The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

While ethicists have directed much attention to controversial biomedical issues--including euthanasia, abortion, and genetic engineering--they have largely ignored the less obvious, but more pervasive, everyday ethical problems faced by family physicians. Ethical Issues in Family Medicine addresses these problems, offering an ethics that reflects the distinctive features of family practice, and helping family physicians to appreciate the extent to which ethical issues influence their practice.

In their article “The Rise of Citizen Science in Health and Biomedical Research,” Wiggins and Wilbanks (2019) present a new typology for understanding the complex landscape of health and biomedical...

Background Citizen science is increasingly prevalent in the biomedical sciences, including the field of human genomics. Genomic citizen science initiatives present new opportunities to engage individuals in scientific discovery, but they also are provoking new questions regarding who owns the outputs of the research, including intangible ideas and discoveries and tangible writings, tools, technologies, and products. The legal and ethical claims of participants to research outputs become stronger—and also more likely to conflict with those of institution-based researchers and other stakeholders—as (...) participants become more involved, quantitatively and qualitatively, in the research process. It is not yet known, however, how genomic citizen science initiatives are managing the interests of their participants in accessing and controlling research outputs in practice. To help fill this gap, we conducted an in-depth review of relevant policies and practices of U.S.-based genomic citizen science initiatives. Methods We queried the peer-reviewed literature and grey literature to identify 22 genomic citizen science initiatives that satisfied six inclusion criteria. A data collection form was used to capture initiative features, policies, and practices relevant to participants’ access to and control over research outputs. Results This analysis revealed that the genomic citizen science landscape is diverse and includes many initiatives that do not have institutional affiliations. Two trends that are in apparent tension were identified: commercialization and operationalization of a philosophy of openness. While most initiatives supported participants’ access to research outputs, including datasets and published findings, none supported participants’ control over results via intellectual property, licensing, or commercialization rights. However, several initiatives disclaimed their own rights to profit from outputs. Conclusions There are opportunities for citizen science initiatives to incorporate more features that support participants’ access to and control over research outputs, consistent with their specific objectives, operations, and technical capabilities. (shrink)

The perspectives of genomic citizen scientists on ownership of research outputs are not well understood, yet they are useful for identifying alignment of participant expectations and project practices and can help guide efforts to develop innovative tools and strategies for managing ownership claims. Here, we report findings from 52 interviews conducted in 2018 and 2019 to understand genomic citizen science stakeholders’ conceptualizations of, experiences with, and preferences for ownership of research outputs. Interviewees identified four approaches for recognizing genomic citizen scientists’ (...) ownership and related credit interests in research outputs: shared governance via commons models; fractional ownership of benefits; full and creative attribution; and offensive and defensive patenting. Interviewees also agreed that the model selected by any project should at least maximize access to research outputs and, as appropriate and to the extent possible, broadly distribute rights of control and entitlements to research benefits. (shrink)

In this article, I highlight some core ideas that are important for understanding the parent-child relationship within the framework of political liberalism. I stress that, although some ideal or conception of the family is part of most, if not all, comprehensive doctrines, for political liberals, the state’s interest in the family is as a social-political institution in which certain needs of persons as free and equal citizens are met. I discuss the main needs and interests of children and parents in (...) the parent-child relationship. I consider that many children are cared for by multiple people, and I discuss how the state should address the recognition of multiple legal parents. I discuss some contexts in which conflicts arise between the interests of children and caregivers and address how such conflicts should be resolved in the politically liberal state. Although Rawls failed to offer an acceptable account of the family as part of the basic structure and did not adequately address the role of caring relationships in a just society, I hope that this article helps to show how political liberals can offer a plausible account. (shrink)

The speed and scale of the COVID‐19 pandemic has highlighted the limits of current health systems and the potential promise of non‐establishment research such as “DIY” research. We consider one example of how DIY research is responding to the pandemic, discuss the challenges faced by DIY research more generally, and suggest that a “trust architecture” should be developed now to contribute to successful future DIY efforts.

The proliferation of personal data collection practices fundamentally reshapes how society is ordered and commercialized, and demands reconsideration of the possibilities for a just and equitable s...

