bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-year progesterone profiles during pregnancy in baleen of humpback whales (Megaptera novaeangliae)
Authors: Lowe Carley L , Hunt Kathleen E , Rogers Matthew C , Neilson Janet L , Robbins Jooke , Gabriele Christine M , Teerlink Suzie S , Seton Rosemary , Buck C Loren 
Published: July 2021

Abstract
Understanding calving rates of wild whale populations is critically important for management and conservation. Reproduction of humpback whales (Megaptera novaeangliae) is difficult to monitor and, even with long-term sighting studies, basic physiological information such as pregnancy rates and calving intervals remain poorly understood in many populations. We hypothesized that pregnant whales have sustained elevations in baleen progesterone that temporally correlate with gestation. To test this hypothesis, baleen progesterone profiles from two adult female North Pacific humpbacks, both with extensive sighting records and documented pregnancies, were compared to those of a nulliparous female (adult female never seen with a calf) and a juvenile male. Baleen specimens recovered during necropsy were subsampled every 2 cm from the base to the tip of the plate, with each interval representing 30–45 days of growth. Homogenized baleen powder was assayed for progesterone using enzyme immunoassays. The date of growth of each sampling location on the baleen plate was estimated based on stable isotope analysis of annual δ15N cycles. Progesterone profiles from both pregnant whales showed sustained high progesterone content (&gt;350 ng/g) in areas corresponding to known pregnancies, inferred from calf sightings and post-mortem data. The younger female, estimated to be 13 years old, had higher progesterone during pregnancy than the 44.5 year old, but levels during non-pregnancy were similar. The nulliparous female and the male had low progesterone throughout their baleen plates. Baleen hormone analysis can determine how progesterone concentrations change throughout gestation and has potential for estimating age at first reproduction, pregnancy intervals, failed pregnancies and early calf mortality. Understanding rates of calving and current and historic reproductive patterns in humpbacks is vital to continuing conservation measures in this species.
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students
Authors: Duek Paula , Mary Camille , Zahn-Zabal Monique , Bairoch Amos , Lane Lydie 
Published: July 2021

Abstract
About 10% of human proteins have no annotated function in protein knowledge bases. A workflow to generate hypotheses for the function of these uncharacterized proteins has been developed, based on predicted and experimental information on protein properties, interactions, tissular expression, subcellular localization, conservation in other organisms, as well as phenotypic data in mutant model organisms. This workflow has been applied to seven uncharacterized human proteins (C6orf118, C7orf25, CXorf58, RSRP1, SMLR1, TMEM53 and TMEM232) in the frame of a course-based undergraduate research experience named Functionathon organized at the University of Geneva to teach undergraduate students how to use biological databases and bioinformatics tools and interpret the results. C6orf118, CXorf58 and TMEM232 were proposed to be involved in cilia-related functions; TMEM53 and SMLR1 were proposed to be involved in lipid metabolism and C7orf25 and RSRP1 were proposed to be involved in RNA metabolism and gene expression. Experimental strategies to test these hypotheses were also discussed. The results of this manual data mining study may contribute to the project recently launched by the Human Proteome Organization (HUPO) Human Proteome Project aiming to fill gaps in the functional annotation of human proteins.
Database URL: http://www.nextprot.org
3D cardiac magnetic resonance stress-perfusion in elderly patients
Authors: Karolyi M , Gotschy A , Plein S , Paetsch I , Jahnke C , Frick M , Gebker R , Alkadhi H , Manka R 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: Foundation. Main funding source(s): Swiss National Science Foundation

Introduction
Age related comorbidities and reduced compliance often limit ischaemia testing in elderly patients.

Purpose
To assessed the accuracy of 3D cardiac magnetic resonance (CMR) stress perfusion in the elderly population.

Methods
56 patients aged ≥75 years underwent 3D CMR stress-perfusion and invasive coronary angiography with quantitative coronary angiography (QCA) and fractional flow reserve (FFR) as part of a multicenter study. The accuracy of 3D CMR stress-perfusion was compared to patients aged &lt;75 years old (n = 360) using qualitative and quantitative imaging parameters.

