Analysis of the barley bract suppression gene Trd1

A typical barley (Hordeum vulgare) floret consists of reproductive organs three stamens and a pistil, and non-reproductive organs-lodicules and two floral bracts, abaxial called 'lemma' and adaxial 'palea'. The floret is subtended by two additional bracts called outer or empty glumes. Together these organs form the basic structural unit of the grass inflorescence, a spikelet. There are commonly three spikelets at each rachis (floral stem of the barley spike) node, one central and two lateral spikelets. Rare naturally occurring or induced phenotypic variants that contain a third bract subtending the central spikelets have been described in barley. The gene responsible for this phenotype was called the THIRD OUTER GLUME1 (Trd1). The Trd1 mutants fail to suppress bract growth and as a result produce leaf-like structures that subtend each rachis node in the basal portion of the spike. Also, floral development at the collar is not always suppressed. In rice and maize, recessive mutations in NECK LEAF1 (Nl1) and TASSEL SHEATH1 (Tsh1) genes, respectively, have been shown to be responsible for orthologous phenotypes. Fine mapping of the trd1 phenotype in an F-3 recombinant population enabled us to position on the long arm of chromosome 1H to a 10 cM region. We anchored this to a conserved syntenic region on rice chromosome Os05 and selected a set of candidate genes for validation by resequencing PCR amplicons from a series of independent mutant alleles. This analysis revealed that a GATA transcription factor, recently proposed to be Trd1, contained mutations in 10 out of 14 independent trd1 mutant alleles that would generate non-functional TRD1 proteins. Together with genetic linkage data, we confirm the identity of Trd1 as the GATA transcription factor ortholog of rice Nl1 and maize Tsh1 genes.

High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H

Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designated dense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC7F3 nearly isogenic line (NIL) of cv. Bowman as potentially containing the dense spike mutant locus dsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808 (Hv_SPL14)-CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum and Brachypodium, Classical map-based isolation of the gene dsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.

Comparison of treatment effect sizes associated with surrogate and final patient relevant outcomes in randomised controlled trials: meta-epidemiological study

Objective To quantify and compare the treatment effect and risk of bias of trials reporting biomarkers or intermediate outcomes (surrogate outcomes) versus trials using final patient relevant primary outcomes. Design Meta-epidemiological study. Data sources All randomised clinical trials published in 2005 and 2006 in six high impact medical journals: Annals of Internal Medicine, BMJ, Journal of the American Medical Association, Lancet, New England Journal of Medicine, and PLoS Medicine. Study selection Two independent reviewers selected trials. Data extraction Trial characteristics, risk of bias, and outcomes were recorded according to a predefined form. Two reviewers independently checked data extraction. The ratio of odds ratios was used to quantify the degree of difference in treatment effects between the trials using surrogate outcomes and those using patient relevant outcomes, also adjusted for trial characteristics. A ratio of odds ratios >1.0 implies that trials with surrogate outcomes report larger intervention effects than trials with patient relevant outcomes. Results 84 trials using surrogate outcomes and 101 using patient relevant outcomes were considered for analyses. Study characteristics of trials using surrogate outcomes and those using patient relevant outcomes were well balanced, except for median sample size (371 v 741) and single centre status (23% v 9%). Their risk of bias did not differ. Primary analysis showed trials reporting surrogate endpoints to have larger treatment effects (odds ratio 0.51, 95% confidence interval 0.42 to 0.60) than trials reporting patient relevant outcomes (0.76, 0.70 to 0.82), with an unadjusted ratio of odds ratios of 1.47 (1.07 to 2.01) and adjusted ratio of odds ratios of 1.46 (1.05 to 2.04). This result was consistent across sensitivity and secondary analyses. Conclusions Trials reporting surrogate primary outcomes are more likely to report larger treatment effects than trials reporting final patient relevant primary outcomes. This finding was not explained by differences in the risk of bias or characteristics of the two groups of trials.

