On the Relationship Between Complex Potentials and Strings of Projection Operators

It is of interest in a variety of contexts, and in particular in the arrival time problem, to consider the quantum state obtained through unitary evolution of an initial state regularly interspersed with periodic projections onto the positive $x$-axis (pulsed measurements). Echanobe, del Campo and Muga have given a compelling but heuristic argument that the state thus obtained is approximately equivalent to the state obtained by evolving in the presence of a certain complex potential of step-function form. In this paper, with the help of the path decomposition expansion of the associated propagators, we give a detailed derivation of this approximate equivalence. The propagator for the complex potential is known so the bulk of the derivation consists of an approximate evaluation of the propagator for the free particle interspersed with periodic position projections. This approximate equivalence may be used to show that to produce significant reflection, the projections must act at time spacing less than 1/E, where E is the energy scale of the initial state.Comment: 29 pages, LaTex, 4 figures. Substantial revision

Three-dimensional coherent X-ray diffraction imaging of a ceramic nanofoam: determination of structural deformation mechanisms

Ultra-low density polymers, metals, and ceramic nanofoams are valued for their high strength-to-weight ratio, high surface area and insulating properties ascribed to their structural geometry. We obtain the labrynthine internal structure of a tantalum oxide nanofoam by X-ray diffractive imaging. Finite element analysis from the structure reveals mechanical properties consistent with bulk samples and with a diffusion limited cluster aggregation model, while excess mass on the nodes discounts the dangling fragments hypothesis of percolation theory.Comment: 8 pages, 5 figures, 30 reference

Integration of Catalysis with Storage for the Design of Multi-Electron Photochemistry Devices for Solar Fuel

Decarbonization of the transport system and a transition to a new diversified energy system that is scalable and sustainable, requires a widespread implementation of carbon-neutral fuels. In biomimetic supramolecular nanoreactors for solar-to-fuel conversion, water-splitting catalysts can be coupled to photochemical units to form complex electrochemical nanostructures, based on a systems integration approach and guided by magnetic resonance knowledge of the operating principles of biological photosynthesis, to bridge between long-distance energy transfer on the short time scale of fluorescence, ~10−9 s, and short-distance proton-coupled electron transfer and storage on the much longer time scale of catalysis, ~10−3 s. A modular approach allows for the design of nanostructured optimized topologies with a tunneling bridge for the integration of storage with catalysis and optimization of proton chemical potentials, to mimic proton-coupled electron transfer processes in photosystem II and hydrogenase

Albedo and Reflection Spectra of Extrasolar Giant Planets

We generate theoretical albedo and reflection spectra for a full range of extrasolar giant planet (EGP) models, from Jovian to 51-Pegasi class objects. Our albedo modeling utilizes the latest atomic and molecular cross sections, a Mie theory treatment of extinction by condensates, a variety of particle size distributions, and an extension of the Feautrier radiative transfer method which allows for a general treatment of the scattering phase function. We find that due to qualitative similarities in the compositions and spectra of objects within each of five broad effective temperature ranges, it is natural to establish five representative EGP albedo classes: a ``Jovian'' class (T$_{\rm eff} \lesssim 150$ K; Class I) with tropospheric ammonia clouds, a ``water cloud'' class (T$_{\rm eff} \sim 250$ K; Class II) primarily affected by condensed H$_2$O, a ``clear'' class (T$_{\rm eff} \gtrsim 350$ K; Class III) which lacks clouds, and two high-temperature classes: Class IV (900 K $\lesssim$ T$_{\rm{eff}}$ $\lesssim$ 1500 K) for which alkali metal absorption predominates, and Class V (T$_{\rm{eff}}$ $\gtrsim$ 1500 K and/or low surface gravity ($\lesssim$ 10$^3$ cm s$^{-2}$)) for which a high silicate layer shields a significant fraction of the incident radiation from alkali metal and molecular absorption. The resonance lines of sodium and potassium are expected to be salient features in the reflection spectra of Class III, IV, and V objects. We derive Bond albedos and effective temperatures for the full set of known EGPs and explore the possible effects of non-equilibrium condensed products of photolysis above or within principal cloud decks. As in Jupiter, such species can lower the UV/blue albedo substantially, even if present in relatively small mixing ratios.Comment: revised LaTeX manuscript accepted to Ap.J.; also available at http://jupiter.as.arizona.edu/~burrows/paper

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA1B2C6D1E1) and a 61-nucleotide CRISPR RNA (crRNA) with 5′-hydroxyl and 2′,3′-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.

Incomplete information about the partner affects the development of collaborative strategies in joint action.

Physical interaction with a partner plays an essential role in our life experience and is the basis of many daily activities. When two physically coupled humans have different and partly conflicting goals, they face the challenge of negotiating some type of collaboration. This requires that both participants understand their partner's state and current actions. But, how would the collaboration be affected if information about their partner were unreliable or incomplete? We designed an experiment in which two players (a dyad) are mechanically connected through a virtual spring, but cannot see each other. They were instructed to perform reaching movements with the same start and end position, but through different via-points. In different groups of dyads we varied the amount of information provided to each player about his/her partner: haptic only (the interaction force perceived through the virtual spring), visuo-haptic (the interaction force is also displayed on the screen), and partner visible (in addition to interaction force, partner position is continuously displayed on the screen). We found that incomplete information about the partner affects not only the speed at which collaboration is achieved (less information, slower learning), but also the actual collaboration strategy. In particular, incomplete or unreliable information leads to an interaction strategy characterized by alternating leader-follower roles. Conversely, more reliable information leads to more synchronous behaviors, in which no specific roles can be identified. Simulations based on a combination of game theory and Bayesian estimation suggested that synchronous behaviors correspond to optimal interaction (Nash equilibrium). Roles emerge as sub-optimal forms of interaction, which minimize the need to account for the partner. These findings suggest that collaborative strategies in joint action are shaped by the trade-off between the task requirements and the uncertainty of the information available about the partner

Neutrophils in cancer: neutral no more

Neutrophils are indispensable antagonists of microbial infection and facilitators of wound healing. In the cancer setting, a newfound appreciation for neutrophils has come into view. The traditionally held belief that neutrophils are inert bystanders is being challenged by the recent literature. Emerging evidence indicates that tumours manipulate neutrophils, sometimes early in their differentiation process, to create diverse phenotypic and functional polarization states able to alter tumour behaviour. In this Review, we discuss the involvement of neutrophils in cancer initiation and progression, and their potential as clinical biomarkers and therapeutic targets

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

<p>Abstract</p> <p>Background</p> <p>Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.</p> <p>Results</p> <p>OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.</p> <p>Conclusions</p> <p>OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases.</p> <p>Availability</p> <p><url>http://www.ontocat.org</url></p

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns