It has been a common assumption that words are substances that instantiate or have properties. In this paper, I question the assumption that our ontology of words requires posting substances by outlining a bundle theory of words, wherein words are bundles of various sorts of properties (such as semantic, phonetic, orthographic, and grammatical properties). I argue that this view can better account for certain phenomena than substance theories, is ontologically more parsimonious, and coheres with claims in linguistics.

What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.

The natural name theory, recently discussed by Johnson (2018), is proposed as an explanation of pure quotation where the quoted term(s) refers to a linguistic object such as in the sentence ‘In the above, ‘bank’ is ambiguous’. After outlining the theory, I raise a problem for the natural name theory. I argue that positing a resemblance relation between the name and the linguistic object it names does not allow us to rule out cases where the natural name fails to resemble (...) the linguistic object it names. I argue that to avoid this problem, we can combine the natural name theory with a type-realist metaphysics of language, and hold that the name is natural because the name is an instance of the kind that it names. I conclude by reflecting on the importance of the metaphysics of language for questions in the philosophy of language. (shrink)

ABSTRACT The idea that two words can be instances of the same word is a central intuition in our conception of language. This fact underlies many of the claims that we make about how we communicate, and how we understand each other. Given this, irrespective of what we think words are, it is common to think that any putative ontology of words, must be able to explain this feature of language. That is, we need to provide criteria of identity for (...) word-types which allow us to individuate words such that it can be the case that two particular word-instances are instances of the same word-type. One solution, recently further developed by Irmak, holds that words are individuated by their history. In this paper, I argue that this view either fails to account for our intuitions about word identity, or is too vague to be a plausible answer to the problem of word individuation. (shrink)

It has been widely argued that words are analogous to species such that words, like species, are natural kinds. In this paper, I consider the metaphysics of word-kinds. After arguing against an essentialist approach, I argue that word-kinds are homeostatic property clusters, in line with the dominant approach to other biological and psychological kinds.

This article examines whether it is possible to uphold one form of deflationism towards metaphysics, ontological pluralism, whilst maintaining metaphysical realism. The focus therefore is on one prominent deflationist who fits the definition of an ontological pluralist, Eli Hirsch, and his self-ascription as a realist. The article argues that ontological pluralism is not amenable to the ascription of realism under some basic intuitions as to what a “realist” position is committed to. These basic intuitions include a commitment to more than (...) a stuff-ontology, and a view that realism carries with it more than a rejection of idealism. This issue is more than merely terminological. The ascription of realism is an important classification in order to understand what sorts of entities can be the truthmakers within a given theory. “Realism” is thus an important term to understand the nature of the entities that a given theory accepts into its ontology. (shrink)

Primitives are both important and unavoidable, and which set of primitives we endorse will greatly shape our theories and how those theories provide solutions to the problems that we take to be important. After introducing the notion of a primitive posit, I discuss the different kinds of primitives that we might posit. Following Cowling (2013), I distinguish between ontological and ideological primitives, and, following Benovsky (2013) between functional and content views of primitives. I then propose that these two distinctions cut (...) across each other leading to four types of primitive posits. I then argue that theoretical virtues should be taken to be meta-theoretical ideological primitives. I close with some reflections on the global nature of comparing sets of primitives. (shrink)

Minimally, metaphysical realists hold that there exist some mind-independent entities. Metaphysical realists also hold that we can speak meaningfully or truthfully about mind-independent entities. Those who reject metaphysical realism deny one or more of these commitments. This Element aims to introduce the reader to the core commitments of metaphysical realism and to illustrate how these commitments have changed over time by surveying some of the main families of views that realism has been contrasted with: such as scepticism, idealism, and anti-realism.

