ALBERT

Description: : We introduce PHOXTRACK (PHOsphosite-X-TRacing Analysis of Causal Kinases), a user-friendly freely available software tool for analyzing large datasets of post-translational modifications of proteins, such as phosphorylation, which are commonly gained by mass spectrometry detection. In contrast to other currently applied data analysis approaches, PHOXTRACK uses full sets of quantitative proteomics data and applies non-parametric statistics to calculate whether defined kinase-specific sets of phosphosite sequences indicate statistically significant concordant differences between various biological conditions. PHOXTRACK is an efficient tool for extracting post-translational information of comprehensive proteomics datasets to decipher key regulatory proteins and to infer biologically relevant molecular pathways. Availability: PHOXTRACK will be maintained over the next years and is freely available as an online tool for non-commercial use at http://phoxtrack.molgen.mpg.de . Users will also find a tutorial at this Web site and can additionally give feedback at https://groups.google.com/d/forum/phoxtrack-discuss . Contact: sauer@molgen.mpg.de . Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser ( http://genome.ucsc.edu/ ) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new ‘multi-region’ track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.

Description: Mountainous headwaters consist of different landscape units including forests, meadows and wetlands. In these headwaters it is unclear which landscape units contribute what percentage to baseflow. In this study, we analysed spatiotemporal differences in baseflow isotope and hydrochemistry to identify catchment-scale runoff contribution. Three baseflow snapshot sampling campaigns were performed in the Swiss pre-alpine headwater catchment the Zwäckentobel (4.25 km 2 ) and six of its adjacent subcatchments. The spatial and temporal variability of δ 2 H, Ca, DOC, AT, pH, SO 4 , Mg, and H 4 SiO 4 of streamflow, groundwater and spring water samples was analysed and related to catchment area and wetland percentage using bivariate and multivariate methods. Our study found that in the six subcatchments, with variable arrangements of landscape units, the inter- and intra catchment variability of isotopic and hydrochemical compositions was small and generally not significant. Stream samples were distinctly different from shallow groundwater. An upper spring zone located near the water divide above 1400 m and a larger wetland were identified by their distinct spatial isotopic and hydrochemical composition. The upstream wetland percentage was not correlated to the hydrochemical streamflow composition, suggesting that wetlands were less connected and act as passive features with a negligible contribution to baseflow runoff. The isotopic and hydrochemical composition of baseflow changed slightly from the upper spring zone towards the subcatchment outlets and corresponded to the signature of deep groundwater. Our results confirm the need and benefits of spatially distributed snapshot sampling to derive process understanding of heterogeneous headwaters during baseflow. This article is protected by copyright. All rights reserved.

Description: The lock-in amplifier is a critical component in many different types of experiments, because of its ability to reduce spurious or environmental noise components by restricting detection to a single frequency and phase. One example application is pump-probe microscopy, a multiphoton technique that leverages excited-state dynamics for imaging contrast. With this application in mind, we present here the design and implementation of a high-speed lock-in amplifier on the field-programmable gate array (FPGA) coprocessor of a data acquisition board. The most important advantage is the inherent ability to filter signals based on more complex modulation patterns. As an example, we use the flexibility of the FPGA approach to enable a novel pump-probe detection scheme based on spread-spectrum communications techniques.

Description: ABSTRACT We explore the fluvial response to faulting in three low-gradient, sand-bed rivers in southeastern Louisiana, USA, that flow across active normal faults from footwall (upstream) to hangingwall (downstream). We calculate sinuosity, migration rate and migration direction in order to identify anomalies spatially associated with fault scarps. In two of the rivers we model 1-D steady water flow to identify anomalies in surface water slope, width-to-depth ratio, and shear stress. In each of these rivers there is one location where flow modeling suggests potential channel incision through the footwall, as indicated by relatively high surface water slopes and shear stress values. In one of these footwall locations, the river straightens and width-to-depth ratios decrease, likely contributing to higher surface water slopes and shear stress. This is in contrast to previous studies that have proposed increased sinuosity across fault footwalls and decreased sinuosity across hangingwalls. However, in two hangingwall locations we also observe relatively less sinuous channels. Other planform changes on the hangingwall include topographic steering of channels along and towards the fault and one example of an avulsion. The most notable anomaly in migration rate occurs on the hangingwall of a fault where a river has cut off a meander loop. Although fluvial response to faulting varies here, comparatively large and small channels exhibit similar responses. Further, Pleistocene fault slip rates are orders of magnitude lower than the channel migration rates, suggesting that faulting should not be a major influence on the fluvial evolution. Nonetheless, notable channel anomalies exist near faults, suggesting that recent fault slip rates are higher than Pleistocene rates, and/or that low-gradient alluvial channels are more sensitive to faulting than previous studies have suggested. Rivers appear to be influenced by faulting in this setting, however background rates of meander loop cut-off may be just as influential as faulting. This article is protected by copyright. All rights reserved.

