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Paola Lecca
We implement a Monte Carlo heuristic algorithm to model drug release from a solid dosage form. We show that with Monte Carlo simulations it is possible to identify and explain the causes of the unsatisfactory predictive power of current drug release models. It is well known that the power-law, the exponential models, as well as those derived from or inspired by them accurately reproduce only the first 60% of the release curve of a drug from a dosage form. In this study, by using Monte Carlo simulation approaches, we show that these models fit quite accurately almost the entire release profile when the release kinetics is not governed by the coexistence of different physico-chemical mechanisms...
2018: MethodsX
Maria Alvarado-Kristensson
When using fluorescence microscope techniques to study cells, it is essential that the cell structure and contents are preserved after preparation of the samples, and that the preparation method employed does not create artefacts that can be perceived as cellular structure/components. γ-Tubulin forms filaments that in some cases are immunostained with an anti-γ-tubulin antibody, but this immunostaining is not reproducible [[1], [2]]. In addition, the C terminal region of γ-tubulin (green fluorescence protein tagged [GFP]-γ-tubulin334--449 ) forms cytosolic GFP-labeled structures, which can easily be imaged in live cells but are not preserved in fixed cells [[1], [3]]...
2018: MethodsX
Tatiana M Minkina, Saglara S Mandzhieva, Marina V Burachevskaya, Tatiana V Bauer, Svetlana N Sushkova
Method of determination of heavy metals loosely bound compounds in the soil was developed using three separate extractions. The group of loosely bound compounds of metals includes exchangeable, complexed, and specifically adsorbed forms. This method is available, rapid and not expensive. Extraction takes less than 24 h. Sample procedure preparation is simple, and the analysis consists of only three steps, which can be performed simultaneously. The parallel extraction gives reliable and reproducible results and provides a relatively complete idea of the metals mobility in the soil, their availability to plants, migratory capacity, and transformation...
2018: MethodsX
Javier Valdes-Abellan, Yakov Pachepsky, Gonzalo Martinez
Data assimilation is becoming a promising technique in hydrologic modelling to update not only model states but also to infer model parameters, specifically to infer soil hydraulic properties in Richard-equation-based soil water models. The Ensemble Kalman Filter method is one of the most widely employed method among the different data assimilation alternatives. In this study the complete Matlab© code used to study soil data assimilation efficiency under different soil and climatic conditions is shown. The code shows the method how data assimilation through EnKF was implemented...
2018: MethodsX
Michael George Zaki Ghali
Tracheostomy is used to obtain airway access to allow for mechanical ventilation in experimental animal models. We present a microsurgical atlas of our technique for tracheostomy in the adult rat.
2018: MethodsX
Elyn M Rowe, Kyle K Biggar
While a number of post-translational modifications (PTM), such as phosphorylation and ubiquitination, have been extensively studied, lysine methylation is emerging as an important PTM with implications in a growing number of diverse cellular processes. To date, there are approximately 5000 identified methylation sites on non-histone proteins, and as the methyllysine proteome expands it becomes important to identify the lysine methyltransferase enzymes responsible for each methylation event. The use of peptide SPOT methylation assay has proven to be a useful in the identification and validation of novel substrates for lysine methyltransferase enzymes as it uses a weak beta emitter coupled with fluorography to detect methylation events...
2018: MethodsX
E S Joel, O Maxwell, O O Adewoyin, C O Ehi-Eromosele, Z Embong, F Oyawoye
In this study, we evaluated the activity concentration of natural radionuclides (226 Ra, 232 Th and 40 K) for fifteen (15) different brands of tile samples used for building purposes in Nigeria. The tile samples were analyzed using High purity Germanium gamma detector. The mean activity concentrations of 226 Ra, 232 Th, and 40 K were observed to be 61.1 ± 5.5 Bq/kg, 70.2 ± 6.08 Bq/kg and 514.7 ± 59.8 Bq/kg respectively. Various hazard indices such as absorbed dose rate, external and internal hazard index, annual effective dose rate, Gamma activity Index (Iγ) and Alpha Index (Iα) were calculated...
