Relevation! : an open source system for information retrieval relevance assessment

Relevation! is a system for performing relevance judgements for information retrieval evaluation. Relevation! is web-based, fully configurable and expandable; it allows researchers to effectively collect assessments and additional qualitative data. The system is easily deployed allowing assessors to smoothly perform their relevance judging tasks, even remotely. Relevation! is available as an open source project at: http://ielab.github.io/relevation.

Why assessing relevance in medical IR is demanding

This study investigates if and why assessing relevance of clinical records for a clinical retrieval task is cognitively demanding. Previous research has highlighted the challenges and issues information retrieval systems are faced with when determining the relevance of documents in this domain, e.g., the vocabulary mismatch problem. Determining if this assessment imposes cognitive load on human assessors, and why this is the case, may shed lights on what are the (cognitive) processes that assessors use for determining document relevance (in this domain). High cognitive load may impair the ability of the user to make accurate relevance judgements and hence the design of IR mechanisms may need to take this into account in order to reduce the load.

Perceptions of document relevance

This article presents a study of how humans perceive and judge the relevance of documents. Humans are adept at making reasonably robust and quick decisions about what information is relevant to them, despite the ever increasing complexity and volume of their surrounding information environment. The literature on document relevance has identified various dimensions of relevance (e.g., topicality, novelty, etc.), however little is understood about how these dimensions may interact. We performed a crowdsourced study of how human subjects judge two relevance dimensions in relation to document snippets retrieved from an internet search engine. The order of the judgment was controlled. For those judgments exhibiting an order effect, a q–test was performed to determine whether the order effects can be explained by a quantum decision model based on incompatible decision perspectives. Some evidence of incompatibility was found which suggests incompatible decision perspectives is appropriate for explaining interacting dimensions of relevance in such instances.

Clinicopathological relevance of BRAF mutations in human cancer

BRAF represents one of the most frequently mutated protein kinase genes in human tumours. The mutation is commonly tested in pathology practice. BRAF mutation is seen in melanoma, papillary thyroid carcinoma (including papillary thyroid carcinoma arising from ovarian teratoma), ovarian serous tumours, colorectal carcinoma, gliomas, hepatobiliary carcinomas and hairy cell leukaemia. In these cancers, various genetic aberrations of the BRAF proto-oncogene, such as different point mutations and chromosomal rearrangements, have been reported. The most common mutation, BRAF V600E, can be detected by DNA sequencing and immunohistochemistry on formalin fixed, paraffin embedded tumour tissue. Detection of BRAF V600E mutation has the potential for clinical use as a diagnostic and prognostic marker. In addition, a great deal of research effort has been spent in strategies inhibiting its activity. Indeed, recent clinical trials involving BRAF selective inhibitors exhibited promising response rates in metastatic melanoma patients. Clinical trials are underway for other cancers. However, cutaneous side effects of treatment have been reported and therapeutic response to cancer is short-lived due to the emergence of several resistance mechanisms. In this review, we give an update on the clinical pathological relevance of BRAF mutation in cancer. It is hoped that the review will enhance the direction of future research and assist in more effective use of the knowledge of BRAF mutation in clinical practice.

Altered JS-2 expression in colorectal cancers and its clinical pathological relevance

JS-2 is a novel gene located at 5p15.2 and originally detected in primary oesophageal cancer. There is no study on the role of JS-2 in colorectal cancer. The aim of this study is to determine the gene copy number and expression of JS-2 in a large cohort of patients with colorectal tumours and correlate these to the clinicopathological features of the cancer patients. We evaluated the DNA copy number and mRNA expression of JS-2 in 176 colorectal tissues (116 adenocarcinomas, 30 adenomas and 30 non-neoplastic tissues) using real-time polymerase chain reaction. JS-2 expression was also evaluated in two colorectal cancer cell lines and a benign colorectal cell line. JS-2 amplification was noted in 35% of the colorectal adenocarcinomas. Significant differences in relative expression levels for JS-2 mRNA between different colorectal tissues were noted (p = 0.05). Distal colorectal adenocarcinoma had significantly higher copy number than proximal adenocarcinoma (p = 0.005). The relative expression level of JS-2 was different between colonic and rectal adenocarcinoma (p = 0.007). Mucinous adenocarcinoma showed higher JS-2 expression than non-mucinous adenocarcinoma (p = 0.02). Early T-stage cancers appear to have higher JS-2 copy number and lower expression of JS-2 mRNA than later stage cancers (p = 0.001 and 0.03 respectively). Colorectal cancer cell lines showed lower expression of JS-2 than the benign colorectal cell line. JS-2 copy number change and expression were shown for the first time to be altered in the carcinogenesis of colorectal cancer. In addition, genetic alteration of JS-2 was found to be related to location, pathological subtypes and staging of colorectal cancer.

