The Gremlin Graph Traversal Machine and Language

Gremlin is a graph traversal machine and language designed, developed, and distributed by the Apache TinkerPop project. Gremlin, as a graph traversal machine, is composed of three interacting components: a graph $G$, a traversal $\Psi$, and a set of traversers $T$. The traversers move about the graph according to the instructions specified in the traversal, where the result of the computation is the ultimate locations of all halted traversers. A Gremlin machine can be executed over any supporting graph computing system such as an OLTP graph database and/or an OLAP graph processor. Gremlin, as a graph traversal language, is a functional language implemented in the user's native programming language and is used to define the $\Psi$ of a Gremlin machine. This article provides a mathematical description of Gremlin and details its automaton and functional properties. These properties enable Gremlin to naturally support imperative and declarative querying, host language agnosticism, user-defined domain specific languages, an extensible compiler/optimizer, single- and multi-machine execution models, hybrid depth- and breadth-first evaluation, as well as the existence of a Universal Gremlin Machine and its respective entailments.Comment: To appear in the Proceedings of the 2015 ACM Database Programming Languages Conferenc

Muon Spin Relaxation Studies of Superconductivity in a Crystalline Array of Weakly Coupled Metal Nanoparticles

We report Muon Spin Relaxation studies in weak transverse fields of the superconductivity in the metal cluster compound, Ga$\_{84}$[N(SiMe$\_{3}$)$\_{2}$]$\_{20}$-Li$\_{6}$Br$\_{2}$(thf)$\_{20}\cdot$2toluene. The temperature and field dependence of the muon spin relaxation rate and Knight shift clearly evidence type II bulk superconductivity below $T\_{\text{c}}\approx7.8$ K, with $B\_{\text{c1}}\approx 0.06$ T, $B\_{\text{c2}}\approx 0.26$ T, $\kappa\sim 2$ and weak flux pinning. The data are well described by the s-wave BCS model with weak electron-phonon coupling in the clean limit. A qualitative explanation for the conduction mechanism in this novel type of narrow band superconductor is presented.Comment: 4 figures, 5 page

Wide-Field Multi-Parameter FLIM: Long-Term Minimal Invasive Observation of Proteins in Living Cells.

Time-domain Fluorescence Lifetime Imaging Microscopy (FLIM) is a remarkable tool to monitor the dynamics of fluorophore-tagged protein domains inside living cells. We propose a Wide-Field Multi-Parameter FLIM method (WFMP-FLIM) aimed to monitor continuously living cells under minimum light intensity at a given illumination energy dose. A powerful data analysis technique applied to the WFMP-FLIM data sets allows to optimize the estimation accuracy of physical parameters at very low fluorescence signal levels approaching the lower bound theoretical limit. We demonstrate the efficiency of WFMP-FLIM by presenting two independent and relevant long-term experiments in cell biology: 1) FRET analysis of simultaneously recorded donor and acceptor fluorescence in living HeLa cells and 2) tracking of mitochondrial transport combined with fluorescence lifetime analysis in neuronal processes

HST/ACS Images of the GG Tauri Circumbinary Disk

Hubble Space Telescope Advanced Camera for Surveys images of the young binary GG Tauri and its circumbinary disk in V and I bandpasses were obtained in 2002 and are the most detailed of this system to date. The confirm features previously seen in the disk including: a "gap" apparently caused by shadowing from circumstellar material; an asymmetrical distribution of light about the line of sight on the near edge of the disk; enhanced brightness along the near edge of the disk due to forward scattering; and a compact reflection nebula near the secondary star. New features are seen in the ACS images: two short filaments along the disk; localized but strong variations in disk intensity ("gaplets"); and a "spur" or filament extending from the reflection nebulosity near the secondary. The back side of the disk is detected in the V band for the first time. The disk appears redder than the combined light from the stars, which may be explained by a varied distribution of grain sizes. The brightness asymmetries along the disk suggest that it is asymmetrically illuminated by the stars due to extinction by nonuniform circumstellar material or the illuminated surface of the disk is warped by tidal effects (or perhaps both). Localized, time-dependent brightness variations in the disk are also seen.Comment: 28 pages, 7 figures, accepted for publication in the Astronomical Journa

Production of Polarized Vector Mesons off Nuclei

Using the light-cone QCD dipole formalism we investigate manifestations of color transparency (CT) and coherence length (CL) effects in electroproduction of longitudinally (L) and transversally (T) polarized vector mesons. Motivated by forthcoming data from the HERMES experiment we predict both the A and Q^2 dependence of the L/T- ratios, for rho^0 mesons produced coherently and incoherently off nuclei. For an incoherent reaction the CT and CL effects add up and result in a monotonic A dependence of the L/T-ratio at different values of Q^2. On the contrary, for a coherent process the contraction of the CL with Q^2 causes an effect opposite to that of CT and we expect quite a nontrivial A dependence, especially at Q^2 >> m_V^2.Comment: Revtex 24 pages and 14 figure

Using Sensors and Generators of H2O2 to Elucidate the Toxicity Mechanism of Piperlongumine and Phenethyl Isothiocyanate

