Amplification of the DFR1 gene in Saccaromyces cerevisiae

A new system was employed to study amplification of t,he DHF'R gene DFB,1 ) in Sa<,:;charoillYCB§. .Q~~Yi...S!i<;1~. . This system consists of a series of yeast strains containing a casset,te which encodes t he yeast, D..ERl gene ttghtly linked tjO a f usion of the yeast 1EU2. regulat,ory region wi tJ1 the LAQZ str ctural gene from E. cO.1-1 (,) . M. Clement , unpubl i,::;hed) . Th's casset;t e was shown t.o be integrat,ed int o a unj que chromosomal l ocati on in each strain . Yeast cells were se l ected for MTX-resistance and overproduction of ~ galac t osi d se ( B-gal ). Since the inserted DF'Rl and ~ACZ genes are independently regulated, it was thought that cel l s with this phenotype probably contain e d ampl if ications of the cassette. A lar ge variat ion in the f requn y o f MTX-resistance was found between the di ff e r ent str ains. These freqlen c ~ es r anged from about 2 x 10 - 7 fo r a population of cells containing the cassette integrated at, the BI J2.l gene in t,he middle of the long arm of chromosome V, to about 5 x 10-4 for a strain with the cassette i nserted in the r DNA cluster Abo It 85% of the MTX- res i stcmt iso l ates examined showed enhanced B·-gal act i v ity rel a t ive t o the parental strain . For the ma jorit y of strains, the mean B- gal activity in drug-r sistant clones was about 3 times that o f the parent following a single se l ect i on step . I n con t r ast, primary MTX-resistant derivat~ves of cells with the cassette inserted 3 at the rDNA cluster showed inc r eases in B- gal activity ranging from 9 - 14 f old r elative to the parent. Analysis of the latte r s train by Southe rn hybr idization indicated that the cassette was inde e d amplified several fold in MTX-re sistant derivatives. A sing l e strain, in which the cassette was inserted at the !lEA;], loc u.s , was used to examine in more detai 1 , the parameters affecting DFRl gene amplificat~ion in yeast . The mean B- gal activity in drug-resistant derivatives of this strain could be increased from 3 to 6 or 7 fold relative to the parent, by stepwise sel ection using increasing MTX concentrations. B-gal overproduction was found to be un stable in all primary and highly -resistant isolates examined. There was no indication, h owever, of a decrease i n growth r a t e in MTX-res i s tant cells which overproduced B - gal

Making Participation Work: A Grounded Theory Describing Participation in Phase I Drug Trials from the Perspective of the Healthy Subject

A qualitative research study was conducted with people who had participated as healthy subjects in phase I drug trials at commercial research facilities, in order to develop a better understanding of their perspective regarding research participation. The participants were recruited using online advertisements posted on the University of Toronto student website (www.my.utoronto.ca) and NOW Magazine online. Thirty-one subjects were interviewed. The audiotaped interviews were transcribed and analyzed using grounded theory methods. A grounded theory was developed that describes the process of participation and the main factors affecting the experience of participation, from the perspective of healthy subjects. The theory, called Making Participation Work, explains how healthy subjects frame participation as an income earning opportunity, and how this framing shapes their behaviour with regard to participation. Participants expressed a range of attitudes about the experience of participation, from very positive to very negative. The main factor affecting the experience is the perceived net burden, which is in turn affected by the degree to which subjects find personal control over their participation. Net burden and finding personal control were both affected by the degree to which subjects felt valued by research staff, and by whether subjects had trust in the research enterprise. Although subjects framed participation as work, the relationship with the study doctors and nurses was viewed as clinical. Most subjects are generally trusting that participation in phase I drug trials is safe. These findings suggest that models of research participation assuming participation motivated by altruism or potential therapeutic benefit cannot accommodate the attitudes and behaviours of healthy subjects in phase I drug trials. New models must be developed which account for the framing of participation as work, while being sensitive to the trust that healthy subjects place in the research enterprise.Ph

Discovering social determinants of health from case reports using natural language processing: algorithmic development and validation

Abstract Background Social determinants of health are non-medical factors that influence health outcomes (SDOH). There is a wealth of SDOH information available in electronic health records, clinical reports, and social media data, usually in free text format. Extracting key information from free text poses a significant challenge and necessitates the use of natural language processing (NLP) techniques to extract key information. Objective The objective of this research is to advance the automatic extraction of SDOH from clinical texts. Setting and data The case reports of COVID-19 patients from the published literature are curated to create a corpus. A portion of the data is annotated by experts to create ground truth labels, and semi-supervised learning method is used for corpus re-annotation. Methods An NLP framework is developed and tested to extract SDOH from the free texts. A two-way evaluation method is used to assess the quantity and quality of the methods. Results The proposed NER implementation achieves an accuracy (F1-score) of 92.98% on our test set and generalizes well on benchmark data. A careful analysis of case examples demonstrates the superiority of the proposed approach in correctly classifying the named entities. Conclusions NLP can be used to extract key information, such as SDOH factors from free texts. A more accurate understanding of SDOH is needed to further improve healthcare outcomes

