An open-source solution for advanced imaging flow cytometry data analysis using machine learning

Imaging flow cytometry (IFC) enables the high throughput collection of morphological and spatial information from hundreds of thousands of single cells. This high content, information rich image data can in theory resolve important biological differences among complex, often heterogeneous biological samples. However, data analysis is often performed in a highly manual and subjective manner using very limited image analysis techniques in combination with conventional flow cytometry gating strategies. This approach is not scalable to the hundreds of available image-based features per cell and thus makes use of only a fraction of the spatial and morphometric information. As a result, the quality, reproducibility and rigour of results are limited by the skill, experience and ingenuity of the data analyst. Here, we describe a pipeline using open-source software that leverages the rich information in digital imagery using machine learning algorithms. Compensated and corrected raw image files (.rif) data files from an imaging flow cytometer (the proprietary .cif file format) are imported into the open-source software CellProfiler, where an image processing pipeline identifies cells and subcellular compartments allowing hundreds of morphological features to be measured. This high-dimensional data can then be analysed using cutting-edge machine learning and clustering approaches using “user-friendly” platforms such as CellProfiler Analyst. Researchers can train an automated cell classifier to recognize different cell types, cell cycle phases, drug treatment/control conditions, etc., using supervised machine learning. This workflow should enable the scientific community to leverage the full analytical power of IFC-derived data set. It will help to reveal otherwise unappreciated populations of cells based on features that may be hidden to the human eye that include subtle measured differences in label free detection channels such as bright-field and dark-field imagery

Running a professional academic-related team in an academic environment

This paper considers the position of a large full-range business school and ways in which it can improve its efficiency and effectiveness, and enhance students' learning environment by the strategic use of academic-related staff within key roles in the School. Some of these roles have traditionally been undertaken by academic staff, but the increased complexity of the Business School environment makes it impossible for academic staff to undertake all roles if the School wants to be innovative and successful in a highly changing external environment. The investigation is carried out via a series of semi-structure interviews, conducted with academic and academic related staff across the School. This is compared with a review of recent literature in the subject. The paper concludes that both the efficient running of the School and the learning environment of students are improved via the partnership of academics and support staff. The findings reveal, however, that the use of academic-related staff must be done sensitively, to ensure that institutions do not become over bureaucratic or academics alienated in the drive to focus on the student experience

Diagnostic Potential of Imaging Flow Cytometry

Imaging flow cytometry (IFC) captures multichannel images of hundreds of thousands of single cells within minutes. IFC is seeing a paradigm shift from low- to high-information-content analysis, driven partly by deep learning algorithms. We predict a wealth of applications with potential translation into clinical practice

Linking performance-related pay to a Business School's mission and objectives

This paper first analyses the Performance Related Pay (PRP) schemes developed from 1992/3 to 2002/3 in a large Business School in England and then the School’s mission and strategic objectives in that period. The PRP schemes changed to include more specific performance indicators and these were increasingly linked to the objectives. The School’s resources allocated to PRP increased from £44,000 in 1992/93 to £355,000 in 2002/3 and from 1.08% in 1995/96 to 2.37% of the School’s income in 2002/3. As well as examining the changing strategic objectives and PRP schemes, the paper charts the development of the School’s reputation and resources and the role which staff motivation via PRP played at different stages. The paper concludes that the PRP scheme was at its most effective when it was clearly linked with the School’s strategic objectives, but that the relationship between objectives and motivation may be more complex than apparent from this study. Although the PRP scheme under consideration also applies to academic related staff, this paper concentrates on the effect on academic staff

Effects of swim-with-dolphin tourism on the behaviour of a threatened species, the Burrunan dolphin Tursiops Australis

Burrunan dolphins Tursiops australis are frequently targeted by tourism operations in Port Phillip Bay, Australia. This study aimed to provide first insights into whether swim-with-dolphin (SWD) vessels in Port Phillip Bay affect the behaviour of Burrunan dolphins via the use of Markov chain models. The presence of SWD vessels affected dolphins' travelling, foraging, milling and socialising behaviours. The time dolphins spent foraging in the presence of SWD vessels was significantly reduced, with average foraging bout length decreasing by 13.6%, foraging recovery time increasing by 47.6%, and the probability of transitioning from foraging to milling increasing 4-fold. Conversely, dolphins spent significantly more time milling and socialising in the presence of SWD vessels. The reduction in time spent foraging when SWD vessels are present could lead to a decrease in dolphins' rate of energy acquisition, whilst the increase in milling could increase their energy expenditure. Collectively, this may lead to reduced biological fitness with population level consequences. However, although the short-term behavioural budget of the dolphin population was significantly affected, SWD vessels did not significantly affect the cumulative (i.e. yearly) behavioural budget of Burrunan dolphins. Thus, the assumption that boat-based cetacean tourism has major negative effects on targeted populations may be flawed in some cases

Corral Monitoring System assessment results

This report describes the results of a functional and operational assessment of the Corral Monitoring Systems (CMS), which was designed to detect and document accountable items entering or leaving a monitored site. Its development was motivated by the possibility that multiple sites in the nuclear weapons states of the former Soviet Union might be opened to such monitoring under the provisions of the Strategic Arms Reduction Treaty. The assessment was performed at three levels. One level evaluated how well the planned approach addressed the target application, and which involved tracking sensitive items moving into and around a site being monitored as part of an international treaty or other agreement. The second level examined the overall design and development approach, while the third focused on individual subsystems within the total package. Unfortunately, the system was delivered as disassembled parts and pieces, with very poor documentation. Thus, the assessment was based on fragmentary operating data coupled with an analysis of what documents were provided with the system. The system design seemed to be a reasonable match to the requirements of the target application; however, important questions about site manning and top level administrative control were left unanswered. Four weaknesses in the overall design and development approach were detected: (1) poor configuration control and management, (2) inadequate adherence to a well defined architectural standard, (3) no apparent provision for improving top level error tolerance, and (4) weaknesses in the object oriented programming approach. The individual subsystems were found to offer few features or capabilities that were new or unique, even at the conceptual level. The CMS might possibly have offered a unique combination of features, but this level of integration was never realized, and it had no unique capabilities that could be readily extracted for use in another system

