Ultra-high-resolution dual-source CT for forensic dental visualization-discrimination of ceramic and composite fillings

Dental identification is the most valuable method to identify human remains in single cases with major postmortem alterations as well as in mass casualties because of its practicability and demanding reliability. Computed tomography (CT) has been investigated as a supportive tool for forensic identification and has proven to be valuable. It can also scan the dentition of a deceased within minutes. In the present study, we investigated currently used restorative materials using ultra-high-resolution dual-source CT and the extended CT scale for the purpose of a color-encoded, in scale, and artifact-free visualization in 3D volume rendering. In 122 human molars, 220 cavities with 2-, 3-, 4- and 5-mm diameter were prepared. With presently used filling materials (different composites, temporary filling materials, ceramic, and liner), these cavities were restored in six teeth for each material and cavity size (exception amalgam n = 1). The teeth were CT scanned and images reconstructed using an extended CT scale. Filling materials were analyzed in terms of resulting Hounsfield units (HU) and filling size representation within the images. Varying restorative materials showed distinctively differing radiopacities allowing for CT-data-based discrimination. Particularly, ceramic and composite fillings could be differentiated. The HU values were used to generate an updated volume-rendering preset for postmortem extended CT scale data of the dentition to easily visualize the position of restorations, the shape (in scale), and the material used which is color encoded in 3D. The results provide the scientific background for the application of 3D volume rendering to visualize the human dentition for forensic identification purposes.

Informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry (GCxGC-HRMS)

This paper describes informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography (GCxGC) and high-resolution mass spectrometry (HRMS). GCxGC-HRMS analysis produces large data sets that are rich with information, but highly complex. The size of the data and volume of information requires automated processing for comprehensive cross-sample analysis, but the complexity poses a challenge for developing robust methods. The approach developed here analyzes GCxGC-HRMS data from multiple samples to extract a feature template that comprehensively captures the pattern of peaks detected in the retention-times plane. Then, for each sample chromatogram, the template is geometrically transformed to align with the detected peak pattern and generate a set of feature measurements for cross-sample analyses such as sample classification and biomarker discovery. The approach avoids the intractable problem of comprehensive peak matching by using a few reliable peaks for alignment and peak-based retention-plane windows to define comprehensive features that can be reliably matched for cross-sample analysis. The informatics are demonstrated with a set of 18 samples from breast-cancer tumors, each from different individuals, six each for Grades 1-3. The features allow classification that matches grading by a cancer pathologist with 78% success in leave-one-out cross-validation experiments. The HRMS signatures of the features of interest can be examined for determining elemental compositions and identifying compounds.

High-resolution imaging of 2D outer membrane protein F (OmpF) crystals by atomic force microscopy

In this chapter the methodological bases are provided to achieve subnanometer resolution on two-dimensional (2D) membrane protein crystals by atomic force microscopy (AFM). This is outlined in detail with the example of AFM studies of the outer membrane protein F (OmpF) from the bacterium Escherichia coli (E. coli). We describe in detail the high-resolution imaging of 2D OmpF crystals in aqueous solution and under near-physiological conditions. The topographs of OmpF, and stylus effects and artifacts encountered when imaging by AFM are discussed.

High-resolution atomic force microscopy imaging of rhodopsin in rod outer segment disk membranes.

Atomic force microscopy (AFM) is a powerful imaging technique that allows recording topographical information of membrane proteins under near-physiological conditions. Remarkable results have been obtained on membrane proteins that were reconstituted into lipid bilayers. High-resolution AFM imaging of native disk membranes from vertebrate rod outer segments has unveiled the higher-order oligomeric state of the G protein-coupled receptor rhodopsin, which is highly expressed in disk membranes. Based on AFM imaging, it has been demonstrated that rhodopsin assembles in rows of dimers and paracrystals and that the rhodopsin dimer is the fundamental building block of higher-order structures.

Structure determination of channel and transport proteins by high-resolution microscopy techniques

High-resolution microscopy techniques provide a plethora of information on biological structures from the cellular level down to the molecular level. In this review, we present the unique capabilities of transmission electron and atomic force microscopy to assess the structure, oligomeric state, function and dynamics of channel and transport proteins in their native environment, the lipid bilayer. Most importantly, membrane proteins can be visualized in the frozen-hydrated state and in buffer solution by cryo-transmission electron and atomic force microscopy, respectively. We also illustrate the potential of the scintillation proximity assay to study substrate binding of detergent-solubilized transporters prior to crystallization and structural characterization.

