Introducing and assessing the explainable AI (XAI)method: SIDU

Explainable Artificial Intelligence (XAI) has in recent years become a well-suited framework to generate human understandable explanations of black box models. In this paper, we present a novel XAI visual explanation algorithm denoted SIDU that can effectively localize entire object regions responsible for prediction in a full extend. We analyze its robustness and effectiveness through various computational and human subject experiments. In particular, we assess the SIDU algorithm using three different types of evaluations (Application, Human and Functionally-Grounded) to demonstrate its superior performance. The robustness of SIDU is further studied in presence of adversarial attack on black box models to better understand its performance.Comment: Preprint-submitted to Journal of Pattern Recognition (Elsevier

Interest shown by medical students at University of San Pablo CEU (Spain) regarding prevention and response to outbreaks of infection

The release of biological hazards during biological incidents, bioterrorism or outbreaks of infection has shown to represent a significant challenge for healthcare professionals as it can involve significant numbers of patients and represent a global public health threat. Healthcare educators should provide students with the necessary skills in medical preparedness and response to these incidents to protect the public. However, this is not standardised in the medical curriculum. An innovative teaching group at De Montfort University (DMU, UK) in collaboration with first responders that worked during the 2014-2016 Ebola outbreak in a Public Health England (PHE) mobile laboratory in Sierra Leone, have developed different, novel teaching training sessions to provide health science students with the necessary skills to respond to these events. We have tested the training sessions with students from three different undergraduate (BSc Biomedical and Medical Science) and postgraduate (MSc Advanced Biomedical Science) human health programmes at DMU. In general, these sessions were shown to be successful in providing students with basic skills to respond to minor biological incidents (Peña-Fernández et al., 2017), although we do not know if these could be adopted to develop standardized curricula across any human health degree in the European Union (EU). Therefore, the purpose of this work was twofold: a) to assess the effectiveness of the specialised training session that covers the medical response to protect public health with medical students; and b) to determine the effectiveness of the training session, initially developed in England, in a non-English EU university. To meet these objectives, we have simplified this specialised training and delivered it to final year students of the Medicine degree at the University of San Pablo CEU (USP-CEU, Spain) during an Eramus+ mobility grant for academics in April 2017. The two hour training provided consisted of developing a complete intervention programme to deal with an outbreak of Crimean-Congo haemorrhagic fever (CCFH) virus following the steps of evidence-based public health. CCFH is a haemorrhagic fever virus causing devastating disease symptoms that result in intense and prolonged suffering in humans and has become an increasing global health concern. This paper will describe the teaching resources used and a comprehensive analysis of students’ feedback to this training. Briefly: the specific questionnaire used has shown high levels of engagement and satisfaction [100% (31.2% agreed; 68.8% strongly agreed)] with the USP-CEU medical students. Despite its short duration, this training would be successful in providing medical students with the necessary skills to respond to a biological event. Thus, 100% (31.2% agreed; 68.8% strongly agreed) of these students reported that they learnt how to establish some public health interventions to protect humans in the aftermath of an outbreak of infection. Moreover, all USP-CEU responders have described that they gained appropriate knowledge of public health prevention and preparedness against these events (37.5% agreed; 62.5 strongly agreed). Finally, the Erasmus+ mobility grant for academics has been shown to be a relevant tool and resource to strengthen curricula development and validation in higher education

Potential presence of microsporidia in clinical faecal specimens from the Isle of Man.

Human-related microsporidia Enterocytozoon bieneusi and Encephalitozoon spp. have emerged as opportunistic infectious agents affecting both immunocompromised and immunocompetent individuals. A pilot study to determine the potential presence of microsporidia in the general population that have attended Nobles’ Hospital in Isle of Man (UK) since January 2018 was performed. Thirty eight faecal samples submitted to the Nobles’ Hospital microbiology lab for routine testing were analysed via microscopy using the Modified Trichrome stain. Encephalitozoon spp. spores were observed in 4 samples, specifically 3 female from a range of ages (24 yr, 65yr and 89 yr old) and one male (69 yr old). These four patients were presented with diarrhoea in a semi-liquid/liquid form. Other symptoms included vomiting (89 yr old female), abdominal pain (24 yr old female), right flank pain (68 yr old male), dehydration (89 yr old female) and acute kidney injury (89 yr old female). Campylobacter spp. growth was also detected in one sample (65 yr old female). Although preliminary, our results indicate Encephalitozoon spp. were observed in faecal samples from patients in the Isle of Man presenting with diarrhoea, for which further studies will be required to determine the species and the pathogenic involvement of these pathogens in these patients. To our knowledge, this is the first study of the presence of microsporidia in human faecal samples in Isle of Man. A more comprehensive study is needed to determine the occurrence of microsporidia in patients attending with a diarrheic picture to focus attention on the need to include microsporidial diagnosis in their management

Applicability of monthly CDC case studies to improve reflection in biomedical science students.

