bluuebunny/crossref_metadata_2025 huggingface dataset:
RAD51C facilitates checkpoint signaling by promoting CHK2 phosphorylation
Authors: Badie Sophie , Liao Chunyan , Thanasoula Maria , Barber Paul , Hill Mark A. , Tarsounas Madalena
Published: May 2009

The RAD51 paralogues act in the homologous recombination (HR) pathway of DNA repair. Human RAD51C (hRAD51C) participates in branch migration and Holliday junction resolution and thus is important for processing HR intermediates late in the DNA repair process. Evidence for early involvement of RAD51 during DNA repair also exists, but its function in this context is not understood. In this study, we demonstrate that RAD51C accumulates at DNA damage sites concomitantly with the RAD51 recombinase and is retained after RAD51 disassembly, which is consistent with both an early and a late function for RAD51C. RAD51C recruitment depends on ataxia telangiectasia mutated, NBS1, and replication protein A, indicating it functions after DNA end resection but before RAD51 assembly. Furthermore, we find that RAD51C is required for activation of the checkpoint kinase CHK2 and cell cycle arrest in response to DNA damage. This suggests that hRAD51C contributes to the protection of genome integrity by transducing DNA damage signals in addition to engaging the HR machinery.
Pro-BDNF–induced synaptic depression and retraction at developing neuromuscular synapses
Authors: Yang Feng , Je Hyun-Soo , Ji Yuanyuan , Nagappan Guhan , Hempstead Barbara , Lu Bai
Published: May 2009

Postsynaptic cells generate positive and negative signals that retrogradely modulate presynaptic function. At developing neuromuscular synapses, prolonged stimulation of muscle cells induces sustained synaptic depression. We provide evidence that pro–brain-derived neurotrophic factor (BDNF) is a negative retrograde signal that can be converted into a positive signal by metalloproteases at the synaptic junctions. Application of pro-BDNF induces a dramatic decrease in synaptic efficacy followed by a retraction of presynaptic terminals, and these effects are mediated by presynaptic pan-neurotrophin receptor p75 (p75NTR), the pro-BDNF receptor. A brief stimulation of myocytes expressing cleavable or uncleavable pro-BDNF elicits synaptic potentiation or depression, respectively. Extracellular application of metalloprotease inhibitors, which inhibits the cleavage of endogenous pro-BDNF, facilitates the muscle stimulation–induced synaptic depression. Inhibition of presynaptic p75NTR or postsynaptic BDNF expression also blocks the activity-dependent synaptic depression and retraction. These results support a model in which postsynaptic secretion of a single molecule, pro-BDNF, may stabilize or eliminate presynaptic terminals depending on its proteolytic conversion at the synapses.
Neurons and Simple Memory Circuits
Authors: Eichenbaum Howard
Published: May 2009

This chapter summarizes some of the key fundamental concepts about the anatomy and physiology of neurons, including the molecular basis of the unusual electrical properties of neurons, different forms of electrical conduction, and the transmission of information between neurons. Neurons are composed of three main elements: dendrites that are specialized for receiving signals from other cells, the cell body, and the axon that is specialized for conduction of the neural impulse. There are specialized areas of these cellular components that mediate communication between cells, called synapses, each composed of a presynaptic element where neurotransmitters are stored and released, and a postsynaptic element where there are receptors that recognize the neurotransmitter and generate signals in the postsynaptic cell.
A Brain System for Emotional Memory
Authors: Eichenbaum Howard
Published: May 2009

This chapter reviews current understanding of the brain pathways that mediate emotional experience and expression. It then considers the notion that some aspects of emotional memories involve a dedicated circuit of the brain that operates in parallel with other memory systems. In particular, it has been proposed that there is a specific memory system that mediates the learning and expression of emotional responses to stimuli of learned significance even in the absence of conscious memory for the events of the learning experience. The chapter first considers the evidence for a specific system for the acquisition of learned fear, and then extends the review to consider whether the same brain system supports the acquisition and expression of a broad range of emotional associations.
Working with Memory
Authors: Eichenbaum Howard
Published: May 2009

This chapter begins by summarizing the anatomy of the prefrontal cortex. It then reviews the functional role of the prefrontal cortex, including a consideration of whether the prefrontal area is involved in memory per se, or other cognitive processes related to memory, and whether the expansive prefrontal area has specialized subdivisions between or within the hemispheres. It considers parcellation of functions and cooperation between the prefrontal cortex and other higher-order cortical areas. Finally, some of the main points made in earlier chapters are reviewed, with the aim of considering how the entire brain participates in ordinary learning and memory processing.
Individual Differences
Authors: Mittleman Guy
Published: May 2009

