Preprocessing of microarray data and analysis and comparison techniques for the resulting graph structures

During our collaborations with scientists interested in high-throughput analysis of biological data, we have made much progress and facilitated some interesting findings using our clique-finding tools. However, we have also uncovered ways in which we can make our tools more efficient but have yet to write the programs to perform these tasks. Part of the problem is time constraints: in order to be useful to us, an application must be quite flexible and run efficiently. Programming such a tool is no small task, so we have resorted to scripting solutions that are geared to the specific task at hand. The first aim of this work is to produce a tool that is usable by both us and our collaborators to meet our common data processing needs. Also during our collaborations, we have been tasked with finding new ways to help find potentially interesting data among a large amount of information that would be prohibitive to analyze by hand. One of our current tools is one that can take a graph and return all the maximal cliques, which, using real data, can be done in a reasonable amount of time. However, the list of maximal cliques itself is usually long and impractical to analyze by hand. Thus, we have needed to come up with new ways to sleuth out those genes and cliques that may be of most interest from a list of millions of cliques. The second aim of this work is to describe new methods that we have been using to achieve this

Spontaneous fission modes and lifetimes of super-heavy elements in the nuclear density functional theory

Lifetimes of super-heavy (SH) nuclei are primarily governed by alpha decay and spontaneous fission (SF). Here we study the competing decay modes of even-even SH isotopes with 108 <= Z <= 126 and 148 <= N <= 188 using the state-of-the-art self-consistent nuclear density functional theory framework capable of describing the competition between nuclear attraction and electrostatic repulsion. The collective mass tensor of the fissioning superfluid nucleus is computed by means of the cranking approximation to the adiabatic time-dependent Hartree-Fock-Bogoliubov approach. Along the path to fission, our calculations allow for the simultaneous breaking of axial and space inversion symmetries; this may result in lowering SF lifetimes by more than seven orders of magnitude in some cases. We predict two competing SF modes: reflection-symmetric and reflection-asymmetric.The shortest-lived SH isotopes decay by SF; they are expected to lie in a narrow corridor formed by $^{280}$Hs, $^{284}$Fl, and $^{284}_{118}$Uuo that separates the regions of SH nuclei synthesized in "cold fusion" and "hot fusion" reactions. The region of long-lived SH nuclei is expected to be centered on $^{294}$Ds with a total half-life of ?1.5 days.Comment: 6 pages, 4 figure

Molecular systematics and phylogenetics of the spider genus Mastigusa Menge, 1854 (Araneae, Cybaeidae)

The palearctic spider genus Mastigusa Menge, 1854 is characterized by a remarkable morphology and wide ecological variability, with free-living, cave dwelling and myrmecophile populations known. This genus has a long and tangled taxonomic history and was placed in different families in the past, all belonging to the “marronoid clade”, an informal grouping of families characterized by the lack of strong synapomorphies. Three species are currently recognized, but their identity and circumscription has been long debated. A molecular approach was never applied for trying to solve these uncertainties, and doubts still remain both about its phylogenetic placement and about the taxonomic status of the described species. For the first time the genus Mastigusa is included in a molecular phylogenetic analysis and strong support is found for its placement within the family Cybaeidae, in sister relationship with the genus Cryphoeca Thorell, 1870. An analysis of Mastigusa populations spanning across the distribution range of the genus identifies a high and previously overlooked genetic diversity, with six distinct genetic lineages showing a strong geographic pattern. Divergence times between Mastigusa and its sister genus and between the distinct Mastigusa lineages are estimated, and the groundwork is laid for a taxonomic revision of the species belonging to the genus

TRAIL induces nuclear translocation and chromatin localization of TRAIL death receptors

