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.

Morphometric stability of the corneal subbasal nerve plexus in healthy individuals a 3-year longitudinal study using corneal confocal microscopy

Purpose We examined the age-dependent alterations and longitudinal course of subbasal nerve plexus (SNP) morphology in healthy individuals. Methods Laser-scanning corneal confocal microscopy, ocular screening, and health and metabolic assessment were performed on 64 healthy participants at baseline and at 12-month intervals for 3 years. At each annual visit, eight central corneal images of the SNP were selected and analyzed using a fully-automated analysis system to quantify corneal nerve fiber length (CNFL). Two linear mixed model approaches were fitted to examine the relationship between age and CNFL, and the longitudinal changes of CNFL over three years. Results At baseline, mean age was 51.9 ± 14.7 years. The cohort was sex balanced (χ2 = 0.56, P = 0.45). Age (t = 1.6, P = 0.12) and CNFL (t = -0.50, P = 0.62) did not differ between sexes. A total of 52 participants completed the 36-month visit and 49 participants completed all visits. Age had a significant effect on CNFL (F1,33 = 5.67, P = 0.02) with a linear decrease of 0.05 mm/mm2 in CNFL per one year increase in age. No significant change in CNFL was observed over the 36-month period (F1,55 = 0.69, P = 0.41). Conclusions The CNFL showed a stable course over a 36-month period in healthy individuals, although there was a slight linear reduction in CNFL with age. The findings of this study have implications for understanding the time-course of the effect of pathology and surgical or therapeutic interventions on the morphology of the SNP, and serves to confirm the suitability of CNFL as a screening/monitoring marker for peripheral neuropathies.

Indirect effects of phytochemicals on offspring performance of Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)

Phytochemical lures such as methyl eugenol (ME) and cue-lure are used in the management of Bactrocera fruit flies for monitoring and control. These lures are not just attractants, but also trigger physiological changes in males that lead to enhanced mating success. Additionally, in the cue-lure-responsive Bactrocera tryoni, females mated with lure-fed males exhibit changes in fecundity, remating receptivity and longevity. While the lures show current generation effects, no research has been carried out on possible multigenerational effects, although such effects have been hypothesized within a ‘sexy-son’ sexual selection model. In this study, we test for indirect, cross-generational effects of lure exposure in F1offspring of B. tryoni females mated with cue-lure-fed, zingerone-fed and lure-unfed (=control) males. The F1 attributes we recorded were immature development time, immature survival, adult survival and adult male lure foraging. No significant differences were found between treatments for any of the three life-history measurements, except that the offspring sired by zingerone-fed males had a longer egg development time than cue-lure and control offspring. However, indirect exposure to lures significantly enhanced the lure-foraging ability of F1 adult males. More offspring of cue-lure-fed males arrived at a lure source in both large flight cages and small laboratory cages over a 2-h period than did control males. The offspring of zingerone-fed males were generally intermediate between cue-lure and control offspring. This study provides the first evidence of a next generation effect of fruit fly male lures. While the results of this study support a ‘sexy-son’ sexual selection mechanism for the evolution of lure response in Bactrocera fruit flies, our discussion urges caution in interpreting our results in this way.

Centroid training to achieve effective text classification

Traditional text classification technology based on machine learning and data mining techniques has made a big progress. However, it is still a big problem on how to draw an exact decision boundary between relevant and irrelevant objects in binary classification due to much uncertainty produced in the process of the traditional algorithms. The proposed model CTTC (Centroid Training for Text Classification) aims to build an uncertainty boundary to absorb as many indeterminate objects as possible so as to elevate the certainty of the relevant and irrelevant groups through the centroid clustering and training process. The clustering starts from the two training subsets labelled as relevant or irrelevant respectively to create two principal centroid vectors by which all the training samples are further separated into three groups: POS, NEG and BND, with all the indeterminate objects absorbed into the uncertain decision boundary BND. Two pairs of centroid vectors are proposed to be trained and optimized through the subsequent iterative multi-learning process, all of which are proposed to collaboratively help predict the polarities of the incoming objects thereafter. For the assessment of the proposed model, F1 and Accuracy have been chosen as the key evaluation measures. We stress the F1 measure because it can display the overall performance improvement of the final classifier better than Accuracy. A large number of experiments have been completed using the proposed model on the Reuters Corpus Volume 1 (RCV1) which is important standard dataset in the field. The experiment results show that the proposed model has significantly improved the binary text classification performance in both F1 and Accuracy compared with three other influential baseline models.

