Analysis of three-dimensional cell imaging obtained with optical microscopy techniques based on defocusing

The properties of an optical microscope are analyzed and analytically evaluated with a simple and effective model in order to understand the true meaning, limitations, and real capabilities of a defocusing technique. Major emphasis is given to the applications related to microscopic objects of biological interest using fluorescence and absorption light microscopy. A procedure for three-dimensional viewing is analyzed and discussed.     

Cell imaging and manipulation by nonlinear optical microscopy

Advances in the technologies for labeling and imaging biological samples drive a constant progress in our capability of studying structures and their dynamics within cells and tissues. In the last decade, the development of numerous nonlinear optical microscopies has led to a new prospective both in basic research and in the potential development of very powerful noninvasive diagnostic tools. These techniques offer large advantages over conventional linear microscopy with regard to penetration depth, spatial resolution, three-dimensional optical sectioning, and lower photobleaching. Additionally, some of these techniques offer the opportunity for optically probing biological functions directly in living cells, as highlighted, for example, by the application of second-harmonic generation to the optical measurement of electrical potential and activity in excitable cells. In parallel with imaging techniques, nonlinear microscopy has been developed into a new area for the selective disruption and manipulation of intracellular structures, providing an extremely useful tool of investigation in cell biology. In this review we present some basic features of nonlinear microscopy with regard both to imaging and manipulation, and show some examples to illustrate the advantages offered by these novel methodologies.     

Applications of second harmonic generation (SHG)/sum-frequency generation (SFG) imaging for biophysical characterization of the plasma membrane

The plasma membrane is a lipid bilayer of < 10 nm width that separates intra- and extra-cellular environments and serves as the site of cell-cell communication, as well as communication between cells and the extracellular environment. As such, biophysical phenomena at and around the plasma membrane play key roles in determining cellular physiology and pathophysiology. Thus, the selective visualization and characterization of the plasma membrane are crucial aspects of research in wide areas of biology and medicine. However, the specific characterization of the plasma membrane has been a challenge using conventional imaging techniques, which are unable to effectively distinguish between signals arising from the plasma membrane and those from intracellular lipid structures. In this regard, interface-specific second harmonic generation (SHG) and sum-frequency generation (SFG) imaging demonstrate great potential. When combined with exogenous SHG/SFG active dyes, SHG/SFG can specifically highlight the plasma membrane as the most prominent interface associated with cells. Furthermore, SHG/SFG imaging can be readily extended to multimodal multiphoton microscopy with simultaneous occurrence of other multiphoton phenomena, including multiphoton excitation and coherent Raman scattering, which shed light on the biophysical properties of the plasma membrane from different perspectives. Here, we review traditional and current applications, as well as the prospects of long-known but unexplored SHG/SFG imaging techniques in biophysics, with special focus on their use in the biophysical characterization of the plasma membrane.     

Comparison of Linear,Nonlinear and Semiparametric Mixed‐effects Models for Estimating HIV Dynamic Parameters

The potency of antiretroviral agents in AIDS clinical trials can be assessed on the basis of an early viral response such as viral decay rate or change in viral load (number of copies of HIV RNA) of the plasma. Linear, parametric nonlinear, and semiparametric nonlinear mixed‐effects models have been proposed to estimate viral decay rates in viral dynamic models. However, before applying these models to clinical data, a critical question that remains to be addressed is whether these models produce coherent estimates of viral decay rates, and if not, which model is appropriate and should be used in practice. In this paper, we applied these models to data from an AIDS clinical trial of potent antiviral treatments and found significant incongruity in the estimated rates of reduction in viral load. Simulation studies indicated that reliable estimates of viral decay rate were obtained by using the parametric and semiparametric nonlinear mixed‐effects models. Our analysis also indicated that the decay rates estimated by using linear mixed‐effects models should be interpreted differently from those estimated by using nonlinear mixed‐effects models. The semiparametric nonlinear mixed‐effects model is preferred to other models because arbitrary data truncation is not needed. Based on real data analysis and simulation studies, we provide guidelines for estimating viral decay rates from clinical data. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Comparison of life history traits between invasive and native populations of purple loosestrife (Lythrum salicaria) using nonlinear mixed effects model

We compared growth patterns of invasive and native populations of purple loosestrife (Lythrum salicaria) while varying water and nutrient levels. We examined three life-history traits (height, number of branches, and the size of largest leaf) during the growth period adopting a nonlinear mixed effects model. Invasive populations were found to be slower in shoot elongation but grew to be taller than native populations. Invasive populations produced more branches than natives only in the high water, high nutrient treatment. Invasive populations had a similar increase in the size of the largest leaf compared to natives, but ultimately produced a greater size of largest leaf than natives. Invasive populations were found to display a greater vegetative expansion, but this was not strongly affected by our treatments.     

Direct evidence for excitonically coupled chlorophylls a and b in LHC II of higher plants by nonlinear polarization spectroscopy in the frequency domain

Occurrence of excitonic interactions in light-harvesting complex II (LHC II) was investigated by nonlinear polarization spectroscopy in the frequency domain (NLPF) at room temperature. NLPF spectra were obtained upon probing in the chlorophyll (Chl) a/b Soret region and pumping in the Q_y region. The lowest energy Chl a absorbing at 678 nm is strongly excitonically coupled to Chl b.     

Can you trust the parametric standard errors in nonlinear least squares? Yes,with provisos

Background

Questions about the reliability of parametric standard errors (SEs) from nonlinear least squares (LS) algorithms have led to a general mistrust of these precision estimators that is often unwarranted.

Global Properties of Infectious Disease Models with Nonlinear Incidence

We consider global properties for the classical SIR, SIRS and SEIR models of infectious diseases, including the models with the vertical transmission, assuming that the horizontal transmission is governed by an unspecified function f(S,I). We construct Lyapunov functions which enable us to find biologically realistic conditions sufficient to ensure existence and uniqueness of a globally asymptotically stable equilibrium state. This state can be either endemic, or infection-free, depending on the value of the basic reproduction number.     

Ultrasound and matter--physical interactions

The basic physical characteristics of ultrasound waves are reviewed in terms of the typical displacements, velocities, accelerations and pressures generated in various fluid media as a function of frequency. The effects on wave propagation of interfaces are considered, and the way in which waves are reflected, transmitted and mode converted at interfaces introduced. Then the nonlinear propagation of high amplitude ultrasound is explained, and its consequences, including the generation of harmonic frequencies and enhanced attenuation, considered. The absorption of ultrasonic waves and the resulting heat deposition in absorbing media are described together with factors determining the resulting temperature rises obtained. In the case of tissue these include conduction and perfusion. The characteristics of cavitation in fluid media are also briefly covered. Finally, secondary nonlinear physical effects are described. These include radiation forces on interfaces and streaming in fluids.     

A prolegomenon to nonlinear empiricism in the human behavioral sciences

We propose a general framework for integrating theory and empiricism in human evolutionary ecology. We specifically emphasize the joint use of stochastic nonlinear dynamics and information theory. To illustrate critical ideas associated with historical contingency and complex dynamics, we review recent research on social preferences and social learning from behavioral economics. We additionally examine recent work on ecological approaches in history, the modeling of chaotic populations, and statistical application of information theory.