A comparative analysis of active learning for biomedical text mining

Data Availability Statement: The code and data are available from https://github.com/usmaann (accessed on 14 March 2021).Copyright © 2021 by the authors. An enormous amount of clinical free-text information, such as pathology reports, progress reports, clinical notes and discharge summaries have been collected at hospitals and medical care clinics. These data provide an opportunity of developing many useful machine learning applications if the data could be transferred into a learn-able structure with appropriate labels for supervised learning. The annotation of this data has to be performed by qualified clinical experts, hence, limiting the use of this data due to the high cost of annotation. An underutilised technique of machine learning that can label new data called active learning (AL) is a promising candidate to address the high cost of the label the data. AL has been successfully applied to labelling speech recognition and text classification, however, there is a lack of literature investigating its use for clinical purposes. We performed a comparative investigation of various AL techniques using ML and deep learning (DL)-based strategies on three unique biomedical datasets. We investigated random sampling (RS), least confidence (LC), informative diversity and density (IDD), margin and maximum representativeness-diversity (MRD) AL query strategies. Our experiments show that AL has the potential to significantly reducing the cost of manual labelling. Furthermore, pre-labelling performed using AL expediates the labelling process by reducing the time required for labelling.This research received no external funding

A novel privacy paradigm for improving serial data privacy

Protecting the privacy of individuals is of utmost concern in today’s society, as inscribed and governed by the prevailing privacy laws, such as GDPR. In serial data, bits of data are continuously released, but their combined effect may result in a privacy breach in the whole serial publication. Protecting serial data is crucial for preserving them from adversaries. Previous approaches provide privacy for relational data and serial data, but many loopholes exist when dealing with multiple sensitive values. We address these problems by introducing a novel privacy approach that limits the risk of privacy disclosure in republication and gives better privacy with much lower perturbation rates. Existing techniques provide a strong privacy guarantee against attacks on data privacy; however, in serial publication, the chances of attack still exist due to the continuous addition and deletion of data. In serial data, proper countermeasures for tackling attacks such as correlation attacks have not been taken, due to which serial publication is still at risk. Moreover, protecting privacy is a significant task due to the critical absence of sensitive values while dealing with multiple sensitive values. Due to this critical absence, signatures change in every release, which is a reason for attacks. In this paper, we introduce a novel approach in order to counter the composition attack and the transitive composition attack and we prove that the proposed approach is better than the existing state-of-the-art techniques. Our paper establishes the result with a systematic examination of the republication dilemma. Finally, we evaluate our work using benchmark datasets, and the results show the efficacy of the proposed technique

Correlation between Attitudes, Concerns, Self-Efficacy and Teaching Intentions in Inclusive Education. Evidence from German pre-service teachers using international scales

The inclusion of pupils with special educational needs (SEN ) in schools is an ongoing challenge – it demands the development of an adapted teaching and learning environment, which, in turn, requires a corresponding teacher education programme. Studies indicate that personal characteristics of the respective teachers are one of the main influencing factors on the classroom environment. This article reports on a study of the role of teacher‐related factors, attitudes, concerns and efficacy in inclusion by testing existing survey instruments of 909 pre‐service teachers in Germany. A confirmatory factor analysis was applied to new German translations of four instruments: Attitudes Towards Inclusion Scale , Intention to Teach in Inclusive Classroom Scale , Concerns about Inclusive Education Scale , and the Teacher Efficacy for Inclusive Practices . With minor modifications, models demonstrated good fit measures and partial measurement invariance between special school pre‐service teachers and general pre‐service teachers. A combined model of all four scales confirmed that lower concerns were related to attitudes that are more positive, greater self‐efficacy and stronger intentions to teaching inclusively. Implications for teacher‐training and comparisons to other international samples are discussed

Using the entomological inoculation rate to assess the impact of vector control on malaria parasite transmission and elimination

Prior studies have shown that annual entomological inoculation rates (EIRs) must be reduced to less than one to substantially reduce the prevalence of malaria infection. In this study, EIR values were used to quantify the impact of insecticide-treated bed nets (ITNs), indoor residual spraying (IRS), and source reduction (SR) on malaria transmission. The analysis of EIR was extended through determining whether available vector control tools can ultimately eradicate malaria. The analysis is based primarily on a review of all controlled studies that used ITN, IRS, and/or SR and reported their effects on the EIR. To compare EIRs between studies, the percent difference in EIR between the intervention and control groups was calculated. Eight vector control intervention studies that measured EIR were found: four ITN studies, one IRS study, one SR study, and two studies with separate ITN and IRS intervention groups. In both the Tanzania study and the Solomon Islands study, one community received ITNs and one received IRS. In the second year of the Tanzania study, EIR was 90% lower in the ITN community and 93% lower in the IRS community, relative to the community without intervention; the ITN and IRS effects were not significantly different. In contrast, in the Solomon Islands study, EIR was 94% lower in the ITN community and 56% lower in the IRS community. The one SR study, in Dar es Salaam, reported a lower EIR reduction (47%) than the ITN and IRS studies. All of these vector control interventions reduced EIR, but none reduced it to zero. These studies indicate that current vector control methods alone cannot ultimately eradicate malaria because no intervention sustained an annual EIR less than one. While researchers develop new tools, integrated vector management may make the greatest impact on malaria transmission. There are many gaps in the entomological malaria literature and recommendations for future research are provided

Successful field trial of attractive toxic sugar bait (ATSB) plant-spraying methods against malaria vectors in the Anopheles gambiae complex in Mali, West Africa

<p>Abstract</p> <p>Background</p> <p>Based on highly successful demonstrations in Israel that attractive toxic sugar bait (ATSB) methods can decimate local populations of mosquitoes, this study determined the effectiveness of ATSB methods for malaria vector control in the semi-arid Bandiagara District of Mali, West Africa.</p> <p>Methods</p> <p>Control and treatment sites, selected along a road that connects villages, contained man-made ponds that were the primary larval habitats of <it>Anopheles gambiae </it>and <it>Anopheles arabiensis</it>. Guava and honey melons, two local fruits shown to be attractive to <it>An. gambiae </it>s.l., were used to prepare solutions of Attractive Sugar Bait (ASB) and ATSB that additionally contained boric acid as an oral insecticide. Both included a color dye marker to facilitate determination of mosquitoes feeding on the solutions. The trial was conducted over a 38-day period, using CDC light traps to monitor mosquito populations. On day 8, ASB solution in the control site and ATSB solution in the treatment site were sprayed using a hand-pump on patches of vegetation. Samples of female mosquitoes were age-graded to determine the impact of ATSB treatment on vector longevity.</p> <p>Results</p> <p>Immediately after spraying ATSB in the treatment site, the relative abundance of female and male <it>An. gambiae </it>s.l. declined about 90% from pre-treatment levels and remained low. In the treatment site, most females remaining after ATSB treatment had not completed a single gonotrophic cycle, and only 6% had completed three or more gonotrophic cycles compared with 37% pre-treatment. In the control site sprayed with ASB (without toxin), the proportion of females completing three or more gonotrophic cycles increased from 28.5% pre-treatment to 47.5% post-treatment. In the control site, detection of dye marker in over half of the females and males provided direct evidence that the mosquitoes were feeding on the sprayed solutions.</p> <p>Conclusion</p> <p>This study in Mali shows that even a single application of ATSB can substantially decrease malaria vector population densities and longevity. It is likely that ATSB methods can be used as a new powerful tool for the control of malaria vectors, particularly since this approach is highly effective for mosquito control, technologically simple, inexpensive, and environmentally safe.</p

Variable expressivity of FGF3 mutations associated with deafness and LAMM syndrome

