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212 protocols using matlab r2019a

1

Statistical Analysis of Bat Behavior

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Statistical analysis of the bat level of focus and call centroid distance, Fig. 3 h and i were conducted in RStudio (Version 1.2.5042, RStudio, Inc.) using the lme4 package by Bates et al.59 (link). Testing for normal distribution was performed with Shapiro-Wilk normality test. Data were analyzed by applying a non-parametric two-sided Wilcoxon signed-rank tests and we fitted a linear model. Data preparation and calculation of basic statistical parameters (mean; standard deviation; median) was performed in Microsoft Excel. Graphs were generated using MATLAB_R2019a, from Mathworks or in Rstudio using the ggplot package from Wickham60 . The data that support these findings are available online61 .
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2

Fluorescence Microscopy Data Analysis

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Fluorescence microscopy setups were controlled by custom built software written in LabView 2016 for Windows (National Instruments, Austin, TX). Single-vesicle fusion data were analyzed using custom built software written in LabView 2016 for Windows (National Instruments) as described39 (link). FLIC intensities were extracted using custom software written in LabView 2016 for Windows (National Instruments, Austin, TX) and fitted using FLIC v.0.5, which was generously provided by Armin Lambacher and Peter Fromherz (Max Planck Institute for Biochemistry, Martinsried/München, D 82152 Germany)35 (link). The simulation of the fluorescent release lineshapes (Fig. 5c) was performed in Matlab_R2019a (Mathworks, Natick, MA). Fits of kinetic fusion data and assembly of data graphs were performed using Igor Pro 8 (Wavemetrics, Lake Oswego, OR). EPR spectra and depth parameters were plotted using OriginPro, versions 7.5 or 2021 (OriginLab, Northhampton, MA). Molecular Structures were rendered using PyMol (Schrodinger, NY, NY).
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3

Functional Segregation of the Parahippocampal Gyrus

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Considering the PHG is a substantial brain region with multifaceted functions (Aminoff et al., 2007 (link); Stenger et al., 2022 (link)), we segregated it into six subdivisions (Figure 1A) to explore the functions of each subdivision, respectively. These divisions, our regions of interest (ROIs), were based on the empirically validated Brainnetome Atlas (BNA) (Fan et al., 2016 (link)).2We used SPM8 software3 within MATLAB R2019a (MathWorks Inc., Natick, MA, USA) to compute each ROI’s mean fALFF values. For each voxel’s time series, we obtained the sum of the amplitudes within the low-frequency range (0.01–0.1 Hz). The fALFF values for each voxel and each participant were then calculated by dividing this fractional low-frequency amplitude sum by the amplitude sum across the total frequency range (0–0.25 Hz) (Zou et al., 2008 (link); Zuo et al., 2010 (link)). As a normalized ALFF index, fALFF minimizes the influence of artifactual signals near vessels or significant pulsatile motion (Zou et al., 2008 (link); Zuo et al., 2010 (link)). The fALFF value maps were registered to the MNI152 space using the previously computed transformation matrix. Furthermore, we estimated each participant’s head motion from the rs-MRI data by incorporating the head motion correction outputs to further minimize the head motion’s influence.
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4

Pitch Estimation Modeling and Simulation

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The auditory encoder as well as the simulation of the bio-physical model of the pitch estimation has been implemented on a PC platform in an interplay of parts implemented in C, C++, MATLAB, NEURON, and Python languages. For evaluation and data visualization, we used MATLAB R2019a from MathWorks and Microsoft Excel 2010. The network models used in the present study were obtained from ModelDB “Duration-tuned neurons from the inferior colliculus of vertebrates,” accession number 144511 (Aubie et al., 2012 (link)). We used NEURON version 7.7 (McDougal et al., 2017 (link)) and Python Anaconda 3 (both 64-bit versions) on a Dell Optiplex 7010 under Microsoft Windows 10. NEURON simulations were run with a time step resolution of 0.05 ms.
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5

Computational Model of Immune Synapse

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The computational model was developed using the Simbiology toolbox of MATLAB R2019a (Mathworks, Natick, MA). The optimization toolbox with fminsearch was used with ode15s for parameter estimations. The local parameter sensitivity analyses were performed by calculating time-dependent sensitivity indices on immune synapse formation in blood, bone marrow, and lymph node with the full dedimensionalization option, and then the indices were integrated throughout the time course.
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6

