Neural architectures for fine-grained entity type classification

In this work, we investigate several neural network architectures for fine-grained entity type classification and make three key contributions. Despite being a natural comparison and addition, previous work on attentive neural architectures have not considered hand-crafted features and we combine these with learnt features and establish that they complement each other. Additionally, through quantitative analysis we establish that the attention mechanism learns to attend over syntactic heads and the phrase containing the mention, both of which are known to be strong hand-crafted features for our task. We introduce parameter sharing between labels through a hierarchical encoding method, that in lowdimensional projections show clear clusters for each type hierarchy. Lastly, despite using the same evaluation dataset, the literature frequently compare models trained using different data. We demonstrate that the choice of training data has a drastic impact on performance, which decreases by as much as 9.85% loose micro F1 score for a previously proposed method. Despite this discrepancy, our best model achieves state-of-the-art results with 75.36% loose micro F1 score on the well-established FIGER (GOLD) dataset and we report the best results for models trained using publicly available data for the OntoNotes dataset with 64.93% loose micro F1 score

Spin and chiral orderings of frustrated quantum spin chains

Ordering of frustrated S=1/2 and 1 XY and Heisenberg spin chains with the competing nearest- and next-nearest-neighbor antiferromagnetic couplings is studied by exact diagonalization and density-matrix renormalization-group methods. It is found that the S=1 XY chain exhibits both gapless and gapped `chiral' phases characterized by the spontaneous breaking of parity, in which the long-range order parameter is a chirality, $\kappa_i = S_i^xS_{i+1}^y-S_i^yS_{i+1}^x$, whereas the spin correlation decays either algebraically or exponentially. Such chiral phases are not realized in the S=1/2 XY chain nor in the Heisenberg chains.Comment: 4 pages, 5 EPS-figures, LaTeX(RevTeX),to appear in J.Phys.Soc.Japa

Microscopic model for the magnetization plateaus in NH4CuCl3

A simple model consisting of three distinct dimer sublattices is proposed to describe the magnetism of NH4CuCl3. It explains the occurrence of magnetization plateaus only at 1/4 and 3/4 of the saturation magnetization. The field dependence of the excitation modes observed by ESR measurements is also explained by the model. The model predicts that the magnetization plateaus should disappear under high pressure.Comment: 4 pages, 5 figures, REVTeX

Semi-classical description of the frustrated antiferromagnetic chain

The antiferromagnetic Heisenberg model on a chain with nearest and next nearest neighbor couplings is mapped onto the $SO(3)$ nonlinear sigma model in the continuum limit. In one spatial dimension this model is always in its disordered phase and a gap opens to excited states. The latter form a doubly degenerate spin-1 branch at all orders in $1/N$. We argue that this feature should be present in the spin-1 Heisenberg model itself. Exact diagonalizations are used to support this claim. The inapplicability of this model to half-integer spin chains is discussed.Comment: 19 pages (RevTeX 3.0), 6 PostScript figures appended (printing instructions included), preprint CRPS-94-1

The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research

The plant organelles database (PODB; http://podb.nibb.ac.jp/Organellome) was built to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement and interactions with other organelles. This database consists of three individual parts, the organellome database, the functional analysis database and external links to other databases and homepages. The organellome database provides images of various plant organelles that were visualized with fluorescent and nonfluorescent probes in various tissues of several plant species at different developmental stages. The functional analysis database is a collection of protocols for plant organelle research. External links give access primarily to other databases and Web pages with information on transcriptomes and proteomes. All the data and protocols in the organellome database and the functional analysis database are populated by direct submission of experimentally determined data from plant researchers and can be freely downloaded. Our database promotes the exchange of information between plant organelle researchers for the comprehensive study of the organelle dynamics that support integrated functions in higher plants. We would also appreciate contributions of data and protocols from all plant researchers to maximize the usefulness of the database

Structural Basis and Kinetics of Force-Induced Conformational Changes of an αA Domain-Containing Integrin

