Particle production and equilibrium properties within a new hadron transport approach for heavy-ion collisions

The microscopic description of heavy-ion reactions at low beam energies is achieved within hadronic transport approaches. In this article a new approach SMASH (Simulating Many Accelerated Strongly-interacting Hadrons) is introduced and applied to study the production of non-strange particles in heavy-ion reactions at $E_{\rm kin}=0.4-2A$ GeV. First, the model is described including details about the collision criterion, the initial conditions and the resonance formation and decays. To validate the approach, equilibrium properties such as detailed balance are presented and the results are compared to experimental data for elementary cross sections. Finally results for pion and proton production in C+C and Au+Au collisions is confronted with HADES and FOPI data. Predictions for particle production in $\pi+A$ collisions are made.Comment: 30 pages, 30 figures, replaced with published version; only minor change

Identification of proteins binding coding and non-coding human RNAs using protein microarrays

Background: The regulation and function of mammalian RNAs has been increasingly appreciated to operate via RNA-protein interactions. With the recent discovery of thousands of novel human RNA molecules by high-throughput RNA sequencing, efficient methods to uncover RNA-protein interactions are urgently required. Existing methods to study proteins associated with a given RNA are laborious and require substantial amounts of cell-derived starting material. To overcome these limitations, we have developed a rapid and large-scale approach to characterize binding of in vitro transcribed labeled RNA to ~9,400 human recombinant proteins spotted on protein microarrays. Results: We have optimized methodology to probe human protein microarrays with full-length RNA molecules and have identified 137 RNA-protein interactions specific for 10 coding and non-coding RNAs. Those proteins showed strong enrichment for common human RNA binding domains such as RRM, RBD, as well as K homology and CCCH type zinc finger motifs. Previously unknown RNA-protein interactions were discovered using this technique, and these interactions were biochemically verified between TP53 mRNA and Staufen1 protein as well as between HRAS mRNA and CNBP protein. Functional characterization of the interaction between Staufen 1 protein and TP53 mRNA revealed a novel role for Staufen 1 in preserving TP53 RNA stability. Conclusions: Our approach demonstrates a scalable methodology, allowing rapid and efficient identification of novel human RNA-protein interactions using RNA hybridization to human protein microarrays. Biochemical validation of newly identified interactions between TP53-Stau1 and HRAS-CNBP using reciprocal pull-down experiments, both in vitro and in vivo, demonstrates the utility of this approach to study uncharacterized RNA-protein interactions.Stem Cell and Regenerative Biolog

Isolation, Characterization, and Mapping of a Human Acid β-Galactosidase cDNA

A λgt11 human testicular cDNA library was screened with degenerate oligonucleotide probe mixtures based on amino acid sequence data generated from cyanogen bromide fragments and tryptic fragments of purified human β-galactosidase.Six positive clones were identified after screening 2 x 106 plaques. The sequences of these six clones were determined and found to be derived from two different cDNAs. The sequence of the longest of these cDNAs is nearly identical to that recently determined by Oshima et al. (1988). It codes for a 76-kD protein and all 11 peptides that were generated from the purified enzyme. The second clone is shorter by 393 bp in the central portion of the coding region. Analysis by Northern blotting revealed the presence of a single mRNA species of 2.45 kb in lymphoblasts and testicular tissue. It is deduced from the amino acid sequence data that proteolytic processing of the precursor form of β-galactosidase must occur by cleavage in the carboxy-terminal portion of the polypeptide perhaps around amino acid 530 at a uniquely hydrophilic sequence. Using a probe generated from the 3\u27 region of the cDNA, we have mapped the locus coding for human β-galactosidase to chromosome 3p21-3pter

Localization of HCN1 channels to presynaptic compartments: novel plasticity that may contribute to hippocampal maturation.