Background Academics from De Montfort University (DMU, UK) in collaboration with other EU universities, virologists and first responders are developing training for health science students to deal with biological incidents. Initially the training is being tested with final year students enrolled on the BSc Biomedical Science (Hons) and in the BMedSci Medical Science (Hons) degree programmes in 2016/17 at DMU. To improve the limited clinical skills of these students, a series of parasitology case studies have been introduced, where students will need to reflect on their knowledge and search for information from different sources to propose possible diagnoses. Reflection is an essential learning tool for developing aspects such autonomous working, critical and analytical thinking and integration of theory with practice (Quintanilla et al., 2016). Methods A series of teaching sessions (theoretical and practical) has been created related to emergency preparedness and response (Peña-Fernández et al., 2016). Students are provided with different scenarios to develop an intervention programme to protect human health in the aftermath of a biological incident involving different biological agents including emerging parasites. During the theoretical component of the training students are provided with different slides collected from the Laboratory Identification of Parasitic Diseases of Public Health Concern (DPDx) (CDC, 2016). Students, by peer group interaction, provide a possible “diagnosis” for each clinical case based on the clinical features presented and microscopic slides provided. Critical thinking is encouraged. Results Although our results are preliminary and we need to evaluate the students’ feedback, the introduction of clinical case-studies has shown to facilitate the acquisition of some clinical skills, particularly in the biomedical science cohort. This is informed by the high level of students’ interaction during these sessions and the formulation of appropriate questions. Students have also shown some gradual improvement in the resolution of clinical case studies throughout the course. Conclusions Despite the fact that student feedback will not be collected until the end of the course, students have display strong engagement and interest in these workshops through interim module level feedback. A priori, these case-studies have been shown to be effective in facilitating the acquisition of different transversal competences including critical thinking, clinical skills, communication and team work

Curriculum modifications for teaching parasitology and infectious diseases in a Biomedical Science degree

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI linkRecent outbreaks threatening public health involving contaminated water or food with different microorganisms such as Escherichia coli or Cyclospora spp. in Europe as well as the 2014-16 Ebola crisis in West Africa have highlighted the relevance of teaching parasitology and infectious diseases to future biomedical scientists. The BSc Biomedical Science (BMS) programme at De Montfort University (DMU, Leicester, UK) is accredited by the Institute of Biomedical Sciences (IBMS). However, the dedicated time to study these topics was very little, limited to two 15 credit modules focused on general and basic medical microbiology. A series of important modifications have been undertaken since 2016 to ensure that our graduates receive comprehensive knowledge in parasitology/infectious diseases following the subject-specific threshold standards described by the Quality Assurance Agency (QAA, 2015). New lectures in these topics (virus, fungi, helminths, infectious diseases) were incorporated in our Basic Microbiology level 4 module after expanding this to 30 credits in the academic course 2016/17. Highly specialised training related with emerging parasites (e.g. Cyclospora, microsporidia) and haemorrhagic fever virus (e.g. Crimean-Congo Haemorrhagic Fever virus) was introduced in our level 6 Medical Microbiology module (15 credits), based on a successful novel teaching experience created by first responders to the Ebola outbreak in West Africa. Validated feedback questionnaires to assess the training were collected as well as final module level feedback (MLF) for each module through Blackboard. Students have highlighted high levels of engagement in both modules, specifically in the training provided in Medical Microbiology (n=121). Thus, some students have highlighted in the MLF that the case studies (e.g. related with free-living amoebas and Cyclospora spp.) “improved my understanding” and were “engaging”. The specific questionnaire has highlighted that 77.5% of final year students enjoyed the novel workshop created to respond to an outbreak of infection affecting the UK following evidence-based public health methodology. However, the module that has shown more improvement in the students’ satisfaction was Basic Microbiology (n=196), which showed a significant increase from 20% in the 2015/16 academic year to 64% in the current academic session. The MLF of Basic Microbiology has also reported the following results: 95% (41% definitely agree, 54% agree) of students have highlighted that this first year module provided them with opportunities to apply what they learnt; and 94% considered that the feedback provided was clear and fair. Despite these results should be considered as preliminary, we consider that the initial changes undertaken in the BMS programme at DMU to date could improve students’ understanding of emerging diseases, specifically about how to study and prevent emerging infectious diseases to protect public health. Future proposed improvements include the development of a complete e-learning package for students and academics for teaching these topics in collaboration with Universities from Spain and practising Biomedical Scientists from the National Health Service. These resources will be accessible throughout 2017/18

Exploring the presence of human pathogenic free-living amoebas in different water ecosystems in Leicester, UK.

