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= Abbreviations

== Full Description of Abbreviations used in the Catalog

<<Special Characters>>, <<A>>, <<B>>, <<C>>, <<D>>, <<E>>, <<F>>, <<G>>, <<H>>, <<I>>, <<K>>, <<L>>, <<M>>, <<N>> ,<<O>>, <<P>>, <<Q>>, <<R>>, <<S>>, <<T>>, <<U>>, <<V>>, <<W>>, <<XYZ>>

=== Special Characters

?: A risk allele not reported

5-HIAA: 5-hydroxyindoleacetic acid

=== A

A2: Biantennary nogalactosylated glycans

AA: African ancestry

AAM-BR: Age at menarche and buckling ratio

AAM-CT: Age at menarche and cortical thickness

AAM-W: Age at menarche and periosteal diameter

AAT: alanine aminotransferase

AAC: abdominal aortic calcium

A action: Aggregatibacter actinomycetemcomitans

Ab: Amyloid-beta

ABI: ankle brachial index

ACA: anti-centromere antibodies

ACE: Angiotensin-converting enzyme

ACPA: antibodies to citrullinated peptide antigens

ACVn: normalised agkistrodon contortrix venom ratio

AD: Alzheimer's Disease

ADM: Adrenomedullin

AF: atrial fibrillation

AFBV: Frontal Brain volume

AFP: ? fetoprotein

AFVB: multivariable-adjusted frontal brain volume

AIMS: Abnormal Involuntary Movements Scale

AIRg: Acute insulin response

Ala: Alaine

ALB: albumin

ALB/GLB: serum albumin:globulin ratio

ALL: all ancestries

ALL-dr: combined tests of verbal delayed recall

ALLV: adjusted log lateral ventricular volume

ALP: alkaline phosphatase

Alpha-TOH: alpha-tocopherol

ALS: amyotrophic lateral sclerosis

ALT: alanine aminotransferase

ALTHBV: multivariable-adjusted temporal horn volume

AlkPhos: Alkaline phosphatase

AMD: Age-related macular degeneration

ANC: Absolute neutrophil count

ANP6: N-terminal pro-atrial natriuretic peptide

AngCAD: angiographic coronary disease

AOI: age of smoking initiation

apoA-1: apolipoprotein A-1

aPTT: activated partial thromboplastin time

ARC: AR-C124910XX

ASD: Ostium secundum atrial septal defect

AST: aspartate aminotransferase

At: antithrombin

ATA: anti-topoisomerase antibodies

ATBV: temporal brain volume

ATCBV: total cerebral brain volume

ATVB: multivariable-adjusted temporal brain volume

AUC: area under the curve

=== B

BABF: baseline brachial artery flow velocity

BARS: Barnes Akathisia Scale

BB:	beta blockers

BD: bipolar disorder

BD-RT: bone density estimated by T score at distal radius

BD-TT: bone density estimated by T score at midshaft tibia

BMD: bone mineral density

BMI: body mass index

BMR: basal metabolic rate

BMR RQ: respiratory quotient during basal metabolic rate measurement

BPV: brain parenchymal volume

BRCA1/2: breast cancer 1 gene and breast cancer 2 gene

BUA: Broadband ultrasound attenuation

BUN: blood urea nitrogen

=== C

C: cholesterol

C3: Propionylcarnitine

C4: Butyrylcarnitine

C9: Nonaylcarnitine

C10: Decanoylcarnitine

C10:2: Decadienylcarnitine

C12: Dodecanoylcarnitine

C14:1-OH: Hydroxytetradecenoylcarnitine

CA19-9: cancer antigen 19-9

CAC: coronary artery calcification

CAL:coronary artery lesions

CB-PWV: carotid brachial pulse wave velocity

CBT: Cortical thickness of the tibia

CC16: Clara cell secretory protein

CCA: common carotid artery

CCA IMT: common carotid artery intimal medial thickness

CCB: calcium channel blockers

CCT: central corneal thickness

CD40L: Ligand, serum & plasma

cDAS28: Disease Activity Score

CDC: Complicated disease course

CE: cholesterol ester

CEA: carcinoembryonic antigen

Cer: ceramide

CERAD-dr: Consortium to Establish a Registry for Alzheimer’s Disease delayed recall

CEU: CEPH (Centre d'Etude du Polymorphisme Humain) from Utah

CF-PWVLTA: carotid-femoral pulse wave velocity, long-term average

CGI: Clinical Global Impressions-Severity

CHS1: 1st principal component on transformed hue and saturation values

CK: creatinine kinase

CKD: chronic kidney disease

cHAQ: health assessment questionnaire score

cHL: Classical Hodgkin lymphoma

CIGSTAT: former/current smokers

cIMT: carotid intima media thickness

CL: cleft lip without cleft palate

CL/P: cleft lip with or without cleft palate

COWA: total number of correct words across three letters

CP: cleft palate

CPd: Chronic periodontitis

CPD: cigarettes per day

CPDBI: 10 or more cigarettes per day

CRP: C-reactive protein

CRP average 2,6,7: C-reactive protein (CRP) averaged from 3 examinations (over about 20 years)

CRP2: C-reactive protein, offspring exam 2

CRP average 2,6,7: C-reactive protein average exam 2,6,7

CRP6: C-reactive protein exam 6

CS: cardioembolic stroke

cSJC: Swollen joint count

cTJC: Tender joint count

CVD: cardiovascular disease

CVLT-dr: California Verbal Learning Test delayed recall (belongs to WL-dr category)

=== D

D: particle diameter

DBP: diastolic blood pressure

DBPLTA: diastolic blood pressure, long-term average

D.f.: Dermatophagoides farina

DG: Desialylated 2AB-labelled human plasma N-glycans groups

DGI+FUSION+WTCCC: combined results from the DGI, FUSION, WTCCC analyses

DHEA-S: dehydroisoandrosterone sulfate

DI: Disposition index

DM: diabetes mellitus

D.p.: Dermatophagoides pteronyssinus

DWRT-dr: Delayed Word Recall Test (belongs to WL-dr category)

DXA: dual energy X-ray absorptiometry

=== E

EA: European Ancestry

EBV: Epstein-Barr virus

EDS: excessive daytime sleepiness

EEG: electroencephalography

EER: estimated energy requirement

eGFR: glomerular filtration rate

eGFRcrea: estimated glomerular filtration rate based on serum creatinine

eGFRcys: serum cystatin C

EIM: Extraintestinal manifestations

EM: Elated mania

ER +ve: Estrogen receptor positive

ER -ve: Estrogen receptor negative

ET-1: Endothelin-1

ET: endocrine treatment

ESCC: esophageal squamous cell carcinoma

ESRD: end-stage renal disease

ESS: Epworth Sleepiness Scale

Est-C: esterified cholesterol

EVNV: ever smokers, never smokers

=== F

F2: Factor 2 (visual memory and organization)

F3: Factor 3 (measure of attention and executive function - Trails A and B)

FA: female athletes

FC: free cholesterol

FEF: forced expiratory flow

FEV1: forced expiratory volume in 1 second

fev1slope: longitudinal slope of forced expiratory volume in one second

FG: fibrinogen

FI: fasting insulin

FLE: female long endurance athletes

FN: femoral neck

FNBMDm: femoral bone mineral density in males

FPG: fasting plasma glucose

fPS: free Protein S

Free T3: fasting serum free triiodothyronine

FS: female-only stroke

FSD: female sexual dysfunction

FSG: fasting serum glucose

FSH: follicle-stimulating hormone

FSIGT: frequently sampled intravenous glucose tolerance test

Ft3: free thyroxine 3

Ft4: free thyroxine

FTD: frontotemporal dementia

FUC-A: Antennary fucosylated glycans

FUC-C: Core fucosylated glycans

funcPS: functional Protein S

FVC:  forced vital capacity

FVII: Coagulation factors VII

FWLTA: forward wave amplitude, long-term average

=== G

G3D: grade 3 diarrhea

GBA: glucocerebrosiadase

GGT: glutamyltranspeptidase

Glc: Glucose

Gln: Glutamine

GLU: glucose

GluCer: glucosylceramide

GOT (AST): Glutamyl oxaloacetic transaminase, Aspartate aminotransferase

GP: Glycan peak

GPT (ALT): glutamate pyruvate transaminase, alanine aminotransferase

GP130: glycoprotein 130

GSE: general side effect burden

=== H

HAM-A: Hamilton Anxiety Scale

HbA1C: hemoglobin A1c

HbF: fetal hemoglobin

Hcy:  homocysteine

HDL-C:  Total cholesterol in HDL

HER2: human epidermal growth factor receptor 2

Hgb: Hemoglobin

His: Histidine

HOMA-IR: homeostasis model assessment of insulin resistance

HIV: human immunodeficiency virus

HDL: high density lipoprotein

HOMA-B: homeostasis model assessment of beta-cell function

HR: hormone receptor

HRmax: maximum heart rate during treadmill fitness test

Ht: hematocrit

HU: Hounsfield units

HVA: homovanillic acid

HVLT-dr: Hopkins Verbal Learning Test delayed recall (belongs to WL-dr category)

=== I

ICAIMT: internal cartotid artery internal and common carotid intimal medial thickness

ICAM: Intercellular adhesion molecule

IED: intra-extradimensional set shifting

IGF1: insulin-like growth factor I precursor

IGFBP-1: fasting serum insulin-like growth factor binding protein-1

IGFBP-3: fasting serum insulin-like growth factor binding protein-3

IL6: Interleukin-6 precursor

IL8: Interleukin-8 precursor

IL10: Interleukin-10 precursor

IL12: interleukin-12 precursor

IL18: Interleukin-18 precursor

IL1B: Interleukin-1, beta

IL1RA: interleukin-1 receptor antagonist protein precursor

IM: irritable mania

IMT: Carotid intimal medial thickness

INS: insulin

int: interaction

IR: insulin resistance

IS: all ischemic stroke

ISI_0-120: 0-120 min insulin sensitivity index

=== K

KD: Kawasaki disease

=== L

LA: linoleic acid

LAA: large artery atherosclerosis

LAD: left atrial diameter

LC: lung cancer

LDL: low density lipoprotein

LDL-C: Total cholesterol in LDL

LF/HF: ratio of low frequency to high frequency power

L-LDL-FC: The free cholesterol content of large LDL

L-HDL-L: Total lipids in large HDL

Lp(a): lipoprotein (a)

LS: lumbar spine

LTG: lamotrigine-induced hypersensitivity

LTL: leukocyte telomere length

LVEF: Left ventricular ejection fraction

LVD: large-vessel disease

LVDD: left ventricular diastolic diameter

LVFS: left ventricular fractional shortening

LVM: left ventricular mass

LVMI: left ventricular mass index

LVSD: left ventricular systolic dimension

LYM: Lymphoma subtypes

=== M

M: from clamp

MA: male athletes

MAP: mean arterial pressure

MAPLTA: mean arterial pressure, long-term average

maxL*: maximum L* (reflectance)

MC: mother's criticism

MCH: mean corpuscular hemoglobin

MCHC: mean corpuscular hemoglobin concentration

MCI: mild cognitive impairment

MCS: Mental Component Summary

MCV: mean corpuscular volume

MCP1: monocyte chemoattractant protein-1

MDC:  Mild disease course

meanFVC: mean forced vital capacity from 2 exams

meanratio: mean FEV1/FVC from 2 exams

METH: Methamphetamine

MHBMA: 2-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene and 1-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene

M-HDL-L: Total lipids in medium HDL

MHPG: 3-methoxy-4-hydroxyphenlglycol

MI: myocardial infarction

MIP-1b: macrophage inflammatory protein beta

M-LDL-C: Total cholesterol in medium LDL

M-LDL-PL: Phospholipids in medium LDL

MLE: male long endurance athletes

MobCH: double-bond protons of mobile lipids

MMnb: mismatch negativity (300-710 ms)

MMR: measles, mumps and rubella vaccination

MMSE: Mini-mental state examination

MSE: middle and short endurance athletes

MSSS: Multiple Sclerosis Severity Scale

M-VLDL-PL: Phospholipids in medium VLDL

MW: mother's warmth

=== N

NA: not applicable

NAP: non-albumin protein

Nam: Boston Naming Test

NCI: neurocognitive impairment

NeckZ1: Neck section modulus

NeckZ1rf: neck section modulus in females

NeckW1rf: neck width in females

NeckZ1rm: neck section modulus in males

NEFA: fasting serum nonesterified fatty acids

NFT: neurofibrillary tangles

NHL: Non-Hodgkin's Lymphoma

NL: neck length

NPC: nasopharyngeal carcinoma

NPG: normal-pressure glaucoma

NR: not reported

NS: none significant

NSA: neck shaft angle

NSAm: neck-shaft angle in males

NSCL/P: nonsyndromic cleft lip with or without cleft palate

NW: neck width

Nvrb: Non Verbal

=== O

OCPD: Childhood Obsessive-Compulsive Personality Disorder

OR: odds ratio

=== P

P: particle concentration

P3MRSBP: post exercise 3 minute recovery systolic blood pressure

PAD: peripheral artery disease

PAI-1: plasminogen activator inhibitor

PAL: paired associates learning

PAR-dr: paragraph delayed recall

PC: Protein C

PC1: principal component axis 1, CANTAB measures

PC2: principal component analysis 2

PC3: principal component analysis 3

PC aa C36:3: Phosphatidylcholine diacyl C36:3

PC aa C36:4: Phosphatidylcholine diacyl C34:4

PCS: Physical Component Summary

PCV: packed cell volume

PD: Parkinson’s disease

P gingi: Porphyromonas gingivalis

Phe: Phenylalanine

PHT: phenytoin-induced hypersensitivity

PKYRS: pack-years

PL: phospholipid

PLT: platelets

pltadp: platelet aggregation (ADP-induced)

pltcoll: platelet aggregation (collagen-induced)

