A protocol for single molecule imaging and tracking of processive myosin motors
We describe the required steps to obtain trajectories of single myosin motors from which fundamental biophysical parameters such as the motor velocity, run length and step size can be derived. We also describe protocols for an ensemble actin gliding assay, which is valuable to test the motor viability and its ensemble properties. The protocols allow probing the effect of changes in nucleotides, ions, and buffer composition on the motor properties and are easily generalizable to track the movements of different motor proteins.Graphical abstract (Source: MethodsX)
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Semi-automated crater depth measurements
We present here this method and its calibration.•Aside to this paper, we provide a simple python code of this pipeline.•This method can rapidly produce crater depth dataset big enough to be interpreted statistically.•We provide solid tests on the precision of measured crater depth. Especially, we show that minimal elevation value within a crater, sometime used as crater floor elevation, is a far less precise approximation than a low percentile of elevation.Graphical abstract (Source: MethodsX)
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Ex Vivo Electrochemical Measurement of Glutamate Release during Spinal Cord Injury
Publication date: Available online 23 August 2019Source: MethodsXAuthor(s): James K. Nolan, Tran N.H. Nguyen, Mara Fattah, Jessica C. Page, Riyi Shi, Hyowon LeeABSTRACTExcessive glutamate release following traumatic spinal cord injury (SCI) has been associated with exacerbating the extent of SCI. However, the mechanism behind sustained high levels of extracellular glutamate is unclear. Spinal cord segments mounted in a sucrose double gap recording chamber are an established model for traumatic spinal cord injury. We have developed a method to record, with micro-scale printed glutamate biosensors, glutamate release from ex ...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Human-Exoskeleton control simulation, kinetic and kinematic modeling and parameters extraction
In this study, a simulation-based method is presented for the designing and analysis of the parameters of an exoskeleton and its wearer’s kinetics and kinematics. Model-based design software, including OpenSim and Inventor, and mathematical software, such as MATLAB, are integrated. This method can assist in the modification of exoskeleton devices and allow physiologists, neuroscientists, and physical therapists to generate new solutions for rehabilitation programs using exoskeletons. •Using the movements parameters of each individual subject in her/his exoskeleton design•Combining the power of OpenSim body ...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Simultaneous Analysis of Betrixaban and Hexazinone using Liquid Chromatography/Tandem Mass Spectrometry in Aqueous Solutions
Publication date: Available online 23 August 2019Source: MethodsXAuthor(s): Tahereh Jasemi Zad, Lokesh P. PadhyeAbstractA new analytical method has been developed, optimised, and validated for simultaneous detection and identification of betrixaban, an oral anticoagulant drug approved recently by food and drug administration (FDA), and hexazinone, a broad-spectrum triazine herbicide, in aqueous media by liquid chromatography/tandem mass spectrometry (LC-MS/MS) using multiple reaction monitoring (MRM). The method was validated by the limit of detection (LOD), the limit of quantification (LOQ), linearity, matrix effect, reco...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

A Working Method for Estimating Dynamic Shear Velocity in the Montney Formation
Publication date: Available online 23 August 2019Source: MethodsXAuthor(s): Sochi C. Iwuoha, Per K. Pedersen, Christopher R. Clarkson, Ian D. GatesAbstractIn this paper, we present a customized method for estimating sonic shear velocity (Vs) from compressional velocity (Vp) logs in the Montney Formation, in wells lacking dipole sonic data. Following a multi-scenario analysis that comprised of assessing empirical Vs estimation relations [including lithology, porosity (Ø), and volume of clay (Vsh)-based Vs estimation techniques], bivariate statistics, and machine learning, we found that the Greenberg & Castagna (1...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

