The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags accounting for 2266 restriction fragments on the homoeologous group 3 chromosomes of hexaploid wheat. Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the (...) chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes ∼21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected. (shrink)

As genetic testing for the presence of potentially health-affecting mutations becomes available for more genetic conditions, many people will soon be faced with the decision of whether or not to have a genetic test. Making an informed decision requires an understanding and evaluation of the arguments for and against having the test. As a case in point, this paper considers argumentation involving the decision of whether to have a BRCA gene test, one of the first commercially available genetic tests. (...) First, argumentation in a five-page patient brochure from a for-profit company that provides BRCA gene testing, is analyzed. Next, for comparison, argumentation on BRCA testing in materials for healthcare consumers written by a not-for-profit health plan and a government organization, is analyzed. In view of the challenges identified by considering these examples, this article discusses how argumentation-oriented computer systems may be able to help the healthcare consumer to make informed decisions about genetic testing. (shrink)

In 1933 Margaret Lasker, a biochemist who worked at the labs of Montefiore Hospital in New York, developed an accurate method for the differentiation between pentosuria and diabetes. Research into pentosuria, and mostly its genetic aspects, became Lasker’s lifelong passion. Since research was not part of her job description, she conducted the chief part of her study in her home kitchen. Lasker’s extensive and personal correspondence with her patients and their families may be the secret key for her success in (...) maintaining a prolonged research career against all odds. Laker’s last article was published in 1955 in Human Biology, presenting data on 72 cases of pentosuria, which occurs almost exclusively in Ashkenazi Jews. More than half a century later, and long after Lasker was gone, her well kept data and family records allowed the discovery of two mutations in the DCXR gene, by Mary-Claire King and her team. (shrink)

Mammalian sperm undergo discharge of a single, anterior secretory granule following their attachment to the zona pellucida surrounding the oocyte. This secretory discharge is known for historical reasons as the acrosome reaction. It fulfils a number of purposes and without it, sperm are unable to penetrate the zona pellucida and fuse with the oocyte. In this review, we focus on the role of the acrosome reaction in the development of fusion competence in sperm. Any naturally occurring membrane fusion has two (...) major sequential steps: a docking or adhesion step, in which two membranes adhere, and a fusion step, in which their lipid bilayers are destabilized and merged and a cellular compartment is either created or destroyed. Recent evidence suggests that there is an important role for oocyte integrins and sperm‐bound disintegrins in mammalian sperm/oocyte adhesion and fusion. The fusion mechanism employed by sperm remains poorly understood, however, and circumstantial evidence suggests it is more complex than the interaction between a single protein species and its target. Sperm/oocyte fusion is probably the most accessible eukaryotic model for intercellular fusion currently available, partly because it is temporally separated from gene expression. Elucidation of the mechanism of sperm/oocyte fusion may throw light on the mechanism of other intercellular fusions such as myoblast fusion, and the evolutionary relationship of intercellular membrane fusion to intracellular membrane fusion. (shrink)

A total of 944 expressed sequence tags generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat. EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and ID with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms (...) was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences, where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses. (shrink)

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with (...) rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7. (shrink)

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat, to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated (...) loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes. (shrink)

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid wheat genome. Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection. Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of (...) ESTs into contigs. These contigs plus singletons were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5′ and 3′ sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics. (shrink)

The eyespot organelle of the green alga Chlamydomonas allows the cell to phototax toward (or away) from light to maximize the light intensity for photosynthesis and minimize photo‐damage. At cytokinesis, the eyespot is resorbed at the cleavage furrow and two new eyespots form in the daughter cells 180° from each other. The eyespots are positioned asymmetrically with respect to the microtubule cytoskeleton. Eyespots are assembled from all three chloroplast membranes and carotenoid‐filled granules, which form a sandwich structure overlaid by (...) the tightly apposed plasma membrane. This review describes (1) my interest in cellular asymmetry and organelle biology, (2) isolation of mutations that describe four genes governing eyespot placement and assembly, (3) the characterization of the EYE2 gene, which encodes a thioredoxin superfamily member, and (4) the characterization of the MIN1 gene, which is required for the layered organization of granules and membranes in the eyespot. BioEssays 25:410–416, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

During the 1980s many communities turned to grassroots activities to promote economic development, rather than relying on industrial recruitment strategies. We evaluate the characteristics of these projects, their benefits and costs, and obstacles they face in the development process. The data are drawn from a survey of more than one hundred communities in the United States. Self-development efforts do not appear to replace traditional rural economic development activities, but may complement them. Self-development activities produce a wide variety of jobs that (...) are taken primarily by local residents. The cost and availability of credit are major obstacles for self-development projects. Although self-development strategies should not be considered the primary economic development strategy for most rural communities, they do enable communities to build a more viable local economy. (shrink)

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We applaud Brown, Elliott, and Paine (2013) for their overarching goal of providing ethical justification for decisions to withdraw nonfutile life-sustaining medical treatments in some cases after...

