A retrospective study of Babesia macropus associated with morbidity and mortality in eastern grey kangaroos (Macropus giganteus) and agile wallabies (Macropus agilis)

This is a retrospective study of 38 cases of infection by Babesia macropus, associated with a syndrome of anaemia and debility in hand-reared or free-ranging juvenile eastern grey kangaroos (Macropus giganteus) from coastal New South Wales and south-eastern Queensland between 1995 and 2013. Infection with B. macropus is recorded for the first time in agile wallabies (Macropus agilis) from far north Queensland. Animals in which B. macropus infection was considered to be the primary cause of morbidity had marked anaemia, lethargy and neurological signs, and often died. In these cases, parasitised erythrocytes were few or undetectable in peripheral blood samples but were sequestered in large numbers within small vessels of visceral organs, particularly in the kidney and brain, associated with distinctive clusters of extraerythrocytic organisms. Initial identification of this piroplasm in peripheral blood smears and in tissue impression smears and histological sections was confirmed using transmission electron microscopy and molecular analysis. Samples of kidney, brain or blood were tested using PCR and DNA sequencing of the 18S ribosomal RNA and heat shock protein 70 gene using primers specific for piroplasms. The piroplasm detected in these samples had 100 sequence identity in the 18S rRNA region with the recently described Babesia macropus in two eastern grey kangaroos from New South Wales and Queensland, and a high degree of similarity to an unnamed Babesia sp. recently detected in three woylies (Bettongia penicillata ogilbyi) in Western Australia.

Genetic characterization of field-evolved resistance to phosphine in the rusty grain beetle, Cryptolestes ferrugineus (Laemophloeidae: Coleoptera)

Inheritance of resistance to phosphine fumigant was investigated in three field-collected strains of rusty grain beetle, Cryptolestes ferrugineus, Susceptible (S-strain), Weakly Resistant (Weak-R) and Strongly Resistant (Strong-R). The strains were purified for susceptibility, weak resistance and strong resistance to phosphine, respectively, to ensure homozygosity of resistance genotype. Crosses were established between S-strain × Weak-R, S-strain × Strong-R and Weak-R × Strong-R, and the dose mortality responses to phosphine of these strains and their F1, F2 and F1-backcross progeny were obtained. The fumigations were undertaken at 25 °C and 55% RH for 72 h. Weak-R and Strong-R showed resistance factors of 6.3 × and 505 × compared with S-strain at the LC50. Both weak and strong resistances were expressed as incompletely recessive with degrees of dominance of − 0.48 and − 0.43 at the LC50, respectively. Responses of F2 and F1-backcross progeny indicated the existence of one major gene in Weak-R, and at least two major genes in Strong-R, one of which was allelic with the major factor in Weak-R. Phenotypic variance analyses also estimated that the number of independently segregating genes conferring weak resistance was 1 (nE = 0.89) whereas there were two genes controlling strong resistance (nE = 1.2). The second gene, unique to Strong-R, interacted synergistically with the first gene to confer a very high level of resistance (~ 80 ×). Neither of the two major resistance genes was sex linked. Despite the similarity of the genetics of resistance to that previously observed in other pest species, a significant proportion (~ 15 to 30%) of F1 individuals survived at phosphine concentrations higher than predicted. Thus it is likely that additional dominant heritable factors, present in some individuals in the population, also influenced the resistance phenotype. Our results will help in understanding the process of selection for phosphine resistance in the field which will inform resistance management strategies. In addition, this information will provide a basis for the identification of the resistance genes.

Genetic characterization of field-evolved resistance to phosphine in the rusty grain beetle, Cryptolestes ferrugineus (Laemophloeidae: Coleoptera)