A tablet-based task for assessing environmental preferences in children and adults
Publication date: Available online 23 August 2019Source: MethodsXAuthor(s): Kimberly L. Meidenbauer, Cecilia U.D. Stenfors, Michael P. Ingram, Marc G. BermanAbstractTo assess environmental preferences in a wide age range of children, a tablet-based task was developed which can be used with children as young as 4-years-old. The current method uses images which have been rated on aesthetic preference in a separate adult sample to ensure that the nature and urban images shown are matched on aesthetics, allowing for a true evaluation of environmental preferences (without any confound of general aesthetics). However, the app is...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Method for the determination of parameters in the sintering process of mixtures of the elemental powders Fe-Cr and Fe-Cr-Ni
Publication date: Available online 23 August 2019Source: MethodsXAuthor(s): Tárique Hernandez Schneider, Luciano Volcanoglo Biehl, Ederson Bitencourt das Neves, Jorge Luiz Braz Medeiros, José de Souza, Fábio Augusto Dornelles do AmaralAbstractThe achievement of varied metal alloys through the sintering of mixtures of elemental metallic powders can provide great flexibility of production of these alloys. The possibilities of controlling the composition and the resulting properties of the alloy are of great importance for metallurgy. Otherwise the alloys involving chromium offer many difficulties for the...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Development of tracheobronchial fluid for in vitro bioaccessibility assessment of particulates-bound trace elements
This study was piloted to evaluate bioaccessibility of particulate-bound trace elements using synthetic epithelia lung fluid; in which dipalmitoylphophatidylcholine was substituted with locus bean gum (LBSFL). The resulting data reveal that no significant change in physicochemical characteristics of the stimulated lung fluid compare with similar synthetic fluids; pH value of 7.3, density (0.998gcm-3), conductivity (13.9 mS m-1), surface viscosity (1.136 × 10-12 pas) and surface tension (50.6 mN m-1). To prove the potential applicability of the fluid in in vitro bioaccessibili...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Generation and morphological quantification of large scale, three-dimensional, self-assembled vascular networks
Publication date: Available online 23 August 2019Source: MethodsXAuthor(s): Jasmine Shirazi, Joshua T. Morgan, Erica M. Comber, Jason P. GleghornAbstractOne of the largest issues facing the field of tissue engineering is scaling due to tissue necrosis as a result of a lack of vascularization. We have developed an accessible method for generating large scale vascular networks of arbitrary geometries through the self-assembly of endothelial cells in a collagen gel, similar to vasculogenesis that occurs in the developing embryo. This system can be applied to a wide range of collagen concentrations and seeding densities, resul...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Scanned Proton Beam Performance and Calibration of the Shanghai Advanced Proton Therapy Facility
Publication date: Available online 24 August 2019Source: MethodsXAuthor(s): Hang Shu, Chongxian Yin, Haiyang Zhang, Ming Liu, Manzhou Zhang, Liying Zhao, Kecheng Chu, Xiaolei Dai, Michael F. MoyersAbstractThe Shanghai Advanced Proton Therapy facility (SAPT) is a hospital-based facility that began construction in December of 2014 with commissioning of the first scanned proton beam line starting in October of 2017. Proton beams are extracted from a synchrotron accelerator with energies between 70 and 235 MeV. Beam delivery uses the modulated scanning and energy stacking techniques to produce a maximal scanning area of...
Source: MethodsX - August 25, 2019 Category: Science Source Type: research

Discrete choice experiments with multiple price vectors for products sold in a wide price range
Publication date: Available online 31 July 2019Source: MethodsXAuthor(s): Caterina Contini, Fabio Boncinelli, Caterina Romano, Gabriele Scozzafava, Leonardo CasiniAbstractThe discrete choice experiment is a widely used methodology in consumer studies. However, applying this method to investigate the market of products sold in a wide price range could present issues as to the quality of the estimate of preferences. In fact, for this type of product, frequently consumers may have different behaviours when faced with different price levels. For example, some market segments may refrain from purchasing products below certain p...
Source: MethodsX - August 1, 2019 Category: Science Source Type: research

The Actor in 4 Dimensions: A Relevant Methodology to Analyze Local Environmental Governance and Inform Ostrom's Social-Ecological Systems Framework
Publication date: Available online 31 July 2019Source: MethodsXAuthor(s): Raphaëlle Dancette, Léa SebastienAbstractThis paper presents the Actor in 4 dimensions (A4D) model as a complementary tool to the Social-ecological systems framework (SESF) in order to better integrate individual and groups' representations into local environmental governance analysis. As the A4D is based on actors' representations of their social-ecological system (SES) and of its governance, it mainly informs the Actors subsystem of the SESF, even if it can also give useful insights for other framework's sub-systems. We define the SESF ...
Source: MethodsX - August 1, 2019 Category: Science Source Type: research

Health Risk Assessment of Nitrate in Groundwater Resources of Iranshahr Using Monte Carlo Simulation and Geographic Information System (GIS)
Publication date: Available online 31 July 2019Source: MethodsXAuthor(s): Naseh Shalyari, Abdolazim Alinejad, Amir Hossein Ghazizadeh Hashemi, Majid RadFard, Mansooreh DehghaniAbstractBecause of exposure to a wide range of chemical contaminants such as nitrate via potable water resources, the use of the approaches to set standards for drinking water quality and also to do a risk assessment is necessary for maintaining the public health. High levels of nitrate in drinking water can have adverse health effects; primarily for infants and pregnant women. So, the present study aimed to the assessment of nitrate health risk in d...
Source: MethodsX - August 1, 2019 Category: Science Source Type: research

