Likelihood inference for particle location in fluorescence microscopy

We introduce a procedure to automatically count and locate the fluorescent particles in a microscopy image. Our procedure employs an approximate likelihood estimator derived from a Poisson random field model for photon emission. Estimates of standard errors are generated for each image along with the parameter estimates, and the number of particles in the image is determined using an information criterion and likelihood ratio tests. Realistic simulations show that our procedure is robust and that it leads to accurate estimates, both of parameters and of standard errors. This approach improves on previous ad hoc least squares procedures by giving a more explicit stochastic model for certain fluorescence images and by employing a consistent framework for analysis.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS299 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Putting theory into practice: The creation of REALs in the context of today's universities

Rich Environments for Active Learning (REALs), as described by R. Scott Grabinger and Joanna Dunlap, are comprehensive educational systems based on constructivist principles that present an intellectual and practical challenge to university lecturers. As teachers and researchers, academics are concerned with improving the learning potential of teaching strategies and, to this end, the theory of the REAL provides inspiration and ideas based on sound theoretical principles. Yet in the context of the current pressured climate, having the time and resources to put such an extensive, theory into practice can seem little more than a pipe‐dream. It is argued that using a computer‐based application such as the Hypermedia Learning Tutorials (HLTs) as the heart of a REAL allows lecturers to take positive steps towards the creation of comprehensive, flexible, integrated learning environments. The concept of the HLT is discussed and a practical application in the field of advanced second‐language acquisition is described. Based on conceptual analysis and the results of preliminary student evaluation, it is argued that the HLT encompasses both in theory and in practice the chief qualities of REALs and can form the basis for their creation in a wide variety of disciplines

Developing a Mammalian Behaviour Ontology

The use of the Entity + Quality (EQ) model in phenotypic descriptions is dependent on the use of specialised domain ontologies to define the entity under observation. A domain currently lacking a specialised ontology is mammalian behaviour, and so the Mammalian Behaviour Ontology is being constructed to address this. Top-level class distinctions are made between behavioural activities and behavioural functions of individuals, and those between two or more individuals. The ontology is manually developed and encourages contributions from domain experts

Growth of III-V films by control of MBE growth front stoichiometry

For the growth of strain-layer materials and high quality single and multiple quantum wells, the instantaneous control of growth front stoichiometry is critical. The process of the invention adjusts the offset or phase of molecular beam epitaxy (MBE) control shutters to program the instantaneous arrival or flux rate of In and As4 reactants to grow InAs. The interrupted growth of first In, then As4, is also a key feature

Editorial: biological ontologies and semantic biology

As the amount of biological information and its diversity accumulates massively there is a critical need to facilitate the integration of this data to allow new and unexpected conclusions to be drawn from it. The Semantic Web is a new wave of web- based technologies that allows the linking of data between diverse data sets via standardised data formats (“big data”). Semantic Biology is the application of semantic web technology in the biological domain (including medical and health informatics). The Special Topic encompasses papers in this very broad area, including not only ontologies (development and applications), but also text mining, data integration and data analysis making use of the technologies of the Semantic Web. Ontologies are a critical requirement for such integration as they allow conclusions drawn about biological experiments, or descriptions of biological entities, to be understandable and integratable despite being contained in different databases and analysed by different software systems. Ontologies are the standard structures used in biology, and more broadly in computer science, to hold standardized terminologies for particular domains of knowledge. Ontologies consist of sets of standard terms, which are defined and may have synonyms for ease of searching and to accommodate different usages by different communities. These terms are linked by standard relationships, such as “is_a” (an eye “is_a” sense organ) or “part_of” (an eye is “part_of” a head). By linking terms in this way, more detailed, or granular, terms can be linked to broader terms, allowing computation to be carried out that takes these relationships into account

NO synthase? Generation of nitric oxide in plants

It has now become well accepted that nitric oxide (NO) has a key role to play in the signalling that takes place in plant cells. However, the sources of NO in plants has been hard to determine and there is considerable debate as to exactly how NO is made by plant cells. In animals nitric oxide synthase (NOS) enzymes have been characterised and such data has been used to inform the studies which have been taking place in plants. However, despite several genomes from higher plants being sequenced, there is no evidence that such species contain NOS sequences. Despite this, a recent search using algal sequences did reveal a NOS-like sequence and such a finding may spark new enthusiasm for the search for a higher plant NOS. However, considerable care needs to be taken in such studies, as the robustness of many of the inhibitors and probes which could be used in such work has been questioned. Here, some of the previous evidence that has been presented for the existence of a plant NOS, along with a discussion of how else plants may produce NO is given

Federalism, Constitutionalism, and the Texas Revolt

Traditional historiography characterizes the period directly following Mexico\u27s independence as one during which the adoption of federalism divided a previously united and uniformed country. Anglo-American settlers in Texas sought to remove the territory from Mexican control by exploiting the resultant political turmoil. This exploitation eventually led to the Texas revolt of 1835, its independence as a republic, and, ultimately, statehood within the United States. The recent focus on Mexico\u27s provincial history challenges this narrative by illustrating that independence did not result in a unified nation. On the contrary, comprising multiple provinces with varying interests, the region\u27s Provincial Deputations adopted federalism as a means of uniting under a federalist national government. Furthermore, Mexico\u27s political turmoil resulted from centralists attempting to undermine the federalist political order. This attack on federalism culminated with the dictatorship of Antonio de Lopez de Santa Anna, who, in 1835, replaced the federal republic with a highly centralized republic controlled by Mexico City. Forces under Santa Anna\u27s command violently suppressed all opposition to the new order until Texas became the last bastion of Mexican federalism and Anglo-American Texans its last defenders