The H1 Forward Track Detector at HERA II

In order to maintain efficient tracking in the forward region of H1 after the luminosity upgrade of the HERA machine, the H1 Forward Track Detector was also upgraded. While much of the original software and techniques used for the HERA I phase could be reused, the software for pattern recognition was completely rewritten. This, along with several other improvements in hit finding and high-level track reconstruction, are described in detail together with a summary of the performance of the detector.Comment: Minor revision requested by journal (JINST) edito

How tropical epiphytes at the Eden Project contribute to rainforest canopy science

Understanding the ecological patterns and ecosystem processes of tropical rainforest canopies is becoming increasingly urgent in the face of widespread deforestation. However, accessing rainforest canopies is far from simple, and performing manipulative experiments in the canopy is particularly challenging. Botanic gardens provide an ideal ‘halfway house’ between field experiments and controlled laboratory conditions. As an ideal venue for testing equipment and refining ideas, botanic gardens also provide scientists with a direct route to public engagement, and potentially to research impact. Here we describe the ‘fernarium’, an adjustable canopy research platform for the standardisation, manipulation and detailed study of epiphytic bird’s nest ferns (Asplenium nidus) at the Eden Project in Cornwall. The fernarium provides a platform not only for the scientific study of bird’s nest ferns, but for public engagement, science communication and a wider understanding of the urgent environmental issues surrounding tropical rainforests. We include some preliminary resultsfrom an experiment in which the microbial community of a fern soil at the Eden Project was found to be similar in composition to that of a fern from lowland tropical rainforest in Malaysian Borneo. This study illustrates how preliminary experiments in an indoor rainforest can inform experimental techniques and procedures fundamental to the scientific study of genuine rainforest canopies

Hot multiboundary wormholes from bipartite entanglement

We analyze the 1+1 CFT states dual to hot (time-symmetric) 2+1 multiboundary AdS wormholes. These are black hole geometries with high local temperature, $n\geqslant 1$ asymptotically-AdS3 regions, and arbitrary internal topology. The dual state at t = 0 is defined on n circles. We show these to be well-described by sewing together tensor networks corresponding to thermofield double states. As a result, the entanglement is spatially localized and bipartite: away from particular boundary points ('vertices') any small connected region A of the boundary CFT is entangled only with another small connected region B, where B may lie on a different circle or may be a different part of the same circle. We focus on the pair-of-pants case, from which more general cases may be constructed. We also discuss finite-temperature corrections, where we note that the states involve a code subspace in each circle

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Molecular motion in cell membranes: analytic study of fence-hindered random walks

A theoretical calculation is presented to describe the confined motion of transmembrane molecules in cell membranes. The study is analytic, based on Master equations for the probability of the molecules moving as random walkers, and leads to explicit usable solutions including expressions for the molecular mean square displacement and effective diffusion constants. One outcome is a detailed understanding of the dependence of the time variation of the mean square displacement on the initial placement of the molecule within the confined region. How to use the calculations is illustrated by extracting (confinement) compartment sizes from experimentally reported published observations from single particle tracking experiments on the diffusion of gold-tagged G-protein coupled mu-opioid receptors in the normal rat kidney cell membrane, and by further comparing the analytical results to observations on the diffusion of phospholipids, also in normal rat kidney cells.Comment: 10 pages, 5 figure

A General Framework for Complex Time-Driven Simulations on Hypercubes

We describe a general framework for building and running complex time-driven simulations with several levels of concurrency. The framework has been implemented on the Caltech/JPL Mark IIIfp hypercube using the Centaur communications protocol. Our framework allows the programmer to break the hypercube up into one or more subcubes of arbitrary size (task parallelism). Each subcube runs a separate application using data parallelism and synchronous communications internal to the subcube. Communications between subcubes are performed with asynchronous messages. Subcubes can each define their own parameters and commands which drive their particular application. These are collected and organized by the Control Processor (CP) in order that the entire simulation can be driven from a single command-driven shell. This system allows several programmers to develop disjoint pieces of a large simulation in parallel and to then integrate them with little effort. Each programmer is, of course, also able to take advantage of the separate data and I/O processors on each hypercube node in order to overlap calculation and communication (on-board parallelism) as well as the pipelined floating point processor on each node (pipelined processor parallelism). We show, as an example of the framework, a large space defense simulation. Functions (sensing, tracking, etc.) each comprise a subcube; functions are collected into defense platforms (satellites); and many platforms comprise the defense architecture. Software in the CP uses simple input to determine the node allocation to each function based on the desired defense architecture and number of platforms simulated in the hypercube. This allows many different architectures to be simulated. The set of simulated platforms, the results, and the messages between them are shown on color graphics displays. The methods used herein can be generalized to other simulations of a similar nature in a straightforward manner

