Transcription factor (TF) signaling regulates gene transcription and requires a complex network of proteins. This network includes co‐activators, co‐repressors, multiple TFs, histone‐modifying complexes, and the basal transcription machinery. It has been widely appreciated that pioneer factors, such as FoxA1 and GATA1, play an important role in opening closed chromatin regions, thereby allowing binding of a secondary factor. In this review we will focus on a newly proposed model wherein multiple TFs, such as steroid receptors (SRs), can function in a pioneering (...) role. This model, termed dynamic assisted loading, integrates data from widely divergent methodologies, including genome wide ChIP‐Seq, digital genomic footprinting, DHS‐Seq, live cell protein dynamics, and biochemical studies of ATP‐dependent remodeling complexes, to present a real time view of TF chromatin interactions. Under this view, many TFs can act as initiating factors for chromatin landscape programming. Furthermore, enhancer and promoter states are more accurately described as energy‐dependent, non‐equilibrium steady states. (shrink)

The available evidence indicates that the music of a culture reflects the speech rhythm of the prevailing language. The normalized pairwise variability index (nPVI) is a measure of durational contrast between successive events that can be applied to vowels in speech and to notes in music. Music–language parallels may have implications for the acquisition of language and music, but it is unclear whether native-language rhythms are reflected in children's songs. In general, children's songs exhibit greater rhythmic regularity than adults' songs, (...) in line with their caregiving goals and frequent coordination with rhythmic movement. Accordingly, one might expect lower nPVI values (i.e., lower variability) for such songs regardless of culture. In addition to their caregiving goals, children's songs may serve an intuitive didactic function by modeling culturally relevant content and structure for music and language. One might therefore expect pronounced rhythmic parallels between children's songs and language of origin. To evaluate these predictions, we analyzed a corpus of 269 English and French songs from folk and children's music anthologies. As in prior work, nPVI values were significantly higher for English than for French children's songs. For folk songs (i.e., songs not for children), the difference in nPVI for English and French songs was small and in the expected direction but non-significant. We subsequently collected ratings from American and French monolingual and bilingual adults, who rated their familiarity with each song, how much they liked it, and whether or not they thought it was a children's song. Listeners gave higher familiarity and liking ratings to songs from their own culture, and they gave higher familiarity and preference ratings to children's songs than to other songs. Although higher child-directedness ratings were given to children's than to folk songs, French listeners drove this effect, and their ratings were uniquely predicted by nPVI. Together, these findings suggest that language-based rhythmic structures are evident in children's songs, and that listeners expect exaggerated language-based rhythms in children's songs. The implications of these findings for enculturation processes and for the acquisition of music and language are discussed. (shrink)

Both target papers cite evidence from infancy and early childhood to support the notion of human musicality as a somewhat static suite of capacities; however, in our view they do not adequately acknowledge the critical role of developmental timing, the acquisition process, or the dynamics of social learning, especially during later periods of development such as middle childhood.

Biological and epidemiological phenomena are often measured with error or imperfectly captured in data. When the true state of this imperfect measure is a confounder of an outcome exposure relationship of interest, it was previously widely believed that adjustment for the mismeasured observed variables provides a less biased estimate of the true average causal effect than not adjusting. However, this is not always the case and depends on both the nature of the measurement and confounding. We describe two sets of (...) conditions under which adjusting for a non-deferentially mismeasured proxy comes closer to the unidentifiable true average causal effect than the unadjusted or crude estimate. The first set of conditions apply when the exposure is discrete or continuous and the confounder is ordinal, and the expectation of the outcome is monotonic in the confounder for both treatment levels contrasted. The second set of conditions apply when the exposure and the confounder are categorical. In all settings, the mismeasurement must be non-differential, as differential mismeasurement, particularly an unknown pattern, can cause unpredictable results. (shrink)

Fusion genes formed by chromosomal rearrangements are common drivers of cancer. Recent innovations in the field of next‐generation sequencing (NGS) have seen a dynamic shift from traditional fusion detection approaches, such as visual characterization by fluorescence, to more precise multiplexed methods. There are many different NGS‐based approaches to fusion gene detection and deciding on the most appropriate method can be difficult. Beyond the experimental approach, consideration needs to be given to factors such as the ease of implementation, processing time, associated (...) costs, and the level of expertise required for data analysis. Here, the different NGS‐based methods for fusion gene detection, the basic principles underlying the techniques, and the benefits and limitations of each approach are reviewed. This article concludes with a discussion of how NGS will impact fusion gene detection in a clinical context and from where the next innovations are evolving. (shrink)

