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16 protocols using pcie 6321

1

Measuring Muscle Activity in Primates

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EMGs of the biceps brachii and triceps brachii muscles were obtained using surface electrodes (NE-05, Nihon Kohden) for monkey K or chronically implanted stainless steel wire electrodes (7-stranded 25.4-μm diameter wire with Teflon coating; A-M Systems, Sequim, WA) for monkey U. Signals from the electrodes were amplified (5000×) and bandpass-filtered (150–3000 Hz) using an amplifier (MEG-5200, Nihon Kohden), digitized at 20 kHz (PCIe-6321, National Instruments), and stored on a computer. The root mean square (RMS) of each EMG was calculated with a 100-ms moving window. The RMS of the EMG was aligned with task events, and the mean and SEM were computed (Supplementary Fig. 5).
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2

Photoreceiver Signal Analysis for Single Particle Detection

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Photoreceiver signals are continuously acquired for 1 minute at 500 kHz using a PCI express data acquisition card (PCIe-6321, National Instruments) and successively analyzed offline using a custom Matlab script. Before analysis, the acquired signal is filtered with a low-pass filter with 20 kHz cut-off frequency to remove high frequency noise. Successively, the signal is segmented into signal events containing single events using a peak-finding procedure. Data are selected and gated using the bivariate distribution fθvs. average intensity (cf. Fig. S5 of the ESI). Coincidences, i.e. the simultaneous presence of 2 or more particles in the measurement region, yield signals with higher intensities which are discarded by thresholding. Coincidences were on average ∼13% of total events measured, but could potentially be recovered by using a more sophisticated signal analysis (e.g. a Bayesian approach46 (link)) to increase system throughput. The start/end points of each event are determined as the first and last time-points where the signal crosses a threshold (3 standard deviations of the baseline noise). A fast-Fourier transform (FFT) is used to compute the frequency power spectrum, and peak-finding is used to find the angular oscillations frequency peak. Single-shell theoretical Mie scattering profiles are computed using Matlab MieScat package.47
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3

Axopatch 200B for Electrical Measurements

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Axopatch 200B (Molecular Devices LLC) was used for electrical measurements. A PCIe-6321 (controlled through a custom LabVIEW script (version 2016, National Instruments)) connected to a BNC 2110 (National Instruments) was used to digitize the output for IV measurements. Signal digitization was carried out using a Digidata 1440A (Molecular Devices LLC) for translocation experiments. Current traces were acquired at a sampling frequency of 250 kHz and lowpass filtered at 10 kHz using the in-built Bessel filter of the Axopatch 200B.
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4

Wrist Flexion/Extension Torque Measurement

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An ATI Mini 27 Ti force sensor integrated in the MR-StretchWrist is used to measure the wrist flexion/extension torque (Full-scale Load (FSL): 2 Nm, Resolution: 0.5 mNm, Measurement uncertainty: 1.5% of FSL). Transducer signals are processed by a preamplifier box (ATI Industrial Automation, Apex, NC, United States), and digitized by an analog/digital I/O device (PCIe-6321, National Instruments, Austin, TX, United States) connected to a laptop.
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5

Surface EMG Sensor Placement and Data Collection

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Surface EMG data were collected from the muscle bellies of the right extensor carpi radialis (ECR), the right medial gastrocnemius, and the right SCM (startle indicator) using the Delsys Trigno Wireless EMG system (fixed 48 ms delay). The EMG sensors (Delsys Trigno Avanti Sensor) were placed parallel to the muscle fibres, and then attached to the skin using double-sided adhesive tape. Prior to electrode application, the recording sites were cleaned using an abrasive gel (Nuprep) and alcohol pads to minimize electrical impedance. The finger switch and the footswitch were used to detect movement onset of the right hand and the right foot, respectively. The finger switch required ~0.38 N to close and showed a voltage of 5 V when closed and 0 V when opened. Similarly, the footswitch required ~18 N to close and showed a voltage of 5 V when closed and 0 V when opened.
All data were digitally sampled at 1000 Hz (National Instruments PCIe-6321) using a customized LabVIEW (National Instruments Inc.) program and stored for offline analysis.
For each trial, data collection was initiated by the computer program 2200 ms prior to the imperative stimulus and continued for 3200 ms.
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6

