bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning deep features and topological structure of cells for clustering of scRNA-sequencing data
Authors: Wang Haiyue , Ma Xiaoke 
Published: February 2022

Abstract
Single-cell RNA sequencing (scRNA-seq) measures gene transcriptome at the cell level, paving the way for the identification of cell subpopulations. Although deep learning has been successfully applied to scRNA-seq data, these algorithms are criticized for the undesirable performance and interpretability of patterns because of the noises, high-dimensionality and extraordinary sparsity of scRNA-seq data. To address these issues, a novel deep learning subspace clustering algorithm (aka scGDC) for cell types in scRNA-seq data is proposed, which simultaneously learns the deep features and topological structure of cells. Specifically, scGDC extends auto-encoder by introducing a self-representation layer to extract deep features of cells, and learns affinity graph of cells, which provide a better and more comprehensive strategy to characterize structure of cell types. To address heterogeneity of scRNA-seq data, scGDC projects cells of various types onto different subspaces, where types, particularly rare cell types, are well discriminated by utilizing generative adversarial learning. Furthermore, scGDC joins deep feature extraction, structural learning and cell type discovery, where features of cells are extracted under the guidance of cell types, thereby improving performance of algorithms. A total of 15 scRNA-seq datasets from various tissues and organisms with the number of cells ranging from 56 to 63 103 are adopted to validate performance of algorithms, and experimental results demonstrate that scGDC significantly outperforms 14 state-of-the-art methods in terms of various measurements (on average 25.51% by improvement), where (rare) cell types are significantly associated with topology of affinity graph of cells. The proposed model and algorithm provide an effective strategy for the analysis of scRNA-seq data (The software is coded using python, and is freely available for academic https://github.com/xkmaxidian/scGDC).
The future of assessing bull fertility: Can the ‘omics fields identify usable biomarkers?
Authors: Klein Erin K , Swegen Aleona , Gunn Allan J , Stephen Cyril P , Aitken Robert John , Gibb Zamira 
Published: February 2022

AbstractBreeding soundness examinations for bulls rely heavily on the subjective, visual assessment of sperm motility and morphology. Although these criteria have the potential to identify infertile males, they cannot be used to guarantee fertility or provide information about varying degrees of bull fertility. Male factor fertility is complex, and the success of the male gamete is not necessarily realized until well after the spermatozoon enters the oocyte. This paper reviews our existing knowledge of the bull’s contribution from a standpoint of the sperm’s cargo and the impact that this can have on fertilization and the development of the embryo. There has been a plethora of recent research characterizing the many molecular attributes that can affect the functional competence of a spermatozoon. A better understanding of the molecular factors influencing fertilization and embryo development in cattle will lead to the identification of biomarkers for the selection of bulls of superior fertility, which will have major implications for livestock production. To see this improvement in reproductive performance, we believe incorporation of modern technology into breeding soundness examinations will be necessary—although many of the discussed technologies are not ready for large-scale field application. Each of the ‘omics fields discussed in this review have shown promise for the identification of biomarkers of fertility, with certain families of biomarkers appearing to be better suited to different evaluations throughout a bull’s lifetime. Further research is needed for the proposed biomarkers to be of diagnostic or predictive value.
A proximal distance algorithm for likelihood-based sparse covariance estimation
Authors: Xu Jason , Lange Kenneth 
Published: February 2022

SummaryThis paper addresses the task of estimating a covariance matrix under a patternless sparsity assumption. In contrast to existing approaches based on thresholding or shrinkage penalties, we propose a likelihood-based method that regularizes the distance from the covariance estimate to a symmetric sparsity set. This formulation avoids unwanted shrinkage induced by more common norm penalties, and enables optimization of the resulting nonconvex objective by solving a sequence of smooth, unconstrained subproblems. These subproblems are generated and solved via the proximal distance version of the majorization-minimization principle. The resulting algorithm executes rapidly, gracefully handles settings where the number of parameters exceeds the number of cases, yields a positive-definite solution, and enjoys desirable convergence properties. Empirically, we demonstrate that our approach outperforms competing methods across several metrics, for a suite of simulated experiments. Its merits are illustrated on international migration data and a case study on flow cytometry. Our findings suggest that the marginal and conditional dependency networks for the cell signalling data are more similar than previously concluded.
Blood pressure targets in CKD 2021: the never-ending guidelines debacle
Authors: Carriazo Sol , Sarafidis Pantelis , Ferro Charles J , Ortiz Alberto 
Published: February 2022