Mating compatibility between bactrocera invadens and bactrocera dorsalis (Diptera: Tephritidae)

The invasive fruit fly, Bactrocera invadens Drew, Tsuruta & White, is a highly polyphagous fruit pest that occurs predominantly in Africa yet has its origins in the Indian subcontinent. It is extremely morphologically and genetically similar to the Oriental fruit fly, Bactrocera dorsalis (Hendel); as such the specific relationship between these two species is unresolved. We assessed prezygotic compatibility between B. dorsalis and B. invadens using standardized field cage mating tests, which have proven effectiveness in tephritid cryptic species studies. These tests were followed by an assessment of postzygotic compatibility by examining egg viability, larval and pupal survival, and sex ratios of offspring produced from parental and subsequent F1 crosses to examine for hybrid breakdown as predicted under a two-species hypothesis. B. dorsalis was sourced from two countries (Pakistan and China), and each population was compared with B. invadens from its type locality of Kenya. B. invadens mated randomly with B. dorsalis from both localities, and there were generally high levels of hybrid viability and survival resulting from parental and F1 crosses. Furthermore, all but one hybrid cross resulted in equal sex ratios, with the single deviation in favor of males and contrary to expectations under Haldane's rule. These data support the hypothesis that B. dorsalis and B. invadens represent the same biological species, an outcome that poses significant implications for pest management and international trade for sub-Saharan Africa.

Tendinopathy alters ultrasound transmission in the patellar tendon during squatting

Measurement of loading patterns of the patellar tendon during activity is important in understanding tendon injury. We used transmission-mode ultrasonography to investigate patellar tendon loading during squatting in adults with and without tendinopathy. It was hypothesized that axial ultrasonic velocity, a surrogate measure of the elastic modulus of tendon, would be lower in tendinopathy. Ultrasound velocity was measured in both patellar tendons of adults with unilateral patellar tendinopathy (n=9) and in healthy controls (n=16) during a bilateral squat manoeuvre. Sagittal knee movement was measured simultaneously with an electrogoniometer. Statistical comparisons between healthy and injured tendons were made using 2–way mixed–design ANOVAs. Axial ultrasound velocity in both symptomatic and asymptomatic patellar tendons in tendinopathy was approximately 15% higher than in healthy tendons at the commencement (F1,23=5.2, P<.05) and completion (F1,23=4.5, P<.05) of the squat. While peak velocity was ≈5% higher during both flexion (F1,23=5.4, P<.05) and extension (F1,23=5.3, P<.05) phases, there was no significant between–group difference at the mid–point of the movement. There were no significant differences in the rate and magnitude of knee movement between groups. Although further research is required, these findings suggest enhanced baseline muscle activity in patellar tendinopathy and highlight fresh avenues for its clinical management.

Effects of laboratory colonization on Bactrocera dorsalis (Diptera, Tephritidae) mating behaviour: ‘what a difference a year makes

