Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation

BACKGROUND: Overlapping transcripts in antisense orientation have the potential to form double-stranded RNA (dsRNA), a substrate for a number of different RNA-modification pathways. One prominent route for dsRNA is its breakdown by Dicer enzyme complexes into small RNAs, a pathway that is widely exploited by RNA interference technology to inactivate defined genes in transgenic lines. The significance of this pathway for endogenous gene regulation remains unclear. RESULTS: We have examined transcription data for overlapping gene pairs in Arabidopsis thaliana. On the basis of an analysis of transcripts with coding regions, we find the majority of overlapping gene pairs to be convergently overlapping pairs (COPs), with the potential for dsRNA formation. In all tissues, COP transcripts are present at a higher frequency compared to the overall gene pool. The probability that both the sense and antisense copy of a COP are co-transcribed matches the theoretical value for coexpression under the assumption that the expression of one partner does not affect the expression of the other. Among COPs, we observe an over-representation of spliced (intron-containing) genes (90%) and of genes with alternatively spliced transcripts. For loci where antisense transcripts overlap with sense transcript introns, we also find a significant bias in favor of alternative splicing and variation of polyadenylation. CONCLUSION: The results argue against a predominant RNA degradation effect induced by dsRNA formation. Instead, our data support alternative roles for dsRNAs. They suggest that at least for a subgroup of COPs, antisense expression may induce alternative splicing or polyadenylation

Toy Model for Pion Production II: The role of three-particle singularities

The influence of three-particle breakup singularities on s-wave meson production in nucleon-nucleon collisions is studied within the distorted wave Born approximation. This study is based on a simple scalar model for the two-nucleon interaction and the production mechanism. An algorithm for the exact numerical treatment of the inherent three-body cuts, together with its straightforward implementation is presented. It is also shown that two often-used approximations to avoid the calculation of the three-body breakup are not justified. The possible impact on pion production observables is discussed.Comment: 14 pages, 6 figure

Cultural intermediaries and the circuit of culture : the digital ambassadors project in Johannesburg, South Africa

Abstract: The question raised by Cheney and Christensen (2001) as to “what a non-Western, nonmanagerial and non-rationalist form of public relations will look like” (p.182), together with the call made by Gregory (2014) for public relations practitioners (PRPs) to be active social change agents, motivated this paper. The aim of this research is to follow a culture-centred approach and apply the circuit of culture (Curtin & Gaither, 2005) to investigate the meanings that young people (aged 18 to 34), as cultural intermediaries, ascribe to their participation in a digital empowerment project implemented by the City of Johannesburg, South Africa. This research forms part of a larger, ongoing multi-disciplinary research project..

An overview of real-world data sources for oncology and considerations for research

Generating evidence on the use, effectiveness, and safety of new cancer therapies is a priority for researchers, health care providers, payers, and regulators given the rapid pace of change in cancer diagnosis and treatments. The use of real-world data (RWD) is integral to understanding the utilization patterns and outcomes of these new treatments among patients with cancer who are treated in clinical practice and community settings. An initial step in the use of RWD is careful study design to assess the suitability of an RWD source. This pivotal process can be guided by using a conceptual model that encourages predesign conceptualization. The primary types of RWD included are electronic health records, administrative claims data, cancer registries, and specialty data providers and networks. Careful consideration of each data type is necessary because they are collected for a specific purpose, capturing a set of data elements within a certain population for that purpose, and they vary by population coverage and longitudinality. In this review, the authors provide a high-level assessment of the strengths and limitations of each data category to inform data source selection appropriate to the study question. Overall, the development and accessibility of RWD sources for cancer research are rapidly increasing, and the use of these data requires careful consideration of composition and utility to assess important questions in understanding the use and effectiveness of new therapies