High-resolution summer temperature reconstruction from Lake Silvaplana based on in-situ reflectance spectroscopy

Annually laminated (varved) sediments of proglacial Lake Silvaplana (46 ̊27’N, 9 ̊48’E, 1791 m a.s.l., Engadine, eastern Swiss Alps) provide an excellent archive for quantitative high-resolution (seasonal – annual) reconstruction of high- and lowfrequency climate signals back to AD 1580. The chronology of the core is based on varve counting, Cs-137, Pb-210 and event stratigraphy. In this study we present a reconstruction based on in-situ reflectance spectroscopy. In situ reflectance spectroscopy is known as a cost- and time-effective non destructtive method for semi-quantitative analysis of pigments (e.g., chlorines and carotenoids) and of lithoclastic sediment fractions. Reflectance-dependent absorption (RDA) was measured with a Gretac Macbeth spectrolino at 2 mm resolution. The spectral coverage ranges from 380 nm to 730 nm at 10 nm band resolution. In proglacial Lake Silvaplana, 99% of the sediment is lithoclastic prior to AD 1950. Therefore, we concentrate on absorption features that are characteristic for lithoclastic sediment fractions. In Lake Silvaplana, two significant correlations that are stable in time were found between RDA typical for lithoclastics and meteorological data: (1) the time series R 570 /R 630 (ratio between RDA at 570 nm and 630 nm) of varves in Lake Silvaplana and May to October temperatures at nearby station of Sils correlate highly significantly (calibration period AD 1864 – 1951, r = 0.74, p < 0.01 for 5ptsmoothed series; RMSE is 0.28 ̊C, RE = 0.41 and CE = 0.38), and (2) the minimum reflectance within the 690nm band (min690) data correlate with May to October (calibration period AD 1864 – 1951, r = 0.68, p < 0.01 for 5pt-smoothed series; RMSE = 0.22 ̊C, RE = 0.5, CE = 0.31). Both proxy series (min690nm and R 570 /R 630 values) are internally highly consistent (r = 0.8, p < 0.001). In proglacial Lake Silvaplana the largest amount of sediment is transported by glacial meltwater. The melting season spans approximately from May to October, which gives us a good understanding of the geophysical processes explaining the correlations between lithoclastic proxies and the meteorological data. The reconstructions were extended back to AD 1580 and show a broad corresponddence with fully independent reconstructions from tree rings and documentary data.

Quantitative high-resolution warm season rainfall recorded in varved sediments of Lake Oeschinen, northern Swiss Alps: calibration and validation AD 1901–2008

High-resolution, well-calibrated records of lake sediments are critically important for quantitative climate reconstructions, but they remain a methodological and analytical challenge. While several comprehensive paleotemperature reconstructions have been developed across Europe, only a few quantitative high-resolution studies exist for precipitation. Here we present a calibration and verification study of lithoclastic sediment proxies from proglacial Lake Oeschinen (46°30′N, 7°44′E, 1,580 m a.s.l., north–west Swiss Alps) that are sensitive to rainfall for the period AD 1901–2008. We collected two sediment cores, one in 2007 and another in 2011. The sediments are characterized by two facies: (A) mm-laminated clastic varves and (B) turbidites. The annual character of the laminae couplets was confirmed by radiometric dating (210Pb, 137Cs) and independent flood-layer chronomarkers. Individual varves consist of a dark sand-size spring-summer layer enriched in siliciclastic minerals and a lighter clay-size calcite-rich winter layer. Three subtypes of varves are distinguished: Type I with a 1–1.5 mm fining upward sequence; Type II with a distinct fine-sand base up to 3 mm thick; and Type III containing multiple internal microlaminae caused by individual summer rainstorm deposits. Delta-fan surface samples and sediment trap data fingerprint different sediment source areas and transport processes from the watershed and confirm the instant response of sediment flux to rainfall and erosion. Based on a highly accurate, precise and reproducible chronology, we demonstrate that sediment accumulation (varve thickness) is a quantitative predictor for cumulative boreal alpine spring (May–June) and spring/summer (May–August) rainfall (rMJ = 0.71, rMJJA = 0.60, p < 0.01). Bootstrap-based verification of the calibration model reveals a root mean squared error of prediction (RMSEPMJ = 32.7 mm, RMSEPMJJA = 57.8 mm) which is on the order of 10–13 % of mean MJ and MJJA cumulative precipitation, respectively. These results highlight the potential of the Lake Oeschinen sediments for high-resolution reconstructions of past rainfall conditions in the northern Swiss Alps, central and eastern France and south-west Germany.

High-resolution mineral dust and sea ice proxy records from the Talos Dome ice core

In this study we report on new non-sea salt calcium (nssCa2+, mineral dust proxy) and sea salt sodium (ssNa+, sea ice proxy) records along the East Antarctic Talos Dome deep ice core in centennial resolution reaching back 150 thousand years (ka) before present. During glacial conditions nssCa2+ fluxes in Talos Dome are strongly related to temperature as has been observed before in other deep Antarctic ice core records, and has been associated with synchronous changes in the main source region (southern South America) during climate variations in the last glacial. However, during warmer climate conditions Talos Dome mineral dust input is clearly elevated compared to other records mainly due to the contribution of additional local dust sources in the Ross Sea area. Based on a simple transport model, we compare nssCa2+ fluxes of different East Antarctic ice cores. From this multi-site comparison we conclude that changes in transport efficiency or atmospheric lifetime of dust particles do have a minor effect compared to source strength changes on the large-scale concentration changes observed in Antarctic ice cores during climate variations of the past 150 ka. Our transport model applied on ice core data is further validated by climate model data. The availability of multiple East Antarctic nssCa2+ records also allows for a revision of a former estimate on the atmospheric CO2 sensitivity to reduced dust induced iron fertilisation in the Southern Ocean during the transition from the Last Glacial Maximum to the Holocene (T1). While a former estimate based on the EPICA Dome C (EDC) record only suggested 20 ppm, we find that reduced dust induced iron fertilisation in the Southern Ocean may be responsible for up to 40 ppm of the total atmospheric CO2 increase during T1. During the last interglacial, ssNa+ levels of EDC and EPICA Dronning Maud Land (EDML) are only half of the Holocene levels, in line with higher temperatures during that period, indicating much reduced sea ice extent in the Atlantic as well as the Indian Ocean sector of the Southern Ocean. In contrast, Holocene ssNa+ flux in Talos Dome is about the same as during the last interglacial, indicating that there was similar ice cover present in the Ross Sea area during MIS 5.5 as during the Holocene.