Results
Sensitivity, specificity, positive and negative predictive values of qualitative 3D perfusion CMR were similar for both age groups in the detection of high-grade (≥50%) coronary stenosis on QCA and hemodynamically relevant (&lt;0.8) stenosis on FFR, p &gt; 0.05 all. Quantitative myocardial ischemia burden was larger in elderly patients (15% ± 17% vs. 9% ± 13%) with similarly high diagnostic accuracy of quantitative 3D CMR perfusion in both age groups to predict pathological FFR (AUC ≥75: 0.906; AUC &lt;75: 0.866).

Conclusions
3D CMR perfusion is well suited for myocardial ischaemia testing in the elderly patients with similarly high diagnostic accuracy as in younger individuals.
Dark blood ischemic LGE segmentation using a deep learning approach
Authors: Torlasco C , Papetti D , Mene R , Artico J , Seraphim A , Badano LP , Moon JC , Parati G , Xue H , Kellman P , Nobile M 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

Introduction
The extent of ischemic scar detected by Cardiac Magnetic Resonance (CMR) with late gadolinium enhancement (LGE) is linked with long-term prognosis, but scar quantification is time-consuming. Deep Learning (DL) approaches appear promising in CMR segmentation. Purpose: To train and apply a deep learning approach to dark blood (DB) CMR-LGE for ischemic scar segmentation, comparing results to 4-Standard Deviation (4-SD) semi-automated method. Methods: We trained and validated a dual neural network infrastructure on a dataset of DB-LGE short-axis stacks, acquired at 1.5T from 33 patients with ischemic scar. The DL architectures were an evolution of the U-Net Convolutional Neural Network (CNN), using data augmentation to increase generalization. The CNNs worked together to identify and segment 1) the myocardium and 2) areas of LGE. The first CNN simultaneously cropped the region of interest (RoI) according to the bounding box of the heart and calculated the area of myocardium. The cropped RoI was then processed by the second CNN, which identified the overall LGE area. The extent of scar was calculated as the ratio of the two areas. For comparison, endo- and epi-cardial borders were manually contoured and scars segmented by a 4-SD technique with a validated software. Results: The two U-Net networks were implemented with two free and open-source software library for machine learning. We performed 5-fold cross-validation over a dataset of 108 and 385 labelled CMR images of the myocardium and scar, respectively. We obtained high performance (&gt; ∼0.85) as measured by the Intersection over Union metric (IoU) on the training sets, in the case of scar segmentation. With regards to heart recognition, the performance was lower (&gt; ∼0.7), although improved (∼ 0.75) by detecting the cardiac area instead of heart boundaries. On the validation set, performances oscillated between 0.8 and 0.85 for scar tissue recognition, and dropped to ∼0.7 for myocardium segmentation. We believe that underrepresented samples and noise might be affecting the overall performances, so that additional data might be beneficial. Figure1: examples of heart segmentation (upper left panel: training; upper right panel: validation) and of scar segmentation (lower left panel: training; lower right panel: validation). Conclusion: Our CNNs show promising results in automatically segmenting LV and quantify ischemic scars on DB-LGE-CMR images. The performances of our method can further improve by expanding the data set used for the training. If implemented in a clinical routine, this process can speed up the CMR analysis process and aid in the clinical decision-making. Abstract Figure.
Reduction of extracellular volume and reverse cardiac remodeling during sacubitril/valsartan therapy assessed by cardiac magnetic resonance in patients with heart failure (REMODELING CMR-HF)
Authors: Plata Mosquera CA , Herrera-Escandon A , Vernaza-Pizarro A , Tamayo-Artunduaga N , Rodriguez-Casanova A , Vivas-Mayor M , Fajardo D 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

OnBehalf
REMODELING HF
Background/Introduction: Extracellular volume (ECV) expansion is a major determinant of cardiac remodeling in heart failure. Cardiac magnetic resonance (CMR) T1 mapping has been developed as a noninvasive technique to estimate ECV.