Integrin α(L)β₂ (lymphocyte function-associated antigen, LFA-1) bears force upon binding to its ligand intercellular adhesion molecule 1 (ICAM-1) when a leukocyte adheres to vascular endothelium or an antigen presenting cell (APC) during immune responses. The ligand binding propensity of LFA-1 is related to its conformations, which can be regulated by force. Three conformations of the LFA-1 αA domain, determined by the position of its α₇-helix, have been suggested to correspond to three different affinity states for ligand binding.The kinetics of the force-driven transitions between these conformations has not been defined and dynamically coupled to the force-dependent dissociation from ligand. Here we show, by steered molecular dynamics (SMD) simulations, that the αA domain was successively transitioned through three distinct conformations upon pulling the C-terminus of its α₇-helix. Based on these sequential transitions, we have constructed a mathematical model to describe the coupling between the αA domain conformational changes of LFA-1 and its dissociation from ICAM-1 under force. Using this model to analyze the published data on the force-induced dissociation of single LFA-1/ICAM-1 bonds, we estimated the force-dependent kinetic rates of interstate transition from the short-lived to intermediate-lived and from intermediate-lived to long-lived states. Interestingly, force increased these transition rates; hence activation of LFA-1 was accelerated by pulling it via an engaged ICAM-1.Our study defines the structural basis for mechanical regulation of the kinetics of LFA-1 αA domain conformational changes and relates these simulation results to experimental data of force-induced dissociation of single LFA-1/ICAM-1 bonds by a new mathematical model, thus provided detailed structural and kinetic characterizations for force-stabilization of LFA-1/ICAM-1 interaction

Nonmuscle myosin heavy chain IIA mediates integrin LFA-1 de-adhesion during T lymphocyte migration

Precise spatial and temporal regulation of cell adhesion and de-adhesion is critical for dynamic lymphocyte migration. Although a great deal of information has been learned about integrin lymphocyte function–associated antigen (LFA)-1 adhesion, the mechanism that regulates efficient LFA-1 de-adhesion from intercellular adhesion molecule (ICAM)-1 during T lymphocyte migration is unknown. Here, we show that nonmuscle myosin heavy chain IIA (MyH9) is recruited to LFA-1 at the uropod of migrating T lymphocytes, and inhibition of the association of MyH9 with LFA-1 results in extreme uropod elongation, defective tail detachment, and decreased lymphocyte migration on ICAM-1, without affecting LFA-1 activation by chemokine CXCL-12. This defect was reversed by a small molecule antagonist that inhibits both LFA-1 affinity and avidity regulation, but not by an antagonist that inhibits only affinity regulation. Total internal reflection fluorescence microscopy of the contact zone between migrating T lymphocytes and ICAM-1 substrate revealed that inactive LFA-1 is selectively localized to the posterior of polarized T lymphocytes, whereas active LFA-1 is localized to their anterior. Thus, during T lymphocyte migration, uropodal adhesion depends on LFA-1 avidity, where MyH9 serves as a key mechanical link between LFA-1 and the cytoskeleton that is critical for LFA-1 de-adhesion

Priming by Chemokines Restricts Lateral Mobility of the Adhesion Receptor LFA-1 and Restores Adhesion to ICAM-1 Nano-Aggregates on Human Mature Dendritic Cells

LFA-1 is a leukocyte specific β2 integrin that plays a major role in regulating adhesion and migration of different immune cells. Recent data suggest that LFA-1 on mature dendritic cells (mDCs) may function as a chemokine-inducible anchor during homing of DCs through the afferent lymphatics into the lymph nodes, by transiently switching its molecular conformational state. However, the role of LFA-1 mobility in this process is not yet known, despite that the importance of lateral organization and dynamics for LFA-1-mediated adhesion regulation is broadly recognized. Using single particle tracking approaches we here show that LFA-1 exhibits higher mobility on resting mDCs compared to monocytes. Lymphoid chemokine CCL21 stimulation of the LFA-1 high affinity state on mDCs, led to a significant reduction of mobility and an increase on the fraction of stationary receptors, consistent with re-activation of the receptor. Addition of soluble monomeric ICAM-1 in the presence of CCL21 did not alter the diffusion profile of LFA-1 while soluble ICAM-1 nano-aggregates in the presence of CCL21 further reduced LFA-1 mobility and readily bound to the receptor. Overall, our results emphasize the importance of LFA-1 lateral mobility across the membrane on the regulation of integrin activation and its function as adhesion receptor. Importantly, our data show that chemokines alone are not sufficient to trigger the high affinity state of the integrin based on the strict definition that affinity refers to the adhesion capacity of a single receptor to its ligand in solution. Instead our data indicate that nanoclustering of the receptor, induced by multi-ligand binding, is required to maintain stable cell adhesion once LFA-1 high affinity state is transiently triggered by inside-out signals.Peer ReviewedPostprint (published version