%Gastrointestinal Methodology {#GastrointestinalMethodology}
===========================

@anchor GI-overview
Overview
========

Abstract
--------

The %BioGears %Gastrointestinal System models the ingestion of macronutrients and their subsequent digestion and transportation into the %Cardiovascular system. 
Digestion rates for each macronutrient can be specified along with the amount, and if no rates are supplied, a default configurable rate will be used.
The macronutrients are then digested by converting the macronutrient into a specific substance from the stomach and 
incrementing the amount of that substance into the small intestine's chyme. 
The substances in the chyme are then absorbed into the vascular system via the small intestine's walls each timestep.

@anchor GI-introduction
Introduction
------------

### %Gastrointestinal Physiology

The %Gastrointestinal tract is responsible for consuming and digesting food, absorbing nutrients, and expelling waste.
The tract consists of the stomach and intestines breaking down food into usable nutrients for the body. 
After being eaten, food is stored in the stomach, gradually digested, then released into the gut chyme. 
At this point, nutrients are either quickly absorbed into the blood through the intestinal wall or further broken down prior to absorption. 
An overview of the digestive tract is shown in Figure 1.

@image html DigestiveTractDetail.png
<center>
<i>
Figure 1. The human digestive tract is composed of several distinct sections @cite LadyofHats2006Digestive. 
Currently, the %BioGears gastrointestinal model replicates the behavior of the stomach and small intestine.
</i>
</center><br>

@anchor GI-system
System Design
=============

@anchor GI-background
Background and Scope
--------------------
The %Gastorintestinal System was created so that end users could supply and replenish substances in the body associated with exercise and clearance.
It provides a rudimentary methodology for getting substances into the body that can be expanded upon in the future.

@anchor GI-dataflow
Data Flow
---------

### Reset

The stomach is initialized with configurable amounts of each macronutrient, sodium, calcium, and water.
The gut chyme is then initialized with substance amounts by calculating 5 hours' worth of digestion of the stomach nutrients,
while not removing mass from the stomach.

### Preprocess

#### Gastric Secretion

A static gastric secretion flow rate of 2.46 mL/min is used to manually move water volume from the gut tissue back into the stomach.

#### Digestion

The amount of macronutrient to decrement from the stomach is based on the nutrient's digestion rate and the engine timestep.
The decremented amount is then multiplied by a configurable absorption amount to calculate the mass of the nutrient absorbed into the body.
This calculated mass is then used to increment a specific substance on the gut chyme compartment.

Nutrient data is converted to substance data in the following manner :
	- Carbohydrates - A transfer mass is directly calculated from the stomach carbohydrate digestion rate and engine timestep.
	                  That mass is then decremented from the stomach carbohydrate mass.
	                  The mass is also multiplied by a configurable carbohydrate absorption factor, 
					  and the amount of glucose in the gut chyme is incremented by that product.
	- Fats - A transfer mass is directly calculated from the stomach fat digestion rate and engine timestep.
	                  That mass is then decremented from the stomach fat mass.
	                  The mass is also multiplied by a configurable fat absorption factor, 
					  and the amount of tristearin in the gut chyme is incremented by that product.
	- Protein - A transfer mass is directly calculated from the stomach protein digestion rate and engine timestep.
	                  That mass is then decremented from the stomach protein mass.
	                  The mass is also multiplied by a configurable ProteinToUrea factor, 
					  and the amount of urea in the gut chyme is incremented by that product.
	- Calcium - A transfer mass is directly calculated from the configurable stomach calcium digestion rate and engine timestep.
	                  That mass is then decremented from the stomach calcium mass.
	                  The mass is also multiplied by a configurable calcium absorption factor, 
					  and the amount of calcium in the gut chyme is incremented by that product.
    - Sodium - A transfer mass is calculated as a function of the concentration of sodium in the stomach and the water digestion rate.
	           This mass is decremented from the stomach sodium mass and the sodium mass is incremented by this transferred mass in the gut chyme compartment.
	- Water -  A transfer volume is directly calculated from the configurable water digestion rate and engine timestep.
			   This volume is decremented from the stomach water volume and the volume is incremented by this transferred volume in the gut chyme compartment.
 
#### Absorption

A static absorption flow rate of 3.3 mL/min is used to manually move water volume and substances from the gut chyme into small intestine vasculature.

### Conditions

#### ConsumeMeal

The ConsumeMeal condition provides a nutrition object along with an elapsed time since those nutrients were in the stomach.
The GI System will then zero out the contents of the stomach and gut chyme and add the nutrient data provided in the condition to the stomach.
The digestion algorithm is executed for the provided elapsed time, removing nutrient mass from the stomach and adding it to substance quantities in the gut chyme.
Next, the absorption algorithm will be executed for the provided elapsed time, removing substance mass from the gut chyme and distributing that mass throughout the blood and tissues.