Inheritance of resistance to phosphine fumigant was investigated in three field-collected strains of rusty grain beetle, Cryptolestes ferrugineus, Susceptible (S-strain), Weakly Resistant (Weak-R) and Strongly Resistant (Strong-R). The strains were purified for susceptibility, weak resistance and strong resistance to phosphine, respectively, to ensure homozygosity of resistance genotype. Crosses were established between S-strain × Weak-R, S-strain × Strong-R and Weak-R × Strong-R, and the dose mortality responses to phosphine of these strains and their F1, F2 and F1-backcross progeny were obtained. The fumigations were undertaken at 25 °C and 55% RH for 72 h. Weak-R and Strong-R showed resistance factors of 6.3 × and 505 × compared with S-strain at the LC50. Both weak and strong resistances were expressed as incompletely recessive with degrees of dominance of − 0.48 and − 0.43 at the LC50, respectively. Responses of F2 and F1-backcross progeny indicated the existence of one major gene in Weak-R, and at least two major genes in Strong-R, one of which was allelic with the major factor in Weak-R. Phenotypic variance analyses also estimated that the number of independently segregating genes conferring weak resistance was 1 (nE = 0.89) whereas there were two genes controlling strong resistance (nE = 1.2). The second gene, unique to Strong-R, interacted synergistically with the first gene to confer a very high level of resistance (~ 80 ×). Neither of the two major resistance genes was sex linked. Despite the similarity of the genetics of resistance to that previously observed in other pest species, a significant proportion (~ 15 to 30%) of F1 individuals survived at phosphine concentrations higher than predicted. Thus it is likely that additional dominant heritable factors, present in some individuals in the population, also influenced the resistance phenotype. Our results will help in understanding the process of selection for phosphine resistance in the field which will inform resistance management strategies. In addition, this information will provide a basis for the identification of the resistance genes.

Semantic Classes in Topic Detection and Tracking

Topic detection and tracking (TDT) is an area of information retrieval research the focus of which revolves around news events. The problems TDT deals with relate to segmenting news text into cohesive stories, detecting something new, previously unreported, tracking the development of a previously reported event, and grouping together news that discuss the same event. The performance of the traditional information retrieval techniques based on full-text similarity has remained inadequate for online production systems. It has been difficult to make the distinction between same and similar events. In this work, we explore ways of representing and comparing news documents in order to detect new events and track their development. First, however, we put forward a conceptual analysis of the notions of topic and event. The purpose is to clarify the terminology and align it with the process of news-making and the tradition of story-telling. Second, we present a framework for document similarity that is based on semantic classes, i.e., groups of words with similar meaning. We adopt people, organizations, and locations as semantic classes in addition to general terms. As each semantic class can be assigned its own similarity measure, document similarity can make use of ontologies, e.g., geographical taxonomies. The documents are compared class-wise, and the outcome is a weighted combination of class-wise similarities. Third, we incorporate temporal information into document similarity. We formalize the natural language temporal expressions occurring in the text, and use them to anchor the rest of the terms onto the time-line. Upon comparing documents for event-based similarity, we look not only at matching terms, but also how near their anchors are on the time-line. Fourth, we experiment with an adaptive variant of the semantic class similarity system. The news reflect changes in the real world, and in order to keep up, the system has to change its behavior based on the contents of the news stream. We put forward two strategies for rebuilding the topic representations and report experiment results. We run experiments with three annotated TDT corpora. The use of semantic classes increased the effectiveness of topic tracking by 10-30\% depending on the experimental setup. The gain in spotting new events remained lower, around 3-4\%. The anchoring the text to a time-line based on the temporal expressions gave a further 10\% increase the effectiveness of topic tracking. The gains in detecting new events, again, remained smaller. The adaptive systems did not improve the tracking results.

Computational Techniques for Haplotype Inference and for Local Alignment Significance

This thesis which consists of an introduction and four peer-reviewed original publications studies the problems of haplotype inference (haplotyping) and local alignment significance. The problems studied here belong to the broad area of bioinformatics and computational biology. The presented solutions are computationally fast and accurate, which makes them practical in high-throughput sequence data analysis. Haplotype inference is a computational problem where the goal is to estimate haplotypes from a sample of genotypes as accurately as possible. This problem is important as the direct measurement of haplotypes is difficult, whereas the genotypes are easier to quantify. Haplotypes are the key-players when studying for example the genetic causes of diseases. In this thesis, three methods are presented for the haplotype inference problem referred to as HaploParser, HIT, and BACH. HaploParser is based on a combinatorial mosaic model and hierarchical parsing that together mimic recombinations and point-mutations in a biologically plausible way. In this mosaic model, the current population is assumed to be evolved from a small founder population. Thus, the haplotypes of the current population are recombinations of the (implicit) founder haplotypes with some point--mutations. HIT (Haplotype Inference Technique) uses a hidden Markov model for haplotypes and efficient algorithms are presented to learn this model from genotype data. The model structure of HIT is analogous to the mosaic model of HaploParser with founder haplotypes. Therefore, it can be seen as a probabilistic model of recombinations and point-mutations. BACH (Bayesian Context-based Haplotyping) utilizes a context tree weighting algorithm to efficiently sum over all variable-length Markov chains to evaluate the posterior probability of a haplotype configuration. Algorithms are presented that find haplotype configurations with high posterior probability. BACH is the most accurate method presented in this thesis and has comparable performance to the best available software for haplotype inference. Local alignment significance is a computational problem where one is interested in whether the local similarities in two sequences are due to the fact that the sequences are related or just by chance. Similarity of sequences is measured by their best local alignment score and from that, a p-value is computed. This p-value is the probability of picking two sequences from the null model that have as good or better best local alignment score. Local alignment significance is used routinely for example in homology searches. In this thesis, a general framework is sketched that allows one to compute a tight upper bound for the p-value of a local pairwise alignment score. Unlike the previous methods, the presented framework is not affeced by so-called edge-effects and can handle gaps (deletions and insertions) without troublesome sampling and curve fitting.

