Monolithic focused reference beam x-ray holography

Fourier transform holography is a highly efficient and robust imaging method, suitable for single-shot imaging at coherent X-ray sources. In its common implementation, the image contrast is limited by the reference signal generated by a small pinhole aperture. Increased pinhole diameters improve the signal, whereas the resolution is diminished. Here we report a new concept to decouple the spatial resolution from the image contrast by employing a Fresnel zone plate to provide the reference beam. Superimposed on-axis images of distinct foci are separated with a novel algorithm. Our method is insensitive to mechanical drift or vibrations and allows for long integration times common at low-flux facilities like high harmonic generation sources. The application of monolithic focused reference beams improves the efficiency of high-resolution X-ray Fourier transform holography beyond all present approaches and paves the path towards sub-10 nm single-shot X-ray imaging

Occurrence and temporal variations of TMDD in the river Rhine, Germany

Background, aim, and scope: The chemical substance 2,4,7,9-tetramethyl-5-decyne-4,7-diol (TMDD) is a non-ionic surfactant used as an industrial defoaming agent and in various other applications. Its commercial name is Surynol 104® and the related ethoxylates are also available as Surfynol® 420, 440, 465 and 485 which are characterized by different grades of ethoxylation of TMDD at both hydroxyl functional groups. TMDD and its ethoxylates offer several advantages in waterborne industrial applications in coatings, inks, adhesives as well as in paper industries. TMDD and its ethoxylates can be expected to reach the aquatic environment due its widespread use and its physico-chemical properties. TMDD has previously been detected in several rivers of Germany with concentrations up to 2.5 µg/L. In the United States, TMDD was also detected in drinking water. However, detailed studies about its presence and distribution in the aquatic environment have not been carried out so far. The aim of the present study was the analysis of the spatial and temporal concentration variations of TMDD in the river Rhine at the Rheingütestation Worms (443.3 km). Moreover, the transported load in the Rhine was investigated during two entire days and 7 weeks between November 2007 and January 2008. Materials and methods: The sampling was carried out at three different sampling points across the river. Sampling point MWL1 is located in the left part of the river, MWL2 in the middle part, and MWL4 in the right part. One more sampling site (MWL3) was run by the monitoring station until the end of 2006, but was put out of service due to financial constrains. The water at the left side of the river Rhine (MWL1) is influenced by sewage from a big chemical plant in Ludwigshafen and by the sewage water from this city. The water at the right side of the river Rhine (MWL4) is largely composed of the water inflow from river Neckar, discharging into Rhine 14.9 km upstream from the sampling point and of communal and industrial wastewater from the city Mannheim. The water from the middle of the river (MWL2) is largely composed of water from the upper Rhine. Water samples were collected in 1-L bottles by an automatic sampler. The water samples were concentrated by use of solid-phase extraction (SPE) using Bond Elut PPL cartridges and quantified by use of gas chromatography-mass spectrometry (GC-MS). The quantification was carried out with the internal standard method. Based on these results, concentration variations were determined for the day profiles and week profiles. The total number of analyzed samples was 219. Results: The results of this study provide information on the temporal concentration variability of TMDD in river Rhine in a cross section at one particular sampling point (443.3 km). TMDD was detected in all analyzed water samples at high concentrations. The mean concentrations during the 2 days were 314 ng/L in MWL1, 246 ng/L in MWL2, and 286 ng/L in MWL4. The variation of concentrations was low in the day profiles. In the week profiles, a trend of increasing TMDD concentrations was detected particularly in January 2008, when TMDD concentrations reached values up to 1,330 ng/L in MWL1. The mean TMDD concentrations during the week profiles were 540 ng/L in MWL1, 484 ng/L in MWL2, and 576 ng/L in MWL4. The loads of TMDD were also determined and revealed to be comparable in all three sections of the river. The chemical plant located at the left side of the Rhine is not contributing additional TMDD to the river. The load of TMDD has been determined to be 62.8 kg/d on average during the entire period. By extrapolation of data obtained from seven week profiles the annual load was calculated to 23 t/a. Discussion: The permanent high TMDD concentrations during the investigation period indicate an almost constant discharge of TMDD into the river. This observation argues for effluents of municipal wastewater treatment plants as the most likely source of TMDD in the river. Another possible source might be the degradation of ethoxylates of TMDD (Surfynol® series 400), in the WWTPs under formation of TMDD followed by discharge into the river. TMDD has to be considered as a high-production-volume (HPV) chemical based on the high concentrations found in this study. In the United States, TMDD is already in the list of HPV chemicals from the Environmental Protection Agency (EPA). However, the amount of TMDD production in Europe is unknown so far and also the biodegradation rates of TMDD in WWTPs have not been investigated. Conclusions: TMDD was found in high concentrations during the entire sampling period in the Rhine river at the three sampling points. During the sampling period, TMDD concentrations remained constant in each part of the river. These results show that TMDD is uniformly distributed in the water collected at three sampling points located across the river. ‘Waves’ of exceptionally high concentrations of TMDD could not be detected during the sampling period. These results indicate that the effluents of WWTPs have to be considered as the most important sources of TMDD in river Rhine. Recommendations and perspectives: Based also on the occurrence of TMDD in different surface waters of Germany with concentrations up to 2,500 ng/L and its presence in drinking water in the USA, more detailed investigations regarding its sources and distribution in the aquatic environment are required. Moreover, the knowledge with respect to its ecotoxicity and its biodegradation pathway is scarce and has to be gained in more detail. Further research is necessary to investigate the rate of elimination of TMDD in municipal and industrial wastewater treatment plants in order to clarify the degradation rate of TMDD and to determine to which extent effluents of WWTPs contribute to the input of TMDD into surface waters. Supplementary studies are needed to clarify whether the ethoxylates of TMDD (known as Surfynol 400® series) are hydrolyzed in the aquatic environment resulting in formation of TMDD similar to the well known cleavage of nonylphenol ethoxylates into nonylphenols. The stability of TMDD under anaerobic conditions in groundwater is also unknown and should be studied

The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain

Abstract Background Cellular RNA polymerases (RNAPs) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-HC) plays a critical role in controlling the catalytic rate. Results Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-HN) is presented. The nanomechanical properties of BH-HN emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC). BH-HN displays functional properties that are distinct from BH-HC, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. Conclusions The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.</p

Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Non-standard errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Monolithic focused reference beam X ray holography

Fourier transform holography is a highly efficient and robust imaging method, suitable for single shot imaging at coherent X ray sources. In its common implementation, the image contrast is limited by the reference signal generated by a small pinhole aperture. Increased pinhole diameters improve the signal, whereas the resolution is diminished. Here we report a new concept to decouple the spatial resolution from the image contrast by employing a Fresnel zone plate to provide the reference beam. Superimposed on axis images of distinct foci are separated with a novel algorithm. Our method is insensitive to mechanical drift or vibrations and allows for long integration times common at low flux facilities like high harmonic generation sources. The application of monolithic focused reference beams improves the efficiency of high resolution X ray Fourier transform holography beyond all present approaches and paves the path towards sub 10[thinsp]nm single shot X ray imagin

Accelerating Screening of 3D Protein Data with a Graph Theoretical Approach

Motivation. The Dictionary of Interfaces in Proteins (DIP) is a data base collecting the three-dimensional structure of interacting parts of proteins that are called patches. It serves as a repository, in which patches similar to given query patches can be found. The computation of the similarity of two patches is time consuming and traversing the entire DIP requires some hours. In this work we address the question how the patches similar to a given query, can be identified by scanning only a small part of DIP. The answer to this question requires the investigation of the distribution of the similarity of patches. Results. The scor