Matlab r2008a

Manufactured by MathWorks

Sourced in United States

MATLAB R2008a is a technical computing software that provides a high-performance environment for numerical computation, visualization, and programming. It is designed to work with large amounts of data, perform complex calculations, and create advanced visualizations.

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Lab products found in correlation

Psychtoolbox 3, by MathWorks (1 mentions) Xenon arc lamp, by Cairn Research (1 mentions) Ni labview 2012, by National Instruments (1 mentions) Ni usb 6361, by National Instruments (1 mentions)

13 protocols using matlab r2008a

Multimodal Sensory Stimulation Protocol

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The visual stimulus was a radial expansion motion stimulus in low-contrast (10%) concentric circles with sinusoidal luminance modulation (Kremláček et al., 2004 (link)). A temporal frequency of 5 cycle/second was kept constant over the whole stimulus field. A black square in the middle of the screen was used as a fixation point. The stimuli had 200 ms motion, followed by a 1,000 ms interstimulus interval stable image. Total stimulus repetition was 60.
The auditory stimulus was a 1,000 Hz tone burst and was presented binaurally via Hosiden DH-05-S circumaural headphones (Hosiden Electronics, Japan) at a level of 70 dB SPL. A gray screen with a white “+” sign was shown to prevent eye movement during recording. The duration of the test stimuli was 200 ms, followed by a 1,000 ms interstimulus interval. The stimulus was presented 60 times.
All stimuli were presented on a 22-inch computer monitor (AOC International GmbH, Germany) with a 60 Hz refresh rate from a 70 cm observing distance. For the presentation of stimuli, an Intel (R) Core (TM)2 Quad CPU Q8300 2.50 GHz computer; ATI Radeon HD 3400 Series graphic card and an Eugene Gavrilov kX 10k1 Audio (3550) sound card were used. The software used to present the stimuli was Psychtoolbox-3.0.8 (Kleiner et al., 2007 (link)) and Matlab-R2008a (MathWorks Inc., United States).

Aykan S., Gürses E., Tokgöz-Yılmaz S, & Kalaycıoğlu C. (2020). Auditory Processing Differences Correlate With Autistic Traits in Males. Frontiers in Human Neuroscience, 14, 584704.

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Unilateral Noise-Induced Hearing Loss Model

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Anesthetized rats were unilaterally exposed to one octave band noise centered at 16 kHz with the peak intensity of 116 dB sound pressure level (SPL). The acoustic signal for generating noise was programmed with RpvdsEx v7 (Tucker-Davis Technologies, USA) and MatLab R2008a (MathWorks Inc., USA), generated with TDT System 3 hardware (RP 2.1, PA 5, ED 1, and HB 7), amplified through an amplifier (MATRX/M-640, USA), and presented via a free-field speaker (CP-75A, Shanghai Chuangmu). The noise was converted into electrical signals by a microphone (model 7016, ACO Pacific Inc., USA) and acquired by the TDT system for calibration of sound levels. One hour continuous noise exposure was conducted within a soundproof chamber. The amplified noise was presented via the speaker positioned 3 cm from the left ear canal, while the right ear was carefully plugged to preserve hearing and make a unilaterally noise-exposed animal model. The material of the plug was a kind of propenoic acid, commonly used to make ear mode in clinic, injected into the right external ear canal and ear nail through a syringe; this material could be turned into solid after ten minutes, and it could be easily pulled out from the external ear canal.

Liu C., Xu T., Liu X., Huang Y., Wang H., Luo B, & Sun J. (2018). Acoustic Trauma Changes the Parvalbumin-Positive Neurons in Rat Auditory Cortex. Neural Plasticity, 2018, 9828070.

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Probiotic Star Fruit Juice Fermentation

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All analyses were carried out based on the data from the triplicate fermentations. One‐way analysis of variance (ANOVA) and Scheffe's test were performed using SPSS 19.0 (Statistical Program for Social Sciences, SPSS Corporation, Chicago, IL), and significant difference was evaluated at the 95% confidence interval. Principal component analysis (PCA) was performed using software MATLAB R2008a (MathWorks, Natick, MA, USA) to analyze the distribution of aroma profiles of star fruit juice and star fruit juice beverages fermented with different probiotic strains.

