Identification Of Phenotypes Research Articles

Identification of antibiotic resistance and virulence-encoding factors in Klebsiella pneumoniae by Raman spectroscopy and deep learning.

Summary Klebsiella pneumoniae has become the number one bacterial pathogen that causes high mortality in clinical settings worldwide. Clinical K. pneumoniae strains with carbapenem resistance and/or hypervirulent phenotypes cause higher mortality comparing with classical K. pneumoniae strains. Rapid differentiation of clinical K. pneumoniae with high resistance/hypervirulence from classical K. pneumoniae would allow us to develop rational and timely treatment plans. In this study, we developed a convolution neural network (CNN) as a prediction method using Raman spectra raw data for rapid identification of ARGs, hypervirulence‐encoding factors and resistance phenotypes from K. pneumoniae strains. A total of 71 K. pneumoniae strains were included in this study. The minimum inhibitory concentrations (MICs) of 15 commonly used antimicrobial agents on K. pneumoniae strains were determined. Seven thousand four hundred fifty‐five spectra were obtained using the InVia Reflex confocal Raman microscope and used for deep learning‐based and machine learning (ML) algorithms analyses. The quality of predictors was estimated in an independent data set. The results of antibiotic resistance and virulence‐encoding factors identification showed that the CNN model not only simplified the classification system for Raman spectroscopy but also provided significantly higher accuracy to identify K. pneumoniae with high resistance and virulence when compared with the support vector machine (SVM) and logistic regression (LR) models. By back‐testing the Raman‐CNN platform on 71 K. pneumoniae strains, we found that Raman spectroscopy allows for highly accurate and rationally designed treatment plans against bacterial infections within hours. More importantly, this method could reduce healthcare costs and antibiotics misuse, limiting the development of antimicrobial resistance and improving patient outcomes.

Heterogeneity of non-alcoholic fatty liver disease: Implications for clinical practice and research activity.

Non-alcoholic fatty liver disease (NAFLD) is a heterogeneous condition with a wide spectrum of clinical presentations and natural history and disease severity. There is also substantial inter-individual variation and variable response to a different therapy. This heterogeneity of NAFLD is in turn influenced by various factors primarily demographic/dietary factors, metabolic status, gut microbiome, genetic predisposition together with epigenetic factors. The differential impact of these factors over a variable period of time influences the clinical phenotype and natural history. Failure to address heterogeneity partly explains the sub-optimal response to current and emerging therapies for fatty liver disease. Consequently, leading experts across the globe have recently suggested a change in nomenclature of NAFLD to metabolic-associated fatty liver disease (MAFLD) which can better reflect current knowledge of heterogeneity and does not exclude concomitant factors for fatty liver disease (e.g. alcohol, viral hepatitis, etc.). Precise identification of disease phenotypes is likely to facilitate clinical trial recruitment and expedite translational research for the development of novel and effective therapies for NAFLD/MAFLD.

Difficult-to-Treat Asthma Management in School-Age Children

The World Health Organization divides severe asthma into three categories: untreated severe asthma; difficult-to-treat severe asthma; and severe, therapy-resistant asthma. The apparent frequency of severe asthma in the general population of asthmatic children is probably around 5%. Upon referral of these children, it is important to evaluate the diagnosis of asthma carefully before modifying management and applying a long-term monitoring plan. Identification of pathophysiologic phenotypes using objective biomarkers is essential in our routine assessments of severe asthma. Although conventional pharmacologic approaches should be attempted first, there is growing recognition that children with difficult-to-treat asthma may have unique clinical phenotypes that may necessitate alternative treatment approaches including asthma biologics. These new medications, especially those with effects on multiple pathologic features of asthma, raise the hope that new treatment strategies could induce remission. Besides introducing new medications, the opportunity for closer monitoring is feasible with advances in digital health. Therefore, we have the opportunity to improve response to medications, individualize treatment, and monitor response along with potential steps to prevent severe asthma.

