The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

1 The Zero-Force Evolutionary Law 2 Randomness, Hierarchy, and Constraint 3 Diversity 4 Complexity 5 Evidence, Predictions, and Tests 6 Philosophical Foundations 7 Implications.

Legal systems often rule that people own objects in their territory. We propose that an early-developing ability to make territory-based inferences of ownership helps children address informational demands presented by ownership. Across 6 experiments (N = 504), we show that these inferences develop between ages 3 and 5 and stem from two aspects of the psychology of ownership. First, we find that a basic ability to infer that people own objects in their territory is already present at age 3 (Experiment (...) 1). Children even make these inferences when the territory owner unintentionally acquired the objects and was unaware of them (Experiments 2 and 3). Second, we find that between ages 3 and 5, children come to consider past events in these judgments. They move from solely considering the current location of an object in territory-based inferences, to also considering and possibly inferring where it originated (Experiments 4 to 6). Together, these findings suggest that territory-based inferences of ownership are unlikely to be constructions of the law. Instead, they may reflect basic intuitions about ownership that operate from early in development. (shrink)

Since its publication in 1965, Brian Barry's seminal work has occupied an important role in the revival of Anglo-American political philosophy. A number of ideas and terms in it have become part of the standard vocabulary, such as the distinction between "ideal-regarding" and "want-regarding" principles and the division of principles into aggregative and distributive. The book provided the first precise analysis of the concept of political values having trade-off relations and its analysis of the notion of the public interest (...) has also been significant. (shrink)

Hoerl & McCormack suggest that saving tools does not require temporal reasoning. However, we identify a class of objects that are only possessed in anticipation of future needs. We propose that investigating these future-oriented objects may help identify temporal reasoning in populations where this ability is uncertain.

Barrett et al. present four puzzles for the ZFEL-view of evolution that we present in our 2010 book, Biology’s First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems. Our intent in writing this book was to present a radically different way to think about evolution. To the extent that it really is radical, it will be easy to misunderstand. We think Barrett et al. have misunderstood several crucial points and so we welcome the opportunity to clarify.

In this Element, we extend our earlier treatment of biology's first law. The law says that in any evolutionary system in which there is variation and heredity, there is a tendency for diversity and complexity to increase. The law plays the same role in biology that Newton's first law plays in physics, explaining what biological systems are expected to do when no forces act, in other words, what happens when nothing happens. Here we offer a deeper explanation of certain features (...) of the law, develop a quantitative version of it, and explore its consequences for our understanding of diversity and complexity. (shrink)

Public discourse is often caustic and conflict-filled. This trend seems to be particularly evident when the content of such discourse is around moral issues (broadly defined) and when the discourse occurs on social media. Several explanatory mechanisms for such conflict have been explored in recent psychological and social-science literatures. The present work sought to examine a potentially novel explanatory mechanism defined in philosophical literature: Moral Grandstanding. According to philosophical accounts, Moral Grandstanding is the use of moral talk to seek social (...) status. For the present work, we conducted six studies, using two undergraduate samples (Study 1, N = 361; Study 2, N = 356); a sample matched to U.S. norms for age, gender, race, income, Census region (Study 3, N = 1,063); a YouGov sample matched to U.S. demographic norms (Study 4, N = 2,000); and a brief, one-month longitudinal study of Mechanical Turk workers in the U.S. (Study 5, Baseline N = 499, follow-up n = 296), and a large, one-week YouGov sample matched to U.S. demographic norms (Baseline N = 2,519, follow-up n = 1,776). Across studies, we found initial support for the validity of Moral Grandstanding as a construct. Specifically, moral grandstanding motivation was associated with status-seeking personality traits, as well as greater political and moral conflict in daily life. (shrink)

Aquinas’s doctrine that infused virtues accompany sanctifying grace raises many questions. We examine one: how do the infused virtues relate to the acquired virtues? More precisely, can the person with the infused virtues possess the acquired virtues? We argue for an answer consistent with and informed by Aquinas’s writings, although it goes beyond textual evidence, as any answer to this question must. There are two plausible, standard interpretations of Aquinas on this issue: the coexistence view and transformation view. After explaining (...) the views, we present plausible reasons for and against each view. The evidence suggests, we argue, that the acquired virtues are both present and absent in the Christian. We then survey Aquinas’s account of virtual presence. Finally, we argue that the case of the presence of acquired virtues in the Christian is a good candidate for virtual presence. (shrink)

The possibility of continuous backwards time travel—time travel for which the traveler follows a continuous path through space between departure and arrival—gives rise to the double-occupancy problem. The trouble is that the time traveler seems bound to have to travel through his or her younger self as the trip begins. Dowe and Le Poidevin agree that this problem is solved by putting the traveler in motion for a gradual trip to the past. Le Poidevin goes on to argue, however, that (...) the gradual trip gives rise to the Cheshire cat problem, a concern about whether the traveler survives the gradual trip. We address the Cheshire cat problem by proposing and considering new continuity constraints on identity over time. Along the way, we come upon an endurantist conception of temporal parts. (shrink)