A simple method for mitochondrial respiration and calcium uptake assessment in pollen tubes
Publication date: Available online 25 July 2019Source: MethodsXAuthor(s): Diana J. Ortiz-Jiménez, Casandra M. López-Aquino, Cesar Flores-Herrera, Gisela Preciado-Linares, Israel González-Vizueth, Roeb García-Arrazola, Daniela Araiza-Olivera, Manuel Gutiérrez AguilarAbstractKey mitochondrial processes are known to be widely conserved throughout the eukaryotic domain. However, the scarce availability of working materials may restrict the assessment of such mitochondrial activities in several working models. Pollen tube mitochondrial studies represent one example of this, where tests have be...
Source: MethodsX - July 27, 2019 Category: Science Source Type: research

Mixed-trophies biofilm cultivation in capillary reactors
Publication date: Available online 25 July 2019Source: MethodsXAuthor(s): Ingeborg Heuschkel, Anna Hoschek, Andreas Schmid, Bruno Bühler, Rohan Karande, Katja BühlerAbstractThe biocatalytic application of photoautotrophic organisms is a promising alternative for the production of biofuels and value-added compounds as they do not rely on carbohydrates as a source of carbon, electrons, and energy. Although the photoautotrophic organisms hold potential for the development of sustainable processes, suitable reactor concepts that allow high cell density (HCD) cultivation of photoautotrophic microorganisms are limited....
Source: MethodsX - July 27, 2019 Category: Science Source Type: research

Evaluation of Carcinogenic Risks Related to Nitrate Exposure in Drinking Water in Iran
Publication date: Available online 24 July 2019Source: MethodsXAuthor(s): Mohammad Darvishmotevalli, Maryam Moradnia, Mohammad Noorisepehr, Ali Fatehizadeh, Saeid Fadaei, Hamed Mohammadi, Mehdi Salari, Hamzeh Ali Jamali, Seyede Shahrbanoo DanialiAbstractNitrate is one of the most important contaminants that can release into the environment predominantly as a result of anthropogenic processes. Excessive intake of nitrates may increase the risk of certain types of cancer. The aim of this study was to investigate the concentration of nitrate in drinking water and its health to people in Iran. This cross-sectional study has pe...
Source: MethodsX - July 25, 2019 Category: Science Source Type: research

Blender interstitial volume: a novel virtual measurement of structural complexity applicable to marine benthic habitats
Publication date: Available online 23 July 2019Source: MethodsXAuthor(s): Saachik Sadchatheeswaran, Coleen L. Moloney, George M Branch, Tamara B. RobinsonAbstractBlender interstitial volume is a novel method that utilizes 3D modeling techniques to accurately and efficiently quantify the volume of interstitial gaps in marine benthic habitats, as well as the space provided by substrate rugosity. This method builds upon the analog methods routinely used on rocky shores and intertidal habitats, including those that measure rugosity, topography, fractals and volume. The method provides a direct Euclidean measurement and uniquel...
Source: MethodsX - July 25, 2019 Category: Science Source Type: research

Modular microporous hydrogels formed from microgel beads with orthogonal thermo-chemical responsivity: Microfluidic fabrication and characterization*
Publication date: Available online 23 July 2019Source: MethodsXAuthor(s): Amir Sheikhi, Joseph de Rutte, Reihaneh Haghniaz, Outman Akouissi, Alireza Sohrabi, Dino Di Carlo, Ali KhademhosseiniAbstractDespite the significant advances in designing injectable bulk hydrogels, the inability to control the pore interconnectivity and decoupling it from the matrix stiffness has tremendously limited the applicability of stiff, flowable hydrogels for 3D cellular engineering, e.g., in hard tissue engineering. To overcome this persistent challenge, here, we introduce a universal method to convert thermosensitive macromolecules with che...
Source: MethodsX - July 23, 2019 Category: Science Source Type: research

Step by Step Procedures: Degradation of Polycyclic Aromatic Hydrocarbons in Potable Water using Photo-Fenton Oxidation Process
Publication date: Available online 20 July 2019Source: MethodsXAuthor(s): Teh Sabariah Binti Abd Manan, Salmia Beddu, Taimur Khan, Wan Hanna Melini Wan Mohtar, Ariyanti Sarwono, Hisyam Jusoh, Nur Liyana Mohd Kamal, Subarna Sivapalan, Abdulnoor A.J. GhanimAbstractPolycyclic aromatic hydrocarbons (PAHs) are carcinogenic compounds, composed of two or more fused benzene rings and abundantly found in mixed-use areas. Mixed-use areas consist of dense population, urbanization, industrial and agricultural activities. River pollution are common in mixed-use areas and 98% of Malaysia's fresh water supply originates from surface wate...
Source: MethodsX - July 21, 2019 Category: Science Source Type: research

