An O(n^3)-Time Algorithm for Tree Edit Distance

The {\em edit distance} between two ordered trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. In this paper, we present a worst-case $O(n^3)$-time algorithm for this problem, improving the previous best $O(n^3\log n)$-time algorithm~\cite{Klein}. Our result requires a novel adaptive strategy for deciding how a dynamic program divides into subproblems (which is interesting in its own right), together with a deeper understanding of the previous algorithms for the problem. We also prove the optimality of our algorithm among the family of \emph{decomposition strategy} algorithms--which also includes the previous fastest algorithms--by tightening the known lower bound of $\Omega(n^2\log^2 n)$~\cite{Touzet} to $\Omega(n^3)$, matching our algorithm's running time. Furthermore, we obtain matching upper and lower bounds of $\Theta(n m^2 (1 + \log \frac{n}{m}))$ when the two trees have different sizes $m$ and~$n$, where $m < n$.Comment: 10 pages, 5 figures, 5 .tex files where TED.tex is the main on

Quark mass and condensate in HQCD

We extend the Sakai-Sugimoto holographic model of QCD (HQCD) by including the scalar bi-fundamental "tachyon" field in the 8-brane-anti-8-brane probe theory. We show that this field is responsible both for the spontaneous breaking of the chiral symmetry, and for the generation of (current algebra) quark masses, from the point of view of the bulk theory. As a by-product we show how this leads to the Gell-Mann- Oakes-Renner relation for the pion mass.Comment: 23 pages, 7 figures; v2: corrected typos in eqs. (4.3), (4.4), (4.5), (4.9) and (4.11), and corrected figures 3, 4, 5 and 6; v3: section 5.3 on the pion mass rewritten in a clearer way, version published in JHE

Imaging Active Infection in vivo Using D-Amino Acid Derived PET Radiotracers.

Occult bacterial infections represent a worldwide health problem. Differentiating active bacterial infection from sterile inflammation can be difficult using current imaging tools. Present clinically viable methodologies either detect morphologic changes (CT/ MR), recruitment of immune cells (111In-WBC SPECT), or enhanced glycolytic flux seen in inflammatory cells (18F-FDG PET). However, these strategies are often inadequate to detect bacterial infection and are not specific for living bacteria. Recent approaches have taken advantage of key metabolic differences between prokaryotic and eukaryotic organisms, allowing easier distinction between bacteria and their host. In this report, we exploited one key difference, bacterial cell wall biosynthesis, to detect living bacteria using a positron-labeled D-amino acid. After screening several 14C D-amino acids for their incorporation into E. coli in culture, we identified D-methionine as a probe with outstanding radiopharmaceutical potential. Based on an analogous procedure to that used for L-[methyl-11C]methionine ([11C] L-Met), we developed an enhanced asymmetric synthesis of D-[methyl-11C]methionine ([11C] D-Met), and showed that it can rapidly and selectively differentiate both E. coli and S. aureus infections from sterile inflammation in vivo. We believe that the ease of [11C] D-Met radiosynthesis, coupled with its rapid and specific in vivo bacterial accumulation, make it an attractive radiotracer for infection imaging in clinical practice

Perturbative Analysis of Nonabelian Aharonov-Bohm Scattering

We perform a perturbative analysis of the nonabelian Aharonov-Bohm problem to one loop in a field theoretic framework, and show the necessity of contact interactions for renormalizability of perturbation theory. Moreover at critical values of the contact interaction strength the theory is finite and preserves classical conformal invariance.Comment: 12 pages in LaTeX, uses epsf.sty, 5 uuencoded Postscript figures sent separately. MIT-CTP-228

Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum

Halobacterium salinarum is a bioenergetically flexible, halophilic microorganism that can generate energy by respiration, photosynthesis, and the fermentation of arginine. In a previous study, using a genome-scale metabolic model, we have shown that the archaeon unexpectedly degrades essential amino acids under aerobic conditions, a behavior that can lead to the termination of growth earlier than necessary. Here, we further integratively investigate energy generation, nutrient utilization, and biomass production using an extended methodology that accounts for dynamically changing transport patterns, including those that arise from interactions among the supplied metabolites. Moreover, we widen the scope of our analysis to include phototrophic conditions to explore the interplay between different bioenergetic modes. Surprisingly, we found that cells also degrade essential amino acids even during phototropy, when energy should already be abundant. We also found that under both conditions considerable amounts of nutrients that were taken up were neither incorporated into the biomass nor used as respiratory substrates, implying the considerable production and accumulation of several metabolites in the medium. Some of these are likely the products of forms of overflow metabolism. In addition, our results also show that arginine fermentation, contrary to what is typically assumed, occurs simultaneously with respiration and photosynthesis and can contribute energy in levels that are comparable to the primary bioenergetic modes, if not more. These findings portray a picture that the organism takes an approach toward growth that favors the here and now, even at the cost of longer-term concerns. We believe that the seemingly "greedy" behavior exhibited actually consists of adaptations by the organism to its natural environments, where nutrients are not only irregularly available but may altogether be absent for extended periods that may span several years. Such a setting probably predisposed the cells to grow as much as possible when the conditions become favorable

