Statistical modelling of transcript profiles of differentially regulated genes

Background: The vast quantities of gene expression profiling data produced in microarray studies, and the more precise quantitative PCR, are often not statistically analysed to their full potential. Previous studies have summarised gene expression profiles using simple descriptive statistics, basic analysis of variance (ANOVA) and the clustering of genes based on simple models fitted to their expression profiles over time. We report the novel application of statistical non-linear regression modelling techniques to describe the shapes of expression profiles for the fungus Agaricus bisporus, quantified by PCR, and for E. coli and Rattus norvegicus, using microarray technology. The use of parametric non-linear regression models provides a more precise description of expression profiles, reducing the "noise" of the raw data to produce a clear "signal" given by the fitted curve, and describing each profile with a small number of biologically interpretable parameters. This approach then allows the direct comparison and clustering of the shapes of response patterns between genes and potentially enables a greater exploration and interpretation of the biological processes driving gene expression. Results: Quantitative reverse transcriptase PCR-derived time-course data of genes were modelled. "Splitline" or "broken-stick" regression identified the initial time of gene up-regulation, enabling the classification of genes into those with primary and secondary responses. Five-day profiles were modelled using the biologically-oriented, critical exponential curve, y(t) = A + (B + Ct)Rt + ε. This non-linear regression approach allowed the expression patterns for different genes to be compared in terms of curve shape, time of maximal transcript level and the decline and asymptotic response levels. Three distinct regulatory patterns were identified for the five genes studied. Applying the regression modelling approach to microarray-derived time course data allowed 11% of the Escherichia coli features to be fitted by an exponential function, and 25% of the Rattus norvegicus features could be described by the critical exponential model, all with statistical significance of p < 0.05. Conclusion: The statistical non-linear regression approaches presented in this study provide detailed biologically oriented descriptions of individual gene expression profiles, using biologically variable data to generate a set of defining parameters. These approaches have application to the modelling and greater interpretation of profiles obtained across a wide range of platforms, such as microarrays. Through careful choice of appropriate model forms, such statistical regression approaches allow an improved comparison of gene expression profiles, and may provide an approach for the greater understanding of common regulatory mechanisms between genes

Towards a deeper understanding of system usage in organizations: A multi-level perspective

The objective of this paper is to contribute towards a deeper understanding of system usage in organizations by examining its multilevel nature. Past research on system usage has suffered from a levels bias, with researchers studying system usage at single levels of analysis only, e.g., the individual, group, or organizational level. Although single-level research can be useful, we suggest that studying organizations one level at a time will ultimately lead to an unnatural, incomplete, and very disjointed view of how information systems are used in practice. To redress this situation, we draw on recent advances in multilevel theory to present system usage as a multilevel construct and provide an illustration for what it takes for IS researchers to study it as such. The multilevel perspective advanced in this article offers rich opportunities for theoretical and empirical insights and suggests a new foundation for in-depth research on the nature of system usage, its emergence and change, and its antecedents and consequences

Face recognition by Metropolitan Police super-recognisers

Face recognition is used to prove identity across a wide variety of settings. Despite this, research consistently shows that people are typically rather poor at matching faces to photos. Some professional groups, such as police and passport officers, have been shown to perform just as poorly as the general public on standard tests of face recognition. However, face recognition skills are subject to wide individual variation, with some people showing exceptional ability—a group that has come to be known as 'super-recognisers'. The Metropolitan Police Force (London) recruits 'super-recognisers' from within its ranks, for deployment on various identification tasks. Here we test four working super-recognisers from within this police force, and ask whether they are really able to perform at levels above control groups. We consistently find that the police 'super-recognisers' perform at well above normal levels on tests of unfamiliar and familiar face matching, with degraded as well as high quality images. Recruiting employees with high levels of skill in these areas, and allocating them to relevant tasks, is an efficient way to overcome some of the known difficulties associated with unfamiliar face recognition

Anthropogenic nitrogen deposition ameliorates the decline in tree growth caused by a drier climate

Most forest ecosystems are simultaneously affected by concurrent global change drivers. However, when assessing these effects, studies have mainly focused on the responses to single factors and have rarely evaluated the joined effects of the multiple aspects of environmental change. Here, we analyzed the combined effects of anthropogenic nitrogen (N) deposition and climatic conditions on the radial growth of Acer saccharum, a dominant tree species in eastern North American forests. We capitalized on a long‐term N deposition study, replicated along a latitudinal gradient, that has been taking place for more than 20 yr. We analyzed tree radial growth as a function of anthropogenic N deposition (ambient and experimental addition) and of summer temperature and soil water conditions. Our results reveal that experimental N deposition enhances radial growth of this species, an effect that was accentuated as temperature increased and soil water became more limiting. The spatial and temporal extent of our data also allowed us to assert that the positive effects of growing under the experimental N deposition are likely due to changes in the physiological performance of this species, and not due to the positive correlation between soil N and soil water holding capacity, as has been previously speculated in other studies. Our simulations of tree growth under forecasted climate scenarios specific for this region also revealed that although anthropogenic N deposition may enhance tree growth under a large array of environmental conditions, it will not mitigate the expected effects of growing under the considerably drier conditions characteristic of our most extreme climatic scenario.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/1/ecy2095-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/2/ecy2095-sup-0001-AppendixS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/3/ecy2095-sup-0006-AppendixS6.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/4/ecy2095-sup-0007-AppendixS7.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/5/ecy2095_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/6/ecy2095-sup-0008-AppendixS8.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/7/ecy2095-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/8/ecy2095-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/9/ecy2095-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142341/10/ecy2095.pd