Background: The presence and distribution of Acanthamoeba spp., Balamuthia mandrillaris and Naegleria fowleri (human pathogenic free-living amoebas, FLA) in different environmental compartments and geographical locations in Europe remains unknown. These FLA can be a public health threat as their cysts are highly resistant to harsh environmental conditions. The aim of this pilot study was to determine the presence of FLA in different water ecosystems close or in Leicester city (Leicestershire, UK) as information on the presence these emerging parasites in the UK is limited in the literature. Materials/methods: A total of 30 water samples were collected from different open water environments in Leicester during winter 2016/17 including: the River Soar and the Grand Union Canal (a canalised section of the River Soar), different lakes highly frequented for fishing or leisure (e.g. John Merricks' Lake, Kings Lears Lake; Bennion Pools Fishing Lake), and a marina near River Soar. The River Soar is rich in wildlife including water birds, fish and plant populations attracting large numbers of users. Water samples were obtained following protocol 1623 described by US EPA and concentrated using IDEXX® Filta Max system following manufacturer's instructions. DNA extraction from concentrated water was performed from each water sample with Fast DNA® Kit. A triplex real-time TaqMan PCR assay was performed to detect FLA; positive controls for the three amoebae were used. Results: All 30 samples assessed for FLA were negative. However these results should be considered as inconclusive as, although rare, several studies have reported the presence of Acanthamoeba spp. in the UK domestic water supplies which may indicate the presence of these human pathogens in other water systems including the environment. Moreover, the incidence of Acanthamoeba keratitis has increased in recent years in England. Conclusions: Further studies will be needed to determine the presence and distribution of FLA in the open water systems monitored to protect the public as recent evidence indicates an increase in infections due to these emerging human pathogens globally. This information is crucial to develop novel strategies to protect humans and increase the awareness of these protozoan parasites in aquatic environments in the UK

Studying the presence of free-living amoeba in parks and recreational areas in Leicester, UK.

Background: Acanthamoeba spp., Naegleria fowleri, and Balamuthia mandrillaris are considered emerging human pathogenic free-living amoebae (FLA), producing severe infections in both immunocompromised and immunocompetent humans. Although FLA have been found in virtually any environmental compartment, little is known about the potential role of wild animals as reservoirs for FLA. The aims of this study were: a) to identify the presence of FLA in animal faeces collected from urban parks in Leicester (UK); b) to identify if animal samples require pre-concentration to improve their detection. Materials/methods: Duplicates of 50 animal faecal samples were collected in March 2016: 13 from Castle Gardens (LE1 5WH), 28 from Abbey Park (LE4 5AQ) and 9 from the River Soar footpath between both parks. Only fresh samples were selected and collected on days where there had been no precipitation in the preceding 48 h. Results: A veterinarian identified the animal species as 20 avian (10 waterfowl, 8 pigeons, 2 uncertain); 24 canine (15 dog, 8 fox, 1 uncertain), 2 cats, 1 herbivore and 3 unidentifiable. Duplicates of each sample were pre-concentrated using the routine coprological method, modified Telemann and MIF (merthiolate-iodine-formaline). The DNA was extracted from each sample (fresh and pre-concentrated) using the Fast-DNA-Spin kit following previously described methodology. The QIAamp micro DNA extraction kit was used to remove PCR inhibitors. A triplex real-time TaqMan PCR assay was performed to detect FLA; positive controls for the three amoebae were used. All samples assessed for FLA were negative. Conclusions: Results were inconclusive as all samples were negative for FLA. However, understanding the zoonotic potential of animals in the presence and distribution of FLA in the environment is critical to protecting the public from these emerging human pathogens. Although the study of FLA in mammals is rare, studies have described the presence of Acanthamoeba spp. and other FLA in the gastrointestinal tract and faeces of cow, pig, and squirrel representing a potential source of transmission for these opportunistic parasites. Further studies are needed to determine the appropriateness of using pre-concentrating methods in future monitoring studies to determine the presence of FLA in mammals as our results were inconclusive

Building on-line materials for teaching parasitology to health sciences’ students: initial impressions.