A site-specific standard for comparing dynamic solar ultraviolet protection characteristics of established tree canopies
Publication date: Available online 20 July 2019Source: MethodsXAuthor(s): N.J. Downs, H.J. Butler, L. Baldwin, A.V. Parisi, A. Amar, J. Vanos, S. HarrisonAbstractA standardised procedure for making fair and comparable assessments of the ultraviolet protection of an established tree canopy that takes into account canopy movement and the changing position of the sun is presented for use by government, planning, and environmental health authorities. The technique utilises video image capture and replaces the need for measurement by ultraviolet radiometers for surveying shade quality characteristics of trees growing in public ...
Source: MethodsX - July 21, 2019 Category: Science Source Type: research

Modeling of Adsorption of Methylene Blue Dye on Ho-CaWO4 Nanoparticles using Response Surface Methodology (RSM) and Artificial Neural Network (ANN) Techniques
Publication date: Available online 19 July 2019Source: MethodsXAuthor(s): Chinenye Adaobi Igwegbe, Leili Mohmmadi, Shahin Ahmadi, Abbas Rahdar, Danial Khadkhodaiy, Rahmin Dehghani, Somayeh RahdarAbstractThe aim of this study is to evaluate the applicability of Ho-CaWO4 nanoparticles prepared using the hydrothermal method for the removal of Methylene blue (MB) from aqueous solution using adsorption process. The effects of contact time, Ho-CaWO4 nanoparticles dose and initial MB concentrationon the removal of MB were studied using the central composite design (CCD) method. Response surface methodology (RSM) and Artificial ne...
Source: MethodsX - July 21, 2019 Category: Science Source Type: research

Carcinogenic and non-carcinogenic health risk assessment of heavy metals in drinking water of Khorramabad, Iran
This study also presents that the carcinogenic risk for Pb, Cr, Cd and Ni were observed higher than the acceptable limit (1 × 10−6). The present study will be quite helpful for both inhabitants in taking protective measures and government officials in reducing heavy metals contamination of urban drinking water.•The data analyzed in this study show a clear situation regarding the quality of drinking water in Khorramabad.•The results of this study can be used to improve and develop the quality of drinking water that directly affects the health of consumers.•The present study will be q...
Source: MethodsX - July 21, 2019 Category: Science Source Type: research

Quantification of ecological complexity and resilience from multivariate biological metrics datasets using singular value decomposition entropy
Publication date: Available online 19 July 2019Source: MethodsXAuthor(s): Antoni Ginebreda, Laia Sabater-Liesa, Damià BarcelóAbstractThe concept of resilience has become popular in many disciplines far beyond its original use in the field of ecology. Despite of its wide use, it has received different definitions not always coincident. Such ambiguity is still more evident in its quantitative characterization. Most of the available methods are heavily context dependent and often difficult to apply in the practice. Here, we propose to define and calculate resilience starting from the data matrices resulting from...
Source: MethodsX - July 21, 2019 Category: Science Source Type: research

Methodology for accounting the net mitigation of China's ecological restoration projects (CANM-EP)
Publication date: Available online 19 July 2019Source: MethodsXAuthor(s): Bojie Liu, Lu Zhang, Fei Lu, Lei Deng, Hong Zhao, Yunjian Luo, Xiuping Liu, Kerong Zhang, Xiaoke Wang, Weiwei Liu, Xueyan Wang, Yafei YuanAbstractThe real emission mitigation by the ecological restoration projects depends upon the integrated effect of all greenhouse gas (GHG) budgets rather than the carbon sequestration alone. However, a comprehensive and robust methodology for estimating the relevant GHG budgets and net mitigation of China's ecological restoration projects is still urgently to await development. Based on the methods from IPCC and st...
Source: MethodsX - July 21, 2019 Category: Science Source Type: research

Biomonitoring of airborne metals using tree leaves: Protocol for biomonitor selection and spatial trend
This study aimed to use leave of local trees for biomonitoring of toxic metals and to evaluate tolerance of the trees against air pollution due to greenbelt development. Leaf samples were taken from four dominant tree species including Vitis vinifera, Juglans regia, Ulmus umbraculifera and Popolus alba in two radial distances (5 and 10 km) around the Urmia Lake in 32 sampling sites. The concentration of Cd, Pb, Ni, As, Cu, Zn and Na in the leaves were extracted according to method 3050B defined by United States Environmental Protection Agency (USEPA) and analyzed by ICP-AES technique. According to the levels of air ...
Source: MethodsX - July 21, 2019 Category: Science Source Type: research