Description: Author(s): Anubhav Jain, Geoffroy Hautier, Shyue Ping Ong, Charles J. Moore, Christopher C. Fischer, Kristin A. Persson, and Gerbrand Ceder Standard approximations to the density functional theory exchange-correlation functional have been extraordinary successful, but calculating formation enthalpies of reactions involving compounds with both localized and delocalized electronic states remains challenging. In this work we examine the sh... [Phys. Rev. B 84, 045115] Published Tue Jul 12, 2011

Description: A straightforward synthesis utilizing the ring-opening metathesis polymerization (ROMP) reaction is described for acid-triggered N,O-chelating ruthenium-based pre-catalysts bearing one or two 8-quinolinolate ligands. The innovative pre-catalysts were tested regarding their behavior in ROMP and especially for their use in the synthesis of poly(dicyclopentadiene) (pDCPD). Bearing either the common phosphine leaving ligand in the first and second Grubbs olefin metathesis catalysts, or the Ru–O bond cleavage for the next Hoveyda-type catalysts, this work is a step forward towards the control of polymer functionalization and living or switchable polymerizations. Beilstein J. Org. Chem. 2016, 12, 154–165. doi:10.3762/bjoc.12.17

Description: The Lower Rhine Embayment in Central Europe hosts a rift system that has very low deformation rates. The faults in this area have slip rates of less than 0.1 mm yr –1 , which does not allow to investigate ongoing tectonic deformation with geodetic techniques, unless they cover very long time spans. Instrumental seismicity does only cover a small fraction of the very long earthquake recurrence intervals of several thousands of years. Palaeoseismological studies are needed to constrain slip rates and the earthquake history of such faults. Destructive earthquakes are rare in the study area, but did occur in historic times. In 1755/1756, a series of strong earthquakes caused significant destruction in the city of Düren (Germany) and the surrounding areas. In this study we document palaeoseismological data from the nearby Rurrand Fault. In contrast to earlier studies on the same fault, we found evidence for a surface rupturing earthquake in the Holocene, and we identified at least one more surface rupturing event. Our study shows that the Rurrand Fault currently accommodates deformation in earthquakes rather than by creeping. The coseismic offsets were determined to be between less than 0.5 m per event. We assign maximum possible magnitudes of M w 5.9–6.8 for the Rurrand Fault and a slip rate of at least 0.02–0.03 mm yr –1 for the last ~130–50 kyr. The surface ruptures did not occur at the main fault trace that has a clear morphological expression due to older tectonic motions, but on a younger fault strand in the hanging wall of the main fault. Terrain analyses based on 1 m resolution airborne LiDAR data have been used to image the subtle morphological expression of this young fault zone. Georadar and electric resistivity tomography were applied to image the fault zone at depth and to test if these shallow geophysical methods can be used to identify and trace the fault zone. Georadar failed to produce reliable results, but geoelectrics were successfully applied and allowed us to retrieve slip rate estimates. Our results indicate that the Düren 1755/1756 earthquakes did not produce surface ruptures at the Rurrand Fault, either because they did not rupture the surface at all, or because they occurred at another, neighbouring fault.

Description: More diverse communities have been shown to have higher and more temporally stable ecosystem functioning than less diverse ones, suggesting they should also have a consistently higher level of functioning over time. Diverse communities could maintain consistently high function because the species driving function change over time (functional turnover) or because they are more likely to contain key species with temporally stable functioning. Across 7 y in a large biodiversity experiment, we show that more diverse plant communities had consistently higher productivity, that is, a higher level of functioning over time. We identify the mechanism for this as turnover in the species driving biomass production; this was substantial, and species that were rare in some years became dominant and drove function in other years. Such high turnover allowed functionally more diverse communities to maintain high biomass over time and was associated with higher levels of complementarity effects in these communities. In contrast, turnover in communities composed of functionally similar species did not promote high biomass production over time. Thus, turnover in species promotes consistently high ecosystem function when it sustains functionally complementary interactions between species. Our results strongly reinforce the argument for conservation of high biodiversity.

Description: Climate models show that particles formed by nucleation can affect cloud cover and, therefore, the earth's radiation budget. Measurements worldwide show that nucleation rates in the atmospheric boundary layer are positively correlated with concentrations of sulfuric acid vapor. However, current nucleation theories do not correctly predict either the observed nucleation...