ABSTRACT
In 2021, two updated clinical guidelines were published, providing guidance on blood pressure (BP) targets for people with chronic kidney disease (CKD). Kidney Disease: Improving Global Outcomes (KDIGO) updated its 2012 Clinical Practice Guideline for the Management of BP in CKD. Different systolic blood pressure (SBP) and diastolic blood pressure (DBP) targets for CKD (&lt;130/80 and &lt;140/90 mmHg, respectively, for people with a urinary albumin: creatinine ratio &gt;30 mg/g or without pathological albuminuria) were replaced by a single number: an SBP target of &lt;120 mmHg is suggested, when tolerated. This represents a major decrease in the SBP target and the abandonment of DBP targets. The European Society of Cardiology (ESC) also published a 2021 Clinical Guideline on Cardiovascular Disease Prevention in Clinical Practice that updates a prior 2016 guideline on prevention and the 2018 ESC/European Society of Hypertension Clinical Practice Guidelines for the Management of Arterial Hypertension. The 2021 ESC guideline was endorsed by 12 European scientific societies. The recommended office BP targets for people with CKD are &lt;140–130 mmHg SBP (lower SBP is acceptable if tolerated) and &lt;80 mmHg DBP. The question is: What should the practicing physician do now: treat hypertension in people with CKD to an SBP target of &lt;120 mmHg or to a target of &lt;140–130 mmHg? Major guideline bodies are aware of the activities of other major players. There is an urgent need for guideline bodies to establish communication channels, search consensus on major issues that impact the health of hundreds of millions of people worldwide and end individualism in guidelines generation.
Towards the integration of ecophysiology with fisheries stock assessment for conservation policy and evaluating the status of the Mediterranean Sea
Authors: Falco F , Bottari T , Ragonese S , Killen S S 
Published: February 2022

Abstract
Recent European Union (EU) regulations have been introduced to discourage the capture of undersized specimens with the aim of reducing the bycatch mortality imposed by commercial fisheries. We argue that we still lack accurate data regarding basic information required to properly implement these regulations for most Mediterranean ecosystems, including the true mortality imposed by fisheries, escape rates from fishing gears and the capability of specimens to survive following discard. We suggest that additional reliance on physiological biomarkers could assist in all aspects of the data collection required to support implementation of the EU discard ban (aka landing obligation), particularly in determining which species should receive special dispensation from this policy. Ideally, this new approach, here termed the ‘Fisheries Environmental and Physiological Stress Analysis’ (FEPSA), would become an important step for any fish stock assessment within the ecosystem approach to fisheries management and the recognition of Good Environmental Status, as established by the EU in the Marine Strategy Framework Directive (2008/56/EC). In particular, the main goal of FEPSA would be applying the study of physiological stressors to exploited stocks to estimate the so-called collateral fishing mortality, which includes the mortality experienced by fish that escape after interacting with fishing gears or that are discarded, with some degree of injury or physiological stress. The approach outlined here, which is described for bottom trawls but adaptable to any other type of fishing gear, is not a trivial undertaking but is a requirement for collecting the data required by recent EU fisheries policies. While we agree that the threats to marine biodiversity posed by fishing and associated discard practices require strong policy interventions, we emphasize that the research programs needed to support such initiatives, including the landing obligation, should be given equal priority. This is particularly true for Mediterranean fisheries, which are at a complex intersection of jurisdictional boundaries, numerous additional ecosystem threats including widespread pollution, thermal variation and hypoxia, and are historically understudied as compared to fisheries and species in more northern climates.
Identifying the limitations of cardiopulmonary exercise testing prior to esophagectomy using a pooled analysis of patient-level data
Authors: Sivakumar Jonathan , Forshaw Matthew J , Lam Stephen , Peters Christopher J , Allum William H , Whibley Jessica , Sinclair Rhona C F , Snowden Christopher P , Hii Michael W , Sivakumar Harry , Read Matthew 
Published: February 2022

Summary
Preoperative cardiopulmonary exercise testing (CPET) provides an objective assessment of aerobic fitness in patients undergoing surgery. While peak oxygen uptake during exercise (VO2peak) and anaerobic threshold have demonstrated a moderate correlation with the development of complications following esophagectomy, no clinically useful threshold values have been defined. By pooling patient level data from existing studies, we aimed to define optimal thresholds for preoperative CPET parameters to predict patients at high risk of postoperative complications. Studies reporting on the relationship between preoperative CPET variables and post-esophagectomy complications were determined from a comprehensive literature search. Patient-level data were obtained from six contributing centers for pooled-analyses. Outcomes of interest included cardiopulmonary and non-cardiopulmonary complications, unplanned intensive care unit readmission, and 90-day and 12-month all-cause mortality. Receiver operating characteristic curves and logistic regression models estimated the predictive value of CPET parameters for each individual outcome of interest. This analysis comprised of 621 patients who underwent CPET prior to esophagectomy during the period from January 2004 to March 2017. For both anaerobic threshold and VO2peak, none of the receiver operating characteristic curves achieved an area under the curve value &gt; 0.66 for the outcomes of interest. The discriminatory ability of CPET for determining high-risk patients was found to be poor in patients undergoing an esophagectomy. CPET may only carry an adjunct role to clinical decision-making.
Real world evaluation of artificial intelligence echocardiography image guidance and acquisition with novice scanners in multiple clinical settings
Authors: Burke DA , Corrigan N , Herlihy M , Nasaj O , Dickson J , Delaney D , Westrup J 
Published: February 2022

