Origin of Discrepancies in Inelastic Electron Tunneling Spectra of Molecular Junctions

We report inelastic electron tunneling spectroscopy (IETS) of multilayer molecular junctions with and without incorporated metal nano-particles. The incorporation of metal nanoparticles into our devices leads to enhanced IET intensity and a modified line-shape for some vibrational modes. The enhancement and line-shape modification are both the result of a low lying hybrid metal nanoparticle-molecule electronic level. These observations explain the apparent discrepancy between earlier IETS measurements of alkane thiolate junctions by Kushmerick \emph{et al.} [Nano Lett. \textbf{4}, 639 (2004)] and Wang \emph{et al.} [Nano Lett. \textbf{4}, 643 (2004)].Comment: 4 pages, 4 figures accepted for publication in Physical Review Letter

Self-supervised automated wrapper generation for weblog data extraction

Data extraction from the web is notoriously hard. Of the types of resources available on the web, weblogs are becoming increasingly important due to the continued growth of the blogosphere, but remain poorly explored. Past approaches to data extraction from weblogs have often involved manual intervention and suffer from low scalability. This paper proposes a fully automated information extraction methodology based on the use of web feeds and processing of HTML. The approach includes a model for generating a wrapper that exploits web feeds for deriving a set of extraction rules automatically. Instead of performing a pairwise comparison between posts, the model matches the values of the web feeds against their corresponding HTML elements retrieved from multiple weblog posts. It adopts a probabilistic approach for deriving a set of rules and automating the process of wrapper generation. An evaluation of the model is conducted on a dataset of 2,393 posts and the results (92% accuracy) show that the proposed technique enables robust extraction of weblog properties and can be applied across the blogosphere for applications such as improved information retrieval and more robust web preservation initiatives

Information Extraction in Illicit Domains

Extracting useful entities and attribute values from illicit domains such as human trafficking is a challenging problem with the potential for widespread social impact. Such domains employ atypical language models, have `long tails' and suffer from the problem of concept drift. In this paper, we propose a lightweight, feature-agnostic Information Extraction (IE) paradigm specifically designed for such domains. Our approach uses raw, unlabeled text from an initial corpus, and a few (12-120) seed annotations per domain-specific attribute, to learn robust IE models for unobserved pages and websites. Empirically, we demonstrate that our approach can outperform feature-centric Conditional Random Field baselines by over 18\% F-Measure on five annotated sets of real-world human trafficking datasets in both low-supervision and high-supervision settings. We also show that our approach is demonstrably robust to concept drift, and can be efficiently bootstrapped even in a serial computing environment.Comment: 10 pages, ACM WWW 201

Effect of Viscosity on Mechanics of Single, Skinned Fibers from Rabbit Psoas Muscle

AbstractMuscle contraction is highly dynamic and thus may be influenced by viscosity of the medium surrounding the myofilaments. Single, skinned fibers from rabbit psoas muscle were used to test this hypothesis. Viscosity within the myofilament lattice was increased by adding to solutions low molecular weight sugars (disaccharides sucrose or maltose or monosaccharides glucose or fructose). At maximal Ca2+ activation, isometric force (Fi) was inhibited at the highest solute concentrations studied, but this inhibition was not directly related to viscosity. Solutes readily permeated the filament lattice, as fiber diameter was unaffected by added solutes (except for an increased diameter with Fi<30% of control). In contrast, there was a linear dependence upon 1/viscosity for both unloaded shortening velocity and also the kinetics of isometric tension redevelopment; these effects were unrelated to either variation in solution osmolarity or inhibition of force. All effects of added solute were reversible. Inhibition of both isometric as well as isotonic kinetics demonstrates that viscous resistance to filament sliding was not the predominant factor affected by viscosity. This was corroborated by measurements in relaxed fibers, which showed no significant change in the strain-rate dependence of elastic modulus when viscosity was increased more than twofold. Our results implicate cross-bridge diffusion as a significant limiting factor in cross-bridge kinetics and, more generally, demonstrate that viscosity is a useful probe of actomyosin dynamics

Thermodynamic and Kinetic Analysis of Sensitivity Amplification in Biological Signal Transduction

Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the free energy from hydrolysis inside cells, $\Delta G$ (phosphorylation potential), controls the amplification and sensitivity of the switch-like cellular module; the response coefficient of the sensitivity amplification approaches the optimal 1 and the Hill coefficient increases with increasing $\Delta G$. We discover that zero-order ultrasensitivity is mathematically equivalent to allosteric cooperativity. Furthermore, we show that the high amplification in ultrasensitivity is mechanistically related to the proofreading kinetics for protein biosynthesis. Both utilize multiple kinetic cycles in time to gain temporal cooperativity, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein.Comment: 19 pages, 7 figure

