Thoracic aortic microcalcification activity in combined positron emission tomography and magnetic resonance imaging.

INTRODUCTION: Non-invasive detection of pathological changes in thoracic aortic disease remains an unmet clinical need particularly for patients with congenital heart disease. Positron emission tomography combined with magnetic resonance imaging (PET-MRI) could provide a valuable low-radiation method of aortic surveillance in high-risk groups. Quantification of aortic microcalcification activity using sodium [18F]fluoride holds promise in the assessment of thoracic aortopathies. We sought to evaluate aortic sodium [18F]fluoride uptake in PET-MRI using three methods of attenuation correction compared to positron emission tomography computed tomography (PET-CT) in patients with bicuspid aortic valve, METHODS: Thirty asymptomatic patients under surveillance for bicuspid aortic valve disease underwent sodium [18F]fluoride PET-CT and PET-MRI of the ascending thoracic aorta during a single visit. PET-MRI data were reconstructed using three iterations of attenuation correction (Dixon, radial gradient recalled echo with two [RadialVIBE-2] or four [RadialVIBE-4] tissue segmentation). Images were qualitatively and quantitatively analysed for aortic sodium [18F]fluoride uptake on PET-CT and PET-MRI. RESULTS: Aortic sodium [18F]fluoride uptake on PET-MRI was visually comparable with PET-CT using each reconstruction and total aortic standardised uptake values on PET-CT strongly correlated with each PET-MRI attenuation correction method (Dixon R = 0.70; RadialVIBE-2 R = 0.63; RadialVIBE-4 R = 0.64; p < 0.001 for all). Breathing related artefact between soft tissue and lung were detected using Dixon and RadialVIBE-4 but not RadialVIBE-2 reconstructions, with the presence of this artefact adjacent to the atria leading to variations in blood pool activity estimates. Consequently, quantitative agreements between radiotracer activity on PET-CT and PET-MRI were most consistent with RadialVIBE-2. CONCLUSION: Ascending aortic microcalcification analysis in PET-MRI is feasible with comparable findings to PET-CT. RadialVIBE-2 tissue attenuation correction correlates best with the reference standard of PET-CT and is less susceptible to artefact. There remain challenges in segmenting tissue types in PET-MRI reconstructions, and improved attenuation correction methods are required.

Noninvasive In Vivo Thrombus Imaging in Patients With Ischemic Stroke or Transient Ischemic Attack-Brief Report.

BACKGROUND: 18F-GP1 is a novel positron-emitting radiotracer that is highly specific for activated platelets and thrombus. In a proof-of-concept study, we aimed to determine its potential clinical application in establishing the role and origin of thrombus in ischemic stroke. METHODS: Eleven patients with recent ischemic stroke (n=9) or transient ischemic attack (n=2) underwent 18F-GP1 positron emission tomography and computed tomography angiography at a median of 11 (range, 2-21) days from symptom onset. 18F-GP1 uptake (maximum target-to-background ratio) was assessed in the carotid arteries and brain. RESULTS: 18F-GP1 uptake was identified in 10 of 11 patients: 4 in the carotid arteries only, 3 in the brain only, and 3 in both the brain and carotid arteries. In those with carotid uptake, 4 participants had >50% stenosis and 3 had nonstenotic disease. One case had bilateral stenotic disease (>70%), but only the culprit carotid artery demonstrated 18F-GP1 uptake. The average uptake was higher in the culprit (median maximum target-to-background ratio, 1.55 [interquartile range, 1.26-1.82]) compared with the contralateral nonculprit carotid artery (maximum target-to-background ratio, 1.22 [1.19-1.6]). In those with brain 18F-GP1 uptake (maximum target-to-background ratio, 6.45 [4.89-7.65]), areas of acute infarction on computed tomography correlated with brain 18F-GP1 uptake in 6 cases. Ex vivo autoradiography of postmortem infarcted brain tissue showed focal uptake corresponding to intraluminal thrombus within the culprit vessel and downstream microvasculature. There was also evidence of diffuse uptake within some of the infarcted brain tissue reflecting parenchymal petechial hemorrhage. CONCLUSIONS: 18F-GP1 positron emission tomography and computed tomography angiography is a novel noninvasive method of identifying in vivo cerebrovascular thrombosis, which holds major promise in understanding the role and origin of thrombosis in stroke. REGISTRATION: URL: https://www. CLINICALTRIALS: gov; Unique identifier: NCT03943966.

Tau induces blood vessel abnormalities and angiogenesis-related gene expression in P301L transgenic mice and human Alzheimer's disease.