This article investigates the propensity for academic dishonesty by university students using the partitioning method of decision tree analysis. A set of prediction rules are presented, and conclusions are drawn. To provide context for the decision tree approach, the partition process is compared with results of more traditional probit regression models. Results of the decision tree analysis complement the probit models in terms of predictive accuracy and confirm results previously found in the literature. In particular, students’ moral character—whether they believe (...) cheating is acceptable—is found to be the most important factor in determining the propensity for academic dishonesty. (shrink)

Even after multiple cycles of ABET accreditation, many engineering programs are unsure of how much curriculum content is needed to meet the requirements of ABET’s Criterion 3.f (an understanding of professional and ethical responsibility). This study represents the first scholarly attempt to assess the impact of curriculum reform following the introduction of ABET Criterion 3.f. This study sought to determine how much professional and ethical responsibility curriculum content was used between 1995 and 2005, as well as how, when, why, and (...) to what effect changes in the amount of content occurred. Subsequently, the study sought to evaluate if different amounts of curriculum content generated differing student outcomes. The amount of curriculum content used by each of the participating programs was identified during semi-structured interviews with program administrators and a review of ABET Self-Study documents. Quantitative methods were applied to determine if a relationship existed between the curriculum content and performance on a nationally administered, engineering-specific standardized examination. The findings indicate a statistical relationship, but a lack of structure between the amount of required content in the curriculum and performance on the examination. Additional findings were also generated regarding the way that programs interpret the Criterion 3.f feedback generated during accreditation visits. The primary impact of this study is that it dispels the myth that more courses or course time on professionalism and ethics will necessarily lead to positive engineering education outcomes. Much of the impetus to add more curriculum content results from a lack of conclusive feedback during ABET accreditation visits. (shrink)

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...) level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

Cyclic nucleotides can regulate the sensitivity of retinal rods to light through phosducin. The phosphorylation state of phosducin determines the amount of G available for activation by Rho*. Phosducin phosphorylation is regulated by cyclic nucleotides through their activation of cAMP-dependent protein kinase. The regulation of phosphodiesterase activity by the noncatalytic cGMP binding sites as well as Ca2+/calmodulin dependent regulation of cGMP binding to the cation channel are also discussed.

Augmentative and alternative communication brain-computer interface systems are intended to offer communication access to people with severe speech and physical impairment without requiring volitional movement. As the field moves toward clinical implementation of AAC-BCI systems, research involving participants with SSPI is essential. Research has demonstrated variability in AAC-BCI system performance across users, and mixed results for comparisons of performance for users with and without disabilities. The aims of this systematic review were to describe study, system, and participant characteristics reported in (...) BCI research, summarize the communication task performance of participants with disabilities using AAC-BCI systems, and explore any differences in performance for participants with and without disabilities. Electronic databases were searched in May, 2018, and March, 2021, identifying 6065 records, of which 73 met inclusion criteria. Non-experimental study designs were common and sample sizes were typically small, with approximately half of studies involving five or fewer participants with disabilities. There was considerable variability in participant characteristics, and in how those characteristics were reported. Over 60% of studies reported an average selection accuracy ≤70% for participants with disabilities in at least one tested condition. However, some studies excluded participants who did not reach a specific system performance criterion, and others did not state whether any participants were excluded based on performance. Twenty-nine studies included participants both with and without disabilities, but few reported statistical analyses comparing performance between the two groups. Results suggest that AAC-BCI systems show promise for supporting communication for people with SSPI, but they remain ineffective for some individuals. The lack of standards in reporting outcome measures makes it difficult to synthesize data across studies. Further research is needed to demonstrate efficacy of AAC-BCI systems for people who experience SSPI of varying etiologies and severity levels, and these individuals should be included in system design and testing. Consensus in terminology and consistent participant, protocol, and performance description will facilitate the exploration of user and system characteristics that positively or negatively affect AAC-BCI use, and support innovations that will make this technology more useful to a broader group of people.Clinical trial registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42018095345, PROSPERO: CRD42018095345. (shrink)

Should society care about Christian morality? Are Christians out of touch with complex moral decision-making? Christian Morality: An Interdisciplinary Framework for Thinking about Contemporary Moral Issues provides readers with a framework for identifying and applying Christian moral principles to divisive issues. First, readers learn of the theological and philosophical foundations of Christian ethics. Two additional chapters explain how personal and social factors influence our capacity to think critically and Christianly about morality. Second, readers will learn about forming Christian moral judgments (...) by seeing how different thinkers address six contemporary moral issues: abortion, same-sex relationships, equal treatment of men and women in the workplace, sex education, and racial bias in incarceration polices. (shrink)

Counterfactuals all the way down? Content Type Journal Article DOI 10.1007/s11016-010-9437-9 Authors Jim Woodward, History and Philosophy of Science, 1017 Cathedral of Learning, University of Pittsburgh, Pittsburgh, PA 15260, USA Barry Loewer, Department of Philosophy, Rutgers University, New Brunswick, NJ 08901, USA John W. Carroll, Department of Philosophy and Religious Studies, North Carolina State University, Raleigh, NC 27695-8103, USA Marc Lange, Department of Philosophy, University of North Carolina at Chapel Hill, CB#3125—Caldwell Hall, Chapel Hill, NC 27599-3125, USA Journal Metascience (...) Online ISSN 1467-9981 Print ISSN 0815-0796 Journal Volume Volume 20 Journal Issue Volume 20, Number 1. (shrink)

