The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Successful therapies to combat microbial diseases and cancers require incorporating ecological and evolutionary principles. Drawing upon the fields of ecology and evolutionary biology, we present a systems‐based approach in which host and disease‐causing factors are considered as part of a complex network of interactions, analogous to studies of “classical” ecosystems. Centering this approach around empirical examples of disease treatment, we present evidence that successful therapies invariably engage multiple interactions with other components of the host ecosystem. Many of these factors interact (...) nonlinearly to yield synergistic benefits and curative outcomes. We argue that these synergies and nonlinear feedbacks must be leveraged to improve the study of pathogenesis in situ and to develop more effective therapies. An eco‐evolutionary systems perspective has surprising and important consequences, and we use it to articulate areas of high research priority for improving treatment strategies. (shrink)

Tropes is a systematic investigation into the metaphysics of properties, aiming to motivate and defend trope theory, and more specifically Natural Class Trope Nominalism (NCTN). Ehring’s book treats an impressive span of relevant positions, considerations, debates and objections with charity and clarity; it’s also a real page-turner, at least if one has (as I do) a taste for analytic twists and turns.

Perception of temporal patterns is fundamental to normal hearing, speech, motor control, and music. Certain types of pattern understanding are unique to humans, such as musical rhythm. Although human responses to musical rhythm are universal, there is much we do not understand about how rhythm is processed in the brain. Here, I consider findings from research into basic timing mechanisms and models through to the neuroscience of rhythm and meter. A network of neural areas, including motor regions, is regularly implicated (...) in basic timing as well as processing of musical rhythm. However, fractionating the specific roles of individual areas in this network has remained a challenge. Distinctions in activity patterns appear between "automatic" and "cognitively controlled" timing processes, but the perception of musical rhythm requires features of both automatic and controlled processes. In addition, many experimental manipulations rely on participants directing their attention toward or away from certain stimulus features, and measuring corresponding differences in neural activity. Many temporal features, however, are implicitly processed whether attended to or not, making it difficult to create controlled baseline conditions for experimental comparisons. The variety of stimuli, paradigms, and definitions can further complicate comparisons across domains or methodologies. Despite these challenges, the high level of interest and multitude of methodological approaches from different cognitive domains (including music, language, and motor learning) have yielded new insights and hold promise for future progress. (shrink)

ABSTRACT:We discuss workers’ dignity in hierarchical organizations. First, we explain why a conflict exists between high-ranking individuals’ authority and low-ranking individuals’ dignity. Then, we ask whether there is any justification that reconciles hierarchical authority with the dignity of workers. We advance a communitarian justification for hierarchical authority, drawing upon Confucianism, which provides that workers can justifiably accept hierarchical authority when it enables a certain type of social functioning critical for the good life of workers and other involved parties. The Confucian (...) communitarian perspective shows that promoting workers’ good life or well-being is an important condition for protecting their dignity. (shrink)

The practical criteria by which developmental biologists choose their model systems have evolutionary correlates. The result is a sample that is not merely small, but biased in particular ways, for example towards species with rapid, highly canalized development. These biases influence both data collection and interpretation, and our views of how development works and which aspects of it are important.

The concept of homology arose from classical studies of comprative morphology, and took on a new signficance with the advent of evolutionary theory. It is currentlyl undergoing antoher metamorphosis: many developmental geneticists now dfine homology as shared patterns of gene expression. However, this ne usage conflaes difinition with criteri, and fails to recognize the meaninful asignments of homology must speify a biologcal level. We argue the although developmental genetic data can help identify homologus structures. they are niether necessary nor sufficient, (...) and do not in any case jutify a new definition of homology. (shrink)

