Light adaptation is modulated almost exclusively by changes in intracellular Ca2+ concentration, and other Ca2+-independent mechanisms are likely to play only a minor role. Changes in Ca2+i may be not only necessary for light adaptation to take place but sufficient to cause it.

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)

Scientists, engineers, and healthcare professionals are currently developing a variety of new devices under the category of brain-computer interfaces (BCIs). Current and future applications are both medical/assistive (e.g., for communication) and non-medical (e.g., for gaming). This array of possibilities comes with ethical challenges for all stakeholders. As a result, BCIs have been an object of both hope and concern in various media. We argue that these conflicting sentiments can be productively understood in terms of personhood, specifically the impact of BCIs (...) on what it means to be a person and to be recognized as such by others. To understand the dynamics of personhood in the context of BCI use and investigate whether ethical guidance is required, a meeting entitled "BCIs and Personhood: A Deliberative Workshop" was held in May 2018. In this article, we describe how BCIs raise important questions about personhood and propose recommendations for BCI development and governance. (shrink)

Talk of different types of cells is commonplace in the biological sciences. We know a great deal, for example, about human muscle cells by studying the same type of cells in mice. Information about cell type is apparently largely projectible across species boundaries. But what defines cell type? Do cells come pre-packaged into different natural kinds? Philosophical attention to these questions has been extremely limited [see e.g., Wilson (Species: New Interdisciplinary Essays, pp 187–207, 1999; Genes and the Agents of Life, (...) 2005; Wilson et al. Philos Top 35(1/2):189–215, 2007)]. On the face of it, the problems we face in individuating cellular kinds resemble those biologists and philosophers of biology encountered in thinking about species: there are apparently many different (and interconnected) bases on which we might legitimately classify cells. We could, for example, focus on their developmental history (a sort of analogue to a species’ evolutionary history); or we might divide on the basis of certain structural features, functional role, location within larger systems, and so on. In this paper, I sketch an approach to cellular kinds inspired by Boyd’s Homeostatic Property Cluster Theory, applying some lessons from this application back to general questions about the nature of natural kinds. (shrink)

Given its non-invasive nature, there is increasing interest in the use of transcutaneous vagus nerve stimulation across basic, translational and clinical research. Contemporaneously, tVNS can be achieved by stimulating either the auricular branch or the cervical bundle of the vagus nerve, referred to as transcutaneous auricular vagus nerve stimulation and transcutaneous cervical VNS, respectively. In order to advance the field in a systematic manner, studies using these technologies need to adequately report sufficient methodological detail to enable comparison of results between (...) studies, replication of studies, as well as enhancing study participant safety. We systematically reviewed the existing tVNS literature to evaluate current reporting practices. Based on this review, and consensus among participating authors, we propose a set of minimal reporting items to guide future tVNS studies. The suggested items address specific technical aspects of the device and stimulation parameters. We also cover general recommendations including inclusion and exclusion criteria for participants, outcome parameters and the detailed reporting of side effects. Furthermore, we review strategies used to identify the optimal stimulation parameters for a given research setting and summarize ongoing developments in animal research with potential implications for the application of tVNS in humans. Finally, we discuss the potential of tVNS in future research as well as the associated challenges across several disciplines in research and clinical practice. (shrink)

This note will challenge G. A. Cohen's view of the interaction between legal systems and economic structures; such interaction raises the so‐called problem of legality, which Cohen sets out to solve in the eighth chapter of Karl Marx's Theory of History . In the course of this note, we shall interrogate the presumed rigor of Cohen's theory of base/superstructure relations, to which his understanding of law is central. His approach will not be simply destroyed, but will be resituated in a (...) network of problems that can highlight a certain fissure between his aspirations and his performance. (shrink)

Given its non-invasive nature, there is increasing interest in the use of transcutaneous vagus nerve stimulation across basic, translational and clinical research. Contemporaneously, tVNS can be achieved by stimulating either the auricular branch or the cervical bundle of the vagus nerve, referred to as transcutaneous auricular vagus nerve stimulation and transcutaneous cervical VNS, respectively. In order to advance the field in a systematic manner, studies using these technologies need to adequately report sufficient methodological detail to enable comparison of results between (...) studies, replication of studies, as well as enhancing study participant safety. We systematically reviewed the existing tVNS literature to evaluate current reporting practices. Based on this review, and consensus among participating authors, we propose a set of minimal reporting items to guide future tVNS studies. The suggested items address specific technical aspects of the device and stimulation parameters. We also cover general recommendations including inclusion and exclusion criteria for participants, outcome parameters and the detailed reporting of side effects. Furthermore, we review strategies used to identify the optimal stimulation parameters for a given research setting and summarize ongoing developments in animal research with potential implications for the application of tVNS in humans. Finally, we discuss the potential of tVNS in future research as well as the associated challenges across several disciplines in research and clinical practice. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

