Experimental study of digital image processing techniques for LANDSAT data

The author has identified the following significant results. Results are reported for: (1) subscene registration, (2) full scene rectification and registration, (3) resampling techniques, (4) and ground control point (GCP) extraction. Subscenes (354 pixels x 234 lines) were registered to approximately 1/4 pixel accuracy and evaluated by change detection imagery for three cases: (1) bulk data registration, (2) precision correction of a reference subscene using GCP data, and (3) independently precision processed subscenes. Full scene rectification and registration results were evaluated by using a correlation technique to measure registration errors of 0.3 pixel rms thoughout the full scene. Resampling evaluations of nearest neighbor and TRW cubic convolution processed data included change detection imagery and feature classification. Resampled data were also evaluated for an MSS scene containing specular solar reflections

Regional moisture change over India during the past Millennium: A comparison of multi-proxy reconstructions and climate model simulations

AbstractThe Indian Monsoon Variability during the past Millennium has been simulated with the ECHAM5 model in two different time slices: Medieval Climate Anomaly and the Little Ice Age. The simulations are compared with new centennial-resolving paleo-reconstructions inferred from various well-dated multi-proxies from two core regions, the Himalaya and Central India. A qualitative moisture index is derived from the proxies and compared with simulated moisture anomalies.The reconstructed paleo-hydrological changes between the Little Ice Age and the Medieval Climate Anomaly depict a dipole pattern between Himalaya and Central India, which is also captured by the model.In the Medieval Climate Anomaly the model exhibits stronger (weaker) dipole signals during summer (winter) compared to Little Ice Age. In summer (winter) months of “Medieval Climate Anomaly minus Little Ice Age” the model simulates wetter conditions over eastern (western and central) Himalaya. Over Central India, a simulated weakening of Indian Summer Monsoon during warmer climate is coincident with reconstructed drying signal in the Lonar Lake record.Based on the model simulations, we can differentiate three physical mechanisms which can lead to the moisture anomalies: (i) the western and central Himalaya are influenced by extra-tropical Westerlies during winter, (ii) the eastern Himalaya is affected by summer variations of temperature gradient between Bay of Bengal and Indian subcontinent and by a zonal band of intensified Indian–East Asian monsoon link north of 25°N, and (iii) Central India is dominated by summer sea surface temperature anomalies in the northern Arabian Sea which have an effect on the large-scale advection of moist air masses. The temperatures in the Arabian Sea are linked to the Indo Pacific Warm Pool, which modulates the Indian monsoon strength

Dynamic multilateral markets

We study dynamic multilateral markets, in which players' payoffs result from intra-coalitional bargaining. The latter is modeled as the ultimatum game with exogenous (time-invariant) recognition probabilities and unanimity acceptance rule. Players in agreeing coalitions leave the market and are replaced by their replicas, which keeps the pool of market participants constant over time. In this infinite game, we establish payoff uniqueness of stationary equilibria and the emergence of endogenous cooperation structures when traders experience some degree of (heterogeneous) bargaining frictions. When we focus on market games with different player types, we derive, under mild conditions, an explicit formula for each type's equilibrium payoff as the market frictions vanish

Rapid and reversible impairment of episodic memory by a high-fat diet in mice.

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request. This work was supported by an EASTBIO BBSRC PhD studentship to F.H.M., L.M.W., C.G., A.C.M., G.W.H. and F.M.C. are supported by Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS).Peer reviewedPublisher PD

Deregulation of the endometrial stromal cell secretome precedes embryo implantation failure

