#include <Gastrointestinal.h>

Inheritance diagram for biogears::Gastrointestinal:

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Public Member Functions
virtual	~Gastrointestinal () override

const char *	classname () const override

size_t	hash_code () const override

void	Clear () override

void	Initialize () override
	Initializes system properties to valid homeostatic values. More...

virtual bool	Load (const CDM::BioGearsGastrointestinalSystemData &in)

virtual CDM::BioGearsGastrointestinalSystemData *	Unload () const override

void	AtSteadyState () override
	Do anything needed between stabilization. More...

void	PreProcess () override
	Gastrointestinal Preprocess function. More...

void	Process () override
	Gastrointestinal Preprocess function. More...

void	PostProcess () override
	Gastrointestinal postprocess function. More...

Public Member Functions inherited from biogears::SEGastrointestinalSystem
	SEGastrointestinalSystem (Logger *logger)

	~SEGastrointestinalSystem () override

const SEScalar *	GetScalar (const char *name) override

const SEScalar *	GetScalar (const std::string &name) override

bool	HasChymeAbsorptionRate () const

SEScalarVolumePerTime &	GetChymeAbsorptionRate ()

double	GetChymeAbsorptionRate (const VolumePerTimeUnit &unit) const

bool	HasStomachContents () const

SENutrition &	GetStomachContents ()

const SENutrition *	GetStomachContents () const

void	RemoveStomachContents ()

std::map< const SESubstance , SEDrugTransitState >	GetDrugTransitStates ()

SEDrugTransitState *	GetDrugTransitState (const SESubstance *sub)

SEDrugTransitState *	NewDrugTransitState (const SESubstance *sub)

bool	Load (const CDM::GastrointestinalSystemData &in)

Tree< const char * >	GetPhysiologyRequestGraph () const override

Public Member Functions inherited from biogears::SESystem
	SESystem (Logger *logger)

virtual	~SESystem ()

bool	Load (const CDM::SystemData &in)

Public Member Functions inherited from biogears::Loggable
	Loggable ()

	Loggable (Logger *log)

virtual	~Loggable ()

virtual Logger *	GetLogger () const

Static Public Member Functions
static size_t	TypeHash ()

static constexpr char const *const	TypeTag ()
	Hopefully this returns a unique ID for every type. More...

Static Public Member Functions inherited from biogears::SEGastrointestinalSystem
static size_t	TypeHash ()

static constexpr char const *const	TypeTag ()
	Hopefully this returns a unique ID for every type. More...

Static Public Member Functions inherited from biogears::SESystem
static const SEScalar *	GetScalar (const char name, std::vector< SESystem > *systems)

static const SEScalar *	GetScalar (const std::string &name, std::vector< SESystem * > *systems)

Protected Member Functions
	Gastrointestinal (BioGears &bg)

virtual void	Unload (CDM::BioGearsGastrointestinalSystemData &data) const

void	SetUp () override

void	GastricSecretion (double duration_s)
	Absorb fluids from the tissues back into the stomach so it always has fluid in it. More...

void	AbsorbNutrients ()
	Absorb substances from the gut into the vascular system via the small intestine. More...

void	DigestNutrient ()
	Digestion code to convert nutrients into appropriate product due to enzyme interaction. More...

void	AbsorbMeal (double duration_s)
	Absorb a meal over a specified length of time. More...

void	AbsorbNutrients (double duration_s)
	Absorb substances from the gut into the vascular system via the small intestine. More...

void	ProcessDrugCAT ()
	Compartment Absorption Transit (CAT) model for drug dissolution and transport through the gastrointestinal system. More...

void	ChymeSecretion ()
	Secrete sodium into the intestinal chyme. More...

