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While the concepts involved in Self-Organized Criticality have stimulated thousands of theoretical models, only recently have these models addressed problems of biological and clinical importance. Here we outline how SOC can be used to engineer hybrid viral proteins whose properties, extrapolated from those of known strains, may be sufficiently effective to cure cancer.

Influenza virus contains two highly variable envelope glycoproteins, hemagglutinin (HA) and neuraminidase (NA). The structure and properties of HA, which is responsible for binding the virus to the cell that is being infected, change significantly when the virus is transmitted from avian or swine species to humans. Previously we identified much smaller human individual evolutionary amino acid mutational changes in NA, which cleaves sialic acid groups and is required for influenza virus replication. We showed that these smaller changes can be monitored very accurately across many Uniprot and NCBI strains using hydropathicity scales to quantify the roughness of water film packages, which increases gradually due to migration, but decreases abruptly under large-scale vaccination pressures. Here we show that, while HA evolution is much more complex, it still shows abrupt punctuation changes linked to those of NA. HA exhibits proteinquakes, which resemble earthquakes and are related to hydropathic shifting of sialic acid binding regions. HA proteinquakes based on sialic acid interactions are required for optimal balance between the receptor-binding and receptor-destroying activities of HA and NA for efficient virus replication. Our comprehensive results present an historical (1945-2011) panorama of HA evolution over thousands of strains, and are consistent with many studies of HA and NA interactions based on a few mutations of a few strains. While the common influenza virus discussed here has been rendered almost harmless by decades of vaccination programs, the sequential decoding lessons learned here are applicable to other viruses that are emerging as powerful weapons for controlling and even curing common organ cancers. Those engineered oncolytic drugs will be discussed in future papers.

Influenza virus contains two highly variable envelope glycoproteins, hemagglutinin (HA) and neuraminidase (NA). The structure and properties of HA, which is responsible for binding the virus to the cell that is being infected, change significantly when the virus is transmitted from avian or swine species to humans. Here we focus on much smaller human individual evolutionary amino acid mutational changes in NA, which cleaves sialic acid groups and is required for influenza virus replication. We show that very small amino acid changes can be monitored very accurately across many Uniprot and NCBI strains using hydropathicity scales to quantify the roughness of water film packages. Quantitative sequential analysis is most effective with the differential hydropathicity scale based on protein self-organized criticality (SOC). NA exhibits punctuated evolution at the molecular scale, millions of times smaller than the more familiar species scale, and thousands of times smaller than the genomic scale. Our analysis shows that large-scale vaccination programs have been responsible for a very large convergent reduction in influenza severity in the last century, a reduction which is hidden from short-term studies of vaccine effectiveness. Hydropathic analysis is capable of interpreting and even predicting trends of functional changes in mutation prolific viruses.

We investigate the structure of the planetary nebula (PN) NGC 2371 using [OIII]-5007 imaging taken with the Jacobus Kapteyn 1.0 m telescope, and [NII]-6584, [OIII]-5007 and Ha results acquired with the Hubble Space Telescope (HST). These are supplemented with archival mid-infrared (MIR) observations taken with the Spitzer Space Telescope (Spitzer). We note the presence of off-axis low-ionization spokes along a PA of 65 degrees, and associated collars of enhanced [OIII] emission. The spokes appear to consist of dense condensations having low-excitation tails, possibly arising due to UV shadowing and/or ram-pressure stripping of material. Line ratios imply that most of the emission arises through photo-ionisation, and is unlikely to derive from post-shock cooling regions. An analysis of these features in the MIR suggests that they may also be associated with high levels of emission from polycyclic aromatic hydrocarbons (PAHs), together with various permitted and forbidden line transitions. Such high levels of PAH emission, where they are confirmed, may develop as a result of preferentially enhanced FUV pumping of the molecules, or shattering of larger grains within local shocks. Although H2 emission may also contribute to these trends, it is argued that shock-excited transitions would lead to markedly differing results. We finally note that thin filaments and ridges of [OIII] emission may indicate the presence of shock activity at the limits of the interior envelope, as well as at various positions within the shell itself. We also note that radially increasing fluxes at 3.6, 5.8 and 8.0 microns, relative to the emission at 4.5 microns, may arise due to enhanced PAH emission in external photo-dissociative regions (PDRs)., Comment: 11 figures and 38 pages in arXiv. Accepted for publication in MNRAS

The behavior of disease-linked mutations of membrane proteins is especially simple in rhodopsin, where they are well-studied, as they are responsible for retinitis pigmentosa, RP (retinal degeneration). Here we show that the frequency of occurrence of single RP mutations is strongly influenced by their posttranslational survival rates, and that this survival correlates well (82%) with a long-range, non-local hydropathic measure of the roughness of the water interfaces of ex-membrane rhodopsin based on self-organized criticality (SOC). It is speculated that this concept may be generally useful in studying survival rates of many mutated proteins.

