Text Mining the History of Medicine

Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform

Liquid phase alkylation of phenol with 1-octene over large pore zeolites

A comparative study is presented of the liquid phase alkylation of phenol with 1-octene over different zeolite catalysts: H-beta (BEA(15)), H-mordenite (MOR(11)) and H-USY (FAU(15)). A wide spectrum of monoalkylated products, identified as isomers of phenyl octyl ether (O-alkylate) and octyl phenol (C-alkylate), was formed in the reaction. The reaction was studied in detail over BEA(15), such studies included the influence of process variables such as temperature, reactant mole ratio, catalyst amount and alkali metal (K) poisoning on its performance in the alkylation reaction. A kinetic analysis of the reaction over BEA(15) was also carried out assuming a second order parallel reaction mechanism. The activity of the different catalysts for the reaction followed the order: BEA(15) > FAU(15) > MOR(11). The poisoning of BEA(15) with potassium resulted in a decrease in the catalyst activity concomitant with a decrease in the number of strong acid centres in the catalyst

Alkylation of anisole with 1-hexene and 1-hexanol over zeolite H-beta

An examination of the kinetics of the alkylation of anisole with 1-hexene and 1-hexanol to produce alkylates over zeolite H-beta is presented. Anisole alkylation is found to occur by a set of parallel reactions when hexene is used as the alkylating agent. When hexyl alcohol is the alkylating agent, the reaction follows a multi-step parallel-series mechanism to form monoalkylates and dihexylether. With 1-hexene, a group of isomeric alkylates, viz., ortho-2-hexyl anisole (2-OHA), ortho-3-hexyl anisole (3-OHA), para-2-hexyl anisole (2-PHA), and para-3-hexyl anisole (3-PHA) was obtained. With hexanol, the olefin (hexene) and dihexyl ether were obtained additionally. The influence of process parameters like temperature, catalyst quantity, and alkylating agent on reaction behavior is reported

Acylation of anisole with long-chain carboxylic acids over wide pore zeolites

The acylation of anisole with long-chain carboxylic acids (hexanoic, octanoic and decanoic) has been studied over three large pore zeolites-beta (BEA), faujasite (FAU) and mordenite (MOR). The acylation of anisole with the long chain acids produced mainly the ketone (4-methoxy phenyl alkyl ketone) and small amounts of the ester (phenyl alkanoate). The results revealed the reaction to be influenced by the type of zeolite and its Si/Al ratio (acidity) besides the chain length (carbon number) of the carboxylic acid. In the acylation of anisole with hexanoic acid, the activity of the zeolites increased with dealumination as it led to the generation of mesopores that resulted in a decrease in diffusion resistance of the zeolites. The reactivity of the acids in the acylation reaction was found to decrease with increase in the carbon number. The experimental data have been fitted into a pseudo first order kinetic model

Claisen rearrangement of allyl phenyl ether over zeolites beta, mordenite and Y

The Claisen rearrangement of allyl phenyl ether (APE) to o-allylphenol was investigated over zeolites beta (BEA), mordenite (MOR) and Y (FAU) with different Si/Al ratios. Over the zeolite catalysts, the allylphenol cyclized to produce 2,3-dihydro-2-methyl benzofuran. Larger catalyst loading, higher reaction temperatures and longer run duration favored the formation of the ring compound. Conversion was small over MOR and FAU although they possessed higher acidity (as measured by the temperature programmed desorption of ammonia) compared to BEA. Studies using BEA revealed that the nature of the solvent influenced the reaction rate. The order of reactivity in the solvents was, benzene > EDC (1,2-dichloroethane) > toluene > TCE (1,1,2,2-tetrachloroethane) ≫ ACN (acetonitrile). The intermediate allylphenol reacted with the aromatic solvents to produce byproducts when benzene and toluene were used as solvents. A kinetic analysis assuming first order series and parallel reactions is presented

Internal drainage of liver hydatid - concerns and solutions

There are a number of procedures for the surgical management of liver hydatid and controversies still persist regarding the best technique Forty-three patients with hydatid disease of the liver were managed surgically between 1991 and 1998. Internal drainage (Roux-en-Y cysto-jejunostomy) was performed in eight cases of liver hydatid with biliary communications. Internal drainage was associated with a high incidence of the infection of the residual cavity with abscess formation (n=3/8, 38%). In all the three patients the cyst was located in the superior segments of the liver (VII, VIII, IVa). In two of the three patients the cyst was larger than 10 cm. Dependent siting of stoma is a key for the successful outcome of internal drainage in liver hydatid. This procedure is best avoided in large cysts, especially those located in the superior segments and with pericyst calcification

Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers.

BackgroundInformatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at over 200 healthcare institutions for querying patient data. The i2b2 platform has several components with numerous dependencies and configuration parameters, which renders the task of installing or upgrading i2b2 a challenging one. Even with the availability of extensive documentation and tutorials, new users often require several weeks to correctly install a functional i2b2 platform. The goal of this work is to simplify the installation and upgrade process for i2b2. Specifically, we have containerized the core components of the platform, and evaluated the containers for ease of installation.ResultsWe developed three Docker container images: WildFly, database, and web, to encapsulate the three major deployment components of i2b2. These containers isolate the core functionalities of the i2b2 platform, and work in unison to provide its functionalities. Our evaluations indicate that i2b2 containers function successfully on the Linux platform. Our results demonstrate that the containerized components work out-of-the-box, with minimal configuration.ConclusionsContainerization offers the potential to package the i2b2 platform components into standalone executable packages that are agnostic to the underlying host operating system. By releasing i2b2 as a Docker container, we anticipate that users will be able to create a working i2b2 hive installation without the need to download, compile, and configure individual components that constitute the i2b2 cells, thus making this platform accessible to a greater number of institutions