Exponentially Modified Peak Functions in Biomedical Sciences and Related Disciplines

In many cases relevant to biomedicine, a variable time, which features a certain distribution, is required for objects of interest to pass from an initial to an intermediate state, out of which they exit at random to a final state. In such cases, the distribution of variable times between exiting the initial and entering the final state must conform to the convolution of the first distribution and a negative exponential distribution. A common example is the exponentially modified Gaussian (EMG), which is widely used in chromatography for peak analysis and is long known as ex-Gaussian in psychophysiology, where it is applied to times from stimulus to response. In molecular and cell biology, EMG, compared with commonly used simple distributions, such as lognormal, gamma, and Wald, provides better fits to the variabilities of times between consecutive cell divisions and transcriptional bursts and has more straightforwardly interpreted parameters. However, since the range of definition of the Gaussian component of EMG is unlimited, data approximation with EMG may extend to the negative domain. This extension may seem negligible when the coefficient of variance of the Gaussian component is small but becomes considerable when the coefficient increases. Therefore, although in many cases an EMG may be an acceptable approximation of data, an exponentially modified nonnegative peak function, such as gamma-distribution, can make more sense in physical terms. In the present short review, EMG and exponentially modified gamma-distribution (EMGD) are discussed with regard to their applicability to data on cell cycle, gene expression, physiological responses to stimuli, and other cases, some of which may be interpreted as decision-making. In practical fitting terms, EMG and EMGD are equivalent in outperforming other functions; however, when the coefficient of variance of the Gaussian component of EMG is greater than ca. 0.4, EMGD is preferable

Impact Factor: outdated artefact or stepping-stone to journal certification?

A review of Garfield's journal impact factor and its specific implementation as the Thomson Reuters Impact Factor reveals several weaknesses in this commonly-used indicator of journal standing. Key limitations include the mismatch between citing and cited documents, the deceptive display of three decimals that belies the real precision, and the absence of confidence intervals. These are minor issues that are easily amended and should be corrected, but more substantive improvements are needed. There are indications that the scientific community seeks and needs better certification of journal procedures to improve the quality of published science. Comprehensive certification of editorial and review procedures could help ensure adequate procedures to detect duplicate and fraudulent submissions.Comment: 25 pages, 12 figures, 6 table

Light propagation and emission in complex photonic media

We provide an introduction to complex photonic media, that is, composite materials with spatial inhomogeneities that are distributed over length scales comparable to or smaller than the wavelength of light. This blossoming field is firmly rooted in condensed matter physics, in optics, and in materials science. Many stimulating analogies exist with other wave phenomena such as sound and seismology, X-rays, neutrons. The field has a rich history, which has led to many applications in lighting, novel lasers, light harvesting, microscopy, and bio optics. We provide a brief overview of complex photonic media with different classes of spatial order, varying from completely random to long-periodically ordered structures, quasi crystalline and aperiodic structures, and arrays of cavities. In addition to shaping optical waves by suitable photonic nanostructures, the realization is quickly arising that the spatial shaping of optical wavefronts with spatial light modulators dramatically increases the number of control parameters. As a result, it is becoming possible for instance to literally see through completely opaque complex media. We discuss a unified view of complex photonic media by means of a photonic interaction strength parameter. This parameter gauges the interaction of light with any complex photonic medium, and allows to compare complex media from different classes for similar applications.Comment: 8 pages, 2 figures, Light Localisation and Lasing: Random and Quasi-Random Photonic Structures, Eds. M. Ghulinyan and L. Pavesi, (Cambridge Univ. Press, Cambridge, 2015) Ch. 1, p.

On Time Series Analysis of Public Health and Biomedical Data

A time series is a sequence of observations made over time. Examples in public health include daily ozone concentrations, weekly admissions to an emergency department or annual expenditures on health care in the United States. Time series models are used to describe the dependence of the response at each time on predictor variables including covariates and possibly previous values in the series. Time series methods are necessary to account for the correlation among repeated responses over time. This paper gives an overview of time series ideas and methods used in public health research

New models involving quantum chemical parameters for assessing the chromatographic retention process

.Knowledge about the theoretical relationship between the analyte properties and the critical chromatographic parameters is mandatory for a better interpretation of the separation mechanism and a more leisurely development of quantitative studies. In a preliminary stage of this work, we introduce the Gumbel distribution, the extreme value distribution type-I widely used in other fields, as a novel tool for modelling the chromatographic peak shape. Further, we develop mathematical models to evaluate the effect of the experimental variables and various quantum parameters on the chromatographic indices, such as the retention time, capacity factor, asymmetry factor, tailing factor and number of theoretical plates. Finally, we propose a mechanistic behaviour for the chromatographic separation process based on the structure-retention relationship of fifteen selected drugs involving several molecular quantum parametersS

Robust visualization and discrimination of nanoparticles by interferometric imaging

Single-molecule and single-nanoparticle biosensors are a growing frontier in diagnostics. Digital biosensors are those which enumerate all specifically immobilized biomolecules or biological nanoparticles, and thereby achieve limits of detection usually beyond the reach of ensemble measurements. Here we review modern optical techniques for single nanoparticle detection and describe the single-particle interferometric reflectance imaging sensor (SP-IRIS). We present challenges associated with reliably detecting faint nanoparticles with SP-IRIS, and describe image acquisition processes and software modifications to address them. Specifically, we describe a image acquisition processing method for the discrimination and accurate counting of nanoparticles that greatly reduces both the number of false positives and false negatives. These engineering improvements are critical steps in the translation of SP-IRIS towards applications in medical diagnostics.R01 AI096159 - NIAID NIH HHSFirst author draf

A systematic literature review of studies analyzing the effect of sex, age, education, marital status, obesity, and smoking on health transitions

Sex, age, education, marital status, obesity, and smoking have been found to affect health transitions between non-disabled, disabled, and death. Our aim is to review the research literature on this topic and provide structured information, first on the availability of results for each risk factor and transition, and then on detailed study characteristics and disability measures. We use expert recommendations and the electronic databases Medline, PsycINFO, and SOCA. The search is confined to the years 1985-2005, and produced a total of 7,778 articles. Sixty-three articles met the selection criteria regarding study population, longitudinal design, risk factors, transition, and outcome measures.gender, health, mortality, obesity, review, sex, smoking, systematic review, transition

Probing and controlling fluorescence blinking of single semiconductor nanoparticles

In this review we present an overview of the experimental and theoretical development on fluorescence intermittency (blinking) and the roles of electron transfer in semiconductor crystalline nanoparticles. Blinking is a very interesting phenomenon commonly observed in single molecule/particle experiments. Under continuous laser illumination, the fluorescence time trace of these single nanoparticles exhibit random light and dark periods. Since its first observation in the mid-1990s, this intriguing phenomenon has attracted wide attention among researchers from many disciplines. We will first present the historical background of the discovery and the observation of unusual inverse power-law dependence for the waiting time distributions of light and dark periods. Then, we will describe our theoretical modeling efforts to elucidate the causes for the power-law behavior, to probe the roles of electron transfer in blinking, and eventually to control blinking and to achieve complete suppression of the blinking, which is an annoying feature in many applications of quantum dots as light sources and fluorescence labels for biomedical imaging