Beam Based Alignment of Interaction Region Magnets

In conventional beam based alignment (BBA) procedures, the relative alignment of a quadrupole to a nearby beam position monitor is determined by finding a beam position in the quadrupole at which the closed orbit does not change when the quadrupole field is varied. The final focus magnets of the interaction regions (IR) of circular colliders often have some specialized properties that make it difficult to perform conventional beam based alignment procedures. At the HERA interaction points, for example, these properties are: (a) The quadrupoles are quite strong and long. Therefore a thin lens approximation is quite imprecise. (b) The effects of angular magnet offsets become significant. (c) The possibilities to steer the beam are limited as long as the alignment is not within specifications. (d) The beam orbit has design offsets and design angles with respect to the axis of the low-beta quadrupoles. (e) Often quadrupoles do not have a beam position monitor in their vicinity. Here we present a beam based alignment procedure that determines the relative offset of the closed orbit from a quadrupole center without requiring large orbit changes or monitors next to the quadrupole. Taking into account the alignment angle allows us to reduce the sensitivity to optical errors by one to two orders of magnitude. We also show how the BBA measurements of all IR quadrupoles can be used to determine the global position of the magnets. The sensitivity to errors of this method is evaluated and its applicability to HERA is shown

Reorganization of interaction networks modulates the persistence of species in late successional stages

Ecological interaction networks constantly reorganize as interspecific interactions change across successional stages and environmental gradients. This reorganization can also be associated with the extent to which species change their preference for types of niches available in their local sites. Despite the pervasiveness of these interaction changes, previous studies have revealed that network reorganizations have a minimal or insignificant effect on global descriptors of network architecture, such as connectance, modularity and nestedness. However, little is known about whether these reorganizations may have an effect on community dynamics and composition.To answer the question above, we study the multi-year dynamics and reorganization of plant–herbivore interaction networks across secondary successional stages of a tropical dry forest. We develop new quantitative tools based on a structural stability approach to estimate the potential impact of network reorganization on species persistence. Then, we investigate whether this impact can explain the likelihood of persistence of herbivore species in the observed communities.We find that resident (early-arriving) herbivore species increase their likelihood of persistence across time and successional stages. Importantly, we demonstrate that, in late successional stages, the reorganization of interactions among resident species has a strong inhibitory effect on the likelihood of persistence of colonizing (late-arriving) herbivores.These findings support earlier predictions suggesting that, in mature communities, changes of species interactions can act as community-control mechanisms (also known as priority effects). Furthermore, our results illustrate that the dynamics and composition of ecological communities cannot be fully understood without attention to their reorganization processes, despite the invariability of global network properties

Evaluation of the LEP Centre-of-Mass Energy Above the W-Pair Production Threshold

Knowledge of the centre-of-mass energy at LEP2 is of primary importance to set the absolute energy scale for the measurement of the W-boson mass. The beam energy above 80 GeV is derived from continuous measurements of the magnetic bending field by 16 NMR probes situated in a number of the LEP dipoles. The relationship between the fields measured by the probes and the beam energy is calibrated against precise measurements of the average beam energy between 41 and 55 GeV made using the resonant depolarisation technique. The linearity of the relationship is tested by comparing the fields measured by the probes with the total bending field measured by a flux loop. This test results in the largest contribution to the systematic uncertainty. Several further corrections are applied to derive the the centre-of-mass energies at each interaction point. In addition the centre-of-mass energy spread is evaluated. The beam energy has been determined with a precision of 25 MeV for the data taken in 1997, corresponding to a relative precision of 2.7x10^{-4}. This is small in comparison to the present uncertainty on the W mass measurement at LEP. However, the ultimate statistical precision on the W mass with the full LEP2 data sample should be around 25 MeV, and a smaller uncertainty on the beam energy is desirable. Prospects for improvements are outlined.Comment: 24 pages, 10 figures, Latex, epsfig; replaced by version accepted by European Physical Journal

States emerging from hybrid political orders: Pacific experiences The Australian Centre for Peace and Conflict Studies Occasional Papers Series.

