GWmodel: an R package for exploring spatial heterogeneity using geographically weighted models

Spatial statistics is a growing discipline providing important analytical techniques in a wide range of disciplines in the natural and social sciences. In the R package GWmodel we present techniques from a particular branch of spatial statistics, termed geographically weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localized calibration provides a better description. The approach uses a moving window weighting technique, where localized models are found at target locations. Outputs are mapped to provide a useful exploratory tool into the nature of the data spatial heterogeneity. Currently, GWmodel includes functions for: GW summary statistics, GW principal components analysis, GW regression, and GW discriminant analysis; some of which are provided in basic and robust forms

Physical Drivers of Phytoplankton Bloom Initiation in the Southern Ocean's Scotia Sea

Abstract: The Scotia Sea is the site of one of the largest spring phytoplankton blooms in the Southern Ocean. Past studies suggest that shelf‐iron inputs are responsible for the high productivity in this region, but the physical mechanisms that initiate and sustain the bloom are not well understood. Analysis of profiling float data from 2002 to 2017 shows that the Scotia Sea has an unusually shallow mixed‐layer depth during the transition from winter to spring, allowing the region to support a bloom earlier in the season than elsewhere in the Antarctic Circumpolar Current. We compare these results to the mixed‐layer depth in the 1/6° data‐assimilating Southern Ocean State Estimate and then use the model output to assess the physical balances governing mixed‐layer variability in the region. Results indicate the importance of lateral advection of Weddell Sea surface waters in setting the stratification. A Lagrangian particle release experiment run backward in time suggests that Weddell outflow constitutes 10% of the waters in the upper 200 m of the water column in the bloom region. This dense Weddell water subducts below the surface waters in the Scotia Sea, establishing a sharp subsurface density contrast that cannot be overcome by wintertime convection. Profiling float trajectories are consistent with the formation of Taylor columns over the region's complex bathymetry, which may also contribute to the unique stratification. Furthermore, biogeochemical measurements from 2016 and 2017 bloom events suggest that vertical exchange associated with this Taylor column enhances productivity by delivering nutrients to the euphotic zone

Polynomial algorithms for partitioning a tree into single-center subtrees to minimize flat service costs

This paper deals with the following graph partitioning problem. Consider a connected graph with n nodes, p of which are centers, while the remaining ones are units. For each unit-center pair there is a fixed service cost and the goal is to find a partition into connected components such that each component contains only one center and the total service cost is minimum. This problem is known to be NP-hard on general graphs, and here we show that it remains such even if the service cost is monotone and the graph is bipartite. However, in this paper we derive some polynomial time algorithms for trees. For this class of graphs we provide several reformulations of the problem as integer linear programs proving the integrality of the corresponding polyhedra. As a consequence, the tree partitioning problem can be solved in polynomial time either by linear programming or by suitable convex nondifferentiable optimization algorithms. Moreover, we develop a dynamic programming algorithm, whose recursion is based on sequences of minimum weight closure problems, which solves the problem on trees in O(np) time

Non-radial sign-changing solutions for the Schroedinger-Poisson problem in the semiclassical limit

We study the existence of nonradial sign-changing solutions to the Schroedinger-Poisson system in dimension N>=3. We construct nonradial sign-changing multi-peak solutions whose peaks are displaced in suitable symmetric configurations and collapse to the same point. The proof is based on the Lyapunov-Schmidt reduction

Ocean variability contributing to basal melt rate near the ice front of Ross Ice Shelf, Antarctica

Author Posting. © American Geophysical Union, 2014. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 119 (2014): 4214–4233, doi:10.1002/2014JC009792.Basal melting of ice shelves is an important, but poorly understood, cause of Antarctic ice sheet mass loss and freshwater production. We use data from two moorings deployed through Ross Ice Shelf, ∼6 and ∼16 km south of the ice front east of Ross Island, and numerical models to show how the basal melting rate near the ice front depends on sub-ice-shelf ocean variability. The moorings measured water velocity, conductivity, and temperature for ∼2 months starting in late November 2010. About half of the current velocity variance was due to tides, predominantly diurnal components, with the remainder due to subtidal oscillations with periods of a few days. Subtidal variability was dominated by barotropic currents that were large until mid-December and significantly reduced afterward. Subtidal currents were correlated between moorings but uncorrelated with local winds, suggesting the presence of waves or eddies that may be associated with the abrupt change in water column thickness and strong hydrographic gradients at the ice front. Estimated melt rate was ∼1.2 ± 0.5 m a−1 at each site during the deployment period, consistent with measured trends in ice surface elevation from GPS time series. The models predicted similar annual-averaged melt rates with a strong annual cycle related to seasonal provision of warm water to the ice base. These results show that accurately modeling the high spatial and temporal ocean variability close to the ice-shelf front is critical to predicting time-dependent and mean values of meltwater production and ice-shelf thinning.The Woods Hole Oceanographic Institution (WHOI) participation in the ANDRILL Coulman High Program was supported by the National Science Foundation Office of Polar Programs (NSF ANT-0839108) through a subcontract from the University of Nebraska, Lincoln (UNL 25-0550-0004-004). I. Arzeno was supported as a 2011 WHOI Summer Student Fellow through the NSF Research Experiences for Undergraduates program (OCE- 0649139). L. Padman and S. Springer were supported by NASA grant NNX10AG19G to Earth & Space Research (ESR). M. Williams and C. Stewart were supported by the New Zealand National Institute of Water and Atmosphere (NIWA) core funding under the National Climate Centre, and the Ministry of Business, Innovation, and Employment (Contract CO5X1001).2015-01-0

