The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Spread transform watermarking for video sources

Spread Transform (ST) is a quantization watermarking algorithm in which vectors of the wavelet coefficients of a host work are quantized, using one of two dithered quantizers, to embed hidden information bits; Loo had some success in applying such a scheme to still images. We extend ST to the video watermarking problem. Visibility considerations require that each spreading vector refer to corresponding pixels in each of several frames, that is, a multi-frame embedding approach. Use of the hierarchical complex wavelet transform (CWT) for a visual mask reduces computation and improves robustness to jitter and valumetric scaling. We present a method of recovering temporal synchronization at the detector, and give initial results demonstrating the robustness and capacity of the scheme.

Transient ventilation dynamics induced by heat sources of unequal strength

We examine theoretically the transient displacement flow and density stratification that develops within a ventilated box after two localized floor-level heat sources of unequal strengths are activated. The heat input is represented by two non-interacting turbulent axisymmetric plumes of constant buoyancy fluxes B1 and B2 > B1. The box connects to an unbounded quiescent external environment of uniform density via openings at the top and base. A theoretical model is developed to predict the time evolution of the dimensionless depths λj and mean buoyancies δj of the 'intermediate' (j = 1) and 'top' (j = 2) layers leading to steady state. The flow behaviour is classified in terms of a stratification parameter S, a dimensionless measure of the relative forcing strengths of the two buoyant layers that drive the flow. We find that dδ1/dτ α 1/λ1 and dδ2/dτ α 1/λ2, where τ is a dimensionless time. When S 1, the intermediate layer is shallow (small λ1), whereas the top layer is relatively deep (large λ2) and, in this limit, δ1 and δ2 evolve on two characteristically different time scales. This produces a time lag and gives rise to a 'thermal overshoot', during which δ1 exceeds its steady value and attains a maximum during the transients; a flow feature we refer to, in the context of a ventilated room, as 'localized overheating'. For a given source strength ratio ψ = B1/B2, we show that thermal overshoots are realized for dimensionless opening areas A < Aoh and are strongly dependent on the time history of the flow. We establish the region of {A, ψ} space where rapid development of δ1 results in δ1 > δ2, giving rise to a bulk overturning of the buoyant layers. Finally, some implications of these results, specifically to the ventilation of a room, are discussed. © Cambridge University Press 2013.

Effects of dietary cyanobacteria of two different sources on growth and recovery of hybrid tilapia (Oreochromis niloticus x O. aureus)

A 115 days feeding trial was conducted to evaluate the effect of dietary cyanobacteria on growth, microcystins (MCs) accumulation in hybrid tilapia (Oreochromis niloticus x O. aureus) and the recovery when the fish were free of cyanobacteria. Three experimental diets were formulated: the control (cyanobacteria free diet); one test diet with cyanobacteria from Lake Taihu (AMt 80.0 mu g MCs g(-1) diet) and one with cyanobacteria from Lake Dianchi (AMd, 410.0 rho g MCs g(-1) diet). Each diet was fed to fish for 60 days and then all fish were free of cyanobacteria for another 55 days. A significant increase in feeding rate (FR) was observed in fish fed AMd diet after a first 30-day exposure (1(st) EP), and in fish fed both AMt diet and AMd diet after a second 30-day exposure (2(nd) EP). Specific growth rates (SGR) of fish fed AMt diet and AMd diet were both obviously affected after the first 30-day exposure, but SGR was only significantly affected in fish fed AMt diet after the second 30-day exposure. After a 55-day recovery, there were no significant differences among diets in the indices mentioned above. Much higher concentrations of MCs were accumulated in tissues of all fish exposed to cyanobacteria. After the 55-day recovery, MC concentrations in fish tissues were significantly lower than those on day 60. (C) 2009 Elsevier Ltd. All rights reserved.

Spatial variability in water quality and surface sediment diatom assemblages in a complex lake basin,lake of the woods,ontario,canada

Lake of the Woods (LOW) is an international waterbody spanning the Canadian provinces of Ontario and Manitoba, and the U.S. state of Minnesota. In recent years, there has been a perception that water quality has deteriorated in northern regions of the lake, with all increase in the frequency and intensity of toxin-producing cyanobacterial blooms. However, given the lack of long-term data these trends are difficult to verify. As a first step, we examine spatial and seasonal patterns in water quality in this highly complex lake on the Canadian Shield. Further, we examine surface sediment diatom assemblages across multiple sites to determine if they track within-take differences in environmental conditions. Our results show that there are significant spatial patterns in water quality in LOW. Principal Component Analysis divides the lake into three geographic zones based primarily on algal nutrients (i.e., total phosphorus, TP), with the highest concentrations at sites proximal to Rainy River. This variation is closely tracked by sedimentary diatom assemblages, with [TP] explaining 43% of the variation in diatom assemblages across sites. The close correlation between water quality and the surface sediment diatom record indicate that paleoecological models could be used to provide data on the relative importance of natural and anthropogenic sources of nutrients to the lake.