This study explores current processes of state formation in the Pacific islands, focusing on Vanuatu, Solomon Islands, Tonga, Bougainville (as an autonomous region of Papua New Guinea), Southern Highlands Province of Papua New Guinea, and East Timor. It challenges the mainstream discourse on fragile states as a framework for analysis of the situation of any of these countries or regions, and argues that it is more appropriate to talk about states emerging from hybrid political orders as a common denominator. Hybrid political orders combine elements of the introduced Western models of governance and elements stemming from local indigenous traditions. In East Timor and the Pacific island countries customary governance, deeply rooted in locality, has significant implications for state capacity and functionality as well as legitimacy. Tonga with its constitutional monarchy is transitioning to more liberal democratic forms of governance. This gradual process is driven by civil society forces that are growing in strength. In the Melanesian cases of Vanuatu, Bougainville and Solomon Islands there is negotiation of the conditions and possibilities of a ‘marriage’ between customary governance and introduced Western forms of governance, based on relatively strong customary spheres and state institutions that struggle with problems of effectiveness and legitimacy. East Timor is engaged in a conventional state-building process (with massive external assistance) focusing on the transfer and strengthening of central government institutions. The process has taken little account of customary institutions and their potential for contributing to governance and order, and has inadvertently marginalised both local culture and rural communities more generally, with considerable negative effects for Timorese state formation. In the Southern Highlands Province of PNG a vacuum of effective and legitimate governance can be found. In all of these countries or regions there is considerable potential for state and non-state actors to play complementary roles in the provision of functions which OECD countries normally assign exclusively to the state. We also found areas of incompatibility and areas of considerable friction between state and customary institutions. These, however, are not due to insurmountable contradictions between customary and liberal democratic principles and could be overcome by processes of mutual adaptation. These findings—large areas of complementarity, at times intense, but surmountable incompatibilities—augur well for constructive interaction between state and customary institutions which might lead to the emergence of networks of resilient governance which are not introduced from the outside, but are embedded in the societal structures on the ground. Keyword(s) state formatio

Massively Parallel Haplotyping on Microscopic Beads for the High-Throughput Phase Analysis of Single Molecules

In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1∶10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases

Rapid kinetics of G protein subunit association: A rate-limiting conformational change?

G protein subunit association and dissociation are thought to play an important role in signal transduction. We measured [alpha][beta][gamma] heterocomplex formation using resonance energy transfer. Fluorescein-labelled [alpha](F-[alpha]) emission was quenched ~ 10% on mixing with eosin-labelled [beta][gamma](E-[beta][gamma]). Unlabelled [beta][gamma] did not quench F-[alpha] fluorescence. Stopped-flow kinetics showed a t1/2 ranging from 2.5 s to 0.25 s for 50 nM to 1200 nM E-[beta][gamma]. The rate saturated at high E-[beta][gamma] concentrations consistent with a two-step mechanism. We report the first rapid-mix studies of G protein subunit association kinetics which suggest that [alpha] and [beta][gamma] combine by a two-step process with a maximal rate of 4.1 +/- 0.4 s-1.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31136/1/0000033.pd

Living long and well: prospects for a personalized approach to the medicine of ageing

Research into ageing and its underlying molecular basis enables us to develop and implement targeted interventions to ameliorate or cure its consequences. However, the efficacy of interventions often differs widely between individuals, suggesting that populations should be stratified or even individualized. Large-scale cohort studies in humans, similar systematic studies in model organisms as well as detailed investigations into the biology of ageing can provide individual validated biomarkers and mechanisms, leading to recommendations for targeted interventions. Human cohort studies are already ongoing, and they can be supplemented by in silico simulations. Systematic studies in animal models are made possible by the use of inbred strains or genetic reference populations of mice. Combining the two, a comprehensive picture of the various determinants of ageing and ‘health span' can be studied in detail, and an appreciation of the relevance of results from model organisms to humans is emerging. The interactions between genotype and environment, particularly the psychosocial environment, are poorly studied in both humans and model organisms, presenting serious challenges to any approach to a personalized medicine of ageing. To increase the success of preventive interventions, we argue that there is a pressing need for an individualized evaluation of interventions such as physical exercise, nutrition, nutraceuticals and calorie restriction mimetics as well as psychosocial and environmental factors, separately and in combination. The expected extension of the health span enables us to refocus health care spending on individual prevention, starting in late adulthood, and on the brief period of morbidity at very old ag