<p>Abstract</p> <p>Background</p> <p>Recessive mutations of fibroblast growth factor 3 (FGF3) can cause LAMM syndrome (OMIM 610706), characterized by fully penetrant complete labyrinthine aplasia, microtia and microdontia.</p> <p>Methods</p> <p>We performed a prospective molecular genetic and clinical study of families segregating hearing loss linked to <it>FGF3 </it>mutations. Ten affected individuals from three large Pakistani families segregating <it>FGF3 </it>mutations were imaged with CT, MRI, or both to detect inner ear abnormalities. We also modeled the three dimensional structure of FGF3 to better understand the structural consequences of the three missense mutations.</p> <p>Results</p> <p>Two families segregated reported mutations (p.R104X and p.R95W) and one family segregated a novel mutation (p.R132GfsX26) of <it>FGF3</it>. All individuals homozygous for p.R104X or p.R132GfsX26 had fully penetrant features of LAMM syndrome. However, recessive p.R95W mutations were associated with nearly normal looking auricles and variable inner ear structural phenotypes, similar to that reported for a Somali family also segregating p.R95W. This suggests that the mild phenotype is not entirely due to genetic background. Molecular modeling result suggests a less drastic effect of p.R95W on FGF3 function compared with known missense mutations detected in fully penetrant LAMM syndrome. Since we detected significant intrafamilial variability of the inner ear structural phenotype in the family segregating p.R95W, we also sequenced <it>FGF10 </it>as a likely candidate for a modifier. However, we did not find any sequence variation, pointing out that a larger sample size will be needed to map and identify a modifier. We also observed a mild to moderate bilateral conductive hearing loss in three carriers of p.R95W, suggesting either a semi-dominant effect of this mutant allele of <it>FGF3</it>, otitis media, or a consequence of genetic background in these three family members.</p> <p>Conclusions</p> <p>We noted a less prominent dental and external ear phenotype in association with the homozygous p.R95W. Therefore, we conclude that the manifestations of recessive <it>FGF3 </it>mutations range from fully penetrant LAMM syndrome to deafness with residual inner ear structures and, by extension, with minimal syndromic features, an observation with implications for cochlear implantation candidacy.</p

Assessing composition in modeling approaches

Modeling approaches are based on various paradigms, e.g., aspect-oriented, feature-oriented, object-oriented, and logic-based. Modeling approaches may cover requirements models to low-level design models, are developed for various purposes, use various means of composition, and thus are difficult to compare. However, such comparisons are critical to help practitioners know under which conditions approaches are most applicable, and how they might be successfully generalized and combined to achieve end-to-end methods. This paper reports on work done at the 2nd International Comparing Modeling Approaches (CMA) workshop towards the goal of identifying potential comprehensive modeling methodologies with a particular emphasis on composition: (i) an improved set of comparison criteria; (ii) 19 assessments of modeling approaches based on the comparison criteria and a common, focused case study

Association of respiratory symptoms and lung function with occupation in the multinational Burden of Obstructive Lung Disease (BOLD) study

Background Chronic obstructive pulmonary disease has been associated with exposures in the workplace. We aimed to assess the association of respiratory symptoms and lung function with occupation in the Burden of Obstructive Lung Disease study. Methods We analysed cross-sectional data from 28 823 adults (≥40 years) in 34 countries. We considered 11 occupations and grouped them by likelihood of exposure to organic dusts, inorganic dusts and fumes. The association of chronic cough, chronic phlegm, wheeze, dyspnoea, forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV1)/FVC with occupation was assessed, per study site, using multivariable regression. These estimates were then meta-analysed. Sensitivity analyses explored differences between sexes and gross national income. Results Overall, working in settings with potentially high exposure to dusts or fumes was associated with respiratory symptoms but not lung function differences. The most common occupation was farming. Compared to people not working in any of the 11 considered occupations, those who were farmers for ≥20 years were more likely to have chronic cough (OR 1.52, 95% CI 1.19–1.94), wheeze (OR 1.37, 95% CI 1.16–1.63) and dyspnoea (OR 1.83, 95% CI 1.53–2.20), but not lower FVC (β=0.02 L, 95% CI −0.02–0.06 L) or lower FEV1/FVC (β=0.04%, 95% CI −0.49–0.58%). Some findings differed by sex and gross national income. Conclusion At a population level, the occupational exposures considered in this study do not appear to be major determinants of differences in lung function, although they are associated with more respiratory symptoms. Because not all work settings were included in this study, respiratory surveillance should still be encouraged among high-risk dusty and fume job workers, especially in low- and middle-income countries.publishedVersio