Volume imaging by tracking sparse topological features in electron micrograph tilt series.

The sensitive coherent interference of electron waves arising from a specimen is useful for revealing subtle structural information in electron micrographs, which can be important for minimising dose and for rapid imaging. In general, dynamical diffraction is expected due to the useful strong interactions of electrons with matter, which can create phase contrast that violates the requisite Radon projection assumption for tomography. It is for these reasons that incoherent imaging modalities such as high angle annular dark field have been favoured to date in electron tomography of crystalline specimens, to access a monotonic relationship between specimen thickness and micrograph intensity. Here we use a geometric approach to track topological features that are robust to perturbation of the imaging conditions, to enable 3D reconstructions from electron microscope tilt series under imaging conditions that violate the Radon projection assumption, with an emphasis on phase contrast. Invoking a sparsity assumption, we demonstrate that topological features can be reliably tracked in 3D using a differential geometric form of stereoscopy, to circumvent departures from the projection approximation and reduce noise by effecting segmentation of interest points from the outset. We demonstrate this approach on a variety of different specimen and data types, from polyhedral nanoparticles, to steel dislocation networks, cryo-EM cellular structures and 3D diffuse diffraction of a relaxor ferroelectric.

Are Groundwater Level Data Collected by Citizen Scientists Trustworthy? A Cautionary Tale.

Public participation in groundwater projects is increasing, however, the efficacy of the data collected in such studies, is not well-documented in the literature. In this study, the authors describe a citizen science project focused on measuring and recording groundwater levels in an aquifer and evaluate whether the groundwater data collected by the participants are trustworthy. A total of 31 participants were initially recruited to measure and record groundwater levels from 29 monitoring wells on a barrier island. Following recruitment, the authors provided training to the citizen scientists by introducing groundwater concepts, and showing the participants how to measure, record and report groundwater level data (over an 81-day period) with an electronic water level meter. The water level data recorded by the citizen scientists (i.e., 35 time series datasets with over 450 unique measurements) were then compared to high frequency data recorded by automated water level loggers that were already deployed in the groundwater monitoring wells to assess the trustworthiness of the data. Trustworthiness was evaluated using measures of reliability (i.e., consistency in measuring the same thing), validity (i.e., degree to which results are truthful), and other standard graphical and statistical techniques. The results suggest that with proper training, guidance, and motivation, citizen scientists can collect trustworthy groundwater level data that could be useful for monitoring the sustainability of aquifers and managing of groundwater levels. It is noted however, that such positive outcomes require significant investments of time and effort on the part of the project managers.

Real-Time Estimates of Escherichia coli Concentrations Using Ultraviolet-Visible Spectrometers.

Substantial effort has been invested in the development and testing of methods to rapidly measure the concentration of indicator bacteria in recreational waters. These efforts are driven by the need to quickly determine whether waters are contaminated and may pose excessive public health risks. In situ ultraviolet-visible (UV-vis) spectrometers have been used to monitor levels of multiple contaminants in surface waters by relating the absorption spectra to the measured concentrations using regression models. In this study, three different regression models were tested to see if spectroscopy could be used to rapidly predict concentrations in a freshwater stream. The regression models did not produce acceptable results when tested for all of the samples collected during an 11-mo period ( < 0.2). When divided into multiple subsets based on temperature, concentration, or rainfall, models produced adequate results for subsets of samples collected in the cooler months ( = 0.72) or on days when rainfall occurred ( = 0.58). Pairing a UV-vis spectrometer with regression models did not result in a model that could be used to estimate levels throughout the year, but the results promote further testing of this method when flow data is available in freshwaters, on beaches where rainfall causes elevated bacteria levels, and in shellfish growing waters.

A menu of electron probes for optimising information from scanning transmission electron microscopy.

We assess a selection of electron probes in terms of the spatial resolution with which information can be derived about the structure of a specimen, as opposed to the nominal image resolution. Using Ge [001] as a study case, we investigate the scattering dynamics of these probes and determine their relative merits in terms of two qualitative criteria: interaction volume and interpretability. This analysis provides a 'menu of probes' from which an optimum probe for tackling a given materials science question can be selected. Hollow cone, vortex and spherical wave fronts are considered, from unit cell to Ångstrom size, and for different defocus and specimen orientations.

The atomic structure of polar and non-polar InGaN quantum wells and the green gap problem.