Magnitude and Timing of Leaf Damage Affect Seed Production in a Natural Population of Arabidopsis thaliana (Brassicaceae)

Background: The effect of herbivory on plant fitness varies widely. Understanding the causes of this variation is of considerable interest because of its implications for plant population dynamics and trait evolution. We experimentally defoliated the annual herb Arabidopsis thaliana in a natural population in Sweden to test the hypotheses that (a) plant fitness decreases with increasing damage, (b) tolerance to defoliation is lower before flowering than during flowering, and (c) defoliation before flowering reduces number of seeds more strongly than defoliation during flowering, but the opposite is true for effects on seed size. Methodology/Principal Findings: In a first experiment, between 0 and 75% of the leaf area was removed in May from plants that flowered or were about to start flowering. In a second experiment, 0, 25%, or 50% of the leaf area was removed from plants on one of two occasions, in mid April when plants were either in the vegetative rosette or bolting stage, or in mid May when plants were flowering. In the first experiment, seed production was negatively related to leaf area removed, and at the highest damage level, also mean seed size was reduced. In the second experiment, removal of 50% of the leaf area reduced seed production by 60% among plants defoliated early in the season at the vegetative rosettes, and by 22% among plants defoliated early in the season at the bolting stage, but did not reduce seed output of plants defoliated one month later. No seasonal shift in the effect of defoliation on seed size was detected. Conclusions/Significance: The results show that leaf damage may reduce the fitness of A. thaliana, and suggest that in this population leaf herbivores feeding on plants before flowering should exert stronger selection on defence traits than those feeding on plants during flowering, given similar damage levels

Structure of a lectin from Canavalia gladiata seeds: new structural insights for old molecules

<p>Abstract</p> <p>Background</p> <p>Lectins are mainly described as simple carbohydrate-binding proteins. Previous studies have tried to identify other binding sites, which possible recognize plant hormones, secondary metabolites, and isolated amino acid residues. We report the crystal structure of a lectin isolated from <it>Canavalia gladiata </it>seeds (CGL), describing a new binding pocket, which may be related to pathogen resistance activity in ConA-like lectins; a site where a non-protein amino-acid, α-aminobutyric acid (Abu), is bound.</p> <p>Results</p> <p>The overall structure of native CGL and complexed with α-methyl-mannoside and Abu have been refined at 2.3 Å and 2.31 Å resolution, respectively. Analysis of the electron density maps of the CGL structure shows clearly the presence of Abu, which was confirmed by mass spectrometry.</p> <p>Conclusion</p> <p>The presence of Abu in a plant lectin structure strongly indicates the ability of lectins on carrying secondary metabolites. Comparison of the amino acids composing the site with other legume lectins revealed that this site is conserved, providing an evidence of the biological relevance of this site. This new action of lectins strengthens their role in defense mechanisms in plants.</p

Genetic Crossovers Are Predicted Accurately by the Computed Human Recombination Map

Hotspots of meiotic recombination can change rapidly over time. This instability and the reported high level of inter-individual variation in meiotic recombination puts in question the accuracy of the calculated hotspot map, which is based on the summation of past genetic crossovers. To estimate the accuracy of the computed recombination rate map, we have mapped genetic crossovers to a median resolution of 70 Kb in 10 CEPH pedigrees. We then compared the positions of crossovers with the hotspots computed from HapMap data and performed extensive computer simulations to compare the observed distributions of crossovers with the distributions expected from the calculated recombination rate maps. Here we show that a population-averaged hotspot map computed from linkage disequilibrium data predicts well present-day genetic crossovers. We find that computed hotspot maps accurately estimate both the strength and the position of meiotic hotspots. An in-depth examination of not-predicted crossovers shows that they are preferentially located in regions where hotspots are found in other populations. In summary, we find that by combining several computed population-specific maps we can capture the variation in individual hotspots to generate a hotspot map that can predict almost all present-day genetic crossovers