| 1. |
- Miliotis, T., et al.
(author)
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Development of silicon microstructures and thin-film MALDI target plates for automated proteomics sample identifications
- 2001
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 1872-678X .- 0165-0270. ; 109:1, s. 41-46
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Journal article (peer-reviewed)abstract
- Here we report on the development of a proteomic platform utilizing a piezoelectric flow-through dispensing unit made from silicon microstructures. The use of a novel surface coating, where matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI MS) targets were uniformly precoated with a thin film of matrix/nitrocellulose, made the sample preparation straightforward and enabled the enrichment and analysis of proteins at low levels in proteomics samples. We demonstrate this by analyzing excised spots in a biological sample originating from a human fetal fibroblast cell line that was subjected to 2D gel-electrophoresis. Furthermore, a sample deposition rate below 30 Hz results in an increased analyte density on the dispensed sample spot, rendering signal amplification. In general, the sensitivity for proteins and peptides can be enhanced 10-50 times compared to traditional MALDI sample preparation techniques. (C) 2001 Elsevier Science B.V. All rights reserved.
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| 2. |
- Bergquist, Jonas, et al.
(author)
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Capillary electrophoresis with laser-induced fluorescence detection : a sensitive method for monitoring extracellular concentrations of amino acids in the periaqueductal grey matter.
- 1996
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 65:1, s. 33-42
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Journal article (peer-reviewed)abstract
- The use of capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) for the analysis of microdialysate samples from the periaqueductal grey matter (PAG) of freely moving rats is described. By employing 3-(4-carboxybenzoyl)-2-quinoline-carboxaldehyde (CBQCA) as a derivatization agent, we simultaneously monitored the concentrations of 8 amino acids (arginine, glutamine, valine, gamma-amino-n-butyric acid (GABA), alanine, glycine, glutamate, and aspartate), with nanomolar and subnanomolar detection limits. Two of the amino acids (GABA and glutamate) were analysed in parallel by conventional high-performance liquid chromatography (HPLC) in order to directly compare the two analytical methods. Other CE methods for analysis of microdialysate have been previously described, and this improved method offers greater sensitivity, ease of use, and the possibility to monitor several amino acids simultaneously. By using this technique together with an optimised form of microdialysis technique, the tiny sample consumption and the improved detection limits permit the detection of fast and transient transmitter changes.
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| 3. |
- Isaac, Giorgis, et al.
(author)
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Analysis of phosphatidylcholine and sphingomyelin molecular species from brain extracts using capillary liquid chromatography electrospray ionization mass spectrometry
- 2003
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In: Journal of Neuroscience Methods. - 0165-0270 .- 1872-678X. ; 128:1-2, s. 111-119
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Journal article (peer-reviewed)abstract
- One feature of complex lipids is that many subtypes of these molecules exist as a diverse mixture in a biological sample. Qualitative and quantitative analysis of these closely related molecules require sensitive and specific analytical methods to detect intact phospholipids (PL) and sphingomyelin (SM) species and to differentiate between them. Conventional analytical methods require laborious procedures including separation by column, argentation thin-layer chromatography or liquid chromatography (LC) after pre- or post-column derivatization. In the present work, a method based on reversed phase capillary LC coupled on-line to electrospray ionization mass spectrometry (LC/ESI/MS) has been developed to gather tools for lipidomic studies, i.e. the profiling of complex mixtures of lipids in small amounts of various cells and tissues. The LC/MS system used consisted of an LC pump in an isocratic elution, a reversed phase capillary column and a single quadrupole mass spectrometer operated in the positive ion mode. A successful separation of phosphatidylcholine (PC) and SM molecular species was obtained with a minimum detectable quantity (MDQ) in the low fmol range injected on column. The method was applied to human brain extracts. Furthermore, the extraction efficiencies of the traditional Folch method and pressurized fluid extraction (PFE) were compared using the human brain. It was found that the intensity of the PC and SM molecular species extracted by PFE is two times that of Folch.
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| 4. |
- Novikov, Lev N
(author)
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Labeling of central projections of primary afferents in adult rats : a comparison between biotinylated dextran amine, neurobiotin and Phaseolus vulgaris-leucoagglutinin.
- 2001
-
In: Journal of Neuroscience Methods. - 0165-0270 .- 1872-678X. ; 112:2, s. 145-154
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Journal article (peer-reviewed)abstract
- The efficacy of anterograde labeling of the central projections of primary afferent fibers were compared between biotinylated dextran amine (BDA), neurobiotin (NB) and Phaseolus vulgaris-leucoagglutinin (PHA-L) after injections into the L5 or T13 dorsal root ganglia (DRGs) of adult rats. Excellent labeling was obtained with BDA, which visualized fibers with fine terminal boutons in the L5 and T13 spinal cord segments, Clarke's nucleus and the gracile nucleus. Rarely observed crossed projections to the gracile nucleus and L5 ventral horn of the contralateral side could also be distinguished. Even in the most successful experiments, however, BDA labeled only about one-third of the axons originating from the injected dorsal root ganglion. BDA was also efficient as transganglionic tracer after application to the transected sciatic nerve. NB produced no significant labeling of the L5 primary afferents, and was only moderately effective on the T13 level. PHA injections resulted in sparse terminal labeling of the T13 and L5 afferents. Thus, BDA is an effective tracer for long-range labeling of primary afferent projections in the spinal cord and brain stem. Since not all stem fibers become labeled, however, the method does not allow quantification of all axon branches and terminals arising from the injected DRGs.