### Actions

#### ConsumeNutrients
Each nutrient is optional in the ConsumeNutrients action. If a nutrient mass is provided with no accompanying digestion rate, the engine will default to the rate specified in the %BioGears configuration. 
If a digestion rate is provided for a macronutrient, it will be combined with the current stomach digestion rate for that macronutrient by volume weighting the two rates together.

### Process
There is no system specific function for Process in %Gastrointestinal.

### Post Process
There is no system specific function for Post Process in %Gastrointestinal.

### Assessments
There are no system specific assessments in %Gastrointestinal.

<br>
<img src="./images/GI/GastrointestinalDataFlow.png" width="600">
<center>
*Figure 2. The data flow for the %Gastrointestinal System consists of a Reset, Conditions, Preprocess, Process, Post Process, and Assessments. 
Only the Reset, Conditions, and Preprocess have system-specific functionality.*
</center><br>

@anchor GI-features
Features, Capabilities, and Dependencies 
----------------------
### Circuit

@anchor GI-circuit
@image html GICircuit.png
<center>
<i>
Figure 4. The %GI circuit is made up of nodes and paths with elements and is connected to extravascular tissue and the cardiovascular system.
</i>
</center><br>

There is a steady secretion of fluid, enzymes, and other substances into the various compartments of the digestive tract.
The constant secretion of fluid into the digestive tract allows for macronutrients to be slowly digested and eventually absorbed through the intestinal wall @cite hall2011guyton. In %BioGears, these macronutrients are placed into the CV system through the an absorption rate that mirrors that of the human GI tract. The calculated flow rate transports substance from the small instestine C1 node to the CV system's small intestine 1 node @ref GI-circuit. Similar transport connects the tissue and the small inestine and determines wanter balance and secretion rate.
The digestion rate of macronutrients is heavily dependent on the nature of the source food, as the digestive tract needs to free substances from the rest of the food's molecular structure before it can be absorbed @cite wolever1991glycemic.
Fats spend several hours being emulsified by the small intestine and are then quickly absorbed once exposed to pancreatic enzymes @cite hall2011guyton. 
Due to the current lack of a hepatic model, the %Gastrointestinal System breaks protein into urea, simulating the deamination of amino acids in the liver @cite hall2011guyton @cite bean1984regulation @cite haussinger1991hepatocyte. 
Many of the small ions like sodium are quickly absorbed with active transport in a manner similar to the %Renal system @cite hall2011guyton.
An exception to this is calcium, which is carefully regulated by parathyroid hormone to ensure that the body's requirements are met @cite hall2011guyton.
Water is absorbed via the osmotic gradient that either naturally exists between the gut chyme and the blood or that is created by the active transport of substances across the intestinal wall @cite hall2011guyton.

| Macronutrient	| Resultant Substance |                       Digestion Rate (R)                         | Absorption Fraction (A<sub>frac</sub>) | Gut Substance Mass(M<sub>g</sub>) Stomach Nutrient Mass (M<sub>s</sub>)|
|:---:	        |:---:                |:---:                                                             |:---:                                   |:---:                                                                   |
| Carbohydrate  | Glucose             | 0.5 - 0.625 g/min @cite hall2011guyton @cite wolever1991glycemic | 0.800 @cite hall2011guyton             | M<sub>g</sub> = R*&Delta;T*A<sub>frac</sub>                            |
| Fat           | Tristearin          | 0.055 g/min @cite hall2011guyton                                 | 0.248 @cite hall2011guyton             | M<sub>g</sub> = R*&Delta;T*A<sub>frac</sub>                            |
| Protein       | Urea                | 0.071 - 0.157 g/min @cite dangin2001digestion                    | 0.405 @cite hall2011guyton             | M<sub>g</sub> = R*&Delta;T*A<sub>frac</sub>                            |
| Calcium       | Calcium             | 2.7 mg/min @cite gallagher1979intestinal                         | 0.25  @cite haussinger1990nitrogen     | M<sub>g</sub> = R*&Delta;T*A<sub>frac</sub>                            |
| Sodium        | Sodium              | N/A                                                              | 1.0                                    | M<sub>g</sub> = M<sub>s</sub>/V<sub>H2O</sub>*R<sub>H2O</sub>*&Delta;T |
| Water         | Water               | 0.417 mL/s @cite Peronnet2012Pharmacokinetic                     | 1.0                                    | V<sub>H2O</sub> = R*&Delta;T                                           |
<center>
*Table 1. How macronutrients are converted into substances.*
</center>

Once substance mass is in the gut, the substances are transported into the cardiovascular circuit with a constant flow source of 3.3mL/s.

@anchor GI-dependencies
Dependencies
------------
The %Gastrointestinal System is not dependent on any other system, but other systems are dependent on GI to provided and replenish substances that they use.

