julilili42/papers huggingface dataset:
[11C]DASB PET: Seasonal changes of cerebral serotonin transporters
2010-05-01

274 Objectives Seasonal changes in the serotonergic system may contribute to seasonal effects in psychiatric disorders and have to be accounted for in imaging studies of the serotonergic system. Recently, reduced serotonin transporter (5HTT) levels in the summer and a neg. correlation with the amount of daylight were reported. Aim of this study was to investigate seasonal effects in our sample of psychiatric patients and healthy controls, and to investigate if previously published results from this sample survive correction for seasonal effects. Methods Results from [11C]DASB PET (binding potential BP=k3/k4, thalamic ROI, explorative voxelwise analysis) in 68 healthy subjects, in 10 pts. with unipolar major depression (UMD) and 14 pts. with obsessive compulsive disorder (OCD) were compared to the time of PET scanning: (1) a sinusoidal function of the month was fitted to thalamic BP (3 d.o.f.), (2) a daylight index (minimum Dec/Jan) was included in previously published regression analyses (3) a voxelwise comparison was carried out for all PET scans between May and Aug and those between Nov and Feb. Results The fit yielded a sinusoidal function with a min. between Dec and Jan and a max. between June and July. Recently published results (reduced BP in UMD, depending on anxiety scores, reduced BP in OCD, depending on disease severity) survived correction for seasonal effects. Among healthy subjects, BP in the summer was 15% higher than in the winter (p=0.003), no significant effect was observed in patients. Conclusions Our results confirm seasonal changes in the serotonergic system which did not affect previously published findings in pts. with UMD and OCD. Surprisingly, the observed effect on 5HTT was opposite to that recently published, indicating seasonal effects being more complex
Application of particle filters to vision-based orientation estimation using harmonic analysis
2010-05-01

We investigate the application of particle filters to estimate the orientation of a mobile agent based on an omnidirectional video stream. By applying spherical signal analysis to sequences of low resolution input images we perform a real-time estimation of the relative camera rotation. We use normalized cross-correlation computed with a fast frequency domain approach that yields unbiased estimates which can be further processed by a particle filter. We discuss the quaternion representation of the rotational state space and evaluate methods for meaningful averaging. A prototype system is presented and experiments with real image sequences show that robust estimation of the rotational motion is achievable even when the input images are corrupted, e.g. due to occlusions.
Soils as sinks or sources for diffuse pollution of the water cycle
2010-05-01

Numerous chemical compounds have been released into environment by human activities and can nowadays be found everywhere, i.e. in compartments water, soil, and air, at poles and in high mountains. Examples for a global distribution of toxic compounds are persistent organic pollutants (PCB, dioxins, PAH, fluorinated surfactants and flame retardants, etc.: the Stockholm dirty dozen) but also mercury and other metals. Many of these compounds reached a global distribution via atmo¬sphere; others have been and are still directly applied to top soils at large scale by agriculture or are released into groundwater at landfill sites or by discharge of treated or untreated waste waters. Sooner or later such compounds end up in water cycle – often via an intermediate storage in soils. Pollutants in soils are leached by seepage waters, transferred to ground¬water, and transported to rivers via groundwater flow. Adsorbed compounds may be transported from soils into surface waters by erosion processes and will end up in sediments.
Analysis of thermal response tests (TRT) using high resolution numerical simulations
2010-05-01

W/m 2 , the computed effective thermal conductivity decreases by 0.14 W/(mK) meaning a decline by 6.4%. At the same time the calculated borehole resistance increases from 0.086 to 0.101 (mK)/W, i.e. it rises by 17.4%. The effect of the geometry is examined by varying the distance between the tubes in the BHE. This leads to no significant change of the calculated thermal conductivity. However, the computed thermal borehole resistance is highly sensitive. The values shift from 0.06 (mK)/W (for the closest arrangement of the tubes) to 0.17 (mK)/W (for the greatest possible distance between the tubes). The presented relationships clearly show the uncertainties in standard TRT interpretation and demonstrate that in many situations a more detailed evaluation concept is needed.
Evolution of habitat and environment of deer during the Late-glacial and early Holocene: the case of red deer in French Jura.
2010-05-01