Introduction This article is a response to Zagouras, Ellick, and Aulisio who presented a case study justifying the questioning of the capacity and autonomy of a young woman with a physical disability who was pregnant and facing coercive pressure to terminate. Case description Julia is described as a 26-year-old woman with a neurological disability that requires her to receive assistance with activities of daily living. She was described as living with her parents who provided her with personal care assistance. Julia (...) became pregnant and her parents wished her to terminate because they did not want to care for her child in addition to her. In fact, Julia's parents threatened her with institutionalization if she did not elect to terminate the pregnancy. Her health care team questioned her decision-making capacity based on her alleged “mental age” and experiences of being sheltered and excluded. The health care team used directive tactics to convince Julia to terminate the pregnancy, which describe as both an ethical and feminist intervention. Discussion The current authors take issue with the case analysis provided by and argue that they neglected to account for numerous instances of systemic ableism that adversely affected Julia, demonstrated prejudicial and judgmental attitudes toward pregnancy and disability, inappropriately questioned her decision-making capacity by infantilizing her, misconstrued the feminist concept of relational autonomy, and colluded with coercive interference from family members. This is a classic example of discriminatory and culturally incompetent reproductive health care for a disabled woman. (shrink)

Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. We hypothesize that the scarcity of disease‐causing Archaea is due, in part, to mutually‐exclusive phage and virus populations infecting Bacteria and Archaea, coupled with an association of bacterial virulence factors with phages or mobile elements. The ability of bacterial phages to infect Bacteria and then use them as a vehicle to infect eukaryotes may be difficult for (...) archaeal viruses to evolve independently. Differences in extracellular structures between Bacteria and Archaea would make adsorption of bacterial phage particles onto Archaea (i.e. horizontal transfer of virulence) exceedingly hard. If phage and virus populations are indeed exclusive to their respective host Domains, this has important implications for both the evolution of pathogens and approaches to infectious disease control. (shrink)

Maize develops separate male and female flowers in different locations on a single plant. Male flowers develop at the tip of the shoot in the tassel, and female flowers develop on the ears, which terminate short branches. The development of male flowers in tassels and female flowers in ears is the result of selective abortion of pistils or stamens, respectively, in developing florets. Genetic analysis has shown that stamen abortion and pistil abortion are under the control of two different genetic (...) pathways. Local levels of the plant hormone gibberellic acid determine whether or not stamens are suppressed. Pistil abortion is under the regulation of the tassel seed genes, one of which has been shown to encode a short‐chain alcohol dehydrogenase. The tassel seed genes play a role in regulating the fate of inflorescence meristems as well as pistil primordium fate. (shrink)

Several studies have indicated that scientists are likely to have an outlook on both facts and values that are different to that of lay people in important ways. This is one significant reason it is currently believed that in order for scientists to exercise a reliable ethical reflection about their research it is necessary for them to engage in dialogue with other stakeholders. This paper reports on an exercise to encourage a group of scientists to reflect on ethical issues without (...) the presence of external stakeholders. It reports on the use of a reflection process with scientists working in the area of animal disease genomics (mainly drawn from the EADGENE EC Network of Excellence). This reflection process was facilitated by using an ethical engagement framework, a modified version of the Ethical Matrix. As judged by two criteria, a qualitative assessment of the outcomes and the participants’ own assessment of the process, this independent reflective exercise was deemed to be successful. The discussions demonstrated a high level of complexity and depth, with participants demonstrating a clear perception of uncertainties and the context in which their research operates. Reflection on stakeholder views and values appeared to be embedded within the discussions. The finding from this exercise seems to indicate that even without the involvement of the wider stakeholder community, valuable reflection and worthwhile discourse can be generated from ethical reflection processes involving only scienitific project partners. Hence, the previous assumption that direct stakeholder engagement is necessary for ethical reflection does not appear to hold true in all cases; however, other reasons for involving a broad group of stakeholders relating to governance and social accountability of science remain. (shrink)

