A stereotaxic, population-averaged T1w ovine brain atlas including cerebral morphology and tissue volumes

Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here, we present a spatial, unbiased ovine brain template with tissue probability maps (TPM) that offer a detailed stereotaxic reference frame for anatomical features and localization of brain areas, thereby enabling inter-individual and cross-study comparability. Three-dimensional data sets from healthy adult Merino sheep (Ovis orientalis aries, 12 ewes and 26 neutered rams) were acquired on a 1.5 T Philips MRI using a T1w sequence. Data were averaged by linear and non-linear registration algorithms. Moreover, animals were subjected to detailed brain volume analysis including examinations with respect to body weight (BW), age, and sex. The created T1w brain template provides an appropriate population-averaged ovine brain anatomy in a spatial standard coordinate system. Additionally, TPM for gray (GM) and white (WM) matter as well as cerebrospinal fluid (CSF) classification enabled automatic prior-based tissue segmentation using statistical parametric mapping (SPM). Overall, a positive correlation of GM volume and BW explained about 15% of the variance of GM while a positive correlation between WM and age was found. Absolute tissue volume differences were not detected, indeed ewes showed significantly more GM per bodyweight as compared to neutered rams. The created framework including spatial brain template and TPM represent a useful tool for unbiased automatic image preprocessing and morphological characterization in sheep. Therefore, the reported results may serve as a starting point for further experimental and/or translational research aiming at in vivo analysis in this species.

Migration and population expansion of Abies, Fagus, Picea, and Quercus since 15000 years in and across the Alps, based on pollen-percentage threshold values

Aims: The aim of this study is to explore the migration (colonization of new areas) and subsequent population expansion (within an area) since 15 ka cal BP of Abies, Fagus, Picea, and Quercus into and through the Alps solely on the basis of high-quality pollen data. Methods: Chronologies of 101 pollen sequences are improved or created. Data from the area delimited by 45.5–48.1°N and 6–14°E are summarized in three ways: (1) in a selection of pollen-percentage threshold maps (thresholds 0.5%, 1%, 2%, 4%, 8%, 16%, and 32% of land pollen); (2) in graphic summaries of 250-year time slices and geographic segments (lengthwise and transverse in relation to the main axis of the Alps) as pollen-percentage curves, pollen-percentage difference curves, and pollen-percentage threshold ages cal BP graphed against both the length and the transverse Alpine axes; and (3) in tables showing statistical relationships of either pollen-percentage threshold ages cal BP or pollen expansion durations (=time lapse between different pollen-percentage threshold ages cal BP) with latitude, longitude, and elevation; to establish these relationships we used both simple linear regression and multiple linear regression after stepwise-forward selection. Results: The statistical results indicate that (a) the use of pollen-percentage thresholds between 0.5% and 8% yield mostly similar directions of tree migration, so the method is fairly robust, (b) Abies migrated northward, Fagus southward, Picea westward, and Quercus northward; more detail does not emerge due to an extreme scarcity of high-quality data especially along the southern foothills of the Alps and in the eastern Alps. This scarcity allows the reconstruction of one immigration route only of Abies into the southern Alps. The speed of population expansion (following arrival) of Abies increased and of Picea decreased during the Holocene, of Fagus it decreased especially during the later Holocene, and of Quercus it increased especially at the start of the Holocene.

A new measure for party coherence: Applying a physics-based concept to the Swiss party system

The paper revives a theoretical definition of party coherence as being composed of two basic elements, cohesion and factionalism, to propose and apply a novel empirical measure based on spin physics. The simultaneous analysis of both components using a single measurement concept is applied to data representing the political beliefs of candidates in the Swiss general elections of 2003 and 2007, proposing a connection between the coherence of the beliefs party members hold and the assessment of parties being at risk of splitting. We also compare our measure with established polarization measures and demonstrate its advantage with respect to multi-dimensional data that lack clear structure. Furthermore, we outline how our analysis supports the distinction between bottom-up and top-down mechanisms of party splitting. In this way, we are able to turn the intuition of coherence into a defined quantitative concept that, additionally, offers a methodological basis for comparative research of party coherence. Our work serves as an example of how a complex systems approach allows to get a new perspective on a long-standing issue in political science.

