Optimization of carbon and energy utilization through differential translational efficiency.

Control of translation is vital to all species. Here we employ a multi-omics approach to decipher condition-dependent translational regulation in the model acetogen Clostridium ljungdahlii. Integration of data from cells grown autotrophically or heterotrophically revealed that pathways critical to carbon and energy metabolism are under strong translational regulation. Major pathways involved in carbon and energy metabolism are not only differentially transcribed and translated, but their translational efficiencies are differentially elevated in response to resource availability under different growth conditions. We show that translational efficiency is not static and that it changes dynamically in response to mRNA expression levels. mRNAs harboring optimized 5'-untranslated region and coding region features, have higher translational efficiencies and are significantly enriched in genes encoding carbon and energy metabolism. In contrast, mRNAs enriched in housekeeping functions harbor sub-optimal features and have lower translational efficiencies. We propose that regulation of translational efficiency is crucial for effectively controlling resource allocation in energy-deprived microorganisms

A computer aided approach for river styles-inspired characterization of large basins: The Magdalena river (Colombia)

This paper addresses the geomorphic characterization and classification of large rivers in a framework of scarce information. This is inspired by the River Styles Framework with some modifications that make the process more straightforward and accessible to practitioners and more applicable to large basins, while reducing the subjective, expert-based inputs, as the process is now more systematic. To this aim, it utilizes innovative criteria and some computer-aided procedures and tools based on GIS, Excel and Python. This approach sheds light on the character and the behavior of rivers, which is key to informing planning, management and restoration. The application to the Magdalena River (Colombia) illustrates the characterization and classification process and the type of results, which ultimately highlight the great geomorphic diversity of that river. The process is applicable to many other rivers worldwide

Effects of Noise, Correlations and errors in the preparation of initial states in Quantum Simulations

In principle a quantum system could be used to simulate another quantum system. The purpose of such a simulation would be to obtain information about problems which cannot be simulated with a classical computer due to the exponential increase of the Hilbert space with the size of the system and which cannot be measured or controlled in an actual experiment. The system will interact with the surrounding environment, with the other particles in the system and be implemented using imperfect controls making it subject to noise. It has been suggested that noise does not need to be controlled to the same extent as it must be for general quantum computing. However the effects of noise in quantum simulations and how to treat them are not completely understood. In this paper we study an existing quantum algorithm for the one-dimensional Fano-Anderson model to be simulated using a liquid-state NMR device. We calculate the evolution of different initial states in the original model, and then we add interacting spins to simulate a more realistic situation. We find that states which are entangled with their environment, and sometimes correlated but not necessarily entangled have an evolution which is described by maps which are not completely positive. We discuss the conditions for this to occur and also the implications.Comment: Revtex 4-1, 14 pages, 21 figures, version 2 has typos corrected and acknowledgement adde

LO-phonon assisted polariton lasing in a ZnO based microcavity

Polariton relaxation mechanisms are analysed experimentally and theoretically in a ZnO-based polariton laser. A minimum lasing threshold is obtained when the energy difference between the exciton reservoir and the bottom of the lower polariton branch is resonant with the LO phonon energy. Tuning off this resonance increases the threshold, and exciton-exciton scattering processes become involved in the polariton relaxation. These observations are qualitatively reproduced by simulations based on the numerical solution of the semi-classical Boltzmann equations

Rheology of distorted nematic liquid crystals

We use lattice Boltzmann simulations of the Beris--Edwards formulation of nematodynamics to probe the response of a nematic liquid crystal with conflicting anchoring at the boundaries under shear and Poiseuille flow. The geometry we focus on is that of the hybrid aligned nematic (HAN) cell, common in devices. In the nematic phase, backflow effects resulting from the elastic distortion in the director field render the velocity profile strongly non-Newtonian and asymmetric. As the transition to the isotropic phase is approached, these effects become progressively weaker. If the fluid is heated just above the transition point, however, another asymmetry appears, in the dynamics of shear band formation.Comment: 7 pages, 4 figures. Accepted for publication in Europhys. Let

DNA-Decorated Carbon Nanotubes as Sensitive Layer for AlN Contour-Mode Resonant-MEMS Gravimetric Sensor