PP: pulse pressure

ppfef: percent predicted FEF25-75 for latest exam

ppfefrat: percent predicted FEF25-75/FVC for latest exam

ppfvc: percent predicted FVC for latest exam

ppfev1: percent predicted FEV1 for latest exam

ppFEV1/FEC/FEE: percent predicted FEV1/FVC/FEF

ppratio: percent predicted FEV1/FVC for latest exam

PRM: pattern recognition memory

PROP: propylthiouracil solution

PS: protein S

PSC: primary sclerosing cholangitis

PT: prothrombin time

PUFA: polyunsaturated fatty acids

pvRSA/HF: peak-valley respiratory sinus arrhythmia or high frequency power

=== Q

QC: quality control

QUICKI: fasting serum quantitative insulin sensitivity check index

=== R

RA: Rheumatoid arthritis

RANTES: fasting serum regulated upon activation, normal T-cell expressed and secreted

RAVLT-dr: Rey’s Auditory Verbal Learning Test delayed recall (belongs to WL-dr category)

RBC: red blood cell

RBCC: red blood cell count

RDW: red cell distribution width

RMSSD: root mean square of the successive differences of inter beat intervals

RQmax: maximum respiratory quotient during treadmill fitness test

RVP: rapid visual processing

RW: reflected wave amplitude

RWLTA: reflected wave amplitude, long-term average

=== S

S2EHR: Stage 2 exercise heart rate

S2ESBP: stage 2 exercise systolic blood pressure

SBM: subset-based meta-analysis approach

SDNN: standard deviation of the normal-to-normal inter beat intervals

serum TG: serum total triglyceride content

SAS: Simpson-Angus Scale

SBP: systolic blood pressure

SBPLTA: systolic blood pressure, long-term average

sCR: serum creatinine

SCZ and BD: Schizophrenia and Bipolar disorder

s.d.: standard deviation

SE: sleep efficiency

SG: Glucose effectiveness

ShaftW1: Shaft width combined

ShaftW1f: shaft width in females

ShaftZ1rf: shaft section modulus in females

ShaftZ1R: shaft section modulus

SHBG: sex hormone binding globulin

SI: SI from FSIGT

sICAM-1: fasting serum soluble intercellular adhesion molecule-1

sIL-6R: soluble interleukin

Sim: Similarities

Sleep RQ: respiratory quotient during sleep

SLE: systemic lupus erythematosus

SM-1: butyrylcarnitine / propionylcarnitine

SM-2: N-acetylornithine

SM-3: 1-arachidonoylglycero phosphoethanolamine / 1-linoleoylglycerophospho-ethanolamine

SM-4: bilirubin (E,E) / oleoylcarnitine

SM-5: hexanoylcarnitine / oleate (18:1n9)

SM-6: myristate (14:0) / myristoleate (14:1n5)

SM-7: 1-methylxanthine / 4-acetamidobutanoate

SM-8: ADpSGEGDFXAEGGGVR / ADSGEGDFXAEGGGVR

SM-9: 10-nonadecenoate (19:1n9) / 10-undecenoate (11:1n1)

SM-10: eicosenoate (20:1n9 or 11) / tetradecanedioate

SM-11: ADpSGEGDFXAEGGGVR / ADSGEGDFXAEGGGVR

SM-12: ADSGEGDFXAEGGGVR / DSGEGDFXAEGGGVR

SM-13: androsterone sulfate / epiandrosterone sulfate

SM-14: ADpSGEGDFXAEGGGVR / DSGEGDFXAEGGGVR

SM-15: 1-eicosatrienoylglycero-phosphocholine / 1-linoleoylglycero phosphocholine

SM-16: docosahexaenoate (DHA; 22:6n3) / eicosapentaenoate (EPA; 20:5n3)

SM-17: 3-(4-hydroxyphenyl)lactate / isovalerylcarnitine

SMKAGE: age of initiation (years)

SMKDU: duration (years)

SM: sphingomyelin

Spc: spectrum

SP-D: surfactant protein D

SPEED: processing speed

SRM: spatial recognition memory

SSP: spatial span

SSRI: selective serotonin reuptake inhibitor

sTfR: Soluble Transferrin Receptor

sTie-2: soluble receptor Tie-2

Str: strict

SVD: small-vessel disease

SWM: spatial working memory

=== T

TA: Tetra-antennary glycans

TAT: Total adipose tissue area

TBLH-BMD: total-body less head bone mineral density

TB-LM: total-body lean mass

TC: total cholesterol

TEE: 24-h total energy expenditure

tFPG: 28 year time averaged fasting plasma glucose (FPG)

TG: triglycerides

TGF-b1: transforming growth factor

TG/HDLC: fasting serum triglycerides/high density lipoprotein cholesterol

TIDN: Type 1 diabetes diabetic nephropathy

Total PS: Total Protein S

Total T3: fasting serum triiodothyronine

Total T4: fasting serum thyroxine

TP: total protein

tPA: tissue plasminogen activator

TNFA: tumor necrosis factor alpha

TRBMD: Trochanter bone mineral density

TRBMDm: Trochanter bone mineral density males

TSH: thyroid stimulating hormone

Tyr: Tyrosine

=== U

UAE: urinary albumin excretion

=== V

Val: Valine

vBMD: volumetric bone mineral density

VitD250H: Vitamin D plasma 25(OH)-D

VitkPhylloq: Vitamin K plasma phylloquinone

VLDL: very-low-density lipoprotein

VLDL-D: Mean diameter for VLDL particles

VO2max: maximum oxygen consumption during treadmill fitness test

VOS: velocity of sound

VPWL-dr: delayed recall for visually presented word list

Vrb: verbal

VRM: verbal recall

vWF: Willebrand factor

=== W

WBC: white blood cell

WC: waist circumference

WCadjBMI: WC adjustment for BMI

WF: weight fluctuation

WGHS: Women's Genome Health Study

WHR: waist hip ratio

WHRadjBMI: WHR adjustment for BMI

WIT: word interference test

WL-dr: word list delayed recall

WRAT: Wide-Range Achievement Test

=== XYZ

XL-HDL-CE: The cholesterol ester content of extra large HD

XL-HDL-TG: Triglycerides in very large HDL

XXL-VLDL-P: extremely large VLDL particles

YKL-40: (Chitinase 3-like 1) protein levels

= Abbreviations

== Full Description of Abbreviations used in the Catalog

<<Special Characters>>, <<A>>, <<B>>, <<C>>, <<D>>, <<E>>, <<F>>, <<G>>, <<H>>, <<I>>, <<K>>, <<L>>, <<M>>, <<N>> ,<<O>>, <<P>>, <<Q>>, <<R>>, <<S>>, <<T>>, <<U>>, <<V>>, <<W>>, <<XYZ>>

=== Special Characters

?: A risk allele not reported

5-HIAA: 5-hydroxyindoleacetic acid

=== A

AA: African ancestry

AAM-BR: Age at menarche and buckling ratio

AAM-CT: Age at menarche and cortical thickness

AAM-W: Age at menarche and periosteal diameter

AAT: alanine aminotransferase

AAC: abdominal aortic calcium

A action: Aggregatibacter actinomycetemcomitans

Ab: Amyloid-beta

ABI: ankle brachial index

ACA: anti-centromere antibodies

ACE: Angiotensin-converting enzyme

ACPA: antibodies to citrullinated peptide antigens

ACVn: normalised agkistrodon contortrix venom ratio

AD: Alzheimer's Disease

ADM: Adrenomedullin

AF: atrial fibrillation

AFBV: Frontal Brain volume

AFP: ? fetoprotein

AFVB: multivariable-adjusted frontal brain volume

AIMS: Abnormal Involuntary Movements Scale

AIRg: Acute insulin response

Ala: Alaine

ALB: albumin

ALB/GLB: serum albumin:globulin ratio

ALL: all ancestries

ALL-dr: combined tests of verbal delayed recall

ALLV: adjusted log lateral ventricular volume

ALP: alkaline phosphatase

Alpha-TOH: alpha-tocopherol

ALS: amyotrophic lateral sclerosis

ALT: alanine aminotransferase

ALTHBV: multivariable-adjusted temporal horn volume

AlkPhos: Alkaline phosphatase

AMD: Age-related macular degeneration

ANC: Absolute neutrophil count

ANP6: N-terminal pro-atrial natriuretic peptide

AngCAD: angiographic coronary disease

AOI: age of smoking initiation

apoA-1: apolipoprotein A-1

aPTT: activated partial thromboplastin time

ARC: AR-C124910XX

ASD: Ostium secundum atrial septal defect

AST: aspartate aminotransferase

At: antithrombin

ATA: anti-topoisomerase antibodies

ATBV: temporal brain volume

ATCBV: total cerebral brain volume

ATVB: multivariable-adjusted temporal brain volume

AUC: area under the curve

=== B

BABF: baseline brachial artery flow velocity

BARS: Barnes Akathisia Scale

BB:	beta blockers

BD: bipolar disorder

BD-RT: bone density estimated by T score at distal radius

BD-TT: bone density estimated by T score at midshaft tibia

BMD: bone mineral density

BMI: body mass index

BMR: basal metabolic rate

BMR RQ: respiratory quotient during basal metabolic rate measurement

BPV: brain parenchymal volume

BRCA1/2: breast cancer 1 gene and breast cancer 2 gene

BUA: Broadband ultrasound attenuation

BUN: blood urea nitrogen

=== C

C: cholesterol

C3: Propionylcarnitine

C4: Butyrylcarnitine

C9: Nonaylcarnitine

C10: Decanoylcarnitine

C10:2: Decadienylcarnitine

C12: Dodecanoylcarnitine

C14:1-OH: Hydroxytetradecenoylcarnitine

CA19-9: cancer antigen 19-9

CAC: coronary artery calcification

CAL:coronary artery lesions

CB-PWV: carotid brachial pulse wave velocity

CBT: Cortical thickness of the tibia

CC16: Clara cell secretory protein

CCA: common carotid artery

CCA IMT: common carotid artery intimal medial thickness

CCB: calcium channel blockers

CCT: central corneal thickness

CD40L: Ligand, serum & plasma

cDAS28: Disease Activity Score

CDC: Complicated disease course

CE: cholesterol ester

CEA: carcinoembryonic antigen

Cer: ceramide

CERAD-dr: Consortium to Establish a Registry for Alzheimer’s Disease delayed recall

CEU: CEPH (Centre d'Etude du Polymorphisme Humain) from Utah

CF-PWVLTA: carotid-femoral pulse wave velocity, long-term average

CGI: Clinical Global Impressions-Severity

CHS1: 1st principal component on transformed hue and saturation values

CK: creatinine kinase

CKD: chronic kidney disease

cHAQ: health assessment questionnaire score

cHL: Classical Hodgkin lymphoma

CIGSTAT: former/current smokers

cIMT: carotid intima media thickness

CL: cleft lip without cleft palate

CL/P: cleft lip with or without cleft palate

COWA: total number of correct words across three letters

CP: cleft palate

CPd: Chronic periodontitis

CPD: cigarettes per day

CPDBI: 10 or more cigarettes per day

CRP: C-reactive protein

CRP average 2,6,7: C-reactive protein (CRP) averaged from 3 examinations (over about 20 years)

CRP2: C-reactive protein, offspring exam 2

CRP average 2,6,7: C-reactive protein average exam 2,6,7

CRP6: C-reactive protein exam 6

CS: cardioembolic stroke

cSJC: Swollen joint count

cTJC: Tender joint count

CVD: cardiovascular disease

CVLT-dr: California Verbal Learning Test delayed recall (belongs to WL-dr category)

=== D

D: particle diameter

DBP: diastolic blood pressure

DBPLTA: diastolic blood pressure, long-term average

D.f.: Dermatophagoides farina

DG: Desialylated 2AB-labelled human plasma N-glycans groups

DGI+FUSION+WTCCC: combined results from the DGI, FUSION, WTCCC analyses

DHEA-S: dehydroisoandrosterone sulfate

DI: Disposition index

DM: diabetes mellitus

D.p.: Dermatophagoides pteronyssinus

DWRT-dr: Delayed Word Recall Test (belongs to WL-dr category)

