General rules on System - Dynamic NPU Manual

System

Abbreviation Syst
Synonym Patient system
Definition

Part or phenomenon of the perceivable or conceivable world consisting of a demarcated arrangement of a set of elements and a set of relationships or processes between these elements (1)

Note 1: The system can be a patient (e.g. body of a patient), a distinct part of the patient (e.g. blood, cerebrospinal fluid), or a part of the patient’s surroundings (e.g., house dust or drinking water).

Note 2: The system is an in vivo system that occurs in the patient. Hence, sample or specimen is an in vitro system that occurs outside the patient and is an artifact. E.g. serum does not occur in the patient but is an artifact created when coagulation of the collected sample is processed.

Scope
  • The system examined is implicitly assumed to be part of the comprehensive system: the patient subject to study including proximate environment
  • The system can be divided into a matrix (a mixture of non-described elements) and component (object, the intended object measured)
Generic NPU syntax

 NPUxxxxx System(specification)—Component(specification); kind-of-property(specification)= ? unit

Specifications

Specifications added to the system may pinpoint or restrict the concept intended.

Specifications to a system usually designate one or more general superordinate systems (Super- or subsystem) of which the system is a part. They are used only if the information is significant different from other similar systems. The intention of specification of the super- or subsystem is stated when the systems are functionally or structurally different.

Reference

  1. Georges Férard, René Dybkaer, Xavier Fuentes-Arderiu. Compendium of Terminology and Nomenclature of Properties in Clinical Laboratory Sciences: Recommendations 2016. Print ISBN: 978-1-78262-107-2, PDF eISBN: 978-1-78262-245-1, EPUB eISBN: 978-1-78262-909-2, DOI:10.1039/9781782622451. Royal Society of Chemistry.
Subjects Examples Notes
Systems without specifications NPU28919 Patient —Urine; volume(procedure) = ? L  
NPU20195 Urine—Urine; colour(procedure) = ? The component and system are the same.
NPU10028 Kidney— Carbamide clearance; volume rate(procedure) = ? mL/s The system comprises both kidneys
NPU56555 Blood— Dextromethadone; substance concentration = ? µmol/L Blood is the system that contains cells and plasma. The component exists intra- and extracellular (plasma) in the blood, which has been measured.
NPU56556 Plasma—Enalaprilat; substance concentration = ? nmol/L  
NPU16870 Exhaled air—1,1-Dichloroethene; substance concentration = ? µmol/m³  
NPU23869 Plasma—Ethanol; mass concentration = ? g/L Plasma part of blood is the system that is being measured in and contains the component.
NPU54578 Blood—Ethanol; mass concentration = ? g/L

Blood is the system that contains cells and plasma. The component exists intra- and extracellular (plasma) in the blood, which has been measured.

Note: Theoretically, the intracellular mass concentration of Ethanol can be found by subtracting the value of mass concentration of Ethanol in blood with the value of mass concentration of Ethanol in plasma.

NPU16857 Drinking water—1,1,2-Trichloroethane; substance concentration = ? nmol/L The system comprises ‘drinking water’ related to the patient
NPU03780 Amniotic fluid cell protein—1,4-alpha-Glucan branching enzyme; catalytic-activity content(37 °C; procedure) = ? 1,4-alpha-Glucan branching enzyme (component) is a type of Amniotic fluid cell protein (system)
Systems with specifications NPU04666 Leukocytes(Marrow)—Basophilocytes; number fraction = ? The system comprises leukocytes derived from the marrow; not all leukocytes.
NPU19111 DNA(specification)—HFE gene; sequence variation = ? Generally, the DNA sequence is the same in any of the patient’s cells. This is expressed by having, why  ‘DNA(spec.)’ as the system. ‘Specification’ is the placeholder for the laboratory to report the exact system and lateralization.
NPU58148 DNA(Plasma)—ABO gene(NG_006669.1:g.20145_20147insG); variation(procedure) = ? The system is plasma derived from plasma that contains the component (‘ABO gene(NG_006669.1:g.20145_20147insG)’). This indicates that the ‘ABO gene sequence’ is different from the ‘ABO gene sequence’ in other tissues.
NPU22069 Plasma(fasting Patient)— Glucose; substance concentration= ? mmol/L  
NPU12459 Secretion(Trachea)—Adenovirus(ag); arbitrary concentration(procedure) = ? Secretion derived from the trachea. Secretion of trachea is (normal physiological) structural and functional different from secretion of the ear, why it’s important to state the origin of the secretion. Specification of whether it is the right or left ear is irrelevant due to the systems are structural and functional the same.
NPU27427 Plasma(Foetus; capillary Blood)—Carbon dioxide; tension(37 °C) = ? kPa Plasma derived from the capillary blood of the foetus that is a part of the system (mater).
 NPU04163 Amylase(Plasma)—Amylase, pancreatic type 3; catalytic fraction(37 °C; procedure) = ? Amylase derived from the plasma. Amylase, pancreatic type 3, the component, is part of all amylase in plasma.
NPU21859 Leukocytes(Blood)—Aberrant cell population; number fraction = ? Leukocytes derived from blood. The aberrant cell population is the component that is part of the leukocytes, in blood..
Unspecific systems NPU14338 System(specification)—Albumin; mass concentration = ? g/L Unspecific system that should be specified by the laboratory. Unspecific systems should be reserved for patient systems that are rarely measured in.
NPU19675 Synovial fluid(specification)—Albumin; mass concentration(procedure) = ? g/L ‘Specification’ is the placeholder for the laboratory to report the exact system and lateralization. E.g. ‘right knee’. (see under ‘Details’)
NPU54370 System—Amoxicillin; threshold mass concentration = ? mg/L This is a special code (context code), being a part of a list code, in which the system and a component are defined. The system without ‘specification’ indicates that the system is defined by the list code, which serves as a ‘header’ for the examination. The component is usually microorganism or cells that are stimulated to observe a given effect on that population.
Date Subjects Notes
2023-10-01 Blood and plasma