Calibration of Plastic Phoswich Detectors for Charged Particle Detection

The response of an array of plastic phoswich detectors to ions of $1\le Z\le 18$ has been measured from $E/A$=12 to 72 MeV. The detector response has been parameterized by a three parameter fit which includes both quenching and high energy delta-ray effects. The fits have a mean variation of $\le 4\%$ with respect to the data.Comment: 17 pages, 5 figure

Tilt order parameters, polarity and inversion phenomena in smectic liquid crystals

The order parameters for the phenomenological description of the smectic-{\it A} to smectic-{\it C} phase transition are formulated on the basis of molecular symmetry and structure. It is shown that, unless the long molecular axis is an axis of two-fold or higher rotational symmetry, the ordering of the molecules in the smectic-{\it C} phase gives rise to more than one tilt order parameter and to one or more polar order parameters. The latter describe the indigenous polarity of the smectic-{\it C} phase, which is not related to molecular chirality but underlies the appearance of spontaneous polarisation in chiral smectics. A phenomenological theory of the phase transition is formulated by means of a Landau expansion in two tilt order parameters (primary and secondary) and an indigenous polarity order parameter. The coupling among these order parameters determines the possibility of sign inversions in the temperature dependence of the spontaneous polarisation and of the helical pitch observed experimentally for some chiral smectic-{\it $C^{\ast}$} materials. The molecular interpretation of the inversion phenomena is examined in the light of the new formulation.Comment: 12 pages, 5 figures, RevTe

Nucleon Polarizabilities from Deuteron Compton Scattering within a Green's-Function Hybrid Approach

We examine elastic Compton scattering from the deuteron for photon energies ranging from zero to 100 MeV, using state-of-the-art deuteron wave functions and NN-potentials. Nucleon-nucleon rescattering between emission and absorption of the two photons is treated by Green's functions in order to ensure gauge invariance and the correct Thomson limit. With this Green's-function hybrid approach, we fulfill the low-energy theorem of deuteron Compton scattering and there is no significant dependence on the deuteron wave function used. Concerning the nucleon structure, we use Chiral Effective Field Theory with explicit \Delta(1232) degrees of freedom within the Small Scale Expansion up to leading-one-loop order. Agreement with available data is good at all energies. Our 2-parameter fit to all elastic $\gamma d$ data leads to values for the static isoscalar dipole polarizabilities which are in excellent agreement with the isoscalar Baldin sum rule. Taking this value as additional input, we find \alpha_E^s= (11.3+-0.7(stat)+-0.6(Baldin)) x 10^{-4} fm^3 and \beta_M^s = (3.2-+0.7(stat)+-0.6(Baldin)) x 10^{-4} fm^3 and conclude by comparison to the proton numbers that neutron and proton polarizabilities are essentially the same.Comment: 47 pages LaTeX2e with 20 figures in 59 .eps files, using graphicx. Minor modifications; extended discussion of theoretical uncertainties of polarisabilities extraction. Version accepted for publication in EPJ

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes

Red cell ABO incompatibility and production of tumour necrosis factor-alpha

Tumour necrosis factor-alpha (TNF) is a major mediator of diverse pathophysiological events similar to those of haemolytic transfusion reactions (HTR), such as fever, intravascular coagulation and organ failure. However, the possible role of TNF in HTR has not been investigated. We have constructed an in vitro whole blood model of HTR to examine whether TNF may be produced in red cell ABO incompatibility. TNF was observed in plasma, in a dose dependent manner, when ABO incompatible red cells were added, but not with compatible (group O) cells. Plasma TNF levels were maximal at 2 h, and declined to control levels by 24 h. Haemolysis of incompatible red cells was accompanied by TNF production. Immune haemolysis induced TNF gene expression by buffy coat leucocytes, as determined by Northern blot analysis. Heat inactivation of plasma abolished TNF production, whereas prior treatment with interferongamma augmented the response. These results demonstrate that a major cytokine is produced in response to red cell incompatibility, and suggest that TNF may play a role in the pathogenesis of haemolytic transfusion reactions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75627/1/j.1365-2141.1991.tb04485.x.pd