DXA: dual energy X-ray absorptiometry

=== E

EA: European Ancestry

EBV: Epstein-Barr virus

EDS: excessive daytime sleepiness

EEG: electroencephalography

EER: estimated energy requirement

eGFR: glomerular filtration rate

eGFRcrea: estimated glomerular filtration rate based on serum creatinine

eGFRcys: serum cystatin C

EIM: Extraintestinal manifestations

EM: Elated mania

ER +ve: Estrogen receptor positive

ER -ve: Estrogen receptor negative

ET-1: Endothelin-1

ET: endocrine treatment

ESCC: esophageal squamous cell carcinoma

ESRD: end-stage renal disease

ESS: Epworth Sleepiness Scale

Est-C: esterified cholesterol

EVNV: ever smokers, never smokers

=== F

F2: Factor 2 (visual memory and organization)

F3: Factor 3 (measure of attention and executive function - Trails A and B)

FA: female athletes

FC: free cholesterol

FEF: forced expiratory flow

FEV1: forced expiratory volume in 1 second

fev1slope: longitudinal slope of forced expiratory volume in one second

FG: fibrinogen

FI: fasting insulin

FLE: female long endurance athletes

FN: femoral neck

FNBMDm: femoral bone mineral density in males

FPG: fasting plasma glucose

fPS: free Protein S

Free T3: fasting serum free triiodothyronine

FS: female-only stroke

FSD: female sexual dysfunction

FSG: fasting serum glucose

FSH: follicle-stimulating hormone

FSIGT: frequently sampled intravenous glucose tolerance test

Ft3: free thyroxine 3

Ft4: free thyroxine

FTD: frontotemporal dementia

FUC-A: Antennary fucosylated glycans

funcPS: functional Protein S

FVC:  forced vital capacity

FVII: Coagulation factors VII

FWLTA: forward wave amplitude, long-term average

=== G

G3D: grade 3 diarrhea

GBA: glucocerebrosiadase

GGT: glutamyltranspeptidase

Glc: Glucose

Gln: Glutamine

GLU: glucose

GluCer: glucosylceramide

GOT (AST): Glutamyl oxaloacetic transaminase, Aspartate aminotransferase

GPT (ALT): glutamate pyruvate transaminase, alanine aminotransferase

GP130: glycoprotein 130

GSE: general side effect burden

=== H

HAM-A: Hamilton Anxiety Scale

HbA1C: hemoglobin A1c

HbF: fetal hemoglobin

Hcy:  homocysteine

HDL-C:  Total cholesterol in HDL

HER2: human epidermal growth factor receptor 2

Hgb: Hemoglobin

His: Histidine

HOMA-IR: homeostasis model assessment of insulin resistance

HIV: human immunodeficiency virus

HDL: high density lipoprotein

HOMA-B: homeostasis model assessment of beta-cell function

HR: hormone receptor

HRmax: maximum heart rate during treadmill fitness test

Ht: hematocrit

HU: Hounsfield units

HVA: homovanillic acid

HVLT-dr: Hopkins Verbal Learning Test delayed recall (belongs to WL-dr category)

=== I

ICAIMT: internal cartotid artery internal and common carotid intimal medial thickness

ICAM: Intercellular adhesion molecule

IED: intra-extradimensional set shifting

IGF1: insulin-like growth factor I precursor

IGFBP-1: fasting serum insulin-like growth factor binding protein-1

IGFBP-3: fasting serum insulin-like growth factor binding protein-3

IL6: Interleukin-6 precursor

IL8: Interleukin-8 precursor

IL10: Interleukin-10 precursor

IL12: interleukin-12 precursor

IL18: Interleukin-18 precursor

IL1B: Interleukin-1, beta

IL1RA: interleukin-1 receptor antagonist protein precursor

IM: irritable mania

IMT: Carotid intimal medial thickness

INS: insulin

int: interaction

IR: insulin resistance

IS: all ischemic stroke

ISI_0-120: 0-120 min insulin sensitivity index

=== K

KD: Kawasaki disease

=== L

LA: linoleic acid

LAA: large artery atherosclerosis

LAD: left atrial diameter

LC: lung cancer

LDL: low density lipoprotein

LDL-C: Total cholesterol in LDL

LF/HF: ratio of low frequency to high frequency power

L-LDL-FC: The free cholesterol content of large LDL

L-HDL-L: Total lipids in large HDL

Lp(a): lipoprotein (a)

LS: lumbar spine

LTG: lamotrigine-induced hypersensitivity

LTL: leukocyte telomere length

LVEF: Left ventricular ejection fraction

LVD: large-vessel disease

LVDD: left ventricular diastolic diameter

LVFS: left ventricular fractional shortening

LVM: left ventricular mass

LVMI: left ventricular mass index

LVSD: left ventricular systolic dimension

LYM: Lymphoma subtypes

=== M

M: from clamp

MA: male athletes

MAP: mean arterial pressure

MAPLTA: mean arterial pressure, long-term average

maxL*: maximum L* (reflectance)

MC: mother's criticism

MCH: mean corpuscular hemoglobin

MCHC: mean corpuscular hemoglobin concentration

MCI: mild cognitive impairment

MCS: Mental Component Summary

MCV: mean corpuscular volume

MCP1: monocyte chemoattractant protein-1

MDC:  Mild disease course

meanFVC: mean forced vital capacity from 2 exams

meanratio: mean FEV1/FVC from 2 exams

METH: Methamphetamine

MHBMA: 2-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene and 1-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene

M-HDL-L: Total lipids in medium HDL

MHPG: 3-methoxy-4-hydroxyphenlglycol

MI: myocardial infarction

MIP-1b: macrophage inflammatory protein beta

M-LDL-C: Total cholesterol in medium LDL

M-LDL-PL: Phospholipids in medium LDL

MLE: male long endurance athletes

MobCH: double-bond protons of mobile lipids

MMnb: mismatch negativity (300-710 ms)

MMR: measles, mumps and rubella vaccination

MMSE: Mini-mental state examination

MSE: middle and short endurance athletes

MSSS: Multiple Sclerosis Severity Scale

M-VLDL-PL: Phospholipids in medium VLDL

MW: mother's warmth

=== N

NA: not applicable

NAP: non-albumin protein

Nam: Boston Naming Test

NCI: neurocognitive impairment

NeckZ1: Neck section modulus

NeckZ1rf: neck section modulus in females

NeckW1rf: neck width in females

NeckZ1rm: neck section modulus in males

NEFA: fasting serum nonesterified fatty acids

NFT: neurofibrillary tangles

NHL: Non-Hodgkin's Lymphoma

NL: neck length

NPC: nasopharyngeal carcinoma

NPG: normal-pressure glaucoma

NR: not reported

NS: none significant

NSA: neck shaft angle

NSAm: neck-shaft angle in males

NSCL/P: nonsyndromic cleft lip with or without cleft palate

NW: neck width

Nvrb: Non Verbal

=== O

OCPD: Childhood Obsessive-Compulsive Personality Disorder

OR: odds ratio

=== P

P: particle concentration

P3MRSBP: post exercise 3 minute recovery systolic blood pressure

PAD: peripheral artery disease

PAI-1: plasminogen activator inhibitor

PAL: paired associates learning

PAR-dr: paragraph delayed recall

PC: Protein C

PC1: principal component axis 1, CANTAB measures

PC2: principal component analysis 2

PC3: principal component analysis 3

PC aa C36:3: Phosphatidylcholine diacyl C36:3

PC aa C36:4: Phosphatidylcholine diacyl C34:4

PCS: Physical Component Summary

PCV: packed cell volume

PD: Parkinson’s disease

P gingi: Porphyromonas gingivalis

Phe: Phenylalanine

PHT: phenytoin-induced hypersensitivity

PKYRS: pack-years

PL: phospholipid

PLT: platelets

pltadp: platelet aggregation (ADP-induced)

pltcoll: platelet aggregation (collagen-induced)

PP: pulse pressure

ppfef: percent predicted FEF25-75 for latest exam

ppfefrat: percent predicted FEF25-75/FVC for latest exam

ppfvc: percent predicted FVC for latest exam

ppfev1: percent predicted FEV1 for latest exam

ppFEV1/FEC/FEE: percent predicted FEV1/FVC/FEF

ppratio: percent predicted FEV1/FVC for latest exam

PRM: pattern recognition memory

PROP: propylthiouracil solution

PS: protein S

PSC: primary sclerosing cholangitis

PT: prothrombin time

PUFA: polyunsaturated fatty acids

pvRSA/HF: peak-valley respiratory sinus arrhythmia or high frequency power

=== Q

QC: quality control

QUICKI: fasting serum quantitative insulin sensitivity check index

=== R

RA: Rheumatoid arthritis

RANTES: fasting serum regulated upon activation, normal T-cell expressed and secreted

RAVLT-dr: Rey’s Auditory Verbal Learning Test delayed recall (belongs to WL-dr category)

RBC: red blood cell

RBCC: red blood cell count

RDW: red cell distribution width

RMSSD: root mean square of the successive differences of inter beat intervals

RQmax: maximum respiratory quotient during treadmill fitness test

RVP: rapid visual processing

RW: reflected wave amplitude

RWLTA: reflected wave amplitude, long-term average

=== S

S2EHR: Stage 2 exercise heart rate

S2ESBP: stage 2 exercise systolic blood pressure

SBM: subset-based meta-analysis approach

SDNN: standard deviation of the normal-to-normal inter beat intervals

serum TG: serum total triglyceride content

SAS: Simpson-Angus Scale

SBP: systolic blood pressure

SBPLTA: systolic blood pressure, long-term average

sCR: serum creatinine

SCZ and BD: Schizophrenia and Bipolar disorder

s.d.: standard deviation

SE: sleep efficiency

SG: Glucose effectiveness

ShaftW1: Shaft width combined

ShaftW1f: shaft width in females

ShaftZ1rf: shaft section modulus in females

ShaftZ1R: shaft section modulus

SHBG: sex hormone binding globulin

SI: SI from FSIGT

sICAM-1: fasting serum soluble intercellular adhesion molecule-1

sIL-6R: soluble interleukin

Sim: Similarities

Sleep RQ: respiratory quotient during sleep

SLE: systemic lupus erythematosus

SM-1: butyrylcarnitine / propionylcarnitine

SM-2: N-acetylornithine

SM-3: 1-arachidonoylglycero phosphoethanolamine / 1-linoleoylglycerophospho-ethanolamine

SM-4: bilirubin (E,E) / oleoylcarnitine

SM-5: hexanoylcarnitine / oleate (18:1n9)

SM-6: myristate (14:0) / myristoleate (14:1n5)

SM-7: 1-methylxanthine / 4-acetamidobutanoate

SM-8: ADpSGEGDFXAEGGGVR / ADSGEGDFXAEGGGVR

SM-9: 10-nonadecenoate (19:1n9) / 10-undecenoate (11:1n1)

SM-10: eicosenoate (20:1n9 or 11) / tetradecanedioate

SM-11: ADpSGEGDFXAEGGGVR / ADSGEGDFXAEGGGVR

SM-12: ADSGEGDFXAEGGGVR / DSGEGDFXAEGGGVR

SM-13: androsterone sulfate / epiandrosterone sulfate

SM-14: ADpSGEGDFXAEGGGVR / DSGEGDFXAEGGGVR

SM-15: 1-eicosatrienoylglycero-phosphocholine / 1-linoleoylglycero phosphocholine

SM-16: docosahexaenoate (DHA; 22:6n3) / eicosapentaenoate (EPA; 20:5n3)

SM-17: 3-(4-hydroxyphenyl)lactate / isovalerylcarnitine

SMKAGE: age of initiation (years)

SMKDU: duration (years)

SM: sphingomyelin

Spc: spectrum

SP-D: surfactant protein D

SPEED: processing speed

SRM: spatial recognition memory

SSP: spatial span

SSRI: selective serotonin reuptake inhibitor

sTfR: Soluble Transferrin Receptor

sTie-2: soluble receptor Tie-2

Str: strict

SVD: small-vessel disease

SWM: spatial working memory

=== T

TAT: Total adipose tissue area

TBLH-BMD: total-body less head bone mineral density

TB-LM: total-body lean mass

TC: total cholesterol

TEE: 24-h total energy expenditure

tFPG: 28 year time averaged fasting plasma glucose (FPG)