Erlebnisse 1940-1944 1940-1944

Exile in Haarlem (Holland); deportation to Westerbork (1943) and Bergen-Belsen (1944) concentration camps; in June 1944 liberation from Bergen-Belsen through special agreement; train-ride to Palestine (summer 1944)

Equivalent rate 1/2 quasi-cyclic codes

Chen et al. [1] give a list of quasi-cyclic (2m,m) codes which have the largest minimum distance of any quasi-cyclic code, for various values ofm. We present the weight distribution of these codes. It will be seen that many of the codes found by Chen et al. [1] are equivalent in the sense of having identical weight distributions.

(v, k, λ) Configurations and self-dual codes

The incidence matrix of a (v, k, λ) configuration is used to construct a (2v, v) and a (2v + 2, v + 1) self-dual code. If the incidence matrix is a circulant, the codes obtained are quasi-cyclic and extended quasi-cyclic, respectively. The weight distributions of some codes of this type are obtained.

The global burden of injury: Incidence, mortality, disability-adjusted life years and time trends from the Global Burden of Disease study 2013

Background The Global Burden of Diseases (GBD), Injuries, and Risk Factors study used the disability-adjusted life year (DALY) to quantify the burden of diseases, injuries, and risk factors. This paper provides an overview of injury estimates from the 2013 update of GBD, with detailed information on incidence, mortality, DALYs and rates of change from 1990 to 2013 for 26 causes of injury, globally, by region and by country. Methods Injury mortality was estimated using the extensive GBD mortality database, corrections for ill-defined cause of death and the cause of death ensemble modelling tool. Morbidity estimation was based on inpatient and outpatient data sets, 26 cause-of-injury and 47 nature-of-injury categories, and seven follow-up studies with patient-reported long-term outcome measures. Results In 2013, 973 million (uncertainty interval (UI) 942 to 993) people sustained injuries that warranted some type of healthcare and 4.8 million (UI 4.5 to 5.1) people died from injuries. Between 1990 and 2013 the global age-standardised injury DALY rate decreased by 31% (UI 26% to 35%). The rate of decline in DALY rates was significant for 22 cause-of-injury categories, including all the major injuries. Conclusions Injuries continue to be an important cause of morbidity and mortality in the developed and developing world. The decline in rates for almost all injuries is so prominent that it warrants a general statement that the world is becoming a safer place to live in. However, the patterns vary widely by cause, age, sex, region and time and there are still large improvements that need to be made.

Eläimen tuttuus ja vieraus : Fenomenologisen empatiateorian uudelleentulkinta ja sen sovellus vieraslajisia eläimiä koskevaan kokemukseen

Within the field of philosophy, animals have traditionally been studied from two perspectives: that of self-knowledge and that of ethics. The analysis of the differences between humans and animals has served our desire to understand our own specificity, whereas ethical discussions have ultimately aimed at finding the right way to treat animals. This dissertation proposes a different way of looking at non-human animals: it investigates the question of how non-human animals appear to us humans in our perceptual experience. The analysis focuses on the empathetic, embodied understanding of animals diverse movements and other expressions. The theoretical point of departure for the research is phenomenological philosophy, in particular Maurice Merleau-Ponty s phenomenology of the body. Edmund Husserl s and Edith Stein s analyses of empathy and embodiment are also crucial to the work. In this tradition, empathy means understanding the other s experience through her bodily expressions and seeing the other body as living, as well as motivated and directed towards the surrounding world. The dissertation both explicates and criticizes the earlier phenomenological notions of empathy and human specificity. In order to elucidate the fundamental structures of our experience of non-human animals, it also applies the phenomenological method, which consists of a phenomenological reduction and a free variation of the different aspects of experience. It is shown that our experiences of non-human animals involve a recognition of both similarities and differences. This recognition, however, is not primarily based on intellectual comparisons but is lived as an embodied relationship to another body, and its manifestations vary from one instant to the next. The analysis also reveals that the object of empathy is not the other s experience as such, not even as it is manifested by the other s movements, but rather the other s embodied situation, enriched by elements that remain outside the scope of the other s experience. The dissertation shows that human existence is intertwined with the existence of non-human animals on four levels: those of empathetic sensations, reciprocal communication, experience of the surrounding world and self-definitions. The animals different modes of perception prove to expand our understanding of what is perceivable and how things can be perceived. The presence of non-human animals in our perceptual world is revealed as something that both shows us the limits of our own embodiment and enables us to overcome these limits in empathetic acts. Finally, it is demonstrated that the life of non-human animals is intertwined with ours in a far more complex way than has been presupposed in traditional descriptions of human-animal differences.

