Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces

An Internet portal accessible at www.gdb.unibe.ch has been set up to automatically generate color-coded similarity maps of the ChEMBL database in relation to up to two sets of active compounds taken from the enhanced Directory of Useful Decoys (eDUD), a random set of molecules, or up to two sets of user-defined reference molecules. These maps visualize the relationships between the selected compounds and ChEMBL in six different high dimensional chemical spaces, namely MQN (42-D molecular quantum numbers), SMIfp (34-D SMILES fingerprint), APfp (20-D shape fingerprint), Xfp (55-D pharmacophore fingerprint), Sfp (1024-bit substructure fingerprint), and ECfp4 (1024-bit extended connectivity fingerprint). The maps are supplied in form of Java based desktop applications called “similarity mapplets” allowing interactive content browsing and linked to a “Multifingerprint Browser for ChEMBL” (also accessible directly at www.gdb.unibe.ch) to perform nearest neighbor searches. One can obtain six similarity mapplets of ChEMBL relative to random reference compounds, 606 similarity mapplets relative to single eDUD active sets, 30 300 similarity mapplets relative to pairs of eDUD active sets, and any number of similarity mapplets relative to user-defined reference sets to help visualize the structural diversity of compound series in drug optimization projects and their relationship to other known bioactive compounds.

On low-dimensional projections of high-dimensional distributions

Let P be a probability distribution on q -dimensional space. The so-called Diaconis-Freedman effect means that for a fixed dimension d<dimensional projections of P look like a scale mixture of spherically symmetric Gaussian distributions. The present paper provides necessary and sufficient conditions for this phenomenon in a suitable asymptotic framework with increasing dimension q . It turns out, that the conditions formulated by Diaconis and Freedman (1984) are not only sufficient but necessary as well. Moreover, letting P ^ be the empirical distribution of n independent random vectors with distribution P , we investigate the behavior of the empirical process n √ (P ^ −P) under random projections, conditional on P ^ .

Local strain distribution in real three-dimensional alveolar geometries

Mechanical ventilation is not only a life saving treatment but can also cause negative side effects. One of the main complications is inflammation caused by overstretching of the alveolar tissue. Previously, studies investigated either global strains or looked into which states lead to inflammatory reactions in cell cultures. However, the connection between the global deformation, of a tissue strip or the whole organ, and the strains reaching the single cells lining the alveolar walls is unknown and respective studies are still missing. The main reason for this is most likely the complex, sponge-like alveolar geometry, whose three-dimensional details have been unknown until recently. Utilizing synchrotron-based X-ray tomographic microscopy, we were able to generate real and detailed three-dimensional alveolar geometries on which we have performed finite-element simulations. This allowed us to determine, for the first time, a three-dimensional strain state within the alveolar wall. Briefly, precision-cut lung slices, prepared from isolated rat lungs, were scanned and segmented to provide a three-dimensional geometry. This was then discretized using newly developed tetrahedral elements. The main conclusions of this study are that the local strain in the alveolar wall can reach a multiple of the value of the global strain, for our simulations up to four times as high and that thin structures obviously cause hotspots that are especially at risk of overstretching.

Mapping material distribution in a heterogeneous sand tank by image analysis

Water flow and solute transport through soils are strongly influenced by the spatial arrangement of soil materials with different hydraulic and chemical properties. Knowing the specific or statistical arrangement of these materials is considered as a key toward improved predictions of solute transport. Our aim was to obtain two-dimensional material maps from photographs of exposed profiles. We developed a segmentation and classification procedure and applied it to the images of a very heterogeneous sand tank, which was used for a series of flow and transport experiments. The segmentation was based on thresholds of soil color, estimated from local median gray values, and of soil texture, estimated from local coefficients of variation of gray values. Important steps were the correction of inhomogeneous illumination and reflection, and the incorporation of prior knowledge in filters used to extract the image features and to smooth the results morphologically. We could check and confirm the success of our mapping by comparing the estimated with the designed sand distribution in the tank. The resulting material map was used later as input to model flow and transport through the sand tank. Similar segmentation procedures may be applied to any high-density raster data, including photographs or spectral scans of field profiles.

Molecular-Based Magnetism in High-Spin Molecular Clusters and Three-Dimensional Networks Based on Cyanometalate Building Blocks

The field of molecule-based magnets is a relatively new branch of chemistry, which involves the design and study of molecular compounds that exhibit a spontaneous magnetic ordering below a critical temperature, Tc. One major goal involves the design of materials with tuneable Tc's for specific applications in memory storage devices. Molecule-based magnets with high magnetic ordering temperatures have recently been obtained from bimetallic and mixed-valence transition metal μ-cyanide complexes of the Prussian blue family. Since the μ-cyanide linkages permit an interaction between paramagnetic metal ions, cyanometalate building blocks have found useful applications in the field of molecule-based magnets. Our work involves the use of octacyanometalate building blocks for the self-assembly of two new classes of magnetic materials namely, high-spin molecular clusters which exhibit both ferromagnetic intra- and intercluster coupling, and specific extended network topologies which show long-range ferromagnetic ordering.