Whole-Body PBPK Model of Nitazoxanide

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A previously published whole‐body PBPK model consisting of compartments to represent select organs and tissues developed in Simbiology (MATLAB R2019a, MathWorks Inc., Natick, MA, USA) was used in this study.45, 46 Nitazoxanide physiochemical and drug‐specific parameters used in the PBPK model were obtained from literature sources as outlined in Table 1. The PBPK model was assumed to be blood‐flow limited, with instant and uniform distribution in each tissue or organ and no reabsorption from the large intestine. Since the data are computer generated, no ethics approval was required for this study.
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7

Biomechanical Assessment of Knee Joint

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At 24 weeks, and following sacrifice, the operative limbs of all animals were disarticulated at the hip and the foot was removed. Skin and other soft-tissues were removed from both the femur and tibia, while taking care to preserve the joint capsule. A 1 cm region of soft-tissue was left on both the femur and tibia nearest to the knee joint. Metal rods were then cemented into the intramedullary canals of the femur and tibia. Once dry, the limb was mounted on a dedicated dynamic load cell device (Figure 3).29 (link),34 (link)
The maximum torque applied to the joint was 20 N·cm and the tibia was moved at a rate of 1°/second. Data were analyzed utilizing Matlab R2019a (Mathworks, USA). A previously defined 'stiffness coefficient' was used to characterize the dynamic stiffness of the joint using the slope of the steepest most linear portion of the exponential curve exported from the load cell device.26 (link)
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8

Roller Skiing Kinematics and GPS Validation

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The design of this study was composed of two parts: a method development using measurements from indoor treadmill roller skiing, and an adoption and validation of the method using dGNSS measurements from a roller skiing test race in a race-like outdoor course. The measurements used in both parts are from previous studies conducted by our group [4 (link),18 (link),19 (link)]. These studies were approved by the ethics committee at the Norwegian School of Sport Sciences (ref. 02-020517) and the Norwegian Centre for Research Data (ref. 54257), and were conducted in accordance with the Declaration of Helsinki and Norwegian law. Data analysis was conducted in Matlab R2019a (The Mathworks Inc., Natick, MA, USA), except for processing of dGNSS measurements and 3D optical motion capture measurements. These were conducted using dedicated software, as described in the text.
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9

Elevated Plus Maze Behavioral Assay

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EPM test was performed according to established protocols39 (link) with slight modifications. We used a custom-made plexiglass EPM. The four arms were 30 cm × 5 cm (L × H); the two closed arms were enclosed by walls 15 cm in height. The apparatus was elevated 50 cm from the ground by sturdy metal posts. Each mouse was allowed to explore the EPM freely for 5 min. Mouse behavior was monitored with a video-tracking system controlled by Bonsai40 (link). We used DeepLabCut41 (link) to track multiple points on the mouse (nose, head, neck, body, and base of the tail) through all video frames, and used custom-written Python 3.6 and Matlab R2019a (MathWorks, Natick, MA) programs to quantify the total distance traveled and the time spent in open vs. closed arms, based on the location of the body point.
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10

Preprocessing of Multimodal Neuroimaging Data

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T1-weighted structural images and resting-state functional images were preprocessed with SPM8 (Wellcome Trust Centre for Neuroimaging, University College London, UK) running on MATLAB R2019a (MathWorks, Inc., Natick, MA, USA). The functional images were corrected for slice-timing and subsequently realigned to the mean image. Next, using the associated parameters obtained through the segmentation of the T1-weighted structural images coregistered to the mean functional image, the fMRI data were normalized and resampled in 2 × 2 × 2 mm3 voxels. All functional images were then smoothed using an isotropic 6-mm full-width half-maximum Gaussian kernel. Finally, a scrubbing procedure58 (link) was used to compensate further for motion, removing any volume (i.e., functional images) with excessive movement (frame displacement > 0.5 mm), based on the relative changes from frame to frame in the fMRI time-series (Supplementary Table S2 for a summary of head motion).
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