bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Real-World Clinical Implementation of Automated Processing Using Intelligent Work Aid for Rapid Reformation at the Orbitomeatal Line in Head Computed Tomography
Authors: Nishii Tatsuya , Okuyama Shun , Horinouchi Hiroki , Chikuda Ryo , Kamei Eisuke , Higuchi Satoshi , Ohta Yasutoshi , Fukuda Tetsuya 
Published: April 2021

Objectives
The aim was to investigate the time savings and plane accuracy of multivendor head computed tomography (CT) using the intelligent work aid with automatic reformatting of the axial head image at the orbitomeatal line.

Materials and Methods
We retrospectively reviewed 781 head CTs (median, 70 years; 441 men) collected by CT systems from 3 vendors. In addition to the orbitomeatal line image reformatted by a CT specialist as a reference, we obtained the fully automated orbitomeatal line image using the intelligent work aid. We calculated the offset angle from the reference of the automatically reformatted image. We defined the large offset angle groups as those with an offset angle greater than 3 degrees. Multivariate logistic regression was used to determine the independent factors for the large offset angle groups. We compared the postprocessing times measured using the intelligent work aid or by a CT specialist.

Results
With the intelligent work aid, 99.7% of CTs were automatically reformatted to the orbitomeatal line without error. Furthermore, 88.1% of CTs were within the 3 degrees' offset angle when compared with the reference produced by a CT specialist. The median offset angle from the reference was 1.41 degrees. Multivariate analysis showed that the offset angle of the positioning plane was an independent factor (odds ratio, 1.045; P = 0.005) for predicting the large offset angle group. Furthermore, this technique was 4 times faster (6.4 ± 0.7 seconds) than a CT specialist (25.6 ± 6.4 seconds).

Conclusions
The intelligent work aid can generate a fast and precise head CT image aligned at the orbitomeatal line, even in real-world clinical CTs. However, precise positioning remains essential.
Evaluation of Iterative Denoising 3-Dimensional T2-Weighted Turbo Spin Echo for the Diagnosis of Deep Infiltrating Endometriosis
Authors: Florin Marie , Vaussy Alexis , Macron Laurent , Bazot Marc , Stemmer Alto , Pinar Ugo , Jarboui Lamia 
Published: April 2021

Objectives
The primary end point of this study was to evaluate the image quality and reliability of a highly accelerated 3-dimensional T2 turbo spin echo (3D-T2-TSE) sequence with prototype iterative denoising (ID) reconstruction compared with conventional 2D T2 sequences for the diagnosis of deep infiltrating endometriosis (DIE). The secondary end point was to demonstrate the 3D-T2-TSE sequence image quality improvement using ID reconstruction.

Material and Methods
Patients were prospectively enrolled to our institution for pelvis magnetic resonance imaging because of a suspicion of endometriosis over a 4-month period. Both conventional 2D-T2 (sagittal, axial, coronal T2 oblique to the cervix) and 3D-T2-TSE sequences were performed with a scan time of 7 minutes 43 seconds and 4 minutes 58 seconds, respectively. Reconstructions with prototype ID (3D-T2-denoised) and without prototype ID (3D-T2) were generated inline at the end of the acquisition. Two radiologists independently evaluated the image quality of 3D-T2, 3D-T2-denoised, and 2D-T2 sequences. Diagnosis confidence of DIE was evaluated for both 3D-T2-denoised and 2D-T2 sequences. Intraobserver and interobserver agreements were calculated using Cohen κ coefficient.

Results
Ninety female patients were included. Both readers found that the ID algorithm significantly improved the image quality and decreased the artifacts of 3D-T2-denoised compared with 3D-T2 sequences (P < 0.001). A significant image quality improvement was found by 1 radiologist for 3D-T2-denoised compared with 2D-T2 sequences (P = 0.002), whereas the other reader evidenced no significant difference. The interobserver agreement of 3D-T2-denoised and 2D-T2 sequences was 0.84 (0.73–0.95) and 0.78 (0.65–0.9), respectively, for the diagnosis of DIE. Intraobserver agreement for readers 1 and 2 was 0.86 (0.79–1) and 0.83 (0.76–1), respectively. For all localization of DIE, interobserver and intraobserver agreements were either almost perfect or substantial for both 3D-T2-denoised and 2D-T2 sequences.