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| 5. |
- Öhberg, Fredrik, 1969-, et al.
(author)
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A neural network appoach to real-time spike discrimination during simultaneous recording from several multi-unit nerve filaments
- 1996
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 64:2, s. 181-187
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Journal article (peer-reviewed)abstract
- A multi-channel, real-time, unsupervised spike discriminator was developed in order to reconstruct single spike trains from several simultaneously recorded multi-unit nerve filaments. The program uses a Self Organising Map (SOM) algorithm for the classification of the spikes. In contrast to previous similar techniques, the described method is made for use on a PC, and the method may thus be implemented at relatively low cost. In order to test the accuracy of the program, a robustness test was performed, where noise with different RMS levels was superimposed on the spikes. Furthermore, the maximal classification rate was determined. The program is easy to use, since the only manual inputs needed are the voltage threshold for spike detection, and the number of units present in each recorded nerve filament.
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| 6. |
- Afzali, Maryam, et al.
(author)
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The sensitivity of diffusion MRI to microstructural properties and experimental factors
- 2021
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In: Journal of Neuroscience Methods. - : ELSEVIER. - 0165-0270 .- 1872-678X. ; 347
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Research review (peer-reviewed)abstract
- Diffusion MRI is a non-invasive technique to study brain microstructure. Differences in the microstructural properties of tissue, including size and anisotropy, can be represented in the signal if the appropriate method of acquisition is used. However, to depict the underlying properties, special care must be taken when designing the acquisition protocol as any changes in the procedure might impact on quantitative measurements. This work reviews state-of-the-art methods for studying brain microstructure using diffusion MRI and their sensitivity to microstructural differences and various experimental factors. Microstructural properties of the tissue at a micrometer scale can be linked to the diffusion signal at a millimeter-scale using modeling. In this paper, we first give an introduction to diffusion MRI and different encoding schemes. Then, signal representation-based methods and multi-compartment models are explained briefly. The sensitivity of the diffusion MRI signal to the microstructural components and the effects of curvedness of axonal trajectories on the diffusion signal are reviewed. Factors that impact on the quality (accuracy and precision) of derived metrics are then reviewed, including the impact of random noise, and variations in the acquisition parameters (i.e., number of sampled signals, b-value and number of acquisition shells). Finally, yet importantly, typical approaches to deal with experimental factors are depicted, including unbiased measures and harmonization. We conclude the review with some future directions and recommendations on this topic.
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| 7. |
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| 8. |
- Ahemaiti, Aikeremu, 1984, et al.
(author)
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A multifunctional pipette for localized drug administration to brain slices
- 2013
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 219:2, s. 292-296
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Journal article (peer-reviewed)abstract
- We have developed a superfusion method utilizing an open-volume microfluidic device for administration of pharmacologically active substances to selected areas in brain slices with high spatio-temporal resolution. The method consists of a hydrodynamically confined flow of the active chemical compound, which locally stimulates neurons in brain slices, applied in conjunction with electrophysiological recording techniques to analyze the response. The microfluidic device, which is a novel free-standing multifunctional pipette, allows diverse superfusion experiments, such as testing the effects of different concentrations of drugs or drug candidates on neurons in different cell layers with high positional accuracy, affecting only a small number of cells. We demonstrate herein the use of the method with electrophysiological recordings of pyramidal cells in hippocampal and prefrontal cortex brain slices from rats, determine the dependence of electric responses on the distance of the superfusion device from the recording site, document a multifold gain in solution exchange time as compared to whole slice perfusion, and show that the device is able to store and deliver up to four solutions in a series. Localized solution delivery by means of open-volume microfluidic technology also reduces reagent consumption and tissue culture expenses significantly, while allowing more data to be collected from a single tissue slice, thus reducing the number of laboratory animals to be sacrificed for a study. (C) 2013 Elsevier B.V. All rights reserved.
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| 9. |
- Ahemaiti, Aikeremu, 1984, et al.
(author)
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Spatial characterization of a multifunctional pipette for drug delivery in hippocampal brain slices
- 2015
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 241, s. 132-136
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Journal article (peer-reviewed)abstract
- Background: Among the various fluidic control technologies, microfluidic devices are becoming powerful tools for pharmacological studies using brain slices, since these devices overcome traditional limitations of conventional submerged slice chambers, leading to better spatiotemporal control over delivery of drugs to specific regions in the slices. However, microfluidic devices are not yet fully optimized for such studies. New method: We have recently developed a multifunctional pipette (MFP), a free standing hydrodynamically confined microfluidic device, which provides improved spatiotemporal control over drug delivery to biological tissues. Results: We demonstrate herein the ability of the MFP to selectively perfuse one dendritic layer in the CA1 region of hippocampus with CNQX, an AMPA receptor antagonist, while not affecting the other layers in this region. Our experiments also illustrate the essential role of hydrodynamic confinement in sharpening the spatial selectivity in brain slice experiments. Concentration-response measurements revealed that the ability of the MFP to control local drug concentration is comparable with that of whole slice perfusion, while in comparison the required amounts of active compounds can be reduced by several orders of magnitude. Comparison with existing method: The multifunctional pipette is applied with an angle, which, compared to other hydrodynamically confined microfluidic devices, provides more accessible space for other probing and imaging techniques. Conclusions: Using the MFP it will be possible to study selected regions of brain slices, integrated with various imaging and probing techniques, without affecting the other parts of the slices.
