Sediment dynamics

This chapter provides descriptions of essential features of modelling of a broad range of problems involving many classes of sediment, flow, applications and research top¬ics. The experimental reproduction of hydraulic processes involving sediment dynam¬ics is focussed on the sediments and not the hydrodynamic processes, which are covered in other chapters. Since a great deal of experimental research on sediment dynamics remains to be done, laboratory experiments to elucidate process knowledge (research) as well as physical modelling of site-specific applications (consultancy) will be covered

An explicit height bound for the classical modular polynomial

For a prime m, let Phi_m be the classical modular polynomial, and let h(Phi_m) denote its logarithmic height. By specializing a theorem of Cohen, we prove that h(Phi_m) <= 6 m log m + 16 m + 14 sqrt m log m. As a corollary, we find that h(Phi_m) <= 6 m log m + 18 m also holds. A table of h(Phi_m) values is provided for m <= 3607.Comment: Minor correction to the constants in Theorem 1 and Corollary 9. To appear in the Ramanujan Journal. 17 pages

Gag-Protease Sequence Evolution Following Protease Inhibitor Monotherapy Treatment Failure in HIV-1 Viruses Circulating in East Africa.

Around 2.5 million HIV-infected individuals failing first-line therapy qualify for boosted protease inhibitor (bPI)-based second-line therapy globally. Major resistance mutations are rarely present at treatment failure in patients receiving bPI and the determinants of failure in these patients remain unknown. There is evidence that Gag can impact PI susceptibility. Here, we have sequenced Gag-Protease before and following failure in 23 patients in the SARA trial infected with subtypes A, C, and D viruses. Before bPI, significant variation in Protease and Gag was observed at positions previously associated with PI exposure and resistance including Gag mutations L449P, S451N, and L453P and Protease K20I and L63P. Following PI failure, previously described mutations in Protease and Gag were observed, including those at the cleavage sites such as R361K and P453L. However, the emergence of clear genetic determinants of therapy failure across patients was not observed. Larger Gag sequence datasets will be required to comprehensively identify mutational correlates of bPI failure across subtypes

De Finetti theorem on the CAR algebra

The symmetric states on a quasi local C*-algebra on the infinite set of indices J are those invariant under the action of the group of the permutations moving only a finite, but arbitrary, number of elements of J. The celebrated De Finetti Theorem describes the structure of the symmetric states (i.e. exchangeable probability measures) in classical probability. In the present paper we extend De Finetti Theorem to the case of the CAR algebra, that is for physical systems describing Fermions. Namely, after showing that a symmetric state is automatically even under the natural action of the parity automorphism, we prove that the compact convex set of such states is a Choquet simplex, whose extremal (i.e. ergodic w.r.t. the action of the group of permutations previously described) are precisely the product states in the sense of Araki-Moriya. In order to do that, we also prove some ergodic properties naturally enjoyed by the symmetric states which have a self--containing interest.Comment: 23 pages, juornal reference: Communications in Mathematical Physics, to appea

Expression of LMO4 and outcome in pancreatic ductal adenocarcinoma

Identification of a biomarker of prognosis and response to therapy that can be assessed preoperatively would significantly improve overall outcomes for patients with pancreatic cancer. In this study, patients whose tumours exhibited high LMO4 expression had a significant survival advantage following operative resection, whereas the survival of those patients whose tumours had low or no LMO4 expression was not significantly different when resection was compared with operative biopsy alone

Life path analysis: scaling indicates priming effects of social and habitat factors on dispersal distances

1. Movements of many animals along a life-path can be separated into repetitive ones within home ranges and transitions between home ranges. We sought relationships of social and environmental factors with initiation and distance of transition movements in 114 buzzards Buteo buteo that were marked as nestlings with long-life radio tags. 2. Ex-natal dispersal movements of 51 buzzards in autumn were longer than for 30 later in their first year and than 35 extra-natal movements between home ranges after leaving nest areas. In the second and third springs, distances moved from winter focal points by birds that paired were the same or less than for unpaired birds. No post-nuptial movement exceeded 2 km. 3. Initiation of early ex-natal dispersal was enhanced by presence of many sibs, but also by lack of worm-rich loam soils. Distances travelled were greatest for birds from small broods and with relatively little short grass-feeding habitat near the nest. Later movements were generally enhanced by the absence of loam soils and short grassland, especially with abundance of other buzzards and probable poor feeding habitats (heathland, long grass). 4. Buzzards tended to persist in their first autumn where arable land was abundant, but subsequently showed a strong tendency to move from this habitat. 5. Factors that acted most strongly in ½-km buffers round nests, or round subsequent focal points, usually promoted movement compared with factors acting at a larger scale. Strong relationships between movement distances and environmental characteristics in ½-km buffers, especially during early ex-natal dispersal, suggested that buzzards became primed by these factors to travel far. 6. Movements were also farthest for buzzards that had already moved far from their natal nests, perhaps reflecting genetic predisposition, long-term priming or poor habitat beyond the study area

