Enhancing Biomedical Lay Summarisation with External Knowledge Graphs

Previous approaches for automatic lay summarisation are exclusively reliant on the source article that, given it is written for a technical audience (e.g., researchers), is unlikely to explicitly define all technical concepts or state all of the background information that is relevant for a lay audience. We address this issue by augmenting eLife, an existing biomedical lay summarisation dataset, with article-specific knowledge graphs, each containing detailed information on relevant biomedical concepts. Using both automatic and human evaluations, we systematically investigate the effectiveness of three different approaches for incorporating knowledge graphs within lay summarisation models, with each method targeting a distinct area of the encoder-decoder model architecture. Our results confirm that integrating graph-based domain knowledge can significantly benefit lay summarisation by substantially increasing the readability of generated text and improving the explanation of technical concepts.Comment: Accepted to the EMNLP 2023 main conferenc

Factores de riesgo de evento tromboembólico en pacientes con infección por COVID-19 que requieren ingreso hospitalario

Resumen del trabajo: La infección por SARS-CoV-2 se ha asociado a un aumento de riesgo de eventos tromboembolicos (ET) sobre todo en pacientes que presentan enfermedad grave, si bien es cierto, los factores predictores no están bien definidos. Se ha diseñado un estudio observacional de cohortes retrospectivo con pacientes con infección por SARS-CoV-2 que ingresaron en el Hospital General Universitario de Elche desde el inicio de la pandemia hasta el 31 Julio 2022, con el objetivo de analizar factores de riesgo de ET. Se analiza una cohorte de 2524 pacientes, de los cuales, 97 (3.7%) desarrollaron un ET en los 90 días del diagnóstico, 76 (78%) trombosis venosas y 17 (22%) arteriales. La tasa de incidencia de ET durante el ingreso hospitalario fue de 3.25 (IC 95% 2.49 - 4.18) x 1000 pacientes-día. El análisis estadístico por regresión de COX muestra un aumento de riesgo en pacientes con un índice severidad en la escala de la OMS >=5 [HR 3.99 (IC 95% 2.23 - 7.18)], sin objetivar otro factor predisponente; en cuanto a parámetros analíticos el dímero D se ha asociado de forma directamente proporcional a ET de forma que por cada mcg/ml aumenta en un 7% el riesgo de desarrollar un ET. Por otra parte, se observa una disminución de la incidencia de ET en pacientes con la variante omicron

A genetic algorithm for the vehicle routing problem with time windows

The objective of the vehicle routing problem (VRP) is to deliver a set of customers with known demands on minimum-cost vehicle routes originating and terminating at the same depot. A vehicle routing problem with time windows (VRPTW) requires the delivery be made within a speci¯c time frame given by the customers. Prins (2004) recently proposed a simple and e®ective genetic algorithm (GA) for VRP. In terms of average solution cost, it outperforms most published tabu search results. We implement this hybrid GA to handle VRPTW. Both the implementation and computational results will be discussed

DEVELOPMENT OF A VERSATILE HIGH SPEED NANOMETER LEVEL SCANNING MULTI-PROBE MICROSCOPE

The motivation for development of a multi-probe scanning microscope, presented in this dissertation, is to provide a versatile measurement tool mainly targeted for biological studies, especially on the mechanical and structural properties of an intracellular system. This instrument provides a real-time, three-dimensional (3D) scanning capability. It is capable of operating on feedback from multiple probes, and has an interface for confocal photo-detection of fluorescence-based and single molecule imaging sensitivity. The instrument platform is called a Scanning Multi-Probe Microscope (SMPM) and enables 45 microm by 45 microm by 10 microm navigation of specimen with simultaneous optical and mechanical probing with each probe location being adjustable for collocation or for probing with known probe separations. The 3D positioning stage where the specimen locates was designed to have nanometer resolution and repeatability at 10 Hz scan speed with either open loop or closed loop operating modes. The fine motion of the stage is comprises three orthogonal flexures driven by piezoelectric actuators via a lever linkage. The flexures design is able to scan in larger range especially in z axis and serial connection of the stages helps to minimize the coupling between x, y and z axes. Closed-loop control was realized by the capacitance gauges attached to a rectangular block mounted to the underside of the fine stage upon which the specimen is mounted. The stage's performance was studied theoretically and verified by experimental test. In a step response test and using a simple proportional and integral (PI) controller, standard deviations of 1.9 nm 1.8 nm and 0.41 nm in the x, y and z axes were observed after settling times of 5 ms and 20 ms for the x and y axes. Scanning and imaging of biological specimen and artifact grating are presented to demonstrate the system operation. For faster, short range scanning, novel ultra-fast fiber scanning system was integrated into the xyz fine stage to achieve a super precision dual scanning system. The initial design enables nanometer positioning resolution and runs at 100 Hz scan speed. Both scanning systems are capable of characterization using dimensional metrology tools. Additionally, because the high-bandwidth, ultra-fast scanning system operates through a novel optical attenuating lever, it is physically separate from the longer range scanner and thereby does not introduce additional positioning noise. The dual scanner provides a fine scanning mechanism at relatively low speed and large imaging area using the xyz stage, and focus on a smaller area of interested in a high speed by the ultra-fast scanner easily. Such functionality is beneficial for researchers to study intracellular dynamic motion which requires high speed imaging. Finally, two high end displacement sensor systems, a knife edge sensor and fiber interferometer, were demonstrated as sensing solutions for potential feedback tools to boost the precision and resolution performance of the SMPM