Residual confounding is a common source of bias in observational studies. In this article, we build upon a series of sensitivity analyses methods for residual confounding developed by Brumback et al. and Chiba whose sensitivity parameters are constructed to quantify deviation from conditional exchangeability, given measured confounders. These sensitivity parameters are combined with the observed data to produce a “bias-corrected” estimate of the causal effect of interest. We provide important generalizations of these sensitivity analyses, by allowing for arbitrary exposures and (...) a wide range of different causal effect measures, through the specification of the target causal effect as a parameter in a generalized linear model with the arbitrary link function. We show how our generalized sensitivity analysis can be easily implemented with standard software, and how its sensitivity parameters can be calibrated against measured confounders. We demonstrate our sensitivity analysis with an application to publicly available data from a cohort study of behavior patterns and coronary heart disease. (shrink)

(2012). A Review of “Contemporary Anarchist Studies: An Introductory Anthology of Anarchy in the Academy”. Educational Studies: Vol. 48, “Anarchism … is a living force within our life …” Anarchism, Education and Alternative Possibilities, pp. 103-107.

Face recognition is one of the most important skills in primate social cognition, enabling the formation of long-lasting, interindividual relationships. This article summarizes existing research on face processing in non-human primates with the goal of understanding the evolution of this important socio-cognitive skill. It describes different levels of configural processing and the importance of early visual expertise in face processing. By reviewing studies on the well-known face inversion effect, evidence for configural face processing in non-human primates is reviewed. The study (...) examines the social salience of faces by employing a variety of gaze tracking and visual orienting techniques. It deals with the ability to recognize individuals across various viewpoints and manipulating configural cues directly. Neuroimaging studies aid in understanding whether the neural correlates of face recognition in non-human primates involve a similar brain regions as humans. (shrink)

This is an excerpt from the content“Accountability” used to be a term that applied primarily to K-12 education, especially following the passage of No Child Left Behind. However, the recent economic downturn and subsequent recovery prompted debates on whether the cost of pursuing a college degree is “worth it” for students. Students’ post-graduation debt and job market prospects have been publicly scrutinized as well as the operations of large research universities. Supporters of higher education posit that these critiques of the (...) system impose a business model where it should not be as they emphasize outputs and efficiency over quality. At the same time, it is hard to ignore that calls for accountability in higher education are getting louder than ever before.In Accountability, Pragmatic Aims, and the American University, Ana M. Martínez-Alemán examines accountability from a historical perspective, arguing that accountability arose in the American university during the early part of the twentieth century. This rise coin. (shrink)

Control of wild animals may give rise to controversy, as is seen in the case of badger control to manage TB in cattle in the UK. However, it is striking that concerns about the potential suffering of the affected animals themselves are often given little attention or completely ignored in policies aimed at dealing with wild animals. McCulloch and Reiss argue that this could be remedied by means of a “mandatory application of formal and systematic Animal Welfare Impact Assessment ”. (...) Optimistically, they consider that an AWIA could help to resolve controversies involving wild animals. The aim of this paper is to evaluate the potential of AWIA. We begin by showing how ideas akin to AWIA already play a significant role in other animal ethics controversies, particularly those concerning laboratory animal use and livestock production; and we bring in lessons learnt from these controversies. Then we comment on the suggested development and application of AWIA in the case of badger control. Finally, we discuss the prospects of applying AWIA to other sorts of wild animal controversy. We argue that the AIWA, as developed by McCulloch and Reiss, relies on several dubious premises, including that killing is a welfare issue. Furthermore, we argue that AWIA is unlikely to prevent serious moral disagreements over how to weigh concerns about wild animals against priorities in human health, the health of domestic and farm animals, and biodiversity, but that it may nonetheless serve to limit harms imposed on the wild animals. (shrink)

Little is known about how employees on husbandry farms perceive animal welfare and the factors influencing the relationship between them and the animals they engage with in their daily work. Reporting the findings of qualitative interviews with 23 employees on five Danish farms (mink, dairy and pig production), this paper describes how the employees viewed animal welfare, and discusses how they dealt with animal welfare issues in their daily work. Four distinct rationales for animal welfare were identified. 1) Animal welfare (...) was supported by concerns about production and health, and could be negotiated – especially when it came to the ability of the animals to perform natural behaviour. 2) Animal welfare was connected with the working conditions on the farm. 3) The employees’ views about animal welfare were affected by working conditions over which they had no influence. 4) An awareness of the condition of the animals was seen as obviously needed in relation to production, but a deeper attachment to some animals was also seen. A specific challenge is presented by the increasingly diverse workforce in farming, with one third of the employees on Danish farms coming from abroad. If farm owners are not able to integrate these employees, there is a risk of creating a second-tier of foreign workers who are isolated. Furthermore, it was seen that negative working conditions can be taken out on the animals, or that animal welfare can come to be seen as unimportant as compared with human welfare. (shrink)