Mixed pathology, with both Alzheimer's disease and vascular abnormalities, is the most common cause of clinical dementia in the elderly. While usually thought to be concurrent diseases, the fact that changes in cerebral blood flow are a prominent early and persistent alteration in Alzheimer's disease raises the possibility that vascular alterations and Alzheimer pathology are more directly linked. Here, we report that aged tau-overexpressing mice develop changes to blood vessels including abnormal, spiraling morphologies; reduced blood vessel diameters; and increased overall blood vessel density in cortex. Blood flow in these vessels was altered, with periods of obstructed flow rarely observed in normal capillaries. These changes were accompanied by cortical atrophy as well as increased expression of angiogenesis-related genes such as Vegfa, Serpine1, and Plau in CD31-positive endothelial cells. Interestingly, mice overexpressing nonmutant forms of tau in the absence of frank neurodegeneration also demonstrated similar changes. Furthermore, many of the genes we observe in mice are also altered in human RNA datasets from Alzheimer patients, particularly in brain regions classically associated with tau pathology such as the temporal lobe and limbic system regions. Together these data indicate that tau pathological changes in neurons can impact brain endothelial cell biology, altering the integrity of the brain's microvasculature.

Estimands in practice: Bridging the gap between study objectives and statistical analysis.

The International Council for Harmonisation (ICH) guideline E9 Statistical Principles for Clinical Trials (1) was issued in 1998. In October 2014, an addendum to ICH E9 was proposed on statistical principles relating to estimands and sensitivity analyses. The final version of the addendum to ICH E9 (R1) (2) was issued in November 2019. This virtual edition of Pharmaceutical Statistics takes a closer look at some of the progress that has been made since 2018 when implementing the estimand framework within clinical research. The articles discussed in this virtual issue are not new, but a compilation from previous issues. This specific article will act as a refresher for those not familiar with the topic and discuss the ABCs of estimands and their proposed deployment for improving the quality of clinical research. An overview of the more recent Pharmaceutical Statistics articles on estimands will be provided, signifying areas where progress have been made. The articles should be considered as contributions to the ongoing discussions rather than the final word. Finally, a personal perspective on the estimand success story and remaining challenges with proposed solutions will be discussed.

20D-dynamic representation of protein sequences.

A new method of comparison of protein sequences has been formulated. The sequence of amino acids is represented by a set of point masses in a 20D space. The distribution of points in the space is obtained by applying the method of a walk in the 20D space. Projections of the 20D representation into 2D or 3D spaces illustrate the distribution of particular amino acids along the sequence. 20D moments of inertia are proposed as new descriptors of protein sequences.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.

Atomistic modeling of a KRT35/KRT85 keratin dimer: folding in aqueous solution and unfolding under tensile load.

We present an atomistic model of a full KRT35/KRT85 dimer, a fundamental building block of human hair. For both monomers initial structures were generated using empirical tools based on homology considerations, followed by the formulation of a naiïve dimer model from docking the monomers in vacuum. Relaxation in aqueous solution was then explored from molecular dynamics simulation. Driven by hydrophobic segregation and protein-protein hydrogen bonding relaxation dynamics result in a folded dimer arrangement which shows a striking encounter of cystein groups. Our simulations hence suggests that (i) cystein groups in the coil regions of keratin are well suited to establish disulfide bonds between the two monomers that constitute the dimer, and (ii) the particularly large number of cystein groups in the head and tail regions promotes the connection of dimers to establish meso- to macroscale fibers. Moreover, we show the molecular mechanisms of elastic and plastic deformation under tensile load. Upon elongation beyond the elastic regime, unfolding was identified as the exposure of hydrophobic moieties and the breaking of protein-protein hydrogen bonds. Therein, the step-wise character of the series of unfolding events leads to a broad regime of constant force in response to further elongation.

Noninvasive In Vivo Coronary Artery Thrombus Imaging.

