Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

In this review, we highlight evidence suggesting that concepts represented in language are used to create a perception of emotion from the constant ebb and flow of other people’s facial muscle movements. In this “construction hypothesis,” (cf. Gendron, Lindquist, Barsalou, & Barrett, 2012) (see also Barrett, 2006b; Barrett, Lindquist, & Gendron, 2007; Barrett, Mesquita, & Gendron, 2011), language plays a constitutive role in emotion perception because words ground the otherwise highly variable instances of an emotion category. We demonstrate that language (...) plays a constitutive role in emotion perception by discussing findings from behavior, neuropsychology, development, and neuroimaging. We close by discussing implications of a constructionist view for the science of emotion. (shrink)

Volume 19, Issue 10, October 2019, Page 61-63.

Background Decisions regarding Cardio-Pulmonary Resuscitation (CPR) and Do Not Attempt Resuscitation (DNAR) orders remain demanding, as does including patients in the process. Objectives To explore physicians’ justification for CPR/DNAR orders and decisions regarding patient inclusion, as well as their reports of how they initiated discussions with patients. Methods We administered a face-to-face survey to residents in charge of 206 patients including DNAR and CPR orders, with or without patient inclusion. Results Justifications were provided for 59% of DNAR orders and included (...) severe comorbidity, patients and families’ resuscitation preferences, patients’ age, or poor prognosis or quality of life. Reasons to include patients in CPR/DNAR decisions were provided in 96% and 84% of cases, and were based on respect for autonomy, clinical assessment of the situation as not too severe, and the view that such inclusion was required. Reasons for not including patients were offered in 84% of cases for CPR and in 70% for DNAR. They included absent decision-making capacity, a clinical situation viewed as good (CPR) or offering little hope of recovery (DNAR), barriers to communication, or concern that discussions could be emotionally difficult or superfluous. Decisions made earlier in the patient's management were infrequently viewed as requiring revision. Residents reported a variety of introductions to discussions with patients. Conclusions These results provide better understanding of reasons for CPR/DNAR decisions, reasons for patient inclusion or lack thereof, and ways in which such inclusion is initiated. They also point to potential side-effects of implementing CPR/DNAR recommendations without in-depth and practical training. This should be part of a regular audit and follow-up process for such recommendations. (shrink)

This paper applies a relational and familial ethic to address concerns relating to nursing home deaths and advance care planning during Covid‐19 and beyond. The deaths of our elderly in nursing homes during this pandemic have been made more complicated by the restriction of visitors even at the end of life, a time when families would normally be present. While we must be vigilant about preventing unnecessary deaths caused by coronavirus outbreaks in nursing homes, some deaths of our elders are (...) inevitable. Thus, it is essential that advanced care planning occurs in a way that upholds the familial and relational aspects of elders’ lives that often matter to them the most. We invoke concepts from feminist ethicists like Hilde Lindemann and Eva Kittay and introduce Avery Weisman and Thomas Hackett’s concept of “appropriate death” to suggest better ways of planning for those deaths of our elderly that cannot be avoided. Our hope is to allow for deaths that are as meaningful as possible for both the elderly and the family members who survive them. (shrink)

Background: This article describes the types of community‐wide benefits provided by investigators conducting public health research in South Asia as well as their self‐reported reasons for providing such benefits.Methods: We conducted 52 in‐depth interviews to explore how public health investigators in low‐resource settings make decisions about the delivery of ancillary care to research subjects. In 39 of the interviews respondents described providing benefits to members of the community in which they conducted their study. We returned to our narrative dataset to (...) find answers to two questions: What types of community‐wide benefits do researchers provide when conducting public health intervention studies in the community setting, and what reasons do researchers give when asked why they provided community‐wide benefits?Findings: The types of community‐wide benefits delivered were directed to the health and well‐being of the population. The most common types of benefits delivered were the facilitation of access to health care for individuals in acute medical need and emergency response to natural disasters. Respondents' self‐reported reasons when asked why they provided such benefits fell into 2 general categories: intrinsic importance and instrumental importance. (shrink)

Collectively these essays inform educators and researchers at different grade levels about the teaching and learning of proof at each level and, thus, help ...