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| 10. |
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| 11. |
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| 12. |
- Bastlund, JF, et al.
(author)
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Measurement of cortical and hippocampal epileptiform activity in freely moving rats by means of implantable radiotelemetry
- 2004
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 1872-678X .- 0165-0270. ; 138:1-2, s. 65-72
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Journal article (peer-reviewed)abstract
- Implanted radiotelemetry has been used for the measurement of cortical electroencephalogram (EEG), locomotor activity, body temperature and cardiovascular parameters. This technique allows high quality data acquisition from freely moving animals with no complications of externalised apparatus. This paper focuses on the methodology for short and long-term monitoring of epileptiform activity by simultaneous cortical EEG, hippocampal (HC) EEG and electromyogram (EMG) in rats. The circadian rhythm of temperature (CRT) was monitored after surgery to estimate the need for post surgical recovery of animals. Different placements of EMG electrodes were assessed in order to minimise artefacts and increase sensitivity. The occurrence of epileptiform ictal and interictal activity following an acute injection of either 40 mg/kg pentylenetetrazole (PTZ) or 13.8 mg/kg kainic acid (KA) was investigated. The occurrence of spontaneous seizures was also monitored 5-8 weeks after administration of KA. The present study demonstrated a sensitive method for monitoring cortical EEG, hippocampal EEG and EMG short and long-term by implantable radiotelemetry in freely moving rats.
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| 13. |
- Bikovski, Lior, et al.
(author)
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Lessons, insights and newly developed tools emerging from behavioral phenotyping core facilities
- 2020
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 334
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Research review (peer-reviewed)abstract
- Scientific investigations, in general, and research in neuroscience, in particular, are becoming ever more complex and require the integration of different techniques. Behavioral assays, which are among the most frequently used methodologies in neuroscience, nowadays rely on advanced, sophisticated technologies that require proficient application. Therefore, behavioral core facilities are becoming essential support units, as they provide the specialized expert research services needed to conduct advanced neuroscience. We here review the lessons learned and insights gathered from managing behavioral core facilities in different academic research institutes. This review addresses several issues, including: the advantages of behavioral core facilities, considerations for establishing a behavioral core facility, and the methodological advances made through calibration and standardization of assay protocols and the development of new assays. Collectively, the review highlights the benefits of both working within and collaborating with behavioral core facility units and emphasizes the potential progress in neuro-phenotyping that such facilities provide.
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| 14. |
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| 15. |
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| 16. |
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| 17. |
- Censoni, Luciano, et al.
(author)
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Verification of multi-structure targeting in chronic microelectrode brain recordings from CT scans
- 2022
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In: Journal of Neuroscience Methods. - : Elsevier. - 0165-0270 .- 1872-678X. ; 382
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Journal article (peer-reviewed)abstract
- Background: Large-scale microelectrode recordings offer a unique opportunity to study neurophysiological processes at the network level with single cell resolution. However, in the small brains of many experimental animals, it is often technically challenging to verify the correct targeting of the intended structures, which inherently limits the reproducibility of acquired data.New method: To mitigate this problem, we have developed a method to programmatically segment the trajectory of electrodes arranged in larger arrays from acquired CT-images and thereby determine the position of individual recording tips with high spatial resolution, while also allowing for coregistration with an anatomical atlas, without pre-processing of the animal samples or post-imaging histological analyses.Results: Testing the technical limitations of the developed method, we found that the choice of scanning angle influences the achievable spatial resolution due to shadowing effects caused by the electrodes. However, under optimal acquisition conditions, individual electrode tip locations within arrays with 250 µm inter-electrode spacing were possible to reliably determine.Comparison to existing methods: Comparison to a histological verification method suggested that, under conditions where individual wires are possible to track in slices, a 90% correspondence could be achieved in terms of the number of electrodes groups that could be reliably assigned to the same anatomical structure.Conclusions: The herein reported semi-automated procedure to verify anatomical targeting of brain structures in the rodent brain could help increasing the quality and reproducibility of acquired neurophysiological data by reducing the risk of assigning recorded brain activity to incorrectly identified anatomical locations.
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| 18. |
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| 19. |
- Dizdar (Dizdar Segrell), Nil, et al.
(author)
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Letter: Untitled
- 2013
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In: Journal of Neuroscience Methods. - : Elsevier. - 0165-0270 .- 1872-678X. ; 212:2, s. 363-363
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Journal article (peer-reviewed)abstract
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| 20. |
- Dublon, Ian, et al.