Although the metaphysics of words remains a relatively understudied domain, one of the more discussed topics has been the question of how to account for the apparent sameness of words. Put one way, the question concerns what it is that makes two word- instances (or tokens) instances of the same word. In this paper, I argue that the existing solutions to the problems all fail as they take the problem of sameness of word to be a problem about how one (...) object relates to another. I propose an alternative solution to the problem of sameness of word which is instead focused on the intrinsic nature of the properties possessed by words. The result is a more thoroughgoing version of nominalism than is currently defended in the literature. (shrink)

This paper addresses the ontological status of the ontological categories as defended within E.J. Lowe’s four-category ontology (kinds, objects, properties/relations, and modes). I consider the arguments in Griffith (2015. “Do Ontological Categories Exist?” Metaphysica 16 (1):25–35) against Lowe’s claim that ontological categories do not exist, and argue that Griffith’s objections to Lowe do not work once we fully take advantage of ontological resources available within Lowe’s four-category ontology. I then argue that the claim that ontological categories do not exist has (...) no undesirable consequences for Lowe’s brand of realism. (shrink)

The objectively best language is intended to refer to some metaphysically privileged language that ‘carves reality at its joints’ perfectly. That is, it is the kind of language that various ‘metaphysical deflationists’ have argued is impossible. One common line of argument amongst deflationists is that we have no means to compare languages that all express true facts about the world in such a way to decide which is ‘better’. For example, the language is physics is not objectively better than the (...) language of economics, as each language has the semantic purpose of expressing some domain of truths about the world inexpressible in the other language, and therefore neither could be ‘objectively best’. In this paper, I argue that metaphysical deflationists have failed to recognise a distinction between fine- and coarse-grained semantic purposes of languages, and that a recognition of that distinction provides us grounds to compare languages to see which is objectively best. I argue that once we recognise the distinction between fine- and coarse-grained semantic purposes, then we can see that it is relative to the coarse-grained purpose that we must compare putative objectively best ontological languages. (shrink)

Providing empirically supportable instances of ontological emergence is notoriously difficult. Typically, the literature has focused on two possible sources. The first is the mind and consciousness; the second is within physics, and more specifically certain quantum effects. In this paper, I wish to suggest that the literature has overlooked a further possible instance of emergence, taken from the special science of linguistics. In particular, I will focus on the property of truth-evaluability, taken to be a property of sentences as created (...) by the language faculty within human minds (or brains). The claim will not be as strong as to suggest that the linguistic data and theories prove emergence. Rather the dialectical aim here is to say that we have some good reasons (even if not conclusive reasons) to think that the property is emergent. (shrink)

This paper will discuss the origin of the human mind, and the qualitative discontinuity between human and animal cognition. We locate the source of this discontinuity within the language faculty, and thus take the origin of the mind to depend on the origin of the language faculty. We will look at one such proposal put forward by Hauser et al. (Science 298:1569-1579, 2002), which takes the evolution of a Merge trait (recursion) to solely explain the differences between human and animal (...) cognition. We argue that the Merge-only hypothesis fails to account for various aspects of the human mind. Instead we propose that the process of lexicalisation is also unique to humans, and that this process is key to explaining the vast qualitative differences. We will argue that lexicalisation is a process through which concepts are reformatted to be able to take on semantic features and to take part in grammatical relations. These are both necessary conditions for a grammatical mind and the increased ability to express conceptual content. We therefore propose a possible explanans for the discontinuity between humans and animals, namely that merge with lexicalisation (and consequently semantic features and grammatical relations) is a minimal requirement for the human mind. (shrink)

Metaphysics has had a long history of debate over its viability, and substantivity. This thesis explores issues connected to the realism question within the domain of metaphysics, ultimately aiming to defend a realist, substantive metaphysics by responding to so-called deflationary approaches, which have become prominent, and well supported within the recent metametaphysical and metaontological literature. To this end, I begin by examining the changing nature of the realism question. I argue that characterising realism and anti-realism through theories of truth unduly (...) places epistemology prior to ontology, and is unwarranted in assuming a non-neutrality between theories of truth and positions within the realism debate. I therefore propose a characterisation of realism and anti-realism understood through truthmaking. This produces a suitable working characterisation of realism that will be used within the remainder of this project. In the second section, I trace the historical influences upon current deflationary approaches to metaphysics, most prominently those of Carnap, and Putnam. I argue that Quine’s supposed attack on Carnap’s anti-metaphysical thought fails, and show how current deflationary thought, most prominently exhibited by Hirsch, came to focus on linguistically derived concerns over the substantivity of metaphysics. In the third section, I outline a number of issues for the deflationist, and defend the coherency and legitimacy of the unrestricted existential quantifier. Focusing on the linguistic aspect of deflationism, I argue that the conception of language that the deflationist relies upon lacks suitable empirical and theoretical support within linguistics and other related domains. Furthermore, I suggest that linguistic analysis in fact supports the claim that the quantifier carries no inherent restrictions. This restores our ability to suitably posit the unrestricted existential quantifier, as a quantifier wherein the domain is only restricted by metaphysically substantive restrictions. Through this, I argue that metaphysics is a substantive domain of discourse. Lastly, I sketch a positive account of how, under an empirically and theoretically justified conception of language, metaphysics can be coherently held to be a realist, substantive enterprise, contra claims that hold that the nature of language inherently prevents metaphysics being considered to be a substantive domain of discourse. (shrink)

