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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
Liam J Hawkins, Kenneth B Storey
Common Western-blot imaging systems have previously been adapted to measure signals from luminescent microplate assays. This can be a cost saving measure as Western-blot imaging systems are common laboratory equipment and could substitute a dedicated luminometer if one is not otherwise available. One previously unrecognized limitation is that the signals captured by the cameras in these systems are not equal for all wells. Signals are dependent on the angle of incidence to the camera, and thus the location of the well on the microplate...
2017: MethodsX
Katie L Hill, Timo Hamers, Jorke H Kamstra, William G Willmore, Robert J Letcher
Thyroid hormones (THs) are involved in the regulation of many physiological processes in vertebrates. Competition for TH binding sites on serum transport proteins can interfere with delivery of THs to target tissues, and this is a potential mechanism of action of exogenous thyroidogenic substances. To date, detailed accounts of in vitro methods for competitive binding with THs on TH transport proteins (human or wildlife) are sparse. In the limited number of published studies on in vitro radio-labelled TH-TH transport protein interactions, method descriptions were brief and with insufficient details for successful replication...
2017: MethodsX
Tesfay Berhe, Omprakash Sahu
Bioethanol is one of the most important alternative renewable energy sources that substitute the fossil fuels. Sugarcane bagasse has a content of cellulose and hemicelluloses, which make it suitable as fermentation substrate when hydrolyzed. The objective of work is ethanol production from sugarcane bagasse (SCB) by the fermentation process. Eight laboratory experiments were conducted to produce bioethanol from sugarcane bagasse. By using Design Expert, it was formulated the dilute acid hydrolysis step to investigate the effects of hydrolysis parameters on a yield of ethanol and optimum condition...
2017: MethodsX
Seyed Ali Sajjadi, Ghasem Zolfaghari, Hamed Adab, Ahmad Allahabadi, Mehri Delsouz
This paper presented the levels of PM2.5 and PM10 in different stations at the city of Sabzevar, Iran. Furthermore, this study was an attempt to evaluate spatial interpolation methods for determining the PM2.5 and PM10 concentrations in the city of Sabzevar. Particulate matters were measured by Haz-Dust EPAM at 48 stations. Then, four interpolating models, including Radial Basis Functions (RBF), Inverse Distance Weighting (IDW), Ordinary Kriging (OK), and Universal Kriging (UK) were used to investigate the status of air pollution in the city...
2017: MethodsX
Nicholas I Cilz, James E Porter, Saobo Lei
Understanding how neuromodulators influence synaptic transmission and intrinsic excitability within the entorhinal cortex (EC) is critical to furthering our understanding of the molecular and cellular aspects of this region. Organotypic cultures can provide a cost-effective means to employ selective molecular biological strategies in elucidating cellular mechanisms of neuromodulation in the EC. We therefore adapted our acute slice model for organotypic culture applications and optimized a protocol for the preparation and biolistic transfection of cultured horizontal EC slices...
2017: MethodsX
Muhammad Shoaib Almas, Luigi Vanfretti
Synchrophasor measurements from Phasor Measurement Units (PMUs) are the primary sensors used to deploy Wide-Area Monitoring, Protection and Control (WAMPAC) systems. PMUs stream out synchrophasor measurements through the IEEE C37.118.2 protocol using TCP/IP or UDP/IP. The proposed method establishes a direct communication between two PMUs, thus eliminating the requirement of an intermediate phasor data concentrator, data mediator and/or protocol parser and thereby ensuring minimum communication latency without considering communication link delays...
2017: MethodsX
Sunil Veeravalli, Kersti Karu, Ian R Phillips, Elizabeth A Shephard
Our method describes the quantification in mouse urine of trimethylamine (TMA), trimethylamine N-oxide (TMAO) and creatinine. The method combines derivatization of TMA, with ethyl bromoacetate, and LC chromatographic separation on an ACE C18 column. The effluent was continuously electrosprayed into the linear ion trap mass spectrometer (LTQ), which operated in selective ion monitoring (SIM) modes set for targeted analytes and their internal standards (IS). All validation parameters were within acceptable ranges of analytical method validation guidelines...
2017: MethodsX
Fabio Granados-Chinchilla, Graciela Artavia
Considering choline (ChCl) as an essential ingredient for animals and that it is administered through feed, we developed an easy, accurate, and sensitive method for its analysis. The method is straightforward, derivatization-free and has no secondary chromatographic interactions. •We demonstrated that the method can be used for quality control for feeds and feed additives containing choline chloride•We report a simple chromatographic method which takes advantage of the hydroxyl moiety present in ChCl and a MS detector...
2017: MethodsX
Fabiola Santos, Saúl Gómez-Manzo, Edgar Sierra-Palacios, Abigail González-Valdez, Adriana Castillo-Villanueva, Horacio Reyes-Vivas, Jaime Marcial-Quino
Purification of nucleic acids is an essential procedure for most experiments in molecular biology. In this paper, the freeze-squeeze method with some modifications is proposed as an alternative methodology for the purification, concentration and recovery of small DNA fragments from agarose gels. The advantage of this alternative methodology is that it enables the recovery of fragments that are less than 100 bp in length and enables suspension of products in smaller volumes compared to several commercially available kits...