This chapter suggests that rats, like humans, display profound individual differences that have relevance for understanding a variety of normal and pathological conditions. Variability in the response to drugs, lesions, or various other experimental manipulations are frequently observed in animals, but they are often attributed to experimental error along with the natural range of variation occurring between individuals of the same species. It is shown that that much within-experiment variability consists of individual differences. Exploiting these individual differences has a potentially large payoff in terms of modeling the behavioral and physiological differences observed between humans as well as providing a means of exploring the factors that control the expression of such differences.
Vision
Authors: Prusky Glen T. , Douglas Robert M.
Published: May 2009

This chapter discusses some of the methodologies used to measure rat vision, the known visual capabilities of rats, and the implications of rat vision for those researchers who use rats in vision-based experiments. Topics covered include experimental methods for measuring rat vision, the rat eye, spatial vision, and implications of rat vision for investigators.
Olfaction
Authors: Slotnick Burton , Schellinck Heather , Brown Richard
Published: May 2009

This chapter discusses the study of olfaction in rats. It argues that rats and other rodents live in an olfactory world and any attempt to understand rodent biology must take into account the importance of olfaction for social behavior, feeding, learning, and orientation in the environment. The role of odors in the control of rodent behavior has long been a primary topic in ethologically oriented studies of rat behavior, and the relatively simple tests used in these studies have served to demonstrate the influence and importance of odors. However, recent advances in odor control of learning and in the molecular biology of olfaction have required the use of more sophisticated test procedures and better control and understanding of the stimulus.
Posture
Authors: Pellis Sergio M. , Pellis Vivien C.
Published: May 2009

Studies with rats have been central to the understanding of postural support mechanisms. This chapter uses examples from this research to illustrate the importance of looking carefully at states of immobility, identifying the sensory controls guiding postural responses, and fractionating such responses into independent modules. For the latter, one type of postural support response, righting, is examined in detail to illustrate the need for using highly specific tests to evaluate these independent modules.
Thermoregulation
Authors: Satinoff Evelyn
Published: May 2009

This chapter sketches behavioral and reflexive thermoregulatory behaviors in adult and immature rats. It also describes some of the methods of studying thermoregulatory behavior and outlines some of the neural mechanisms that mediate temperature regulation.
Adolescence
Authors: Brown Russell W.
Published: May 2009

This chapter begins by describing the appearance of motor abilities, social and play behavior, sexual maturity, and sensory function in laboratory rats. It then discusses cognitive function, the development of simple stimulus associations made in conditioned taste aversion, and complex associations necessitated in spatial memory. The development of brain structures and their possible role in these behaviors are also discussed.
Aggressive, Defensive, and Submissive Behavior
Authors: Miczek Klaus A. , de Boer Sietse F.
Published: May 2009

This chapter discusses aggressive behavior in rats. Aggressive behavior, although infrequent, is part of life in a colony, particularly during its formation, and these interactions within the group are referred to as dominance or within-group aggressive behavior. As in their feral counterparts, the most potent trigger for aggressive behavior in resident male laboratory rats is the intrusion by an unfamiliar adult male, and these interactions are called resident-intruder aggression. Aggressive behavior by a female resident is more likely in the initial postpartum period, at which time the dam attacks both male and female intruders (maternal aggression).
Object Recognition
Authors: Mumby Dave G.
Published: May 2009

This chapter discusses object recognition in rats. It describes the two paradigms most often used to assess object recognition in rats: delayed nonmatching-to-sample (DNMS) and novel-object-preference (NOP). It shows that despite superficial similarities, DNMS and NOP tests engage different behavioral and motivational systems and therefore entail different procedural pitfalls and interpretational challenges. Still, findings from lesion experiments using either task have so far been fairly consistent, suggesting that the hippocampus is not critical for object-recognition memory, whereas the perirhinal cortex plays a more significant role. These conclusions are consistent with findings of changes in single-unit responses and c-fos expression within the perirhinal cortex produced by repeatedly presented visual stimuli.
Piloting
Authors: Save Etienne , Poucet Bruno
Published: May 2009

This chapter describes allothetic navigation and the methods for studying allothetic navigation in the laboratory. Topics covered include theories of spatial learning, spatial strategies, behavioral tests, and brain substrates of navigation.
Fear
Authors: Tinsley Matthew R. , Fanselow Michael S.
Published: May 2009

This chapter presents defensive behavior as a functional behavior system, describes the neural substrates of many of the various defensive behaviors described, and presents a model that integrates the behavioral and neural organizations of defensive behavior. The functional mapping of behavioral organization onto a network of brain structures has provided an invaluable and productive framework for generating testable hypotheses of the effects of experimental manipulations and may be beginning to inform studies of the substrates of clinical disorders related to dysfunction of defensive behavior in people.
Cognitive Processes
Authors: Sutherland Robert J.
Published: May 2009

This chapter seeks to provide a kind of thinking about behavioral processes in rats that is characteristic of a cognitive approach and to provide some examples of experimental paradigms that have been used with some success to probe the nature of the rat's representations of its environment and its own actions. The examples are drawn mainly from recent work on attentional and memory processes, two of the traditional subject matters in cognitive science.
Psychiatric Models
Authors: Szechtman Henry , Eilam David
Published: May 2009

