mstadt / neph_preght

Multiple nephron model for virgin, mid-pregnant, late-pregnant, and hypertensive rats

About

This version of the nephron model was used for the paper Stadt et al. Effect of pregnancy and hypertension on kidney function in female rats: Modeling and functional implications, under review

Directory information

model_code/

Model code files used to generate simulations. Simulation results given in plot_results/data_files/

plot_results/

data_files/ contains data files created from model simulation results

Instructions for model simulations

Note: These instructions are for running simulations using files under model_code/. Move model output to directory with files from plot_results/ to make figures.

To run the parallel simulation code use command: python3 parallel_simulate.py --sex [option] --species [option] --type [option] --diabetes [option] --inhibition [option] --pregnant [option]

The options here are:

sex: Male, Female (required);

species: human, rat, mouse (required);

type: superficial, multiple (required);

diabetes: Severe, Moderate, Non (optional, default: Non);

pregnant: mid, late (optional, default: non, only for female rat);

inhibition: ACE, SGLT2, NHE3-50, NHE3-80, NKCC2-70, NKCC2-100, NCC-70, NCC-100, ENaC-70, ENaC-100, SNB-70, SNB-100, HKA-100, HKApreg-100 (optional, default: None).

unx: N, Y (optional, default: N)

Notes:

• Human only have ACE and SGLT2 inhibition cases. The others are for rats.
• pregnancy: only has been characterized for normal pregnant rat nephron models at this time (i.e., not done for humans and for diabetes)
• mouse model is not finished for any case

Understanding output

All the output files' names are in following structure: 'sex_species_segment_concentration/flow_of_solute_in_compartment.txt'.

Here is an example: female_rat_ccd_con_of_Cl_in_Bath.txt. It contains interstitial concentration of Chloride along cortical collecting duct in female rat.

Another example: male_hum_pt_flow_of_Na_in_Lumen.txt. It contains luminal flow of Sodium along proximal convolute tubule in male human.

These results are scaled per nephron.

The unit of concentration from outputs is mmol/L (mM).

The unit of volume is nl/min.

The unit of flow is pmol/min.

Research Papers

Please cite appropriate paper(s) when using this model. Published papers related to/using model:

• superficial nephron (sex-specific): 2019 Hu et al. "Functional implications of the sex differences in transporter abundance along the rat nephron: Modeling and analysis"
• multiple nephron (sex-specific): 2020 Hu et al. "Sex differences in solute transport along the nephrons: effects of Na+ transport inhibition"
• human multiple nephron (male only): 2019 Layton and Layton "A computational model of epithelial solute and water transport along a human nephron"
• human multiple nephron (sex-specific): 2021 Hu et al. "Sex differences in solute and water handling in the human kidney: Modeling and functional implications"
• diabetic human (sex-specific): 2021 Hu et al. "A Computational Model of Kidney Function in a Patient with Diabetes"
• pregnant rat nephron (superficial): 2022 Stadt and Layton "Adaptive changes in single-nephron GFR, tubular morphology, and transport in a pregnant rat nephron: Modeling and analysis"