Algorithms for sequence analysis via mutagenesis

Despite many successes of conventional DNA sequencing methods, some DNAs remain difficult or impossible to sequence. Unsequenceable regions occur in the genomes of many biologically important organisms, including the human genome. Such regions range in length from tens to millions of bases, and may contain valuable information such as the sequences of important genes. The authors have recently developed a technique that renders a wide range of problematic DNAs amenable to sequencing. The technique is known as sequence analysis via mutagenesis (SAM). This paper presents a number of algorithms for analysing and interpreting data generated by this technique.

Constructing and Deconstructing Latin Trades

This paper discusses existence results for latin trades and provides a Glueing Construction which is subsequently used to construct all latin trades of finite order greater than three.

Variants of temporal defeasible logics for modelling norm modifications

This paper proposes some variants of Temporal Defeasible Logic (TDL) to reason about normative modifications. These variants make it possible to differentiate cases in which, for example, modifications at some time change legal rules but their conclusions persist afterwards from cases where also their conclusions are blocked.

Equational Reasoning as a Tool for Data Analysis

A combination of deductive reasoning, clustering, and inductive learning is given as an example of a hybrid system for exploratory data analysis. Visualization is replaced by a dialogue with the data.

Strategic argumentation: A game theoretical investigation

Argumentation is modelled as a game where the payoffs are measured in terms of the probability that the claimed conclusion is, or is not, defeasibly provable, given a history of arguments that have actually been exchanged, and given the probability of the factual premises. The probability of a conclusion is calculated using a standard variant of Defeasible Logic, in combination with standard probability calculus. It is a new element of the present approach that the exchange of arguments is analysed with game theoretical tools, yielding a prescriptive and to some extent even predictive account of the actual course of play. A brief comparison with existing argument-based dialogue approaches confirms that such a prescriptive account of the actual argumentation has been almost lacking in the approaches proposed so far.

What is the Problem of Ad Hoc Hypotheses?

The received view of an ad hoc hypothesis is that it accounts for only the observation(s) it was designed to account for, and so non-adhocness is generally held to be necessary or important for an introduced hypothesis or modification to a theory. Attempts by Popper and several others to convincingly explicate this view, however, prove to be unsuccessful or of doubtful value, and familiar and firmer criteria for evaluating the hypotheses or modified theories so classified are characteristically available. These points are obscured largely because the received view fails to adequately separate psychology from methodology or to recognise ambiguities in the use of 'ad hoc'.

Unlocking hidden genomic sequence

Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs.

Common multiples of complete graphs

A graph H is said to divide a graph G if there exists a set S of subgraphs of G, all isomorphic to H, such that the edge set of G is partitioned by the edge sets of the subgraphs in S. Thus, a graph G is a common multiple of two graphs if each of the two graphs divides G.

Gauge fields, geometric phases, and quantum adiabatic pumps

Quantum adiabatic pumping of charge and spin between two reservoirs (leads) has recently been demonstrated in nanoscale electronic devices. Pumping occurs when system parameters are varied in a cyclic manner and sufficiently slowly that the quantum system always remains in its ground state. We show that quantum pumping has a natural geometric representation in terms of gauge fields (both Abelian and non-Abelian) defined on the space of system parameters. Tunneling from a scanning tunneling microscope tip through a magnetic atom could be used to demonstrate the non-Abelian character of the gauge field.

Superconducting Correlations in Metallic Nanoparticles: Exact Solution of the BCS Model by the Algebraic Bethe Ansatz

Superconducting pairing of electrons in nanoscale metallic particles with discrete energy levels and a fixed number of electrons is described by the reduced Bardeen, Cooper, and Schrieffer model Hamiltonian. We show that this model is integrable by the algebraic Bethe ansatz. The eigenstates, spectrum, conserved operators, integrals of motion, and norms of wave functions are obtained. Furthermore, the quantum inverse problem is solved, meaning that form factors and correlation functions can be explicitly evaluated. Closed form expressions are given for the form factors and correlation functions that describe superconducting pairing.

Proof Explanation in the DR-DEVICE System

Trust is a vital feature for Semantic Web: If users (humans and agents) are to use and integrate system answers, they must trust them. Thus, systems should be able to explain their actions, sources, and beliefs, and this issue is the topic of the proof layer in the design of the Semantic Web. This paper presents the design and implementation of a system for proof explanation on the Semantic Web, based on defeasible reasoning. The basis of this work is the DR-DEVICE system that is extended to handle proofs. A critical aspect is the representation of proofs in an XML language, which is achieved by a RuleML language extension.

A hybrid planning method for transmission networks in a deregulated environment

The reconstruction of power industries has brought fundamental changes to both power system operation and planning. This paper presents a new planning method using multi-objective optimization (MOOP) technique, as well as human knowledge, to expand the transmission network in open access schemes. The method starts with a candidate pool of feasible expansion plans. Consequent selection of the best candidates is carried out through a MOOP approach, of which multiple objectives are tackled simultaneously, aiming at integrating the market operation and planning as one unified process in context of deregulated system. Human knowledge has been applied in both stages to ensure the selection with practical engineering and management concerns. The expansion plan from MOOP is assessed by reliability criteria before it is finalized. The proposed method has been tested with the IEEE 14-bus system and relevant analyses and discussions have been presented.

Modeling control objectives for business process compliance

Business process design is primarily driven by process improvement objectives. However, the role of control objectives stemming from regulations and standards is becoming increasingly important for businesses in light of recent events that led to some of the largest scandals in corporate history. As organizations strive to meet compliance agendas, there is an evident need to provide systematic approaches that assist in the understanding of the interplay between (often conflicting) business and control objectives during business process design. In this paper, our objective is twofold. We will firstly present a research agenda in the space of business process compliance, identifying major technical and organizational challenges. We then tackle a part of the overall problem space, which deals with the effective modeling of control objectives and subsequently their propagation onto business process models. Control objective modeling is proposed through a specialized modal logic based on normative systems theory, and the visualization of control objectives on business process models is achieved procedurally. The proposed approach is demonstrated in the context of a purchase-to-pay scenario.

Quantum-state protection in cavities

We show how an initially prepared quantum state of a radiation mode in a cavity can be preserved for a long time using a feedback scheme based on the injection of appropriately prepared atoms. We present a feedback scheme both for optical cavities, which can be continuously monitored by a photodetector, and for microwave cavities, which can be monitored only indirectly via the detection of atoms that have interacted with the cavity field. We also discuss the possibility of applying these methods for decoherence control in quantum information processing.