Conclusions
Three-dimensional T2-denoised imaging is a promising tool to replace conventional 2D-T2 sequences, offering a significant scan time reduction without compromising image quality or diagnosis information for the assessment of DIE.
Rapid Cycle Deliberate Practice Versus Traditional Simulation for Training Extracorporeal Membrane Oxygenation Specialists in Circuit Air Emergency Management
Authors: Swinger Nathan , Hocutt Gail , Medsker Brock H. , Gray Brian W. , Abulebda Kamal 
Published: April 2021

Introduction
Extracorporeal membrane oxygenation (ECMO) is a highly complex therapy used to support critically ill patients. Simulation-based training of ECMO specialists in the management of ECMO emergencies has been described in the literature, but optimal methods are not currently established. The objective of this study was to compare rapid cycle deliberate practice (RCDP) simulation versus traditional simulation (TS) with reflective debriefing for training ECMO specialists in the management of arterial air emergencies.

Methods
A prospective, randomized, pre-post interventional design was used to compare the impact of RCDP training with that of TS training on ECMO specialist performance during a simulated ECMO circuit emergency. Participants were divided into 2 training groups—RCDP and TS. Each participant completed a simulated arterial air emergency scenario before training, immediately after training, and again 3 months later. The primary outcome was the time required by individual participants to complete critical clinical actions.

Results
Twenty-four ECMO specialists completed the study. Immediately after the training, the RCDP group had faster times to dissociate the patient from the ECMO circuit (11-seconds RCDP vs. 16-seconds TS, P = 0.03) and times to re-establish ECMO support (59-seconds RCDP vs. 82.5-seconds TS, P = 0.01). Follow-up testing at 3 months showed persistence in faster times to re-establish ECMO support in the RCDP group (114-seconds RCDP vs. 199-seconds TS, P = 0.01).

Conclusions
Rapid cycle deliberate practice simulation provides a superior curriculum and method of training ECMO specialists in the management of arterial air emergencies in comparison with traditional simulation.
Evaluating Nontechnical Skills in US Emergency Departments Using Simulation
Authors: Meguerdichian David A. , Huancahuari Nadia , Pozner Charles N. , Eyre Andrew , Schuur Jeremiah , Yule Steven 
Published: April 2021

Introduction
Nontechnical skills (NTS) in medicine are the “cognitive, social, and personal resource skills that complement technical skills contributing to safe and efficient care.” We aimed to (1) evaluate the validity and reliability of a 12-element United Kingdom emergency medicine (EM) NTS assessment tool in the context of United States (US) EM practice and (2) identify behaviors unique to US clinical practice.

Methods
This was a mixed methods study conducted in 2 phases, following Kane's validity framework. The intended use of the NTS tool is to provide formative assessment of US EM physicians (EPs) from a video of simulated clinical encounters. In phase I, a focus group assessed the appropriateness of each aspect of the tool in the context of US EM practice by reviewing and identifying the NTS of an EP in a simulated clinical scenario. In phase II, EPs (N = 208) attending a national EM conference evaluated an EP's behaviors in 1 of 2 video simulations. Reliability in the form of internal consistency was calculated using Cronbach α. All participants suggested exemplar behaviors for the 12 elements in the context of their own clinical practice and generated new assessment elements.

Results
Internal consistency was acceptable (α > 0.7) for all categories, except teamwork and cooperation. Participants proposed 4 novel behavioral elements and suggested US exemplar behaviors for all 12 original elements.

Conclusions
This tool can be used to assess US EP's NTS for the purpose of formative assessment. Refinement of exemplar behaviors and inclusion of novel US-specific elements may optimize usability.
Rapid Cycle Deliberate Practice Improves Retention of Pediatric Resuscitation Skills Compared With Postsimulation Debriefing
Authors: Won Sharon K. , Doughty Cara B. , Young Ann L. , Welch-Horan T. Bram , Rus Marideth C. , Camp Elizabeth A. , Lemke Daniel S. 
Published: April 2021

Introduction
Rapid cycle deliberate practice (RCDP) for teaching team-based resuscitation is associated with similar improvements in immediate performance as compared with postsimulation debriefing (PSD). Limited studies compare skill retention between these 2 modalities. Our objective was to compare retention of team leader performance in residents trained with RCDP versus PSD.

