A Formalism for Scattering of Complex Composite Structures. 2 Distributed Reference Points

Recently we developed a formalism for the scattering from linear and acyclic branched structures build of mutually non-interacting sub-units.{[}C. Svaneborg and J. S. Pedersen, J. Chem. Phys. 136, 104105 (2012){]} We assumed each sub-unit has reference points associated with it. These are well defined positions where sub-units can be linked together. In the present paper, we generalize the formalism to the case where each reference point can represent a distribution of potential link positions. We also present a generalized diagrammatic representation of the formalism. Scattering expressions required to model rods, polymers, loops, flat circular disks, rigid spheres and cylinders are derived. and we use them to illustrate the formalism by deriving the generic scattering expression for micelles and bottle brush structures and show how the scattering is affected by different choices of potential link positions.Comment: Paper no. 2 of a serie

A Formalism for Scattering of Complex Composite Structures. 1 Applications to Branched Structures of Asymmetric Sub-Units

We present a formalism for the scattering of an arbitrary linear or acyclic branched structure build by joining mutually non-interacting arbitrary functional sub-units. The formalism consists of three equations expressing the structural scattering in terms of three equations expressing the sub-unit scattering. The structural scattering expressions allows a composite structures to be used as sub-units within the formalism itself. This allows the scattering expressions for complex hierarchical structures to be derived with great ease. The formalism is furthermore generic in the sense that the scattering due to structural connectivity is completely decoupled from internal structure of the sub-units. This allows sub-units to be replaced by more complex structures. We illustrate the physical interpretation of the formalism diagrammatically. By applying a self-consistency requirement we derive the pair distributions of an ideal flexible polymer sub-unit. We illustrate the formalism by deriving generic scattering expressions for branched structures such as stars, pom-poms, bottle-brushes, and dendrimers build out of asymmetric two-functional sub-units.Comment: Complete rewrite generalizing the formalism to arbitrary functional sub-units and including a new Feynmann like diagrammatic interpretatio

Noise Induced Coherence in Neural Networks

We investigate numerically the dynamics of large networks of $N$ globally pulse-coupled integrate and fire neurons in a noise-induced synchronized state. The powerspectrum of an individual element within the network is shown to exhibit in the thermodynamic limit ($N\to \infty$) a broadband peak and an additional delta-function peak that is absent from the powerspectrum of an isolated element. The powerspectrum of the mean output signal only exhibits the delta-function peak. These results are explained analytically in an exactly soluble oscillator model with global phase coupling.Comment: 4 pages ReVTeX and 3 postscript figure

Improving advanced intraoperative MRI methods during pediatric neurosurgery

Advanced intraoperative MR images (ioMRI) acquired during the resection of pediatric brain tumors could offer additional physiological information to preserve healthy tissue. With this work, we aimed to develop a protocol for ioMRI with increased sensitivity for arterial spin labeling (ASL) and diffusion MRI (dMRI), optimized for patient positioning regularly used in the pediatric neurosurgery setting. For ethical reasons, ASL images were acquired in healthy adult subjects that were imaged in the prone and supine position. After this, the ASL cerebral blood flow (CBF) was quantified and compared between both positions. To evaluate the impact of the RF coils setups on image quality, we compared different setups (two vs. four RF coils) by looking at T1-weighted (T1w) signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), as well as undertaking a qualitative evaluation of T1w, T2w, ASL, and dMR images. Mean ASL CBF did not differ between the surgical prone and supine positions in any of the investigated regions of interest or the whole brain. T1w SNR (gray matter: p = 0.016, 34% increase; white matter: p = 0.016, 32% increase) and CNR were higher (p = 0.016) in the four versus two RF coils setups (18.0 ± 1.8 vs. 13.9 ± 1.8). Qualitative evaluation of T1w, T2w, ASL, and dMR images resulted in acceptable to good image quality and did not differ statistically significantly between setups. Only the nonweighted diffusion image maps and corticospinal tract reconstructions yielded higher image quality and reduced susceptibility artifacts with four RF coils. Advanced ioMRI metrics were more precise with four RF coils as the standard deviation decreased. Taken together, we have investigated the practical use of advanced ioMRI during pediatric neurosurgery. We conclude that ASL CBF quantification in the surgical prone position is valid and that ASL and dMRI acquisition with two RF coils can be performed adequately for clinical use. With four versus two RF coils, the SNR of the images increases, and the sensitivity to artifacts reduces

Coupling GIS and LCA for biodiversity assessments of land use

Geospatial details about land use are necessary to assess its potential impacts on biodiversity. Geographic information systems (GIS) are adept at modeling land use in a spatially explicit manner, while life cycle assessment (LCA) does not conventionally utilize geospatial information. This study presents a proof-of-concept approach for coupling GIS and LCA for biodiversity assessments of land use and applies it to a case study of ethanol production from agricultural crops in California. GIS modeling was used to generate crop production scenarios for corn and sugar beets that met a range of ethanol production targets. The selected study area was a four-county region in the southern San Joaquin Valley of California, USA. The resulting land use maps were translated into maps of habitat types. From these maps, vectors were created that contained the total areas for each habitat type in the study region. These habitat compositions are treated as elementary input flows and used to calculate different biodiversity impact indicators in a second paper (Geyer et al., submitted). Ten ethanol production scenarios were developed with GIS modeling. Current land use is added as baseline scenario. The parcels selected for corn and sugar beet production were generally in different locations. Moreover, corn and sugar beets are classified as different habitat types. Consequently, the scenarios differed in both the habitat types converted and in the habitat types expanded. Importantly, land use increased nonlinearly with increasing ethanol production targets. The GIS modeling for this study used spatial data that are commonly available in most developed countries and only required functions that are provided in virtually any commercial or open-source GIS software package. This study has demonstrated that GIS-based inventory modeling of land use allows important refinements in LCA theory and practice. Using GIS, land use can be modeled as a geospatial and nonlinear function of output. For each spatially explicit process, land use can be expressed within the conventional structure of LCA methodology as a set of elementary input flows of habitat types

