Monoenergetic computed tomography reconstructions reduce beam hardening artifacts from dental restorations

The aim of this study was to assess the potential of monoenergetic computed tomography (CT) images to reduce beam hardening artifacts in comparison to standard CT images of dental restoration on dental post-mortem CT (PMCT). Thirty human decedents (15 male, 58 ± 22 years) with dental restorations were examined using standard single-energy CT (SECT) and dual-energy CT (DECT). DECT data were used to generate monoenergetic CT images, reflecting the X-ray attenuation at energy levels of 64, 69, 88 keV, and at an individually adjusted optimal energy level called OPTkeV. Artifact reduction and image quality of SECT and monoenergetic CT were assessed objectively and subjectively by two blinded readers. Subjectively, beam artifacts decreased visibly in 28/30 cases after monoenergetic CT reconstruction. Inter- and intra-reader agreement was good (k = 0.72, and k = 0.73 respectively). Beam hardening artifacts decreased significantly with increasing monoenergies (repeated-measures ANOVA p < 0.001). Artifact reduction was greatest on monoenergetic CT images at OPTkeV. Mean OPTkeV was 108 ± 17 keV. OPTkeV yielded the lowest difference between CT numbers of streak artifacts and reference tissues (-163 HU). Monoenergetic CT reconstructions significantly reduce beam hardening artifacts from dental restorations and improve image quality of post-mortem dental CT.

Dependence of Eemian Greenland temperature reconstructions on the ice sheet topography

The influence of a reduced Greenland Ice Sheet (GrIS) on Greenland's surface climate during the Eemian interglacial is studied using a set of simulations with different GrIS realizations performed with a comprehensive climate model. We find a distinct impact of changes in the GrIS topography on Greenland's surface air temperatures (SAT) even when correcting for changes in surface elevation, which influences SAT through the lapse rate effect. The resulting lapse-rate-corrected SAT anomalies are thermodynamically driven by changes in the local surface energy balance rather than dynamically caused through anomalous advection of warm/cold air masses. The large-scale circulation is indeed very stable among all sensitivity experiments and the Northern Hemisphere (NH) flow pattern does not depend on Greenland's topography in the Eemian. In contrast, Greenland's surface energy balance is clearly influenced by changes in the GrIS topography and this impact is seasonally diverse. In winter, the variable reacting strongest to changes in the topography is the sensible heat flux (SHF). The reason is its dependence on surface winds, which themselves are controlled to a large extent by the shape of the GrIS. Hence, regions where a receding GrIS causes higher surface wind velocities also experience anomalous warming through SHF. Vice-versa, regions that become flat and ice-free are characterized by low wind speeds, low SHF, and anomalous low winter temperatures. In summer, we find surface warming induced by a decrease in surface albedo in deglaciated areas and regions which experience surface melting. The Eemian temperature records derived from Greenland proxies, thus, likely include a temperature signal arising from changes in the GrIS topography. For the Eemian ice found in the NEEM core, our model suggests that up to 3.1 °C of the annual mean Eemian warming can be attributed to these topography-related processes and hence is not necessarily linked to large-scale climate variations.

Clinical Performance of Screw- Versus Cement-Retained Fixed Implant-Supported Reconstructions- A Systematic Review.

PURPOSE To assess the survival outcomes and reported complications of screw- and cement-retained fixed reconstructions supported on dental implants. MATERIALS AND METHODS A Medline (PubMed), Embase, and Cochrane electronic database search from 2000 to September 2012 using MeSH and free-text terms was conducted. Selected inclusion and exclusion criteria guided the search. All studies were first reviewed by abstract and subsequently by full-text reading by two examiners independently. Data were extracted by two examiners and statistically analyzed using a random effects Poisson regression. RESULTS From 4,324 abstracts, 321 full-text articles were reviewed. Seventy-three articles were found to qualify for inclusion. Five-year survival rates of 96.03% (95% confidence interval [CI]: 93.85% to 97.43%) and 95.55% (95% CI: 92.96% to 97.19%) were calculated for cemented and screw-retained reconstructions, respectively (P = .69). Comparison of cement and screw retention showed no difference when grouped as single crowns (I-SC) (P = .10) or fixed partial dentures (I-FDP) (P = .49). The 5-year survival rate for screw-retained full-arch reconstructions was 96.71% (95% CI: 93.66% to 98.31). All-ceramic reconstruction material exhibited a significantly higher failure rate than porcelain-fused-to-metal (PFM) in cemented reconstructions (P = .01) but not when comparing screw-retained reconstructions (P = .66). Technical and biologic complications demonstrating a statistically significant difference included loss of retention (P ≤ .01), abutment loosening (P ≤ .01), porcelain fracture and/or chipping (P = .02), presence of fistula/suppuration (P ≤ .001), total technical events (P = .03), and total biologic events (P = .02). CONCLUSIONS Although no statistical difference was found between cement- and screw-retained reconstructions for survival or failure rates, screw-retained reconstructions exhibited fewer technical and biologic complications overall. There were no statistically significant differences between the failure rates of the different reconstruction types (I-SCs, I-FDPs, full-arch I-FDPs) or abutment materials (titanium, gold, ceramic). The failure rate of cemented reconstructions was not influenced by the choice of a specific cement, though cement type did influence loss of retention.

