From Sensor Readings to Predictions: On the Process of Developing Practical Soft Sensors.

Automatic data acquisition systems provide large amounts of streaming data generated by physical sensors. This data forms an input to computational models (soft sensors) routinely used for monitoring and control of industrial processes, traffic patterns, environment and natural hazards, and many more. The majority of these models assume that the data comes in a cleaned and pre-processed form, ready to be fed directly into a predictive model. In practice, to ensure appropriate data quality, most of the modelling efforts concentrate on preparing data from raw sensor readings to be used as model inputs. This study analyzes the process of data preparation for predictive models with streaming sensor data. We present the challenges of data preparation as a four-step process, identify the key challenges in each step, and provide recommendations for handling these issues. The discussion is focused on the approaches that are less commonly used, while, based on our experience, may contribute particularly well to solving practical soft sensor tasks. Our arguments are illustrated with a case study in the chemical production industry

Comparative Analysis of the Heptahelical Transmembrane Bundles of G Protein-Coupled Receptors

Background: G protein-coupled receptors represent a large family of eukaryotic membrane proteins, and are involved in almost all physiological processes in humans. Recent advances in the crystallographic study of these receptors enable a detailed comparative analysis of the commonly shared heptahelical transmembrane bundle. Systematic comparison of the bundles from a variety of receptors is indispensable for understanding not only of the structural diversification optimized for the binding of respective ligands but also of the structural conservation required for the common mechanism of activation accompanying the interaction changes among the seven helices. Methodology/Principal Findings: We have examined the bundles of 94 polypeptide chains from almost all available structures of 11 receptors, which we classified into either inactivated chain or activated chain, based on the type of bound ligand. For the inactivated chains, superposition of 200 residue bundles by secondary structure matching demonstrated that the bound ligands share a laterally limited cavity in the extracellular section of the bundle. Furthermore, a distinct feature was found for helix III of bovine rhodopsin, which might have evolved to lower its activity in the presence of 11-cis-retinal, to a level that other receptors could hardly achieve with any currently available ligands. Conclusions/Significance: Systematic analysis described here would be valuable for understanding of the rearrangement o

Electronic sculpting of ligand-GPCR subtype selectivity:the case of angiotensin II

GPCR subtypes possess distinct functional and pharmacological profiles, and thus development of subtype-selective ligands has immense therapeutic potential. This is especially the case for the angiotensin receptor subtypes AT1R and AT2R, where a functional negative control has been described and AT2R activation highlighted as an important cancer drug target. We describe a strategy to fine-tune ligand selectivity for the AT2R/AT1R subtypes through electronic control of ligand aromatic-prolyl interactions. Through this strategy an AT2R high affinity (<i>K</i>_i = 3 nM) agonist analogue that exerted 18,000-fold higher selectivity for AT2R versus AT1R was obtained. We show that this compound is a negative regulator of AT1R signaling since it is able to inhibit MCF-7 breast carcinoma cellular proliferation in the low nanomolar range

ICIRAS: Research and reconciliation with indigenous peoples in rural health journals.

AIM: We aim to promote discussion about an Indigenous Cultural Identity of Research Authors Standard (ICIRAS) for academic journal publications. CONTEXT: This is based on a gap in research publishing practice where Indigenous peoples' identity is not systematically and rigorously flagged in rural health research publications. There are widespread reforms, in different research areas, to counter the reputation of scientific research as a vehicle of racism and discrimination against the world's Indigenous peoples. Reflecting on these broader movements, the editorial teams of three rural health journals-the Australian Journal of Rural Health, the Canadian Journal of Rural Medicine, and Rural and Remote Health-recognised that Indigenous peoples' identity could be embedded in authorship details. APPROACH: An environmental scan (through a cultural safety lens where Indigenous cultural authority is respected, valued, and empowered) of literature was undertaken to detect the signs of inclusion of Indigenous peoples in research. This revealed many ways in which editorial boards of Journals could systematically improve their process so that there is 'nothing about Indigenous people, without Indigenous people' in rural health research publications. CONCLUSION: Improving the health and wellbeing of Indigenous peoples worldwide requires high quality research evidence. The philosophy of cultural safety supports the purposeful positioning of Indigenous peoples within the kaleidoscope of cultural knowledges as identified contributors and authors of research evidence. The ICIRAS is a call-to-action for research journals and institutions to rigorously improve publication governance that signals "Editing with IndigenUs and for IndigenUs"

The Atacama Cosmology Telescope: A Measurement of the 600< ell <8000 Cosmic Microwave Background Power Spectrum at 148 GHz