High Resolution Transmission Spectroscopy as a Diagnostic for Jovian Exoplanet Atmospheres: Constraints from Theoretical Models

We present high resolution transmission spectra of giant planet atmospheres from a coupled 3-D atmospheric dynamics and transmission spectrum model that includes Doppler shifts which arise from winds and planetary motion. We model jovian planets covering more than two orders of magnitude in incident flux, corresponding to planets with 0.9 to 55 day orbital periods around solar-type stars. The results of our 3-D dynamical models reveal certain aspects of high resolution transmission spectra that are not present in simple 1-D models. We find that the hottest planets experience strong substellar to anti-stellar (SSAS) winds, resulting in transmission spectra with net blue shifts of up to 3 km s−1, whereas less irradiated planets show almost no net Doppler shifts. Compared to 1-D models, peak line strengths are significantly reduced for the hottest atmospheres owing to Doppler broadening from a combination of rotation (which is faster for close-in planets under the assumption of tidal locking) and atmospheric winds. Finally, high resolution transmission spectra may be useful in studying the atmospheres of exoplanets with optically thick clouds since line cores for very strong transitions should remain optically thick to very high altitude. High resolution transmission spectra are an excellent observational test for the validity of 3-D atmospheric dynamics models, because they provide a direct probe of wind structures and heat circulation. Ground-based exoplanet spectroscopy is currently on the verge of being able to verify some of our modeling predictions, most notably the dependence of SSAS winds on insolation. We caution that interpretation of high resolution transmission spectra based on 1-D atmospheric models may be inadequate, as 3-D atmospheric motions can produce a noticeable effect on the absorption signatures.

A high-resolution map of direct and indirect connectivity of erosion risk areas to surface waters in Switzerland: A risk assessment tool for planning and policy-making

Off-site effects of soil erosion are becoming increasingly important, particularly the pollution of surface waters. In order to develop environmentally efficient and cost effective mitigation options it is essential to identify areas that bear both a high erosion risk and high connectivity to surface waters. This paper introduces a simple risk assessment tool that allows the delineation of potential critical source areas (CSA) of sediment input into surface waters concerning the agricultural areas of Switzerland. The basis are the erosion risk map with a 2 m resolution (ERM2) and the drainage network, which is extended by drained roads, farm tracks, and slope depressions. The probability of hydrological and sedimentological connectivity is assessed by combining soil erosion risk and extended drainage network with flow distance calculation. A GIS-environment with multiple-flow accumulation algorithms is used for routing runoff generation and flow pathways. The result is a high resolution connectivity map of the agricultural area of Switzerland (888,050 ha). Fifty-five percent of the computed agricultural area is potentially connected with surface waters, 45% is not connected. Surprisingly, the larger part of 34% (62% of the connected area) is indirectly connected with surface waters through drained roads, and only 21% are directly connected. The reason is the topographic complexity and patchiness of the landscape due to a dense road and drainage network. A total of 24% of the connected area and 13% of the computed agricultural area, respectively, are rated with a high connectivity probability. On these CSA an adapted land use is recommended, supported by vegetated buffer strips preventing sediment load. Even areas that are far away from open water bodies can be indirectly connected and need to be included in planning of mitigation measures. Thus, the connectivity map presented is an important decision-making tool for policy-makers and extension services. The map is published on the web and thus available for application.

High-resolution MALDI-FT-ICR MS imaging for the analysis of metabolites from formalin-fixed, paraffin-embedded clinical tissue samples.

We present the first analytical approach to demonstrate the in situ imaging of metabolites from formalin-fixed, paraffin-embedded (FFPE) human tissue samples. Using high-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR MSI), we conducted a proof-of-principle experiment comparing metabolite measurements from FFPE and fresh frozen tissue sections, and found an overlap of 72% amongst 1700 m/z species. In particular, we observed conservation of biomedically relevant information at the metabolite level in FFPE tissues. In biomedical applications, we analysed tissues from 350 different cancer patients and were able to discriminate between normal and tumour tissues, and different tumours from the same organ, and found an independent prognostic factor for patient survival. This study demonstrates the ability to measure metabolites in FFPE tissues using MALDI-FT-ICR MSI, which can then be assigned to histology and clinical parameters. Our approach is a major technical, histochemical, and clinicopathological advance that highlights the potential for investigating diseases in archived FFPE tissues.