Laboratory-reared insects are widely known to have significantly reduced genetic diversity in comparison to wild populations; however, subtle behavioural changes between laboratory-adapted and wild or ‘wildish’ (i.e., within one or very few generations of field collected material) populations are less well understood. Quantifying alterations in behaviour, particularly sexual, in laboratory-adapted insects is important for mass-reared insects for use in pest management strategies, especially those that have a sterile insect technique component. We report subtle changes in sexual behaviour between ‘wildish’ Bactrocera dorsalis flies (F1 and F2) from central and southern Thailand and the same colonies 12 months later when at six generations from wild. Mating compatibility tests were undertaken under standardised semi-natural conditions, with number of homo/heterotypic couples and mating location in field cages analysed via compatibility indices. Central and southern populations of B. dorsalis displayed positive assortative mating in the 2010 trials but mated randomly in the 2011 trials. ‘Wildish’ southern Thailand males mated significantly earlier than central Thailand males in 2010; this difference was considerably reduced in 2011, yet homotypic couples from southern Thailand still formed significantly earlier than all other couple combinations. There was no significant difference in couple location in 2010; however, couple location significantly differed among pair types in 2011 with those involving southern Thailand females occurring significantly more often on the tree relative to those with central Thailand females. Relative participation also changed with time, with more southern Thailand females forming couples relative to central Thailand females in 2010; this difference was considerably decreased by 2011. These results reveal how subtle changes in sexual behaviour, as driven by laboratory rearing conditions, may significantly influence mating behaviour between laboratory-adapted and recently colonised tephritid fruit flies over a relatively short period of time.

Resolving cryptic species complexes of major tephritid pests

An FAO/IAEA Co-ordinated Research Project (CRP) on “Resolution of Cryptic Species Complexes of Tephritid Pests to Overcome Constraints to SIT Application and International Trade” was conducted from 2010 to 2015. As captured in the CRP title, the objective was to undertake targeted research into the systematics and diagnostics of taxonomically challenging fruit fly groups of economic importance. The scientific output was the accurate alignment of biological species with taxonomic names; which led to the applied outcome of assisting FAO and IAEA Member States in overcoming technical constraints to the application of the Sterile Insect Technique (SIT) against pest fruit flies and the facilitation of international agricultural trade. Close to 50 researchers from over 20 countries participated in the CRP, using coordinated, multidisciplinary research to address, within an integrative taxonomic framework, cryptic species complexes of major tephritid pests. The following progress was made for the four complexes selected and studied: Anastrepha fraterculus complex – Eight morphotypes and their geographic and ecological distributions in Latin America were defined. The morphotypes can be considered as distinct biological species on the basis of differences in karyotype, sexual incompatibility, post-mating isolation, cuticular hydrocarbon, pheromone, and molecular analyses. Discriminative taxonomic tools using linear and geometric morphometrics of both adult and larval morphology were developed for this complex. Bactrocera dorsalis complex – Based on genetic, cytogenetic, pheromonal, morphometric, and behavioural data, which showed no or only minor variation between the Asian/African pest fruit flies Bactrocera dorsalis, B. papayae, B. philippinensis and B. invadens, the latter three species were synonymized with B. dorsalis. Of the five target pest taxa studied, only B. dorsalis and B. carambolae remain as scientifically valid names. Molecular and pheromone markers are now available to distinguish B. dorsalis from B. carambolae. Ceratitis FAR Complex (C. fasciventris, C. anonae, C. rosa) – Morphology, morphometry, genetic, genomic, pheromone, cuticular hydrocarbon, ecology, behaviour, and developmental physiology data provide evidence for the existence of five different entities within this fruit fly complex from the African region. These are currently recognised as Ceratitis anonae, C. fasciventris (F1 and F2), C. rosa and a new species related to C. rosa (R2). The biological limits within C. fasciventris (i.e. F1 and F2) are not fully resolved. Microsatellites markers and morphological identification tools for the adult males of the five different FAR entities were developed based on male leg structures. Zeugodacus cucurbitae (formerly Bactrocera (Zeugodacus) cucurbitae) – Genetic variability was studied among melon fly populations throughout its geographic range in Africa and the Asia/Pacific region and found to be limited. Cross-mating studies indicated no incompatibility or sexual isolation. Host preference and genetic studies showed no evidence for the existence of host races. It was concluded that the melon fly does not represent a cryptic species complex, neither with regard to geographic distribution nor to host range. Nevertheless, the higher taxonomic classification under which this species had been placed, by the time the CRP was started, was found to be paraphyletic; as a result the subgenus Zeugodacus was elevated to genus level.