Abstract

Funding Acknowledgements
Type of funding sources: Private company. Main funding source(s): Caption Health, US

OnBehalf
Beacon Hospital Research Institute

Background
Cardiac echocardiographic scanning requires significant training and experience. The FDA approved Caption Echocardiography system uses a deep learning artificial intelligence software that guides novice scanners to optimal position and then automatically acquires the highest quality image. Further advances to this novel technology have allowed for immediate calculation of left ventricular ejection fraction directly from these images.

Methods
Following only brief training, we sought to evaluate study quality by novice scanners in four clinical settings, both acute and ambulatory – the Emergency Department, Intensive Care Unit, Heart Failure clinic, and the Oncology Day Unit. 120 patients (30 per clinical area) were recruited and underwent 2 echo scans – one by a novice scanner using the Caption AI system, and one by an expert scanner using the same ultrasound system but without AI guidance. Both studies were evaluated blindly and independently side by side by 3 accredited experts judging diagnostic quality. ‘AutoEF’ measurements were compared with expert scanners measurements by Simpson’s biplane technique.

Results
120 patients with mean age 62.04 years old (range 18 – 92) were enrolled, consisting of 30 from each clinical area. 8 novice scanners – nursing staff and junior doctors – scanned 15 patients each, allowing their first 3 cases to be excluded. 75% of patients were male. BMI ranged from 18 – 37 with mean 27.48. Image quality allowed left ventricular function to be sufficiently captured in 97.5% of studies, right ventricular function in 95% and outrule of pericardial effusion in 97.5%. ‘AutoEF’ was determined in 88.3% of studies and matched the expert measurement in 84% of cases. Blinded expert assessment found that 60% of Caption studies were of equal or better quality than the experienced sonographer scan.

Conclusion
The Caption AI technology safely allows novice users to provide efficient and accurate point of care echo in differing clinical settings to a standard comparable to expert scanners, and automatically determines left ventricular ejection fraction.
Prevention of stroke and atrial arrhythmia consequences in hypertrophic cardiomyopathies: a clinical challenge that could be best managed by a better echocardiographic left atrial characterization
Authors: Al Wazzan A , Galli E , Panis V , Paven E , L"official G , Schnell F , Oger E , Donal E 
Published: February 2022

Abstract

Funding Acknowledgements
Type of funding sources: None.
Background
There is a need to better predict the risk of atrial arrhythmia (AA) and stroke in patients with hypertrophic cardiomyopathy (HCM).
Purpose
We sought to look at atrial remodeling and atrial function by echocardiography in a HCM-cohort to assess the association with occurrence of AA and stroke.
Methods
We retrospectively studied 216 patients diagnosed for HCM (mean age 52 ± 16 years) from 2015 to 2020. All patients underwent transthoracic echocardiography with the assessment of left atrial volume (LAV) and peak left atrial strain (PLAS). Patients were followed-up for 2,9 years for the development of a composite endpoint comprising occurrence of atrial arrhythmias and/or stroke.
Results
78 patients had an event (24 stroke and 54 documented atrial arrhythmia). Univariate comparison analysis showed that LAV (37.2 ± 15.7 vs. 47 ± 20 ml/m², p = 0.0001) and anteroposterior LA diameter (41.7 ±7.58 vs. 45.8 ± 8.9 mm; p = 0.0006) were significantly higher in patients who met the composite endpoint, whereas PLAS was significantly impaired (27.1 ± 9.77 vs. 20.4 ± 10.5%; p &lt; 0.0001). Other echographic parameters associated with the composite endpoint were mean E/e" ratio (0.65 [0.55-0.85] vs. 0.60 [0.45-0.75]; p = 0.0204) and tricuspid annular peak systolic velocity (S") (cm/s) (13.3 ± 2.92 vs. 12.2 ± 3.26; p = 0.0148). NTproBNP level (216 vs. 818 ; p &lt; 0.0001), history of hypertension (42.3% vs. 62.3%; p = 0.005) and age at diagnosis (50.3 ± 16.7 vs. 57.1 ± 14.4; p = 0.0035) were the clinical parameters different between groups.
In a multivariable analysis, PLAS was the only independent maker associated with the occurrence of AA and stroke, particularly for stroke with an odd ratio of 0.53 ([0.32-0.86]; p = 0.00097).
Interestingly, 19 of 28 stroke patients (67%) did not experience any documented AA.

