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Takaki Waritani, Jessica Chang, Bonnie McKinney, Kuniaki Terato
To assay serum antibodies by indirect ELISA, it is critical to eliminate a variety of false positive and negative reactions attributed to the principle. These include 1) the background (BG) noise reaction caused by hydrophobic binding of immunoglobulin components in sample specimens to solid surfaces, 2) false positive reaction caused by non-specific binding of immunoglobulins to target-antigens by protein-protein interactions, and 3) other false positive and negative reactions caused by buffer components. No current blocking agents can prevent these false positive and negative reactions, and antibody assay results vary significantly depending on the buffer system used...
2017: MethodsX
Jara Laso, María Margallo, Pére Fullana, Alba Bala, Cristina Gazulla, Ángel Irabien, Rubén Aldaco
To be able to fulfil high market expectations for a number of practical applications, Environmental Product Declarations (EPDs) have to meet and comply with specific and strict methodological prerequisites. These expectations include the possibility to add up Life Cycle Assessment (LCA)-based information in the supply chain and to compare different EPDs. To achieve this goal, common and harmonized calculation rules have to be established, the so-called Product Category Rules (PCRs), which set the overall LCA calculation rules to create EPDs...
2017: MethodsX
Jelmer J Nijp, Klaas Metselaar, Juul Limpens, Harm P A Gooren, Sjoerd E A T M van der Zee
The saturated hydraulic conductivity (Ks ) is a key characteristic of porous media, describing the rate of water flow through saturated porous media. It is an indispensable parameter in a broad range of simulation models that quantify saturated and/or unsaturated water flow. The constant-head permeameter test is a common laboratory method to determine Ks on undisturbed soil samples collected from the field. In this paper we show that the application of this conventional method may result in a biased Ks in the case of highly permeable media, such as the top layer of Sphagnum peat and gravel...
2017: MethodsX
Afroze Alam, Kamlesh Kumar Naik, Navneet Kumar Upadhaya, Shailendra Kumar, K L Dhar
The study was undertaken to develop a simplified procedure for the isolation of bioactive isoflavone from Iris kashmiriana, using a direct method of isolation, avoiding the use of chromatographic techniques. The compound was isolated by commercially viable procedure. The extraction of powdered drug (500 g) was done with petroleum ether (60-80) using a Soxhlet apparatus (24 h run). The petroleum ether extract (gums and resins 2.13 g) was obtained and the marc (400 g) was subjected to extraction with 95% methanol using a Soxhlet apparatus (24 h run)...
2017: MethodsX
Sumedha Liyanage, Rohan S Dassanayake, Amal Bouyanfif, Erandathi Rajakaruna, Latha Ramalingam, Naima Moustaid-Moussa, Noureddine Abidi
In Fourier transform infrared (FTIR) microspectrocopy, the tissue preparation method is crucial, especially how the tissue is cryo-sectioned prior to the imaging requires special consideration. Having a temperature difference between the cutting blade and the specimen holder of the cryostat greatly affects the quality of the sections. Therefore, we have developed an optimal protocol for cryo-sectioning of biological tissues by varying the temperature of both the cutting blade and the specimen holder. Using this protocol, we successfully cryo-sectioned four different difficult-to-section tissues including white adipose tissue (WAT), brown adipose tissue (BAT), lung, and liver...
2017: MethodsX
Zubairu Darma Umar, Nor Azwady Abd Aziz, Syaizwan Zahmir Zulkifli, Muskhazli Mustafa
Polycyclic Aromatic Hydrocarbons (PAHs) are complex and widely distributed environmental pollutants that can affect living ecosystems. This study was conducted to rapidly degrade phenanthrene and pyrene representing low and high molecular weight of PAHs, respectively. Cronobacter sakazakii MM045 (KT933253) was identified from used engine oil of contaminated soil. PAHs biodegradation was carried out using 2,6-dichlorophenol indophenol (DCPIP) assay. Biodegradation influencing factors including agitation, temperature, pH, inoculums volume and salinity were enhanced using Response Surface Methodology (RSM) by Central Composite Design (CCD)...
