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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
Eric Zluhan, Kathleen Kelly, Nick LeClair, Danique Wortel, Kesley Moody
Historically, the routine use of laboratory automation solutions has been prohibitively expensive for many laboratories. As legacy hardware has begun to emerge on the secondary market, automation is becoming an increasingly affordable option to augment workflow in virtually any laboratory. To assess the utility of legacy liquid handling in stem cell differentiation, a used liquid handling robot was purchased at auction to automate a stem cell differentiation protocol that gives rise to CD14 + CD45+ mononuclear cells...
2016: MethodsX
Tywanquila Walker
Twenty-three infants (M = 13.7 months, SD = 3.73) and their primary caregivers were observed and video-taped in three 20-min play sessions. Over the course of a month, changes in infant behaviors and caregiver responsiveness to those behaviors were monitored. Repeated-measures ANOVAs indicated that caregiver responsiveness to infant object-related and dyadic behaviors significantly increased over the course of the sessions. However, the ANOVAs did not specify exactly which caregiver behaviors changed. Sequential data analysis revealed that caregivers specifically increased their use of dyadic vocal behaviors in response to all infant behaviors...
2016: MethodsX
Anton Strunov, Lidiya V Boldyreva, Gera A Pavlova, Alexey V Pindyurin, Maurizio Gatti, Elena Kiseleva
The Drosophila S2 tissue culture cells are a widely used system for studies on mitosis. S2 cells are particularly sensitive to gene silencing by RNA interference (RNAi), allowing targeted inactivation of mitotic genes. S2 cells are also well suited for high-resolution light microscopy analysis of mitosis in fixed cells, and can be easily immunostained to detect mitotic components. In addition, S2 cells are amenable to transformation with plasmid encoding fluorescently tagged mitotic proteins, allowing in vivo analysis of their behavior throughout cell division...
2016: MethodsX
Meenu Thakur, R Dubey, S R Abhilash, B R Behera, B P Mohanty, D Kabiraj, Sunil Ojha, Heena Duggal
Thin carbon-backed isotopically enriched (208)Pb targets were required for our experiment aimed to study the reaction dynamics for (48)Ti + (208)Pb system, populating the near super-heavy nucleus (256)Rf, through mass-energy correlation of the fission fragments. Purity and thickness of the targets are of utmost importance in such studies as these factors have strong influence on the measurement accuracy of mass and energy distribution of fission fragments. (208)Pb targets with thickness ranging from 60 μg/cm(2) to 250 μg/cm(2) have been fabricated in high vacuum environment using physical vapor deposition method...
2016: MethodsX
Pavel Trtik, Manuel Morgano, Roman Bentz, Eberhard Lehmann
The recent developments in scientific complementary metal oxide semiconductor (sCMOS) detector technology allow for imaging of relevant processes with very high temporal resolution with practically negligible readout time. However, it is neutron intensity that limits the high temporal resolution neutron imaging. In order to partially overcome the neutron intensity problem for the high temporal resolution imaging, a parabolic neutron focussing guide was utilized in the test arrangement and placed upstream the detector in such a manner that the focal point of the guide was positioned slightly behind the scintillator screen...
2016: MethodsX
Christopher Stone, Derrick Williams, Jeremy Price
The Extended Q-range Small-angle Neutron Scattering Diffractometer (EQ-SANS) instrument at the spallation neutron source (SNS), Oak Ridge, Tennessee, incorporates a 69 m(3) detector vessel with a vacuum system which required an upgrade with respect to performance, ease of operation, and maintenance. The upgrade focused on improving pumping performance as well as optimizing system design to minimize opportunity for operational error. This upgrade provided the following practical contributions: •Reduced time required to evacuate from atmospheric pressure to 2 mTorr from 500 to 1000 min to 60-70 min•Provided turn-key automated control with a multi-faceted interlock for personnel and machine safety...
