Geometric View of Measurement Errors

The slope of the best fit line from minimizing the sum of the squared oblique errors is the root of a polynomial of degree four. This geometric view of measurement errors is used to give insight into the performance of various slope estimators for the measurement error model including an adjusted fourth moment estimator introduced by Gillard and Iles (2005) to remove the jump discontinuity in the estimator of Copas (1972). The polynomial of degree four is associated with a minimun deviation estimator. A simulation study compares these estimators showing improvement in bias and mean squared error

Quantitative resistance can lead to evolutionary changes in traits not targeted by the resistance QTLs.

This paper addresses the general concern in plant pathology that the introduction of quantitative resistance in the landscape can lead to increased pathogenicity. Hereto, we study the hypothetical case of a quantitative trait loci (QTL) acting on pathogen spore production per unit lesion area. To regain its original fitness, the pathogen can break the QTL, restoring its spore production capacity leading to an increased spore production per lesion. Or alternatively, it can increase its lesion size, also leading to an increased spore production per lesion. A data analysis shows that spore production per lesion (affected by the resistance QTL) and lesion size (not targeted by the QTL) are positively correlated traits, suggesting that a change in magnitude of a trait not targeted by the QTL (lesion size) might indirectly affect the targeted trait (spore production per lesion). Secondly, we model the effect of pathogen adaptation towards increased lesion size and analyse its consequences for spore production per lesion. The model calculations show that when the pathogen is unable to overcome the resistance associated QTL, it may compensate for its reduced fitness by indirect selection for increased pathogenicity on both the resistant and susceptible cultivar, but whereby the QTLs remain effective.Rothamsted Research receives support from the Biotechnology and Biological Sciences Research Council (BBSRC) of the United Kingdom. F v d Berg was funded by an INRA-BBSRC funded project entitled ‘Epidemiological and evolutionary models for invasion and persistence of disease’. CAG gratefully acknowledges support of a BBSRC Professional Fellowship

Ethiopian agriculture has greater potential for carbon sequestration than previously estimated

More than half of the cultivation-induced carbon loss from agricultural soils could be restored through improved management. To incentivise carbon sequestration, the potential of improved practices needs to be verified. To date, there is sparse empirical evidence of carbon sequestration through improved practices in East-Africa. Here, we show that agroforestry and restrained grazing had a greater stock of soil carbon than their bordering pair-matched controls, but the difference was less obvious with terracing. The controls were treeless cultivated fields for agroforestry, on slopes not terraced for terracing, and permanent pasture for restrained grazing, representing traditionally managed agricultural practices dominant in the case regions. The gain by the improved management depended on the carbon stocks in the control plots. Agroforestry for 6-20 years led to 11.4 Mg ha(-1) and restrained grazing for 6-17 years to 9.6 Mg ha(-1) greater median soil carbon stock compared with the traditional management. The empirical estimates are higher than previous process-model-based estimates and indicate that Ethiopian agriculture has greater potential to sequester carbon in soil than previously estimated.Peer reviewe

Negative and positive selection of antigen-specific cytotoxic T lymphocytes affected by the α3 domain of MHC I molecules

THE α1 and α2 domains of major histocompatibility complex (MHC) class I molecules function in the binding and presentation of foreign peptides to the T-cell antigen receptor and control both negative and positive selection of the T-cell repertoire. Although the α3 domain of class I is not involved in peptide binding, it does interact with the T-cell accessory molecule, CDS. CDS is important in the selection of T cells as anti-CDS antibody injected into perinatal mice interfers with this process. We previously used a hybrid class I molecule with the α1/α2 domains from L^d and the α3 domain from Q7^b and showed that this molecule binds an L^d-restricted peptide but does not interact with CD8-dependent cytotoxic T lymphocytes. Expression of this molecule in transgenic mice fails to negatively select a subpopulation of anti-L^d cytotoxic T lymphocytes. In addition, positive selection of virus-specific L^d-restricted cytotoxic T lymphocytes does not occur. We conclude that besides the α1/α2 domains of class I, the α3 domain plays an important part in both positive and negative selection of antigen-specific cells

The development of a mouse model to explore resistance and susceptibility to early Ascaris suum infection

