QSRA – a quality-value guided de novo short read assembler

<p>Abstract</p> <p>Background</p> <p>New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data.</p> <p>Results</p> <p>We have designed and implemented an assembler, Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality.</p> <p>Conclusion</p> <p>QSRA generally produced the highest genomic coverage, while being faster than VCAKE. QSRA is extremely competitive in its longest contig and N50/N80 contig lengths, producing results of similar quality to those of EDENA and VELVET. QSRA provides a step closer to the goal of de novo assembly of complex genomes, improving upon the original VCAKE algorithm by not only drastically reducing runtimes but also increasing the viability of the assembly algorithm through further error handling capabilities.</p

'Surely the most natural scenario in the world’: Representations of ‘Family’ in BBC Pre-school Television

Historically, the majority of work on British children’s television has adopted either an institutional or an audience focus, with the texts themselves often overlooked. This neglect has meant that questions of representation in British children’s television – including issues such as family, gender, class or ethnicity - have been infrequently analysed in the UK context. In this article, we adopt a primarily qualitative methodology and analyse the various textual manifestations of ‘family’, group, or community as represented in a selected number of BBC pre-school programmes. In doing so, we question the (limited amount of) international work that has examined representations of the family in children’s television, and argue that nuclear family structures do not predominate in this sphere

Orientifolds of K3 and Calabi-Yau Manifolds with Intersecting D-branes

We investigate orientifolds of type II string theory on K3 and Calabi-Yau 3-folds with intersecting D-branes wrapping special Lagrangian cycles. We determine quite generically the chiral massless spectrum in terms of topological invariants and discuss both orbifold examples and algebraic realizations in detail. Intriguingly, the developed techniques provide an elegant way to figure out the chiral sector of orientifold models without computing any explicit string partition function. As a new example we derive a non-supersymmetric Standard-like Model from an orientifold of type IIA on the quintic Calabi-Yau 3-fold with wrapped D6-branes. In the case of supersymmetric intersecting brane models on Calabi-Yau manifolds we discuss the D-term and F-term potentials, the effective gauge couplings and the Green-Schwarz mechanism. The mirror symmetric formulation of this construction is provided within type IIB theory. We finally include a short discussion about the lift of these models from type IIB on K3 to F-theory and from type IIA on Calabi-Yau 3-folds to M-theory on G_2 manifolds.Comment: 82 pages, harvmac, 5 figures. v2: references added. v3: T^6 orientifold corrected, JHEP versio

Fire Promotes Pollinator Visitation: Implications for Ameliorating Declines of Pollination Services

Pollinators serve critical roles for the functioning of terrestrial ecosystems, and have an estimated annual value of over $150 billion for global agriculture. Mounting evidence from agricultural systems reveals that pollinators are declining in many regions of the world, and with a lack of information on whether pollinator communities in natural systems are following similar trends, identifying factors which support pollinator visitation and services are important for ameliorating the effects of the current global pollinator crisis. We investigated how fire affects resource structure and how that variation influences floral pollinator communities by comparing burn versus control treatments in a southeastern USA old-field system. We hypothesized and found a positive relationship between fire and plant density of a native forb, Verbesina alternifolia, as well as a significant difference in floral visitation of V. alternifolia between burn and control treatments. V. alternifolia density was 44% greater and floral visitation was 54% greater in burned treatments relative to control sites. When the density of V. alternifolia was experimentally reduced in the burn sites to equivalent densities observed in control sites, floral visitation in burned sites declined to rates found in control sites. Our results indicate that plant density is a proximal mechanism by which an imposed fire regime can indirectly impact floral visitation, suggesting its usefulness as a tool for management of pollination services. Although concerns surround the negative impacts of management, indirect positive effects may provide an important direction to explore for managing future ecological and conservation issues. Studies examining the interaction among resource concentration, plant apparency, and how fire affects the evolutionary consequences of altered patterns of floral visitation are overdue. DOI: 10.1371/journal.pone.007985

The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of <i>Synechococcus</i> inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

© 2015 Becraft, Wood, Rusch, Kühl, Jensen, Bryant, Roberts, Cohan and Ward. Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species (putative ecotypes), which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same putative ecotype formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the putative ecotypes are ecologically distinct, the members of each ecotype are ecologically homogeneous. Putative ecotypes responded differently to experimental perturbations of temperature and light, but the genetic variation within each putative ecotype was maintained as the relative abundances of putative ecotypes changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to putative ecotypes that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for putative ecotypes that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time

