Relationship between continuous aerosol measurements and firn core chemistry over a 10-year period at the South Pole

Before ice core chemistry can be used to estimate past atmospheric chemistry it is necessary to establish an unambiguous link between concentrations of chemical species in the air and snow. For the first time a continuous long-term record of aerosol properties (aerosol light scattering coefficient, σsp, and Ångström exponent, å) at the South Pole are compared with the chemical record from a high resolution firn core (∼10 samples per year) covering the period from 1981 to 1991. Seasonal signals in å, associated with winter minima due to coarse mode seasalt and summer maxima due to accumulation mode sulfate aerosol, are reflected in the firn core SO42−/Na+ concentration ratio. Summertime ratios of σsp and aerosol optical depth, τ to corresponding firn core sulfur concentrations are determined and the ‘calibrations’ are applied to sulfur concentrations in snowpits from a previous study. Results show that σsp estimates from snowpit sulfur concentrations are in agreement with atmospheric measurements while τ estimates are significantly different, which is likely due to the lack of understanding of the processes that mix surface air with air aloft

Online optimization with switching cost

We consider algorithms for "smoothed online convex optimization (SOCO)" problems. SOCO is a variant of the class of "online convex optimization (OCO)" problems that is strongly related to the class of "metrical task systems", each of which have been studied extensively. Prior literature on these problems has focused on two performance metrics: regret and competitive ratio. There exist known algorithms with sublinear regret and known algorithms with constant competitive ratios; however no known algorithms achieve both. In this paper, we show that this is due to a fundamental incompatibility between regret and the competitive ratio -- no algorithm (deterministic or randomized) can achieve sublinear regret and a constant competitive ratio, even in the case when the objective functions are linear

Relationship between Continuous Aerosol Measurements and Firn Core Chemistry over a 10‐year Period at the South Pole

Before ice core chemistry can be used to estimate past atmospheric chemistry it is necessary to establish an unambiguous link between concentrations of chemical species in the air and snow. For the first time a continuous long‐term record of aerosol properties (aerosol light scattering coefficient, σsp , and Ångström exponent, å) at the South Pole are compared with the chemical record from a high resolution firn core (∼10 samples per year) covering the period from 1981 to 1991. Seasonal signals in å, associated with winter minima due to coarse mode seasalt and summer maxima due to accumulation mode sulfate aerosol, are reflected in the firn core SO42−/Na+ concentration ratio. Summertime ratios of σsp and aerosol optical depth, τ to corresponding firn core sulfur concentrations are determined and the ‘calibrations’ are applied to sulfur concentrations in snowpits from a previous study. Results show that σsp estimates from snowpit sulfur concentrations are in agreement with atmospheric measurements while τ estimates are significantly different, which is likely due to the lack of understanding of the processes that mix surface air with air aloft

High dimensional decision dilemmas in climate models

An important source of uncertainty in climate models is linked to the calibration of model parameters. Interest in systematic and automated parameter optimization procedures stems from the desire to improve the model climatology and to quantify the average sensitivity associated with potential changes in the climate system. Building upon on the smoothness of the response of an atmospheric circulation model (AGCM) to changes of four adjustable parameters, Neelin et al. (2010) used a quadratic metamodel to objectively calibrate the AGCM. The metamodel accurately estimates global spatial averages of common fields of climatic interest, from precipitation, to low and high level winds, from temperature at various levels to sea level pressure and geopotential height, while providing a computationally cheap strategy to explore the influence of parameter settings. Here, guided by the metamodel, the ambiguities or dilemmas related to the decision making process in relation to model sensitivity and optimization are examined. Simulations of current climate are subject to considerable regional-scale biases. Those biases may vary substantially depending on the climate variable considered, and/or on the performance metric adopted. Common dilemmas are associated with model revisions yielding improvement in one field or regional pattern or season, but degradation in another, or improvement in the model climatology but degradation in the interannual variability representation. Challenges are posed to the modeler by the high dimensionality of the model output fields and by the large number of adjustable parameters. The use of the metamodel in the optimization strategy helps visualize trade-offs at a regional level, e.g., how mismatches between sensitivity and error spatial fields yield regional errors under minimization of global objective functions

Nonnative \u3ci\u3ePhragmites australis\u3c/i\u3e Invasion into Utah Wetlands

Phragmites australis (Cav.) Trin. ex Steud. (common reed), already one of the world’s most widespread plant species, has realized rapid range expansion in coastal wetlands of North America in the past century, but little is known about P. australis range expansion in inland wetland systems. We used genetic analyses, aerial photographs, field surveys, and a greenhouse experiment to study the extent and mechanism of nonnative P. australis invasion of Utah wetlands. We collected and genetically analyzed 39 herbarium samples across the state and 225 present-day samples from northern Utah’s major wetland complexes. All samples collected before 1993 and all samples collected outside the major wetlands of northern Utah, including some as recent as 2001, were identified as native (haplotypes A, B, D, and H). Only 10 (4%) of the present-day samples were native, each from small, discrete, low-density stands; the remaining samples were nonnative (haplotype M). Our earliest nonnative sample was collected near the Great Salt Lake in 1993. Around the Great Salt Lake, which contains 40% of Utah’s wetlands, P. australis cover has increased from 20% to 56% over the past 27 years—an increase that appears attributable to the nonnative strain. In a 3-month-long greenhouse experiment, the nonnative haplotype grew taller, had more aboveground biomass, and had a greater above- to belowground biomass ratio than the native haplotypes regardless of nitrogen, phosphorus, or water availability. Nonnative P. australis is rapidly invading the wetlands of northern Utah. Areas in Utah where the native P. australis remains should be identified and protected