Abstract 13977: Identification of Intermediate Right Ventricular Phenotypes Using Consensus Clustering in Patients With Pulmonary Hypertension

Introduction: Current right ventricular (RV) function phenotypes in pulmonary hypertension (PH) rely on few hemodynamic parameters to quantify RV dysfunction disease severity. The aim of the study was to identify novel RV phenotypes using RV hemodynamics and unsupervised machine learning in patients with PH. Methods: Participants were identified from the UArizona PH Registry (n=190). Correlation analyses identified 9 RV variables to include in clustering analysis. Consensus clustering was used to identify an unsupervised clustering method with a large inter-cluster, and small intra-cluster distance (Fig 1A). Significance was tested with Dunn and chi-square tests. Results: K-Medoids with a Pearson distance matrix over >1000 resampling iterations identified 5 clusters (consensus range: 0.8-0.9). World Symposium PH groups were distributed across clusters (Fig 1B). Clusters 1, 2 and 5 exhibit mild RV dysfunction with low diastolic stiffness (Eed) and afterload (Ea, Fig 1C). However, RV-PA coupling (Ees/Ea) was decreased in clusters 1 and 5. Clusters 3 and 4 have moderate to severe RV dysfunction with increased Eed and Ea but cluster 4 had decreased Ees/Ea. For pulmonary hemodynamics, clusters 3 and 4 have increased mean PA pressure (mPAP), increased pulmonary vascular resistance (PVR) and decreased PA compliance (Ca) compared to clusters 1 and 2. Cluster 5 has increased mPAP and high cardiac output resulting in moderately elevated PVR and decreased Ca. Conclusions: Unsupervised clustering identified 5 unique RV phenotypes ranging from mild to severe dysfunction. Further investigations are needed to identify factors modulating intermediate phenotypes to provide insight into RV dysfunction and disease progression.

Chemical phenotypes of intrinsic cardiac neurons in the newborn pig (Sus scrofa domesticus Erxleben, 1777).

Intrinsic cardiac neurons (ICNs) are crucial cells in the neural regulation of heart rhythm, myocardial contractility, and coronary blood flow. ICNs exhibit diversity in their morphology and neurotransmitters that probably are age-dependent. Therefore, neuroanatomical heart studies have been currently focused on the identification of chemical phenotypes of ICNs to disclose their possible functions in heart neural regulation. Employing whole-mount immunohistochemistry, we examined ICNs from atria of the newborn pigs (Sus scrofa domesticus) as ICNs at this stage of development have never been neurochemically characterized so far. We found that the majority of the examined ICNs (>60%) were of cholinergic phenotype. Biphenotypic neuronal somata (NS), that is, simultaneously positive for two neuronal markers, were also rather common and distributed evenly within the sampled ganglia. Simultaneous positivity for cholinergic and adrenergic neuromarkers was specific in 16.4%, for cholinergic and nitrergic-in 3.5% of the examined NS. Purely either adrenergic or nitrergic ICNs were observed at 13% and 3.1%, correspondingly. Purely adrenergic and nitrergic NS were the most frequent in the ventral left atrial subplexus. Similarly to neuronal phenotype, sizes of NS also varied depending on the atrial region providing insights into their functional implications. Axons, but not NS, positive for classic sensory neuronal markers (vesicular glutamate transporter 2 and calcitonin gene-related peptide) were identified within epicardiac nerves and ganglia. Moreover, a substantial number of ICNs could not be attributed to any phenotype as they were not immunoreactive for antisera used in this study. Numerous dendrites with putative peptidergic and adrenergic contacts on cholinergic NS contributed to neuropil of ganglia. Our observations demonstrate that intrinsic cardiac ganglionated plexus is not fully developed in the newborn pig despite of dense network of neuronal processes and numerous signs of neural contacts within ganglia.

Genetic biomarkers in osteoarthritis: a quick overview

Osteoarthritis (OA) is a chronic musculoskeletal disease with a polygenic and heterogeneous nature. In addition, when clinical manifestations appear, the evolution of the disease is usually already irreversible. Therefore, the efforts on OA research are focused mainly on the discovery of therapeutic targets and reliable biomarkers that permit the early identification of different OA-related parameters such as diagnosis, prognosis, or phenotype identification. To date, potential candidate protein biomarkers have been associated with different aspects of the disease; however, there is currently no gold standard. In this sense, genomic data could act as complementary biomarkers of diagnosis and prognosis or even help to identify therapeutic targets of the disease. In this review, we will describe the most recent advances in genetic biomarkers in OA over the past three years.