NGC 6369 is a double-shell planetary nebula (PN) consisting of a bright annular inner shell with faint bipolar extensions and a filamentary envelope. We have used ground- and space-based narrow-band optical and near-IR images, broad-band mid-IR images, optical long-slit echelle spectra, and mid-IR spectra to investigate its physical structure. These observations indicate that the inner shell of NGC 6369 can be described as a barrel-like structure shape with polar bubble-like protrusions, and reveal evidence for H2 and strong polycyclic aromatic hydrocarbons (PAHs) emission from a photo-dissociative region (PDR) with molecular inclusions located outside the bright inner shell. High-resolution HST narrow-band images reveal an intricate excitation structure of the inner shell and a system of "cometary" knots. The knotty appearance of the envelope, the lack of kinematical evidence for shell expansion and the apparent presence of emission from ionized material outside the PDR makes us suggest that the envelope of NGC 6369 is not a real shell, but a flattened structure at its equatorial regions. We report the discovery of irregular knots and blobs of diffuse emission in low-excitation and molecular line emission that are located up to 80" from the central star, well outside the main nebular shells. We also show that the filaments associated to the polar protrusions have spatial extents consistent with post-shock cooling regimes, and likely represent regions of interaction of these structures with surrounding material., Comment: 14 pages, 13 figures. Accepted for publication in MNRAS

We focus here on the scaling properties of small interspecies differences between red cone opsin transmembrane proteins, using a hydropathic elastic roughening tool previously applied to the rhodopsin rod transmembrane proteins. This tool is based on a non-Euclidean hydropathic metric realistically rooted in the atomic coordinates of 5526 protein segments, which thereby encapsulates universal non-Euclidean long-range differential geometrical features of water films enveloping globular proteins in the Protein Data Bank. Whereas the rhodopsin blue rod water films are smoothest in humans, the red cone opsins' water films are optimized in cats and elephants, consistent with protein species landscapes that evolve differently in different contexts. We also analyze red cone opsins in the chromatophore-containing family of chameleons, snakes, zebrafish and goldfish, where short- and long-range (BLAST and hydropathic) aa correlations are found with values as large as 97-99%. We use hydropathic amino acid (aa) optimization to estimate the maximum number Nmax of color shades that the human eye can discriminate, and obtain 10^6 < Nmax < 10^7, in good agreement with experiment.

Although the planetary nebula NGC 6781 appears to possess an elliptical morphology, its kinematic and emission characteristics are in many ways unusual, and it is possible that it may represent a bipolar source oriented close to the line of sight. We shall present deep imaging of this nebula in [O III], Ha and [N II], and using broad-band (F555W and F814W) filters. These were taken with the 2.56-m Nordic Optical Telescope and Hubble Space Telescope. This is combined with mid-infrared (MIR) imaging and spectroscopy acquired with the Spitzer Space Telescope (Spitzer), and near-infrared spectroscopy deriving from the Infrared Space Observatory (ISO). These reveal details of the complex [N II] structure associated with extended shell emission, perhaps associated with highly inclined bipolar lobes. We also note the presence of narrow absorbing filaments and clumps projected against the surface of the envelope, components which may be responsible for much of the molecular emission. We point out that such clumps may be responsible for complex source structure in the MIR, and give rise to asymmetries in emission along the major axis of the source., Comment: 12 pages, 10 figures, Accepted for publication in MNRAS. 32 pages in arXiv

Measured exponents associated with Stretched Exponential Relaxation (SER) are widely scattered in microscopically inhomogeneous glasses, but accurately bifurcate into two "magic" values, 3/5 and 3/7, in a wide variety of microscopically homogeneous glasses. These bifurcated values are derived here from a statistical product model that involves diffusion of excitations to native traps in the presence of short-range forces only, or combined short- and long- range forces, respectively. Bifurcated SER can be used to monitor sample homogeneity. It explains a wide range of experimental data, and even includes multiple aspects of the citation distributions of 20th century science, involving 25 million papers and 600 million citations, and why these changed radically in 1960. It also shows that the distribution of country population sizes has compacted glassy character, and is strongly influenced by migration.

Self-organized criticality (SOC) is a popular concept that has been the subject of more than 3000 articles in the last 25 years. Here we show that SOC may enable theory to connect standard Web-based (BLAST) short-range amino acid (aa) similarities to long-range aa roughening form factors that accurately describe evolutionary trends in water-membrane protein interactions. Our method utilizes a hydropathic aa metric based on 5526 protein segments and thereby encapsulates differential geometrical features of the Protein Data Bank. It easily organizes small aa sequence differences between humans and proximate species. For rhodopsin, the most studied transmembrane signaling protein associated with night vision, it shows that short- and long-range aa sequence properties correlate with 96% success for humans, monkeys, cats, mice and rabbits. Proper application of SOC promises unprecedented simplifications of exponentially complex protein sequence-structure-function problems, both conceptual and practical.

We provide mid- and far-infrared photometry of 857 Galactic planetary nebulae (PNe) using data derived from the AKARI All-Sky Survey. These include fluxes at 9 and 18 {\mu}m obtained with the Infrared Camera (IRC), and at 65, 90, 140 and 160 {\mu}m using the far-Infrared Surveyor (FIS). It is noted that the IR luminosities of the youngest PNe are comparable to the total luminosities of the central stars, and subsequently decline to ~ 5102 L where D > 0.08 pc. This is consistent with an evolution of PNe dust opacities, and appreciable absorption in young and proto-PNe. We also note that whilst there is little evidence for the evolution in IR/radio flux ratios suggested by previous authors. The fall-off in dust temperatures is similar to that determined in previous studies, whilst levels of Ly heating are < 0.5 of the total energy budget of the grains. There appears to be an evolution in the infrared excess (IRE) as nebulae expand, with the largest values occurring in the most compact PNe., Comment: 76 pages, 13 figures (1 in color), 2 tables

Proteins appear to be the most dramatic natural example of self-organized network criticality (SONC), a concept that explains many otherwise apparently exponentially unlikely phenomena. Adaptive plasticity is a term which has become much more specific as a result of recent physiological and genetic studies. Here we show that the molecular properties of rhodopsin, the transmembrane protein associated with night vision, can be quantified species by species using the Moret-Zebende hydropathicity scale based on SONC. The results show that long-range adaptive plasticity optimizes proximate species molecular functionality far more effectively than one would infer using only standard amino acid sequence (local similarity) tools such as BLAST for multiple alignments. These results should be universal, and they suggest new paths for analyzing and predicting protein functionality from amino acid sequences alone.