Thus, we have studied the habitat and environment evolution of red deer (Cervus elaphus) during the Late-glacial and early Holocene using stable isotopes and radiocarbon investigations. The analyzed bone material was selected from archaeological sites in French Jura. Performing direct radiocarbon dating on the bone collagen of the selected remains solved the problem of possible chronological uncertainties of the stratigraphical record of the sites. The same bone collagen samples were used for stable isotope measurements. We investigated the relative abundances in 13 C to examine changes in habitat closure (canopy effect), in 15 N to decipher changes in pedogenic activities (soil maturation) of the animals dwelling, and in 18 O to track changes in altitude and/or local temperatures of the occupied territories. The results demonstrate that the stable isotopic composition of red deer bone collagen can be a valuable and sensitive indicator of habitat use and environmental conditions. The associated direct dating allows us to reconstruct the chronology of ecological changes. The combined chronological and ecological results evidence local differences in red deer adaptation at a small geographical scale.
The analysis of a hydrothermal breccia system, Mount Painter Inlier, South Australia
2010-05-01

(1) Institut fur Geowissenschaften, Universitat Tubingen, Wilhelmstrasse 56, 72074 Tuebingen, Germany (anett.weisheit@uni-tuebingen.de / fax: +497071293060), (2) Institut fur Geowissenschaften, Universitat Tubingen, Wilhelmstrasse 56, 72074 Tuebingen, Germany (paul.bons@uni-tuebingen.de / fax: +497071293060), (3) Department of Geology and Soil Science, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium (marlina.elburg@UGent.be / fax: +3292644984)
Contribution of stable isotopes (C,N,S) in collagen of late Pleistocene large mammal trophic ecology and landscape use: a case study in Goyet and Scladina cave (30-40,000 years BP)
2010-05-01

Two Belgian caves yielded very rich large mammal associations dating around 30 to 40,000 years ago: Goyet and Scladina cave (layer 1A). These sites are only 5 km apart but the cave entrances open on different valleys, in a quite diverse landscape ranging between open, unprotected uplands, steep cliffs and sheltered sun-exposed gorges, with the larger Meuse valley nearby. This mosaic scenery permitted during the Last Glacial a rich diversity of fossil flora and fauna. The faunal association includes a large diversity of taxa including Aurochs Bos primigenius, steppe bison Bison priscus, reindeer Rangifer tarandus, giant deer Megaloceros giganteus, horse Equus ferus, woolly rhinoceros Coelodonta antiquitatis, woolly mammoth Mammuthus primigenius, cave bear Ursus spelaeus, brown bear Ursus arctos, wolf Canis lupus, cave lion Panthera leo spelaea, and cave hyaena Crocuta crocuta spelaea. All the 90 studied bones and teeth yielded collagen with excellent collagen preservation, allowing reliable investigations of carbon, nitrogen and sulfur isotopic biogeochemistry. The combination of three different isotopic tracers allows to deciphering the effects of food selection and landscape use by different herbivorous and carnivorous taxa. This is the first study to include sulfur isotopic signatures in the study of late Quaternary large mammal palaeobiology. This new tracer yields evidence on mobility and differences in pasture areas, as different geological bedrock may exhibit various sulfur isotopic signatures that will pass on the herbivores and further on their predators. Using this feature in addition to the trophic information provided by carbon and nitrogen isotopic signatures, it appears that for some species present in both sites, such as horse and woolly rhinoceros, the individuals found in each site probably did not use the same pasture areas. This seems to also the case for the overwhelmingly vegetarian cave bears. In addition, individuals from the same species found in one site sometimes exhibit clear isotopic differences in the three isotopic tracers that suggest different pasture grounds as well, and therefore the possibility of different herds in the vicinity of the cave site. In the case of cave hyeanas, the isotopic signatures of individuals from both caves are not significantly different and suggest that these predators obtained their prey from a large territory including the pasture grounds of herbivores from both caves. In addition, direct radiocarbon dating of some of the studied collagen allows to investigating possible chronological trends.
Quantifying Landscape Response to Past (Last Glacial) and Present Day Erosion with Detrital Thermochronology
2010-05-01

