[Herd problem: udder health. Retrospective study of farms assessed by the Swiss Bovine Health Service (BHS) from 1999 to 2004]

Data from 59 farms with complaints of udder health problems and insufficient quality of delivered milk that had been assessed by the Swiss Bovine Health Service (BHS) between 1999 and 2004 were retrospectively analysed. Data evaluated included farm characteristics such as farm size, herd size, average milk yield, milking system and housing system, deficits of the milking equipment and the milking practices, and bacteriological results of milk samples from all cows in lactation. The average size of the farms assessed by the BHS was larger than the size of the were evaluated, 42 showed obvious failures which the farm managers could have noticed. Only 5 of the 57 milkers carried out their work according to the generally valid guidelines of the National Mastitis Council. More than 2 basic mistakes were observed in the milking practices of 36 milkers. In 51 farms, mixed infections with several problem bacteria (those present in at least 20 % of the tested cows on a farm) were found. Staphylococcus aureus proved to be the most common problem germ. As the bacteria responsible for the herd problem (the sole problem bacteria detectable on a particular farm) Staphylococcus aureus was detected in 4 farms. The current study revealed that education in the area of milking techniques and milking practices of farmers should be improved in order to reduce the incidence of udder health problems on herd level. Staphylococcus aureus is the most important problem bacteria involved in herds with udder health problems in Switzerland. Staphylococcus aureus might be used in practice as the indicator germ for early recognition of management problems in dairy farms.

Towards greater accuracy in individual-tree mortality regression

Background mortality is an essential component of any forest growth and yield model. Forecasts of mortality contribute largely to the variability and accuracy of model predictions at the tree, stand and forest level. In the present study, I implement and evaluate state-of-the-art techniques to increase the accuracy of individual tree mortality models, similar to those used in many of the current variants of the Forest Vegetation Simulator, using data from North Idaho and Montana. The first technique addresses methods to correct for bias induced by measurement error typically present in competition variables. The second implements survival regression and evaluates its performance against the traditional logistic regression approach. I selected the regression calibration (RC) algorithm as a good candidate for addressing the measurement error problem. Two logistic regression models for each species were fitted, one ignoring the measurement error, which is the “naïve” approach, and the other applying RC. The models fitted with RC outperformed the naïve models in terms of discrimination when the competition variable was found to be statistically significant. The effect of RC was more obvious where measurement error variance was large and for more shade-intolerant species. The process of model fitting and variable selection revealed that past emphasis on DBH as a predictor variable for mortality, while producing models with strong metrics of fit, may make models less generalizable. The evaluation of the error variance estimator developed by Stage and Wykoff (1998), and core to the implementation of RC, in different spatial patterns and diameter distributions, revealed that the Stage and Wykoff estimate notably overestimated the true variance in all simulated stands, but those that are clustered. Results show a systematic bias even when all the assumptions made by the authors are guaranteed. I argue that this is the result of the Poisson-based estimate ignoring the overlapping area of potential plots around a tree. Effects, especially in the application phase, of the variance estimate justify suggested future efforts of improving the accuracy of the variance estimate. The second technique implemented and evaluated is a survival regression model that accounts for the time dependent nature of variables, such as diameter and competition variables, and the interval-censored nature of data collected from remeasured plots. The performance of the model is compared with the traditional logistic regression model as a tool to predict individual tree mortality. Validation of both approaches shows that the survival regression approach discriminates better between dead and alive trees for all species. In conclusion, I showed that the proposed techniques do increase the accuracy of individual tree mortality models, and are a promising first step towards the next generation of background mortality models. I have also identified the next steps to undertake in order to advance mortality models further.

Dirichlet-Neumann inverse spectral problem for a star graph of Stieltjes strings

We solve two inverse spectral problems for star graphs of Stieltjes strings with Dirichlet and Neumann boundary conditions, respectively, at a selected vertex called root. The root is either the central vertex or, in the more challenging problem, a pendant vertex of the star graph. At all other pendant vertices Dirichlet conditions are imposed; at the central vertex, at which a mass may be placed, continuity and Kirchhoff conditions are assumed. We derive conditions on two sets of real numbers to be the spectra of the above Dirichlet and Neumann problems. Our solution for the inverse problems is constructive: we establish algorithms to recover the mass distribution on the star graph (i.e. the point masses and lengths of subintervals between them) from these two spectra and from the lengths of the separate strings. If the root is a pendant vertex, the two spectra uniquely determine the parameters on the main string (i.e. the string incident to the root) if the length of the main string is known. The mass distribution on the other edges need not be unique; the reason for this is the non-uniqueness caused by the non-strict interlacing of the given data in the case when the root is the central vertex. Finally, we relate of our results to tree-patterned matrix inverse problems.

