proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.

The transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motivate its broad dissemination and reuse, which is currently an unmet need in the prokaryotic domain. To fill this gap, we present proChIPdb (prochipdb.org), an information-rich, interactive web database. This website collects public ChIP-seq/-exo data across several prokaryotes and presents them in dashboards that include curated binding sites, nucleotide-resolution genome viewers, and summary plots such as motif enrichment sequence logos. Users can search for TFs of interest or their target genes, download all data, dashboards, and visuals, and follow external links to understand regulons through biological databases and the literature. This initial release of proChIPdb covers diverse organisms, including most major TFs of Escherichia coli, and can be expanded to support regulon discovery across the prokaryotic domain.

Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is an opportunistic pathogen and major cause of hospital-acquired infections. The virulence of P. aeruginosa is largely determined by its transcriptional regulatory network (TRN). We used 411 transcription profiles of P. aeruginosa from diverse growth conditions to construct a quantitative TRN by identifying independently modulated sets of genes (called iModulons) and their condition-specific activity levels. The current study focused on the use of iModulons to analyze the biofilm production and antibiotic resistance of P. aeruginosa. Our analysis revealed: (i) 116 iModulons, 81 of which show strong association with known regulators; (ii) novel roles of regulators in modulating antibiotics efflux pumps; (iii) substrate-efflux pump associations; (iv) differential iModulon activity in response to beta-lactam antibiotics in bacteriological and physiological media; (v) differential activation of 'Cell Division' iModulon resulting from exposure to different beta-lactam antibiotics and (vi) a role of the PprB iModulon in the stress-induced transition from planktonic to biofilm lifestyle. In light of these results, the construction of an iModulon-based TRN provides a transcriptional regulatory basis for key aspects of P. aeruginosa infection, such as antibiotic stress responses and biofilm formation. Taken together, our results offer a novel mechanistic understanding of P. aeruginosa virulence.

Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family.

Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.

Fractional Flow Reserve Cardio-Oncology Effects on Inpatient Mortality, Length of Stay, and Cost Based on Malignancy Type: Machine Learning Supported Nationally Representative Case-Control Study of 30 Million Hospitalizations.

Background and Objectives: There are no nationally representative studies of mortality and cost effectiveness for fractional flow reserve (FFR) guided percutaneous coronary interventions (PCI) in patients with cancer. Our study aims to show how this patient population may benefit from FFR-guided PCI. Materials and Methods: Propensity score matched analysis and backward propagation neural network machine learning supported multivariable regression was performed for inpatient mortality in this case-control study of the 2016 National Inpatient Sample (NIS). Regression results were adjusted for age, race, income, geographic region, metastases, mortality risk, and the likelihood of undergoing FFR versus non-FFR PCI. All analyses were adjusted for the complex survey design to produce nationally representative estimates. Results: Of the 30,195,722 hospitalized patients meeting criteria, 3.37% of the PCIs performed included FFR. In propensity score adjusted multivariable regression, FFR versus non-FFR PCI significantly reduced inpatient mortality (OR 0.47, 95%CI 0.35−0.63; p < 0.001) and length of stay (LOS) (in days; beta −0.23, 95%CI −0.37−−0.09; p = 0.001) while increasing cost (in USD; beta $5708.63, 95%CI, 3042.70−8374.57; p < 0.001), without significantly increasing complications overall. FFR versus non-FFR PCI did not specifically change cancer patients' inpatient mortality, LOS, or cost. However, FFR versus non-FFR PCI significantly increased inpatient mortality for Hodgkin's lymphoma (OR 52.48, 95%CI 7.16−384.53; p < 0.001) and rectal cancer (OR 24.38, 95%CI 2.24−265.73; p = 0.009). Conclusions: FFR-guided PCI may be safely utilized in patients with cancer as it does not significantly increase inpatient mortality, complications, and LOS. These findings support the need for an increased utilization of FFR-guided PCI and further studies to evaluate its long-term impact.

Geographical Differences in Cardiovascular Comorbidities and Outcomes of COVID-19 Hospitalized Patients in the USA.