Ascaris suum and Ascaris lumbricoides exhibit an over-dispersed frequency distribution in their host populations in both the adult and larval stages. The impact of host factors on this observed distribution is still poorly understood and difficult to investigate in the natural host populations. The use of a mouse model has been supported by the observations that the larval migratory pattern, in this host, mimics the pattern observed in the pig. We explored the extrinsic factors that might affect the quantitative recovery of larvae during this migration in order to standardize a model system facilitating accurate future assessment of host genetic variation on this phase of the infection. In Exp. 1 larvae accumulated in the livers of both C57BL/6j and BALB/c mice up to and including days 4–5 p.i. and then declined in both strains until day 9. Loss of larvae from the livers corresponded to arrival in the lungs and maximum accumulation on day 7 p.i. but recovery was considerably higher in C57BL/6j mice. It was concluded that day 7 recoveries gave the best indication of relative resistance/susceptibility to this parasite. In Exp. 2 A/J, BALB/c, CBA/Ca, C57BL/6j, C3H/HeN, DBA/2, NIH, SJL, and SWR mice were compared. C57BL/6j mice were identified as the most susceptible strain and CBA/Ca mice as having the most contrasting phenotype, but with a similar kinetic pattern of migration. Finally, in Exp. 3, a strong positive correlation between the size of the inoculum and the mean worm recovery from the lungs was found in CBA/Ca and C57BL/6j mice, but the difference between these strains was highly consistent, 66.6–80%, regardless of the initial dose. These results demonstrate that, using our protocols for infection and recovery, between-experiment variation in A. suum worm burdens is minimal, and that C57BL/6j mice are highly susceptible to infection compared to other strains. The mechanistic basis of this susceptibility in relation to the resistance of other strains is unknown, but the possibilities are reviewed

Involvement of Mhc Loci in immune responses that are not Ir-gene-controlled

Twenty-nine randomly chosen, soluble antigens, many of them highly complex, were used to immunize mice of two strains, C3H and B10.RIII. Lymphnode cells from the immunized mice were restimulated in vitro with the priming antigens and the proliferative response of the cells was determined. Both strains were responders to 28 of 29 antigens. Eight antigens were then used to immunize 11 congenic strains carrying different H-2 haplotypes, and the T-cell proliferative responses of these strains were determined. Again, all the strains responded to seven of the eight antigens. These experiments were then repeated, but this time -antibodies specific for the A (AA) or E (EE) molecules were added to the culture to block the in vitro responsiveness. In all but one of the responses, inhibition with both A-specific and E-specific antibodies was observed. The response to one antigen (Blastoinyces) was exceptional in that some strains were nonresponders to this antigen. Furthermore, the response in the responder strains was blocked with A-specific, but not with E-specific, antibodies. The study demonstrates that responses to antigens not controlled by Irr genes nevertheless require participation of class II Mhc molecules. In contrast to Ir gene-controlled responses involving either the A- or the E-molecule controlling loci (but never both), the responses not Ir-controlled involve participation of both A- and E-controlling loci. The lack of Ir-gene control is probably the result of complexity of the responses to multiple determinants. There is thus no principal difference between responses controlled and those not controlled by Ir genes: both types involve the recognition of the antigen, in the context of Mhc molecules

Spelling errors and keywords in born-digital data: a case study using the Teenage Health Freak Corpus

The abundance of language data that is now available in digital form, and the rise of distinct language varieties that are used for digital communication, means that issues of non-standard spellings and spelling errors are, in future, likely to become more prominent for compilers of corpora. This paper examines the effect of spelling variation on keywords in a born-digital corpus in order to explore the extent and impact of this variation for future corpus studies. The corpus used in this study consists of e-mails about health concerns that were sent to a health website by adolescents. Keywords are generated using the original version of the corpus and a version with spelling errors corrected, and the British National Corpus (BNC) acts as the reference corpus. The ranks of the keywords are shown to be very similar and, therefore, suggest that, depending on the research goals, keywords could be generated reliably without any need for spelling correction

A Model for the Development of the Rhizobial and Arbuscular Mycorrhizal Symbioses in Legumes and Its Use to Understand the Roles of Ethylene in the Establishment of these two Symbioses