(author)
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Scintillate : An open-source graphical viewer for time-series calcium imaging evaluation and pre-processing
- 2016
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 273, s. 120-127
-
Journal article (peer-reviewed)abstract
- Background Calcium imaging is based on the detection of minute signal changes in an image time-series encompassing pre- and post-stimuli. Depending on the function of the elicited response, change may be pronounced, as in the case of a genetically encoded calcium-reporter protein, or subtle, as is the case in a bath-applied dye system. Large datasets are thus often acquired and appraised only during post-processing where specific Regions of Interest (ROIs) are examined. New method The scintillate software provides a platform allowing for near instantaneous viewing of time-sequenced tiffs within a discrete GUI environment. Whole sequences may be evaluated. In its simplest form scintillate provides change in florescence (ΔF) across the entire tiff image matrix. Evaluating image intensity level differences across the whole image allows the user to rapidly establish the value of the preparation, without a priori ROI-selection. Additionally, an implementation of Independent Component Analysis (ICA) provides additional rapid insights into areas of signal change. Results We imaged transgenic flies expressing Calcium-sensitive reporter proteins within projection neurons and moth mushroom bodies stained with a Ca2+ sensitive bath-applied dye. Instantaneous pre-stimulation background subtraction allowed us to appraise strong genetically encoded neuronal Ca2+ responses in flies and weaker, less apparent, responses within moth mushroom bodies. Comparison with existing methods At the time of acquisition, whole matrix ΔF analysis alongside ICA is ordinarily not performed. We found it invaluable, minimising time spent with unresponsive samples, and assisting in optimisation of subsequent acquisitions. Conclusions We provide a multi-platform open-source system to evaluate time-series images.
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| 21. |
- Edin, Benoni B, et al.
(author)
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Single unit retrieval in microneurography : a microprocessor-based device controlled by an operator.
- 1988
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In: Journal of Neuroscience Methods. - 0165-0270 .- 1872-678X. ; 24:2, s. 137-144
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Journal article (peer-reviewed)abstract
- A microprocessor-based device was constructed to retrieve single unit activity from nerve recordings contaminated by other units and EMG activity. The microneurographic signal is sampled at 10 kHz and an algorithm applied to identify impulses from a single nerve fibre. On line, a TTL pulse is delivered when an event, i.e. a provisional nerve impulse, is selected. The wave form and clock time of events are stored. Moreover, the latest selected event and the actual selection criteria are continuously displayed on a standard oscilloscope. Off line, the wave form and clock time of events as well as an instantaneous frequency plot can be displayed on the oscilloscope. The final selection of events is done with a combination of a second algorithm, which essentially is a wave form comparator, and a manual check. The device is controlled either by hardware, with knobs on the front panel, or by software through a data bus connected to a microcomputer. Clock times and wave forms of the events, which are stored in the microprocessor memory, may also be presented on the data bus for later off-line analysis and coordination with other related signals collected during the experiment, e.g. transducer and electromyography records, whether these were stored on analog or digital tape or computer disc. Compared to other available techniques, the device has a superior discriminative power when electromyographic artefacts are present.
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| 22. |
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
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| 28. |
- Grand, Laszlo, et al.
(author)
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Short and long term biocompatibility of NeuroProbes silicon probes
- 2010
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 189:2, s. 216-229
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Journal article (peer-reviewed)abstract
- Brain implants provide exceptional tools to understand and restore cerebral functions. The utility of these devices depends crucially on their biocompatibility and long term viability. We addressed these points by implanting non-functional, NeuroProbes silicon probes, without or with hyaluronic acid (Hya), dextran (Dex), dexamethasone (DexM), Hya + DexM coating, into rat neocortex. Light and transmission electron microscopy were used to investigate neuronal survival and glial response. The surface of explanted probes was examined in the scanning electron microscope. We show that blood vessel disruption during implantation could induce considerable tissue damage. If, however, probes could be inserted without major bleeding, light microscopical evidence of damage to surrounding neocortical tissue was much reduced. At distances less than 100 mu m from the probe track a considerable neuron loss (similar to 40%) occurred at short survival times, while the neuronal numbers recovered close to control levels at longer survival. Slight gliosis was observed at both short and long term survivals. Electron microscopy showed neuronal cell bodies and synapses close (<10 mu m) to the probe track when bleeding could be avoided. The explanted probes were usually partly covered by tissue residue containing cells with different morphology. Our data suggest that NeuroProbes silicon probes are highly biocompatible. If major blood vessel disruption can be avoided, the low neuronal cell loss and gliosis should provide good recording and stimulating results with future functional probes. We found that different bioactive molecule coatings had small differential effects on neural cell numbers and gliosis, with optimal results achieved using the DexM coated probes. (C) 2010 Elsevier B.V. All rights reserved.
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| 29. |
- Hanrieder, Jörg, 1980, et al.
(author)
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Temporally resolved differential proteomic analysis of human ventricular CSF for monitoring traumatic brain injury biomarker candidates.