An overview of the concept of Strong Emergence, and a summary of the papers within the special issue.

A summary of the papers within the Philosophica special issue on Strong Emergence.

A review of A Philosophical Guide to Chance by Toby Handfield. Cambridge CUP 2012.

A review of E.J. Lowe and Ontology, Edited By Mirosław Szatkowski. (New York, Oxford: Routledge, 2022. Pp. 326. Price £130.00.).

A review of Eli Hirsch, Quantifier Variance and Realism: Essays in Metaontology, Oxford University Press, 2011.

A review of The Limits of Realism, by Tim Button. Oxford University Press, 2013.

The Orbiting Carbon Observatory mission will make the first global, space-based measurements of atmospheric carbon dioxide with the precision, resolution, and coverage needed to characterize CO2 sources and sinks on regional scales. The measurement approach and instrument specifications were determined through an analysis of existing carbon cycle data and a series of observing system simulation experiments. During its 2-year mission, OCO will fly in a 1:15 PM sun-synchronous orbit with a 16-day ground-track repeat time, just ahead of the EOS Aqua (...) platform. It will carry a single instrument that incorporates three bore-sighted high-resolution spectrometers designed to measure reflected sunlight in the 0.76-μm O 2 A-band and in the CO2 bands at 1.61 and 2.06 μm. Soundings recorded in these three bands will be used to retrieve the column-averaged CO2 dry air mole fraction. A comprehensive validation program was included in the mission to ensure that the space-based XCO2 measurements have precisions of ∼0.3% on regional scales. OCO measurements will be used in global synthesis inversion and data assimilation models to quantify CO2 sources and sinks. While OCO will have a nominal lifetime of only 2 years, it will serve as a pathfinder for future long-term CO2 monitoring missions. © 2004 COSPAR. Published by Elsevier Ltd. All rights reserved. (shrink)

Background: Neuroimaging studies examining neural substrates of impaired self-awareness in patients with neurodegenerative diseases have shown divergent results depending on the modality of awareness. Evidence is accumulating to suggest that self-awareness arises from a combination of modality-specific and large-scale supramodal neural networks. Methods: We investigated the structural substrates of patients' tendency to overestimate or underestimate their own capacity to demonstrate empathic concern for others. Subjects' level of empathic concern was measured using the Interpersonal Reactivity Index, and subject-informant discrepancy scores were (...) used to predict regional atrophy pattern, using voxel-based morphometry analysis. Of the 102 subjects, 83 were patients with neurodegenerative diseases such as behavioral variant frontotemporal dementia or semantic variant primary progressive aphasia ; the other 19 were healthy older adults. Results: bvFTD and svPPA patients typically overestimated their level of empathic concern compared to controls, and overestimating one's empathic concern predicted damage to predominantly right-hemispheric anterior infero-lateral temporal regions, whereas underestimating one's empathic concern showed no neuroanatomical basis. Conclusions: These findings suggest that overestimation and underestimation of one's capacity for empathic concern cannot be interpreted as varying degrees of the same phenomenon, but may arise from different pathophysiological processes. Damage to anterior infero-lateral temporal regions has been associated with semantic self-knowledge, emotion processing, and social perspective taking; neuropsychological functions partly associated with empathic concern itself. These findings support the hypothesis that-at least in the socioemotional domain-neural substrates of self-awareness are partly modality-specific. © 2014 The Authors. (shrink)

Polymorphisms, deletions and translocations have been identified in some of the Chinese Spring nullisomic-tetrasomic and ditelosomic lines. In this paper, we present a comprehensive overview of the status of these materials.

© 2016. The American Astronomical Society. All rights reserved.We present DES14X3taz, a new hydrogen-poor superluminous supernova discovered by the Dark Energy Survey supernova program, with additional photometric data provided by the Survey Using DECam for Superluminous Supernovae. Spectra obtained using Optical System for Imaging and low-Intermediate-Resolution Integrated Spectroscopy on the Gran Telescopio CANARIAS show DES14X3taz is an SLSN-I at z = 0.608. Multi-color photometry reveals a double-peaked light curve: a blue and relatively bright initial peak that fades rapidly prior to (...) the slower rise of the main light curve. Our multi-color photometry allows us, for the first time, to show that the initial peak cools from 22,000 to 8000 K over 15 rest-frame days, and is faster and brighter than any published core-collapse supernova, reaching 30% of the bolometric luminosity of the main peak. No physical 56Ni-powered model can fit this initial peak. We show that a shock-cooling model followed by a magnetar driving the second phase of the light curve can adequately explain the entire light curve of DES14X3taz. Models involving the shock-cooling of extended circumstellar material at a distance of ≃400 R⊙ are preferred over the cooling of shock-heated surface layers of a stellar envelope. We compare DES14X3taz to the few double-peaked SLSN-I events in the literature. Although the rise times and characteristics of these initial peaks differ, there exists the tantalizing possibility that they can be explained by one physical interpretation. (shrink)

© 2015 by the Society of Critical Care Medicine and Lippincott Williams & Wilkins. Objectives: In the Fluid and Catheter Treatment Trial of the National Institutes of Health Acute Respiratory Distress Syndrome Network, a conservative fluid protocol resulted in a lower cumulative fluid balance and better outcomes than a liberal fluid protocol. Subsequent Acute Respiratory Distress Syndrome Network studies used a simplified conservative fluid protocol. The objective of this study was to compare the performance of FACTT Lite, FACTT Conservative, and (...) FACTT Liberal protocols. (shrink)

© 2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised (...) by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method. (shrink)

© 2014 Johnson et al.Introduction: We have previously shown that a tag single nucleotide polymorphism, which maps to the CYP3A locus, was associated with a reduction in premenopausal urinary estrone glucuronide levels and a modest reduction in risk of breast cancer in women age ≤50 years. Methods: We further investigated the association of rs10235235 with breast cancer risk in a large case control study of 47,346 cases and 47,570 controls from 52 studies participating in the Breast Cancer Association Consortium. Genotyping (...) of rs10235235 was conducted using a custom Illumina Infinium array. Stratified analyses were conducted to determine whether this association was modified by age at diagnosis, ethnicity, age at menarche or tumor characteristics. Results: We confirmed the association of rs10235235 with breast cancer risk for women of European ancestry but found no evidence that this association differed with age at diagnosis. Heterozygote and homozygote odds ratios were OR = 0.98 and OR = 0.80, respectively. There was no evidence of effect modification by tumor characteristics. rs10235235 was, however, associated with age at menarche in controls but not cases. Consequently the association between rs10235235 and breast cancer risk differed according to age at menarche ; the rare allele of rs10235235 was associated with a reduction in breast cancer risk for women who had their menarche age ≥15 years but not for those who had their menarche age ≤11 years. Conclusions: To our knowledge rs10235235 is the first single nucleotide polymorphism to be associated with both breast cancer risk and age at menarche consistent with the well-documented association between later age at menarche and a reduction in breast cancer risk. These associations are likely mediated via an effect on circulating hormone levels. (shrink)

