The California Current System: A multiscale overview and the development of a feature-oriented regional modeling system (FORMS)

17 USC 105 interim-entered record; under review.Over the past decade, the feature-oriented regional modeling methodology has been developed and applied in several ocean domains, including the western North Atlantic and tropical North Atlantic. This methodology is model-independent and can be utilized with or without satellite and/or in situ observations. Here we develop new feature-oriented models for the eastern North Pacific from 36◦ to 48◦N – essentially, most of the regional eastern boundary current. This is the firsttime feature-modeling has been applied to a complex eastern boundary current system. As a prerequisite to feature modeling, prevalent features that comprise the multiscale and complex circulation in the California Current system (CCS) are first overviewed. This description is based on contemporary understanding ofthe features and their dominant space and time scales of variability. A synergistic configuration of circulation features interacting with one another on multiple and sometimes overlapping space and time scales as a meander-eddy-upwelling system is presented. The second step is to define the feature-oriented regional modeling system (FORMS). The major multiscale circulation features include the mean flow and southeastward meandering jet(s) of the California Current (CC), the poleward flowing California Undercurrent (CUC), and six upwelling regions along the coastline. Next, the typical synoptic width, location, vertical extent, and core characteristics of these features and their dominant scales of variability are identified from past observational, theoretical and modeling studies. The parameterized features are then melded with the climatology, in situ and remotely sensed data, as available. The methodology is exemplified here for initialization of primitiveequation models. Dynamical simulations are run as nowcasts and short-term (4–6 weeks) forecasts using these feature models (FM) as initial fields and the Princeton Ocean Model (POM) for dynamics. The set of simulations over a 40-day period illustrate the applicability of FORMS to a transient eastern boundary current region such as the CCS. Comparisons are made with simulations initialized from climatology only. The FORMS approach increases skill in severalfactors, including the: (i) maintenance of the low-salinity pool in the core of the CC; (ii) representation of eddy activity inshore of the coastal transition zone; (iii) realistic eddy kinetic energy evolution; (iv) subsurface (intermediate depth) mesoscale feature evolution; and (v) deep poleward flow evolution.This work was funded by the Office of Naval Research grants N00014-03-1-0411 and N00014-03-1-0206 at the University of Massachusetts at Dartmouth. Leslie Rosenfeld’s participation was supported by ONR grant N00014-03-WR-20009. PFJL, PJH and WGL are grateful to ONR for support under grant N00014-08-1-1097, N00014-08-1-0680 and MURI-ASAP to the Massachusetts Institute of Technology

Constraints on Pluto’s H and CH₄ profiles from New Horizons Alice Lyα observations

The Alice spectrograph on New Horizons performed several far-ultraviolet (FUV) airglow observations during the July 2015 flyby of Pluto. One of these observations, named PColor2, was a short (226 s) scan across the dayside disk of Pluto from a range of ∼34,000 km, at about 40 minutes prior to closest approach. The brightest observed FUV airglow signal at Pluto is the Lyman alpha (Lyα) emission line of atomic hydrogen, which arises primarily through the resonant scattering of solar Lyα by H atoms in the upper atmosphere, with a brightness of about 30 Rayleighs. Pluto appears dark against the much brighter (∼100 Rayleigh) sky background; this sky background is likewise the result of resonantly scattered solar Lyα, in this case by H atoms in the interplanetary medium (IPM). Here we use an updated photochemical model and a resonance line radiative transfer model to perform detailed simulations of the Lyα emissions observed in the Alice PColor2 scan. The photochemical models show that H and CH₄ abundances in Pluto’s upper atmosphere are a very strong function of the near-surface mixing ratio of CH₄, and could provide a useful way to remotely monitor seasonal climate variations in Pluto’s lower atmosphere. The morphology of the PColor2 Lyα emissions provides constraints on the current abundance profiles of H atoms and CH₄ molecules in Pluto’s atmosphere, and indicate that the globally averaged near-surface mixing ratio of CH₄ is currently close to 0.4%. This new result thus provides independent confirmation of one of the primary results from the solar occultation, also observed with the New Horizons Alice ultraviolet spectrograph

Constraints on Pluto’s H and CH₄ profiles from New Horizons Alice Lyα observations

