CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures

We present CATHEDRAL, an iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures. CATHEDRAL builds on the features of a fast secondary-structure–based method (using graph theory) to locate known folds within a multidomain context and a residue-based, double-dynamic programming algorithm, which is used to align members of the target fold groups against the query protein structure to identify the closest relative and assign domain boundaries. To increase the fidelity of the assignments, a support vector machine is used to provide an optimal scoring scheme. Once a domain is verified, it is excised, and the search protocol is repeated in an iterative fashion until all recognisable domains have been identified. We have performed an initial benchmark of CATHEDRAL against other publicly available structure comparison methods using a consensus dataset of domains derived from the CATH and SCOP domain classifications. CATHEDRAL shows superior performance in fold recognition and alignment accuracy when compared with many equivalent methods. If a novel multidomain structure contains a known fold, CATHEDRAL will locate it in 90% of cases, with <1% false positives. For nearly 80% of assigned domains in a manually validated test set, the boundaries were correctly delineated within a tolerance of ten residues. For the remaining cases, previously classified domains were very remotely related to the query chain so that embellishments to the core of the fold caused significant differences in domain sizes and manual refinement of the boundaries was necessary. To put this performance in context, a well-established sequence method based on hidden Markov models was only able to detect 65% of domains, with 33% of the subsequent boundaries assigned within ten residues. Since, on average, 50% of newly determined protein structures contain more than one domain unit, and typically 90% or more of these domains are already classified in CATH, CATHEDRAL will considerably facilitate the automation of protein structure classification

Diagnosing Acute Heart Failure in Patients With Undifferentiated Dyspnea: A Lung and Cardiac Ultrasound (LuCUS) Protocol

Objectives The primary goal of this study was to determine accuracy for diagnosing acutely decompensated heart failure (ADHF) in the undifferentiated dyspneic emergency department (ED) patient using a lung and cardiac ultrasound (LuCUS) protocol. Secondary objectives were to determine if US findings acutely change management and if findings are more accurate than clinical gestalt. Methods This was a prospective, observational study of adult patients presenting to the ED with undifferentiated dyspnea. The intervention consisted of a 12-view LuCUS protocol performed by experienced emergency physician sonographers. The primary objective was measured by comparing US findings to the final diagnosis independently determined by two physicians blinded to the LuCUS result. Acute treatment changes based on US findings were tracked in real time through a standardized data collection form. Results Data on 99 patients were analyzed; ADHF was the final diagnosis in 36%. The LuCUS protocol had sensitivity of 83% (95% confidence interval [CI] = 67% to 93%), specificity of 83% (95% CI = 70% to 91%), positive likelihood ratio of 4.8 (95% CI = 2.7 to 8.3), and negative likelihood ratio of 0.20 (95% CI = 0.09 to 0.42). Forty-seven percent of patients had changes in acute management, and 42% had changes in acute treatment. Observed agreement for the LuCUS protocol was 93% between coinvestigators. Overall, accuracy improved by 20% (83% vs. 63%, 95% CI = 8% to 31% for the difference) over clinical gestalt alone. Conclusions The LuCUS protocol may accurately identify ADHF and may improve acute clinical management in dyspneic ED patients. This protocol has improved diagnostic accuracy over clinical gestalt alone

Impact of bedside lung ultrasound on physician clinical decision-making in an emergency department in Nepal

Background Lung ultrasound is an effective tool for the evaluation of undifferentiated dyspnea in the emergency department. Impact of lung ultrasound on clinical decisions for the evaluation of patients with dyspnea in resource-limited settings is not well-known. The objective of this study was to evaluate the impact of lung ultrasound on clinical decision-making for patients presenting with dyspnea to an emergency department in the resource-limited setting of Nepal. Methods A prospective, cross-sectional study of clinicians working in the Patan Hospital Emergency Department was performed. Clinicians performed lung ultrasounds on patients presenting with dyspnea and submitted ultrasounds with their pre-test diagnosis, lung ultrasound interpretation, post-test diagnosis, and any change in management. Results Twenty-two clinicians participated in the study, completing 280 lung ultrasounds. Diagnosis changed in 124 (44.3%) of patients with dyspnea. Clinicians reported a change in management based on the lung ultrasound in 150 cases (53.6%). Of the changes in management, the majority involved treatment (83.3%) followed by disposition (13.3%) and new consults (2.7%). Conclusions In an emergency department in Nepal, bedside lung ultrasound had a significant impact on physician clinical decision-making, especially on patient diagnosis and treatment

Emergency Physicians Are Able to Detect Right Ventricular Dilation With Good Agreement Compared to Cardiology