INTRODUCTION: We have previously shown that a tag single nucleotide polymorphism, which maps to the CYP3A locus, was associated with a reduction in premenopausal urinary estrone glucuronide levels and a modest reduction in risk of breast cancer in women age ≤50 years.METHODS: We further investigated the association of rs10235235 with breast cancer risk in a large case control study of 47,346 cases and 47,570 controls from 52 studies participating in the Breast Cancer Association Consortium. Genotyping of rs10235235 was conducted using (...) a custom Illumina Infinium array. Stratified analyses were conducted to determine whether this association was modified by age at diagnosis, ethnicity, age at menarche or tumor characteristics.RESULTS: We confirmed the association of rs10235235 with breast cancer risk for women of European ancestry but found no evidence that this association differed with age at diagnosis. Heterozygote and homozygote odds ratios were OR = 0.98 and OR = 0.80, respectively = 0.02). There was no evidence of effect modification by tumor characteristics. rs10235235 was, however, associated with age at menarche in controls = 0.005) but not cases = 0.97). Consequently the association between rs10235235 and breast cancer risk differed according to age at menarche = 0.02); the rare allele of rs10235235 was associated with a reduction in breast cancer risk for women who had their menarche age ≥15 years = 0.84, 95% CI 0.75, 0.94; OR = 0.81, 95% CI 0.51, 1.30; P = 0.002) but not for those who had their menarche age ≤11 years = 1.06, 95% CI 0.95, 1.19, OR = 1.07, 95% CI 0.67, 1.72; P = 0.29).CONCLUSIONS: To our knowledge rs10235235 is the first single nucleotide polymorphism to be associated with both breast cancer risk and age at menarche consistent with the well-documented association between later age at menarche and a reduction in breast cancer risk. These associations are likely mediated via an effect on circulating hormone levels. (shrink)

Investigation of neural and cognitive processes underlying individual variation in moral preferences is underway, with notable similarities emerging between moral- and risk-based decision-making. Here we specifically assessed moral distributive justice preferences and non-moral financial gambling preferences in the same individuals, and report an association between these seemingly disparate forms of decision-making. Moreover, we find this association between distributive justice and risky decision-making exists primarily when the latter is assessed with the Iowa Gambling Task. These findings are consistent with neuroimaging studies (...) of brain function during moral and risky decision-making. This research also constitutes the first replication of a novel experimental measure of distributive justice decision-making, for which individual variation in performance was found. Further examination of decision-making processes across different contexts may lead to an improved understanding of the factors affecting moral behaviour. (shrink)

Ultra-high isotropic resolution imaging of retinal structures was made possible with an adaptive optics system using dual deformable mirrors and a Fourier-domain optical coherence tomography system with correction for longitudinal chromatic aberration. This system was used to image microscopic retinal structures of healthy as well as diseased retinas in vivo. The improved resolution and contrast enhanced visualization of morphological structures in the retina can be clearly seen. The benefits of this instrument are apparent from comparison of new images with those (...) acquired using a previous generation AO-OCT instrument. Big change in the appearance of speckle field can be observed as well. Additionally, further improvements in volumetric data acquisition and image representation will be discussed. This includes creation of large Field of View AO-OCT volume from multiple sub-volumes and its visualization. Also techniques and results of reducing speckle contrast by averaging multiple B-scans will be presented. (shrink)

© 2004 Nature Publishing Group.We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome - composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes - provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance (...) between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture. (shrink)

This new translation of the first volume of Hegel's Lectures on the History of Philosophy is a welcome and valuable addition to the new translations of Hegel's works, and now appears in paperback for the first time. Hegel's History of Philosophy has been described as perhaps one of his greatest achievements, and also as the first systematic history of philosophy since Aristotle. The translation included material from lecture notes taken by Hegel's pupils in 1923-4, 1925-6, and 1927-8. This material was (...) not available to Haldane and Simson when they made their translation nearly 100 years ago. The present volume, which supersedes that earlier one, besides being indispensable for the professional student, will also introduce those unfamiliar with Hegel to his conception of philosophy. (shrink)

© 2016 Elsevier Ltd All rights reserved.Crystallographic studies of ligands bound to biological macromolecules represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models (...) to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. (shrink)