2017: MethodsX
Matthew C Pharris, Tzu-Ching Wu, Xinping Chen, Xu Wang, David M Umulis, Vikki M Weake, Tamara L Kinzer-Ursem
Advanced molecular probing techniques such as single molecule fluorescence in situ hybridization (smFISH) or RNAscope can be used to assess the quantity and spatial location of mRNA transcripts within cells. Quantifying mRNA expression in large image sets usually involves automated counting of fluorescent spots. Though conventional spot counting algorithms may suffice, they often lack high-throughput capacity and accuracy in cases of crowded signal or excessive noise. Automatic identification of cells and processing of many images is still a challenge...
2017: MethodsX
Mario Plattes, Christian Köhler, Tom Gallé
The two most characteristic properties of an ultrasonic wave are the frequency and the power. It is therefore important to determine the power in a given reactor. This can be done by calorimetry, i.e. by measuring the temperature rise in the vessel during sonication starting at thermal equilibrium with the surroundings (classic calorimetry) [1-3]. However, the classic ultrasonic calorimetry has drawbacks. In particular it is difficult to evaluate the temperature rise at thermal equilibrium, because the relevant initial time and temperature intervals are small and measurement errors in the temperature readings are large...
2017: MethodsX
Rodrigo Montoro, Renee Dickie
The vascular system, the pipeline for oxygen and nutrient delivery to tissues, is essential for vertebrate development, growth, injury repair, and regeneration. With their capacity to regenerate entire appendages throughout their lifespan, axolotls are an unparalleled model for vertebrate regeneration, but they lack many of the molecular tools that facilitate vascular imaging in other animal models. The determination of vascular metrics requires high quality image data for the discrimination of vessels from background tissue...
2017: MethodsX
Stanislav Naryzhny, Victor Zgoda, Artur Kopylov, Elena Petrenko, Аlexander Archakov
A method for increasing the productivity of ESI LC-MS/MS (electrospray ionization-liquid chromatography-tandem mass spectrometry) was proposed and applied. After IF (isoelectric focusing) of the sample using IPG (immobilized pH gradient) strip, the strip was cut to sections, and every section was treated according to trypsinolysis protocol for MS/MS analysis. The peptides produced were further analyzed by ESI LC-MS/MS. The procedure allows to: •identify many more proteins and proteoforms compared to shotgun analysis of extracts...
2017: MethodsX
Mahin Basha Syed
High-performance liquid chromatography (HPLC) was used for the determination of compounds occurring during the production of biodiesel from karanja and jatropha oil. Methanol was used for fast monitoring of conversion of karanja and jatropha oil triacylglycerols to fatty acid methyl esters and for quantitation of residual triacylglycerols (TGs), in the final biodiesel product. The individual sample compounds were identified using HPLC. Analysis of fatty acid methyl esters (FAMES) in blends of biodiesel by HPLC using a refractive index and a UV detector at 238 nm...
2017: MethodsX
Leonid Livshits, Einav Gross
Cysteine catabolism by gut microbiota produces high levels of sulfide. Excessive sulfide can interfere with colon function, and therefore may be involved in the etiology and risk of relapse of ulcerative colitis, an inflammatory bowel disease affecting millions of people worldwide. Therefore, it is crucial to understand how cells/animals regulate the detoxification of sulfide generated by bacterial cysteine catabolism in the gut. Here we describe a simple and cost-effective way to explore the mechanism of sulfide toxicity in the nematode Caenorhabditis elegans (C...
2017: MethodsX
Mauro Holzman, Raúl Rivas, Facundo Carmona, Raquel Niclòs
Optimization of field techniques is crucial to ensure high quality soil moisture data. The aim of the work is to present a sampling method for undisturbed soil and soil water content to calibrated soil moisture probes, in a context of the SMOS (Soil Moisture and Ocean Salinity) mission MIRAS Level 2 soil moisture product validation in Pampean Region of Argentina. The method avoids soil alteration and is recommended to calibrated probes based on soil type under a freely drying process at ambient temperature...
2017: MethodsX
Mehdi Jalili, Mahmoud Nikkhah Shahmirzadi, Mahdi Kaseb Hazrati, Hamed Ahmadi
Liquids coming from different sources like wastewaters, agricultural and industrial activities and leakages of chemical substances often have high concentration of chemical compositions and the osmotic gradient generated around such sources causes a considerable transmission of the Contamination. The steam transmitted by non-polluted soils moves to polluted masses, causing an increase in the volume of pollution zone and movement of pollutants. Therefore, such physical and chemical processes should be taken into account in pollution transmission models...
2017: MethodsX
Chenlong Zhang, Sandra Cvetanovic, Joshua M Pearce
Recent advances in the use of plasmonic metamaterials to improve absorption of light in thin-film solar photovoltaic devices has created a demand for a scalable method of patterning large areas with metal nanostructures deposited in an ordered array. This article describes two methods of fabricating ordered 2D nanosphere colloidal films: spin coating and interface coating. The two methods are compared and parameter optimization discussed. The study reveals that: •For smaller nanosphere sizes, spin coating is more favorable, while for larger nanospheres, the angled interface coating provides more coverage and uniformity...
2017: MethodsX
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