Towards the Amplituhedron Volume

21 pages; v2: version published in JHEPIt has been recently conjectured that scattering amplitudes in planar N=4 super Yang-Mills are given by the volume of the (dual) amplituhedron. In this paper we show some interesting connections between the tree-level amplituhedron and a special class of differential equations. In particular we demonstrate how the amplituhedron volume for NMHV amplitudes is determined by these differential equations. The new formulation allows for a straightforward geometric description, without any reference to triangulations. Finally we discuss possible implications for volumes related to generic N^kMHV amplitudes.Peer reviewe

High-power Soliton-induced Supercontinuum Generation and Tunable Sub-10-fs VUV Pulses from Kagome-lattice HC-PCFs

We theoretically study a novel approach for soliton-induced high-power supercontinuum generation by using kagome lattice HC-PCFs filled with a noble gas. Anomalous dispersion and broad-band low loss of these fibers enable the generation of two-octave broad spectra by fs pulses, with high coherence and high spectral peak power densities up to five orders of magnitude larger than in standard PCFs. In addition, up to 20 percents of the output radiation energy forms a narrow UV/VUV band, which can be tuned by contolling the pressure in the range from 350 nm to 120 nm. In the temporal domain this corresponds to sub-10-fs UV/VUV pulses with pulse energy of few tens of microjoule, caused by the formation of a high-order soliton emitting non-solitonic radiation.Comment: 4 pages, 4 figure

Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

Treatment Outcomes and Cost-Effectiveness of Shifting Management of Stable ART Patients to Nurses in South Africa: An Observational Cohort

Lawrence Long and colleagues report that “down-referring” stable HIV patients from a doctor-managed, hospital-based ART clinic to a nurse-managed primary health facility provides good health outcomes and cost-effective treatment for patients

Conformal algebra: R-matrix and star-triangle relation

The main purpose of this paper is the construction of the R-operator which acts in the tensor product of two infinite-dimensional representations of the conformal algebra and solves Yang-Baxter equation. We build the R-operator as a product of more elementary operators S_1, S_2 and S_3. Operators S_1 and S_3 are identified with intertwining operators of two irreducible representations of the conformal algebra and the operator S_2 is obtained from the intertwining operators S_1 and S_3 by a certain duality transformation. There are star-triangle relations for the basic building blocks S_1, S_2 and S_3 which produce all other relations for the general R-operators. In the case of the conformal algebra of n-dimensional Euclidean space we construct the R-operator for the scalar (spin part is equal to zero) representations and prove that the star-triangle relation is a well known star-triangle relation for propagators of scalar fields. In the special case of the conformal algebra of the 4-dimensional Euclidean space, the R-operator is obtained for more general class of infinite-dimensional (differential) representations with nontrivial spin parts. As a result, for the case of the 4-dimensional Euclidean space, we generalize the scalar star-triangle relation to the most general star-triangle relation for the propagators of particles with arbitrary spins.Comment: Added references and corrected typo

mPSQed: A Software for the Design of Multiplex Pyrosequencing Assays

Molecular-based diagnostic assays are the gold standard for infectious diseases today, since they allow a rapid and sensitive identification and typing of various pathogens. While PCR can be designed to be specific for a certain pathogen, a subsequent sequence analysis is frequently required for confirmation or typing. The design of appropriate PCR-based assays is a complex task, especially when conserved discriminating polymorphisms are rare or if the number of types which need to be differentiated is high. One extremely useful but underused method for this purpose is the multiplex pyrosequencing technique. Unfortunately there is no software available to aid researchers in designing multiplex pyrosequencing assays. Here, we present mPSQed (Multiplex PyroSeQuencing EDitor), a program targeted at closing this gap. We also present the design of an exemplarily theoretical assay for the differentiation of human adenovirus types A–F using two pyrosequencing primers on two distinct PCR products, designed quickly and easily using our software

Ectopic A-lattice seams destabilize microtubules

Natural microtubules typically include one A-lattice seam within an otherwise helically symmetric B-lattice tube. It is currently unclear how A-lattice seams influence microtubule dynamic instability. Here we find that including extra A-lattice seams in GMPCPP microtubules, structural analogues of the GTP caps of dynamic microtubules, destabilizes them, enhancing their median shrinkage rate by >20-fold. Dynamic microtubules nucleated by seeds containing extra A-lattice seams have growth rates similar to microtubules nucleated by B-lattice seeds, yet have increased catastrophe frequencies at both ends. Furthermore, binding B-lattice GDP microtubules to a rigor kinesin surface stabilizes them against shrinkage, whereas microtubules with extra A-lattice seams are stabilized only slightly. Our data suggest that introducing extra A-lattice seams into dynamic microtubules destabilizes them by destabilizing their GTP caps. On this basis, we propose that the single A-lattice seam of natural B-lattice MTs may act as a trigger point, and potentially a regulation point, for catastrophe

Localisation of RNAs into the germ plasm of vitellogenic xenopus oocytes

We have studied the localisation of mRNAs in full-grown Xenopus laevis oocytes by injecting fluorescent RNAs, followed by confocal microscopy of the oocyte cortex. Concentrating on RNA encoding the Xenopus Nanos homologue, nanos1 (formerly Xcat2), we find that it consistently localised into aggregated germ plasm ribonucleoprotein (RNP) particles, independently of cytoskeletal integrity. This implies that a diffusion/entrapment-mediated mechanism is active, as previously reported for previtellogenic oocytes. Sometimes this was accompanied by localisation into scattered particles of the “late”, Vg1/VegT pathway; occasionally only late pathway localisation was seen. The Xpat RNA behaved in an identical fashion and for neither RNA was the localisation changed by any culture conditions tested. The identity of the labelled RNP aggregates as definitive germ plasm was confirmed by their inclusion of abundant mitochondria and co-localisation with the germ plasm protein Hermes. Further, the nanos1/Hermes RNP particles are interspersed with those containing the germ plasm protein Xpat. These aggregates may be followed into the germ plasm of unfertilized eggs, but with a notable reduction in its quantity, both in terms of injected molecules and endogenous structures. Our results conflict with previous reports that there is no RNA localisation in large oocytes, and that during mid-oogenesis even germ plasm RNAs localise exclusively by the late pathway. We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs, Vg1 and VegT, also may localise into germ plasm. Our results support the view that mechanistically the two modes of localisation are extremely similar, and that in an injection experiment RNAs might utilise either pathway, the distinction in fates being very subtle and subject to variation. We discuss these results in relation to their biological significance and the results of others

The Cost of Antibiotic Mass Drug Administration for Trachoma Control in a Remote Area of South Sudan

Trachoma is one of a group of so-called “neglected tropical diseases” (NTDs) for which safe and effective treatments are available. The International Trachoma Initiative oversees donation of the antibiotic azithromycin to endemic countries. Delivery of this drug to communities affected by trachoma is the responsibility of national programmes and their implementing partners, and should be conducted as part of a comprehensive control strategy termed “SAFE,” which includes trichiasis surgery, health education and water/sanitation interventions. There are little data on how much the different components of a trachoma control programme cost and none from South Sudan. To inform budgeting to scale up control of trachoma, and of other NTDs whose control relies on large-scale mass drug administration (MDA), the present study set out to determine the cost per person treated when antibiotics were delivered through a vertical campaign that covered 94% of the target population in a remote trachoma endemic area of South Sudan. The average economic cost per person treated was USD 1.53, which included all inputs not paid for in cash except for the cost of the donated azithromycin and the opportunity cost of community members attending treatment