Tree-ring-reconstructed summer temperatures from northwestern North America during the last nine centuries

Northwestern North America has one of the highest rates of recent temperature increase in the world, but the putative “divergence problem” in dendroclimatology potentially limits the ability of tree-ring proxy data at high latitudes to provide long-term context for current anthropogenic change. Here, summer temperatures are reconstructed from a Picea glauca maximum latewood density (MXD) chronology that shows a stable relationship to regional temperatures and spans most of the last millennium at the Firth River in northeastern Alaska. The warmest epoch in the last nine centuries is estimated to have occurred during the late twentieth century, with average temperatures over the last 30 yr of the reconstruction developed for this study [1973–2002 in the Common Era (CE)] approximately 1.3° ± 0.4°C warmer than the long-term preindustrial mean (1100–1850 CE), a change associated with rapid increases in greenhouse gases. Prior to the late twentieth century, multidecadal temperature fluctuations covary broadly with changes in natural radiative forcing. The findings presented here emphasize that tree-ring proxies can provide reliable indicators of temperature variability even in a rapidly warming climate.

Roy-Steiner equations for piN scattering

In this talk, we present a coupled system of integral equations for the πN → πN (s-channel) and ππ → N̅N (t-channel) lowest partial waves, derived from Roy–Steiner equations for pion–nucleon scattering. After giving a brief overview of this system of equations, we present the solution of the t-channel sub-problem by means of Muskhelishvili–Omnès techniques, and solve the s-channel sub-problem after finding a set of phase shifts and subthreshold parameters which satisfy the Roy–Steiner equations.

Alarm tree analysis using statistical techniques

This work presents a systematic method for the generation and treatment of the alarms' graphs, being its final object to find the Alarm Root Cause of the Massive Alarms that are produced in the dispatching centers. Although many works about this matter have been already developed, the problem about the alarm management in the industry is still completely unsolved. In this paper, a simple statistic analysis of the historical data base is conducted. The results obtained by the acquisition alarm systems, are used to generate a directed graph from which the more significant alarms are extracted, previously analyzing any possible case in which a great quantity of alarms are produced.

Nonparametric generalized belief propagation based on pseudo-junction tree for cooperative localization in wireless networks

Non-parametric belief propagation (NBP) is a well-known message passing method for cooperative localization in wireless networks. However, due to the over-counting problem in the networks with loops, NBP’s convergence is not guaranteed, and its estimates are typically less accurate. One solution for this problem is non-parametric generalized belief propagation based on junction tree. However, this method is intractable in large-scale networks due to the high-complexity of the junction tree formation, and the high-dimensionality of the particles. Therefore, in this article, we propose the non-parametric generalized belief propagation based on pseudo-junction tree (NGBP-PJT). The main difference comparing with the standard method is the formation of pseudo-junction tree, which represents the approximated junction tree based on thin graph. In addition, in order to decrease the number of high-dimensional particles, we use more informative importance density function, and reduce the dimensionality of the messages. As by-product, we also propose NBP based on thin graph (NBP-TG), a cheaper variant of NBP, which runs on the same graph as NGBP-PJT. According to our simulation and experimental results, NGBP-PJT method outperforms NBP and NBP-TG in terms of accuracy, computational, and communication cost in reasonably sized networks.

Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

Competing hypotheses seek to explain the evolution of oxygenic and anoxygenic processes of photosynthesis. Since chlorophyll is less reduced and precedes bacteriochlorophyll on the modern biosynthetic pathway, it has been proposed that chlorophyll preceded bacteriochlorophyll in its evolution. However, recent analyses of nucleotide sequences that encode chlorophyll and bacteriochlorophyll biosynthetic enzymes appear to provide support for an alternative hypothesis. This is that the evolution of bacteriochlorophyll occurred earlier than the evolution of chlorophyll. Here we demonstrate that the presence of invariant sites in sequence datasets leads to inconsistency in tree building (including maximum-likelihood methods). Homologous sequences with different biological functions often share invariant sites at the same nucleotide positions. However, different constraints can also result in additional invariant sites unique to the genes, which have specific and different biological functions. Consequently, the distribution of these sites can be uneven between the different types of homologous genes. The presence of invariant sites, shared by related biosynthetic genes as well as those unique to only some of these genes, has misled the recent evolutionary analysis of oxygenic and anoxygenic photosynthetic pigments. We evaluate an alternative scheme for the evolution of chlorophyll and bacteriochlorophyll.

Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications.

