Bounds on the Complexity of Halfspace Intersections when the Bounded Faces have Small Dimension

We study the combinatorial complexity of D-dimensional polyhedra defined as the intersection of n halfspaces, with the property that the highest dimension of any bounded face is much smaller than D. We show that, if d is the maximum dimension of a bounded face, then the number of vertices of the polyhedron is O(n^d) and the total number of bounded faces of the polyhedron is O(n^d^2). For inputs in general position the number of bounded faces is O(n^d). For any fixed d, we show how to compute the set of all vertices, how to determine the maximum dimension of a bounded face of the polyhedron, and how to compute the set of bounded faces in polynomial time, by solving a polynomial number of linear programs

Getting into hot water:sick guppies frequent warmer thermal conditions

Ectotherms depend on the environmental temperature for thermoregulation and exploit thermal regimes that optimise physiological functioning. They may also frequent warmer conditions to up-regulate their immune response against parasite infection and/or impede parasite development. This adaptive response, known as ‘behavioural fever’, has been documented in various taxa including insects, reptiles and fish, but only in response to endoparasite infections. Here, a choice chamber experiment was used to investigate the thermal preferences of a tropical freshwater fish, the Trinidadian guppy (Poecilia reticulata), when infected with a common helminth ectoparasite Gyrodactylus turnbulli, in female-only and mixed-sex shoals. The temperature tolerance of G. turnbulli was also investigated by monitoring parasite population trajectories on guppies maintained at a continuous 18, 24 or 32 °C. Regardless of shoal composition, infected fish frequented the 32 °C choice chamber more often than when uninfected, significantly increasing their mean temperature preference. Parasites maintained continuously at 32 °C decreased to extinction within 3 days, whereas mean parasite abundance increased on hosts incubated at 18 and 24 °C. We show for the first time that gyrodactylid-infected fish have a preference for warmer waters and speculate that sick fish exploit the upper thermal tolerances of their parasites to self medicate

The AFLOW Fleet for Materials Discovery

The traditional paradigm for materials discovery has been recently expanded to incorporate substantial data driven research. With the intent to accelerate the development and the deployment of new technologies, the AFLOW Fleet for computational materials design automates high-throughput first principles calculations, and provides tools for data verification and dissemination for a broad community of users. AFLOW incorporates different computational modules to robustly determine thermodynamic stability, electronic band structures, vibrational dispersions, thermo-mechanical properties and more. The AFLOW data repository is publicly accessible online at aflow.org, with more than 1.7 million materials entries and a panoply of queryable computed properties. Tools to programmatically search and process the data, as well as to perform online machine learning predictions, are also available.Comment: 14 pages, 8 figure

A bovine lymphosarcoma cell line infected with theileria annulata exhibits an irreversible reconfiguration of host cell gene expression

Theileria annulata, an intracellular parasite of bovine lymphoid cells, induces substantial phenotypic alterations to its host cell including continuous proliferation, cytoskeletal changes and resistance to apoptosis. While parasite induced modulation of host cell signal transduction pathways and NFκB activation are established, there remains considerable speculation on the complexities of the parasite directed control mechanisms that govern these radical changes to the host cell. Our objectives in this study were to provide a comprehensive analysis of the global changes to host cell gene expression with emphasis on those that result from direct intervention by the parasite. By using comparative microarray analysis of an uninfected bovine cell line and its Theileria infected counterpart, in conjunction with use of the specific parasitacidal agent, buparvaquone, we have identified a large number of host cell gene expression changes that result from parasite infection. Our results indicate that the viable parasite can irreversibly modify the transformed phenotype of a bovine cell line. Fifty percent of genes with altered expression failed to show a reversible response to parasite death, a possible contributing factor to initiation of host cell apoptosis. The genes that did show an early predicted response to loss of parasite viability highlighted a sub-group of genes that are likely to be under direct control by parasite infection. Network and pathway analysis demonstrated that this sub-group is significantly enriched for genes involved in regulation of chromatin modification and gene expression. The results provide evidence that the Theileria parasite has the regulatory capacity to generate widespread change to host cell gene expression in a complex and largely irreversible manner

