Principal Investigator Views of the IRB System

We undertook a qualitative e-mail survey of federally-funded principal investigators of their views of the US human subjects protection system, intended to identify the range of investigator attitudes. This was an exploratory study with a 14% response rate. Twenty-eight principal investigators responded; their comments were analyzed to show underlying themes, which are here presented along with supporting quotations

Disc orientations in pre-main-sequence multiple systems. A study in southern star formation regions

Classical T Tauri stars are encircled by accretion discs most of the time unresolved by conventional imaging observation. However, numerical simulations show that unresolved aperture linear polarimetry can be used to extract information about the geometry of the immediate circumstellar medium that scatter the starlight. Monin, Menard & Duchene (1998) previously suggested that polarimetry can be used to trace the relative orientation of discs in young binary systems in order to shed light on the stellar and planet formation process. In this paper, we report on new VLT/FORS1 optical linear polarisation measurements of 23 southern binaries spanning a range of separation from 0.8'' to 10''. In each field, the polarisation of the central binary is extracted, as well as the polarisation of nearby stars in order to estimate the local interstellar polarisation. We find that, in general, the linear polarisation vectors of individual components in binary systems tend to be parallel to each other. The amplitude of their polarisations are also correlated. These findings are in agreement with our previous work and extend the trend to smaller separations. They are also similar to other studies, e.g., Donar et al. 1999; Jensen et al. 2000, 2004; Wolf et al. 2001. However, we also find a few systems showing large differences in polarisation level, possibly indicating different inclinations to the line-of-sight for their discs.Comment: 13 pages, 11 figures, accepted in Astronomy and Astrophysics. accepted in Astronomy and Astrophysics (A&A

Line Graphs of Weighted Networks for Overlapping Communities

In this paper, we develop the idea to partition the edges of a weighted graph in order to uncover overlapping communities of its nodes. Our approach is based on the construction of different types of weighted line graphs, i.e. graphs whose nodes are the links of the original graph, that encapsulate differently the relations between the edges. Weighted line graphs are argued to provide an alternative, valuable representation of the system's topology, and are shown to have important applications in community detection, as the usual node partition of a line graph naturally leads to an edge partition of the original graph. This identification allows us to use traditional partitioning methods in order to address the long-standing problem of the detection of overlapping communities. We apply it to the analysis of different social and geographical networks.Comment: 8 Pages. New title and text revisions to emphasise differences from earlier paper

Virus Infection of Plants Alters Pollinator Preference: A Payback for Susceptible Hosts?

Plant volatiles play important roles in attraction of certain pollinators and in host location by herbivorous insects. Virus infection induces changes in plant volatile emission profiles, and this can make plants more attractive to insect herbivores, such as aphids, that act as viral vectors. However, it is unknown if virus-induced alterations in volatile production affect plant-pollinator interactions. We found that volatiles emitted by cucumber mosaic virus (CMV)-infected tomato (Solanum lycopersicum) and Arabidopsis thaliana plants altered the foraging behaviour of bumblebees (Bombus terrestris). Virus-induced quantitative and qualitative changes in blends of volatile organic compounds emitted by tomato plants were identified by gas chromatography-coupled mass spectrometry. Experiments with a CMV mutant unable to express the 2b RNA silencing suppressor protein and with Arabidopsis silencing mutants implicate microRNAs in regulating emission of pollinator-perceivable volatiles. In tomato, CMV infection made plants emit volatiles attractive to bumblebees. Bumblebees pollinate tomato by 'buzzing' (sonicating) the flowers, which releases pollen and enhances self-fertilization and seed production as well as pollen export. Without buzz-pollination, CMV infection decreased seed yield, but when flowers of mock-inoculated and CMV-infected plants were buzz-pollinated, the increased seed yield for CMV-infected plants was similar to that for mock-inoculated plants. Increased pollinator preference can potentially increase plant reproductive success in two ways: i) as female parents, by increasing the probability that ovules are fertilized; ii) as male parents, by increasing pollen export. Mathematical modeling suggested that over a wide range of conditions in the wild, these increases to the number of offspring of infected susceptible plants resulting from increased pollinator preference could outweigh underlying strong selection pressures favoring pathogen resistance, allowing genes for disease susceptibility to persist in plant populations. We speculate that enhanced pollinator service for infected individuals in wild plant populations might provide mutual benefits to the virus and its susceptible hosts.Major funding for this project was provided to JPC by the Leverhulme Trust (Grant numbers RPG-2012-667 and F/09741/F: https://www. leverhulme.ac.uk/). Additional funding to JPC and studentships to support JHW and SCG came from the Biotechnological and Biological Sciences Research Council (Grant number BB/J011762/1: http://www.bbsrc.ac.uk/). Other additional funding was obtained from the Isaac Newton Trust (http://www. newtontrust.cam.ac.uk/: grant number 12.07/I to AMM).This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/:10.1371/journal.ppat.100579