Cue-Evoked Licking Behavior Dynamics

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The licking behavior was sampled at 1 kHz (PCIe-6321; National Instruments) and, for analysis, was binned every 500 ms and converted to frequency (licks / s). For each trial, licking frequency was normalized to the 2 second period before the cue presentation. All mice developed cue-evoked licking that was significantly greater than baseline licking. As a measure of the rate of learning as determined by cue-evoked licking, we first normalized each mouse’s cue-evoked licking to the maximum lick rate across all four days. We then quantified the latency to reach 50 % of the maximum cue-evoked lick rate.
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7

Olfactory Stimulation Protocol with Custom Olfactometer

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Odour stimulation was performed through a custom-made olfactometer40 (link), where a constant air stream is split into eight channels, each composed of two alternate paths: an odour chamber (1:500 dilutions in mineral oil) and a blank chamber (mineral oil). Single channels are switched by electronic valves controlled by a PCIe-6321 multifunction board (National Instruments) and programmed via a LabView-based user interface41 (link). Acetophenone, benzaldehyde, 1-hexanol, 1-octanol (all Sigma-Aldrich) were applied sequentially as pulsed stimuli. Each odour pulse (duration: 1 s, inter-stimulus interval: 7 s) was repeated 25 times. Because the 4 odours were alternated, this produced an interval of 32 s between subsequent stimulations with the same odour.
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8

Wireless Cortical Recording in Gerbils

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Trained gerbils were tested while cortical potentials were simultaneously recorded, amplified and transmitted wirelessly to a receiver positioned approximately 1 m from the cage (W16, Triangle BioSystems International). All input/output channels were synchronized at 100,000 samples/s and 16 bits by sharing the sampling clock pulse of two data acquisition cards (DAQs, PCIe-6321 and PCIe-6341, National Instruments Corporation) via a Real-Time System Integration bus cable. Specifically, custom written software, called Electrophysiology Auditory Recording System (EARS), synchronously controlled auditory stimuli delivery and recorded both behavioral and physiological responses23 . EARS communicated with the loudspeaker, nose poke, licks spout, W16 and a personal computer for data storage and analysis via the two DAQs. In addition, EARS interfaced with a syringe pump (NE-1000 Programmable Single Syringe Pump, New Era Pump Systems, Inc.) via a USB-RS232 emulator.
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9

Simultaneous Neural and EMG Recording Protocols

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Neural activity was recorded simultaneously in both IOS and 2PLSM as the differential potentials between the two leads of either the PFA-coated tungsten microwires (#795500, A-M Systems, Sequim, WA) (Huo et al., 2014 (link); Winder et al., 2017 (link)) for cortical and hippocampal stereotrodes. EMG activity was identically recorded with PFA-coated 7-strand stainless-steel microwires (#793200, A-M systems, Sequim, WA). Stereotrode tungsten microwires were threaded through polyimide tubing (#822200, A-M Systems, Sequim, WA) giving an interelectrode spacing of ~100 µm. The tungsten microwires were crimped to gold pin connectors, with impedances typically between 70 and 120 kΩ at 1 kHz. EMG stainless-steel microwires were fabricated in a similar fashion, but with an interelectrode spacing of several mm. Each signal was amplified and hardware bandpass filtered between 0.1 Hz and 10 kHz (DAM80, World Precision Instruments, Sarasota, FL) and then digitized at 20 kHz (PCIe-6341 for IOS experiments, PCIe-6321 and PCIe-6353 for 2PLSM experiments, National Instruments, Austin, TX).
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10

Fiber Photometry Recordings in Head-Fixed Mice

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Fiber photometry recordings were performed using head-fixed mice that were free to run on a circular treadmill. Fiber optic cables (1 m long; 400 μm core; 0.48 NA; Doric Lenses) were coupled to implanted optic fibers with zirconia sleeves (Precision Fiber Products). Black heat shrink material was placed around the fiber coupling to prevent external sources of light (e.g. from the visual stimulus) from interfering with recordings. Excitation and emission light was passed through a GFP fluorescence minicube (FMC3_E(460–490)_F(500–550); Doric Lenses). Excitation light (~ 100 μW) was provided by a 465 nm LED (Plexon LED and driver) which was modulated at either 217 Hz or 319 Hz using TTL output from two lock-in amplifiers (SR830; Stanford Instruments). Emission light was collected by a femtowatt photoreceiver (Newport 2151), demodulated using a lock-in amplifier (SR830; Stanford Instruments) and digitized at 1 kHz sample rate (PCIe-6321; National Instruments). Data acquisition was controlled using a custom script in MATLAB (MathWorks).
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