Objective Focused cardiac ultrasound (FOCUS) is a useful tool in evaluating patients presenting to the emergency department (ED) with acute dyspnea. Prior work has shown that right ventricular (RV) dilation is associated with repeat hospitalizations and shorter life expectancy. Traditionally, RV assessment has been evaluated by cardiologist-interpreted comprehensive echocardiography. The primary goal of this study was to determine the inter-rater reliability between emergency physicians (EPs) and a cardiologist for determining RV dilation on FOCUS performed on ED patients with acute dyspnea. Methods This was a prospective, observational study at two urban academic EDs; patients were enrolled if they had acute dyspnea and a computed tomographic pulmonary angiogram without acute disease. All patients had an EP-performed FOCUS to assess for RV dilation. RV dilation was defined as an RV to left ventricular ratio greater than 1. FOCUS interpretations were compared to a blinded cardiologist FOCUS interpretation using agreement and kappa statistics. Results Of 84 FOCUS examinations performed on 83 patients, 17% had RV dilation. Agreement and kappa, for EP-performed FOCUS for RV dilation were 89% (95% confidence interval [CI] 80–95%) and 0.68 (95% CI 0.48–0.88), respectively. Conclusions Emergency physician sonographers are able to detect RV dilation with good agreement when compared to cardiology. These results support the wider use of EP-performed FOCUS to evaluate for RV dilation in ED patients with dyspnea

Derivation of a screening tool to identify patients with right ventricular dysfunction or tricuspid regurgitation after negative computerized tomographic pulmonary angiography of the chest

Many dyspneic patients who undergo computerized tomographic pulmonary angiography (CTPA) for presumed acute pulmonary embolism (PE) have no identified cause for their dyspnea yet have persistent symptoms, leading to more CTPA scanning. Right ventricular (RV) dysfunction or overload can signal treatable causes of dyspnea. We report the rate of isolated RV dysfunction or overload after negative CTPA and derive a clinical decision rule (CDR). We performed secondary analysis of a multicenter study of diagnostic accuracy for PE. Inclusion required persistent dyspnea and no PE. Echocardiography was ordered at clinician discretion. A characterization of isolated RV dysfunction or overload required normal left ventricular function and RV hypokinesis, or estimated RV systolic pressure of at least 40 mmHg. The CDR was derived from bivariate analysis of 97 candidate variables, followed by multivariate logistic regression. Of 647 patients, 431 had no PE and persistent dyspnea, and 184 (43%) of these 431 had echocardiography ordered. Of these, 64 patients (35% [95% confidence interval (CI): 28%-42%]) had isolated RV dysfunction or overload, and these patients were significantly more likely to have a repeat CTPA within 90 days (P = .02, [Formula: see text] test). From univariate analysis, 4 variables predicted isolated RV dysfunction: complete right bundle branch block, normal CTPA scan, active malignancy, and CTPA with infiltrate, the last negatively. Logistic regression found only normal CTPA scanning significant. The final rule (persistent dyspnea + normal CTPA scan) had a positive predictive value of 53% (95% CI: 37%-69%). We conclude that a simple CDR consisting of persistent dyspnea plus a normal CTPA scan predicts a high probability of isolated RV dysfunction or overload on echocardiography

Stereodivergent cyclopropanation of unactivated alkenes with heme proteins

Cyclopropyl motifs are present in a variety of compounds important to pharmaceutical, agrochemical, and fragrance industries. The asymmetric synthesis of cyclopropanes is often performed under harsh conditions with toxic, precious metal chiral catalysts. In 2013, the first example of biocatalytic alkene cyclopropanation was reported, using an engineered cytochrome P450 enzyme [1]. Since then, several heme proteins were reported to cyclopropanate a variety of styrenyl alkenes [2], but none have been shown to asymmetrically cyclopropanate more challenging substrates such as unactivated, aliphatic alkenes using the native iron-heme cofactor. Here we report that heme proteins can cyclopropanate unactivated alkenes and that stereoselectivity and activity can be tuned by directed evolution. A few rounds of site-saturation mutagenesis and screening yielded four protein variants with high enantio- and diastereoselectivity for complementary isomers, enabling stereodivergent synthesis of aliphatic cyclopropanes. These iron-porphyrin proteins are fully genetically encoded, and the reactions can be performed under mild, aqueous conditions with whole cells or purified protein. The protein enhances the activity of the native iron-heme cofactor, giving access to a broad array of cyclopropanated products. This example showcases the ability to quickly and efficiently engineer proteins for non-natural biocatalytic function. [1] P.S. Coelho, E.M. Brustad, A. Kannan, F.H. Arnold, Olefin cyclopropanation via carbene transfer catalyzed by engineered cytochrome P450 enzymes., Science. 339 (2013) 307–10. [2] O.F. Brandenberg, R. Fasan, F.H. Arnold, Exploiting and engineering hemoproteins for abiological carbene and nitrene transfer reactions, Curr. Opin. Biotechnol. 38 (2017) in press

Independent evaluation of a simple clinical prediction rule to identify right ventricular dysfunction in patients with shortness of breath