Background: It is widely recognised that the use of web-based teaching resources is an increasingly important method for delivering education, and it will be particularly important in the near future due to the progressively increasing number of health science students and the current number of academics in the “European Higher Education Area”. The study of parasitology and infectious diseases is essential to build professionals in the health sector with the key knowledge and skills to face global public health threats such as food-, water- or vector-borne infectious diseases outbreaks. However, the current time dedicated to the teaching of this discipline in all health sciences degrees at De Montfort University (DMU, Leicester, UK) is very little or non-existent depending on the degree/master. Methods: An innovative teaching group at DMU is trying to fill this gap in the currently available teaching offer in line with new trends in global health education, the large number of students enrolled in any health degree and the increasing number of students that would like to study this discipline (but due to different commitments do not have enough time or resources to study on a full time basis). Thus, an innovative teaching group from different EU Universities (DMU and the Spanish universities: University of San Pablo CEU, University of Alcalá, and University Miguel Hernández de Elche) and clinicians (University Hospitals of Leicester, UK) have started to design, create and develop a complete on-line package in Parasitology for undergraduate and postgraduate students that study health sciences. Results: The e-Parasitology package will be accessible through the DMU website (http://parasitology.dmu.ac.uk) in 2017 and will be focused on infection, prevention and treatment of major and emerging parasitological diseases. Conclusions: This teaching resource will aid our undergraduate and postgraduate students to gain a significant knowledge in parasitology by promoting self-learning and internationalization. This poster will explore one of the first mini-modules developed so far related with Toxocara, a helminthiasis with prevalence rates that can reach as high as 40% or more in parts of the world, and the challenges for its development

Development of a virtual environment for teaching and learning biomedical techniques and equipment for the study of human pathogens.

An international innovative teaching group from different EU Universities (De Montfort University, Leicester, UK; University of San Pablo CEU, Madrid, Spain; University of Miguel Hernandez, Elche, Spain) and biomedical scientists registered by the Health and Care Professions Council (HCPC, UK) are developing a complete e-learning package in medical parasitology for undergraduate and postgraduate students that study Health Sciences. This package, named DMU e-Parasitology, is accessible through the DMU website (http://parasitology.dmu.ac.uk) and will present different modules including a virtual laboratory module for the study of traditional and novel biomedical laboratory techniques and equipment for detecting, identifying and studying human pathogens, specifically parasites. These techniques could also be potentially used to study other pathogens such as bacteria or viruses. The virtual biomedical laboratory is under development, but is available in the DMU website here: http://parasitology.dmu.ac.uk/learn/laboratory.htm. To develop this new module of the DMU e-Parasitology, we are using Storyline 360 software and the scaffolding and methods used to build the theoretical module (Peña-Fernández et al., 2017) [1]. To facilitate the navigation, study and comprehension of the final user, we have divided the virtual laboratory into a series of sub-sections that include different units; the sub-sections so far are: microscopes (with units such as the electron microscope); molecular biology (e.g. polymerase chain reaction and gel electrophoresis); biological safety cabinets and cell/parasite culture; biochemical and immunological techniques (e.g. magnetic immunoseparation); histology (e.g. microtome) and staining techniques (e.g. Kinyoun staining). The virtual laboratory units are highly interactive and present short videos of academics and/or technicians working in real conditions with the different laboratory equipment such as a thermocycler, a microtome, or a biological safety cabinet, as well as performing a specific technique such as a staining to determine pathogens. Therefore, the user of this virtual environment will receive a complete and “real” experience of the work in a biomedical laboratory. The DMU e-Parasitology package, and specifically its virtual laboratory environment, could help technicians and students across the world to learn how to work in a biomedical laboratory as well as to perform techniques to identify and diagnose human pathogens such as microsporidia or Plasmodium spp. Thus, the virtual resource is supported by a virtual library that includes a real collection of clinical slides that will provide the user with the functionality of a light and/or an immunofluorescence microscope. In conclusion, the virtual laboratory may serve as a high quality and reliable on-line environment for the learning of techniques and equipment. These resources can be used to improve the learning of undergraduate and postgraduate students of human health sciences as well as to develop CPD training. Moreover, the virtual laboratory module may impact in the teaching of laboratory techniques and skills in developing countries due to their limited resources. This communication will explore the design and development of the virtual laboratory environment that will be publicly accessible by the end of 2018