In vitro accuracy evaluation of image-guided robot system for direct cochlear access

HYPOTHESIS A previously developed image-guided robot system can safely drill a tunnel from the lateral mastoid surface, through the facial recess, to the middle ear, as a viable alternative to conventional mastoidectomy for cochlear electrode insertion. BACKGROUND Direct cochlear access (DCA) provides a minimally invasive tunnel from the lateral surface of the mastoid through the facial recess to the middle ear for cochlear electrode insertion. A safe and effective tunnel drilled through the narrow facial recess requires a highly accurate image-guided surgical system. Previous attempts have relied on patient-specific templates and robotic systems to guide drilling tools. In this study, we report on improvements made to an image-guided surgical robot system developed specifically for this purpose and the resulting accuracy achieved in vitro. MATERIALS AND METHODS The proposed image-guided robotic DCA procedure was carried out bilaterally on 4 whole head cadaver specimens. Specimens were implanted with titanium fiducial markers and imaged with cone-beam CT. A preoperative plan was created using a custom software package wherein relevant anatomical structures of the facial recess were segmented, and a drill trajectory targeting the round window was defined. Patient-to-image registration was performed with the custom robot system to reference the preoperative plan, and the DCA tunnel was drilled in 3 stages with progressively longer drill bits. The position of the drilled tunnel was defined as a line fitted to a point cloud of the segmented tunnel using principle component analysis (PCA function in MatLab). The accuracy of the DCA was then assessed by coregistering preoperative and postoperative image data and measuring the deviation of the drilled tunnel from the plan. The final step of electrode insertion was also performed through the DCA tunnel after manual removal of the promontory through the external auditory canal. RESULTS Drilling error was defined as the lateral deviation of the tool in the plane perpendicular to the drill axis (excluding depth error). Errors of 0.08 ± 0.05 mm and 0.15 ± 0.08 mm were measured on the lateral mastoid surface and at the target on the round window, respectively (n =8). Full electrode insertion was possible for 7 cases. In 1 case, the electrode was partially inserted with 1 contact pair external to the cochlea. CONCLUSION The purpose-built robot system was able to perform a safe and reliable DCA for cochlear implantation. The workflow implemented in this study mimics the envisioned clinical procedure showing the feasibility of future clinical implementation.

Impact of different cultivation methods on the metabolic profile of apples studied by 1H HR-MAS NMR spectroscopy

The cultivation of dessert apples has to meet the consumer's increasing demand for high fruit quality and a sustainable mostly residue-free production while ensuring a competitive agricultural productivity. It is therefore of great interest to know the impact of different cultivation methods on the fruit quality and the chemical composition, respectively. Previous studies have demonstrated the feasibility of High Resolution Magic Angle Spinning (HR-MAS) NMR spectroscopy directly performed on apple tissue as analytical tool for metabonomic studies. In this study, HR-MAS NMR spectroscopy is applied to apple tissue to analyze the metabolic profiles of apples grown under 3 different cultivation methods. Golden Delicious apples were grown applying organic (Bio), integrated (IP) and low-input (LI) plant protection strategies. A total of 70 1H HR-MAS NMR spectra were analyzed by means of principle component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). Apples derived from Bio-production could be well separated from the two other cultivation methods applying both, PCA and PLS-DA. Apples obtained from integrated (IP) and low-input (LI) production discriminated when taking the third PLS-component into account. The identified chemical composition and the compounds responsible for the separation, i.e. the PLS-loadings, are discussed. The results are compared with fruit quality parameters assessed by conventional methods. The present study demonstrates the potential of HR-MAS NMR spectroscopy of fruit tissue as analytical tool for finding markers for specific fruit production conditions like the cultivation method.

