Deep Learning Based Segmentation of Various Brain Lesions for Radiosurgery

Semantic segmentation of medical images with deep learning models is rapidly developed. In this study, we benchmarked state-of-the-art deep learning segmentation algorithms on our clinical stereotactic radiosurgery dataset, demonstrating the strengths and weaknesses of these algorithms in a fairly practical scenario. In particular, we compared the model performances with respect to their sampling method, model architecture, and the choice of loss functions, identifying the suitable settings for their applications and shedding light on the possible improvements

The genome sequence of the orchid Phalaenopsis equestris

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers. (Résumé d'auteur

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Adaptive Radar Waveform Design Based on Weighted MI and the Difference of Two Mutual Information Metrics

This study deals with the problem of radar waveform design based on the weighted mutual information (MI) and the difference of two mutual information metrics (DMI) in signal-dependent interference. Since the target and clutter information are included in the received signal at the beginning of the design, DMI-based waveform is designed according to the following criterion: maximizing the MI between the received signal and target impulse response while minimizing the MI between the received signal and the clutter impulse response. This criterion is equivalent to maximizing the difference between the first MI and the second MI. Then maximizing the difference of two types of MI is used as the objective function, and the optimization model with the transmitted waveform energy constraint is established. In order to solve it, we resort to maximum marginal allocation (MMA) method to find the DMI-based waveform. Since DMI-based waveform does not allocate energy to the frequency band where the clutter power spectral density (PSD) is greater than the target PSD, we propose to weight the MI-based waveform and DMI-based waveform to synthesize the final optimal waveform. It could provide different trade-offs between two types of MI. Simulation results show the proposed algorithm is valid

Oral Anticoagulant Prescription in Patients With Atrial Fibrillation and a Low Risk of Thromboembolism

OBJECTIVES: We sought to investigate the prevalence and predictors of oral anticoagulation prescription among patients with atrial fibrillation (AF) at the lowest risk for thromboembolism, despite contemporary consensus guidelines that do not recommend anticoagulation therapy in this population. BACKGROUND: In young and healthy AF patients without significant thromboembolic risk factors, anticoagulant treatment carries bleeding risks that outweigh stroke prevention benefit. METHODS: Within a large contemporary registry of cardiology outpatients, we identified low-risk patients with AF meeting criteria for a contemporary consensus guideline class III indication against use of anticoagulation (age < 60 years, CHADS(2) Score=0, and no structural heart disease) between 2008–2012, and a second cohort with the same criteria and a CHA(2)DS(2)-VASc Score of 0. Using hierarchical modified Poisson regression models adjusted for patient characteristics, we examined predictors of oral anticoagulation treatment in these low thromboembolic risk AF patients. RESULTS: Oral anticoagulation was prescribed in a total of 2,561 of 10,995 (23.2%) AF patients with a CHADS(2) score of 0 and 1,787 of 6,730 (26.6%) AF patients with a CHA(2)DS(2)-VASc score of 0. In multivariable analysis, older age (RR 1.48 per 10 years; 95% CI, 1.41–1.56; p<0.0001), male sex (RR 1.34; 95% CI, 1.22–1.46; p<0.0001), higher body mass index (RR 1.18 per 5 kg/m(2); 95% CI, 1.14–1.22; p<0.0001), and Medicare insurance (reference: private insurance; RR,1.32; 95% CI, 1.17–1.49; overall p<0.0001) were associated with a higher likelihood of oral anticoagulant prescription, whereas treatment in Southern states (reference: Northeast; RR 0.69; 95% CI, 0.49–0.98;overall p=0.1187) was associated with a lower likelihood of oral anticoagulant prescription. CONCLUSIONS: In a large, real-world population of AF patients with the lowest thrombotic risk, approximately 1 in 4 were treated with oral anticoagulation against contemporary guideline recommendations

Differences in Anticoagulant Therapy Prescription in Patients with Paroxysmal Versus Persistent Atrial Fibrillation

