photosynthesis was determined together with amounts of carbohydrates, anthocyanins, organic acids and enzyme activities of the central carbohydrate metabolism. Starch deficiency was found to significantly delay soluble sugar accumulation during cold acclimation, while starch overaccumulation did not affect accumulation dynamics but resulted in lower total amounts of \sucrose and glucose. Anthocyanin amounts were lowered in both starch deficient and overaccumulating mutants. Vice versa, flavonoid deficiency did not result in a changed starch amount, which suggested a unidirectional signalling link between starch and flavonoid metabolism. Mathematical modelling of carbon metabolism indicated kinetics of sucrose biosynthesis to be limiting for carbon partitioning in leaf tissue during cold exposure. Together with cold-induced dynamics of citrate, fumarate and malate amounts, this provided evidence for a central role of sucrose phosphate synthase activity in carbon partitioning between biosynthetic and dissimilatory pathways which stabilizes photosynthesis and metabolism at low temperature.

Acoustic Resonance Frequencies of Underwater Toroidal Bubbles.

Underwater bubbles display an acoustic resonance frequency close to spherical ones. In order to obtain a resonance significantly deviating from the spherical case, we stabilize bubbles in toroidal frames, resulting in bubbles which can be slender while still compact. For thin tori the resonance frequency increases greatly. Between a pair of bubble rings, we can achieve a flat acoustic pressure field for a critical distance between rings, a condition reminiscent of Helmholtz coils in magnetostatics. This opens the possibility to shape the acoustic field using long tunnels of rings.

A yeast cell cycle model integrating stress, signaling, and physiology.

The cell division cycle in eukaryotic cells is a series of highly coordinated molecular interactions that ensure that cell growth, duplication of genetic material, and actual cell division are precisely orchestrated to give rise to two viable progeny cells. Moreover, the cell cycle machinery is responsible for incorporating information about external cues or internal processes that the cell must keep track of to ensure a coordinated, timely progression of all related processes. This is most pronounced in multicellular organisms, but also a cardinal feature in model organisms such as baker's yeast. The complex and integrative behavior is difficult to grasp and requires mathematical modeling to fully understand the quantitative interplay of the single components within the entire system. Here, we present a self-oscillating mathematical model of the yeast cell cycle that comprises all major cyclins and their main regulators. Furthermore, it accounts for the regulation of the cell cycle machinery by a series of external stimuli such as mating pheromones and changes in osmotic pressure or nutrient quality. We demonstrate how the external perturbations modify the dynamics of cell cycle components and how the cell cycle resumes after adaptation to or relief from stress.

Identification of small non-coding RNAs responsive to GUN1 and GUN5 related retrograde signals in Arabidopsis thaliana.

Chloroplast perturbations activate retrograde signalling pathways, causing dynamic changes of gene expression. Besides transcriptional control of gene expression, different classes of small non-coding RNAs (sRNAs) act in gene expression control, but comprehensive analyses regarding their role in retrograde signalling are lacking. We performed sRNA profiling in response to norflurazon (NF), which provokes retrograde signals, in Arabidopsis thaliana wild type (WT) and the two retrograde signalling mutants gun1 and gun5. The RNA samples were also used for mRNA and long non-coding RNA profiling to link altered sRNA levels to changes in the expression of their cognate target RNAs. We identified 122 sRNAs from all known sRNA classes that were responsive to NF in the WT. Strikingly, 142 and 213 sRNAs were found to be differentially regulated in both mutants, indicating a retrograde control of these sRNAs. Concomitant with the changes in sRNA expression, we detected about 1500 differentially expressed mRNAs in the NF-treated WT and around 900 and 1400 mRNAs that were differentially regulated in the gun1 and gun5 mutants, with a high proportion (~30%) of genes encoding plastid proteins. Furthermore, around 20% of predicted miRNA targets code for plastid-localised proteins. Among the sRNA-target pairs, we identified pairs with an anticorrelated expression as well pairs showing other expressional relations, pointing to a role of sRNAs in balancing transcriptional changes upon retrograde signals. Based on the comprehensive changes in sRNA expression, we assume a considerable impact of sRNAs in retrograde-dependent transcriptional changes to adjust plastidic and nuclear gene expression.

Efficient ptychographic phase retrieval via a matrix-free Levenberg-Marquardt algorithm.