A small, stainless-steel sieve optimized for laboratory beaker-based extraction of microplastics from environmental samples
Publication date: Available online 20 July 2019Source: MethodsXAuthor(s): Ryota Nakajima, Dhugal J. Lindsay, Masashi Tsuchiya, Rie Matsui, Tomo Kitahashi, Katsunori Fujikura, Tomohiko FukushimaAbstractRemoving non-plastic materials is a mandatory process for studying microplastics in environmental samples, and non-plastic materials, both inorganic and organic matter, are often removed chemically through sequential processes. In the multiple chemical treatment processes, the samples need to be collected and the reagent removed at the end of each chemical treatment before the samples are again exposed to a different reagent ...
Source: MethodsX - July 21, 2019 Category: Science Source Type: research

Evaluation of two independent protocols for the extraction of DNA and RNA from different tissues of sea cucumber Isostichopus badionotus
In this study, we describe the first protocols to obtain DNA and RNA from different tissues of I. badionotus, which include the respiratory tree, gonad, longitudinal muscle bands, anterior intestine and cloaca. The extraction of high-quality DNA was performed using the DNeasy Blood & Tissue kit (Qiagen, Valencia, CA, USA) with minor modifications in different points of the protocol.Concerning the RNA, the method of TRIzol was used. This method is particularly advantageous in situations where cells or tissues are enriched for endogenous RNases or when the separation of cytoplasmic RNA from nuclear RNA is impractical. Th...
Source: MethodsX - July 13, 2019 Category: Science Source Type: research

Optimization of Contact Angle and Interfacial Tension Measurements for Fluid/Rock Systems at Ambient Conditions
Publication date: Available online 12 July 2019Source: MethodsXAuthor(s): Wajdi Alnoush, Amr Sayed, Nayef AlyafeiAbstractQuantification of interfacial tension (IFT) and contact angles is essential to characterize reservoir fluid-fluid and rock-fluid interactions. However, these measurements are highly dependent on chemical structure, surface residues, system conditions, flow dynamics and interface interactions. Interfacial interactions are specifically important for secondary and tertiary oil recovery processes where water or brine is injected to recover residual oil through complex multi-phase - rock/brine/oil- interactio...
Source: MethodsX - July 13, 2019 Category: Science Source Type: research

HLIBCov: Parallel hierarchical matrix approximation of large covariance matrices and likelihoods with applications in parameter identification
Publication date: Available online 11 July 2019Source: MethodsXAuthor(s): Alexander Litvinenko, Ronald Kriemann, Marc G. Genton, Ying Sun, David E. KeyesAbstractWe provide more technical details about the HLIBCov package, which is using parallel hierarchical (H-) matrices to:•approximates large dense inhomogeneous covariance matrices with a log-linear computational cost and storage requirement;•computes matrix-vector product, Cholesky factorization and inverse with a log-linear complexity;•identify unknown parameters of the covariance function (variance, smoothness, and covariance length); These unknown para...
Source: MethodsX - July 12, 2019 Category: Science Source Type: research

An effective white spot syndrome virus challenge test for cultured shrimp using different biomass of the infected papilla
Publication date: Available online 10 July 2019Source: MethodsXAuthor(s): Cristóbal Domínguez-Borbor, Irma Betancourt, Fanny Panchana, Stanislaus Sonnenholzner, Bonny BayotAbstractWhite spot syndrome virus (WSSV) is one of the most virulent pathogens of cultured penaeid shrimp. Several control strategies are used commonly to mitigate the economic losses caused by the pathogen, such as application of antiviral products at farm level. One of the most practical method for the screening of potential anti-WSSV products is through challenge tests. Therefore, it is essential to develop simple, reproducible and effec...
Source: MethodsX - July 10, 2019 Category: Science Source Type: research

Sensitive detection of antigen-specific T-cells using bead-bound antigen for in vitro re-stimulation
Publication date: Available online 8 July 2019Source: MethodsXAuthor(s): Mattias Bronge, Andreas Kaiser, Claudia Carvalho-Queiroz, Ola B. Nilsson, Sabrina Ruhrmann, Erik Holmgren, Tomas Olsson, Guro Gafvelin, Hans GrönlundAbstractReliable and sensitive detection of antigen specific cells is essential in several fields of research, whether it concerns monitoring responses to infectious agents or exploring the auto-antigen repertoire in autoimmune diseases. Identification of these cells is however difficult, especially when the cells often are rare and methods not sensitive, specific or practical enough. We propose a no...
Source: MethodsX - July 9, 2019 Category: Science Source Type: research

