Development of novel multiplex microsatellite polymerase chain reactions to enable high-throughput population genetic studies of Schistosoma haematobium

© 2015 Webster et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The attached file is the published version of the article

Pattern Reduction in Paper Cutting

A large part of the paper industry involves supplying customers with reels of specified width in specifed quantities. These 'customer reels' must be cut from a set of wider 'jumbo reels', in as economical a way as possible. The first priority is to minimize the waste, i.e. to satisfy the customer demands using as few jumbo reels as possible. This is an example of the one-dimensional cutting stock problem, which has an extensive literature. Greycon have developed cutting stock algorithms which they include in their software packages. Greycon's initial presentation to the Study Group posed several questions, which are listed below, along with (partial) answers arising from the work described in this report. (1) Given a minimum-waste solution, what is the minimum number of patterns required? It is shown in Section 2 that even when all the patterns appearing in minimum-waste solutions are known, determining the minimum number of patterns may be hard. It seems unlikely that one can guarantee to find the minimum number of patterns for large classes of realistic problems with only a few seconds on a PC available. (2) Given an n → n-1 algorithm, will it find an optimal solution to the minimum- pattern problem? There are problems for which n → n - 1 reductions are not possible although a more dramatic reduction is. (3) Is there an efficient n → n-1 algorithm? In light of Question 2, Question 3 should perhaps be rephrased as 'Is there an efficient algorithm to reduce n patterns?' However, if an algorithm guaranteed to find some reduction whenever one existed then it could be applied iteratively to minimize the number of patterns, and we have seen this cannot be done easily. (4) Are there efficient 5 → 4 and 4 → 3 algorithms? (5) Is it worthwhile seeking alternatives to greedy heuristics? In response to Questions 4 and 5, we point to the algorithm described in the report, or variants of it. Such approaches seem capable of catching many higher reductions. (6) Is there a way to find solutions with the smallest possible number of single patterns? The Study Group did not investigate methods tailored specifically to this task, but the algorithm proposed here seems to do reasonably well. It will not increase the number of singleton patterns under any circumstances, and when the number of singletons is high there will be many possible moves that tend to eliminate them. (7) Can a solution be found which reduces the number of knife changes? The algorithm will help to reduce the number of necessary knife changes because it works by bringing patterns closer together, even if this does not proceed fully to a pattern reduction. If two patterns are equal across some of the customer widths, the knives for these reels need not be changed when moving from one to the other

Train Positioning Using Video Odometry

Reliable Data Systems have developed a video-based odometry system that enables trains to measure velocities and distances travelled without the need for trackside infrastructure. The Study Group was asked to investigate ways of improving the accuracy of such a system, and to suggest any improvements that might be made. The work performed in the week followed along these strands: (a). Elimination of errors in video odometery induced by pitch and height; (b) Robust calculation of (i) the train velocity and (ii) the track curvature; (c). Accurate determination of the position of a train on a track by assimilating Curvature information; (d). Determining where on UK’s railway map a train journey takes place, based purely on video odometry and (e). Drawing a track map

Phylogenetic relationships of African Caecilians (Amphibia: Gymnophiona): insights from mitochondrial rRNA gene sequences

Africa (excluding the Seychelles) has a diverse caecilian fauna, including the endemic family Scolecomorphidae and six endemic genera of the more cosmopolitan Caeciliidae. Previous molecular phylogenetic studies have not included any caecilians from the African mainland. Partial 12S and 16S mitochondrial gene sequences were obtained for two species of the endemic African Scolecomorphidae and five species and four genera of African Caeciliids, aligned against previously reported sequences for 16 caecilian species, and analysed using parsimony, maximum likelihood, Bayesian and distance methods. Results are in agreement with traditional taxonomy in providing support for the monophyly of the African Caeciliid genera Boulengerula and Schistometopum and for the Scolecomorphidae. They disagree in indicating that the Caeciliidae is paraphyletic with respect to the Scolecomorphidae. Although more data from morphology and/or molecules will be required to resolve details of the interrelationships of the African caecilian genera, the data provide strong support for at least two origins of caecilians in which the eye is reduced and covered with bone, and do not support the hypotheses that the caecilian assemblages of Africa, and of East and of West Africa are monophyletic