Blocking Zika virus vertical transmission.

The outbreak of the Zika virus (ZIKV) has been associated with increased incidence of congenital malformations. Although recent efforts have focused on vaccine development, treatments for infected individuals are needed urgently. Sofosbuvir (SOF), an FDA-approved nucleotide analog inhibitor of the Hepatitis C (HCV) RNA-dependent RNA polymerase (RdRp) was recently shown to be protective against ZIKV both in vitro and in vivo. Here, we show that SOF protected human neural progenitor cells (NPC) and 3D neurospheres from ZIKV infection-mediated cell death and importantly restored the antiviral immune response in NPCs. In vivo, SOF treatment post-infection (p.i.) decreased viral burden in an immunodeficient mouse model. Finally, we show for the first time that acute SOF treatment of pregnant dams p.i. was well-tolerated and prevented vertical transmission of the virus to the fetus. Taken together, our data confirmed SOF-mediated sparing of human neural cell types from ZIKV-mediated cell death in vitro and reduced viral burden in vivo in animal models of chronic infection and vertical transmission, strengthening the growing body of evidence for SOF anti-ZIKV activity

Use of bioremediation for the removal of petroleum hydrocarbons from the soil: an overview

Large amount of organic and inorganic compounds are released constantly in the environment as a consequence of human activity and technological and industrial advancement. Environmental pollution by petroleum and petrochemicals, such as petroleum hydrocarbons (PHCs), is considered one of the most serious hazards today due to its worldwide distribution. Contamination by these pollutants causes degradation of global environment and a substantial reduction in biodiversity. In addition, a deep removal of the pollutants is often required to prevent their migration into the water, air and therefore threaten human health. In this way, the search for ecologically sustainable approaches to repair contaminated environments have been of great concern in society. Bioremediation is a technique, based on the metabolic activity of living organisms, which aims to reduce, degrade and/or remove contaminants from the marine and terrestrial ecosystems. It is a more economical and more efficient process to minimize waste, compared to the usual physical-chemical treatment methods. Historically, bioremediation has been used to restore environments polluted by PHCs, where microbial communities play a key role during this course, either by the direct degradation of pollutants or by interaction with other microorganisms. Finally, this review discusses about the soil contamination by PHCs, the role of living organisms in this mechanism and their recent application in bioremediation process

Comparative analysis of the complete genome sequence of the California MSW strain of myxoma virus reveals potential host adaptations

Myxomatosis is a rapidly lethal disease of European rabbits that is caused by myxoma virus (MYXV). The introduction of a South American strain of MYXV into the European rabbit population of Australia is the classic case of host-pathogen coevolution following cross-species transmission. The most virulent strains of MYXV for European rabbits are the Californian viruses, found in the Pacific states of the United States and the Baja Peninsula, Mexico. The natural host of Californian MYXV is the brush rabbit, Sylvilagus bachmani. We determined the complete sequence of the MSW strain of Californian MYXV and performed a comparative analysis with other MYXV genomes. The MSW genome is larger than that of the South American Lausanne (type) strain of MYXV due to an expansion of the terminal inverted repeats (TIRs) of the genome, with duplication of the M156R, M154L, M153R, M152R, and M151R genes and part of the M150R gene from the right-hand (RH) end of the genome at the left-hand (LH) TIR. Despite the extreme virulence of MSW, no novel genes were identified; five genes were disrupted by multiple indels or mutations to the ATG start codon, including two genes, M008.1L/R and M152R, with major virulence functions in European rabbits, and a sixth gene, M000.5L/R, was absent. The loss of these gene functions suggests that S. bachmani is a relatively recent host for MYXV and that duplication of virulence genes in the TIRs, gene loss, or sequence variation in other genes can compensate for the loss of M008.1L/R and M152R in infections of European rabbits.This work was funded in part by grant R01 AI093804 from the National Institute of Allergy and Infectious Diseases, National Institutes of Health. E.C.H. was supported by an NHMRC Australia Fellowship, and D.C.T. was supported by an ARC Future Fellowship