Identify disorders in health records using Conditional Random Fields and Metamap: AEHRC at ShARe/CLEF 2013 eHealth Evaluation Lab Task 1

The Australian e-Health Research Centre (AEHRC) recently participated in the ShARe/CLEF eHealth Evaluation Lab Task 1. The goal of this task is to individuate mentions of disorders in free-text electronic health records and map disorders to SNOMED CT concepts in the UMLS metathesaurus. This paper details our participation to this ShARe/CLEF task. Our approaches are based on using the clinical natural language processing tool Metamap and Conditional Random Fields (CRF) to individuate mentions of disorders and then to map those to SNOMED CT concepts. Empirical results obtained on the 2013 ShARe/CLEF task highlight that our instance of Metamap (after ltering irrelevant semantic types), although achieving a high level of precision, is only able to identify a small amount of disorders (about 21% to 28%) from free-text health records. On the other hand, the addition of the CRF models allows for a much higher recall (57% to 79%) of disorders from free-text, without sensible detriment in precision. When evaluating the accuracy of the mapping of disorders to SNOMED CT concepts in the UMLS, we observe that the mapping obtained by our ltered instance of Metamap delivers state-of-the-art e ectiveness if only spans individuated by our system are considered (`relaxed' accuracy).

Bike share's impact on car use : evidence from the United States, Great Britain, and Australia

There are currently more than 400 cities operating bike share programs. Purported benefits of bike share programs include flexible mobility, physical activity, reduced congestion, emissions and fuel use. Implicit or explicit in the calculation of program benefits are assumptions regarding the modes of travel replaced by bike share journeys. This paper examines the degree to which car trips are replaced by bike share, through an examination of survey and trip data from bike share programs in Melbourne, Brisbane, Washing, D.C., London, and Minneapolis/St. Paul. A secondary and unique component of this analysis examines motor vehicle support services required for bike share fleet rebalancing and maintenance. These two components are then combined to estimate bike share’s overall contribution to changes in vehicle kilometres traveled. The results indicate that the estimated mean reduction in car use due to bike share is at least twice the distance covered by operator support vehicles, with the exception of London, in which the relationship is reversed, largely due to a low car mode substitution rate. As bike share programs mature, evaluation of their effectiveness in reducing car use may become increasingly important. This paper reveals that by increasing the convenience of bike share relative to car use and by improving perceptions of safety, the capacity of bike share programs to reduce vehicle trips and yield overall net benefits will be enhanced. Researchers can adapt the analytical approach proposed in this paper to assist in the evaluation of current and future bike share programs.

Overview of the ShARe/CLEF eHealth Evaluation Lab 2013

Discharge summaries and other free-text reports in healthcare transfer information between working shifts and geographic locations. Patients are likely to have difficulties in understanding their content, because of their medical jargon, non-standard abbreviations,and ward-specific idioms. This paper reports on an evaluation lab with an aim to support the continuum of care by developing methods and resources that make clinical reports in English easier to understand for patients, and which helps them in finding information related to their condition.

ShARe/CLEF eHealth Evaluation Lab 2013, Task 3: Information retrieval to address patients' questions when reading clinical reports

This paper presents the results of task 3 of the ShARe/CLEF eHealth Evaluation Lab 2013. This evaluation lab focuses on improving access to medical information on the web. The task objective was to investigate the effect of using additional information such as the discharge summaries and external resources such as medical ontologies on the IR effectiveness. The participants were allowed to submit up to seven runs, one mandatory run using no additional information or external resources, and three each using or not using discharge summaries.

