Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks

Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because ADAGE models, like many neural networks, are over-parameterized, different ADAGE models perform equally well. To enhance model robustness and better build signatures consistent with biological pathways, we developed an ensemble ADAGE (eADAGE) that integrated stable signatures across models. We applied eADAGE to a compendium of Pseudomonas aeruginosa gene expression profiling experiments performed in 78 media. eADAGE revealed a phosphate starvation response controlled by PhoB in media with moderate phosphate and predicted that a second stimulus provided by the sensor kinase, KinB, is required for this PhoB activation. We validated this relationship using both targeted and unbiased genetic approaches. eADAGE, which captures stable biological patterns, enables cross-experiment comparisons that can highlight measured but undiscovered relationships.Gordon and Betty Moore Foundation (GBMF 4552)National Institutes of Health (U.S.) (grant R01-AI091702)Cystic Fibrosis Foundation (STANTO15R0

Safety and efficacy of the hybrid approach in coronary chronic total occlusion percutaneous coronary intervention: The Hybrid Video Registry

Objectives The aim of the Hybrid Video Registry (HVR) is to assess the acute safety and efficacy of the Hybrid Approach in comparison to other contemporary methods of CTO‐PCI. Background: Recently, multiple techniques in Percutaneous Coronary Intervention (PCI) for coronary Chronic Total Occlusions (CTO) have been synthesized into a method referred to as the “Hybrid Approach”. Methods About 194 video‐taped timed live cases from CTO‐PCI training workshops were analyzed by independent data abstractors and compared to three contemporary CTO‐PCI registries stratified by case complexity based on the J‐CTO score. Results Overall procedural success was 95% of all cases attempted with an excellent safety profile. In the most complex lesion subset, which made up 45% of all HVR cases, success was 92.8%, which was significantly higher than either the Royal Bromptom (78.9%), or Japanese‐CTO (73.3%) registries, P = 0.04 Hybrid vs. Royal Brompton, P = 0.006 Hybrid vs. Japanese‐CTO). The Hybrid Approach was also associated with shorter procedure times and lower contrast utilization. Conclusions In a real world angiographic registry of complex CTOs, the Hybrid Approach to CTO‐PCI is safe, and may be superior to other contemporary approaches to CTO intervention with respect to procedural success and efficiency among a diverse group of operators and lesion complexity

Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14.

Pseudomonas aeruginosa is an opportunistic pathogen that causes difficult-to-treat infections. Two well-studied divergent P. aeruginosa strain types, PAO1 and PA14, have significant genomic heterogeneity, including diverse accessory genes present in only some strains. Genome content comparisons find core genes that are conserved across both PAO1 and PA14 strains and accessory genes that are present in only a subset of PAO1 and PA14 strains. Here, we use recently assembled transcriptome compendia of publicly available P. aeruginosa RNA sequencing (RNA-seq) samples to create two smaller compendia consisting of only strain PAO1 or strain PA14 samples with each aligned to their cognate reference genome. We confirmed strain annotations and identified other samples for inclusion by assessing each sample\u27s median expression of PAO1-only or PA14-only accessory genes. We then compared the patterns of core gene expression in each strain. To do so, we developed a method by which we analyzed genes in terms of which genes showed similar expression patterns across strain types. We found that some core genes had consistent correlated expression patterns across both compendia, while others were less stable in an interstrain comparison. For each accessory gene, we also determined core genes with correlated expression patterns. We found that stable core genes had fewer coexpressed neighbors that were accessory genes. Overall, this approach for analyzing expression patterns across strain types can be extended to other groups of genes, like phage genes, or applied for analyzing patterns beyond groups of strains, such as samples with different traits, to reveal a deeper understanding of regulation

Extraction and sensitive detection of toxins A and B from the human pathogen Clostridium difficile in 40 seconds using microwave-accelerated metal-enhanced fluorescence.

Clostridium difficile is the primary cause of antibiotic associated diarrhea in humans and is a significant cause of morbidity and mortality. Thus the rapid and accurate identification of this pathogen in clinical samples, such as feces, is a key step in reducing the devastating impact of this disease. The bacterium produces two toxins, A and B, which are thought to be responsible for the majority of the pathology associated with the disease, although the relative contribution of each is currently a subject of debate. For this reason we have developed a rapid detection assay based on microwave-accelerated metal-enhanced fluorescence which is capable of detecting the presence of 10 bacteria in unprocessed human feces within 40 seconds. These promising results suggest that this prototype biosensor has the potential to be developed into a rapid, point of care, real time diagnostic assay for C. difficile

Do twins share the same dress code?:Quantifying relative genetic and environmental contributions to subjective perceptions of "the dress" in a classical twin study