We present mapping, profiles and photometry for 24 planetary nebulae (PNe) detected in the GLIMPSE 3D mid-infrared (MIR) survey of the Galactic plane. The PNe show many of the properties observed in previous studies of these sources, including evidence for longer wave emission from outside of the ionised zones, a likely consequence of emission from polycyclic aromatic hydrocarbons (PAHs) within the nebular photo-dissociation regimes (PDRs). We also note variations in 5.8/4.5 and 8.0/4.5 microns flux ratios with distance from the nuclei; present evidence for enhanced MIR emission in the halos of the sources; and note evidence for variations in colour with nebular evolution., Comment: 35 pages, 28 figures, Accepted for publication in Revista Mexicana de Astronomia y Astrofisica (RevMexAA). 61 pages in arXiv

Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein conformational functionality is often dominated by long-range hydro(phobic/philic) interactions which both drive protein compaction and mediate protein-protein interactions. Superfamily transmembrane GPCR are the largest family of proteins in the human genome; their amino acid sequences form the largest data base for protein-membrane interactions. While there are now structural data on the heptad transmembrane structures of representatives of several heptad families, here we show that fresh insights into global and some local chemical trends in GPCR properties can be obtained accurately from sequences alone, especially by separating the extracellular and cytoplasmic loops from transmembrane segments. The global mediation of long-range water-protein interactions occurs in conjunction with modulation of these interactions by roughened interfaces. Hydropathic roughening profiles are defined here solely in terms of amino acid sequences, and knowledge of protein coordinates is not required. Roughening profiles both for GPCR and some simpler protein families display accurate and transparent connections to protein functionality.

We present imaging and spectroscopy of NGC 40 acquired using the Spitzer Space Telescope (Spitzer), and the Infrared Space observatory (ISO). These are used to investigate the nature of emission from the central nebular shell, from the nebular halo, and from the associated circumnebular rings. It is pointed out that a variety of mechanisms may contribute to the mid-infrared (MIR) fluxes, and there is evidence for a cool dust continuum, strong ionic transitions, and appreciable emission by polycyclic aromatic hydrocarbons (PAHs). Prior observations at shorter wavelengths also indicate the presence of warmer grains, and the possible contribution of H2 transitions. It is suggested that an apparent jet-like structure to the NE of the halo represents one of the many emission spokes that permeate the shell. The spokes are likely to be caused by the percolation of UV photons through a clumpy interior shell, whilst the jet-like feature is enhanced due to locally elevated electron densities; a result of interaction between NGC 40 and the interstellar medium. It is finally noted that the presence of the PAH, 21 microns and 30 microns spectral features testifies to appreciable C/O ratios within the main nebular shell. Such a result is consistent with abundance determinations using collisionally excited lines, but not with those determined using optical recombination lines, Comment: 13 pages, 8 figures, Accepted for publication in MNRAS. 37 pages in arXiv

We report a measurement of the positive muon lifetime to a precision of 1.0 parts per million (ppm); it is the most precise particle lifetime ever measured. The experiment used a time-structured, low-energy muon beam and a segmented plastic scintillator array to record more than 2 x 10^{12} decays. Two different stopping target configurations were employed in independent data-taking periods. The combined results give tau_{mu^+}(MuLan) = 2196980.3(2.2) ps, more than 15 times as precise as any previous experiment. The muon lifetime gives the most precise value for the Fermi constant: G_F(MuLan) = 1.1663788 (7) x 10^-5 GeV^-2 (0.6 ppm). It is also used to extract the mu^-p singlet capture rate, which determines the proton's weak induced pseudoscalar coupling g_P., Comment: Accepted for publication in Phys. Rev. Lett

At vertical edges, thin films of silicon oxide (SiO_{2-x}) contain semiconductive c-Si layered nanocrystals (Si NC) embedded in and supported by an insulating g-SiO2 matrix. Tour et al. have shown that a trenched thin film geometry enables the NC to form switchable nanowires (SNW) when trained by an applied field. The field required to form SNW decreases rapidly within a few cycles, or by annealing at 600 C in even fewer cycles, and is stable to 700C. Here we describe the intrinsic evolution of Si NC and SNW in terms of the competition between internal stresses and electro-osmosis. The analysis relies heavily on experimental data from a wide range of thin film studies, and it explains why a vertical edge across the planar Si-SiOx interface is necessary to form SNW. The discussion also shows that the formation mechanisms of Si NC and Si/SiO_{2-x} SNW are intrinsic and result from optimization of nanowire conductivity in the presence of residual host misfit stresses.