Protected Member Functions inherited from biogears::SEGastrointestinalSystem
void	Unload (CDM::GastrointestinalSystemData &data) const

Protected Member Functions inherited from biogears::SESystem
void	Unload (CDM::SystemData &data) const

Protected Member Functions inherited from biogears::Loggable
virtual void	Debug (const char msg, const char origin="") const

virtual void	Debug (const std::string &msg, const std::string &origin=empty) const

virtual void	Debug (std::ostream &msg, const std::string &origin=empty) const

virtual void	Info (const char msg, const char origin="") const

virtual void	Info (const std::string &msg, const std::string &origin=empty) const

virtual void	Info (std::ostream &msg, const std::string &origin=empty) const

virtual void	Warning (const char msg, const char origin="") const

virtual void	Warning (const std::string &msg, const std::string &origin=empty) const

virtual void	Warning (std::ostream &msg, const std::string &origin=empty) const

virtual void	Error (const char msg, const char origin="") const

virtual void	Error (const std::string msg, const std::string origin=empty) const

virtual void	Error (std::ostream &msg, const std::string &origin=empty) const

virtual void	Fatal (const char msg, const char origin="") const

virtual void	Fatal (const std::string &msg, const std::string &origin=empty) const

virtual void	Fatal (std::ostream &msg, const std::string &origin=empty) const

Protected Member Functions inherited from biogears::BioGearsSystem
virtual void	LoadState ()

Static Protected Member Functions
static auto	make_unique (BioGears &bg) -> std::unique_ptr< Gastrointestinal >

Protected Attributes
BioGears &	m_data

SELiquidCompartment *	m_SmallIntestineChyme

SELiquidCompartment *	m_vSmallIntestine

SELiquidCompartment *	m_Lymph

SELiquidSubstanceQuantity *	m_SmallIntestineChymeAlbumin

SELiquidSubstanceQuantity *	m_SmallIntestineChymeAminoAcids

SELiquidSubstanceQuantity *	m_SmallIntestineChymeGlucose

SELiquidSubstanceQuantity *	m_SmallIntestineChymeTriacylglycerol

SELiquidSubstanceQuantity *	m_SmallIntestineChymeCalcium

SELiquidSubstanceQuantity *	m_SmallIntestineChymeSodium

SELiquidSubstanceQuantity *	m_SmallIntestineChymeUrea

SELiquidSubstanceQuantity *	m_SmallIntestineVascularSodium

SELiquidSubstanceQuantity *	m_smallIntestineVascularGlucose

SELiquidSubstanceQuantity *	m_smallIntestineVascularAminoAcids

SELiquidSubstanceQuantity *	m_SmallIntestineVascularCalcium

SELiquidSubstanceQuantity *	m_LymphTriacylglycerol

SELiquidSubstanceQuantity *	m_smallintestineVAscularTriacylglycerol

SEFluidCircuitPath *	m_GItoCVPath

SEFluidCircuitPath *	m_GutE3ToGroundPath

SEScalarMassPerTime	m_CalciumDigestionRate

SEScalarVolumePerTime	m_WaterDigestionRate

std::vector< double >	m_TransitPH

std::vector< double >	m_TransitVolume_mL

std::vector< double >	m_TransitSurfaceArea_cm2

std::vector< double >	m_EnterocyteVolumeFraction

std::vector< double >	m_TransitRate_Per_s

std::vector< double >	m_TransitBileSalts_mM

std::map< SELiquidSubstanceQuantity *, double >	m_InitialSubstanceMasses_ug

bool	m_ConsumeRate

bool	m_DecrementNutrients

double	m_secretionRate_mL_Per_s

double	m_dT_s

Protected Attributes inherited from biogears::SEGastrointestinalSystem
SEScalarVolumePerTime *	m_ChymeAbsorptionRate

SENutrition *	m_StomachContents

std::map< const SESubstance , SEDrugTransitState >	m_DrugTransitStates

Protected Attributes inherited from biogears::SESystem
std::stringstream	m_ss

Protected Attributes inherited from biogears::Loggable
Logger *	m_Logger

Friends
class	BioGears

class	BioGearsEngineTest

Additional Inherited Members
Static Public Attributes inherited from biogears::Loggable
static const std::string	empty

static const char *	empty_cStr

Detailed Description

Constructor & Destructor Documentation

biogears::Gastrointestinal::Gastrointestinal ( BioGears & bg )

protected

biogears::Gastrointestinal::~Gastrointestinal ( )

overridevirtual

Member Function Documentation

void biogears::Gastrointestinal::AbsorbMeal ( double duration_min )

protected

Absorb a meal over a specified length of time.