2017: MethodsX
Jean-Pierre Trezzi, Christian Jäger, Sara Galozzi, Katalin Barkovits, Katrin Marcus, Brit Mollenhauer, Karsten Hiller
Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids...
2017: MethodsX
Khadijeh Shekoohi, Fatemeh Sadat Hosseini, Amir Hossein Haghighi, Atefe Sahrayian
Hydrotalcites are quite prevalent in nature and their importance is growing more and more because of their very wide range of potential applications and uses. Because hydrotalcite does not exist in significant quantities in nature, coprecipitation methods are the most used for prepartion of hydrotalcite. In this study: Two types of Nano hydrotalcite compounds containing one divalent (Mg-Al) and two divalent cation(Co-Mg-Al) were synthesized based on aqueous solutions of corresponding nitrates by co-precipitation method...
2017: MethodsX
Palash Dutta
Health risk assessments have been carried out worldwide to examine potential health risk due to exposure to toxic contaminants in various environments. In risk assessment, it is most important to know the nature of all available information, data or model parameters. It is observed that available information/data are tainted with uncertainty and variability in the same time, i.e., uncertainty and variability co-exist. In such situation it is important to devise method for processing both uncertainty and variability into same framework and which is an open issue...
2017: MethodsX
Thomas Kroshko, Luciene Kapronczai, Marc R L Cattet, Bryan J Macbeth, Gordon B Stenhouse, Martyn E Obbard, David M Janz
Methodological differences among laboratories are recognized as significant sources of variation in quantification of hair cortisol concentration (HCC). An important step in processing hair, particularly when collected from wildlife, is the choice of solvent used to remove or "wash" external hair shaft cortisol prior to quantification of HCC. The present study systematically compared methanol and isopropanol as wash solvents for their efficiency at removing external cortisol without extracting internal hair shaft cortisol in samples collected from free-ranging grizzly bears and polar bears...
2017: MethodsX
Purvi Zaveri, Rushika Patel, Meghavi Patel, Devki Sarodia, Nasreen S Munshi
To overcome the issue of interferences by salt and compactness in release of bacterial cell required for lysis, method described by Yeates et al. (1998), was optimized for isolation of genomic material (Deoxyribo Nucleic Acid, DNA) from soil microbial community by addition of Al(NH4)SO4. Very low total viable count was observed in the samples tested and hence use of higher amount of soil is required primarily for DNA isolation from wasteland soils. The method proves itself efficient where commercially available bead beating and enzymatic lysis methods could not give isolation of any amount of community genomic DNA due to compact nature and salt concentrations present in soil...
2017: MethodsX
G Sreenivasulu, N Jayaraju, B C Sundara Raja Reddy, T Lakshmi Prasad, K Nagalakshmi, B Lakshmanna
Fourier Transform Infrared Spectroscopy (FTIR) was used to study the variations in organic matters of benthic foraminifera (Ammonia beccarii) from four samples collected from beach environments from brackish environments along Tupilipalem coast (South east coast of India). Common absorption bands were observed as peaks in the range of 3600-3400 cm(-1), 3000-2850 cm(-1), 1750-1740 cm(-1), 1640-1600 cm(-1), 1450-1350 cm(-1), 885-870 cm(-1) and 725-675 cm(-1) in all the shells of Ammonia beccarii. The FTIR spectrum of station-1 represents the presence of alkanes (CH3) and alkyl halide (C-F stretching) with absorptions at the range 1385-1255 and 1350-1150 cm(-1) were observed and ether (C-O stretching) absorption band was observed at stations 1 and 3 with wavenumber of 1115 cm(-1) and 1117 cm(-1) respectively...
2017: MethodsX
Guembou Shouop Cebastien Joel, Samafou Penabei, Moyo Maurice Ndontchueng, Gregoire Chene, Eric Jilbert Nguelem Mekontso, Alexandre Ngwa Ebongue, Motapon Ousmanou, Strivay David
To obtain high quality of results in gamma spectrometry, it is necessary to select the best HPGe detector for particular measurements, to calibrate energy and efficiency of gamma detector as accurate as possible. To achieve this aim, the convenient detector model and gamma source can be very useful. The purpose of this study was to evaluate the soil specific activity using two HPGe model (BEGe-6530 and GC0818-7600SL) by comparing the results of the two detectors and the technics used according to the detector type...
