Modelling dependencies in genetic-marker data and its application to haplotype analysis

The objective of this thesis is to develop new methods to reconstruct haplotypes from phaseunknown genotypes. The need for new methodologies is motivated by the increasing avail¬ ability of high-resolution marker data for many species. Such markers typically exhibit correlations, a phenomenon known as Linkage Disequilibrium (LD). It is believed that re¬ constructed haplotypes for markers in high LD can be valuable for a variety of application areas in population genetics, including reconstructing population history and identifying genetic disease variantsTraditionally, haplotype reconstruction methods can be categorized according to whether they operate on a single pedigree or a collection of unrelated individuals. The thesis begins with a critical assessment of the limitations of existing methods, and then presents a uni¬ fied statistical framework that can accommodate pedigree data, unrelated individuals and tightly linked markers. The framework makes use of graphical models, where inference entails representing the relevant joint probability distribution as a graph and then using associated algorithms to facilitate computation. The graphical model formalism provides invaluable tools to facilitate model specification, visualization, and inference.Once the unified framework is developed, a broad range of simulation studies are conducted using previously published haplotype data. Important contributions include demonstrating the different ways in which the haplotype frequency distribution can impact the accuracy of both the phase assignments and haplotype frequency estimates; evaluating the effectiveness of using family data to improve accuracy for different frequency profiles; and, assessing the dangers of treating related individuals as unrelated in an association study

A cryogenic amplifier for fast real-time detection of single-electron tunneling

We employ a cryogenic High Electron Mobility Transistor (HEMT) amplifier to increase the bandwidth of a charge detection setup with a quantum point contact (QPC) charge sensor. The HEMT is operating at 1K and the circuit has a bandwidth of 1 MHz. The noise contribution of the HEMT at high frequencies is only a few times higher than that of the QPC shot noise. We use this setup to monitor single-electron tunneling to and from an adjacent quantum dot and we measure fluctuations in the dot occupation as short as 400 nanoseconds, 20 times faster than in previous work.Comment: 4 pages, 3 figure

Commuting symmetry operators of the Dirac equation, Killing-Yano and Schouten-Nijenhuis brackets

In this paper we derive the most general first-order symmetry operator commuting with the Dirac operator in all dimensions and signatures. Such an operator splits into Clifford even and Clifford odd parts which are given in terms of odd Killing-Yano and even closed conformal Killing-Yano inhomogeneous forms respectively. We study commutators of these symmetry operators and give necessary and sufficient conditions under which they remain of the first-order. In this specific setting we can introduce a Killing-Yano bracket, a bilinear operation acting on odd Killing-Yano and even closed conformal Killing-Yano forms, and demonstrate that it is closely related to the Schouten-Nijenhuis bracket. An important non-trivial example of vanishing Killing-Yano brackets is given by Dirac symmetry operators generated from the principal conformal Killing-Yano tensor [hep-th/0612029]. We show that among these operators one can find a complete subset of mutually commuting operators. These operators underlie separability of the Dirac equation in Kerr-NUT-(A)dS spacetimes in all dimensions [arXiv:0711.0078].Comment: 37 pages, no figure

Approximations for the delivery splitting model

Consumer Demand;Operational Research;Stocks

Anecic earthworms and associated ecosystem services in a ley-arable crop

Een vruchtwisseling van gras en maïs zou duurzaam kunnen zijn in termen van nutriëntengebruik, maar het effect op regenwormen is nog onvoldoende bekend. Regenwormen zijn verzameld in permanent akkerland, permanent grasland en grond waarop een vruchtwisseling was toegepast. De hoeveelheid regenwormen was het hoogst in permanent grasland. Na gebruik als akkerland heeft de populatie heeft minstens drie jaar nodig om te herstellen. De populatie anenic wormen waren echter na deze periode nog niet hersteld

QND measurement of a superconducting qubit in the weakly projective regime

Quantum state detectors based on switching of hysteretic Josephson junctions biased close to their critical current are simple to use but have strong back-action. We show that the back-action of a DC-switching detector can be considerably reduced by limiting the switching voltage and using a fast cryogenic amplifier, such that a single readout can be completed within 25 ns at a repetition rate of 1 MHz without loss of contrast. Based on a sequence of two successive readouts we show that the measurement has a clear quantum non-demolition character, with a QND fidelity of 75 %.Comment: submitted to PR