Using plant functional traits and phylogenies to understand patterns of plant community assembly in a seasonal tropical forest in Lao PDR

Plant functional traits reflect different evolutionary responses to environmental variation, and among extant species determine the outcomes of interactions between plants and their environment, including other plant species. Thus, combining phylogenetic and trait-based information can be a powerful approach for understanding community assembly processes across a range of spatial scales. We used this approach to investigate tree community composition at Phou Khao Khouay National Park (18°14’-18°32’N; 102°38’- 102°59’E), Laos, where several distinct forest types occur in close proximity. The aim of our study was to examine patterns of plant community assembly across the strong environmental gradients evident at our site. We hypothesized that differences in tree community composition were being driven by an underlying gradient in soil conditions. Thus, we predicted that environmental filtering would predominate at the site and that the filtering would be strongest on sandier soil with low pH, as these are the conditions least favorable to plant growth. We surveyed eleven 0.25 ha (50x50 m) plots for all trees above 10 cm dbh (1221 individual trees, including 47 families, 70 genera and 123 species) and sampled soils in each plot. For each species in the community, we measured 11 commonly studied plant functional traits covering both the leaf and wood economic spectrum traits and we reconstructed a phylogenetic tree for 115 of the species in the community using rbcL and matK sequences downloaded from Genebank (other species were not available). Finally we compared the distribution of trait values and species at two scales (among plots and 10x10m subplots) to examine trait and phylogenetic community structures. Although there was strong evidence that an underlying soil gradient was determining patterns of species composition at the site, our results did not support the hypothesis that the environmental filtering dominated community assembly processes. For the measured plant functional traits there was no consistent pattern of trait dispersion across the site, either when traits were considered individually or when combined in a multivariate analysis. However, there was a significant correlation between the degree of phylogenetic dispersion and the first principle component axis (PCA1) for the soil parameters.Moreover, the more phylogenetically clustered plots were on sandier soils with lower pH. Hence, we suggest that the community assembly processes across our sitemay reflect the influence ofmore conserved traits that we did not measure. Nevertheless, our results are equivocal and other interpretations are possible. Our study illustrates some difficulties in combining trait and phylogenetic approaches that may result from the complexities of integrating spatial and evolutionary processes that vary at different scales.

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

Investigations on sediments from Lake Nam Co (Tibetan Plateau)

This study focuses on the analysis of lake sediments retrieved from the deepest part of Lake Nam Co (Tibetan Plateau). One gravity core of 115 cm length, covering the last ~ 4000 cal BP, was analyzed for geochemical and biological parameters. High organic content at ~ 4000 cal BP and the coinciding presence of pyrite framboids until ~ 2000 cal BP point to hampered decomposition of organic material due to anoxic conditions within the lake sediments. At the same time sedimentological and biological proxies suggest a rather high lake level, but still ~ 5 m below the recent one, with less saline lake water due to enhanced monsoonal activity. During this time a change in the source of organic matter to lowered input of terrestrial components is observed. A rather quick shift to a dry environment with less monsoonal influence and a lake level ~ 15 m lower than today at ~ 2000 cal BP lead to the oxygenation of sediment, the degradation of organic matter and the absence of pyrite. Oscillations of the lake level thereafter were of minor amplitude and not able to establish anoxia at the lake bottom again. A wet spell between ~ 1500 cal BP and ~ 1150 cal BP is visible in proxies referring to catchment hydrology and the ostracod-based water depth transfer function gives only a slightly elevated lake level. The last ~ 300 years are characterized by low TOC and rising TN values reflecting enhanced nutrient supply and hence an advancing influence of human activity in the catchment. Decreasing TOC/TN values point to a complete shift to almost solely aquatic biomass production. These results show that hydrological variations in terms of lake level change based on monsoonal strength can be linked to redox conditions at the lake bottom of Nam Co. Comparison with other archives over larger parts of the Tibetan Plateau and beyond exhibits a rather homogeneous climatic pattern throughout the late Holocene.

Planktic foraminiferal Mg/Ca and oxygen isotopes, plus estimated d18Oseawater and ice volume corrected d18Oseawater for the past 35000 years of sediment core GeoB10069-3