BackgroundIn the Canadian Alliance for Healthy Hearts and Minds (CAHHM) cohort, participants underwent magnetic resonance imaging (MRI) of the brain, heart, and abdomen, that generated incidental findings (IFs). The approach to managing these unexpected results remain a complex issue. Our objectives were to describe the CAHHM policy for the management of IFs, to understand the impact of disclosing IFs to healthy research participants, and to reflect on the ethical obligations of researchers in future MRI studies.MethodsBetween 2013 and 2019, 8252 participants (...) (mean age 58 ± 9 years, 54% women) were recruited with a follow-up questionnaire administered to 909 participants (40% response rate) at 1-year. The CAHHM policy followed a restricted approach, whereby routine feedback on IFs was not provided. Only IFs of severe structural abnormalities were reported.ResultsSevere structural abnormalities occurred in 8.3% (95% confidence interval 7.7–8.9%) of participants, with the highest proportions found in the brain (4.2%) and abdomen (3.1%). The majority of participants (97%) informed of an IF reported no change in quality of life, with 3% of participants reporting that the knowledge of an IF negatively impacted their quality of life. Furthermore, 50% reported increased stress in learning about an IF, and in 95%, the discovery of an IF did not adversely impact his/her life insurance policy. Most participants (90%) would enrol in the study again and perceived the MRI scan to be beneficial, regardless of whether they were informed of IFs. While the implications of a restricted approach to IF management was perceived to be mostly positive, a degree of diagnostic misconception was present amongst participants, indicating the importance of a more thorough consent process to support participant autonomy.ConclusionThe management of IFs from research MRI scans remain a challenging issue, as participants may experience stress and a reduced quality of life when IFs are disclosed. The restricted approach to IF management in CAHHM demonstrated a fair fulfillment of the overarching ethical principles of respect for autonomy, concern for wellbeing, and justice. The approach outlined in the CAHHM policy may serve as a framework for future research studies.Clinical trial registrationhttps://clinicaltrials.gov/ct2/show/nct02220582. (shrink)

A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat, five other hexaploid wheat genotypes, tetraploid durum wheat, diploid wheat, and two other diploid members of the grass tribe Triticeae. The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags were examined (...) by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAPS. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 "unigenes." Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature. (shrink)

Frontotemporal dementia and Alzheimers disease are sometimes difficult to differentiate clinically because of overlapping symptoms. Using diffusion tensor imaging measurements of fractional anisotropy can be useful in distinguishing the different patterns of white matter degradation between the two dementias. In this study, we performed MRI scans in a 4 Tesla MRI machine including T1-weighted structural images and diffusion tensor images in 18 patients with FTD, 18 patients with Alzheimers disease and 19 cognitively normal controls. FA was measured selectively in specific (...) fibre tracts as well as globally in a voxel-by-voxel analysis. Patients with FTD were associated with reductions of FA in frontal and temporal regions including the anterior corpus callosum, bilateral anterior, descending cingulum tracts, and uncinate tracts, compared to controls. Patients with Alzheimers disease were associated with reductions of FA in parietal, temporal and frontal regions including the left anterior and posterior cingulum tracts, bilateral descending cingulum tracts and left uncinate tracts compared to controls. When compared with Alzheimers disease, FTD was associated with greater reductions of FA in frontal brain regions, whereas no region in Alzheimers disease showed greater reductions of FA when compared to FTD. In conclusion, the regional patterns of anisotropy reduction in FTD and Alzheimers disease compared to controls suggest a characteristic distribution of white matter degradation in each disease. Moreover, the white matter degradation seems to be more prominent in FTD than in Alzheimers disease. Taken together, the results suggest that white matter degradation measured with DTI may improve the diagnostic differentiation between FTD and Alzheimers disease. (shrink)

The behavior of antigen-specific CD4+ T lymphocytes during initial exposure to antigen probably influences their decision to become primed or tolerized, but this has not been examined directly in vivo. We have therefore tracked such cells in real time, in situ during the induction of oral priming versus oral tolerance. There were marked contrasts with respect to rate and type of movement and clustering between naive T cells and those exposed to antigen in immunogenic or tolerogenic forms. However, the major (...) difference when comparing tolerized and primed T cells was that the latter formed larger and longerlived clusters within mucosal and peripheral lymph nodes. This is the first comparison of the behavior of antigen-specific CD4+ T cells in situ in mucosal and systemic lymphoid tissues during the induction of priming versus tolerance in a physiologically relevant model in vivo. JEM © The Rockefeller University Press. (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)