Background Empirical studies of surrogate decision-making tend to assume that surrogates should make only a 'substituted judgement'—that is, judge what the patient would want if they were mentally competent. Objectives To explore what people want in a surrogate decision-maker whom they themselves select and to test the assumption that people want their chosen surrogate to make only a substituted judgement. Methods 30 undergraduate students were recruited. They were presented with a hypothetical scenario about their expected loss of mental capacity in (...) the future and asked to answer some questions about their choice of surrogate. These data were analysed qualitatively using thematic content analysis. Results Most respondents talked about choosing someone who was caring and competent in certain ways, giving interesting evidence for their judgements. Surprisingly few highlighted how well they thought their chosen surrogate knew their preferences and would be able to make a substituted judgement. Moreover, few specified that their chosen surrogate had similar attitudes and values to their own and so would make a similar decision to theirs in the circumstances presented. Some respondents also referred to the social role of their chosen surrogate or the social dynamics of their situation which influenced their choices, as well as to ideas of reciprocity and characteristics of honesty and loyalty. Conclusion In the event that they lose mental capacity, many people will not select a surrogate to decide about medical treatments on their behalf solely on the basis that they expect their surrogate to make a substituted judgement. (shrink)

Insurance coverage of abortion varies widely across the United States and is an extensively debated issue. Medicaid coverage of abortion is particularly relevant because the majority of abortion patients are poor or low‐income and are thus often covered by Medicaid. Since the Hyde Amendment was first passed in 1976, federal Medicaid funds have been banned from covering the costs of elective abortion. Although states are allowed to use their own funds to cover abortions for their Medicaid recipients, only 17 states (...) currently do so. Of these 17 states, only five cover abortion costs voluntarily; the others do so pursuant to court order. The medical literature includes few ethical analyses of the Hyde Amendment’s ban on Medicaid funding of elective abortions. To fill this gap, we perform an ethical analysis of federal policy to fund elective abortions using a consequentialist approach focused on consequences for pregnant women and their children. (shrink)

This paper concludes a special feature of Sustainability Science that explores a broad range of social value theoretical traditions, such as religious studies, social psychology, indigenous knowledge, economics, sociology, and philosophy. We introduce a novel transdisciplinary conceptual framework that revolves around concepts of 'lenses' and 'tensions' to help navigate value diversity. First, we consider the notion of lenses: perspectives on value and valuation along diverse dimensions that describe what values focus on, how their sociality is envisioned, and what epistemic and (...) procedural assumptions are made. We characterise fourteen of such dimensions. This provides a foundation for exploration of seven areas of tension, between: (1) the values of individuals vs collectives; (2) values as discrete and held vs embedded and constructed; (3) value as static or changeable; (4) valuation as descriptive vs normative and transformative; (5) social vs relational values; (6) different rationalities and their relation to value integration; (7) degrees of acknowledgment of the role of power in navigating value conflicts. In doing so, we embrace the 'mess' of diversity, yet also provide a framework to organise this mess and support and encourage active transdisciplinary collaboration. We identify key research areas where such collaborations can be harnessed for sustainability transformation. Here it is crucial to understand how certain social value lenses are privileged over others and build capacity in decision-making for understanding and drawing on multiple value, epistemic and procedural lenses. (shrink)

Background Investigative genetic genealogy (IGG) is a technique that involves uploading genotypes developed from perpetrator DNA left at a crime scene, or DNA from unidentified remains, to public genetic genealogy databases to identify genetic relatives and, through the creation of a family tree, the individual who was the source of the DNA. As policymakers demonstrate interest in regulating IGG, it is important to understand public perspectives on IGG to determine whether proposed policies are aligned with public attitudes.Methods We conducted eight (...) focus groups with members of the public (N = 72), sampled from four geographically diverse US regions, to explore general attitudes and perspectives regarding aspects of IGG practices, applications, and policies. Five major topics were explored in each focus group: when IGG should be used; who should perform IGG; how to approach consent for genetic database users; what systems of oversight should govern IGG practitioners; and whether to notify database users if their data are involved in law enforcement (LE) matching.Results Participants were supportive of IGG in most scenarios, especially for cold and violent cases. The favorable attitudes toward IGG were, however, tempered by distrust of law enforcement among some participants. All participants agreed that databases must inform users if IGG is allowed, but they did not agree on how individual database users should be allowed to opt out or whether to notify them if their data are involved in specific investigations. All participants agreed that IGG should be subject to some prescriptive guidelines, regulations, or accountability mechanisms.Conclusions These findings suggest broad public support for IGG, and interest in developing systems of accountability for its practice. Our study provides useful insight for policy makers, genomic database stewards, law enforcement, and other stakeholders in IGG’s practice, and suggests multiple directions for future research. (shrink)

