Photophysiological and photosynthetic complex changes during iron starvation in Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942

Iron is an essential component in many protein complexes involved in photosynthesis, but environmental iron availability is often low as oxidized forms of iron are insoluble in water. To adjust to low environmental iron levels, cyanobacteria undergo numerous changes to balance their iron budget and mitigate the physiological effects of iron depletion. We investigated changes in key protein abundances and photophysiological parameters in the model cyanobacteria Synechococcus PCC 7942 and Synechocystis PCC 6803 over a 120 hour time course of iron deprivation. The iron stress induced protein (IsiA) accumulated to high levels within 48 h of the onset of iron deprivation, reaching a molar ratio of ~42 IsiA : Photosystem I in Synechococcus PCC 7942 and ~12 IsiA : Photosystem I in Synechocystis PCC 6803. Concomitantly the iron-rich complexes Cytochrome b6f and Photosystem I declined in abundance, leading to a decrease in the Photosystem I : Photosystem II ratio. Chlorophyll fluorescence analyses showed a drop in electron transport per Photosystem II in Synechococcus, but not in Synechocystis after iron depletion. We found no evidence that the accumulated IsiA contributes to light capture by Photosystem II complexes

CODE DEFENDERS: A Mutation Testing Game

Mutation testing is endorsed by software testing researchers for its unique capability of providing pragmatic estimates of a test suite's fault detection capability, and for guiding testers in improving their test suites. In practice, however, wide-spread adoption of mutation testing is hampered because any non-trivial program results in huge numbers of mutants, many of which are either trivial or equivalent, and thus useless. Trivial mutants reduce the motivation of developers in trusting and using the technique, while equivalent mutants are frustratingly difficult to handle. These problems are exacerbated by insufficient education on testing, which often means that mutation testing is not well understood in practice. These are examples of the types of problems that gamification aims to overcome by making such tedious activities competitive and entertaining. In this paper, we introduce the first steps towards building Code Defenders, a mutation testing game where players take the role of an attacker, who aims to create the most subtle non-equivalent mutants, or a defender, who aims to create strong tests to kill these mutants. The benefits of such an approach are manifold: The game can serve an educational role by engaging learners in mutation testing activities in a fun way. Experienced players will produce strong test suites, capable of detecting even the most subtle bugs that other players can conceive. Equivalent mutants are handled by making them a special part of the gameplay, where points are at stake in duels between attackers and defenders

A detailed investigation of the effectiveness of whole test suite generation

© 2016 The Author(s)A common application of search-based software testing is to generate test cases for all goals defined by a coverage criterion (e.g., lines, branches, mutants). Rather than generating one test case at a time for each of these goals individually, whole test suite generation optimizes entire test suites towards satisfying all goals at the same time. There is evidence that the overall coverage achieved with this approach is superior to that of targeting individual coverage goals. Nevertheless, there remains some uncertainty on (a) whether the results generalize beyond branch coverage, (b) whether the whole test suite approach might be inferior to a more focused search for some particular coverage goals, and (c) whether generating whole test suites could be optimized by only targeting coverage goals not already covered. In this paper, we perform an in-depth analysis to study these questions. An empirical study on 100 Java classes using three different coverage criteria reveals that indeed there are some testing goals that are only covered by the traditional approach, although their number is only very small in comparison with those which are exclusively covered by the whole test suite approach. We find that keeping an archive of already covered goals along with the tests covering them and focusing the search on uncovered goals overcomes this small drawback on larger classes, leading to an improved overall effectiveness of whole test suite generation

Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis

Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we introduce tools from topological data analysis to characterize the frequency and scale of lateral gene transfer in bacteria, focusing on a set of pathogens of significant public health relevance. As a case study, we examine the spread of antibiotic resistance in Staphylococcus aureus. Finally, we consider the possible role of the human microbiome as a reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on Advanced Methods of Interactive Data Mining for Personalized Medicin

Structure factor measurement in TiAl and silicon

It proved impossible to obtain results with sufficient precision for TiAl reproducibly (<0.1%) from samples of different thicknesses. In order to ascertain the origin of this inconsistency, this study concentrates on the development of the experimental and theoretical tools required for such refinement and measurements for Si have been performed

A corpus-assisted study of the discourse marker well as an indicator of judges' institutional roles in court cases with litigants in person

In this paper, I concentrate on court cases with litigants in person (lay people who act on their own behalf in legal proceedings without a counsel or solicitor) and discuss the challenges of building a corpus of courtroom discourse where it is crucial to distinguish between speakers due to their distinct institutional roles. The corpus incorporates seven sub-corpora of verbatim transcripts from different court cases with litigants in person and comprises over eleven-million tokens. The focus of this paper is on the interplay between the legal and lay discourse types and how judges project their institutional roles through well-initiated turns directed at litigants in person and counsels. As a versatile discourse marker, well provides a good opportunity to explore how judges have to adapt their roles to ensure lay litigants in person receive the necessary support and that their lack of competence does not impede on the fairness of the proceedings. Given the breadth and importance of the topic of litigation in person, I discuss how the tools and approaches of corpus linguistics can be helpful in this multi-disciplinary area where multiple functions and uses of individual linguistic features need to be explored in depth

Longitudinal effects of environmental enrichment on behaviour and physiology of pigs reared on an intensive-stock farm

The aim of this paper was to provide a longitudinal evaluation of the effects of physical enrichments on the behaviour and physiology of intensive stock-farming pigs. Twenty-eight crossbred pigs of both sexes, were exposed to four types of enrichments (hemp ropes, steel chains, plastic balls, rubber hoses) over a period of eleven weeks. This investigation was based on specific abnormal behaviours and physiological indicators, including hematologic parameters. For behavioural score, focal sampling was used with recording of abnormal behaviours (body-, tail- and ear-biting), belly nosing, running, and interaction with objects (for Enriched pigs). The presence of skin injuries was also recorded. In general, the frequency of abnormal behaviours was significantly reduced in the Enriched group. A timerelated profile appeared in the use of the enrichments. Males showed higher occurrence of skin injuries than females. Physiological measurements, such as levels of complement system, white blood cells and neutrophils, were lower in pigs from the Enriched group. Enriched pigs, as a whole, presented much lower levels of serum DHEA-S concentration over two weeks. The findings of this study show the successful provision of appropriate enrichments to encourage behaviours which may result in satisfactory animal oral interaction with the enriching objects, preventing them biting pen-mates. In this respect, the objects proposed were strongly effective in producing changes in behaviour which could mitigate inadequate conditions, such as the relationship between animal body weight and the available space allowance