The phase retrieval problem, where one aims to recover a complex-valued image from far-field intensity measurements, is a classic problem encountered in a range of imaging applications. Modern phase retrieval approaches usually rely on gradient descent methods in a nonlinear minimization framework. Calculating closed-form gradients for use in these methods is tedious work, and formulating second order derivatives is even more laborious. Additionally, second order techniques often require the storage and inversion of large matrices of partial derivatives, with memory requirements that can be prohibitive for data-rich imaging modalities. We use a reverse-mode automatic differentiation (AD) framework to implement an efficient matrix-free version of the Levenberg-Marquardt (LM) algorithm, a longstanding method that finds popular use in nonlinear least-square minimization problems but which has seen little use in phase retrieval. Furthermore, we extend the basic LM algorithm so that it can be applied for more general constrained optimization problems (including phase retrieval problems) beyond just the least-square applications. Since we use AD, we only need to specify the physics-based forward model for a specific imaging application; the first and second-order derivative terms are calculated automatically through matrix-vector products, without explicitly forming the large Jacobian or Gauss-Newton matrices typically required for the LM method. We demonstrate that this algorithm can be used to solve both the unconstrained ptychographic object retrieval problem and the constrained "blind" ptychographic object and probe retrieval problems, under the popular Gaussian noise model as well as the Poisson noise model. We compare this algorithm to state-of-the-art first order ptychographic reconstruction methods to demonstrate empirically that this method outperforms best-in-class first-order methods: it provides excellent convergence guarantees with (in many cases) a superlinear rate of convergence, all with a computational cost comparable to, or lower than, the tested first-order algorithms.

Nonuniform Flow Dynamics Probed by Nanosecond X-Ray Speckle Visibility Spectroscopy.

We report observations of nanosecond nonuniform colloidal dynamics in a free flowing liquid jet using ultrafast x-ray speckle visibility spectroscopy. Utilizing a nanosecond double-bunch mode, the Linac Coherent Light Source free electron laser produced pairs of femtosecond coherent hard x-ray pulses. By exploring anisotropy in the visibility of summed speckle patterns which relates to the correlation functions, we evaluate not only the average particle flow rate in a colloidal nanoparticle jet, but also the nonuniform flow field within. The methodology presented here establishes the foundation for the study of nano- and atomic-scale inhomogeneous fluctuations in complex matter using x-ray free electron laser sources.

Comparative assessment of left atrial volume in healthy cats by two-dimensional and three-dimensional echocardiography.

BACKGROUND: The left atrium (LA) is an important prognostic parameter in cardiac pathologies of cats. Its size is currently measured in one-dimensional methods, while human medicine considers two- and three-dimensional echocardiography as standard. The objectives of this study were to compare monoplane, biplane, triplane and real-time three dimensional echocardiography for volumetric measurement of the left atrium in healthy cats and establish a reference interval for further studies on cats with heart disease. Additionally, the influence of age, sex and weight on left atrial volume (LAV) was tested. RESULTS: One dimensional monoplane Simpson method of discs (SMOD) in the right parasternal four chamber view (r4) and the left apical 2 chamber view (l2) as well as biplane SMOD had no significant difference for left atrial maximum volume (LAMax). They can be used as equivalent in future studies and one common reference range was set up (1.96 ± 0.54 ml). Those three methods produced significantly higher volumes than triplane echocardiography (RTTPE) and real time three dimensional echocardiography (RT3DE) using TomTec® software. LA volumetry with RTTPE and RT3DE-TomTec™ was more feasible than expected, but low RT3DE image quality was the main reason for excluding patients. Neither age nor weight had an influence on LA volume in healthy cats. Male LAV results were only slightly, but in 2D and RTTPE significantly higher than those of female cats with a range of + 10.46% to + 19.58%. CONCLUSIONS: Monoplane, biplane, triplane and real-time three dimensional echocardiography were feasible for LA volumetry in healthy cats and showed acceptable intra- and interobserver variability. One common LAMax reference range for monoplane r4, l2 and biplane SMOD was set up. Raw data can be used for LA volumes and does not need to be correlated with the cat's weight or age. Male cats have only slightly but significantly larger atria than females in 2D and RTTPE. Therefore, under reservation, also sex related limit values were defined.

Correlated Nanoscale Analysis of the Emission from Wurtzite versus Zincblende (In,Ga)As/GaAs Nanowire Core-Shell Quantum Wells.