Optimal number of oral implants for fixed reconstructions: a review of the literature.

BACKGROUND AND AIM So far there is little evidence from randomised clinical trials (RCT) or systematic reviews on the preferred or best number of implants to be used for the support of a fixed prosthesis in the edentulous maxilla or mandible, and no consensus has been reached. Therefore, we reviewed articles published in the past 30 years that reported on treatment outcomes for implant-supported fixed prostheses, including survival of implants and survival of prostheses after a minimum observation period of 1 year. MATERIAL AND METHODS MEDLINE and EMBASE were searched to identify eligible studies. Short and long-term clinical studies were included with prospective and retrospective study designs to see if relevant information could be obtained on the number of implants related to the prosthetic technique. Articles reporting on implant placement combined with advanced surgical techniques such as sinus floor elevation (SFE) or extensive grafting were excluded. Two reviewers extracted the data independently. RESULTS A primary search was broken down to 222 articles. Out of these, 29 studies comprising 26 datasets fulfilled the inclusion criteria. From all studies, the number of planned and placed implants was available. With two exceptions, no RCTs were found, and these two studies did not compare different numbers of implants per prosthesis. Eight studies were retrospective; all the others were prospective. Fourteen studies calculated cumulative survival rates for 5 and more years. From these data, the average survival rate was between 90% and 100%. The analysis of the selected articles revealed a clear tendency to plan 4 to 6 implants per prosthesis. For supporting a cross-arch fixed prosthesis in the maxilla, the variation is slightly greater. CONCLUSIONS In spite of a dispersion of results, similar outcomes are reported with regard to survival and number of implants per jaw. Since the 1990s, it was proven that there is no need to install as many implants as possible in the available jawbone. The overwhelming majority of articles dealing with standard surgical procedures to rehabilitate edentulous jaws uses 4 to 6 implants.

Pollen-based quantitative reconstructions of Holocene regional vegetation cover (plant-functional types and land-cover types) in Europe suitable for climate modelling

We present quantitative reconstructions of regional vegetation cover in north-western Europe, western Europe north of the Alps, and eastern Europe for five time windows in the Holocene around 6k, 3k, 0.5k, 0.2k, and 0.05k calendar years before present (bp)] at a 1 degrees x1 degrees spatial scale with the objective of producing vegetation descriptions suitable for climate modelling. The REVEALS model was applied on 636 pollen records from lakes and bogs to reconstruct the past cover of 25 plant taxa grouped into 10 plant-functional types and three land-cover types evergreen trees, summer-green (deciduous) trees, and open land]. The model corrects for some of the biases in pollen percentages by using pollen productivity estimates and fall speeds of pollen, and by applying simple but robust models of pollen dispersal and deposition. The emerging patterns of tree migration and deforestation between 6k bp and modern time in the REVEALS estimates agree with our general understanding of the vegetation history of Europe based on pollen percentages. However, the degree of anthropogenic deforestation (i.e. cover of cultivated and grazing land) at 3k, 0.5k, and 0.2k bp is significantly higher than deduced from pollen percentages. This is also the case at 6k in some parts of Europe, in particular Britain and Ireland. Furthermore, the relationship between summer-green and evergreen trees, and between individual tree taxa, differs significantly when expressed as pollen percentages or as REVEALS estimates of tree cover. For instance, when Pinus is dominant over Picea as pollen percentages, Picea is dominant over Pinus as REVEALS estimates. These differences play a major role in the reconstruction of European landscapes and for the study of land cover-climate interactions, biodiversity and human resources.

A regional climate palaeosimulation for Europe in the period 1500–1990 – Part 2: Shortcomings and strengths of models and reconstructions

