Table Summary of taxa, feeding behaviors, and developmental stages in feed




Дата канвертавання21.04.2016
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Table 1. Summary of taxa, feeding behaviors, and developmental stages in FEED . The 16 species included in the public demo version of FEED as of June, 2011 are highlighted in bold. The remaining species indicate taxa that will be added to FEED at the next data release, which is scheduled for January 2013.
Taxon Species Behavior Developmental Stage

Marsupialia Macropus eugenii M A



Macropus rufus M A

Lasiorhinus latifrons M A

Potorus tridactylus M A

Sarcophilus harrasii M A

Trichosurus vulpecula M A

Didelphis virginiana M A

Afrosoricida Tenrec ecaudatus M A

Hyracoidea Procavia syriacus M A

P. capensis M A

Scandentia Tupaia belangeri M A

Primates Otolemur crassicaudatus B, M A

O. garnetti B A

Eulemur fulvus M A

Lemur catta M A

Varecia variegata M A

Hapalemur griseus M A

Propithecus verreauxi M A

Callithrix jacchus B, M A

Saguinus fuscicollis B, M A

Aotus trivirgatus M A

Allouatta palliata M A

Ateles geoffroyi M A

Cebus apella M A

Macaca fascicularis M A

M. fuscata M A

Papio anubis B, M S, A

Hylobates lar M, S A

Pongo pygmaeus M, S S

Pan troglodytes M S

Homo sapiens M A

Lagomorpha Oryctolagus cuniculus Continuous I, J, A

Rodentia Rattus norvegicus M A

Kerodon rupestris M A

Aplodontia rufa M A

Marmota monax M A

Sciurus caroliensis M A

Cavia porcellus M A

Pedetes capensis M A

Carnivora Felis domesticus M, Sk I, A



Canis familiaris M I, A

Table 1, continued.
Taxon Species Behavior Developmental Stage
Perissodactyla Equus caballus M A

Cetartiodactyla Llama pacos M A



Capra hircus M A

Sus scrofa M, Sk, S I, J, A

Chiroptera Pteropus giganteus M A


Key: Behavior, Continuous=multiple-day, continuous recordings of EMG activity; B=isometric bite; M=mastication; S=swallowing; Sk=suckle.

Developmental Stage, I=infant; J=juvenile; S=subadult; A=adult.

Table 2. Sensor Types and the Controlled Vocabulary for technical, directional, and measurement terms in FEED. If technical or directional information in each category is not available, then “Unknown” may be specified during data entry.
Sensor Type Notes

Electromyography Much of the raw data were collected using bi-polar, indwelling electrodes.

Force Much of the raw data were collected using a bite force transducer.

Strain Typically in vivo bone strain measured with a strain gage.

Kinematics 2- and 3-dimensional coordinate data from a wide variety of recording techniques, including cinefluorography, cineradiography, and standard light movies.
Pressure Much of the raw data are intraoral pressures measured during suckling.

Sonomicrometry Much of the raw data were collected within muscles or across patent sutures.


Classes & Names of Terms:

Technical Terms

Restraint Type If restraint type differs, then data entry options include Other and Unknown.

Box


Chair

Hand-held

Sling

Stall


None
Electrode Type These terms are specific to electromyography. If electrode type is not known, then data entry options include Unknown.

Bipolar indwelling

Indwelling patch

Surface
EMG Filtering

Band pass

60Hz Notch

Notch

Table 2, continued.
Classes & Names of Terms:

Directional Terms These terms are standard anatomical directions.

Side

Left


Middle

Right


Anterior-Posterior Axis

Anterior


Middle

Posterior



Dorsal-Ventral Axis

Dorsal


Ventral

Medial-Lateral Axis

Medial


Lateral

Proximal-Distal Axis

Proximal


Middle

Distal


Depth Axis

Deep


Superficial
Measurement Terms
Sensor Type Term

EMG volt, millivolt

Sonomicrometry volt, mm

Strain gage volt, microstrain

Strain angle of E1 degrees

Bite force volt, kg, Newton

Pressure volt, mmHg, kPa

Kinematics cm, mm

Table 3. Controlled vocabulary: terms to describe the developmental stage of a research subject. If developmental stage is not known, the category “unknown” can be specified during data entry. Currently, accuracy in correlating across species and stages is provided by additional data entry fields for Research Subject Age in which the terms available for age units are days, weeks, months, or years. Precise definitions of developmental stage have not yet been specified.
Developmental Stage