GRB 051221A and Tests of Lorentz Symmetry

Various approaches to quantum gravity suggest the possibility of violation of Lorentz symmetry at very high energies. In these cases we expect a modification at low energies of the dispersion relation of photons that contains extra powers of the momentum suppressed by a high energy scale. These terms break boost invariance and can be tested even at relatively low energies. We use the light curves of the very bright short Gamma-Ray Burst GRB 051221A and compare the arrival times of photons at different energies with the expected time delay due to a modified dispersion relation. As no time delay was observed, we set a lower bound of 0.0066 E_{pl} \sim 0.66 10^{17} GeV on the scale of Lorentz invariance violation.Comment: 9 pages, 2 figure

Multi Visualization and Dynamic Query for Effective Exploration of Semantic Data

Semantic formalisms represent content in a uniform way according to ontologies. This enables manipulation and reasoning via automated means (e.g. Semantic Web services), but limits the user’s ability to explore the semantic data from a point of view that originates from knowledge representation motivations. We show how, for user consumption, a visualization of semantic data according to some easily graspable dimensions (e.g. space and time) provides effective sense-making of data. In this paper, we look holistically at the interaction between users and semantic data, and propose multiple visualization strategies and dynamic filters to support the exploration of semantic-rich data. We discuss a user evaluation and how interaction challenges could be overcome to create an effective user-centred framework for the visualization and manipulation of semantic data. The approach has been implemented and evaluated on a real company archive

Canopy nitrogen, carbon assimilation, and albedo in temperate and boreal forests: Functional relations and potential climate feedbacks

The availability of nitrogen represents a key constraint on carbon cycling in terrestrial ecosystems, and it is largely in this capacity that the role of N in the Earth\u27s climate system has been considered. Despite this, few studies have included continuous variation in plant N status as a driver of broad-scale carbon cycle analyses. This is partly because of uncertainties in how leaf-level physiological relationships scale to whole ecosystems and because methods for regional to continental detection of plant N concentrations have yet to be developed. Here, we show that ecosystem CO2 uptake capacity in temperate and boreal forests scales directly with whole-canopy N concentrations, mirroring a leaf-level trend that has been observed for woody plants worldwide. We further show that both CO2 uptake capacity and canopy N concentration are strongly and positively correlated with shortwave surface albedo. These results suggest that N plays an additional, and overlooked, role in the climate system via its influence on vegetation reflectivity and shortwave surface energy exchange. We also demonstrate that much of the spatial variation in canopy N can be detected by using broad-band satellite sensors, offering a means through which these findings can be applied toward improved application of coupled carbon cycle–climate models

The Herbertsmithite Hamiltonian: μ\muSR measurements on single crystals

We present transverse field muon spin rotation/relaxation measurements on single crystals of the spin-1/2 kagome antiferromagnet Herbertsmithite. We find that the spins are more easily polarized when the field is perpendicular to the kagome plane. We demonstrate that the difference in magnetization between the different directions cannot be accounted for by Dzyaloshinksii-Moriya type interactions alone, and that anisotropic axial interaction is present.Comment: 8 pages, 3 figures, accepted to JPCM special issue on geometrically frustrated magnetis

Tunable pentapeptide self-assembled β-sheet hydrogels

Oligopeptide-based supramolecular hydrogels hold promise in a range of applications. The gelation of these systems is hard to control with minor alterations in the peptide sequence significantly influencing the self-assembly process. This makes sequence design difficult whereby typical self-assembly rules cannot be applied. We explored the design of pentapeptide sequences with different charge distributions and discovered that they formed robust, pH-responsive hydrogels. Through altering the concentration and charge distribution of the peptide sequence, we demonstrated that the stiffness of the hydrogels can be tuned across two orders of magnitude (2-200 kPa). Also, through the reassembly of the b-sheet interactions, the hydrogels can both selfheal and shear thin. Using spectroscopic and cryo-imaging techniques, we investigated the relationship between peptide sequence, molecular structure and how these influence the mechanical properties of the hydrogel. These pentapetide hydrogels attributed with tunable morphology and mechanical properties have promise in tissue engineering, injectable delivery vectors and 3D printing applications