The Alice spectrograph on New Horizons performed several far-ultraviolet (FUV) airglow observations during the July 2015 flyby of Pluto. One of these observations, named PColor2, was a short (226 s) scan across the dayside disk of Pluto from a range of ∼34,000 km, at about 40 minutes prior to closest approach. The brightest observed FUV airglow signal at Pluto is the Lyman alpha (Lyα) emission line of atomic hydrogen, which arises primarily through the resonant scattering of solar Lyα by H atoms in the upper atmosphere, with a brightness of about 30 Rayleighs. Pluto appears dark against the much brighter (∼100 Rayleigh) sky background; this sky background is likewise the result of resonantly scattered solar Lyα, in this case by H atoms in the interplanetary medium (IPM). Here we use an updated photochemical model and a resonance line radiative transfer model to perform detailed simulations of the Lyα emissions observed in the Alice PColor2 scan. The photochemical models show that H and CH₄ abundances in Pluto’s upper atmosphere are a very strong function of the near-surface mixing ratio of CH₄, and could provide a useful way to remotely monitor seasonal climate variations in Pluto’s lower atmosphere. The morphology of the PColor2 Lyα emissions provides constraints on the current abundance profiles of H atoms and CH₄ molecules in Pluto’s atmosphere, and indicate that the globally averaged near-surface mixing ratio of CH₄ is currently close to 0.4%. This new result thus provides independent confirmation of one of the primary results from the solar occultation, also observed with the New Horizons Alice ultraviolet spectrograph

Time-evolving acoustic propagation modeling in a complex ocean environment

During naval operations, sonar performance estimates often need to be computed in-situ with limited environmental information. This calls for the use of fast acoustic propagation models. Many naval operations are carried out in challenging and dynamic environments. This makes acoustic propagation and sonar performance behavior particularly complex and variable, and complicates prediction. Using data from a field experiment, we have investigated the accuracy with which acoustic propagation loss (PL) can be predicted, using only limited modeling capabilities. Environmental input parameters came from various sources that may be available in a typical naval operation. The outer continental shelf shallow-water experimental area featured internal tides, packets of nonlinear internal waves, and a meandering water mass front. For a moored source/receiver pair separated by 19.6 km, the acoustic propagation loss for 800 Hz pulses was computed using the peak amplitude. The variations in sound speed translated into considerable PL variability of order 15 dB. Acoustic loss modeling was carried out using a data-driven regional ocean model as well as measured sound speed profile data for comparison. The acoustic model used a two-dimensional parabolic approximation (vertical and radial outward wavenumbers only). The variance of modeled propagation loss was less than that measured. The effect of the internal tides and sub-tidal features was reasonably well modeled; these made use of measured sound speed data. The effects of nonlinear waves were not well modeled, consistent with their known three-dimensional effects but also with the lack of measurements to initialize and constrain them.Netherlands. Ministry of DefenceUnited States. Office of Naval Research (Grant N00014-12-1-0944 (ONR6.2))United States. Office of Naval Research (Grant N00014-08-1-1097 (ONR6.1))United States. Office of Naval Research (Grant N00014-08-1-0680 (PLUS-SEAS)

Comparing the DNA Hypermethylome with Gene Mutations in Human Colorectal Cancer

We have developed a transcriptome-wide approach to identify genes affected by promoter CpG island DNA hypermethylation and transcriptional silencing in colorectal cancer. By screening cell lines and validating tumor-specific hypermethylation in a panel of primary human colorectal cancer samples, we estimate that nearly 5% or more of all known genes may be promoter methylated in an individual tumor. When directly compared to gene mutations, we find larger numbers of genes hypermethylated in individual tumors, and a higher frequency of hypermethylation within individual genes harboring either genetic or epigenetic changes. Thus, to enumerate the full spectrum of alterations in the human cancer genome, and to facilitate the most efficacious grouping of tumors to identify cancer biomarkers and tailor therapeutic approaches, both genetic and epigenetic screens should be undertaken

Visualizing the Anthropocene dialectically: Jessica Woodworth and Peter Brosens’ eco-crisis trilogy

The ambition of this article is to propose a way of visualizing the Anthropocene dialectically. As suggested by the Dutch atmospheric chemist Paul Crutzen and the professor of biology Eugene F. Stoermer, the term Anthropocene refers to a historical period in which humankind has turned into a geological force that transforms the natural environment in such a way that it is hard to distinguish between the human and the natural world. Crutzen and Stoermer explain that the Anthropocene has begun after the Holocene, the geological epoch that followed the last ice age and lasted until the industrial revolution. Drawing on a number of figures such as the “tenfold” increase in urbanisation, the extreme transformation of land surface by human action, the use of more than 50% of all accessible fresh water by humans, and the massive increase in greenhouse emissions, Crutzen and Stoermer conclude that the term Anthropocene describes aptly mankind's influence on ecological and geological cycles (Crutzen & Stoermer, 2000, p.17). The wager of this article is that we need to identify ways to visualize the Anthropocene dialectically and I proceed to do so using as a case study Jessica Woodworth's and Peter Brosen's trilogy on the conflict between humans and nature, which consists of Khadak (2006), Altiplano (2009), and The Fifth Season (La Cinquième Saison, 2012)