Leading animal models are powerful tools for translational research, but they also present obstacles. Poorly conducted preclinical research in animals is a common cause of translational failure, but even when such research is well-designed and carefully executed, challenges remain. In particular, dominant models may bias research directions, elide essential aspects of human disease, omit important context, or subtly shift research targets. Recognizing these stumbling blocks can help us find ways to avoid them: employing a wider range of models, incorporating more (...) realistic environmental conditions, better aligning studies between animals and patients, and focusing on human biology and therapeutic goals. Such changes are costly; but insisting it would be impractical or unrealistic to change strategies offers no way out of the current impasse. Rather, we must acknowledge the obstacles as well as the advantages presented by core models, and direct some of our investments in translational research toward getting around them. The dominance of biomedical research by a handful of animal models introduces subtle but significant obstacles to translation. Recognizing these obstacles is a critical first step toward finding ways around them; this paper describes how dominant models can create roadblocks, and suggests strategies to improve the efficiency of translation from animal models to humans. (shrink)

Music uses the evolutionarily unique temporal sensitivity of the auditory system and its tight coupling to the motor system to create a common neurophysiological clock between individuals that facilitates action coordination. We propose that this shared common clock arises from entrainment to musical rhythms, the process by which partners' brains and bodies become temporally aligned to the same rhythmic pulse.

Much critical attention has been paid to the use of qualitative research in the medical sciences, with proponents advancing discussions of what it is and how it may be appraised, and critics arguing that it is of exploratory use only. Using philosophical analysis, I argue that such discussions are flawed insofar as they endorse the idea that qualitative and quantitative research are epistemically distinct categories involving different types of knowledge. Rather, I claim that such approaches are actually culturally distinct involving (...) different intellectual histories. Thus highlighting that qualitative research may not necessarily be exploratory, and that the qualitative-quantitative divide could be closed through the development of innovative social strategies. This makes possible not only shared standard setting practices, but also novel techniques which could optimise medical research to improve health care and save lives. (shrink)

The American Journal of Bioethics, Volume 12, Issue 10, Page 47-49, October 2012.

With the aim of studying foundations for self-other relations and understanding, we conducted an experimental investigation of a specific aspect of imitation in children with autism: the propensity to copy self-other orientation. We hypothesised that children with autism would show limitations inidentifying withthe stance of another person. We tested 16 children with autism and 16 non-autistic children with learning difficulties, matched on both chronological and verbal mental age, for their propensity to imitate the self- or other-orientated aspects of another person’s (...) actions. All participants were attentive to the demonstrator and copied her actions, but the children with autism were significantly less likely to imitate those aspects of her actions that involved movement in relation to her own vis-à-vis the child’s body. There were a number of children with autism who copied the identical geometric orientation of objects acted-upon. These results suggest that children with autism have a diminished propensity to identify with other people, and point to the importance of this mechanism for shaping self-other relations and flexible thinking. (shrink)

New technologies coupled with high energy prices, a desire for energy independence, and cleaner energy, have led to many energy companies investing large amounts of capital into rural places. In the last decade, along with solar and wind, unconventional shale oil and gas production has risen steeply throughout the United States boosting economic growth and stimulating wealth creation in many communities. Because farmers own or operate over half of rural lands in the lower 48 states, the possibility is high for (...) shale development to contribute to the financial well-being of farmers with land in shale regions. However, by focusing on the large royalties of some landowners, environmental and social risks that farmers encounter may be overlooked. To address the gap of farmer impacts, I examine the experiences and perceptions of crop farm owners who reside in two established shale plays: the Bakken region in North Dakota and the Marcellus region in Pennsylvania and in one emerging shale play: the New Albany region in Southern Illinois. I survey farm owners of both large and small crop farms, who farm a variety of crops both by conventional and organic methods. By having such a diverse sample of farm owners in both established shale plays and emerging shale plays, I explore how farmers’ experiences differ with respect to their finances and investments, environmental degradation as well as how their perceptions of trust in oil and gas companies and community rifts differ. (shrink)

