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  • 1
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    GPZ: non-stationary sparse Gaussian processes for heteroscedastic uncertainty estimation in photometric redshifts (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-07
    Description: The next generation of cosmology experiments will be required to use photometric redshifts rather than spectroscopic redshifts. Obtaining accurate and well-characterized photometric redshift distributions is therefore critical for Euclid , the Large Synoptic Survey Telescope and the Square Kilometre Array. However, determining accurate variance predictions alongside single point estimates is crucial, as they can be used to optimize the sample of galaxies for the specific experiment (e.g. weak lensing, baryon acoustic oscillations, supernovae), trading off between completeness and reliability in the galaxy sample. The various sources of uncertainty in measurements of the photometry and redshifts put a lower bound on the accuracy that any model can hope to achieve. The intrinsic uncertainty associated with estimates is often non-uniform and input-dependent, commonly known in statistics as heteroscedastic noise. However, existing approaches are susceptible to outliers and do not take into account variance induced by non-uniform data density and in most cases require manual tuning of many parameters. In this paper, we present a Bayesian machine learning approach that jointly optimizes the model with respect to both the predictive mean and variance we refer to as Gaussian processes for photometric redshifts (GP z ). The predictive variance of the model takes into account both the variance due to data density and photometric noise. Using the Sloan Digital Sky Survey (SDSS) DR12 data, we show that our approach substantially outperforms other machine learning methods for photo-z estimation and their associated variance, such as tpz and annz2 . We provide a matlab and python implementations that are available to download at https://github.com/OxfordML/GPz .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    A sparse Gaussian process framework for photometric redshift estimation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-25
    Description: Accurate photometric redshifts are a lynchpin for many future experiments to pin down the cosmological model and for studies of galaxy evolution. In this study, a novel sparse regression framework for photometric redshift estimation is presented. Synthetic data set simulating the Euclid survey and real data from SDSS DR12 are used to train and test the proposed models. We show that approaches which include careful data preparation and model design offer a significant improvement in comparison with several competing machine learning algorithms. Standard implementations of most regression algorithms use the minimization of the sum of squared errors as the objective function. For redshift inference, this induces a bias in the posterior mean of the output distribution, which can be problematic. In this paper, we directly minimize the target metric z = ( z s – z p )/(1 + z s ) and address the bias problem via a distribution-based weighting scheme, incorporated as part of the optimization objective. The results are compared with other machine learning algorithms in the field such as artificial neural networks (ANN), Gaussian processes (GPs) and sparse GPs. The proposed framework reaches a mean absolute z = 0.0026(1 + z s ), over the redshift range of 0 ≤ z s ≤ 2 on the simulated data, and z = 0.0178(1 + z s ) over the entire redshift range on the SDSS DR12 survey, outperforming the standard ANNz used in the literature. We also investigate how the relative size of the training sample affects the photometric redshift accuracy. We find that a training sample of 〉30 per cent of total sample size, provides little additional constraint on the photometric redshifts, and note that our GP formalism strongly outperforms ANNz in the sparse data regime for the simulated data set.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Analysis of the minimal specificity of caspase-2 and identification of Ac-VDTTD-AFC as a caspase-2-selective peptide substrate (2014)
    Portland Press
    Details
    Publication Date: 2014-02-18
    Description: Caspase-2 is an evolutionarily conserved but enigmatic protease whose biological role remains poorly understood. To date, research into the functions of caspase-2 has been hampered by an absence of reagents that can distinguish its activity from that of the downstream apoptotic caspase, caspase-3. Identification of protein substrates of caspase-2 that are efficiently cleaved within cells may also provide clues to the role of this protease. We used a yeast-based transcriptional reporter system to define the minimal substrate specificity of caspase-2. The resulting profile enabled the identification of candidate novel caspase-2 substrates. Caspase-2 cleaved one of these proteins, the cancer-associated transcription factor Runx1, although with relatively low efficiency. A fluorogenic peptide was derived from the sequence most efficiently cleaved in the context of the transcriptional reporter. This peptide, Ac-VDTTD-AFC, was efficiently cleaved by purified caspase-2 and auto-activating caspase-2 in mammalian cells, and exhibited better selectivity for caspase-2 relative to caspase-3 than reagents that are currently available. We suggest that this reagent, used in parallel with the traditional caspase-3 substrate Ac-DEVD-AFC, will enable researchers to monitor caspase-2 activity in cell lysates and may assist in the determination of stimuli that activate caspase-2 in vivo .