We have obtained 24 {\mu}m imaging, profiles and fluxes for 224 planetary nebulae (PNe) lying within the limits of the Spitzer MIPSGAL survey. It is noted that most of the PNe having extended 24 {\mu}m emission also possess circular morphologies, suggesting that the emission derives from cool grains located within the AGB mass-loss regimes. Certain of these halos are found to have a surface brightness fall-off which may be consistent with secularly invariant mass-loss within the PNe progenitors. By contrast, the 8.0 {\mu}m envelopes are detected out to smaller distances from the nuclei, and have a steeper rate of surface brightness fall-off; a phenomenon which may arise from changes in the excitation of polycyclic aromatic hydrocarbons (PAHs) within external photo-dissociation regimes (PDRs). Our 24{\mu}m fluxes are compared to those in previously published studies, and this appears to indicate that many of the prior fluxes have been underestimated; a disparity may imply that previous aperture sizes were too small. We have also combined our 24 {\mu}m fluxes with measures at shorter mid-infrared (MIR) wavelengths, taken with the Infrared Array Camera (IRAC). These are used to investigate the positioning of PNe within the IRAC-MIPSGAL colour planes. The [8.0]-[24] and [5.8]-[24] colours are found to be large, and extend over the respective ranges 3.4-8.7 mag, and 5.4-10.3 mag; indices which are only explainable where a broad range of mechanisms contribute to the fluxes, including PAH bands, cool dust continua, and a variety of ionic transitions. These and other components also affect the morphologies of the sources, and lead to wavelength dependent changes in the widths of the profiles., Comment: 44 pages, 6 figures (3 in color), 2 tables

Thin films of silicon oxide (SiOx) are mixtures of semiconductive c-Si nanoclusters (NC) embedded in an insulating g-SiO2 matrix. Tour et al. have shown that a trenched thin film geometry enables the NC to form semiconductive filamentary arrays when driven by an applied field. The field required to form reversible nanoscale switching networks (NSN) decreases rapidly within a few cycles, or by annealing at 600 C in even fewer cycles, and is stable to 700C. Here we discuss an elastic mechanism that explains why a vertical edge across the planar Si-SiOx interface is necessary to form NSN. The discussion shows that the formation mechanism is intrinsic and need not occur locally at the edge, but can occur anywhere in the SiOx film, given the unpinned nanoscale vertical edge geometry.

The supernova remnant (SNR) G357.7+0.3 appears to have caused considerable shredding of the local interstellar medium (ISM), leading to the formation of multiple cloud fragments having bright rims and cometary structures. We investigate five of these regions using mid-infrared (MIR) imaging and photometry deriving from the Spitzer Space Telescope (SST), as well as photometry deriving from the 2MASS near-infrared all sky survey, the Mid-Course Science Experiment (MSX), and the Multiband Imaging Photometer for Spitzer (MIPSGAL) survey of the Galactic plane. It is noted that two of the rims show evidence for emission by shock excited H2 transitions, whilst the centres of the clouds also show evidence for dark extinction cores, observed in silhouette against the bright emission rims. Levels of extinction for these cores are determined to be of order AV ~ 17-26 mag, whilst densities n(HI) are of order ~ 10^4 cm^(-3), and masses in the region of ~40-100 Msun. It is shown that the wavelength dependence of extinction is probably similar to that of Cardelli et al. and Martin & Whittet, but differs from the MIR extinction trends of Indebetouw et al. The distributions of Class I young stellar objects (YSOs) implies that many of them are physically associated with the clouds, and were likely formed as a result of interaction between the clouds and SN winds. A determination of the spectral energy distributions (SEDs) of these stars, together with 2-D radiative transfer modelling of their continua is used to place constraints upon their properties., Comment: The paper contains 18 figures and 2 tables

NGC 7009 is a fascinating example of a high excitation, elliptical planetary nebula (PN) containing circum-nebular rings, and FLIERs and jets along the major axis. We present visual spectroscopy along multiple position angles through the nucleus, taken with the Observatorio Astronomico Nacional (Mexico); mid-infrared (MIR) spectroscopy and imaging acquired using the Infrared Space Observatory (ISO) and Spitzer Space Telescope (SST), and narrow band imaging obtained using the Hubble Space Telescope (HST). The data show that the mid-infrared (MIR) continuum is dominated by a broad ~ 100K continuum, and a strong excess attributable to crystalline silicate emission. The primary peaks in this excess are similar to those observed in Forsterite and clino- and ortho-enstatite. We use the ground-based spectroscopy, and ratioing of HST images to investigate the presence of shocks in the ansae and interior envelope. It is concluded that line ratios in the ansae may be partially consistent with shock excitation, although these features are primarily dominated by photo-ionisation. We also note evidence for shock excitation at the limits of the interior elliptical shell, and for multiple bow-shock structures centered upon the ansae., Comment: 22 pages, 19 figures. Accepted for publication in MNRAS. 52 pages in arXiv

Scientific communication is an essential part of modern science: whereas Archimedes worked alone, Newton (correspondence with Hooke, 1676) acknowledged that "If I have seen a little further, it is by standing on the shoulders of Giants." How is scientific communication reflected in the patterns of citations in scientific papers? How have these patterns changed in the 20th century, as both means of communication and individual transportation changed rapidly, compared to the earlier post-Newton 18th and 19th centuries? Here we discuss a glass model for scientific communications, based on a unique 2009 scientometric study of 25 million papers and 600 million citations that encapsulates the epistemology of modern science. The glass model predicts and explains, using no adjustable parameters, a surprisingly universal internal structure in the development of scientific research, which is essentially constant across the natural sciences, but which because of globalization changed qualitatively around 1960. Globalization corresponds physically to anomalous superdiffusion, which has been observed near the molecular glass transition, and can enhance molecular diffusion by factors as large as 100.

