An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces

Recent progress in the biochemical classification and structural determination of allergens and allergen–antibody complexes has enhanced our understanding of the molecular determinants of allergenicity. Databases of allergens and their epitopes have facilitated the clustering of allergens according to their sequences and, more recently, their structures. Groups of similar sequences are identified for allergenic proteins from diverse sources, and all allergens are classified into a limited number of protein structural families. A gallery of experimental structures selected from the protein classes with the largest number of allergens demonstrate the structural diversity of the allergen universe. Further comparison of these structures and identification of areas that are different from innocuous proteins within the same protein family can be used to identify features specific to known allergens. Experimental and computational results related to the determination of IgE binding surfaces and methods to define allergen-specific motifs are highlighted

Disentangling habitat concepts for demersal marine fish management

Fishing and other anthropogenic impacts have led to declines in many fish stocks and modification of the seabed. As a result, efforts to restore marine ecosystems have become increasingly focused on spatially explicit management methods to protect fish and the habitats they require for survival. This has led to a proliferation of investigations trying to map ‘habitats’ vulnerable to anthropogenic impacts and identify fish resource requirements in order to meet conservation and management needs. A wide range of habitat-related concepts, with different uses and understandings of the word ‘habitat’ itself has arisen as a consequence. Inconsistencies in terminology can cause confusion between studies, making it difficult to investigate and understand the ecology of fish and the factors that affect their survival. Ultimately, the inability to discern the relationships between fish and their environment clearly can hinder conservation and management measures for fish populations. This review identifies and addresses the present ambiguity surrounding definitions of ‘habitat’ and habitat-related concepts currently used in spatial management of demersal marine fish populations. The role of spatial and temporal scales is considered, in addition to examples of how to assess fish habitat for conservation and management purposes

Fast evaluation of appointment schedules for outpatients in health care

We consider the problem of evaluating an appointment schedule for outpatients in a hospital. Given a fixed-length session during which a physician sees K patients, each patient has to be given an appointment time during this session in advance. When a patient arrives on its appointment, the consultations of the previous patients are either already finished or are still going on, which respectively means that the physician has been standing idle or that the patient has to wait, both of which are undesirable. Optimising a schedule according to performance criteria such as patient waiting times, physician idle times, session overtime, etc. usually requires a heuristic search method involving a huge number of repeated schedule evaluations. Hence, the aim of our evaluation approach is to obtain accurate predictions as fast as possible, i.e. at a very low computational cost. This is achieved by (1) using Lindley's recursion to allow for explicit expressions and (2) choosing a discrete-time (slotted) setting to make those expression easy to compute. We assume general, possibly distinct, distributions for the patient's consultation times, which allows us to account for multiple treatment types, as well as patient no-shows. The moments of waiting and idle times are obtained. For each slot, we also calculate the moments of waiting and idle time of an additional patient, should it be appointed to that slot. As we demonstrate, a graphical representation of these quantities can be used to assist a sequential scheduling strategy, as often used in practice

Evaluating the role of hydrocarbon seepage in carbonate mound formation (offshore Ireland) using basin modelling

The goal of this project was to assess whether deep water coral mound growth on the continental slope of the north Atlantic could be related to active hydrocarbon leakage. The objects of interest are numerous buried and non-buried carbonate mounds, consisting mainly of corals, carbonate crusts and fine grained clastic sediments in the Porcupine Basin, which is located on the eastern Atlantic continental slope 200 km offshore Ireland and contains the sub-commercial Connemara oil field.To evaluate the possible link between hydrocarbon leakage and mound growth we used 2D and 3D basin modelling in combination with geochemical analysis of sediments from gravity cores. A total of 5 intersecting seismic lines were used as a basis for 2D modelling of basin evolution, hydrocarbon generation and migration. Data from six exploration wells were used for calibration of the basin burial and thermal history using vitrinite reflectance, bottom hole temperatures and apatite fission track data. 3D basin modelling was performed using data provided by UCD in the northern part of the Porcupine Basin.The results of this study indicate that a link between modelled hydrocarbon leakage and carbonate mound growth is possible both in the Belgica mound province on the eastern flank of the basin where stratigraphic pinch outs of carrier beds can lead to the localised leakage of hydrocarbons to the seafloor, as well as in the Hovland Magellan mound area in the northern half of the Porcupine Basin, where small-scale structural closures mapped on the main Miocene surfaces correlate roughly to observed mound locations.This study demonstrates the applicability of basin modelling in testing and identifying geologic processes related to geosphere/biosphere interactions

Alpha scattering and capture reactions in the A = 7 system at low energies

Differential cross sections for $^3$He-$\alpha$ scattering were measured in the energy range up to 3 MeV. These data together with other available experimental results for $^3$He $+ \alpha$ and $^3$H $+ \alpha$ scattering were analyzed in the framework of the optical model using double-folded potentials. The optical potentials obtained were used to calculate the astrophysical S-factors of the capture reactions $^3$He$(\alpha,\gamma)^7$Be and $^3$H$(\alpha,\gamma)^7$Li, and the branching ratios for the transitions into the two final $^7$Be and $^7$Li bound states, respectively. For $^3$He$(\alpha,\gamma)^7$Be excellent agreement between calculated and experimental data is obtained. For $^3$H$(\alpha,\gamma)^7$Li a $S(0)$ value has been found which is a factor of about 1.5 larger than the adopted value. For both capture reactions a similar branching ratio of $R = \sigma(\gamma_1)/\sigma(\gamma_0) \approx 0.43$ has been obtained.Comment: submitted to Phys.Rev.C, 34 pages, figures available from one of the authors, LaTeX with RevTeX, IK-TUW-Preprint 930540