Lung Pattern Classification for Interstitial Lung Diseases Using a Deep Convolutional Neural Network

Automated tissue characterization is one of the most crucial components of a computer aided diagnosis (CAD) system for interstitial lung diseases (ILDs). Although much research has been conducted in this field, the problem remains challenging. Deep learning techniques have recently achieved impressive results in a variety of computer vision problems, raising expectations that they might be applied in other domains, such as medical image analysis. In this paper, we propose and evaluate a convolutional neural network (CNN), designed for the classification of ILD patterns. The proposed network consists of 5 convolutional layers with 2×2 kernels and LeakyReLU activations, followed by average pooling with size equal to the size of the final feature maps and three dense layers. The last dense layer has 7 outputs, equivalent to the classes considered: healthy, ground glass opacity (GGO), micronodules, consolidation, reticulation, honeycombing and a combination of GGO/reticulation. To train and evaluate the CNN, we used a dataset of 14696 image patches, derived by 120 CT scans from different scanners and hospitals. To the best of our knowledge, this is the first deep CNN designed for the specific problem. A comparative analysis proved the effectiveness of the proposed CNN against previous methods in a challenging dataset. The classification performance (~85.5%) demonstrated the potential of CNNs in analyzing lung patterns. Future work includes, extending the CNN to three-dimensional data provided by CT volume scans and integrating the proposed method into a CAD system that aims to provide differential diagnosis for ILDs as a supportive tool for radiologists.

From stellar to planetary composition: Galactic chemical evolution of Mg/Si mineralogical ratio

Aims. The main goal of this work is to study element ratios that are important for the formation of planets of different masses. Methods. We study potential correlations between the existence of planetary companions and the relative elemental abundances of their host stars. We use a large sample of FGK-type dwarf stars for which precise Mg, Si, and Fe abundances have been derived using HARPS high-resolution and high-quality data. Results. A first analysis of the data suggests that low-mass planet host stars show higher [Mg/Si] ratios, while giant planet hosts present [Mg/Si] that is lower than field stars. However, we found that the [Mg/Si] ratio significantly depends on metallicity through Galactic chemical evolution. After removing the Galactic evolution trend only the difference in the [Mg/Si] elemental ratio between low-mass planet hosts and non-hosts was present in a significant way. These results suggest that low-mass planets are more prevalent around stars with high [Mg/Si]. Conclusions. Our results demonstrate the importance of Galactic chemical evolution and indicate that it may play an important role in the planetary internal structure and composition. The results also show that abundance ratios may be a very relevant issue for our understanding of planet formation and evolution.

Visualizing the Simulation of 3-D Underwater Sensor Networks

The majority of sensor network research deals with land-based networks, which are essentially two-dimensional, and thus the majority of simulation and animation tools also only handle such networks. Underwater sensor networks on the other hand, are essentially 3D networks because the depth at which a sensor node is located needs to be considered as well. Due to that additional dimension, specialized tools need to be used when conducting simulations for experimentation. The School of Engineering’s Underwater Sensor Network (UWSN) lab is conducting research on underwater sensor networks and requires simulation tools for 3D networks. The lab has extended NS-2, a widely used network simulator, so that it can simulate three-dimensional networks. However, NAM, a widely used network animator, currently only supports two-dimensional networks and no extensions have been implemented to give it three-dimensional capabilities. In this project, we develop a network visualization tool that functions similarly to NAM but is able to render network environments in full 3-D. It is able to take as input a NS-2 trace file (the same file taken as input by NAM), create the environment, position the sensor nodes, and animate the events of the simulation. Further, the visualization tool is easy to use, especially friendly to NAM users, as it is designed to follow the interfaces and functions similar to NAM. So far, the development has fulfilled the basic functionality. Future work includes fully functional capabilities for visualization and much improved user interfaces.

