The Effect of Social Proof on Tag Selection in Social Bookmarking Applications

The growing popularity of social bookmaking applications like flickr and del.icio.us present new challenges to system designers because the effects of social psychological factors on users' tag choices have not been examined. The social psychological principle of social proof is particularly applicable to social bookmarking because it predicts that the tags applied by users will be more similar to each other if they are provided with a list of suggested tags. This study examines the effect of social proof on tag selection by comparing the degree of similarity between tags provided by a sample group and a collection of suggested tags provided to the treatment group. The results indicate that social proof can have an effect on users' tag selection. The conclusion briefly examines the beneficial effect of social proof on the quality of social bookmarking applications and other collaborative tagging applications

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

Lead isotope ratio measurements as indicators for the source of lead poisoning in Mute swans ('Cygnus olor') wintering in Puck Bay (northern Poland)

Lead (Pb) poisoning is most commonly linked amongst anthropogenically-caused deaths in waterfowl and this is often associated with hunting and fishing activities. However, the exact identification of the source may be difficult with commonly-used techniques. We have studied isotope ratios using Inductively-Coupled Plasma Mass Spectrometry (ICP-MS) to investigate the source of Pb in the blood of Mute swans (n = 49) wintering in northern Poland. We compared the values of isotopic ratios from blood and ammunition pellets available on the Polish market. The mean Pb concentrations found was 0.241 μg/g (w/w) and nearly half of the blood specimens had elevated Pb levels (higher than the cited 0.23 μg/g w/w threshold of poisoning). Only the mean 208/206 Pb isotope ratio was similar in blood and pellet samples. Mean ratios of isotopes 206/204, 206/207 and 208/207 in swans' blood and in pellets differed significantly. Moreover, coefficients of variation were higher in blood samples than in pellets. These discrepancies and significant differences in abundance of (204)Pb and (207)Pb isotopes in both materials indicated that pellets available today on the Polish market were not the source of Pb in the blood of Mute swans wintering in northern Poland

From barren plateaus through fertile valleys: Conic extensions of parameterised quantum circuits

Optimisation via parameterised quantum circuits is the prevalent technique of near-term quantum algorithms. However, the omnipresent phenomenon of barren plateaus - parameter regions with vanishing gradients - sets a persistent hurdle that drastically diminishes its success in practice. In this work, we introduce an approach - based on non-unitary operations - that favours jumps out of a barren plateau into a fertile valley. These operations are constructed from conic extensions of parameterised unitary quantum circuits, relying on mid-circuit measurements and a small ancilla system. We further reduce the problem of finding optimal jump directions to a low-dimensional generalised eigenvalue problem. As a proof of concept we incorporate jumps within state-of-the-art implementations of the Quantum Approximate Optimisation Algorithm (QAOA). We demonstrate the extensions' effectiveness on QAOA through extensive simulations, showcasing robustness against barren plateaus and highly improved sampling probabilities of optimal solutions.Comment: 6+2 pages, 3 figure

SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns

SplitPocket (http://pocket.uchicago.edu/) is a web server to identify functional surfaces of protein from structure coordinates. Using the Alpha Shape Theory, we previously developed an analytical approach to identify protein functional surfaces by the geometric concept of a split pocket, which is a pocket split by a binding ligand. Our geometric approach extracts site-specific spatial information from coordinates of structures. To reduce the search space, probe radii are designed according to the physicochemical textures of molecules. The method uses the weighted Delaunay triangulation and the discrete flow algorithm to obtain geometric measurements and spatial patterns for each predicted pocket. It can also measure the hydrophobicity on a surface patch. Furthermore, we quantify the evolutionary conservation of surface patches by an index derived from the entropy scores in HSSP (homology-derived secondary structure of proteins). We have used the method to examine ∼1.16 million potential pockets and identified the split pockets in >26 000 structures in the Protein Data Bank. This integrated web server of functional surfaces provides a source of spatial patterns to serve as templates for predicting the functional surfaces of unbound structures involved in binding activities. These spatial patterns should also be useful for protein functional inference, structural evolution and drug design

Correcting errors in synthetic DNA through consensus shuffling

Although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1–3 random errors/kb of DNA. Here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic DNA. In this method, errors are revealed as mismatches by re-hybridization of the population. The DNA is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding protein (MutS). PCR assembly of the remaining fragments yields a new population of full-length sequences enriched for the consensus sequence of the input population. We show that two iterations of consensus shuffling improved a population of synthetic green fluorescent protein (GFPuv) clones from ∼60 to >90% fluorescent, and decreased errors 3.5- to 4.3-fold to final values of ∼1 error per 3500 bp. In addition, two iterations of consensus shuffling corrected a population of GFPuv clones where all members were non-functional, to a population where 82% of clones were fluorescent. Consensus shuffling should facilitate the rapid and accurate synthesis of long DNA sequences

Relationship between air pollution and metal levels in cancerous and non-cancerous lung tissues

We aimed to check the relationships between levels of metals (Ca, Cd, Cu, Fe, Hg and Zn) in cancerous and non-cancerous lung tissues and their link to air pollution, expressed as particulate matter (PM) concentrations. The study also examines the influence on metal concentration in the lung tissue of patients' sex and the distance of their homes from the nearest emitter. We found that the general pattern of ascending concentrations in tumor tissue was as follows: Hg < Cd < Cu < Ca < Zn < Fe. In non-affected lung tissue the order of concentrations of Ca and Fe was reversed. With the exception of Cd and Cu, levels of metals were found in higher accumulations in non-cancerous tissue (e.g., Fe 326.423 and Ca 302.730 μg/g d.w) than in tumorous tissue (Fe 150.735 and Ca 15.025 μg/g d.w). Neither the PM10 (PM of a diameter of 10 μm) concentration nor sex revealed any connection with metal concentrations. The shorter the distance from the emitter, the higher the metal concentrations that tended to be observed for almost all metals, but a statistically significant (but weak) relationship was noted only for Cu in tumor tissue (rs: -0.4869)

A quantum algorithm for the solution of the 0-1 Knapsack problem

Here we present two novel contributions for achieving quantum advantage in solving difficult optimisation problems, both in theory and foreseeable practice. (1) We introduce the ''Quantum Tree Generator'', an approach to generate in superposition all feasible solutions of a given instance, yielding together with amplitude amplification the optimal solutions for $0$-$1$-Knapsack problems. The QTG offers exponential memory savings and enables competitive runtimes compared to the state-of-the-art Knapsack solver COMBO for instances involving as few as 600 variables. (2) By introducing a high-level simulation strategy that exploits logging data from COMBO, we can predict the runtime of our method way beyond the range of existing quantum platforms and simulators, for various benchmark instances with up to 1600 variables. Combining both of these innovations, we demonstrate the QTG's potential advantage for large-scale problems, indicating an effective approach for combinatorial optimisation problems.Comment: 6+9 pages, 7 figure

Variation in Stemmatal Morphology of Larvae of Liodessus noviaffinis Miller (Dytiscidae: Hydroporinae: Bidessini)

Second and third instars tentatively identified as Liodessus noviaffinis Miller have six dorsolateral stemmata near the origin of each antenna. However, each stemma lacks a corneal (cuticular) lens on the surface exterior to its internal sensory pigmented components