Phenotypic and genotypic monitoring of Schistosoma mansoni in Tanzanian schoolchildren five years into a preventative chemotherapy national control programme

We conducted combined in vitro PZQ efficacy testing with population genetic analyses of S. mansoni collected from children from two schools in 2010, five years after the introduction of a National Control Programme. Children at one school had received four annual PZQ treatments and the other school had received two mass treatments in total. We compared genetic differentiation, indices of genetic diversity, and estimated adult worm burden from parasites collected in 2010 with samples collected in 2005 (before the control programme began) and in 2006 (six months after the first PZQ treatment). Using 2010 larval samples, we also compared the genetic similarity of those with high and low in vitro sensitivity to PZQ

Multiband description of the upper critical field of bulk FeSe

The upper critical field of multiband superconductors can be an essential quantity to unravel the nature of superconducting pairing and its interplay with the electronic structure. Here we experimentally map out the complete upper critical field phase diagram of FeSe for different magnetic field orientations at temperatures down to 0.3 K using both resistivity and torque measurements. The temperature dependence of the upper critical field reflects that of a multiband superconductor and requires a two-band description in the clean limit with band coupling parameters favoring interband over intraband interactions. Despite the relatively small Maki parameter in FeSe of α ∼ 1.6, the multiband description of the upper critical field is consistent with the stabilization of a Fulde-Ferrell-Larkin-Ovchinnikov state below T /Tc ∼ 0.3. We find that the anomalous behavior of the upper critical field is linked to a departure from the single-band picture, and FeSe provides a clear example of where multiband effects and the strong anisotropy of the superconducting gap need to be taken into account

The origin of the Narrow Line Region of Mrk 3: an overpressured jet cocoon

We have obtained HST FOC long-slit optical spectroscopy of the Narrow Line Region of the Seyfert 2 galaxy Mrk 3. In the region cospatial with the radio-jet the velocity field is highly perturbed and shows two velocity systems separated by as much as 1700 km/s. We interpret this to be the consequence of the rapid expansion of a cocoon of hot gas, shocked and heated by the radio-emitting outflow, which compresses and accelerates the ambient gas. The NLR itself is essentially a cylindrical shell expanding supersonically. From the size and velocity of the expanding region, we derive an upper limit to the radio-source age, ~ 2 E42 erg/s required to inflate the cocoon and estimate that the jet minimum advance speed is 3 E-3 pc per year. The total kinetic energy of the high velocity NLR gas can be estimated as ~6 E54 erg, comparable to the total energy carried by the jet over its lifetime and this quantitatively supports the idea that the NLR gas is accelerated by the jet. If the advance speed of Mrk 3 is representative of the Seyfert population then these sources must also be short lived and probably recurrent. The jet kinetic luminosity of Mrk 3 is between 2 and 3 orders of magnitude smaller than that derived for radio-loud AGNs with similar emission-line luminosity. On the other hand, the fraction of jet power dissipated in radio-emission is similar. We speculate that the main distinction between radio-quiet and radio-loud AGN is ascribed to a difference in jet power rather than to a different efficiency in synchrotron emission production.Comment: 13 pages, 8 figures, Astrophysical Journal in pres

Preasymptotic Convergence of Randomized Kaczmarz Method

Kaczmarz method is one popular iterative method for solving inverse problems, especially in computed tomography. Recently, it was established that a randomized version of the method enjoys an exponential convergence for well-posed problems, and the convergence rate is determined by a variant of the condition number. In this work, we analyze the preasymptotic convergence behavior of the randomized Kaczmarz method, and show that the low-frequency error (with respect to the right singular vectors) decays faster during first iterations than the high-frequency error. Under the assumption that the inverse solution is smooth (e.g., sourcewise representation), the result explains the fast empirical convergence behavior, thereby shedding new insights into the excellent performance of the randomized Kaczmarz method in practice. Further, we propose a simple strategy to stabilize the asymptotic convergence of the iteration by means of variance reduction. We provide extensive numerical experiments to confirm the analysis and to elucidate the behavior of the algorithms.Comment: 20 page