Rapamycin Regulates Bleomycin-Induced Lung Damage in SP-C-Deficient Mice

Injury to the distal respiratory epithelium has been implicated as an underlying cause of idiopathic lung diseases. Mutations that result in SP-C deficiencies are linked to a small subset of spontaneous and familial cases of interstitial lung disease (ILD) and interstitial pulmonary fibrosis (IPF). Gene-targeted mice that lack SP-C (Sftpc−/−) develop an irregular ILD-like disease with age and are a model of the human SP-C related disease. In the current study, we investigated whether rapamycin could ameliorate bleomycin-induced fibrosis in the lungs of Sftpc−/− mice. Sftpc+/+ and −/− mice were exposed to bleomycin with either preventative administration of rapamycin or therapeutic administration beginning eight days after the bleomycin injury. Rapamycin-treatment increased weight loss and decreased survival of bleomycin-treated Sftpc+/+ and Sftpc−/− mice. Rapamycin did not reduce the fibrotic disease in the prophylactic or rescue experiments of either genotype of mice. Further, rapamycin treatment augmented airway resistance and reduced lung compliance of bleomycin-treated Sftpc−/− mice. Rapamycin treatment was associated with an increased expression of profibrotic Th2 cytokines and reduced expression of INF-γ. These findings indicate that novel therapeutics will be required to treat individuals with SP-C deficient ILD/IPF

Genetic replacement of surfactant protein-C reduces respiratory syncytial virus induced lung injury

BACKGROUND: Individuals with deficiencies of pulmonary surfactant protein C (SP-C) develop interstitial lung disease (ILD) that is exacerbated by viral infections including respiratory syncytial virus (RSV). SP-C gene targeted mice (Sftpc -/-) lack SP-C, develop an ILD-like disease and are susceptible to infection with RSV. METHODS: In order to determine requirements for correction of RSV induced injury we have generated compound transgenic mice where SP-C expression can be induced on the Sftpc -/- background (SP-C/Sftpc -/-) by the administration of doxycycline (dox). The pattern of induced SP-C expression was determined by immunohistochemistry and processing by Western blot analysis. Tissue and cellular inflammation was measured following RSV infection and the RSV-induced cytokine response of isolated Sftpc +/+ and -/- type II cells determined. RESULTS: After 5 days of dox administration transgene SP-C mRNA expression was detected by RT-PCR in the lungs of two independent lines of bitransgenic SP-C/Sftpc -/- mice (lines 55.3 and 54.2). ProSP-C was expressed in the lung, and mature SP-C was detected by Western blot analysis of the lavage fluid from both lines of SP-C/Sftpc -/- mice. Induced SP-C expression was localized to alveolar type II cells by immunostaining with an antibody to proSP-C. Line 55.3 SP-C/Sftpc -/- mice were maintained on or off dox for 7 days and infected with 2.6x10(7) RSV pfu. On day 3 post RSV infection total inflammatory cell counts were reduced in the lavage of dox treated 55.3 SP-C/Sftpc -/- mice (p = 0.004). The percentage of neutrophils was reduced (p = 0.05). The viral titers of lung homogenates from dox treated 55.3 SP-C/Sftpc -/- mice were decreased relative to 55.3 SP-C/Sftpc -/- mice without dox (p = 0.01). The cytokine response of Sftpc -/- type II cells to RSV was increased over that of Sftpc +/+ cells. CONCLUSIONS: Transgenic restoration of SP-C reduced inflammation and improved viral clearance in the lungs of SP-C deficient mice. The loss of SP-C in alveolar type II cells compromises their response to infection. These findings show that the restoration of SP-C in Sftpc -/- mice in response to RSV infection is a useful model to determine parameters for therapeutic intervention

Physical conditions regulate the fungal to bacterial ratios of a tropical suspended soil

As a source of ‘suspended soils’, epiphytes contribute large amounts of organic matter to the canopy of tropical rain forests. Microbes associated with epiphytes are responsible for much of the nutrient cycling taking place in rain forest canopies. However, soils suspended far above the ground in living organisms differ from soil on the forest floor, and traditional predictors of soil microbial community composition and functioning (nutrient availability and the activity of soil organisms) are likely to be less important. We conducted an experiment in the rain forest biome at the Eden Project in Cornwall to explore how biotic and abiotic conditions determine microbial community composition and functioning in a suspended soil. To simulate their natural epiphytic lifestyle, 20 bird’s nest ferns (Asplenium nidus) were placed on a custom-built canopy platform suspended 8m above the ground. Ammonium nitrate and earthworm treatments were applied to ferns in a factorial design. Extracellular enzyme activity and Phospholipid Fatty Acid (PLFA) profiles were determined at zero, three and six months. We observed no significant differences in either enzyme activity or PLFA profiles between any of the treatments. Instead, we observed decreases in β-glucosidase and N-acetyl-glucosaminidase activity, and an increase in phenol oxidase activity across all treatments and controls. An increase in the relative abundance of fungi during the experiment meant that the microbial communities in the Eden Project ferns after six months were comparable with 20 ferns sampled from pristine tropical rain forest in Borneo

Excitability in autonomous Boolean networks

We demonstrate theoretically and experimentally that excitable systems can be built with autonomous Boolean networks. Their experimental implementation is realized with asynchronous logic gates on a reconfigurabe chip. When these excitable systems are assembled into time-delay networks, their dynamics display nanosecond time-scale spike synchronization patterns that are controllable in period and phase.Comment: 6 pages, 5 figures, accepted in Europhysics Letters (epljournal.edpsciences.org