The quantum communication complexity of sampling

Sampling is an important primitive in probabilistic and quantum algorithms. In the spirit of communication complexity, given a function f : X × Y → {0, 1} and a probability distribution D over X × Y , we define the sampling complexity of (f,D) as the minimum number of bits that Alice and Bob must communicate for Alice to pick x ∈ X and Bob to pick y ∈ Y as well as a value z such that the resulting distribution of (x, y, z) is close to the distribution (D, f(D)). In this paper we initiate the study of sampling complexity, in both the classical and quantum models. We give several variants of a definition. We completely characterize some of these variants and give upper and lower bounds on others. In particular, this allows us to establish an exponential gap between quantum and classical sampling complexity for the set-disjointness function

The role of horizontal gene transfer in the evolution of the oomycetes

This is the final version of the article. Available from Public Library of Science via the DOI in this record.Horizontal gene transfer (HGT) or lateral gene transfer (LGT) involves the transmission of genetic material between distinct evolutionary lineages and can be an important source of biological innovation. For instance, the acquisition of foreign genes can allow recipient organisms to adapt to new lifestyles or to exploit a novel ecological niche, such as a host environment. HGT has long been recognised as an important factor contributing to the evolution of prokaryotic lineages especially in connection to the evolution of pathogencity [1,2]. However, it is becoming increasingly apparent that HGT has also played a role in the evolution of pathogenic traits in eukaryotes [3,4]. Here, we consider how HGT has contributed to genome evolution in the oomycetes

Expression of interleukin 2 receptors on activated human B cells.

Using anti-Tac, a monoclonal anti-interleukin 2 (IL-2) receptor antibody, we have explored the possibility that certain activated B cells display receptors for IL-2. Resting normal B cells and unselected B cell lines established from normal individuals were Tac antigen negative. In contrast, the cell surface Tac antigen expression was demonstrable on 6 of 10 B cell lines from patients with Burkitt's lymphoma, 5 of 6 B cell lines derived from patients with HTLV-I-associated adult T cell leukemia (including all four that had integrated HTLV-I into their genome), and on certain normal B cells activated with pokeweed mitogen. Furthermore, cloned Epstein-Barr virus-transformed B cell lines derived from Tac-positive normal B cells continued to express the Tac antigen in long-term cultures and manifested high affinity IL-2 receptors identified in binding studies with purified radiolabeled IL-2. The line 5B4 developed in the present study could be induced with purified JURKAT-derived or recombinant IL-2 to express a larger number of IL-2 receptors. Furthermore, the addition of IL-2 to the 5B4 B cell line augmented IgM synthesis, which could be blocked by the addition of anti-Tac. The size of the IL-2 receptors expressed on the cloned normal B cell lines was similar (53,000-57,000 daltons) to that of receptors on phytohemagglutinin-stimulated T cell lymphoblasts. Thus, certain malignant and activated normal B cells display the Tac antigen and manifest high affinity receptors for IL-2. These data suggest that IL-2 may play a role in the differentiation of activated B cells into immunoglobulin-synthesizing and -secreting cells

The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer

This is the final version. Available on open access from Oxford University Press via the DOI in this recordSaprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the "secretome" and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here, we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle.University of Rhode Island College of the Environment and Life SciencesU.S. Department of AgricultureNational Institutes of Health (NIH)National Science FoundationDivision of Biology and Medicine, Brown Universit

