Estimation of errors in text and data processing

The company Adiss Lab Lts. obtained 1 000 000 medical reports that are either in free form text, or in XML format. One of the main goals of their development is to integrate an algorithm for information extraction (IE) in their platform. The verification of the algorithm’s output for a report is done by a medical doctor (MD) for a certain fee. Validating the correctness of all data would be overwhelming and very expensive. Hence, the problem, as presented by the company, is to provide a method (algorithm) which determines the minimum amount of reports that will validate the correctness of the IE algorithm and a procedure for selecting these reports. In order to solve the problem we have considered an algorithm-centric approach uses active learning and semi-supervised learning

Magnetic and quadrupolar order in a one-dimensional ferromagnet with cubic crystal-field anisotropy

The zero temperature phase diagram of a one-dimensional S=2 Heisenberg ferromagnet with single-ion cubic anisotropy is studied numerically using the density-matrix renormalization group method. Evidence is found that although the model does not involve quadrupolar couplings, there is a purely quadrupolar phase for large values of the anisotropy. The phase transition between the magnetic and quadrupolar phases is continuous and it seems to be characterized by Ising critical exponents.Comment: 11 pages, 7 figures, REVTeX, accepted in Phys. Rev. B (scheduled on June 99

Quantum phase transitions and thermodynamic properties in highly anisotropic magnets

The systems exhibiting quantum phase transitions (QPT) are investigated within the Ising model in the transverse field and Heisenberg model with easy-plane single-site anisotropy. Near QPT a correspondence between parameters of these models and of quantum phi^4 model is established. A scaling analysis is performed for the ground-state properties. The influence of the external longitudinal magnetic field on the ground-state properties is investigated, and the corresponding magnetic susceptibility is calculated. Finite-temperature properties are considered with the use of the scaling analysis for the effective classical model proposed by Sachdev. Analytical results for the ordering temperature and temperature dependences of the magnetization and energy gap are obtained in the case of a small ground-state moment. The forms of dependences of observable quantities on the bare splitting (or magnetic field) and renormalized splitting turn out to be different. A comparison with numerical calculations and experimental data on systems demonstrating magnetic and structural transitions (e.g., into singlet state) is performed.Comment: 46 pages, RevTeX, 6 figure

Anomalous resistivity and the electron-polaron effect in the two-band Hubbard model with one narrow band

We search for anomalous normal and superconductive behavior in the two-band Hubbard model with one narrow band. We analyze the influence of electron-polaron effect and Altshuler-Aronov effect on effective mass enhancement and scattering times of heavy and light components in the clean case. We find anomalous behavior of resistivity at high temperatures $T>W_{h}^{*}$ both in 3D and 2D situation. The SC instability in the model is governed by enhanced Kohn-Luttinger effect for p-wave pairing of heavy electrons via polarization of light electrons.Comment: 8 pages, 4 figures, accepted for publication in Journal of Superconductivity and Novel Magnetism, based on the invited talk on Stripes XI Conference in Rome, July 201

Prognostic impact of peritumoral lymphocyte infiltration in soft tissue sarcomas

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to clarify the prognostic significance of peritumoral lymphocyte infiltration in the capsule of soft tissue sarcomas (STS). Multiple observations in preclinical and clinical studies have shown that the immune system has a role in controlling tumor growth and progression. Prognostic markers in potentially curable STS should guide therapy after surgical resection. The immune status at the time of resection may be important, but the prognostic significance of peritumoral lymphocytes is unknown.</p> <p>Methods</p> <p>Tissue microarrays from 80 patients with STS were constructed from duplicate cores of tissue from the tumor and the peritumoral capsule. Immunohistochemistry was used to evaluate the CD3+, CD4+, CD8+ and CD20+ lymphocytes in the tumor and the peritumoral capsule.</p> <p>Results</p> <p>In univariate analyses, increasing numbers of CD20+ (<it>P </it>= 0.032) peritumoral lymphocytes were associated with a reduced disease free survival (DSS). In multivariate analyses, a high number of CD20+ peritumoral lymphocytes (<it>P </it>= 0.030) in the capsule was an independent negative prognostic factor for DSS. There were no such associations of lymphocyte infiltration in the tumor.</p> <p>Conclusions</p> <p>A high density of CD20+ peritumoral lymphocytes is an independent negative prognostic indicator for patients with STS. Further research is needed to determine whether CD20 cells in the peritumoral capsule of STS may promote tumor invasion in the surrounding tissue and increase the metastatic potential.</p

Construction of plant transformation vectors carrying beet necrotic yellow vein virus coat protein gene (ii)- plant transformation