Methods
This was a cluster-randomized trial comparing RCDP and PSD from January 2018 to April 2019. Pediatric and emergency medicine residents participated in simulation-based pediatric resuscitation education, and teams were randomized to undergo either RCDP or PSD. Each participant's team leader performance was assessed 1 to 12 months after training via a simulated cardiac arrest. The primary outcome was time to defibrillation. Secondary outcomes included overall team leader performance and time to chest compressions.

Results
Thirty-two residents (90.6% pediatrics, 9.4% emergency medicine) met inclusion criteria (16 RCDP, 16 PSD). Of the 32 residents, 40% returned in 1 to 3 months, 25% 3 to 6 months, 16% 6 to 9 months, and 19% 10 to 12 months. Participants in RCDP had more than 5 times the odds of achieving defibrillation versus those in the PSD group (odds ratio = 5.57, 95% confidence interval = 1.13–27.52, P = 0.04). The RCDP group had a higher mean Resident Team Leader Evaluation score (0.54 ± 0.19) than the PSD group (0.34 ± 0.16, P < 0.001).

Conclusions
This study shows significant differences in subsequent performance in the team leader trained with RCDP and suggests that RCDP may improve retention of pediatric resuscitation skills compared with PSD. Future studies should focus on best applications for RCDP with attention to knowledge and skill decay.
Simulation in Upper and Lower Limb Trauma Skill Acquisition
Authors: Heskin Leonie , Galvin Rose , Traynor Oscar , Simms Ciaran 
Published: April 2021

Summary Statement
This review aimed to explore the published evidence with regard to the types and composition of both full- and part-task trainers to teach surgeons extremity exploration procedures in limb trauma management. Studies were included if they reported the development and/or validation of synthetic or virtual task trainers. Studies were evaluated to determine their derivation, usability, and clinical utility.
A total of 638 citations were identified and 63 satisfied the inclusion criteria. Twenty-five articles addressed simulator validation and 36 addressed level of learning achieved with simulator engagement. Two studies described a dedicated limb simulator. Simulators were developed to repair limb structures including skin (n = 15), tendon (n = 7), nerve (n = 1), fascia (n = 1), muscle (n = 1), vascular (n = 24), and bone (n = 11). Considerations such as material fidelity, learning outcomes, cost or reusability, validity, and effectiveness are inconsistently reported. Future studies should address design standards for the effective production of synthetic or virtual simulators for limb trauma management.
Q-Methodology
Authors: Klein Barbie A. 
Published: April 2021

Summary Statement
Learner perceptions of simulation can be challenging to assess and are usually limited to qualitative strategies. Q-methodology is an exploratory, systematic research technique that combines quantitative and qualitative procedures to measure differences in subjectivity. This article briefly reviews Q-methodology, provides an example of how it could be applied to assess the affective domain of simulation-based learning, and discusses implications for the use of Q-methodology in future simulation scholarship.
Computational Simulation Is a Vital Resource for Navigating the COVID-19 Pandemic
Authors: Page Andrew , Diallo Saikou Y. , Wildman Wesley J. , Hodulik George , Weisel Eric W. , Gondal Neha , Voas David 
Published: April 2021

Introduction
COVID-19 has prompted the extensive use of computational models to understand the trajectory of the pandemic. This article surveys the kinds of dynamic simulation models that have been used as decision support tools and to forecast the potential impacts of nonpharmaceutical interventions (NPIs). We developed the Values in Viral Dispersion model, which emphasizes the role of human factors and social networks in viral spread and presents scenarios to guide policy responses.

Methods
An agent-based model of COVID-19 was developed with individual agents able to move between 3 states (susceptible, infectious, or recovered), with each agent placed in 1 of 7 social network types and assigned a propensity to comply with NPIs (quarantine, contact tracing, and physical distancing). A series of policy questions were tested to illustrate the impact of social networks and NPI compliance on viral spread among (1) populations, (2) specific at-risk subgroups, and (3) individual trajectories.

Results
Simulation outcomes showed large impacts of physical distancing policies on number of infections, with substantial modification by type of social network and level of compliance. In addition, outcomes on metrics that sought to maximize those never infected (or recovered) and minimize infections and deaths showed significantly different epidemic trajectories by social network type and among higher or lower at-risk age cohorts.