STUDY QUESTION Is implantation failure following ART associated with a perturbed decidual response in endometrial stromal cells (EnSCs)? SUMMARY ANSWER Dynamic changes in the secretome of decidualizing EnSCs underpin the transition of a hostile to a supportive endometrial microenvironment for embryo implantation; perturbation in this transitional pathway prior to ART is associated with implantation failure. WHAT IS KNOWN ALREADY Implantation is the rate-limiting step in ART, although the contribution of an aberrant endometrial microenvironment in IVF failure remains ill defined. STUDY DESIGN, SIZE, DURATION In vitro characterization of the temporal changes in the decidual response of primary EnSCs isolated prior to a successful or failed ART cycle. An analysis of embryo responses to secreted cues from undifferentiated and decidualizing EnSCs was performed. The primary clinical outcome of the study was a positive urinary pregnancy test 14 days after embryo transfer. PARTICIPANTS/MATERIALS, SETTING, METHODS Primary EnSCs were isolated from endometrial biopsies obtained prior to IVF treatment and cryopreserved. EnSCs from 10 pregnant and 10 non-pregnant patients were then thawed, expanded in culture, subjected to clonogenic assays, and decidualized for either 2 or 8 days. Transcript levels of decidual marker gene [prolactin (PRL), insulin-like growth factor binding protein 1 (IGFBP1) and 11β-hydroxysteroid dehydrogenase (HSD11B1)] were analysed using real-time quantitative PCR and temporal secretome changes of 45 cytokines, chemokines and growth factors were measured by multiplex suspension bead immunoassay. The impact of the EnSC secretome on human blastocyst development was scored morphologically; and embryo secretions in response to EnSC cues analyzed by multiplex suspension bead immunoassay. MAIN RESULTS AND THE ROLE OF CHANCE Clonogenicity and induction of decidual marker genes were comparable between EnSC cultures from pregnant and non-pregnant group groups (P > 0.05). Analysis of 23 secreted factors revealed that successful implantation was associated with co-ordinated secretome changes in decidualizing EnSCs, which were most pronounced on Day 2 of differentiation: 17 differentially secreted proteins on Day 2 of decidualization relative to undifferentiated (Day 0) EnSCs (P 0.05)

Bringing numerous methods for expression and promoter analysis to a public cloud computing service

Every year, a large number of novel algorithms are introduced to the scientific community for a myriad of applications, but using these across different research groups is often troublesome, due to suboptimal implementations and specific dependency requirements. This does not have to be the case, as public cloud computing services can easily house tractable implementations within self-contained dependency environments, making the methods easily accessible to a wider public. We have taken 14 popular methods, the majority related to expression data or promoter analysis, developed these up to a good implementation standard and housed the tools in isolated Docker containers which we integrated into the CyVerse Discovery Environment, making these easily usable for a wide community as part of the CyVerse UK project

A pilot study to evaluate the application of a generic protein standard panel for quality control of biomarker detection technologies

<p>Abstract</p> <p>Background</p> <p>Protein biomarker studies are currently hampered by a lack of measurement standards to demonstrate quality, reliability and comparability across multiple assay platforms. This is especially pertinent for immunoassays where multiple formats for detecting target analytes are commonly used.</p> <p>Findings</p> <p>In this pilot study a generic panel of six non-human protein standards (50 - 10^7 pg/mL) of varying abundance was prepared as a quality control (QC) material. Simulated "normal" and "diseased" panels of proteins were prepared in pooled human plasma and incorporated into immunoassays using the Meso Scale Discovery^®(MSD^®) platform to illustrate reliable detection of the component proteins. The protein panel was also evaluated as a spike-in material for a model immunoassay involving detection of ovarian cancer biomarkers within individual human plasma samples. Our selected platform could discriminate between two panels of the proteins exhibiting small differences in abundance. Across distinct experiments, all component proteins exhibited reproducible signal outputs in pooled human plasma. When individual donor samples were used, half the proteins produced signals independent of matrix effects. These proteins may serve as a generic indicator of platform reliability.</p> <p>Each of the remaining proteins exhibit differential signals across the distinct samples, indicative of sample matrix effects, with the three proteins following the same trend. This subset of proteins may be useful for characterising the degree of matrix effects associated with the sample which may impact on the reliability of quantifying target diagnostic biomarkers.</p> <p>Conclusions</p> <p>We have demonstrated the potential utility of this panel of standards to act as a generic QC tool for evaluating the reproducibility of the platform for protein biomarker detection independent of serum matrix effects.</p

Evidence for self-similar bedload transport on Andean alluvial fans, Iglesia basin, south Central Argentina