In this article, I respond to important questions raised by Gallagher and Jacobson in the field of cognitive science about face-to-face interactions in Heidegger’s account of ‘intersubjectivity’ in Being and Time. They have criticized his account for a lack of attention to primary intersubjectivity, or immediate, face-to-face interactions; he favours, they argue, embodied interactions via objects. I argue that the same assumption underlies their argument as did earlier critiques of a lack of an account of the body in Heidegger ; (...) namely that because the body is not explicitly discussed in Being and Time, embodiment, rather than stressing the immediacy of experience, is insufficiently acknowledged in his emphasis on ‘being-in-the-world’. Through placing Gallagher and Jacobson’s accounts of intersubjectivity and the body alongside Heidegger’s accounts of Mitsein and Leib, this article shows Heidegger’s radical position on the body as immersed in a holistic environment, and its reverberations on his account of intersubjectivity. I argue that Dasein’s embodied engagement in the world is always one of immediacy and that the body of the other is perceived as ‘tied into’ its context, as well. In so doing, I offer an Heideggerian account of ecstatic involvement which moves away from the distinction between primary and secondary intersubjectivity toward an immediate engagement with objects and people always already ‘tied into’ a context; an account that, through the concept of Fürsorge, includes shifts of attention between objects and people that allow for the ethical distinctions Gallagher and Jacobson are looking for. (shrink)

Animal ethicists have recently debated the ethical questions raised by disenhancing animals to improve their welfare. Here, we focus on the particular case of breeding hens for commercial egg-laying systems to become blind, in order to benefit their welfare. Many people find breeding blind hens intuitively repellent, yet ‘welfare-only’ positions appear to be committed to endorsing this possibility if it produces welfare gains. We call this the ‘Blind Hens’ Challenge’. In this paper, we argue that there are both empirical and (...) theoretical reasons why even those adopting ‘welfare-only’ views should be concerned about breeding blind hens. But we also argue that alternative views, which (for example) claim that it is important to respect the telos or rights of an animal, do not offer a more convincing solution to questions raised by the possibility of disenhancing animals for their own benefit. (shrink)

The aim of the present paper is to describe three different attempts, which have been made by philosophers, to define what quality of life is; and to spell out some of the difficulties that faces each definition. One, Perfectionism, focuses on the capacities that human beings possess: capacities for friendship, knowledge and creative activity, for instance. It says that the good life consists in the development and use of these capacities. Another account, the Preference Theory, urges that satisfying one's preferences, (...) or desires, is what improves one's quality of life. And a third account, Hedonism, sees life-quality as consisting in the enjoyment of pleasure and the avoidance of pain. The paper describes and evaluates objections to each of these views, thereby displaying their weaknesses and strengths. Since no view comes out as the right one there is a choice to be made. At the end of the paper it is being discussed how well each of the views cohere with different methodologies used in quality of life research. Also it is suggested that considerations about what the research is to be used for are relevant. (shrink)

Recently it has been argued that some instances of germ‐line gene therapy will change the identity of the person who receives the benefit of therapy, and that in these instances there is no good moral reason to conduct germ‐line gene therapy. Against this we argue that even if gene therapy should have an effect on the identity of the resulting person, this would not diminish the urgency of the therapy. Not only would impersonal moral reasons speak in favour of such (...) radical gene therapy, there would also be person‐affecting reasons to perform it. (shrink)

The paper addresses issues of scientific conduct regarding relations between science and the media, relations between scientists and journalists, and attitudes towards the public at large. In the large and increasing body of literature on scientific conduct and misconduct, these issues seem underexposed as ethical challenges. Consequently, individual scientists here tend to be left alone with problems and dilemmas, with no guidance for good conduct. Ideas are presented about how to make up for this omission. Using a practical, ethical approach, (...) the paper attempts to identify ways scientists might deal with ethical public relations issues, guided by a norm or maxim of openness. Drawing on and rethinking the CUDOS codification of the scientific ethos, as it was worked out by Robert K. Merton in 1942, we propose that this, which is echoed in current codifications of norms for good scientific conduct, contains a tacit maxim of openness which may naturally be extended to cover the public relations of science. Discussing openness as access, accountability, transparency and receptiveness, the argumentation concentrates on the possible prevention of misconduct with respect to, on the one hand, sins of omission—withholding important information from the public—and, on the other hand, abuses of the authority of science in order to gain publicity. Statements from interviews with scientists are used to illustrate how scientists might view the relevance of the issues raised. (shrink)