Conclusions
Although dynamic simulation models have important limitations, which are discussed, these decision support tools should be a key resource for navigating the ongoing impacts of the COVID-19 pandemic and can help local and national decision makers determine where, when, and how to invest resources.
Structure, function and parallel evolution of the bivalve byssus, with insights from proteomes and the zebra mussel genome
Authors: McCartney Michael A. 
Published: April 2021

The byssus is a structure unique to bivalves. Byssal threads composed of many proteins extend like tendons from muscle cells, ending in adhesive pads that attach underwater. Crucial to settlement and metamorphosis, larvae of virtually all species are byssate. By contrast, in adults, the byssus is scattered throughout bivalves, where it has had profound effects on morphological evolution and been key to adaptive radiations of epifaunal species. I compare byssus structure and proteins in blue mussels (Mytilus), by far the best characterized, to zebra mussels (Dreissena polymorpha), in which several byssal proteins have been isolated and sequenced. By mapping the adult byssus onto a recent phylogenomic tree, I confirm its independent evolution in these and other lineages, likely parallelisms with common origins in development. While the byssus is superficially similar inDreissenaandMytilus, in finer detail it is not, and byssal proteins are dramatically different. I used the chromosome-scaleD. polymorphagenome we recently assembled to search for byssal genes and found 37 byssal loci on 10 of the 16 chromosomes. Most byssal genes are in small families, with several amino acid substitutions between paralogs. Byssal proteins of zebra mussels and related quagga mussels (D. rostriformis) are divergent, suggesting rapid evolution typical of proteins with repetitive low complexity domains. Opportunities abound for proteomic and genomic work to further our understanding of this textbook example of a marine natural material. A priority should be invasive bivalves, given the role of byssal attachment in the spread of, and ecological and economic damage caused by zebra mussels, quagga mussels and others.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Whole-genome re-sequencing data to infer historical demography and speciation processes in land snails: the study of twoCandidulasister species
Authors: Chueca Luis J. , Schell Tilman , Pfenninger Markus 
Published: April 2021

Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two closely related species of land snails from western Europe,Candidula unifasciataandC. rugosiuscula. Historical demographic analysis indicated fluctuations in the size of ancestral populations, probably driven by Pleistocene climatic fluctuations. Although the current population distributions of both species do not overlap, our approximate Bayesian computation model selection approach on several speciation scenarios suggested that gene flow has occurred throughout the divergence process until recently. Positively selected genes diverging early in the process were associated with intragenomic and cyto-nuclear incompatibilities, respectively, potentially fostering reproductive isolation as well as ecological divergence. Our results suggested that the speciation between species entails complex processes involving both gene flow and ecological speciation, and that further research based on whole-genome data can provide valuable understanding on species divergence.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
MolluscDB: a genome and transcriptome database for molluscs
Authors: Caurcel Carlos , Laetsch Dominik R. , Challis Richard , Kumar Sujai , Gharbi Karim , Blaxter Mark 
Published: April 2021

As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Examining adaptive evolution of immune activity: opportunities provided by gastropods in the age of ‘omics’
Authors: Seppälä Otto , Çetin Cansu , Cereghetti Teo , Feulner Philine G. D. , Adema Coen M. 
Published: April 2021

Parasites threaten all free-living organisms, including molluscs. Understanding the evolution of immune defence traits in natural host populations is crucial for predicting their long-term performance under continuous infection risk. Adaptive trait evolution requires that traits are subject to selection (i.e. contribute to organismal fitness) and that they are heritable. Despite broad interest in the evolutionary ecology of immune activity in animals, the understanding of selection on and evolutionary potential of immune defence traits is far from comprehensive. For instance, empirical observations are only rarely in line with theoretical predictions of immune activity being subject to stabilizing selection. This discrepancy may be because ecoimmunological studies can typically cover only a fraction of the complexity of an animal immune system. Similarly, molecular immunology/immunogenetics studies provide a mechanistic understanding of immunity, but neglect variation that arises from natural genetic differences among individuals and from environmental conditions. Here, we review the current literature on natural selection on and evolutionary potential of immune traits in animals, signal how merging ecological immunology and genomics will strengthen evolutionary ecological research on immunity, and indicate research opportunities for molluscan gastropods for which well-established ecological understanding and/or ‘immune-omics’ resources are already available.
This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Molluscan mitochondrial genomes break the rules
Authors: Ghiselli Fabrizio , Gomes-dos-Santos André , Adema Coen M. , Lopes-Lima Manuel , Sharbrough Joel , Boore Jeffrey L. 
Published: April 2021

The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a ‘textbook description’. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed ‘doubly uniparental inheritance’. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology.
This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.