    Print ISSN: 0144-8463
    Electronic ISSN: 1573-4935
    Topics: Biology , Chemistry and Pharmacology
    Published by Portland Press
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  • 4
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    Langerhans cells facilitate epithelial DNA damage and squamous cell carcinoma (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-10
    Description: Polyaromatic hydrocarbons (PAHs) are prevalent, potent carcinogens, and 7,12-dimethylbenz[a]anthracene (DMBA) is a model PAH widely used to study tumorigenesis. Mice lacking Langerhans cells (LCs), a signatory epidermal dendritic cell (DC), are protected from cutaneous chemical carcinogenesis, independent of T cell immunity. Investigation of the underlying mechanism revealed that LC-deficient skin was relatively resistant to DMBA-induced DNA damage. LCs efficiently metabolized DMBA to DMBA-trans-3,4-diol, an intermediate proximal to oncogenic Hras mutation, and DMBA-treated LC-deficient skin contained significantly fewer Hras mutations. Moreover, DMBA-trans-3,4-diol application bypassed tumor resistance in LC-deficient mice. Additionally, the genotoxic impact of DMBA on human keratinocytes was significantly increased by prior incubation with human-derived LC. Thus, tissue-associated DC can enhance chemical carcinogenesis via PAH metabolism, highlighting the complex relation between immune cells and carcinogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753811/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753811/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Modi, Badri G -- Neustadter, Jason -- Binda, Elisa -- Lewis, Julia -- Filler, Renata B -- Roberts, Scott J -- Kwong, Bernice Y -- Reddy, Swapna -- Overton, John D -- Galan, Anjela -- Tigelaar, Robert -- Cai, Lining -- Fu, Peter -- Shlomchik, Mark -- Kaplan, Daniel H -- Hayday, Adrian -- Girardi, Michael -- 085780/Wellcome Trust/United Kingdom -- K08 AR002072/AR/NIAMS NIH HHS/ -- P30 CA016359/CA/NCI NIH HHS/ -- R01 AR056632/AR/NIAMS NIH HHS/ -- R01 CA102703/CA/NCI NIH HHS/ -- R01-AR044077/AR/NIAMS NIH HHS/ -- R01-AR056632/AR/NIAMS NIH HHS/ -- R01CA102703/CA/NCI NIH HHS/ -- T32 AR007016/AR/NIAMS NIH HHS/ -- Cancer Research UK/United Kingdom -- Department of Health/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Jan 6;335(6064):104-8. doi: 10.1126/science.1211600.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223807" target="_blank"〉PubMed〈/a〉
    Keywords: 9,10-Dimethyl-1,2-benzanthracene/*analogs & derivatives/metabolism/toxicity ; Animals ; Aryl Hydrocarbon Hydroxylases/metabolism ; Carcinogens/*metabolism/*toxicity ; Carcinoma, Squamous Cell/*chemically induced/metabolism ; Cell Transformation, Neoplastic ; Cells, Cultured ; Cytochrome P-450 CYP1A1/metabolism ; Cytochrome P-450 CYP1B1 ; *DNA Damage ; Genes, ras ; Humans ; Keratinocytes/metabolism/pathology ; Langerhans Cells/immunology/*metabolism ; Mice ; Mice, Transgenic ; Skin Neoplasms/*chemically induced/metabolism ; T-Lymphocytes/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Enhanced glacial discharge from the eastern Antarctic Peninsula since the 1700s associated with a positive Southern Annular Mode (2019)
    In:  EPIC3Scientific Reports, 9(1), ISSN: 2045-2322
    Details
    Publication Date: 2019-11-17
    Description: The Antarctic Peninsula Ice Sheet is currently experiencing sustained and accelerating loss of ice. Determining when these changes were initiated and identifying the main drivers is hampered by the short instrumental record (1992 to present). Here we present a 6,250 year record of glacial discharge based on the oxygen isotope composition of diatoms (δ18Odiatom) from a marine core located at the north-eastern tip of the Antarctic Peninsula. We find that glacial discharge - sourced primarily from ice shelf and iceberg melting along the eastern Antarctic Peninsula – remained largely stable between ~6,250 to 1,620 cal. yr BP, with a slight increase in variability until ~720 cal. yr. BP. An increasing trend in glacial discharge occurs after 550 cal. yr BP (A.D. 1400), reaching levels unprecedented during the past 6,250 years after 244 cal. yr BP (A.D. 1706). A marked acceleration in the rate of glacial discharge is also observed in the early part of twentieth century (after A.D. 1912). Enhanced glacial discharge, particularly after the 1700s is linked to a positive Southern Annular Mode (SAM). We argue that a positive SAM drove stronger westerly winds, atmospheric warming and surface ablation on the eastern Antarctic Peninsula whilst simultaneously entraining more warm water into the Weddell Gyre, potentially increasing melting on the undersides of ice shelves. A possible implication of our data is that ice shelves in this region have been thinning for at least ~300 years, potentially predisposing them to collapse under intensified anthropogenic warming.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 6
    Electronic Resource
    Electronic Resource
    Effect of bacterial blight (Pseudomonas syringae pv. pisi) on the growth and yield of single pea (Pisum sativum) plants under glasshouse conditions (1993)
    Oxford, UK : Blackwell Publishing Ltd
    Plant pathology 42 (1993), S. 0 
    Details
    ISSN: 1365-3059