This paper concludes a special feature of Sustainability Science that explores a broad range of social value theoretical traditions, such as religious studies, social psychology, indigenous knowledge, economics, sociology, and philosophy. We introduce a novel transdisciplinary conceptual framework that revolves around concepts of ‘lenses’ and ‘tensions’ to help navigate value diversity. First, we consider the notion of lenses: perspectives on value and valuation along diverse dimensions that describe what values focus on, how their sociality is envisioned, and what epistemic and (...) procedural assumptions are made. We characterise fourteen of such dimensions. This provides a foundation for exploration of seven areas of tension, between: (1) the values of individuals vs collectives; (2) values as discrete and held vs embedded and constructed; (3) value as static or changeable; (4) valuation as descriptive vs normative and transformative; (5) social vs relational values; (6) different rationalities and their relation to value integration; (7) degrees of acknowledgment of the role of power in navigating value conflicts. In doing so, we embrace the ‘mess’ of diversity, yet also provide a framework to organise this mess and support and encourage active transdisciplinary collaboration. We identify key research areas where such collaborations can be harnessed for sustainability transformation. Here it is crucial to understand how certain social value lenses are privileged over others and build capacity in decision-making for understanding and drawing on multiple value, epistemic and procedural lenses. (shrink)

This invaluable resource is the first one-volume, in-depth, comprehensive history of modern science ever published.

Rationale: Deep brain stimulation (DBS) of the hippocampus is proposed for enhancement of memory impaired by injury or disease. Many pre-clinical DBS paradigms can be addressed in epilepsy patients undergoing intracranial monitoring for seizure localization, since they already have electrodes implanted in brain areas of interest. Even though epilepsy is usually not a memory disorder targeted by DBS, the studies can nevertheless model other memory-impacting disorders, such as Traumatic Brain Injury (TBI). Methods: Human patients undergoing Phase II invasive monitoring for (...) intractable epilepsy were implanted with depth electrodes capable of recording neurophysiological signals. Subjects performed a delayed-match-to-sample (DMS) memory task while hippocampal ensembles from CA1 and CA3 cell layers were recorded to estimate a multi-input, multi-output (MIMO) model of CA3-to-CA1 neural encoding and a memory decoding model (MDM) to decode memory information from CA3 and CA1 neuronal signals. After model estimation, subjects again performed the DMS task while either MIMO-based or MDM-based patterned stimulation was delivered to CA1 electrode sites during the encoding phase of the DMS trials. Each subject was sorted (post hoc) by prior experience of repeated and/or mild-to-moderate brain injury (RMBI), TBI, or no history (control) and scored for percentage successful delayed recognition (DR) recall on stimulated vs. non-stimulated DMS trials. The subject’s medical history was unknown to the experimenters until after individual subject memory retention results were scored. Results: When examined compared to control subjects, both TBI and RMBI subjects showed increased memory retention in response to both MIMO and MDM-based hippocampal stimulation. Furthermore, effects of stimulation were also greater in subjects who were evaluated as having pre-existing mild-to-moderate memory impairment. Conclusion: These results show that hippocampal stimulation for memory facilitation was more beneficial for subjects who had previously suffered a brain injury (other than epilepsy), compared to control (epilepsy) subjects who had not suffered a brain injury. This study demonstrates that the epilepsy/intracranial recording model can be extended to test the ability of DBS to restore memory function in subjects who previously suffered a brain injury other than epilepsy, and support further investigation into the beneficial effect of DBS in TBI patients. (shrink)

Generative artificial intelligence (AI) has the potential to transform many aspects of scholarly publishing. Authors, peer reviewers, and editors might use AI in a variety of ways, and those uses might augment their existing work or might instead be intended to replace it. We are editors of bioethics and humanities journals who have been contemplating the implications of this ongoing transformation. We believe that generative AI may pose a threat to the goals that animate our work but could also be (...) valuable for achieving those goals. In the interests of fostering a wider conversation about how generative AI may be used, we have developed a preliminary set of recommendations for its use in scholarly publishing. We hope that the recommendations and rationales set out here will help the scholarly community navigate toward a deeper understanding of the strengths, limits, and challenges of AI for responsible scholarly work. (shrink)

The new generative artificial intelligence (AI) tools, and especially the large language models (LLMs) of which ChatGPT is the most prominent example, have the potential to transform many aspects o...

This book provides practical and research-based chapters that offer greater clarity about the particular kinds of teacher reflection that matter and avoids talking about teacher reflection generically, which implies that all kinds of reflection are of equal value.