P7‐13: Identification of exacerbation phenotypes across asthma and COPD

P7‐13: Identification of exacerbation phenotypes across asthma and COPD

Identification of clinical phenotypes of peripheral involvement in patients with spondyloarthritis, including psoriatic arthritis: a cluster analysis in the worldwide ASAS-PerSpA study

ObjectiveTo identify clusters of peripheral involvement according to the specific location of peripheral manifestations (ie, arthritis, enthesitis and dactylitis) in patients with spondyloarthritis (SpA) including psoriatic arthritis (PsA), and to...

Syncope: new solutions for an old problem.

Syncope is a frequent event in the general population. Approximately 1%-2% of all emergency department admissions are due to syncope and at least one-third of all people experience fainting in their life. Although consequences of cardiac syncope are generally feared, non-cardiac syncope is much more common and may be associated with severe injuries and quality-of-life impairment, particularly in older adults. Various diagnostic and therapeutic strategies have been created and implemented over decades, leading to significant improvements in diagnostic accuracy and treatment effectiveness. In recent years, diagnosis and treatment have further evolved according to an innovative approach focused on the hemodynamic mechanism underlying syncope, based upon the assumption that knowledge of the syncope mechanism is a prerequisite for effective syncope prevention and treatment. Therefore, a new classification of syncope has been proposed, which defines two main syncope phenotypes with different predominant mechanisms: the hypotensive phenotype, where hypotension or vasodepression prevails, and the bradycardic phenotype, where cardioinhibition prevails. Identification of syncope phenotype - bradycardic or hypotensive/vasodepressive - represents the first step towards personalized management of syncope, characterized by customized interventions for prevention. The present review aims to illustrate these new developments in the diagnosis and therapy of non-cardiac syncope within a mechanism-based perspective. Diagnosis and therapy of bradycardic and hypotensive phenotypes are discussed, with a focus on recent evidence.

Molecular-Genetic Portrait of Breast Cancer with Triple Negative Phenotype.

Simple SummaryBreast cancer is a genetically heterogeneous disease with different molecular biological and clinical characteristics. The available knowledge about the genetic heterogeneity of the most aggressive molecular subtype of breast cancer—triple-negative—has led to discoveries in drug treatment. Identification of the molecular-genetic phenotype of breast cancer is an important prognostic factor of the disease and allows personalization of the patient’s treatment.Understanding of the genetic mechanisms and identification of the biological markers of tumor progression that form the individual molecular phenotype of transformed cells can characterize the degree of tumor malignancy, the ability to metastasize, the hormonal sensitivity, and the effectiveness of chemotherapy, etc. Breast cancer (BC) is a genetically heterogeneous disease with different molecular biological and clinical characteristics. The available knowledge about the genetic heterogeneity of the most aggressive molecular subtype of breast cancer—triple-negative (TN)—has led to discoveries in drug treatment, including the use of DNA damaging agents (platinum and PARP inhibitors) for these tumors, as well as the use of immunotherapy. Most importantly, the ability to prescribe optimal drug treatment regimens for patients with TNBC based on knowledge of the molecular-genetic characteristics of this subtype of BC will allow the achievement of high rates of overall and disease-free survival. Thus, identification of the molecular-genetic phenotype of breast cancer is an important prognostic factor of the disease and allows personalization of the patient’s treatment.

Clinicopathological features and BRCA1 and BRCA2 mutation status in a prospective cohort of young women with breast cancer.