While the properties of wurtzite GaAs have been extensively studied during the past decade, little is known about the influence of the crystal polytype on ternary (In,Ga)As quantum well structures. We address this question with a unique combination of correlated, spatially resolved measurement techniques on core-shell nanowires that contain extended segments of both the zincblende and wurtzite polytypes. Cathodoluminescence hyperspectral imaging reveals a blue-shift of the quantum well emission energy by 75 ± 15 meV in the wurtzite polytype segment. Nanoprobe X-ray diffraction and atom probe tomography enable k·p calculations for the specific sample geometry to reveal two comparable contributions to this shift. First, there is a 30% drop in In mole fraction going from the zincblende to the wurtzite segment. Second, the quantum well is under compressive strain, which has a much stronger impact on the hole ground state in the wurtzite than in the zincblende segment. Our results highlight the role of the crystal structure in tuning the emission of (In,Ga)As quantum wells and pave the way to exploit the possibilities of three-dimensional band gap engineering in core-shell nanowire heterostructures. At the same time, we have demonstrated an advanced characterization toolkit for the investigation of semiconductor nanostructures.

Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality.

Temperature influences the life of many organisms in various ways. A great number of organisms live under conditions where their ability to adapt to changes in temperature can be vital and largely determines their fitness. Understanding the mechanisms and principles underlying this ability to adapt can be of great advantage, for example, to improve growth conditions for crops and increase their yield. In times of imminent, increasing climate change, this becomes even more important in order to find strategies and help crops cope with these fundamental changes. There is intense research in the field of acclimation that comprises fluctuations of various environmental conditions, but most acclimation research focuses on regulatory effects and the observation of gene expression changes within the examined organism. As thermodynamic effects are a direct consequence of temperature changes, these should necessarily be considered in this field of research but are often neglected. Additionally, compensated effects might be missed even though they are equally important for the organism, since they do not cause observable changes, but rather counteract them. In this work, using a systems biology approach, we demonstrate that even simple network motifs can exhibit temperature-dependent functional features resulting from the interplay of network structure and the distribution of activation energies over the involved reactions. The demonstrated functional features are (i) the reversal of fluxes within a linear pathway, (ii) a thermo-selective branched pathway with different flux modes and (iii) the increased flux towards carbohydrates in a minimal Calvin cycle that was designed to demonstrate temperature compensation within reaction networks. Comparing a system's response to either temperature changes or changes in enzyme activity we also dissect the influence of thermodynamic changes versus genetic regulation. By this, we expand the scope of thermodynamic modelling of biochemical processes by addressing further possibilities and effects, following established mathematical descriptions of biophysical properties.

Using automatic differentiation as a general framework for ptychographic reconstruction.

Coherent diffraction imaging methods enable imaging beyond lens-imposed resolution limits. In these methods, the object can be recovered by minimizing an error metric that quantifies the difference between diffraction patterns as observed, and those calculated from a present guess of the object. Efficient minimization methods require analytical calculation of the derivatives of the error metric, which is not always straightforward. This limits our ability to explore variations of basic imaging approaches. In this paper, we propose to substitute analytical derivative expressions with the automatic differentiation method, whereby we can achieve object reconstruction by specifying only the physics-based experimental forward model. We demonstrate the generality of the proposed method through straightforward object reconstruction for a variety of complex ptychographic experimental models.

Gas-Induced Segregation in Pt-Rh Alloy Nanoparticles Observed by In Situ Bragg Coherent Diffraction Imaging.

Bimetallic catalysts can undergo segregation or redistribution of the metals driven by oxidizing and reducing environments. Bragg coherent diffraction imaging (BCDI) was used to relate displacement fields to compositional distributions in crystalline Pt-Rh alloy nanoparticles. Three-dimensional images of internal composition showed that the radial distribution of compositions reverses partially between the surface shell and the core when gas flow changes between O_{2} and H_{2}. Our observation suggests that the elemental segregation of nanoparticle catalysts should be highly active during heterogeneous catalysis and can be a controlling factor in synthesis of electrocatalysts. In addition, our study exemplifies applications of BCDI for in situ 3D imaging of internal equilibrium compositions in other bimetallic alloy nanoparticles.

Measuring Three-Dimensional Strain and Structural Defects in a Single InGaAs Nanowire Using Coherent X-ray Multiangle Bragg Projection Ptychography.