Adiponectin isoform distribution in serum and in follicular fluid of women undergoing treatment by ICSI

Adiponectin is an adipokine, present in the circulation in comparatively high concentrations and different molecular weight isoforms. For the first time, the distribution of these isoforms in serum and follicular fluid (FF) and their usefulness as biological markers for infertility investigations was studied.

dGEMRIC and subsequent T1 mapping of the hip at 1.5 Tesla: normative data on zonal and radial distribution in asymptomatic volunteers

To characterize the zonal distribution of three-dimensional (3D) T1 mapping in the hip joint of asymptomatic adult volunteers.

Quality of life in high-risk patients: comparison of transcatheter aortic valve implantation with surgical aortic valve replacement

OBJECTIVES To compare health-related quality of life (QoL) in patients undergoing transcatheter aortic valve implantation via transapical access (TA TAVI) with patients undergoing surgical aortic valve replacement (SAVR). METHODS One hundred and forty-four high-risk patients referred for aortic valve replacement underwent TAVI screening and were assigned to either TA TAVI (n = 51, age 79.7 ± 9.2 years, logistic EuroSCORE 26.5 ± 16.1%, 51% males) or SAVR (n = 93, age 81.1 ± 5.3 years, logistic EuroSCORE 12.1 ± 9.3%, 42% males) by the interdisciplinary heart team. QoL was assessed using the Short Form 36 (SF-36) Health Survey Questionnaire and the Hospital Anxiety and Depression Scale. Furthermore, current living conditions and the degree of independence at home were evaluated. RESULTS Patients undergoing TA TAVI were at higher risk as assessed by EuroSCORE (26.5 ± 16 vs. 12.1 ± 9, P < 0.001) and STS score (6.7 ± 4 vs. 4.4 ± 3, P < 0.001) compared with SAVR patients. At the 30-day follow-up, the rate of mortality was similar and amounted to 7.8% for TA TAVI and 7.5% for SAVR patients and raised to 25.5% in TA TAVI and 18.3% in SAVR patients after a follow-up period of 15 ± 10 months. Assessment of QoL revealed no differences in terms of anxiety and depression between TA TAVI and SAVR patients. The SF-36 mental health metascore was similar in both groups (65.6 ± 19 vs. 68.8 ± 22, P = 0.29), while a significant difference was observed in the physical health metascore (49.7 ± 21 vs. 62.0 ± 21, P = 0.015). After adjustment for baseline characteristics, this difference disappeared. However, every added point in the preoperative risk assessment with the STS score decreased the SF-36 physical health dimension by two raw points at the follow-up assessment. CONCLUSIONS Selected high-risk patients undergoing TAVI by using a transapical access achieve similar clinical outcomes and QoL compared with patients undergoing SAVR. Increased STS scores predict worse QoL outcomes.

Quantitative measurements in 3-dimensional datasets of mouse lymph nodes resolve organ-wide functional dependencies

Deep tissue imaging has become state of the art in biology, but now the problem is to quantify spatial information in a global, organ-wide context. Although access to the raw data is no longer a limitation, the computational tools to extract biologically useful information out of these large data sets is still catching up. In many cases, to understand the mechanism behind a biological process, where molecules or cells interact with each other, it is mandatory to know their mutual positions. We illustrate this principle here with the immune system. Although the general functions of lymph nodes as immune sentinels are well described, many cellular and molecular details governing the interactions of lymphocytes and dendritic cells remain unclear to date and prevent an in-depth mechanistic understanding of the immune system. We imaged ex vivo lymph nodes isolated from both wild-type and transgenic mice lacking key factors for dendritic cell positioning and used software written in MATLAB to determine the spatial distances between the dendritic cells and the internal high endothelial vascular network. This allowed us to quantify the spatial localization of the dendritic cells in the lymph node, which is a critical parameter determining the effectiveness of an adaptive immune response.

Drug targeting using OX7-immunoliposomes: correlation between Thy1.1 antigen expression and tissue distribution in the rat

OX7 monoclonal antibody F((ab')2) fragments directed against Thy1.1 antigen can be used for drug targeting by coupling to the surface of drug-loaded liposomes. Such OX7-conjugated immunoliposomes (OX7-IL) were used recently for drug delivery to rat glomerular mesangial cells, which are characterized by a high level of Thy1.1 antigen expression. In the present study, the relationship between OX7-IL tissue distribution and target Thy1.1 antigen localization in different organs in rat was investigated. Western blot and immunohistofluorescence analysis revealed a very high Thy1.1 expression in brain cortex and striatum, thymus and renal glomeruli. Moderate Thy1.1 levels were observed in the collecting ducts of kidney, lung tissue and spleen. Thy1.1 was not detected in liver and heart. There was a poor correlation between Thy1.1 expression levels and organ distribution of fluorescence- or (14)C-labeled OX7-IL. The highest overall organ density of OX7-IL was observed in the spleen, followed by lung, liver and kidney. Heart and brain remained negative. With respect to intra-organ distribution, a localized and distinct signal was observed in renal glomerular mesangial cells only. As a consequence, acute pharmacological (i.e. toxic) effects of doxorubicin-loaded OX7-IL were limited to renal glomeruli. The competition with unbound OX7 monoclonal antibody F((ab')2) fragments demonstrated that the observed tissue distribution and acute pharmacological effects of OX7-IL were mediated specifically by the conjugated OX7 antibody. It is concluded that both the high target antigen density and the absence of endothelial barriers are needed to allow for tissue-specific accumulation and pharmacological effects of OX7-IL. The liposomal drug delivery strategy used is therefore specific toward renal glomeruli and can be expected to reduce the risk of unwanted side effects in other tissues.