@anchor GI-assumptions
Assumptions and Limitations
---------------------------

Currently there is no modeling of defecation or the lower portion of the digestive tract. This means that all food that is ingested will eventually be absorbed.
The current digestion methodology is rudimentary and assumes all digestive rates are constant and move with the water flow after leaving the stomach. Active transport is used across cell walls with no diffusion currently implemented. Contraction of the small intestines to allow for transport and defecation is also not modeled.

@anchor GI-results
Results and Conclusions
=======================
Validation - Resting Physiologic State
--------------------------------------

The %BioGears %Gastrointestinal System was validated qualitatively by observing the relative changes in the substance and nutrient masses between the stomach contents
and the gut contents. The transport to the CV system was then shown by demonstrating an increase in substance concentration in the blood.
Concentrations are not solely a function of GI; other systems are potentially using substances in the blood.

<center>
*Table 2. Macronutrient mass in the stomach, gut, and blood as a function of time.*
</center>

|  Macronutrient/Substance |                           Stomach Mass(g) vs. Time(s)                            |                               Gut Mass(g) vs. Time(s)                                  |                     Blood Concentration (ug/mL) vs. Time (s)                         |
|:---:                     |:---:                                                                             |:---:                                                                                   |:---:                                                                                 |
| Carbohydrate/Glucose     | <img src="./plots/GI/12hr_StomachCarbs.jpg" height="100" width="200"> | <img src="./plots/GI/12hr_IntestineGlucose.jpg" height="100" width="200">    | <img src="./plots/GI/12hr_BloodGlucose.jpg" height="100" width="200">    |
| Fat/Tristearin           | <img src="./plots/GI/12hr_StomachFat.jpg" height="100" width="200">          | <img src="./plots/GI/12hr_IntestineTristearin.jpg" height="100" width="200"> | <img src="./plots/GI/12hr_BloodTristearin.jpg" height="100" width="200"> |
| Protein/Urea             | <img src="./plots/GI/12hr_StomachProtein.jpg" height="100" width="200">      | <img src="./plots/GI/12hr_IntestineUrea.jpg" height="100" width="200">       | <img src="./plots/GI/12hr_BloodUrea.jpg" height="100" width="200">       |
| Calcium                  | <img src="./plots/GI/12hr_StomachCalcium.jpg" height="100" width="200">      | <img src="./plots/GI/12hr_IntestineCalcium.jpg" height="100" width="200">    | <img src="./plots/GI/12hr_BloodCalcium.jpg" height="100" width="200">    |
| Sodium                   | <img src="./plots/GI/12hr_StomachSodium.jpg" height="100" width="200">       | <img src="./plots/GI/12hr_IntestineSodium.jpg" height="100" width="200">     | <img src="./plots/GI/12hr_BloodSodium.jpg" height="100" width="200">     |
| Water                    | <img src="./plots/GI/12hr_StomachWater.jpg" height="100" width="200">        | <img src="./plots/GI/12hr_IntestineVolume.jpg" height="100" width="200">          | <img src="./plots/GI/12hr_BV.jpg" height="100" width="200">             |


As seen in Table 2, the macronutrient masses in the stomach are depleted based on different digestion rates and eventually reach zero. 
The center column of plots shows the associated mass of substances in the gut chyme increase as the nutrients are removed from the stomach.
Concentrations are provided in the far right column demonstrating the effect of the increasing mass on the blood concentrations.
These overall trends meet the expectations of the model performance.

@anchor GI-conclusions
Conclusions
-----------

The %BioGears %Gastrointestinal System lays a foundation for future efforts in modeling digestive physiology. The flexible definition of food allows for easy extensibility
of the system by creating the ability for users to add to a library of meals. 

@anchor GI-futurework
Future Work
===========

Coming Soon
-----------
The osmolarity of the digested material is not currently measured. Implementing this would allow for the creation of a more realistic osmolar gradient to determine the water absorption rate and gastric secretion. Permeability of the tissue matrix and substance concentration levels will be added to allow for actual diffusion of substances and fluid instead of active transport being implemented currently.

@anchor GI-recommended
Recommended Improvements
------------------------

- More %Substances: By expanding the list of %substances %BioGears works with, the %Gastrointestinal model will inherently gain fidelity as mechanisms
	are constructed to properly handle new inputs.

- Defecation: The %Gastrointestinal system should eventually be able to handle undigestible material and the fluid loss due to defecation. This
	will also allow for a variety of disease states to be implemented.
	
- Vomiting: This can be added either as a symptom or an intervention to aid someone who has ingested a harmful substance.

@anchor GI-appendices
Appendices
==========

Acronyms
--------

GI - %Gastrointestinal

CV - %Cardiovascular


Data Model Implementation
-------------------------

@ref CardiovascularSystemTable "Cardiovascular"

@ref GastrointestinalSystemTable "Gastrointestinal"

Compartments
------------

The GI system is integrated into the %cardiovascular system, please refer to the compartement description associated with @ref cardiovascular-appendices "Cardiovascular Methodology".