Nonlinear soliton propagation in a few mode optical fibre

We experimentally demonstrate adiabatic soliton propagation in the fundamental mode of a few mode optical fibre and more complex behaviour in a higher order mode, indicating that the impact of nonlinearities differs for each mode

Motmot, an open-source toolkit for realtime video acquisition and analysis

<p>Abstract</p> <p>Background</p> <p>Video cameras sense passively from a distance, offer a rich information stream, and provide intuitively meaningful raw data. Camera-based imaging has thus proven critical for many advances in neuroscience and biology, with applications ranging from cellular imaging of fluorescent dyes to tracking of whole-animal behavior at ecologically relevant spatial scales.</p> <p>Results</p> <p>Here we present 'Motmot': an open-source software suite for acquiring, displaying, saving, and analyzing digital video in real-time. At the highest level, Motmot is written in the Python computer language. The large amounts of data produced by digital cameras are handled by low-level, optimized functions, usually written in C. This high-level/low-level partitioning and use of select external libraries allow Motmot, with only modest complexity, to perform well as a core technology for many high-performance imaging tasks. In its current form, Motmot allows for: (1) image acquisition from a variety of camera interfaces (package motmot.cam_iface), (2) the display of these images with minimal latency and computer resources using wxPython and OpenGL (package motmot.wxglvideo), (3) saving images with no compression in a single-pass, low-CPU-use format (package motmot.FlyMovieFormat), (4) a pluggable framework for custom analysis of images in realtime and (5) firmware for an inexpensive USB device to synchronize image acquisition across multiple cameras, with analog input, or with other hardware devices (package motmot.fview_ext_trig). These capabilities are brought together in a graphical user interface, called 'FView', allowing an end user to easily view and save digital video without writing any code. One plugin for FView, 'FlyTrax', which tracks the movement of fruit flies in real-time, is included with Motmot, and is described to illustrate the capabilities of FView.</p> <p>Conclusion</p> <p>Motmot enables realtime image processing and display using the Python computer language. In addition to the provided complete applications, the architecture allows the user to write relatively simple plugins, which can accomplish a variety of computer vision tasks and be integrated within larger software systems. The software is available at <url>http://code.astraw.com/projects/motmot</url></p

Genetic improvement technologies to support the sustainable growth of UK aquaculture

While the UK is the fourth largest aquaculture producer in Europe by volume, it is the second largest by value with an annual first sale value of around £1 billion. Over 90% of this value is from Atlantic salmon farmed in Scotland, but other finfish and shellfish aquaculture species are important to several UK regions. In this review, we describe the state of the art in UK aquaculture breeding and stock supply, and how innovation in genetics technologies can help achieve the Scottish Government’s ambitious target of doubling its aquaculture industry by 2030. Particular attention is given to the four most important UK aquaculture species: Atlantic salmon, rainbow trout, blue mussel and Pacific oyster, and we contrast the highly variable level of selective breeding and genomics technologies used in these sectors. A major factor in the success of Atlantic salmon farming has been large‐scale investment in modern breeding programmes, including family selection programmes and genomic selection. This has proven cost‐effective at scale, leading to improved production efficiency and reduction of some infectious diseases. We discuss the feasibility of applying similar technologies to the UK shellfish sectors, to ensure consistent and robust spat supply and begin trait selection. Furthermore, we discuss species‐specific application of modern breeding technologies in a global context, and the future potential of genomics and genome editing technologies to improve commercially desirable traits. Increased adoption of modern breeding technologies will assist UK aquaculture industries to meet the challenges for sustainable expansion, and remain competitive in a global market

Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study.

Ulcerative colitis is a chronic inflammatory disease of the colon that presents as diarrhea and gastrointestinal bleeding. We performed a genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry. In an analysis that controlled for gender and population structure, ulcerative colitis loci attaining genome-wide significance and subsequent replication in two independent populations were identified on chromosomes 1p36 (rs6426833, combined P = 5.1 x 10(-13), combined odds ratio OR = 0.73) and 12q15 (rs1558744, combined P = 2.5 x 10(-12), combined OR = 1.35). In addition, combined genome-wide significant evidence for association was found in a region spanning BTNL2 to HLA-DQB1 on chromosome 6p21 (rs2395185, combined P = 1.0 x 10(-16), combined OR = 0.66) and at the IL23R locus on chromosome 1p31 (rs11209026, combined P = 1.3 x 10(-8), combined OR = 0.56; rs10889677, combined P = 1.3 x 10(-8), combined OR = 1.29)

Dietary garlic and hip osteoarthritis: evidence of a protective effect and putative mechanism of action

Background Patterns of food intake and prevalent osteoarthritis of the hand, hip, and knee were studied using the twin design to limit the effect of confounding factors. Compounds found in associated food groups were further studied in vitro. Methods Cross-sectional study conducted in a large population-based volunteer cohort of twins. Food intake was evaluated using the Food Frequency Questionnaire; OA was determined using plain radiographs. Analyses were adjusted for age, BMI and physical activity. Subsequent in vitro studies examined the effects of allium-derived compounds on the expression of matrix-degrading proteases in SW1353 chondrosarcoma cells. Results Data were available, depending on phenotype, for 654-1082 of 1086 female twins (median age 58.9 years; range 46-77). Trends in dietary analysis revealed a specific pattern of dietary intake, that high in fruit and vegetables, showed an inverse association with hip OA (p = 0.022). Consumption of 'non-citrus fruit' (p = 0.015) and 'alliums' (p = 0.029) had the strongest protective effect. Alliums contain diallyl disulphide which was shown to abrogate cytokine-induced matrix metalloproteinase expression. Conclusions Studies of diet are notorious for their confounding by lifestyle effects. While taking account of BMI, the data show an independent effect of a diet high in fruit and vegetables, suggesting it to be protective against radiographic hip OA. Furthermore, diallyl disulphide, a compound found in garlic and other alliums, represses the expression of matrix-degrading proteases in chondrocyte-like cells, providing a potential mechanism of action