Sensitivity of the Mott Transition to Non-cubic Splitting of the Orbital Degeneracy: Application to NH3 K3C60

Within dynamical mean-field theory, we study the metal-insulator transition of a twofold orbitally degenerate Hubbard model as a function of a splitting \Delta of the degeneracy. The phase diagram in the U-\Delta plane exhibits two-band and one-band metals, as well as the Mott insulator. The correlated two-band metal is easily driven to the insulator state by a strikingly weak splitting \Delta << W of the order of the Kondo-peak width zW, where z << 1 is the metal quasiparticle weight. The possible relevance of this result to the insulator-metal transition in the orthorhombic expanded fulleride NH3 K3C60 is discussed.Comment: revtex, 15 pages including 6 ps figures. Submitted to Phys. Rev.

Coherent states for exactly solvable potentials

A general algebraic procedure for constructing coherent states of a wide class of exactly solvable potentials e.g., Morse and P{\"o}schl-Teller, is given. The method, {\it a priori}, is potential independent and connects with earlier developed ones, including the oscillator based approaches for coherent states and their generalizations. This approach can be straightforwardly extended to construct more general coherent states for the quantum mechanical potential problems, like the nonlinear coherent states for the oscillators. The time evolution properties of some of these coherent states, show revival and fractional revival, as manifested in the autocorrelation functions, as well as, in the quantum carpet structures.Comment: 11 pages, 4 eps figures, uses graphicx packag

Methylation-capture and Next-Generation sequencing of free circulating DNA from human plasma

Background Free circulating DNA (fcDNA) has many potential clinical applications, due to the non-invasive way in which it is collected. However, because of the low concentration of fcDNA in blood, genome-wide analysis carries many technical challenges that must be overcome before fcDNA studies can reach their full potential. There are currently no definitive standards for fcDNA collection, processing and whole-genome sequencing. We report novel detailed methodology for the capture of high-quality methylated fcDNA, library preparation and downstream genome-wide Next-Generation Sequencing. We also describe the effects of sample storage, processing and scaling on fcDNA recovery and quality. Results Use of serum versus plasma, and storage of blood prior to separation resulted in genomic DNA contamination, likely due to leukocyte lysis. Methylated fcDNA fragments were isolated from 5 donors using a methyl-binding protein-based protocol and appear as a discrete band of ~180 bases. This discrete band allows minimal sample loss at the size restriction step in library preparation for Next-Generation Sequencing, allowing for high-quality sequencing from minimal amounts of fcDNA. Following sequencing, we obtained 37×106-86×106 unique mappable reads, representing more than 50% of total mappable reads. The methylation status of 9 genomic regions as determined by DNA capture and sequencing was independently validated by clonal bisulphite sequencing. Conclusions Our optimized methods provide high-quality methylated fcDNA suitable for whole-genome sequencing, and allow good library complexity and accurate sequencing, despite using less than half of the recommended minimum input DNA

Can forest management based on natural disturbances maintain ecological resilience?

Given the increasingly global stresses on forests, many ecologists argue that managers must maintain ecological resilience: the capacity of ecosystems to absorb disturbances without undergoing fundamental change. In this review we ask: Can the emerging paradigm of natural-disturbance-based management (NDBM) maintain ecological resilience in managed forests? Applying resilience theory requires careful articulation of the ecosystem state under consideration, the disturbances and stresses that affect the persistence of possible alternative states, and the spatial and temporal scales of management relevance. Implementing NDBM while maintaining resilience means recognizing that (i) biodiversity is important for long-term ecosystem persistence, (ii) natural disturbances play a critical role as a generator of structural and compositional heterogeneity at multiple scales, and (iii) traditional management tends to produce forests more homogeneous than those disturbed naturally and increases the likelihood of unexpected catastrophic change by constraining variation of key environmental processes. NDBM may maintain resilience if silvicultural strategies retain the structures and processes that perpetuate desired states while reducing those that enhance resilience of undesirable states. Such strategies require an understanding of harvesting impacts on slow ecosystem processes, such as seed-bank or nutrient dynamics, which in the long term can lead to ecological surprises by altering the forest's capacity to reorganize after disturbance