Background: This article describes the types of community-wide benefits provided by investigators conducting public health research in South Asia as well as their self-reported reasons for providing such benefits. Methods: We conducted 52 in-depth interviews to explore how public health investigators in low-resource settings make decisions about the delivery of ancillary care to research subjects. In 39 of the interviews respondents described providing benefits to members of the community in which they conducted their study. We returned to our narrative dataset (...) to find answers to two questions: What types of community-wide benefits do researchers provide when conducting public health intervention studies in the community setting, and what reasons do researchers give when asked why they provided community-wide benefits? Findings: The types of community-wide benefits delivered were directed to the health and well-being of the population. The most common types of benefits delivered were the facilitation of access to health care for individuals in acute medical need and emergency response to natural disasters. Respondents' self-reported reasons when asked why they provided such benefits fell into 2 general categories: intrinsic importance and instrumental importance. (shrink)

As social and economic injustice spreads from the historically marginalized to the 99 per cent both symbolically and realistically that which concerned the few now openly confronts the majority. This publication inquires into the contemporary moment through the proposition of the Roma model of existence as it resonates within artistic practice and civic imagination. By reversing outsider status, can we, with the emblematic claim that we are all Roma, invoke alternate futures? Artists, theorists and activists of both Roma and non-Roma (...) origin speculate upon the possibilities in this selection of new and anthologized texts. Includes contributions by Zygmunt Bauman, Ethel Brooks, Sanja Ivekovic' and Salman Rushdie, among others. (shrink)

RESUMO Este texto apresenta parte de pesquisa recém-concluída, que delineia dimensões e balizas para o que vem sendo denominado perspectiva discursiva de alfabetização. Princípios da teoria da enunciação e de estudos que analisam as relações entre sujeito e linguagem e o papel das interações discursivas nos processos de ensino e aprendizagem organizam a base teórico-metodológica do estudo, em que se analisam relatos escritos por cinco professoras alfabetizadoras durante 18 meses. Duas dimensões teórico-metodológicas de análise são trabalhadas: discursiva e indiciária. Mergulha-se (...) nos modos como a prática pedagógica é movimentada em sala de aula, em busca de indícios para descrever a situação discursiva em que foram colhidos, analisá-los e interpretá-los. A pesquisa tem como horizonte compreender como podem ser concebidas metodologias de alfabetização em que o trabalho com a vida das crianças na cultura escrita se sobreponha ao trabalho tradicionalmente realizado com foco no sistema de escrita. ABSTRACT This paper presents data from a recently finished research that outlines dimensions and guidelines for what has been named discursive perspective on literacy. Principles of the theory of enunciation and studies that analyze the relationships between subject and language as well as the role of discursive interactions in the teaching and learning processes, organize the theoretical and methodological basis of the study. We analyzed reports written by five literacy teachers for 18 months. Two theoretical-methodological dimensions of analysis were employed, the discursive and the evidential. We focus on the ways the pedagogical practice is developed in the classroom, seeking for indexes to describe the discursive situation from which they were collected, and to analyze and interpret them. The aim of the research was to understand how to construct literacy methodologies in which working with children's lives in written culture overcomes the traditional work focused on the writing system. (shrink)

The potential for genetically modified (GM) crops to threaten biodiversity conservation and sustainable agriculture is substantial. Megadiverse countries and centers of origin and/or diversity of crop species are particularly vulnerable regions. The future of sustainable agriculture may be irreversibly jeopardized by contamination of in situ preserved genetic resources threatening a strategic resource for the world—s food security. Because GM crops are truly biological novelties, their release into the environment poses concerns about the unpredictable ecological and evolutionary responses that GM species (...) themselves and the interacting biota may express in the medium and long term. One of the consequences of these processes may be a generalized contamination of natural flora by GM traits and a degradation and erosion of the commonly owned genetic resources available today for agricultural development. GM plants carrying pharmaceutical and industrial traits will pose even more dangerous risks if released in the environment. (shrink)

Chronic pain affects a large part of the population causing functional disability, being often associated with coexisting psychological disorders, such as depression and anxiety, besides cognitive deficits, and sleep disturbance. The world elderly population has been growing over the last decades and the negative consequences of chronic pain for these individuals represent a current clinical challenge. The main painful complaints in the elderly are related to neurodegenerative and musculoskeletal conditions, peripheral vascular diseases, arthritis, and osteoarthritis, contributing toward poorly life quality, (...) social isolation, impaired physical activity, and dependence to carry out daily activities. Organ dysfunction and other existing diseases can significantly affect the perception and responses to chronic pain in this group. It has been proposed that elderly people have an altered pain experience, with changes in pain processing mechanisms, which might be associated with the degeneration of circuits that modulate the descending inhibitory pathways of pain. Aging has also been linked to an increase in the pain threshold, a decline of painful sensations, and a decrease in pain tolerance. Still, elderly patients with chronic pain show an increased risk for dementia and cognitive impairment. The present review article is aimed to provide the state-of-art of pre-clinical and clinical research about chronic pain in elderly, emphasizing the altered mechanisms, comorbidities, challenges, and potential therapeutic alternatives. (shrink)