2016: MethodsX
Marko Rožman, Mira Petrović
Quantitative target analysis by liquid chromatography coupled to mass spectrometry (LCMS) is ubiquitous in environmental, metabolomic and toxicological studies. Targeted LCMS methods are capable of the simultaneous determination of literally hundreds of analytes. Although acquiring of instrumental data is very fast, data post-processing i.e. quantification can be time consuming step (and)or dependent to various commercial software packages. In attempt to facilitate this drawback Wolfram Mathematica script for batch quantification of LCMS data was created...
2016: MethodsX
Ileana Frasier, Elke Noellemeyer, Romina Fernández, Alberto Quiroga
The present article describes a field auger sampling method for row-crop root measurements. In agroecosystems where crops are planted in a specific design (row crops), sampling procedures for root biomass quantification need to consider the spatial variability of the root system. This article explains in detail how to sample and calculate root biomass considering the sampling position in the field and the differential weight of the root biomass in the inter-row compared to the crop row when expressing data per area unit...
2016: MethodsX
Alejandro Cardoso Landaburu, María Pomares, Alfredo Avalos, Silvia Lapertosa, Gustavo Frechtel, Edgardo Poskus
The prevalence and high levels of anti-insulin antibodies (IA) have frequently been associated with brittle diabetes, lipodystrophy in the areas where the insulin is injected and/or poor metabolic control. When this happens the usual criterion adopted is the empirical change of insulin type and/or formulation intending to diminish the IA level and then to decrease the undesirable side-effects. Here, we present a rational two step radiometric method consisting in: A) a first-line radioligand binding assay (RBA) to assess IA in sera of these patients and detecting those with high levels...
2016: MethodsX
J Scholz, S Suppmann
Wave-mixed bioreactors have increasingly replaced stainless steel stirred tank reactors in seed inoculum productions and mammalian cell-based process developments. Pre-sterilized, single-use plastic bags are used for cultivation, eliminating the risk of cross-contamination and cleaning procedures. However, these advantages come with high consumable costs which is the main barrier to more uptakes of the technology by academic institutions. As an academic Core Facility that faces high demand in protein production from insect cells, we have therefore developed a cost-effective alternative to disposable wave bags...
2016: MethodsX
Russell F Cole, Graham A Mills, Adil Bakir, Ian Townsend, Anthony Gravell, Gary R Fones
Tributyltin (TBT) is a legacy pollutant in the aquatic environment, predominantly from its use in anti-foulant paints and is listed as a priority hazardous substance in the European Union's Water Framework Directive (WFD). Measuring low concentrations of TBT and other organotins (e.g. monobutyltin (MBT), dibutyltin (DBT), diphenyltin (DPhT) and triphenyltin (TPhT)) at sub ng/L concentrations in coastal waters using standard laboratory instrumentation is very challenging. Conventional, low injection volume gas chromatography/mass spectrometry (GC/MS) combined with liquid-liquid extraction typically achieves limits of detection for TBT ∼10 ng L(-1)...
2016: MethodsX
Sung Bae Kim, Takeaki Ozawa, Yoshio Umezawa
We introduce a method to evaluate the activities of cytokines based on the nuclear transport of NF-κB. A pair of bioluminescent indicators was made for conferring cytokine sensitivity to cervical carcinoma-derived HeLa cells. The principle is based on reconstitution of split fragments of Renilla reniformis luciferase (RLuc) by protein splicing with a DnaE intein from Synechocystis sp. PCC6803. The bioluminescence intensity of thus reconstituted RLuc in the HeLa cells was used as a measure of the activities for cytokines...
2016: MethodsX
Thomas E Gladwin, Matthijs Vink, Roger B Mars
Cluster-based analysis methods in neuroimaging provide control of whole-brain false positive rates without the need to conservatively correct for the number of voxels and the associated false negative results. The current method defines clusters based purely on shapes in the landscape of activation, instead of requiring the choice of a statistical threshold that may strongly affect results. Statistical significance is determined using permutation testing, combining both size and height of activation. A method is proposed for dealing with relatively small local peaks...
