Natural language processing for aviation safety: Extracting knowledge from publicly-available loss of separation reports

Background: The air traffic management (ATM) system has historically coped with a global increase in traffic demand ultimately leading to increased operational complexity. When dealing with the impact of this increasing complexity on system safety it is crucial to automatically analyse the losses of separation (LoSs) using tools able to extract meaningful and actionable information from safety reports. Current research in this field mainly exploits natural language processing (NLP) to categorise the reports,with the limitations that the considered categories need to be manually annotated by experts and that general taxonomies are seldom exploited. Methods: To address the current gaps,authors propose to perform exploratory data analysis on safety reports combining state-of-the-art techniques like topic modelling and clustering and then to develop an algorithm able to extract the Toolkit for ATM Occurrence Investigation (TOKAI) taxonomy factors from the free-text safety reports based on syntactic analysis. TOKAI is a tool for investigation developed by EUROCONTROL and its taxonomy is intended to become a standard and harmonised approach to future investigations. Results: Leveraging on the LoS events reported in the public databases of the Comisión de Estudio y Análisis de Notificaciones de Incidentes de Tránsito Aéreo and the United Kingdom Airprox Board,authors show how their proposal is able to automatically extract meaningful and actionable information from safety reports,other than to classify their content according to the TOKAI taxonomy. The quality of the approach is also indirectly validated by checking the connection between the identified factors and the main contributor of the incidents. Conclusions: Authors' results are a promising first step toward the full automation of a general analysis of LoS reports supported by results on real-world data coming from two different sources. In the future,authors' proposal could be extended to other taxonomies or tailored to identify factors to be included in the safety taxonomies

Managing the complexity of doing it all : an exploratory study on students' experiences when trained stepwise in conducting consultations

Background: At most medical schools the components required to conduct a consultation, medical knowledge, communication, clinical reasoning and physical examination skills, are trained separately. Afterwards, all the knowledge and skills students acquired must be integrated into complete consultations, an art that lies at the heart of the medical profession. Inevitably, students experience conducting consultations as complex and challenging. Literature emphasizes the importance of three didactic course principles: moving from partial tasks to whole task learning, diminishing supervisors' support and gradually increasing students' responsibility. This study explores students' experiences of an integrated consultation course using these three didactic principles to support them in this difficult task. Methods: Six focus groups were conducted with 20 pre-clerkship and 19 clerkship students in total. Discussions were audiotaped, transcribed and analysed by Nvivo using the constant comparative strategy within a thematic analysis. Results: Conducting complete consultations motivated students in their learning process as future physician. Initially, students were very much focused on medical problem solving. Completing the whole task of a consultation obligated them to transfer their theoretical medical knowledge into applicable clinical knowledge on the spot. Furthermore, diminishing the support of a supervisor triggered students to reflect on their own actions but contrasted with their increased appreciation of critical feedback. Increasing students' responsibility stimulated their active learning but made some students feel overloaded. These students were anxious to miss patient information or not being able to take the right decisions or to answer patients' questions, which sometimes resulted in evasive coping techniques, such as talking faster to prevent the patient asking questions. Conclusion: The complex task of conducting complete consultations should be implemented early within medical curricula because students need time to organize their medical knowledge into applicable clinical knowledge. An integrated consultation course should comprise a step-by-step teaching strategy with a variety of supervisors' feedback modi, adapted to students' competence. Finally, students should be guided in formulating achievable standards to prevent them from feeling overloaded in practicing complete consultations with simulated or real patients

Attitudes toward and experiences of gender issues among physician teachers: A survey study conducted at a university teaching hospital in Sweden

<p>Abstract</p> <p>Background</p> <p>Gender issues are important to address during medical education, however research about the implementation of gender in medical curricula reports that there are obstacles. The aim of this study was to explore physician teachers' attitudes to gender issues.</p> <p>Methods</p> <p>As part of a questionnaire, physician teachers at Umeå University in Sweden were given open-ended questions about explanations for and asked to write examples why they found gender important or not. The 1 469 comments from the 243 respondents (78 women, 165 men) were analyzed by way of content analysis. The proportion of comments made by men and women in each category was compared.</p> <p>Results</p> <p>We found three themes in our analysis: Understandings of gender, problems connected with gender and approaches to gender. Gender was associated with differences between women and men regarding behaviour and disease, as well as with inequality of life conditions. Problems connected with gender included: delicate situations involving investigations of intimate body parts or sexual attraction, different expectations on male and female physicians and students, and difficulty fully understanding the experience of people of the opposite sex. The three approaches to gender that appeared in the comments were: 1) avoidance, implying that the importance of gender in professional relationships was recognized but minimized by comparing gender with aspects, such as personality and neutrality; 2) simplification, implying that gender related problems were easy to address, or already solved; and 3) awareness, implying that the respondent was interested in gender issues or had some insights in research about gender. Only a few individuals described gender as an area of competence and knowledge. There were comments from men and women in all categories, but there were differences in the relative weight for some categories. For example, recognizing gender inequities was more pronounced in the comments from women and avoidance more common in comments from men.</p> <p>Conclusion</p> <p>The surveyed physician teachers gave many examples of gender-related problems in medical work and education, but comments describing gender as an area of competence and knowledge were few. Approaches to gender characterized by avoidance and simplification suggest that faculty development programs on gender need to address and reflect on attitudes as well as knowledge.</p