This chapter begins with a discussion of the conflicts associated with a rise of a biological psychiatry perspective on mental illness, suggesting that the current preeminence of this viewpoint has aligned clinical psychiatry with behavioral neuroscience for the source of much of its basic science knowledge. It then elaborates on the methods of behavioral neuroscience and shows how this methodology is in fact just what is needed to investigate mechanisms of mental disorders of interest to psychiatry. The chapter attempts to clear up some confusion revolving around the distinction between tests, models, and theories. Finally, it illustrates some of the discussed principles by examining a rat model of a psychiatric illness—obsessive-compulsive disorder.
The Patient as Victim and Vector
Authors: Battin Margaret P. , Francis Leslie P. , Jacobson Jay A. , Smith Charles B.
Published: May 2009

Bioethics emerged at a time when infectious disease was not a major concern, and thus never developed a normative framework sensitive to disease transmission. This book develops the “patient as victim and vector” view to explore issues in clinical medicine, research, public health, and health policy. The central idea of this book is that a patient with a communicable infectious disease should be understood both as a victim of that disease and also as a potential vector—both a person who is ill and may die but who also may transmit an illness that could sicken or kill others. Bioethics has in general failed to see one part of this duality, and public health the other: that the patient is both victim and vector at one and the same time. Part I of the book shows why patient-centered concepts like autonomy and informed consent need to change in the context of communicable infectious diseases; Part II develops a normative theory for doing so. Part III examines traditional and new issues: the ethics of quarantine and isolation, research, disease screening, rapid testing, antibiotic use, and immunization, in contexts like multi-drug-resistant tuberculosis, syphilis, hepatitis, HIV/AIDS, and HPV. Part IV begins with a controversial thought experiment to consider constraints in the control of infectious disease, including pandemics, and Part V “thinks big” about global efforts to prevent, treat, or eradicate infectious disease.
The Next Frontier
Authors: Johnson David T. , Zimring Franklin E.
Published: May 2009

Asia is the next frontier in the campaign to end state execution because more than 95 percent of the executions in the world take place there. This book combines detailed case studies of the death penalty in major Asian nations with cross-national comparisons. It demonstrates decline in the number of Asian countries using execution as a criminal sanction and a decline in the rate of executions in most nations that retain the death penalty. Few Asian nations conduct executions with any regularity, and even major nations with death penalties in their criminal codes use the sanction rarely. What separates the low-execution nations from the very few states with high execution rates is, more than anything, politics. All of Asia's high execution states are hard-line authoritarian regimes of the left or right. When former right-wing authoritarian states experience democratic reforms, the rate of executions drops sharply and the only noncommunist government that maintains high executions is Singapore. The key question is not whether Asia will end state executions, but when it can be expected to do so. If the end of executions depends on the democratization of relatively stable hard-line communist regimes, many decades may be required, but if the stigma of state executions continues to increase, the end of capital punishment in Asia could happen before more comprehensive political change occurs.
2 Varieties of Capital Punishment in Contemporary Asia
Authors: Johnson David T. , Zimring Franklin E.
Published: May 2009

This chapter extends the analysis by profiling the great variety of death penalty policies in Asia, and it also outlines the research strategy employed in the chapters that follow. Its first and second sections provide an overview of the varieties of death penalty policy found in contemporary Asia by examining the region, first cross-sectionally and then temporally. The chapter's third section presents the book's case study methodology and explains the selection of five nations in East and Southeast Asia as the book's central subjects.
7 The Political Origins of China's Death Penalty Exceptionalism
Authors: Johnson David T. , Zimring Franklin E.
Published: May 2009

This chapter begins by providing a context for Chinese capital punishment through descriptions of the scale of criminal justice in the PRC and of the political organization of its criminal justice system. The second section estimates execution incidence in the post-Mao reform period, 1976 to the present. The third section contrasts two explanations for the high rates of execution in recent years: Chinese history as an influence on contemporary penal culture, and the political legacy of the past half century. The chapter argues that the proximate causes of China's death penalty exceptionalism are more rooted in the nation's recent history—and in the PRC's founding fathers, Joseph Stalin, Mao Zedong, and Deng Xiaoping. The fourth section of this case study analyzes the 2007 reinstitution of death sentence review by the Supreme People's Court. The fifth section describes the likely impact of the 2007 reform, the administrative character and costs of the PRC's death penalty system, and the types of reform proposals that may emerge from China's renewed experience with Supreme People's Court review. The sixth and final section of this chapter focuses on the long-term future of capital punishment in China.
8 Lessons
Authors: Johnson David T. , Zimring Franklin E.
Published: May 2009