An empirical evaluation of the Random Forests classifier models for variable selection in a large-scale lung cancer case-control study

Random Forests™ is reported to be one of the most accurate classification algorithms in complex data analysis. It shows excellent performance even when most predictors are noisy and the number of variables is much larger than the number of observations. In this thesis Random Forests was applied to a large-scale lung cancer case-control study. A novel way of automatically selecting prognostic factors was proposed. Also, synthetic positive control was used to validate Random Forests method. Throughout this study we showed that Random Forests can deal with large number of weak input variables without overfitting. It can account for non-additive interactions between these input variables. Random Forests can also be used for variable selection without being adversely affected by collinearities. ^ Random Forests can deal with the large-scale data sets without rigorous data preprocessing. It has robust variable importance ranking measure. Proposed is a novel variable selection method in context of Random Forests that uses the data noise level as the cut-off value to determine the subset of the important predictors. This new approach enhanced the ability of the Random Forests algorithm to automatically identify important predictors for complex data. The cut-off value can also be adjusted based on the results of the synthetic positive control experiments. ^ When the data set had high variables to observations ratio, Random Forests complemented the established logistic regression. This study suggested that Random Forests is recommended for such high dimensionality data. One can use Random Forests to select the important variables and then use logistic regression or Random Forests itself to estimate the effect size of the predictors and to classify new observations. ^ We also found that the mean decrease of accuracy is a more reliable variable ranking measurement than mean decrease of Gini. ^

Oxygen isotopes, IRD and SST reconstruction for the interval MIS31-19 of IODP Site 306-U1314

Early and Mid-Pleistocene climate, ocean hydrography and ice sheet dynamics have been reconstructed using a high-resolution data set (planktonic and benthic d18O time series, faunal-based sea surface temperature (SST) reconstructions and ice-rafted debris (IRD)) record from a high-deposition-rate sedimentary succession recovered at the Gardar Drift formation in the subpolar North Atlantic (Integrated Ocean Drilling Program Leg 306, Site U1314). Our sedimentary record spans from late in Marine Isotope Stage (MIS) 31 to MIS 19 (1069-779 ka). Different trends of the benthic and planktonic oxygen isotopes, SST and IRD records before and after MIS 25 (~940 ka) evidence the large increase in Northern Hemisphere ice-volume, linked to the cyclicity change from the 41-kyr to the 100-kyr that occurred during the Mid-Pleistocene Transition (MPT). Beside longer glacial-interglacial (G-IG) variability, millennial-scale fluctuations were a pervasive feature across our study. Negative excursions in the benthic d18O time series observed at the times of IRD events may be related to glacio-eustatic changes due to ice sheets retreats and/or to changes in deep hydrography. Time series analysis on surface water proxies (IRD, SST and planktonic d18O) of the interval between MIS 31 to MIS 26 shows that the timing of these millennial-scale climate changes are related to half-precessional (10 kyr) components of the insolation forcing, which are interpreted as cross-equatorial heat transport toward high latitudes during both equinox insolation maxima at the equator.

Global raster maps indicating the habitat suitability for 7 suborders of cold water octocorals (Octocorallia found deeper than 50m)

This dataset consists of global raster maps indicating the habitat suitability for 7 suborders of cold water octocorals (Octocorallia found deeper than 50m). Maps present a relative habitat suitability index ranging from 0 (unsuitable) to 100 (highly suitable). Two maps are provided for each suborder (Alcyoniina, Calcaxonia, Holaxonia, Scleraxonia, Sessiliflorae, Stolonifera, and Subselliflorae). A publicly accessable low resolution map (grid size 10x10 arc-minutes) and a restricted access high resolution map (grid size 30x30 arc-seconds). Maps are geotiff format incorporating LZW compression to reduce file size. Please contact the corresponding author (Chris Yesson) for access to the high resolution data.

Isotope ratios of osmiun, carbon and oxygen of Miocene sediments and benthic foraminifera

Seawater 187Os/188Os ratios for the Middle Miocene were reconstructed by measuring the 187Os/188Os ratios of metalliferous carbonates from the Pacific (DSDP 598) and Atlantic (DSDP 521) oceans. Atlantic and Pacific 187Os/188Os measurements are nearly indistinguishable and are consistent with previously published Os isotope records from Pacific cores. The Atlantic data reported here provide the first direct evidence that the long-term sedimentary 187Os/188Os record reflects whole-ocean changes in the Os isotopic composition of seawater. The Pacific and the Atlantic Os measurements confirm a long-term 0.01/Myr increase in marine 187Os/188Os ratios that began no later than 16 Ma. The beginning of the Os isotopic increase coincided with a decrease in the rate of increase of marine 87Sr/86Sr ratios at 16 Ma. A large increase of 1? in benthic foraminiferal delta18O values, interpreted to reflect global cooling and ice sheet growth, began approximately 1 million years later at 14.8 Ma, and the long-term shift toward lower bulk carbonate delta13C values began more than 2 Myr later around 13.6 Ma. The post-16 Ma increase in marine 187Os/188Os ratios was most likely forced by weathering of radiogenic materials, either old sediments or sialic crust with a sedimentary protolith. We consider two possible Miocene-specific geologic events that can account for both this increase in marine 187Os/188Os ratios and also nearly constant 87Sr/86Sr ratios: (1) the first glacial erosion of sediment-covered cratons in the Northern Hemisphere; (2) the exhumation of the Australian passive margin-New Guinea arc system. The latter event offers a mechanism, via enhanced availability of soluble Ca and Mg silicates in the arc terrane, for the maintenance of assumed low CO2 levels after 15 Ma. The temporal resolution (three samples/Myr) of the 187Os/188Os record from Site 598, for which a stable isotope stratigraphy was also constructed, is significantly higher than that of previously published records. These high resolution data suggest oscillations with amplitudes of 0.01 to 0.02 and periods of around 1 Myr. Although variations in the 187Os/188Os record of this magnitude can be easily resolved analytically, this higher frequency signal must be verified at other sites before it can be safely interpreted as global in extent. However, the short-term 187Os/188Os variations may correlate inversely with short-term benthic foraminiferal delta18O and bulk carbonate delta13C variations that reflect glacioeustatic events.

Stable isotope record of DSDP Hole 81-552A in the northeastern Atlantic Ocean

Oxygen and carbon isotope ratios in benthic foraminifers have been determined at 10 cm intervals through the top 59 m of DSDP Hole 552A. This provides a glacial record of remarkable resolution for the late Pliocene and Pleistocene. The major glacial event which marked the onset of Pleistocene-like glacial-interglacial alternations was at about 2.4 m.y. ago. These very high-resolution data do not support the notion of significant Northern Hemisphere glaciation between 3.2 and 2.4 m.y. ago.

Age model and stable oxygen isotope mean values of ice core SZ99 from Akademii Nauk ice cap on Severnaya Zemlya

Between 1999 and 2001, a 724 m long ice core was drilled on Akademii Nauk, the largest glacier on Severnaya Zemlya, Russian Arctic. The drilling site is located near the summit. The core is characterized by high melt-layer content. The melt layers are caused by melting and even by rain during the summer. We present high-resolution data of density, electrical conductivity (dielectrical profiling), stable water isotopes and melt-layer content for the upper 136 m (120 m w.e.) of the ice core. The dating by isotopic cycles and electrical conductivity peak identification suggests that this core section covers approximately the past 275 years. Singularities of volcanogenic and anthropogenic origin provide well-defined additional time markers. Long-term temperatures inferred from 12 year running mean averages of d18O reach their lowest level in the entire record around 1790. Thereafter the d18O values indicate a continuously increasing mean temperature on the Akademii Nauk ice cap until 1935, interrupted only by minor cooling episodes. The 20th century is found to be the warmest period in this record.