Purpose
The objective of this study is to assess the response to Sacubitril/Valsartan by measuring changes in myocardial ECV and their association with reverse cardiac remodeling in patients with heart failure with reduced ejection fraction (HFrEF).

Methods
Prospective, single-center, open-label study of two hundred-four HFrEF patients underwent CMR T1 mapping using the modified Look-Locker inversion recovery (MOLLI) sequence for ECV calculation, and initiated with sacubitril-valsartan treatment according to Guideline-Directed Medical Therapy. Absolute change in myocardial ECV, serum levels of procollagen type I amino-terminal peptide (PINP) and procollagen type III amino-terminal peptide (PIIINP), left ventricular end-diastolic volume index, left ventricular end-systolic volume index and left ventricle ejection fraction (LVEF) were analyzed from baseline to 12-month follow-up.

Results
Baseline MOLLI-ECV was 48.2% ± 2.4 in 106 patients with ischemic cardiomyopathy (ICM) and 38.7% ± 2.7 in 98 with idiopathic dilated cardiomyopathy (DCM), decreasing to 34% ± 2.4 for ICM and 29.5% ± 2.7 for DCM (P &lt; 0.001), at 12 months with sacubitril-valsartan therapy. These changes were correlated with a reduction of -36 μg/L for PINP (CI 95% 78-93, P &lt; 0.001), and -3.0 μg/L for PIIINP (CI 95% 73-91, P &lt; 0.001), -20 ml/m² in left ventricle end-diastolic and -18 ml/m² in end-systolic volumes, and an improvement in LVEF from 29% to 36% in both groups (P &lt; 0.001).

Conclusions
For the first time, we observe that changes in extracellular volume induced by sacubitril-valsartan therapy are related to reverse cardiac remodeling in patients with in HFrEF. These findings suggest that there may be an opportunity to decrease adverse remodeling with the use of a CMR-guided therapeutic approach aimed at decreasing fibrogenic activity and modulate the remodeling process.
High interstudy repeatability of automatic deep learnt biventricular CMR measurements
Authors: Alabed S , Karunasaagarar K , Alandejani F , Garg P , Uthoff J , Metherall P , Sharkey M , Lu H , Wild JM , Kiely DG , Van Der Geest RJ , Swift AJ 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: Foundation. Main funding source(s): Wellcome Trust (UK), NIHR (UK)

Introduction
Cardiac magnetic resonance (CMR) measurements have significant diagnostic and prognostic value. Accurate and repeatable measurements are essential to assess disease severity, evaluate therapy response and monitor disease progression. Deep learning approaches have shown promise for automatic left ventricular (LV) segmentation on CMR, however fully automatic right ventricular (RV) segmentation remains challenging. We aimed to develop a biventricular automatic contouring model and evaluate the interstudy repeatability of the model in a prospectively recruited cohort.
Methods
A deep learning CMR contouring model was developed in a retrospective multi-vendor (Siemens and General Electric), multi-pathology cohort of patients, predominantly with heart failure, pulmonary hypertension and lung diseases (n = 400, ASPIRE registry). Biventricular segmentations were made on all CMR studies across cardiac phases. To test the accuracy of the automatic segmentation, 30 ASPIRE CMRs were segmented independently by two CMR experts. Each segmentation was compared to the automatic contouring with agreement assessed using the Dice similarity coefficient (DSC).
A prospective validation cohort of 46 subjects (10 healthy volunteers and 36 patients with pulmonary hypertension) were recruited to assess interstudy agreement of automatic and manual CMR assessments. Two CMR studies were performed during separate sessions on the same day. Interstudy repeatability was assessed using intraclass correlation coefficient (ICC) and Bland-Altman plots.

Results
DSC showed high agreement (figure 1) comparing automatic and expert CMR readers, with minimal bias towards either CMR expert. The scan-scan repeatability CMR measurements were higher for all automatic RV measurements (ICC 0.89 to 0.98) compared to manual RV measurements (0.78 to 0.98). LV automatic and manual measurements were similarly repeatable (figure 2). Bland-Altman plots showed strong agreement with small mean differences between the scan-scan measurements (figure 2).