Experienced stressors and coping strategies among Iranian nursing students

<p>Abstract</p> <p>Background</p> <p>College students are prone to stress due to the transitional nature of college life. High levels of stress are believed to affect students' health and academic functions. If the stress is not dealt with effectively, feelings of loneliness, nervousness, sleeplessness and worrying may result. Effective coping strategies facilitate the return to a balanced state, reducing the negative effects of stress.</p> <p>Methods</p> <p>This descriptive cross-sectional study was performed to determine sources of stress and coping strategies in nursing students studying at the Iran Faculty of Nursing & Midwifery. All undergraduate nursing students enrolled in years 1-4 during academic year 2004-2005 were included in this study, with a total of 366 questionnaires fully completed by the students. The Student Stress Survey and the Adolescent Coping Orientation for Problem Experiences Inventory (ACOPE) were used for data collection.</p> <p>Results</p> <p>Most students reported "finding new friends" (76.2%), "working with people they did not know" (63.4%) as interpersonal sources of stress, "new responsibilities" (72.1%), "started college" (65.8%) as intrapersonal sources of stress more than others. The most frequent academic source of stress was "increased class workload" (66.9%) and the most frequent environmental sources of stress were being "placed in unfamiliar situations" (64.2%) and "waiting in long lines" (60.4%). Interpersonal and environmental sources of stress were reported more frequently than intrapersonal and academic sources. Mean interpersonal (P=0.04) and environmental (P=0.04) sources of stress were significantly greater in first year than in fourth year students. Among coping strategies in 12 areas, the family problem solving strategies, "trying to reason with parents and compromise" (73%) and "going along with family rules" (68%) were used "often or always" by most students. To cope with engaging in demanding activity, students often or always used "trying to figure out how to deal with problems" (66.4%) and "trying to improve themselves" (64.5%). The self-reliance strategy, "trying to make their own decisions" (62%); the social support strategies, "apologizing to people" (59.6%), "trying to help other people solve their problems" (56.3%), and "trying to keep up friendships or make new friends" (54.4%); the spiritual strategy, "praying" (65.8%); the seeking diversions strategy, "listening to music" (57.7%), the relaxing strategy "day dreaming" (52.5%), and the effort to "be close with someone cares about you" (50.5%) were each used "often or always" by a majority of students. Most students reported that the avoiding strategies "smoking" (93.7%) and "drinking beer or wine" (92.9%), the ventilating strategies "saying mean things to people" and "swearing" (85.8%), the professional support strategies "getting professional counseling" (74.6%) and "talking to a teacher or counselor" (67.2%) and the humorous strategy "joking and keeping a sense of humor" (51.9%) were used "seldom or never".</p> <p>Conclusion</p> <p>First year nursing students are exposed to a variety of stressors. Establishing a student support system during the first year and improving it throughout nursing school is necessary to equip nursing students with effective coping skills. Efforts should include counseling helpers and their teachers, strategies that can be called upon in these students' future nursing careers.</p

Computational Micromodel for Epigenetic Mechanisms

Characterization of the epigenetic profile of humans since the initial breakthrough on the human genome project has strongly established the key role of histone modifications and DNA methylation. These dynamic elements interact to determine the normal level of expression or methylation status of the constituent genes in the genome. Recently, considerable evidence has been put forward to demonstrate that environmental stress implicitly alters epigenetic patterns causing imbalance that can lead to cancer initiation. This chain of consequences has motivated attempts to computationally model the influence of histone modification and DNA methylation in gene expression and investigate their intrinsic interdependency. In this paper, we explore the relation between DNA methylation and transcription and characterize in detail the histone modifications for specific DNA methylation levels using a stochastic approach

A novel approach to the clustering of microarray data via nonparametric density estimation

<p>Abstract</p> <p>Background</p> <p>Cluster analysis is a crucial tool in several biological and medical studies dealing with microarray data. Such studies pose challenging statistical problems due to dimensionality issues, since the number of variables can be much higher than the number of observations.</p> <p>Results</p> <p>Here, we present a general framework to deal with the clustering of microarray data, based on a three-step procedure: (i) gene filtering; (ii) dimensionality reduction; (iii) clustering of observations in the reduced space. Via a nonparametric model-based clustering approach we obtain promising results both in simulated and real data.</p> <p>Conclusions</p> <p>The proposed algorithm is a simple and effective tool for the clustering of microarray data, in an unsupervised setting.</p