BackgroundPatients with paroxysmal and persistent atrial fibrillation experience a similar risk of thromboembolism. Therefore, consensus guidelines recommend anticoagulant therapy in those at risk for thromboembolism irrespective of atrial fibrillation classification. We sought to examine whether there are differences in rates of appropriate oral anticoagulant treatment among patients with paroxysmal vs persistent atrial fibrillation in real-world cardiology practices.MethodsWe studied 71,316 outpatients with atrial fibrillation and intermediate to high thromboembolic risk (CHADS2 score ≥2) enrolled in the American College of Cardiology PINNACLE Registry between 2008 and 2012. Using hierarchical modified Poisson regression models adjusted for patient characteristics, we examined whether anticoagulant treatment rates differed between patients with paroxysmal vs persistent atrial fibrillation.ResultsThe majority of outpatients (78.4%, n&nbsp;= 55,905) had paroxysmal atrial fibrillation. In both unadjusted and multivariable adjusted analyses, patients with paroxysmal atrial fibrillation were less frequently prescribed oral anticoagulant therapy than those with persistent atrial fibrillation (50.3% vs 64.2%; adjusted risk ratio [RR] 0.74; 95% confidence interval [CI], 0.72-0.76). Instead, patients with paroxysmal atrial fibrillation were prescribed more frequently only antiplatelet therapy (35.1% vs 25.0%; adjusted RR 1.77; 95% CI, 1.69-1.86) or neither antiplatelet nor anticoagulant therapy (14.6% vs 10.8%; adjusted RR 1.35; 95% CI, 1.26-1.44; P &lt; .0001 for differences across all 3 comparisons).ConclusionsIn a large, real-world cardiac outpatient population, patients with paroxysmal atrial fibrillation with a moderate to high risk of stroke were less likely to be prescribed appropriate oral anticoagulant therapy and more likely to be prescribed less effective or no therapy for thromboembolism prevention

Oral Anticoagulant Prescription in Patients With Atrial Fibrillation and a Low Risk of Thromboembolism: Insights From the NCDR PINNACLE Registry

OBJECTIVES: We sought to investigate the prevalence and predictors of oral anticoagulation prescription among patients with atrial fibrillation (AF) at the lowest risk for thromboembolism, despite contemporary consensus guidelines that do not recommend anticoagulation therapy in this population. BACKGROUND: In young and healthy AF patients without significant thromboembolic risk factors, anticoagulant treatment carries bleeding risks that outweigh stroke prevention benefit. METHODS: Within a large contemporary registry of cardiology outpatients, we identified low-risk patients with AF meeting criteria for a contemporary consensus guideline class III indication against use of anticoagulation (age &lt; 60 years, CHADS2 Score=0, and no structural heart disease) between 2008–2012, and a second cohort with the same criteria and a CHA2DS2-VASc Score of 0. Using hierarchical modified Poisson regression models adjusted for patient characteristics, we examined predictors of oral anticoagulation treatment in these low thromboembolic risk AF patients. RESULTS: Oral anticoagulation was prescribed in a total of 2,561 of 10,995 (23.2%) AF patients with a CHADS2 score of 0 and 1,787 of 6,730 (26.6%) AF patients with a CHA2DS2-VASc score of 0. In multivariable analysis, older age (RR 1.48 per 10 years; 95% CI, 1.41–1.56; p&lt;0.0001), male sex (RR 1.34; 95% CI, 1.22–1.46; p&lt;0.0001), higher body mass index (RR 1.18 per 5 kg/m2; 95% CI, 1.14–1.22; p&lt;0.0001), and Medicare insurance (reference: private insurance; RR,1.32; 95% CI, 1.17–1.49; overall p&lt;0.0001) were associated with a higher likelihood of oral anticoagulant prescription, whereas treatment in Southern states (reference: Northeast; RR 0.69; 95% CI, 0.49–0.98;overall p=0.1187) was associated with a lower likelihood of oral anticoagulant prescription. CONCLUSIONS: In a large, real-world population of AF patients with the lowest thrombotic risk, approximately 1 in 4 were treated with oral anticoagulation against contemporary guideline recommendations