Quantifying landscape response to climate change is limited by insufficient knowledge of spatial and temporal variations in catchment erosion. Detrital cooling ages collected from Quaternary glacial moraines and modern river sediments provide a tool to address these problems. We use detrital thermochronology to quantify spatial variations in alpine glacial erosion during the Last Glacial Maximum (LGM). Results are compared to the distribution of present-day erosion recorded in samples from modern river sediments, and predicted patterns in glacial erosion from a plan-form (shallow-ice approximation) glacial erosion model.
PAHs in soils: Sorption versus degradation - elucidation of rate-limiting processes
2010-05-01

Polycyclic aromatic hydrocarbons (PAHs) belong to the class of persistent organic pollutants, and are of special interest due to their ubiquituous distribution in the environment at relatively high concentrations. Subsequent to their emmission into the environment through incomplete combustion processes of natural and anthropogenic sources (e.g. vulcano eruptions, forest fires, industry, traffic), PAHs can be transported over long distances. Following atmospheric deposition they accumulate in particular in top-soils and have been found to be stable over long periods of time (decades to centuries). Based on that this study targets on the elucidation of the long-term PAH-fate in top-soils by means of degradation experiments under well-controlled laboratory conditions with well mixed batch experiments at a water to solids ratio 10:1. From a rural site in the Black Forest Mountains, Germany, top-soil samples were taken, which contains approximately 7-8 mg 18 PAHs per kg soil. This soil was sieved through 2 mm to sort out stones, roots- and leaf-parts and homogenised afterwards. Within the first month of incubation a depletion of native PAHs were observed. However, an exhaustive sequential extraction using accelerated solvent extraction with 3 cycles of acteone and 4 cycles of toluene (100 bar pressure, 10 min static time, 100°C and 150°C respectively) revealed a reduced extractability of PAHs subsequent to incubation. In order to stimulate PAH degradation a second experiment with a higher water to solid ratio (1000:1) was carried out, and phenanthrene was spiked to the water phase of this set up. Results revealed a reduction of phenanthrene concentration more likely to be due to sorption rather than degradation. The set up was changed to aqueous soil solutions without soil in the batch and spiked again with phenanthrene. Degradation of phenanthrene occurred within 10 days in these batches. The experiments show that the microorganisms present in the Black Forest soil are capable to degrade PAHs. Nevertheless strong sorption and high organic carbon content in this soil prevent these microorganisms from degrading the native PAHs. The results were implemented into a mass balance model considering both, sorption and degradation. The calculations were conducted with first order rate constant taken from the non-soil-containing experiment, and revealed a half-life of phenanthrene up to almost one century.
Biophysical analysis of plant gas exchange and reconstruction of palaeoclimate
2010-05-01

We present a systematic derivation of the relation between stomatal density and CO2concentration based upon (i) a quantitative model of C3-photosynthesis, (ii) the physics of diffusion, and (iii) an optimisation principle which asserts that plants adjust stomatal conductance such that assimilation is maximised and transpiration is minimised. Since maximum stomatal conductance per leaf area is related to stomatal density the model leads to an equation connecting parameters which describe (a) the environment (stomatal density, atmospheric CO2-concentration, leaf temperature, atmospheric humidity, soil water content, insolation, wind velocity) (b) leaf and stoma anatomy, (c) C3photosynthesis. Due to the formulation of the model in terms of analytic functions, sensitivity studies can easily be performed. According to the results, stomatal density depends strongly on atmospheric CO2concentration, leaf temperature, atmospheric humidity, soil water content, stomatal area, stomatal depth and one of the photosynthetic parameters. Compared to these, the influence of the other parameters (for example, wind speed) is negligible. It is usually assumed that the stomatal index is largely independent from climate and represents therefore a more robust quantity for reconstructing CO2. However, the stomatal index does 1) not consider the changes in stomatal anatomy that can often observed in a lineage (for example, pore length) and 2) the stomatal index itself may also be influenced by climate. Additionally, it is often not possible to determine the density of epidermal cells which is a prerequisite for calculating the stomatal index. We suggest to focus on stomatal density for CO2 reconstruction. Stomata of fossil leaves are often well preserved and photosynthetic biochemical parameters are comparatively conservative. Hence, the model ties essentially the four environmental quantities atmospheric CO2-concentration, temperature, atmospheric humidity and soil water content to the fossil stomatal density and stomatal anatomy. In other words, if three of these environmental quantities are already known, the fourth is provided by the mathematics of the model. Attempts to obtain the atmospheric CO2concentration from stomatal density (or stomatal index) should therefore accompanied by additional palaeoclimate studies of the considered sites.
Mechanistic modelling of Middle Eocene atmospheric carbon dioxide using fossil plant material
2010-05-01

