Collection and analysis of a global marine phytoplankton primary-production dataset

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Lessons Learned from Development of a Software Tool to Support Academic Advising

We detail some lessons learned while designing and testing a decision-theoretic advising support tool for undergraduates at a large state university. Between 2009 and 2011 we conducted two surveys of over 500 students in multiple majors and colleges. These surveys asked students detailed questions about their preferences concerning course selection, advising, and career paths. We present data from this study which may be helpful for faculty and staff who advise undergraduate students. We find that advising support software tools can augment the student-advisor relationship, particularly in terms of course planning, but cannot and should not replace in-person advising.Comment: 5 Figures, revised version including more figures and cross-referencin

Chloroquine supplementation increases the cytotoxic effect of curcumin against Her2/neu overexpressing breast cancer cells in vitro and in vivo in nude mice while counteracts it in immune competent mice

Autophagy is usually a pro-survival mechanism in cancer cells, especially in the course of chemotherapy, thus autophagy inhibition may enhance the chemotherapy-mediated anti-cancer effect. However, since autophagy is strongly involved in the immunogenicity of cell death by promoting ATP release, its inhibition may reduce the immune response against tumors, negatively influencing the overall outcome of chemotherapy. In this study, we evaluated the in vitro and in vivo anti-cancer effect of curcumin (CUR) against Her2/neu overexpressing breast cancer cells (TUBO) in the presence or in the absence of the autophagy inhibitor chloroquine (CQ). We found that TUBO cell death induced by CUR was increased in vitro by CQ and slightly in vivo in nude mice. Conversely, CQ counteracted the Cur cytotoxic effect in immune competent mice, as demonstrated by the lack of in vivo tumor regression and the reduction of overall mice survival as compared with CUR-treated mice. Immunohistochemistry analysis revealed the presence of a remarkable FoxP3 T cell infiltrate within the tumors in CUR/CQ treated mice and a reduction of T cytotoxic cells, as compared with single CUR treatment. These findings suggest that autophagy is important to elicit anti-tumor immune response and that autophagy inhibition by CQ reduces such response also by recruiting T regulatory (Treg) cells in the tumor microenvironment that may be pro-tumorigenic and might counteract CUR-mediated anti-cancer effects

Web-Beagle: a web server for the alignment of RNA secondary structures

Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods

A Robust Filter for the BeppoSAX Gamma Ray Burst Monitor Triggers

The BeppoSAX Gamma Ray Burst Monitor (GRBM) is triggered any time a statistically significant counting excess is simultaneously revealed by at least two of its four independent detectors. Several spurious effects, including highly ionizing particles crossing two detectors, are recorded as onboard triggers. In fact, a large number of false triggers is detected, in the order of 10/day. A software code, based on an heuristic algorithm, was written to discriminate between real and false triggers. We present the results of the analysis on an homogeneous sample of GRBM triggers, thus providing an estimate of the efficiency of the GRB detection system consisting of the GRBM and the software.Comment: Proc. 5th Huntsville GRB Symposiu