The Time Machine: A Simulation Approach for Stochastic Trees

In the following paper we consider a simulation technique for stochastic trees. One of the most important areas in computational genetics is the calculation and subsequent maximization of the likelihood function associated to such models. This typically consists of using importance sampling (IS) and sequential Monte Carlo (SMC) techniques. The approach proceeds by simulating the tree, backward in time from observed data, to a most recent common ancestor (MRCA). However, in many cases, the computational time and variance of estimators are often too high to make standard approaches useful. In this paper we propose to stop the simulation, subsequently yielding biased estimates of the likelihood surface. The bias is investigated from a theoretical point of view. Results from simulation studies are also given to investigate the balance between loss of accuracy, saving in computing time and variance reduction.Comment: 22 Pages, 5 Figure

Politics by other means?:STS and research in education

Science and Technology Studies (STS) has been surprisingly slow to become widely known and deployed in the field of education. Yet STS has a rich array of concepts and analytical methods to offer to studies of: knowledge practices and epistemic cultures; the interrelationship between states and knowledge; regulatory practices, governance and institutions; and classrooms, pedagogy, teaching and learning. Most importantly, it provides a fresh perspective on how power operates in ordering societies, disciplining actors and promoting ideas and practices. In this paper, we provide an introduction to STS and elaborate what it offers education scholars. Using examples from the emerging body of STS work in the field of education, and in particular from the papers in this special issue, we argue that STS is not only useful, but an exciting and generative form of critique–one that is especially suited to investigating contemporary issues in education policies and practices

DC Inclined-Plane Tracking and Erosion Test of Insulating Materials

The paper reviews previous work on the DC inclined plane test and suggests equivalent DC voltage levels in parallel to AC voltage in the ASTM inclined plane tracking and erosion test. The aim of this work is to provide a basis for standardizing the inclined plane test for DC voltage. Round robin tests done in five laboratories on five specimens of a silicone rubber material were done with the purpose of establishing appropriate ratios by which the equivalent DC voltages can be determined with respect to the corresponding AC voltages. These levels were determined as 67% and 87%, for +DC and-DC respectively, of the AC initial tracking voltage, and for practical purposes, these levels are rounded to 70 and 90%.Peer reviewed: YesNRC publication: Ye

(un)Doing standards in education with actor-network theory

Recent critiques have drawn important attention to the depoliticized consensus and empty promises embedded in network discourses of educational policy. While acceding this critique, this discussion argues that some forms of network analysis – specifically those adopting actor-network theory (ANT) approaches - actually offer useful theoretical resources for policy studies. Drawing from ANT-inspired studies of policy processes associated with educational standards, the article shows the ambivalences and contradictions as well as the possibilities that can be illuminated by ANT analysis of standards as networks. The discussion outlines the diverse network conceptions, considerations and sensibilities afforded by ANT approaches. Then it shows four phenomena that have been highlighted by ANT studies of educational standards: ordering (and rupturing) practice through ‘immutable mobiles’, local universality, tensions among networks of prescription and networks of negotiation, and different co-existing ontological forms of the same standards. The conclusion suggests starting points, drawing from these ANT-inspired network analyses, for examining policy processes associated with educational standards

Uropathogenic Escherichia coli P and Type 1 Fimbriae Act in Synergy in a Living Host to Facilitate Renal Colonization Leading to Nephron Obstruction

The progression of a natural bacterial infection is a dynamic process influenced by the physiological characteristics of the target organ. Recent developments in live animal imaging allow for the study of the dynamic microbe-host interplay in real-time as the infection progresses within an organ of a live host. Here we used multiphoton microscopy-based live animal imaging, combined with advanced surgical procedures, to investigate the role of uropathogenic Escherichia coli (UPEC) attachment organelles P and Type 1 fimbriae in renal bacterial infection. A GFP+ expressing variant of UPEC strain CFT073 and genetically well-defined isogenic mutants were microinfused into rat glomerulus or proximal tubules. Within 2 h bacteria colonized along the flat squamous epithelium of the Bowman's capsule despite being exposed to the primary filtrate. When facing the challenge of the filtrate flow in the proximal tubule, the P and Type 1 fimbriae appeared to act in synergy to promote colonization. P fimbriae enhanced early colonization of the tubular epithelium, while Type 1 fimbriae mediated colonization of the center of the tubule via a mechanism believed to involve inter-bacterial binding and biofilm formation. The heterogeneous bacterial community within the tubule subsequently affected renal filtration leading to total obstruction of the nephron within 8 h. Our results reveal the importance of physiological factors such as filtration in determining bacterial colonization patterns, and demonstrate that the spatial resolution of an infectious niche can be as small as the center, or periphery, of a tubule lumen. Furthermore, our data show how secondary physiological injuries such as obstruction contribute to the full pathophysiology of pyelonephritis

Microwave processing of cement and concrete materials - towards an industrial reality?

