Algebraic Approach to Interacting Quantum Systems

We present an algebraic framework for interacting extended quantum systems to study complex phenomena characterized by the coexistence and competition of different states of matter. We start by showing how to connect different (spin-particle-gauge) {\it languages} by means of exact mappings (isomorphisms) that we name {\it dictionaries} and prove a fundamental theorem establishing when two arbitrary languages can be connected. These mappings serve to unravel symmetries which are hidden in one representation but become manifest in another. In addition, we establish a formal link between seemingly unrelated physical phenomena by changing the language of our model description. This link leads to the idea of {\it universality} or equivalence. Moreover, we introduce the novel concept of {\it emergent symmetry} as another symmetry guiding principle. By introducing the notion of {\it hierarchical languages}, we determine the quantum phase diagram of lattice models (previously unsolved) and unveil hidden order parameters to explore new states of matter. Hierarchical languages also constitute an essential tool to provide a unified description of phases which compete and coexist. Overall, our framework provides a simple and systematic methodology to predict and discover new kinds of orders. Another aspect exploited by the present formalism is the relation between condensed matter and lattice gauge theories through quantum link models. We conclude discussing applications of these dictionaries to the area of quantum information and computation with emphasis in building new models of computation and quantum programming languages.Comment: 44 pages, 14 psfigures. Advances in Physics 53, 1 (2004

VEZF1 elements mediate protection from DNA methylation

There is growing consensus that genome organization and long-range gene regulation involves partitioning of the genome into domains of distinct epigenetic chromatin states. Chromatin insulator or barrier elements are key components of these processes as they can establish boundaries between chromatin states. The ability of elements such as the paradigm β-globin HS4 insulator to block the range of enhancers or the spread of repressive histone modifications is well established. Here we have addressed the hypothesis that a barrier element in vertebrates should be capable of defending a gene from silencing by DNA methylation. Using an established stable reporter gene system, we find that HS4 acts specifically to protect a gene promoter from de novo DNA methylation. Notably, protection from methylation can occur in the absence of histone acetylation or transcription. There is a division of labor at HS4; the sequences that mediate protection from methylation are separable from those that mediate CTCF-dependent enhancer blocking and USF-dependent histone modification recruitment. The zinc finger protein VEZF1 was purified as the factor that specifically interacts with the methylation protection elements. VEZF1 is a candidate CpG island protection factor as the G-rich sequences bound by VEZF1 are frequently found at CpG island promoters. Indeed, we show that VEZF1 elements are sufficient to mediate demethylation and protection of the APRT CpG island promoter from DNA methylation. We propose that many barrier elements in vertebrates will prevent DNA methylation in addition to blocking the propagation of repressive histone modifications, as either process is sufficient to direct the establishment of an epigenetically stable silent chromatin stat

Measuring V_ub and probing SUSY with double ratios of purely leptonic decays of B and D mesons

The experimental prospects for precise measurements of the leptonic decays B_u -> tau nu / mu nu, B_s -> mu+ mu-, D -> mu nu and D_s -> mu nu / tau nu are very promising. Double ratios involving four of these decays can be defined in which the dependence on the values of the decay constants is essentially eliminated, thus enabling complementary measurements of the CKM matrix element V_ub with a small theoretical error. We quantify the experimental error in a possible future measurement of |V_ub| using this approach, and show that it is competitive with the anticipated precision from the conventional approaches. Moreover, it is shown that such double ratios can be more effective than the individual leptonic decays as a probe of the parameter space of supersymmetric models. We emphasize that the double ratios have the advantage of using |V_ub| as an input parameter (for which there is experimental information), while the individual decays have an uncertainty from the decay constants (e.g. f_B_s), and hence a reliance on theoretical techniques such as lattice QCD.Comment: 21 pages, 4 figure

PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

Machine learning-based classification of rock discontinuity trace: SMOTE oversampling integrated with GBT ensemble learning

This paper presents a hybrid ensemble classifier combined synthetic minority oversampling technique (SMOTE), random search (RS) hyper-parameters optimization algorithm and gradient boosting tree (GBT) to achieve efficient and accurate rock trace identification. A thirteen-dimensional database consisting of basic, vector, and discontinuity features is established from image samples. All data points are classified as either “trace” or “non-trace” to divide the ultimate results into candidate trace samples. It is found that the SMOTE technology can effectively improve classification performance by recommending an optimized imbalance ratio of 1:5 to 1:4. Then, sixteen classifiers generated from four basic machine learning (ML) models are applied for performance comparison. The results reveal that the proposed RS-SMOTE-GBT classifier outperforms the other fifteen hybrid ML algorithms for both trace and non-trace classifications. Finally, discussions on feature importance, generalization ability and classification error are conducted for the proposed classifier. The experimental results indicate that more critical features affecting the trace classification are primarily from the discontinuity features. Besides, cleaning up the sedimentary pumice and reducing the area of fractured rock contribute to improving the overall classification performance. The proposed method provides a new alternative approach for the identification of 3D rock trace

Gastrojejunocolic fistula after gastrojejunostomy: a case series

<p>Abstract</p> <p>Introduction</p> <p>Gastrojejunocolic (GJC) fistulae represent a significant post-surgical cause of morbidity and mortality. GJC fistulae represent rare post-surgical complications, and most are associated with gastric surgery. In the past, this complication has been under-recognized because a fistula may form years after surgery.</p> <p>Case presentation</p> <p>We describe two cases of gastrojejunocolic fistula in men aged 67 and 60 who both initially presented with watery diarrhea and weight loss. Upper GI studies with small bowel follow-through or barium contrast enema studies allowed a conclusive diagnosis to be made. Both patients underwent one-stage en bloc resection, and their postoperative course was uneventful.</p> <p>Conclusion</p> <p>With surgery, this condition is entirely correctable. Pre-operative nutritional status should be evaluated in patients undergoing corrective surgery, and total parenteral nutrition plays a major role in the provision of bowel rest to allow recovery in malnourished patients.</p