Breast cancer in young women is more likely to have higher risk features and be associated with germline BRCA1/BRCA2 mutations. We present the clinicopathologic features of breast cancers in a prospective cohort of young women, and associations between surrogate molecular subtype and BRCA1/BRCA2 mutation status. Histopathological features, biomarker status, tumour stage and BRCA status were collected. Invasive tumours were categorised as luminal A-like (ER + and/or PR + , HER2-, grade 1/2), luminal B-like (ER + and/or PR + , HER2 + , or ER + and/or PR + , HER2-, and grade 3), HER2-enriched (ER/PR-, HER2 + ) or triple-negative. In all, 57.3% (654/1143) of invasive tumours were high grade. In total, 32.9% were luminal A-like, 42.4% luminal B-like, 8.3% HER2-enriched, and 16.4% triple-negative. Among different age groups, there were no differences in molecular phenotype, stage, grade or histopathology. 11% (131) of tumours were from BRCA mutation carriers; 64.1% BRCA1 (63.1% triple-negative), and 35.9% BRCA2 (55.3% luminal B-like). The opportunity to provide comparisons across young age groups, BRCA mutation status, surrogate molecular phenotype, and the identification of more aggressive hormone receptor-positive phenotypes in this population provides direction for future work to further understand and improve disparate outcomes for young women with luminal B-like cancers, particularly BRCA2-associated cancers, with potential implications for tailored prevention and treatment.

Natural Competence for Transformation in Lactobacili

Natural Competence for Transformation in Lactobacili

Validation of the optical Aktiia bracelet in different body positions for the persistent monitoring of blood pressure

The diagnosis of hypertension and the adjustment of antihypertensive drugs are evolving from isolated measurements performed at the physician offices to the full phenotyping of patients in real-life conditions. Indeed, the strongest predictor of cardiovascular risk comes from night measurements. The aim of this study was to demonstrate that a wearable device (the Aktiia Bracelet) can accurately estimate BP in the most common body positions of daily life and thus become a candidate solution for the BP phenotyping of patients. We recruited 91 patients with BP ranging from low to hypertensive levels and compared BP values from the Aktiia Bracelet against auscultatory reference values for 4 weeks according to an extended ISO 81060-2 protocol. After initializing on day one, the observed means and standard deviations of differences for systolic BP were of 0.46 ± 7.75 mmHg in the sitting position, − 2.44 ± 10.15 mmHg in the lying, − 3.02 ± 6.10 mmHg in the sitting with the device on the lap, and − 0.62 ± 12.51 mmHg in the standing position. Differences for diastolic BP readings were respectively of 0.39 ± 6.86 mmHg, − 1.93 ± 7.65 mmHg, − 4.22 ± 6.56 mmHg and − 4.85 ± 9.11 mmHg. This study demonstrates that a wearable device can accurately estimate BP in the most common body positions compared to auscultation, although precision varies across positions. While wearable persistent BP monitors have the potential to facilitate the identification of individual BP phenotypes at scale, their prognostic value for cardiovascular events and its association with target organ damage will need cross-sectional and longitudinal studies. Deploying this technology at a community level may be also useful to drive public health interventions against the epidemy of hypertension.

The Quest for Signals in Noise: Leveraging Experiential Variation to Identify Bilingual Phenotypes.

Increasing evidence suggests that bilingualism does not, in itself, result in a particular pattern of response, revealing instead a complex and multidimensional construct that is shaped by evolutionary and ecological sources of variability. Despite growing recognition of the need for a richer characterization of bilingual speakers and of the different contexts of language use, we understand relatively little about the boundary conditions of putative “bilingualism” effects. Here, we review recent findings that demonstrate how variability in the language experiences of bilingual speakers, and also in the ability of bilingual speakers to adapt to the distinct demands of different interactional contexts, impact interactions between language use, language processing, and cognitive control processes generally. Given these findings, our position is that systematic variation in bilingual language experience gives rise to a variety of phenotypes that have different patterns of associations across language processing and cognitive outcomes. The goal of this paper is thus to illustrate how focusing on systematic variation through the identification of bilingual phenotypes can provide crucial insights into a variety of performance patterns, in a manner that has implications for previous and future research.