Intelligent Self-Repairable Web Wrappers

The amount of information available on the Web grows at an incredible high rate. Systems and procedures devised to extract these data from Web sources already exist, and different approaches and techniques have been investigated during the last years. On the one hand, reliable solutions should provide robust algorithms of Web data mining which could automatically face possible malfunctioning or failures. On the other, in literature there is a lack of solutions about the maintenance of these systems. Procedures that extract Web data may be strictly interconnected with the structure of the data source itself; thus, malfunctioning or acquisition of corrupted data could be caused, for example, by structural modifications of data sources brought by their owners. Nowadays, verification of data integrity and maintenance are mostly manually managed, in order to ensure that these systems work correctly and reliably. In this paper we propose a novel approach to create procedures able to extract data from Web sources -- the so called Web wrappers -- which can face possible malfunctioning caused by modifications of the structure of the data source, and can automatically repair themselves.\u

Electronic and optical properties of electromigrated molecular junctions

Electromigrated nanoscale junctions have proven very useful for studying electronic transport at the single-molecule scale. However, confirming that conduction is through precisely the molecule of interest and not some contaminant or metal nanoparticle has remained a persistent challenge, typically requiring a statistical analysis of many devices. We review how transport mechanisms in both purely electronic and optical measurements can be used to infer information about the nanoscale junction configuration. The electronic response to optical excitation is particularly revealing. We briefly discuss surface-enhanced Raman spectroscopy on such junctions, and present new results showing that currents due to optical rectification can provide a means of estimating the local electric field at the junction due to illumination.Comment: 19 pages, 8 figures, invited paper for forthcoming special issue of Journal of Physics: Condensed Matter. For other related papers, see http://www.ruf.rice.edu/~natelson/publications.htm

Quantum transport in a resonant tunnel junction coupled to a nanomechanical oscillator

We discuss the quantum transport of electrons through a resonant tunnel junction coupled to a nanomechanical oscillator at zero temperature. By using the Green's function technique we calculate the transport properties of electrons through a single dot strongly coupled to a single oscillator. We consider a finite chemical potential difference between the right and left leads. In addition to the main resonant peak of electrons on the dot, we find satellite peaks due to the creation of phonons. These satellite peaks become sharper and more significant with increasing coupling strength between the electrons and the oscillator. We also consider the energy transferred from the electrons to the oscillator.Comment: Updated in response to referees' comments. Section IV amended including figure

Instabilities in the transient response of muscle

We investigate the isometric transient response of muscle using a quantitative stochastic model of the actomyosin cycle based on the swinging lever-arm hypothesis. We first consider a single pair of filaments, and show that when values of parameters such as the lever-arm displacement and the crossbridge elasticity are chosen to provide effective energy transduction, the T2 curve (the tension recovered immediately after a step displacement) displays a region of negative slope. If filament compliance and the discrete nature of the binding sites are taken into account, the negative slope is diminished, but not eliminated. This implies that there is an instability in the dynamics of individual half-sarcomeres. However, when the symmetric nature of whole sarcomeres is taken into account, filament rearrangement becomes important during the transient: as tension is recovered, some half-sarcomeres lengthen while others shorten. This leads to a flat T2 curve, as observed experimentally. In addition, we investigate the isotonic transient response and show that for a range of parameter values the model displays damped oscillations, as recently observed in experiments on single muscle fibers. We conclude that it is essential to consider the collective dynamics of many sarcomeres, rather than the dynamics of a single pair of filaments, when interpreting the transient response of muscle.Comment: 11 pages, 11 figures, Submitted to Biophysical Journa

Using the words/leafs ratio in the DOM tree for content extraction

The main content in a webpage is usually centered and visible without the need to scroll. It is often rounded by the navigation menus of the website and it can include advertisements, panels, banners, and other not necessarily related information. The process to automatically extract the main content of a webpage is called content extraction. Content extraction is an area of research of widely interest due to its many applications. Concretely, it is useful not only for the final human user, but it is also frequently used as a preprocessing stage of different systems (i.e., robots, indexers, crawlers, etc.) that need to extract the main content of a web document to avoid the treatment and processing of other useless information. In thisworkwe present a newtechnique for content extraction that is based on the information contained in theDOMtree. The technique analyzes the hierarchical relations of the elements in the webpage and the distribution of textual information in order to identify the main block of content. Thanks to the hierarchy imposed by the DOM tree the technique achieves a considerable recall and precision. Using theDOMstructure for content extraction gives us the benefits of other approaches based on the syntax of the webpage (such as characters, words and tags), but it also gives us a very precise information regarding the related components in a block (not necessarily textual such as images or videos), thus, producing very cohesive blocks. © 2013 Elsevier Inc. All rights reserved.This work has been partially supported by the Spanish Ministerio de Economia y Competitividad (Secretaria de Estado de Investigacion, Desarrollo e Innovacion) under Grant TIN2008-06622-C03-02 and by the Generalitat Valenciana under Grant PROMETEO/2011/052. Salvador Tamarit was partially supported by the Spanish MICINN under FPI Grant BES-2009-015019. David Insa was partially supported by the Spanish Ministerio de Eduacion under FPU Grant AP2010-4415.Insa Cabrera, D.; Silva Galiana, JF.; Tamarit, S. (2013). Using the words/leafs ratio in the DOM tree for content extraction. Journal of Logic and Algebraic Programming. 82(8):311-325. https://doi.org/10.1016/j.jlap.2013.01.002S31132582