We provide mid-infrared (MIR) imaging, photometry and profiles for the Galactic supernova remnants (SNRs) G001.0-00.1, G355.9-02.5, G355.6-00.0, and W28 based upon data deriving for the Galactic Legacy Infrared Midplane Survey Extraordinaire (GLIMPSE). All of the sources show evidence for interaction with the interstellar medium (ISM), leading to curved frontal structures and apparent voids in the ISM. An analysis of the spectral energy distributions (SEDs) of Class I young stellar objects (YSOs) within the north-westerly interaction region of W28, and of the density of stars within the borders of the SNR, suggests that many of them may have been triggered by the SN event. 2-D radiative transfer modelling permits us to constrain the physical parameters of the sources. It is also noted that the location of Class I YSOs about the perimeter of G001.0-00.1, and close to frontal arcs associated with SNR G355.9-02.5, suggests that star formation may have been triggered by these SNRs as well. Finally, it is found that the MIR colours of the frontal structures appear consistent with shock excitation of the v = 0->0 transitions of H2, although it is conceivable that emission by polycyclic aromatic hydrocarbons (PAHs) may also play a role. Where the latter mechanism is relevant, then it is possible that emission derives from the shattering of larger grains in frontal regions, leading to increased volume densities of PAH carrying grains., Comment: The paper contains 14 figures and 0 tables

Left Cheban loops are loops that satisfy the identity x(xy.z) = yx.xz. Right Cheban loops satisfy the mirror identity {(z.yx)x = zx.xy}. Loops that are both left and right Cheban are called Cheban loops. Cheban loops can also be characterized as those loops that satisfy the identity x(xy.z) = (y.zx)x. These loops were introduced in Cheban, A. M. Loops with identities of length four and of rank three. II. (Russian) General algebra and discrete geometry, pp. 117-120, 164, "Shtiintsa", Kishinev, 1980. Here we initiate a study of their structural properties. Left Cheban loops are left conjugacy closed. Cheban loops are weak inverse property, power associative, conjugacy closed loops; they are centrally nilpotent of class at most two., Comment: 6 pages

Because the theory of SER is still a work in progress, the phenomenon itself can be said to be the oldest unsolved problem in science, as it started with Kohlrausch in 1847. Many electrical and optical phenomena exhibit SER with probe relaxation I(t) ~ exp[-(t/{\tau}){\beta}], with 0 < {\beta} < 1. Here {\tau} is a material-sensitive parameter, useful for discussing chemical trends. The "shape" parameter {\beta} is dimensionless and plays the role of a non-equilibrium scaling exponent; its value, especially in glasses, is both practically useful and theoretically significant. The mathematical complexity of SER is such that rigorous derivations of this peculiar function were not achieved until the 1970's. The focus of much of the 1970's pioneering work was spatial relaxation of electronic charge, but SER is a universal phenomenon, and today atomic and molecular relaxation of glasses and deeply supercooled liquids provide the most reliable data. As the data base grew, the need for a quantitative theory increased; this need was finally met by the diffusion-to-traps topological model, which yields a remarkably simple expression for the shape parameter {\beta}, given by d*/(d* + 2). At first sight this expression appears to be identical to d/(d + 2), where d is the actual spatial dimensionality, as originally derived. The original model, however, failed to explain much of the data base. Here the theme of earlier reviews, based on the observation that in the presence of short-range forces only d* = d = 3 is the actual spatial dimensionality, while for mixed short- and long-range forces, d* = fd = d/2, is applied to four new spectacular examples, where it turns out that SER is useful not only for purposes of quality control, but also for defining what is meant by a glass in novel contexts. (Please see full abstract in main text)

We have investigated the mid-infrared (MIR) and visual structures of seven bipolar planetary nebulae (BPNe), using imaging and spectroscopy acquired using the Spitzer Space Telescope (SST), and the Observatorio Astronomico Nacional in Mexico. The results show that the sources are more extended towards longer MIR wavelengths, as well as having higher levels of surface brightness in the 5.8 and 8.0 microns bands. It is also noted that the 5.8/4.5 and 8.0/4.5 microns flux ratios increase with increasing distance from the nuclei of the sources. All of these latter trends may be attributable to emission by polycyclic aromatic hydrocarbons (PAHs) and/or warm dust continua within circum-nebular photo-dissociation regions (PDRs). A corresponding decrease in the flux ratios 8.0/5.8 microns may, by contrast, arise due to changes in the properties of the PAH emitting grains. We note evidence for possible 8.0 microns ring-like structures in the envelope of NGC 2346, located in a region beyond the minor axis limits of the ionized envelope. An analysis of the inner two rings shows that whilst they have higher surface brightnesses at longer MIR wavelengths, they are relatively stronger (compared to underlying emission) at 3.6 and 4.5 microns. There is also evidence for point reflection symmetry along the major axis of the outflow., Comment: 27 pages, 22 figures, Accepted for publication in MNRAS. 69 pages in arXiv

We present an analysis of the structure and properties of the compact HII region Sh 2-89, and certain of the young stellar objects (YSOs) within this regime, using mid-infrared (MIR) mapping derived from the Spitzer Space Telescope (SST) and visual slit spectroscopy of the inner regions of the source. We show that the region has a bipolar structure, and contains a variety of Class I and II YSOs. Much of the MIR emission appears to be dominated by PAH emission bands, which cause strong increases in flux in the 5.8 and 8.0 microns photometric channels, whilst the variation of H_alpha, [NII] at 6583 A, [SII] at 6716+6731 A, and MIR emission profiles confirms the presence of complex ionisation fronts, and ionisation stratification., Comment: 12 pages, 6 figures, Accepted for publication in MNRAS. 33 pages in arXiv