This chapter makes the case for a regional focus by reviewing the materials in the preceding chapters for insights from Asia about capital punishment in the world in the 21st century. The lessons are organized into three sections. The first section describes features of death penalty policy in Asia that are consistent with the experiences recorded in Europe and with the theories developed to explain Western changes. The second section identifies some of the most significant diversities within the Asian region—in rates of execution, trends over time, and patterns of change—that contrast with the recent history of capital punishment in non-Asian locations and hence challenge conventional interpretations of death penalty policy and change. The third section discusses three ways the politics of capital punishment in Asia is distinctive: the limited role of international standards and transnational influences in most Asian jurisdictions; the presence of single-party domination in many Asian political systems; and the persistence of communist versions of capital punishment in the Asian region. Overall, the study of death penalty policy in Asia confirms many of the major themes that have emerged from studies of the postwar European and Commonwealth experiences.
CHAPTER 13 A New Starting Place for the Semantics of Belief Sentences
Authors: Eaker Erin L.
Published: May 2009

This chapter focuses on the semantics of believes that sentences, that is, sentences like, “Stella believes that Joe Tobacco won the hand.” It argues that semantic theories for believes that sentences have been unnecessarily complicated by an unsupported assumption about the primary function of believes that sentences, namely, that they relate their subjects to contents of belief in a way that reflects the role that those beliefs play in the subject's thinking, reasoning, and behavior. This assumption, referred to as the Explanatory Function Assumption (EFA), leads to a distorted understanding of believes that sentences and to the mistaken conclusion that any adequate account of the semantics of these sentences must provide solutions to certain well‐known but illusory puzzles. It is argued that when we reject the EFA, the puzzles are no longer puzzles, the semantic account of believes that sentences is suddenly much simpler, and the burden for explaining the so‐called belief puzzles is put where it should be, that is, on the pragmatic account of how belief descriptions are used.
CHAPTER 14 What Is De Re Belief?
Authors: Stalnaker Robert
Published: May 2009

This chapter brings out some of the interconnections between the specific issues about the logical form of de re belief attributions and the broader issues about intentionality. It begins by going over some familiar ground: reviewing the Quine/Kaplan analysis, spelling out the problem that originally motivated it, and considering some different assumptions about the objects or contents of belief. It then looks at Kaplan's modifications of Quine's analysis, and at a way that it might be further generalized, in light of its internalist motivation. The chapter concludes by looking at de re belief, and belief generally, from a contrasting externalist perspective.
CHAPTER 15 Five Theses on De Re States and Attitudes
Authors: Burge Tyler
Published: May 2009

This chapter proposes five theses on de re states and attitudes. The first thesis formulates the perspectival nature of representation. The second outlines attributional resources necessary to perceptually based representation. The third thesis holds that some of these attributional resources must apply veridically if perceptually based singular reference is to occur. The fourth sketches how these resources provide a basis for a priori knowledge, although they are much less rich than those postulated by the neo-Kantian views. The fifth outlines a nonempiricist conception of de re states and attitudes that builds on the empirical cases.
The Moral Skeptic
Authors: Superson Anita M.
Published: May 2009

This book challenges the traditional picture of the skeptic who asks, “Why be moral?” and demands a demonstration that acting in morally required ways is rationally required. It argues that we defeat the action skeptic, as well as the disposition skeptic, who denies that being morally disposed is rationally required, and the motive skeptic, who believes that merely going through the motions in acting morally is rationally permissible. It argues, against internalism, that we address the amoralist, who is not moved by moral reasons he recognizes. It argues for expanding the skeptic's position from self-interest to privilege, to include morally unjustified behavior typically directed against disenfranchised social groups. It argues for revising the traditional expected utility model of rationality to exclude desires deformed by patriarchy as ones it is not irrational to have. It defends the Interdependency Thesis, which assesses the rationality of moral dispositions and of actions interdependently, and allows us to fine tune the demands of the skeptic by not focusing on acts and dispositions in themselves, but on their interconnection. It defends the view that our rational assessments of agents should reflect the complex connection between the agent's reasons for adopting a moral disposition, and for having and acting from it, whether these cohere with her reasons for acting and for wanting to be a morally good person, and the justification for the moral theory or principles she endorses. Acts come in degrees of rationality, as measured by how they contribute to the agent's consistent life plan.
4 Deformed Desires
Authors: Superson Anita M.
Published: May 2009

This chapter argues that since the formal version of expected utility theory does not exclude desires deformed by patriarchy as irrational, the traditional picture of the skeptic who adopts this theory runs the risk of recapitulating women's oppression in the emergent moral code, and threatens a satisfactory defeat of skepticism. The chapter examines some traditional informed desire tests, and argues that they ultimately fail to exclude deformed desires as irrational. It proposes an additional condition of rationality, according to which the agent recognizes herself as having intrinsic worth. Narrowing the skeptic's position by excluding deformed desires from any theory of rational choice the skeptic is assumed to adopt helps to achieve a satisfactory defeat of action skepticism.
Bilateral Investment Treaties and Foreign Direct Investment: A Political Analysis
Authors: Büthe Tim , Milner Helen V.
Published: May 2009