A multiplier theorem for the sublaplacian on the Heisenberg group

A multiplier theorem for the sublaplacian on the Heisenberg group is proved using Littlewood-Paley-Stein theory of g-functions.

A maximal operator, Carleson's embedding, and tent spaces for vector-valued functions

This thesis is concerned with the area of vector-valued Harmonic Analysis, where the central theme is to determine how results from classical Harmonic Analysis generalize to functions with values in an infinite dimensional Banach space. The work consists of three articles and an introduction. The first article studies the Rademacher maximal function that was originally defined by T. Hytönen, A. McIntosh and P. Portal in 2008 in order to prove a vector-valued version of Carleson's embedding theorem. The boundedness of the corresponding maximal operator on Lebesgue-(Bochner) -spaces defines the RMF-property of the range space. It is shown that the RMF-property is equivalent to a weak type inequality, which does not depend for instance on the integrability exponent, hence providing more flexibility for the RMF-property. The second article, which is written in collaboration with T. Hytönen, studies a vector-valued Carleson's embedding theorem with respect to filtrations. An earlier proof of the dyadic version assumed that the range space satisfies a certain geometric type condition, which this article shows to be also necessary. The third article deals with a vector-valued generalizations of tent spaces, originally defined by R. R. Coifman, Y. Meyer and E. M. Stein in the 80's, and concerns especially the ones related to square functions. A natural assumption on the range space is then the UMD-property. The main result is an atomic decomposition for tent spaces with integrability exponent one. In order to suit the stochastic integrals appearing in the vector-valued formulation, the proof is based on a geometric lemma for cones and differs essentially from the classical proof. Vector-valued tent spaces have also found applications in functional calculi for bisectorial operators. In the introduction these three themes come together when studying paraproduct operators for vector-valued functions. The Rademacher maximal function and Carleson's embedding theorem were applied already by Hytönen, McIntosh and Portal in order to prove boundedness for the dyadic paraproduct operator on Lebesgue-Bochner -spaces assuming that the range space satisfies both UMD- and RMF-properties. Whether UMD implies RMF is thus an interesting question. Tent spaces, on the other hand, provide a method to study continuous time paraproduct operators, although the RMF-property is not yet understood in the framework of tent spaces.

Arvoja näkyvissä : Kaunokirjallisuuden etiikka Ludwig Wittgensteinin filosofian valossa

