Genomic control of patterning

The development of multicellular organisms involves the partitioning of the organism into territories of cells of specific structure and function. The information for spatial patterning processes is directly encoded in the genome. The genome determines its own usage depending on stage and position, by means of interactions that constitute gene regulatory networks (GRNs). The GRN driving endomesoderm development in sea urchin embryos illustrates different regulatory strategies by which developmental programs are initiated, orchestrated, stabilized or excluded to define the pattern of specified territories in the developing embryo

Identifying and managing asbestiform minerals in geological collections

Asbestos is widely recognised as a serious hazard, and its industrial use is now banned within the UK, and EU, and strict regulations govern the use of older manufactured materials which may contain asbestos. However, asbestos is also a natural geological material, and may occur in museum collections as minerals or constituents of rock specimens. In the UK the Control of Asbestos Regulations 2012 (CAR 2012) provides the legal framework for the safe identification, use and disposal of asbestos. However, these regulations, and other EU regulations, provide no specific guidance on dealing with potentially asbestos-containing natural materials. CAR 2012 specifies just six asbestos minerals although a number of other minerals in museum collections are known to have asbestiform structures and be hazard-ous, including other amphiboles, and the zeolite erionite. Despite the lack of specific guid-ance, museums must comply with CAR 2012, and this paper outlines the professional ad-vice, training and procedures which may be needed for this. It provides guidance on identifi-cation of potential asbestos-bearing specimens and on procedures to document them and store them for future use, or to prepare them for professional disposal. It also makes sug-gestions how visitors, employees and others in a museum can be protected from asbestos as incoming donations and enquiries, managed in the event of an emergency, and safely included in displays

The word problem for Pride groups

Pride groups are defined by means of finite (simplicial) graphs and examples include Artin groups, Coxeter groups and generalized tetrahedron groups. Under suitable conditions we calculate an upper bound of the first order Dehn function for a finitely presented Pride group. We thus obtain sufficient conditions for when finitely presented Pride groups have solvable word problems. As a corollary to our main results we show that the first order Dehn function of a generalized tetrahedron groups, containing finite generalized triangle groups, is at most cubic

Understanding and valuing the economic, social and environmental components of System Harmonisation

The aim of the Products and Markets component of the System Harmonisation project is to value the economic and environmental outcomes from an irrigation scheme that is operated by and in the interests of society. In this conceptual note the thinking underlying this component of the project are outlined. The aim of this note is to provide elements for debated. The nature and requirements of System Harmonisation demands that a 'systems approach' be taken throughout the project. What becomes important within this approach is how the different elements within a system are isolated and yet linked with one another. In many instances the extent and nature of irrigation systems are defined by the relevant Regional Irrigation Business Partnership (RIBP) under investigation. It is recognised that society has multiple uses for the water (agriculture, industry, households, recreation and the environment) as well as non-use (intrinsic) values for which it derives benefits from and incurs costs in distributing the water in any select manner. Further, it is assumed that the irrigation schemes are run for the benefit of society as a whole. Thus, there is a necessity to evaluate both the private and public costs and benefits associated with irrigation schemes. In order to identify what society values from an irrigation scheme, it is argued that a social matrix approach is needed. This analysis allows for a clustering of the issues people feel is important to them regarding the use of an irrigation scheme. Such an analysis will allow identification of the perceived most and least beneficial activities connected to water allocation, economic modelling of the most productive activities, evaluation of externalities and Cost Benefit Analysis. The net economic benefits that arise from irrigation need to be evaluated. The sectors where benefits are derived can be segregated into agriculture, households, the environment, recreation and industrial uses. The largest of these, by pure scale of the use of water, is agriculture. A gross margins approach is used to evaluate the returns for water in the agricultural sector. In the industrial and household sectors, a simple evaluation approach is used where the quantity of water demanded is multiplied by the price paid in each sector. Non-market valuation techniques are used to evaluate the recreational and environmental uses of water. The difficulty that arises in this analysis is how to evaluate the performance of irrigation schemes, where the outcomes are multifaceted. A 'meta' model approach is suggested in which the different elements from the project are brought together and assessed using a technique derived from the theory surrounding production possibility frontiers. This technique can be used to hypothesise a value for the ecosystem services derived from an irrigation scheme. The performance of an irrigation scheme is evaluated in terms of the suggestions raised to change it. Cost Effective Analysis is to be utilised to evaluate this performance. Then two issues need to be addressed. First, it is necessary to converse with those from other components, particularly those involved in the hydrological programs, to determine the nature of the schemes to be investigated. Second, it is necessary to implement the approach in each of the RIBPs. This work needs to commence with the evaluation of the social values in each region