Evidence from geologic archives suggests that there were large changes in the tropical hydrologic cycle associated with the two prominent northern hemisphere deglacial cooling events, Heinrich Stadial 1 (HS1; ~19 to 15 kyr BP; kyr BP = 1000 yr before present) and the Younger Dryas (~12.9 to 11.7 kyr BP). These hydrologic shifts have been alternatively attributed to high and low latitude origin. Here, we present a new record of hydrologic variability based on planktic foraminifera-derived d18O of seawater (d18Osw) estimates from a sediment core from the tropical Eastern Indian Ocean, and using 12 additional d18Osw records, construct a single record of the dominant mode of tropical Eastern Equatorial Pacific and Indo-Pacific Warm Pool (IPWP) hydrologic variability. We show that deglacial hydrologic shifts parallel variations in the reconstructed interhemispheric temperature gradient, suggesting a strong response to variations in the Atlantic Meridional Overturning Circulation and the attendant heat redistribution. A transient model simulation of the last deglaciation suggests that hydrologic changes, including a southward shift in the Intertropical Convergence Zone (ITCZ) which likely occurred during these northern hemisphere cold events, coupled with oceanic advection and mixing, resulted in increased salinity in the Indonesian region of the IPWP and the eastern tropical Pacific, which is recorded by the d18Osw proxy. Based on our observations and modeling results we suggest the interhemispheric temperature gradient directly controls the tropical hydrologic cycle on these time scales, which in turn mediates poleward atmospheric heat transport.

Early Oligocene dinoflagellate cysts from the Upper Rhine Graben

Using principal component analysis and cyst diversity and equity trends, we can recognize four distinct dinoflagellate cyst (dinocyst) assemblages from four Rupelian (Early Oligocene) cores in the Mainz Embayment of the northern Rhine Graben (SW Germany). These assemblages are the Spiniferites ramosus (PC1), Thalassiphora pelagica (PC2), Homotryblium tenuispinosum (PC3), and Vozzhennikovia spinula (PC4) assemblages. The four cores provide an onshore-offshore transect in the Mainz Embayment. The H. tenuispinosum assemblage shows high factor loadings in proximal to intermediate cores, which is interpreted to reflect temporary high-salinity conditions. Mean dinocyst diversity and equity increase with distance from the Mid-Rupelian shoreline, indicating increasingly stable paleoenvironmental conditions towards the center of the Mainz Embayment. Within individual cores, changes in dinocyst assemblages through time are related to paleoenvironmental and paleoclimatological changes. The three proximal to intermediate cores show dominance of the H. tenuispinosum assemblage repeatedly alternating with high factor loadings of the T. pelagica assemblage. In both cases, dinocyst diversity and equity tend to be reduced. Highest factor loadings of the S. ramosus assemblage occur in intervals where neither of the above assemblages is dominant and tend to coincide with dinocyst diversity and equity maxima. We interpret this distribution pattern to denote different paleoceanographic conditions, reflecting drier and more humid phases in the Early Oligocene of Central Europe. During relatively dry periods, increased salinity conditions prevailed in proximal to intermediate settings of the Mainz Embayment, as reflected by the dominance of the H. tenuispinosum assemblage. During more humid periods, increased runoff led to higher nutrient availability and the formation of a pycnocline separating slightly less saline surface waters from higher saline deeper waters, thus impeding vertical circulation. These environmental conditions are documented in high loadings of the T. pelagica assemblage which is indicative of increased eutrophication and/or oxygen-depleted bottom waters. Transitions between drier and more humid periods, i.e. episodes of normal marine conditions, are characterized by high loadings predominantly of the S. ramosus assemblage as well as increased dinocyst diversity and equity values. We propose that the alternations between drier and more humid phases may be related to variations in the ocean-atmosphere moisture flux from the North Atlantic into Central Europe bearing a high-latitude climate signal.

Diatom, ice rafted debris and Neogloboquadrina pachyderma (sinistral) abundance in sediment core OCE326-GGC14