Stereotaxic Surgery for Implantation of Guide Cannulas for Microinjection into the Dorsomedial Hypothalamus in Young Rats
Publication date: Available online 8 July 2019Source: MethodsXAuthor(s): Emily I. Poole, Jacob J. McGavin, Nicholas L. Cochkanoff, Karen M. CrosbyAbstractStereotaxic surgery to implant guide cannulas into the rodent brain is a frequently used technique to deliver drugs to targeted brain regions in awake, freely moving animals. There are limited reports, however, of central injections in young animals, and no information on cannula implantation for drug administration into the dorsomedial hypothalamus in young rats. Our protocol describes a simple and successful method for implanting guide cannulas in the brains of young, m...
Source: MethodsX - July 9, 2019 Category: Science Source Type: research

A Framework to Characterize the Performance of Early Warning Index Alarm Systems for Patient Monitoring
Publication date: Available online 8 July 2019Source: MethodsXAuthor(s): Chathuri Daluwatte, Farid Yaghouby, Christopher ScullyAbstractIn [Scully, C.G., and Daluwatte, C., Evaluating performance of early warning indices to predict physiological instabilities. J Biomed Inform. 75 (2017) 14-21.], a framework was presented to characterize the performance of warning indices to provide information on the 1) probability a critical health event will occur when a warning is given (analogous to positive predictive value) and 2) proportion of warned events to all events (analogous to sensitivity). This framework also provides inform...
Source: MethodsX - July 9, 2019 Category: Science Source Type: research

The submerged plus maze as an assay for studying anxiety-like behaviour in fish
Publication date: Available online 8 July 2019Source: MethodsXAuthor(s): Brittany V. Hope, Trevor J. Hamilton, Peter L. HurdAbstractThe elevated plus maze is a commonly used and well-validated test of anxiety-related behaviour in rodents. The use of fish in behavioural neuroscience paradigms is increasing, necessitating an equivalent test for studying anxiety-like behaviour in fish. Because behaviour in the elevated plus maze is driven by aversion to open space, the submerged plus maze described here uses transparent walls to elicit similar behaviour in fish. The tendency of fish to explore or avoid the sections of the maz...
Source: MethodsX - July 9, 2019 Category: Science Source Type: research

Radiogenic Heat Production in the Coastal Plain Sands of Ipokia, Dahomey Basin, Nigeria
This study is aimed at establishing the radiogenic heat production in the Benin Formation of Dahomey Basin using in-situ measurements of elemental concentrations of uranium, thorium and potassium over a kaolin deposits in Ifonyintedo, Ipokia LGA, Ogun State. Super-Spec gamma ray spectrometer is used to obtain varied data of naturally occurring radionuclides over eleven different stations in the Coastal Plain Sands at 1 m height above the ground. The mean heat produced by uranium, thorium and potassium are 294.3, 410.5 and 0.001 ρW kg-1 respectively. The total heat produced in the study area varied from 544.0 to ...
Source: MethodsX - July 9, 2019 Category: Science Source Type: research

Manual Grasparatus: A nifty tool for presenting real objects in fMRI research
Publication date: 2019Source: MethodsX, Volume 6Author(s): Agnieszka M. Nowik, Piotr P. Styrkowiec, Gregory KroliczakAbstractOne of the greatest challenges in functional magnetic resonance imaging (fMRI) research using real objects as stimuli is their timely delivery and (pseudo)randomized presentation. To this end, we designed an apparatus which solves the majority of problems that fMRI researchers may encounter during testing. The display apparatus – here: delivering objects for manual exploration and grasping (hence the “Grasparatus”) – is equipped with semi-attachable stimulus belts and, therefo...
Source: MethodsX - June 30, 2019 Category: Science Source Type: research

A microwave assisted method to synthesize nanoCoFe2O4@methyl cellulose as a novel metal-organic framework for antibiotic degradation
Publication date: Available online 26 June 2019Source: MethodsXAuthor(s): Alireza Nasiri, Fatemeh Tamaddon, Mohammad Hossein Mosslemin, Maryam FarajiAbstractIn this research, magnetically separable nanoCoFe2O4@methyl cellulose (MC) as a novel metal-organic framework was designed by a facile, fast, and new microwave-assisted method and then characterized. To assay the photocatalytic activity of nanoCoFe2O4@MC, its ability in metronidazole (MNZ) removal was investigated by considering the effect of some variables such as initial MNZ concentrations (5– 20 mg/L), pH (3–11), nanophotocatalyst loading (0.0&nda...
Source: MethodsX - June 27, 2019 Category: Science Source Type: research