The role and scope of practice of midwives in humanitarian settings:a systematic review and content analysis

Abstract Background Midwives have an essential role to play in preparing for and providing sexual and reproductive health (SRH) services in humanitarian settings due to their unique knowledge and skills, position as frontline providers and geographic and social proximity to the communities they serve. There are considerable gaps in the international guidance that defines the scope of practice of midwives in crises, particularly for the mitigation and preparedness, and recovery phases. We undertook a systematic review to provide further clarification of this scope of practice and insights to optimise midwifery performance. The review aimed to determine what SRH services midwives are involved in delivering across the emergency management cycle in humanitarian contexts, and how they are working with other professionals to deliver health care. Methods Four electronic databases and the websites of 33 organisations were searched between January and March 2017. Papers were eligible for inclusion if they were published in English between 2007 and 2017 and reported primary research pertaining to the role of midwives in delivering and performing any component of sexual and/or reproductive health in humanitarian settings. Content analysis was used to map the study findings to the Minimum Initial Service Package (MISP) for SRH across the three phases of the disaster management cycle and identify how midwives work with other members of the health care team. Results Fourteen studies from ten countries were included. Twelve studies were undertaken in conflict settings, and two were conducted in the context of the aftermath of natural disasters. We found a paucity of evidence from the research literature that examines the activities and roles undertaken by midwives across the disaster management cycle. This lack of evidence was more apparent during the mitigation and preparedness, and recovery phases than the response phase of the disaster management cycle. Conclusion Research-informed guidelines and strategies are required to better align the scope of practice of midwives with the objectives of multi-agency guidelines and agreements, as well as the activities of the MISP, to ensure that the potential of midwives can be acknowledged and optimised across the disaster management cycle

A New Evolutionary Algorithm-Based Home Monitoring Device for Parkinson’s Dyskinesia

Parkinson’s disease (PD) is a neurodegenerative movement disorder. Although there is no cure, symptomatic treatments are available and can significantly improve quality of life. The motor, or movement, features of PD are caused by reduced production of the neurotransmitter dopamine. Dopamine deficiency is most often treated using dopamine replacement therapy. However, this therapy can itself lead to further motor abnormalities referred to as dyskinesia. Dyskinesia consists of involuntary jerking movements and muscle spasms, which can often be violent. To minimise dyskinesia, it is necessary to accurately titrate the amount of medication given and monitor a patient’s movements. In this paper, we describe a new home monitoring device that allows dyskinesia to be measured as a patient goes about their daily activities, providing information that can assist clinicians when making changes to medication regimens. The device uses a predictive model of dyskinesia that was trained by an evolutionary algorithm, and achieves AUC>0.9 when discriminating clinically significant dyskinesia

Recommendations for a ‘Wellbeing Curriculum’ to Mitigate Undergraduate Psychological Distress Associated with Lack of Careers Confidence and Poor University Engagement

To foster a ‘wellbeing curriculum’ in a climate with an increasingly competitive graduate jobs market, we believe it is critical to support undergraduate career development and to develop positive peer and educator relationships, particularly for non vocational degree programs. However, these relationships between undergraduate wellbeing and their career development or peer/educator relationships have not been specifically examined. This study used a mixed methods approach to examine if poor career development or university engagement (quality of relationships with peers or educators, use of the university careers and counselling services, time studying) were associated with psychological distress for students in non vocational degree programs. Undergraduates (biomedical science; n=1100) from five Australian universities participated in a survey to investigate relationships between psychological distress, as determined by their responses to the Depression, Anxiety and Stress Scales, and their career development or university engagement. Almost half of the students lacked confidence in their ‘future employment and job prospects’. Students’ psychological distress was significantly correlated with lack of confidence with their career development, poor relationships with their peers and educators and little use of the counselling service. Further exploration of these factors in student focus groups highlighted stress associated with academic competition between students and a critical need for undergraduate career development, especially industry placements. We provide pivotal recommendations to promote undergraduate and educator wellbeing, by developing a ‘wellbeing curriculum’ that supports career development and positive relationships between students and their peers and educators, particularly vital for non vocational degrees

Molecular psychiatry of zebrafish

Due to their well-characterized neural development and high genetic homology to mammals, zebrafish (Danio rerio) have emerged as a powerful model organism in the field of biological psychiatry. Here, we discuss the molecular psychiatry of zebrafish, and its implications for translational neuroscience research and modeling central nervous system (CNS) disorders. In particular, we outline recent genetic and technological developments allowing for in vivo examinations, high-throughput screening and whole-brain analyses in larval and adult zebrafish. We also summarize the application of these molecular techniques to the understanding of neuropsychiatric disease, outlining the potential of zebrafish for modeling complex brain disorders, including attention-deficit/hyperactivity disorder (ADHD), aggression, post-traumatic stress and substance abuse. Critically evaluating the advantages and limitations of larval and adult fish tests, we suggest that zebrafish models become a rapidly emerging new field in modern molecular psychiatry research