HypTrails: A Bayesian Approach for Comparing Hypotheses About Human Trails on the Web

When users interact with the Web today, they leave sequential digital trails on a massive scale. Examples of such human trails include Web navigation, sequences of online restaurant reviews, or online music play lists. Understanding the factors that drive the production of these trails can be useful for e.g., improving underlying network structures, predicting user clicks or enhancing recommendations. In this work, we present a general approach called HypTrails for comparing a set of hypotheses about human trails on the Web, where hypotheses represent beliefs about transitions between states. Our approach utilizes Markov chain models with Bayesian inference. The main idea is to incorporate hypotheses as informative Dirichlet priors and to leverage the sensitivity of Bayes factors on the prior for comparing hypotheses with each other. For eliciting Dirichlet priors from hypotheses, we present an adaption of the so-called (trial) roulette method. We demonstrate the general mechanics and applicability of HypTrails by performing experiments with (i) synthetic trails for which we control the mechanisms that have produced them and (ii) empirical trails stemming from different domains including website navigation, business reviews and online music played. Our work expands the repertoire of methods available for studying human trails on the Web.Comment: Published in the proceedings of WWW'1

ISO/IEC 15504 measurement applied to COBIT process maturity

Purpose: The assessment of COBIT process maturity levels is fraught with a number of problems regarding the objectivity of the assessment results. Unlike ISO/IEC 15504, COBIT does not define an assessment model. The purpose of this paper is to align the behavioural aspects of the six COBIT process attributes with achievement results defined for the nine process attributes associated with the ISO/IEC 15504-2 measurement scale. The authors believe that this alignment permits a translation of the ISO/IEC 15504 assessment data into an objective COBIT process maturity rating. Design/methodology/approach: The tables presented in the paper identify the COBIT process attributes, the applicable ISO/IEC 15504 process attribute achievement results and the aggregated rating that pertains to the selected achievement results. A final table lists the derived COBIT process maturity level in terms of the ratings for the ISO/IEC 15504 process attribute achievement results for an assessed process. Findings: The objectivity of the aggregated result (COBIT process maturity level) appeals strongly to end-users of this measurement result, particularly where contractual obligations must be satisfied. Practical implications: The method is useful where measurement rigour must be demonstrated in the computation of the COBIT process maturity levels. Originality/value: This assessment and computational method was developed and trialled in the second half of 2010 in the context of the assessment of 13 information technology (IT) service management processes at two different customer sites. The material is of special value to service managers in companies that have outsourced IT service management processes to external IT service providers. © Emerald Group Publishing Limited

Host-Derived Artificial MicroRNA as an Alternative Method to Improve Soybean Resistance to Soybean Cyst Nematode

Citation: Tian, B., Li, J. R., Oakley, T. R., Todd, T. C., & Trick, H. N. (2016). Host-Derived Artificial MicroRNA as an Alternative Method to Improve Soybean Resistance to Soybean Cyst Nematode. Genes, 7(12), 13. doi:10.3390/genes7120122Citation: Tian, B., . . . & Trick, H. (2016). Host-Derived Artificial MicroRNA as an Alternative Method to Improve Soybean Resistance to Soybean Cyst Nematode. Genes, 7(12), 13. https://doi.org/10.3390/genes7120122The soybean cyst nematode (SCN), Heterodera glycines, is one of the most important pests limiting soybean production worldwide. Novel approaches to managing this pest have focused on gene silencing of target nematode sequences using RNA interference (RNAi). With the discovery of endogenous microRNAs as a mode of gene regulation in plants, artificial microRNA (amiRNA) methods have become an alternative method for gene silencing, with the advantage that they can lead to more specific silencing of target genes than traditional RNAi vectors. To explore the application of amiRNAs for improving soybean resistance to SCN, three nematode genes (designated as J15, J20, and J23) were targeted using amiRNA vectors. The transgenic soybean hairy roots, transformed independently with these three amiRNA vectors, showed significant reductions in SCN population densities in bioassays. Expression of the targeted genes within SCN eggs were downregulated in populations feeding on transgenic hairy roots. Our results provide evidence that host-derived amiRNA methods have great potential to improve soybean resistance to SCN. This approach should also limit undesirable phenotypes associated with off-target effects, which is an important consideration for commercialization of transgenic crops

