bluuebunny/crossref_metadata_2025 huggingface dataset:
Study Sample and Demographics of the Participating Agencies
Authors: Pecora Peter J. , Kessler Ronald C. , Williams Jason , Downs A. Chris , English Diana J. , White James , O'Brien Kirk
Published: September 2009

This chapter provides the background for two research questions concerning youth spending extended periods of time in care: (1) Are there key factors or program components linked to better functioning of youth from foster care as they reach adulthood? (2) Is one family foster care program approach more successful than another in helping youth achieve desired outcomes? Answers to these questions could be used by policymakers to promote changes in public and voluntary foster care programs. This chapter consists of two sections. The first section (Sample Characteristics and Matching Criteria) explains how the Northwest Alumni Study sample was formed, including eligibility, sample matching, data weighting, and power analyses. The second section (Alumni Demographics: Ethnicity, Gender, and Age at the Time of the Interview) provides demographic information on the Northwest alumni including ethnicity, gender, and age.
Data Sources, Variables, and Data Collection Procedures
Authors: Pecora Peter J. , Kessler Ronald C. , Williams Jason , Downs A. Chris , English Diana J. , White James , O'Brien Kirk
Published: September 2009

This chapter discusses the two means of data collection (case record reviews and interviews); the description of study variables, predictors, and outcomes; and the response rate, the handling of missing data, and how the data were weighted to adjust for interview nonresponse.
Mental and Physical Health Functioning
Authors: Pecora Peter J. , Kessler Ronald C. , Williams Jason , Downs A. Chris , English Diana J. , White James , O'Brien Kirk
Published: September 2009

Based on alumni interviews, this chapter reports on the mental and physical health functioning of alumni, thus providing more empirical data about the short-term and long-term functioning of maltreated youth who were placed in foster care. The primary hypothesis was that alumni would exhibit mental and physical health difficulties that would be more severe than those of the general population.
Employment and Finances
Authors: Pecora Peter J. , Kessler Ronald C. , Williams Jason , Downs A. Chris , English Diana J. , White James , O'Brien Kirk
Published: September 2009

Previous research has shown that youth who have been placed in foster care experience a wide range of economic-related adversities after leaving care, such as homelessness, unemployment, and low wages and income. Table 8.1 summarizes studies that have examined some of these adversities. This chapter will present current alumni achievement and functioning with respect to homelessness and living situation, employment, public assistance, and finances. Findings are compared not only to those of other foster care follow-up studies but also to general population information gathered from the U.S. Census Bureau. Currently, there are few studies with which to compare follow-up data (especially for older alumni), but the literature is slowly building, with longitudinal follow-up studies such as the Midwest study (Courtney et al., 2007) and studies that use state employment or other databases.
Summary and Recommendations
Authors: Pecora Peter J. , Kessler Ronald C. , Williams Jason , Downs A. Chris , English Diana J. , White James , O'Brien Kirk
Published: September 2009

This chapter summarizes the Northwest Alumni Study's main study research questions, hypotheses, and findings. Recommendations tied directly to the study data are discussed, along with other strategies that have been identified through discussions with alumni from foster care, staff, and others. The summary of major study findings is divided into findings from the (1) primary research questions and corresponding hypotheses and (2) supplemental research questions. Many of the questions and hypotheses concern the overall status of outcomes such as mental health functioning, while other questions concern relations among variables, such as the effect of child maltreatment on future financial health. In addition to answering the questions and testing hypotheses, data presented in previous chapters have provided answers to many unasked questions. These findings are presented where appropriate.
3 New Wine Words
Authors: Lehrer Adrienne
Published: September 2009

Wine descriptors that became common after the 1980s tended to be synthetic, as opposed to the earlier analytic words. Structure, a popular current word, deals with the balance and interaction of the elements (acidity, tannin, alcohol, sugar). New words for body are based on metaphors of the human form (big-boned, broad-shouldered, muscular vs. svelte). Age and drinkability can be described by age metaphors (backward, precocious), and tightness vs. openness. Many new evaluative descriptors are based on personality: charming, diplomatic, friendly, intellectual, and hedonistic. A common word is terroir, borrowed from the French, for the complete growing environment. Verbs of motion are frequently used to describe the progression of the tasting experience. A wine bursts from the glass or an aroma sneaks up on one.
The public health response to the World Trade Center disaster
Authors: Holtz Timothy H. , Jessica Leighton , Balter Sharon , Weiss Don , Blank Susan , Weisfuse Isaac
Published: September 2009