Relational reasoning is a complex form of human cognition involving the evaluation of relations between mental representations of information. Prior studies have modified stimulus properties of relational reasoning problems and examined differences in difficulty between different problem types. While subsets of these stimulus properties have been addressed in separate studies, there has not been a comprehensive study, to our knowledge, which investigates all of these properties in the same set of stimuli. This investigative gap has resulted in different findings across (...) studies which vary in task design, making it challenging to determine what stimulus properties make relational reasoning—and the putative formation of mental models underlying reasoning—difficult. In this article, we present the Multidimensional Relational Reasoning Task, a task which systematically varied an array of stimulus properties within a single set of relational reasoning problems. Using a mixed-effects framework, we demonstrate that reasoning problems containing a greater number of the premises as well as multidimensional relations led to greater task difficulty. The MRRT has been made publicly available for use in future research, along with normative data regarding the relative difficulty of each problem. (shrink)

Integral Science provides the empirical rigor needed to shift medicine's worldview. The shift in science will give rise to Integral Medicine, which will emerge from the integration and transformational change of biomedicine, psychosocial approaches, Complementary and Alternative Medicine, and other reform movements. The root metaphor of Integral Medicine is a healthy and sustainable ecosystem. At its heart are mind-body holism and collaborative learning. Healing and the creation of health will emphasize educational, self-care, and community support models. Implications are discussed for (...) practice, research, and education. (shrink)

The role of imagery in encoding event-based prospective memories has yet to be fully clarified. Herein, it is argued that imagery augments a cue-to-context association that supports event-based prospective memory performance. By this account, imagery encoding not only improves prospective memory performance but also reduces interference to intention-related information that occurs outside of context. In the current study, when lure words occurred outside of the appropriate responding context, the use of imagery encoding strategies resulted in less interference when compared with (...) a standard event-based intention condition. This difference was eliminated when participants were not given a specific context to associate their intention . These results support a cue-to-context association account of how imagery operates in certain event-based prospective memory tasks. (shrink)

Revenant sur les prémisses mêmes de la Cité nationale de l’Histoire de l’immigration , Nancy L. Green retrace la politique entourant le projet ainsi que le choix du bâtiment. Contestée depuis le début dans le fond comme dans la forme, la CNHI doit affronter le problème de ses origines et sa tentative de renverser la symbolique de la colonisation par une reconnaissance de l’immigration, elle-même sujette à des définitions multiples. Passant en revue différentes « options » dans la représentation (...) des immigrés au sein d’un musée d’immigration – une chronologie des vagues d’arrivées, une présentation par groupe ou des choix thématiques –, l’auteur s’interroge sur les tensions entre historiens et scénographes, entre art et histoire au sein du musée, ainsi que sur l’idée de procéder par thèmes, finalement retenue. Si cette approche permet de souligner les similitudes dans l’expérience migratoire, elle peut également en gommer les spécificités. La CNHI elle-même représente un moment spécifique dans la représentation des immigrés en France.From the beginning, the Cité nationale de l’Histoire de l’immigration project was plagued by both political and symbolic difficulties. Nancy L. Green discusses the choices made and the politics surrounding the choice of the building, a former colonial arts museum. How successful is the idea of using an old symbol of France’s hubris at the height of her colonial empire to highlight the historical irony of her former colonies arriving to live in France? In analysing the multiple meanings of immigration itself and the different “options” available to represent a history of immigration in France – a chronological view of successive waves of immigrants, displays highlighting different groups – Green discusses the tensions between researchers and exhibition designers, between art and history as modes of representation, and the idea of the thematic approach, which was the option eventually chosen. While this approach brings out similarities in experiences of migration, it can also detract from an understanding of specific circumstances. The CNHI itself reflects a specific moment in the representation of immigrants in French history. (shrink)