BACKGROUND: The diagnosis and management of myocardial infarction are increasingly complex, and establishing the presence of intracoronary thrombosis has major implications for both the classification and treatment of myocardial infarction. OBJECTIVES: The aim of this study was to investigate whether positron emission tomographic (PET) and computed tomographic (CT) imaging could noninvasively detect in vivo thrombus formation in human coronary arteries using a novel glycoprotein IIb/IIIa receptor antagonist-based radiotracer, 18F-GP1. METHODS: In a single-center observational case-control study, patients with or without acute myocardial infarction underwent coronary 18F-GP1 PET/CT angiography. Coronary artery 18F-GP1 uptake was assessed visually and quantified using maximum target-to-background ratios. RESULTS: 18F-GP1 PET/CT angiography was performed in 49 patients with and 50 patients without acute myocardial infarction (mean age: 61 ± 9 years, 75% men). Coronary 18F-GP1 uptake was apparent in 39 of the 49 culprit lesions (80%) in patients with acute myocardial infarction. False negative results appeared to relate to time delays to scan performance and low thrombus burden in small-caliber distal arteries. On multivariable regression analysis, culprit vessel status was the only independent variable associated with higher 18F-GP1 uptake. Extracoronary cardiac 18F-GP1 findings included a high frequency of infarct-related intramyocardial uptake (35%) as well as left ventricular (8%) or left atrial (2%) thrombus. CONCLUSIONS: Coronary 18F-GP1 PET/CT angiography is the first noninvasive selective technique to identify in vivo coronary thrombosis in patients with acute myocardial infarction. This novel approach can further define the role and location of thrombosis within the heart and has the potential to inform the diagnosis, management, and treatment of patients with acute myocardial infarction. (In-Vivo Thrombus Imaging With 18F-GP1, a Novel Platelet PET Radiotracer [iThrombus]; NCT03943966).

18F-Sodium Fluoride Positron Emission Tomography and Computed Tomography in Acute Aortic Syndrome.

BACKGROUND: Acute aortic syndrome is associated with aortic medial degeneration. 18F-sodium fluoride (18F-NaF) positron emission tomography (PET) detects microscopic tissue calcification as a marker of disease activity. OBJECTIVES: In a proof-of-concept study, this investigation aimed to establish whether 18F-NaF PET combined with computed tomography (CT) angiography could identify aortic medial disease activity in patients with acute aortic syndrome. METHODS: Patients with aortic dissection or intramural hematomas and control subjects underwent 18F-NaF PET/CT angiography of the aorta. Aortic 18F-NaF uptake was measured at the most diseased segment, and the maximum value was corrected for background blood pool activity (maximum tissue-to-background ratio [TBRmax]). Radiotracer uptake was compared with change in aortic size and major adverse aortic events (aortic rupture, aorta-related death, or aortic repair) over 45 ± 13 months. RESULTS: Aortic 18F-NaF uptake co-localized with histologically defined regions of microcalcification and elastin disruption. Compared with control subjects, patients with acute aortic syndrome had increased 18F-NaF uptake (TBRmax: 1.36 ± 0.39 [n = 20] vs 2.02 ± 0.42 [n = 47] respectively; P < 0.001) with enhanced uptake at the site of intimal disruption (+27.5%; P < 0.001). 18F-NaF uptake in the false lumen was associated with aortic growth (+7.1 mm/year; P = 0.011), and uptake in the outer aortic wall was associated with major adverse aortic events (HR: 8.5 [95% CI: 1.4-50.4]; P = 0.019). CONCLUSIONS: In patients with acute aortic syndrome, 18F-NaF uptake was enhanced at sites of disease activity and was associated with aortic growth and clinical events. 18F-NaF PET/CT holds promise as a noninvasive marker of disease severity and future risk in patients with acute aortic syndrome. (18F Sodium Fluoride PET/CT in Acute Aortic Syndrome [FAASt]; NCT03647566).

18F-GP1 Positron Emission Tomography and Bioprosthetic Aortic Valve Thrombus.

BACKGROUND: Bioprosthetic valve thrombosis may have implications for valve function and durability. OBJECTIVES: Using a novel glycoprotein IIb/IIIa receptor radiotracer 18F-GP1, we investigated whether positron emission tomography (PET)-computed tomography (CT) could detect thrombus formation on bioprosthetic aortic valves. METHODS: Ex vivo experiments were performed on human platelets and explanted bioprosthetic aortic valves. In a prospective cross-sectional study, patients with either bioprosthetic or normal native aortic valves underwent echocardiography, CT angiography, and 18F-GP1 PET-CT. RESULTS: Flow cytometric analysis, histology, immunohistochemistry, and autoradiography demonstrated selective binding of 18F-GP1 to activated platelet glycoprotein IIb/IIIa receptors and thrombus adherent to prosthetic valves. In total, 75 participants were recruited: 53 with bioprosthetic valves (median time from implantation 37 months [IQR: 12-80 months]) and 22 with normal native aortic valves. Three participants had obstructive valve thrombosis, and a further 3 participants had asymptomatic hypoattenuated leaflet thickening on CT angiography. All bioprosthetic valves, but none of the native aortic valves, demonstrated focal 18F-GP1 uptake on the valve leaflets: median maximum target-to-background ratio 2.81 (IQR: 2.29-3.48) vs 1.43 (IQR: 1.28-1.53) (P < 0.001). Higher 18F-GP1 uptake was independently associated with duration of valve implantation and hypoattenuated leaflet thickening. All 3 participants with obstructive valve thrombosis were anticoagulated for 3 months, leading to resolution of their symptoms, improvement in mean valve gradients, and a reduction in 18F-GP1 uptake. CONCLUSIONS: Adherence of activated platelets is a common and sustained finding on bioprosthetic aortic valves. 18F-GP1 uptake is higher in the presence of thrombus, regresses with anticoagulation, and has potential use as an adjunctive clinical tool. (18F-GP1 PET-CT to Detect Bioprosthetic Aortic Valve Thrombosis; NCT04073875).