Fragments containing the coat protein gene of beet necrotic yellow vein virus were cloned in two plant transformation vectors: pCAMBIA3301M with the bar gene as selectable marker, and pCAMBIA1304M, with resistance to hygromycin. Three constructs were made of each vector: CPL, containing coat protein gene with leader sequence; CPS with coat protein gene, and CPSas with coat protein gene in antisense orientation. Vectors pC3301MCPL, pC3301MCPS. and pC3301MCPSas were used in Agrobacterium—mediated transformation of Nicotiana tabacum (tobacco), Nicotiana excelsior and Nicotiana benthamiana. Regenerants that developed roots on selective media were tested for the presence of CP fragments and the bar gene, but most regenerants were nontransformed (50-83% escapes). After all rooted plants had been selfed, and T1 seed germinated on selective media, only plants descending from one N. excelsior regenerant transformed with pC3301MCPS were positive for presence of bar gene and CPS fragment. Tobacco and Nicotiana benthamiana were transformed with constructs pC1304MCPS and pC1304MCPSas. Transformation efficiency was much higher and approximately 50% of regenerants that rooted on media with 20 mg l−1 hygromycin were positive for the presence of CP fragments. All T1 plants were positive for presence of CP fragments

Structural Insights into TIR Domain Specificity of the Bridging Adaptor Mal in TLR4 Signaling

MyD88 adaptor-like protein (Mal) is a crucial adaptor that acts as a bridge to recruit the MyD88 molecule to activated TLR4 receptors in response to invading pathogens. The specific assembly of the Toll/interleukin-1 receptor (TIR) domains of TLR4, Mal and MyD88 is responsible for proper signal transduction in the TLR4 signaling pathway. However, the molecular mechanism for the specificity of these TIR domains remains unclear. Here, we present the crystal structure of the TIR domain of the human Mal molecule (Mal-TIR) at a resolution of 2.4 Å. Unexpectedly, Mal-TIR exhibits an extraordinarily long AB loop, but no αB helix or BB loop, distinguishing it from other TIR domains. More importantly, the Mal-TIR AB loop is capable of mediating direct binding to the TIR domains of TLR4 and MyD88 simultaneously. We also found that Mal-TIR can form a back-to-back dimer that may resemble the dimeric assembly of the entire Mal molecule. Our data demonstrate the bridge role of the Mal-TIR domain and provide important information about TIR domain specificity

Structural Basis for Functional Tetramerization of Lentiviral Integrase

Experimental evidence suggests that a tetramer of integrase (IN) is the protagonist of the concerted strand transfer reaction, whereby both ends of retroviral DNA are inserted into a host cell chromosome. Herein we present two crystal structures containing the N-terminal and the catalytic core domains of maedi-visna virus IN in complex with the IN binding domain of the common lentiviral integration co-factor LEDGF. The structures reveal that the dimer-of-dimers architecture of the IN tetramer is stabilized by swapping N-terminal domains between the inner pair of monomers poised to execute catalytic function. Comparison of four independent IN tetramers in our crystal structures elucidate the basis for the closure of the highly flexible dimer-dimer interface, allowing us to model how a pair of active sites become situated for concerted integration. Using a range of complementary approaches, we demonstrate that the dimer-dimer interface is essential for HIV-1 IN tetramerization, concerted integration in vitro, and virus infectivity. Our structures moreover highlight adaptable changes at the interfaces of individual IN dimers that allow divergent lentiviruses to utilize a highly-conserved, common integration co-factor

HIVToolbox, an Integrated Web Application for Investigating HIV

Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com

Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF

The essential herpesvirus adaptor protein HVS ORF57, which has homologs in all other herpesviruses, promotes viral mRNA export by utilizing the cellular mRNA export machinery. ORF57 protein specifically recognizes viral mRNA transcripts, and binds to proteins of the cellular transcription-export (TREX) complex, in particular ALYREF. This interaction introduces viral mRNA to the NXF1 pathway, subsequently directing it to the nuclear pore for export to the cytoplasm. Here we have used a range of techniques to reveal the sites for direct contact between RNA and ORF57 in the absence and presence of ALYREF. A binding site within ORF57 was characterized which recognizes specific viral mRNA motifs. When ALYREF is present, part of this ORF57 RNA binding site, composed of an a-helix, binds preferentially to ALYREF. This competitively displaces viral RNA from the a-helix, but contact with RNA is still maintained by a flanking region. At the same time, the flexible N-terminal domain of ALYREF comes into contact with the viral RNA, which becomes engaged in an extensive network of synergistic interactions with both ALYREF and ORF57. Transfer of RNA to ALYREF in the ternary complex, and involvement of individual ORF57 residues in RNA recognition, were confirmed by UV cross-linking and mutagenesis. The atomic-resolution structure of the ORF57-ALYREF interface was determined, which noticeably differed from the homologous ICP27-ALYREF structure. Together, the data provides the first site-specific description of how viral mRNA is locked by a herpes viral adaptor protein in complex with cellular ALYREF, giving herpesvirus access to the cellular mRNA export machinery. The NMR strategy used may be more generally applicable to the study of fuzzy protein-protein-RNA complexes which involve flexible polypeptide regions