Enforcing public data archiving policies in academic publishing: A study of ecology journals

To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage or mandate data sharing within and across disciplines, with varying degrees of success. Academic journals in ecology and evolution have adopted several types of public data archiving policies requiring authors to make data underlying scholarly manuscripts freely available. Yet anecdotes from the community and studies evaluating data availability suggest that these policies have not obtained the desired effects, both in terms of quantity and quality of available datasets. We conducted a qualitative, interview-based study with journal editorial staff and other stakeholders in the academic publishing process to examine how journals enforce data archiving policies. We specifically sought to establish who editors and other stakeholders perceive as responsible for ensuring data completeness and quality in the peer review process. Our analysis revealed little consensus with regard to how data archiving policies should be enforced and who should hold authors accountable for dataset submissions. Themes in interviewee responses included hopefulness that reviewers would take the initiative to review datasets and trust in authors to ensure the completeness and quality of their datasets. We highlight problematic aspects of these thematic responses and offer potential starting points for improvement of the public data archiving process.Comment: 35 pages, 1 figure, 1 tabl

Hack Weeks as a model for Data Science Education and Collaboration

Across almost all scientific disciplines, the instruments that record our experimental data and the methods required for storage and data analysis are rapidly increasing in complexity. This gives rise to the need for scientific communities to adapt on shorter time scales than traditional university curricula allow for, and therefore requires new modes of knowledge transfer. The universal applicability of data science tools to a broad range of problems has generated new opportunities to foster exchange of ideas and computational workflows across disciplines. In recent years, hack weeks have emerged as an effective tool for fostering these exchanges by providing training in modern data analysis workflows. While there are variations in hack week implementation, all events consist of a common core of three components: tutorials in state-of-the-art methodology, peer-learning and project work in a collaborative environment. In this paper, we present the concept of a hack week in the larger context of scientific meetings and point out similarities and differences to traditional conferences. We motivate the need for such an event and present in detail its strengths and challenges. We find that hack weeks are successful at cultivating collaboration and the exchange of knowledge. Participants self-report that these events help them both in their day-to-day research as well as their careers. Based on our results, we conclude that hack weeks present an effective, easy-to-implement, fairly low-cost tool to positively impact data analysis literacy in academic disciplines, foster collaboration and cultivate best practices.Comment: 15 pages, 2 figures, submitted to PNAS, all relevant code available at https://github.com/uwescience/HackWeek-Writeu

Robust Local Explanations for Healthcare Predictive Analytics: An Application to Fragility Fracture Risk Modeling

With recent advancements in data analytics, healthcare predictive analytics (HPA) is garnering growing interest among practitioners and researchers. However, it is risky to blindly accept the results and users will not accept the HPA model if transparency is not guaranteed. To address this challenge, we propose the RObust Local EXplanations (ROLEX) method, which provides robust, instance-level explanations for any HPA model. The applicability of the ROLEX method is demonstrated using the fragility fracture prediction problem. Analysis with a large real-world dataset demonstrates that our method outperforms state-of-the-art methods in terms of local fidelity. The ROLEX method is applicable to various types of HPA problems beyond the fragility fracture problem. It is applicable to any type of supervised learning model and provides fine-grained explanations that can improve understanding of the phenomenon of interest. Finally, we discuss theoretical implications of our study in light of healthcare IS, big data, and design science

Functional outcome of minimally invasive posterior stabilisation in dorsal and lumbar spine fractures

This record was migrated from the OpenDepot repository service in June, 2017 before shutting down

Development of a Finite Element Model for the study of impact behaviour of sandwich panels

Sandwich structures based on Fibre Reinforced Polymer (FRP) skins bonded to either side of a low density core material, such as polymer foams are finding increasing use in aerospace and marine industries. It is necessary to study the impact response of sandwich structures in order to ensure the reliability and safety of these structures. It is particularly important due to the susceptibility of sandwich structures to damage, including Barely Visible Impact Damage (BVID) caused by foreign object impact. The study of the behaviour of sandwich structures to impact loading is usually accomplished by experimental testing, for example in a drop tower setup. However, experiments are time consuming and expensive. It requires instruments such as strain gauges and high speed cameras to find stress and deformation state of the structure. Experimental costs can be reduced by using numerical methods, which can help in predicting the energy absorption and peak loads for a given combination of materials and geometry. A finite element (FE) analysis provides the capability to model the impact event, including the contribution of the individual elements of the sandwich panel to the energy absorption. The damage inflicted on a sandwich plate is a complex phenomenon due to the different damage mechanisms involved: matrix cracking, tensile and compressive fibre breakage, delamination, core crushing and shear, etc. An accurate FE analysis requires including complex material models capable of capturing the mechanical behaviour of the facesheets as well as the core. The purpose of this work is to develop a numerical model of sandwich panels with Kevlar FRP facesheets and core of Rohacell foam, subjected to low velocity impact loading. An approach for modelling sandwich structures in the commercial finite element code LS-DYNA is presented. The force and energy absorption characteristics of the sandwich structure are analysed