We propose a model depicting the development of nodulation and arbuscular mycorrhizae. Both processes are dissected into many steps, using Pisum sativum L. nodulation mutants as a guideline. For nodulation, we distinguish two main developmental programs, one epidermal and one cortical. Whereas Nod factors alone affect the cortical program, bacteria are required to trigger the epidermal events. We propose that the two programs of the rhizobial symbiosis evolved separately and that, over time, they came to function together. The distinction between these two programs does not exist for arbuscular mycorrhizae development despite events occurring in both root tissues. Mutations that affect both symbioses are restricted to the epidermal program. We propose here sites of action and potential roles for ethylene during the formation of the two symbioses with a specific hypothesis for nodule organogenesis. Assuming the epidermis does not make ethylene, the microsymbionts probably first encounter a regulatory level of ethylene at the epidermis–outermost cortical cell layer interface. Depending on the hormone concentrations there, infection will either progress or be blocked. In the former case, ethylene affects the cortex cytoskeleton, allowing reorganization that facilitates infection; in the latter case, ethylene acts on several enzymes that interfere with infection thread growth, causing it to abort. Throughout this review, the difficulty of generalizing the roles of ethylene is emphasized and numerous examples are given to demonstrate the diversity that exists in plants

Geometry of River Networks I: Scaling, Fluctuations, and Deviations

This article is the first in a series of three papers investigating the detailed geometry of river networks. Large-scale river networks mark an important class of two-dimensional branching networks, being not only of intrinsic interest but also a pervasive natural phenomenon. In the description of river network structure, scaling laws are uniformly observed. Reported values of scaling exponents vary suggesting that no unique set of scaling exponents exists. To improve this current understanding of scaling in river networks and to provide a fuller description of branching network structure, we report here a theoretical and empirical study of fluctuations about and deviations from scaling. We examine data for continent-scale river networks such as the Mississippi and the Amazon and draw inspiration from a simple model of directed, random networks. We center our investigations on the scaling of the length of sub-basin's dominant stream with its area, a characterization of basin shape known as Hack's law. We generalize this relationship to a joint probability density and show that fluctuations about scaling are substantial. We find strong deviations from scaling at small scales which can be explained by the existence of linear network structure. At intermediate scales, we find slow drifts in exponent values indicating that scaling is only approximately obeyed and that universality remains indeterminate. At large scales, we observe a breakdown in scaling due to decreasing sample space and correlations with overall basin shape. The extent of approximate scaling is significantly restricted by these deviations and will not be improved by increases in network resolution.Comment: 16 pages, 13 figures, Revtex4, submitted to PR

CELL-TO-CELL INTERACTION IN THE IMMUNE RESPONSE : VI. CONTRIBUTION OF THYMUS-DERIVED CELLS AND ANTIBODY-FORMING CELL PRECURSORS TO IMMUNOLOGICAL MEMORY

Collaboration between thymus-derived lymphocytes and nonthymus-derived antibody-forming cell precursors occurs in the primary antibody response of mice to heterologous erythrocytes and serum proteins. The purpose of the experiments reported here was to determine whether collaboration took place in an adoptive secondary antibody response. A chimeric population of lymphocytes was produced by reconstituting neonatally thymectomized CBA mice soon after birth with (CBA x C57BL)F1 thymus lymphocytes. These mice could be effectively primed to fowl immunoglobulin G (FγG) and their thoracic duct lymphocytes adoptively transferred memory responses to irradiated mice. The activity of these cells was impaired markedly by preincubation with CBA anti-C57BL serum and to a lesser extent by anti-θ-serum. Reversal of this deficiency was obtained by adding T cells in the form of thoracic duct cells from normal CBA mice. Cells from FγG-primed mice were at least 10 times as effective as cells from normal mice or from CBA mice primed to horse erythrocytes. These results were considered to support the concept that memory resides in the T cell population and that collaboration between T and B cells is necessary for an optimal secondary antibody response. Poor antibody responses were obtained in irradiated mice given mixtures of thoracic duct cells from primed mice and of B cells from unprimed mice (in the form of spleen or thoracic duct cells from thymectomized donors). In contrast to the situation with T cells, the deficiency in the B cell population could not be reversed by adding B cells from unprimed mice. It was considered that memory resides in B cells as well as in T cells and that priming probably entails a change in the B cell population which is fundamentally different from that produced in the T cell population