The phenomenon of contrasting color perceptions of "the dress" photograph has gained scientific interest. The mechanism underlying why individuals differ is yet to be fully explained. We use the powerful twin model design to ascertain the relative contribution of genetic and environmental factors on perception variation. A sample of 466 twins from the British TwinsUK registry were invited to report what color they saw in a standard image of the dress in standard illumination. The mean age of the participants was 49.5 (SD = 17.8) years, and 85% were female. When asked to choose between white and gold (WG) or blue and black (BB), 328 reported WG (70.4%) and 135 (29.0%) reported BB. Subjects choosing WG were significantly older (p &lt; 0.01), but there was no significant difference in gender. Monozygotic (MZ) twins were more concordant in their responses than dizygotic (DZ) twins (0.46 vs. 0.36). Twin modeling revealed that genetic factors accounted for 34% (95% confidence interval, 5%-59%) of variation in the reported color of the dress when adjusted for age, whereas environmental factors contributed 66% (95% CI, 41%-95%). This study suggests environmental factors play a significant role in how an individual perceives the color of "the dress."</p

Using genome-wide expression compendia to study microorganisms

A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a tremendous opportunity for gaining a systems level understanding of the transcriptional responses that influence phenotypes. Variety in experimental design is particularly important for studying microbes, where the transcriptional responses integrate many signals and demonstrate plasticity across strains including response to what nutrients are available and what microbes are present. Advances in high-throughput measurement technology have made it feasible to construct compendia for many microbes. In this review we discuss how these compendia are constructed and analyzed to reveal transcriptional patterns

In-hospital Outcomes of Attempting More Than One Chronic Total Coronary Occlusion Through Percutaneous Intervention During the Same Procedure

The frequency and outcomes of patients who underwent chronic total occlusion (CTO) percutaneous coronary intervention (PCI) of more than one CTO during the same procedure have received limited study. We compared the clinical and angiographic characteristics and procedural outcomes of patients who underwent treatment of single versus >1 CTOs during the same procedure in 20 centers from the United States, Europe, and Russia. A total of 2,955 patients were included: mean age was 65 ± 10 years and 85% were men with high prevalence of previous myocardial infarction (46%), and previous coronary artery bypass graft surgery (33%). More than one CTO lesions were attempted during the same procedure in 58 patients (2.0%) and 70% of them were located in different major epicardial arteries. Compared with patients who underwent PCI of a single CTO, those who underwent PCI of >1 CTOs during the same procedure had similar J-CTO (2.4 ± 1.3 vs 2.5 ± 1.3, p = 0.579) and Prospective Global Registry for the Study of Chronic Total Occlusion Intervention (1.5 ± 1.2 vs 1.3 ± 1.0 p = 0.147) scores. The multi-CTO PCI group had similar technical success (86% vs 87%, p = 0.633), but higher risk of in-hospital major complications (10.3% vs 2.7%, p = 0.005), and consequently numerically lower procedural success (79% vs 85%, p = 0.197). The multi-CTO PCI group had higher in-hospital mortality (5.2% vs 0.5%, p = 0.005) and stroke (5.2%vs 0.2%, p 1 CTO lesions requiring revascularization, as treatment during a single procedure was associated with higher risk for periprocedural complications

Prevalence and Outcomes of Percutaneous Coronary Interventions for Ostial Chronic Total Occlusions: Insights From a Multicenter Chronic Total Occlusion Registry

Ostial chronic total occlusions (CTOs) can be challenging to recanalize.We sought to examine the prevalence, angiographic presentation, and procedural outcomes of ostial (side-branch ostial and aorto-ostial) CTOs among 1000 CTO percutaneous coronary interventions (PCIs) performed in 971 patients between 2015 and 2017 at 14 centres in the US, Europe, and Russia.Ostial CTOs represented 16.9% of all CTO PCIs: 9.6% were aorto-ostial, and 7.3% were side-branch ostial occlusions. Compared with nonostial CTOs, ostial CTOs were longer (44 ± 33 vs 29 ± 19 mm, P < 0.001) and more likely to have proximal-cap ambiguity (55% vs 33%, P < 0.001), moderate/severe calcification (67% vs 45%, P < 0.001), a diffusely diseased distal vessel (41% vs 26%, P < 0.001), interventional collaterals (64% vs 53%, P = 0.012), and previous coronary artery bypass graft surgery (CABG) (51% vs 27%, P < 0.001). The retrograde approach was used more often in ostial CTOs (54% vs 29%, P < 0.001) and was more often the final successful crossing strategy (30% vs 18%, P = 0.003). Technical (81% vs 84%, P = 0.280), and procedural (77% vs 83%, P = 0.112) success rates and the incidence of in-hospital major complication were similar (4.8% vs 2.2%, P = 0.108), yet in-hospital mortality (3.0% vs 0.5%, P = 0.010) and stroke (1.2% vs 0.0%, P = 0.030) were higher in the ostial CTO PCI group. In multivariable analysis, ostial CTO location was not independently associated with higher risk for in-hospital major complications (adjusted odds ratio 1.27, 95% confidence intervals 0.37 to 4.51, P = 0.694).Ostial CTOs can be recanalized with similar rates of success as nonostial CTOs but are more complex, more likely to require retrograde crossing and may be associated with numerically higher risk for major in-hospital complications