Axiomatic foundations of quantum mechanics revisited: the case for systems

We present an axiomatization of non-relativistic Quantum Mechanics for a system with an arbitrary number of components. The interpretation of our system of axioms is realistic and objective. The EPR paradox and its relation with realism is discussed in this framework. It is shown that there is no contradiction between realism and recent experimental results.Comment: submitted to International Journal of Theoretical Physics, uses Latex, no figure

Ground and excited states of Li−^-, Be−^- through a density-based approach

Density functional calculations are performed for ground [He]2s$^2$ $^1$S$^e$, and three metastable bound excited states, 1s2s2p$^2$ $^5$P$^e$, 1s2p$^3$ $^5$S$^o$, 1s2s2p3p $^5$P$^e$ of Li$^-$ and [He]2s2p$^2$ $^4$P$^e$, [He]2p$^3$ $^4$S$^o$, 1s2s2p$^3$ $^6$S$^o$ of Be$^-$ each. The work-function-based exchange potential is used, while the correlation effects are included by employing the Lee-Yang-Parr potential. The relevant nonrelativistic KS equation is solved by means of a generalized pseudospectral discretization scheme offering nonuniform and optimal spatial grid. Computed total energies, radial densities, selected density moments, as well as two transition wavelengths (1s2s2p$^2$ $^5$P$^e \to$1s2p$^3$ $^5$S$^o$ of Li$^-$, [He]2s2p$^2$ $^4$P$^e \to$ [He]2p$^3$ $^4$S$^o$ of Be$^-$) show reasonably good agreement with the available theoretical and experimental data. The term energies show an absolute deviation of 0.007--0.171% with the largest deviation being observed for the even-parity $^5$P state of Li$^-$. The transition wavelengths of Li$^-$, Be$^-$ are calculated within 0.891 and 0.438% of the experimental values. This offers a simple practical route towards accurate reliable calculation of excited states of anions within density functional theory.Comment: 12 pages, 35 ref

Estimation of viral richness from shotgun metagenomes using a frequency count approach

BACKGROUND: Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communities. One ecological characteristic is species richness, which is the number of different species in a community. Viruses do not have a phylogenetic marker analogous to the bacterial 16S rRNA gene with which to estimate richness, and so contig spectra are employed to measure the number of virus taxa in a given community. A contig spectrum is generated from a viral shotgun metagenome by assembling the random sequence reads into groups of sequences that overlap (contigs) and counting the number of sequences that group within each contig. Current tools available to analyze contig spectra to estimate phage richness are limited by relying on rank-abundance data. RESULTS: We present statistical estimates of virus richness from contig spectra. The program CatchAll (http://www.northeastern.edu/catchall/) was used to analyze contig spectra in terms of frequency count data rather than rank-abundance, thus enabling formal statistical analyses. Also, the influence of potentially spurious low-frequency counts on richness estimates was minimized by two methods, empirical and statistical. The results show greater estimates of viral richness than previous calculations in nearly all environments analyzed, including swine feces and reclaimed fresh water. CONCLUSIONS: CatchAll yielded consistent estimates of richness across viral metagenomes from the same or similar environments. Additionally, analysis of pooled viral metagenomes from different environments via mixed contig spectra resulted in greater richness estimates than those of the component metagenomes. Using CatchAll to analyze contig spectra will improve estimations of richness from viral shotgun metagenomes, particularly from large datasets, by providing statistical measures of richness

Neural circuitry underlying rule use in humans and nonhuman primates

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Best-Fit Ellipsoids of Atom-Probe Tomographic Data to Study Coalescence of Gamma Prime (L1_2) Precipitates in Ni-Al-Cr

An algorithm is presented to fit precipitates in atom probe tomographic data sets as equivalent ellipsoids. Unlike previous techniques, which measure only the radius of gyration, these ellipsoids retain the moments of inertia and principle axes of the original precipitate, preserving crystallographic orientational information. The algorithm is applied to study interconnected gamma prime precipitates (L1_2) in the Gamma-matrix (FCC) of a Ni-Al-Cr alloy. The precipitates are found to coagulate along -type directions.Comment: Accepted for publication in Scripta Materialia, added information about local magnification effect

Cross‐scale seismic anisotropy analysis in metamorphic rocks from the COSC‐1 borehole in the Scandinavian Caledonides

