87 research outputs found
Roy-Steiner equations for pion-nucleon scattering
Starting from hyperbolic dispersion relations, we derive a closed system of
Roy-Steiner equations for pion-nucleon scattering that respects analyticity,
unitarity, and crossing symmetry. We work out analytically all kernel functions
and unitarity relations required for the lowest partial waves. In order to
suppress the dependence on the high-energy regime we also consider once- and
twice-subtracted versions of the equations, where we identify the subtraction
constants with subthreshold parameters. Assuming Mandelstam analyticity we
determine the maximal range of validity of these equations. As a first step
towards the solution of the full system we cast the equations for the
partial waves into the form of a Muskhelishvili-Omn\`es
problem with finite matching point, which we solve numerically in the
single-channel approximation. We investigate in detail the role of individual
contributions to our solutions and discuss some consequences for the spectral
functions of the nucleon electromagnetic form factors.Comment: 106 pages, 18 figures; version published in JHE
Electro-Magnetic Nucleon Form Factors and their Spectral Functions in Soliton Models
It is demonstrated that in simple soliton models essential features of the
electro-magnetic nucleon form factors observed over three orders of magnitude
in momentum transfer are naturally reproduced. The analysis shows that
three basic ingredients are required: an extended object, partial coupling to
vector mesons, and relativistic recoil corrections. We use for the extended
object the standard skyrmion, one vector meson propagator for both isospin
channels, and the relativistic boost to the Breit frame. Continuation to
timelike leads to quite stable results for the spectral functions in the
regime from the 2- or 3-pion threshold to about two rho masses. Especially the
onset of the continuous part of the spectral functions at threshold can be
reliably determined and there are strong analogies to the results imposed on
dispersion theoretic approaches by the unitarity constraint.Comment: 24 pages, (RevTeX), 5 PS-figures; Data points in fig.2 and
corresponding references added. Final version, to be published in Z.Physik
Ioffe Times in DIS from a Dipole Model Fit
We present a study of Ioffe times in deep inelastic electron-proton
scattering. We deduce 'experimental' Ioffe-time distributions from the small-x
HERA data as described by a particular colour-dipole-model fit. We show
distributions for three representative gamma*-proton c.m. energies W and
various values of the photon virtuality Q^2. These distributions are rather
broad for transversely and very narrow for longitudinally polarised virtual
photons. The Ioffe times for W=150 GeV, for example, range from around 1000 fm
for Q^2=1 GeV^2 to around 10 fm for Q^2=100 GeV^2. Based on our results we
discuss consequences for the limitations of applicability of the dipole
picture.Comment: 20 page
Dijet resonances, widths and all that
The search for heavy resonances in the dijet channel is part of the on-going
physics programme, both at the Tevatron and at the LHC. Lower limits have been
placed on the masses of dijet resonances predicted in a wide variety of models.
However, across experiments, the search strategy assumes that the effect of the
new particles is well-approximated by on-shell production and subsequent decay
into a pair of jets. We examine the impact of off-shell effects on such
searches, particularly for strongly interacting resonances.Comment: Version published in JHE
Dispersive analysis of the scalar form factor of the nucleon
Based on the recently proposed Roy-Steiner equations for pion-nucleon
scattering, we derive a system of coupled integral equations for the pi pi -->
N-bar N and K-bar K --> N-bar N S-waves. These equations take the form of a
two-channel Muskhelishvili-Omnes problem, whose solution in the presence of a
finite matching point is discussed. We use these results to update the
dispersive analysis of the scalar form factor of the nucleon fully including
K-bar K intermediate states. In particular, we determine the correction
Delta_sigma=sigma(2M_pi^2)-sigma_{pi N}, which is needed for the extraction of
the pion-nucleon sigma term from pi N scattering, as a function of pion-nucleon
subthreshold parameters and the pi N coupling constant.Comment: 24 pages, 6 figures; version published in JHE
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes
BACKGROUND: The recent accumulation of closely related genomic sequences provides a valuable resource for the elucidation of the evolutionary histories of various organisms. However, although numerous alignment calculation and visualization tools have been developed to date, the analysis of complex genomic changes, such as large insertions, deletions, inversions, translocations and duplications, still presents certain difficulties. RESULTS: We have developed a comparative genome analysis tool, named CGAT, which allows detailed comparisons of closely related bacteria-sized genomes mainly through visualizing middle-to-large-scale changes to infer underlying mechanisms. CGAT displays precomputed pairwise genome alignments on both dotplot and alignment viewers with scrolling and zooming functions, and allows users to move along the pre-identified orthologous alignments. Users can place several types of information on this alignment, such as the presence of tandem repeats or interspersed repetitive sequences and changes in G+C contents or codon usage bias, thereby facilitating the interpretation of the observed genomic