We have used high resolution transmission electron microscopy (HRTEM), aberration-corrected quantitative scanning transmission electron microscopy (Q-STEM), atom probe tomography (APT) and X-ray diffraction (XRD) to study the atomic structure of (0001) polar and (11-20) non-polar InGaN quantum wells (QWs). This paper provides an overview of the results. Polar (0001) InGaN in QWs is a random alloy, with In replacing Ga randomly. The InGaN QWs have atomic height interface steps, resulting in QW width fluctuations. The electrons are localised at the top QW interface by the built-in electric field and the well-width fluctuations, with a localisation energy of typically 20meV. The holes are localised near the bottom QW interface, by indium fluctuations in the random alloy, with a localisation energy of typically 60meV. On the other hand, the non-polar (11-20) InGaN QWs contain nanometre-scale indium-rich clusters which we suggest localise the carriers and produce longer wavelength (lower energy) emission than from random alloy non-polar InGaN QWs of the same average composition. The reason for the indium-rich clusters in non-polar (11-20) InGaN QWs is not yet clear, but may be connected to the lower QW growth temperature for the (11-20) InGaN QWs compared to the (0001) polar InGaN QWs.

The spatial coherence function in scanning transmission electron microscopy and spectroscopy.

We investigate the implications of the form of the spatial coherence function, also referred to as the effective source distribution, for quantitative analysis in scanning transmission electron microscopy, and in particular for interpreting the spatial origin of imaging and spectroscopy signals. These questions are explored using three different source distribution models applied to a GaAs crystal case study. The shape of the effective source distribution was found to have a strong influence not only on the scanning transmission electron microscopy (STEM) image contrast, but also on the distribution of the scattered electron wavefield and hence on the spatial origin of the detected electron intensities. The implications this has for measuring structure, composition and bonding at atomic resolution via annular dark field, X-ray and electron energy loss STEM imaging are discussed.

Enhanced minority carrier lifetimes in GaAs/AlGaAs core-shell nanowires through shell growth optimization.

The effects of AlGaAs shell thickness and growth time on the minority carrier lifetime in the GaAs core of GaAs/AlGaAs core-shell nanowires grown by metal-organic chemical vapor deposition are investigated. The carrier lifetime increases with increasing AlGaAs shell thickness up to a certain value as a result of reducing tunneling probability of carriers through the AlGaAs shell, beyond which the carrier lifetime reduces due to the diffusion of Ga-Al and/or impurities across the GaAs/AlGaAs heterointerface. Interdiffusion at the heterointerface is observed directly using high-angle annular dark field scanning transmission electron microscopy. We achieve room temperature minority carrier lifetimes of 1.9 ns by optimizing the shell growth with the intention of reducing the effect of interdiffusion.

Measurement of chromatic aberration in STEM and SCEM by coherent convergent beam electron diffraction.

A simple method is described for the accurate and precise measurement of chromatic aberration under electron-optical conditions pertinent to scanning transmission electron microscopy (STEM) and scanning confocal electron microscopy (SCEM). The method requires only the measurement of distances in a coherent CBED pattern and knowledge of the electron wavelength and the lattice spacing of a calibration specimen. The chromatic aberration of a spherical-aberration corrected 300 kV thermal field emission TEM is measured in STEM and SCEM operating modes and under different condenser lens settings. The effect of the measured chromatic aberrations on the 3 dimensional intensity distribution of the electron probe is also considered.

Addressing the fouling of in situ ultraviolet-visual spectrometers used to continuously monitor water quality in brackish tidal marsh waters.

The introduction of portable in situ ultraviolet-visual spectrometers has made possible the collection of water quality parameters at a high frequency in dynamic systems such as tidal marshes. The usefulness of this technology is inhibited by fouling of the instrument's optics. In this study, a spectrometer fitted with manufacturer-recommended compressed air optical cleaning was installed in a brackish marsh to determine if fouling interfered with measurements between bi-weekly servicing. During a 2-wk period, the absorbance measured in air at 220 nm increased from 9 to 549 m, indicating major fouling. An antifouling system was developed that reduced the time of exposure of the optics to stream water and used a pressurized fresh water cleaning. After implementation of the system, the absorbance in air increased to at most 63 m after 2 wk of data collection. The dramatic reduction in fouling will allow quality long-term data to be collected using this technology.

Image formation in the scanning transmission electron microscope using object-conjugate detectors.

This work presents a theoretical analysis of image formation in a scanning transmission electron microscope equipped with electron detectors in a plane conjugate to the specimen. This optical geometry encompasses both the three-dimensional imaging technique of scanning confocal electron microscopy (SCEM) and a recently developed atomic resolution imaging technique coined real-space scanning transmission electron microscopy (R-STEM). Image formation in this geometry is considered from the viewpoints of both wave optics and geometric optics, and the validity of the latter is analysed by means of Wigner distributions. Relevant conditions for the validity of a geometric interpretation of image formation are provided. For R-STEM, where a large detector is used, it is demonstrated that a geometric optics description of image formation provides an accurate approximation to wave optics, and that this description offers distinct advantages for interpretation and numerical implementation. The resulting description of R-STEM is also demonstrated to be in good agreement with experiment. For SCEM, it is emphasized that a geometric optics description of image formation is valid provided that higher-order aberrations can be ignored and the detector size is large enough to average out diffraction from the angle-limiting aperture.