Compared to our understanding of positive prediction error signals occurring due to unexpected reward outcomes, less is known about the neural circuitry in humans that drives negative prediction errors during omission of expected rewards. While classical learning theories such as Rescorla–Wagner or temporal difference learning suggest that both types of prediction errors result from a simple subtraction, there has been recent evidence suggesting that different brain regions provide input to dopamine neurons which contributes to specific components of this prediction error (...) computation. Here, we focus on the brain regions responding to negative prediction error signals, which has been well-established in animal studies to involve a distinct pathway through the lateral habenula. We examine the activity of this pathway in humans, using a conditioned inhibition paradigm with high-resolution functional MRI. First, participants learned to associate a sensory stimulus with reward delivery. Then, reward delivery was omitted whenever this stimulus was presented simultaneously with a different sensory stimulus, the conditioned inhibitor. Both reward presentation and the reward-predictive cue activated midbrain dopamine regions, insula and orbitofrontal cortex. While we found significant activity at an uncorrected threshold for the CI in the habenula, consistent with our predictions, it did not survive correction for multiple comparisons and awaits further replication. Additionally, the pallidum and putamen regions of the basal ganglia showed modulations of activity for the inhibitor that did not survive the corrected threshold. (shrink)

Although widely studied in other domains, relatively little is known about the metacognitive processes that monitor and control behaviour during reasoning and decision-making. In this paper, we examined the conditions under which two fluency cues are used to monitor initial reasoning: answer fluency, or the speed with which the initial, intuitive answer is produced, and perceptual fluency, or the ease with which problems can be read. The first two experiments demonstrated that answer fluency reliably predicted Feeling of Rightness judgments to (...) conditional inferences and base rate problems, which subsequently predicted the amount of deliberate processing as measured by thinking time and answer changes; answer fluency also predicted retrospective confidence judgments. Moreover, the effect of answer fluency on reasoning was independent from the effect of perceptual fluency, establishing that these are empirically independent constructs. In five experiments with a variety of reasoning problems similar to those of Alter et al., we found no effect of perceptual fluency on FOR, retrospective confidence or accuracy; however, we did observe that participants spent more time thinking about hard to read stimuli, although this additional time did not result in answer changes. In our final two experiments, we found that perceptual disfluency increased accuracy on the CRT, but only amongst participants of high cognitive ability. As Alter et al.’s samples were gathered from prestigious universities, collectively, the data to this point suggest that perceptual fluency prompts additional processing in general, but this processing may results in higher accuracy only for the most cognitively able. (shrink)

With the aim of studying foundations for self-other relations and understanding, we conducted an experimental investigation of a specific aspect of imitation in children with autism: the propensity to copy self-other orientation. We hypothesised that children with autism would show limitations inidentifying withthe stance of another person. We tested 16 children with autism and 16 non-autistic children with learning difficulties, matched on both chronological and verbal mental age, for their propensity to imitate the self- or other-orientated aspects of another person’s (...) actions. All participants were attentive to the demonstrator and copied her actions, but the children with autism were significantly less likely to imitate those aspects of her actions that involved movement in relation to her own vis-à-vis the child’s body. There were a number of children with autism who copied the identical geometric orientation of objects acted-upon. These results suggest that children with autism have a diminished propensity to identify with other people, and point to the importance of this mechanism for shaping self-other relations and flexible thinking. (shrink)

While utopians cannot produce what they can imagine, we can no longer imagine what we produce. It is increasingly the case that undergraduate teacher candidates find themselves enrolled in courses that have been developed “in partnership” with local school districts—districts adjacent to the actual universities where they are enrolled. Recently, one such partnership arrangement had a foundation of education professor and initial certification students oscillating between two school districts located in the same large suburban area. One side of town is (...) inhabited by mostly minority children in underfunded schools—commonly viewed as the “bad” district. The other side of town has the “better” district, as it .. (shrink)

"A frontier is not a wall, but a threshold."The last four decades have witnessed a marked change in the perception of identity in Spain. The country's rapid transformation from dictatorship to democracy with the death of its dictator, General Francisco Franco, in 1975, accelerated the economic modernization begun in the 1960s. Soon after, Spain joined Western countries as a significant entity in world events, and became an appealing destination for immigrants looking for a better chance at economic sustainability. Consequently, the (...) country's population shifted from one of net emigration in the 1960s and '70s, to one with a slight immigrant population of.52 percent in 1981, to harboring an immigrant population of. (shrink)