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)

This article explores some implications of the counterfactual aspect of freedom and unfreedom. Because actions can be unprevented even if they are not undertaken, and conversely because actions can be prevented even if they are not attempted and are thus not overtly thwarted, any adequate account of negative liberty must ponder numerous counterfactual chains of events. Each person's freedom or unfreedom is affected not only by what others in fact do, but also by what they are disposed to do. Their (...) dispositions play a key role in determining whether the abilities and inabilities of each person would continue as such if the person's conduct or situation were altered in various respects. Until one knows whether people would or would not have acted in certain ways if a given person had sought to do something, one cannot know whether that person was free to do that thing. Nor can one know whether the person was free to perform that action in combination with manifold subsequent actions. Thus, whether tacit or explicit, counterfactual scenarios are indispensable for any enquiry into a person's liberty. By relying on such scenarios, which trace how people are disposed to act vis-a-vis one another, one takes account of the central role of unmanifested dispositions in setting the bounds of people's sociopolitical freedom. Among the principal theorists whose work is critically examined in this article are Hillel Steiner, Ian Carter, and G.A. Cohen. Key Words: freedom • liberty • unfreedom • negative liberty • counterfactuals • disposition. (shrink)

Researchers from diverse disciplines, including organismal and cellular physiology, sports science, human nutrition, evolution and ecology, have sought to understand the causes and consequences of the surprising variation in metabolic rate found among and within individual animals of the same species. Research in this area has been hampered by differences in approach, terminology and methodology, and the context in which measurements are made. Recent advances provide important opportunities to identify and address the key questions in the field. By bringing together (...) researchers from different areas of biology and biomedicine, we describe and evaluate these developments and the insights they could yield, highlighting the need for more standardisation across disciplines. We conclude with a list of important questions that can now be addressed by developing a common conceptual and methodological toolkit for studies on metabolic variation in animals. (shrink)

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (shrink)

This volume explores how Catholicism began and continues to open its doors to the wider world and to other confessions in embracing ecumenism, thanks to the vision and legacy of the Second Vatican Council. It explores such themes as the twentieth century context preceding the council; parallels between Vatican II and previous councils; its distinctively pastoral character; the legacy of the council in relation to issues such as church-world dynamics, as well as to ethics, social justice, economic activity. Several chapters (...) discuss the role of women in the church before, during, and since the council. Others discern inculturation in relation to Vatican II. The book also contains a wide and original range of ecumenical considerations of the council, including by and in relation to Free Church, Reformed, Orthodox, and Anglican perspectives. Finally, it considers the Council’s ongoing promise and remaining challenges with regard to ecumenical issues, including a groundbreaking essay on the future of ecumenical dialogue by Cardinal Walter Kasper. (shrink)

The reasoning abilities of large language models (LLMs) are the topic of a growing body of research in artificial intelligence and cognitive science. In this paper, we probe the extent to which a dozen LLMs are able to distinguish logically correct inferences from logically fallacious ones. We focus on inference patterns involving conditionals (e.g., 'If Ann has a queen, then Bob has a jack') and epistemic modals (e.g., 'Ann might have an ace', 'Bob must have a king'). These inference patterns (...) have been of special interest to logicians, philosophers, and linguists, since they plausibly play a central role in human reasoning. Assessing LLMs on these inference patterns is thus highly relevant to the question of how much the reasoning abilities of LLMs match those of humans. Among the LLMs we tested, all but GPT-4 often make basic mistakes with conditionals. Moreover, even GPT-4 displays logically inconsistent judgments across inference patterns involving epistemic modals. (shrink)

