Topological Defect Lines and Renormalization Group Flows in Two Dimensions

We consider topological defect lines (TDLs) in two-dimensional conformal field theories. Generalizing and encompassing both global symmetries and Verlinde lines, TDLs together with their attached defect operators provide models of fusion categories without braiding. We study the crossing relations of TDLs, discuss their relation to the 't Hooft anomaly, and use them to constrain renormalization group flows to either conformal critical points or topological quantum field theories (TQFTs). We show that if certain non-invertible TDLs are preserved along a RG flow, then the vacuum cannot be a non-degenerate gapped state. For various massive flows, we determine the infrared TQFTs completely from the consideration of TDLs together with modular invariance.Comment: 101 pages, 63 figures, 2 tables; v3: minor changes, added footnotes and references, published versio

Little String Amplitudes (and the Unreasonable Effectiveness of 6D SYM)

We study tree level scattering amplitudes of four massless states in the double scaled little string theory, and compare them to perturbative loop amplitudes in six-dimensional super-Yang-Mills theory. The little string amplitudes are computed from correlators in the cigar coset CFT and in N=2 minimal models. The results are expressed in terms of integrals of conformal blocks and evaluated numerically in the alpha' expansion. We find striking agreements with up to 2-loop scattering amplitudes of massless gluons in 6D SU(k) SYM at a Z_k invariant point on the Coulomb branch. We comment on the issue of UV divergence at higher loop orders in the gauge theory and discuss the implication of our results.Comment: 58 pages, 5 figures, 3 tables, comments added, references adde

Assessing the quality of steady-state visual-evoked potentials for moving humans using a mobile electroencephalogram headset.

Recent advances in mobile electroencephalogram (EEG) systems, featuring non-prep dry electrodes and wireless telemetry, have enabled and promoted the applications of mobile brain-computer interfaces (BCIs) in our daily life. Since the brain may behave differently while people are actively situated in ecologically-valid environments versus highly-controlled laboratory environments, it remains unclear how well the current laboratory-oriented BCI demonstrations can be translated into operational BCIs for users with naturalistic movements. Understanding inherent links between natural human behaviors and brain activities is the key to ensuring the applicability and stability of mobile BCIs. This study aims to assess the quality of steady-state visual-evoked potentials (SSVEPs), which is one of promising channels for functioning BCI systems, recorded using a mobile EEG system under challenging recording conditions, e.g., walking. To systematically explore the effects of walking locomotion on the SSVEPs, this study instructed subjects to stand or walk on a treadmill running at speeds of 1, 2, and 3 mile (s) per hour (MPH) while concurrently perceiving visual flickers (11 and 12 Hz). Empirical results of this study showed that the SSVEP amplitude tended to deteriorate when subjects switched from standing to walking. Such SSVEP suppression could be attributed to the walking locomotion, leading to distinctly deteriorated SSVEP detectability from standing (84.87 ± 13.55%) to walking (1 MPH: 83.03 ± 13.24%, 2 MPH: 79.47 ± 13.53%, and 3 MPH: 75.26 ± 17.89%). These findings not only demonstrated the applicability and limitations of SSVEPs recorded from freely behaving humans in realistic environments, but also provide useful methods and techniques for boosting the translation of the BCI technology from laboratory demonstrations to practical applications

Reconstruction of phyletic trees by global alignment of multiple metabolic networks

Background: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information. Results: We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis. Conclusions: We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification.National Institutes of Health (U.S.) (Grant GM081871

The Nuclear Chaperone Nucleophosmin Escorts an Epstein-Barr Virus Nuclear Antigen to Establish Transcriptional Cascades for Latent Infection in Human B Cells

Epstein-Barr Virus (EBV) is an oncogenic γ-herpesvirus that capably establishes both latent and lytic modes of infection in host cells and causes malignant diseases in humans. Nuclear antigen 2 (EBNA2)-mediated transcription of both cellular and viral genes is essential for the establishment and maintenance of the EBV latency program in B lymphocytes. Here, we employed a protein affinity pull-down and LC-MS/MS analysis to identify nucleophosmin (NPM1) as one of the cellular proteins bound to EBNA2. Additionally, the specific domains that are responsible for protein-protein interactions were characterized as EBNA2 residues 300 to 360 and the oligomerization domain (OD) of NPM1. As in c-MYC, dramatic NPM1 expression was induced in EBV positively infected B cells after three days of viral infection, and both EBNA2 and EBNALP were implicated in the transactivation of the NPM1 promoter. Depletion of NPM1 with the lentivirus-expressed short-hairpin RNAs (shRNAs) effectively abrogated EBNA2-dependent transcription and transformation outgrowth of lymphoblastoid cells. Notably, the ATP-bound state of NPM1 was required to induce assembly of a protein complex containing EBNA2, RBP-Jκ, and NPM1 by stabilizing the interaction of EBNA2 with RBP-Jκ. In a NPM1-knockdown cell line, we demonstrated that an EBNA2-mediated transcription defect was fully restored by the ectopic expression of NPM1. Our findings highlight the essential role of NPM1 in chaperoning EBNA2 onto the latency-associated membrane protein 1 (LMP1) promoters, which is coordinated with the subsequent activation of transcriptional cascades through RBP-Jκ during EBV infection. These data advance our understanding of EBV pathology and further imply that NPM1 can be exploited as a therapeutic target for EBV-associated diseases

Conceptualizing socioscientific decision making from a review of research in science education

Abstract: This article proposes a theoretical framework for conceptualizing socioscientific decision making, reviews current research in this area, and intends to shed some light on the instructional design for the classroom implementation of socioscientific decision making. The framework involves 3 phases: formulate the decision-making space, posit a decision-making strategy, and reflect on the decision-making process. A total of 24 articles that specifically focused on socioscientific decision making were included. They were classified into 2 groups. The first group explored students’ socioscientific decision-making behavior and its relationships with their cognitive conditions. The second examined the effectiveness of the interventions, that is, task conditions. The analysis showed that most of the studies in both groups focused on phase 1 and studied 3 research themes: informal reasoning, evidence-based reasoning, and social interactions. The findings indicated the challenges phases 1 and 2 posed to students, such as prioritizing criteria and employing a suitable decision-making strategy. Two cognitive conditions, scientific knowledge and scientific epistemological beliefs, appeared to have a more direct impact on evidence-based reasoning rather than on informal reasoning. Group 2 studies designed various interventions and looked into divergent socioscientific decision-making performances across 3 phases. The framework helps conceptualize socioscientific decision making in a more structural and holistic way. The content review provides instructional insights for the socioscientific decision-making process and suggests several future research directions

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database (http://mirtarbase.mbc.nctu.edu.tw/) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for >100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system