This chapter examines the effect of bilateral investment treaties (BITs) on inward foreign direct investment flows (FDI) into least developed countries (LDCs). It suggests that BITs should not only boost FDI between the signatory states but more broadly increase inward FDI into the developing country signatory. The chapter begins with a discussion of the often narrow, legalistic conceptualization of BITs in previous studies, as well as previous dyadic and monadic empirical findings. It presents a statistical analysis of inward FDI flows into 122 developing countries with a population of more than 1 million from 1970 to 2000, and a qualitative analysis of the hypothesized causal mechanisms. It shows that the positive correlation between BITs and subsequent FDI is driven by the hypothesized causal mechanisms.
New Institutional Economics and FDI Location in Central and Eastern Europe
Authors: Grosse Robert , Trevino Len J.
Published: May 2009

This chapter demonstrates that institutions matter in the context of foreign direct investment (FDI) in the transitional economies of Central and Eastern Europe (CEE). It employs the new institutional economics (NIE) as a theoretical foundation and applies related concepts in an examination of FDI activity that may respond to institutional development in CEE. It shows that the flow of FDI into the transitional economies of CEE tends to follow patterns similar to those in other emerging markets, with the added dimension that institutional factors appear to play a larger role than elsewhere. In particular, bilateral investment treaties, the degree of enterprise reform, and repatriation rules tend to stimulate FDI, while political risk and the level of corruption in government tend to constrain FDI into these countries. This outcome provides strong support for this reasoning based on the new institutional economics.
Do Investment Agreements Attract Investment? Evidence from Latin America
Authors: Gallagher Kevin P. , Birch Melissa B.L.
Published: May 2009

This chapter attempts to identify the determinants of foreign direct investment (FDI) into Latin American Countries (LAC) and the Caribbean (LAC) during the period from 1980 to 2003. Although a number of countries are aggressively pursuing investment agreements with the United States in order to increase investment, there is no evidence that signing such an agreement with the United States will bring increased investment. This is largely consistent with previous work on the relationship between BITs and investment. The analysis is also consistent with broader literature on FDI determinants in Latin America and the Caribbean, which shows that the size of the domestic economy and the ability to serve as an export platform are key drivers of FDI inflows.
The Impact on Foreign Direct Investment of BITs
Authors: Unctad
Published: May 2009

This chapter examines whether the conclusion of BITs does indeed contribute to an increase in FDI. Time-series data analysis based on bilateral FDI flows between the BIT signatory countries shows that the influence of BITs on FDI is weak, especially in redirecting the share of FDI flowing from or to BIT signatory countries. In other words, following the signing of a BIT, it is more likely than not that the host country will marginally increase its share in the outward FDI of the home country; the same applies to the share of the home country in the FDI inflows of the host country. The effect, however, is usually small. In the cross-country comparison of FDI determinants, the overall conclusion is that BITs appear to play a minor and secondary role in influencing FDI flows.
Bilateral Investment Treaties and Foreign Direct Investment: Correlation Versus Causation
Authors: Aisbett Emma
Published: May 2009

This chapter examines whether participation in bilateral investment treaties (BITs) leads to increased foreign direct investment (FDI) inflows from the treaty partner countries. The chapter is organized as follows. It begins in Section A with a short overview of the basic theory and case evidence on the potential of BITs to function as a commitment device for the host. Section B presents a theoretical model of BIT function and the decision of a host country to participate in one. Section C introduces and motivates an empirical approach to the endogeneity of BIT participation, and shows that selection bias is not a concern in the specifications. Section D presents the results of the regression analysis, followed by the graphical event study of BIT participation. The final subsection of results shows that BITs do not attract investment from nonpartner countries through signaling.
Host-country Governance, Tax Treaties, and U.S. Direct Investment Abroad
Authors: Louie Henry J. , Rousslang Donald J.
Published: May 2009

This chapter takes a different approach from earlier studies to determine how host-country governance affects U.S. foreign direct investment (FDI). Instead of looking at the effect on the amount of investment, it looks at the effect on the rates of return that companies require on their FDI. It shows that poor host-country governance, as indicated by indexes measuring corruption or political instability, causes U.S. companies to require a significantly higher rate of return on their FDI. There is no evidence that a bilateral income tax treaty with the United States reduces the required rates of return to U.S. FDI. This finding is consistent with theoretical predictions, particularly those of Sinn (1991, 1993), and with the conclusions reached by Blonigen and Davies (2001). Failing to include a variable for the quality of host-country governance can cause a simple cross-section regression to yield the misleading implication that a tax treaty encourages U.S. FDI.
CHAPTER 1 Expected Utility Theory
Authors: Grant Simon , Van Zandt Timothy
Published: May 2009