- 2009
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In: Journal of neuroscience methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 177:2, s. 469-78
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Journal article (peer-reviewed)abstract
- A shotgun proteomic approach based on nanoflow liquid chromatography (nanoLC) in conjunction with matrix assisted laser desorption/ionization time of flight tandem mass spectrometry (MALDI TOF MS/MS) was utilized to quantitatively analyze the protein content of consecutive ventricular cerebrospinal fluid (CSF) samples of severe traumatic brain injury (TBI) patients on an individual basis. CSF was acquired from the lateral ventricle 1-9 days after the TBI incident by canula drain to investigate temporally resolved protein changes in three patients that required intracranial pressure monitoring during neurointensive care. The samples were subjected to at once tryptic digestion followed by isobaric tag labeling before multiplexed peptide separation and MS analysis. By using this approach, we were able to follow characteristic changes in protein concentrations over time allowing new conclusions to be drawn about ongoing pathological processes during TBI. Certain suggested protein-biomarker candidates for TBI, like acute phase reactants (APRs), fibrinogens (FIB), cystatin C (CC) or more brain specific proteins like glial fibrillary acid protein (GFAP) and neuron-specific enolase (NSE) were found to be significantly up-regulated which is in strong consistence with previously reported results. This methodology appears to be a promising tool for studying candidate biomarkers of neurovascular and traumatic brain injuries in the neurointensive care setting.
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| 30. |
- Hanssen, Katrine Sjaastad, et al.
(author)
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Dissection and culturing of adult lateral entorhinal cortex layer II neurons from APP/PS1 Alzheimer model mice
- 2023
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In: Journal of Neuroscience Methods. - : Elsevier. - 0165-0270 .- 1872-678X. ; 390
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Journal article (peer-reviewed)abstract
- Background: Primary neuronal cultures enable cell-biological studies of Alzheimer's disease (AD), albeit typically non-neuron-specific. The first cortical neurons affected in AD reside in layer II of the lateralmost part of the entorhinal cortex, and they undergo early accumulation of intracellular amyloid-β, form subsequent tau pathology, and start degenerating pre-symptomatically. These vulnerable entorhinal neurons uniquely express the glycoprotein reelin and provide selective inputs to the hippocampal memory system. Gaining a more direct access to study these neurons is therefore highly relevant.New method: We demonstrate a methodological approach for dissection and long-term culturing of adult lateral entorhinal layer II-neurons from AD-model mice.Results: We maintain adult dissected lateralmost entorhinal layer II-neurons beyond two months in culture. We show that they express neuronal markers, and that they are electrophysiologically active by 15 days in vitro and continuing beyond 2 months.Comparison with existing methods: Primary neurons are typically harvested from embryonic or early postnatal brains because such neurons are easier to culture compared to adult neurons. Methods to culture adult primary neurons have been reported, however, to our knowledge, culturing of adult entorhinal neuron-type specific primary neurons from AD-model animals have not been reported.Conclusions: Our methodological approach offers a window to study initial pathological changes in the AD disease-cascade. This includes the study of proteinopathy, single-neuron changes, and network-level dysfunction.
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| 31. |
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| 32. |
- Havton, LA, et al.
(author)
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Systemic administration of cholera toxin B subunit conjugated to horseradish peroxidase in the adult rat labels preganglionic autonomic neurons, motoneurons, and select primary afferents for light and electron microscopic studies
- 2005
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 1872-678X .- 0165-0270. ; 149:2, s. 101-109
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Journal article (peer-reviewed)abstract
- Retrograde and transganglionic labeling techniques are commonly used to visualize subsets of neurons and sensory afferent projections in the nervous system. These methods commonly require anesthesia and surgical methods. However, some tracers can also be administered systemically in awake animals, thus reducing risks associated with anesthesia and surgery and allowing for labeling of neuronal populations that are difficult to label with local tracer injections. Here, we demonstrate in the adult rat that intraperitoneal administration of cholera toxin subunit B conjugated to horseradish peroxidase labels preganglionic autonomic neurons, motoneurons, and the terminal projections of select primary afferents for both light and electron microscopic studies. We demonstrate also that this method can be combined with post-embedding immunogold labeling to detect amino acid transmitters in synaptic boutons.
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| 33. |
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| 34. |
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| 35. |
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| 36. |
- Jacob, Stefan, et al.
(author)
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A digital heterodyne laser interferometer for studying cochlear mechanics
- 2009
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 179:2, s. 271-277
-
Journal article (peer-reviewed)abstract
- Laser interferometry is the technique of choice for studying the smallest displacements of the hearing organ. For low intensity sound stimulation, these displacements may be below 1 nm. This cannot be reliably measured with other presently available techniques in an intact organ of Corti. In a heterodyne interferometer, light is projected against an object of study and motion of the target along the optical axis causes phase and frequency modulations of the back-reflected light. To recover object motion, the reflected light is made to interfere with a reference beam of artificially altered frequency, producing a beating signal. In conventional interferometers, this carrier signal is demodulated with analog electronics. In this paper, we describe a digital implementation of the technique, using direct carrier sampling. In order to obtain the necessary reference signal for demodulation we introduce an additional third light path. Together, this results in lower noise and reduces the cost of the system.Within the hearing organ, different structures may move in different directions. It is therefore necessary to precisely measure the angle of incidence of the laser light, and to precisely localize the anatomical structure where the measurement is performed. Therefore, the interferometer is integrated with a laser scanning confocal microscope that permits us to map crucial morphometric parameters in each experiment. We provide key construction parameters and a detailed performance characterization. We also show that the system accurately measures the diminutive vibrations present in the apical turn of the cochlea during low-level sound stimulation.