This study compares gridded European seasonal series of surface air temperature (SAT) and precipitation (PRE) reconstructions with a regional climate simulation over the period 1500–1990. The area is analysed separately for nine subareas that represent the majority of the climate diversity in the European sector. In their spatial structure, an overall good agreement is found between the reconstructed and simulated climate features across Europe, supporting consistency in both products. Systematic biases between both data sets can be explained by a priori known deficiencies in the simulation. Simulations and reconstructions, however, largely differ in the temporal evolution of past climate for European subregions. In particular, the simulated anomalies during the Maunder and Dalton minima show stronger response to changes in the external forcings than recorded in the reconstructions. Although this disagreement is to some extent expected given the prominent role of internal variability in the evolution of regional temperature and precipitation, a certain degree of agreement is a priori expected in variables directly affected by external forcings. In this sense, the inability of the model to reproduce a warm period similar to that recorded for the winters during the first decades of the 18th century in the reconstructions is indicative of fundamental limitations in the simulation that preclude reproducing exceptionally anomalous conditions. Despite these limitations, the simulated climate is a physically consistent data set, which can be used as a benchmark to analyse the consistency and limitations of gridded reconstructions of different variables. A comparison of the leading modes of SAT and PRE variability indicates that reconstructions are too simplistic, especially for precipitation, which is associated with the linear statistical techniques used to generate the reconstructions. The analysis of the co-variability between sea level pressure (SLP) and SAT and PRE in the simulation yields a result which resembles the canonical co-variability recorded in the observations for the 20th century. However, the same analysis for reconstructions exhibits anomalously low correlations, which points towards a lack of dynamical consistency between independent reconstructions.

Antarctic temperature changes during the last millennium: evaluation of simulations and reconstructions

Temperature changes in Antarctica over the last millennium are investigated using proxy records, a set of simulations driven by natural and anthropogenic forcings and one simulation with data assimilation. Over Antarctica, a long term cooling trend in annual mean is simulated during the period 1000–1850. The main contributor to this cooling trend is the volcanic forcing, astronomical forcing playing a dominant role at seasonal timescale. Since 1850, all the models produce an Antarctic warming in response to the increase in greenhouse gas concentrations. We present a composite of Antarctic temperature, calculated by averaging seven temperature records derived from isotope measurements in ice cores. This simple approach is supported by the coherency displayed between model results at these data grid points and Antarctic mean temperature. The composite shows a weak multi-centennial cooling trend during the pre-industrial period and a warming after 1850 that is broadly consistent with model results. In both data and simulations, large regional variations are superimposed on this common signal, at decadal to centennial timescales. The model results appear spatially more consistent than ice core records. We conclude that more records are needed to resolve the complex spatial distribution of Antarctic temperature variations during the last millennium.

Quantitative summer and winter temperature reconstructions from pollen and chironomid data between 15 and 8 ka BP in the Baltic–Belarus area

New pollen based reconstructions of summer (May-to-August) and winter (December-to-February) temperatures between 15 and 8 ka BP along a S-N transect in the Baltic-Belarus (BB) area display trends in temporal and spatial changes in climate variability. These results are completed by two chironomid-based July mean temperature reconstructions. The magnitude of change compared with modern temperatures was more prominent in the northern part of BB area. The 4 C degrees winter and 2 C degrees summer warming at the start of GI-1 was delayed in the BB area and Lateglacial maximum temperatures were reached at ca 13.6 ka BP, being 4 C degrees colder than the modern mean. The Younger Dryas cooling in the area was 5 C degrees colder than present, as inferred by all proxies. In addition, our analyses show an early Holocene divergence in winter temperature trends with modern values reaching 1 ka earlier (10 ka BP) in southern BB compared to the northern part of the region (9 ka BP).

Effect of low count sums on quantitative environmental reconstructions: an example using subfossil chironomids

The concentrations of chironomid remains in lake sediments are very variable and, therefore, chironomid stratigraphies often include samples with a low number of counts. Thus, the effect of low count sums on reconstructed temperatures is an important issue when applying chironomid‐temperature inference models. Using an existing data set, we simulated low count sums by randomly picking subsets of head capsules from surface‐sediment samples with a high number of specimens. Subsequently, a chironomid‐temperature inference model was used to assess how the inferred temperatures are affected by low counts. The simulations indicate that the variability of inferred temperatures increases progressively with decreasing count sums. At counts below 50 specimens, a further reduction in count sum can cause a disproportionate increase in the variation of inferred temperatures, whereas at higher count sums the inferences are more stable. Furthermore, low count samples may consistently infer too low or too high temperatures and, therefore, produce a systematic error in a reconstruction. Smoothing reconstructed temperatures downcore is proposed as a possible way to compensate for the high variability due to low count sums. By combining adjacent samples in a stratigraphy, to produce samples of a more reliable size, it is possible to assess if low counts cause a systematic error in inferred temperatures.