This method supports the ConsumeMeal Condition, it will move the provided meal into the stomach Digest food for the specified length of time and move it to the Gut, then calculate the amount of substance that would then have been absorbed from the Gut and distributes that mass throughout the body tissues

void biogears::Gastrointestinal::AbsorbNutrients ( )

protected

Absorb substances from the gut into the vascular system via the small intestine.

Move substances from the chyme system into the vascular system based on a rate that is a function of the sodium mass in the chyme. co-transporters are used to carry glucose and amino acids Sodium absorption rate is determined by a hill-type function that increases during heavy nutrient loads. Water moves at a constant rate and doesn't transport substances with it because there isn't a compartment link connecting the chyme and vasculature.

void biogears::Gastrointestinal::AbsorbNutrients ( double duration_s )

protected

Absorb substances from the gut into the vascular system via the small intestine.

Move substances from the chyme system into the vascular system based on a rate that is a function of the sodium concentration in the body. This function is deprecated as of 6.2 but is included to support meal conditions that will be updated as of 6.3

void biogears::Gastrointestinal::AtSteadyState ( )

overridevirtual

Do anything needed between stabilization.

At the end of resting stabilization we apply a ConsumeMeal condition to modify the body state if no condition is present we reset the body state substance levels to their original level

Reimplemented from biogears::BioGearsSystem.

void biogears::Gastrointestinal::ChymeSecretion ( )

protected

Secrete sodium into the intestinal chyme.

Secretion of sodium into the small intestine chyme is computed as a function of digested amount a hill function determines rates of sodium transport. Sodium is then used as a co-transporter to facilitate movement into the blood. Could be expanded to support other ions and substances to get correct pH balance

const char* biogears::Gastrointestinal::classname ( ) const

inlineoverridevirtual

Reimplemented from biogears::SEGastrointestinalSystem.

void biogears::Gastrointestinal::Clear ( )

overridevirtual

Reimplemented from biogears::SEGastrointestinalSystem.

void biogears::Gastrointestinal::DigestNutrient ( )

protected

Digestion code to convert nutrients into appropriate product due to enzyme interaction.

Simulates digestion in the stomach between the three major nutrients and their corresponding enzymes Computes the rate of conversion and then increments that amount per time step into the chyme Handles all movement into the small intestine: ions and nutrients

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void biogears::Gastrointestinal::GastricSecretion ( double duration_s )

protected

Absorb fluids from the tissues back into the stomach so it always has fluid in it.

Fluid absorption is based on time step at a constant rate

size_t biogears::Gastrointestinal::hash_code ( ) const

inlineoverridevirtual

Reimplemented from biogears::SEGastrointestinalSystem.

void biogears::Gastrointestinal::Initialize ( )

overridevirtual

Initializes system properties to valid homeostatic values.

Reimplemented from biogears::BioGearsSystem.

bool biogears::Gastrointestinal::Load ( const CDM::BioGearsGastrointestinalSystemData & in )

virtual

auto biogears::Gastrointestinal::make_unique ( BioGears & bg ) -> std::unique_ptr<Gastrointestinal>

staticprotected

void biogears::Gastrointestinal::PostProcess ( )

overridevirtual

Gastrointestinal postprocess function.

The current BioGears implementation has no specific postprocess functionality.

Implements biogears::BioGearsSystem.

void biogears::Gastrointestinal::PreProcess ( )

overridevirtual

Gastrointestinal Preprocess function.

Apply any meal consumption actions Absorb fluids from the tissues back into the stomach so it always has fluid in it Digest substances based on our time step and transfer them to the Gut Absorb substances from the gut into the vascular system via the small intestine

Error:: Unable to read consume meal action file

Implements biogears::BioGearsSystem.

void biogears::Gastrointestinal::Process ( )

overridevirtual

Gastrointestinal Preprocess function.