Increasing evidence supports roles for the current mediated by hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, I(h), in hippocampal maturation and specifically in the evolving changes of intrinsic properties as well as network responses of hippocampal neurons. Here, we describe a novel developmental plasticity of HCN channel expression in axonal and presynaptic compartments: HCN1 channels were localized to axon terminals of the perforant path (the major hippocampal afferent pathway) of immature rats, where they modulated synaptic efficacy. However, presynaptic expression and functions of the channels disappeared with maturation. This was a result of altered channel transport to the axons, because HCN1 mRNA and protein levels in entorhinal cortex neurons, where the perforant path axons originate, were stable through adulthood. Blocking action potential firing in vitro increased presynaptic expression of HCN1 channels in the perforant path, suggesting that network activity contributed to regulating this expression. These findings support a novel developmentally regulated axonal transport of functional ion channels and suggest a role for HCN1 channel-mediated presynaptic I(h) in hippocampal maturation

Experimental study of pedestrian flow through a bottleneck

In this work the results of a bottleneck experiment with pedestrians are presented in the form of total times, fluxes, specific fluxes, and time gaps. A main aim was to find the dependence of these values from the bottleneck width. The results show a linear decline of the specific flux with increasing width as long as only one person at a time can pass, and a constant value for larger bottleneck widths. Differences between small (one person at a time) and wide bottlenecks (two persons at a time) were also found in the distribution of time gaps.Comment: accepted for publication in J. Stat. Mec

An MPEG-7 scheme for semantic content modelling and filtering of digital video

Abstract Part 5 of the MPEG-7 standard specifies Multimedia Description Schemes (MDS); that is, the format multimedia content models should conform to in order to ensure interoperability across multiple platforms and applications. However, the standard does not specify how the content or the associated model may be filtered. This paper proposes an MPEG-7 scheme which can be deployed for digital video content modelling and filtering. The proposed scheme, COSMOS-7, produces rich and multi-faceted semantic content models and supports a content-based filtering approach that only analyses content relating directly to the preferred content requirements of the user. We present details of the scheme, front-end systems used for content modelling and filtering and experiences with a number of users

Particle production and equilibrium properties within a new hadron transport approach for heavy-ion collisions

The microscopic description of heavy-ion reactions at low beam energies is achieved within hadronic transport approaches. In this article a new approach called "Simulating Many Accelerated Strongly interacting Hadrons" (SMASH) is introduced and applied to study the production of nonstrange particles in heavy-ion reactions at Ekin=0.4A-2A GeV. First, the model is described including details about the collision criterion, the initial conditions and the resonance formation and decays. To validate the approach, equilibrium properties such as detailed balance are presented and the results are compared to experimental data for elementary cross sections. Finally results for pion and proton production in C+C and Au+Au collisions is confronted with data from the high-acceptance dielectron spectrometer (HADES) and FOPI. Predictions for particle production in π+A collisions are made

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations

This is the peer reviewed version of the following article: Bray, MS, Wu, J, Reed, BC, et al. Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations. Geobiology. 2017; 15: 678– 689. https://doi.org/10.1111/gbi.12239, which has been published in final form at https://doi.org/10.1111/gbi.12239. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.Reactive Fe(III) minerals can influence methane (CH4) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4 oxidation. The balance between Fe(III) reduction, methanogenesis, and CH4 oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4 fluxes to the atmosphere, thereby regulating the capacity for CH4 to warm the early Earth under the Faint Young Sun. We studied CH4 and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH4 oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH4 production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH4 oxidation, although some incubations displayed CH4-stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH4 as a greenhouse gas throughout the first half of Earth history

The Snail repressor recruits EZH2 to specific genomic sites through the enrollment of the lncRNA HOTAIR in epithelial-to-mesenchymal transition

The transcription factor Snail is a master regulator of cellular identity and epithelial-to-mesenchymal transition (EMT) directly repressing a broad repertoire of epithelial genes. How chromatin modifiers instrumental to its activity are recruited to Snail-specific binding sites is unclear. Here we report that the long non-coding RNA (lncRNA) HOTAIR (for HOX Transcript Antisense Intergenic RNA) mediates a physical interaction between Snail and enhancer of zeste homolog 2 (EZH2), an enzymatic subunit of the polycomb-repressive complex 2 and the main writer of chromatin-repressive marks. The Snail-repressive activity, here monitored on genes with a pivotal function in epithelial and hepatic morphogenesis, differentiation and cell-type identity, depends on the formation of a tripartite Snail/HOTAIR/EZH2 complex. These results demonstrate an lncRNA-mediated mechanism by which a transcriptional factor conveys a general chromatin modifier to specific genes, thereby allowing the execution of hepatocyte transdifferentiation; moreover, they highlight HOTAIR as a crucial player in the Snail-mediated EMT.Oncogene advance online publication, 25 July 2016; doi:10.1038/onc.2016.260