A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

Geometric methods in the study of Pride groups and relative presentations

Combinatorial group theory is the study of groups given by presentations. Algebraic and geometric methods pervade this area of mathematics and it is the latter which forms the main theme of this thesis. In particular, we use diagrams and pictures over presentations to study problems in the domain of finitely presented groups. Our thesis is split into two distinct halves, though the techniques used in each are very similar. In Chapters 2 - 4 we study Pride groups with the aim to solve their word and conjugacy problems. We also study the second homotopy module of a natural presentation of a Pride group. Chapters 6 and 7 are devoted to the study of relative presentations, with particular attention being paid to those of the form . Determining when such presentations are aspherical is our main objective. Chapter 1 covers the basic material that is used throughout this thesis. The main topics of interest are free groups; presentations of groups; the word, conjugacy, and isomorphism problems for finitely presented groups; first and second order Dehn functions of finitely presented groups; diagrams and pictures over finite presentations; and the second homotopy module of a finite presentation. The reader may skip Chapter 1 if they are familiar with this material. A Pride group is a finitely presented group which can be defined by means of a finite simplicial graph; this is done in Chapter 2. Examples of Pride groups are given in Section 2.1. This section also contains the statements of Conditions (I), (II), (H-I), (H-II), and the asphericity condition. We will always assume that a Pride group satisfies one of these conditions. In Section 2.2 we survey the known results that appear in the literature, while in Section 2.3 we present our original results. We obtain isoperimetric functions for a vertex-finite Pride group G which satisfies (I), (II), (H-I) or (H-II). Sufficient conditions are then obtained for G to have a soluble word problem. Solutions of the conjugacy problem for G are also obtained. However, we require that G satisfies some extra conditions. We calculate a generating set for the second homotopy module of the natural presentation of a non-spherical Pride group, i.e. one which satisfies the asphericity condition. Using this generating set, we obtain an upper bound for the second order Dehn function of a non-spherical vertex-free Pride group. We also obtain information about the second order Dehn function of an arbitrary non-spherical Pride group. Chapter 3 contains various technical results that are needed in Chapter 4. The main focus is that of diagrams over the standard presentation of a vertex-finite Pride group. We study simply-connected r-diagrams in Section 3.1 and in Section 3.2 we study annular r-diagrams. Propositions 3.1.1, 3.2.1, 3.2.2, and Theorems 3.2.1 and 3.2.2 are the main results of this chapter. Chapters 4 and 5 are devoted to the proofs of our main results. Proofs of our results for the word and conjugacy problems of a vertex-finite Pride group are contained in Chapter 4, while Chapter 5 contains proofs of our results about the second homotopy module of a non-spherical Pride group. Chapter 5 also contains a study of pictures over the natural presentation of such a group. In Chapter 6, we turn our attention to relative presentations. Our interest lies in determining when such presentations are aspherical. Relevant background material and definitions are given in this chapter and pictures over relative presentations are also studied. Five tests which are used to determine whether or not a relative presentation is aspherical are given in Section 6.4. Chapter 6 also contains a brief survey of known results in this area. In Chapter 7, the final chapter of this thesis, we present our original contribution to the area of aspherical relative presentations. In particular, we determine when the relative presentation is aspherical where n is greater than or equal to 4 and a, b are elements of H each of order at least 3. There are four exceptional cases for which asphericity cannot be determined