Identifying hybridizing taxa within the Daphnia longispina species complex: a comparison of genetic methods and phenotypic approaches

Daphnia galeata Sars, D. longispina O. F. Muller and D. cucullata Sars (Crustacea: Cladocera) are closely related species which often produce interspecific hybrids in natural populations. Several marker systems are available for taxon determination in this hybridizing complex, but their performance and reliability has not been systematically assessed. We compared results from identifications by three molecular methods. More than 1,200 individuals from 10 localities in the Czech Republic were identified as parental species or hybrids by allozyme electrophoresis and the analysis of the restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP); over 440 of them were additionally analyzed and identified by 12 microsatellite loci. Identification by microsatellite markers corresponded well with allozyme analyses. However, consistent discrepancies between ITS-RFLP and other markers were observed in two out of 10 studied localities. Although some marker discrepancies may have been caused by occasional recent introgression, consistent deviations between ITS-RFLP and other markers suggest a long-term maintenance of introgressed alleles. These results warn against its use as a sole identification method in field studies. Additionally, we quantitatively evaluated the discriminatory power of geometric morphometric (elliptic Fourier) analysis of body shapes based on photos of over 1,300 individuals pre-classified by allozyme markers. Furthermore, a randomly selected subset of 240 individuals was independently determined from photos by several experts. Despite a tendency for morphological divergence among parental Daphnia species, some taxa (especially D. galeata, D. longispina, and their hybrids) substantially overlapped in their body shapes. This was reflected in different determination success for particular species and hybrids in discriminant analysis based on shape data as well as from photograph

On-Line Monitoring for Temporal Logic Robustness

In this paper, we provide a Dynamic Programming algorithm for on-line monitoring of the state robustness of Metric Temporal Logic specifications with past time operators. We compute the robustness of MTL with unbounded past and bounded future temporal operators MTL over sampled traces of Cyber-Physical Systems. We implemented our tool in Matlab as a Simulink block that can be used in any Simulink model. We experimentally demonstrate that the overhead of the MTL robustness monitoring is acceptable for certain classes of practical specifications

Design by taking perspectives: How engineers explore problems

BackgroundProblem exploration includes identifying, framing, and defining design problems and bounding problem spaces. Intentional and unintentional changes in problem understanding naturally occur as designers explore design problems to create solutions. Through problem exploration, new perspectives on the problem can emerge along with new and diverse ideas for solutions. By considering multiple problem perspectives varying in scope and focus, designers position themselves to increase their understandings of the “real” problem and engage in more diverse idea generation processes leading to an increasing variety of potential solutions.Purpose/HypothesisThe purpose of this study was to investigate systematic patterns in problem exploration in the early design phases of mechanical engineers.Design/MethodThirty‐five senior undergraduate students and experienced designers with mechanical engineering backgrounds worked individually following a think‐aloud protocol. They explored problems and generated solutions for two of four randomly assigned design problems. After generating solutions, participants framed and rewrote problem statements to reflect their perspectives on the design problem their solutions addressed. Thematic analysis and a priori codes guided the identification of problem exploration patterns within and across problems.ResultsThe set of patterns in engineers’ problem exploration that emerged from the analysis documents alternative strategies in exploring problems to arrive at solutions. The results provide evidence that engineering designers, working individually, apply both problem‐specific and more general strategies to explore design problems.ConclusionsOur study identified common patterns in the explorations of presented problems by individual engineering designers. The observed patterns, described as Problem Exploration Perspectives, capture alternative approaches to discovering problems and taking multiple problem perspectives during design. Learning about Problem Exploration Perspectives may be helpful in creating alternative perspectives on a design problem, potentially leading to more varied and innovative solutions. This paper concludes with an extended example illustrating the process of applying Problem Exploration Perspectives to move between problem perspectives to generate varied design outcomes.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149675/1/jee20263_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149675/2/jee20263.pd

On acceptance conditions for membrane systems: characterisations of L and NL

In this paper we investigate the affect of various acceptance conditions on recogniser membrane systems without dissolution. We demonstrate that two particular acceptance conditions (one easier to program, the other easier to prove correctness) both characterise the same complexity class, NL. We also find that by restricting the acceptance conditions we obtain a characterisation of L. We obtain these results by investigating the connectivity properties of dependency graphs that model membrane system computations

Equivariant cohomology over Lie groupoids and Lie-Rinehart algebras

Using the language and terminology of relative homological algebra, in particular that of derived functors, we introduce equivariant cohomology over a general Lie-Rinehart algebra and equivariant de Rham cohomology over a locally trivial Lie groupoid in terms of suitably defined monads (also known as triples) and the associated standard constructions. This extends a characterization of equivariant de Rham cohomology in terms of derived functors developed earlier for the special case where the Lie groupoid is an ordinary Lie group, viewed as a Lie groupoid with a single object; in that theory over a Lie group, the ordinary Bott-Dupont-Shulman-Stasheff complex arises as an a posteriori object. We prove that, given a locally trivial Lie groupoid G and a smooth G-manifold f over the space B of objects of G, the resulting G-equivariant de Rham theory of f boils down to the ordinary equivariant de Rham theory of a vertex manifold relative to the corresponding vertex group, for any vertex in the space B of objects of G; this implies that the equivariant de Rham cohomology introduced here coincides with the stack de Rham cohomology of the associated transformation groupoid whence this stack de Rham cohomology can be characterized as a relative derived functor. We introduce a notion of cone on a Lie-Rinehart algebra and in particular that of cone on a Lie algebroid. This cone is an indispensable tool for the description of the requisite monads.Comment: 47 page