Bike share's impact on car use : evidence from the United States, Great Britain, and Australia

There are currently more than 700 cities operating bike share programs. Purported benefits of bike share include flexible mobility, physical activity, reduced congestion, emissions and fuel use. Implicit or explicit in the calculation of program benefits are assumptions regarding the modes of travel replaced by bike share journeys. This paper examines the degree to which car trips are replaced by bike share, through an examination of survey and trip data from bike share programs in Melbourne, Brisbane, Washington, D.C., London, and Minneapolis/St. Paul. A secondary and unique component of this analysis examines motor vehicle support services required for bike share fleet rebalancing and maintenance. These two components are then combined to estimate bike share’s overall contribution to changes in vehicle kilometers traveled. The results indicate an estimated reduction in motor vehicle use due to bike share of approx. 90,000 km per annum in Melbourne and Minneapolis/St. Paul and 243,291 km for Washington, D.C. London’s bike share program however recorded an additional 766,341 km in motor vehicle use. This was largely due to a low car mode substitution rate and substantial truck use for rebalancing of bicycles. As bike share programs mature, evaluation of their effectiveness in reducing car use may become increasingly important. Researchers can adapt the analytical approach proposed in this paper to assist in the evaluation of current and future bike share programs.

Overview of the ShARe/CLEF eHealth Evaluation Lab 2014

This paper reports on the 2nd ShARe/CLEFeHealth evaluation lab which continues our evaluation resource building activities for the medical domain. In this lab we focus on patients' information needs as opposed to the more common campaign focus of the specialised information needs of physicians and other healthcare workers. The usage scenario of the lab is to ease patients and next-of-kins' ease in understanding eHealth information, in particular clinical reports. The 1st ShARe/CLEFeHealth evaluation lab was held in 2013. This lab consisted of three tasks. Task 1 focused on named entity recognition and normalization of disorders; Task 2 on normalization of acronyms/abbreviations; and Task 3 on information retrieval to address questions patients may have when reading clinical reports. This year's lab introduces a new challenge in Task 1 on visual-interactive search and exploration of eHealth data. Its aim is to help patients (or their next-of-kin) in readability issues related to their hospital discharge documents and related information search on the Internet. Task 2 then continues the information extraction work of the 2013 lab, specifically focusing on disorder attribute identification and normalization from clinical text. Finally, this year's Task 3 further extends the 2013 information retrieval task, by cleaning the 2013 document collection and introducing a new query generation method and multilingual queries. De-identified clinical reports used by the three tasks were from US intensive care and originated from the MIMIC II database. Other text documents for Tasks 1 and 3 were from the Internet and originated from the Khresmoi project. Task 2 annotations originated from the ShARe annotations. For Tasks 1 and 3, new annotations, queries, and relevance assessments were created. 50, 79, and 91 people registered their interest in Tasks 1, 2, and 3, respectively. 24 unique teams participated with 1, 10, and 14 teams in Tasks 1, 2 and 3, respectively. The teams were from Africa, Asia, Canada, Europe, and North America. The Task 1 submission, reviewed by 5 expert peers, related to the task evaluation category of Effective use of interaction and targeted the needs of both expert and novice users. The best system had an Accuracy of 0.868 in Task 2a, an F1-score of 0.576 in Task 2b, and Precision at 10 (P@10) of 0.756 in Task 3. The results demonstrate the substantial community interest and capabilities of these systems in making clinical reports easier to understand for patients. The organisers have made data and tools available for future research and development.

Working notes for TopSig at ShARe/CLEF 2013

We used our TopSig open-source indexing and retrieval tool to produce runs for the ShARe/CLEF eHealth 2013 track. TopSig was used to produce runs using the query fields and provided discharge summaries, where appropriate. Although the improvement was not great TopSig was able to gain some benefit from utilising the discharge summaries, although the software needed to be modified to support this. This was part of a larger experiment involving determining the applicability and limits to signature-based approaches.