Drought Reduces Root Respiration In Sugar Maple Forests

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117195/1/eap199883771.pd

A Pilot Survey for the H2_2O Southern Galactic Plane Survey (HOPS)

We describe observations with the Mopra radiotelescope designed to assess the feasibility of the H$_2$O maser southern Galactic plane survey (HOPS). We mapped two one-square-degree regions along the Galactic plane using the new 12 mm receiver and the UNSW Mopra spectrometer (MOPS). We covered the entire spectrum between 19.5 and 27.5 GHz using this setup with the main aims of finding out which spectral lines can be detected with a quick mapping survey. We report on detected emission from H$_2$O masers, NH$_3$ inversion transitions (1,1), (2,2) and (3,3), HC$_3$N (3-2), as well as several radio recombination lines.Comment: accepted by PAS

International Data Sharing in Practice:New Technologies Meet Old Governance

The social structures that govern data/sample release aim to safeguard the confidentiality and privacy of cohort research participants (without whom there would be no data or samples) and enable the realization of societal benefit through optimizing the scientific use of those cohorts. Within collaborations involving multiple cohorts and biobanks, however, the local, national, and supranational institutional and legal guidelines for research (which produce a multiplicity of data access governance structures and guidelines) risk impeding the very science that is the raison d'etre of these consortia. We present an ethnographic study, which examined the epistemic and nonepistemic values driving decisions about data access and their consequences in the context of the pilot of an integrated approach to co-analysis of data. We demonstrate how the potential analytic flexibility offered by this approach was lost under contemporary data access governance. We identify three dominant values: protecting the research participant, protecting the study, and protecting the researcher. These values were both supported by and juxtaposed against a “public good” argument, and each was used as a rationale to both promote and inhibit sharing of data. While protection of the research participants was central to access permissions, decisions were also attentive to the desire of researchers to see their efforts in building population biobanks and cohorts realized in the form of scientific outputs. We conclude that systems for governing and enabling data access in large consortia need to (1) protect disclosure of research participant information or identity, (2) ensure the specific expectations of research participants are met, (3) embody systems of review that are transparent and not compromised by the specific interests of one particular group of stakeholders, and (4) facilitate data access procedures that are timely and efficient. Practical solutions are urgently needed. New approaches to data access governance should be trialed (and formally evaluated) with input from and discussion with stakeholders

Complete replication of hepatitis C virus in cell culture.

Many aspects of the hepatitis C virus (HCV) life cycle have not been reproduced in cell culture, which has slowed research progress on this important human pathogen. Here, we describe a full-length HCV genome that replicates and produces virus particles that are infectious in cell culture (HCVcc). Replication of HCVcc was robust, producing nearly 10(5) infectious units per milliliter within 48 hours. Virus particles were filterable and neutralized with a monoclonal antibody against the viral glycoprotein E2. Viral entry was dependent on cellular expression of a putative HCV receptor, CD81. HCVcc replication was inhibited by interferon-alpha and by several HCV-specific antiviral compounds, suggesting that this in vitro system will aid in the search for improved antivirals

Spectral Decomposition of Broad-Line AGNs and Host Galaxies

Using an eigenspectrum decomposition technique, we separate the host galaxy from the broad line active galactic nucleus (AGN) in a set of 4666 spectra from the Sloan Digital Sky Survey (SDSS), from redshifts near zero up to about 0.75. The decomposition technique uses separate sets of galaxy and quasar eigenspectra to efficiently and reliably separate the AGN and host spectroscopic components. The technique accurately reproduces the host galaxy spectrum, its contributing fraction, and its classification. We show how the accuracy of the decomposition depends upon S/N, host galaxy fraction, and the galaxy class. Based on the eigencoefficients, the sample of SDSS broad-line AGN host galaxies spans a wide range of spectral types, but the distribution differs significantly from inactive galaxies. In particular, post-starburst activity appears to be much more common among AGN host galaxies. The luminosities of the hosts are much higher than expected for normal early-type galaxies, and their colors become increasingly bluer than early-type galaxies with increasing host luminosity. Most of the AGNs with detected hosts are emitting at between 1% and 10% of their estimated Eddington luminosities, but the sensitivity of the technique usually does not extend to the Eddington limit. There are mild correlations among the AGN and host galaxy eigencoefficients, possibly indicating a link between recent star formation and the onset of AGN activity. The catalog of spectral reconstruction parameters is available as an electronic table.Comment: 18 pages; accepted for publication in A