Conclusion
The decrease of PLAS is strongly associated with the risk of stroke, even in patients without documented atrial arrhythmia. Its use to guide the indication for an implantable holter monitoring and perhaps a prophylactic oral anticoagulation in HCM requires further investigation. Abstract Figure. Impaired PLAS in an HCM patient
Can 2D speckle tracking echocardiography be useful in venesection therapy monitoring in hereditary hemochromatosis patients?
Authors: Wabich E , Swiatczak M , Sikorska K , Lipinski P , Raczak G , Danilowicz - Szymanowicz L 
Published: February 2022

Abstract

Funding Acknowledgements
Type of funding sources: None.
Background. Hereditary hemochromatosis (HH) is a widespread genetic disease. Abnormally increased intestinal iron absorption and accelerated recycling of iron lead to progressive body iron accumulation and the generation of oxidative stress in tissues. Venesection is the primary treatment of such patients. Based on the fact that two-dimensional speckle tracking echocardiography (2D STE) can evaluate left ventricle (LV) dysfunction more accurately and earlier than conventional echocardiography, the purpose of our study was to check whether it could be helpful in venesection therapy monitoring.
Methods. We prospectively enrolled 20 patients with genetically confirmed HH. Classic echocardiographic and 2D STE parameters (GE VIVID E9, EchoPAC v202) were analyzed at the moment of diagnosis, and after three years of treatment with venesection; 20 healthy age- and sex-matched persons constituted the control group.
Results. The HH patients had all standard echo parameters within the normal range at the first and second examinations. The rotation parameters were initially worse than in healthy people at the first visit and significantly increased after three years of treatment. The radial strain after the treatment was significantly better for the apex but not for basal LV, apart from the epicardial layer (known as the layer of iron overload in the heart). Global longitudinal strain (GLS), significantly lower than in healthy people at the first visit, did not change within the treatment (Table).
Conclusions. Venesection leads to significant improvement in the rotation function of LV and increases radial strain mainly in the epicardium, which seems to help monitor the treatment and guide the intensity of venesections. GLS, which is known as a parameter for early detection of heart abnormalities in asymptomatic HH patients, did not increase within the treatment and could reveal irreversible changes in LV. Abstract Figure.
Comprehensive stress echocardiography in hypertrophic cardiomyopathy
Authors: Palinkas ED , Ciampi Q , Tesic M , Palinkas A , Torres MAR , Djordievic-Dikic A , Beleslin B , Sepp R , Mori F , Picano E 
Published: February 2022

Abstract

Funding Acknowledgements
Type of funding sources: None.

OnBehalf
Stress Echo 2020 study group of the Italian Society of Echocardiography and Cardiovascular Imaging

Background
Stress echocardiography (SE) in hypertrophic cardiomyopathy (HCM) has more to offer beyond dynamic left ventricular outflow obstruction (LVOTO) to capture the functional heterogeneity of the disease.

Objectives
To determine the feasibility of comprehensive SE in HCM.

Methods
We prospectively enrolled 235 HCM patients (age = 48 ± 15 years, 113 men) assessed with exercise stress echocardiography (ESE) in 4 centers. ESE modality was semi-supine bicycle in 29 patients in one center, and treadmill in 206 (followed by same-day, same session, adenosine for step D) in another centers. During SE, we assessed stress-induced new regional wall motion abnormalities (RWMA, step A), coronary flow velocity reserve (CFVR) in left anterior descending coronary artery with Doppler (step D) by semi-supine exercise or adenosine, heart rate reserve (peak/rest heart rate) for EKG-based step E, mitral regurgitation (MR) flow for step F, and LVOTO (step G for gradient). A comprehensive SE score was generated from 0 (all parameters normal) to 5 (all abnormal).

Results
Technical success rate was 100% for all steps, except step D (80% with semi-supine, 100% with adenosine after treadmill) and F (232/235, 99%). Extra-analysis time was &lt; 3 minutes for steps A + D + E + F + G. Rate of abnormal results ranged from 73% for step E (peak/rest heart rate reserve &lt; 1.80) to 1% for step A (inducible RWMA), with intermediate values for step D (CFVR &lt; 2.0, 44%), step F (at least moderate MR, 32%) and step G (LVOTG &gt; 50 mm Hg, 26%): see figure. SE score was 0 in 14 pts (6%), 1 or 2 in 202 patients (86%) and ≥ 3 in 19 patients (8%).

Conclusions
Comprehensive SE is feasible in HCM with single stress (semi-supine exercise) or hybrid treadmill exercise followed by adenosine for step D. Phenotyping of the multiform manifestations of HCM with a personalized functional blueprint is now possible. Abstract Figure.