Sapropel cycles in the Mediterranean Sea

Water column stratification increased at climatic transitions from cold to warm periods during the late Quaternary and led to anoxic conditions and sapropel formation in the deep eastern Mediterranean basins. High-resolution data sets on sea-surface temperatures (SST) (estimated from UK'37 indices) and d18O of planktonic foraminifer calcite (d18Ofc) across late Pleistocene sapropel intervals show that d18Ofc decreased (between 1 and 4.6 per mil) and SST increased (between 0.7° and 6.7°C). Maximal d18Oseawater depletion of eastern Mediterranean surface waters at the transition is between 0.5 and 3.0 per mil, and in all but one case exceeded the depletion seen in a western Mediterranean core. The depletion in d18Oseawater is most pronounced at sapropel bases, in agreement with an initial sudden input of monsoon-derived freshwater. Most sapropels coincide with warming trends of SST. The density decrease by initial freshwater input and continued warming of the sea surface pooled fresh water in the surface layer and prohibited deep convection down to ageing deep water emplaced during cold and arid glacial conditions. An exception to this pattern is "glacial" sapropel S6; its largest d18Oseawater depletion (3 per mil) is almost matched by the depletion in the western Mediterranean Sea, and it is accompanied by surface water cooling following an initially rapid warming phase. A second period of significant isotopic depletion is in isotope stage 6 at the 150 kyr insolation maximum. While not expressed as a sapropel due to cold SST, it is in accord with a strengthened monsoon in the southern catchment.

Benthic foraminifera of the Labrador Sea and Buffin Bay

Trigger weight (TWC) and piston (PC) cores obtained from surveys of the three sites drilled during Ocean Drilling Program (ODP) Leg 105 were studied in detail for benthic foraminiferal assemblages, total carbonate (all sites), planktonic foraminiferal abundances (Sites 645 and 647), and stable isotopes (Sites 646 and 647). These high-resolution data provide the link between modern environmental conditions represented by the sediment in the TWC and the uppermost cores of the ODP holes. This link provides essential control data for interpretating late Pleistocene paleoceanographic records from these core holes. At Site 645 in Baffin Bay, local correlation is difficult because the area is dominated by ice-rafted deposits and by debris flows and/or turbidite sedimentation. At the two Labrador Sea sites (646 and 647), the survey cores and uppermost ODP cores can be correlated. High-resolution data from the site survey cores also provide biostratigraphic data that refine the interpretations compiled from core-catcher samples at each ODP site.

Plant Functional Type (PFT) map over Siberia derived from GlobCover 2005 dataset, link to dataset in NetCDF format

High-latitude ecosystems play an important role in the global carbon cycle and in regulating the climate system and are presently undergoing rapid environmental change. Accurate land cover data sets are required to both document these changes as well as to provide land-surface information for benchmarking and initializing Earth system models. Earth system models also require specific land cover classification systems based on plant functional types (PFTs), rather than species or ecosystems, and so post-processing of existing land cover data is often required. This study compares over Siberia, multiple land cover data sets against one another and with auxiliary data to identify key uncertainties that contribute to variability in PFT classifications that would introduce errors in Earth system modeling. Land cover classification systems from GLC 2000, GlobCover 2005 and 2009, and MODIS collections 5 and 5.1 are first aggregated to a common legend, and then compared to high-resolution land cover classification systems, vegetation continuous fields (MODIS VCFs) and satellite-derived tree heights (to discriminate against sparse, shrub, and forest vegetation). The GlobCover data set, with a lower threshold for tree cover and taller tree heights and a better spatial resolution, tends to have better distributions of tree cover compared to high-resolution data. It has therefore been chosen to build new PFT maps for the ORCHIDEE land surface model at 1 km scale. Compared to the original PFT data set, the new PFT maps based on GlobCover 2005 and an updated cross-walking approach mainly differ in the characterization of forests and degree of tree cover. The partition of grasslands and bare soils now appears more realistic compared with ground truth data. This new vegetation map provides a framework for further development of new PFTs in the ORCHIDEE model like shrubs, lichens and mosses, to represent the water and carbon cycles in northern latitudes better. Updated land cover data sets are critical for improving and maintaining the relevance of Earth system models for assessing climate and human impacts on biogeochemistry and biophysics.