Screening for prostate cancer with the prostate-specific antigen blood test is controversial, as evidence to date has not demonstrated such screening does more good than harm. While the potential benefit of PSA screening on reducing prostate cancer mortality has not been documented in randomized trials, many risks of PSA screening have been well documented. These risks include a substantially higher risk of a prostate cancer diagnosis over a screenee’s lifetime, false-positive and false-negative test results, possible complications from biopsies done in (...) response to suspicious test results, and substantial risks of side effects from subsequent prostate cancer treatments. Nevertheless, PSA screening is widespread in the United States, and many physicians in a national survey reported supporting routine PSA screening as well as getting PSA tests themselves, despite the lack of evidence. (shrink)

We conducted focus groups with 47 potential jurors who were presented with diferent scenarios in a hypothetical malpractice case involving failure to order a PSA test. Better documentation that a patient made an informed decision to decline a PSA test appeared to provide more medical-legal protection for physicians, especially with the use of a decision aid.

Media multitasking entails simultaneously engaging in multiple tasks when at least one of the tasks involves media. Across two studies, we investigated one potential trigger of media multitasking, state boredom, and its relation to media multitasking. To this end, we manipulated participants’ levels of state boredom using video mood inductions prior to administering an attention-demanding 2-back task during which participants could media multitask by playing a task-irrelevant video. We also examined whether trait boredom proneness was associated media multitasking. We found (...) no direct evidence that state boredom leads to media multitasking. However, trait boredom proneness correlated with greater amounts of media multitasking in Experiment 1, but not in Experiment 2. Surprisingly, in both experiments, post-task ratings of state boredom were equivalent across conditions, alerting us to the short-lived effects of video mood inductions and the boring nature of cognitive tasks. (shrink)

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva (...) diagnostics made possible by the Saliva Ontology and SDxMart. (shrink)

Childhood adversity is associated with altered or dysregulated stress reactivity; these altered patterns of physiological functioning persist into adulthood. Evidence from both preclinical animal models and human neuroimaging studies indicates that early life experience differentially influences stressor-evoked activity within central visceral neural circuits proximally involved in the control of stress responses, including the subgenual anterior cingulate cortex (sgACC), paraventricular nucleus of the hypothalamus (PVN), bed nucleus of the stria terminalis (BNST) and amygdala. However, the relationship between childhood adversity and the (...) resting-state connectivity of this central visceral network remains unclear. To this end, we examined relationships between childhood threat and childhood socioeconomic deprivation, the resting-state connectivity between our regions of interest (ROIs), and affective symptom severity and diagnoses. We recruited a transdiagnostic sample of young adult males and females (n= 100; mean age = 27.28,SD= 3.99; 59 females) with a full distribution of maltreatment history and symptom severity across multiple affective disorders. Resting-state data were acquired using a 7.2-min functional magnetic resonance imaging (fMRI) sequence; noted ROIs were applied as masks to determine ROI-to-ROI connectivity. Threat was determined by measures of childhood traumatic events and abuse. Socioeconomic deprivation (SED) was determined by a measure of childhood socioeconomic status (parental education level). Covarying for age, race and sex, greater childhood threat was significantly associated with lower BNST-PVN, amygdala-sgACC and PVN-sgACC connectivity. No significant relationships were found between SED and resting-state connectivity. BNST-PVN connectivity was associated with the number of lifetime affective diagnoses. Exposure to threat during early development may entrain altered patterns of resting-state connectivity between these stress-related ROIs in ways that contribute to dysregulated neural and physiological responses to stress and subsequent affective psychopathology. (shrink)

Access to communication is critical for individuals with late-stage amyotrophic lateral sclerosis and minimal volitional movement, but they sometimes present with concomitant visual or ocular motility impairments that affect their performance with eye tracking or visual brain-computer interface systems. In this study, we explored the use of modified eye tracking and steady state visual evoked potential BCI, in combination with the Shuffle Speller typing interface, for this population. Two participants with late-stage ALS, visual impairments, and minimal volitional movement completed a (...) single-case experimental research design comparing copy-spelling performance with three different typing systems: commercially available eye tracking communication software, Shuffle Speller with modified eye tracking, and Shuffle Speller with SSVEP BCI. Participant 1 was unable to type any correct characters with the commercial system, but achieved accuracies of up to 50% with Shuffle Speller eye tracking and 89% with Shuffle Speller BCI. Participant 2 also had higher maximum accuracies with Shuffle Speller, typing with up to 63% accuracy with eye tracking and 100% accuracy with BCI. However, participants’ typing accuracy for both Shuffle Speller conditions was highly variable, particularly in the BCI condition. Both the Shuffle Speller interface and SSVEP BCI input show promise for improving typing performance for people with late-stage ALS. Further development of innovative BCI systems for this population is needed. (shrink)