Complex patterns of gene fission in the eukaryotic folate biosynthesis pathway

This is the final version. Available on open access from Oxford University Press via the DOI in this recordShared derived genomic characters can be useful for polarizing phylogenetic relationships, for example, gene fusions have been used to identify deep-branching relationships in the eukaryotes. Here, we report the evolutionary analysis of a three-gene fusion of folB, folK, and folP, which encode enzymes that catalyze consecutive steps in de novo folate biosynthesis. The folK-folP fusion was found across the eukaryotes and a sparse collection of prokaryotes. This suggests an ancient derivation with a number of gene losses in the eukaryotes potentially as a consequence of adaptation to heterotrophic lifestyles. In contrast, the folB-folK-folP gene is specific to a mosaic collection of Amorphea taxa (a group encompassing: Amoebozoa, Apusomonadida, Breviatea, and Opisthokonta).Next, we investigated the stability of this character.We identified numerous gene losses and a total of nine gene fission events, either by break up of an open reading frame (four events identified) or loss of a component domain (five events identified). This indicates that this three gene fusion is highly labile. These data are consistent with a growing body of data indicating gene fission events occur at high relative rates. Accounting for these sources of homoplasy, our data suggest that the folB-folK-folP gene fusion was present in the last common an castor of Amoebozoa and Opisthokonta but absent inthe Metazoa including the human genome. Comparative genomic data of these genes provides an important resource for designing therapeutic strategies targeting the de novo folate biosynthesis pathway of a variety of eukaryotic pathogens such as Acanthamoeba castellanii.Society of General MicrobiologyTula Foundation (The Centre for Comparative Genomics and Evolutionary Bioinformatics at Dalhousie University)Gordon and Betty Moore FoundationLeverhulme TrustRoyal SocietyNatural Environment Research Council (NERC)Biotechnology and Biological Sciences Research Council (BBSRC

Emerging technologies in physics education

Three emerging technologies in physics education are evaluated from the interdisciplinary perspective of cognitive science and physics education research. The technologies - Physlet Physics, the Andes Intelligent Tutoring System (ITS), and Microcomputer-Based Laboratory (MBL) Tools - are assessed particularly in terms of their potential at promoting conceptual change, developing expert-like problem-solving skills, and achieving the goals of the traditional physics laboratory. Pedagogical methods to maximize the potential of each educational technology are suggested.Comment: Accepted for publication in the Journal of Science Education and Technology; 20 page

BRIDGING MECHANICAL STIMULATION OF CELLULAR AND MOLECULAR STRUCTURE THROUGH LATTICE BASED COMPUTATIONAL SIMULATIONS

ABSTRACT Understanding the connection between mechanics and cell structure requires a critical exploration of molecular structure. One of these molecular bridges is known to be the cytoskeleton, which is involved with intracellular organization and mechanotransduction. In order to examine the structure in cells, we have developed a computational simulation that is able to probe the self-assembly of actin filaments through a lattice based Monte Carlo method. We have modeled the polymerization of these filaments based upon the interactions of globular actin through a probabilistic scheme with both inert and active proteins. The results show similar response to classic ordinary differential equations at low molecular concentrations, but a bi-phasic divergence at realistic concentrations for living mammalian cells. Further, these inert monomers have a limiting effect based upon their relative density ratios, which alter the polymerization process. Finally, by introducing localized mobility parameters, we are able to set up molecular gradients that are found in non-homogeneous protein distributions in vitro. This method and results have potential applications in cell and molecular biology as well as self assembly in inorganic systems

Computation of reactive thermosolutal micropolar nanofluid Sakiadis convection flow with gold/silver metallic nanoparticles

In the present study, a mathematical model is developed by combining the Tiwari-Das nanofluidformulation with the Eringen micro-morphic model to simulate the thermo-solutal natural convection chemicallyreacting micropolar nanofluid flow from a permeable stretching surface with non-uniform heat source/sink effects.The transformed ordinary differential equation boundary value problem features linear momentum, angularmomentum, energy and species conservation boundary layer equations with appropriate boundary conditions.This ninth order nonlinear system is solved with Runge-Kutta 45 Fehlberg method (Maple dsolve routine).Several nanoparticles i.e., gold, and silver with aqueous base fluid are studied. The influence of the effect of theemerging parameters on the velocity, angular velocity, temperature, nanoparticle concentration, skin friction,couple stress, Nusselt number and Sherwood number distributions are visualized and tabulated. It is observed thatIncreasing volume fraction decreases velocity whereas it elevates microrotation, temperature and nanoparticleconcentration. Nanoparticle concentrations are elevated for stronger destructive chemical reaction effect whereasthey are suppressed with constructive chemical reaction. With greater micropolar boundary condition parameter,the velocity is elevated, microrotation but reduces temperature and thermal boundary layer thickness. Increasingnanoparticle volume fraction enhances both skin friction and couple stress but marginally reduces the Nusseltnumber. Finally, Au-water micropolar nanofluids achieve the highest skin friction and couple stress magnitudes,then Ag-water and finally Cu-water. Validation of solutions with earlier non-reactive studies in the absence ofnanoparticle mass transfer are included