Factors influencing bike share membership : an analysis of Melbourne and Brisbane

The number of bike share programs has increased rapidly in recent years and there are currently over 700 programs in operation globally. Australia’s two bike share programs have been in operation since 2010 and have significantly lower usage rates compared to Europe, North America and China. This study sets out to understand and quantify the factors influencing bike share membership in Australia’s two bike share programs located in Melbourne and Brisbane. An online survey was administered to members of both programs as well as a group with no known association with bike share. A logistic regression model revealed several significant predictors of membership including reactions to mandatory helmet legislation, riding activity over the previous month, and the degree to which convenience motivated private bike riding. In addition, respondents aged 18 - 34 and having docking station within 250m of their workplace were found to be statistically significant predictors of bike share membership. Finally, those with relatively high incomes increased the odds of membership. These results provide insight as to the relative influence of various factors impacting on bike share membership in Australia. The findings may assist bike share operators to maximize membership potential and help achieve the primary goal of bike share – to increase the sustainability of the transport system.

On the need for an international effort to capture, share and use crystallization screening data

When crystallization screening is conducted many outcomes are observed but typically the only trial recorded in the literature is the condition that yielded the crystal(s) used for subsequent diffraction studies. The initial hit that was optimized and the results of all the other trials are lost. These missing results contain information that would be useful for an improved general understanding of crystallization. This paper provides a report of a crystallization data exchange (XDX) workshop organized by several international large-scale crystallization screening laboratories to discuss how this information may be captured and utilized. A group that administers a significant fraction of the worlds crystallization screening results was convened, together with chemical and structural data informaticians and computational scientists who specialize in creating and analysing large disparate data sets. The development of a crystallization ontology for the crystallization community was proposed. This paper (by the attendees of the workshop) provides the thoughts and rationale leading to this conclusion. This is brought to the attention of the wider audience of crystallographers so that they are aware of these early efforts and can contribute to the process going forward. © 2012 International Union of Crystallography All rights reserved.

The equity and efficiency of the Australian share market with respect to director trading

Purpose – The purpose of this paper is to investigate the extent of directors breaching the reporting requirements of the Australian Stock Exchange (ASX) and the Corporations Act in Australia. Further, it seeks to assess whether directors in Australia achieve abnormal returns from trades in their own companies. Design/methodology/approach – Using an event study approach on an Australian sample, abnormal returns for a range of situations were estimated. Findings – A total of 13 (seven) per cent of own‐company directors trades do not meet the ASX (Corporations Act) requirement of reporting within five (14) business days. Directors do achieve abnormal returns through trading in shares of their own companies. Ignoring transaction costs, outsiders can achieve abnormal returns by imitating directors' trades. Analysis of returns to directors after they trade but before they announce the trade to the market shows that directors are making small but statistically significant returns that are not available to the market. Analysis of returns to directors subsequent to the ASX reporting requirement up to the day the trade is reported shows that directors are making small but statistically significant returns that should be available to the market. Research limitations/implications – Future research should investigate the linkages between late reporting by directors and disadvantages to outside shareholders and the implementation of internal policies implemented to mitigate insider trading. Practical implications – Market participants should remain vigilant regarding the potential for late/non‐reporting of directors' trades. Originality/value – Uncovering breaches of reporting regulations are particularly important given that directors tend to purchase (sell) shares when the price is low (high), thereby achieving abnormal returns.