Lu Y., Tan C., Chen D, & Liu S. (2018). Potential of three probiotic lactobacilli in transforming star fruit juice into functional beverages. Food Science & Nutrition, 6(8), 2141-2150.

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Multiblock Consensus PCA of Wheat Leaf Metabolomics

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The deconvolved and internal standard normalised GC-TOF/MS peak areas were directly imported from Microsoft Excel into MatLab R2008a (The MathWorks Inc., www.mathworks.com). Multiblock Consensus (C)-PCA was performed as described previously (Biais et al., 2009 (link)). The first C-PCA model arranged the data into two blocks consisting of nitrate supplemented and nitrate deprived samples. The second C-PCA model arranged the data into three blocks consisting of leaf base, mid leaf, and leaf tip, wheat leaf sections. After arrangement of data into blocks, with each experimental class consisting of a balanced number of sample replicates (6), each block was auto-scaled (i.e. each variable has a mean of 0 and a standard deviation of 1), and C-PCA was applied with results displayed as scores and loadings multiblock bi-plots. Additionally, a Wilcoxon rank-sum test was applied to test the difference between GC-TOF/MS profile variables at a 95% confidence limit (FDR q-value 0.05).

Allwood J.W., Chandra S., Xu Y., Dunn W.B., Correa E., Hopkins L., Goodacre R., Tobin A.K, & Bowsher C.G. (2015). Profiling of spatial metabolite distributions in wheat leaves under normal and nitrate limiting conditions. Phytochemistry, 115, 99-111.

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Precision Display for Cognitive Experiments

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Stimuli were presented on an ASUS ROG Swift PG278Q GSYNC monitor with 1 ms response time and 120 Hz refresh rate, driven by two SLI linked NVIDIA GeForce 980GT GPUs, at a screen resolution of 2560 × 1440³¹. The display subtended approximately 31 degrees horizontal and 22 vertical degrees of visual angle. The display was controlled by a custom-built workstation running Gentoo Linux with a 64 bit kernel that was tuned for real-time processing. The paradigm was programmed in Matlab R2008a (The Mathworks, MA) using Psychtoolbox version 3^{32 (link),33 (link)}. We recorded target onset presentation times with a photodiode that was time-synchronized with the eyetracker.

Martin J.G., Davis C.E., Riesenhuber M, & Thorpe S.J. (2018). Zapping 500 faces in less than 100 seconds: Evidence for extremely fast and sustained continuous visual search. Scientific Reports, 8, 12482.

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Pupillary Light Reflex Measurement Protocol

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Pupillary light reflex (PLR) was conducted as previously described [21] (link), [22] (link). Mice were entrained to a 24 h LD cycle then dark-adapted for 1 to 1.5 hours prior to the beginning of the experiment. Measurements were taken between ZT5 and ZT8 (where ZT12 = time lights off). Pupillary responses were elicited by applying a light stimulus (200 µW/cm²) provided by Xenon arc lamp (Cairn Research Ltd.) filtered with a 480 nm monochromatic interference filter (half bandwidth ≤10 nm) and transmitted to the integrating sphere using a quartz fibre optic. Consensual pupil constriction could then be monitored in the left eye by illuminating it with infrared (>900 nm) and recording it with a CCD camera fitted with a 140 mm lens in a parallel plane to the cornea. The eye was recorded for 2 s with no light stimulus, then for a further 58 s as the light stimulus was applied. Pupil area was measured in images captured from the videotaped records using VirtualDub (web-based software package, VirtualDub.org) and Matlab R2008a (The Mathworks, Cambridge, UK).

Brooks E., Patel D, & Canal M.M. (2014). Programming of Mice Circadian Photic Responses by Postnatal Light Environment. PLoS ONE, 9(5), e97160.

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Structural Brain Imaging Data Processing

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Images were processed using Statistical Parametric Mapping (SPM8, Wellcome Department of Cognitive Neurology) implemented in MATLAB R2008a (version 7.6.0, MathWorks, ). All the steps for data processing were followed as described in detail by Ashburner and Friston[36 (link)])).¹ In order to improve the registration of the MRI images, DARTEL toolbox for SPM8 was used. Briefly, the anatomical images were firstly reoriented so that the mm coordinate of the anterior commissure matched the origin (0, 0, 0), and the orientation approximated MNI space. Then, T1-weighted images were segmented and classified into GM, white matter (WM), and cerebrospinal fluid (CSF) probability maps using the ‘new-segment’ option implemented in SPM8, which gives both the native space versions and DARTEL imported versions of the tissues. All the GM and WM images were spatially nonlinearly normalized to the population template which was created by GM and WM maps and DARTEL, and then Jacobian modulated. These images were affine transformed to MNI space and, finally, were smoothed with a 10 mm FWHM Gaussian kernel.
Total GM volume, WM volume, CSF volume, and total intracranial volume (TIV) were calculated using a MATLAB script downloaded from the SPM email list.²