eXframe: reusable framework for storage, analysis and visualization of genomics experiments.

BACKGROUND: Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types. RESULTS: We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple data types including microarrays and next generation sequencing 3) query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples) and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients. CONCLUSION: The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications.

Building biomedical web communities using a semantically aware content management system.

Web-based biomedical communities are becoming an increasingly popular vehicle for sharing information amongst researchers and are fast gaining an online presence. However, information organization and exchange in such communities is usually unstructured, rendering interoperability between communities difficult. Furthermore, specialized software to create such communities at low cost-targeted at the specific common information requirements of biomedical researchers-has been largely lacking. At the same time, a growing number of biological knowledge bases and biomedical resources are being structured for the Semantic Web. Several groups are creating reference ontologies for the biomedical domain, actively publishing controlled vocabularies and making data available in Resource Description Framework (RDF) language. We have developed the Science Collaboration Framework (SCF) as a reusable platform for advanced structured online collaboration in biomedical research that leverages these ontologies and RDF resources. SCF supports structured 'Web 2.0' style community discourse amongst researchers, makes heterogeneous data resources available to the collaborating scientist, captures the semantics of the relationship among the resources and structures discourse around the resources. The first instance of the SCF framework is being used to create an open-access online community for stem cell research-StemBook (http://www.stembook.org). We believe that such a framework is required to achieve optimal productivity and leveraging of resources in interdisciplinary scientific research. We expect it to be particularly beneficial in highly interdisciplinary areas, such as neurodegenerative disease and neurorepair research, as well as having broad utility across the natural sciences.

Electron-vibron coupling in halogenated acenaphthenequinone upon O K-edge soft x-ray absorption.

We present high resolution oxygen K near-edge x-ray absorption spectra of the acenaphthenequinone (ANQ) derivative 3,8-dibromo-5,6-dichloro-ANQ (Br(2)Cl(2)-ANQ). The spectral features exhibit an almost identical vibronic fine structure compared to that shown by ANQ. The unequal distances of the vibronic levels as derived from the least-squares fit analysis of the vibronic progressions allows us to determine the anharmonicity of the excited state potentials involved. We conclude that a single vibrational progression couples to the resonant excitation of O 1s core electrons preferentially. Comparison of the two ANQ derivatives gives a clear indication that the vibronic mode corresponds to a C=O stretching mode, rather than coupling to a C-H mode as suggested previously. These conclusions are supported by density functional theory calculations.

Recognizing the value of software: a software citation guide.

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience. This article (and those community-specific versions) are aimed at authors citing software, including software developed by the authors or by others. We also include brief instructions on how software can be made citable, directing readers to more comprehensive guidance published elsewhere. The guidance presented in this article helps to support proper attribution and credit, reproducibility, collaboration and reuse, and encourages building on the work of others to further research.

A data citation roadmap for scholarly data repositories.

This article presents a practical roadmap for scholarly data repositories to implement data citation in accordance with the Joint Declaration of Data Citation Principles, a synopsis and harmonization of the recommendations of major science policy bodies. The roadmap was developed by the Repositories Expert Group, as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of FORCE11.org and the NIH-funded BioCADDIE ( https://biocaddie.org ) project. The roadmap makes 11 specific recommendations, grouped into three phases of implementation: a) required steps needed to support the Joint Declaration of Data Citation Principles, b) recommended steps that facilitate article/data publication workflows, and c) optional steps that further improve data citation support provided by data repositories. We describe the early adoption of these recommendations 18 months after they have first been published, looking specifically at implementations of machine-readable metadata on dataset landing pages.

The SWAN biomedical discourse ontology.

Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. SWAN (Semantic Web Applications in Neuromedicine) is an interdisciplinary project to develop a practical, common, semantically structured, framework for biomedical discourse initially applied, but not limited, to significant problems in Alzheimer Disease (AD) research. The SWAN ontology has been developed in the context of building a series of applications for biomedical researchers, as well as in extensive discussions and collaborations with the larger bio-ontologies community. In this paper, we present and discuss the SWAN ontology of biomedical discourse. We ground its development theoretically, present its design approach, explain its main classes and their application, and show its relationship to other ongoing activities in biomedicine and bio-ontologies.