2016: MethodsX
Teresa Gazzotti, Andrea Barbarossa, Elisa Zironi, Paola Roncada, Marco Pietra, Giampiero Pagliuca
Although budesonide is frequently used in veterinary medicine for the treatment of canine respiratory and bowel inflammatory diseases, knowledge is lacking regarding its kinetics in this species. We developed and validated a liquid chromatography-tandem mass spectrometry method for the determination of budesonide and its metabolite 16α-hydroxyprednisolone in dog plasma. The analytes were extracted by solid phase extraction and analysis was performed by high performance liquid chromatography-tandem mass spectrometry, with positive electrospray ionization...
2016: MethodsX
Pirouz Nourian, Romulo Gonçalves, Sisi Zlatanova, Ken Arroyo Ohori, Anh Vu Vo
Voxel representations have been used for years in scientific computation and medical imaging. The main focus of our research is to provide easy access to methods for making large-scale voxel models of built environment for environmental modelling studies while ensuring they are spatially correct, meaning they correctly represent topological and semantic relations among objects. In this article, we present algorithms that generate voxels (volumetric pixels) out of point cloud, curve, or surface objects. The algorithms for voxelization of surfaces and curves are a customization of the topological voxelization approach [1]; we additionally provide an extension of this method for voxelization of point clouds...
2016: MethodsX
Stephanie R A Botelho, Thais P Martins, Macária F Duarte, Andreza V Barbosa, Douglas Lau, Fernanda R Fernandes, Marcio M Sanches
Seeds that contain large amounts of oil, starch, fibers and phenols are the most difficult tissues for RNA extraction. Currently, there are some reports of virus detection in seeds using commercial kits for RNA extraction. However, individual seeds were used, which may not be always suitable for analyses that deal with large amounts of seeds. Sangha [1] described a simple, quick and efficient protocol for RNA extraction and downstream applications in a group of seeds of jatropha (Jatropha curcas), mustard (Brassica sp...
2016: MethodsX
Eduardo Vitarelli de Queiroz, João Luiz Baptista de Carvalho
The curvature of the sea wave was tested as a parameter for estimating wave direction in the search for better results in estimates of wave direction in shallow waters, where waves of different sizes, frequencies and directions intersect and it is difficult to characterize. We used numerical simulations of the sea surface to determine wave direction calculated from the curvature of the waves. Using 1000 numerical simulations, the statistical variability of the wave direction was determined. The results showed good performance by the curvature parameter for estimating wave direction...
2016: MethodsX
Navid Ziaei-Darounkalaei, Mehrdad Ameri, Taghi Zahraei-Salehi, Omid Ziaei-Darounkalaei, Tahereh Mohajer-Tabrizi, Lotfollah Bornaei
The attempts via introducing many methods have been conducted to select the best antibiotic combination in the treatment of seriously ill patients. Operational or interpretational complexity or time-consuming along with sufficient accuracy led to postpone routine clinical use of these tests until today, despite the urgent need for them. By this study and proposed method, selection of the best double antibiotic synergistic combination against resistant pathogen is simply same as Kirby-Bauer antibiotic susceptibility test...
2016: MethodsX
Maria Chiara Fontanella, Gian Maria Beone
This work provides a method with application of valid techniques to extract and determinate inorganic species of antimony (Sb) for water. The procedure involves•the simultaneous accumulation of Sb(III) and Sb(V) on passive samplers like Diffusive Gradient in Thin Films (DGT) with iron (Fe) oxide gel, eliminating the risk of speciation changes due to transport and storage;•application of less concentrated acid (50 mM Na2EDTA) for elution and preservation of Sb species from DGT resin;•subsequent analytical determination of inorganic species with High Performance Liquid Chromatography-Isotopic Dilution-Inductively Coupled Plasma Mass Spectrometer (HPLC-ID-ICP MS) based on determination of the isotope ratio ((123)Sb/(121)Sb) of isotopes in the samples after spiking with 123Sb enriched standard solution, reducing the effect of signal drift and matrix effect on the final value...
2016: MethodsX
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