Singh S., Goyal S., Modi S., Kumar P., Singh N., Bhatia T., Deshpande S.N, & Khushu S. (2014). Motor function deficits in schizophrenia: an fMRI and VBM study. Neuroradiology, 56(5), 413-422.

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Structural Brain Imaging Analysis of MDD Patients

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The structural T1‐weighted imaging data of the MDD patients and the HCs were processed using statistical parametric mapping software (SPM8, Wellcome Department of Cognitive Neurology, UK; http://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037) on the Matrix Laboratory, MATLAB R2008a platform (MathWorks, Natick MA, USA). VBM (http://dbm.neuro.uni-jena.de/vbm) and IBASPM (http://www.thomaskoenig.ch/Lester/ibaspm.htm; RRID:SCR_014196) were performed for all subjects.

Xu L., Xu F., Liu C., Ji Y., Wu J., Wang Y., Wang H, & Yu Y. (2017). Relationship between cerebellar structure and emotional memory in depression. Brain and Behavior, 7(7), e00738.

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PVDF Transducer for Laser-Induced Pressure Measurement

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The PVDF sensor had dimensions of 41.40 × 16.26 mm² and was made up of a piezoelectric PVDF polymer film with 28 μm thickness laminated onto 0.125 mm thickness polyester. The sensitivity of the PVDF film was 13 mV/N. Output signals from the sensor were amplified by 40 dB and stored in PC using a data acquisition board (NI USB-6361, National Instruments, Austin, TX, USA) and LabVIEW (NI LabVIEW 2012, National Instruments, Austin, TX, USA). By considering the sensitivity of the PVDF film, amplification gain, and the spot size of laser irradiation, the sensitivity of the PVDF transducer was recalculated in terms of pressure, i.e., 235.2 mV/MPa, and used to convert the output signals in mV to MPa. One hundred one-pulse single shots were repeatedly performed at each energy level and output signals were averaged for improving the signal-to-noise ratio (SNR). Any damage to the sample was checked every ten single shots using a digital microscope (AM3713TB, AnMo Electronics Corp., Taiwan). Output signals were processed with home-built programs based on MATLAB (R2008a, Mathworks, Portola Valley, CA, USA).

Jun J.H., Park J.R., Kim S.P., Min Bae Y., Park J.Y., Kim H.S., Choi S., Jung S.J., Hwa Park S., Yeom D.I., Jung G.I., Kim J.S, & Chung S.C. (2015). Laser-induced thermoelastic effects can evoke tactile sensations. Scientific Reports, 5, 11016.

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Visual Stimuli Presentation for Cognitive Research

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Stimuli were presented on an ASUS ROG Swift PG278Q GSYNC monitor with 1 ms response time and 120 Hz refresh rate at a screen resolution of 2560 × 1440 pixels. The size of screen in cm was 61.5 cm width × 35.5 cm height. Subjects’ eyes were at an approximate distance of 85.0 cm to the screen (as measured with a laser distance measure device with distance measurement precision of ±2 mm). The display therefore subtended approximately 31° horizontal and 22° vertical of visual angle. There was no gamma correction done during image presentation. The default parameters for the monitor were used. We have included data on the luminance of each background image. The display was controlled by a custom-built workstation running Gentoo Linux with a 64 bit kernel that was tuned for real-time processing. The paradigm was programmed in MATLAB R2008a (The Mathworks, MA) using Psychtoolbox version 3 (Brainard, 1997 (link); Pelli, 1997 (link)). Target onset presentation times were recorded using a photodiode that was linked with the high-speed analog input of the eye-tracker recording through the Cedrus StimTracker system.

Martin J.G., Davis C.E., Riesenhuber M, & Thorpe S.J. (2018). High Resolution Human Eye Tracking During Continuous Visual Search. Frontiers in Human Neuroscience, 12, 374.

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