This chapter reviews classic normative expected utility theory. The goal is to frame the subsequent chapters (which consider more modern extensions to and deviations from this classic theory) in a way that is accessible to the nonspecialist but also useful to the specialist. The chapter starts from scratch with a revealed preference approach to the existence of a utility function. It then presents the mathematical structure of additive and linear utility representations and their axiomatizations, in the context of abstract choice theory and using intertemporal choice as a source of examples. The chapter is thus able to focus on this mathematical structure without interference the specific interpretation and notation for decision under uncertainty. Furthermore, this approach allows the chapter to focus on the interpretation of the axioms when it turns to decision under uncertainty.
CHAPTER 3 Applications of Non‐Expected Utility
Authors: Bleichrodt Han , Schmidt Ulrich
Published: May 2009

Expected utility is the dominant framework for analyzing decisions under risk and uncertainty. Many empirical studies show that people deviate systematically from expected utility. To accommodate these deviations new, non‐expected utility models have been proposed. Among these models prospect theory is the most influential. This chapter studies applications of non‐expected utility and in particular prospect theory in insurance economics, auctions, and health economics. This chapter shows how the insights from non‐expected utility have improved understanding of people's choices and have led to improved decisions and more accurate measurements of utility.
CHAPTER 4 Ambiguity
Authors: Eichberger Jürgen , Kelsey David
Published: May 2009

Ambiguity refers to a decision situation under uncertainty where there is incomplete information about the likelihood of events. Different formal models of this notion have been developed with differing implications the representation of ambiguity and ambiguity aversion.
Antibody against infectious salmon anaemia virus among feral Atlantic salmon (Salmo salar)
Authors: Cipriano Rocco C.
Published: May 2009

Cipriano, R. C. 2009. Antibody against infectious salmon anaemia virus among feral Atlantic salmon (Salmo salar). – ICES Journal of Marine Science, 66: 865–870. Archived sera from Atlantic salmon (Salmo salar) that returned to the Penobscot River (Maine), Merrimack River (Massachusetts), and Connecticut River (in Massachusetts) from 1995 to 2002 were analysed for antibodies against infectious salmon anaemia virus (ISAV) using an enzyme-linked immunosorbent assay (ELISA). Up to 60 samples were archived per river system per year. In a given year, the number of fish sampled by ELISA for ISAV antibodies in the Penobscot River ranged from 2.9 to 11.2%, and the range of salmon sampled in the Merrimack River and the Connecticut River was 31.3–100% and 20.0–67.5%, respectively. Archived sera were not available for the 1995 and 2002 year classes from the Connecticut River. In all, 1141 samples were processed; 14 serum samples tested positive for antibodies to ISAV. In the Penobscot River, serum from one fish tested positive in each of the 1995 and 1999 year-class returns, and sera from two fish tested positive in the 1998 returns. In the Merrimack River, sera from four fish tested positive in each of the 1996 and 1997 returns, and sera from two fish were positive in the 2002 return. None of the archived sera from Atlantic salmon that returned to the Connecticut River tested positive.
Seasonal occurrence and sexual maturation of Japanese pygmy squid (Idiosepius paradoxus) at the northern limits of their distribution
Authors: Sato Noriyosi , Awata Satoshi , Munehara Hiroyuki
Published: May 2009

Sato, N., Awata, S., and Munehara, H. 2009. Seasonal occurrence and sexual maturation of Japanese pygmy squid (Idiosepius paradoxus) at the northern limits of their distribution. – ICES Journal of Marine Science, 66: 811–815. The distribution of aquatic animals is limited by water temperature. However, little is known about migration patterns, overwintering, and reproduction at the extremities of their distribution. To investigate the sexual maturation of Japanese pygmy squid (Idiosepius paradoxus) and their ability to survive during winter at the northern limits of their distribution, we collected samples monthly at Usujiri in northern Japan and carried out experiments on low-temperature tolerance. Squid were collected during 4 months in autumn and early winter. In autumn, all squid were large and sexually mature, and many egg masses were found on the surface of seagrass, whereas in early winter, only small immature squid were collected. A warm north-flowing current reached the Usujiri area during autumn, so the squid were likely transported by the current and some of the small squid were recruits that hatched there. Field data and the results of experiments on tolerance of the species to low temperatures showed that it cannot survive at the low temperatures around Usujiri in winter. The migration pattern of I. paradoxus may differ from the traditional pattern for marine resources, where young fish are transported passively and do not reproduce at the extremities of their distribution.
Impact of Cropping Sequences and Alternative Hosts on Take-all Management of Winter Wheat in Arkansas
Authors: Milus Eugene A. , Cartwright Richard D. , Rothrock Craig S. , Anders Merle , Slaton Nathan
Published: May 2009

Cultural practices are the principle means for managing take-all of wheat caused by Gaeumannomyces graminis var. tritici. This research identified cropping sequences that can be used to manage take-all in Arkansas. For dryland fields where the opportunity to grow rotational crops is limited, summer fallow was the best option for managing take-all. For irrigated fields, rotation out of wheat for at least one year reduced incidence and severity of take-all, and rice was the most effective rotational crop. Summer fallow or a rice crop was more detrimental to survival of take-all inoculum compared to corn or soybean. Reductions in inoculum were associated with elevated soil temperatures during the summer in fallow fields and with soil anoxia in flooded rice fields. Managing grassy weeds is important during rotations out of wheat. Rescuegrass was the most susceptible grassy weed to G. graminis var. tritici in this study. Although Italian ryegrass was only moderately susceptible, it likely plays a major role in maintaining inoculum because of its wide distribution and large population size.