Neotethys closure history of Anatolia: insights from 40Ar–39Ar geochronology and P–T estimation in high pressure metasedimentary rocks

The multiple high-pressure (HP), low-temperature (LT) metamorphic units of Western and Central Anatolia offer a great opportunity to investigate the subduction- and continental accretion-related evolution of the eastern limb of the long-lived Aegean subduction system. Recent reports of the HP–LT index mineral Fe-Mg-carpholite in three metasedimentary units of the Gondwana-derived Anatolide–Tauride continental block (namely the Afyon Zone, the Ören Unit and the southern Menderes Massif) suggest a more complicated scenario than the single-continental accretion model generally put forward in previous studies. This study presents the first isotopic dates (white mica 40Ar–39Ar geochronology), and where possible are combined with P–T estimates (chlorite thermometry, phengite barometry, multi-equilibrium thermobarometry), on carpholite-bearing rocks from these three HP–LT metasedimentary units. It is shown that, in the Afyon Zone, carpholite-bearing assemblages were retrogressed through greenschist-facies conditions at c. 67–62 Ma. Early retrograde stages in the Ören Unit are dated to 63–59 Ma. In the Kurudere–Nebiler Unit (HP Mesozoic cover of the southern Menderes Massif), HP retrograde stages are dated to c. 45 Ma, and post-collisional cooling to c. 26 Ma. These new results support that the Ören Unit represents the westernmost continuation of the Afyon Zone, whereas the Kurudere–Nebiler Unit correlates with the Cycladic Blueschist Unit of the Aegean Domain. In Western Anatolia, three successive HP–LT metamorphic belts thus formed: the northernmost Tavşanlı Zone (c. 88–82 Ma), the Ören–Afyon Zone (between 70 and 65 Ma), and the Kurudere–Nebiler Unit (c. 52–45 Ma). The southward younging trend of the HP–LT metamorphism from the upper and internal to the deeper and more external structural units, as in the Aegean Domain, points to the persistence of subduction in Western Anatolia between 93–90 and c. 35 Ma. After the accretion of the Menderes–Tauride terrane, in Eocene times, subduction stopped, leading to continental collision and associated Barrovian-type metamorphism. Because, by contrast, the Aegean subduction did remain active due to slab roll-back and trench migration, the eastern limb (below Southwestern Anatolia) of the Hellenic slab was dramatically curved and consequently teared. It therefore is suggested that the possibility for subduction to continue after the accretion of buoyant (e.g. continental) terranes probably depends much on palaeogeography.

Radiometric Method for Emissivity Retrieval in High Reflective Materials

High reflective materials in the microwave region play a very important role in the realization of antenna reflectors for a broad range of applications, including radiometry. These reflectors have a characteristic emissivity which needs to be characterized accurately in order to perform a correct radiometric calibration of the instrument. Such a characterization can be performed by using open resonators, waveguide cavities or by radiometric measurements. The latter consists of comparative radiometric observations of absorbers, reference mirrors and the sample under test, or using the cold sky radiation as a direct reference source. While the first two mentioned techniques are suitable for the characterization of metal plates and mirrors, the latter has the advantages to be also applicable to soft materials. This paper describes how, through this radiometric techniques, it is possible to characterize the emissivity of the sample relative to a reference mirror and how to characterize the absolute emissivity of the latter by performing measurements at different incident angles. The results presented in this paper are based on our investigations on emissivity of a multilayer insulation material (MLI) for space mission, at the frequencies of 22 and 90 GHz.

Measurement of the Z/ѵ* boson transverse momentum distribution in pp collisions at √s = 7 TeV with the ATLAS detector

This paper describes a measurement of the Z/ѵ* boson transverse momentum spectrum using ATLAS proton-proton collision data at a centre-of-mass energy of √s = 7 TeV at the LHC. The measurement is performed in the Z/ѵ* → e+e− and Z/ѵ* → μ+μ− channels, using data corresponding to an integrated luminosity of 4.7 fb−1. Normalized differential cross sections as a function of the Z/ѵ* boson transverse momentum are measured for transverse momenta up to 800 GeV. The measurement is performed inclusively for Z/ѵ* rapidities up to 2.4, as well as in three rapidity bins. The channel results are combined, compared to perturbative and resummed QCD calculations and used to constrain the parton shower parameters of Monte Carlo generators.