Quasielastic 12C(e,e'p) Reaction at High Momentum Transfer

We measured the 12C(e,e'p) cross section as a function of missing energy in parallel kinematics for (q,w) = (970 MeV/c, 330 MeV) and (990 MeV/c, 475 MeV). At w=475 MeV, at the maximum of the quasielastic peak, there is a large continuum (E_m > 50 MeV) cross section extending out to the deepest missing energy measured, amounting to almost 50% of the measured cross section. The ratio of data to DWIA calculation is 0.4 for both the p- and s-shells. At w=330 MeV, well below the maximum of the quasielastic peak, the continuum cross section is much smaller and the ratio of data to DWIA calculation is 0.85 for the p-shell and 1.0 for the s-shell. We infer that one or more mechanisms that increase with $\omega$ transform some of the single-nucleon-knockout into multinucleon knockout, decreasing the valence knockout cross section and increasing the continuum cross section.Comment: 14 pages, 7 figures, Revtex (multicol, prc and aps styles), to appear in Phys Rev

A Measurement of the Interference Structure Function, R_LT, for the 12C(e,e'p) reaction in the Quasielastic Region

The coincidence cross-section and the interference structure function, R_LT, were measured for the 12C(e,e'p) 11B reaction at quasielastic kinematics and central momentum transfer of q=400 MeV/c. The measurement was at an opening angle of theta_pq=11 degrees, covering a range in missing energy of E_m = 0 to 65 MeV. The R_LT structure function is found to be consistent with zero for E_m > 50 MeV, confirming an earlier study which indicated that R_L vanishes in this region. The integrated strengths of the p- and s-shell are compared with a Distorted Wave Impulse Approximation calculation. The s-shell strength and shape are compared with a Hartree Fock-Random Phase Approximation calculation. The DWIA calculation overestimates the cross sections for p- and s-shell proton knockout as expected, but surprisingly agrees with the extracted R_LT value for both shells. The HF-RPA calculation describes the data more consistently, which may be due to the inclusion of 2-body currents in this calculation.Comment: 8 Pages LaTex, 5 postscript figures. Submitted to Phys. Rev.

Spanning forests and the q-state Potts model in the limit q \to 0

We study the q-state Potts model with nearest-neighbor coupling v=e^{\beta J}-1 in the limit q,v \to 0 with the ratio w = v/q held fixed. Combinatorially, this limit gives rise to the generating polynomial of spanning forests; physically, it provides information about the Potts-model phase diagram in the neighborhood of (q,v) = (0,0). We have studied this model on the square and triangular lattices, using a transfer-matrix approach at both real and complex values of w. For both lattices, we have computed the symbolic transfer matrices for cylindrical strips of widths 2 \le L \le 10, as well as the limiting curves of partition-function zeros in the complex w-plane. For real w, we find two distinct phases separated by a transition point w=w_0, where w_0 = -1/4 (resp. w_0 = -0.1753 \pm 0.0002) for the square (resp. triangular) lattice. For w > w_0 we find a non-critical disordered phase, while for w < w_0 our results are compatible with a massless Berker-Kadanoff phase with conformal charge c = -2 and leading thermal scaling dimension x_{T,1} = 2 (marginal operator). At w = w_0 we find a "first-order critical point": the first derivative of the free energy is discontinuous at w_0, while the correlation length diverges as w \downarrow w_0 (and is infinite at w = w_0). The critical behavior at w = w_0 seems to be the same for both lattices and it differs from that of the Berker-Kadanoff phase: our results suggest that the conformal charge is c = -1, the leading thermal scaling dimension is x_{T,1} = 0, and the critical exponents are \nu = 1/d = 1/2 and \alpha = 1.Comment: 131 pages (LaTeX2e). Includes tex file, three sty files, and 65 Postscript figures. Also included are Mathematica files forests_sq_2-9P.m and forests_tri_2-9P.m. Final journal versio

Acting while perceiving: assimilation precedes contrast

To explore the nature of specific interactions between concurrent perception and action, participants were asked to move one of their hands in a certain direction while simultaneously observing an independent stimulus motion of a (dis)similar direction. The kinematics of the hand trajectories revealed a form of contrast effect (CE) in that the produced directions were biased away from the perceived directions (“Experiment 1”). Specifically, the endpoints of horizontal movements were lower when having watched an upward as opposed to a downward motion. However, when participants moved under higher speed constraints and were not presented with the stimulus motion prior to initiating their movements, the CE was preceded by an assimilation effect, i.e., movements were biased toward the stimulus motion directions (“Experiment 2”). These findings extend those of related studies by showing that CEs of this type actually correspond to the second phase of a bi-phasic pattern of specific perception–action interference

Rubisco evolution in C₄ eudicots: an analysis of Amaranthaceae sensu lato.

BACKGROUND: Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots. METHODOLOGY/PRINCIPAL FINDINGS: We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution. CONCLUSIONS/SIGNIFICANCE: Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco