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Pediatric Cardiology Jun 2024Transcatheter stent implantation is a widely performed procedure for treating native coarctation of the aorta (CoA) in pediatric patients. However, data on mid- to...
Transcatheter stent implantation is a widely performed procedure for treating native coarctation of the aorta (CoA) in pediatric patients. However, data on mid- to long-term outcomes are limited. The aim of this study was to evaluate the mid-term safety and efficacy of transcatheter CoA stenting based on centrally adjudicated outcomes. This retrospective cohort study included patients aged 15 years or younger undergoing de novo stenting for CoA or recoarctation (reCoA) between 2006 and 2017. Immediate and 5-year outcomes were assessed. Immediate outcomes (procedural and in-hospital) were retrieved from electronic records. Rates of 5-year reCoA, stent fractures, aneurysmal/pseudoaneurysmal formation, and all-cause mortality were mid-term outcomes. The study included 274 patients (64% male and 36% female) with a median (interquartile range) age of 9 (6-12) years. Procedural success was achieved in 251 patients (91.6%). Procedural complications occurred in 4 patients (1.4%), consisting of stent migration in 1 (0.3%) and small non-expanding non-flow-limiting aortic wall injuries in 3 (1.1%). Major vascular access complications were observed in 18 patients (6.6%), acute limb ischemia in 8 (2.9%). In-hospital mortality occurred in 4 patients (1.4%). Five-year cumulative incidence rates of stent fractures, reCoA, and aortic aneurysmal/pseudoaneurysmal formation were 17/100 (17%), 73/154 (48%), and 8/101 (7.92%), respectively. Of 73 reCoAs, 47 were treated with balloon angioplasty, and 15 underwent a second stent implantation. Five-year all-cause mortality occurred in 4/251 (1.6%) patients. Coarctoplasty with stents was safe and effective in our pediatric population during a 5-year follow-up despite a high rate of reCoA.
PubMed: 38940826
DOI: 10.1007/s00246-024-03551-4 -
Bioinformatics (Oxford, England) Jun 2024World Health Organization estimates that there were over 10 million cases of tuberculosis (TB) worldwide in 2019, resulting in over 1.4 million deaths, with a worrisome...
MOTIVATION
World Health Organization estimates that there were over 10 million cases of tuberculosis (TB) worldwide in 2019, resulting in over 1.4 million deaths, with a worrisome increasing trend yearly. The disease is caused by Mycobacterium tuberculosis (MTB) through airborne transmission. Treatment of TB is estimated to be 85% successful, however, this drops to 57% if MTB exhibits multiple antimicrobial resistance (AMR), for which fewer treatment options are available.
RESULTS
We develop a robust machine-learning classifier using both linear and nonlinear models (i.e. LASSO logistic regression (LR) and random forests (RF)) to predict the phenotypic resistance of Mycobacterium tuberculosis (MTB) for a broad range of antibiotic drugs. We use data from the CRyPTIC consortium to train our classifier, which consists of whole genome sequencing and antibiotic susceptibility testing (AST) phenotypic data for 13 different antibiotics. To train our model, we assemble the sequence data into genomic contigs, identify all unique 31-mers in the set of contigs, and build a feature matrix M, where M[i, j] is equal to the number of times the ith 31-mer occurs in the jth genome. Due to the size of this feature matrix (over 350 million unique 31-mers), we build and use a sparse matrix representation. Our method, which we refer to as MTB++, leverages compact data structures and iterative methods to allow for the screening of all the 31-mers in the development of both LASSO LR and RF. MTB++ is able to achieve high discrimination (F-1 >80%) for the first-line antibiotics. Moreover, MTB++ had the highest F-1 score in all but three classes and was the most comprehensive since it had an F-1 score >75% in all but four (rare) antibiotic drugs. We use our feature selection to contextualize the 31-mers that are used for the prediction of phenotypic resistance, leading to some insights about sequence similarity to genes in MEGARes. Lastly, we give an estimate of the amount of data that is needed in order to provide accurate predictions.
AVAILABILITY
The models and source code are publicly available on Github at https://github.com/M-Serajian/MTB-Pipeline.
Topics: Mycobacterium tuberculosis; Machine Learning; Drug Resistance, Bacterial; Microbial Sensitivity Tests; Anti-Bacterial Agents; Whole Genome Sequencing; Genome, Bacterial; Humans
PubMed: 38940175
DOI: 10.1093/bioinformatics/btae243 -
Bioinformatics (Oxford, England) Jun 2024One of the core problems in the analysis of protein tandem mass spectrometry data is the peptide assignment problem: determining, for each observed spectrum, the peptide...
MOTIVATION
One of the core problems in the analysis of protein tandem mass spectrometry data is the peptide assignment problem: determining, for each observed spectrum, the peptide sequence that was responsible for generating the spectrum. Two primary classes of methods are used to solve this problem: database search and de novo peptide sequencing. State-of-the-art methods for de novo sequencing use machine learning methods, whereas most database search engines use hand-designed score functions to evaluate the quality of a match between an observed spectrum and a candidate peptide from the database. We hypothesized that machine learning models for de novo sequencing implicitly learn a score function that captures the relationship between peptides and spectra, and thus may be re-purposed as a score function for database search. Because this score function is trained from massive amounts of mass spectrometry data, it could potentially outperform existing, hand-designed database search tools.
RESULTS
To test this hypothesis, we re-engineered Casanovo, which has been shown to provide state-of-the-art de novo sequencing capabilities, to assign scores to given peptide-spectrum pairs. We then evaluated the statistical power of this Casanovo score function, Casanovo-DB, to detect peptides on a benchmark of three mass spectrometry runs from three different species. In addition, we show that re-scoring with the Percolator post-processor benefits Casanovo-DB more than other score functions, further increasing the number of detected peptides.
Topics: Databases, Protein; Peptides; Machine Learning; Mass Spectrometry; Algorithms; Sequence Analysis, Protein; Tandem Mass Spectrometry
PubMed: 38940129
DOI: 10.1093/bioinformatics/btae218 -
Journal of Arrhythmia Jun 2024Hypertrophic cardiomyopathy (HCM) is frequently associated with atrial fibrillation (AF). We compared clinical, echocardiographic, and electrophysiological parameters...
BACKGROUND
Hypertrophic cardiomyopathy (HCM) is frequently associated with atrial fibrillation (AF). We compared clinical, echocardiographic, and electrophysiological parameters between HCM subtypes and those without HCM at AF catheter ablation (AFCA) and analyzed post-AFCA reverse remodeling and AF recurrence based on HCM presence and subtype.
METHODS
Among 5161 consecutive patients who underwent de novo AFCA, we included HCM patients and control patients who were age-, gender-, and AF type-matched. Between AF-HCM patients and controls, we compared baseline values for left atrium (LA) wall thickness (LAWT), reverse remodeling at 1-year follow-up, and procedural outcomes over the course of follow-up between two groups.
RESULTS
A total of 122 AF-HCM patients and 318 control patients were included. AF-HCM patients had more frequent heart failure and higher LA diameter, E/Em, and LA pressure (all, < .001). However, LAWT did not differ from control group. A year after AFCA, degree of LA reverse remodeling was significantly lower in AF-HCM than in control group (ΔLA dimension, = .025). Nonapical HCM (HR 1.71; 95% CI 1.05-2.80), persistent AF (HR 1.46; 95% CI 1.05-2.04), and LA dimension (HR 1.04; 95% CI 1.01-1.06) were independent risk factors for AF recurrence. During 78.0 months of follow-up, nonapical HCM patients showed higher AF recurrence rate than both apical HCM (log-rank = .005) and control patients (log-rank = .002).
CONCLUSIONS
The presence of HCM, particularly nonapical HCM, displayed increased LA hemodynamic loading with diastolic dysfunction and had poorer rhythm outcomes after AFCA compared to both apical HCM and control group.
PubMed: 38939784
DOI: 10.1002/joa3.13061 -
JACC. Advances Jun 2024Decompensated heart failure (HF) can be categorized as de novo or worsening of chronic HF. In PARAGLIDE-HF (Prospective comparison of ARNI with ARB Given following...
BACKGROUND
Decompensated heart failure (HF) can be categorized as de novo or worsening of chronic HF. In PARAGLIDE-HF (Prospective comparison of ARNI with ARB Given following stabiLization In DEcompensated HFpEF), among patients with an ejection fraction >40% that stabilized after worsening HF, sacubitril/valsartan led to a significantly greater reduction in N-terminal pro-B-type natriuretic peptide (NT-proBNP) and was associated with clinical benefit compared to valsartan.
OBJECTIVES
This prespecified analysis characterized patients with de novo vs worsening chronic HF in PARAGLIDE-HF and assessed the interaction between HF chronicity and the effect of sacubitril/valsartan.
METHODS
Patients were classified as de novo (first diagnosis of HF) or chronic (known HF prior to the index event). Time-averaged proportional change in NT-proBNP from baseline to weeks 4 and 8 was analyzed using an analysis of covariance model. A win ratio consisting of time to cardiovascular death, number and times of HF hospitalizations during follow-up, number and times of urgent HF visits during follow-up, and time-averaged proportional change in NT-proBNP was assessed for each group.
RESULTS
Of the 466 participants, 153 (33%) had de novo HF and 313 (67%) had chronic HF. De novo patients had lower rates of atrial fibrillation/flutter and lower creatinine. There was a nonsignificant reduction in NT-proBNP with sacubitril/valsartan vs valsartan for de novo (0.82; 95% CI: 0.62-1.07) and chronic HF (0.88; 95% CI: 0.73-1.07), interaction = 0.66. The win ratio was nominally in favor of sacubitril/valsartan for both de novo (1.12; 95% CI: 0.70-1.58) and chronic HF (1.24; 95% CI: 0.89-1.71).
CONCLUSIONS
There is no interaction between HF chronicity and the effect of sacubitril-valsartan.
PubMed: 38938861
DOI: 10.1016/j.jacadv.2024.100984 -
JACS Au Jun 2024Sample efficiency is a fundamental challenge in molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls...
Sample efficiency is a fundamental challenge in molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparent when using oracles that can provide increased predictive accuracy but impose significant computational cost. Consequently, designing molecules that are optimized for such oracles cannot be achieved under a practical computational budget. Molecular generative models based on simplified molecular-input line-entry system (SMILES) have shown remarkable sample efficiency when coupled with reinforcement learning, as demonstrated in the practical molecular optimization (PMO) benchmark. Here, we first show that experience replay drastically improves the performance of multiple previously proposed algorithms. Next, we propose a novel algorithm called Augmented Memory that combines data augmentation with experience replay. We show that scores obtained from oracle calls can be reused to update the model multiple times. We compare Augmented Memory to previously proposed algorithms and show significantly enhanced sample efficiency in an exploitation task, a drug discovery case study requiring both exploration and exploitation, and a materials design case study optimizing explicitly for quantum-mechanical properties. Our method achieves a new state-of-the-art in sample-efficient molecular design, outperforming all of the previously reported methods. The code is available at https://github.com/schwallergroup/augmented_memory.
PubMed: 38938817
DOI: 10.1021/jacsau.4c00066 -
Brain : a Journal of Neurology Jun 2024Charcot-Marie-Tooth (CMT) disease is a neuromuscular disorder affecting the peripheral nervous system. The diagnostic yield in demyelinating CMT (CMT1) is typically...
Charcot-Marie-Tooth (CMT) disease is a neuromuscular disorder affecting the peripheral nervous system. The diagnostic yield in demyelinating CMT (CMT1) is typically ∼80-95%, of which at least 60% is due to the PMP22 gene duplication. The remainder of CMT1 is more genetically heterogeneous. We used whole exome and whole genome sequencing data included in the GENESIS database to investigate novel causal genes and mutations in a cohort of ∼2,670 individuals with CMT neuropathy. A recurrent heterozygous missense variant p.Thr1424Met in the recently described CMT gene ITPR3, encoding IP3R3 (inositol 1,4,5-trisphosphate receptor 3) was identified. This previously reported p.Thr1424Met change was present in 33 affected individuals from nine unrelated families from multiple populations, representing an unusual recurrence rate at a mutational hotspot, strengthening the gene-disease relationship (GnomADv4 allele frequency 1.76e-6). Sanger sequencing confirmed the co-segregation of the CMT phenotype with the presence of the mutation in autosomal dominant and de novo inheritance patterns, including a four-generation family with multiple affected second-degree cousins. Probands from all families presented with slow nerve conduction velocities, matching the diagnostic category of CMT1. Remarkably, we observed a uniquely variable clinical phenotype for age at onset and phenotype severity in p.Thr1424Met carrying patients, even within families. Finally, we present data supportive of a dominant-negative effect of the p.Thr1424Met mutation with associated changes in protein expression in patient-derived cells.
PubMed: 38938188
DOI: 10.1093/brain/awae206 -
Plant Disease Jun 2024The first tri-segmented viruses in the family Rhabdoviridae were recently discovered by exploring publicly available plant datasets in several hosts, including alfalfa...
The first tri-segmented viruses in the family Rhabdoviridae were recently discovered by exploring publicly available plant datasets in several hosts, including alfalfa (Medicago sativa L.) (Bejerman et al. 2023). They were classified in a novel genus "Trirhavirus" within the family Rhabdoviridae. The trirhavirus identified in alfalfa was named Medicago trirhavirus 1 (MeTRV1). Here we report the first confirmation of MeTRV1 in commercial alfalfa fields in Washington State, USA. Samples were collected in 2019-2021 in Benton and Grant Counties, WA. The alfalfa leaves in which the virus was detected displayed irregular chlorotic spotting (Fig.1). Total RNA extraction, library preparation, high throughput sequencing, and bioinformatics analysis were performed as described in Nemchinov et al (2023). Raw reads were trimmed with Trimmomatic 0.39 (Bolger at al. 2014). SPAdes 3.15.5 (Bankevich et al. 2012) was used for assembly. MeTRV1 was identified in four plants out of 100 tested and three complete RNA segments were recovered from one of them. For clarity, the virus found in the alfalfa field samples was designated MeTRV1-Wa. De novo assembly resulted in three contigs, which, when subjected to BLASTn analyses, aligned to the respective RNA segments of MeTRV1. The first contig was 6,498 nucleotides (nts)-long, 99.4% identical to RNA1 of MeTRV1 (BK064256.1), and 5,922 reads mapped to it (coverage 125x). RNA1 of MeTRV1-Wa encoded a protein 2,040 amino acid (aa)-long that aligned with protein L of MeTRV1 (DBA36559.1, 99.8%). The second contig was 4,014 nts-long and 95.2% identical to the RNA2 of MetRV1 (BK064257.1) with 1,751 reads mapping (coverage 59x). It contained four open reading frames (ORFs) encoding proteins N (445 aa, 99.8%, DBA36560.1); P2 (343 aa, 99.4%, DBA36561.1); P3 (183 aa, 99.4%, DBA36562.1); and P4 (72 aa, 98.6%, DBA36563.1). Altogether, 4,653 reads mapped to the third contig (coverage 131x) that was 4,889 nts-long and 99.1% identical to the RNA 3 segment of MeTRV1 (BK064258.1). RNA3 of MeTRV1-Wa encoded four proteins: P6 (274 aa, 100%, DBA36565.1); P7 (189 aa, 99.5%, DBA36566.1); P8 (514 aa, 99 %, DBA36567.1); and P5 (303 aa, 99.7%, DBA36564.1). The 5' trailer of each RNA segment had a nearly identical 24 nts at the end. Genomic organization of the MeTRV1-Wa and the locations of its ORFs are shown in Fig.2. To confirm the virus's presence, two sets of primers were designed based on the predicted sequence of the viral RNA 3 segment. The correct-size products were amplified in RT-PCR assays with RNA extracted from infected plants (Fig.3) and verified by Sanger sequencing. Besides MeTRV1-Wa, sequences of the following viruses known to cause symptoms in alfalfa were identified in the same library: alfalfa mosaic virus, bean leafroll virus, lucerne transient streak virus, and pea streak virus. Thus, the observed symptomatology may not be clearly attributed to MeTRV1-Wa due to coinfecting organisms. However, a possible association of the disease symptoms with the virus presence could be suggested based on comparison with both asymptomatic and symptomatic plants negative for MeTRV1-Wa (Fig.1). Since plant rhabdoviruses are recognized as a cause of economic losses in alfalfa and other major crops and are transmitted by insects (Bejerman et al. 2011, 2015; Jackson et al. 2005; Man and Dietzgen 2014), this first experimental confirmation of the occurrence of the new virus in the U.S. alfalfa is important for understanding its origin, distribution, and pathogenic potential.