(1) Institute for Geosciences, University of Tubingen, Germany (michaela.grein@uni-tuebingen.de, wilfried.konrad@uni-tuebingen.de), (2) State Museum of Natural History Stuttgart, Germany (grein.smns@naturkundemuseum-bw.de, rothnebelsick.smns@naturkundemuseum-bw.de), (3) Senckenberg Research Institute, Palaeobotany, Frankfurt am Main, Germany (vwilde@senckenberg.de), (4) Steinmann-Institute, Bonn University, Germany (utescher@geo.uni-bonn.de)
Automatic pharmacophore model generation using weighted substructure assignments
2010-05-01

The generation of a pharmacophore model is a challenging process, which often requires the interaction of medicinal chemists. Given a number of ligands for a specific target, the aim is to identify the pharmacophore patterns that are responsible for the biological activities of chemical compounds. A recent study of optimal assignment methods has shown that the assignment of chemical substructures is able to detect active compounds in a data set [1]. Therefore, we investigated the possibility to use this technique to identify key features of a set of active compounds. To determine important substructures of active compounds, we integrated n weight factors, where n is the number of substructures. The substructures were defined using the pharmacophore definitions of Phase 3.0 [2]. To define the individual weights of the pharmacophore patterns, we integrated a genetic algorithm which assigns weight factors to the previously defined patterns. The experimental setup was designed as follows: Given a data set with active compounds, the most active compound was selected as query structure for the experiment. The remaining active compounds were inserted into a background data set containing inactive compounds. The genetic algorithm evolved n weights for the pharmacophore patterns of the query structure. To evaluate the fitness of an individual, we performed a single query screening with the weights of the individual. During the optimization process, the BEDROC score [3] is optimized which puts emphasis on the early recognition performance. The result of the genetic algorithm was a weight vector that assigns each pharmacophore feature the weight of the best individual. We evaluated our approach on a subset of the Directory of Useful Decoys that is suitable for ligand-based virtual screening [1][4]. The query structure was extracted from the same complexed crystal structure used by Huang et al. [4] to determine the binding site of the protein. The presented method is able to provide valuable information about key features that are important for the biological activity of a compound. Additionally, information of the protein structure is not needed. Therefore, the method can also be used to derive a pharmacophore model if no protein structure is available (e.g. GPCRs).
Efficient extraction of canonical spatial relationships using a recursive enumeration of k-subsets
2010-05-01

The spatial arrangement of a chemical compound plays an important role regarding the related properties or activities. A straightforward approach to encode the geometry is to enumerate pairwise spatial relationships between k substructures, like functional groups or subgraphs. This leads to a combinatorial explosion with the number of features of interest and redundant information. The goal of this work is to compute all possible k-subsets of spatial points and to extract a single canonical descriptor for each subset in sub-polynomial computation time. More precisely, the problem is to reduce the complexity of nk = n·(n - 1)...(n - k) possible relationships (patterns or descriptors) for n features and k-point relationships. We propose a two-step algorithm to solve this problem. A modified algorithm for the computation of the binomial coefficient computes the k-subsets [1] containing the possible combinations of the n relevant features. If a k-subset is completed in the inner recursion, the algorithm computes a canonical representation for it. By defining a natural order by means of the geometrical center of gravity of the k points, we extract k patterns that describe the distance to the center of gravity and type of the spatial feature k ∈ F. Then, the algorithm returns a unique identifier for the lexicographically sorted array of patterns. If applicable (), an additional identifier is added which has the form , where dij denotes the geometrical distance between features i, j. Else (), this step is omitted. Therefore, this approach also considers stereochemistry. Finally, one feature is returned for each k-subset resulting in a set of C(n, k) patterns describing the structure. The main result is that the number of features is reduced from nk to C(n, k), which equals the binomial coefficient. This procedure is useful in combination with similarity approaches that use spatial relationships, like pharmacophore searches, fingerprints, or graph kernels. We experimentally validated the algorithm on numerous QSAR benchmark sets in combination with the pharmacophore kernel [2].
Geochemical changes in pore water and reservoir rock due to CO2 injection
2010-05-01