III-As nanowires are candidates for near-infrared light emitters and detectors that can be directly integrated onto silicon. However, nanoscale to microscale variations in structure, composition, and strain within a given nanowire, as well as variations between nanowires, pose challenges to correlating microstructure with device performance. In this work, we utilize coherent nanofocused X-rays to characterize stacking defects and strain in a single InGaAs nanowire supported on Si. By reconstructing diffraction patterns from the 21̅1̅0 Bragg peak, we show that the lattice orientation varies along the length of the wire, while the strain field along the cross-section is largely unaffected, leaving the band structure unperturbed. Diffraction patterns from the 011̅0 Bragg peak are reproducibly reconstructed to create three-dimensional images of stacking defects and associated lattice strains, revealing sharp planar boundaries between different crystal phases of wurtzite (WZ) structure that contribute to charge carrier scattering. Phase retrieval is made possible by developing multiangle Bragg projection ptychography (maBPP) to accommodate coherent nanodiffraction patterns measured at arbitrary overlapping positions at multiple angles about a Bragg peak, eliminating the need for scan registration at different angles. The penetrating nature of X-ray radiation, together with the relaxed constraints of maBPP, will enable the in operando imaging of nanowire devices.

Utilizing broadband X-rays in a Bragg coherent X-ray diffraction imaging experiment.

A method is presented to simplify Bragg coherent X-ray diffraction imaging studies of complex heterogeneous crystalline materials with a two-stage screening/imaging process that utilizes polychromatic and monochromatic coherent X-rays and is compatible with in situ sample environments. Coherent white-beam diffraction is used to identify an individual crystal particle or grain that displays desired properties within a larger population. A three-dimensional reciprocal-space map suitable for diffraction imaging is then measured for the Bragg peak of interest using a monochromatic beam energy scan that requires no sample motion, thus simplifying in situ chamber design. This approach was demonstrated with Au nanoparticles and will enable, for example, individual grains in a polycrystalline material of specific orientation to be selected, then imaged in three dimensions while under load.

Interfacial Control of Magnetic Properties at LaMnO3/LaNiO3 Interfaces.

The functional properties of oxide heterostructures ultimately rely on how the electronic and structural mismatches occurring at interfaces are accommodated by the chosen materials combination. We discuss here LaMnO3/LaNiO3 heterostructures, which display an intrinsic interface structural asymmetry depending on the growth sequence. Using a variety of synchrotron-based techniques, we show that the degree of intermixing at the monolayer scale allows interface-driven properties such as charge transfer and the induced magnetic moment in the nickelate layer to be controlled. Further, our results demonstrate that the magnetic state of strained LaMnO3 thin films dramatically depends on interface reconstructions.

Quantification of left ventricular volumes and function in anesthetized beagles using real-time three-dimensional echocardiography: 4D-TomTec™ analysis versus 4D-AutLVQ™ analysis in comparison with cardiac magnetic resonance imaging.

BACKROUND: Real-time three-dimensional echocardiography (RT3DE) enables accurate volume determination of the left ventricle (LV), since measurements in foreshortened depicted views are avertable. Different analyzing programs are available for this RT3DE. The commonly used semi-automatic software 4D-AutLVQ™ showed underestimation of LV volumes in comparison with CMRI in healthy anesthetized dogs (Am J Vet Res 74(9):1223-1230, 2013). TomTec 4D LV-Function™ is an offline analysis program for morphological and functional analyses of the left ventricle by using manual measurement optimization, showing excellent agreement with CMRI in human medicine (Echocardiography 27(10):1263-1273, 2010; Eur J Echocardiogr 11(4):359-368, 2010; Echocardiography 24(9):967-974, 2007). The aim of the present study was to compare these different RT3DE analyzing software programs to test the possibility of one performing better than the other by assessing accuracy and reproducibility in comparison with the reference method cardiac magnetic resonance imaging (CMRI) by determining the left ventricular end-diastolic volume (EDV), end-systolic volume (ESV), stroke volume (SV) and ejection fraction (EF). RT3DE and CMRI were performed during anesthesia in 10 healthy beagles. The analyzing programs 4D-AutLVQ™ (based on semi-automated border detection) and TomTec 4D LV-Function™ (primary manual tracking with semi-automated border detection) were used for RT3DE volume analysis of the left ventricle. Left ventricular EDV, ESV, SV and EF were measured and compared to those measured by the reference method CMRI. Repeated measurements were performed to determine inter- and intra-observer variability. RESULTS: Both, 4D-AutLVQ™ and 4D-TomTec™ showed small but significant underestimation for EDV and ESV with quite good correlation (r = 0.34-0.69) in comparison with CMRI, without significant difference between each of them. Ejection fraction (EF) measured by 4D-TomTec™ showed no significant differences compared to CMRI (p = 0.12), while 4D-AutLVQ™ significantly underestimated LV-EF (p = 0.03). Analyzing time was shorter using 4D-AutLVQ™ compared to 4D-TomTec™. The inter-observer variability was higher using 4D-TomTec™ than with 4D-AutLVQ™, whereas both methods present excellent intra-observer variability. CONCLUSION: 4D-TomTec™ and 4D-AutLVQ™ are feasible RT3DE analyzing programs, allowing accurate volume quantification of the left ventricle, albeit with significant underestimation of ventricular volumes in comparison with the gold standard CMRI. 4D-AutLVQ™ is performed faster with less inter-observer variability than 4D-TomTec™. Therefore, 4D-AutLVQ™ is the more practicable measurement method when comparing the different analyzing programs.