INTRODUCTION: Cardiovascular comorbidities may predispose to adverse outcomes in hospitalized patients with coronavirus disease 2019 (COVID-19). However, across the USA, the burden of cardiovascular comorbidities varies significantly. Whether clinical outcomes of hospitalized patients with COVID-19 differ between regions has not yet been studied systematically. Here, we report differences in underlying cardiovascular comorbidities and clinical outcomes of patients hospitalized with COVID-19 in Texas and in New York state. METHODS: We established a multicenter retrospective registry including patients hospitalized with COVID-19 between March 15 and July 12, 2020. Demographic and clinical data were manually retrieved from electronic medical records. We focused on the following outcomes: mortality, need for pharmacologic circulatory support, need for mechanical ventilation, and need for hemodialysis. Univariate and multivariate logistic regression analyses were performed. RESULTS: Patients in the Texas cohort (n = 296) were younger (57 vs. 63 years, p value <0.001), they had a higher BMI (30.3 kg/m2 vs. 28.5 kg/m2, p = 0.015), and they had higher rates of diabetes mellitus (41 vs. 30%; p = 0.014). In contrast, patients in the New York state cohort (n = 218) had higher rates of coronary artery disease (19 vs. 10%, p = 0.005) and atrial fibrillation (11 vs. 5%, p = 0.012). Pharmacologic circulatory support, mechanical ventilation, and hemodialysis were more frequent in the Texas cohort (21 vs. 13%, p = 0.020; 30 vs. 12%, p < 0.001; and 11 vs. 5%, p = 0.009, respectively). In-hospital mortality was similar between the 2 cohorts (16 vs. 18%, p = 0.469). After adjusting for differences in underlying comorbidities, only the use of mechanical ventilation remained significantly higher in the participating Texas hospitals (odds ratios [95% CI]: 3.88 [1.23, 12.24]). Median time to pharmacologic circulatory support was 8 days (interquartile range: 2, 13.8) in the Texas cohort compared to 1 day (0, 3) in the New York state cohort, while median time to in-hospital mortality was 16 days (10, 25.5) and 7 days (4, 14), respectively (both p < 0.001). In-hospital mortality was higher in the late versus the early study phase in the New York state cohort (24 vs. 14%, p = 0.050), while it was similar between the 2 phases in the Texas cohort (16 vs. 15%, p = 0.741). CONCLUSIONS: Geographical differences, including practice pattern variations and the impact of disease burden on provision of health care, are important for the evaluation of COVID-19 outcomes. Unadjusted data may cause bias affecting future regulatory policies and proper allocation of resources.

Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures.

Establishing transcriptional regulatory networks (TRNs) in bacteria has been limited to well-characterized model strains. Using machine learning methods, we established the transcriptional regulatory networks of six Salmonella enterica serovar Typhimurium strains from their transcriptomes. By decomposing a compendia of RNA sequencing (RNA-seq) data with independent component analysis, we obtained 400 independently modulated sets of genes, called iModulons. We (i) performed pan-genome analysis of the phylogroup structure of S. Typhimurium and analyzed the iModulons against this background, (ii) revealed different genetic signatures in pathogenicity islands that explained phenotypes, (iii) discovered three transport iModulons linked to antibiotic resistance, (iv) described concerted responses to cationic antimicrobial peptides, and (v) uncovered new regulons. Thus, by combining pan-genome and transcriptomic analytics, we revealed variations in TRNs across six strains of serovar Typhimurium. IMPORTANCE Salmonella enterica serovar Typhimurium is a pathogen involved in human nontyphoidal infections. Treating S. Typhimurium infections is difficult due to the species's dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN) that is different across strains. In this study, we describe the use of independent component analysis to characterize the differential TRNs across the S. Typhimurium pan-genome using a compendium of high-quality RNA-seq data. This approach provided unprecedented insights into the differences between regulation of key cellular functions and pathogenicity in the different strains. The study provides an impetus to initiate a large-scale effort to reveal the TRN differences between the major phylogroups of the pathogenic bacteria, which could fundamentally impact personalizing treatments of bacterial pathogens.

Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection.

Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, and some studies have performed system-level analysis, few have been able to provide a network-based model of the TRN that also provides the relative shifts in transcriptional regulator activity triggered by changing environments. Here, we compiled a compendium of nearly 650 publicly available, high quality M. tuberculosis RNA-sequencing data sets and applied an unsupervised machine learning method to obtain a quantitative, top-down TRN. It consists of 80 independently modulated gene sets known as "iModulons," 41 of which correspond to known regulons. These iModulons explain 61% of the variance in the organism's transcriptional response. We show that iModulons (i) reveal the function of poorly characterized regulons, (ii) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and infection events, and (iii) identify intrinsic clusters of regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date. IMPORTANCE Mycobacterium tuberculosis H37Rv is one of the world's most impactful pathogens, and a large part of the success of the organism relies on the differential expression of its genes to adapt to its environment. The expression of the organism's genes is driven primarily by its transcriptional regulatory network, and most research on the TRN focuses on identifying and quantifying clusters of coregulated genes known as regulons. While previous studies have relied on molecular measurements, in the manuscript we utilized an alternative technique that performs machine learning to a large data set of transcriptomic data. This approach is less reliant on hypotheses about the role of specific regulatory systems and allows for the discovery of new biological findings for already collected data. A better understanding of the structure of the M. tuberculosis TRN will have important implications in the design of improved therapeutic approaches.

Post-cardiac arrest PCI is underutilized among cancer patients: Machine learning augmented nationally representative case-control study of 30 million hospitalizations.

BACKGROUND: Cancer patients are less likely to undergo percutaneous coronary intervention (PCI) after cardiac arrest, although they demonstrate improved mortality benefit from the procedure. We produced the largest nationally representative analysis of mortality of cardiac arrest and PCI for patients with cancer versus non-cancer. METHODS: Propensity score adjusted multivariable regression for mortality was performed in this case-control study of the United States' largest all-payer hospitalized dataset, the 2016 National Inpatient Sample. Regression models of mortality and PCI weighted by the complex survey design were fully adjusted for age, race, income, cancer metastases, NIS-calculated mortality risk by Diagnosis Related Group (DRG), acute coronary syndrome, and likelihood of undergoing PCI. RESULTS: Of the 30,195,722 hospitalized adult patients, 15.43% had cancer, and 0.79% of the whole sample presented with cardiac arrest (of whom 20.57% underwent PCI). In fully adjusted regression analysis among patients with cardiac arrest, PCI significantly reduced mortality (OR 0.15, 95 %CI 0.13-0.19; p < 0.001) among patients with cancer greater than those without it (OR 0.21, 95 %CI 0.20-0.23; p < 0.001). CONCLUSIONS: This nationally representative study suggests that post-cardiac arrest PCI is underutilized among patients with cancer despite its significant mortality reduction for such patients (independent of clinical acuity).

Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius.

Dynamic cellular responses to environmental constraints are coordinated by the transcriptional regulatory network (TRN), which modulates gene expression. This network controls most fundamental cellular responses, including metabolism, motility, and stress responses. Here, we apply independent component analysis, an unsupervised machine learning approach, to 95 high-quality Sulfolobus acidocaldarius RNA-seq datasets and extract 45 independently modulated gene sets, or iModulons. Together, these iModulons contain 755 genes (32% of the genes identified on the genome) and explain over 70% of the variance in the expression compendium. We show that five modules represent the effects of known transcriptional regulators, and hypothesize that most of the remaining modules represent the effects of uncharacterized regulators. Further analysis of these gene sets results in: (1) the prediction of a DNA export system composed of five uncharacterized genes, (2) expansion of the LysM regulon, and (3) evidence for an as-yet-undiscovered global regulon. Our approach allows for a mechanistic, systems-level elucidation of an extremophile's responses to biological perturbations, which could inform research on gene-regulator interactions and facilitate regulator discovery in S. acidocaldarius. We also provide the first global TRN for S. acidocaldarius. Collectively, these results provide a roadmap toward regulatory network discovery in archaea.

Pseudo-Acute Myocardial Infarction in a Young COVID-19 Patient.

A 29-year-old man tested positive for COVID-19 and developed acute respiratory distress syndrome. While mechanically ventilated, his electrocardiogram showed inferior ST-segment elevations, with normal serial cardiac troponin I and transthoracic echocardiograms. He was treated conservatively, with complete clinical recovery and resolution of his electrocardiographic abnormalities. (Level of Difficulty: Beginner.).