Kinetic and Spectroscopic Characterisation of Highly Reactive Methanesulfonates. Leaving Group Effects for Solvolyses and Comments on Geminal Electronic Effects Influencing SN_N1 Reactivity

Highly reactive methanesulfonates (mesylates, ROMs) have been prepared from 1-phenylethanol. cyclohex-2-en-1-ol, diphenylmethanol and p-methoxybenzyl alcohol by treatment with methanesulfonyl chloride and triethylamine in dichloro- or trichloro-methane at - 20 to 0 °C. The mesylates. characterised in solution by $^1$H and $^{13}$C NMR at -20 °C, were obtained in satisfactory purity (ca. 95%) in cold solutions but they decomposed by reaction with chloride, triethylamine or the parent alcohol. Rate constants for solvolyses in aqueous acetone and aqueous ethanol have been determined by a fast response conductimetric method. Product selectivities for solvolyses of pmethoxybenzyl mesylate in aqueous ethanol and methanol at 0 °C have been determined by HPLC. From additional new or Iiterature kinetic data for solvolyses of corresponding bromides. chlorides and p-nitrobenzoates (OPNB). Br/CI. OMs/Br and OMs/OPNB rate ratios were calculated; the results are consistent with electronic effects stabilising the carbocationic transition states and increasing OMs/Br rate ratios for these SN 1 solvolyses; none of the evidence supports a geminal electronic effect on Br/CI rate ratios (e.g. caused by stabilisation of the initial state in pmethoxybenzyl chloride). Steric effects on ester /halide rate ratios for solvolyses of tertiary substrates are confirmed. Relative rates over a 10$^{16}$ range for ester and halide leaving groups are evaluated for solvolyses of 1-phenylethyl substrates in 80% ethanol-water. updating previous work by Noyce et al. (1972)

Phylogenetic distance does not predict competition in green algal communities

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/116355/1/ecs214005021.pd

Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology

An Efficient System for Heterologous Expression of Secondary Metabolite Genes in Aspergillus nidulans

This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ja401945a.Fungal secondary metabolites (SMs) are an important source of medically valuable compounds. Genome projects have revealed that fungi have many SM biosynthetic gene clusters that are not normally expressed. To access these potentially valuable, cryptic clusters, we have developed a heterologous expression system in Aspergillus nidulans. We have developed an efficient system for amplifying genes from a target fungus, placing them under control of a regulatable promoter, transferring them into A. nidulans and expressing them. We have validated this system by expressing non-reducing polyketide synthases of Aspergillus terreus and additional genes required for compound production and release. We have obtained compound production and release from six of these NR-PKSs and have identified the products. To demonstrate that the procedure allows transfer and expression of entire secondary metabolite biosynthetic pathways, we have expressed all the genes of a silent A. terreus cluster and demonstrate that it produces asperfuranone. Further, by expressing the genes of this pathway in various combinations, we have clarified the asperfuranone biosynthetic pathway. We have also developed procedures for deleting entire A. nidulans SM clusters. This allows us to remove clusters that might interfere with analyses of heterologously expressed genes and to eliminate unwanted toxins

A Suborbital Payload for Soft X-ray Spectroscopy of Extended Sources

We present a suborbital rocket payload capable of performing soft X-ray spectroscopy on extended sources. The payload can reach resolutions of ~100(lambda/dlambda) over sources as large as 3.25 degrees in diameter in the 17-107 angstrom bandpass. This permits analysis of the overall energy balance of nearby supernova remnants and the detailed nature of the diffuse soft X-ray background. The main components of the instrument are: wire grid collimators, off-plane grating arrays and gaseous electron multiplier detectors. This payload is adaptable to longer duration orbital rockets given its comparatively simple pointing and telemetry requirements and an abundance of potential science targets.Comment: Accepted to Experimental Astronomy, 12 pages plus 1 table and 17 figure

Quantum Monte Carlo Calculations of Pion Scattering from Li

We show that the neutron and proton transition densities predicted by recent quantum Monte Carlo calculations for A=6,7 nuclei are consistent with pion scattering from 6Li and 7Li at energies near the Delta resonance. This has provided a microscopic understanding of the enhancement factors for quadrople excitations, which were needed to describe pion inelastic scattering within the nuclear shell model of Cohen and Kurath.Comment: 10 pages, REVTeX, 3 postscript figures; added calculation of elastic and inelastic pion scattering from 6Li at multiple energie