Optimism : what it is and its relevance in the school context

"For myself, I am an optimist - it does not seem to be much use to be anything else". Winston Churchill Optimism has its modern roots in philosophy dating back to the 17th century in the writings of philosophers such as Descartes and Voltaire (Domino & Conway, 2001). Previous to these philosophical writings, the concept of optimism was revealed in the teaching of many of the great spiritual traditions such as Buddhism and Christianity (Miller, Richards, & Keller, 2001). In the 20th century, optimism became defined in juxtaposition to pessimism, sometimes conceptualized as a bipolar unidimensional construct and by others as two related but separate constructs (Garber, 2000). Contemporary models (Scheier & Carver, 1985; Seligman, 1991) have increasingly focused on distinguishing optimism-pessimism as a general dispositional orientation, as described by expectancy theory, and as an explanatory process, described by explanatory style theory.

Marx as a Critical Discourse Analyst : The Genesis of a Critical Method and its Relevance to the Critique of Global Capital (with Phil Graham)

In this paper we identify elements in Marx’s economic and political writings that are relevant to contemporary critical discourse analysis (CDA). We argue that Marx can be seen to be engaging in a form of discourse analysis. We identify the elements in Marx’s historical materialist method that support such a perspective, and exemplify these in longitudinal comparison of Marx’s texts.

Relevance of the deletion polymorphisms of the glutathione S-transferases GSTT1 and GSTM1 in pharmacology and toxicology

Although cytosolic glutathione S-transferase (GST) enzymes occupy a key position in biological detoxification processes, two of the most relevant human isoenzymes, GSTT1-1 and GSTM1-1, are genetically deleted (non-functional alleles GSTT1*0 and GSTM1*0) in a high percentage of the human population, with major ethnic differences. The structures of the GSTT and GSTM gene areas explain the underlying genetic processes. GSTT1-1 is highly conserved during evolution and plays a major role in phase-II biotransformation of a number of drugs and industrial chemicals, e.g. cytostatic drugs, hydrocarbons and halogenated hydrocarbons. GSTM1-1 is particularly relevant in the deactivation of carcinogenic intermediates of polycyclic aromatic hydrocarbons. Several lines of evidence suggest that hGSTT1-1 and/or hGSTM1-1 play a role in the deactivation of reactive oxygen species that are likely to be involved in cellular processes of inflammation, ageing and degenerative diseases. There is cumulating evidence that combinations of the GSTM1*0 state with other genetic traits affecting the metabolism of carcinogens (CYP1A1, GSTP1) may predispose the aero-digestive tract and lung, especially in smokers, to a higher risk of cancer. The GSTM1*0 status appears also associated with a modest increase in the risk of bladder cancer, consistent with a GSTM1 interaction with carcinogenic tobacco smoke constituents. Both human GST deletions, although largely counterbalanced by overlapping substrate affinities within the GST superfamily, have consequences when the organism comes into contact with distinct man-made chemicals. This appears relevant in industrial toxicology and in drug metabolism.

Conjugation of carcinogens by 6 class glutathione S-transferases : mechanisms and relevance to variations in human risk

Conjugation of chemicals with glutathione (GSH) can lead to decreased or increased toxicity. A genetic deficiency in the GSH S-transferase μ class gene M1 has been hypothesized to lead to greater risk of lung cancer in smokers. Recently a gene deletion polymorphism involving the human θ enzyme T1 has been described; the enzyme is present in erythrocytes and can be readily assayed. A rat θ class enzyme, 5-5, has structural and catalytic similarity and the protein was expressed in the Salmonella typhimurium tester strain TA1535. Expression of the cDNA vector increased the mutagenicity of ethylene dibromide and several methylene dihalides. Mutations resulting from the known GSH S-transferase substrate 1,2-epoxy-3-(4′nitrophenoxy)propane were decreased in the presence of the transferase. Expression of transferase 5-5 increased mutations when 1,2,3,4-diepoxybutane (butadiene diepoxide), 4-bromo-1,2-epoxybutane, or 1,3-dichloracetone were added. The latter compound is a model for the putative 1,2-dibromo-3-chloropropane oxidation product 1-bromo-3-chloroacetone. These genotoxicity and genotyping assays may be of use in further studies of the roles of GSH S-transferase θ enzymes in bioactivation and detoxication and any changes in risk due to polymorphism.