Aims: Chemotherapeutics target vital functions that ensure survival of cancer cells, including their increased reliance on defense mechanisms against oxidative stress compared to normal cells. Many chemotherapeutics exploit this vulnerability to oxidative stress by elevating the levels of intracellular reactive oxygen species (ROS). A quantitative understanding of the oxidants generated and how they induce toxicity will be important for effective implementation and design of future chemotherapeutics. Molecular tools that facilitate measurement and manipulation of individual chemical species within the context of the larger intracellular redox network present a means to develop this understanding. In this work, we demonstrate the use of such tools to elucidate the roles of H[subscript 2]O[subscript 2] and glutathione (GSH) in the toxicity mechanism of two ROS-based chemotherapeutics, piperlongumine and phenethyl isothiocyanate. Results: Depletion of GSH as a result of treatment with these compounds is not an important part of the toxicity mechanisms of these drugs and does not lead to an increase in the intracellular H[subscript 2]O[subscript 2] level. Measuring peroxiredoxin-2 (Prx-2) oxidation as evidence of increased H[subscript 2]O[subscript 2], only piperlongumine treatment shows elevation and it is GSH independent. Using a combination of a sensor (HyPer) along with a generator (D-amino acid oxidase) to monitor and mimic the drug-induced H[subscript 2O[subscript 2] production, it is determined that H[subscript 2]O[subscript 2] produced during piperlongumine treatment acts synergistically with the compound to cause enhanced cysteine oxidation and subsequent toxicity. The importance of H[subscript 2]O[subscript 2] elevation in the mechanism of piperlongumine promotes a hypothesis of why certain cells, such as A549, are more resistant to the drug than others. Innovation and Conclusion: The approach described herein sheds new light on the previously proposed mechanism of these two ROS-based chemotherapeutics and advocates for the use of both sensors and generators of specific oxidants to isolate their effects. Antioxid. Redox Signal. 24, 924–938.National Science Foundation (U.S.). Graduate Research Fellowship ProgramBurroughs Wellcome Fund (Career Award at the Scientific Interface

The association between green space and cause-specific mortality in urban New Zealand: an ecological analysis of green space utility

<b>Background:</b> There is mounting international evidence that exposure to green environments is associated with health benefits, including lower mortality rates. Consequently, it has been suggested that the uneven distribution of such environments may contribute to health inequalities. Possible causative mechanisms behind the green space and health relationship include the provision of physical activity opportunities, facilitation of social contact and the restorative effects of nature. In the New Zealand context we investigated whether there was a socioeconomic gradient in green space exposure and whether green space exposure was associated with cause-specific mortality (cardiovascular disease and lung cancer). We subsequently asked what is the mechanism(s) by which green space availability may influence mortality outcomes, by contrasting health associations for different types of green space. <b>Methods:</b> This was an observational study on a population of 1,546,405 living in 1009 small urban areas in New Zealand. A neighbourhood-level classification was developed to distinguish between usable (i.e., visitable) and non-usable green space (i.e., visible but not visitable) in the urban areas. Negative binomial regression models were fitted to examine the association between quartiles of area-level green space availability and risk of mortality from cardiovascular disease (n = 9,484; 1996 - 2005) and from lung cancer (n = 2,603; 1996 - 2005), after control for age, sex, socio-economic deprivation, smoking, air pollution and population density. <b>Results:</b> Deprived neighbourhoods were relatively disadvantaged in total green space availability (11% less total green space for a one standard deviation increase in NZDep2001 deprivation score, p < 0.001), but had marginally more usable green space (2% more for a one standard deviation increase in deprivation score, p = 0.002). No significant associations between usable or total green space and mortality were observed after adjustment for confounders. <b>Conclusion</b> Contrary to expectations we found no evidence that green space influenced cardiovascular disease mortality in New Zealand, suggesting that green space and health relationships may vary according to national, societal or environmental context. Hence we were unable to infer the mechanism in the relationship. Our inability to adjust for individual-level factors with a significant influence on cardiovascular disease and lung cancer mortality risk (e.g., diet and alcohol consumption) will have limited the ability of the analyses to detect green space effects, if present. Additionally, green space variation may have lesser relevance for health in New Zealand because green space is generally more abundant and there is less social and spatial variation in its availability than found in other contexts

Modelling trade offs between public and private conservation policies

To reduce global biodiversity loss, there is an urgent need to determine the most efficient allocation of conservation resources. Recently, there has been a growing trend for many governments to supplement public ownership and management of reserves with incentive programs for conservation on private land. At the same time, policies to promote conservation on private land are rarely evaluated in terms of their ecological consequences. This raises important questions, such as the extent to which private land conservation can improve conservation outcomes, and how it should be mixed with more traditional public land conservation. We address these questions, using a general framework for modelling environmental policies and a case study examining the conservation of endangered native grasslands to the west of Melbourne, Australia. Specifically, we examine three policies that involve: i) spending all resources on creating public conservation areas; ii) spending all resources on an ongoing incentive program where private landholders are paid to manage vegetation on their property with 5-year contracts; and iii) splitting resources between these two approaches. The performance of each strategy is quantified with a vegetation condition change model that predicts future changes in grassland quality. Of the policies tested, no one policy was always best and policy performance depended on the objectives of those enacting the policy. This work demonstrates a general method for evaluating environmental policies and highlights the utility of a model which combines ecological and socioeconomic processes.Comment: 20 pages, 5 figure

Infrared generation in low-dimensional semiconductor heterostructures via quantum coherence

A new scheme for infrared generation without population inversion between subbands in quantum-well and quantum-dot lasers is presented and documented by detailed calculations. The scheme is based on the simultaneous generation at three frequencies: optical lasing at the two interband transitions which take place simultaneously, in the same active region, and serve as the coherent drive for the IR field. This mechanism for frequency down-conversion does not rely upon any ad hoc assumptions of long-lived coherences in the semiconductor active medium. And it should work efficiently at room temperature with injection current pumping. For optimized waveguide and cavity parameters, the intrinsic efficiency of the down-conversion process can reach the limiting quantum value corresponding to one infrared photon per one optical photon. Due to the parametric nature of IR generation, the proposed inversionless scheme is especially promising for long-wavelength (far- infrared) operation.Comment: 4 pages, 1 Postscript figure, Revtex style. Replacement corrects a printing error in the authors fiel