TG: triglycerides

TGF-b1: transforming growth factor

TG/HDLC: fasting serum triglycerides/high density lipoprotein cholesterol

TIDN: Type 1 diabetes diabetic nephropathy

Total PS: Total Protein S

Total T3: fasting serum triiodothyronine

Total T4: fasting serum thyroxine

TP: total protein

tPA: tissue plasminogen activator

TNFA: tumor necrosis factor alpha

TRBMD: Trochanter bone mineral density

TRBMDm: Trochanter bone mineral density males

TSH: thyroid stimulating hormone

Tyr: Tyrosine

=== U

UAE: urinary albumin excretion

=== V

Val: Valine

vBMD: volumetric bone mineral density

VitD250H: Vitamin D plasma 25(OH)-D

VitkPhylloq: Vitamin K plasma phylloquinone

VLDL: very-low-density lipoprotein

VLDL-D: Mean diameter for VLDL particles

VO2max: maximum oxygen consumption during treadmill fitness test

VOS: velocity of sound

VPWL-dr: delayed recall for visually presented word list

Vrb: verbal

VRM: verbal recall

vWF: Willebrand factor

=== W

WBC: white blood cell

WC: waist circumference

WCadjBMI: WC adjustment for BMI

WF: weight fluctuation

WGHS: Women's Genome Health Study

WHR: waist hip ratio

WHRadjBMI: WHR adjustment for BMI

WIT: word interference test

WL-dr: word list delayed recall

WRAT: Wide-Range Achievement Test

=== XYZ

XL-HDL-CE: The cholesterol ester content of extra large HD

XL-HDL-TG: Triglycerides in very large HDL

XXL-VLDL-P: extremely large VLDL particles

YKL-40: (Chitinase 3-like 1) protein levels


Update abbreviations-content.adoc

Update abbreviations-content.adoc

= Abbreviations

== Full Description of Abbreviations used in the Catalog

<<Special Characters>>, <<A>>, <<B>>, <<C>>, <<D>>, <<E>>, <<F>>, <<G>>, <<H>>, <<I>>, <<K>>, <<L>>, <<M>>, <<N>> ,<<O>>, <<P>>, <<Q>>, <<R>>, <<S>>, <<T>>, <<U>>, <<V>>, <<W>>, <<XYZ>>

=== Special Characters

?: A risk allele not reported

5-HIAA: 5-hydroxyindoleacetic acid

=== A

AA: African-American

AAM-BR: Age at menarche and buckling ratio

AAM-CT: Age at menarche and cortical thickness

AAM-W: Age at menarche and periosteal diameter

AAT: alanine aminotransferase

AAC: abdominal aortic calcium

A action: Aggregatibacter actinomycetemcomitans

Ab: Amyloid-beta

ABI: ankle brachial index

ACE: Angiotensin-converting enzyme

ACPA: antibodies to citrullinated peptide antigens

ACVn: normalised agkistrodon contortrix venom ratio

AD: Alzheimer's Disease

ADM: Adrenomedullin

AF: atrial fibrillation

AFBV: Frontal Brain volume

AFP: ? fetoprotein

AFVB: multivariable-adjusted frontal brain volume

AIMS: Abnormal Involuntary Movements Scale

AIRg: Acute insulin response

Ala: Alaine

ALB: albumin

ALB/GLB: serum albumin:globulin ratio

ALL: all ancestries

ALL-dr: combined tests of verbal delayed recall

ALLV: adjusted log lateral ventricular volume

ALP: alkaline phosphatase

Alpha-TOH: alpha-tocopherol

ALT: alanine aminotransferase

ALTHBV: multivariable-adjusted temporal horn volume

AlkPhos: Alkaline phosphatase

AMD: Age-related macular degeneration

ANP6: N-terminal pro-atrial natriuretic peptide

AngCAD: angiographic coronary disease

AOI: age of smoking initiation

apoA-1: apolipoprotein A-1

aPTT: activated partial thromboplastin time

ASD: Ostium secundum atrial septal defect

AST: aspartate aminotransferase

At: antithrombin

ATBV: temporal brain volume

ATCBV: total cerebral brain volume

ATVB: multivariable-adjusted temporal brain volume

=== B

BABF: baseline brachial artery flow velocity

BARS: Barnes Akathisia Scale

BD: bipolar disorder

BD-RT: bone density estimated by T score at distal radius

BD-TT: bone density estimated by T score at midshaft tibia

BMD: bone mineral density

BMI: body mass index

BMR: basal metabolic rate

BMR RQ: respiratory quotient during basal metabolic rate measurement

BPV: brain parenchymal volume

BRCA1/2: breast cancer 1 gene and breast cancer 2 gene

BUA: Broadband ultrasound attenuation

BUN: blood urea nitrogen

=== C

C: cholesterol

C3: Propionylcarnitine

C4: Butyrylcarnitine

C9: Nonaylcarnitine

C10: Decanoylcarnitine

C10:2: Decadienylcarnitine

C12: Dodecanoylcarnitine

C14:1-OH: Hydroxytetradecenoylcarnitine

CA19-9: cancer antigen 19-9

CAC: coronary artery calcification

CAL:coronary artery lesions

CB-PWV: carotid brachial pulse wave velocity

CBT: Cortical thickness of the tibia

CC16: Clara cell secretory protein

CCA: common carotid artery

CCA IMT: common carotid artery intimal medial thickness

CCT: central corneal thickness

CD40L: Ligand, serum & plasma

cDAS28: Disease Activity Score

CDC: Complicated disease course

CE: cholesterol ester

CEA: carcinoembryonic antigen

Cer: ceramide

CERAD-dr: Consortium to Establish a Registry for Alzheimer’s Disease delayed recall

CEU: CEPH (Centre d'Etude du Polymorphisme Humain) from Utah

CF-PWVLTA: carotid-femoral pulse wave velocity, long-term average

CHS1: 1st principal component on transformed hue and saturation values

CK: creatinine kinase

CKD: chronic kidney disease

cHAQ: health assessment questionnaire score

cHL: Classical Hodgkin lymphoma

CIGSTAT: former/current smokers

cIMT: carotid intima media thickness

CL: cleft lip without cleft palate

CL/P: cleft lip with or without cleft palate

COWA: total number of correct words across three letters

CP: cleft palate

CPd: Chronic periodontitis

CPD: cigarettes per day

CPDBI: 10 or more cigarettes per day

CRP: C-reactive protein

CRP average 2,6,7: C-reactive protein (CRP) averaged from 3 examinations (over about 20 years)

CRP2: C-reactive protein, offspring exam 2

CRP average 2,6,7: C-reactive protein average exam 2,6,7

CRP6: C-reactive protein exam 6

CS: cardioembolic stroke

cSJC: Swollen joint count

cTJC: Tender joint count

CVD: cardiovascular disease

CVLT-dr: California Verbal Learning Test delayed recall (belongs to WL-dr category)

=== D

D: particle diameter

DBP: diastolic blood pressure

DBPLTA: diastolic blood pressure, long-term average

D.f.: Dermatophagoides farina

DG: Desialylated 2AB-labelled human plasma N-glycans groups

DGI+FUSION+WTCCC: combined results from the DGI, FUSION, WTCCC analyses

DHEA-S: dehydroisoandrosterone sulfate

DI: Disposition index

DM: diabetes mellitus

D.p.: Dermatophagoides pteronyssinus

DWRT-dr: Delayed Word Recall Test (belongs to WL-dr category)

DXA: dual energy X-ray absorptiometry

=== E

EA: European Ancestry

EBV: Epstein-Barr virus

EDS: excessive daytime sleepiness

EER: estimated energy requirement

eGFR: glomerular filtration rate

eGFRcrea: estimated glomerular filtration rate based on serum creatinine

eGFRcys: serum cystatin C

EIM: Extraintestinal manifestations

EM: Elated mania

ET-1: Endothelin-1

ESCC: esophageal squamous cell carcinoma

ESRD: end-stage renal disease

ESS: Epworth Sleepiness Scale

Est-C: esterified cholesterol

EVNV: ever smokers, never smokers

=== F

F2: Factor 2 (visual memory and organization)

F3: Factor 3 (measure of attention and executive function - Trails A and B)

FA: female athletes

FC: free cholesterol

FEF: forced expiratory flow

FEV1: forced expiratory volume in 1 second

fev1slope: longitudinal slope of forced expiratory volume in one second

FG: fibrinogen

FI: fasting insulin

FLE: female long endurance athletes

FN: femoral neck

FNBMDm: femoral bone mineral density in males

FPG: fasting plasma glucose

fPS: free Protein S

Free T3: fasting serum free triiodothyronine

FS: female-only stroke

FSD: female sexual dysfunction

FSG: fasting serum glucose

FSH: follicle-stimulating hormone

Ft3: free thyroxine 3

Ft4: free thyroxine

FUC-A: Antennary fucosylated glycans

funcPS: functional Protein S

FVC:  forced vital capacity

FVII: Coagulation factors VII

FWLTA: forward wave amplitude, long-term average

=== G

G3D: grade 3 diarrhea

GGT: glutamyltranspeptidase

Glc: Glucose

Gln: Glutamine

GLU: glucose

GluCer: glucosylceramide

GOT (AST): Glutamyl oxaloacetic transaminase, Aspartate aminotransferase

GPT (ALT): glutamate pyruvate transaminase, alanine aminotransferase

GP130: glycoprotein 130

GSE: general side effect burden

=== H

HbA1C: hemoglobin A1c

HbF: fetal hemoglobin

Hcy:  homocysteine

HDL-C:  Total cholesterol in HDL

Hgb: Hemoglobin

His: Histidine

HOMA-IR: homeostasis model insulin resistance

HIV: human immunodeficiency virus

HDL: high density lipoprotein

HOMA-B: beta-cell function

HRmax: maximum heart rate during treadmill fitness test

Ht: hematocrit

HU: Hounsfield units

HVA: homovanillic acid

HVLT-dr: Hopkins Verbal Learning Test delayed recall (belongs to WL-dr category)

=== I

ICAIMT: internal cartotid artery internal and common carotid intimal medial thickness

ICAM: Intercellular adhesion molecule

IED: intra-extradimensional set shifting

IGF1: insulin-like growth factor I precursor

IGFBP-1: fasting serum insulin-like growth factor binding protein-1

IGFBP-3: fasting serum insulin-like growth factor binding protein-3

IL6: Interleukin-6 precursor

IL8: Interleukin-8 precursor

IL10: Interleukin-10 precursor

IL12: interleukin-12 precursor

IL18: Interleukin-18 precursor

IL1B: Interleukin-1, beta

IL1RA: interleukin-1 receptor antagonist protein precursor

IM: irritable mania

IMT: Carotid intimal medial thickness

INS: insulin

int: interaction

IR: insulin resistance

IS: all ischemic stroke

ISI_0-120: 0-120 min insulin sensitivity index

=== K

KD: Kawasaki disease

=== L

LA: linoleic acid

LAA: large artery atherosclerosis

LAD: left atrial diameter

LC: lung cancer

LDL: low density lipoprotein

LDL-C: Total cholesterol in LDL

LF/HF: ratio of low frequency to high frequency power

L-LDL-FC: The free cholesterol content of large LDL

L-HDL-L: Total lipids in large HDL

LS: lumbar spine

LTG: lamotrigine-induced hypersensitivity

LTL: leukocyte telomere length

LVD: large-vessel disease

LVDD: left ventricular diastolic diameter

LVFS: left ventricular fractional shortening

LVM: left ventricular mass

LVMI: left ventricular mass index

LVSD: left ventricular systolic dimension

LYM: Lymphoma subtypes

=== M

M: from clamp

MA: male athletes

MAP: mean arterial pressure

MAPLTA: mean arterial pressure, long-term average

maxL*: maximum L* (reflectance)

MC: mother's criticism

MCH: mean corpuscular hemoglobin

MCHC: mean corpuscular hemoglobin concentration

MCI: mild cognitive impairment

MCS: Mental Component Summary

MCV: mean corpuscular volume

MCP1: monocyte chemoattractant protein-1

MDC:  Mild disease course

meanFVC: mean forced vital capacity from 2 exams

meanratio: mean FEV1/FVC from 2 exams

METH: Methamphetamine

M-HDL-L: Total lipids in medium HDL

MHPG: 3-methoxy-4-hydroxyphenlglycol

MI: myocardial infarction

MIP-1b: macrophage inflammatory protein beta

M-LDL-C: Total cholesterol in medium LDL

M-LDL-PL: Phospholipids in medium LDL

MLE: male long endurance athletes

MobCH: double-bond protons of mobile lipids

MMnb: mismatch negativity (300-710 ms)

MMR: measles, mumps and rubella vaccination

MMSE: Mini-mental state examination

MSE: middle and short endurance athletes

MSSS: Multiple Sclerosis Severity Scale

M-VLDL-PL: Phospholipids in medium VLDL

MW: mother's warmth

=== N

NA: not applicable

NAP: non-albumin protein

Nam: Boston Naming Test

NCI: neurocognitive impairment

NeckZ1: Neck section modulus

NeckZ1rf: neck section modulus in females

NeckW1rf: neck width in females

NeckZ1rm: neck section modulus in males

NEFA: fasting serum nonesterified fatty acids

NFT: neurofibrillary tangles

NHL: Non-Hodgkin's Lymphoma

NL: neck length

NPC: nasopharyngeal carcinoma

NPG: normal-pressure glaucoma

NR: not reported

NS: none significant

NSA: neck shaft angle

NSAm: neck-shaft angle in males

NSCL/P: nonsyndromic cleft lip with or without cleft palate

NW: neck width

Nvrb: Non Verbal

=== O

OCPD: Childhood Obsessive-Compulsive Personality Disorder

OR: odds ratio

=== P

P: particle concentration

P3MRSBP: post exercise 3 minute recovery systolic blood pressure

PAD: peripheral artery disease

PAI-1: plasminogen activator inhibitor

PAL: paired associates learning

PAR-dr: paragraph delayed recall

PC: Protein C

PC1: principal component axis 1, CANTAB measures

PC2: principal component analysis 2

PC3: principal component analysis 3

PC aa C36:3: Phosphatidylcholine diacyl C36:3

PC aa C36:4: Phosphatidylcholine diacyl C34:4

PCS: Physical Component Summary

PCV: packed cell volume

P gingi: Porphyromonas gingivalis

Phe: Phenylalanine

PHT: phenytoin-induced hypersensitivity

PKYRS: pack-years

PL: phospholipid

PLT: platelets

pltadp: platelet aggregation (ADP-induced)

pltcoll: platelet aggregation (collagen-induced)