Upright exercise stress echocardiography may unmask dynamic left ventricular obstruction also beyond hypertrophic cardiomyopathy

Abstract Background Dynamic left ventricular outflow obstruction (LVOTO) during exercise stress echocardiography (ESE) is recommended in hypertrophic cardiomyopathy (HCM) to identify the obstructive phenotype. Aim To assess left ventricular outflow gradient (LVOTG) during ESE in different conditions. Methods In a single-group, prospective, observational study, we performed peak and/or post-treadmill ESE with systematic assessment of LVOTG in the orthostatic position by continuous-wave Doppler in 1333 subjects (837 males, mean age 38,2±20 ranging from 6 to 87 years) recruited over a period of twenty years, from 2001 to 2021. Peak LVOTG ≥30 mm Hg was considered abnormal for LVOTO during ESE. We enrolled 7 different populations: asymptomatic healthy controls (n=35); HCM (n=81); genotype-positive, phenotype negative asymptomatic HCM (n=6); patients with chest pain symptoms, suspected myocardial ischemia and either normal coronary arteries (INOCA, n=131,or with very low pre-test probability of coronary artery disease (probable INOCA, n=416) and; fatigue and suspected heart failure with preserved ejection fraction (HFpEF, n=206); amateur athletes with ischemia-like ECG changes during exercise-test or symptoms such as near syncope or chest pain or dizziness (n=457); aborted sudden death and with negative screening (n=1). Results Technical success rate of LVOTG assessment was 1333/1333 at rest and at peak stress (feasibility 100%). Imaging and analysis time were <1 minute. LVOTG at rest was present in 25 pts (2.8%) of the overall population: 23 HCM, 1 INOCA, and 1 HFpEF. Overall prevalence during ESE was 432/1333 (32%). During ESE, LVOTO (see Figure 1 and 2) was 0% (0/35) in normals, 58% (47/81) in HCM (23 with obstruction at rest), 33% (2/6) in genotype-positive, phenotype negative HCM, 37% (33/131) in INOCA, 40% (135/416) in athletes and 1/1 in the patient with aborted sudden death on strenuous exercise. Conclusion LVOTO in orthostatic position is detectable during treadmill ESE in several cardiovascular conditions associated with symptoms such as dyspnea, chest pain or near syncope, and even in asymptomatic patients with genotype-positive, phenotype-negative HCM. The identification of the obstructive phenotype is easy to capture during ESE without any significant additional imaging and analysis burden and can be important also outside HCM. Funding Acknowledgement Type of funding sources: None. Figure 1Figure 2

The associations of serum homoarginine to long-term prognosis in patients with chronic coronary syndrome and non-obstructive coronary artery disease

Abstract Background Although generally at lower risk than those with obstructive CAD, patients with non-obstructive CAD (NOCAD) are heterogeneous concerning long-term prognosis. Notably, reversible ischemia due to vascular dysfunction is a frequent finding in NOCAD patients (1). The endogenous, non-proteinogenic amino acid homoarginine (hArg) increases the availability of nitric oxide (NO) and thereby the NO-dependent vasodilatation (2). Several studies have reported a strong inverse relation between serum hArg levels and cardiovascular disease (CVD) risk among patients with obstructive CAD. However, the prognostic implications of serum hArg levels in NOCAD patients have not been explored previously. Purpose We evaluated serum hArg as a predictor of long-term risk of CVD mortality among patients with NOCAD. Methods 1046 patients with chronic coronary syndrome (CCS) underwent elective coronary angiography during 2000–2004, with the findings of NOCAD. Serum hArg was measured by liquid chromatography-tandem mass spectrometry in samples that had been frozen and stored at −80°C. The association of serum hArg to CVD mortality risk was visualized in a generalized additive regression plot and further explored using Cox regression. The models included age, sex, body mass index, hypertension, diabetes, smoking status, serum LDL cholesterol and estimated glomerular filtration rate as independent covariables. We evaluated model discrimination and risk classification by calculating C-statistics and net reclassification improvement (NRI >0), respectively. Results Median (25th-75th percentiles) age at inclusion was 57 (51–65) years, 48.5% were women and median (25th-75th percentiles) level of serum hArg was 1.87 (1.47–2.38) μmol/L. During median (25th- 75th percentiles) 14.1 (13.2–15.4) years of follow-up 5.7% of the patients died from CVD. The multivariable adjusted hazard ratio (95% confidence interval) per SD increment of (log transformed) hArg was 0.53 (0.40–0.70) in relation to CVD mortality. The multivariable model without biomarker provided a C- statistics for CVD mortality of 0.79 which increased to 0.82 by the addition of serum-hArg to the model (Δ area =0.03, P=0.01). Further, serum hArg provided a high NRI (95% CI) of 0.53 (0.40–0.70), P<0.001. Conclusion We demonstrated a strong inverse relationship between serum hArg and long-term risk of CVD mortality among patients with NOCAD. Our study adds to previous literature linking low hArg with vascular dysfunction and adverse CVD prognosis. The potential clinical usefulness of serum hArg measurements for the identification of a high-risk phenotype in NOCAD warrants further evaluation. Funding Acknowledgement Type of funding sources: Public hospital(s). Main funding source(s): The Western Norway Regional Health Authority