Universal trees based on sequences of single gene homologs cannot be rooted. Iwabe et al. [Iwabe, N., Kuma, K.-I., Hasegawa, M., Osawa, S. & Miyata, T. (1989) Proc. Natl. Acad. Sci. USA 86, 9355-9359] circumvented this problem by using ancient gene duplications that predated the last common ancestor of all living things. Their separate, reciprocally rooted gene trees for elongation factors and ATPase subunits showed Bacteria (eubacteria) as branching first from the universal tree with Archaea (archaebacteria) and Eucarya (eukaryotes) as sister groups. Given its topical importance to evolutionary biology and concerns about the appropriateness of the ATPase data set, an evaluation of the universal tree root using other ancient gene duplications is essential. In this study, we derive a rooting for the universal tree using aminoacyl-tRNA synthetase genes, an extensive multigene family whose divergence likely preceded that of prokaryotes and eukaryotes. An approximately 1600-bp conserved region was sequenced from the isoleucyl-tRNA synthetases of several species representing deep evolutionary branches of eukaryotes (Nosema locustae), Bacteria (Aquifex pyrophilus and Thermotoga maritima) and Archaea (Pyrococcus furiosus and Sulfolobus acidocaldarius). In addition, a new valyl-tRNA synthetase was characterized from the protist Trichomonas vaginalis. Different phylogenetic methods were used to generate trees of isoleucyl-tRNA synthetases rooted by valyl- and leucyl-tRNA synthetases. All isoleucyl-tRNA synthetase trees showed Archaea and Eucarya as sister groups, providing strong confirmation for the universal tree rooting reported by Iwabe et al. As well, there was strong support for the monophyly (sensu Hennig) of Archaea. The valyl-tRNA synthetase gene from Tr. vaginalis clustered with other eukaryotic ValRS genes, which may have been transferred from the mitochondrial genome to the nuclear genome, suggesting that this amitochondrial trichomonad once harbored an endosymbiotic bacterium.

Heat stress, heat strain, and productivity in Washington State tree fruit harvesters

Thesis (Master's)--University of Washington, 2016-06

Existence and embeddings of partial Steiner triple systems of order ten with cubic leaves

Denote the set of 21 non-isomorphic cubic graphs of order 10 by L. We first determine precisely which L is an element of L occur as the leave of a partial Steiner triple system, thus settling the existence problem for partial Steiner triple systems of order 10 with cubic leaves. Then we settle the embedding problem for partial Steiner triple systems with leaves L is an element of L. This second result is obtained as a corollary of a more general result which gives, for each integer v greater than or equal to 10 and each L is an element of L, necessary and sufficient conditions for the existence of a partial Steiner triple system of order v with leave consisting of the complement of L and v - 10 isolated vertices. (C) 2004 Elsevier B.V. All rights reserved.

Physiological evidence for reproductive suppression in the introduced population of brown tree snakes (Boiga irregularis) on Guam

Introduced species are an increasingly pervasive problem. While studies on the ecology and behavior of these pests are numerous, there is relatively little known of their physiology, specifically their reproductive and stress physiology. One of the best documented introduced pest species is the brown tree snake, Boiga irregularis, which was introduced onto the Pacific island of Guam sometime around World War II. The snake is responsible for severely reducing Guam's native vertebrates. We captured free-living individuals throughout the year and measured plasma levels of stress and sex hormones in an effort to determine when they were breeding. These data were compared to reproductive cycles from a captive population originally collected from Guam. Free-living individuals had chronically elevated plasma levels of the stress hormone corticosterone and basal levels of sex steroids and a remarkably low proportion were reproductively active. These data coincide with evidence that the wild population may be in decline. Captive snakes, had low plasma levels of corticosterone with males displaying a peak in plasma testosterone levels during breeding. Furthermore, we compared body condition between the free-living and captive snakes from Guam and free-living individuals captured from their native range in Australia. Male and female free-living snakes from Guam exhibited significantly reduced body condition compared to free-living individuals from Australia. We suggest that during the study period, free-living brown tree snakes on Guam were living under stressful conditions, possibly due to overcrowding and overexploitation. of food resources, resulting in decreased body condition and suppressed reproduction. (C) 2004 Elsevier Ltd. All rights reserved.

Steiner triple systems with two disjoint subsystems

It is shown that there exists a triangle decomposition of the graph obtained from the complete graph of order v by removing the edges of two vertex disjoint complete subgraphs of orders u and w if and only if u, w, and v are odd, ((v)(2)) - ((u)(2)) - ((w)(2)) equivalent to 0 (mod 3), and v >= w + u + max {u, w}. Such decompositions are equivalent to group divisible designs with block size 3, one group of size u, one group of size w, and v - u - w groups of size 1. This result settles the existence problem for Steiner triple systems having two disjoint specified subsystems, thereby generalizing the well-known theorem of Doyen and Wilson on the existence of Steiner triple systems with a single specified subsystem. (c) 2005 Wiley Periodicals, Inc.

Deficits in dyslexia:Barking up the wrong tree?

Reviews of the dyslexia literature often seem to suggest that children with dyslexia perform at a lower level on almost any task. Richards et al. (Dyslexia 2002; 8: 1-8) note the importance of being able to demonstrate dissociations between tasks. However, increasingly elegant experiments, in which dissociations are found, almost inevitably find that the performance of children with dyslexia is lower as tasks become more difficult! By looking for deficits in dyslexia, could we be barking up the wrong tree? A methodological approach for circumventing this potential problem is discussed. Copyright © 2004 John Wiley & Sons, Ltd.