A facile and green method for synthesis of ZnFe2O4@CMC as a new magnetic nanophotocatalyst for ciprofloxacin removal from aqueous media
This study aimed to synthesize a ZnFe2O4@carboxymethyl cellulose (CMC) nanophotocatalyst using a simple, facile, and green hydrothermal method for ciprofloxacin (CIP) removal from aqueous solutions. At first, ZnFe2O4@CMC was synthesized using the hydrothermal method, and then it was characterized. To assay the photocatalytic activity of ZnFe2O4@CMC, its ability was investigated in CIP and total organic carbon (TOC) removal by considering the effect of some variables such as initial CIP concentrations (5–30 mg/L), pH (3–11), nanophotocatalyst loading (0.1–0.5 g), and reaction time (20–1...
Source: MethodsX - June 27, 2019 Category: Science Source Type: research

Evaluation of skeletal age based on Greulich-Pyle method in Tehran
Publication date: Available online 25 June 2019Source: MethodsXAuthor(s): Mohammadreza Ebrahimzade, Dariush Rahban, Aarman Baboli Bahmaei, Safdar Masoumi, Vahid Changizi, Mohammad MirdoraghiAbstractAlthough bone age plays a special role in determining the child's age, there are some variations in skeletal growth of different people. The aim of this study was to compare the bone age with chronological age of children aged 2-18 years old in order to recognize whether Greulich-pyle (GP) method could be reliable for Iranian children? The standard radiograph of Left hand was taken in 40 healthy subjects, then the bone age was d...
Source: MethodsX - June 27, 2019 Category: Science Source Type: research

Protocol Measuring Horizontal Gene Transfer from Algae to Non-Photosynthetic Organisms
Publication date: Available online 25 June 2019Source: MethodsXAuthor(s): James Weifu LeeAbstractHorizontal gene transfer (HGT) is a natural process for an organism to transfer genetic material to another organism that is a completely different species, for example, from a blue-green alga to a non-photosynthetic bacterium. The phenomenon of HGT is not only of an interest to the science of molecular genetics and biology, but also to the biosafety issue of genetic engineering. The novel protocol reported here for the first time teaches how to measure HGT from a genetically engineered (GE) blue-green alga (gene donor) to wild...
Source: MethodsX - June 27, 2019 Category: Science Source Type: research

Two MATLAB programs for computing paleo-elevations and burial ages from paired-cosmogenic nuclide
Publication date: Available online 25 June 2019Source: MethodsXAuthor(s): Pierre-Henri Blard, Maarten Lupker, Moïse Rousseau, Jim TessonAbstractMethods based on cosmic-ray produced nuclides are key to improve our understanding of the Earth surface dynamic. Measuring multiple cosmogenic nuclides in the same rock sample has a great potential, but data interpretation requires rigorous and often complex mathematical treatments. In order to make progress on this topic, this paper presents two easy-to-use MATLAB© programs permitting to derive information from pairs of cosmogenic nuclides (26Al-10Be or 10Be-21Ne) measur...
Source: MethodsX - June 25, 2019 Category: Science Source Type: research

IRT Scoring Procedures for TIMSS Data
Publication date: Available online 21 June 2019Source: MethodsXAuthor(s): Gregory Camilli, John A. DosseyAbstractIn large-scale international assessment programs, results for mathematics proficiency are typically reported for jurisdictions such as provinces or countries. An overall score is provided along with subscores based on content subdomains defined in the test specifications. In this paper, an alternative method for obtaining empirical subscores is described, where the empirical subscores are based on an exploratory item response theory (IRT) factor solution. This alternative scoring is intended to augment rather th...
Source: MethodsX - June 22, 2019 Category: Science Source Type: research

Landfill site selection using a hybrid system of AHP-Fuzzy in GIS environment: A case study in Shiraz city, Iran
Publication date: 2019Source: MethodsX, Volume 6Author(s): Hasan Pasalari, Ramin Nabizadeh Nodehi, Amir Hossein Mahvi, Kamyar Yaghmaeian, Zabihalah CharrahiAbstractLandfilling with simplicity and economic advantages is the most common element for waste management in both developed and developing countries. Landfill site selection in a proper way is an important municipal planning process which prevent environmental issues including water pollution imposed for insanitary landfills. The present research was developed to exhibit a simplified method of multi criteria decision making (MCDM) and Fuzzy memberships in GIS environm...
Source: MethodsX - June 21, 2019 Category: Science Source Type: research

Biohydrogen production from alkaline wastewater: The Stoichiometric reactions, Modeling, and Electron Equivalent
Publication date: Available online 20 June 2019Source: MethodsXAuthor(s): Bijan Bina, Mohammad Mehdi Amin, Hamidreza Pourzamani, Ali Fatehizadeh, Mohammad Ghasemian, Mokhtar Mahdavi, Ensiyeh TaheriAbstractHydrogen gas (H2) is the cleanest energy carrier with 142 kJ/g energy content and without toxic byproducts release during combustion. There is interest to H2 production by biological process from sustainable resources including municipal and industrial wastewater and also solid waste. Here, we describe the biohydrogen production that involves first survey the effect of alkalinity on biohydrogen production based on ...
Source: MethodsX - June 21, 2019 Category: Science Source Type: research