Determinants of response to fluticasone propionate and salmeterol/fluticasone propionate combination in the Gaining Optimal Asthma controL study.

BACKGROUND: During the Gaining Optimal Asthma controL study, 3416 patients with uncontrolled asthma were randomized to receive salmeterol/fluticasone propionate combination (SFC) or fluticasone propionate (FP) for 1 year. Approximately two thirds of patients achieved well-controlled (WC) asthma, and one third continued to have asthma that was not well controlled (NWC). OBJECTIVE: This analysis aimed to (1) identify factors influencing treatment response and (2) assess the clinical benefits of SFC and FP in patients with NWC asthma. METHODS: Logistic regression analysis was used to investigate whether covariates influenced the achievement of at least WC asthma in the study population. In patients with NWC asthma, predefined criteria were used to assess improvements in 6 clinical outcomes. RESULTS: Factors affecting the probability of having NWC asthma included smoking status (current vs never: odds ratio [OR], 2.757; 95% CI, 2.061-3.689; P < .0001; former vs never: OR, 1.274; 95% CI, 1.031-1.574; P = 0.0273), sex (women vs men: OR, 0.652; 95% CI, 0.527-0.806; P < .0001), history of inhaled corticosteroid use (no history vs history: OR, 0.546; 95% CI, 0.437-0.683; P < .0001), and treatment (FP vs SFC: OR, 1.972; 95% CI, 1.686-2.308; P < .0001). Of patients with NWC asthma, 86% to 96% showed improvements in 1 or more clinical outcomes. CONCLUSION: It is imperative for good asthma control that patients stop smoking. Patients who did not have at least WC asthma demonstrated clinical improvements in individual asthma outcomes. CLINICAL IMPLICATIONS: Although not all patients can achieve guideline-defined control, long-term treatment with SFC or FP is associated with clinical improvements in nearly all patients, regardless of smoking history or inhaled corticosteroid use.

Cross-sectional analysis of UK research studies in 2015: results from a scoping project with the UK Health Research Authority.

OBJECTIVES: To determine whether data on research studies held by the UK Health Research Authority (HRA) could be summarised automatically with minimal manual intervention. There are numerous initiatives to reduce research waste by improving the design, conduct, analysis and reporting of clinical studies. However, quantitative data on the characteristics of clinical studies and the impact of the various initiatives are limited. DESIGN: Feasibility study, using 1 year of data. SETTING: We worked with the HRA on a pilot study using research applications submitted for UK-wide ethical review. We extracted into a single dataset, information held in anonymised XML files by the Integrated Research Application System (IRAS) and the HRA Assessment Review Portal (HARP). Research applications from 2014 to 2016 were provided. We used standard text extraction methods to assess information held in free-text fields. We use simple, descriptive methods to summarise the research activities that we extracted. PARTICIPANTS: Not applicable-records-based study INTERVENTIONS: Not applicable. PRIMARY AND SECONDARY OUTCOME MEASURES: Feasibility of extraction and processing. RESULTS: We successfully imported 1775 non-duplicate research applications from the XML files into a single database. Of these, 963 were randomised controlled trials and 812 were other studies. Most studies received a favourable opinion. There was limited patient and public involvement in the studies. Most, but not all, studies were planned for publication of results. Novel study designs (eg, adaptive and Bayesian designs) were infrequently reported. CONCLUSIONS: We have demonstrated that the data submitted from IRAS to the HRA and its HARP system are accessible and can be queried for information. We strongly encourage the development of fully resourced collaborative projects to further this work. This would aid understanding of how study characteristics change over time and across therapeutic areas, as well as the progress of initiatives to improve the quality and relevance of research studies.

A data citation roadmap for scientific publishers.

This article presents a practical roadmap for scholarly publishers to implement data citation in accordance with the Joint Declaration of Data Citation Principles (JDDCP), a synopsis and harmonization of the recommendations of major science policy bodies. It was developed by the Publishers Early Adopters Expert Group as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of FORCE11.org and the NIH BioCADDIE program. The structure of the roadmap presented here follows the "life of a paper" workflow and includes the categories Pre-submission, Submission, Production, and Publication. The roadmap is intended to be publisher-agnostic so that all publishers can use this as a starting point when implementing JDDCP-compliant data citation. Authors reading this roadmap will also better know what to expect from publishers and how to enable their own data citations to gain maximum impact, as well as complying with what will become increasingly common funder mandates on data transparency.