Generative artificial intelligence (AI) has the potential to transform many aspects of scholarly publishing. Authors, peer reviewers, and editors might use AI in a variety of ways, and those uses might augment their existing work or might instead be intended to replace it. We are editors of bioethics and humanities journals who have been contemplating the implications of this ongoing transformation. We believe that generative AI may pose a threat to the goals that animate our work but could also be (...) valuable for achieving those goals. In the interests of fostering a wider conversation about how generative AI may be used, we have developed a preliminary set of recommendations for its use in scholarly publishing. We hope that the recommendations and rationales set out here will help the scholarly community navigate toward a deeper understanding of the strengths, limits, and challenges of AI for responsible scholarly work. (shrink)

Understanding the clinical significance of variants associated with hereditary cancer risk requires access to a pooled data resource or network of resources—a “cancer gene variant commons”—incorporating representative, well-characterized genetic data, metadata, and, for some purposes, pathways to case-level data. Several initiatives have invested significant resources into collecting and sharing cancer gene variant data, but further progress hinges on identifying and addressing unresolved policy issues. This commentary provides insights from a modified policy Delphi process involving experts from a range of stakeholder (...) groups involved in the data-sharing ecosystem. In particular, we describe policy issues and options generated by Delphi participants in five domains critical to the development of an effective cancer gene variant commons: incentives, financial sustainability, privacy and security, equity, and data quality. Our intention is to stimulate wider discussion and lay a foundation for further work evaluating policy options more in-depth and mapping them to those who have the power to bring about change. Addressing issues in these five domains will contribute to a cancer gene variant commons that supports better care for at-risk and affected patients, empowers patient communities, and advances research on hereditary cancers. (shrink)

The new generative artificial intelligence (AI) tools, and especially the large language models (LLMs) of which ChatGPT is the most prominent example, have the potential to transform many aspects o...

White matter tracts are known to be susceptible to injury following concussion. The objective of this study was to determine whether contact play in sport could alter white matter metabolite levels in female varsity athletes independent of changes induced by long-term exercise. Metabolite levels were measured by single voxel proton magnetic resonance spectroscopy in the prefrontal white matter at the beginning and end of season in contact and non-contact varsity athletes. Sedentary women were scanned once, at a time equivalent to (...) the Off-Season time point. Metabolite levels in non-contact athletes did not change over a season of play, or differ from age matched sedentary women except that non-contact athletes had a slightly lower myo-inositol level. The contact athletes had lower levels of myo-inositol and glutamate, and higher levels of glutamine compared to both sedentary women and non-contact athletes. Lower levels of myo-inositol in non-contact athletes compared to sedentary women indicates long-term exercise may alter glial cell profiles in these athletes. The metabolite differences observed between contact and non-contact athletes suggest that non-contact athletes should not be used as controls in studies of concussion in high-impact sports because repetitive impacts from physical contact can alter white matter metabolite level profiles. It is imperative to use athletes engaged in the same contact sport as controls to ensure a matched metabolite profile at baseline. (shrink)

Background As citizen science continues to grow in popularity, there remains disagreement about what terms should be used to describe citizen science activities and participants. The question of how to self-identify has important ethical, political, and practical implications to the extent that shared language reflects a common ethos and goals and shapes behavior. Biomedical citizen science in particular has come to be associated with terms that reflect its unique activities, concerns, and priorities. To date, however, there is scant evidence regarding (...) how biomedical citizen scientists prefer to describe themselves, their work, and the values that they attach to these terms.Methods In 2018, we conducted semi-structured interviews with 35 biomedical citizen scientists in connection with a larger study to understand ownership preferences. Interview data were analyzed to identify the terms that interviewees used and avoided to describe themselves and their work, as well as the reasons for their preferences.Results Biomedical citizen scientists self-identified using three main terms: citizen scientist, biohacker, and community scientist. However, there was a lack of consensus among interviewees on the appropriateness of each term, two of which prompted conflicting responses. Self-identification preferences were based on personal judgments about whether specific terms convey respect, are provocative, or are broad and inclusive, as well as the desirability of each of these messages.Conclusions The lack of consensus about self-identification preferences in biomedical citizen science reflects the diversity of experiences and goals of individuals participating in this field, as well as different perceptions of the values signaled by and implications of using each term. Heterogeneity of preferences also may signal the parallel development of multiple communities in biomedical citizen science. (shrink)