Practical methods for the measurement of spatial coherence--a comparative study.

Two new methods for the measurement of transverse spatial coherence in a transmission electron microscope (TEM) are developed and applied to measure the spatial coherence in a field emission gun TEM. Measurements are made under different illumination and operating conditions, illustrating the effect of these conditions on the spatial coherence. The relative merits and limitations of these methods are discussed and compared, together with the previously described "Ronchigram" method.

Differential use of identical food resources by Reticulitermes flavipes (Isoptera: Rhinotermitidae) in two types of habitats.

A year-long field experiment showed that Reticulitermes flavipes attacked and used single stakes and wooden stake bundles differently in two habitats that varied in alternative forage. In both habitats, the number of termites present in single stakes and stake-bundles increased with stake resource size, and the number of larvae recorded from feeding sites was a close reflection of the number of workers attracted to a given food source. Over 12 mo, more single stakes and stake bundles were heavily attacked and abandoned in the pine woods compared with grassy clearings. Paradoxically, the number of termites present in single stakes and stake bundles was greater in the food-poor habitat (grassy clearings), yet the wood was less consumed compared with the food-rich habitat (pine woods). Use of stake bundles as nests and the slower rate of wood consumption in grassy clearings indicated that termites seemed to value food resources in relative terms, i.e., those termites with abundant alternative food resources consumed quickly and departed, whereas those lacking extra resources ate slowly and settled in. These field results confirm earlier laboratory results that showed that termites modified wood consumption rates dependent on the amount of food available to the colony as a whole. The appearance of mature (physogastric) reproductives (>> yr old) in stake bundles in both habitats further indicated that termites track resources and opportunistically shift colony activities and possibly territory boundaries depending on the nature of the resources and other environmental factors. Implications for managing termites with a baiting strategy are discussed.

CBED contrast in the lower order Laue zone.

Contrast in a systematic arrangement of lower order Laue zone (LOLZ) beams is reported and analysed using a Bloch wave description. Observations are reported for hexagonal barium ruthenium zirconate (Ba4Ru3ZrO12) and barium ruthenium titanate (Ba3Ti2RuO9), both near the c-axis orientation. The specific scattering dynamics invoked by this diffraction geometry may have novel uses in the exploration of crystallographic parameters.

Scattering of A-scale electron probes in silicon.

We use frozen phonon multislice calculations to examine the scattering behaviour of A-scale electron probes in <001> and <110> silicon. For each crystal orientation, we consider the distribution of scattered intensity in real space as a function of crystal thickness, probe size and probe position. The scattered intensity distribution is found to vary drastically for different probe sizes. For a given probe size, the scattered intensity distribution is also significantly influenced by the crystal orientation. We discuss the implications for the simultaneous acquisition of an annular dark-field image and electron energy loss spectra in the scanning transmission electron microscope, with specific reference to the spatial resolution with which electron energy loss spectra can be related to local atomic structure.

Cellular angiofibroma of the vulva.

BACKGROUND: The cellular angiofibroma is a benign mesenchymal neoplasm that clinically and histologically must be distinguished from biologically more aggressive lesions. It typically arises in women of late reproductive age and lends itself to cure by complete local excision. A report of an unusual case in a postmenopausal patient is presented. CASE: A 77-year-old woman presented with a painless vulvar mass that slowly enlarged over 3 years. Past history included a hysterectomy and bilateral salpingo-oophorectomy followed by estrogen replacement therapy. Surgical excision of the mass was performed and there is no evidence of recurrence 1 year postoperatively. Histopathologic examination revealed an admixture of hyalinized blood vessels and loose cellular stroma characteristic of a cellular angiofibroma. Immunohistochemical studies revealed stromal cell immunoreactivity for vimentin and CD34 and nonreactivity for desmin, actin, and S100 protein. The nuclei of the stromal cells demonstrated strong reactivity for estrogen and progesterone receptors. CONCLUSION: Mesenchymal lesions of the vulva and perineum include both benign and malignant neoplasms. The cellular angiofibroma is benign; however, other lesions including the aggressive angiomyxoma must be excluded when arriving at that diagnosis. The role of long-term estrogen therapy in the genesis of this tumor awaits further analysis.

A study of Li2TiOSiO4 and Li2TiOGeO4 by X-ray powder and electron single-crystal diffraction, 17O MAS NMR andO K-edge and Ti L2,3-edge EELS.