How to develop a comprehensive Mangrove Quality Index?
Publication date: Available online 20 June 2019Source: MethodsXAuthor(s): Faridah-Hanum Ibrahim, Fatimah Mohd Yusoff, Anwar Fitrianto, Ahmad Ainuddin Nuruddin, Seca Gandaseca, Zaiton Samdin, Norizah Kamarudin, Siti Nurhidayu Abu Bakar, Mohamad Roslan Kassim, Khalid Rehman Hakeem, Shamsuddin Ibrahim, Ismail Adnan, Awang Noor Abdul Ghani, Rhyma Purnamasayangsukasih Parman, Siti Balqis Abd Razak, Siti Aminah Ibrahim, Fareha Hilaluddin, Fatin Ramli, Nik Harun Al-Rashid Nik ZaidinAbstractCurrently, the available indices to measure mangrove health are not comprehensive. An integrative ecological-socio economic index could give a...
Source: MethodsX - June 21, 2019 Category: Science Source Type: research

Establishment of specific enzyme-linked immunosorbent assay (ELISA) for measuring Fsh and Lh levels in medaka (Oryzias latipes), using recombinant gonadotropins
Publication date: Available online 17 June 2019Source: MethodsXAuthor(s): Susann Burow, Romain Fontaine, Kristine von Krogh, Ian Mayer, Rasoul Nourizadeh-Lillabadi, Lian Hollander-Cohen, Yaron Cohen, Michal Shpilman, Berta Levavi-Sivan, Finn-Arne WeltzienAbstractThe paucity of information on understanding the regulatory mechanisms that are involved in the control of piscine Fsh and Lh synthesis, secretion, and function, prompted the present work. Part of the problem is related to the molecular heterogeneity and the unavailability of Fsh and Lh assays for quantifying gonadotropins, in particular assays regarding the measure...
Source: MethodsX - June 18, 2019 Category: Science Source Type: research

Circulating tumour cell RNA characterisation from colorectal cancer patient blood after inertial microfluidic enrichment
Publication date: Available online 17 June 2019Source: MethodsXAuthor(s): Marnie Winter, Zhen Cai, Katharina Winkler, Kristen Georgiou, Daniel Inglis, Tina Lavranos, Meysam Rezaei, Majid Warkiani, Benjamin ThierryAbstractThe detection and molecular analysis of circulating tumour cells (CTCs) potentially provides a significant insight to the characterisation of disease, stage of progression and therapeutic options for cancer patients. Following on from the protocol by Warkiani et al. 2016, which describes a method of enriching CTCs from cancer patient blood with inertial microfluidics, we describe a method to measure the CT...
Source: MethodsX - June 18, 2019 Category: Science Source Type: research

Estimation of air pollutants emission (PM10, CO, SO2 and NOx) during development of the industry using AUSTAL 2000 model: a new method for sustainable development
Publication date: Available online 14 June 2019Source: MethodsXAuthor(s): Ali Atamaleki, Saeed Motesaddi Zarandi, Yadolah Fakhri, Ehsan Abouee Mehrizi, Ghasem Hesam, Meysam Faramarzi, Mahdiyeh DarbandiAbstractThere is well-documented relationship between industrial development and environmental pollution, but there are no enough studies that have predicted development impacts on pollutants emission. In the current study, impacts of three development periods of Bojnourd cement factory on pollutants emission (CO, SO2, NOx, and PM10) were investigated using the AUSTAL 2000 model. The collected emission data during 19 years we...
Source: MethodsX - June 15, 2019 Category: Science Source Type: research

Corrigendum to “Mann-Kendall Monotonic Trend Test and Correlation Analysis using Spatio-temporal Dataset: the case of Asia using vegetation greenness and climate factors” [MethodsX 5 (2018) 803–807]
Publication date: 2019Source: MethodsX, Volume 6Author(s): Munkhnasan Lamchin, Woo-Kyun Lee, Seong Woo Jeon, Sonam Wangyel Wang, Chul-Hee Lim, Cholho Song, Minjun SungAbstractThe Earth Trends Modeler (ETM) is an earth observation software tool that allows for modeling environmental changes and trend analyses of earth observation data. We used Global Inventory Modeling and Mapping Studies (GIMMS)-Normalized Difference Vegetation Index-3rd generation (NDVI3g) and Climatic Research Unit Time Series (CRU-TS) for climate data. We applied Mann-Kendall Monotonic Trend (MKMT) test using the ETM for changing trend analyses, correla...
Source: MethodsX - June 15, 2019 Category: Science Source Type: research