We report the results of visual spectroscopy, mid-infrared (MIR) mapping and photometry, and near-infrared photometry of two candidate symbiotic stars (IPHAS J193108.67+164950.5 and IPHAS J193709.65+202655.7) associated with extended MIR emission. Our analysis of the continua of these sources shows that they are likely to represent Class I-II young stellar objects (YSOs) in which most of the IR emission arises from circumstellar discs, and for which the physical characteristics (stellar temperatures, radii, masses and luminosities) are similar. The extended emission is characterized by a substantial increase in fluxes and dimensions to longer MIR wavelengths. This is likely to arise as a result of emission by polycyclic aromatic hydrocarbons within extended photodissociation regimes, centred upon more compact ionized regions responsible for much of the shorter wave emission. Such dual emission structures are characteristic of those observed in many compact HII regions. Finally, we note that the clouds have asymmetrical structures and wind-swept morphologies, conceivably indicative of shock interaction with external winds. Where this is the case, then it is possible that the YSOs are located in regions of triggered star formation., Comment: 10 pages, 7 figures, Accepted for publication in MNRAS. 25 pages in arXiv

We construct a family of purely infinite $C^*$-algebras, $\mathcal{Q}^\lambda$ for $\lambda\in (0,1)$ that are classified by their $K$-groups. There is an action of the circle $\T$ with a unique ${\rm KMS}$ state $\psi$ on each $\mathcal{Q}^\lambda.$ For $\lambda=1/n,$ $\mathcal{Q}^{1/n}\cong O_n$, with its usual $\T$ action and ${\rm KMS}$ state. For $\lambda=p/q,$ rational in lowest terms, $\mathcal{Q}^\lambda\cong O_n$ ($n=q-p+1$) with UHF fixed point algebra of type $(pq)^\infty.$ For any $n>0,$ $\mathcal{Q}^\lambda\cong O_n$ for infinitely many $\lambda$ with distinct KMS states and UHF fixed-point algebras. For any $\lambda\in (0,1),$ $\mathcal{Q}^\lambda\neq O_\infty.$ For $\lambda$ irrational the fixed point algebras, are NOT AF and the $\mathcal{Q}^\lambda$ are usually NOT Cuntz algebras. For $\lambda$ transcendental, $K_1\cong K_0\cong\Z^\infty$, so that $\mathcal{Q}^\lambda$ is Cuntz' $\mathcal Q_{\N}$, \cite{Cu1}. If $\lambda^{\pm 1}$ are both algebraic integers, the {\bf only} $O_n$ which appear satisfy $n\equiv 3(mod 4).$ For each $\lambda$, the representation of $\mathcal{Q}^\lambda$ defined by the KMS state $\psi$ generates a type ${\rm III}_\lambda$ factor. These algebras fit into the framework of modular index (twisted cyclic) theory of \cite{CPR2,CRT} and \cite{CNNR}.

Scientific communication is an essential part of modern science: whereas Archimedes worked alone, Newton (1676) acknowledged that "If I have seen a little further, it is by standing on the shoulders of Giants." How is scientific communication reflected in the patterns of citations in scientific papers? How have these patterns changed in the 20th century, as both means of communication and individual transportation changed rapidly, compared to the earlier post-Newton 18th and 19th centuries? Here we discuss a physical model for scientific communications, based on an informetric study of 25 million papers and 600 million citations; the physical model itself relies on analogies with glass relaxation, where virtually identical patterns have been identified in 50 well designed experiments. The model reveals a surprisingly universal internal structure in the development of scientific research, which is essentially constant across the natural sciences, but which changed qualitatively around 1960.

We present mid-infrared (MIR) photometry for 367 Galactic disk, bulge and Large Magellanic Cloud (LMC) planetary nebulae, determined using GLIMPSE II and SAGE data acquired using the Spitzer Space Telescope. This has permitted us to make a comparison between the luminosity functions of bulge and LMC planetary nebulae, and between the MIR colours of all three categories of source. It is determined that whilst the 3.6 microns luminosity function of the LMC and bulge sources are likely to be closely similar, the [3.6]-[5.8] and [5.8]-[8-0] indices of LMC nebulae are different from those of their disk and bulge counterparts. This may arise because of enhanced 6.2 microns PAH emission within the LMC sources, and/or as a result of differences between the spectra of LMC PNe and those of their Galactic counterparts. We also determine that the more evolved disk sources listed in the MASH catalogues of Parker et al. and Miszalski et al. (2008) have similar colours to those of the less evolved (and higher surface brightness) sources in the catalogue of Acker et al. (1992); a result which appears at variance with previous studies of these sources., Comment: 14 pages, 9 figures, Publicated in MNRAS. 58 pages in arXiv

We present evidence for interaction between the supernova remnant (SNR) G357.7+0.3 and nearby molecular clouds, leading to the formation of wind-swept structures and bright emission rims. These features are not observed at visual wavelengths, but are clearly visible in mid-infrared (MIR) mapping undertaken using the Spitzer Space Telescope (SST). Analysis of one of these clouds, the bright cometary structure G357.46+0.60, suggests that it contains strong polycyclic aromatic hydrocarbon (PAH) emission features in the 5.8 and 8.0 microns photometric bands, and that these are highly variable over relatively small spatial scales. This source also appears to contain a YSO within the bright rim structure, with a steeply rising spectrum between 1.25 and 24 microns. Finally, it is noted that a further, conical emission region appears to be associated with the Mira V1139 Sco, and it is suggested that this may represent the case of a Mira outflow interacting with a SNR., Comment: 13 pages, 9 figures, Publicated in MNRAS. 43 pages in arXiv