PubMed: 38937929
DOI: 10.1094/PDIS-05-24-1132-PDN -
Nature Chemistry Jun 2024The 1,2-arylheteroaryl ethane motif stands as a privileged scaffold with promising implications in drug discovery. Conventional de novo syntheses of these molecules have...
The 1,2-arylheteroaryl ethane motif stands as a privileged scaffold with promising implications in drug discovery. Conventional de novo syntheses of these molecules have relied heavily on pre-functionalized synthons, entailing harsh conditions and multi-step processes. Here, to address these limitations, we present a modular approach for the direct synthesis of 1,2-arylheteroaryl ethanes using feedstock chemicals, including ethylene, arenes and heteroarenes. We disclosed a photo triplet-energy-transfer-initiated radical cascade process, leveraging homolytic cleavage of C-S bonds in aryl sulfonium salts as the key step to access aryl radicals with excellent regioselectivity. This method allows for rapid structural diversification of bioactive molecules, showcasing excellent functional group tolerance and streamlining the synthesis of bioactive compounds and their derivatives. Furthermore, our approach can be extended to propylene, non-gaseous terminal alkenes and various other electrophilic radical precursors, including heteroaryl radicals, hydroxyl radicals, trifluoromethyl radicals and α-carbonyl alkyl radicals. This study highlights the significance of radical polarity matching in designing selective multi-component couplings.
PubMed: 38937591
DOI: 10.1038/s41557-024-01560-7 -
Journal of Medical Genetics Jun 2024Tatton-Brown-Rahman syndrome (TBRS; OMIM 615879), also known as DNA methyltransferase 3 alpha ()-overgrowth syndrome (DOS), was first described by Tatton-Brown in 2014....
BACKGROUND
Tatton-Brown-Rahman syndrome (TBRS; OMIM 615879), also known as DNA methyltransferase 3 alpha ()-overgrowth syndrome (DOS), was first described by Tatton-Brown in 2014. This syndrome is characterised by overgrowth, intellectual disability and distinctive facial features and is the consequence of germline loss-of-function variants in , which encodes a DNA methyltransferase involved in epigenetic regulation. Somatic variants of are frequently observed in haematological malignancies, including acute myeloid leukaemia (AML). To date, 100 individuals with TBRS with de novo germline variants have been described. We aimed to further characterise this disorder clinically and at the molecular level in a nationwide series of 24 French patients and to investigate the correlation between the severity of intellectual disability and the type of variant.
METHODS
We collected genetic and medical information from 24 individuals with TBRS using a questionnaire released through the French National AnDDI-Rares Network.
RESULTS
Here, we describe the first nationwide French cohort of 24 individuals with germline likely pathogenic/pathogenic variants in , including 17 novel variants. We confirmed that the main phenotypic features were intellectual disability (100% of individuals), distinctive facial features (96%) and overgrowth (87%). We highlighted novel clinical features, such as hypertrichosis, and further described the neurological features and EEG results.
CONCLUSION
This study of a nationwide cohort of individuals with TBRS confirms previously published data and provides additional information and clarifies clinical features to facilitate diagnosis and improve care. This study adds value to the growing body of knowledge on TBRS and broadens its clinical and molecular spectrum.
PubMed: 38937076
DOI: 10.1136/jmg-2024-110031