A high-resolution diatom census coupled with other proxy data from Laurentian Fan (LF) provides a detailed description of the last deglaciation, bringing new insight to that period by revealing directly the timing of sea-ice formation and melting. Cold events Heinrich Event 1 (H1) and the Younger Dryas (YD) were multiphase events. H1 (~16.8-15.7 cal kyr BP) was defined by a two-pulse release of icebergs promoting sea-ice formation. Melting of sea-ice after H1 corresponds to a cold and fresh anomaly that may have kept the Bølling colder than the Allerød. At ~13.6 cal kyr BP, a cooling trend culminated with sea-ice formation, marking the YD onset (~12.8 cal kyr BP). The decrease in sea-ice (~12.2 cal kyr BP) led to a YD second phase characterized by very cold winters. However, the contribution of warm water diatoms tends to increase at the same time and the YD gradual end (~11.6 cal kyr BP) contrasts with its abrupt end in Greenland ice cores. The YD cannot be regarded as an event triggered by a fresh water input through the Laurentian Channel since only one weak brief input nearly 1000 yrs after its onset is recorded. Very cold and cool conditions without ice mark the following Preboreal. A northward heat flux between 10.8 and 10.2 cal kyr BP was interrupted by the increased influence of coastal waters likely fed by inland melting. There was no further development of sea-ice or ice-drift then.

Sediment composition in NE Greenland Fjords, Shelf, and Slope

In order to document changes in Holocene glacier extent and activity in NE Greenland (~73° N) we study marine sediment records that extend from the fjords (PS2631 and PS2640), across the shelf (PS2623 and PS2641), to the Greenland Sea (JM07-174GC). The primary bedrock geology of the source areas is the Caledonian sediment outcrop, including Devonian red beds, plus early Neoproterozoic gneisses and early Tertiary volcanics. We examine the variations in colour (CIE*), grain size, and bulk mineralogy (from X-ray diffraction of the <2 mm sediment fraction). Fjord core PS2640 in Sofia Sund, with a marked red hue, is distinct in grain size, colour and mineralogy from the other fjord and shelf cores. Five distinct grain-size modes are distinguished of which only one is associated with a coarse ice-rafting signal - this mode is rare in the mid- and late Holocene. A sediment unmixing program (SedUnMixMC) is used to characterize down-core changes in sediment composition based on the upper late Holocene sediments from cores PS2640 (Sofia Sund), PS2631 (Kaiser Franz Joseph Fjord) and PS2623 (south of Shannon Is), and surface samples from the Kara Sea (as an indicator of transport from the Russian Arctic shelves). Major changes in mineral composition are noted in all cores with possible coeval shifts centred c. 2.5, 4.5 and 7.5 cal. ka BP (±0.5 ka) but are rarely linked with changes in the grain-size spectra. Coarse IRD (>2 mm) and IRD-grain-size spectra are rare in the last 9-10 cal. ka BP and, in contrast with areas farther south (~68° N), there is no distinct IRD signal at the onset of neoglaciation. Our paper demonstrates the importance of the quantitative analysis of sediment properties in clarifying source to sink changes in glacial marine environments.

Giant clams and rising CO2: light may ameliorate effects of ocean acidification on a solar-powered animal

Global climate change and ocean acidification pose a serious threat to marine life. Marine invertebrates are particularly susceptible to ocean acidification, especially highly calcareous taxa such as molluscs, echinoderms and corals. The largest of all bivalve molluscs, giant clams, are already threatened by a variety of local pressures, including overharvesting, and are in decline worldwide. Several giant clam species are listed as 'Vulnerable' on the IUCN Red List of Threatened Species and now climate change and ocean acidification pose an additional threat to their conservation. Unlike most other molluscs, giant clams are 'solar-powered' animals containing photosynthetic algal symbionts suggesting that light could influence the effects of ocean acidification on these vulnerable animals. In this study, juvenile fluted giant clams Tridacna squamosa were exposed to three levels of carbon dioxide (CO2) (control ~400, mid ~650 and high ~950 µatm) and light (photosynthetically active radiation 35, 65 and 304 µmol photons/m**2/s). Elevated CO2 projected for the end of this century (~650 and ~950 µatm) reduced giant clam survival and growth at mid-light levels. However, effects of CO2 on survival were absent at high-light, with 100% survival across all CO2 levels. Effects of CO2 on growth of surviving clams were lessened, but not removed, at high-light levels. Shell growth and total animal mass gain were still reduced at high-CO2. This study demonstrates the potential for light to alleviate effects of ocean acidification on survival and growth in a threatened calcareous marine invertebrate. Managing water quality (e.g. turbidity and sedimentation) in coastal areas to maintain water clarity may help ameliorate some negative effects of ocean acidification on giant clams and potentially other solar-powered calcifiers, such as hard corals.