Methods for Answer Extraction in Textual Question Answering

In this thesis we present and evaluate two pattern matching based methods for answer extraction in textual question answering systems. A textual question answering system is a system that seeks answers to natural language questions from unstructured text. Textual question answering systems are an important research problem because as the amount of natural language text in digital format grows all the time, the need for novel methods for pinpointing important knowledge from the vast textual databases becomes more and more urgent. We concentrate on developing methods for the automatic creation of answer extraction patterns. A new type of extraction pattern is developed also. The pattern matching based approach chosen is interesting because of its language and application independence. The answer extraction methods are developed in the framework of our own question answering system. Publicly available datasets in English are used as training and evaluation data for the methods. The techniques developed are based on the well known methods of sequence alignment and hierarchical clustering. The similarity metric used is based on edit distance. The main conclusions of the research are that answer extraction patterns consisting of the most important words of the question and of the following information extracted from the answer context: plain words, part-of-speech tags, punctuation marks and capitalization patterns, can be used in the answer extraction module of a question answering system. This type of patterns and the two new methods for generating answer extraction patterns provide average results when compared to those produced by other systems using the same dataset. However, most answer extraction methods in the question answering systems tested with the same dataset are both hand crafted and based on a system-specific and fine-grained question classification. The the new methods developed in this thesis require no manual creation of answer extraction patterns. As a source of knowledge, they require a dataset of sample questions and answers, as well as a set of text documents that contain answers to most of the questions. The question classification used in the training data is a standard one and provided already in the publicly available data.

Similarities in Different Experiments of Erosion Caused by Cavitation and Liquid Impingement

Correlations of erosion resistances of materials tested in different equipment are reported. Analysis of the authors' data from rotating disk and venturi equipment indicates that there exists a good correlation between the erosion resistances of materials tested at different intensities. The study indicates that time effects on erosion are important in correlations of this type. The erosion resistances of materials tested in two different devices exhibit good correlations indicating a quantitative similarity between different forms of erosion. The investigations also show that the prediction of erosion resistances of materials in a field device may be made with the data from a laboratory device which may not fully reproduce the flow conditions in the field. These conclusions are also checked with data reported from other laboratories.

Turbulence measurements in an equilibrium axisymmetric wall jet

This paper reports measurements of turbulent quantities in an axisymmetric wall jet subjected to an adverse pressure gradient in a conical diffuser, in such a way that a suitably defined pressure-gradient parameter is everywhere small. Self-similarity is observed in the mean velocity profile, as well as the profiles of many turbulent quantities at sufficiently large distances from the injection slot. Autocorrelation measurements indicate that, in the region of turbulent production, the time scale of ν fluctuations is very much smaller than the time scale of u fluctuations. Based on the data on these time scales, a possible model is proposed for the Reynolds stress. One-dimensional energy spectra are obtained for the u, v and w components at several points in the wall jet. It is found that self-similarity is exhibited by the one-dimensional wavenumber spectrum of $\overline{q^2}(=\overline{u^2}+\overline{v^2}+\overline{w^2})$, if the half-width of the wall jet and the local mean velocity are used for forming the non-dimensional wavenumber. Both the autocorrelation curves and the spectra indicate the existence of periodicity in the flow. The rate of dissipation of turbulent energy is estimated from the $\overline{q^2}$ spectra, using a slightly modified version of a previously suggested method.

Similar solutions for the incompressible laminar boundary layer with pressure gradient in micropolar

This paper presents the similarity solution for the steady incompressible laminar boundary layer flow of a micropolar fluid past an infinite wedge. The governing equations have been solved numerically using fourth orderRunge-Kutta-Gill method. The results indicate the extent to which the velocity and microrotation profiles, and the surface shear stress are influenced by coupling, microrotation, and pressure gradient parameters. The important role played by the standard length of the micropolar fluid in determining the structure of the boundary layer has also been discussed.

