Evaluating performance in three-dimensional fluorescence microscopy

In biological fluorescence microscopy, image contrast is often degraded by a high background arising from out of focus regions of the specimen. This background can be greatly reduced or eliminated by several modes of thick specimen microscopy, including techniques such as 3-D deconvolution and confocal. There has been a great deal of interest and some confusion about which of these methods is ‘better’, in principle or in practice. The motivation for the experiments reported here is to establish some rough guidelines for choosing the most appropriate method of microscopy for a given biological specimen. The approach is to compare the efficiency of photon collection, the image contrast and the signal-to-noise ratio achieved by the different methods at equivalent illumination, using a specimen in which the amount of out of focus background is adjustable over the range encountered with biological samples. We compared spot scanning confocal, spinning disk confocal and wide-field/deconvolution (WFD) microscopes and find that the ratio of out of focus background to in-focus signal can be used to predict which method of microscopy will provide the most useful image. We also find that the precision of measurements of net fluorescence yield is very much lower than expected for all modes of microscopy. Our analysis enabled a clear, quantitative delineation of the appropriate use of different imaging modes relative to the ratio of out-of-focus background to in-focus signal, and defines an upper limit to the useful range of the three most common modes of imaging

Dynamical large deviations of countable reaction networks under a weak reversibility condition

A dynamic large deviations principle for a countable reaction network including coagulation-fragmentation models is proved. The rate function is represented as the infimal cost of the reaction fluxes and a minimiser for this variational problem is shown to exist. A weak reversibility condition is used to control the boundary behaviour and to guarantee a representation for the optimal fluxes via a Lagrange multiplier that can be used to construct the changes of measure used in standard tilting arguments. Reflecting the pure jump nature of the approximating processes, their paths are treated as elements of a BV function space

Initial commissioning results from the APS loss monitor system

The design of the beam loss monitor system for the Argonne National Laboratory Advanced Photon Source is based on using a number of air dielectric coaxial cables as long ionization chambers. Results to date show that the loss monitor is useful in helping to determine the cause of injection losses and losses large enough to limit circulating currents in the storage ring to short lifetimes. Sensitivities ranging from 13 to 240 pC of charge collected in the injector BTS (booster-to-storage-ring) loss monitor per picocoulomb of loss have been measured, depending on the loss location. These results have been used to predict that the storage ring loss monitor leakage current limit of 10 pA per cable should allow detection of losses resulting in beam lifetimes of 100 hours or less with 100 mA stored beam. Significant DC bias levels associated with the presence of stored beam have been observed. These large bias levels are most likely caused by the loss monitor responding to hard x-ray synchrotron radiation. No such response to synchrotron radiation was observed during earlier tests at SSRL. However, the loss monitor response to average stored beam current in APS has provided a reasonable alternative to the DC current transformer (DCCT) for measuring beam lifetimes

Variational structures beyond gradient flows: a macroscopic fluctuation-theory perspective

Macroscopic equations arising out of stochastic particle systems in detailed balance (called dissipative systems or gradient flows) have a natural variational structure, which can be derived from the large-deviation rate functional for the density of the particle system. While large deviations can be studied in considerable generality, these variational structures are often restricted to systems in detailed balance. Using insights from macroscopic fluctuation theory, in this work we aim to generalise this variational connection beyond dissipative systems by augmenting densities with fluxes, which encode non-dissipative effects. Our main contribution is an abstract framework, which for a given flux-density cost and a quasipotential, provides a decomposition into dissipative and non-dissipative components and a generalised orthogonality relation between them. We then apply this abstract theory to various stochastic particle systems – independent copies of jump processes, zero-range processes, chemical-reaction networks in complex balance and lattice-gas models

Charge Form Factor and Cluster Structure of 6^6Li Nucleus

The charge form factor of ${}^6$Li nucleus is considered on the basis of its cluster structure. The charge density of ${}^6$Li is presented as a superposition of two terms. One of them is a folded density and the second one is a sum of ${}^4$He and the deuteron densities. Using the available experimental data for ${}^4$He and deuteron charge form factors, a good agreement of the calculations within the suggested scheme is obtained with the experimental data for the charge form factor of ${}^6$Li, including those in the region of large transferred momenta.Comment: 12 pages 5 figure

Endemic fungal infections in solid organ and hematopoietic cell transplant recipients enrolled in the Transplant‐Associated Infection Surveillance Network ( TRANSNET )

Background Invasive fungal infections are a major cause of morbidity and mortality among solid organ transplant ( SOT ) and hematopoietic cell transplant ( HCT ) recipients, but few data have been reported on the epidemiology of endemic fungal infections in these populations. Methods Fifteen institutions belonging to the Transplant‐Associated Infection Surveillance Network prospectively enrolled SOT and HCT recipients with histoplasmosis, blastomycosis, or coccidioidomycosis occurring between March 2001 and March 2006. Results A total of 70 patients (64 SOT recipients and 6 HCT recipients) had infection with an endemic mycosis, including 52 with histoplasmosis, 9 with blastomycosis, and 9 with coccidioidomycosis. The 12‐month cumulative incidence rate among SOT recipients for histoplasmosis was 0.102%. Occurrence of infection was bimodal; 28 (40%) infections occurred in the first 6 months post transplantation, and 24 (34%) occurred between 2 and 11 years post transplantation. Three patients were documented to have acquired infection from the donor organ. Seven SOT recipients with histoplasmosis and 3 with coccidioidomycosis died (16%); no HCT recipient died. Conclusions This 5‐year multicenter prospective surveillance study found that endemic mycoses occur uncommonly in SOT and HCT recipients, and that the period at risk extends for years after transplantation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106980/1/tid12186.pd

Dynamical mean-field approach to materials with strong electronic correlations

We review recent results on the properties of materials with correlated electrons obtained within the LDA+DMFT approach, a combination of a conventional band structure approach based on the local density approximation (LDA) and the dynamical mean-field theory (DMFT). The application to four outstanding problems in this field is discussed: (i) we compute the full valence band structure of the charge-transfer insulator NiO by explicitly including the p-d hybridization, (ii) we explain the origin for the simultaneously occuring metal-insulator transition and collapse of the magnetic moment in MnO and Fe2O3, (iii) we describe a novel GGA+DMFT scheme in terms of plane-wave pseudopotentials which allows us to compute the orbital order and cooperative Jahn-Teller distortion in KCuF3 and LaMnO3, and (iv) we provide a general explanation for the appearance of kinks in the effective dispersion of correlated electrons in systems with a pronounced three-peak spectral function without having to resort to the coupling of electrons to bosonic excitations. These results provide a considerable progress in the fully microscopic investigations of correlated electron materials.Comment: 24 pages, 14 figures, final version, submitted to Eur. Phys. J. for publication in the Special Topics volume "Cooperative Phenomena in Solids: Metal-Insulator Transitions and Ordering of Microscopic Degrees of Freedom