Mindfulness and compassion meditation are thought to cultivate prosocial behavior. However, the lack of diverse representation within both scientific and participant populations in contemplative neuroscience may limit generalizability and translation of prior findings. To address these issues, we propose a research framework calledIntersectional Neurosciencewhich adapts research procedures to be more inclusive of under-represented groups. Intersectional Neuroscience builds inclusive processes into research design using two main approaches: 1) community engagement with diverse participants, and 2) individualized multivariate neuroscience methods to accommodate neural (...) diversity. We tested the feasibility of this framework in partnership with a diverse U.S. meditation center (East Bay Meditation Center, Oakland, CA). Using focus group and community feedback, we adapted functional magnetic resonance imaging (fMRI) screening and recruitment procedures to be inclusive of participants from various under-represented groups, including racial and ethnic minorities, gender and sexual minorities, people with disabilities, neuropsychiatric disorders, and/or lower income. Using person-centered screening and study materials, we recruited and scanned 15 diverse meditators (80% racial/ethnic minorities, 53% gender and sexual minorities). The participants completed the EMBODY task – which applies individualized machine learning algorithms to fMRI data – to identify mental states during breath-focused meditation, a basic skill that stabilizes attention to support interoception and compassion. All 15 meditators’ unique brain patterns were recognized by machine learning algorithms significantly above chance levels. These individualized brain patterns were used to decode the internal focus of attention throughout a 10-min breath-focused meditation period, specific to each meditator. These data were used to compile individual-level attention profiles during meditation, such as the percentage time attending to the breath, mind wandering, or engaging in self-referential processing. This study provides feasibility of employing an intersectional neuroscience approach to include diverse participants and develop individualized neural metrics of meditation practice. Through inclusion of more under-represented groups while developing reciprocal partnerships, intersectional neuroscience turns the research process into an embodied form of social action. (shrink)

The use of conventional manufacturing methods is mainly limited by the size of the production run and the geometrical complexity of the component, and as a result we are occasionally forced to use processes and tools that increase the final cost of the element being produced. Additive manufacturing techniques provide major competitive advantages due to the fact that they adapt to the geometrical complexity and customised design of the part to be manufactured. The following may also be achieved according to (...) field of application: lighter weight products, multimaterial products, ergonomic products, efficient short production runs, fewer assembly errors and, therefore, lower associated costs, lower tool investment costs, a combination of different manufacturing processes, an optimised use of materials, and a more sustainable manufacturing process. Additive manufacturing is seen as being one of the major revolutionary industrial processes of the next few years. Additive manufacturing has several alternatives ranging from simple RepRap machines to complex fused metal deposition systems. This paper will expand upon the structural design of the machines, their history, classification, the alternatives existing today, materials used and their characteristics, the technology limitations, and also the prospects that are opening up for different technologies both in the professional field of innovation and the academic field of research. It is important to say that the choice of technology is directly dependent on the particular application being planned: first the application and then the technology. (shrink)

Most studies investigating the relationship between cultural constructs and ethical perception have focused on individual- and societal-level values without much attention to other type of cultural constructs such as social beliefs. In addition, we need to better understand how social beliefs are linked to ethical perception and the level of analysis at which social beliefs may best predict ethical perceptions. This research contributes to the cross-cultural ethical perception literature by examining the relationship of individual-level social cynicism belief, one of five (...) universally endorsed social beliefs, together with individual social dominance orientation and the perception of unethical behavior. By means of two studies, we examine these relationships across societies that significantly differ on societal-level social cynicism belief. Using 371 business students from Russia and the U.S. in Study 1 and 268 professionals from Portugal and the U.S. in Study 2, we found that individual-level social cynicism belief was positively associated with social dominance orientation. Social dominance orientation, in turn, mediated the relationship between individual social cynicism belief and the perception of unethical behavior. Although we found significant societal-level differences in social cynicism belief in both studies, the relationships between individual-level social cynicism belief, social dominance orientation, and the perception of unethical behavior were structurally equivalent across societies in both studies, suggesting that societal-level differences did not significantly affect these relationships. Implications for cross-cultural business ethics research and practice are discussed. (shrink)

