In the Death of a Phoenix

The male form classically elicits thoughts of certain characteristics, including strength, security, power, all of which lie deep within a hardened outer shell. But on closer inspection there is something much more primal to the nature of a man . Man tends to fall short of their female counterparts when it comes to understanding and verbalizing their emotions. Thus they are faced with strange tumultuous insecurities, fears, judgements, and expectations, with no way to express the struggles they may face within themselves. Man has many stories to tell, but lacks the language to begin speaking. This poem is the closest I came to finding words for these primal emotions

Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota

Microscopic algae release organic compounds to the region immediately surrounding their cells, known as the phycosphere, constituting a niche for colonization by heterotrophic bacteria. These bacteria take up algal photoassimilates and provide beneficial functions to their host, in a process that resembles the establishment of microbial communities associated with the roots and rhizospheres of land plants. Here, we characterize the microbiota of the model alga Chlamydomonas reinhardtii and reveal extensive taxonomic and functional overlap with the root microbiota of land plants. Using synthetic communities derived from C. reinhardtii and Arabidopsis thaliana, we show that phycosphere and root bacteria assemble into taxonomically similar communities on either host. We show that provision of diffusible metabolites is not sufficient for phycosphere community establishment, which additionally requires physical proximity to the host. Our data suggest the existence of shared ecological principles driving the assembly of the A. thaliana root and C. reinhardtii phycosphere microbiota, despite the vast evolutionary distance between these two photosynthetic organisms

Psi-series solutions of the cubic H\'{e}non-Heiles system and their convergence

The cubic H\'enon-Heiles system contains parameters, for most values of which, the system is not integrable. In such parameter regimes, the general solution is expressible in formal expansions about arbitrary movable branch points, the so-called psi-series expansions. In this paper, the convergence of known, as well as new, psi-series solutions on real time intervals is proved, thereby establishing that the formal solutions are actual solutions

Origin of land plants: Do conjugating green algae hold the key?

<p>Abstract</p> <p>Background</p> <p>The terrestrial habitat was colonized by the ancestors of modern land plants about 500 to 470 million years ago. Today it is widely accepted that land plants (embryophytes) evolved from streptophyte algae, also referred to as charophycean algae. The streptophyte algae are a paraphyletic group of green algae, ranging from unicellular flagellates to morphologically complex forms such as the stoneworts (Charales). For a better understanding of the evolution of land plants, it is of prime importance to identify the streptophyte algae that are the sister-group to the embryophytes. The Charales, the Coleochaetales or more recently the Zygnematales have been considered to be the sister group of the embryophytes However, despite many years of phylogenetic studies, this question has not been resolved and remains controversial.</p> <p>Results</p> <p>Here, we use a large data set of nuclear-encoded genes (129 proteins) from 40 green plant taxa (Viridiplantae) including 21 embryophytes and six streptophyte algae, representing all major streptophyte algal lineages, to investigate the phylogenetic relationships of streptophyte algae and embryophytes. Our phylogenetic analyses indicate that either the Zygnematales or a clade consisting of the Zygnematales and the Coleochaetales are the sister group to embryophytes.</p> <p>Conclusions</p> <p>Our analyses support the notion that the Charales are not the closest living relatives of embryophytes. Instead, the Zygnematales or a clade consisting of Zygnematales and Coleochaetales are most likely the sister group of embryophytes. Although this result is in agreement with a previously published phylogenetic study of chloroplast genomes, additional data are needed to confirm this conclusion. A Zygnematales/embryophyte sister group relationship has important implications for early land plant evolution. If substantiated, it should allow us to address important questions regarding the primary adaptations of viridiplants during the conquest of land. Clearly, the biology of the Zygnematales will receive renewed interest in the future.</p

Using functional annotations to study pairwise interactions in urinary tract infection communities

The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities

Having Fun in Learning Formal Specifications

There are many benefits in providing formal specifications for our software. However, teaching students to do this is not always easy as courses on formal methods are often experienced as dry by students. This paper presents a game called FormalZ that teachers can use to introduce some variation in their class. Students can have some fun in playing the game and, while doing so, also learn the basics of writing formal specifications in the form of pre- and post-conditions. Unlike existing software engineering themed education games such as Pex and Code Defenders, FormalZ takes the deep gamification approach where playing gets a more central role in order to generate more engagement. This short paper presents our work in progress: the first implementation of FormalZ along with the result of a preliminary users' evaluation. This implementation is functionally complete and tested, but the polishing of its user interface is still future work

Satellite-derived volume loss rates and glacier speeds for the Juneau Icefield, Alaska

Abstract We provide a high-resolution map of elevation change rates at the Juneau Icefield (JIF), southeastern Alaska, in order to quantify its contribution to sea-level rise between 2000 and 2009/2013. We also produce the first high-resolution map of ice speeds at the JIF, which we use to constrain flux and look for acceleration. We calculate using stacked digital elevation models (DEMs) from the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) instrument and the Shuttle Radar Topography Mission (SRTM), taking into account SRTM C-band penetration via comparison with SRTM X-band elevations. Overall, the JIF is losing mass less rapidly (0.13 ± 0.12 m w.e. a –1 ) than other Alaskan icefields (0.79 m w.e. a –1 ). We determine glacier speeds using pixel-tracking on optical image pairs acquired from 2001 to 2010 by ASTER, from radar image pairs acquired between 2007 and 2011 and from radar interferometry in 1995. We detect seasonal speed variations but no interannual acceleration, ruling out dynamics as the cause of the observed thinning. Thinning must therefore be due to the documented warming in the region. Flux measurements confirm this for Mendenhall Glacier, showing that calving constitutes only 2.5–5% of mass loss there