Double standard polynucleotides: two typical alternative conformations for nucleic acids

Two typical alternative conformations for double strandee polynucleotides with Watson-Crick base pairing scheme are presented. these types avoid tangling of the chains. Representative models of these types with two different views, to show the similarity and dissimilarity between these models and the Watson-Crick model, are given.

Unsteady laminar boundary layers in a compressible stagnation flow

The unsteady laminar compressible boundary-layer flow in the immediate vicinity of a two-dimensional stagnation point due to an incident stream whose velocity varies arbitrarily with time is considered. The governing partial differential equations, involving both time and the independent similarity variable, are transformed into new co-ordinates with finite ranges by means of a transformation which maps an infinite interval into a finite one. The resulting equations are solved by converting them into a matrix equation through the application of implicit finite-difference formulae. Computations have been carried out for two particular unsteady free-stream velocity distributions: (1) a constantly accelerating stream and (2) a fluctuating stream. The results show that in the former case both the skin-friction and the heat-transfer parameter increase steadily with time after a certain instant, while in the latter they oscillate thus responding to the fluctuations in the free-stream velocity.

Holistic Spirituality in the Thinking of Ellen White

Spiritualiteetti viittaa syvälliseen, inhimilliseen ulottuvuuteen ja ominaisuuteen, jonka tarkka määritteleminen on haasteellista, ellei mahdotonta. Sitä vastaa yhtäältä uskonnollisuuden kautta toteutuva, elämän tarkoitukseen ja syvemmän olemuksen etsintään liittyvä hengellisyys, mutta toisaalta myös kaikkea muuta hengen viljelyä ja mielekkään olemisen tavoittelua tarkoittava henkisyys. John Swintonin mukaan hengen ulottuvuus on se inhimilliseen olemukseen kuuluva, dynaaminen elinvoima, joka virkistää ja elävöittää ihmistä ja motivoi häntä etsimään Jumalaa, arvoja, merkitystä, tarkoitusta ja toivoa. Tämä tutkimus nostaa tarkastelun kohteeksi kokonaisvaltaisen hengellisyyden, jolloin huomio kiinnitetään niihin sidoksiin, joiden kautta hengen ulottuvuus liittyy muihin inhimillisen elämän olennaisiin toimintoihin ja näkökulmiin. Tällaisia ovat 1) ajattelu 2) teot ja käytännön toiminta 3) suhteet ja vuorovaikutusverkostot 4) tunteet ja kanssakäymistä ohjaavat asenteet 5) olemassaolon ja olemisen ulottuvuudet. Kokemusten merkitys, arvo ja mielekkyys hahmottuvat juuri hengen alueella, toisin sanoen sisäisesti, hengellisenä ja henkisenä asiana. Tutkimusmateriaalina tässä tutkimuksessa on amerikkalaisen vuosina 1827 1915 eläneen Ellen Whiten kuusi myöhäiskauden teosta vuosilta 1892 1905 ja tutkimusmenetelmänä on käytetty systemaattista analyysiä. Olennaista Whiten tavassa käsitellä uskonnon harjoitukseen liittyviä aiheita on hänen käytännöllinen ja elämän arkeen kiinteästi niveltyvä otteensa. Tutkimus paljastaa, että Martti Lutherin käsitykset ovat merkittävästi vaikuttaneet Whiten ajatteluun. Lähteistä paljastuu samankaltaisuutta hänen näkemystensä ja uusimman suomalaisen Luther-tutkimuksen Martti Lutherin tuotannosta esiin nostaman ajattelutavan välillä. Vaikka teologisen oppineisuuden kannalta White ja Luther ovat eri tasoilla, kummankin käsitys ihmisen ja Jumalan välisen suhteen perusolemuksesta on samankaltainen: Lähtökohtana sille on Jumalan rakkaus ja hänen armostaan lähtenyt toiminta. Toiseksi, ihmisen ja Kristuksen välinen, olemuksellinen yhteys, unio , on perustana sille, että Jumala hyväksyy ihmisen ja huolehtii hänestä nyt ja ikuisesti. Kolmanneksi, tämä ihmisen ja Kristuksen liittoutuminen ja yhdistyminen ilmenee yhteistoimintana ja kumppanuutena yhteisten tavoitteiden saavuttamiseksi maailmassa. White korostaa ihmisen ja Kristuksen välisen hengellisen suhteen vuorovaikutteista ja toiminnallista luonnetta, joka tulee ilmi epäitsekkyytenä, toisten ihmisten ja heidän tarpeittensa huomioimisena sekä myötätuntona ja kykynä asettua toisen asemaan. Terveellistä elämäntapaa ja kasvatusta koskevat ajatuksensa White liittää siihen laaja-alaiseen näkemykseen hengellisyydestä, jonka tavoitteena on ihmisen kokonaisvaltainen hyvinvointi. Hän ei näe spiritualiteettia elämän arjesta irrallisena tai erillisenä saarekkeena, vaan ihmistä kaikessa ohjaavana, voimaannuttavana ja mielekkyyttä tuottavana, ensisijaisena ulottuvuutena. Tutkimuksen kuluessa myös Whiten usein käyttämät Jumalalle antautumisen ja luonteen käsitteet nousevat tarkastelun kohteiksi. Hänen mukaansa ihminen ei tahdonponnistuksillaan yksin pysty tavoittamaan Jumalaa vaan hänen on lakattava Jumalan rakastavan kutsun edessä itse tahtomasta ja suostuttava liittymään Jumalan tahtoon ja tarkoitukseen. Tämä liittyy siihen sisäiseen muutokseen, jota White kuvaa luonteen käsitteen avulla. Jumalan armon vaikuttama tahdon uudelleen suuntaaminen muuttaa ihmisen olemusta, arvoja, asennoitumisen tapaa ja myötätuntoisen vuorovaikutuksen kykyä niin ettei ihminen ole enää aivan sama kuin ennen. Kysymys on toisaalta yhtäkkisestä ja kertakaikkisesta olemuksellisesta muuttumisesta, mutta samalla myös hiljaisesta, elämänmittaisesta kasvusta ja kypsymisestä. Juuri luonteen käsitteen avulla White kuvaa hengellisyyttä ja siihen kuuluvaa sisästä matkaa. Tässä tutkimuksessa spiritualiteettia lähestytään yleisinhimillisenä piirteenä ja ominaisuutena, jolloin huomio ei ole ensisijaisesti yksittäisissä opillisissa käsityksissä tai uskonnollisuuden harjoittamisen muodoissa. Tarkoituksena on luoda kokoava rakenne, jonka puitteissa holistinen spiritualiteetti voidaan selkeämmin hahmottaa ja yksilöidymmin ymmärtää.