BACKGROUND: Many patients have unexplained persistent dyspnea after negative computed tomographic pulmonary angiography (CTPA). We hypothesized that many of these patients have isolated right ventricular (RV) dysfunction from treatable causes. We previously derived a clinical decision rule (CDR) for predicting RV dysfunction consisting of persistent dyspnea and normal CTPA, finding that 53% of CDR-positive patients had isolated RV dysfunction. Our goal is to validate this previously derived CDR by measuring the prevalence of RV dysfunction and outcomes in dyspneic emergency department patients. METHODS: A secondary analysis of a prospective observational multicenter study that enrolled patients presenting with suspected PE was performed. We included patients with persistent dyspnea, a nonsignificant CTPA, and formal echo performed. Right ventricular dysfunction was defined as RV hypokinesis and/or dilation with or without moderate to severe tricuspid regurgitation. RESULTS: A total of 7940 patients were enrolled. Two thousand six hundred sixteen patients were analyzed after excluding patients without persistent dyspnea and those with a significant finding on CTPA. One hundred ninety eight patients had echocardiography performed as standard care. Of those, 19% (95% confidence interval [CI], 14%-25%) and 33% (95% CI, 25%-42%) exhibited RV dysfunction and isolated RV dysfunction, respectively. Patients with isolated RV dysfunction or overload were more likely than those without RV dysfunction to have a return visit to the emergency department within 45 days for the same complaint (39% vs 18%; 95% CI of the difference, 4%-38%). CONCLUSION: This simple clinical prediction rule predicted a 33% prevalence of isolated RV dysfunction or overload. Patients with isolated RV dysfunction had higher recidivism rates and a trend toward worse outcomes

Lung ultrasound training and evaluation for proficiency among physicians in a low-resource setting

Background: Lung ultrasound (LUS) is helpful for the evaluation of patients with dyspnea in the emergency department (ED). However, it remains unclear how much training and how many LUS examinations are needed for ED physicians to obtain proficiency. The objective of this study was to determine the threshold number of LUS physicians need to perform to achieve proficiency for interpreting LUS on ED patients with dyspnea. Methods: A prospective study was performed at Patan Hospital in Nepal, evaluating proficiency of physicians novice to LUS. After eight hours of didactics and hands-on training, physicians independently performed and interpreted ultrasounds on patients presenting to the ED with dyspnea. An expert sonographer blinded to patient data and LUS interpretation reviewed images and provided an expert interpretation. Interobserver agreement was performed between the study physician and expert physician interpretation. Cumulative sum analysis was used to determine the number of scans required to attain an acceptable level of training. Results: Nineteen physicians were included in the study, submitting 330 LUS examinations with 3288 lung zones. Eighteen physicians (95%) reached proficiency. Physicians reached proficiency for interpreting LUS accurately when compared to an expert after 4.4 (SD 2.2) LUS studies for individual zone interpretation and 4.8 (SD 2.3) studies for overall interpretation, respectively. Conclusions: Following 1 day of training, the majority of physicians novice to LUS achieved proficiency with interpretation of lung ultrasound after less than five ultrasound examinations performed independently

Interpretation and application of carbon isotope ratios in freshwater diatom silica

Carbon incorporated into diatom frustule walls is protected from degradation enabling analysis for carbon isotope composition (δ13Cdiatom). This presents potential for tracing carbon cycles via a single photosynthetic host with well-constrained ecophysiology. Improved understanding of environmental processes controlling carbon delivery and assimilation is essential to interpret changes in freshwater δ13Cdiatom. Here relationships between water chemistry and δ13Cdiatom from contemporary regional data sets are investigated. Modern diatom and water samples were collected from river catchments within England and lake sediments from across Europe. The data suggest dissolved, biogenically produced carbon supplied proportionately to catchment productivity was critical in the rivers and soft water lakes. However, dissolved carbon from calcareous geology overwhelmed the carbon signature in hard water catchments. Both results demonstrate carbon source characteristics were the most important control on δ13Cdiatom, with a greater impact than productivity. Application of these principles was made to a sediment record from Lake Tanganyika. δ13Cdiatom co-varied with δ13Cbulk through the last glacial and Holocene. This suggests carbon supply was again dominant and exceeded authigenic demand. This first systematic evaluation of contemporary δ13Cdiatom controls demonstrates that diatoms have the potential to supply a record of carbon cycling through lake catchments from sediment records over millennial timescales

Measurement Instruments for Integration within Children and Young People Healthcare Systems and Networks: A Rapid Review of the International Literature

Introduction: Robust measures of integration are essential for assessment of the development, design and implementation of integration within healthcare systems. This review aimed to identify measurement instruments for integration within children and young people’s (CYP) healthcare systems (PROSPERO registration number CRD42021235383).Methods: We searched electronic databases (PubMED and Ovid Embase) using three main concepts: ‘(integrated care) AND (child population) AND (measurement)’, along with additional searches.Results: Fifteen studies describing 16 measurement instruments were eligible for inclusion. The majority of studies were conducted in the USA. There was a diversity of health conditions included in the studies. The most frequent type of assessment used was a questionnaire (11 identified), but interviews, patient data and healthcare records, and focus groups were also used. Integration outcomes assessed were quality of care coordination, quality of collaboration, continuity of care, completeness of care, structure of care, quality of communication, and local implementation of integrated care.Conclusion: A variety of instruments for the measurement of integration within CYP healthcare systems were identified. Further work on the standardisation of integrated care measures would be valuable; however, it is important that instruments and measures meet the needs of specific settings, populations and conditions being studied