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| 37. |
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| 38. |
- Keenan, Thomas M, et al.
(author)
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Automated identification of axonal growth cones in time-lapse image sequences.
- 2006
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 151:2, s. 232-8
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Journal article (peer-reviewed)abstract
- The isolation and purification of axon guidance molecules has enabled in vitro studies of the effects of axon guidance molecule gradients on numerous neuronal cell types. In a typical experiment, cultured neurons are exposed to a chemotactic gradient and their growth is recorded by manual identification of the axon tip position from two or more micrographs. Detailed and statistically valid quantification of axon growth requires evaluation of a large number of neurons at closely spaced time points (e.g. using a time-lapse microscopy setup). However, manual tracing becomes increasingly impractical for recording axon growth as the number of time points and/or neurons increases. We present a software tool that automatically identifies and records the axon tip position in each phase-contrast image of a time-lapse series with minimal user involvement. The software outputs several quantitative measures of axon growth, and allows users to develop custom measurements. For, example analysis of growth velocity for a dissociated E13 mouse cortical neuron revealed frequent extension and retraction events with an average growth velocity of 0.05 +/- 0.14 microm/min. Comparison of software-identified axon tip positions with manually identified axon tip positions shows that the software's performance is indistinguishable from that of skilled human users.
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| 39. |
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| 40. |
- Kuznetsova, Tatiana, et al.
(author)
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Visual stimulation with blue wavelength light drives V1 effectively eliminating stray light contamination during two-photon calcium imaging
- 2021
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In: Journal of Neuroscience Methods. - : Elsevier. - 0165-0270 .- 1872-678X. ; 362
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Journal article (peer-reviewed)abstract
- Background: Brain visual circuits are often studied in vivo by imaging Ca2+ indicators with green-shifted emission spectra. Polychromatic white visual stimuli have a spectrum that partially overlaps indicators´ emission spectra, resulting in significant contamination of calcium signals.New method: To overcome light contamination problems we choose blue visual stimuli, having a spectral composition not overlapping with Ca2+ indicator´s emission spectrum. To compare visual responsiveness to blue and white stimuli we used electrophysiology (visual evoked potentials –VEPs) and 3D acousto-optic two-photon (2P) population Ca2+ imaging in mouse primary visual cortex (V1).Results: VEPs in response to blue and white stimuli had comparable peak amplitudes and latencies. Ca2+ imaging in a Thy1 GP4.3 line revealed that the populations of neurons responding to blue and white stimuli were largely overlapping, that their responses had similar amplitudes, and that functional response properties such as orientation and direction selectivities were also comparable.Comparison with existing methods: Masking or shielding the microscope are often used to minimize the contamination of Ca2+ signal by white light, but they are time consuming, bulky and thus can limit experimental design, particularly in the more and more frequently used awake set-up. Blue stimuli not interfering with imaging allow to omit shielding.Conclusions: Together, our results show that the selected blue light stimuli evoke responses comparable to those evoked by white stimuli in mouse V1. This will make complex designs of imaging experiments in behavioral set-ups easier, and facilitate the combination of Ca2+ imaging with electrophysiology and optogenetics.
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| 41. |
- Langer, Dominik, et al.
(author)
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HelioScan : A software framework for controlling in vivo microscopy setups with high hardware flexibility, functional diversity and extendibility
- 2013
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 215:1, s. 38-52
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Journal article (peer-reviewed)abstract
- Intravital microscopy such as in vivo imaging of brain dynamics is often performed with custom-built microscope setups controlled by custom-written software to meet specific requirements. Continuous technological advancement in the field has created a need for new control software that is flexible enough to support the biological researcher with innovative imaging techniques and provide the developer with a solid platform for quickly and easily implementing new extensions. Here, we introduce HelioScan, a software package written in LabVIEW, as a platform serving this dual role. HelioScan is designed as a collection of components that can be flexibly assembled into microscope control software tailored to the particular hardware and functionality requirements. Moreover, HelioScan provides a software framework, within which new functionality can be implemented in a quick and structured manner. A specific HelioScan application assembles at run-time from individual software components, based on user-definable configuration files. Due to its component-based architecture, HelioScan can exploit synergies of multiple developers working in parallel on different components in a community effort. We exemplify the capabilities and versatility of HelioScan by demonstrating several in vivo brain imaging modes, including camera-based intrinsic optical signal imaging for functional mapping of cortical areas, standard two-photon laser-scanning microscopy using galvanometric mirrors, and high-speed in vivo two-photon calcium imaging using either acousto-optic deflectors or a resonant scanner. We recommend HelioScan as a convenient software framework for the in vivo imaging community.
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| 42. |
- Larsson, Linnéa, et al.