Antimalarial plants used by indigenous people of the Upper Rio Negro in Amazonas, Brazil

AbstractEthnopharmacological relevanceThis is the first intercultural report of antimalarial plants in this region. The aim of this study was to document the medicinal plants used against malaria by indigenous people in the Upper Rio Negro region and to review the literature on antimalarial activity and traditional use of the cited species.Materials and methodsParticipant observation, semi-structured interviews, and ethnobotanical walks were conducted with 89 informants in five indigenous communities between April 2010 and November 2013 to obtain information on the use of medicinal plants against malaria. We reviewed academic databases for papers published in scientific journals up to January 2014 in order to find works on ethnopharmacology, ethnobotany, and antimalarial activity of the species cited.ResultsForty-six plant species belonging to 24 families are mentioned. Fabaceae (17.4%), Arecaceae (13.0%) and Euphorbiaceae (6.5%) account together for 36.9% of these species. Only seven plant species showed a relatively high consensus. Among the plant parts, barks (34.0%) and roots (28.0%) were the most widely used. Of the 46 species cited, 18 (39.1%) have already been studied for their antimalarial properties according to the literature, and 26 species (56.5%) have no laboratory essays on antimalarial activity.ConclusionsLocal traditional knowledge of the use of antimalarials is still widespread in indigenous communities of the Upper Rio Negro, where 46 plants species used against malaria were recorded. Our studies highlight promising new plants for future studies: Glycidendron amazonicum, Heteropsis tenuispadix, Monopteryx uaucu, Phenakospermum guianensis, Pouteria ucuqui, Sagotia brachysepala and notably Aspidosperma schultesii, Ampelozizyphus amazonicus, Euterpe catinga, E. precatoria, Physalis angulata, Cocos nucifera and Swartzia argentea with high-use consensus. Experimental validation of these remedies may help in developing new drugs for malaria

Analytic functions and complex integration

This paper presents some basic theory of analytic function. The class of analytic functions is formed by the complex functions of a complex variable which possess a derivative wherever the function is defined. Beginning with the definition of the derivative, the necessary and sufficient conditions for a function to be analytic at a point are developed. In order to prove that the derivative of an analytic function is itself analytic, the line integrals are defined. The exact differential and its relation to line integrals are discussed. Then Cauchy's theorem is stated. Since the proof of Cauchy's theorem is so complicated and can be found in most texts on complex variable, it is skipped. Lastly Cauchy's integral formula is developed. The formula is an ideal tool for the study of local properties of analytic functions. Particularly it helps to show that an analytic function has derivatives of all orders, which are then analytic. With this result, the converse of Cauchy's theorem, known as Morera's theorem, can be proved. Last, the paper discusses Liouville's theorem concerning entire function

Neurocysticercotic Calcifications And Hippocampal Sclerosis: A Case-control Study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Objective The exact role of calcified neurocysticercotic lesions (CNLs) in epilepsy is yet unknown and controversial. Although the relationship between CNLs, epilepsy and mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS) has already been addressed, to our knowledge, no study has actually provided strong statistical evidence, nor reported the ODDS ratio for these associations. Therefore, we designed this case-control study to assess the likelihood of having MTLE-HS versus other forms of epilepsy in the presence of CNLs. Methods In this case-control study we included 119 consecutive patients with epilepsy and 106 disease controls (headache) with previous CT scans. We subdivided cases into MTLE-HS and other epilepsies. We used brain CT scans to define presence or absence of CNLs. After exploratory analyses, we used logistic regression to analyze the association between CNLs, epilepsy subgroups and disease controls. Results CNLs were found in 31.09% of cases and in 11.32% of controls (p<0.001). The initial analysis comparing epilepsy versus controls revealed a significant association between CNLs and epilepsy (OR = 5.32; 95%CI = 2.43-11.54; p<0.001). However, when we compared MTLE-HS versus other epilepsies versus controls we confirmed that CNLs were associated with MTLE-HS (OR = 11.27, 95%CI = 4.73-26.85; p<0.001) but other epilepsies were not. We found no difference in the CNLs load and no difference in the location of the CNLs when we compared patients with MTLE-HS, other epilepsies and disease controls. Significance The inclusion of controls allowed us to estimate the likelihood of having epilepsy in the presence of CNLs. We found that patients with CNLs were 11 times more likely to have MTLE-HS; however, the presence of CNLs did not change the odds of having other types of epilepsy. These findings raise the possibility of neurocysticercosis playing a role in the pathophysiology of MTLE-HS and need further confirmation in other series.107Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP [2013/21265-2, 2013/07559-3

Overview of the BioLaySumm 2023 Shared Task on Lay Summarization of Biomedical Research Articles