Binding of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) to the plasma membrane TRAIL-R1/-R2 selectively kills tumor cells. This discovery led to evaluation of TRAIL-R1/-R2 as targets for anti-cancer therapy, yet the corresponding clinical trials were disappointing. Meanwhile, it emerged that many cancer cells are TRAIL-resistant and that TRAIL-R1/R2-triggering may lead to tumor-promoting effects. Intriguingly, recent studies uncovered specific functions of long ignored intracellular TRAIL-R1/-R2, with tumor-promoting functions of nuclear (n)TRAIL-R2 as the regulator of let-7-maturation. As nuclear trafficking of TRAIL-Rs is not well understood, we addressed this issue in our present study. Cell surface biotinylation and tracking of biotinylated proteins in intracellular compartments revealed that nTRAIL-Rs originate from the plasma membrane. Nuclear TRAIL-Rs-trafficking is a fast process, requiring clathrin-dependent endocytosis and it is TRAIL-dependent. Immunoprecipitation and immunofluorescence approaches revealed an interaction of nTRAIL-R2 with the nucleo-cytoplasmic shuttle protein Exportin-1/CRM-1. Mutation of a putative nuclear export sequence (NES) in TRAIL-R2 or the inhibition of CRM-1 by Leptomycin-B resulted in the nuclear accumulation of TRAIL-R2. In addition, TRAIL-R1 and TRAIL-R2 constitutively localize to chromatin, which is strongly enhanced by TRAIL-treatment. Our data highlight the novel role for surface-activated TRAIL-Rs by direct trafficking and signaling into the nucleus, a previously unknown signaling principle for cell surface receptors that belong to the TNF-superfamily

New association between red wood ant species (Formica rufa group) and the myrmecophilic spiders Mastigusa arietina and Thyreosthenius biovatus

Ants belonging to the Formica rufa species group, counting 10 representatives in Europe, are often referred to as red wood ants (RWAs). These dominant, mound building species are known to host in their nests an extremely diverse fauna of associated myrmecophilic arthropods, among which are the two W-Palaearctic spider species Mastigusa arietina (Thorell 1871) and Thyreosthenius biovatus (O. Pickard-Cambridge 1875). The actual host range of these spiders within the Formica rufa group is little known, due to the taxonomic uncertainties that have characterized RWAs in the past. We conducted a large-scale survey for assessing the occurrence of both spider species in association with different RWAs, with a focus on an accurate identification of the ant species. We recorded co-occurrence data for 5 European representatives of the Formica rufa group, and we reported for the first time on the co-occurrence of M. arietina with Formica aquilonia Yarrow 1955, Formica lugubris Zetterstedt 1838 and Formica paralugubris Seifert 1996, and of T. biovatus with F. aquilonia. We found no association between the rate of presence/absence of the two spiders and host ant species or sampling localities, which suggests a non-selective exploitation of RWA hosts by the two myrmecophilic spiders

Developing and Assessing Respect for Human Dignity in College Students

Academic institutions are now expected to engage in developing and assessing learning outcomes; however, responsibility outcomes, such as respect for human dignity (RFHD), can be particularly challenging. As part of our Biopsychology course and Sensation and Perception course over the past decade, we applied the scientist-educator model of learning and drew from the literature on prejudice reduction to develop our RFHD interventions, which involved face-to-face interactions with others who had sensory deficits or brain/spinal cord injuries. We iteratively created two pre-post measures to assess development of different aspects of RFHD: a Behavioral Tendencies Questionnaire and a 4-Factor RFHD Model Questionnaire. Recently, we modified the intervention and the assessments for adoption in our Class, Race, and Ethnicity in Society course. This paper reports findings from these three courses and a control course in engineering (n = 153). Findings support our two sets of hypotheses, regarding 1) the efficacy of the assessments to capture different likelihoods for interacting with others targeted by the interventions and changes over time in these factors, and 2) positive effects of the face-to-face intervention activities. This study demonstrates RFHD can be developed and assessed in a college course and provides new assessments for RFHD that are easily modified for a variety of types of others (e.g., individuals who are homeless versus blind or of a particular race). Click here to read the corresponding ISSOTL blog post

Powers of the Vandermonde determinant, Schur Functions, and recursive formulas

Since every even power of the Vandermonde determinant is a symmetric polynomial, we want to understand its decomposition in terms of the basis of Schur functions. We investigate several combinatorial properties of the coefficients in the decomposition. In particular, we give recursive formulas for the coefficient of the Schur function s_{\m} in the decomposition of an even power of the Vandermonde determinant in $n + 1$ variables in terms of the coefficient of the Schur function s_{\l} in the decomposition of the same even power of the Vandermonde determinant in $n$ variables if the Young diagram of \m is obtained from the Young diagram of \l by adding a tetris type shape to the top or to the left. An extended abstract containing the statement of the results presented here appeared in the Proceedings of FPSAC11Comment: 23 pages; extended abstract appeared in the Proceedings of FPSAC1