GRACKLE: a chemistry and cooling library for astrophysics

We present the Grackle chemistry and cooling library for astrophysical simulations and models. Grackle provides a treatment of non-equilibrium primordial chemistry and cooling for H, D, and He species, including H2 formation on dust grains; tabulated primordial and metal cooling; multiple UV background models; and support for radiation transfer and arbitrary heat sources. The library has an easily implementable interface for simulation codes written in C, C++, and Fortran as well as a Python interface with added convenience functions for semi-analytical models. As an open-source project, Grackle provides a community resource for accessing and disseminating astrochemical data and numerical methods. We present the full details of the core functionality, the simulation and Python interfaces, testing infrastructure, performance, and range of applicability. Grackle is a fully open-source project and new contributions are welcome.Comment: 20 pages, 8 figures, accepted for publication in MNRAS. For more info, visit grackle.readthedocs.i

Autophagy Inhibition Delays Early but Not Late-Stage Metastatic Disease s

ABSTRACT The autophagy pathway has been recognized as a mechanism of survival and therapy resistance in cancer, yet the extent of autophagy&apos;s function in metastatic progression is still unclear. Therefore, we used murine models of metastatic cancer to investigate the effect of autophagy modulation on metastasis development. Pharmacologic and genetic autophagy inhibition were able to impede cell proliferation in culture, but did not impact the development of experimentally induced 4T1 and B16-F10 metastases. Similarly, autophagy inhibition by adjuvant chloroquine (CQ) treatment did not delay metastasis in an orthotopic 4T1, tumor-resection model. However, neoadjuvant CQ treatment or genetic autophagy inhibition resulted in delayed metastasis development, whereas stimulation of autophagy by trehalose hastened development. Cisplatin was also administered either as a single agent or in combination with CQ. The combination of cisplatin and CQ was antagonistic. The effects of autophagy modulation on metastasis did not appear to be due to alterations in the intrinsic metastatic capability of the cells, as modulating autophagy had no impact on migration, invasion, or anchorage-independent growth in vitro. To explore the possibility of autophagy&apos;s influence on the metastatic microenvironment, bone marrow-derived cells (BMDCs), which mediate the establishment of the premetastatic niche, were measured in the lung and in circulation. Trehalose-treated mice had significantly more BMDCs than either vehicle-or CQ-treated mice. Autophagy inhibition may be most useful as a treatment to impede early metastatic development. However, modulating autophagy may also alter the efficacy of platinum-based therapies, requiring caution when considering combination therapies

Surface orientation, modulation frequency and the detection and perception of depth defined by binocular disparity and motion parallax

Binocular disparity and motion parallax provide information about the spatial structure and layout of the world. Descriptive similarities between the two cues have often been noted which have been taken as evidence of a close relationship between them. Here, we report two experiments which investigate the effect of surface orientation and modulation frequency on (i) a threshold detection task and (ii) a supra-threshold depth-matching task using sinusoidally corrugated surfaces defined by binocular disparity or motion parallax. For low frequency corrugations, an orientation anisotropy was observed in both domains, with sensitivity decreasing as surface orientation was varied from horizontal to vertical. In the depth-matching task, for surfaces defined by binocular disparity the greatest depth was seen for oblique orientations. For surfaces defined by motion parallax, perceived depth was found to increase as surface orientation was varied from horizontal to vertical. In neither case was perceived depth for supra-threshold surfaces related to threshold performance in any simple manner. These results reveal clear differences between the perception of depth from binocular disparity or motion parallax, and between perception at threshold and supra-threshold levels of performance. © 2006 Elsevier Ltd. All rights reserved

Molecular Gas and Star Formation in Bars of Nearby Spiral Galaxies

We compare the distribution of molecular gas and star formation activity in the bar region of six spirals (NGC 2903, NGC 3627, NGC 4321, NGC 5457, NGC 6946, & IC 342) from the BIMA Survey of Nearby Galaxies (SONG). The molecular gas, traced using the CO (J=1--0) emission line, is brightest along the leading edge of the stellar bar in the bar dust lanes. The star formation activity, traced using the Halpha emission line, is offset towards the leading side of the CO emission. A cross-correlation analysis shows that a) the HII regions are offset 0--800 pc on the leading side of the CO emission, b) the largest offsets are found in the strongest bars, and c) there is a wide range in offsets in a single bar with no systematic pattern as a function of the galacto-centric radius. The CO-Halpha offset constrains how stars may form depending on the gas flow. We examine possible star formation scenarios in context of the two main classes of bar gas flow simulations, the N-body/sticky particle and hydrodynamic models. Though both model gas flows are generally consistent with the observed offsets, we suggest the inclusion of a two- or multi-phase medium to improve the agreement between models and observation.Comment: Accepted for publication in the Astronomical Journal, schedule for November 2002. 28 pages, 12 figures in PNG format. Paper available in emulateapj style (gzipped-postscript format) at http://www.astro.caltech.edu/~kartik/papers/haco.ps.g