Effective elimination of laser interference fringing in fluorescence microscopy by spinning azimuthal incidence angle

Laser illumination used in both conventional widefield epi-fluorescence as well as in total internal reflection fluorescence (TIRF) microscopy is subject to nonuniformities in intensity that obscure true image details. These intensity variations are interference fringes arising from coherent light scattering and diffraction at every surface in the laser light's optical path, including the lenses, mirrors, and coverslip. We present an inexpensive technique for effectively eliminating these interference fringes based upon introduction of the excitation laser beam by oblique through-the-objective incidence coupled with rapid azimuthal rotation of the plane of incidence. Although this rotation can be accomplished in several ways, a particularly simple method applicable to a free laser beam is to use an optical wedge, spun on a motor, which diverts the beam into a hollow cone of fixed angle. A system of lenses converts this collimated beam cone into a focused spot that traces a circle at the objective's back focal plane. Consequently, a collimated beam with fixed polar angle and spinning azimuthal angle illuminates the sample. If the wedge is spun rapidly, then the different interference patterns at every particular azimuthal incidence angle average out over a single camera exposure to produce an effectively uniform field of illumination. Microsc. Res. Tech., 2006. © 2006 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55799/1/20334_ftp.pd

Refractive index within the lens of a goldfish eye determined from the paths of thin laser beams

The paths of 15 [mu]m diameter laser beams traversing goldfish eye lenses were photographed. Measurements of these photographs gave experimental data for the distance of the exit point of each ray from the lens axis as a function of the corresponding entrance distance. A number of mathematical models with distinct distributions of refractive index within the lens were analysed by tracing rays to simulate the experimental data. The only distributions for which the simulated and experimental data were in agreement have a refractive index N which varies continuously with distance r from the lens center in a manner consistent with that originally proposed by Matthiessen: N2 = a - br2. Estimates for the central (1.55-1.57) and surface (1.35-1.38) refractive indices of the goldfish eye lens are derived from the preferred model, but these differ from those previously given by Matthiessen for other species. The optical performance of the lens models is also compared by third-order analyses.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27459/1/0000499.pd

Differential Regularization of Topologically Massive Yang-Mills Theory and Chern-Simons Theory

We apply differential renormalization method to the study of three-dimensional topologically massive Yang-Mills and Chern-Simons theories. The method is especially suitable for such theories as it avoids the need for dimensional continuation of three-dimensional antisymmetric tensor and the Feynman rules for three-dimensional theories in coordinate space are relatively simple. The calculus involved is still lengthy but not as difficult as other existing methods of calculation. We compute one-loop propagators and vertices and derive the one-loop local effective action for topologically massive Yang-Mills theory. We then consider Chern-Simons field theory as the large mass limit of topologically massive Yang-Mills theory and show that this leads to the famous shift in the parameter $k$. Some useful formulas for the calculus of differential renormalization of three-dimensional field theories are given in an Appendix.Comment: 25 pages, 4 figures. Several typewritten errors and inappropriate arguments are corrected, especially the correct adresses of authors are give

The UN in the lab

We consider two alternatives to inaction for governments combating terrorism, which we term Defense and Prevention. Defense consists of investing in resources that reduce the impact of an attack, and generates a negative externality to other governments, making their countries a more attractive objective for terrorists. In contrast, Prevention, which consists of investing in resources that reduce the ability of the terrorist organization to mount an attack, creates a positive externality by reducing the overall threat of terrorism for all. This interaction is captured using a simple 3×3 “Nested Prisoner’s Dilemma” game, with a single Nash equilibrium where both countries choose Defense. Due to the structure of this interaction, countries can benefit from coordination of policy choices, and international institutions (such as the UN) can be utilized to facilitate coordination by implementing agreements to share the burden of Prevention. We introduce an institution that implements a burden-sharing policy for Prevention, and investigate experimentally whether subjects coordinate on a cooperative strategy more frequently under different levels of cost sharing. In all treatments, burden sharing leaves the Prisoner’s Dilemma structure and Nash equilibrium of the game unchanged. We compare three levels of burden sharing to a baseline in a between-subjects design, and find that burden sharing generates a non-linear effect on the choice of the efficient Prevention strategy and overall performance. Only an institution supporting a high level of mandatory burden sharing generates a significant improvement in the use of the Prevention strategy

Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.

The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation

Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity

Social Experiments in the Mesoscale: Humans Playing a Spatial Prisoner's Dilemma

Background: The evolutionary origin of cooperation among unrelated individuals remains a key unsolved issue across several disciplines. Prominent among the several mechanisms proposed to explain how cooperation can emerge is the existence of a population structure that determines the interactions among individuals. Many models have explored analytically and by simulation the effects of such a structure, particularly in the framework of the Prisoner’s Dilemma, but the results of these models largely depend on details such as the type of spatial structure or the evolutionary dynamics. Therefore, experimental work suitably designed to address this question is needed to probe these issues. Methods and Findings: We have designed an experiment to test the emergence of cooperation when humans play Prisoner’s Dilemma on a network whose size is comparable to that of simulations. We find that the cooperation level declines to an asymptotic state with low but nonzero cooperation. Regarding players ’ behavior, we observe that the population is heterogeneous, consisting of a high percentage of defectors, a smaller one of cooperators, and a large group that shares features of the conditional cooperators of public goods games. We propose an agent-based model based on the coexistence of these different strategies that is in good agreement with all the experimental observations. Conclusions: In our large experimental setup, cooperation was not promoted by the existence of a lattice beyond a residual level (around 20%) typical of public goods experiments. Our findings also indicate that both heterogeneity and a ‘‘moody’