(author)
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Head Movement Compensation and Multi-Modal Event Detection in Eye-Tracking Data for Unconstrained Head Movements
- 2016
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 1872-678X .- 0165-0270. ; 274, s. 13-26
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Journal article (peer-reviewed)abstract
- BackgroundThe complexity of analyzing eye-tracking signals increases as eye-trackers become more mobile. The signals from a mobile eye-tracker are recorded in relation to the head coordinate system and when the head and body move, the recorded eye-tracking signal is influenced by these movements, which render the subsequent event detection difficult.New methodThe purpose of the present paper is to develop a method that performs robust event detection in signals recorded using a mobile eye-tracker. The proposed method performs compensation of head movements recorded using an inertial measurement unit and employs a multi-modal event detection algorithm. The event detection algorithm is based on the head compensated eye-tracking signal combined with information about detected objects extracted from the scene camera of the mobile eye-tracker.ResultsThe method is evaluated when participants are seated 2.6 m in front of a big screen, and is therefore only valid for distant targets. The proposed method for head compensation decreases the standard deviation during intervals of fixations from 8° to 3.3° for eye-tracking signals recorded during large head movements.Comparison with existing methodsThe multi-modal event detection algorithm outperforms both an existing algorithm (I-VDT) and the built-in-algorithm of the mobile eye-tracker with an average balanced accuracy, calculated over all types of eye movements, of 0.90, compared to 0.85 and 0.75, respectively for the compared algorithms.ConclusionsThe proposed event detector that combines head movement compensation and information regarding detected objects in the scene video enables for improved classification of events in mobile eye-tracking data.
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| 43. |
- Latini, Francesco, et al.
(author)
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The use of a cerebral perfusion and immersion-fixation process for subsequent white matter dissection
- 2015
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 253, s. 161-169
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Journal article (peer-reviewed)abstract
- Background: The Klingler's method for white matter dissection revolutionized the study of deep cerebral anatomy. Although this technique made white matter dissection more feasible and widely used, it still presents some intrinsic limitations. New method: We evaluated the quality of different methods for specimen preparation based on an intra-carotidal formalin perfusion fixation process. Ten post-mortem human hemispheres were prepared with this method and dissected in a stepwise manner. Results: The homogeneous and rapid fixation of the brain allowed documentation of several fine additional anatomical details. Intra-cortical white matter terminations were described during the first stage of dissection on each specimen. No limitations were encountered during dissection of the major associative bundles. On the contrary, the quality of the fixation of the specimens made it possible to isolate them en bloc. One of the most complex and deep bundles (accumbo-frontal fasciculus) was dissected without technical limitations. Deep vascular structures were very well preserved and dissected within the white matter until their sub-millimetric terminations. Comparison with existing method: Short time for preparation, a more homogeneous fixation, no technical limitation for a detailed description of superficial and deep white matter anatomy, the possibility to dissect with a single technique the fibre organization and the white matter vascular architecture are the advantages reported with the perfusion fixation. Conclusion: These results provide encouraging data about the possibility to use a perfusion fixation process, which may help in improving the quality of white matter dissection for research, didactic purposes and surgical training.
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| 44. |
- Liu, Jia, et al.
(author)
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Analysis of modulations of mental fatigue on intra-individual variability from single-trial event related potentials
- 2024
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In: JOURNAL OF NEUROSCIENCE METHODS. - 0165-0270 .- 1872-678X. ; 406
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Journal article (peer-reviewed)abstract
- Background: Intra-individual variability (IIV), a measure of variance within an individual's performance, has been demonstrated as metrics of brain responses for neural functionality. However, how mental fatigue modulates IIV remains unclear. Consequently, the development of robust mental fatigue detection methods at the single-trial level is challenging. New methods: Based on a long-duration flanker task EEG dataset, the modulations of mental fatigue on IIV were explored in terms of response time (RT) and trial-to-trial latency variations of event-related potentials (ERPs). Specifically, latency variations were quantified using residue iteration decomposition (RIDE) to reconstruct latency-corrected ERPs. We compared reconstructed ERPs with raw ERPs by means of temporal principal component analysis (PCA). Furthermore, a single-trial classification pipeline was developed to detect the changes of mental fatigue levels. Results: We found an increased IIV in the RT metric in the fatigue state compared to the alert state. The same sequence of ERPs (N1, P2, N2, P3a, P3b, and slow wave, or SW) was separated from both raw and reconstructed ERPs using PCA, whereas differences between raw and reconstructed ERPs in explained variances for separated ERPs were found owing to IIV. Particularly, a stronger N2 was detected in the fatigue than alert state after RIDE. The single-trial fatigue detection pipeline yielded an acceptable accuracy of 73.3%. Comparison with existing methods: The IIV has been linked to aging and brain disorders, and as an extension, our finding demonstrates IIV as an efficient indicator of mental fatigue. Conclusions: This study reveals significant modulations of mental fatigue on IIV at the behavioral and neural levels and establishes a robust mental fatigue detection pipeline.
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| 45. |
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| 46. |
- Lu, Han, et al.