We present a measurement of the angular power spectrum of the cosmic microwave background (CMB) radiation observed at 148 GHz. The measurement uses maps with 1.4' angular resolution made with data from the Atacama Cosmology Telescope (ACT). The observations cover 228 square degrees of the southern sky, in a 4.2-degree-wide strip centered on declination 53 degrees South. The CMB at arcminute angular scales is particularly sensitive to the Silk damping scale, to the Sunyaev-Zel'dovich (SZ) effect from galaxy clusters, and to emission by radio sources and dusty galaxies. After masking the 108 brightest point sources in our maps, we estimate the power spectrum between 600 < \ell < 8000 using the adaptive multi-taper method to minimize spectral leakage and maximize use of the full data set. Our absolute calibration is based on observations of Uranus. To verify the calibration and test the fidelity of our map at large angular scales, we cross-correlate the ACT map to the WMAP map and recover the WMAP power spectrum from 250 < ell < 1150. The power beyond the Silk damping tail of the CMB is consistent with models of the emission from point sources. We quantify the contribution of SZ clusters to the power spectrum by fitting to a model normalized at sigma8 = 0.8. We constrain the model's amplitude ASZ < 1.63 (95% CL). If interpreted as a measurement of sigma8, this implies sigma8^SZ < 0.86 (95% CL) given our SZ model. A fit of ACT and WMAP five-year data jointly to a 6-parameter LCDM model plus terms for point sources and the SZ effect is consistent with these results.Comment: 15 pages, 8 figures. Accepted for publication in Ap

The Atacama Cosmology Telescope (ACT): Beam Profiles and First SZ Cluster Maps

The Atacama Cosmology Telescope (ACT) is currently observing the cosmic microwave background with arcminute resolution at 148 GHz, 218 GHz, and 277 GHz. In this paper, we present ACT's first results. Data have been analyzed using a maximum-likelihood map-making method which uses B-splines to model and remove the atmospheric signal. It has been used to make high-precision beam maps from which we determine the experiment's window functions. This beam information directly impacts all subsequent analyses of the data. We also used the method to map a sample of galaxy clusters via the Sunyaev-Zel'dovich (SZ) effect, and show five clusters previously detected with X-ray or SZ observations. We provide integrated Compton-y measurements for each cluster. Of particular interest is our detection of the z = 0.44 component of A3128 and our current non-detection of the low-redshift part, providing strong evidence that the further cluster is more massive as suggested by X-ray measurements. This is a compelling example of the redshift-independent mass selection of the SZ effect.Comment: 16 pages, 10 figures. Accepted for publication in ApJS. See Marriage et al. (arXiv:1010.1065) and Menanteau et al. (arXiv:1006.5126) for additional cluster result

The Atacama Cosmology Telescope: Cosmological Parameters from the 2008 Power Spectra

We present cosmological parameters derived from the angular power spectrum of the cosmic microwave background (CMB) radiation observed at 148 GHz and 218 GHz over 296 deg^2 with the Atacama Cosmology Telescope (ACT) during its 2008 season. ACT measures fluctuations at scales 500<l<10000. We fit a model for the lensed CMB, Sunyaev-Zel'dovich (SZ), and foreground contribution to the 148 GHz and 218 GHz power spectra, including thermal and kinetic SZ, Poisson power from radio and infrared point sources, and clustered power from infrared point sources. The power from thermal and kinetic SZ at 148 GHz is estimated to be B_3000 = 6.8+-2.9 uK^2, where B_l=l(l+1)C_l/2pi. We estimate primary cosmological parameters from the 148 GHz spectrum, marginalizing over SZ and source power. The LCDM cosmological model is a good fit to the data, and LCDM parameters estimated from ACT+WMAP are consistent with the 7-year WMAP limits, with scale invariant n_s = 1 excluded at 99.7% CL (3sigma). A model with no CMB lensing is disfavored at 2.8sigma. By measuring the third to seventh acoustic peaks, and probing the Silk damping regime, the ACT data improve limits on cosmological parameters that affect the small-scale CMB power. The ACT data combined with WMAP give a 6sigma detection of primordial helium, with Y_P = 0.313+-0.044, and a 4sigma detection of relativistic species, assumed to be neutrinos, with Neff = 5.3+-1.3 (4.6+-0.8 with BAO+H0 data). From the CMB alone the running of the spectral index is constrained to be dn/dlnk = -0.034 +- 0.018, the limit on the tensor-to-scalar ratio is r<0.25 (95% CL), and the possible contribution of Nambu cosmic strings to the power spectrum is constrained to string tension Gmu<1.6 \times 10^-7 (95% CL).Comment: 20 pages, 13 figures. Submitted to ApJ. This paper is a companion to Hajian et al. (2010) and Das et al. (2010

