Text Mining of Biomedical Articles Using the Konstanz Information Miner (KNIME) Platform: Hemolytic Uremic Syndrome as a Case Study

Objectives

Automated systems for information extraction are becoming very useful due to the enormous scale of the existing literature and the increasing number of scientific articles published worldwide in the field of medicine. We aimed to develop an accessible method using the open-source platform KNIME to perform text mining (TM) on indexed publications. Material from scientific publications in the field of life sciences was obtained and integrated by mining information on hemolytic uremic syndrome (HUS) as a case study.

Methods

Text retrieved from Europe PubMed Central (PMC) was processed using specific KNIME nodes. The results were presented in the form of tables or graphical representations. Data could also be compared with those from other sources.

Results

By applying TM to the scientific literature on HUS as a case study, and by selecting various fields from scientific articles, it was possible to obtain a list of individual authors of publications, build bags of words and study their frequency and temporal use, discriminate topics (HUS vs. atypical HUS) in an unsupervised manner, and cross-reference information with a list of FDA-approved drugs.

Conclusions

Following the instructions in the tutorial, researchers without programming skills can successfully perform TM on the indexed scientific literature. This methodology, using KNIME, could become a useful tool for performing statistics, analyzing behaviors, following trends, and making forecast related to medical issues. The advantages of TM using KNIME include enabling the integration of scientific information, helping to carry out reviews, and optimizing the management of resources dedicated to basic and clinical research.

[Obtaining new information on hemolytic uremic syndrome by text mining]

Hemolytic uremic syndrome (HUS) is characterized by thrombotic microangiopathy, hemolytic anemia, thrombocytopenia and acute renal failure. It can cause from permanent sequelae to death, mainly in children. In this work, using text mining (TM), we analyzed the explicit and implicit text of 16 192 original scientific articles on HUS indexed in the Europe PMC database. The objectives were to examine behaviors, track trends, and make predictions and cross-check data with other sources of information. For the analysis we used -among other computational tools- specially developed workflows (WF) in the KNIME platform. The TM on the words of the abstracts of the publications made it possible to: detect undescribed associations between events related to HUS; extract underlying information; make thematic clustering using unsupervised algorithms; make forecasting about the course of research associated with the topic. Both the approach and the WFs developed to perform Data Science on HUS can be applied to other biomedical topics and other scientific databases, making it possible to analyze relevant aspects in the field of human health to improve research, prevention and treatment of multiples diseases.

[Text mining in scientific publications with Argentine authors]

In the present work we use text mining as a treatment tool for a large scientific database, with the aim of obtaining new information about all the publications signed by Argentine authors and indexed until 2019, in the area of life sciences. More than 75 000 articles were analysed, published in around 5000 media, signed by about 186 000 authors with a workplace in Argentina or in collaborations with Argentine laboratories. Using automated tools that were developed ad hoc, the text of around 70 800 abstracts was analysed, seeking, through non-supervised digital detection, the main topics addressed by the authors, and the relationship with health problems in Argentina and their treatment. Results are also presented regarding the number of publications per year, the journals that have published them, and their authors and collaborations. These results, together with the predictions that were obtained, could become a useful tool to optimize the management of resources dedicated to basic and clinical research.

Human AQP1 is a constitutively open channel that closes by a membrane-tension-mediated mechanism

This work presents experimental results combined with model-dependent predictions regarding the osmotic-permeability regulation of human aquaporin 1 (hAQP1) expressed in Xenopus oocyte membranes. Membrane elastic properties were studied under fully controlled conditions to obtain a function that relates internal volume and pressure. This function was used to design a model in which osmotic permeability could be studied as a pressure-dependent variable. The model states that hAQP1 closes with membrane-tension increments. It is important to emphasize that the only parameter of the model is the initial osmotic permeability coefficient, which was obtained by model-dependent fitting. The model was contrasted with experimental records from emptied-out Xenopus laevis oocytes expressing hAQP1. Simulated results reproduce and predict volume changes in high-water-permeability membranes under hypoosmotic gradients of different magnitude, as well as under consecutive hypo- and hyperosmotic conditions. In all cases, the simulated permeability coefficients are similar to experimental values. Predicted pressure, volume, and permeability changes indicate that hAQP1 water channels can transit from a high-water-permeability state to a closed state. This behavior is reversible and occurs in a cooperative manner among monomers. We conclude that hAQP1 is a constitutively open channel that closes mediated by membrane-tension increments.

Water flux through human aquaporin 1: inhibition by intracellular furosemide and maximal response with high osmotic gradients

This work studies water permeability properties of human aquaporin 1 (hAQP1) expressed in Xenopus laevis oocyte membranes, applying a technique where cellular content is replaced with a known medium, with the possibility of measuring intracellular pressure. Consequences on water transport-produced by well-known anisotonic gradients and by the intracellular effect of probable aquaporin inhibitors-were tested. In this way, the specific intracellular inhibition of hAQP1 by the diuretic drug furosemide was demonstrated. In addition, experiments imposing anisotonic mannitol gradients with a constant ionic strength showed that the relationship between water flux and the applied mannitol gradient deflects from a perfect osmometer response when the gradient is higher than 150 mosmol kg (W) (-1) . These results would indicate that the passage of water molecules through hAQP1 may have a maximum rate. As a whole, this work demonstrates the technical advantage of controlling both intracellular pressure and medium composition in order to study biophysical properties of hAQP1, and contributes information on water channel behavior under osmotic challenges and the discovery of new inhibitors.

From membrane pores to aquaporins: 50 years measuring water fluxes

This review focuses on studies of water movement across biological membranes performed over the last 50 years. Different scientific approaches had tried to elucidate such intriguing mechanism, from hypotheses emphasizing the role of the lipid bilayer to the cloning of aquaporins, the ubiquitous proteins described as specific water channels. Pioneering and clarifying biophysical work are reviewed beside results obtained with the help of recent sophisticated techniques, to conclude that great advances in the subject live together with old questions without definitive answers.

A new data-acquisition system for the measurement of the net water flux across epithelia

We describe a computer-based data-acquisition system designed for the measurement of net water flux across epithelia. It is based on the detection of a liquid meniscus position in a capillary tube using an electro-optical device. Then the data are digitized, transferred to the computer main memory and saved in a file. The advantages of the system are: (a) to measure net water transfer with an accuracy of 50 nl; (b) to switch from absorptive to secretory conditions in real time; (c) data are directly digitized to be analytically, graphically and statistically treated; (d) the specially developed software allows change of time intervals for data acquirement and the scale in graphic events; (e) the software also allows recall to the monitor screen of graphics from previous tests or to print them on paper; (f) a simple mechanical structure, saving maintenance and time; and (g) high reliability.