Feasibility randomised controlled trial comparing TRAK-ACL digital rehabilitation intervention plus treatment as usual versus treatment as usual for patients following anterior cruciate ligament reconstruction

Objectives: To evaluate the feasibility of trialling taxonomy for the rehabilitation of knee conditions-ACL (TRAK-ACL), a digital health intervention that provides health information, personalised exercise plans and remote clinical support combined with treatment as usual (TAU), for people following ACL reconstruction. Methods: The study design was a two-arm parallel randomised controlled trial (RCT). Eligible participants were English-speaking adults who had undergone ACL reconstruction within the last 12 weeks, had access to the internet and could provide informed consent. Recruitment took place at three sites in the UK. TRAK-ACL intervention was an interactive website informed by behaviour change technique combined with TAU. The comparator was TAU. Outcomes were: recruitment and retention; completeness of outcome measures at follow-up; fidelity of intervention delivery and engagement with the intervention. Individuals were randomised using a computer-generated random number sequence. Blinded assessors allocated groups and collected outcome measures. Results: Fifty-nine people were assessed for eligibility at two of the participating sites, and 51 were randomised; 26 were allocated to TRAK-ACL and 25 to TAU. Follow-up data were collected on 44 and 40 participants at 3 and 6 months, respectively. All outcome measures were completed fully at 6 months except the Client Service Receipt Inventory. Two patients in each arm did not receive the treatment they were randomised to. Engagement with TRAK-ACL intervention was a median of 5 logins (IQR 3-13 logins), over 18 weeks (SD 12.2 weeks). Conclusion: TRAK-ACL would be suitable for evaluation of effectiveness in a fully powered RCT

Application of homotopy-perturbation method to fractional IVPs

Fractional initial-value problems (fIVPs) arise from many fields of physics and play a very important role in various branches of science and engineering. Finding accurate and efficient methods for solving fIVPs has become an active research undertaking. In this paper, both linear and nonlinear fIVPs are considered. Exact and/or approximate analytical solutions of the fIVPs are obtained by the analytic homotopy-perturbation method (HPM). The results of applying this procedure to the studied cases show the high accuracy, simplicity and efficiency of the approach

Neurological Disorders and Publication Abstracts Follow Elements of Social Network Patterns when Indexed Using Ontology Tree-Based Key Term Search

Disorders of the Central Nervous System (CNS) are worldwide causes of morbidity and mortality. In order to further investigate the nature of the CNS research, we generate from an initial reference a controlled vocabulary of CNS disorder-related terms and ontological tree structure for this vocabulary, and then apply the vocabulary in an analysis of the past ten years of abstracts (N = 10,488) from a major neuroscience journal. Using literal search methodology with our terminology tree, we find over 5,200 relationships between abstracts and clinical diagnostic topics. After generating a network graph of these document-topic relationships, we find that this network graph contains characteristics of document-author and other human social networks, including evidence of scale-free and power law-like node distributions. However, we also found qualitative evidence for Z-normal-type (albeit logarithmically skewed) distributions within disorder popularity. Lastly, we discuss potential consumer-centered as well as clinic-centered uses for our ontology and search methodology

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Spatial movement of the Wels catfish (Silurus glanis) in the Danube

Wels catfish (Silurus glanis, Linnaeus, 1758) is one of the most targeted species for recreational and commercial fishing in the Danube River, even though studies of behavior and movement patterns of Wels catfish in the Danube are rare. Wels catfish was caught downstream of Iron Gate II hydropower dam and tagged with an ultrasonic transmitter (Vemco Ltd, V16TP). Nine autonomous receivers (Vemco Ltd, VR 2W) recorded detections of spatial movement downstream of Iron Gate II dam between Serbia and Romania for almost two years, between the years 2015 and 2017. Our telemetry data found that Wels catfish exhibit relatively short movements within a maximum range (≈ 12 km), but as a territorial species most of the time it was recorded by the two receivers, close to the Iron Gate dam and location where it was caught. The longest displacement from the preferable place under Iron Gate II dam was migration to Romanian ship lock and turbines located in the right arm of the Danube River. Location under the river dam is already recognized as a place of aggregation of the fish and thus preference of predatory catfish is strongly connected with food availability. Our data revealed that dam and ship lock blocked further migration of this fish. The last signal received was during the winter 2017, which was a period with extremely low temperature and ice cover on the Danube River. Considering the fact that the ice displaced whole receiver deployment downstream the dam, we might conclude that the tagged catfish disappeared because of ice movement during the winter season. Results can be used for management ensuring habitat requirements and developing of restoration and conservation strategies

Ontology-driven indexing of public datasets for translational bioinformatics

The volume of publicly available genomic scale data is increasing. Genomic datasets in public repositories are annotated with free-text fields describing the pathological state of the studied sample. These annotations are not mapped to concepts in any ontology, making it difficult to integrate these datasets across repositories. We have previously developed methods to map text-annotations of tissue microarrays to concepts in the NCI thesaurus and SNOMED-CT

Annotation and query of tissue microarray data using the NCI Thesaurus

<p>Abstract</p> <p>Background</p> <p>The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample. These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult.</p> <p>Results</p> <p>We developed methods to map these annotations to the NCI thesaurus. Using the NCI-T we can effectively represent annotations for about 86% of the samples. We demonstrate how this mapping enables ontology driven integration and querying of tissue microarray data. We have deployed the mapping and ontology driven querying tools at the TMAD site for general use.</p> <p>Conclusion</p> <p>We have demonstrated that we can effectively map the diagnosis-related terms describing a sample in TMAD to the NCI-T. The NCI thesaurus terms have a wide coverage and provide terms for about 86% of the samples. In our opinion the NCI thesaurus can facilitate integration of this resource with other biological data.</p

EnvMine: A text-mining system for the automatic extraction of contextual information

<p>Abstract</p> <p>Background</p> <p>For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind.</p> <p>Results</p> <p>EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.</p> <p>Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.</p> <p>Conclusion</p> <p>EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.</p

OntoFox: web-based support for ontology reuse

<p>Abstract</p> <p>Background</p> <p>Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms.</p> <p>Findings</p> <p>OntoFox <url>http://ontofox.hegroup.org/</url> is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated.</p> <p>Conclusions</p> <p>OntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies.</p