We present a one per cent measurement of the cosmic distance scale from the detections of the baryon acoustic oscillations in the clustering of galaxies from the Baryon Oscillation Spectroscopic Survey, which is part of the Sloan Digital Sky Survey III. Our results come from the Data Release 11 sample, containing nearly one million galaxies and covering approximately 8500 square degrees and the redshift range 0.2 < z < 0.7. We also compare these results with those from the publicly released (...) DR9 and DR10 samples. Assuming a concordance Λ cold dark matter cosmological model, the DR11 sample covers a volume of 13 Gpc3 and is the largest region of the Universe ever surveyed at this density. We measure the correlation function and power spectrum, including density-field reconstruction of the BAO feature. The acoustic features are detected at a significance of over 7σ in both the correlation function and power spectrum. Fitting for the position of the acoustic features measures the distance relative to the sound horizon at the drag epoch, rd, which has a value of rd,fid = 149.28 Mpc in our fiducial cosmology. We find DV = at z = 0.32 and DV = at z = 0.57. At 1.0 per cent, this latter measure is the most precise distance constraint ever obtained from a galaxy survey. Separating the clustering along and transverse to the line of sight yields measurements at z = 0.57 of DA = and H =. Our measurements of the distance scale are in good agreement with previous BAO measurements and with the predictions from cosmic microwave background data for a spatially flat CDM model with a cosmological constant. © 2014 The Author Published by Oxford University Press on behalf of the Royal Astronomical Society. (shrink)

The problem of inferring probability comparisons between events from an initial set of comparisons arises in several contexts, ranging from decision theory to artificial intelligence to formal semantics. In this paper, we treat the problem as follows: beginning with a binary relation ≥ on events that does not preclude a probabilistic interpretation, in the sense that ≥ has extensions that are probabilistically representable, we characterize the extension ≥+ of ≥ that is exactly the intersection of all probabilistically representable extensions of (...) ≥. This extension ≥+ gives us all the additional comparisons that we are entitled to infer from ≥, based on the assumption that there is some probability measure of which ≥ gives us partial qualitative information. We pay special attention to the problem of extending an order on states to an order on events. In addition to the probabilistic interpretation, this problem has a more general interpretation involving measurement of any additive quantity: e.g., given comparisons between the weights of individual objects, what comparisons between the weights of groups of objects can we infer? (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Ius Gentium as Publicly Articulated Moral ScienceMatthew K. MinerdAmong the various types of law discussed in St. Thomas's theological "treatise on law"—questions 90–108 of Summa theologia [ST] I-II—the classification known as the "law of nations" (ius gentium) holds an ambiguous epistemological position. Marking a kind of halfway point between the natural law and civil law, it seems to straddle both domains. In fact, in a particularly important text dedicated (...) to this topic in the ST (I-II, q. 95, a. 4), Aquinas classes the ius gentium as being closely connected to the natural law, though in a way that is somewhat derivative, not as immediately flowing from human nature (especially in its animality) as does the natural law, but also not as marked by human contingency as is human civil law.As was recently discussed in a well-documented and insightful article by Barrett H. Turner in The Thomist, there have historically been two main lines of Thomist interpretation concerning the exact character of the "law of nations." Very broadly stated, what he refers to as the "Salamancan" line, indebted to Francisco de Vitoria, "interprets Thomas's doctrine of the ius gentium as a body of universal positive institutions (that is, specifications, determinationes) added to the natural law by agreement of the human race."1 [End Page 1043] This position, which would be common for several centuries among members of the Thomist school, would locate the law of nations essentially in the domain of nearly universally adopted customs and institutions, not strictly deduced from the natural law, but rather grounded on "the quasi-political authority of the entire human race, which promulgates the ius gentium by customs whose utility for attaining the ends of the natural law under a certain set of social conditions is easily recognized by rational creatures."2Turner calls the other line of thought "Maritain's Neo-Thomist Line,"3 an outlook that would be shared with various nuances by thinkers like Jean-Marie Aubert, Yves Simon, Marie-Michel Labourdette, John Finnis, and others. Setting aside my qualms about his appellation "neo-Thomist," which does more to obscure than to illumine (for it covers a host of Thomistic figures who have significantly different views on what constitutes "Thomism"), Turner does fairly lay out the major lines of Jacques Maritain's position, which is most directly articulated in Man and the State and La loi naturelle ou loi non-écrite.4 Basing himself on his particular view of knowledge of the natural law through connaturality,5 Maritain contrasted this sort of moral cognition with that which develops in the line of conceptual articulation, thus having a different "gnoseological" character from our knowledge of the natural law, while nonetheless still sharing the same "ontological" foundation. Such conceptually articulated law would be the ius gentium.Rather than add my voice to the dialectic of the various thinkers arrayed by Turner into the two aforementioned camps, I would like to propose a slightly different approach to the "moral epistemology of the law of nations," though one that I believe lies in line with the best aspects of Maritain's approach. Continuing a series of reflections that I have undertaken [End Page 1044] concerning moral epistemology during the past few years,6 I propose that it is most helpful to consider the "law of nations" as being a form of reasoning pertaining to what Scholastic vocabulary would refer to as "moral science,"7 namely discursive philosophical reasoning concerning the essences, properties, effects, and various other essential relationships that belong to a human acts, morally considered (the principal subject of moral philosophy), along with other subjects that are studied in relation to this principal subject (e.g., the principles of human acts, most particularly, the structure of human acts and the moral virtues). Moral science is the activity of reasoning that can be undertaken by knowing agents living together in community, seeking to discursively articulate and explain the moral truth that forms the essential basis for the contingent determinations that will then be codified in particular civil laws, the latter of which are not concerned with questions like "what are the ultimate foundations for property... (shrink)