Conclusion
Fully automatic biventricular short-axis segmentations are comparable with expert manual segmentations, and have shown excellent interstudy repeatability.
Assessing access to mri in patients with cardiac implantable electronic devices in australia
Authors: Page N , Chia K , Brazier D , Manisty C , Kozor R 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

Background
"Legacy" cardiac implantable electronic devices (CIEDs) have historically been considered non-MRI-conditional. However, a number of recent studies indicate that if certain protocols are followed, patients with such devices may undergo MRI without significant adverse outcomes. Nowadays, industry standards dictate that "modern" CIEDs are MRI compatible. Despite these developments, some patients with CIEDs are denied MRI. Paucity of access to this vital service has been shown to increase expense, lead to more invasive imaging and later diagnosis, and poorer patient outcomes.
This study aims to identify if Australian public hospitals provide MRI services for patients with modern and legacy CIEDs, the characteristics of the services, and the barriers to implementing such a service.

Methods
This study surveyed all Australian Tertiary Referral Public Hospitals (n = 38), with a mixed qualitative and quantitative questionnaire.

Results
35 of the 38 sites completed the survey. Figure 1A shows that the majority of hospitals (30/35, 85.7%) offer MRIs for modern MRI-conditional CIEDs. In contrast, Figure 1B shows that only a minority of hospitals (3/35, 8.6%) offer MRIs for legacy CIEDs.
Protocols governing patient eligibility vary greatly among hospitals that scan modern devices. Locations either allow all CIEDs to be scanned, only non-dependent CIEDs, or only pacemaker CIEDs. 1.5 Tesla is the preferred strength to scan Modern CIEDs (59%), however a sizeable proportion scan at only 3.0 Tesla (10%) or both strengths (31%). A majority (80%) of staff in attendance of the scan were ACLS-trained (Advanced Cardiac Life Support), with no correlation to strength of MRI used. A range of different personnel attend the scan with varied patient monitoring strategies, and a majority (79%) offer thoracic as well as extra-thoracic scanning.
The few hospitals that scan legacy devices only scan at 1.5 tesla, and follow individualised protocols. These sites offer more personnel in attendance for the scan than for modern CIED scans, with all staff ACLS-trained including a physician who can direct CIED programming of required. These sites have more involved patient monitoring, and all also offer thoracic and extra-thoracic MRI scanning.
The predominant barrier identified was an absence of National Guidelines, followed by a lack of formal training or logistical device support.

Conclusions
The majority (85.7%) of Australian Tertiary Referral Public Hospitals have a MRI service for patients with modern CIEDs, but only 8.6% offer this service to patients with legacy CIEDs.
This highlights the need for a national effort to guide the provision of MRI services for patients with CIEDs, and address the identified barriers.
Prognostic value of pulmonary transit time by cardiac magnetic resonance in patients with heart failure with preserved ejection fraction
Authors: Elshibly M , Kanagala P , Budgeon C , Wright R , Jerosch-Herold M , Gulsin GS , Squire IB , Ng LL , Mccann GP , Arnold JR 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: Other. Main funding source(s): National Institute for Health Research Leicester Cardiovascular Biomedical Research Centre

Background
Quantifying pulmonary transit time (PTT) from cardiac magnetic resonance (CMR) first pass perfusion imaging is a novel technique for the evaluation of haemodynamic congestion in heart failure. Previous studies have demonstrated that PTT is prolonged in patients with heart failure with reduced ejection fraction (HFrEF) and that it provides independent prognostic information in this patient group. However, the potential diagnostic and prognostic roles of PTT assessment in patients with heart failure with preserved ejection fraction (HFpEF) remain to be established.

Aim
To compare PTT in healthy controls and in patients with HFpEF, and to determine the prognostic value of PTT in HFpEF.