The goal of this dissertation was to study whether it is possible and meaningful to apply Ludwig Wittgenstein s distinction between saying (Sagen) and showing (Zeigen) to ethically oriented literary criticism. The following questions were used as the primary guidelines: 1. Is it possible, in the context of literary criticism, to put in practice Wittgenstein s ethical conceptions, which are quite theoretical and metaphysical by nature? 2. If so, what practical literary devices do authors use if they want to demonstrate their ethical values within the frame of a fictional work? 3. Does philosophy offer useful ethical consepts that open us new and interesting readings in fiction? The philosophical background of Wittgenstein s distinction is clarified in chapter I. This clarification is based on his main works, Tractatus logico-philosophicus and Philosophishe Untersuchungen, the published correspondence between Wittgenstein and Paul Engelmann, and selected Wittgenstein research and papers. Analyzing ethics and it s expression in Georg Trakl s poetry further elucidates Wittgenstein s concept of showing. The concept that a literary work is an act of an author was used as a starting point. The presumption was that analyzing this act of an author will reveal how ethical values can be demonstrated in literature. Categorizing an author s act at different levels of literary expression provides the structure of this study. In chapters IV - XIII literary devices useful for demonstrating ethics are examined and explained using examples from the works of Joseph Conrad, Charles Dickens, Nikolay Leskov, Ludwig Uhland, Eino Leino, Pentti Haanpää and Maria Jotuni. The concepts and views of researchers and writers such as Mihail Bahtin, Peter Juhl, E. D. Hirsch, Peter Lamarque and Stein Haugom Olsen are used. The concepts outlined in previous chapters are then applied in three case studies: Aeschylus s Oresteia trilogy, J-L. Runeberg s poem Sven Dufva and Sofi Oksanen s novel Puhdistus (Purge). On the whole, Wittgenstein s idea that ethical values can be demonstrated (shown) by means of literature is revealed as a fruitful point of departure for a more exact ethical reading, offering a new perspective on literary works.

Lopsidedness in WHISP galaxies I. Rotation curves and kinematic lopsidedness

The frequently observed lopsidedness of the distribution of stars and gas in disc galaxies is still considered as a major problem in galaxy dynamics. It is even discussed as an imprint of the formation history of discs and the evolution of baryons in dark matter haloes. Here, we analyse a selected sample of 70 galaxies from the Westerbork Hi Survey of Spiral and Irregular Galaxies. The Hi data allow us to follow the morphology and the kinematics out to very large radii. In the present paper, we present the rotation curves and study the kinematic asymmetry. We extract the rotation curves of the receding and approaching sides separately and show that the kinematic behaviour of disc galaxies can be classified into five different types: symmetric velocity fields where the rotation curves of the receding and approaching sides are almost identical; global distortions where the rotation velocities of the receding and approaching sides have an offset that is constant with radius; local distortions leading to large deviations in the inner and negligible deviations in the outer parts (and vice versa); and distortions that divide the galaxies into two kinematic systems that are visible in terms of the different behaviour of the rotation curves of the receding and approaching sides, which leads to a crossing and a change in side. The kinematic lopsidedness is measured from the maximum rotation velocities, averaged over the plateau of the rotation curves. This gives a good estimate of the global lopsidedness in the outer parts of the sample galaxies. We find that the mean value of the perturbation parameter denoting the lopsided potential as obtained from the kinematic data is 0.056. Altogether, 36% of the sample galaxies are globally lopsided, which can be interpreted as the disc responding to a halo that was distorted by a tidal encounter. In Paper II, we study the morphological lopsidedness of the same sample of galaxies.

Lopsidedness in WHISP galaxies II. Morphological lopsidedness

The distribution of stars and gas in many galaxies is asymmetric. This so-called lopsidedness is expected to significantly affect the dynamics and evolution of the disc, including the star formation activity. Here, we measure the degree of lopsidedness for the gas distribution in a selected sample of 70 galaxies from the Westerbork Hi Survey of Spiral and Irregular Galaxies. This complements our earlier work (Paper I) where the kinematic lopsidedness was derived for the same galaxies. The morphological lopsidedness is measured by performing a harmonic decomposition of the surface density maps. The amplitude of lopsidedness A(1), the fractional value of the first Fourier component, is typically quite high (about 0.1) within the optical disc and has a constant phase. Thus, lopsidedness is a common feature in galaxies and indicates a global mode. We measure A(1) out to typically one to four optical radii, sometimes even further. This is, on average, four times larger than the distance to which lopsidedness was measured in the past using near-IR as a tracer of the old stellar component, and therefore provides a new, more stringent constraint on the mechanism for the origin of lopsidedness. Interestingly, the value of A(1) saturates beyond the optical radius. Furthermore, the plot of A(1) versus radius shows fluctuations that we argue are due to local spiral features. We also try to explain the physical origin of this observed disc lopsidedness. No clear trend is found when the degree of lopsidedness is compared to a measure of the isolation or interaction probability of the sample galaxies. However, this does not rule out a tidal origin if the lopsidedness is long-lived. In addition, we find that the early-type galaxies tend to be more morphologically lopsided than the late-type galaxies. Both results together indicate that lopsidedness has a tidal origin.