Fusion transcript loci share many genomic features with non-fusion loci

Background Fusion transcripts are found in many tissues and have the potential to create novel functional products. Here, we investigate the genomic sequences around fusion junctions to better understand the transcriptional mechanisms mediating fusion transcription/splicing. We analyzed data from prostate (cancer) cells as previous studies have shown extensively that these cells readily undergo fusion transcription. Results We used the FusionMap program to identify high-confidence fusion transcripts from RNAseq data. The RNAseq datasets were from our (N = 8) and other (N = 14) clinical prostate tumors with adjacent non-cancer cells, and from the LNCaP prostate cancer cell line that were mock-, androgen- (DHT), and anti-androgen- (bicalutamide, enzalutamide) treated. In total, 185 fusion transcripts were identified from all RNAseq datasets. The majority (76 %) of these fusion transcripts were ‘read-through chimeras’ derived from adjacent genes in the genome. Characterization of sequences at fusion loci were carried out using a combination of the FusionMap program, custom Perl scripts, and the RNAfold program. Our computational analysis indicated that most fusion junctions (76 %) use the consensus GT-AG intron donor-acceptor splice site, and most fusion transcripts (85 %) maintained the open reading frame. We assessed whether parental genes of fusion transcripts have the potential to form complementary base pairing between parental genes which might bring them into physical proximity. Our computational analysis of sequences flanking fusion junctions at parental loci indicate that these loci have a similar propensity as non-fusion loci to hybridize. The abundance of repetitive sequences at fusion and non-fusion loci was also investigated given that SINE repeats are involved in aberrant gene transcription. We found few instances of repetitive sequences at both fusion and non-fusion junctions. Finally, RT-qPCR was performed on RNA from both clinical prostate tumors and adjacent non-cancer cells (N = 7), and LNCaP cells treated as above to validate the expression of seven fusion transcripts and their respective parental genes. We reveal that fusion transcript expression is similar to the expression of parental genes. Conclusions Fusion transcripts maintain the open reading frame, and likely use the same transcriptional machinery as non-fusion transcripts as they share many genomic features at splice/fusion junctions.

Head motion and Inattention/Hyperactivity share common genetic influences: Implications for fMRI studies of ADHD

Head motion (HM) is a well known confound in analyses of functional MRI (fMRI) data. Neuroimaging researchers therefore typically treat HM as a nuisance covariate in their analyses. Even so, it is possible that HM shares a common genetic influence with the trait of interest. Here we investigate the extent to which this relationship is due to shared genetic factors, using HM extracted from resting-state fMRI and maternal and self report measures of Inattention and Hyperactivity-Impulsivity from the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scales. Our sample consisted of healthy young adult twins (N = 627 (63% females) including 95 MZ and 144 DZ twin pairs, mean age 22, who had mother-reported SWAN; N = 725 (58% females) including 101 MZ and 156 DZ pairs, mean age 25, with self reported SWAN). This design enabled us to distinguish genetic from environmental factors in the association between head movement and ADHD scales. HM was moderately correlated with maternal reports of Inattention (r = 0.17, p-value = 7.4E-5) and Hyperactivity-Impulsivity (r = 0.16, p-value = 2.9E-4), and these associations were mainly due to pleiotropic genetic factors with genetic correlations [95% CIs] of rg = 0.24 [0.02, 0.43] and rg = 0.23 [0.07, 0.39]. Correlations between self-reports and HM were not significant, due largely to increased measurement error. These results indicate that treating HM as a nuisance covariate in neuroimaging studies of ADHD will likely reduce power to detect between-group effects, as the implicit assumption of independence between HM and Inattention or Hyperactivity-Impulsivity is not warranted. The implications of this finding are problematic for fMRI studies of ADHD, as failing to apply HM correction is known to increase the likelihood of false positives. We discuss two ways to circumvent this problem: censoring the motion contaminated frames of the RS-fMRI scan or explicitly modeling the relationship between HM and Inattention or Hyperactivity-Impulsivity

Sign and share: What influences our participation in online microvolunteering

Microvolunteering is bite-size volunteering with no commitment to repeat and minimum formality, involving short and specific actions. Online microvolunteering occurs through an internet-connected device. University students' online microvolunteering decisions were investigated using an extended theory of planned behavior (TPB) comprising attitudes and normative and control perceptions, with the additional variables of moral norm and group norm. Participants (N = 303) completed the main TPB questionnaire and 1-month follow-up survey (N = 171) assessing engagement in online microvolunteering. Results generally supported standard and additional TPB constructs predicting intention. Intention predicted behavior. The findings suggest an important role for attitudes and moral considerations in understanding what influences this increasingly popular form of online activity.

Evaluating the regional and distributional impacts of forestry cost-share payments.

XVIII IUFRO World Congress, Ljubljana 1986.