Commercial food health branding is a challenging branch of marketing because it might, at the same time, promote healthy living and be commercially viable. However, the power to influence individuals’ health behavior and overall health status makes it crucial for marketing professionals to take into account the ethical dimensions of health branding: this article presents a conceptual analysis of potential ethical problems in health branding. The analysis focuses on ethical concerns related to the application of three health brand elements (functional (...) claims, process claims, and health symbols) as well as a number of general concerns that apply to health branding as such. Being a pioneering analysis, this article advances the academic understanding of health branding and provides practitioners with knowledge of important concerns to take into account when marketing health brands. (shrink)

Outlining the characteristics of “wicked” and “super‐wicked” problems, climate change is considered as a global super‐wicked problem that is primarily about the future. Being global‐ and future‐oriented makes climate change something we have to learn to live with but cannot expect to solve. Because the Institute on Religion in an Age of Science (IRAS) is a multidisciplinary society that yokes the natural and social sciences with values, it is in a position to explore strategies for living with climate change—exemplified by (...) the articles in this section. Finally, asking “who/what is in charge,” it is suggested that in a dynamically interrelated and evolving world no one is. It is important to distinguish between good that is already created and the creative interactions that give rise to new good. In order to live with climate change, our primary orientation should be to live with the creativity that has created and continues to create our life on Planet Earth—since we are not able to know what the future holds. (shrink)

Riverside Park is an illustrated tribute to Frederick Law Olmsted's "other" New York City sanctuary. Since its conception in the 1870s, the park has undergone a number of transformations and suffered from periods of misuse and neglect, but in 1984, much-needed renovations turned this city oasis into what is today one of Manhattan's most beautiful attractions. "If the West Side does not stir you, you are a clod, past redemption."-Robert Moses Millions visit the Upper West Side landmark annually, and despite (...) the heavy use, thousands of volunteers keep the grounds pristine. The park is now being extended southward as part of Manhattan's plan to reclaim the island's six hundred miles of waterfront, and Riverside Drive-Olmsted's curving thoroughfare flanking the park-has long been one of Manhattan's premier addresses. "I often feel drawn to the Hudson River.... I never get tired of looking at it; it hypnotizes me."-Joseph Mitchell, from The Rivermen From the time it was carved out of an unpromising landscape, Riverside Park has continued to reinvent itself. Using photographs, illustrations, poems, and original and excerpted narrative, Edward Grimm and E. Peter Schroeder tell the intriguing story of a symbol of the modern revitalization of New York City. "Riverside Park will be a genuine riverside reservation, dedicated forever to the use of the people, beautiful in the highest sense."-The New York World, April 24, 1892 *Includes the official Riverside Park Fund Map of 2007*. (shrink)

In this chapter we will use the case of beaver reintroduction in southern Scandinavia to illuminate the philosophical issues underlying the value of biodiversity. First, we rehearse some of the main types of argument relating to the practice of ecological restoration. This is followed by a description of the case study, and by a summary of what we take to be the main positions in the ongoing debate over reintroduction of beavers. We then interpret these different positions, asking in each (...) case how ‘biodiversity’ is being understood. In this way, we try to establish the causes of the disagreement. It is important to distinguish between disagreements caused by conflicting interests and disagreements caused by conflicting values. We shall focus on a special type of disagreement where there seems to be a genuine conflict of values pertaining to biodiversity. Finally, we show how the claim that biodiversity should be protected is made by several participants in the debate and taken to have remarkably different implications: the need to protect biodiversity has been invoked both in attacks on, and defenses of, reintroduction and other forms of ecological restoration. (shrink)

It is well-known that dichotomization can cause bias and loss of efficiency in estimation. One can easily construct examples where adjusting for a dichotomized confounder causes bias in causal estimation. There are additional examples in the literature where adjusting for a dichotomized confounder can be more biased than not adjusting at all. The message is clear, do not dichotomize. What is unclear is if there are scenarios where adjusting for the dichotomized confounder always leads to lower bias than not adjusting. (...) We propose several sets of conditions that characterize scenarios where one should always adjust for the dichotomized confounder to reduce bias. We then highlight scenarios where the decision to adjust should be made more cautiously. To our knowledge, this is the first formal presentation of conditions that give information about when one should and potentially should not adjust for a dichotomized confounder. (shrink)