Blood comprises of cells and plasma (extracellular part). “Whole blood” and “full blood” are synonyms for blood.

  • When “blood” is annotated as system, the component has been measured in/on the cells AND in plasma. 
  • When “plasma” is annotated as system, the component has been measured in plasma.
  • When a cell in blood, e.g. “erythrocyte”, is annotated as system, the component has been measured in/on the erythrocytes.

Note: Even though, an instrument can measure on the primary sample, e.g. “blood”, it should be distinguished whether the component has been measured intracellular and plasma OR only plasma. The system should be annotated accordingly.

2019-12-09 Limits of granularity

There is a limit of granularity to specify all anatomical locations in the NPU codes. The threshold to determine whether to include or exclude the anatomical location is arbitrary, and the request of a code with a certain location must be assessed every time. In some NPU codes, anatomical locations have been included because there is a physiological or structural difference between the specified system and other systems. To this date, the subject of threshold is still under discussion. One pro-argument is that it is clinically relevant to include a specific anatomical location, e.g. ‘fifth right finger.’ The opposite argument is that the number of NPU codes will increase exponentially, and that, in their definitions, would be very similar.

A system is different from alike system when there is a structural (and/or functional) difference between the systems. The threshold is an arbitrary distinction.Secretion from trachea is structural different from secretion from bronchus. (although the difference may not be determined yet)

2019-12-09 Lateralization Lateralization of anatomical locations should be specified somewhere else than in the NPU entries. The word ‘specification’ is the placeholder for the laboratory to specify the anatomical location and lateralization. E.g. ‘right knee’.
2023-10-01 System is not synonym to specimen

Specimen, specimen type or sample have a broader definition, being either biological material (e.g. serum) or a patient system (e.g. blood). A patient system (e.g. blood) that has undergone coagulation proces has become an in vitro system that does not exist in the patient.

System is an in vivo patient system that the NPU terminology intends to describe. A primary sample is collected from the in vivo system into an in vitro system that contains additives to preserve specific components. The “primary sample” can be processed by e.g. centrifugation in which the supernatant of the sample may be alliqoted into a tube and is designated as “secondary sample”. The “secondary sample” may be processed by other procedures untill it is meaured. The final sample that is measured is designated as the “analytical sample” (which may be the same as the primary, secondary, etc, sample depending on the number of processes it is going through).

Figure 1. Illustration of the different systems.

As the scientific knowledge increases, the in vitro systems may evolve in variety and numbers. To describe one or more in vitro systems in measurands will multiply the numbers of measurand codes exponentially, causing confusions for the patients, clinicians and laboratorians and may comprimise patient safety and be econimically inefficient. The laboratorians may have difficulties in choosing a measurand code and a further harmonization work will to be performed. Moreover, presenting the details of the sample processes to the clinicians and patients is irrelevant and does not provide further knowledge. Hence

Table 1. It demonstrates the consequences of including concepts that evolve in variety and in numbers through time in measurand codes.

2019-12-09 Preanalytical conditions Information on the preparation of the patient or medication in connection with the examination is usually not included in the NPU code; this should be part of the examination procedure, the laboratory manual, or the medical record. But if the examination is performed under conditions having a special clinical significance, then a particular state of the superordinate system is added. E.g. ‘fasting patient’ is particular preanalytical condition.
2019-12-09 Unspecified specification When ‘specification’ is used as a term in the specification to system, it indicates that the the laboratory need to specify the system further in the laboratory records. in other words, ‘specification’ is the placeholder for the information that the laboratory need to specify.