Each year a substantial body of literature is published on the use of microwaves to process cement and concrete materials. Yet to date, very few if any have lead the realisation of a commercial scale industrial system and is the context under which this review has been undertaken. The state-of the–art is evaluated for opportunities, and the key barriers to the development of new microwave-based processing techniques to enhance production, processing and recycling of cement and concrete materials. Applications reviewed include pyro-processing of cement clinker; accelerated curing, non-destructive testing and evaluation (NDT&E), and end-of-life processing including radionuclide decontamination

A missense mutation in Katnal1 underlies behavioural, neurological and ciliary anomalies

Microtubule severing enzymes implement a diverse range of tissue-specific molecular functions throughout development and into adulthood. Although microtubule severing is fundamental to many dynamic neural processes, little is known regarding the role of the family member Katanin p60 subunit A-like 1, KATNAL1, in central nervous system (CNS) function. Recent studies reporting that microdeletions incorporating the KATNAL1 locus in humans result in intellectual disability and microcephaly suggest that KATNAL1 may play a prominent role in the CNS; however, such associations lack the functional data required to highlight potential mechanisms which link the gene to disease symptoms. Here we identify and characterise a mouse line carrying a loss of function allele in Katnal1. We show that mutants express behavioural deficits including in circadian rhythms, sleep, anxiety and learning/memory. Furthermore, in the brains of Katnal1 mutant mice we reveal numerous morphological abnormalities and defects in neuronal migration and morphology. Furthermore we demonstrate defects in the motile cilia of the ventricular ependymal cells of mutants, suggesting a role for Katnal1 in the development of ciliary function. We believe the data we present here are the first to associate KATNAL1 with such phenotypes, demonstrating that the protein plays keys roles in a number of processes integral to the development of neuronal function and behaviour.Molecular Psychiatry advance online publication, 4 April 2017; doi:10.1038/mp.2017.54

Host-plant genotypic diversity and community genetic interactions mediate aphid spatial distribution.

Genetic variation in plants can influence the community structure of associated species, through both direct and indirect interactions. Herbivorous insects are known to feed on a restricted range of plants, and herbivore preference and performance can vary among host plants within a species due to genetically based traits of the plant (e.g., defensive compounds). In a natural system, we expect to find genetic variation within both plant and herbivore communities and we expect this variation to influence species interactions. Using a three-species plant-aphid model system, we investigated the effect of genetic diversity on genetic interactions among the community members. Our system involved a host plant (Hordeum vulgare) that was shared by an aphid (Sitobion avenae) and a hemi-parasitic plant (Rhinanthus minor). We showed that aphids cluster more tightly in a genetically diverse host-plant community than in a genetic monoculture, with host-plant genetic diversity explaining up to 24% of the variation in aphid distribution. This is driven by differing preferences of the aphids to the different plant genotypes and their resulting performance on these plants. Within the two host-plant diversity levels, aphid spatial distribution was influenced by an interaction among the aphid's own genotype, the genotype of a competing aphid, the origin of the parasitic plant population, and the host-plant genotype. Thus, the overall outcome involves both direct (i.e., host plant to aphid) and indirect (i.e., parasitic plant to aphid) interactions across all these species. These results show that a complex genetic environment influences the distribution of herbivores among host plants. Thus, in genetically diverse systems, interspecific genetic interactions between the host plant and herbivore can influence the population dynamics of the system and could also structure local communities. We suggest that direct and indirect genotypic interactions among species can influence community structure and processes

Loss of PTB or Negative Regulation of Notch mRNA Reveals Distinct Zones of Notch and Actin Protein Accumulation in Drosophila Embryo

Polypyrimidine Tract Binding (PTB) protein is a regulator of mRNA processing and translation. Genetic screens and studies of wing and bristle development during the post-embryonic stages of Drosophila suggest that it is a negative regulator of the Notch pathway. How PTB regulates the Notch pathway is unknown. Our studies of Drosophila embryogenesis indicate that (1) the Notch mRNA is a potential target of PTB, (2) PTB and Notch functions in the dorso-lateral regions of the Drosophila embryo are linked to actin regulation but not their functions in the ventral region, and (3) the actin-related Notch activity in the dorso-lateral regions might require a Notch activity at or near the cell surface that is different from the nuclear Notch activity involved in cell fate specification in the ventral region. These data raise the possibility that the Drosophila embryo is divided into zones of different PTB and Notch activities based on whether or not they are linked to actin regulation. They also provide clues to the almost forgotten role of Notch in cell adhesion and reveal a role for the Notch pathway in cell fusions