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

ABSTRACT Greek historical accounts of ancient eclipses were an important, if peculiar, focus of scientific attention in the nineteenth century. Victorian-era astronomers tried to correct the classical histories using scientific methods, then used those histories as data with which to calibrate their lunar theories, then rejected the histories as having any relevance at all. The specific dating of these eclipses—apparently a simple exercise in celestial mechanics—became bound up with tensions between scientific and humanistic approaches to the past as well as (...) with wider social debates over the power and authority of science in general. The major figures discussed here, including G. B. Airy, Simon Newcomb, and T. H. Huxley, argued that the critical question was whether science could speak authoritatively about the past. To them, the ability of science to talk about the past indicated its power to talk about the future; it was also the fulcrum of fierce boundary disputes among science, history, and religion. (shrink)

ABSTRACT Greek historical accounts of ancient eclipses were an important, if peculiar, focus of scientific attention in the nineteenth century. Victorian-era astronomers tried to correct the classical histories using scientific methods, then used those histories as data with which to calibrate their lunar theories, then rejected the histories as having any relevance at all. The specific dating of these eclipses—apparently a simple exercise in celestial mechanics—became bound up with tensions between scientific and humanistic approaches to the past as well as (...) with wider social debates over the power and authority of science in general. The major figures discussed here, including G. B. Airy, Simon Newcomb, and T. H. Huxley, argued that the critical question was whether science could speak authoritatively about the past. To them, the ability of science to talk about the past indicated its power to talk about the future; it was also the fulcrum of fierce boundary disputes among science, history, and religion. (shrink)

This bilingual volume—English and German on facing pages—brings together the writings Wittgenstein composed during his stay in Dublin between October 1948 and March 1949, one of his most fruitful periods. He later drew more than half of his remarks for Part II of Philosophical Investigations from this Dublin manuscript. A direct continuation of the writing that makes up the two volumes of Remarks on the Philosophy of Psychology, this collection offers scholars a glimpse of Wittgenstein's preliminary thinking on one of (...) his most important works. G. H. von Wright and Heikki Nyman both teach at the University of Helsinki. (shrink)

Ecological theory is built upon assumptions about the fundamental nature of organism-environment interactions. We argue that two mutually exclusive sets of such assumptions are available and that they have given rise to alternative approaches to studying ecology. The fundamentally different premises of these approaches render them irreconcilable with one another. In this paper, we present the first logical formalisation of these two paradigms.The more widely-accepted approach - which we label the demographic paradigm - includes both population ecology and community ecology (...) (synecology). Demographic ecology assumes that the environment is relatively stable and that biotic processes, governed predominantly by resource availability, are the most important of ecological and evolutionary influences. Moreover, ecological processes are assumed to translate into directional selection pressures that drive significant evolutionary change on a local scale through the process of optimisation. (shrink)

Explaining the persistence of populations is an important quest in ecology, and is a modern manifestation of the balance of nature metaphor. Increasingly, however, ecologists see populations (and ecological systems generally) as not being in equilibrium or balance. The portrayal of ecological systems as “non-equilibrium” is seen as a strong alternative to deterministic or equilibrium ecology, but this approach fails to provide much theoretical or practical guidance, and warrants formalisation at a more fundamental level. This is available in adaptation theory, (...) which allows population persistence to be explained as an epiphenomenon stemming from the maintenance, survival, movement and reproduction of individual organisms. These processes take place within a physicochemical and biotic environment that persists through structured annual cycles, but which is also spatiotemporally dynamic and subject to stochastic variation. The focus is thus shifted from the overproduction of offspring and the consequent density dependent population pressure thought to follow, to the adaptations and ecological circumstances that support those relatively few individuals that do survive. (shrink)