Evaluation of Normalization Methods on GeLC-MS/MS Label-Free Spectral Counting Data to Correct for Variation during Proteomic Workflows

Normalization of spectral counts (SpCs) in label-free shotgun proteomic approaches is important to achieve reliable relative quantification. Three different SpC normalization methods, total spectral count (TSpC) normalization, normalized spectral abundance factor (NSAF) normalization, and normalization to selected proteins (NSP) were evaluated based on their ability to correct for day-to-day variation between gel-based sample preparation and chromatographic performance. Three spectral counting data sets obtained from the same biological conidia sample of the rice blast fungus Magnaporthe oryzae were analyzed by 1D gel and liquid chromatography-tandem mass spectrometry (GeLC-MS/MS). Equine myoglobin and chicken ovalbumin were spiked into the protein extracts prior to 1D-SDS- PAGE as internal protein standards for NSP. The correlation between SpCs of the same proteins across the different data sets was investigated. We report that TSpC normalization and NSAF normalization yielded almost ideal slopes of unity for normalized SpC versus average normalized SpC plots, while NSP did not afford effective corrections of the unnormalized data. Furthermore, when utilizing TSpC normalization prior to relative protein quantification, t-testing and fold-change revealed the cutoff limits for determining real biological change to be a function of the absolute number of SpCs. For instance, we observed the variance decreased as the number of SpCs increased, which resulted in a higher propensity for detecting statistically significant, yet artificial, change for highly abundant proteins. Thus, we suggest applying higher confidence level and lower fold-change cutoffs for proteins with higher SpCs, rather than using a single criterion for the entire data set. By choosing appropriate cutoff values to maintain a constant false positive rate across different protein levels (i.e., SpC levels), it is expected this will reduce the overall false negative rate, particularly for proteins with higher SpCs.     

On modeling with multiplicative differential equations

This work is aimed to show that various problems from different fields can be modeled more efficiently using multiplicative calculus, in place of Newtonian calculus. Since multiplicative calculus is still in its infancy, some effort is put to explain its basic principles such as exponential arithmetic, multiplicative calculus, and multiplicative differential equations. Examples from finance, actuarial science, economics, and social sciences are presented with solutions using multiplicative calculus concepts. Based on the encouraging results obtained it is recommended that further research into this field be vested to exploit the applicability of multiplicative calculus in different fields as well as the development of multiplicative calculus concepts.     

Multiplicative Adams Bashforth–Moulton methods

The multiplicative version of Adams Bashforth–Moulton algorithms for the numerical solution of multiplicative differential equations is proposed. Truncation error estimation for these numerical algorithms is discussed. A specific problem is solved by methods defined in multiplicative sense. The stability properties of these methods are analyzed by using the standart test equation.     

Extension of gamma, beta and hypergeometric functions

The main object of this paper is to present generalizations of gamma, beta and hypergeometric functions. Some recurrence relations, transformation formulas, operation formulas and integral representations are obtained for these new generalizations.     

The cogyrolines of Möbius gyrovector spaces are metric but not periodic

In this paper, we prove that every metric line of a Möbius gyrovector space ${(\mathbb{R}_{1}^{n}, \oplus, \otimes)}$ is exactly a cogyroline of itself, and also we prove the nonexistence of periodic lines in ${(\mathbb{R}_{1}^{n}, \oplus, \otimes)}$ .     

Determination of Cadmium Separated Selectively with Ion Exchange Method from Solution by ICP- AES

The removal of heavy metals, such as cadmium, from solution was investigated by using modified asphaltite ash as an ion exchange. Analysis were determined using inductively coupled plasma atomic emission spectrometry (i.e., ICP- AES). The effect of time, temperature, pH and concentration of cadmium on the removal process of cadmium was examined. An optimum condition for complete removal of cadmium from solution has been found. Therefore pretreated asphaltite ash can be used as an alternative material for removal of cadmium from industrial waste waters.     