The motion of planetary nebulae (PNe) through the interstellar medium (ISM) is thought to lead to a variety of observational consequences, including the formation of bright rims; deformation and fragmentation of the shells; and a shift of the central stars away from the geometric centres of the envelopes. These and other characteristics have been noted through imaging in the visual wavelength regime. We report further observations of such shells taken in the mid-infrared (MIR), acquired through programs of IRAC imaging undertaken using the Spitzer Space Telescope (SST). NGC 2440 and NGC 6629 are shown to possess likely interacting halos, together with ram-pressure stripped material to one side of their shells. Similarly, the outer halos of NGC 3242 and NGC 6772 appear to have been fragmented through Rayleigh-Taylor (RT) instabilities, leading to a possible flow of ISM material towards the inner portions of their envelopes. If this interpretation is correct, then it would suggest that NGC 3242 is moving towards the NE; a suggestion which is also supported through the presence of a 60 microns tail extending in the opposite direction, and curved bands of H-alpha emission in the direction of motion - components which may arise through RT instabilities in the magnetized ISM., Comment: 14 pages, 9 figures, Accepted for publication in MNRAS. 42 pages in arXiv

We present images of the planetary nebulae (PNe) NGC 7354 and NGC 3242 in four mid-infrared (MIR) photometric bands centred at 3.6, 4.5, 5.8 and 8.0 microns; the results of observations undertaken using the Spitzer Space Telescope (SST). The resulting images show the presence of a halo and rings in NGC 3242, as previously observed through narrow band imaging at visual wavelengths, as well as evidence for a comparable halo and ring system in NGC 7354. This is the first time that a halo and rings have been observed in the latter source. We have analysed the formation of halos as a result of radiatively accelerated mass loss in the AGB progenitors. Although the models assume that dust formation occurs in C-rich environments, we note that qualitatively similar results would be expected for O-rich progenitors as well. The model fall-offs in halo density are found to result in gradients in halo surface brightness which are similar to those observed in the visible and MIR., Comment: 19 pages, 12 figures, Accepted for publication in MNRAS. 56 pages in arXiv

Optimally doped ceramic superconductors (cuprates, pnictides, ...) exhibit transition temperatures Tc much larger than strongly coupled metallic superconductors like Pb (Tc= 7.2K, Eg/kTc = 4.5), and exhibit many universal features that appear to contradict the BCS theory of superconductivity based on attractive electron-phonon pairing interactions. Here I argue that this paradoxical simplicity is plausibly resolved within the framework of the Pauling-Phillips self-organized, hard-wired dopant network model of ceramic superconductors, which has previously explained many features of the normal-state transport properties of these materials and successfully predicted strict lowest upper bounds for Tc in the cuprate and pnictide families.

Right groups are direct products of right zero semigroups and groups and they play a significant role in the semilattice decomposition theory of semigroups. Right groups can be characterized as associative right quasigroups (magmas in which left translations are bijective). If we do not assume associativity we get right quasigroups which are not necessarily representable as direct products of right zero semigroups and quasigroups. To obtain such a representation, we need stronger assumptions which lead us to the notion of \emph{right product quasigroup}. If the quasigroup component is a (one-sided) loop, then we have a \emph{right product (left, right) loop}. We find a system of identities which axiomatizes right product quasigroups, and use this to find axiom systems for right product (left, right) loops; in fact, we can obtain each of the latter by adjoining just one appropriate axiom to the right product quasigroup axiom system. We derive other properties of right product quasigroups and loops, and conclude by showing that the axioms for right product quasigroups are independent., Comment: 15 pages; v2: minor corrections to author data

Ceramic superconductors (cuprates, pnictides, ...) exhibit universal features in both Tcmax and in their planar lattice disordering measured by EXAFS, as reflected by three phase transitions. The two highest temperature transitions are known to be associated with formation of pseudogaps and superconductive gaps, with corresponding Landau order parameters, but no new gap is associated with the third transition below Tc. It is argued that the third transition is a dopant glass transition, which is remarkably similar to transitions previously observed in chalcogenide and oxide alloy network glasses (like window glass).

The prediction of transition temperatures can be regarded in several ways, either as an exacting test of theory, or as a tool for identifying theoretical rules for defining new homology models. Popular "first principle" methods for predicting transition temperatures in conventional crystalline superconductors have failed for cuprate HTSC, as have parameterized models based on CuO2 planes (with or without apical oxygen). Following a path suggested by Bayesian probability, we find that the glassy, self-organized dopant network percolative model is so successful that it defines a new homology class appropriate to ceramic superconductors. The reasons for this success are discussed, and a critical comparison is made with previous theories. The predictions are successful for all ceramics, including new non-cuprates based on FeAs in place of CuO2.

The Scher-Lax-Phillips (SLP) universal minimalist model quantitatively explains stretching fractions beta(Tg) for a wide variety of relaxation experiments (nearly 50 altogether) on electronic and molecular glasses and deeply supercooled liquids by assuming that quasi-particle excitations indexed by Breit-Wigner channels diffuse to traps (sinks). This model is effective here in discussing in detail three experiments: luminescence in isoelectronic Zn(Se,Te) alloys, fibrous relaxation in orthoterphenyl (OTP) and related glasses and melts up to 1.15Tg, and relaxation of binary chalcogen melts probed by spin-polarized neutrons (T as high as 1.5Tg). The model is also compared to several other recent theories.

The realization of high-transition-temperature superconductivity (HTSC) confined to nanometre-sized interfaces has been a long-standing goal because of potential applications and the opportunity to study quantum phenomena in reduced dimensions. Here we discuss HTSC at free surfaces, interfaces, and nanoscale cluster surfaces, and show that the percolative self-organized model of bulk HTSC also gives an excellent description of HTSC in quasi-two-dimensional contexts.

Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein functionality is dominated by long range hydro(phobic/philic) interactions which both drive protein compaction and mediate protein-protein interactions. In contrast to previous reductionist short range hydrophobicity scales, the holistic Moret-Zebende hydrophobicity scale represents a hydroanalytic tool that bioinformatically quantifies SOC in a way fully compatible with evolution. Hydroprofiling identifies chemical trends in the activities and substrate binding abilities of model enzymes and antibiotic animal lysozymes c and antibiotic human defensins, which have been the subject of tens of thousands of experimental studies. The analysis is simple and easily performed, and immediately yields insights not obtainable by traditional methods based on short-range real-space interactions, as described either by classical force fields (CFF) used in molecular dynamics simulations (MDS), or hydrophobicity scales based on transference energies from water to organic solvents.

Reversible switching of the complex network dynamics of proteins is mimicked in selected network glasses and compacted small carbohydrate molecules. Protein transitions occur on long time scales ~ us -ms, evocative of the exponentially large viscosities found in glass-forming supercooled liquids just above the glass transition; in searching for mechanisms for reversibly slowed "geared activation", Kauzmann was led from proteins to glasses. I show here that selected network glasses and small carbohydrate molecules can be used to model such transitions, and elucidate in particular some universal aspects of tandem repeats. The human ankyrin tandem repeat D34, with a superhelical "coiled spring" structure which has 426 residues, folds reversibly and plastically. Such molecules are too large for present transition-state numerical simulations, currently limited to ~ 100 residues solvated by ~ 3000 water molecules for times ~ ns. The transition states of D34 exhibit a surprisingly simple collective ("geared") pattern when studied by fluorescence near its center, in samples modified mutageneously along its 12 helical repeats. One can understand this "plastic" pattern by taking advantage of a symmetric 45-atom carbohydrate molecular bridge to "cross over" from proteins to inorganic network glasses. There one easily identifies gears, and can show that the collective pattern is the signature of nonlocal, water-mediated [hydro(phobic/philic)] switching. Details of the transition patterns emerge from analyzing the amino acid alpha helical repeat sequences with water-only hydrophobicity scales. Freezing and melting of monolayer water films at physiological temperatures can enable ankyrin repeats to direct cell dynamics in muscles, membranes and cytoskeletons.

The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess water-induced medium-range order that is sometimes similar, but can also be complementary, to structural order. Study of these hitherto "phantom" order parameters promises far-reaching incremental improvements in the theory of protein dynamics. A by-product of the theory is an independent evaluation of the reliability of different hydrophobicity scales.

Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino acids, and protein scientists have long described protein-water interactions in terms of qualitative amino acid hydrophobicity scales. Here we examine several recent scales and argue plausibly (in terms of self-organized criticality) that one of them should be regarded as an absolute scale (within the protein universe), analogous to the dielectric scale of bond ionicity in inorganic octet compounds. Applications to repeat proteins (containing upwards of 900 amino acids) are successful, far beyond reasonable expectations, in all cases studied so far. While some of the results are obvious and can be obtained from the ex vitro spatial structures alone, many are hidden from plain view, and can be called phantom relations. As a byproduct, the network theory explains the exceptional functionality of leucine in zippers, heptads, and repeat consensus sites.

This paper presents, by example, an index theory appropriate to algebras without trace. Whilst we work exclusively with the Cuntz algebras the exposition is designed to indicate how to develop a general theory. Our main result is an index theorem (formulated in terms of spectral flow) using a twisted cyclic cocycle where the twisting comes from the modular automorphism group for the canonical gauge action on the Cuntz algebra. We introduce a modified $K_1$-group of the Cuntz algebra so as to pair with this twisted cocycle. As a corollary we obtain a noncommutative geometry interpretation for Araki's notion of relative entropy in this example. We also note the connection of this example to the theory of noncommutative manifolds., Comment: 27 pages, minor corrections

We investigate an extension of ideas of Atiyah-Patodi-Singer (APS) to a noncommutative geometry setting framed in terms of Kasparov modules. We use a mapping cone construction to relate odd index pairings to even index pairings with APS boundary conditions in the setting of KK-theory, generalising the commutative theory. We find that Cuntz-Kreiger systems provide a natural class of examples for our construction and the index pairings coming from APS boundary conditions yield complete K-theoretic information about certain graph C*-algebras., Comment: 40 pages, minor corrections to final section

C-loops are loops satisfying $x(y(yz))=((xy)y)z$. They often behave analogously to Moufang loops and they are closely related to Steiner triple systems and combinatorics. We initiate the study of C-loops by proving: (i) Steiner loops are C-loops, (ii) C-loops are alternative, inverse property loops with squares in the nucleus, (iii) the nucleus of a C-loop is a normal subgroup, (iv) C-loops modulo their nucleus are Steiner loops, (v) C-loops are power associative, power alternative but not necessarily diassociative, (vi) torsion commutative C-loops are products of torsion abelian groups and torsion commutative 2-C-loops; and several other results. We also give examples of the smallest nonassociative C-loops, and explore the analogy between commutative C-loops and commutative Moufang loops., Comment: 15 pages

A quasigroup identity is of Bol-Moufang type if two of its three variables occur once on each side, the third variable occurs twice on each side, the order in which the variables appear on both sides is the same, and the only binary operation used is the multiplication, viz. $((xy)x)z=x(y(xz))$. Many well-known varieties of quasigroups are of Bol-Moufang type. We show that there are exactly 26 such varieties, determine all inclusions between them, and provide all necessary counterexamples. We also determine which of these varieties consist of loops or one-sided loops, and fully describe the varieties of commutative quasigroups of Bol-Moufang type. Some of the proofs are computer-generated., Comment: 15 pages