Accepted for publication 11 April 2009. Published 12 May 2009.
High-performance computing for Monte Carlo radiotherapy calculations
Authors: Downes P. , Yaikhom G. , Giddy J.P. , Walker D.W. , Spezi E. , Lewis D.G.
Published: May 2009

We report on the RTGrid project, which investigates approaches for using high-performance computing infrastructures, such as the grid, in order to reduce the turnaround time of Monte Carlo (MC) simulation-based radiotherapy treatment planning. The main aim of this project is to render accurate dose calculations using MC simulations clinically feasible. To this end, we have successfully implemented and deployed the RTGrid distributed simulation framework for MC dose calculations. In this paper, we present the main experimental findings.
The Archaeotools project: faceted classification and natural language processing in an archaeological context
Authors: Jeffrey S. , Richards J. , Ciravegna F. , Waller S. , Chapman S. , Zhang Z.
Published: May 2009

This paper describes ‘Archaeotools’, a major e-Science project in archaeology. The aim of the project is to use faceted classification and natural language processing to create an advanced infrastructure for archaeological research. The project aims to integrate over 1×10
6
structured database records referring to archaeological sites and monuments in the UK, with information extracted from semi-structured grey literature reports, and unstructured antiquarian journal accounts, in a single faceted browser interface. The project has illuminated the variable level of vocabulary control and standardization that currently exists within national and local monument inventories. Nonetheless, it has demonstrated that the relatively well-defined ontologies and thesauri that exist in archaeology mean that a high level of success can be achieved using information extraction techniques. This has great potential for unlocking and making accessible the information held in grey literature and antiquarian accounts, and has lessons for allied disciplines.
Flexible selection of heterogeneous and unreliable services in large-scale grids
Authors: Stein Sebastian , Payne Terry R. , Jennings Nicholas R.
Published: May 2009

As grids become larger and more interconnected in nature, scientists can benefit from a growing number of distributed services that may be invoked on demand to complete complex computational workflows. However, it also means that these scientists become dependent on the cooperation of third-party service providers, whose behaviour may be uncertain, failure prone and highly heterogeneous. To address this, we have developed a novel decision-theoretic algorithm that automatically selects appropriate services for the tasks of an abstract workflow and deals with failures through redundancy and dynamic re-invocation of functionally equivalent services. In this paper, we summarize our approach, describe in detail how it can be applied to a real-world bioinformatics workflow and show that it offers a significant improvement over current service selection techniques.
Building a scientific data grid with D
i
GS
Authors: Beckett Mark G. , Allton Chris R. , Davies Christine T.H. , Davis Ilan , Flynn Jonathan M. , Grant Eilidh J. , Hamilton Russell S. , Irving Alan C. , Kenway R.D. , Ostrowski Radosław H. , Perry James T. , Swedlow Jason R. , Trew Arthur
Published: May 2009

We provide an insight into the challenge of building and supporting a scientific data infrastructure with reference to our experience working with scientists from computational particle physics and molecular biology. We illustrate how, with modern high-performance computing resources, even small scientific groups can generate huge volumes (petabytes) of valuable scientific data and explain how grid technology can be used to manage, publish, share and curate these data. We describe the D
i
GS software application, which we have developed to meet the needs of smaller communities and we have highlighted the key elements of its functionality.
Using food web dominator trees to catch secondary extinctions in action
Authors: Bodini Antonio , Bellingeri Michele , Allesina Stefano , Bondavalli Cristina
Published: May 2009

In ecosystems, a single extinction event can give rise to multiple ‘secondary’ extinctions. Conservation effort would benefit from tools that help forecast the consequences of species removal. One such tool is the dominator tree, a graph-theoretic algorithm that when applied to food webs unfolds their complex architecture, yielding a simpler topology made of linear pathways that are essential for energy delivery. Each species along these chains is responsible for passing energy to the taxa that follow it and, as such, it is indispensable for their survival. To assess the predictive potential of the dominator tree, we compare its predictions with the effects that followed the collapse of the capelin (
Mallotus villosus
) in the Barents Sea ecosystem. To this end, we first compiled a food web for this ecosystem, then we built the corresponding dominator tree and, finally, we observed whether model predictions matched the empirical observations. This analysis shows the potential and the drawbacks of the dominator trees as a tool for understanding the causes and consequences of extinctions in food webs.
Contrasting spatial patterns of taxonomic and functional richness offer insights into potential loss of ecosystem services
Authors: Cumming Graeme S. , Child Matthew F.
Published: May 2009