(author)
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A microfluidic perspective on conventional in vitro transcranial direct current stimulation methods
- 2023
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In: Journal of Neuroscience Methods. - : Elsevier B.V.. - 0165-0270 .- 1872-678X. ; 385
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Research review (peer-reviewed)abstract
- Transcranial direct current stimulation (tDCS) is a promising non-invasive brain stimulation method to treat neurological and psychiatric diseases. However, its underlying neural mechanisms warrant further investigation. Indeed, dose–response interrelations are poorly understood. Placing explanted brain tissue, mostly from mice or rats, into a uniform direct current electric field (dcEF) is a well-established in vitro system to elucidate the neural mechanism of tDCS. Nevertheless, we will show that generating a defined, uniform, and constant dcEF throughout a brain slice is challenging. This article critically reviews the methods used to generate and calibrate a uniform dcEF. We use finite element analysis (FEA) to evaluate the widely used parallel electrode configuration and show that it may not reliably generate uniform dcEF within a brain slice inside an open interface or submerged chamber. Moreover, equivalent circuit analysis and measurements inside a testing chamber suggest that calibrating the dcEF intensity with two recording electrodes can inaccurately capture the true EF magnitude in the targeted tissue when specific criteria are not met. Finally, we outline why microfluidic chambers are an effective and calibration-free approach of generating spatiotemporally uniform dcEF for DCS in vitro studies, facilitating accurate and fine-scale dcEF adjustments. We are convinced that improving the precision and addressing the limitations of current experimental platforms will substantially improve the reproducibility of in vitro experimental results. A better mechanistic understanding of dose–response relations will ultimately facilitate more effective non-invasive stimulation therapies in patients.
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| 47. |
- Martens-Lobenhoffer, Jens, et al.
(author)
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Determination of cerebrospinal fluid concentrations of arginine and dimethylarginines in patients with subarachnoid haemorrhage
- 2007
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In: Journal of Neuroscience Methods. - : Elsevier. - 0165-0270 .- 1872-678X. ; 164:1, s. 155-160
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Journal article (peer-reviewed)abstract
- Elevated cerebrospinal fluid (CSF) concentrations of asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthase (NOS), are assumed to be related to delayed vasospasm after subarachnoid haemorrhage (SAH). However, data on CSF concentrations of L-arginine, ADMA and its structural isomer symmetric dimethylarginine (SDMA) are very sparse in humans. We here present a new hydrophilic interaction chromatography-tandem mass spectrometry (HILIC-MS-MS) method for the precise determination of these substances in CSF. The method requires only minimal sample preparation and features isotope labeled internal standards. First data of patients with SAH showed that on the day of admission CSF concentration values of L-arginine and ADMA were not significantly different from controls, but increased markedly during the course of the hospital stay. The decrease of the L-arginine to ADMA ratio points to a progressive impairment of the NO production rate in the brain after SAH which is confirmed by a simultaneous decrease in nitrate and nitrite concentrations in CSF.
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| 48. |
- Mohlin, Camilla, 1972-, et al.
(author)
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Death of photoreceptors in organotypic retinal explant cultures: implication of rhodopsin accumulation and endoplasmic reticulum stress.
- 2011
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 0165-0270 .- 1872-678X. ; 197:1, s. 56-64
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Journal article (peer-reviewed)abstract
- Here we suggest that endoplasmic reticulum (ER)-stress may be induced following aberrant rhodopsin accumulation in photoreceptors in explanted rat retinas. Rhodopsin accumulation was accompanied by increased phosphorylation of pancreatic ER-kinase and eukaryotic initiator factor 2α as well as increased levels of C/EBP homologous protein, glucose-regulated protein 78 and eventually increased cleaved caspase-12 and cleaved caspase-3. Glucose-regulated protein 78, pancreatic ER-kinase, caspase-12 and cleaved caspase-3 were present in photoreceptors, indicating that ER-stress and apoptosis are induced in this cell population. These results suggest that ER-stress and subsequent apoptosis is induced in healthy photoreceptors, presumably by aberrant accumulation of rhodopsin and the phosphorylation of eukaryotic initiator factor 2α. The explant culture system may allow investigations of neuroprotective strategies.
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| 49. |
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| 50. |
- Moore, Richard JD, et al.
(author)
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FicTrac: A visual method for tracking spherical motion and generating fictive animal paths
- 2014
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In: Journal of Neuroscience Methods. - : Elsevier BV. - 1872-678X .- 0165-0270. ; 225, s. 106-119
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Journal article (peer-reviewed)abstract
- Studying how animals interface with a virtual reality can further our understanding of how attention, learning and memory, sensory processing, and navigation are handled by the brain, at both the neurophysiological and behavioural levels. To this end, we have developed a novel vision-based tracking system, FicTrac (Fictive path Tracking software), for estimating the path an animal makes whilst rotating an air-supported sphere using only input from a standard camera and computer vision techniques. We have found that the accuracy and robustness of FicTrac outperforms a low-cost implementation of a standard optical mouse-based approach for generating fictive paths. FicTrac is simple to implement for a wide variety of experimental configurations and, importantly, is fast to execute, enabling real-time sensory feedback for behaving animals. We have used FicTrac to record the behaviour of tethered honeybees, Apis mellifera, whilst presenting visual stimuli in both open-loop and closed-loop experimental paradigms. We found that FicTrac could accurately register the fictive paths of bees as they walked towards bright green vertical bars presented on an LED arena. Using FicTrac, we have demonstrated closed-loop visual fixation in both the honeybee and the fruit fly, Drosophila melanogaster, establishing the flexibility of this system. FicTrac provides the experimenter with a simple yet adaptable system that can be combined with electrophysiological recording techniques to study the neural mechanisms of behaviour in a variety of organisms, including walking vertebrates
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