A novel image-based approach for interactive characterization of rock fracture spacing in a tunnel face

This paper presents a novel integrated method for interactive characterization of fracture spacing in rock tunnel sections. The main procedure includes four steps: (1) Automatic extraction of fracture traces, (2) digitization of trace maps, (3) disconnection and grouping of traces, and (4) interactive measurement of fracture set spacing, total spacing, and surface rock quality designation (S-RQD) value. To evaluate the performance of the proposed method, sample images were obtained by employing a photogrammetry-based scheme in tunnel faces. Experiments were then conducted to determine the optimal parameter values (i.e. distance threshold, angle threshold, and number of fracture trace grouping) for characterizing rock fracture spacing. By applying the identified optimal parameters involved in the model, the proposed method could lead to excellent qualitative results to a new tunnel face. To perform a quantitative analysis, three methods (i.e. field, straightening, and the proposed method) were employed in the same study and comparisons were made. The proposed method agrees well with the field measurement in terms of the maximum and average values of measured spacing distribution. Overall, the proposed method has reasonably good accuracy and interactive advantage for estimating the ultimate fracture spacing and S-RQD. It can be a possible extension of existing methods for fracture spacing characterization for two-dimensional (2D) rock tunnel faces

Noncommutative cosmological models coupled to a perfect fluid and a cosmological constant

In this work we carry out a noncommutative analysis of several Friedmann-Robert-Walker models, coupled to different types of perfect fluids and in the presence of a cosmological constant. The classical field equations are modified, by the introduction of a shift operator, in order to introduce noncommutativity in these models. We notice that the noncommutative versions of these models show several relevant differences with respect to the correspondent commutative ones.Comment: 27 pages. 7 figures. JHEP style.arXiv admin note: substantial text overlap with arXiv:1104.481

Roles for Treg expansion and HMGB1 signaling through the TLR1-2-6 axis in determining the magnitude of the antigen-specific immune response to MVA85A

© 2013 Matsumiya et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedA better understanding of the relationships between vaccine, immunogenicity and protection from disease would greatly facilitate vaccine development. Modified vaccinia virus Ankara expressing antigen 85A (MVA85A) is a novel tuberculosis vaccine candidate designed to enhance responses induced by BCG. Antigen-specific interferon-γ (IFN-γ) production is greatly enhanced by MVA85A, however the variability between healthy individuals is extensive. In this study we have sought to characterize the early changes in gene expression in humans following vaccination with MVA85A and relate these to long-term immunogenicity. Two days post-vaccination, MVA85A induces a strong interferon and inflammatory response. Separating volunteers into high and low responders on the basis of T cell responses to 85A peptides measured during the trial, an expansion of circulating CD4+ CD25+ Foxp3+ cells is seen in low but not high responders. Additionally, high levels of Toll-like Receptor (TLR) 1 on day of vaccination are associated with an increased response to antigen 85A. In a classification model, combined expression levels of TLR1, TICAM2 and CD14 on day of vaccination and CTLA4 and IL2Rα two days post-vaccination can classify high and low responders with over 80% accuracy. Furthermore, administering MVA85A in mice with anti-TLR2 antibodies may abrogate high responses, and neutralising antibodies to TLRs 1, 2 or 6 or HMGB1 decrease CXCL2 production during in vitro stimulation with MVA85A. HMGB1 is released into the supernatant following atimulation with MVA85A and we propose this signal may be the trigger activating the TLR pathway. This study suggests an important role for an endogenous ligand in innate sensing of MVA and demonstrates the importance of pattern recognition receptors and regulatory T cell responses in determining the magnitude of the antigen specific immune response to vaccination with MVA85A in humans.This work was funded by the Wellcome Trust. MM has a Wellcome Trust PhD studentship and HM is a Wellcome Trust Senior Fello

Spectroscopic investigation of quantum confinement effects in ion implanted silicon-on-sapphire films

Crystalline Silicon-on-Sapphire (SOS) films were implanted with boron (B$^+$) and phosphorous (P$^+$) ions. Different samples, prepared by varying the ion dose in the range $10^{14}$ to 5 x $10^{15}$ and ion energy in the range 150-350 keV, were investigated by the Raman spectroscopy, photoluminescence (PL) spectroscopy and glancing angle x-ray diffraction (GAXRD). The Raman results from dose dependent B$^+$ implanted samples show red-shifted and asymmetrically broadened Raman line-shape for B$^+$ dose greater than $10^{14}$ ions cm$^{-2}$. The asymmetry and red shift in the Raman line-shape is explained in terms of quantum confinement of phonons in silicon nanostructures formed as a result of ion implantation. PL spectra shows size dependent visible luminescence at $\sim$ 1.9 eV at room temperature, which confirms the presence of silicon nanostructures. Raman studies on P$^+$ implanted samples were also done as a function of ion energy. The Raman results show an amorphous top SOS surface for sample implanted with 150 keV P$^+$ ions of dose 5 x $10^{15}$ ions cm$^{-2}$. The nanostructures are formed when the P$^+$ energy is increased to 350 keV by keeping the ion dose fixed. The GAXRD results show consistency with the Raman results.Comment: 9 Pages, 6 Figures and 1 Table, \LaTex format To appear in SILICON(SPRINGER