The effective action of D6-branes in N=1 type IIA orientifolds

We use a Kaluza-Klein reduction to compute the low-energy effective action for the massless modes of a spacetime-filling D6-brane wrapped on a special Lagrangian 3-cycle of a type IIA Calabi-Yau orientifold. The modifications to the characteristic data of the N=1 bulk orientifold theory in the presence of a D6-brane are analysed by studying the underlying Type IIA supergravity coupled to the brane worldvolume in the democratic formulation and performing a detailed dualisation procedure. The N=1 chiral coordinates are found to be in agreement with expectations from mirror symmetry. We work out the Kahler potential for the chiral superfields as well as the gauge kinetic functions for the bulk and the brane gauge multiplets including the kinetic mixing between the two. The scalar potential resulting from the dualisation procedure can be formally interpreted in terms of a superpotential. Finally, the gauging of the Peccei-Quinn shift symmetries of the complex structure multiplets reproduces the D-term potential enforcing the calibration condition for special Lagrangian 3-cycles.Comment: 48 pages, v2: typos corrected, references adde

Why do banks promise to pay par on demand?

We survey the theories of why banks promise to pay par on demand and examine evidence about the conditions under which banks have promised to pay the par value of deposits and banknotes on demand when holding only fractional reserves. The theoretical literature can be broadly divided into four strands: liquidity provision, asymmetric information, legal restrictions, and a medium of exchange. We assume that it is not zero cost to make a promise to redeem a liability at par value on demand. If so, then the conditions in the theories that result in par redemption are possible explanations of why banks promise to pay par on demand. If the explanation based on customers’ demand for liquidity is correct, payment of deposits at par will be promised when banks hold assets that are illiquid in the short run. If the asymmetric-information explanation based on the difficulty of valuing assets is correct, the marketability of banks’ assets determines whether banks promise to pay par. If the legal restrictions explanation of par redemption is correct, banks will not promise to pay par if they are not required to do so. If the transaction explanation is correct, banks will promise to pay par value only if the deposits are used in transactions. After the survey of the theoretical literature, we examine the history of banking in several countries in different eras: fourth-century Athens, medieval Italy, Japan, and free banking and money market mutual funds in the United States. We find that all of the theories can explain some of the observed banking arrangements, and none explain all of them

Priority setting in developing countries health care institutions: the case of a Ugandan hospital

BACKGROUND: Because the demand for health services outstrips the available resources, priority setting is one of the most difficult issues faced by health policy makers, particularly those in developing countries. However, there is lack of literature that describes and evaluates priority setting in these contexts. The objective of this paper is to describe priority setting in a teaching hospital in Uganda and evaluate the description against an ethical framework for fair priority setting processes – Accountability for Reasonableness. METHODS: A case study in a 1,500 bed national referral hospital receiving 1,320 out patients per day and an average budget of US$ 13.5 million per year. We reviewed documents and carried out 70 in-depth interviews (14 health planners, 40 doctors, and 16 nurses working at the hospital). Interviews were recorded and transcribed. Data analysis employed the modified thematic approach to describe priority setting, and the description was evaluated using the four conditions of Accountability for Reasonableness: relevance, publicity, revisions and enforcement. RESULTS: Senior managers, guided by the hospital strategic plan make the hospital budget allocation decisions. Frontline practitioners expressed lack of knowledge of the process. Relevance: Priority is given according to a cluster of factors including need, emergencies and patient volume. However, surgical departments and departments whose leaders "make a lot of noise" are also prioritized. Publicity: Decisions, but not reasons, are publicized through general meetings and circulars, but this information does not always reach the frontline practitioners. Publicity to the general public was through ad hoc radio programs and to patients who directly ask. Revisions: There were no formal mechanisms for challenging the reasoning. Enforcement: There were no mechanisms to ensure adherence to the four conditions of a fair process. CONCLUSION: Priority setting decisions at this hospital do not satisfy the conditions of fairness. To improve, the hospital should: (i) engage frontline practitioners, (ii) publicize the reasons for decisions both within the hospital and to the general public, and (iii) develop formal mechanisms for challenging the reasoning. In addition, capacity strengthening is required for senior managers who must accept responsibility for ensuring that the above three conditions are met