With the aim of studying foundations for self-other relations and understanding, we conducted an experimental investigation of a specific aspect of imitation in children with autism: the propensity to copy self-other orientation. We hypothesised that children with autism would show limitations in identifying with the stance of another person. We tested 16 children with autism and 16 non-autistic children with learning difficulties, matched on both chronological and verbal mental age, for their propensity to imitate the self- or other-orientated aspects of (...) another person’s actions. All participants were attentive to the demonstrator and copied her actions, but the children with autism were significantly less likely to imitate those aspects of her actions that involved movement in relation to her own vis-à-vis the child’s body. There were a number of children with autism who copied the identical geometric orientation of objects acted-upon. These results suggest that children with autism have a diminished propensity to identify with other people, and point to the importance of this mechanism for shaping self-other relations and flexible thinking. (shrink)

Matrices that cannot be handled using conventional clustering, regression or classification methods are often found in every big data research area. In particular, datasets with thousands or millions of rows and less than a hundred columns regularly appear in biological so-called omic problems. The effectiveness of conventional data analysis approaches is hampered by this matrix structure, which necessitates some means of reduction. An evolutionary method called PreCLAS is presented in this article. Its main objective is to find a submatrix with (...) fewer rows that exhibits some group structure. Three stages of experiments were performed. First, a benchmark dataset was used to assess the correct functionality of the method for clustering purposes. Then, a microarray gene expression data matrix was used to analyze the method’s performance in a simple classification scenario, where differential expression was carried out. Finally, several classification methods were compared in terms of classification accuracy using an RNA-seq gene expression dataset. Experiments showed that the new evolutionary technique significantly reduces the number of rows in the matrix and intelligently performs unsupervised row selection, improving classification and clustering methods. (shrink)

In “Obligations of the ‘Gift’: Reciprocity and Responsibility in Precision Medicine,” Lee rightly points out that disparities in health care access also lead to disparities in precision medi...

The United States has a population of three hundred million, according to latest Census Bureau estimates. Forty-seven million, including many non-citizens, are uninsured. That is, 16% of the total United States population has no health insurance. Millions more have inadequate coverage and are in danger of losing that. Private, corporatized medical coverage, structured by the insurance industry, is the basis for the current system. This article is an attempt to lay out the principal health care issues, to look at the (...) alternatives and the cost of those alternatives, and to try to determine whether there is a particular regime that, despite its imperfections, is the best available to us now. (shrink)

Although compelling and insightful, the proposal by Uchiyama et al. largely neglects within-person change over time, arguably the central topic of interest within their framework. Longitudinal behavioural genetics modelling suggests that the heritability of trajectories is low, in contrast to high and increasing cross-sectional heritability across development. Better understanding of the mechanisms of trajectories remains a crucial outstanding challenge.

Bowers et al. rightly emphasise that deep learning models often fail to capture constraints on visual perception that have been discovered by previous research. However, the solution is not to discard deep learning altogether, but to design stimuli and tasks that more closely reflect the problems that biological vision evolved to solve, such as understanding scenes and preparing skilled action.

The target article raises important questions about the applicability of experimental social psychology research on topics with policy implications. This commentary focuses on the importance of attending to a variety of factors to improve ecological validity as well as considering the ultimate factors shaping behavior and the role of natural categories in the stability of stereotypes and their influence.

The term "viewing stones" is primarily associated with two traditions of stone appreciation: Chinese Gongshi and Japanese suiseki. Today, viewing-stone associations around the world take inspiration from these traditions and are creating new ways of displaying stones. Petraphiles, whether ancient or contemporary, are often drawn to express their appreciation of favored stones in writing.The Petraphiles represented in this virtual exhibition are diverse in their expressions of geo-affection. They are, by turns, both scholarly and poetic. In each entry there is a (...) sense of discovery. Thomas Elias finds his Liaoshan Green Stone talking to him about the vicissitudes of life. Kemin Hu's research on a... (shrink)