Genetic variation and phylogeographic history of Picea likiangensis revealed by RAPD markers

Repeated cycles of retreat and recolonization during the Quaternary ice ages are thought to have greatly influenced current species distributions and their genetic diversity. It remains unclear how this climatic oscillation has affected the distribution of genetic diversity between populations of wind-pollinated conifers in the Qinghai-Tibetan region. In this study, we investigated the within-species genetic diversity and phylogenetic relationships of Picea likiangensis, a dominant forest species in this region using polymorphic DNA (RAPD) markers. Our results suggest that this species has high overall genetic diversity, with 85.42% of loci being polymorphic and an average expected heterozygosity (H (E)) of 0.239. However, there were relatively low levels of polymorphism at population levels and the differences between populations were not significant, with percentages of polymorphic bands (PPB) ranging from 46.88 to 69.76%, Nei's gene diversity (H (E)) from 0.179 to 0.289 and Shannon's indices (Hpop) from 0.267 to 0.421. In accordance with our proposed hypothesis, a high level of genetic differentiation among populations was detected based on Nei's genetic diversity (G (ST) = 0.256) and AMOVA analysis (Phi (st) = 0.236). Gene flow between populations was found to be limited (Nm = 1.4532) and far lower than reported for other conifer species with wide distribution ranges from other regions. No clusters corresponding to three morphological varieties found in the south, north and west, respectively, were detected in either UPGMA or PCO analyses. Our results suggest that this species may have had different refugia during the glacial stages in the southern region and that the northern variety may have multiple origins from these different refugia.

Use and non-use of electronic information sources by undergraduates at the University of the West Indies

Ramlogan, R.,& Tedd, L. (2006). Use and non-use of electronic information sources by undergraduates at the University of the West Indies. Online Information Review, 30(1), 24-42.

The Jesus Chapel in St Paul's Cathedral, London: a reconstruction of its appearance before the Reformation

New, Elizabeth, 'The Jesus Chapel in St Paul's Cathedral, London: a reconstruction of its appearance before the Reformation', Antiquaries Journal (2005) 85, pp.103-124 RAE2008

Lordship and the peasant economy, c.1250-c.1400: Robert Kyng and the Abbot of Bury St Edmunds

Schofield, P. (2007). Lordship and the peasant economy, c.1250-c.1400: Robert Kyng and the Abbot of Bury St Edmunds. Past and Present. 195(Sup. 2), pp.53-68. RAE2008

Relation de la Mission Abnaquise de St. Franðcois de Sales L'Annâee 1702 / par le Páere Jacques Bigot, de la Compagnie de Jâesus.

http://www.archive.org/details/missionabnaquise00bigorich

Rambo's Interdisciplinary Approach to Religious Conversion: The Case of St. Augustine

This dissertation illustrates the merits of an interdisciplinary approach to religious conversion by employing Lewis Rambo’s systemic stage model to illumine the process of St. Augustine’s conversion. Previous studies of Augustine’s conversion have commonly explored his narrative of transformation from the perspective of one specific discipline, such as theology, history, or psychology. In doing so, they have necessarily restricted attention to a limited set of questions and problems. By bringing these disciplines into a structured, critical conversation, this study demonstrates how formulating and responding to the interplay among personal, social, cultural, and religious dimensions of Augustine’s conversion process may eventuate in the consideration of issues previously unarticulated and thus unaddressed. Rambo (1993) formulates a model of religious change that consists of what he calls context, crisis, quest, encounter, interaction, commitment, and consequences. Change is explained by drawing upon the research and scholarship of psychologists, sociologists, anthropologists, and religionists, in conjunction with the contributions of theologians. This study unfolds in the following chapters: I. Introduction; II. Literature review of scholarship about conversion, with emphasis on explication of Rambo’s model; III. A description of the case of Augustine, drawn from a close reading of the Confessions; IV. Literature review of scholarship about Augustine’s conversion; V. Interdisciplinary interpretation of Augustine’s conversion; and VI. Implications for scholars of conversion, and for pastoral caregivers, as well as recommendations for future research. This dissertation demonstrates how Augustine’s conversion experience was deeply influenced by 1) psychological distress and crisis; 2) the quest to know himself and the divine; 3) interactions with significant others; 4) participation in Christian communities; 5) philosophical and cultural changes; and 6) the encounter with the divine. As such, this study reveals the value of interpreting Augustine’s conversion as an evolving process constituted in multiple factors that can be differentiated from one another, yet clearly interact with one another. It examines the implications of constructing an interdisciplinary approach to Augustine’s conversion narrative for both the academy and the Christian community, and recommends the use of Rambo’s model in studies of other cases of religious change.

St. Columba, Silnán, and the 'Male Bovine' (VC 2.17)

At Vita Columbae VC 2.17, Adomnán has severely misunderstood a written source which originally described how Columba ordered one party to a dispute, an alleged maleficus ‘evil-doer’ called Silnán, to milk a sick cow in order to settle the dispute by demonstrating that its contaminated milk was the real, hidden cause of the harm which had occasioned the dispute. Adomnán misread a description of a bos maculosus ‘pock-marked bovine’ to refer to a bos masculus ‘male bovine’, and proceeded to misunderstand the story as the description of some form of contest between Columba and a maleficus ‘sorcerer’.

The Queen's College, Cork: its origins and early history, 1803-1858

This work examines the origins and early history of the Queen's College, Cork. Designedly there is as much stress on the origins as on the early history, for it is the contention of the work that the College was something more than a legislative mushroom. It was very much in the tradition of the civic universities which added an exciting new dimension to academic life in these islands in the nineteenth century. The first chapter surveys university practice and thinking at the opening of the century, relying exclusively on published sources. The second chapter is devoted specifically to the state of learning in Cork during the period, and makes extensive use of hitherto unpublished manuscript material in relation to the Royal Cork Institution. The third chapter deals with the highly significant evidence on education embodied in the Report of the Select Committee on Irish Education of 1838. This material has not previously been published. In chapter four an extended study is made of relevant letters in the manuscript correspondence of Sir Robert Peel - even the most recent authoritative biography has ignored this material. The remaining three chapters are devoted more specifically to the College, both in the formulation or policy and in its practical working. In chapter six there is an extended survey of early College life based exclusively on hitherto unpublished manuscript material in the College Archives. All of these sources, together with incidental published material, are set out at the end of each chapter.