Dielectric and Electron Spin Resonance Spectroscopic Studies of Glassy Crystalline States of Organic Compounds

Dielectric studies of the glassy crystalline states of cyclohexanol, cyclohexanone, and camphor obtained by upercooling the plastic crystalline phase demonstrate the presence of characteristic a- and p-relaxations. The parameters of the a-relaxation fit the Vogel-Tammann-Fulcher (VTF) equation. ESR spin-probe studies of the glassy crystalline phase of cyclohexanol show that there is a marked decrease in the correlation time above the glasslike transition temperature. The present studies suggest the similarity between glassy crystals having long-range orientational disorder and glasses which are known to betra nslationally disordered.

Laminar compressible boundary layers with vectored mass transfer

The paper studies the influence of vectored suction or injection on the flow and heat transfer at the stagnation point of a two-dimensional body (a cylinder) and an axisymmetric body (a sphere) with allowance for the effects of variable gas properties. The analysis is based on the boundary-layer equations in dimensionless form for the steady compressible fluid with variable properties in the stagnation region of a two-dimensional or an axisymmetric body with tangential and normal surface mass transfer under similarity requirements. It is shown that the variation of the density-viscosity product across the boundary layer has a strong effect on the skin friction and heat transfer. This gives rise to a point of inflection which can be removed by suction and by increasing the wall temperature. The skin friction and heat transfer are significantly affected by the pressure gradient parameter.

Nonsimilar incompressible laminar boundary layers with magnetic field.

The solution of the steady laminar incompressible nonsimilar magneto-hydrodynamic boundary layer flow and heat transfer problem with viscous dissipation for electrically conducting fluids over two-dimensional and axisymmetric bodies with pressure gradient and magnetic field has been presented. The partial differential equations governing the flow have been solved numerically using an implicit finite-difference scheme. The computations have been carried out for flow over a cylinder and a sphere. The results indicate that the magnetic field tends to delay or prevent separation. The heat transfer strongly depends on the viscous dissipation parameter. When the dissipation parameter is positive (i.e. when the temperature of the wall is greater than the freestream temperature) and exceeds a certain value, the hot wall ceases to be cooled by the stream of cooler air because the ‘heat cushion’ provided by the frictional heat prevents cooling whereas the effect of the magnetic field is to remove the ‘heat cushion’ so that the wall continues to be cooled. The results are found to be in good agreement with those of the local similarity and local nonsimilarity methods except near the point of separation, but they are in excellent agreement with those of the difference-differential technique even near the point of separation.