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https://www.readbyqxmd.com/read/28070500/chimeric-influenza-haemagglutinins-generation-and-use-in-pseudotype-neutralization-assays
#1
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
https://www.readbyqxmd.com/read/28053880/adapting-axelrod-s-cultural-dissemination-model-for-simulating-peer-effects
#2
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
https://www.readbyqxmd.com/read/28003965/a-method-to-implement-the-reservoir-wave-hypothesis-using-phase-contrast-magnetic-resonance-imaging
#3
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
https://www.readbyqxmd.com/read/27942465/longqt-a-cardiac-electrophysiology-simulation-platform
#4
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
https://www.readbyqxmd.com/read/27924282/a-computationally-efficient-algorithm-for-fitting-ion-channel-parameters
#5
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
https://www.readbyqxmd.com/read/27872822/automating-hesc-differentiation-with-3d-printing-and-legacy-liquid-handling-solutions
#6
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
https://www.readbyqxmd.com/read/27822451/so-much-data-so-little-time-using-sequential-data-analysis-to-monitor-behavioral-changes
#7
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
https://www.readbyqxmd.com/read/27822450/a-simple-and-effective-method-for-ultrastructural-analysis-of-mitosis-in-drosophila-s2-cells
#8
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
https://www.readbyqxmd.com/read/27818948/fabrication-and-characterization-of-carbon-backed-thin-208-pb-targets
#9
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
https://www.readbyqxmd.com/read/27774412/100%C3%A2-hz-neutron-radiography-at-the-boa-beamline-using-a-parabolic-focussing-guide
#10
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
https://www.readbyqxmd.com/read/27766212/vacuum-system-upgrade-for-extended-q-range-small-angle-neutron-scattering-diffractometer-eq-sans-at-sns
#11
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
https://www.readbyqxmd.com/read/27709068/bquant-novel-script-for-batch-quantification-of-lcms-data
#12
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
https://www.readbyqxmd.com/read/27630821/direct-field-method-for-root-biomass-quantification-in-agroecosystems
#13
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
https://www.readbyqxmd.com/read/27617231/use-of-cross-reactivity-immunoassay-to-orient-insulin-replacement-in-diabetic-patients-with-high-levels-of-insulin-antibodies
#14
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
https://www.readbyqxmd.com/read/27556015/a-re-usable-wave-bioreactor-for-protein-production-in-insect-cells
#15
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
https://www.readbyqxmd.com/read/27504267/a-simple-low-cost-gc-ms-method-for-the-sub-nanogram-per-litre-measurement-of-organotins-in-coastal-water
#16
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
https://www.readbyqxmd.com/read/27489781/a-genetically-encoded-bioluminescent-indicator-for-illuminating-proinflammatory-cytokines
#17
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
https://www.readbyqxmd.com/read/27489780/a-landscape-based-cluster-analysis-using-recursive-search-instead-of-a-threshold-parameter
#18
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
https://www.readbyqxmd.com/read/27408833/an-lc-ms-ms-method-for-the-determination-of-budesonide-and-16%C3%AE-hydroxyprednisolone-in-dog-plasma
#19
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
https://www.readbyqxmd.com/read/27408832/voxelization-algorithms-for-geospatial-applications-computational-methods-for-voxelating-spatial-datasets-of-3d-city-models-containing-3d-surface-curve-and-point-data-models
#20
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
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