Most studies investigating the relationship between cultural constructs and ethical perception have focused on individual- and societal-level values without much attention to other type of cultural constructs such as social beliefs. In addition, we need to better understand how social beliefs are linked to ethical perception and the level of analysis at which social beliefs may best predict ethical perceptions. This research contributes to the cross-cultural ethical perception literature by examining the relationship of individual-level social cynicism belief, one of five (...) universally endorsed social beliefs, together with individual social dominance orientation and the perception of unethical behavior. By means of two studies, we examine these relationships across societies that significantly differ on societal-level social cynicism belief. Using 371 business students from Russia and the U.S. in Study 1 and 268 professionals from Portugal and the U.S. in Study 2, we found that individual-level social cynicism belief was positively associated with social dominance orientation. Social dominance orientation, in turn, mediated the relationship between individual social cynicism belief and the perception of unethical behavior. Although we found significant societal-level differences in social cynicism belief in both studies, the relationships between individual-level social cynicism belief, social dominance orientation, and the perception of unethical behavior were structurally equivalent across societies in both studies, suggesting that societal-level differences did not significantly affect these relationships. Implications for cross-cultural business ethics research and practice are discussed. (shrink)

Recent studies have pointed to the existence of a strong relationship between memory and mental representation, while others have shown that images are open to reinterpretation and manipulation; this volume offers a historical overview of the problem as well as a review of the research in psychology and related fields.

O objetivo do presente artigo é desenvolver uma reflexão acerca de relações existentes entre informação e ação, no contexto das tecnologias informacionais de comunicação. O problema central que guiará o artigo pode ser assim formulado: Qual é a influência da informação disponível nas TICs na ação autônoma? O direcionamento de pesquisas em relação ao conceito de informação possui geralmente uma orientação técnica, não focalizando questões éticas, ontológicas e epistemológicas, que são igualmente relevantes ao se tratar desse conceito. Em contraste com (...) a orientação técnica vigente, ressaltamos a abordagem proposta por Charles S. Peirce, que caracteriza informação a partir de diferentes perspectivas: lógico-semântica, pragmática e semiótica. Partindo da hipótese que processos informacionais têm uma participação fundamental no direcionamento da ação, investigamos impactos das TICs presentes nas relações cotidianas. Discutimos transformações que as TICs têm possibilitado na relação agente-ambiente, ressaltando recursos computacionais de mineração de dados, que propiciam ações, muitas vezes direcionadas por interesses alheios àqueles dos usuários. Argumentamos que o estudo da informação é importante para entender possíveis implicações das TICs no direcionamento da ação humana. (shrink)

BackgroundSerious ethical problems have been anecdotally identified in the care of children with osteogenesis imperfecta (OI), which may negatively impact their moral experiences, defined as their sense of fulfillment towards personal values and beliefs.Research aimsTo explore children’s actual and desired participation in discussions, decisions, and actions in an OI hospital setting and their community using art-making to facilitate their self-expression.Research designA focused ethnography was conducted using the moral experiences framework with data from key informant interviews; participant observations, semi-structured interviews, and (...) practice-based research (art-making) with 10 children with OI; and local documents.Participants and research contextThe study was conducted at a pediatric, orthopedic hospital.Ethical considerationsThis study was approved by McGill University Institutional Review Board.Findings/resultsChildren expressed desires to participate in their care, but sometimes lacked the necessary resources and encouragement from healthcare providers. Art-making facilitated children’s voice and participation in health-related discussions.ConclusionsHealthcare providers are recommended to consider the benefits of art-making and educational resources to reduce discrepancies between children’s actual and desired participation in care and promote positive moral experiences. (shrink)

El presente trabajo recupera, caracteriza y evalúa el marco antropológico subyacente en la Declaración de los Derechos Humanos de 1948. Para este propósito, se utilizó como metodología el análisis del discurso y una evaluación antropológica de su contenido en relación directa con la Bioética contemporánea y sus problemas más sobresalientes. doi: 10.5294/pebi.2015.19.2.4.

This study is an investigation of both comprehension and production of Wh- questions in Malay-speaking children with a developmental language disorder. A total of 15 Malay children with DLD were tested on a set of Wh- questions, comparing their performance with two control groups [15 age-matched typically developing children and 15 younger TD language-matched children]. Malay children with DLD showed a clear asymmetry in comprehension of Wh- questions, with a selective impairment for which NP questions compared with who questions. Age-matched (...) controls performed at ceiling in all Wh- questions, while the language-matched group reported a subject/object asymmetry selective for the which NP, as reported in other languages. In production, both children with DLD and younger children showed a preference for questions with in situ Wh- elements, a structure that is allowed in colloquial Malay, but which is not produced by the age-matched TD group. Several non-adult-like strategies were adopted particularly by the children with DLD to avoid complex sentences, including substitution with yes/no echo questions, production of the wrong Wh- question, and use of a generic Wh- element. The study provides an insight on the mastery of Wh- questions in both typical Malay children and children with DLD. Implications for the definition of a clinical marker for DLD in a free word order language with Wh- in situ option will be discussed. (shrink)