NT-ProBNP levels in saliva and its clinical relevance to heart failure

Background: Current blood based diagnostic assays to detect heart failure (HF) have large intra-individual and inter-individual variations which have made it difficult to determine whether the changes in the analyte levels reflect an actual change in disease activity. Human saliva mirrors the body's health and well being and similar to 20% of proteins that are present in blood are also found in saliva. Saliva has numerous advantages over blood as a diagnostic fluid which allows for a non-invasive, simple, and safe sample collection. The aim of our study was to develop an immunoassay to detect NT-proBNP in saliva and to determine if there is a correlation with blood levels. Methods: Saliva samples were collected from healthy volunteers (n = 40) who had no underlying heart conditions and HF patients (n = 45) at rest. Samples were stored at -80 degrees C until analysis. A customised homogeneous sandwich AlphaLISA((R)) immunoassay was used to quantify NT-proBNP levels in saliva. Results: Our NT-proBNP immunoassay was validated against a commercial Roche assay on plasma samples collected from HF patients (n = 37) and the correlation was r(2) = 0.78 (p<0.01, y = 1.705 x +1910.8). The median salivary NT-proBNP levels in the healthy and HF participants were <16 pg/mL and 76.8 pg/mL, respectively. The salivary NT-proBNP immunoassay showed a clinical sensitivity of 82.2% and specificity of 100%, positive predictive value of 100% and negative predictive value of 83.3%, with an overall diagnostic accuracy of 90.6%. Conclusion: We have firstly demonstrated that NT-proBNP can be detected in saliva and that the levels were higher in heart failure patients compared with healthy control subjects. Further studies will be needed to demonstrate the clinical relevance of salivary NT-proBNP in unselected, previously undiagnosed populations.

On the (ir)relevance of rates of return measures of economic performance to small boats

A common measure of the economic performance of different fleet segments in fisheries is the rate of return on capital. However, in the English Channel (UK), observed changes in the fleet structure are at odds with expectations given the observed rates of return on capital. This disjunction between expected and observed behaviour raises the question as to the appropriateness of rate of return on capital as a measure of economic performance for small boats whose main input is often non-wage labour. In this paper, an alternative performance indicator is developed based on returns on owner-operator labour. This indicator appears to be of more relevance to small scale boats than the traditional returns on capital, and a better indicator of the direction of adjustment in the fishery.

Explanation of relevance judgement discrepancy with quantum interference

A key concept in many Information Retrieval (IR) tasks, e.g. document indexing, query language modelling, aspect and diversity retrieval, is the relevance measurement of topics, i.e. to what extent an information object (e.g. a document or a query) is about the topics. This paper investigates the interference of relevance measurement of a topic caused by another topic. For example, consider that two user groups are required to judge whether a topic q is relevant to a document d, and q is presented together with another topic (referred to as a companion topic). If different companion topics are used for different groups, interestingly different relevance probabilities of q given d can be reached. In this paper, we present empirical results showing that the relevance of a topic to a document is greatly affected by the companion topic’s relevance to the same document, and the extent of the impact differs with respect to different companion topics. We further analyse the phenomenon from classical and quantum-like interference perspectives, and connect the phenomenon to nonreality and contextuality in quantum mechanics. We demonstrate that quantum like model fits in the empirical data, could be potentially used for predicting the relevance when interference exists.

Learning-based Relevance Feedback for Web-based Relation Completion

In a pilot application based on web search engine calledWeb-based Relation Completion (WebRC), we propose to join two columns of entities linked by a predefined relation by mining knowledge from the web through a web search engine. To achieve this, a novel retrieval task Relation Query Expansion (RelQE) is modelled: given an entity (query), the task is to retrieve documents containing entities in predefined relation to the given one. Solving this problem entails expanding the query before submitting it to a web search engine to ensure that mostly documents containing the linked entity are returned in the top K search results. In this paper, we propose a novel Learning-based Relevance Feedback (LRF) approach to solve this retrieval task. Expansion terms are learned from training pairs of entities linked by the predefined relation and applied to new entity-queries to find entities linked by the same relation. After describing the approach, we present experimental results on real-world web data collections, which show that the LRF approach always improves the precision of top-ranked search results to up to 8.6 times the baseline. Using LRF, WebRC also shows performances way above the baseline.

Relevance feature discovery for text mining

It is a big challenge to guarantee the quality of discovered relevance features in text documents for describing user preferences because of large scale terms and data patterns. Most existing popular text mining and classification methods have adopted term-based approaches. However, they have all suffered from the problems of polysemy and synonymy. Over the years, there has been often held the hypothesis that pattern-based methods should perform better than term-based ones in describing user preferences; yet, how to effectively use large scale patterns remains a hard problem in text mining. To make a breakthrough in this challenging issue, this paper presents an innovative model for relevance feature discovery. It discovers both positive and negative patterns in text documents as higher level features and deploys them over low-level features (terms). It also classifies terms into categories and updates term weights based on their specificity and their distributions in patterns. Substantial experiments using this model on RCV1, TREC topics and Reuters-21578 show that the proposed model significantly outperforms both the state-of-the-art term-based methods and the pattern based methods.