Metamorphic and deformed rocks in thrust zones show particularly high seismic anisotropy causing challenges for seismic imaging and interpretation. A good example is the Seve Nappe Complex in central Sweden, an old exhumed orogenic thrust zone that is characterized by a strong but incoherent seismic reflectivity and considerable seismic anisotropy. However, only little is known about their origin in relation to composition and structural influences on measurements at different seismic scales. Here, we present a new integrative study of cross‐scale seismic anisotropy analyses combining mineralogical composition, microstructural analyses and seismic laboratory experiments from the COSC‐1 borehole, which sampled a 2.5 km‐deep section of metamorphic rocks deformed in an orogenic root now preserved in the Lower Seve Nappe. While there is strong crystallographic preferred orientation in most samples in general, variations in anisotropy depend mostly on bulk mineral composition and dominant core lithology as shown by a strong correlation between these. This relationship enables to identify three distinct seismic anisotropy facies providing a continuous anisotropy profile along the borehole. Moreover, comparison of laboratory seismic measurements and electron‐backscatter diffraction data reveals a strong scale‐dependence, which is more pronounced in the highly deformed, heterogeneous samples. This highlights the need for comprehensive cross‐validation of microscale anisotropy analyses with additional lithological data when integrating seismic anisotropy over seismic scales

The nucleotide-binding domain and leucine-rich repeat protein-3 inflammasome is not activated in airway smooth muscle upon toll-like receptor-2 ligation

Inflammasomes have emerged as playing key roles in inflammation and innate immunity. A growing body of evidence has suggested that the nucleotide-binding domain and leucine-rich repeat protein-3 (NLRP3) inflammasomeisimportant inchronic airwaydiseases suchas asthma and chronic obstructive pulmonary disease. Inflammasome activation results, in part, in pro-IL-1β processing and the secretion of the proinflammatory cytokine IL-1β. Because asthma exacerbations are associated with elevated concentrations of secreted IL-1β, we addressed whether the NLRP3 inflammasome is activated under in vitro conditions that mimic infectious exacerbations in asthma. Primary cultures of airway smoothmuscle (ASM) cells were treated with infectious stimuli (mimicked using the Toll-like receptor-2 agonist Pam3CSK4, a synthetic bacterial lipopeptide).Whereas Pam3CSK4 robustlyup-regulatedASMcytokineexpressionin response toTNF-αand significantly enhanced IL-1β mRNA expression, we were unable to detect IL-1β in the cell supernatants. Thus, IL-1β was not secreted and therefore was unable to act in an autocrine manner to promote the amplification of ASMinflammatory responses.Moreover, Toll-like receptor-2 ligation did not enhanceNLRP3 or caspase-1 expression in ASM cells, and NLRP3 and caspase-1 protein were not present in the ASM layer of tracheal sections from human donors. In conclusion, these data demonstrate that the enhanced synthetic function of ASM cells, induced by infectious exacerbations of airway inflammation, is NLRP3 inflammasome-independent and IL-1β-independent. Activation of the NLRP3 inflammasome by invading pathogens may prove cell type-specific in exacerbations of airway inflammation in asthma. Copyright © 2013 by the American Thoracic Society

Hotspot motion caused the Hawaiian-Emperor Bend and LLSVPs are not fixed

Controversy surrounds the fixity of both hotspots and large low shear velocity provinces (LLSVPs). Paleomagnetism, plate-circuit analyses, sediment facies, geodynamic modeling, and geochemistry suggest motion of the Hawaiian plume in Earth's mantle during formation of the Emperor seamounts. Herein, we report new paleomagnetic data from the Hawaiian chain (Midway Atoll) that indicate the Hawaiian plume arrived at its current latitude by 28 Ma. A dramatic decrease in distance between Hawaiian-Emperor and Louisville chain seamounts between 63 and 52 Ma confirms a high rate of southward Hawaiian hotspot drift (similar to 47 mm yr(-1)), and excludes true polar wander as a relevant factor. These findings further indicate that the Hawaiian-Emperor chain bend morphology was caused by hotspot motion, not plate motion. Rapid plume motion was likely produced by ridge-plume interaction and deeper influence of the Pacific LLSVP. When compared to plate circuit predictions, the Midway data suggest similar to 13 mm yr(-1) of African LLSVP motion since the Oligocene. LLSVP upwellings are not fixed, but also wander as they attract plumes and are shaped by deep mantle convection

Citizen Science 2.0 : Data Management Principles to Harness the Power of the Crowd

Citizen science refers to voluntary participation by the general public in scientific endeavors. Although citizen science has a long tradition, the rise of online communities and user-generated web content has the potential to greatly expand its scope and contributions. Citizens spread across a large area will collect more information than an individual researcher can. Because citizen scientists tend to make observations about areas they know well, data are likely to be very detailed. Although the potential for engaging citizen scientists is extensive, there are challenges as well. In this paper we consider one such challenge – creating an environment in which non-experts in a scientific domain can provide appropriate and accurate data regarding their observations. We describe the problem in the context of a research project that includes the development of a website to collect citizen-generated data on the distribution of plants and animals in a geographic region. We propose an approach that can improve the quantity and quality of data collected in such projects by organizing data using instance-based data structures. Potential implications of this approach are discussed and plans for future research to validate the design are described