In this work a nano-enabled gravimetric chemical sensor prototype based on single-stranded DNA (ss-DNA) decorated single-walled carbon nanotubes (SWNT) as nano-functionalization layer for Aluminun Nitride (AIN) contour-mode resonant-MEMS gravimetric sensors has been demonstrated. Two resonators fabricated on the same silicon chip and operating at different resonance frequencies, 287 and 450 MHz, were functionalized with this novel bio-coating layer to experimentally prove the capability of two distinct single strands of DNA bound to SWNT to enhance differently the adsorption of volatile organic compounds such as dinitroluene (DNT, simulant for explosive vapor) and dymethyl-methylphosphonate (DMMP, a simulant for nerve agent sarin). The introduction of this bio-coating layer addresses the major drawbacks of recovery time (50% recovery in less than 29 seconds has been achieved) and lack of selectivity associated with gas sensor based on polymers and pristine carbon nanotube functionalization layers

Patterned silicon substrates: a common platform for room temperature GaN and ZnO polariton lasers

A new platform for fabricating polariton lasers operating at room temperature is introduced: nitride-based distributed Bragg reflectors epitaxially grown on patterned silicon substrates. The patterning allows for an enhanced strain relaxation thereby enabling to stack a large number of crack-free AlN/AlGaN pairs and achieve cavity quality factors of several thousands with a large spatial homogeneity. GaN and ZnO active regions are epitaxially grown thereon and the cavities are completed with top dielectric Bragg reflectors. The two structures display strong-coupling and polariton lasing at room temperature and constitute an intermediate step in the way towards integrated polariton devices

IL-27R signalling mediates early viral containment and impacts innate and adaptive immunity after chronic lymphocytic choriomeningitis virus infection

Chronic viral infections represent a major challenge to host's immune response and a unique network of immunological elements, including cytokines, are required for their containment. By using a model persistent infection with the natural murine pathogen lymphocytic choriomeningitis virus clone 13 (LCMV Cl13) we investigated the role of one such cytokine, interleukin 27 (IL-27), in the control of chronic infection. We found that IL-27R signalling promoted control of LCMV Cl13 as early as day 1 and 5 after infection and that il27p28 transcripts were rapidly elevated in multiple subsets of dendritic cells (DCs) and myeloid cells. In particular, plasmacytoid DCs (pDCs), the most potent type-1-interferon (IFN-I) producing cells, significantly increased il27p28 in a TLR7 dependent fashion. Notably, mice deficient in IL-27 specific receptor (R), WSX-1, exhibited a pleiotropy of innate and adaptive immune alterations after chronic LCMV infection, including compromised NK cell cytotoxicity and antibody responses. While, the majority of these immune alterations appeared cell-extrinsic, cell-intrinsic IL-27R was necessary to maintain early pDC numbers, which, alongside lower IFN-I transcription in CD11b+ DCs and myeloid cells, may explain the compromised IFN-I elevation that we observed early after LCMV Cl13 infection in IL-27R-deficient mice. Together these data highlight the critical role of IL-27 in enabling optimal anti-viral immunity early and late after infection with a systemic persistent virus and suggest that a previously unrecognized positive feedback-loop mediated by IL-27 in pDCs might be involved in this process

A Tool to Enable Intraoperative Insertion Force Measurements for Cochlear Implant Surgery

Objective: Residual hearing preservation during cochlear implant (CI) surgery is closely linked to the magnitude of intracochlear forces acting during the insertion process. So far, these forces have only been measured in vitro. Therefore, the range of insertion forces and the magnitude of damage-inducing thresholds in the human cochlea in vivo remain unknown. We aimed to develop a method to intraoperatively measure insertion forces without negatively affecting the established surgical workflow. Initial experiments showed that this requires the compensation of orientation-dependent gravitational forces. Methods: We devised design requirements for a force-sensing manual insertion tool. Experienced CI surgeons evaluated the proposed design for surgical safety and handling quality. Measured forces from automated and manual insertions into an artificial cochlea model were evaluated against data from a static external force sensor representing the gold standard. Results: The finalized manual insertion tool uses an embedded force sensor and inertial measurement unit to measure insertion forces. The evaluation of the proposed design shows the feasibility of orientation-independent insertion force measurements. Recorded forces correspond well to externally recorded reference forces after reliable removal of gravitational disturbances. CI surgeons successfully used the tool to insert electrode arrays into human cadaver cochleae. Conclusion: The presented positive evaluation poses the first step towards intraoperative use of the proposed tool. Further in vitro experiments with human specimens will ensure reliable in vivo measurements. Significance: Intraoperative insertion force measurements enabled by this tool will provide insights on the relationship between forces and hearing outcomes in cochlear implant surgery