Methods
In a prospective, observational study, HFpEF and age-matched control subjects underwent multi-parametric CMR at 3-Tesla, comprising quantitative left ventricular volumetric assessment using a standard steady-state free precession (SSFP) pulse sequence, and first-pass perfusion imaging at rest using a T1-weighted segmented inversion recovery gradient echo sequence (following injection of 0.04mmol/kg of contrast). PTT was calculated as the time interval between the peaks of signal intensity curves in the right and left ventricular blood pools (defined on the basal slice of the rest perfusion images). The primary endpoint was the composite of death or hospitalisation with heart failure.

Results
88 HFpEF patients (age 73 ± 9 years, 51% male, EF 56.4 ± 5.6%) and 40 controls (age 73 ± 5 years, 43% male, EF 58.5 ± 4.7%) were studied. PTT was comparable in HFpEF patients (7.7 ± 3.8s) and in healthy controls (7.5 ± 1.8, p = 0.69). Normalised to cardiac cycle lengths, PTT remained comparable in HFpEF patients and healthy controls (8.5 ± 4.0 cardiac cycles versus 7.8 ± 1.6 cardiac cycles, respectively, p = 0.19). In the HFpEF group, during median follow-up of 3.4 years, there were 38 events (25 hospitalisations with heart failure, 13 deaths); a significant relationship between survival and PTT was not demonstrated (HR 1.06 [0.99,1.14] for a one-unit increase, p = 0.098).

Conclusion
In HFpEF, PTT is not prolonged compared with PTT in healthy subjects. Unlike in HFrEF, PTT does not appear to be diagnostically or prognostically significant in HFpEF.
Figure 1: Graph showing signal intensity curves in the right (red) and left (green) ventricular blood pools
Figure 2: Kaplan-Meier plot showing comparable rates of the composite endpoint in patients with PTT greater/less than median PTT (8 cardiac cycles)
Value of cardiac magnetic resonance imaging derived spectral myocardial strain pattern for non-invasive diagnosis of myocarditis
Authors: Laqua FC , Polacin M , Luecke C , Klingel K , Alkadhi H , Manka R , Thiele H , Gutberlet M , Lurz P , Baessler B 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: Public grant(s) – EU funding. Main funding source(s): European Society of Radiology European Institute for Biomedical Imaging Research

Background
Traditionally, cardiac function is quantified by measures of peak excursion, for example ejection fraction. However, myocardial strain estimation from cine- cardiac MRI allows quantification of cardiac motion over the whole heart cycle. We propose a spectral decomposition of the strain curves applying Discrete Fourier transformation (DFT).

Purpose
To evaluate a potential additive diagnostic value of spectral temporal strain curve quantification for non-invasive diagnosis of myocarditis using cardiac MRI.

Methods
In the single-center prospective study patients with suspected myocarditis underwent comprehensive cardiac MRI followed by biventricular endomyocardial biopsy (EMB) between 2012 and 2014. DFT was applied to myocardial strain curves extracted from cine-Images. As reference model, a L1- and L2-penalized logistic regression model using global native T1 time, T2 time and presence of late-gadolinium enhancement was trained to predict EMB results and compared to two models which additionally include three orders of DFT coefficients and ejection fraction, respectively. Predictive performance was evaluated in a tournament-leave-pair-out cross-validation approach with a bootstrap correction for testing of multiple hyperparameter configurations.

Results
Out of 100 patients (28 % female, median age 40 [IQR 32 to 56) years) with acute symptom-onset (&lt;30 days) 65 had pathologically proven myocarditis in EMB. The DFT model showed best discrimination (Area under the receiver-operating-curve [AUC] 0.72 [95% CI 52 to 87]). Addition of ejection fraction (AUC 0.60 [95% CI: 0.43 to 0.74]) did not increase AUC compared to the reference (AUC 0.60 [95% CI: 0.43 to 0.74]). Posterior distribution of the bootstrap-corrected AUC difference between DFT and reference model was gaussian (mean 12%, standard deviation 12%) with a posterior probability of 86%, that DFT has a greater AUC.

Conclusions
Discrimination of myocarditis from similar clinical presentations remains challenging. The results support incremental discriminatory value of DFT-decomposed myocardial strain for non-invasive diagnosis of myocarditis. Future research should address the value of the spectral decomposition of cardiac motion trajectories in larger samples and different disease entities.