A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

The synthesis of this dataset was enabled by funding from the Canada Foundation for Innovation, from Genome Canada through Ontario Genomics, from NSERC, and from the Ontario Ministry of Research, Innovation and Science in support of the International Barcode of Life project. It was also enabled by philanthropic support from the Gordon and Betty Moore Foundation and from Ann McCain Evans and Chris Evans. The release of the data on GGBN was supported by a GGBN – Global Genome Initiative Award and we thank G. Droege, L. Loo, K. Barker, and J. Coddington for their support. Our work depended heavily on the analytical capabilities of the Barcode of Life Data Systems (BOLD, www.boldsystems.org). We also thank colleagues at the CBG for their support, including S. Adamowicz, S. Bateson, E. Berzitis, V. Breton, V. Campbell, A. Castillo, C. Christopoulos, J. Cossey, C. Gallant, J. Gleason, R. Gwiazdowski, M. Hajibabaei, R. Hanner, K. Hough, P. Janetta, A. Pawlowski, S. Pedersen, J. Robertson, D. Roes, K. Seidle, M. A. Smith, B. St. Jacques, A. Stoneham, J. Stahlhut, R. Tabone, J.Topan, S. Walker, and C. Wei. For bioblitz-related assistance, we are grateful to D. Ireland, D. Metsger, A. Guidotti, J. Quinn and other members of Bioblitz Canada and Ontario Bioblitz. For our work in Canada’s national parks, we thank S. Woodley and J. Waithaka for their lead role in organizing permits and for the many Parks Canada staff who facilitated specimen collections, including M. Allen, D. Amirault-Langlais, J. Bastick, C. Belanger, C. Bergman, J.-F. Bisaillon, S. Boyle, J. Bridgland, S. Butland, L. Cabrera, R. Chapman, J. Chisholm, B. Chruszcz, D. Crossland, H. Dempsey, N. Denommee, T. Dobbie, C. Drake, J. Feltham, A. Forshner, K. Forster, S. Frey, L. Gardiner, P. Giroux, T. Golumbia, D. Guedo, N. Guujaaw, S. Hairsine, E. Hansen, C. Harpur, S. Hayes, J. Hofman, S. Irwin, B. Johnston, V. Kafa, N. Kang, P. Langan, P. Lawn, M. Mahy, D. Masse, D. Mazerolle, C. McCarthy, I. McDonald, J. McIntosh, C. McKillop, V. Minelga, C. Ouimet, S. Parker, N. Perry, J. Piccin, A. Promaine, P. Roy, M. Savoie, D. Sigouin, P. Sinkins, R. Sissons, C. Smith, R. Smith, H. Stewart, G. Sundbo, D. Tate, R. Tompson, E. Tremblay, Y. Troutet, K. Tulk, J. Van Wieren, C. Vance, G. Walker, D. Whitaker, C. White, R. Wissink, C. Wong, and Y. Zharikov. For our work near Canada’s ports in Vancouver, Toronto, Montreal, and Halifax, we thank R. Worcester, A. Chreston, M. Larrivee, and T. Zemlak, respectively. Many other organizations improved coverage in the reference library by providing access to specimens – they included the Canadian National Collection of Insects, Arachnids and Nematodes, Smithsonian Institution’s National Museum of Natural History, the Canadian Museum of Nature, the University of Guelph Insect Collection, the Royal British Columbia Museum, the Royal Ontario Museum, the Pacifc Forestry Centre, the Northern Forestry Centre, the Lyman Entomological Museum, the Churchill Northern Studies Centre, and rare Charitable Research Reserve. We also thank the many taxonomic specialists who identifed specimens, including A. Borkent, B. Brown, M. Buck, C. Carr, T. Ekrem, J. Fernandez Triana, C. Guppy, K. Heller, J. Huber, L. Jacobus, J. Kjaerandsen, J. Klimaszewski, D. Lafontaine, J-F. Landry, G. Martin, A. Nicolai, D. Porco, H. Proctor, D. Quicke, J. Savage, B. C. Schmidt, M. Sharkey, A. Smith, E. Stur, A. Tomas, J. Webb, N. Woodley, and X. Zhou. We also thank K. Kerr and T. Mason for facilitating collections at Toronto Zoo and D. Iles for servicing the trap at Wapusk National Park. This paper contributes to the University of Guelph’s Food from Thought research program supported by the Canada First Research Excellence Fund. The Barcode of Life Data System (BOLD; www.boldsystems.org)8 was used as the primary workbench for creating, storing, analyzing, and validating the specimen and sequence records and the associated data resources48. The BOLD platform has a private, password-protected workbench for the steps from specimen data entry to data validation (see details in Data Records), and a public data portal for the release of data in various formats. The latter is accessible through an API (http://www.boldsystems.org/index.php/resources/api?type=webservices) that can also be controlled through R75 with the package ‘bold’76.Peer reviewedPublisher PD

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques

Extensive experimental information supports the formation of ligand-specific conformations of G protein-coupled receptors (GPCRs) as a possible molecular basis for their functional selectivity for signaling pathways. Taking advantage of the recently published inactive and active crystal structures of GPCRs, we have implemented an all-atom computational strategy that combines different adaptive biasing techniques to identify ligand-specific conformations along pre-determined activation pathways. Using the prototypic GPCR β2-adrenergic receptor as a suitable test case for validation, we show that ligands with different efficacies (either inverse agonists, neutral antagonists, or agonists) modulate the free-energy landscape of the receptor by shifting the conformational equilibrium towards active or inactive conformations depending on their elicited physiological response. Notably, we provide for the first time a quantitative description of the thermodynamics of the receptor in an explicit atomistic environment, which accounts for the receptor basal activity and the stabilization of different active-like states by differently potent agonists. Structural inspection of these metastable states reveals unique conformations of the receptor that may have been difficult to retrieve experimentally