Compartir l'esforç per millorar els serveis d'aigua i sanejament

La gestión comunitaria de los sistemas de suministro de agua será el enfoque primordial para conseguir los principales Objetivos de Desarrollo del Milenio en las zonas rurales. Discutimos tres aspectos específicos: el concepto de gestión comunitaria, los distintos papeles que pueden jugar los principales actores implicados en el desarrollo y la implementación de los servicios de agua y saneamiento; y la crucial necesidad de proveer capacitación utilizando técnicas participativas, de las cuales se describen algunas, apuntando a una toma de decisiones informada. Señalamos también que capacitar y estimular a los miembros de la comunidad es importante, pero aun lo es más, capacitar a los actores del nivel intermedio (gobierno local, ONG, sector privado, etc.) que son quienes respaldan y facilitan la implementación del proceso inicialmente, y luego el apoyo para asegurar la sostenibilidad del servicio proporcionado.La gestió comunitària dels sistemes de subministrament d'aigua serà l'enfocament primordial per a aconseguir els principals Objectius de Desenvolupament del Mil·lenni a les zones rurals. Discutim tres aspectes específics: el concepte de gestió comunitària, els distints papers que poden jugar els principals actors implicats en el desenvolupament i la implementació dels serveis d'aigua i sanejament; i la crucial necessitat de proveir capacitació utilitzant tècniques participatives, de les quals es descriuen algunes, apuntant a una presa de decisions informada. Assenyalem també que capacitar i estimular els membres de la comunitat és important, però fins i tot ho és més, capacitar als actors del nivell intermedi (govern local, ONG, sector privat, etc.) que són els qui donen suport i faciliten la implementació del procés inicialment, i després el suport per a assegurar la sostenibilitat del servei proporcionat.Peer Reviewe

Soil biological quality of grassland fertilized with adjusted cattle manure slurries in comparison with organic and inorganic fertilizers

We studied the effect of five fertilizers (including two adjusted manure slurries) and an untreated control on soil biota and explored the effect on the ecosystem services they provided. Our results suggest that the available N (NO3- and NH4+) in the soil plays a central role in the effect of fertilizers on nematodes and microorganisms. Microorganisms are affected directly through nutrient availability and indirectly through grass root mass. Nematodes are affected indirectly through microbial biomass and grass root mass. A lower amount of available N in the treatment with inorganic fertilizer was linked to a higher root mass and a higher abundance and proportion of herbivorous nematodes. A higher amount of available N in the organic fertilizer treatments resulted in a twofold higher bacterial activity (measured as bacterial growth rate, viz. thymidine incorporation), a higher proportion of bacterivorous nematodes, a 30% higher potential N mineralization (aerobic incubation), and 25–50% more potentially mineralizable N (anaerobic incubation). Compared to inorganic fertilizer, organic fertilization increased the C total, the N total, the activity of decomposers, and the supply of nutrients via the soil food web. Within the group of organic fertilizers, there was no significant difference in C total, abundances of soil biota, and the potential N mineralization rate. There were no indications that farmyard manure or the adjusted manure slurries provided the ecosystem service “supply of nutrients” better than normal manure slurry. Normal manure slurry provided the highest bacterial activity and the highest amount of mineralizable N and it was the only fertilizer resulting in a positive trend in grass yield over the years 2000–2005. The number of earthworm burrows was higher in the treatments with organic fertilizers compared to the one with the inorganic fertilizer, which suggests that organic fertilizers stimulate the ecosystem service of water regulation more than inorganic fertilizer. The trend towards higher epigeic earthworm numbers with application of farmyard manure and one of the adjusted manure slurries, combined with the negative relation between epigeic earthworms and bulk density and a significantly lower penetration resistance in the same fertilizer types, is preliminary evidence that these two organic fertilizer types contribute more to the service of soil structure maintenance than inorganic fertilize

Do Killing-Yano tensors form a Lie Algebra?

Killing-Yano tensors are natural generalizations of Killing vectors. We investigate whether Killing-Yano tensors form a graded Lie algebra with respect to the Schouten-Nijenhuis bracket. We find that this proposition does not hold in general, but that it does hold for constant curvature spacetimes. We also show that Minkowski and (anti)-deSitter spacetimes have the maximal number of Killing-Yano tensors of each rank and that the algebras of these tensors under the SN bracket are relatively simple extensions of the Poincare and (A)dS symmetry algebras.Comment: 17 page