Cytoscape: the network visualization tool for GenomeSpace workflows.

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013

Comparison of the High-Temperature Oxidation Behavior of Subsolvus and Supersolvus Treated Advanced Powder Metallurgy Disk Alloys

No abstract availabl

Usability-Focused Development and Usage of NeoTree-Beta, an App for Newborn Care in a Low-Resource Neonatal Unit, Malawi

Background: Neonatal mortality is high in low-resource settings. NeoTree is a digital intervention for neonatal healthcare professionals (HCPs) aiming to achieve data-driven quality improvement and improved neonatal survival in low-resource hospitals. Optimising usability with end-users could help digital health interventions succeed beyond pilot stages in low-resource settings. Usability is the quality of a user's experience when interacting with an intervention, encompassing their effectiveness, efficiency, and overall satisfaction. Objective: To evaluate the usability and usage of NeoTree beta-app and conduct Agile usability-focused intervention development. Method: A real-world pilot of NeoTree beta-app was conducted over 6 months at Kamuzu Central Hospital neonatal unit, Malawi. Prior to deployment, think-aloud interviews were conducted to guide nurses through the app whilst voicing their thoughts aloud (n = 6). System Usability Scale (SUS) scores were collected before the implementation of NeoTree into usual clinical care and 6 months after implementation (n = 8 and 8). During the pilot, real-world user-feedback and user-data were gathered. Feedback notes were subjected to thematic analysis within an Agile “product backlog.” For usage, number of users, user-cadre, proportion of admissions/outcomes recorded digitally, and median app-completion times were calculated. Results: Twelve overarching usability themes generated 57 app adjustments, 39 (68%) from think aloud analysis and 18 (32%) from the real-world testing. A total of 21 usability themes/issues with corresponding app features were produced and added to the app. Six themes relating to data collection included exhaustiveness of data schema, prevention of errors, ease of progression, efficiency of data entry using shortcuts, navigation of user interface (UI), and relevancy of content. Six themes relating to the clinical care included cohesion with ward process, embedded education, locally coherent language, adaptability of user-interface to available resources, and printout design to facilitate handover. SUS scores were above average (88.1 and 89.4 at 1 and 6 months, respectively). Ninety-three different HCPs of 5 cadres, recorded 1,323 admissions and 1,197 outcomes over 6 months. NeoTree achieved 100% digital coverage of sick neonates admitted. Median completion times were 16 and 8 min for admissions and outcomes, respectively. Conclusions: This study demonstrates optimisation of a digital health app in a low-resource setting and could inform other similar usability studies apps in similar settings

The Effect of Prior Exposures on the Notched Fatigue Behavior of Disk Superalloy ME3

Environmental attack has the potential to limit turbine disk durability, particularly in next generation engines which will run hotter; there is a need to understand better oxidation at potential service conditions and develop models that link microstructure to fatigue response. More efficient gas turbine engine designs will require higher operating temperatures. Turbine disks are regarded as critical flight safety components; a failure is a serious hazard. Low cycle fatigue is an important design criteria for turbine disks. Powder metallurgy alloys, like ME3, have led to major improvements in temperature performance through refractory additions (e.g. Mo,W) at the expense of environmental resistance (Al, Cr). Service conditions for aerospace disks can produce major cycle periods extending from minutes to hours and days with total service times exceeding 1,000 hours in aerospace applications. Some of the effects of service can be captured by extended exposures at elevated temperature prior to LCF testing. Some details of the work presented here have been published

N=2 supergravity in five dimensions revisited

We construct matter-coupled N=2 supergravity in five dimensions, using the superconformal approach. For the matter sector we take an arbitrary number of vector-, tensor- and hyper-multiplets. By allowing off-diagonal vector-tensor couplings we find more general results than currently known in the literature. Our results provide the appropriate starting point for a systematic search for BPS solutions, and for applications of M-theory compactifications on Calabi-Yau manifolds with fluxes.Comment: 35 pages; v.2: A sign changed in a bilinear fermion term in (5.7

Software development process of Neotree - a data capture and decision support system to improve newborn healthcare in low-resource settings

The global priority of improving neonatal survival could be tackled through the universal implementation of cost-effective maternal and newborn health interventions. Despite 90% of neonatal deaths occurring in low-resource settings, very few evidence-based digital health interventions exist to assist healthcare professionals in clinical decision-making in these settings. To bridge this gap, Neotree was co-developed through an iterative, user-centered design approach in collaboration with healthcare professionals in the UK, Bangladesh, Malawi, and Zimbabwe. It addresses a broad range of neonatal clinical diagnoses and healthcare indicators as opposed to being limited to specific conditions and follows national and international guidelines for newborn care. This digital health intervention includes a mobile application (app) which is designed to be used by healthcare professionals at the bedside. The app enables real-time data capture and provides education in newborn care and clinical decision support via integrated clinical management algorithms. Comprehensive routine patient data are prospectively collected regarding each newborn, as well as maternal data and blood test results, which are used to inform clinical decision making at the bedside. Data dashboards provide healthcare professionals and hospital management a near real-time overview of patient statistics that can be used for healthcare quality improvement purposes. To enable this workflow, the Neotree web editor allows fine-grained customization of the mobile app. The data pipeline manages data flow from the app to secure databases and then to the dashboard. Implemented in three hospitals in two countries so far, Neotree has captured routine data and supported the care of over 21,000 babies and has been used by over 450 healthcare professionals. All code and documentation are open source, allowing adoption and adaptation by clinicians, researchers, and developers

Implementing a Cross-Institutional Staffing Model for Curating Research Data

Poster presented at the Research Data Alliance (RDA) 11th Plenary in Berlin, Germany.“Launching the Data curation Network: A cross-institutional staffing model for curating research data” funded 2018-2021 by the Alfred P. Sloan Foundation grant G-2018-10072

Integrating sequence and structural biology with DAS.

BACKGROUND: The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. RESULTS: Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources. CONCLUSION: Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

American Step-Up and Step-Down Default Swaps under Levy Models

This paper studies the valuation of a class of default swaps with the embedded option to switch to a different premium and notional principal anytime prior to a credit event. These are early exercisable contracts that give the protection buyer or seller the right to step-up, step-down, or cancel the swap position. The pricing problem is formulated under a structural credit risk model based on Levy processes. This leads to the analytic and numerical studies of several optimal stopping problems subject to early termination due to default. In a general spectrally negative Levy model, we rigorously derive the optimal exercise strategy. This allows for instant computation of the credit spread under various specifications. Numerical examples are provided to examine the impacts of default risk and contractual features on the credit spread and exercise strategy.Comment: 35 pages, 5 figure