Development of pancreatic diseases during long-term follow-up after acute pancreatitis:a post-hoc analysis of a prospective multicenter cohort

Background and Aim: More insight into the incidence of and factors associated with progression following a first episode of acute pancreatitis (AP) would offer opportunities for improvements in disease management and patient counseling. Methods: A long-term post hoc analysis of a prospective cohort of patients with AP (2008–2015) was performed. Primary endpoints were recurrent acute pancreatitis (RAP), chronic pancreatitis (CP), and pancreatic cancer. Cumulative incidence calculations and risk analyses were performed. Results: Overall, 1184 patients with a median follow-up of 9 years (IQR: 7–11) were included. RAP and CP occurred in 301 patients (25%) and 72 patients (6%), with the highest incidences observed for alcoholic pancreatitis (40% and 22%). Pancreatic cancer was diagnosed in 14 patients (1%). Predictive factors for RAP were alcoholic and idiopathic pancreatitis (OR 2.70, 95% CI 1.51–4.82 and OR 2.06, 95% CI 1.40–3.02), and no pancreatic interventions (OR 1.82, 95% CI 1.10–3.01). Non-biliary etiology (alcohol: OR 5.24, 95% CI 1.94–14.16, idiopathic: OR 4.57, 95% CI 2.05–10.16, and other: OR 2.97, 95% CI 1.11–7.94), RAP (OR 4.93, 95% CI 2.84–8.58), prior pancreatic interventions (OR 3.10, 95% CI 1.20–8.02), smoking (OR 2.33, 95% CI 1.14–4.78), and male sex (OR 2.06, 95% CI 1.05–4.05) were independently associated with CP. Conclusion: Disease progression was observed in a quarter of pancreatitis patients. We identified several risk factors that may be helpful to devise personalized strategies with the intention to reduce the impact of disease progression in patients with AP.</p

Development of pancreatic diseases during long-term follow-up after acute pancreatitis:a post-hoc analysis of a prospective multicenter cohort

Background and Aim: More insight into the incidence of and factors associated with progression following a first episode of acute pancreatitis (AP) would offer opportunities for improvements in disease management and patient counseling. Methods: A long-term post hoc analysis of a prospective cohort of patients with AP (2008–2015) was performed. Primary endpoints were recurrent acute pancreatitis (RAP), chronic pancreatitis (CP), and pancreatic cancer. Cumulative incidence calculations and risk analyses were performed. Results: Overall, 1184 patients with a median follow-up of 9 years (IQR: 7–11) were included. RAP and CP occurred in 301 patients (25%) and 72 patients (6%), with the highest incidences observed for alcoholic pancreatitis (40% and 22%). Pancreatic cancer was diagnosed in 14 patients (1%). Predictive factors for RAP were alcoholic and idiopathic pancreatitis (OR 2.70, 95% CI 1.51–4.82 and OR 2.06, 95% CI 1.40–3.02), and no pancreatic interventions (OR 1.82, 95% CI 1.10–3.01). Non-biliary etiology (alcohol: OR 5.24, 95% CI 1.94–14.16, idiopathic: OR 4.57, 95% CI 2.05–10.16, and other: OR 2.97, 95% CI 1.11–7.94), RAP (OR 4.93, 95% CI 2.84–8.58), prior pancreatic interventions (OR 3.10, 95% CI 1.20–8.02), smoking (OR 2.33, 95% CI 1.14–4.78), and male sex (OR 2.06, 95% CI 1.05–4.05) were independently associated with CP. Conclusion: Disease progression was observed in a quarter of pancreatitis patients. We identified several risk factors that may be helpful to devise personalized strategies with the intention to reduce the impact of disease progression in patients with AP.</p

Diagnostic accuracy of endoscopic ultrasonography-guided tissue acquisition prior to resection of pancreatic carcinoma:a nationwide analysis

