Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell

Phylogenetic inference is considered to be one of the grand challenges in Bioinformatics due to the immense computational requirements. RAxML is currently among the fastest and most accurate programs for phylogenetic tree inference under the Maximum Likelihood (ML) criterion. First, we introduce new tree search heuristics that accelerate RAxML by a factor of 2.43 while returning equally good trees. The performance of the new search algorithm has been assessed on 18 real-world datasets comprising 148 up to 4,843 DNA sequences. We then present the implementation, optimization, and evaluation of RAxML on the IBM Cell Broadband Engine. We address the problems and provide solutions pertaining to the optimization of floating point code, control flow, communication, and scheduling of multi-level parallelism on the Cel

Novel expression of Haemonchus contortus vaccine candidate aminopeptidase H11 using the free-living nematode Caenorhabditis elegans

With the problem of parasitic nematode drug resistance increasing, vaccine development offers an alternative sustainable control approach. For some parasitic nematodes, native extracts enriched for specific proteins are highly protective. However, recombinant forms of these proteins have failed to replicate this protection. This is thought to be due to differences in glycosylation and/or conformation between native and recombinant proteins. We have exploited the free-living nematode Caenorhabditis elegans to examine its suitability as an alternative system for recombinant expression of parasitic nematode vaccine candidates. We focussed on Haemonchus contortus aminopeptidase H11 glycoprotein, which is enriched in a gut membrane fraction capable of inducing significant protection against this important ovine gastrointestinal nematode. We show that H. contortus H11 expressed in C. elegans is enzymatically active and MALDI mass spectrometry identifies similar di- and tri-fucosylated structures to those on native H11, with fucose at the 3- and/or 6-positions of the proximal GlcNAc. Some glycan structural differences were observed, such as lack of LDNF. Serum antibody to native H11 binds to C. elegans recombinant H11 and most of the antibody to rH11 or native H11 is directed to glycan moieties. Despite these similarities, no reduction in worm burden or faecal egg count was observed following immunisation of sheep with C. elegans-expressed recombinant H11 protein. The findings suggest that the di- and tri-fucosylated N-glycans expressed on rH11 do not contribute to the protective effect of H11 and that additional components present in native H11-enriched extract are likely required for enhancing the antibody response necessary for protection

A Drop in the Bucket or a Pebble in a Pond: Commercial Building Partners’ Replication of EEMs Across Their Portfolios

This study presents findings from questionnaire and interview data investigating replication efforts of Commercial Building Partnerships (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered with 12 organizations on new and retrofit construction projects as part of the U.S. Department of Energy (DOE) CBP program. PNNL and other national laboratories collaborate with industry leaders that own large portfolios of buildings to develop high performance projects for new construction and renovation. This project accelerates market adoption of commercially available energy saving technologies into the design process for new and upgraded commercial buildings. The labs provide assistance to the partners’ design teams and make a business case for energy investments. From the owner’s perspective, a sound investment results in energy savings based on corporate objectives and design. Through a feedback questionnaire, along with personal interviews, PNNL gathered qualitative and quantitative information relating to replication efforts by each organization. Data gathered through this process were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used in the CBP project to the rest of the organization’s building portfolio (including replication verification), and 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the entire CBP program. Conclusions of this study indicate by 2030, a range of 2,957 to 97,101 buildings will be impacted by the CBP program through partner replication efforts, representing over 22% of all buildings in partner portfolios, and an energy savings potential between 2.3 and 77 trillion Btus annually

A Drop in the Bucket or a Pebble in a Pond: Commercial Building Partners’ Replication of EEMs Across Their Portfolios

This study presents findings from questionnaire and interview data investigating replication efforts of Commercial Building Partnerships (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered with 12 organizations on new and retrofit construction projects as part of the U.S. Department of Energy (DOE) CBP program. PNNL and other national laboratories collaborate with industry leaders that own large portfolios of buildings to develop high performance projects for new construction and renovation. This project accelerates market adoption of commercially available energy saving technologies into the design process for new and upgraded commercial buildings. The labs provide assistance to the partners’ design teams and make a business case for energy investments. From the owner’s perspective, a sound investment results in energy savings based on corporate objectives and design. Through a feedback questionnaire, along with personal interviews, PNNL gathered qualitative and quantitative information relating to replication efforts by each organization. Data gathered through this process were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used in the CBP project to the rest of the organization’s building portfolio (including replication verification), and 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the entire CBP program. Conclusions of this study indicate by 2030, a range of 2,957 to 97,101 buildings will be impacted by the CBP program through partner replication efforts, representing over 22% of all buildings in partner portfolios, and an energy savings potential between 2.3 and 77 trillion Btus annually

Time--Evolving Statistics of Chaotic Orbits of Conservative Maps in the Context of the Central Limit Theorem

We study chaotic orbits of conservative low--dimensional maps and present numerical results showing that the probability density functions (pdfs) of the sum of $N$ iterates in the large $N$ limit exhibit very interesting time-evolving statistics. In some cases where the chaotic layers are thin and the (positive) maximal Lyapunov exponent is small, long--lasting quasi--stationary states (QSS) are found, whose pdfs appear to converge to $q$--Gaussians associated with nonextensive statistical mechanics. More generally, however, as $N$ increases, the pdfs describe a sequence of QSS that pass from a $q$--Gaussian to an exponential shape and ultimately tend to a true Gaussian, as orbits diffuse to larger chaotic domains and the phase space dynamics becomes more uniformly ergodic.Comment: 15 pages, 14 figures, accepted for publication as a Regular Paper in the International Journal of Bifurcation and Chaos, on Jun 21, 201