Si isotope variability in Proterozoic cherts

We report Si-isotopic compositions of 75 sedimentologically and petrographically characterized chert samples with ages ranging from similar to 2600 to 750 Ma using multi-collector inductively coupled plasma mass spectrometry. delta Si-30 values of the cherts analyzed in this study show a similar to 7 parts per thousand range, from -4.29 to +2.85. This variability can be explained in part by (1) simple mixing of silica derived from continental (higher delta Si-30) and hydrothermal (lower delta Si-30) sources, (2) multiple mechanisms of silica precipitation and (3) Rayleigh-type fractionations within pore waters of individual basins. We observe similar to 3 parts per thousand variation in peritidal cherts from a single Neoproterozoic sedimentary basin (Spitsbergen). This variation can be explained by Rayleigh-type fractionation during precipitation from silica-saturated porewaters. In some samples, post-dissolution and reprecipitation of silica could have added to this effect. Our data also indicate that peritidal cherts are enriched in the heavier isotopes of Si whereas basinal cherts associated with banded iron formations (BIF) show lower delta Si-30. This difference could partly be due to Si being derived from hydrothermal sources in BIFs. We postulate that the difference in delta Si-30 between non-BIF and BIF cherts is consistent with the contrasting genesis of these deposits. Low delta Si-30 in BIF is consistent with laboratory experiments showing that silica adsorbed onto Fe-hydroxide particles preferentially incorporates lighter Si isotopes. Despite large intrabasinal variation and environmental differences, the data show a clear pattern of secular variation. Low delta Si-30 in Archean cherts is consistent with a dominantly hydrothermal source of silica to the oceans at that time. The monotonically increasing delta Si-30 from 3.8 to 1.5 Ga appears to reflect a general increase in continental versus hydrothermal sources of Si in seawater, as well as the preferential removal of lighter Si isotopes during silica precipitation in iron-associated cherts from silica-saturated seawater. The highest delta Si-30 values are observed in 1.5 Ga peritidal cherts; in part, these enriched values could reflect increasing sequestration of light silica during soil-forming processes, thus, delivering relatively heavy dissolved silica to the oceans from continental sources. The causes behind the reversal in trend towards lower delta Si-30 in cherts younger than 1.5 Ga old are less clear. Cherts deposited 1800-1900 Ma are especially low delta Si-30, a possible indication of transiently strong hydrothermal input at this time. (C) 2012 Elsevier Ltd. All rights reserved.

SURE-FAST BILATERAL FILTERS

Edge-preserving smoothing is widely used in image processing and bilateral filtering is one way to achieve it. Bilateral filter is a nonlinear combination of domain and range filters. Implementing the classical bilateral filter is computationally intensive, owing to the nonlinearity of the range filter. In the standard form, the domain and range filters are Gaussian functions and the performance depends on the choice of the filter parameters. Recently, a constant time implementation of the bilateral filter has been proposed based on raisedcosine approximation to the Gaussian to facilitate fast implementation of the bilateral filter. We address the problem of determining the optimal parameters for raised-cosine-based constant time implementation of the bilateral filter. To determine the optimal parameters, we propose the use of Stein's unbiased risk estimator (SURE). The fast bilateral filter accelerates the search for optimal parameters by faster optimization of the SURE cost. Experimental results show that the SURE-optimal raised-cosine-based bilateral filter has nearly the same performance as the SURE-optimal standard Gaussian bilateral filter and the Oracle mean squared error (MSE)-based optimal bilateral filter.