Oil induced cardiac effects in embryonic sheepshead minnows, Cyprinodon variegatus

Following the Deepwater Horizon oil spill in April 2010, much research has been conducted on the cardiotoxic effects of oil on fish. Sensitive life history stages, such as the embryonic period, have been targeted to elucidate the effects of polycyclic aromatic hydrocarbons (PAHs) on the developing cardiovascular systems of fish. However, much of this research has focused on rapidly developing pelagic species, with little emphasis on estuarine species with longer embryological periods. Moreover, previous studies have used heart rate as the primary endpoint to measure cardiac performance in embryos and larvae; an endpoint that on its own may overlook impairment in cardiac performance. This study aims to fill these knowledge gaps and provide a more holistic approach for assessing the effects of PAHs on cardiac function by exposing sheepshead minnow (Cyprinodon variegatus) embryos to two oil doses (150 and 300 μg/L tPAH nominally) throughout embryonic development and measuring cardiac responses through the identification of cardiotoxic phenotypes (pericardial edema) as well as calculation of cardiac output at 4 days post fertilization. Results of this study show significant increases in pericardial edema at both oil doses relative to controls as well as significantly reduced cardiac output – driven by reductions in ventricular stroke volume. This study is one of the first to assess cardiac output in embryonic fish exposed to oil and methods described here allow for more physiologically relevant measures of cardiac performance in early life stages through established and non-invasive measures.

Phenotypic characterization of Cdkl5-knockdown neurons establishes elongated cilia as a functional assay for CDKL5 Deficiency Disorder

CDKL5 Deficiency Disorder (CDD) is a severe encephalopathy characterized by intractable epilepsy, infantile spasms, and cognitive disabilities. The detrimental CNS manifestations and lack of therapeutic interventions represent unmet needs, necessitating identification of CDD-dependent phenotypes for in vitro disease modeling and therapeutic testing. Here, we optimized a high-content assay to quantify cilia in CDKL5-deficient neurons. Our work shows that Cdkl5-knockdown neurons have elongated cilia and uncovers cilium lengthening in hippocampi of Cdkl5 knockout mice. Collectively, our findings identify cilia length alterations under CDKL5 activity loss in vitro and in vivo and reveal elongated cilia as a robust functional phenotype for CDD.

Electrical Impedance Tomography might be a Practical Tool to Provide Information about COVID-19 Pneumonia Progression

Abstract COVID-19 induced acute respiratory distress syndrome (ARDS) could have two different phenotypes, which might have different response and outcome to the traditional ARDS positive end-expiration pressure (PEEP) treatment. The identification of the different phenotypes in terms of the PEEP recruitment can help improve the patients’ outcome. In this contribution we reported a COVID-19 patient with seven-day electrical impedance tomography monitoring. From the conductivity distribution difference image analysis of the data, a clear course developing trend can be observed in addition to the phenotype identification. This case might suggest that EIT can be a practical tool to identify phenotypes and to provide progressive information of COVID-19 pneumonia.

Fast decliner phenotype of chronic obstructive pulmonary disease (COPD): applying machine learning for predicting lung function loss

BackgroundChronic obstructive pulmonary disease (COPD) is a heterogeneous group of lung conditions challenging to diagnose and treat. Identification of phenotypes of patients with lung function loss may allow early intervention...