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Single pea (Pisum sativum) plants cvs Kelvedon Wonder and Solara, growing in pots in a glasshouse, showed significant reductions in seed yield of 24, 47 or 71% following inoculation with pea bacterial blight (Pseudomonas syringae pv. pisi) during reproductive, vegetative or both reproductive and vegetative growth stages, respectively. These yield reductions were seen as reduced numbers of seeds per pod combined with changes in the numbers of pods per plant. Examination of the importance of different disease parameters on yield showed that mean disease on the whole plant was the most important. Equations describing the relationship between seed yield or the natural log of the total weight and mean disease were derived.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-3059.1993.tb01537.x
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  • 7
    Electronic Resource
    Electronic Resource
    Effect of soil moisture on the transmission of pea bacterial blight (Pseudomonas syringae pv. pisi) from seed to seedling (1992)
    Oxford, UK : Blackwell Publishing Ltd
    Plant pathology 41 (1992), S. 0 
    Details
    ISSN: 1365-3059
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Controlled-environment studies in which pea seed cv. Solara, inoculated with Pseudomonas syringae pv. pisi, was sown in pots of compost maintained at different moisture contents showed that soil moisture had a considerable influence on the transmission of the disease from seed to seedling. An equation was derived from this data which described the relationship between the proportion of seedlings infected (p) and the soil water stress (s) in MPa: -In(-In(1 −p)) = 0.64 In(s) + 4.5. This equation was used to produce predicted transmission rates for each year from 1987 to 1990, which were compared with measured transmission rates in field experiments at Wellesbourne in the same years. Although agreement between the observed and predicted transmission rates was poor, years of severe and slight disease transmission were successfully predicted.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-3059.1992.tb02330.x
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  • 8
    Electronic Resource
    Electronic Resource
    Eradication of plant pathogens and nematodes during composting: a review (2004)
    Oxford, UK : Blackwell Science Ltd
    Plant pathology 53 (2004), S. 0 
    Details
    ISSN: 1365-3059
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: The effects of temperature–time combinations and other sanitizing factors during composting on 64 plant pathogenic fungi, plasmodiophoromycetes, oomycetes, bacteria, viruses and nematodes were reviewed. In most cases pathogen survival was determined by bioassays of unknown sensitivity and minimum detection limits of 5% infection or more. For 33 out of 38 fungal and oomycete pathogens, all seven bacterial pathogens and nine nematodes, and three out of nine plant viruses, a peak temperature of 64–70°C and duration of 21 days, were sufficient to reduce numbers to below the detection limits of the tests used. Shorter periods and/or lower temperatures than those quoted in these tests may be satisfactory for eradication, but they were not always examined in detail in composting systems. Plasmodiophora brassicae (clubroot of Brassica spp.), Fusarium oxysporum f.sp. lycopersici (tomato wilt) and Macrophomina phaseolina (dry root rot) were more temperature-tolerant, as they survived a peak compost temperature of at least 62°C (maximum 74°C) and a composting duration of 21 days. Synchytrium endobioticum (potato wart disease) survived in water at 60°C for 2 h, but was not examined in compost. For Tobacco mosaic virus (TMV), peak compost temperatures in excess of 68°C and composting for longer than 20 days were needed to reduce numbers below detection limits. However, TMV and Tomato mosaic virus (TomMV) were inactivated over time in compost, even at temperatures below 50°C. Temperatures in excess of 60°C were achieved in different composting systems, with a wide range of organic feedstocks. The potential survival of plant pathogens in cooler zones of compost, particularly in systems where the compost is not turned, has not been quantified. This may be an important risk factor in composting plant wastes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.0032-0862.2004.01059.x
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  • 9
    Electronic Resource
    Electronic Resource
    Pseudomonas syringae causing a leaf spot and flower blight of Mock Orange, Philadelphus coronarius, in England (1983)
    Oxford, UK : Blackwell Publishing Ltd
    Plant pathology 32 (1983), S. 0 
    Details
    ISSN: 1365-3059
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-3059.1983.tb02863.x
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  • 10
    Electronic Resource
    Electronic Resource
    Real-time brain-computer interfacing: A preliminary study using Bayesian learning (2000)
    Springer
    Medical & biological engineering & computing 38 (2000), S. 56-61 
    Details
    ISSN: 1741-0444
    Keywords: Brain-computer interfacing ; Real-time EEG analysis ; Biosignal analysis ; Bayesian learning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract Preliminary results from real-time ‘brain-computer interface’ experiments are presented. The analysis is based on autoregressive modelling of a single EEG channel coupled with classification and temporal smoothing under a Bayesian paradigm. It is shown that uncertainty in decisions is taken into account under such a formalism and that this may be used to reject uncertain samples, thus dramatically improving system performance. Using the strictest rejection method, a classification performance of 86.5±6.9% is achieved over a set of seven subjects in two-way cursor movement experiments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02344689
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