PP: pulse pressure

ppfef: percent predicted FEF25-75 for latest exam

ppfefrat: percent predicted FEF25-75/FVC for latest exam

ppfvc: percent predicted FVC for latest exam

ppfev1: percent predicted FEV1 for latest exam

ppFEV1/FEC/FEE: percent predicted FEV1/FVC/FEF

ppratio: percent predicted FEV1/FVC for latest exam

PRM: pattern recognition memory

PROP: propylthiouracil solution

PS: protein S

PSC: primary sclerosing cholangitis

PT: prothrombin time

PUFA: polyunsaturated fatty acids

=== Q

QC: quality control

QUICKI: fasting serum quantitative insulin sensitivity check index

=== R

RA: Rheumatoid arthritis

RANTES: fasting serum regulated upon activation, normal T-cell expressed and secreted

RAVLT-dr: Rey’s Auditory Verbal Learning Test delayed recall (belongs to WL-dr category)

RBC: red blood cell

RBCC: red blood cell count

RDW: red cell distribution width

RQmax: maximum respiratory quotient during treadmill fitness test

RVP: rapid visual processing

RW: reflected wave amplitude

RWLTA: reflected wave amplitude, long-term average

=== S

S2EHR: Stage 2 exercise heart rate

S2ESBP: stage 2 exercise systolic blood pressure

serum TG: serum total triglyceride content

SAS: Simpson-Angus Scale

SBP: systolic blood pressure

SBPLTA: systolic blood pressure, long-term average

sCR: serum creatinine

SCZ and BD: Schizophrenia and Bipolar disorder

s.d.: standard deviation

SE: sleep efficiency

SG: Glucose effectiveness

ShaftW1: Shaft width combined

ShaftW1f: shaft width in females

ShaftZ1rf: shaft section modulus in females

ShaftZ1R: shaft section modulus

SHBG: sex hormone binding globulin

SI: SI from FSIGT

sICAM-1: fasting serum soluble intercellular adhesion molecule-1

sIL-6R: soluble interleukin

Sim: Similarities

Sleep RQ: respiratory quotient during sleep

SLE: systemic lupus erythematosus

SM-1: butyrylcarnitine / propionylcarnitine

SM-2: N-acetylornithine

SM-3: 1-arachidonoylglycero phosphoethanolamine / 1-linoleoylglycerophospho-ethanolamine

SM-4: bilirubin (E,E) / oleoylcarnitine

SM-5: hexanoylcarnitine / oleate (18:1n9)

SM-6: myristate (14:0) / myristoleate (14:1n5)

SM-7: 1-methylxanthine / 4-acetamidobutanoate

SM-8: ADpSGEGDFXAEGGGVR / ADSGEGDFXAEGGGVR

SM-9: 10-nonadecenoate (19:1n9) / 10-undecenoate (11:1n1)

SM-10: eicosenoate (20:1n9 or 11) / tetradecanedioate

SM-11: ADpSGEGDFXAEGGGVR / ADSGEGDFXAEGGGVR

SM-12: ADSGEGDFXAEGGGVR / DSGEGDFXAEGGGVR

SM-13: androsterone sulfate / epiandrosterone sulfate

SM-14: ADpSGEGDFXAEGGGVR / DSGEGDFXAEGGGVR

SM-15: 1-eicosatrienoylglycero-phosphocholine / 1-linoleoylglycero phosphocholine

SM-16: docosahexaenoate (DHA; 22:6n3) / eicosapentaenoate (EPA; 20:5n3)

SM-17: 3-(4-hydroxyphenyl)lactate / isovalerylcarnitine

SMKAGE: age of initiation (years)

SMKDU: duration (years)

SM: sphingomyelin

Spc: spectrum

SP-D: surfactant protein D

SPEED: processing speed

SRM: spatial recognition memory

SSP: spatial span

sTfR: Soluble Transferrin Receptor

sTie-2: soluble receptor Tie-2

Str: strict

SVD: small-vessel disease

SWM: spatial working memory

=== T

TAT: Total adipose tissue area

TC: total cholesterol

TEE: 24-h total energy expenditure

tFPG: 28 year time averaged fasting plasma glucose (FPG)

TG: triglycerides

TGF-b1: transforming growth factor

TG/HDLC: fasting serum triglycerides/high density lipoprotein cholesterol

TIDN: Type 1 diabetes diabetic nephropathy

Total PS: Total Protein S

Total T3: fasting serum triiodothyronine

Total T4: fasting serum thyroxine

TP: total protein

tPA: tissue plasminogen activator

TNFA: tumor necrosis factor alpha

TRBMD: Trochanter bone mineral density

TRBMDm: Trochanter bone mineral density males

TSH: thyroid stimulating hormone

Tyr: Tyrosine

=== U

UAE: urinary albumin excretion

=== V

Val: Valine

vBMD: volumetric bone mineral density

VitD250H: Vitamin D plasma 25(OH)-D

VitkPhylloq: Vitamin K plasma phylloquinone

VLDL: very-low-density lipoprotein

VLDL-D: Mean diameter for VLDL particles

VO2max: maximum oxygen consumption during treadmill fitness test

VOS: velocity of sound

VPWL-dr: delayed recall for visually presented word list

Vrb: verbal

VRM: verbal recall

vWF: Willebrand factor

=== W

WBC: white blood cell

WC: waist circumference

WCadjBMI: WC adjustment for BMI

WF: weight fluctuation

WGHS: Women's Genome Health Study

WHR: waist hip ratio

WHRadjBMI: WHR adjustment for BMI

WL-dr: word list delayed recall

WRAT: Wide-Range Achievement Test

=== XYZ

XL-HDL-CE: The cholesterol ester content of extra large HD

XL-HDL-TG: Triglycerides in very large HDL

XXL-VLDL-P: extremely large VLDL particles

YKL-40: (Chitinase 3-like 1) protein levels

= Abbreviations

== Full Description of Abbreviations used in the Catalog

<<Special Characters>>, <<A>>, <<B>>, <<C>>, <<D>>, <<E>>, <<F>>, <<G>>, <<H>>, <<I>>, <<K>>, <<L>>, <<M>>, <<N>> ,<<O>>, <<P>>, <<Q>>, <<R>>, <<S>>, <<T>>, <<U>>, <<V>>, <<W>>, <<XYZ>>

=== Special Characters

?: A risk allele not reported

5-HIAA: 5-hydroxyindoleacetic acid

=== A

AA: African-American

AAM-BR: Age at menarche and buckling ratio

AAM-CT: Age at menarche and cortical thickness

AAM-W: Age at menarche and periosteal diameter

AAT: alanine aminotransferase

AAC: abdominal aortic calcium

A action: Aggregatibacter actinomycetemcomitans

Ab: Amyloid-beta

ABI: ankle brachial index

ACE: Angiotensin-converting enzyme

ACPA: antibodies to citrullinated peptide antigens

ACVn: normalised agkistrodon contortrix venom ratio

AD: Alzheimer's Disease

ADM: Adrenomedullin

AF: atrial fibrillation

AFBV: Frontal Brain volume

AFP: ? fetoprotein

AFVB: multivariable-adjusted frontal brain volume

AIMS: Abnormal Involuntary Movements Scale

AIRg: Acute insulin response

Ala: Alaine

ALB: albumin

ALB/GLB: serum albumin:globulin ratio

ALL: all ancestries

ALL-dr: combined tests of verbal delayed recall

ALLV: adjusted log lateral ventricular volume

ALP: alkaline phosphatase

Alpha-TOH: alpha-tocopherol

ALT: alanine aminotransferase

ALTHBV: multivariable-adjusted temporal horn volume

AlkPhos: Alkaline phosphatase

AMD: Age-related macular degeneration

ANP6: N-terminal pro-atrial natriuretic peptide

AngCAD: angiographic coronary disease

AOI: age of smoking initiation

apoA-1: apolipoprotein A-1

aPTT: activated partial thromboplastin time

ASD: Ostium secundum atrial septal defect

AST: aspartate aminotransferase

At: antithrombin

ATBV: temporal brain volume

ATCBV: total cerebral brain volume

ATVB: multivariable-adjusted temporal brain volume

=== B

BABF: baseline brachial artery flow velocity

BARS: Barnes Akathisia Scale

BD: bipolar disorder

BD-RT: bone density estimated by T score at distal radius

BD-TT: bone density estimated by T score at midshaft tibia

BMD: bone mineral density

BMI: body mass index

BMR: basal metabolic rate

BMR RQ: respiratory quotient during basal metabolic rate measurement

BPV: brain parenchymal volume

BRCA1/2: breast cancer 1 gene and breast cancer 2 gene

BUA: Broadband ultrasound attenuation

BUN: blood urea nitrogen

=== C

C: cholesterol

C3: Propionylcarnitine

C4: Butyrylcarnitine

C9: Nonaylcarnitine

C10: Decanoylcarnitine

C10:2: Decadienylcarnitine

C12: Dodecanoylcarnitine

C14:1-OH: Hydroxytetradecenoylcarnitine

CA19-9: cancer antigen 19-9

CAC: coronary artery calcification

CAL:coronary artery lesions

CB-PWV: carotid brachial pulse wave velocity

CBT: Cortical thickness of the tibia

CC16: Clara cell secretory protein

CCA: common carotid artery

CCA IMT: common carotid artery intimal medial thickness

CCT: central corneal thickness

CD40L: Ligand, serum & plasma

cDAS28: Disease Activity Score

CDC: Complicated disease course

CE: cholesterol ester

CEA: carcinoembryonic antigen

Cer: ceramide

CERAD-dr: Consortium to Establish a Registry for Alzheimer’s Disease delayed recall

CEU: CEPH (Centre d'Etude du Polymorphisme Humain) from Utah

CF-PWVLTA: carotid-femoral pulse wave velocity, long-term average

CHS1: 1st principal component on transformed hue and saturation values

CK: creatinine kinase

CKD: chronic kidney disease

cHAQ: health assessment questionnaire score

cHL: Classical Hodgkin lymphoma

CIGSTAT: former/current smokers

cIMT: carotid intima media thickness

CL: cleft lip without cleft palate

CL/P: cleft lip with or without cleft palate

COWA: total number of correct words across three letters

CP: cleft palate

CPd: Chronic periodontitis

CPD: cigarettes per day

CPDBI: 10 or more cigarettes per day

CRP: C-reactive protein

CRP average 2,6,7: C-reactive protein (CRP) averaged from 3 examinations (over about 20 years)

CRP2: C-reactive protein, offspring exam 2

CRP average 2,6,7: C-reactive protein average exam 2,6,7

CRP6: C-reactive protein exam 6

CS: cardioembolic stroke

cSJC: Swollen joint count

cTJC: Tender joint count

CVD: cardiovascular disease

CVLT-dr: California Verbal Learning Test delayed recall (belongs to WL-dr category)

=== D

D: particle diameter

DBP: diastolic blood pressure

DBPLTA: diastolic blood pressure, long-term average

D.f.: Dermatophagoides farina

DG: Desialylated 2AB-labelled human plasma N-glycans groups

DGI+FUSION+WTCCC: combined results from the DGI, FUSION, WTCCC analyses

DHEA-S: dehydroisoandrosterone sulfate

DI: Disposition index

DM: diabetes mellitus

D.p.: Dermatophagoides pteronyssinus

DWRT-dr: Delayed Word Recall Test (belongs to WL-dr category)

DXA: dual energy X-ray absorptiometry

=== E

EA: European Ancestry

EBV: Epstein-Barr virus

EDS: excessive daytime sleepiness

EER: estimated energy requirement

eGFR: glomerular filtration rate

eGFRcrea: estimated glomerular filtration rate based on serum creatinine

eGFRcys: serum cystatin C

EIM: Extraintestinal manifestations

EM: Elated mania

ET-1: Endothelin-1

ESCC: esophageal squamous cell carcinoma

ESRD: end-stage renal disease

ESS: Epworth Sleepiness Scale

Est-C: esterified cholesterol

EVNV: ever smokers, never smokers

=== F

F2: Factor 2 (visual memory and organization)

F3: Factor 3 (measure of attention and executive function - Trails A and B)

FA: female athletes

FC: free cholesterol

FEF: forced expiratory flow

FEV1: forced expiratory volume in 1 second

fev1slope: longitudinal slope of forced expiratory volume in one second

FG: fibrinogen

FI: fasting insulin

FLE: female long endurance athletes

FN: femoral neck

FNBMDm: femoral bone mineral density in males

FPG: fasting plasma glucose

fPS: free Protein S

Free T3: fasting serum free triiodothyronine

FS: female-only stroke

FSD: female sexual dysfunction

FSG: fasting serum glucose

FSH: follicle-stimulating hormone

Ft3: free thyroxine 3

Ft4: free thyroxine

FUC-A: Antennary fucosylated glycans

funcPS: functional Protein S

FVC:  forced vital capacity

FVII: Coagulation factors VII

FWLTA: forward wave amplitude, long-term average

=== G

G3D: grade 3 diarrhea

GGT: glutamyltranspeptidase

Glc: Glucose

Gln: Glutamine

GLU: glucose

GluCer: glucosylceramide

GOT (AST): Glutamyl oxaloacetic transaminase, Aspartate aminotransferase

GPT (ALT): glutamate pyruvate transaminase, alanine aminotransferase

GP130: glycoprotein 130

GSE: general side effect burden

=== H

HbA1C: hemoglobin A1c

HbF: fetal hemoglobin

Hcy:  homocysteine

HDL-C:  Total cholesterol in HDL

Hgb: Hemoglobin

His: Histidine

HOMA-IR: homeostasis model insulin resistance

HIV: human immunodeficiency virus

HDL: high density lipoprotein

HOMA-B: beta-cell function

HRmax: maximum heart rate during treadmill fitness test

Ht: hematocrit

HU: Hounsfield units

HVA: homovanillic acid

HVLT-dr: Hopkins Verbal Learning Test delayed recall (belongs to WL-dr category)

=== I

ICAIMT: internal cartotid artery internal and common carotid intimal medial thickness

ICAM: Intercellular adhesion molecule

IED: intra-extradimensional set shifting

IGF1: insulin-like growth factor I precursor

IGFBP-1: fasting serum insulin-like growth factor binding protein-1

IGFBP-3: fasting serum insulin-like growth factor binding protein-3

IL6: Interleukin-6 precursor

IL8: Interleukin-8 precursor

IL10: Interleukin-10 precursor

IL12: interleukin-12 precursor

IL18: Interleukin-18 precursor

IL1B: Interleukin-1, beta

IL1RA: interleukin-1 receptor antagonist protein precursor

IM: irritable mania

IMT: Carotid intimal medial thickness

INS: insulin

int: interaction

IR: insulin resistance

IS: all ischemic stroke

ISI_0-120: 0-120 min insulin sensitivity index

=== K

KD: Kawasaki disease

=== L

LA: linoleic acid

LAA: large artery atherosclerosis

LAD: left atrial diameter

LC: lung cancer

LDL: low density lipoprotein

LDL-C: Total cholesterol in LDL

LF/HF: ratio of low frequency to high frequency power

L-LDL-FC: The free cholesterol content of large LDL

L-HDL-L: Total lipids in large HDL

LS: lumbar spine

LTG: lamotrigine-induced hypersensitivity

LTL: leukocyte telomere length

LVD: large-vessel disease

LVDD: left ventricular diastolic diameter

LVFS: left ventricular fractional shortening

LVM: left ventricular mass

LVMI: left ventricular mass index

LVSD: left ventricular systolic dimension

LYM: Lymphoma subtypes

=== M

M: from clamp

MA: male athletes

MAP: mean arterial pressure

MAPLTA: mean arterial pressure, long-term average

maxL*: maximum L* (reflectance)

MC: mother's criticism

MCH: mean corpuscular hemoglobin

MCHC: mean corpuscular hemoglobin concentration

MCI: mild cognitive impairment

MCS: Mental Component Summary

MCV: mean corpuscular volume

MCP1: monocyte chemoattractant protein-1

MDC:  Mild disease course

meanFVC: mean forced vital capacity from 2 exams

meanratio: mean FEV1/FVC from 2 exams

METH: Methamphetamine

M-HDL-L: Total lipids in medium HDL

MHPG: 3-methoxy-4-hydroxyphenlglycol

MI: myocardial infarction

MIP-1b: macrophage inflammatory protein beta

M-LDL-C: Total cholesterol in medium LDL

M-LDL-PL: Phospholipids in medium LDL

MLE: male long endurance athletes

MobCH: double-bond protons of mobile lipids

MMnb: mismatch negativity (300-710 ms)

MMR: measles, mumps and rubella vaccination

MMSE: Mini-mental state examination

MSE: middle and short endurance athletes

MSSS: Multiple Sclerosis Severity Scale

M-VLDL-PL: Phospholipids in medium VLDL

MW: mother's warmth

=== N

NA: not applicable

NAP: non-albumin protein

Nam: Boston Naming Test

NCI: neurocognitive impairment

NeckZ1: Neck section modulus

NeckZ1rf: neck section modulus in females

NeckW1rf: neck width in females

NeckZ1rm: neck section modulus in males

NEFA: fasting serum nonesterified fatty acids

NFT: neurofibrillary tangles

NHL: Non-Hodgkin's Lymphoma

NL: neck length

NPC: nasopharyngeal carcinoma

NPG: normal-pressure glaucoma

NR: not reported

NS: none significant

NSA: neck shaft angle

NSAm: neck-shaft angle in males

NSCL/P: nonsyndromic cleft lip with or without cleft palate

NW: neck width

Nvrb: Non Verbal

=== O

OCPD: Childhood Obsessive-Compulsive Personality Disorder

OR: odds ratio

=== P

P: particle concentration

P3MRSBP: post exercise 3 minute recovery systolic blood pressure

PAD: peripheral artery disease

PAI-1: plasminogen activator inhibitor

PAL: paired associates learning

PAR-dr: paragraph delayed recall

PC: Protein C

PC1: principal component axis 1, CANTAB measures

PC2: principal component analysis 2

PC3: principal component analysis 3

PC aa C36:3: Phosphatidylcholine diacyl C36:3

PC aa C36:4: Phosphatidylcholine diacyl C34:4

PCS: Physical Component Summary

PCV: packed cell volume

P gingi: Porphyromonas gingivalis

Phe: Phenylalanine

PHT: phenytoin-induced hypersensitivity

PKYRS: pack-years

PL: phospholipid

PLT: platelets

pltadp: platelet aggregation (ADP-induced)

pltcoll: platelet aggregation (collagen-induced)

PP: pulse pressure

ppfef: percent predicted FEF25-75 for latest exam

ppfefrat: percent predicted FEF25-75/FVC for latest exam

ppfvc: percent predicted FVC for latest exam

ppfev1: percent predicted FEV1 for latest exam

ppFEV1/FEC/FEE: percent predicted FEV1/FVC/FEF

ppratio: percent predicted FEV1/FVC for latest exam

PRM: pattern recognition memory

PROP: propylthiouracil solution

PS: protein S

PSC: primary sclerosing cholangitis

PT: prothrombin time

PUFA: polyunsaturated fatty acids

=== Q

QC: quality control

QUICKI: fasting serum quantitative insulin sensitivity check index

=== R

RA: Rheumatoid arthritis

RANTES: fasting serum regulated upon activation, normal T-cell expressed and secreted

RAVLT-dr: Rey’s Auditory Verbal Learning Test delayed recall (belongs to WL-dr category)

RBC: red blood cell

RBCC: red blood cell count

RDW: red cell distribution width

RQmax: maximum respiratory quotient during treadmill fitness test

RVP: rapid visual processing

RW: reflected wave amplitude

RWLTA: reflected wave amplitude, long-term average

=== S

S2EHR: Stage 2 exercise heart rate

S2ESBP: stage 2 exercise systolic blood pressure

serum TG: serum total triglyceride content

SAS: Simpson-Angus Scale

SBP: systolic blood pressure

SBPLTA: systolic blood pressure, long-term average

sCR: serum creatinine

SCZ and BD: Schizophrenia and Bipolar disorder

s.d.: standard deviation

SE: sleep efficiency

SG: Glucose effectiveness

ShaftW1: Shaft width combined

ShaftW1f: shaft width in females

ShaftZ1rf: shaft section modulus in females

ShaftZ1R: shaft section modulus

SHBG: sex hormone binding globulin

SI: SI from FSIGT

sICAM-1: fasting serum soluble intercellular adhesion molecule-1

sIL-6R: soluble interleukin

Sim: Similarities

Sleep RQ: respiratory quotient during sleep

SLE: systemic lupus erythematosus

SM-1: butyrylcarnitine / propionylcarnitine

SM-2: N-acetylornithine

SM-3: 1-arachidonoylglycero phosphoethanolamine / 1-linoleoylglycerophospho-ethanolamine

SM-4: bilirubin (E,E) / oleoylcarnitine

SM-5: hexanoylcarnitine / oleate (18:1n9)

SM-6: myristate (14:0) / myristoleate (14:1n5)

SM-7: 1-methylxanthine / 4-acetamidobutanoate

SM-8: ADpSGEGDFXAEGGGVR / ADSGEGDFXAEGGGVR

SM-9: 10-nonadecenoate (19:1n9) / 10-undecenoate (11:1n1)

SM-10: eicosenoate (20:1n9 or 11) / tetradecanedioate

SM-11: ADpSGEGDFXAEGGGVR / ADSGEGDFXAEGGGVR

SM-12: ADSGEGDFXAEGGGVR / DSGEGDFXAEGGGVR

SM-13: androsterone sulfate / epiandrosterone sulfate

SM-14: ADpSGEGDFXAEGGGVR / DSGEGDFXAEGGGVR

SM-15: 1-eicosatrienoylglycero-phosphocholine / 1-linoleoylglycero phosphocholine

SM-16: docosahexaenoate (DHA; 22:6n3) / eicosapentaenoate (EPA; 20:5n3)

SM-17: 3-(4-hydroxyphenyl)lactate / isovalerylcarnitine

SMKAGE: age of initiation (years)

SMKDU: duration (years)

SM: sphingomyelin

Spc: spectrum

SP-D: surfactant protein D

SPEED: processing speed

SRM: spatial recognition memory

SSP: spatial span

sTfR: Soluble Transferrin Receptor

Str: strict

SVD: small-vessel disease

SWM: spatial working memory

=== T

TAT: Total adipose tissue area

TC: total cholesterol

TEE: 24-h total energy expenditure

tFPG: 28 year time averaged fasting plasma glucose (FPG)

TG: triglycerides

TGF-b1: transforming growth factor

TG/HDLC: fasting serum triglycerides/high density lipoprotein cholesterol

TIDN: Type 1 diabetes diabetic nephropathy

Total PS: Total Protein S

Total T3: fasting serum triiodothyronine

Total T4: fasting serum thyroxine

TP: total protein

tPA: tissue plasminogen activator

TNFA: tumor necrosis factor alpha

TRBMD: Trochanter bone mineral density

TRBMDm: Trochanter bone mineral density males

TSH: thyroid stimulating hormone

Tyr: Tyrosine

=== U

UAE: urinary albumin excretion

=== V

Val: Valine

vBMD: volumetric bone mineral density

VitD250H: Vitamin D plasma 25(OH)-D

VitkPhylloq: Vitamin K plasma phylloquinone

VLDL: very-low-density lipoprotein

VLDL-D: Mean diameter for VLDL particles

VO2max: maximum oxygen consumption during treadmill fitness test

VOS: velocity of sound

VPWL-dr: delayed recall for visually presented word list

Vrb: verbal

VRM: verbal recall

vWF: Willebrand factor

=== W

WBC: white blood cell

WC: waist circumference

WCadjBMI: WC adjustment for BMI

WF: weight fluctuation

WGHS: Women's Genome Health Study

WHR: waist hip ratio

WHRadjBMI: WHR adjustment for BMI

WL-dr: word list delayed recall

WRAT: Wide-Range Achievement Test

=== XYZ

XL-HDL-CE: The cholesterol ester content of extra large HD

XL-HDL-TG: Triglycerides in very large HDL

XXL-VLDL-P: extremely large VLDL particles

YKL-40: (Chitinase 3-like 1) protein levels


improves main behind spec documentation

improves main behind spec documentation

//
//  Copyright (c) 2018 Otávio Santana and others
//   All rights reserved. This program and the accompanying materials
//   are made available under the terms of the Eclipse Public License v1.0
//   and Apache License v2.0 which accompanies this distribution.
//   The Eclipse Public License is available at http://www.eclipse.org/legal/epl-v10.html
//   and the Apache License v2.0 is available at http://www.opensource.org/licenses/apache2.0.php.
//
//   You may elect to redistribute this code under either of these licenses.
//
//   Contributors:
//
//   Otavio Santana

== The main idea behind the API

The divide-and-conquer strategy decreases the complexity of systems within modules or structures. These structure levels split responsibility and make maintenance and replaceability more clear. The new Jakarta NoSQL API proposal is going to be a bridge between the logic tier and the data tier. To do this, we need to create two APIs: one to communicate to a database and another one to be a high abstraction to the Java application.

In software, there are structures: tiers, physical structures, and layers. The multi-tier application has three levels:

* **Presentation** tier: Has a primary duty to translate results so the user can understand.
* **Logic tier**: Has all business rules, processes, conditions, saved information, etc. This level moves and processes information between other levels.
* **Data tier**: Retrieves and stores information in either a database or a system file.

image::tiers.png[Tiers from a classic application structure]

Talking more precisely about the physical layer and the logic to separate responsibilities, there are other layers.

The logic tier, where the application and the business rules stay, has additional layers:

* **Application layer**: The bridge between the view tier and logic tier, e.g. convert an object into either JSON or HTML.
* **Service layer**: The service layer; this can be either a Controller or a Resource.
* **Business Layer**: This is the part of the program that encodes the real-world business or domain rules that determine how data will be created, stored, and changed.
* **Persistence Layer**: This is a layer that provides simplified access to data stored in persistent storage of some kind.

image::logic_tier.png[Logic tier on details]

Within a persistence layer, it has its layers: A Data Access Object, DAO. This structure connects business layer and persistence layer. Inside it has an API that does database. Currently, there is a difference between SQL and NoSQL database:

In the relational database, there are two mechanisms under DAO, JDBC, and JPA:

* **JDBC**: a deep layer with a database that has communications, underlying transactions, and is basically a driver to a particular database.
* **JPA**: A high layer that has communication with either JDBC or JPA. This layer has a high mapping to Java; this place has annotations and an EntityManager. In general, a JPA has integrations with other specifications, such as CDI and Bean Validation.

A considerable advantage of this strategy is that one change, either JDBC or JPA, can happen quickly. When you change a database, you need to supersede to a respective driver by a database, and then you're done! The code is ready for a new database change.

.A usual Java application with JPA layer architecture
image::jpa.png[A usual Java application with JPA layer architecture]

In a NoSQL database, there isn't a strategy to save code, and there is little impact for change. All APIs are different and don't follow any one standard, so one change to a new database can result in a lot of work.

* The database vendor needs to be worried about the high-level mapping to Java world, and the solution provider needs to be concerned about the low level of communication with a particular database.
* The database vendor needs to “copy” these communication solutions to all Java vendors.
* To a Java developer, there are two lock-in types: If a developer uses an API directly for a change, it loses code. If a developer uses high-level mapping, they lock-in a Java solution because if this high level doesn't have the support to a particular NoSQL database, the developer needs to change to either a Java solution or use a NoSQL API directly.

.A NoSQL Java application that has lock-in to each NoSQL provider
image::nosql_issue.png[A NoSQL Java application that has locking to each NoSQL provider]

A wise recommendation might be to use the JPA because once the developer already knows this standard SQL API, they can use the same API for a relational database and apply it to a NoSQL database. Using an API with SQL concepts in NoSQL is the same as using a knife as a spoon; the result is a disaster! Furthermore, the NoSQL world has diversity with several data structures and particular behavior to each provider, and both matter in a software solution. Indeed, the merge strategy to use just one API is still a discussion nowadays.

A good point about using NoSQL as a consequence polyglot persistence is that data storage is about choice. When a database offers gains, it sacrifices other aspects; it is the CAP theorem slamming the door. Hence, an API generic enough to encapsulate all kinds of databases might be useless.

The history between Java and NoSQL has several solutions that can be split by two:

1. NoSQL Drivers
2. Mapper
   * Mapper Agnostic
   * Mapper Specific

The first one is the driver API; this API has a low communication level, such as JDBC to NoSQL. It guarantees full power over the NoSQL database, a semantic closer to a database. However, it requires more code to move it forward to the entity domain the portability is pretty down; therefore, the learning curve.

The Object Mapper lets the developer work in terms of domains, thus it can help a developer follow ethical practices. A mapper may be specific, which means that a mapper is made for a particular database, so the mapper will support all the database features but with the price of a lock-in API. On the other hand, there is the agnostic mapper that uses a generic API to encapsulate the database API, which allows a developer with an API to connect several databases; however, it tends to either not cover numerous features in a database or many databases.

The rapid adoption of NoSQL combined with the vast assortment of implementations has driven a desire to create a set of standardized APIs. In the Java world, this was initially proposed in an effort by Oracle to define a NoSQL API for Java EE 9. The justification for the definition of a new API, separate form JDBC and JPA, was the following:

* JPA was not designed with NoSQL in mind
* A single set of APIs or annotations isn’t adequate for all database types
* JPA over NoSQL implies the inconsistent use of annotations
* The diversity in the NoSQL world matters

Unfortunately, what Oracle proposed for Java EE 9 was not completed when Java EE was donated to the Eclipse Foundation.

To bring innovation under the Jakarta EE umbrella, Jakarta NoSQL was born. The goal of this specification is to ease integration between Java applications and NoSQL databases, with a standard API to work with different types and vendors of NoSQL databases. To achieve this, the spec has two APIs that work like layers, and each layer has a specific goal that can integrate between each and use in isolation:

* **Communication API**: Exactly what JDBC is to SQL. This API has four specializations, one for each type of database (column, document, key-value and graph). The specialties are independent of each other, optional from the point of the database vendor and have their specific TCKs.
* **Mapping API**: This layer is based on Annotations, analogous to JPA and CDI, and preserves integration with other Jakarta EE technologies like Bean Validation and so on.

Jakarta EE NoSQL is the first specification in the Java enterprise. As any Java specification, it analyzes solutions that already exist, checks the history with both success and failure cases, and then goes in a direction that has a lesser number of trade-offs in an API architecture. The divide and conquer method fits well in the layer, communication, mapping, and NoSQL types. Thus, it will provide a straightforward specification, light maintenance; it will define the scope of each API; and it will work better in extensibility once the particular features matter to a NoSQL database.ut CDI events is how easy it creates and add new functionalities without changing the core code that is easy to use bean validation just to listen to an event.

Jakarta EE has a bright future with a significant integration with the community and open source. More transparency, after all, is the most meaningful power of Jakarta. It's not the technology itself, but the heart of the community, therefore, the success is in the hand of each developer.

//
//  Copyright (c) 2018 Otávio Santana and others
//   All rights reserved. This program and the accompanying materials
//   are made available under the terms of the Eclipse Public License v1.0
//   and Apache License v2.0 which accompanies this distribution.
//   The Eclipse Public License is available at http://www.eclipse.org/legal/epl-v10.html
//   and the Apache License v2.0 is available at http://www.opensource.org/licenses/apache2.0.php.
//
//   You may elect to redistribute this code under either of these licenses.
//
//   Contributors:
//
//   Otavio Santana

== The main idea behind the API

Once, we talked about the importance of the standard of a NoSQL database API; the next step is to discuss, in more details, about API. However, to make a natural explanation, we are first going to talk about both layer and tier. These structure levels make communication, maintenance, and split the responsibility clearer. The new API proposal is going to be responsible for being a bridge between the logic tier and data tier, and to do this; we need to create two APIs - one to communicate to a database and another one to be a high abstraction to Java application.

In software, the word is common that application has structures: tier, physical structure, and layer, logic one. The multi-tier application has three levels:

* **Presentation tier**: This, as primary duty, translates the result from below tiers to what the user can understand.

* **Logic tier**: The tier where has all business rules, process, conditions, etc. This level moves and processes information between other levels.

* **Data tier**: Stores and retrieve information, either in a database or a system file.

Talking more precisely about the physical layer, logic to separate responsibilities, there are layers

The logic tier, where the application and the business rule stay. It has layers:

* *Application layer*: The bridge between the view tier and logic tier, e.g., Convert an object into either JSON or HTML.
* *Service layer*: The service layer can either be a Controller or a Resource.
* *Business Layer*: Where the whole business and the model be.
* *Persistence Layer*: The platform between the logic tier and data tier. The layer has an integration such as DAO or repository.

Within a persistence layer, it has its layers: A Data Access Object, DAO. This structure connects business layer and persistence layer. Inside it has an API that does database. Currently, there is a difference between SQL and NoSQL database:

In the relational database, there are two mechanisms beyond DAO: JDBC, and JPA.

* *JDBC*: A deep layer with a database that has communications, basic transactions; basically, it's a driver to a particular database.
* *JPA*: A high layer that has communication, either JDBC and JPA. This layer has high mapping to Java; this place has annotations and an EntityManager. In general, a JPA has integration with other specifications such as CDI and Bean Validation.

A huge advantage of this strategy is that one change, either JDBC or JPA, can happen quickly. When a developer changes a database, he just needs the switch to a respective driver by a database and done! Code ready for a new database changed.

.A usual Java application with JPA layer architecture
image::jpa.png[A usual Java application with JPA layer architecture]

In a NoSQL database, there isn’t a strategy to save code or little impact for a change. All APIs are different and don’t follow any one standard, so one change to new database results in a lot of work. There are some solutions such as Spring Data, Hibernate OGM, TopLink NoSQL, but at a high level. In other words, if this high-level API has no support for a particular database, the result is going to be either changing a high-level API or using the API from NoSQL database directly; so, loss of a lot of code. This solution has several issues:

* The database vendor needs to be worried about the high-level mapping to Java world
* The solution provider needs to be concerned about the low level of communication with a particular database. The database vendor needs to “copy” this communication solutions to all Java vendors.
* To a Java developer, there are two lock-in types: If a developer uses an API directly for a change, it will lose code. If a developer uses a high-level mapping, this developer has locked-in a Java solution because if this high level hasn’t support for a particular NoSQL database, the developer needs to change to either Java solution or use a NoSQL API directly.

.A NoSQL Java application that has lock-in to each NoSQL provider
image::nosql_issue.png[A NoSQL Java application that has locking to each NoSQL provider]

The solve this problem, the API should have two layers:

* The communication layer: the driver from a particular database that connects Java to an accurate database. This layer has four specializations, one for each NoSQL type.
* The mapping level: its duty is to high concept to Java developers; this layer has annotations and integration to other specializations.

These APIs are optional to each other. In other words, a Java solution just needs to implement a great solution, and the database vendors need to implement the connection API.

=== Eclipse JNoSQL

The Eclipse JNoSQL is a several tool to make easy integration between the Java Application with the NoSQL. JNoSQL has a standard API. However, NoSQL has a diversity even when both are the same type. E.g. two column family databases, HBase and Cassandra, they have particular behavior and resource that make their individual, such as Cassandra Query Language and consistency level that just does exist on Cassandra. So, the API must be extensive and configurable to have support also to a specific database. To solve this problem, the project gonna have two layers:

* **Communication API**: An API just to communicate with the database, exactly what JDBC does to SQL. This API is going to have four specializations, one for each kind of database.
* **Mapping API**: An API to do integration and do the best integration with the Java developer. That is going to be annotation driven and going to have integration with other technologies like Bean Validation, etc.

.Eclipse JNoSQL
image::jnosql.png[Eclipse JNoSQL]

==== Communication API

The communication has a goal to the low-level API; in other words, communicate with the NoSQL databases. This project is going to work as a driver to NoSQL databases. At overall, it has four APIs inside; three new APIs and Apache TinkePop to graph one for each NoSQL kind, beyond its own TCK. A test compatibility kit, the TCK, is a test group that makes sure a NoSQL database does support a database.

==== Mapping API

Mapping API is the integration and mapping layer. In other words, it takes the communication level, and it does integration with other technologies such as Bean Validation and also with an entity model. It has a CDI engine.

As communication has, mapping also has an API to each database flavor. Using CDI as the engine, each component is configurable, and it has features such as:

* Persist an object through annotation
* Make replaceable any component (reflections, entity conversions, cache, persistence lifecycle and more).
* Observe event: a continued existence database lifecycle (each database's kind has an individual event).

An important point about CDI events is how easy it creates and add new functionalities without changing the core code that is easy to use bean validation just to listen to an event.


fix refs

fix refs

= Level of Detail (LOD) Optimization
:revnumber: 2.0
:revdate: 2020/07/15
:uri-jme3: https://github.com/jMonkeyEngine/jmonkeyengine/blob/master

A mesh with a high level of detail has lots of polygons and looks good close up. But when the mesh is further away (and the detail is not visible), the high-polygon count slows down performance unnecessarily.

One solution for this problem is to use high-detail meshes for objects close to the camera, and low-detail meshes for objects far from the camera. As the player moves through the scene, you must keep replacing close objects by more detailed meshes, and far objects by less detailed meshes. The goal is to keep few high-quality slow-rendering objects in the foreground, and many low-quality fast-rendering objects in the background. (Experienced users can compare this approach to xref:jme3/advanced/terrain.adoc[JME's TerraMonkey terrain system], which internally uses the specialized GeoMipMapping algorithm to generate a terrain's Levels of Detail.)

You see now why you may want to be able to generate Levels of Detail for complex Geometries automatically. JME3 supports a Java implementation of the Ogre engine's LOD generator (originally by Péter Szücs and Stan Melax): You use link:{uri-jme3}/jme3-core/src/tools/java/jme3tools/optimize/LodGenerator.java[jme3tools.optimize.LodGenerator] in conjunction with link:{uri-jme3}/jme3-core/src/main/java/com/jme3/scene/control/LodControl.java[com.jme3.scene.control.LodControl].

For a demo, run link:{uri-jme3}/jme3-examples/src/main/java/jme3test/stress/TestLodGeneration.java[TestLodGeneration.java] from xref:sdk:sample_code.adoc[JmeTests], then press +/- and spacebar to experiment. The following screenshots show a monkey model with three reduced Levels of Detail:

image::jme3/advanced/jmonkey-lod.gif[jmonkey-lod.gif,width="",height="",align="center"]

== Usage

To activate this optimization:

.  Pick a reduction method and values for the Geometry. (Trial and error…)
.  Generate LODs for the Geometry, either in the SDK or in code.
.  Add an LOD control to the Geometry.

== Pick Reduction Methods and Values

There are several reduction methods to generate a low-polygon version from a high-polygon model. Don't worry, the reduction does not modify the original model.
[cols="35,55,10", options="header"]
|===

a|Reduction Method
a|Description
a|Reduction Value

a|LodGenerator.TriangleReductionMethod.COLLAPSE_COST
a|Collapses polygon vertices from the mesh until the reduction cost (= amount of ugly artifacts caused) exceeds the given threshold.
a|0.0f - 1.0f

a|LodGenerator.TriangleReductionMethod.PROPORTIONAL
a|Removes the given percentage of polygons from the mesh.
a| 0.0f - 1.0f

a|LodGenerator.TriangleReductionMethod.CONSTANT
a|Removes the given number of polygons from the mesh.
a| integer

|===

If you don't know which to choose, experiment. For example start by trying COLLAPSE_COST and .5f-.9f.

== Generate LOD

You must generate and cache several LODs for each mesh, ranging from many to few polygons. The LOD generator algorithm attempts to collaps vertices automatically, while avoiding ugly artifacts. The LOD generator doesn't generate new meshes, it only creates separate reduced index buffers for the more highly reduced levels.

*  If you create geometries manually (3D models), use the SDK to generate LODs.
*  If you create geometries programmatically, generate LODs from your Java code.

=== Generating LODs in the SDK

The SDK contains a user-friendly interface to generate LODs for a model (.j3o file).

.  Open the Projects or Files window.
.  Select the .j3o file in the `Project Assets/Models` directory.
.  Choose `menu:Window[Edit in SceneExplorer]` if the SceneExplorer is not open. Info about the selected model is now displayed in the SceneExplorer.
.  btn:[RMB] select the model in SceneExplorer. Choose the `menu:Tools[Generate Levels of Detail]` menu. +
image:jme3/advanced/jme-sdk-generate-lod-menu.png[The Tools Generate LOD context menu in the SceneExplorer,width="300",height="180"]
.  The `Generate LOD` settings wizard opens: +
image:jme3/advanced/jme-sdk-generate-lod-window.png[The Generate LOD settings wizard,width="300",height="150"]
.  Choose a reduction method and reduction values for one or more levels.
+
[TIP]
====
Enter higher reduction values for higher levels.
====

.  Click btn:[Finish] to generate the LODs for this model.

The LODs are saved in the .j3o model file.

[TIP]
====
Choose `menu:Window[Properties]` if the Properties window is not open. Choose the generated LODs from the dropdown in the Properties window, and verify their quality in the SceneComposer.
====

image::jme3/advanced/jme-sdk-generate-lod-full.png[jme-sdk-generate-lod-full.png,width="",height="",align="center"]

=== Generating LODs in Code

The `jme3tools.optimize.LodGenerator` utility class helps you generate LODs for an arbitrary mesh (a Geometry object) programmatically from your Java code. You create and bake one LodGenerator for each Geometry.

[source,java]
----
LodGenerator lod = new LodGenerator(geometry);
lod.bakeLods(reductionMethod,reductionValue);
----

The LODs are stored inside the Geometry object.

*Example:* How to generate an LOD of myPrettyGeo's mesh with the same settings as used in the SDK example above:

[source,java]
----
LodGenerator lod = new LodGenerator(myPrettyGeo);
lod.bakeLods(LodGenerator.TriangleReductionMethod.PROPORTIONAL,0.25, 0.5f, 0.75f);
----

== Activate the LOD Control

After generating the LODs for the geometry, you create and add a `com.jme3.scene.control.LodControl` to the geometry. Adding the LodControl activates the LOD optimizaton for this geometry.

[source,java]
----
LodControl lc = new LodControl();
myPrettyGeo.addControl(lc);
rootNode.attachChild(myPrettyGeo);
----

The LodControl internally gets the camera from the game's viewport to calculate the distance to this geometry. Depending on the distance, the LodControl selects an appropriate level of detail, and passes more (or less) detailed vertex data to the renderer.

== Impact on Quality and Speed
[cols="10,30,20,20,20", options="header"]
|===

a|Level number
a|Purpose
a|Distance
a|Rendering Speed
a|Rendering Quality

a|Level 0
a|The original mesh is used automatically for close-ups, and it's the default if no LODs have been generated.
a|Closest
a|Slowest.
a|Best.

a|Level 1 +
Level 2 +
Level 3
a|If you generated LODs, JME3 uses them automatically as soon as the object moves into the background.
a|The higher the level, +
the further away.
a|The higher the level, +
the faster.
a|The higher the level, +
the lower the quality.

|===

== See also

*  link:https://hub.jmonkeyengine.org/t/brand-new-lod-generator/26341[https://hub.jmonkeyengine.org/t/brand-new-lod-generator/26341]
*  link:https://github.com/worldforge/ember/tree/master/src/components/ogre/lod[https://github.com/worldforge/ember/tree/master/src/components/ogre/lod]
*  link:http://www.melax.com/polychop[http://www.melax.com/polychop]
*  link:http://sajty.elementfx.com/progressivemesh/GSoC2012.pdf[http://sajty.elementfx.com/progressivemesh/GSoC2012.pdf]
*  xref:jme3/advanced/terrain.adoc[JME3 TerraMonkey Terrain]

= Level of Detail (LOD) Optimization
:author:
:revnumber:
:revdate: 2016/03/17 20:48
:relfileprefix: ../../
:imagesdir: ../..
:experimental:
:uri-jme3: https://github.com/jMonkeyEngine/jmonkeyengine/blob/master
ifdef::env-github,env-browser[:outfilesuffix: .adoc]

A mesh with a high level of detail has lots of polygons and looks good close up. But when the mesh is further away (and the detail is not visible), the high-polygon count slows down performance unnecessarily.

One solution for this problem is to use high-detail meshes for objects close to the camera, and low-detail meshes for objects far from the camera. As the player moves through the scene, you must keep replacing close objects by more detailed meshes, and far objects by less detailed meshes. The goal is to keep few high-quality slow-rendering objects in the foreground, and many low-quality fast-rendering objects in the background. (Experienced users can compare this approach to <<jme3/advanced/terrain#,JME's TerraMonkey terrain system>>, which internally uses the specialized GeoMipMapping algorithm to generate a terrain's Levels of Detail.)

You see now why you may want to be able to generate Levels of Detail for complex Geometries automatically. JME3 supports a Java implementation of the Ogre engine's LOD generator (originally by Péter Szücs and Stan Melax): You use link:{uri-jme3}/jme3-core/src/tools/java/jme3tools/optimize/LodGenerator.java[jme3tools.optimize.LodGenerator] in conjunction with link:{uri-jme3}/jme3-core/src/main/java/com/jme3/scene/control/LodControl.java[com.jme3.scene.control.LodControl].

For a demo, run link:{uri-jme3}/jme3-examples/src/main/java/jme3test/stress/TestLodGeneration.java[TestLodGeneration.java] from <<sdk/sample_code#,JmeTests>>, then press +/- and spacebar to experiment. The following screenshots show a monkey model with three reduced Levels of Detail:

image::jme3/advanced/jmonkey-lod.gif[jmonkey-lod.gif,width="",height="",align="center"]

== Usage

To activate this optimization:

.  Pick a reduction method and values for the Geometry. (Trial and error…)
.  Generate LODs for the Geometry, either in the SDK or in code.
.  Add an LOD control to the Geometry.

== Pick Reduction Methods and Values

There are several reduction methods to generate a low-polygon version from a high-polygon model. Don't worry, the reduction does not modify the original model.
[cols="35,55,10", options="header"]
|===

a|Reduction Method
a|Description
a|Reduction Value

a|LodGenerator.TriangleReductionMethod.COLLAPSE_COST
a|Collapses polygon vertices from the mesh until the reduction cost (= amount of ugly artifacts caused) exceeds the given threshold.
a|0.0f - 1.0f

a|LodGenerator.TriangleReductionMethod.PROPORTIONAL
a|Removes the given percentage of polygons from the mesh.
a| 0.0f - 1.0f

a|LodGenerator.TriangleReductionMethod.CONSTANT
a|Removes the given number of polygons from the mesh.
a| integer

|===

If you don't know which to choose, experiment. For example start by trying COLLAPSE_COST and .5f-.9f.

== Generate LOD

You must generate and cache several LODs for each mesh, ranging from many to few polygons. The LOD generator algorithm attempts to collaps vertices automatically, while avoiding ugly artifacts. The LOD generator doesn't generate new meshes, it only creates separate reduced index buffers for the more highly reduced levels.

*  If you create geometries manually (3D models), use the SDK to generate LODs.
*  If you create geometries programmatically, generate LODs from your Java code.

=== Generating LODs in the SDK

The SDK contains a user-friendly interface to generate LODs for a model (.j3o file).

.  Open the Projects or Files window.
.  Select the .j3o file in the `Project Assets/Models` directory.
.  Choose `menu:Window[Edit in SceneExplorer]` if the SceneExplorer is not open. Info about the selected model is now displayed in the SceneExplorer.
.  btn:[RMB] select the model in SceneExplorer. Choose the `menu:Tools[Generate Levels of Detail]` menu. +
image:jme3/advanced/jme-sdk-generate-lod-menu.png[The Tools Generate LOD context menu in the SceneExplorer,width="300",height="180"]
.  The `Generate LOD` settings wizard opens: +
image:jme3/advanced/jme-sdk-generate-lod-window.png[The Generate LOD settings wizard,width="300",height="150"]
.  Choose a reduction method and reduction values for one or more levels.
+
[TIP]
====
Enter higher reduction values for higher levels.
====

.  Click btn:[Finish] to generate the LODs for this model.

The LODs are saved in the .j3o model file.

[TIP]
====
Choose `menu:Window[Properties]` if the Properties window is not open. Choose the generated LODs from the dropdown in the Properties window, and verify their quality in the SceneComposer.
====

image::jme3/advanced/jme-sdk-generate-lod-full.png[jme-sdk-generate-lod-full.png,width="",height="",align="center"]

=== Generating LODs in Code

The `jme3tools.optimize.LodGenerator` utility class helps you generate LODs for an arbitrary mesh (a Geometry object) programmatically from your Java code. You create and bake one LodGenerator for each Geometry.

[source,java]
----
LodGenerator lod = new LodGenerator(geometry);
lod.bakeLods(reductionMethod,reductionValue);
----

The LODs are stored inside the Geometry object.

*Example:* How to generate an LOD of myPrettyGeo's mesh with the same settings as used in the SDK example above:

[source,java]
----
LodGenerator lod = new LodGenerator(myPrettyGeo);
lod.bakeLods(LodGenerator.TriangleReductionMethod.PROPORTIONAL,0.25, 0.5f, 0.75f);
----

== Activate the LOD Control

After generating the LODs for the geometry, you create and add a `com.jme3.scene.control.LodControl` to the geometry. Adding the LodControl activates the LOD optimizaton for this geometry.

[source,java]
----
LodControl lc = new LodControl();
myPrettyGeo.addControl(lc);
rootNode.attachChild(myPrettyGeo);
----

The LodControl internally gets the camera from the game's viewport to calculate the distance to this geometry. Depending on the distance, the LodControl selects an appropriate level of detail, and passes more (or less) detailed vertex data to the renderer.

== Impact on Quality and Speed
[cols="10,30,20,20,20", options="header"]
|===

a|Level number
a|Purpose
a|Distance
a|Rendering Speed
a|Rendering Quality

a|Level 0
a|The original mesh is used automatically for close-ups, and it's the default if no LODs have been generated.
a|Closest
a|Slowest.
a|Best.

a|Level 1 +
Level 2 +
Level 3
a|If you generated LODs, JME3 uses them automatically as soon as the object moves into the background.
a|The higher the level, +
the further away.
a|The higher the level, +
the faster.
a|The higher the level, +
the lower the quality.

|===

== See also

*  link:https://hub.jmonkeyengine.org/t/brand-new-lod-generator/26341[https://hub.jmonkeyengine.org/t/brand-new-lod-generator/26341]
*  link:https://github.com/worldforge/ember/tree/master/src/components/ogre/lod[https://github.com/worldforge/ember/tree/master/src/components/ogre/lod]
*  link:http://www.melax.com/polychop[http://www.melax.com/polychop]
*  link:http://sajty.elementfx.com/progressivemesh/GSoC2012.pdf[http://sajty.elementfx.com/progressivemesh/GSoC2012.pdf]
*  <<jme3/advanced/terrain#,JME3 TerraMonkey Terrain>>