Posterior Vertical Bite Reconstructions of Erosively Worn Dentitions and the "Stamp Technique" - A Case Series with a Mean Observation Time of 40 Months

PURPOSE In the present case series, the authors report on seven cases of erosively worn dentitions (98 posterior teeth) which were treated with direct resin composite. MATERIALS AND METHODS In all cases, both arches were restored by using the so-called stamp technique. All patients were treated with standardized materials and protocols. Prior to treatment, a waxup was made on die-cast models to build up the loss of occlusion as well as ensure the optimal future anatomy and function of the eroded teeth to be restored. During treatment, teeth were restored by using templates of silicone (ie, two "stamps," one on the vestibular, one on the oral aspect of each tooth), which were filled with resin composite in order to transfer the planned, future restoration (ie, in the shape of the waxup) from the extra- to the intraoral situation. Baseline examinations were performed in all patients after treatment, and photographs as well as radiographs were taken. To evaluate the outcome, the modified United States Public Health Service criteria (USPHS) were used. RESULTS The patients were re-assessed after a mean observation time of 40 months (40.8 ± 7.2 months). The overall outcome of the restorations was good, and almost exclusively "Alpha" scores were given. Only the marginal integrity and the anatomical form received a "Charlie" score (10.2%) in two cases. CONCLUSION Direct resin composite restorations made with the stamp technique are a valuable treatment option for restoring erosively worn dentitions.

Morphological variation within the diatom taxon Cyclotella comensis and its importance for quantitative temperature reconstructions

1. The morphologically complex taxon Cyclotella comensis Grunow had no clear relationship with environmental parameters in a study using sediment surface samples from the Swiss Alps. The morphological heterogeneity of the taxon was investigated by applying a principal component analysis (PCA) to 9000 presence/absence descriptions of valves from surface samples of six lakes from different altitudes (15 characteristics, 100 valves each lake). The PCA allowed the classification of six morphs, which differed mainly in size and length of striae. Photographs of the morphs are shown in this paper. 2. Sixty-eight sediment surface samples were analysed using these newly defined six morphs. Summer temperature explained a major part of the variance between the morphs as assessed by a redundancy analysis (RDA). Summer temperature optima and tolerances were estimated using weighted averaging. 3. The influence of the revised C. comensis taxonomy on the diatom inferred summer temperature of a high alpine lake is discussed in a multiproxy context for the past 800 years.

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Multi-sensor global compilation of mid-Holocene sea surface temperatures, based on Mg/Ca and alkenone palaeothermometry and reconstructions obtained using planktonic foraminifera and organic-walled dinoflagellate cyst

We present and examine a multi-sensor global compilation of mid-Holocene (MH) sea surface temperatures (SST), based on Mg/Ca and alkenone palaeothermometry and reconstructions obtained using planktonic foraminifera and organic-walled dinoflagellate cyst census counts. We assess the uncertainties originating from using different methodologies and evaluate the potential of MH SST reconstructions as a benchmark for climate-model simulations. The comparison between different analytical approaches (time frame, baseline climate) shows the choice of time window for the MH has a negligible effect on the reconstructed SST pattern, but the choice of baseline climate affects both the magnitude and spatial pattern of the reconstructed SSTs. Comparison of the SST reconstructions made using different sensors shows significant discrepancies at a regional scale, with uncertainties often exceeding the reconstructed SST anomaly. Apparent patterns in SST may largely be a reflection of the use of different sensors in different regions. Overall, the uncertainties associated with the SST reconstructions are generally larger than the MH anomalies. Thus, the SST data currently available cannot serve as a target for benchmarking model simulations.

Paleoclimate reconstructions from sediment core MD01-2378

On the basis of the radiocarbon (14C) plateau-tuning method a new age model for Timor Sea Core MD01-2378 was established. It revealed a precise centennial-scale phasing of climate events in the ocean, cryo-, and atmosphere during the last deglacial and provides important new insights into causal linkages controlling events of global climate change. At Site MD01-2378 reservoir ages of surface waters dropped from 1600 yr prior to 20 cal ka to 250-500 yr after 18.8 cal ka. This evidence was crucial for generating a high-resolution age model for deglacial events in the Indo-Pacific Warm Pool. Sea-surface temperatures (SST) started to change near 18.8 cal ka, that is ~500 yr after the start of, presumably northern hemispheric, deglacial melt and sea level rise as shown by the benthic foraminiferal oxygen isotope ratio (d18O). However, the SST rise occurred 500-1000 yr prior to the onset of deglacial Antarctic warming and the first major rise in atmospheric carbon dioxide at about 18 ka. The increase in SST may partly reflect reduced seasonal upwelling of cold subsurface waters along the eastern margin of the Indian Ocean, which is reflected by a doubling of the thermal gradient between the sea surface and the thermocline, a halving of chlorin productivity from 19 to 18.5 cal ka, and in particular, by the strong decrease in surface water reservoir ages. Two significant increases in deglacial Timor Sea surface salinities from 19-18.5 and 15.5-14.5 cal ka, may partly reflect the deglacial increase in the distance of local river mouths, partly an inter-hemispheric millennial-scale see-saw in tropical monsoon intensity, possibly linked to a deglacial increase in the dominance of Pacific El Niño regimes over Heinrich stadial 1.