Bootstrap Approximations in Contractor Renormalization

We propose a bootstrap method for approximating the long-range terms in the Contractor Renormalization (CORE) method. The idea is tested on the 2-D Heisenberg antiferromagnet and the frustrated J_2-J_1 model. We obtain renormalization group flows that directly reveal the Neel phase of the unfrustrated HAF and the existence of a phase transition in the J_2-J_1 model for weak frustration. However, we find that this bootstrap method is dependent on blocking and truncation schemes. For this reason, we discuss these dependencies and unresolved issues that researchers who use this approach must consider.Comment: Some clarifications added for Phys Rev submissio

Humoral autoimmunity after solid organ transplantation: Germinal ideas may not be natural

Non-HLA antibody responses following solid organ transplantation have become increasingly emphasised, with several large clinical series suggesting that such responses contribute to late graft failure. Many of the responses described recognise both recipient and donor moieties of the target antigen and thus represent auto-, rather than allo-immunity. Within this rapidly evolving field, many questions remain unanswered: what triggers the response; how innate and adaptive humoral autoimmunity integrate; and most pressingly, how autoimmunity contributes to graft damage and its relationship to other effector mechanisms of graft rejection. This review summarises recent clinical and experimental studies of humoral autoimmunity in transplant rejection, and considers some of the answers to these questions

KnowLife: A Versatile Approach for Constructing a Large Knowledge Graph for Biomedical Sciences

BACKGROUND: Biomedical knowledge bases (KB’s) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at which new findings are published. Second, for automatic information extraction (IE), the text genre of choice has been scientific publications, neglecting sources like health portals and online communities. Third, most prior work on IE has focused on the molecular level or chemogenomics only, like protein-protein interactions or gene-drug relationships, or solely address highly specific topics such as drug effects. RESULTS: We address these three limitations by a versatile and scalable approach to automatic KB construction. Using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a huge number of facts in an automated manner without requiring any explicit training. We extend previous techniques for pattern-based IE with confidence statistics, and we combine this recall-oriented stage with logical reasoning for consistency constraint checking to achieve high precision. To our knowledge, this is the first method that uses consistency checking for biomedical relations. Our approach can be easily extended to incorporate additional relations and constraints. We ran extensive experiments not only for scientific publications, but also for encyclopedic health portals and online communities, creating different KB’s based on different configurations. We assess the size and quality of each KB, in terms of number of facts and precision. The best configured KB, KnowLife, contains more than 500,000 facts at a precision of 93% for 13 relations covering genes, organs, diseases, symptoms, treatments, as well as environmental and lifestyle risk factors. CONCLUSION: KnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from different text genres such as scientific publications, health portals, and online communities. Thus, it has the potential to serve as one-stop portal for a wide range of relations and use cases. To showcase the breadth and usefulness, we make the KnowLife KB accessible through the health portal (http://knowlife.mpi-inf.mpg.de). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0549-5) contains supplementary material, which is available to authorized users

Finite Generation of Canonical Ring by Analytic Method

In the 80th birthday conference for Professor LU Qikeng in June 2006 I gave a talk on the analytic approach to the finite generation of the canonical ring for a compact complex algebraic manifold of general type. This article is my contribution to the proceedings of that conference from my talk. In this article I give an overview of the analytic proof and focus on explaining how the analytic method handles the problem of infinite number of interminable blow-ups in the intuitive approach to prove the finite generation of the canonical ring. The proceedings of the LU Qikeng conference will appear as Issue No. 4 of Volume 51 of Science in China Series A: Mathematics (www.springer.com/math/applications/journal/11425)

Direct plastic analysis of steel structures by flexibility-based element with initial imperfection

[EN] Second-order direct analysis has been used in some regions for reliable analysis and design of steel structures. Currently, the stiffness-based element is widely used with accuracy improved by enforcing equilibrium along mid-span or “stations” along the member length in order to achieve equilibrium which is not guaranteed along an element. In this paper, a flexibility-based beam-column element considering member imperfection based on Hellinger-Reissner functional is developed and used for practical second-order direct analysis. This new element is a flexibility-based element with member initial bowing at the element level for direct analysis of three-dimensional frame analysis whereas previous flexibility-based elements assumed perfectly straight geometry for the element. The fiber plastic hinge approach is adopted to account for the distributed plasticity of a section. The new flexibility-based element performs excellently for modeling of members under high stress with material yielded as the conventional stiffness-based element has less accuracy when few elements are used in modeling a plastic member. This will significantly enhance accuracy and computational efficiency for direct plastic analysis which can then be more widely used in practical design. Several examples are employed to validate the accuracy and efficiency of the proposed element along this line of thought.The authors are grateful for financial support from the Research Grant Council of the Hong Kong SAR Government on the projects “Second-order Analysis of Shallow Dome Structures made of Tapering Members (PolyU 152047/17E)” and “Second-Order Analysis of Flexible Steel Cable Nets Supporting Debris (PolyU 152008/15E) ”; from the Innovation and Technology Fund of the Hong Kong SAR Government for the project “Development of an Energy Absorbing Device for Flexible RockFall Barriers (ITS/059/16FP) ”; and from the Hong Kong Branch of the Chinese National Engineering Research Centre for Steel Construction of The Innovation and Technology Fund of the Hong Kong SAR Government for the project “Advanced Numerical Analyses for Building Structures Using High Performance Steel Materials”.Liu, Y.; Shu, GP.; Chan, SL. (2018). Direct plastic analysis of steel structures by flexibility-based element with initial imperfection. En Proceedings of the 12th International Conference on Advances in Steel-Concrete Composite Structures. ASCCS 2018. Editorial Universitat Politècnica de València. 393-400. https://doi.org/10.4995/ASCCS2018.2018.7281OCS39340

Higher-order splitting algorithms for solving the nonlinear Schr\"odinger equation and their instabilities

Since the kinetic and the potential energy term of the real time nonlinear Schr\"odinger equation can each be solved exactly, the entire equation can be solved to any order via splitting algorithms. We verified the fourth-order convergence of some well known algorithms by solving the Gross-Pitaevskii equation numerically. All such splitting algorithms suffer from a latent numerical instability even when the total energy is very well conserved. A detail error analysis reveals that the noise, or elementary excitations of the nonlinear Schr\"odinger, obeys the Bogoliubov spectrum and the instability is due to the exponential growth of high wave number noises caused by the splitting process. For a continuum wave function, this instability is unavoidable no matter how small the time step. For a discrete wave function, the instability can be avoided only for \dt k_{max}^2{<\atop\sim}2 \pi, where $k_{max}=\pi/\Delta x$.Comment: 10 pages, 8 figures, submitted to Phys. Rev.