Hydralazine-Induced Lupus Syndrome Manifesting as Large Pericardial Effusion.

Hydralazine-induced lupus syndrome (HILS) is a rare clinical entity with variable manifestations. Pericardial involvement is an uncommon but serious manifestation of the condition. In this report, we present a case of large symptomatic pericardial effusion secondary to HILS. We highlight the important considerations in the evaluation and management of this rare syndrome. HILS should be considered in the differential diagnosis for cardiac tamponade of otherwise unclear etiology in patients taking 100 mg daily or more of hydralazine for longer than three months. A temporal association between the offending drug and presenting symptoms, resolution of symptoms upon discontinuation, and a positive anti-histone antibody test can all support the diagnosis of this syndrome.

Massive TAVR: Complex Transcatheter Aortic Valve Replacement in the Setting of an Enormous Adnexal Mass.

A 65-year-old woman with a large adnexal mass was found to have severe bicuspid aortic valve stenosis. Transcatheter aortic valve replacement was chosen rather than surgical aortic valve replacement because of concerns over risks. We demonstrate the value of pre-operative transcatheter aortic valve replacement before prompt noncardiac surgery. Furthermore, it illustrates some useful bailout techniques in this challenging scenario. (Level of Difficulty: Intermediate.).

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Adverse reproductive outcomes associated with teenage pregnancy.

INTRODUCTION: It is debated whether teenage pregnancy is associated with an adverse reproductive outcome. This study assessed the reproductive outcomes in teenage pregnancy in Nepal, a developing setting. METHODS: A hospital based retrospective cohort study of 4,101 deliveries to compare the outcomes between teenage and non-teenage pregnancies. RESULTS: Pregnancy in teenagers was associated with significantly increased risk (P<0.05) of delivery of very and moderately preterm births and Low Birth Weight babies. There was no significant difference in risk of having small for gestational age babies, low APGAR score at birth at 1 min and 5 min, stillbirth, neonatal death, and post partum hemorrhage. However, the risk of having delivery by episiotomy, vacuum or forceps and Caesarean section was significantly lower (P<0.05) among teenage mothers. CONCLUSION: Teenage women were more likely to have preterm births and low birth weight babies. However, they were less likely to have delivery by episiotomy, forceps or vacuum and Caesarean sections. In other respects, there were no significant differences between teenage and non-teenage mothers.

Variability of forearm collateral circulation: An observational study of serial hand plethysmography testing.

OBJECTIVES: Evaluation of plethysmography as a reliable triage tool to access collateral circulation in the hand prior to transradial access. BACKGROUND: Hand plethysmographic testing has been used for access site triage prior to cardiac catheterization despite a lack of data supporting its result's stability. METHODS: Cohort of consecutive outpatients presenting for evaluation prior to cardiac catheterization underwent hand plethysmographic testing at the beginning of the office visit and before discharge. Demographics and clinical data was recorded. RESULTS: Hands (N = 887) in 445 patients were evaluated using the Barbeau plethysmography technique. Barbeau Test (BT) patterns A, B, C, and D were observed in 58%, 30%, 8% and 4% on initial evaluation. On preliminary evaluation, 780 (88%) hands had a "low-risk" pattern (A or B) and 107 (12%) hands had a "high-risk" pattern (C or D). Repeat evaluation performed 50 ±â€¯26 min later revealed a 'low-risk' pattern in 809 (91%) hands with 78 (9%) of hands showing a persistent "high risk" pattern. In 29 (27%) high-risk hands, spontaneous conversion to pattern B within <1 h occurred. Reverse Barbeau Test (RBT) at baseline showed pattern A, B, C and D in 95.9%, 2.8%, 1% and .4% respectively. There was no significant change in RBT upon follow-up evaluation. Strength of the radial artery pulsation was significantly associated with the pattern of RBT and the strength of ulnar pulsation was associated with the results of the BT. CONCLUSIONS: Plethysmographic testing of forearm circulation demonstrates variability over short intervals suggesting poor reliability for access site triage.