Parameterized Complexity of the k-anonymity Problem

The problem of publishing personal data without giving up privacy is becoming increasingly important. An interesting formalization that has been recently proposed is the $k$-anonymity. This approach requires that the rows of a table are partitioned in clusters of size at least $k$ and that all the rows in a cluster become the same tuple, after the suppression of some entries. The natural optimization problem, where the goal is to minimize the number of suppressed entries, is known to be APX-hard even when the records values are over a binary alphabet and $k=3$, and when the records have length at most 8 and $k=4$ . In this paper we study how the complexity of the problem is influenced by different parameters. In this paper we follow this direction of research, first showing that the problem is W[1]-hard when parameterized by the size of the solution (and the value $k$). Then we exhibit a fixed parameter algorithm, when the problem is parameterized by the size of the alphabet and the number of columns. Finally, we investigate the computational (and approximation) complexity of the $k$-anonymity problem, when restricting the instance to records having length bounded by 3 and $k=3$. We show that such a restriction is APX-hard.Comment: 22 pages, 2 figure

AXL modulates extracellular matrix protein expression and is essential for invasion and metastasis in endometrial cancer

The receptor tyrosine kinase AXL promotes migration, invasion, and metastasis. Here, we evaluated the role of AXL in endometrial cancer. High immunohistochemical expression of AXL was found in 76% (63/83) of advanced-stage, and 77% (82/107) of high-grade specimens and correlated with worse survival in uterine serous cancer patients. In vitro, genetic silencing of AXL inhibited migration and invasion but had no effect on proliferation of ARK1 endometrial cancer cells. AXL-deficient cells showed significantly decreased expression of phospho-AKT as well as uPA, MMP-1, MMP-2, MMP-3, and MMP-9. In a xenograft model of human uterine serous carcinoma with AXL-deficient ARK1 cells, there was significantly less tumor burden than xenografts with control ARK1 cells. Together, these findings underscore the therapeutic potentials of AXL as a candidate target for treatment of metastatic endometrial cancer

Oncogenic RIT1 mutations in lung adenocarcinoma

Lung adenocarcinoma is comprised of distinct mutational subtypes characterized by mutually exclusive oncogenic mutations in RTK/RAS pathway members KRAS, EGFR, BRAF and ERBB2, and translocations involving ALK, RET and ROS1. Identification of these oncogenic events has transformed the treatment of lung adenocarcinoma via application of therapies targeted toward specific genetic lesions in stratified patient populations. However, such mutations have been reported in only ∼55% of lung adenocarcinoma cases in the United States, suggesting other mechanisms of malignancy are involved in the remaining cases. Here we report somatic mutations in the small GTPase gene RIT1 in ∼2% of lung adenocarcinoma cases that cluster in a hotspot near the switch II domain of the protein. RIT1 switch II domain mutations are mutually exclusive with all other known lung adenocarcinoma driver mutations. Ectopic expression of mutated RIT1 induces cellular transformation in vitro and in vivo, which can be reversed by combined PI3K and MEK inhibition. These data identify RIT1 as a driver oncogene in a specific subset of lung adenocarcinomas and suggest PI3K and MEK inhibition as a potential therapeutic strategy in RIT1-mutated tumors

Competition among native and invasive Phragmites australis populations: An experimental test of the effects of invasion status, genome size, and ploidy level

Among the traits whose relevance for plant invasions has recently been suggested are genome size (the amount of nuclear DNA) and ploidy level. So far, research on the role of genome size in invasiveness has been mostly based on indirect evidence by comparing species with different genome sizes, but how karyological traits influence competition at the intraspecific level remains unknown. We addressed these questions in a common-garden experiment evaluating the outcome of direct intraspecific competition among 20 populations of Phragmites australis, represented by clones collected in North America and Europe, and differing in their status (native and invasive), genome size (small and large), and ploidy levels (tetraploid, hexaploid, or octoploid). Each clone was planted in competition with one of the others in all possible combinations with three replicates in 45-L pots. Upon harvest, the identity of 21 shoots sampled per pot was revealed by flow cytometry and DNA analysis. Differences in performance were examined using relative proportions of shoots of each clone, ratios of their aboveground biomass, and relative yield total (RYT). The performance of the clones in competition primarily depended on the clone status (native vs. invasive). Measured in terms of shoot number or aboveground biomass, the strongest signal observed was that North American native clones always lost in competition to the other two groups. In addition, North American native clones were suppressed by European natives to a similar degree as by North American invasives. North American invasive clones had the largest average shoot biomass, but only by a limited, nonsignificant difference due to genome size. There was no effect of ploidy on competition. Since the North American invaders of European origin are able to outcompete the native North American clones, we suggest that their high competitiveness acts as an important driver in the early stages of their invasion

Diagnostic applications of next generation sequencing: working towards quality standards

Over the past 6 years, next generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. All major NGS technology companies providing commercially available instruments (Roche 454, Illumina, Life Technologies) have recently marketed bench top sequencing instruments with lower throughput and shorter run times, thereby broadening the applications of NGS and opening the technology to the potential use for clinical diagnostics. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry and data analysis need to be overcome. To facilitate the implementation of NGS as a routine method in molecular diagnostics, consistent quality standards need to be developed. Here the authors give an overview of the current standards in protocols and workflows and discuss possible approaches to define quality criteria for NGS in molecular genetic diagnostics