Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.Comment: 14 pages, 8 figures, 10 table

Identification of HLA-A2–restricted CD8+ Cytotoxic T Cell Responses in Primary Biliary Cirrhosis: T Cell Activation Is Augmented by Immune Complexes Cross-Presented by Dendritic Cells

Primary biliary cirrhosis (PBC) is characterized by an intense biliary inflammatory CD4+ and CD8+ T cell response. Very limited information on autoantigen-specific cytotoxic T lymphocyte (CTL) responses is available compared with autoreactive CD4+ T cell responses. Using peripheral blood mononuclear cells (PBMCs) from PBC, we identified an HLA-A2–restricted CTL epitope of the E2 component of pyruvate dehydrogenase (PDC-E2), the immunodominant mitochondrial autoantigen. This peptide, amino acids 159–167 of PDC-E2, induces specific MHC class I–restricted CD8+ CTL lines from 10/12 HLA-A2+ PBC patients, but not controls, after in vitro stimulation with antigen-pulsed dendritic cells (DCs). PDC-E2–specific CTLs could also be generated by pulsing DCs with full-length recombinant PDC-E2 protein. Furthermore, using soluble PDC-E2 complexed with either PDC-E2–specific human monoclonal antibody or affinity-purified autoantibodies against PDC-E2, the generation of PDC-E2–specific CTLs, occurred at 100-fold and 10-fold less concentration, respectively, compared with soluble antigen alone. Collectively, these data demonstrate that autoantibody, helper, and CTL epitopes all contain a shared peptide sequence. The finding that autoantigen–immune complexes can not only cross-present but also that presentation of the autoantigen is of a higher relative efficiency, for the first time defines a unique role for autoantibodies in the pathogenesis of an autoimmune disease

Axial Higgs Mode Detected by Quantum Pathway Interference in RTe3

The observation of the Higgs boson solidified the standard model of particle physics. However, explanations of anomalies (e.g. dark matter) rely on further symmetry breaking calling for an undiscovered axial Higgs mode. In condensed matter the Higgs was seen in magnetic, superconducting and charge density wave(CDW) systems. Uncovering a low energy mode's vector properties is challenging, requiring going beyond typical spectroscopic or scattering techniques. Here, we discover an axial Higgs mode in the CDW system RTe3 using the interference of quantum pathways. In RTe3 (R=La,Gd), the electronic ordering couples bands of equal or different angular momenta. As such, the Raman scattering tensor associated to the Higgs mode contains both symmetric and antisymmetric components, which can be excited via two distinct, but degenerate pathways. This leads to constructive or destructive interference of these pathways, depending on the choice of the incident and Raman scattered light polarization. The qualitative behavior of the Raman spectra is well-captured by an appropriate tight-binding model including an axial Higgs mode. The elucidation of the antisymmetric component provides direct evidence that the Higgs mode contains an axial vector representation (i.e. a pseudo-angular momentum) and hints the CDW in RTe3 is unconventional. Thus we provide a means for measuring collective modes quantum properties without resorting to extreme experimental conditions

Academic Senate - Meeting Minutes, 4/18/2017

<p>All values are presented with SD. Differences between <i>LDLR−/−</i> and the other two genotypes are significant where indicated, ANOVA: *p<0.05, **p<0.01.</p

Alleviating Human-level Shift : A Robust Domain Adaptation Method for Multi-person Pose Estimation

Human pose estimation has been widely studied with much focus on supervised learning requiring sufficient annotations. However, in real applications, a pretrained pose estimation model usually need be adapted to a novel domain with no labels or sparse labels. Such domain adaptation for 2D pose estimation hasn't been explored. The main reason is that a pose, by nature, has typical topological structure and needs fine-grained features in local keypoints. While existing adaptation methods do not consider topological structure of object-of-interest and they align the whole images coarsely. Therefore, we propose a novel domain adaptation method for multi-person pose estimation to conduct the human-level topological structure alignment and fine-grained feature alignment. Our method consists of three modules: Cross-Attentive Feature Alignment (CAFA), Intra-domain Structure Adaptation (ISA) and Inter-domain Human-Topology Alignment (IHTA) module. The CAFA adopts a bidirectional spatial attention module (BSAM)that focuses on fine-grained local feature correlation between two humans to adaptively aggregate consistent features for adaptation. We adopt ISA only in semi-supervised domain adaptation (SSDA) to exploit the corresponding keypoint semantic relationship for reducing the intra-domain bias. Most importantly, we propose an IHTA to learn more domain-invariant human topological representation for reducing the inter-domain discrepancy. We model the human topological structure via the graph convolution network (GCN), by passing messages on which, high-order relations can be considered. This structure preserving alignment based on GCN is beneficial to the occluded or extreme pose inference. Extensive experiments are conducted on two popular benchmarks and results demonstrate the competency of our method compared with existing supervised approaches.Comment: Accepted By ACM MM'202

Danggui Buxue Tang – A Chinese herbal decoction activates the phosphorylations of extracellular signal-regulated kinase and estrogen receptor α in cultured MCF-7 cells

AbstractDanggui Buxue Tang (DBT), a Chinese herbal decoction used to treat ailments in women, contains Radix Astragali (Huangqi; RA) and Radix Angelicae Sinensis (Danggui; RAS). The weight ratio of RA to RAS used in DBT must be 5:1 as stipulated as early as AD 1247; however, DBT’s mechanism of action has never been described. Here, the estrogenic effects of DBT were investigated by determining the phosphorylations of estrogen receptor α (ERα) and extracellular signal-regulated kinase 1/2 (Erk1/2) in cultured MCF-7 cells. The application of DBT triggered the phosphorylation of ERα and Erk1/2 in a time-dependent manner. In contrast to the effect of estrogen, DBT triggered ERα phosphorylation at both S118 and S167. This DBT-specific phosphorylation was not triggered by an extract of one of the individual herbs, or by mixing the extracts of RA and RAS. DBT-induced downstream signals are described here. These signals suggest the uniqueness of this Chinese herbal decoction that requires a well-defined formulation

Placing the library at the heart of plagiarism prevention: The University of Bradford experience.

yesPlagiarism is a vexed issue for Higher Education, affecting student transition, retention and attainment. This paper reports on two initiatives from the University of Bradford library aimed at reducing student plagiarism. The first initiative is an intensive course for students who have contravened plagiarism regulations. The second course introduces new students to the concepts surrounding plagiarism with the aim to prevent plagiarism breaches. Since the Plagiarism Avoidance for New Students course was introduced there has been a significant drop in students referred to the disciplinary programme. This paper discusses the background to both courses and the challenges of implementation