Conformational flexibility of RNA polymerase III during transcriptional elongation

RNA polymerase (Pol) III is responsible for the transcription of genes encoding small RNAs, including tRNA, 5S rRNA and U6 RNA. Here, we report the electron cryomicroscopy structures of yeast Pol III at 9.9 Å resolution and its elongation complex at 16.5 Å resolution. Particle sub-classification reveals prominent EM densities for the two Pol III-specific subcomplexes, C31/C82/C34 and C37/C53, that can be interpreted using homology models. While the winged-helix-containing C31/C82/C34 subcomplex initiates transcription from one side of the DNA-binding cleft, the C37/C53 subcomplex accesses the transcription bubble from the opposite side of this cleft. The transcribing Pol III enzyme structure not only shows the complete incoming DNA duplex, but also reveals the exit path of newly synthesized RNA. During transcriptional elongation, the Pol III-specific subcomplexes tightly enclose the incoming DNA duplex, which likely increases processivity and provides structural insights into the conformational switch between Pol III-mediated initiation and elongation

Erufosine, a novel alkylphosphocholine, in acute myeloid leukemia: single activity and combination with other antileukemic drugs

Alkylphosphocholines represent a new class of cytostatic drugs with a novel mode of action. Erufosine (ErPC3), the first compound of this class that can be administered intravenously, has recently been shown to be active against human tumor and leukemic cell lines. METHODS: In order to evaluate the antileukemic potential of ErPC3 in acute myeloid leukemia (AML) the lethal concentration 50% (LC 50) was determined using WST-1 assay. For analysis of cell death, staining for Annexin V and activated caspase 3 was performed. An interaction analysis was performed by calculation of combination index and construction of isobolograms. RESULTS: The LC 50 was 7.4 microg/ml after 24 h and 3.2 microg/ml after 72 h in HL 60 cells and 30.1 and 8.6 microg/ml, respectively, in 19 fresh samples from patients with AML. ErPC3 was found to be cytotoxic in HL60 cells with distinct activation of caspase 3. ErPC3 was not cross-resistant with cytarabine, idarubicine and etoposide as shown by the linear relation of respective LC 50s. The latter agents, however, exerted an additive cytotoxicity in combination with ErPC3 as revealed by isobologram analysis and combination index, although results are uneven for idarubicine. CONCLUSION: Based on these data ErPC3 appears as a novel antileukemic candidate drug, which needs to be explored further in the treatment of AML

Practical examination of bystanders performing Basic Life Support in Germany: a prospective manikin study

<p>Abstract</p> <p>Background</p> <p>In an out-of-hospital emergency situation bystander intervention is essential for a sufficient functioning of the chain of rescue. The basic measures of cardiopulmonary resuscitation (Basic Life Support – BLS) by lay people are therefore definitely part of an effective emergency service of a patient needing resuscitation. Relevant knowledge is provided to the public by various course conceptions. The learning success concerning a one day first aid course ("LSM" course in Germany) has not been much investigated in the past. We investigated to what extent lay people could perform BLS correctly in a standardised manikin scenario. An aim of this study was to show how course repetitions affected success in performing BLS.</p> <p>Methods</p> <p>The "LSM course" was carried out in a standardised manner. We tested prospectively 100 participants in two groups (<b>Group 1: </b>Participants with previous attendance of a BLS course; <b>Group 2: </b>Participants with no previous attendance of a BLS course) in their practical abilities in BLS after the course. Success parameter was the correct performance of BLS in accordance with the current ERC guidelines.</p> <p>Results</p> <p>Twenty-two (22%) of the 100 investigated participants obtained satisfactory results in the practical performance of BLS. Participants with repeated participation in BLS obtained significantly better results (<b>Group 1: </b>32.7% vs. <b>Group 2: </b>10.4%; p < 0.01) than course participants with no relevant previous knowledge.</p> <p>Conclusion</p> <p>Only 22% of the investigated participants at the end of a "LSM course" were able to perform BLS satisfactorily according to the ERC guidelines. Participants who had previously attended comparable courses obtained significantly better results in the practical test. Through regular repetitions it seems to be possible to achieve, at least on the manikin, an improvement of the results in bystander resuscitation and, consequently, a better patient outcome. To validate this hypothesis further investigations are recommended by specialised societies.</p

Characterization of the Single Stranded DNA Binding Protein SsbB Encoded in the Gonoccocal Genetic Island

Background: Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in genetic islands of different proteobacteria. This cluster encodes DNA-processing enzymes such as the ParA and ParB partitioning proteins, the TopB topoisomerase, and four conserved hypothetical proteins. The SsbB homologs found in these clusters form a family separated from other ssDNA binding proteins. Methodology/Principal Findings: In contrast to most other SSBs, SsbB did not complement the Escherichia coli ssb deletion mutant. Purified SsbB forms a stable tetramer. Electrophoretic mobility shift assays and fluorescence titration assays, as well as atomic force microscopy demonstrate that SsbB binds ssDNA specifically with high affinity. SsbB binds single-stranded DNA with minimal binding frames for one or two SsbB tetramers of 15 and 70 nucleotides. The binding mode was independent of increasing Mg 2+ or NaCl concentrations. No role of SsbB in ssDNA secretion or DNA uptake could be identified, but SsbB strongly stimulated Topoisomerase I activity