The Prevalence of TNFα-Induced Necrosis over Apoptosis Is Determined by TAK1-RIP1 Interplay

Death receptor-induced programmed necrosis is regarded as a secondary death mechanism dominating only in cells that cannot properly induce caspase-dependent apoptosis. Here, we show that in cells lacking TGFβ-activated Kinase-1 (TAK1) expression, catalytically active Receptor Interacting Protein 1 (RIP1)-dependent programmed necrosis overrides apoptotic processes following Tumor Necrosis Factor-α (TNFα) stimulation and results in rapid cell death. Importantly, the activation of the caspase cascade and caspase-8-mediated RIP1 cleavage in TNFα-stimulated TAK1 deficient cells is not sufficient to prevent RIP1-dependent necrosome formation and subsequent programmed necrosis. Our results demonstrate that TAK1 acts independently of its kinase activity to prevent the premature dissociation of ubiquitinated-RIP1 from TNFα-stimulated TNF-receptor I and also to inhibit the formation of TNFα-induced necrosome complex consisting of RIP1, RIP3, FADD, caspase-8 and cFLIPL. The surprising prevalence of catalytically active RIP1-dependent programmed necrosis over apoptosis despite ongoing caspase activity implicates a complex regulatory mechanism governing the decision between both cell death pathways following death receptor stimulation

Communications in cellular automata

The goal of this paper is to show why the framework of communication complexity seems suitable for the study of cellular automata. Researchers have tackled different algorithmic problems ranging from the complexity of predicting to the decidability of different dynamical properties of cellular automata. But the difference here is that we look for communication protocols arising in the dynamics itself. Our work is guided by the following idea: if we are able to give a protocol describing a cellular automaton, then we can understand its behavior

Poor prognostic clinicopathologic features correlate with VEGF expression but not with PTEN expression in squamous cell carcinoma of the larynx

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to assess the relationship between expression of vascular endothelial growth factor (VEGF) and phosphatase and tensin homolog deleted in chromosome ten (PTEN), angiogenesis and clinicopathological parameters of squamous cell carcinoma of the larynx.</p> <p>Methods</p> <p>We examined immunohistochemical expression of VEGF and PTEN and CD34 for microvessel density (MVD) in sections of formalin-fixed, paraffin embedded tissue blocks of 140 patients with squamous cell carcinoma of the larynx. The intensity of VEGF and PTEN staining and the proportion of cells staining were scored.</p> <p>Results</p> <p>The tumor grade was not significantly related to PTEN expression, but it was to VEGF expression (p = 0.400; p = 0.015, respectively). While there was no significant relationship between PTEN expression and tumor size and cartilage invasion (p = 0.311, p = 0.128), there was a significant relationship between the severity of VEGF expression and tumor size (p = 0.006) and lymph node metastasis (p = 0.048) but not cartilage invasion (p = 0.129). MVD was significantly higher in high-grade tumors (p = 0.003) but had no significant relationship between MVD, lymph node metastasis, and cartilage invasion (p = 0.815, p = 0.204). There was also no significant relationship between PTEN and VEGF expression (p = 0.161) and between PTEN and VEGF expression and the MVD (p = 0.120 and p = 0.175, respectively).</p> <p>Conclusions</p> <p>Increased VEGF expression may play an important role in the outcome of squamous cell carcinoma of the larynx. PTEN expression was not related to VEGF expression and clinicopathological features of squamous cell carcinoma of the larynx.</p

Clique-based data mining for related genes in a biomedical database

<p>Abstract</p> <p>Background</p> <p>Progress in the life sciences cannot be made without integrating biomedical knowledge on numerous genes in order to help formulate hypotheses on the genetic mechanisms behind various biological phenomena, including diseases. There is thus a strong need for a way to automatically and comprehensively search from biomedical databases for related genes, such as genes in the same families and genes encoding components of the same pathways. Here we address the extraction of related genes by searching for densely-connected subgraphs, which are modeled as cliques, in a biomedical relational graph.</p> <p>Results</p> <p>We constructed a graph whose nodes were gene or disease pages, and edges were the hyperlink connections between those pages in the Online Mendelian Inheritance in Man (OMIM) database. We obtained over 20,000 sets of related genes (called 'gene modules') by enumerating cliques computationally. The modules included genes in the same family, genes for proteins that form a complex, and genes for components of the same signaling pathway. The results of experiments using 'metabolic syndrome'-related gene modules show that the gene modules can be used to get a coherent holistic picture helpful for interpreting relations among genes.</p> <p>Conclusion</p> <p>We presented a data mining approach extracting related genes by enumerating cliques. The extracted gene sets provide a holistic picture useful for comprehending complex disease mechanisms.</p