A risk screening tool for ethical appraisal of evidence-generating initiatives

Abstract Background The boundaries between health-related research and practice have become blurred as initiatives traditionally considered to be practice (e.g., quality improvement, program evaluation) increasingly use the same methodology as research. Further, the application of different ethical requirements based on this distinction raises concerns because many initiatives commonly labelled as “non-research” are associated with risks to patients, participants, and other stakeholders, yet may not be subject to any ethical oversight. Accordingly, we sought to develop a tool to facilitate the systematic identification of risks to human participants and determination of risk level across a broad range of projects (e.g., clinical research, laboratory-based projects, population-based surveillance, and program evaluation) and health-related contexts. This paper describes the development of the Public Health Ontario (PHO) Risk Screening Tool. Method Development of the PHO Risk Screening Tool included: (1) preparation of a draft risk tool (n = 47 items); (2) expert appraisal; (3) internal stakeholder validation; (4) external validation; (5) pilot testing and evalution of the draft tool; and (6) revision after 1 year of testing. Results A risk screening tool was generated consisting of 20 items organized into five risk domains: Sensitivity; Participant Selection, Recruitment and Consent; Data/Sample Collection; Identifiability and Privacy Risk; and Commercial Interests. The PHO Risk Screening Tool is an electronic tool, designed to identify potential project-associated risks to participants and communities and to determine what level of ethics review is required, if any. The tool features an easy to use checklist format that generates a risk score (0–3) associated with a suggested level of ethics review once all items have been completed. The final score is based on a threshold approach to ensure that the final score represents the highest level of risk identified in any of the domains of the tool. Conclusions The PHO Risk Screening Tool offers a practical solution to the problem of how to maintain accountability and appropriate risk oversight that transcends the boundaries of research and practice. We hope that the PHO Risk Screening Tool will prove useful in minimizing the problems of over and under protection across a wide range of disciplines and jurisdictions

What makes public health studies ethical? Dissolving the boundary between research and practice

Abstract Background The generation of evidence is integral to the work of public health and health service providers. Traditionally, ethics has been addressed differently in research projects, compared with other forms of evidence generation, such as quality improvement, program evaluation, and surveillance, with review of non-research activities falling outside the purview of the research ethics board. However, the boundaries between research and these other evaluative activities are not distinct. Efforts to delineate a boundary – whether on grounds of primary purpose, temporality, underlying legal authority, departure from usual practice, or direct benefits to participants – have been unsatisfactory. Public Health Ontario has eschewed this distinction between research and other evaluative activities, choosing to adopt a common framework and process to guide ethical reflection on all public health evaluative projects throughout their lifecycle – from initial planning through to knowledge exchange. Discussion The Public Health Ontario framework was developed by a working group of public health and ethics professionals and scholars, in consultation with individuals representing a wide range of public health roles. The first part of the framework interprets the existing Canadian research ethics policy statement (commonly known as the TCPS 2) through a public health lens. The second part consists of ten questions that guide the investigator in the application of the core ethical principles to public health initiatives. The framework is intended for use by those designing and executing public health evaluations, as well as those charged with ethics review of projects. The goal is to move toward a culture of ethical integrity among investigators, reviewers and decision-makers, rather than mere compliance with rules. The framework is consonant with the perspective of the learning organization and is generalizable to other public health organizations, to health services organizations, and beyond. Summary Public Health Ontario has developed an ethics framework that is applicable to any evidence-generating activity, regardless of whether it is labelled research. While developed in a public health context, it is readily adaptable to other health services organizations and beyond

What makes public health studies ethical? Dissolving the boundary between research and practice

Abstract Background The generation of evidence is integral to the work of public health and health service providers. Traditionally, ethics has been addressed differently in research projects, compared with other forms of evidence generation, such as quality improvement, program evaluation, and surveillance, with review of non-research activities falling outside the purview of the research ethics board. However, the boundaries between research and these other evaluative activities are not distinct. Efforts to delineate a boundary – whether on grounds of primary purpose, temporality, underlying legal authority, departure from usual practice, or direct benefits to participants – have been unsatisfactory. Public Health Ontario has eschewed this distinction between research and other evaluative activities, choosing to adopt a common framework and process to guide ethical reflection on all public health evaluative projects throughout their lifecycle – from initial planning through to knowledge exchange. Discussion The Public Health Ontario framework was developed by a working group of public health and ethics professionals and scholars, in consultation with individuals representing a wide range of public health roles. The first part of the framework interprets the existing Canadian research ethics policy statement (commonly known as the TCPS 2) through a public health lens. The second part consists of ten questions that guide the investigator in the application of the core ethical principles to public health initiatives. The framework is intended for use by those designing and executing public health evaluations, as well as those charged with ethics review of projects. The goal is to move toward a culture of ethical integrity among investigators, reviewers and decision-makers, rather than mere compliance with rules. The framework is consonant with the perspective of the learning organization and is generalizable to other public health organizations, to health services organizations, and beyond. Summary Public Health Ontario has developed an ethics framework that is applicable to any evidence-generating activity, regardless of whether it is labelled research. While developed in a public health context, it is readily adaptable to other health services organizations and beyond