An electron spin probe study was made of the effect of a number of mitogenic agents on the ordering and state of aggregation of the plasma membrane lipids of lymphocytes. These agents, which included phytohemagglutinin, Concanavalin A, the calcium ionophore A23187 and periodate, caused a 20% decrease in lipid ordering in the region of the bilayer probed by 5-nitroxide stearic acid. The corresponding methyl ester probe showed marked probe-probe interaction under the same conditions indicating an aggregation of lipids in the area probed by this label. Studies with mixed lipid vesicles and ganglioside-free cells indicate that these areas are rich in glycolipids capable of hydrogen bonding to the ester probe. The decrease in ordering and the increase in aggregation of the membrane lipids were correlated with the patching and capping of the ligand-receptor complexes. Furthermore, the disappearance of fluorescent ligand from the surface of treated cells corresponded with the return of the spectral parameters of the probes to control cell values. It was concluded that glycolipids might play an important role in ligand-induced cell surface changes either as bearers of receptor groups, as in the case of some gangliosides, or in association by hydrogen-bonding with receptor proteins.
Comparison of bone scintigraphy with Tc-99m-DPD and PET/CT with C-11-choline for the detection of bone metastases in patients with prostate cancer
2010-05-01

1275 Objectives PET/CT with C-11-choline (choline-PET/CT) is a promising tool for imaging prostate carcinomas and its metastases. We compared the value of Choline-PET/CT for the detection of bone metastases with the standard imaging modality Tc-99m-bone-scintigraphy (scintigraphy). Methods Retrospective analysis of scintigraphy and choline-PET/CT in 31 patients with histological proven prostate cancer and clinical suspicion of metastases, who were examined by both methods (mean time lapse of 13 days between the examinations). The examinations were evaluated lesion wise and region wise by a radiologist and a nuclear medicine physician. A consensus of all further examinations and a clinical follow-up of at least 6 months served as gold standard. Results The mean PSA at the time of the examinations was 3,62 ng/ml (range: 0,97 to 26 ng/ml). In total 82 bone lesions were identified. In 11 of 31 patients (35%) neither cholin-PET/CT nor scintigraphy detected bone metastases. 20 of 31 patients (65%) had bone metastases and in 6 of these 20 patients the results of cholin-PET/CT and scintigraphy were identical. The accuracy for the detection of bone metastases was 92% for scintigraphy and 81% for choline-PET/CT. Scintigraphy showed a higher sensitivity whereas choline-PET/CT showed a superior specificity (82% vs. 36%). The lowest sensitivity of choline-PET/CT was found for metastases in ribs. In the examined patients there was no correlation between the choline-uptake of bone metastases and clinical parameters (grading, PSA). Conclusions PET/CT with C-11-Choline is a method with a high specificity for the detection of bone metastases in whole body staging of patients with advanced prostate cancer. Nevertheless, due to its limited sensitivity it can not replace the widely available bone scintigraphy in many cases
New Results on the Palaeobiology of Bears on the Swabian Alb (Chronology, Isotopic Geochemistry and Palaeogenetics)
2010-05-01

Paleogenetic investigations at three geographically close caves in the Ach Valley near Blaubeuren have revealed two different cave bear haplogroups. These two haplogroups correspond to Ursus spelaeus (haplogroup 1) and Ursus ingressus (haplogroup 4) (Rabeder & Hofreiter 2004, Die Hohle 55, 58-77). This genetic variability was first attested for Geisenklosterle and Sirgenstein cave, but the new genetic data attest them also for Hohle Fels. In all three caves Ursus ingressus replaced Ursus spelaeus around 28 000 B.P.