This article outlines the rationale for a molecular genetic study of social behavior, and explains why social insects are good models. Summaries of research on brain and behavior in two species, honey bees and fire ants, are presented to illustrate the richness of the behavioral phenomena that can be addressed with social insects and to show how they are beginning to be used to study genes that influence social behavior. We conclude by considering the problems and potential of this emerging (...) field. (shrink)

Early last year, the GenEthics Consortium (GEC) of the Washington Metropolitan Area convened at George Washington University to consider a complex case about genetic testing for Alzheimer disease (AD). The GEC consists of scientists, bioethicists, lawyers, genetic counselors, and consumers from a variety of institutions and affiliations. Four of the 8 co-authors of this paper delivered presentations on the case. Supplemented by additional ethical and legal observations, these presentations form the basis for the following discussion.

Various argumentation analysis tools permit the analyst to represent functional components of an argument (e.g., data, claim, warrant, backing), how arguments are composed of subarguments and defenses against potential counterarguments, and argumentation schemes. In order to facilitate a study of argument presentation in a biomedical corpus, we have developed a hybrid scheme that enables an analyst to encode argumentation analysis within the framework of Rhetorical Structure Theory (RST), which can be used to represent the discourse structure of a text. This (...) paper describes the hybrid representation scheme and illustrates its use for investigation of contexts that license omission of elements of an argument. The analyses given in the paper involve reconstruction of enthymemes. Defeasible argumentation schemes serve as a constraint on reconstruction. In addition, the examples illustrate several other types of contextual constraints on reconstruction of enthymemes. (shrink)

Diligent citizens must critically analyze arguments for science policy recommendations, such as cutting greenhouse gas emissions or growing genetically modified food crops. Science policy articles present arguments for and against such recommendations using scientific evidence and rhetorical devices. In this paper we present an in-depth analysis of argumentation and rhetorical devices in two journal articles on climate change issues. One objective was to gain a better understanding of use of rhetorical devices in this genre, as a prerequisite for designing and (...) building a rhetorically-annotated digital corpus of full-text science policy articles. The near term objective was to inform the design of pedagogical tools to help students analyze science policy arguments. (shrink)

To be radical about pornography used to mean that one favored less censorship; now it often means that one favors more. That political change reflects a shift in the dominant paradigm of pornography and its putative evils. Until quite recently, most people who believed pornography wrong thought that it offended against decency and propriety and was therefore obscene. That was certainly the view of the law. English judges first created the crime of obscene libel in 1727 on the basis that (...) such expression tended to corrupt the morals of the King's subjects, a thought that inspired most subsequent legislation in the common‐law world. Sometimes the underlying concern really was paternalistic: pornography degrades and corrupts its producers and consumers; the law forces them to become better people. More often, however, it was just moralism of the familiar sorts: the view that a majority of a community is entitled to enforce its moral views on the rest, either because that is democratic or because that is just what it means to be a community. The obscenity paradigm thus had two features. First, it was illiberal: it ranked personal autonomy below realizing the good, enforcing the majority will, or embodying communitarian values. Second, it was gender neutral: to understand the nature of pornography did not require theorizing relations between men and women. On the obscenity paradigm, pornography was a matter of virtue versus vice, majorities versus minorities. (shrink)

Argumentation schemes have played a key role in our research projects on computational models of natural argument over the last decade. The catalogue of schemes in Walton, Reed and Macagno’s 2008 book, Argumentation Schemes, served as our starting point for analysis of the naturally occurring arguments in written text, i.e., text in different genres having different types of author, audience, and subject domain, for different argument goals, and for different possible future applications. We would often first attempt to analyze the (...) arguments in our corpora in terms of those schemes, then adapt schemes as needed for the goals of the project, and in some cases implement them for use in computational models. Among computational researchers, the main interest in argumentation schemes has been for use in argument mining by applying machine learning methods to existing argument corpora. In contrast, a primary goal of our research has been to learn more about written arguments themselves in various contemporary fields. Our approach has been to manually analyze semantics, discourse structure, argumentation, and rhetoric in texts. Another goal has been to create sharable digital corpora containing the results of our studies. Our approach has been to define argument schemes for use by human corpus annotators or for use in logic programs for argument mining. The third goal is to design useful computer applications based upon our studies, such as argument diagramming systems that provide argument schemes as building blocks. This paper describes each of the various projects: the methods, the argument schemes that were identified, and how they were used. Then a synthesis of the results is given with a discussion of open issues. (shrink)