Strain imaging of nanoscale semiconductor heterostructures with x-ray Bragg projection ptychography.

We report the imaging of nanoscale distributions of lattice strain and rotation in complementary components of lithographically engineered epitaxial thin film semiconductor heterostructures using synchrotron x-ray Bragg projection ptychography (BPP). We introduce a new analysis method that enables lattice rotation and out-of-plane strain to be determined independently from a single BPP phase reconstruction, and we apply it to two laterally adjacent, multiaxially stressed materials in a prototype channel device. These results quantitatively agree with mechanical modeling and demonstrate the ability of BPP to map out-of-plane lattice dilatation, a parameter critical to the performance of electronic materials.

Quantification of right ventricular volume in dogs: a comparative study between three-dimensional echocardiography and computed tomography with the reference method magnetic resonance imaging.

BACKGROUND: Right ventricular (RV) volume and function are important diagnostic and prognostic factors in dogs with primary or secondary right-sided heart failure. The complex shape of the right ventricle and its retrosternal position make the quantification of its volume difficult. For that reason, only few studies exist, which deal with the determination of RV volume parameters. In human medicine cardiac magnetic resonance imaging (CMRI) is considered to be the reference technique for RV volumetric measurement (Nat Rev Cardiol 7(10):551-563, 2010), but cardiac computed tomography (CCT) and three-dimensional echocardiography (3DE) are other non-invasive methods feasible for RV volume quantification. The purpose of this study was the comparison of 3DE and CCT with CMRI, the gold standard for RV volumetric quantification. RESULTS: 3DE showed significant lower and CCT significant higher right ventricular volumes than CMRI. Both techniques showed very good correlations (R > 0.8) with CMRI for the volumetric parameters end-diastolic volume (EDV) and end-systolic volume (ESV). Ejection fraction (EF) and stroke volume (SV) were not different when considering CCT and CMRI, whereas 3DE showed a significant higher EF and lower SV than CMRI. The 3DE values showed excellent intra-observer variability (<3%) and still acceptable inter-observer variability (<13%). CONCLUSION: CCT provides an accurate image quality of the right ventricle with comparable results to the reference method CMRI. CCT overestimates the RV volumes; therefore, it is not an interchangeable method, having the disadvantage as well of needing general anaesthesia. 3DE underestimated the RV-Volumes, which could be explained by the worse image resolution. The excellent correlation between the methods indicates a close relationship between 3DE and CMRI although not directly comparable. 3DE is a promising technique for RV volumetric quantification, but further studies in awake dogs and dogs with heart disease are necessary to evaluate its usefulness in veterinary cardiology.

Direct evidence of Fe(2+)-Fe3+ charge ordering in the ferrimagnetic hematite-ilmenite Fe(1.35)Ti(0.65)O(3-δ) thin films.

In this Letter we highlight direct experimental evidence of Fe(2+)-Fe3+ charge ordering at room temperature in hematite-ilmenite Fe(1.35)Ti(0.65)O(3-δ) epitaxial thin films grown by pulsed laser deposition, using aberration-corrected scanning transmission electron microscopy coupled to high-resolution energy electron-loss spectroscopy. These advanced spectromicroscopy techniques demonstrate a strong modulation of the Fe2+ valence state along the c axis. Density functional theory calculations provide crucial information on the key role of oxygen vacancies in the observed charge distributions. Their presence at significant levels leads to the localization of extra electrons onto reduced Fe2+ sites, while Ti remains solely +4. The magnetic and transport properties of these films are reviewed in the light of the present results regarding their ferrimagnetic character correlated with the Fe2+ modulation and their semiconducting behavior interpreted by an Efros-Shklovskii variable-range hopping conduction regime via Fe2+ and Fe3+ centers. The experimental evidence of only one type of mixed valence state, i.e., Fe2+ and Fe3+, in the Fe(2-x)Ti(x)O(3-δ) system will thus help to interpret further the origin of its geomagnetic properties and to illuminate fundamental issues regarding its spintronic potential.