Circulation and intrusions northeast of Taiwan : chasing and predicting uncertainty in the cold dome

Author Posting. © The Oceanography Society, 2011. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 24 no. 4 (2011): 110–121, doi:10.5670/oceanog.2011.99.An important element of present oceanographic research is the assessment and quantification of uncertainty. These studies are challenging in the coastal ocean due to the wide variety of physical processes occurring on a broad range of spatial and temporal scales. In order to assess new methods for quantifying and predicting uncertainty, a joint Taiwan-US field program was undertaken in August/September 2009 to compare model forecasts of uncertainties in ocean circulation and acoustic propagation, with high-resolution in situ observations. The geographical setting was the continental shelf and slope northeast of Taiwan, where a feature called the "cold dome" frequently forms. Even though it is hypothesized that Kuroshio subsurface intrusions are the water sources for the cold dome, the dome's dynamics are highly uncertain, involving multiple scales and many interacting ocean features. During the experiment, a combination of near-surface and profiling drifters, broad-scale and high-resolution hydrography, mooring arrays, remote sensing, and regional ocean model forecasts of fields and uncertainties were used to assess mean fields and uncertainties in the region. River runoff from Typhoon Morakot, which hit Taiwan August 7–8, 2009, strongly affected shelf stratification. In addition to the river runoff, a cold cyclonic eddy advected into the region north of the Kuroshio, resulting in a cold dome formation event. Uncertainty forecasts were successfully employed to guide the hydrographic sampling plans. Measurements and forecasts also shed light on the evolution of cold dome waters, including the frequency of eddy shedding to the north-northeast, and interactions with the Kuroshio and tides. For the first time in such a complex region, comparisons between uncertainty forecasts and the model skill at measurement locations validated uncertainty forecasts. To complement the real-time model simulations, historical simulations with another model show that large Kuroshio intrusions were associated with low sea surface height anomalies east of Taiwan, suggesting that there may be some degree of predictability for Kuroshio intrusions.We thank the National Science Council of Taiwan as well as the Office of Naval Research for generous support of this effort

Pre-processing Agilent microarray data

<p>Abstract</p> <p>Background</p> <p>Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction software with pre-processing methods that have become the standard for normalization of cDNA arrays. These include log transformation followed by loess normalization with or without background subtraction and often a between array scale normalization procedure. The larger goal is to define best study design and pre-processing practices for Agilent arrays, and we offer some suggestions.</p> <p>Results</p> <p>Simple loess normalization without background subtraction produced the lowest variability. However, without background subtraction, fold changes were biased towards zero, particularly at low intensities. ROC analysis of a spike-in experiment showed that differentially expressed genes are most reliably detected when background is not subtracted. Loess normalization and no background subtraction yielded an AUC of 99.7% compared with 88.8% for Agilent processed fold changes. All methods performed well when error was taken into account by t- or z-statistics, AUCs ≥ 99.8%. A substantial proportion of genes showed dye effects, 43% (99%<it>CI </it>: 39%, 47%). However, these effects were generally small regardless of the pre-processing method.</p> <p>Conclusion</p> <p>Simple loess normalization without background subtraction resulted in low variance fold changes that more reliably ranked gene expression than the other methods. While t-statistics and other measures that take variation into account, including Agilent's z-statistic, can also be used to reliably select differentially expressed genes, fold changes are a standard measure of differential expression for exploratory work, cross platform comparison, and biological interpretation and can not be entirely replaced. Although dye effects are small for most genes, many array features are affected. Therefore, an experimental design that incorporates dye swaps or a common reference could be valuable.</p

Measurement of the t t-bar production cross section in the dilepton channel in pp collisions at sqrt(s) = 7 TeV

The t t-bar production cross section (sigma[t t-bar]) is measured in proton-proton collisions at sqrt(s) = 7 TeV in data collected by the CMS experiment, corresponding to an integrated luminosity of 2.3 inverse femtobarns. The measurement is performed in events with two leptons (electrons or muons) in the final state, at least two jets identified as jets originating from b quarks, and the presence of an imbalance in transverse momentum. The measured value of sigma[t t-bar] for a top-quark mass of 172.5 GeV is 161.9 +/- 2.5 (stat.) +5.1/-5.0 (syst.) +/- 3.6(lumi.) pb, consistent with the prediction of the standard model.Comment: Replaced with published version. Included journal reference and DO