Context-Specific Target Definition in Influenza A Virus Hemagglutinin-Glycan Receptor Interactions

Protein-glycan interactions are important regulators of a variety of biological processes, ranging from immune recognition to anticoagulation. An important area of active research is directed toward understanding the role of host cell surface glycans as recognition sites for pathogen protein receptors. Recognition of cell surface glycans is a widely employed strategy for a variety of pathogens, including bacteria, parasites, and viruses. We present here a representative example of such an interaction: the binding of influenza A hemagglutinin (HA) to specific sialylated glycans on the cell surface of human upper airway epithelial cells, which initiates the infection cycle. We detail a generalizable strategy to understand the nature of protein-glycan interactions both structurally and biochemically, using HA as a model system. This strategy combines a top-down approach using available structural information to define important contacts between glycans and HA, with a bottom-up approach using data-mining and informatics approaches to identify the common motifs that distinguish glycan binders from nonbinders. By probing protein-glycan interactions simultaneously through top-down and bottom-up approaches, we can scientifically validate a series of observations. This in turn provides additional confidence and surmounts known challenges in the study of protein-glycan interactions, such as accounting for multivalency, and thus truly defines concepts such as specificity, affinity, and avidity. With the advent of new technologies for glycomics—including glycan arrays, data-mining solutions, and robust algorithms to model protein-glycan interactions—we anticipate that such combination approaches will become tractable for a wide variety of protein-glycan interactions.National Institute of General Medical Sciences (U.S.) (GM 57073)National Institute of General Medical Sciences (U.S.) (U54 GM62116)Singapore-MIT Alliance for Research and Technolog

Outcome analysis of surgically managed unstable burst fracture

Background:Burst fractures are common injuries of dorsolumbar spine. In indicated cases, surgery is the treatment of choice. Significant controversy exists regarding surgical intervention for these fractures. Posterior decompression, anterior decompression and instrumentation, and combined anterior decompression and posterior instrumentation have been recommended in various studies. Here we are going to evaluate unstable burst fractures of thoracic and lumbar spine treated by isolated anterior decompression and instrumented fusion with TSM-Bone graft composite.Methods: Prospective study of thirty-six cases of unstable fracture of thoracic and lumbar spine treated in Sri Ramachandra Medical centre from January 2011 to January 2014. The inclusion criteria were burst fractures of thoracic or lumbar spine complete or incomplete neurological deficit and burst fractures of thoracic or lumbar spine without neurological deficit but with mechanical instability. The exclusion criteria were pathological fractures, chance fracture, stable burst, wedge compression and osteoporotic compression fractures. The results were analyzed during the follow-up using the Pain – Visual analogue scale, Fusion status and radiographic parameter – K-angle .For pain score were given as 3,2,1 for absent, moderate and severe pain respectively. Regarding fusion status score of 3,2,1 were given when fusion was good, fair and no sign of fusion respectively.Results:Mean pre-operative K-angle was 28o. Average loss of correction at final follow up was 3o.Mean correction of K-angle was 140.Moderate to severe loss of correction of K- angle was observed in 4 patients. Mild to moderate pain in 5 patients treated with analgesics. Average TSM subsidence was 3mm.Conclusions:Bone graft composite provides stable biomechanical support to deficient anterior column in burst fractures and allows early rehabilitation and mobilization. Neural recovery may occur after anterior decompression, stabilization and fusion with TSM-Bone graft composite in dorsolumbar burst fractures with incomplete cord injury

Impact damage resistance of novel adhesively bonded natural fibre composite:Steel hybrid laminates

Synthetic fibre reinforcements are increasingly replaced with plant fibres but an improvement in the mechanical performance of biocomposites is required. Flax composite exhibits fibre failure and perforation even at low impact energies. This paper investigates the viability of improving the impact resistance of flax-epoxy biocomposite by hybridisation with a thin metal layer. High-speed cameras and optical microscopy were used to measure the dissipated energy and to identify the different damage modes. The impact response of hybrid biocomposites was compared to a reference GFRP composite and monolithic biocomposites and it was shown that the deformation and damage is significantly reduced in the hybrid configuration. Additionally, a numerical model was developed in Abaqus/Explicit and validated in terms of the displacement history and damage modes. The study reveals the effect of various material configurations and thicknesses on impact damage resistance and proves that the penetration resistance of biocomposites is improved by hybrid construction.publishedVersionPeer reviewe