Infant


Juvenile

Subadult


Adult

Table 4. Controlled vocabulary: anatomical terms to describe the structure in which or on which sensor(s) are located. This list contains the names of 43 muscles and 9 bones or regions of the head and neck. The Working Group plans to add names to this list as work on FEED proceeds.
Anatomical Term (Muscle, Bone, or Region Name)

Anterior Digastric (Muscle)

Buccinator (Muscle)

Cricopharyngeus (Muscle)

Cricothyroid (Muscle)

Genioglossus (Muscle)

Geniohyoid (Muscle)

Hyoglossus (Muscle)

Inferior Constrictor (Muscle)

Internal Intrinsic Laryngeal Muscles (Muscle)

Intrinsic Tongue (Muscle)

Lateral Pterygoid, Inferior Head (Muscle)

Lateral Pterygoid, Superior Head (Muscle)

Masseter, Superficial (Muscle)

Masseter, Deep (Muscle)

Masseter, Zygomaticomandibularis (Muscle)

Masseter, Maxillomandibularis (Muscle)

Medial Pterygoid (Muscle)

Middle Constrictor (Muscle)

Mylohyoid (Muscle)

Omohyoid (Muscle)

Orbiculari Oris (Muscle)

Palatoglossus (Muscle)

Palatopharyngeus (Muscle)

Panniculus Carnosus (Muscle)

Posterior Digastric (Muscle)

Salpingopharyngeus (Muscle)

Sternohyoid (Muscle)

Sternothyroid (Muscle)

Styloglossus (Muscle)

Stylohyoid (Muscle)

Stylopharyngeus (Muscle)

Superior Constrictor (Muscle)

Temporalis, Superficial (Muscle)

Temporalis, Deep (Muscle)

Temporalis, Zygomatic (Muscle)

Tensor Veli Palatini (Muscle)

Thyroepiglotticus (Muscle)

Thyrohyoid (Muscle)

Uvular Muscle (Muscle)



Table 4, continued.
Anatomical Term (Muscle, Bone, or Region Name)

Frontal (Bone)

Mandible (Bone)

Maxilla (Bone)

Parietal (Bone)

Sphenoid (Bone)

Temporal (Bone)

Zygomatic (Bone)

Temporomandibular Joint (Region)

Mandibular Symphysis (Region)



Description of Data Containers with Guidelines and Recommended Practices for Contributions to and Use of FEED, including Table 5 of Required, Highly Recommended, and Other Data Entry Fields

Registered users will be able to upload physiologic data into FEED and download accessioned data. In case of data recorded using several types of sensors simultaneously (e.g., EMG together with bone strain), the recordings should be properly combined into a single tab-delimited file in order to be deposited.



Study. A Study is a set of experiments on a collection of individuals, typically treated with a specific experimental protocol for answering a set of related questions concerning the physiology of the feeding apparatus. This data container contains both public and private information. The public information will be available to all registered users of FEED. The private information is visible only to the user who deposited the data. The public information includes the title of the Study, its start and end date, the funding source, and whether institutional approval for the research was secured.

Experiment. The metadata in this and subsequent data containers are public. Each Experiment has a Title and refers to one of the Individual Research Subjects defined in the Study. Developmental stage and age (including units) of the Subject are ascribed at this level. In addition, other relevant descriptors of the Subject pertinent to the experiment can be entered here.

Sensors used in data collection are associated with an Experiment. Channels are named under Experiment but are designated as to position (channel lineup) within the raw data file under Recording Session (see below). For EMG data, sensor and channel have a one-to-one correspondence and the sensor name is also the channel name (e.g., masseterEMG). For the other techniques, sensors and channels are named separately. This is because some techniques use two sensors to calculate a single channel of data (e.g., sonomicrometry) and other techniques record several channels of data from a single sensor (e.g., kinematic markers). For each sensor and channel, there are metadata that are specific to the Experiment, the sensor type, and the channel.



Recording Session. A Recording Session corresponds to a single hook-up of a particular group of sensors. One might, for example, implant 16 EMG electrodes (sensors) for an Experiment, and have two separate Recording Sessions, one including data on sensors 1 to 12, and the second including data on sensors 5 to 16. Thus, a channel lineup is specified for each Recording Session. In addition, the metadata tie the Recording Session to an Experiment and provide information about the preparation of the subject (e.g., type of restraint). The channel lineup is the order of occurrence of the numeric data streams in the raw data file. It is specified by its position and channel name.