Self‐similar downstream grain‐size fining trends in fluvial deposits are being increasingly used to simplify equilibrium sediment transport dynamics in numerical models. Their ability to collapse time‐averaged behavior of a depositional system into a simple mass balance framework makes them ideal for exploring the sensitivity of sediment routing systems to their climatic and tectonic boundary conditions. This is important if we want to better understand the sensitivity of landscapes to environmental change over timescales >102 years. However, the extent to which self‐similarity is detectable in the deposits of natural rivers is not fully constrained. In transport‐limited rivers, stored sediment can be remobilized or “recycled” and this behavior has been highlighted as a mechanism by which externally forced grain‐size fining trends are distorted. Here we evaluate evidence of self‐similarity in surface gravel‐size distributions on three geomorphically diverse alluvial fans in the Iglesia basin, south Central Argentine Andes. We find that size distributions are self‐similar, deviating from that condition only when significant variability occurs in the coarse tails of the distributions. Our analysis indicates a strong correlation between the degree of sediment recycling and the proportion of coarse clasts present on the bed surface. However, by fitting a relative mobility transfer function, we demonstrate that size‐selectivity alone can explain the bulk size distributions observed. This strengthens the application of self‐similar grain size fining models to solving problems of mass balance in a range of geomorphic settings, with an aim for reconstructing environmental boundary conditions from stratigraphy

GJ 1252b: A Hot Terrestrial Super-Earth With No Atmosphere

The increasing numbers of rocky, terrestrial exoplanets known to orbit nearby stars (especially M dwarfs) has drawn increased attention to the possibility of studying these planets' surface properties, and atmospheric compositions & escape histories. Here we report the detection of the secondary eclipse of the terrestrial exoplanet GJ1252b using the Spitzer Space Telescope's IRAC2 4.5 micron channel. We measure an eclipse depth of 149(+25/-32) ppm, corresponding to a day-side brightness temperature of 1410(+91/-125) K and consistent with the prediction for no atmosphere. Comparing our measurement to atmospheric models indicates that GJ1252b has a surface pressure of <10 bar, substantially less than Venus. Assuming energy-limited escape, even a 100 bar atmosphere would be lost in <1 Myr, far shorter than estimated age of 3.9+/-0.4 Gyr. The expected mass loss could be overcome by mantle outgassing, but only if the mantle's carbon content were >7% by mass - over two orders of magnitude greater than that found in Earth. We therefore conclude that GJ1252b has no significant atmosphere. Model spectra with granitoid or feldspathic surface composition, but with no atmosphere, are disfavored at >2 sigma. The eclipse occurs just +1.4(+2.8/-1.0) min after orbital phase 0.5, indicating e cos omega=+0.0025(+0.0049/-0.0018), consistent with a circular orbit. Tidal heating is therefore likely to be negligible to GJ1252b's global energy budget. Finally, we also analyze additional, unpublished TESS transit photometry of GJ1252b which improves the precision of the transit ephemeris by a factor of ten, provides a more precise planetary radius of 1.180+/-0.078 R_E, and rules out any transit timing variations with amplitudes <1 min.Comment: ApJL in press. 16 pages, 12 figures, 10 eclipses, 1 bandpass. Models will be available at journal websit

The Effect of Pre-Analytical Variability on the Measurement of MRM-MS-Based Mid- to High-Abundance Plasma Protein Biomarkers and a Panel of Cytokines

Blood sample processing and handling can have a significant impact on the stability and levels of proteins measured in biomarker studies. Such pre-analytical variability needs to be well understood in the context of the different proteomics platforms available for biomarker discovery and validation. In the present study we evaluated different types of blood collection tubes including the BD P100 tube containing protease inhibitors as well as CTAD tubes, which prevent platelet activation. We studied the effect of different processing protocols as well as delays in tube processing on the levels of 55 mid and high abundance plasma proteins using novel multiple-reaction monitoring-mass spectrometry (MRM-MS) assays as well as 27 low abundance cytokines using a commercially available multiplexed bead-based immunoassay. The use of P100 tubes containing protease inhibitors only conferred proteolytic protection for 4 cytokines and only one MRM-MS-measured peptide. Mid and high abundance proteins measured by MRM are highly stable in plasma left unprocessed for up to six hours although platelet activation can also impact the levels of these proteins. The levels of cytokines were elevated when tubes were centrifuged at cold temperature, while low levels were detected when samples were collected in CTAD tubes. Delays in centrifugation also had an impact on the levels of cytokines measured depending on the type of collection tube used. Our findings can help in the development of guidelines for blood collection and processing for proteomic biomarker studies