2018: MethodsX
Samer Salameh, Dominique Nouel, Cecilia Flores, Daniel Hoops
Netrin-1, an axon guidance protein, is difficult to detect using immunohistochemistry. We performed a multi-step, blinded, and controlled protocol optimization procedure to establish an efficient and effective fluorescent immunohistochemistry protocol for characterizing Netrin-1 expression. Coronal mouse brain sections were used to test numerous antigen retrieval methods and combinations thereof in order to optimize the stain quality of a commercially available Netrin-1 antibody. Stain quality was evaluated by experienced neuroanatomists for two criteria: signal intensity and signal-to-noise ratio...
2018: MethodsX
Elisabeth Mohammed, Terry Mohammed, Azad Mohammed
A simple, efficient and cost effective method was developed and optimized for the digestion of fish tissue for the determination of Lead, Cadmium, Mercury, Antimony, Arsenic and Selenium by FAAS, CVAAS and HGAAS. Three of the more common classical open tubed acid digestion procedures were explored with the purpose of optimizing the variables and selecting the single most efficient, convenient and inexpensive digestion method. The effect of parameters such as digestion media, digestion time and digestion temperature on the efficiency of extraction of heavy metals from fish tissue was examined...
2017: MethodsX
Negar Motayagheni
Oscar Langendorff introduced the first method for isolating a heart with contractile activity in 1895. Since then, the Langendorff method has remained a powerful technique in cardiac research and has led to major advances in medicine. The primary goal of the Langendorff method is to provide an isolated heart with oxygen and metabolites via a cannula inserted into the aorta. The Langendorff heart is a complex in vitro technique used primarily in pharmacological and physiological research that allows the evaluation of multiple cardiac hemodynamic parameters including, but not limited to, contractility and heart rate...
2017: MethodsX
Pavel Trtik
Pilot attempt of the neutron microtomography of voids in gold carried out using the Neutron Microscope instrument is presented in the paper. The paper demonstrates that neutron microtomography provides viable alternative to X-ray imaging for the assessment of porosity in high atomic number materials. The model sample based on gold with artificially induced void system reveals segmented porosity with 5.4 micrometres voxel size and the spatial resolution close to 10 micrometres.
2017: MethodsX
Norhayati Abu Bakar, Muhamad Mat Salleh, Akrajas Ali Umar, Joseph George Shapter
Silver nanoparticles deposited on quartz substrates are widely used as SERS substrates. The nanoparticles can be deposited directly from colloidal solution by dipping technique. However, the adhesion of the particles on the quartz surface is very poor. Normally the substrate is pre-treated with hydroxylation or silanisation process. In this paper, we have demonstrated that the application of the sequence pre-treatment hydroxylation and silanisation have improved the density of silver nanoplates desposited on the quartz surface...
2017: MethodsX
Heather A Hintz, Courtney Weihing, Rachel Bayer, David Lonzarich, Winnifred Bryant
In various species of fishes, the importance of visual cues in the determination of environmental threat and subsequent predator avoidance is clear. Chemical cues also play an essential role facilitating predator avoidance. Among fish in the superorder Ostariophysi, club cells in the epidermis produce an alarm substance. Damage to the skin during a predation event releases an alarm substance (AS), which diffuses through the water column and binds to olfactory receptors of conspecifics. Fish then engage in a number of anti-predator behaviors that may include darting, schooling, or hiding...
2017: MethodsX
T V S Udaya Bhaskar, R Venkat Shesu, Timothy P Boyer, E Pattabhi Rama Rao
A new method of identifying anomalous oceanic temperature and salinity (T/S) data from Argo profiling floats is proposed. The proposed method uses World Ocean Database 2013 climatology to classify good against anomalous data by using convex hulls. An n-sided polygon (convex hull) with least area encompassing all the climatological points is constructed using Jarvis March algorithm. Subsequently Points In Polygon (PIP) principle implemented using ray casting algorithm is used to classify the T/S data as within or without acceptable bounds...