The current BioGears implementation has no functionality in the process function for Gastrointestinal.

Implements biogears::BioGearsSystem.

void biogears::Gastrointestinal::ProcessDrugCAT ( )

protected

Compartment Absorption Transit (CAT) model for drug dissolution and transport through the gastrointestinal system.

This CAT model tracks a drugs progress from the stomach through the small intestine to the large intestine. The model accounts for both solid and dissolved drug in each compartment. The stomach is the first compartment in the model. The small intestine is divided in to seven compartments to generate an estimate of spatial resolution. Each small intestine compartment (not the stomach) communicates with an enterocyte layer–this is the intestinal lining that drugs must pass through in which many drugs are subjected to intestinal metabolism. Currently, the degree of metabolism is a substance specific tuning modifier. Drug in the enterocyte layer diffuses in to the portal vein. This model is based on the work in Yang2016Application and most parameters are derived from this source.

void biogears::Gastrointestinal::SetUp ( )

overrideprotectedvirtual

Implements biogears::BioGearsSystem.

static size_t biogears::Gastrointestinal::TypeHash ( )

inlinestatic

static constexpr char const* const biogears::Gastrointestinal::TypeTag ( )

inlinestatic

Hopefully this returns a unique ID for every type.

CDM::BioGearsGastrointestinalSystemData * biogears::Gastrointestinal::Unload ( ) const

overridevirtual

Reimplemented from biogears::SEGastrointestinalSystem.

void biogears::Gastrointestinal::Unload ( CDM::BioGearsGastrointestinalSystemData & data ) const

protectedvirtual

Friends And Related Function Documentation

friend class BioGears

friend

friend class BioGearsEngineTest

friend

Member Data Documentation

SEScalarMassPerTime biogears::Gastrointestinal::m_CalciumDigestionRate

protected

bool biogears::Gastrointestinal::m_ConsumeRate

protected

BioGears& biogears::Gastrointestinal::m_data

protected

bool biogears::Gastrointestinal::m_DecrementNutrients

protected

double biogears::Gastrointestinal::m_dT_s

protected

std::vector<double> biogears::Gastrointestinal::m_EnterocyteVolumeFraction

protected

SEFluidCircuitPath* biogears::Gastrointestinal::m_GItoCVPath

protected

SEFluidCircuitPath* biogears::Gastrointestinal::m_GutE3ToGroundPath

protected

std::map<SELiquidSubstanceQuantity*, double> biogears::Gastrointestinal::m_InitialSubstanceMasses_ug

protected

SELiquidCompartment* biogears::Gastrointestinal::m_Lymph

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_LymphTriacylglycerol

protected

double biogears::Gastrointestinal::m_secretionRate_mL_Per_s

protected

SELiquidCompartment* biogears::Gastrointestinal::m_SmallIntestineChyme

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineChymeAlbumin

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineChymeAminoAcids

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineChymeCalcium

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineChymeGlucose

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineChymeSodium

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineChymeTriacylglycerol

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineChymeUrea

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_smallIntestineVascularAminoAcids

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineVascularCalcium

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_smallIntestineVascularGlucose

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_SmallIntestineVascularSodium

protected

SELiquidSubstanceQuantity* biogears::Gastrointestinal::m_smallintestineVAscularTriacylglycerol

protected

std::vector<double> biogears::Gastrointestinal::m_TransitBileSalts_mM

protected

std::vector<double> biogears::Gastrointestinal::m_TransitPH

protected

std::vector<double> biogears::Gastrointestinal::m_TransitRate_Per_s

protected

std::vector<double> biogears::Gastrointestinal::m_TransitSurfaceArea_cm2

protected

std::vector<double> biogears::Gastrointestinal::m_TransitVolume_mL

protected

SELiquidCompartment* biogears::Gastrointestinal::m_vSmallIntestine

protected

SEScalarVolumePerTime biogears::Gastrointestinal::m_WaterDigestionRate

protected

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation