A survey on deep learning in medical image analysis

ACCF
: American College of Cardiology Foundation
ACS
: acute coronary syndrome
AHA
: American Heart Association
CAD
: coronary artery disease
CABG
: coronary artery bypass grafting
CKMB
: creatine kinase MB isoform
cTn
: cardiac troponin
CT
: computed tomography
CV
: coefficient of variation
ECG
: electrocardiogram
ESC
: European Society of Cardiology
FDG
: fluorodeoxyglucose
h
: hour(s)
HF
: heart failure
LBBB
: left bundle branch block
LV
: left ventricle
LVH
: left ventricular hypertrophy
MI
: myocardial infarction
mIBG
: meta-iodo-benzylguanidine
min
: minute(s)
MONICA
: Multinational MONItoring of trends and determinants in CArdiovascular disease)
MPS
: myocardial perfusion scintigraphy
MRI
: magnetic resonance imaging
mV
: millivolt(s)
ng/L
: nanogram(s) per litre
Non-Q MI
: non-Q wave myocardial infarction
NSTEMI
: non-ST-elevation myocardial infarction
PCI
: percutaneous coronary intervention
PET
: positron emission tomography
pg/mL
: pictogram(s) per millilitre
Q wave MI
: Q wave myocardial infarction
RBBB
: right bundle branch block
sec
: second(s)
SPECT
: single photon emission computed tomography
STEMI
: ST elevation myocardial infarction
ST–T
: ST-segment –T wave
URL
: upper reference limit
WHF
: World Heart Federation
WHO
: World Health Organization

Myocardial infarction (MI) can be recognised by clinical features, including electrocardiographic (ECG) findings, elevated values of biochemical markers (biomarkers) of myocardial necrosis, and by imaging, or may be defined by pathology. It is a major cause of death and disability worldwide. MI may be the first manifestation of coronary artery disease (CAD) or it may occur, repeatedly, in patients with established disease. Information on MI rates can provide useful information regarding the burden of CAD within and across populations, especially if standardized data are collected in a manner that …

/pdf/third-universal-definition-of-myocardial-infarction-1nbq846anm.pdf

Third universal definition of myocardial infarction

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Modern Applied Statistics With S

The UK Biobank project is a prospective cohort study with deep genetic and phenotypic data collected on approximately 500,000 individuals from across the United Kingdom, aged between 40 and 69 at recruitment. The open resource is unique in its size and scope. A rich variety of phenotypic and health-related information is available on each participant, including biological measurements, lifestyle indicators, biomarkers in blood and urine, and imaging of the body and brain. Follow-up information is provided by linking health and medical records. Genome-wide genotype data have been collected on all participants, providing many opportunities for the discovery of new genetic associations and the genetic bases of complex traits. Here we describe the centralized analysis of the genetic data, including genotype quality, properties of population structure and relatedness of the genetic data, and efficient phasing and genotype imputation that increases the number of testable variants to around 96 million. Classical allelic variation at 11 human leukocyte antigen genes was imputed, resulting in the recovery of signals with known associations between human leukocyte antigen alleles and many diseases.

/pdf/the-uk-biobank-resource-with-deep-phenotyping-and-genomic-2fs3jmksld.pdf

The UK Biobank resource with deep phenotyping and genomic data

Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Infusion of the nitric oxide (NO) donor, glyceryl trinitrate (GTN), provokes a migraine-like attack in migraineurs and cFos up-regulation in rat trigeminal nucleus caudalis. We studied the level of dura mast cell degranulation after infusion of GTN in awake, freely moving rats and hypothesized that the degranulation is secondary to NO.

/pdf/ehmti-0234-glyceryl-trinitrate-provoked-mast-cell-2jptrt3uky.pdf

EHMTI-0234. Glyceryl trinitrate provoked mast cell degranulation is secondary to the release of nitric oxide in vivo

Background The quantitative measures used to assess the performance of automated methods often do not reflect the clinical acceptability of contouring. A quality-based assessment of automated cardiac magnetic resonance (CMR) segmentation more relevant to clinical practice is therefore needed. Objective We propose a new method for assessing the quality of machine learning (ML) outputs. We evaluate the clinical utility of the proposed method as it is employed to systematically analyse the quality of an automated contouring algorithm. Methods A dataset of short-axis (SAX) cine CMR images from a clinically heterogeneous population (n = 217) were manually contoured by a team of experienced investigators. On the same images we derived automated contours using a ML algorithm. A contour quality scoring application randomly presented manual and automated contours to four blinded clinicians, who were asked to assign a quality score from a predefined rubric. Firstly, we analyzed the distribution of quality scores between the two contouring methods across all clinicians. Secondly, we analyzed the interobserver reliability between the raters. Finally, we examined whether there was a variation in scores based on the type of contour, SAX slice level, and underlying disease. Results The overall distribution of scores between the two methods was significantly different, with automated contours scoring better than the manual (OR (95% CI) = 1.17 (1.07–1.28), p = 0.001; n = 9401). There was substantial scoring agreement between raters for each contouring method independently, albeit it was significantly better for automated segmentation (automated: AC2 = 0.940, 95% CI, 0.937–0.943 vs manual: AC2 = 0.934, 95% CI, 0.931–0.937; p = 0.006). Next, the analysis of quality scores based on different factors was performed. Our approach helped identify trends patterns of lower segmentation quality as observed for left ventricle epicardial and basal contours with both methods. Similarly, significant differences in quality between the two methods were also found in dilated cardiomyopathy and hypertension. Conclusions Our results confirm the ability of our systematic scoring analysis to determine the clinical acceptability of automated contours. This approach focused on the contours' clinical utility could ultimately improve clinicians' confidence in artificial intelligence and its acceptability in the clinical workflow.

A Systematic Quality Scoring Analysis to Assess Automated Cardiovascular Magnetic Resonance Segmentation Algorithms

Assisted text input techniques can save time and effort and improve text quality. In this paper, we investigate how grounded and conditional extensions to standard neural language models can bring improvements in the tasks of word prediction and completion. These extensions incorporate a structured knowledge base and numerical values from the text into the context used to predict the next word. Our automated evaluation on a clinical dataset shows extended models significantly outperform standard models. Our best system uses both conditioning and grounding, because of their orthogonal benefits. For word prediction with a list of 5 suggestions, it improves recall from 25.03% to 71.28% and for word completion it improves keystroke savings from 34.35% to 44.81%, where theoretical bound for this dataset is 58.78%. We also perform a qualitative investigation of how models with lower perplexity occasionally fare better at the tasks. We found that at test time numbers have more influence on the document level than on individual word probabilities.

Clinical Text Prediction with Numerically Grounded Conditional Language Models

Aim: Delayed enhancement MRI (DE-MRI) of the heart has been shown to reliably identify areas of irreversible myocardial damage. We sought to determine if the term anteroseptal MI is appropriate by correlating electrocardiographic, angiographic, cine MRI and DE-MRI findings. Methods and Results: Nineteen patients admitted to our hospital with their first acute anterior MI and whose ECG showed new Q waves in leads V1 –V 4 were studied. All patients underwent cardiac catheterization, cine MRI, and DE-MRI. The mean left ventricular ejection fraction was 53% ± 16%. All 19 patients had evidence of delayed hyperenhancement in one or more myocardial segments (mean number of affected segments 5.5 ± 2.1). The mean mass of hyperenhanced myocardium was 14 ± 8 grams, or 10% ± 6% of absolute LV mass. Nineteen (100%) and 15 (79%) patients showed evidence of delayed hyperenhancement of the apex and apical anterior segments respectively. Seven (37%) patients showed evidence of mid ventricular anteroseptal hyperenhancement and none had any hyperenhancement of basal anteroseptal segments. Conclusion: High resolution cardiac MRI applied in patients with acute infarction and new Q waves in leads V1 –V 4 demonstrates the presence of predominantly apical, but not isolated septal or anteroseptal infarction.

Steffen E. Petersen

Papers

EHMTI-0234. Glyceryl trinitrate provoked mast cell degranulation is secondary to the release of nitric oxide in vivo

A Systematic Quality Scoring Analysis to Assess Automated Cardiovascular Magnetic Resonance Segmentation Algorithms

Clinical Text Prediction with Numerically Grounded Conditional Language Models

Anteroseptal or Apical Myocardial Infarction: A Controversy addressed using Delayed Enhancement Cardiovascular Magnetic Resonance Imaging

Myocardial Tissue Phase Mapping with Cine Phase- Contrast MR Imaging: Regional WallMotionAnalysisinHealthy