2017: MethodsX
Ileana F Márquez, Marisela Vélez
We describe a simple way of fusing E. coli lipid vesicles onto a gold surface. Supported lipid bilayers on metal surfaces are interesting for several reasons: transducing a biological signal to an electric readout, using surface analytical tools such as Surface Plasmon Resonance (SPR), Infrared Reflection Absorption Spectroscopy, Neutron Reflectivity or Electrochemistry. The most widely used method to prepare supported lipid membranes is fusion of preexisting liposomes. It is quite efficient on hydrophilic surfaces such as glass, mica or SiO2 , but vesicle fusion on metals and metal oxide surfaces (as gold, titanium oxide or indium tin oxide), remains a challenge, particularly for vesicles containing charged lipids, as is the case of bacterial lipids...
2017: MethodsX
Prathap Moothamadathil Baby, Sanu Susan Jacob, Rajesh Kumar, Pramod Kumar
Serial injection into marginal vein and blood collection through auricular artery in New Zealand white Rabbit (Oryctolagus cuniculus) is an important procedure for various types of experimental studies. Limitations of the existing methods for serial injection and blood collection includes complex procedures, causes considerable discomfort to rabbits, whole blood samples obtained are highly prone to hemolysis and lastly detailed protocol is not available in the literature. Approximately 10 min before commencement of the experiment, a local anesthetic cream was applied over the right and left ear lobes...
2017: MethodsX
Tariq J Al-Musawi, Ibrahim A Mohammed, Huda M Atiea
The present study aims to manage and determine the most economical efficiency of five wastewater treatment plants discharging wastewater into the Tigris River in Iraq. The management system was based on ensuring the five-day biological oxygen demand concentration in the river is <30 mg/L according to the Iraqi standards. In many cases, the determined optimized efficiencies were found to be lower than the present working efficiencies. Although this was good for the environment, it was not cost-effective...
2017: MethodsX
Alexander A Loshkarev, Maria F Vlasova, Natalya I Sapronova, Yuri M Tokunov, Ivan A Volkov, Victor V Ivanov, Thomas Maeder
A method for determining the critical values of the flow speed and the flow constriction degree characteristic of the alignment of cylindrical nano-objects in a flowing suspension is proposed. Previously, the alignment process of cylindrical nano-objects in suspensions was investigated by using birefringence of the polarized light and the small-angle X-ray scattering. While both methods are suitable for measuring the alignment degree of cylindrical nano-objects in suspensions diluted down to low concentrations, they are restricted for the application to undiluted concentrated suspensions because of non-transparency and multiple scattering of X-rays...
2017: MethodsX
Khalil Ur Rehman, Abid Ali Khan, M Y Malik, Usman Ali
We have found that few attempts are reported on Williamson fluid flow yields by an inclined cylindrical surface. To be more specific, Williamson fluid flow regime characteristics under stagnation point region especially when it is manifested with mutual interaction of double stratification and mixed convection effects are not proposed as yet. Therefore, we have considered stagnation point mixed convection Williamson fluid flow brought by an inclined cylinder in the presence of temperature and concentration stratification phenomena...
2017: MethodsX
Christoph Bauer, Eugenia Niculescu-Morzsa, Stefan Nehrer
RNA isolation from human or animal cartilage tissue is necessary when performing mechanical or biotribological applications. Despite no influence on the cells and no alterations in gene expression patterns, enzymatic digestion of tissues should be avoided as it's known that the expression of collagen 2 can be effected (Hayman et al., 2006 [1]). After mechanical or biotribological tests alternative options with an immediate disruption of the tissue should be contemplated. To obtain RNA, different tissue homogenization and disruption methods are available on the market (Yu et al...
2017: MethodsX
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