X-ray powder and electron single-crystal diffraction of crystals of Li(2)TiOSiO(4) and Li(2)TiOGeO(4) showed them to be tetragonal, space group P4/nmm unit-cell parameters a = 6.4379(2), c = 4.40032(2) Å for Li(2)TiOSiO(4) and a = 6.6110(8), c = 4.4372(6) Å for Li(2)TiGeO(4). The compounds are isostructural with their sodium analogues but are considerably compressed along the c axis owing to the smaller size of lithium compared with sodium atoms. Square-pyramidal TiO(5) groups are joined in these compounds by tetrahedral SiO(4) and GeO(4) groups, respectively. (17)O nuclear magnetic resonance spectra of the two compounds, isotopically enriched with (17)O, showed peaks due to the apical titanyl, Ti-O, and basal, bridging, Ti-O-Si or Ti-O-Ge, oxygen atoms of the title compounds. By comparison with reference spectra, oxygen K edges and titanium L(2,3) edges of electron energy-loss spectra were tentatively assigned.

High-resolution electron-microscope images of crystals with correlated atomic displacements.

A coordinate-space multislice description of the scattering of high-energy electrons is constructed from consecutions of differential operators acting upon atomic potentials. It is used to find expressions for the intensity distribution in high-resolution electron-microscope images of crystals whose atoms are periodically displaced relative to a reference lattice according to a modulation wave. Both static correlated displacements, such as occur in modulated structures, and time-dependent correlated displacements, as are generated by phonons, are considered. Two aspects of the image are examined in detail; its translational symmetry and its dependence upon the correlations between the atomic displacements. It is shown that the intensity distribution due to scattering from static correlated displacements has the translational symmetry of the modulated structure in that projection, as determined by the component of the modulation wavevector perpendicular to the incident beam, whereas that due to scattering from phonons has the translational symmetry of the reference lattice in that projection. The former is a consequence of higher-order Laue-zone interactions. The intensity distribution due to scattering from static displacements depends upon the absolute phase of the displacement at each scattering atomic site whereas that due to scattering from phonons depends only upon the relative phase of the displacements between different scattering sites, both within the same atomic column parallel to the beam and in adjacent columns. In both cases, the influence of the component of the correlation wavevector parallel to the incident beam is different to that perpendicular to the beam; the former affects the intensity mostly at the atomic sites whilst the latter affects the intensity mostly between the atomic sites. It is also observed that, as a consequence of the periodic nature of the polarization-vector function, the interference terms are small, both relative to the non-interference term and in an absolute sense, particularly for phonon scattering. For this reason, the contribution to the image due to scattering from correlated atomic displacements will have greater and sharper atomic contrast than that due to scattering from the reference structure without displacements. In addition, this component of the intensity distribution will not exhibit strong contrast reversal when the objective-lens defocus is changed.

103Pd brachytherapy and external beam irradiation for clinically localized, high-risk prostatic carcinoma.

PURPOSE: To summarize biochemical failure rates and morbidity of external beam irradiation (EBRT) combined with palladium (103Pd) boost for clinically localized high-risk prostate carcinoma. METHODS AND MATERIALS: Seventy-three consecutive patients with stage T2a-T3 prostatic carcinoma were treated from 1991 through 1994. Each patient had at least one of the following risk factors for extracapsular disease extension: Stage T2b or greater (71 patients), Gleason score 7-10 (40 patients), prostate specific antigen (PSA) > 15 (32 patients), or elevated prostatic acid phosphatase (PAP) (17 patients). Patients received 41 Gy EBRT to a limited pelvic field, followed 4 weeks later by a 103Pd boost (prescription dose: 80 Gy). Biochemical failure was defined as a PSA greater than 1.0 ng/ml (normal < 4.0 ng/ml). Patients whose PSA was still decreasing at the last follow-up were censored at that time. Patients whose PSA plateaued at a value greater than 1.0 were scored as failures at the time the PSA first plateaued. RESULTS: The overall, actuarial freedom from biochemical failure at 3 years after treatment was 79%. In Cox proportional hazard multivariate analysis, the strongest predictor of failure was elevated acid phosphatase (p = 0.04), followed by PSA (p = 0.17), Stage (p = 0.23), and Gleason score (p = 0.6). Treatment-related morbidity was usually limited to temporary, RTOG Grade 1-2 urinary symptoms. One patient, who had both a transurethral incision of the prostate (TUIP) and a transurethral resection of the prostate (TURP), developed low-volume urinary incontinence. The actuarial potency rate at 3 years after implantation was 77% for 46 patients who were sexually potent prior to implant. CONCLUSION: Biochemical freedom from failure rates following combined EBRT and 103Pd brachytherapy for clinically localized, high-risk prostate cancer compare favorably with that reported after conventional dose EBRT alone. Morbidity has been acceptable.