This paper presents the results of the shared task on Lay Summarisation of Biomedical Research Articles (BioLaySumm), hosted at the BioNLP Workshop at ACL 2023. The goal of this shared task is to develop abstractive summarisation models capable of generating "lay summaries" (i.e., summaries that are comprehensible to non-technical audiences) in both a controllable and non-controllable setting. There are two subtasks: 1) Lay Summarisation, where the goal is for participants to build models for lay summary generation only, given the full article text and the corresponding abstract as input; and 2) Readability-controlled Summarisation, where the goal is for participants to train models to generate both the technical abstract and the lay summary, given an article's main text as input. In addition to overall results, we report on the setup and insights from the BioLaySumm shared task, which attracted a total of 20 participating teams across both subtasks.Comment: Published at BioNLP@ACL202

Thermodynamic Analysis and Process System Comparison of the Exhaust Gas Recirculated, Steam Injected and Humidified Micro Gas Turbine

Stringent environmental emission regulations and continuing efforts to reduce carbon dioxide (CO2) from the energy sector, in the context of global warming, have promoted interest to improve the efficiency of power generation systems whilst reducing emissions. Further, this has led to the development of innovative gas turbine systems which either result in higher electrical efficiency or the reduction of CO2 emissions. Micro gas turbines are one of the secure, economical and environmentally viable options for power and heat generation. Here, a Turbec T100 micro gas turbine (MGT) is simulated using Aspen HYSYS® V8.4 and validated through experimental data. Due to the consistency and robustness of the steady state model developed, it is further extended to three different innovative cycles: (i) an exhaust gas recirculated (EGR) cycle, in which part of the exhaust gas is dried and re-circulated to the MGT inlet; (ii) a steam injected (STIG) cycle, and (iii) a humid air turbine (HAT) cycle. The steam and hot water are generated through the exhaust of the recuperator for the STIG and HAT cycle, respectively. Further, the steam is directly injected into the recuperator for power augmentation, while for the HAT cycle; the compressed air is saturated with water in the humid tower before entering the recuperator. This study evaluates the impact of the EGR ratio, steam to air ratio, and water to air ratio on the performance and efficiency of the system. The comparative potential for each innovative cycle is assessed by thermodynamic properties estimation of process parameters through the models developed to better understand the behavior of each cycle. The thermodynamic assessment indicates that CO2 enrichment occurs for the three innovative cycles. Further, the results indicate that the electrical efficiency increases for the STIG and HAT cycle while it decreases for the EGR cycle. In conclusion, the innovative cycles indicates the possibilities to improve the system performance and efficiency

Food groups and risk of coronary heart disease, stroke and heart failure : a systematic review and dose-response meta-analysis of prospective studies

Background: Despite growing evidence for food-based dietary patterns' potential to reduce cardiovascular disease risk, knowledge about the amounts of food associated with the greatest change in risk of specific cardiovascular outcomes and about the quality of meta-evidence is limited. Therefore, the aim of this meta-analysis was to synthesize the knowledge about the relation between intake of 12 major food groups (whole grains, refined grains, vegetables, fruits, nuts, legumes, eggs, dairy, fish, red meat, processed meat, and sugar-sweetened beverages [SSB]) and the risk of coronary heart disease (CHD), stroke and heart failure (HF). Methods: We conducted a systematic search in PubMed and Embase up to March 2017 for prospective studies. Summary risk ratios (RRs) and 95% confidence intervals (95% CI) were estimated using a random effects model for highest versus lowest intake categories, as well as for linear and non-linear relationships. Results: Overall, 123 reports were included in the meta-analyses. An inverse association was present for whole grains (RRCHD: 0.95 (95% CI: 0.92-0.98), RRHF: 0.96 (0.95-0.97)), vegetables and fruits (RRCHD: 0.97 (0.96-0.99), and 0.94 (0.90-0.97); RRstroke: 0.92 (0.86-0.98), and 0.90 (0.84-0.97)), nuts (RRCHD: 0.67 (0.43-1.05)), and fish consumption (RRCHD: 0.88 (0.79-0.99), RRstroke: 0.86 (0.75-0.99), and RRHF: 0.80 (0.67-0.95)), while a positive association was present for egg (RRHF: 1.16 (1.03-1.31)), red meat (RRCHD: 1.15 (1.08-1.23), RRstroke: 1.12 (1.06-1.17), RRHF: 1.08 (1.02-1.14)), processed meat (RRCHD: 1.27 (1.09-1.49), RRstroke: 1.17 (1.02-1.34), RRHF: 1.12 (1.05-1.19)), and SSB consumption (RRCHD: 1.17 (1.11-1.23), RRstroke: 1.07 (1.02-1.12), RRHF: 1.08 (1.05-1.12)) in the linear dose-response meta-analysis. There were clear indications for non-linear dose-response relationships between whole grains, fruits, nuts, dairy, and red meat and CHD. Conclusion: An optimal intake of whole grains, vegetables, fruits, nuts, legumes, dairy, fish, red and processed meat, eggs and SSB showed an important lower risk of CHD, stroke, and HF