The G0 Experiment: Apparatus for Parity-Violating Electron Scattering Measurements at Forward and Backward Angles

In the G0 experiment, performed at Jefferson Lab, the parity-violating elastic scattering of electrons from protons and quasi-elastic scattering from deuterons is measured in order to determine the neutral weak currents of the nucleon. Asymmetries as small as 1 part per million in the scattering of a polarized electron beam are determined using a dedicated apparatus. It consists of specialized beam-monitoring and control systems, a cryogenic hydrogen (or deuterium) target, and a superconducting, toroidal magnetic spectrometer equipped with plastic scintillation and aerogel Cerenkov detectors, as well as fast readout electronics for the measurement of individual events. The overall design and performance of this experimental system is discussed.Comment: Submitted to Nuclear Instruments and Method

Horizontal Branch Stars: The Interplay between Observations and Theory, and Insights into the Formation of the Galaxy

We review HB stars in a broad astrophysical context, including both variable and non-variable stars. A reassessment of the Oosterhoff dichotomy is presented, which provides unprecedented detail regarding its origin and systematics. We show that the Oosterhoff dichotomy and the distribution of globular clusters (GCs) in the HB morphology-metallicity plane both exclude, with high statistical significance, the possibility that the Galactic halo may have formed from the accretion of dwarf galaxies resembling present-day Milky Way satellites such as Fornax, Sagittarius, and the LMC. A rediscussion of the second-parameter problem is presented. A technique is proposed to estimate the HB types of extragalactic GCs on the basis of integrated far-UV photometry. The relationship between the absolute V magnitude of the HB at the RR Lyrae level and metallicity, as obtained on the basis of trigonometric parallax measurements for the star RR Lyrae, is also revisited, giving a distance modulus to the LMC of (m-M)_0 = 18.44+/-0.11. RR Lyrae period change rates are studied. Finally, the conductive opacities used in evolutionary calculations of low-mass stars are investigated. [ABRIDGED]Comment: 56 pages, 22 figures. Invited review, to appear in Astrophysics and Space Scienc

D* Production in Deep Inelastic Scattering at HERA

This paper presents measurements of D^{*\pm} production in deep inelastic scattering from collisions between 27.5 GeV positrons and 820 GeV protons. The data have been taken with the ZEUS detector at HERA. The decay channel $D^{*+}\to (D^0 \to K^- \pi^+) \pi^+$ (+ c.c.) has been used in the study. The $e^+p$ cross section for inclusive D^{*\pm} production with $5<Q^2<100 GeV^2$ and $y<0.7$ is 5.3 \pms 1.0 \pms 0.8 nb in the kinematic region {$1.3<p_T(D^{*\pm})<9.0$ GeV and $| \eta(D^{*\pm}) |<1.5$}. Differential cross sections as functions of p_T(D^{*\pm}), $\eta(D^{*\pm}), W$ and $Q^2$ are compared with next-to-leading order QCD calculations based on the photon-gluon fusion production mechanism. After an extrapolation of the cross section to the full kinematic region in p_T(D^{*\pm}) and $\eta$(D^{*\pm}), the charm contribution $F_2^{c\bar{c}}(x,Q^2)$ to the proton structure function is determined for Bjorken $x$ between 2 $\cdot$ 10$^{-4}$ and 5 $\cdot$ 10$^{-3}$.Comment: 17 pages including 4 figure

Observation of Scaling Violations in Scaled Momentum Distributions at HERA

Charged particle production has been measured in deep inelastic scattering (DIS) events over a large range of $x$ and $Q^2$ using the ZEUS detector. The evolution of the scaled momentum, $x_p$, with $Q^2,$ in the range 10 to 1280 $GeV^2$, has been investigated in the current fragmentation region of the Breit frame. The results show clear evidence, in a single experiment, for scaling violations in scaled momenta as a function of $Q^2$.Comment: 21 pages including 4 figures, to be published in Physics Letters B. Two references adde

Observation of hard scattering in photoproduction events with a large rapidity gap at HERA

Events with a large rapidity gap and total transverse energy greater than 5 GeV have been observed in quasi-real photoproduction at HERA with the ZEUS detector. The distribution of these events as a function of the $\gamma p$ centre of mass energy is consistent with diffractive scattering. For total transverse energies above 12 GeV, the hadronic final states show predominantly a two-jet structure with each jet having a transverse energy greater than 4 GeV. For the two-jet events, little energy flow is found outside the jets. This observation is consistent with the hard scattering of a quasi-real photon with a colourless object in the proton.Comment: 19 pages, latex, 4 figures appended as uuencoded fil