Introduction: Endoscopic ultrasonography guided tissue acquisition (EUS + TA) is used to provide a tissue diagnosis in patients with suspected pancreatic cancer. Key performance indicators (KPI) for these procedures are rate of adequate sample (RAS) and sensitivity for malignancy (SFM). Aim: assess practice variation regarding KPI of EUS + TA prior to resection of pancreatic carcinoma in the Netherlands. Patients and methods: Results of all EUS + TA prior to resection of pancreatic carcinoma from 2014–2018, were extracted from the national Dutch Pathology Registry (PALGA). Pathology reports were classified as: insufficient for analysis (b1), benign (b2), atypia (b3), neoplastic other (b4), suspected malignant (b5), and malignant (b6). RAS was defined as the proportion of EUS procedures yielding specimen sufficient for analysis. SFM was calculated using a strict definition (malignant only, SFM-b6), and a broader definition (SFM-b5+6). Results: 691 out of 1638 resected patients (42%) underwent preoperative EUS + TA. RAS was 95% (range 89–100%), SFM-b6 was 44% (20–77%), and SFM-b5+6 was 65% (53–90%). All centers met the performance target RAS&gt;85%. Only 9 out of 17 met the performance target SFM-b5+6 &gt; 85%. Conclusion: This nationwide study detected significant practice variation regarding KPI of EUS + TA procedures prior to surgical resection of pancreatic carcinoma. Therefore, quality improvement of EUS + TA is indicated

Paternal mtDNA and Maleness Are Co-Inherited but Not Causally Linked in Mytilid Mussels

BACKGROUND: In marine mussels of the genus Mytilus there are two mitochondrial genomes. One is transmitted through the female parent, which is the normal transmission route in animals, and the other is transmitted through the male parent which is an unusual phenomenon. In males the germ cell line is dominated by the paternal mitochondrial genome and the somatic cell line by the maternal. Research to date has not allowed a clear answer to the question of whether inheritance of the paternal genome is causally related to maleness. METHODOLOGY/PRINCIPAL FINDINGS: Here we present results from hybrid crosses, from triploid mussels and from observations of sperm mitochondria in fertilized eggs which clearly show that maleness and presence of the paternal mitochondrial genome can be decoupled. These same results show that the female mussel has exclusive control of whether her progeny will inherit the mitochondrial genome of the male parent. CONCLUSIONS/SIGNIFICANCE: These findings are important in our efforts to understand the mechanistic basis of this unusual mode of mitochondrial DNA inheritance that is common among bivalves

Complementarity Between a Docking and a High-Throughput Screen in Discovering New Cruzain Inhibitors†

Virtual and high-throughput screens (HTS) should have complementary strengths and weaknesses, but studies that prospectively and comprehensively compare them are rare. We undertook a parallel docking and HTS screen of 197861 compounds against cruzain, a thiol protease target for Chagas disease, looking for reversible, competitive inhibitors. On workup, 99 % of the hits were eliminated as false positives, yielding 146 well-behaved, competitive ligands. These fell into five chemotypes: two were prioritized by scoring among the top 0.1 % of the docking-ranked library, two were prioritized by behavior in the HTS and by clustering, and one chemotype was prioritized by both approaches. Determination of an inhibitor/cruzain crystal structure and comparison of the high-scoring docking hits to experiment illuminated the origins of docking false-negatives and false-positives. Prioritizing molecules that are both predicted by docking and are HTS-active yields well-behaved molecules, relatively unobscured by the false-positives to which both techniques are individually prone

One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening†

The enzyme pteridine reductase 1 (PTR1) is a potential target for new compounds to treat human African trypanosomiasis. A virtual screening campaign for fragments inhibiting PTR1 was carried out. Two novel chemical series were identified containing aminobenzothiazole and aminobenzimidazole scaffolds, respectively. One of the hits (2-amino-6-chloro-benzimidazole) was subjected to crystal structure analysis and a high resolution crystal structure in complex with PTR1 was obtained, confirming the predicted binding mode. However, the crystal structures of two analogues (2-amino-benzimidazole and 1-(3,4-dichloro-benzyl)-2-amino-benzimidazole) in complex with PTR1 revealed two alternative binding modes. In these complexes, previously unobserved protein movements and water-mediated protein-ligand contacts occurred, which prohibited a correct prediction of the binding modes. On the basis of the alternative bindingmode of 1-(3,4-dichloro-benzyl)-2-amino-benzimidazole, derivatives were designed and selective PTR1 inhibitors with low nanomolar potency and favorable physicochemical properties were obtained