changes. In addition to displaying precomputed alignments, the viewer can dynamically calculate the alignments between specified regions; this feature is especially useful for examining the alignment boundaries, as these boundaries are often obscure and can vary between programs. Besides the alignment browser functionalities, CGAT also contains an alignment data construction module, which contains various procedures that are commonly used for pre- and post-processing for large-scale alignment calculation, such as the split-and-merge protocol for calculating long alignments, chaining adjacent alignments, and ortholog identification. Indeed, CGAT provides a general framework for the calculation of genome-scale alignments using various existing programs as alignment engines, which allows users to compare the outputs of different alignment programs. Earlier versions of this program have been used successfully in our research to infer the evolutionary history of apparently complex genome changes between closely related eubacteria and archaea. CONCLUSION: CGAT is a practical tool for analyzing complex genomic changes between closely related genomes using existing alignment programs and other sequence analysis tools combined with extensive manual inspection
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies
The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized enzyme superfamilies
Training Genetic Counsellors to Deliver an Innovative Therapeutic Intervention: their views and experience of facilitating multi-family discussion groups
Innovations in clinical genetics have increased diagnosis, treatment and prognosis of inherited genetic conditions (IGCs). This has led to an increased number of families seeking genetic testing and / or genetic counselling and increased the clinical load for genetic counsellors (GCs). Keeping pace with biomedical discoveries, interventions are required to support families to understand, communicate and cope with their Inherited Genetic Condition. The Socio-Psychological Research in Genomics (SPRinG) collaborative have developed a new intervention, based on multi-family discussion groups (MFDGs), to support families affected by IGCs and train GCs in its delivery. A potential challenge to implementing the intervention was whether GCs were willing and able to undergo the training to deliver the MFDG. In analysing three multi-perspective interviews with GCs, this paper evaluates the training received. Findings suggests that MFDGs are a potential valuable resource in supporting families to communicate genetic risk information and can enhance family function and emotional well-being. Furthermore, we demonstrate that it is feasible to train GCs in the delivery of the intervention and that it has the potential to be integrated into clinical practice. Its longer term implementation into routine clinical practice however relies on changes in both organisation of clinical genetics services and genetic counsellors' professional development
The supernatural characters and powers of sacred trees in the Holy Land
This article surveys the beliefs concerning the supernatural characteristics and powers of sacred trees in Israel; it is based on a field study as well as a survey of the literature and includes 118 interviews with Muslims and Druze. Both the Muslims and Druze in this study attribute supernatural dimensions to sacred trees which are directly related to ancient, deep-rooted pagan traditions. The Muslims attribute similar divine powers to sacred trees as they do to the graves of their saints; the graves and the trees are both considered to be the abode of the soul of a saint which is the source of their miraculous powers. Any violation of a sacred tree would be strictly punished while leaving the opportunity for atonement and forgiveness. The Druze, who believe in the transmigration of souls, have similar traditions concerning sacred trees but with a different religious background. In polytheistic religions the sacred grove/forest is a centre of the community's official worship; any violation of the trees is regarded as a threat to the well being of the community. Punishments may thus be collective. In the monotheistic world (including Christianity, Islam and Druze) the pagan worship of trees was converted into the worship/adoration of saints/prophets; it is not a part of the official religion but rather a personal act and the punishments are exerted only on the violating individual
Functional Copy-Number Alterations in Cancer
Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples. Computational analysis is needed (1) to deduce from raw array data actual amplification or deletion events for chromosomal fragments and (2) to distinguish causal chromosomal alterations from functionally neutral ones. We present a comprehensive computational approach, RAE, designed to robustly map chromosomal alterations in tumor samples and assess their functional importance in cancer. To demonstrate the methodology, we experimentally profile copy number changes in a clinically aggressive subtype of soft-tissue sarcoma, pleomorphic liposarcoma, and computationally derive a portrait of candidate oncogenic alterations and their target genes. Many affected genes are known to be involved in sarcomagenesis; others are novel, including mediators of adipocyte differentiation, and may include valuable therapeutic targets. Taken together, we present a statistically robust methodology applicable to high-resolution genomic data to assess the extent and function of copy-number alterations in cancer
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