Optimization of Release Conditions of Alzheimer's Drug Donepezil Hydrochloride from Sodium Alginate/Sodium Carboxymethyl Cellulose Blend Microspheres

Microspheres of blends of sodium alginate (NaAlg) and sodium carboxymethyl cellulose (NaCMC) were prepared by a water-in-oil (w/o) emulsion crosslinking method and used for the release of donepezil hydrochloride (DP), which is an Alzheimer's drug. The microspheres were characterized with Fourier transform infrared spectroscopy (FTIR), differantial scanning calorimetry (DSC), and scanning electron microscopy (SEM). The microsphere characteristics, including DP entrapment efficiency, particle size, equilibrium swelling degree (ESD), and DP release kinetics, were determined. The effects of the preparation conditions, including the NaAlg/NaCMC (w/w) ratio, drug/polymer (w/w) ratio, cross-linker concentration and time of exposure to the cross-linker, on the release of DP were investigated for successive gastrointestinal tract pH values of 1.2, 6.8, and 7.4 at 37°C. The release of DP increased with the increase in NaAlg/NaCMC (w/w) ratio and drug/polymer (d/p) ratio, while it decreased with increasing extent of cross-linking. The optimum DP release was obtained as 99.13% for a NaAlg/NaCMC (w/w) ratio of 2/1, d/p ratio of 1/4, CaCl₂ concentration of 5% and crosslinking time of 30 min. It was also observed from release results that DP release from the microspheres through the external medium was higher at low pH (1.2) values than that at high pH (6.8 and 7.4) values. The DP release of the microspheres followed either Fickian transport below a value of n < 0.5 or anomalous transport (n = 0.5–1.0).     

Nonlinear Intersubband Transitions in Square and Graded Quantum Wells Modulated by Intense Laser Field

There has been increasing interest, both exper- imentally and theoretically, in the investigation of low-dimensional semiconductor heterostructures due to their intrinsic physical properties and technological applications in electronic and optoelectronic devices. The studies on quantum heterostructures have opened a new field in fundamental physics, and also offer a wide range of potential applications for optoelectronic devices. By varying the profile of a semiconductor quantum well （QW）, both the subband state energies and their wave functions change, and so do various physical properties depending on them.     

The Detailed Comparison of Cell Death Detected by Annexin V-PI Counterstain Using Fluorescence Microscope,Flow Cytometry and Automated Cell Counter in Mammalian and Microalgae Cells

The evaluation of cell wellness is an important task for molecular biology research. This mainly comprises the assessment for morphology and viability of culturing cells. Annexin V-Propidium iodide counterstaining has been currently one of the common and easy methods to discriminate apoptotic and necrotic cell profiles. The method is operated by fluorescence-based detection of counterstain via laser beam-employed instruments including flow cytometer, fluorescence microscope and automated cell counter. The detection is primarily conducted based on the same principle; however the efficiency of instruments may vary. Here we evaluated the efficiency of those instruments for the clear-cut detection of cell death through various mammalian and microalgae cell lines. To the best of our knowledge, this is the first study revealing comparative analyses of apoptotic and necrotic cells in mammalian and microalgae cells using Annexin V-PI counterstain detected by flow cytometer, fluorescence microscope and automated cell counter. Fluorescence microscope and cell counter instruments were also tested and compared for the traditional trypan blue-based cell viability detection performance. For these, cell death was induced by UV-irradiation and/or bee venom for mammalian (pancreatic cancer, metastatic breast cancer and mouse fibroblasts) and microalgae cells (Chlorella vulgaris), respectfully. Findings postulated that automated cell counter and fluorescence microscopy revealed similar patterns for the detection by both counterstain and trypan blue in mammalian cells. Interestingly, flow cytometry did provide an accurate and significant detection for only one mammalian cell line when UV-treatment was followed by routine Annexin V-Propidium iodide counterstaining. Unlike, only flow cytometry revealed a significant change in the detection of death of microalgae cells by Annexin V-Propidium iodide method, but both Annexin and conventional trypan blue methods were not applicable for the automated cell counter and microscopic detections for microalgae cells. The related outputs propose that the obtaining reliable quantitation strongly depends on cell type and instruments used. These suggest the necessity of optimization and validation endeavors before any cell death detection initiative. The analytical outcomes present insights into detailed assessment of cell death detection of eukaryotic cells and provide a direction to researchers to consider.