Functional and trophic perspectives on patterns of species occurrences have the potential to offer new and interesting insights into a range of spatially explicit problems in ecology and conservation. We present the function–area relationship (FAR) and explore linkages between functional and taxonomic species richness for South African birds. We first used beak morphology to classify a subset of 151 South African bird species into 18 functional groups and calculated both the species–area relationship and the FAR at quarter-degree resolution for South Africa. The relationship between functional and taxonomic richness by cell was quadratic rather than linear, with considerable scatter around the curve. We next looked at the spatial relationships between taxonomic diversity and response diversity (i.e. diversity within functional groups) using an
a priori
categorization of nearly all South African birds into nine functional groups. The spatial distribution of response richness also showed considerable variation in relation to taxonomic richness. Our results demonstrate a novel approach to linking taxonomic, functional and trophic patterns in space and suggest a way in which conservation planning, which has traditionally had a taxonomic focus, could formally incorporate a more functional and food-web-based approach.
Keystone species and food webs
Authors: Jordán Ferenc
Published: May 2009

Different species are of different importance in maintaining ecosystem functions in natural communities. Quantitative approaches are needed to identify unusually important or influential, ‘keystone’ species particularly for conservation purposes. Since the importance of some species may largely be the consequence of their rich interaction structure, one possible quantitative approach to identify the most influential species is to study their position in the network of interspecific interactions. In this paper, I discuss the role of network analysis (and centrality indices in particular) in this process and present a new and simple approach to characterizing the interaction structures of each species in a complex network. Understanding the linkage between structure and dynamics is a condition to test the results of topological studies, I briefly overview our current knowledge on this issue. The study of key nodes in networks has become an increasingly general interest in several disciplines: I will discuss some parallels. Finally, I will argue that conservation biology needs to devote more attention to identify and conserve keystone species and relatively less attention to rarity.
PKR acts early in infection to suppress Semliki Forest virus production and strongly enhances the type I interferon response
Authors: Barry Gerald , Breakwell Lucy , Fragkoudis Rennos , Attarzadeh-Yazdi Ghassem , Rodriguez-Andres Julio , Kohl Alain , Fazakerley John K.
Published: May 2009

The double-stranded RNA-activated protein kinase (PKR) is a key regulator of protein translation, interferon (IFN) expression and cell survival. Upon infection of vertebrate cells in continuous culture, the alphavirus Semliki Forest virus (SFV) initiates apoptosis and IFN synthesis. To determine the effect of PKR on SFV infection, we studied the course of infection in wild-type (wt) mice, mice with a genetic deletion of PKR (PKR−/−) and mouse embryo fibroblasts (MEFs) derived from these mice. In MEFs, PKR delayed virus protein synthesis, production of infectious virus and caspase-3-activated cell death and reduced the yield of infectious virus by 90 %. Small interfering RNA suppression of PKR levels in NIH-3T3 cells also reduced virus production and apoptosis. In MEFs, PKR was not required for initiation of IFN-β gene transcription, but contributed strongly to the magnitude of this response. Levels of IFN-β transcripts in PKR−/− MEFs at 8 h were 80 % lower than those in wt MEFs and levels of functional IFN at 24 h were 95 % lower. Following infection of wt and PKR−/− mice, SFV4 and SFV A7(74) were avirulent. PKR increased levels of serum IFN and the rate of clearance of infectious virus from the brain. In summary, in response to SFV, PKR exerts an early antiviral effect that delays virus protein production and release of infectious virus and, whilst PKR is not required for induction of apoptosis or activation of the type I IFN response, it strongly augments the type I IFN response and contributes to clearance of infectious virus from the mouse brain.
Peptide inhibitors of hepatitis C virus core oligomerization and virus production
Authors: Kota S. , Coito C. , Mousseau G. , Lavergne J.-P. , Strosberg A. D.
Published: May 2009

Hepatitis C virus (HCV) nucleocapsid assembly requires dimerization of the core protein, an essential step in the formation of the virus particle. We developed a novel quantitative assay for monitoring this protein–protein interaction, with the goal of identifying inhibitors of core dimerization that might block HCV production in infected Huh-7.5 hepatoma cells. Two core-derived, 18-residue peptides were found that inhibited the dimerization of a fragment of core comprising residues 1–106 (core106) by 68 and 63 %, respectively. A third, related 15-residue peptide displayed 50 % inhibition, with an IC50 of 21.9 μM. This peptide was shown, by fluorescence polarization, to bind directly to core106 with a K
d of 1.9 μM and was displaced by the unlabelled peptide with an IC50 of 18.7 μM. When measured by surface plasmon resonance, the same peptide bound core169 with a K
d of 7.2 μM. When added to HCV-infected cells, each of the three peptides blocked release, but not replication, of infectious virus. When measured by real-time RT-PCR, the RNA levels were reduced by 7-fold. The 15-residue peptide had no effect on HIV propagation. Such inhibitors may constitute useful tools to investigate the role of core dimerization in the virus cycle.