2017: MethodsX
Ritika Verma, K S Daya
Bio-molecule when isolated from its natural ecological condition is subjected to rapid decay. This decay leads to change in polarization and permittivity of molecule. This study presents an experimental analysis of the decay pattern of pM concentration of insulin using whispering gallery mode (WGM) dielectric resonator (DR) method. Analysis is carried out by comparing the permittivity, relaxation time and time delay for three days. It is observed that different pM concentrations of insulin solutions start to decay after 24 h at 5°C...
2017: MethodsX
Stefano Morotti, Eleonora Grandi
Population-based computational approaches have been developed in recent years and helped to gain insight into arrhythmia mechanisms, and intra- and inter-patient variability (e.g., in drug responses). Here, we illustrate the use of multivariable logistic regression to analyze the factors that enhance or reduce the susceptibility to cellular arrhythmogenic events. As an example, we generate 1000 model variants by randomly modifying ionic conductances and maximal rates of ion transports in our atrial myocyte model and simulate an arrhythmia-provoking protocol that enhances early afterdepolarization (EAD) proclivity...
2017: MethodsX
Francesca Ferrara, Nigel Temperton
Recently chimeric influenza haemagglutinins (cHAs) have been generated as potential 'universal' vaccination antigens and as tools to identify HA stalk-directed antibodies via their use as antigens in ELISA, and virus or pseudotype-based neutralization assays. The original methods [1], [2] used for their generation require the amplification of regions of interest (head and stalk) using primers containing SapI sites and subsequent cloning into pDZ plasmid. This requires precise primer design, checking for the absence of SapI sites in the sequence of interest, and multi-segment ligation...
2017: MethodsX
Christian Hofer, Gernot Lechner, Thomas Brudermann, Manfred Füllsack
We present a generic method for considering incomplete but gradually expandable sociological data in agent-based modeling based on the classic model of cultural dissemination by Axelrod. Our method extension was inspired by research on the diffusion of citizen photovoltaic initiatives, i.e. by initiatives in which citizens collectively invest in photovoltaic plants and share the profits. Owing to the absence of empirical interaction parameters, the Axelrod model was used as basis for considering peer effects with contrived interaction data that can be updated from empirical surveys later on...
2017: MethodsX
Robert D M Gray, Kim H Parker, Michael A Quail, Andrew M Taylor, Giovanni Biglino
The reservoir-wave hypothesis states that the blood pressure waveform can be usefully divided into a "reservoir pressure" related to the global compliance and resistance of the arterial system, and an "excess pressure" that depends on local conditions. The formulation of the reservoir-wave hypothesis applied to the area waveform is shown, and the analysis is applied to area and velocity data from high-resolution phase-contrast cardiovascular magnetic resonance (CMR) imaging. A validation study shows the success of the principle, with the method producing largely robust and physically reasonable parameters, and the linear relationship between flow and wave pressure seen in the traditional pressure formulation is retained...
2016: MethodsX
Birce Onal, Daniel Gratz, Thomas Hund
Mathematical modeling has been used for over half a century to advance our understanding of cardiac electrophysiology and arrhythmia mechanisms. Notably, computational studies using mathematical models of the cardiac action potential (AP) have provided important insight into the fundamental nature of cell excitability, mechanisms underlying both acquired and inherited arrhythmia, and potential therapies. Ultimately, an approach that tightly integrates mathematical modeling and experimental techniques has great potential to accelerate discovery...
2016: MethodsX
Zachary R Teed, Jonathan R Silva
Continuous time Markov models have been widely used to describe ion channel kinetics, providing explicit representation of channel states and transitions. Fitting models to experimental data remains a computationally demanding task largely due to the high cost of model evaluation. Here, we propose a method to efficiently optimize model parameters and structure. Voltage clamp channel protocols can be decomposed into a series of fixed steps of constant voltage resulting in a set of linear systems of differential equations...
2016: MethodsX
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