Trial. A trial is a single episode of physiologic data recording within a Recording Session. Trials are typically identified by food type and/or sequence number within the Recording Session. Each Trial can have one raw data file of physiologic recordings as described above.
Table 5. Required, Highly Recommended, and Other data entry fields in FEED. Data containers, sensors, and channels in BOLD.
REQUIRED DATA ENTRY FIELDS: These fields were determined by the Mammalian Feeding Working Group to meet the minimum standards to support re-use of the data in FEED for research and education purposes.
STUDY

Title


Start (date and time)

Description


SUBJECTS

Study


Taxon

Name
EXPERIMENTS

Title

Study


Subject

Subject developmental stage


STRAIN

Experiment Name



Strain Sensors

Name


Location

Side


Strain channels

Recording rate

Strain units

Sensor
BITE FORCE

Experiment Name

Bite Force Sensors

Name


Location

Side


Bite Force Channels

Name


Table 5, continued.

Bite Force Channels

Recording rate

Bite force units

Sensor
PRESSURE

Experiment Name

Technique



Pressure Sensors

Name


Location

Side


Pressure Channels

Name


Recording rate

Pressure units

Sensor
EMG

Experiment Name



EMG Electrodes

Name


Side

Muscle


Recording rate

EMG units

EMG filtering
SONOMICROMETRY (SONO)

Experiment Name



Sono Crystals

Name


Muscle

Side


Sono Channels

Name


Recording rate

Sono units

Crystal 1

Crystal 2


KINEMATICS

Experiment Name



Kinematics Markers (i.e., sensors)

Name


Location

Side


Table 5, continued

Kinematics Channels

Name


Recording rate

Kinematics units


RECORDING SESSION

Title


Experiment

Position


Subject restraint

Channel lineup (specify numeric position here, and this is linked to previously specified name)


TRIALS

Title


Session

Position


Primary behavior

Data File



HIGHLY RECOMMENDED DATA ENTRY FIELDS: These fields were determined by the Mammalian Feeding Working Group to be important for completing planned analyses by the original collectors of the data. Though not required, it is highly recommended that information be provided in these fields when uploading data in FEED. Inclusion of relevant citations, data concerning anatomy of the species and/or research subjects, and illustrations of raw data are particularly encouraged.
STUDY

Funding agency

Approval secured

External sources



SUBJECTS

Breed


Sex

Notes


Picture

Notes


EXPERIMENTS

Description

Subject age

Age units

Subject weight (kg)

Subject teeth

Subject notes

Implantation notes

Picture

Notes



Table 5, continued

STRAIN

Notes about all sensors and channels in this setup

Sampling Rate (Hz)

Picture


Notes

Strain Sensors

AP

DV



PD

ML

Notes



Strain Channels

Notes


BITE FORCE

Notes about all sensors and channels in this setup

Sampling rate (Hz)

Picture


Notes

Bite Force Sensors

AP

DV



PD

ML

Notes



PRESSURE

Notes about all sensors and channels in this setup

Sampling rate (Hz)

Picture


Notes

Pressure Sensors

AP

DV



PD

ML

Notes



EMG

Notes about all sensors and channels in this setup

Sampling rate (Hz)

Picture


Notes

Preamplifiers

Picture

Notes


EMG Electrodes

Anatomical Location (free text)

AP

DV

PD



ML

Table 5, continued

SONOMICROMETRY

Notes about all sensors and channels in this setup

Sampling rate (Hz)

Sonomicrometer

Picture

Sono crystals

AP

DV



PD

ML

Crystal depth


KINEMATICS

Notes about all sensors and channels in this setup

Sampling rate (Hz)

Picture


Notes

Kinematics markers

AP

DV



PD

ML

RECORDING SESSION

Subject notes

Subject anesthesia / sedation



TRIALS

Estimated duration

Subject treatment

Food type

Food size

Food property

Secondary behavior (e.g., a mastication sequence might contain one or more swallows)

Waveform picture



OTHER DATA ENTRY FIELDS: These fields were determined by the Mammalian Feeding Working Group to meet a very high standard of providing relevant information on species, subject, and data acquisition protocols for future use in education and in meta-analyses by re-users of the data.
STUDY

Bookkeeping

End

SUBJECTS

Source


EXPERIMENTS

Bookkeeping

Start

End
Table 5, continued



STRAIN

BITE FORCE

Bite Force channels

Notes


PRESSURE

Pressure channels

Notes


EMG

EMG Electrodes

Notes


SONOMICROMETRY

Sono crystals

Notes


Sono channels

Notes


KINEMATICS

Kinematics markers

Notes


Kinematics channels

Notes


RECORDING SESSION

Bookkeeping

Start: Date:

Start: Time:

End: Date:

End: Time:



TRIALS

Bookkeeping

Start: Date:

Start: Time:

End: Date:

End: Time:

Subject notes

Behavior notes



end tables







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