Software and methods for oligonucleotide and cDNA array data analysis.

Two HTML-based programs were developed to analyze and filter gene-expression data: 'Bullfrog' for Affymetrix oligonucleotide arrays and 'Spot' for custom cDNA arrays. The programs provide intuitive data-filtering tools through an easy-to-use interface. A background subtraction and normalization program for cDNA arrays was also built that provides an informative summary report with data-quality assessments. These programs are freeware to aid in the analysis of gene-expression results and facilitate the search for genes responsible for interesting biological processes and phenotypes

Studies in Medium-Sized-Ring Compounds

Abstract Not Provided

Species delimitation and phylogeny of a New Zealand plant species radiation

<p>Abstract</p> <p>Background</p> <p>Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation <it>Ourisia </it>species (Plantaginaceae) in the New Zealand archipelago.</p> <p>Results</p> <p>New Zealand <it>Ourisia </it>are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4–1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of <it>Ourisia </it>produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties.</p> <p>Conclusion</p> <p><it>Ourisia </it>radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters allowing species boundaries to be delimited in <it>Ourisia</it>. Importantly, Structure analyses suggest some degree of admixture with most species, which may also explain why the AFLP data do not exhibit sufficient tree-like properties necessary for reconstructing some species relationships. We discuss this feature and highlight the importance of improving models for phylogenetic analyses of species radiations using AFLP and SNP data.</p

Solutions of the Einstein Constraint Equations with Apparent Horizon Boundaries

We construct asymptotically Euclidean solutions of the vacuum Einstein constraint equations with an apparent horizon boundary condition. Specifically, we give sufficient conditions for the constant mean curvature conformal method to generate such solutions. The method of proof is based on the barrier method used by Isenberg for compact manifolds without boundary, suitably extended to accommodate semilinear boundary conditions and low regularity metrics. As a consequence of our results for manifolds with boundary, we also obtain improvements to the theory of the constraint equations on asymptotically Euclidean manifolds without boundary.Comment: 27 pages, 1 figure, TeX, v3. Final version to appear in CMP. Exposition has been extensively tightened and the proof of Proposition 3.5 has been simplifie

HST/WFC3 Observations of an Off-Nuclear Superbubble in Arp 220

We present a high spatial resolution optical and infrared study of the circumnuclear region in Arp 220, a late-stage galaxy merger. Narrowband imaging using HST/WFC3 has resolved the previously observed peak in H$\alpha$+[NII] emission into a bubble-shaped feature. This feature measures 1.6" in diameter, or 600 pc, and is only 1" northwest of the western nucleus. The bubble is aligned with the western nucleus and the large-scale outflow axis seen in X-rays. We explore several possibilities for the bubble origin, including a jet or outflow from a hidden active galactic nucleus (AGN), outflows from high levels of star formation within the few hundred pc nuclear gas disk, or an ultraluminous X-ray source. An obscured AGN or high levels of star formation within the inner $\sim$100 pc of the nuclei are favored based on the alignment of the bubble and energetics arguments.Comment: Accepted for publication in ApJ. 12 pages, 10 figure

Antarctic macrobenthic communities: a compilation of circumpolar information

Comprehensive information on Antarctic macrobenthic community structure has been publicly available since the 1960s. It stems from trawl, dredge, grab, and corer samples as well as from direct and camera observations (Table 1–2). The quality of this information varies considerably; it consists of pure descriptions, figures for presence (absence) and abundance of some key taxa or proxies for such parameters, e.g. sea-floor cover. Some data sets even cover a defined and complete proportion of the macrobenthos with further analyses on diversity and zoogeography. As a consequence the acquisition of data from approximately 90 different campaigns assembled here was not standardised. Nevertheless, it was possible to classify this broad variety of known macrobenthic assemblages to the best of expert knowledge (Gutt 2007; Fig. 1). This overview does not replace statistically sound community and diversity analyses. However, it shows from where which kind of information is available and it acts as an example of the feasibility and power of such data collections. The data set provides unique georeferenced biological basic information for the planning of future coordinated research activities, e.g. under the umbrella of the biology program “Antarctic Thresholds - Ecosystem Resilience and Adaptation” (AnT-ERA) of the Scientific Committee on Antarctic Research (SCAR) and especially for actual conservation issues, e.g. the planning of Marine Protected Areas (MPAs) by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR)

A Bi-objective Optimization Study of an Acid-Base Flow Battery for High Efficiency and Improved Power Density

Electrical energy storage is critical for a broader penetration of renewable energies with intermittent nature, such as solar and wind energy. The Acid/Base Flow Battery (AB-FB) is a unique, sustainable, and environmental-friendly storage technology with high electrolyte solution energy density. The method relies on reversible electrodialytic technologies using bipolar membranes to transform electrical energy into chemical energy related to pH gradients and vice versa. The charge phase is accomplished by using bipolar membrane electrodialysis, whereas the discharge phase is performed via bipolar membrane reverse electrodialysis. In a previous work, we developed an advanced multi-scale process model (Culcasi et al., 2021b), revealing the importance of operating conditions and design features for the AB-FB battery performance. For the first time, the current work attempts to optimize the AB-FB. The net Round Trip Efficiency and average net discharge power density were maximized in a two-objective optimization. The ε-constraint method was used to construct curves of Pareto optimal solutions under various scenarios, thereby systematically assessing the effect of decision variables consisting of operating and design parameters. The gPROMS Model Builder® software package's optimization tool was used. This optimization study demonstrated that in a closed-loop configuration, optimized operating conditions and design features can be chosen to maximize net Round Trip Efficiency up to 64% and average net discharge power density up to 19.5 W m-2 using current commercial membranes