Dataset DOI: 10.5061/dryad.ngf1vhj8q

Description of the data and file structure

Nine male TgF344-AD and 6 Wildtype Fisher 344 rats underwent deglutition assessments and PET imaging using the radiotracer [^11^C]PiB to assess brain and brainstem amyloid beta (Aβ) pathology at 11 months of age—a time point corresponding to early-middle stage AD progression. A priori brain regions of interest (ROIs) included those commonly associated with Aβ pathology and more specific swallowing associated structures such as brainstem nuclei and cortical motor areas. Deglutition was assessed using a videofluoroscopic swallow study and a pasta biting task.

Files and variables

General Description: The data comes in 3 CSVs, labeled "PET data" (Positron Emission Tomography data), "VFSS" (Videofluoroscopic Swallowing Study), and "Pastabiting". The subjects are given numbers and group identifiers, either AD (Alzheimer's Disease) or WT (Wild Type).  The subjects are SD (Sprague-Dawley) rats. They are the same subjects in all 3 .csvs. 

• Animal ID/Subject numbers are used only for identification
• AD = Alzheimer's Disease (signifies the animal is the transgenic model studied)
• WT = Wild Type (signifies the animal is a non-diseased model
• Sex = Denotes the sex of the animal. M is Male, F is Female

Variables + Acronyms + Terms by sheet occurrence

File: PET_data.csv

Description: This CSV contains the Positron emission Tomography data for the rats which underwent this study. Each number associated with the animal represents the Standard Uptake Value Ratio for that region, using the provided Waxholm Space Atlas values.

• Condition = Baseline denotes that the animal was at the beginning of its life when this data was acquired.
• WB = Whole Brain
• Medulla = Medulla
• Pons = Pons
• Midbrain = Midbrain
• Nucl 12 = hypoglossal nucleus
• Nucl-sol = Solitary Nucleus
• Nucl-amb = Nucleus ambiguous
• LC = Locus Coeruleus
• PAG = periaqueductal gray
• Amyg = Amygdala
• Hipp = Hippocampus
• neocortex = Neocortex
• thalamus = Thalamus
• perirhinal = Perirhinal Cortex
• SMA = Secondary Motor Area
• PMA = Primary Motor Area
• WHS = Waxholm Space Atlas. A detailed volumetric atlas of the rat brain, which contains comprehensive anatomical delineations of the adult rat brain's regions and fiber tracts.

File: VFSS.csv

• Average Residue Score - Score assigned to an animal based on the presence or lack thereof of residue before or after a swallow. Larger numbers denote a higher occurrence of residue pre or post-swallow.
• % Post Swallow Inhales - This column denotes the percentage of swallows in which aberrant post-swallow inhale is observed (diaphragm pulls down caudally / pleural space expands after obligatory swallow apnea)
• Oropharyngeal Transit Duration - This column denotes in msec the average duration from swallow onset (bolus head enters posterior oropharynx) until bolus head touches the UES
• Pharyngoesophageal Transit Duration - This column denotes in msec the average duration from bolus head first touching UES, until bolus passes completely through UES and enters proximal esophagus (bolus tail is pinched by UES closure behind it)
• Inter-Swallow Interval - This column denotes the average time between swallows. There are two columns labeled as Inter-Swallow Interval, one in msec and the other in seconds. These units are indicated in the column's header
• Apnea Duration - This column denotes the average duration where the diaphragm has a net movement of zero (i.e., the diaphragm is not moving toward the inhale or exhale position) for at least 2 consecutive frames
• Swallow Onset Delay - Swallow Apnea Onset Latency Duration. This column denotes the average difference/duration between the onset of the swallow (as marked by bolus head entering the posterior oropharynx) versus onset of apnea (as assessed by cessation of diaphragm movement).
• Respiratory Reset Delay - This column denotes the difference/duration between the offset of the OP swallow (as marked by the bolus head first touching the UES) versus offset of apnea (as marked by the first frame of diaphragm movement toward post-swallow respiration).
• Bolus Area - This column denotes the size of the bolus at the moment of bolus contact with the upper esophageal sphincter. This column is in square millimeters. 

File: PastaBiting.csv

This sheet contains the ID, Sex, and Genotype of the studied rats. Then, 5 columns labeled as Piece 1 - Piece 5. Then a final column called Event Rate Average. An event was classified as the sound of the animal biting or chewing a piece of pasta. The sound was assessed for 5 pieces per animal, with each event's temporal point noted. The columns denote the average events per second for that piece of pasta. The final column is an average of the previous pieces together for a final score.

Code/software

Microsoft Excel, any version.