This chapter describes the public health response to the World Trade Center disaster on 9/11. It describes the initial public health response, environmental health assessment and risk communication, surveillance, support systems, mental health issues, and other key issues in the public health response to the World Trade Center disaster.
Improving epidemiology, surveillance, and laboratory capabilities
Authors: Conrad J. Lyle , Pearson James L.
Published: September 2009

This chapter describes ways to improve epidemiology, surveillance, and laboratory capabilities. It discusses the current status of epidemiology, surveillance, and laboratory capabilities in the United States; the challenges posed by terrorism; and deficiencies identified in epidemiology, surveillance, and laboratory capabilities. It describes ways of improving epidemiology, surveillance, and public health laboratories.
Improving vaccines, antimicrobials, and antitoxins through research
Authors: Margolskee Dorothy
Published: September 2009

This chapter describes ways to improve vaccines, antimicrobials, and antitoxins through research. It describes and discusses a number of issues, including the need for rapid diagnostic tests for several pathogens, the potential role of antitoxins, the potential post-exposure utility of vaccines, and the need for fundamental research on the viruses that cause hemorrhagic fever.
Amico
Authors: Lister Warwick
Published: September 2009

This book is a full-length biography in English of Giovanni Battista Viotti (1755–1824), one of the great violinist-composers in the history of music, and arguably the most influential violinist who ever lived. He rose from humble origins as a blacksmith's son in a village near Turin, Italy, and early studies with Gaetano Pugnani, to a triumphant international career, particularly in Paris and London. His multifarious career as concert performer, composer, teacher, opera theater director, and impresario was played out against the backdrop of a dramatically changing world: from the ancien régime patronage of an Italian prince and the Queen of France, Marie Antoinette, to the commercial and box-office–centered institutions of the early 19th century. Viotti's life was intensely dramatic. He knew tragedy as well as success: he was forced to flee the French Revolution, he was exiled from England for an extended period, his attempt to establish himself in business met with failure, and he died heavily in debt. His correspondence with an English family, the Chinnerys, with whom he was intimately associated for the last half of his life, provides an unusually revealing glimpse into his personal life. Viotti's biography is not without its mysteries, among which is his renunciation, twice in his life, of public performance. This study is based on extensive documentary research, much of it here revealed for the first time. Viotti's works are considered in the context of his life. Eleven appendices include translations of various Viotti-related archival documents, and additional information on Viotti's siblings, his places of residence, his violins, his unfinished violin method, and financial matters.
CHAPTER NINE Paris and the Opéra, 1819–21
Authors: Lister Warwick
Published: September 2009

This chapter describes Viotti in his role as director of the Paris Opéra and the Théâtre Italien in the period 1819–21. Several letters are cited showing how he dealt with disciplinary, financial, and artistic matters involving composers, such as Gaspare Spontini, colleagues, such as Ferdinando Paer and Kreutzer, lead singers, chorus and orchestra members, dancers, and his superiors in the Opéra administration. His attempts to improve artistic standards among the singers and the orchestra are documented. Viotti's role in the increasing popularity of Rossini's operas at the Théâtre Italien is considered. His friendships with the Duke of Cambridge, the poet Thomas Moore, Lady Bessborough, his pupil Robberechts, and others, is described. Viotti's unsuccessful attempts to recoup his losses from the failure of his wine business in 1818 are given due attention.
Epidemiology and world health
Authors: Mathers Colin
Published: September 2009

This chapter examines major developments in summarizing population health over the last thirty years, focusing on developments in global descriptive epidemiology, on the global burden of disease approach to summarizing population health, and on the issues and controversies surrounding these developments. Reliable and comparable information about levels and trends in population health, about the main causes of loss of health in populations, and how these are changing, is a critical input for debates about international and national health policies and priorities.
Epidemiology as a common European endeavour
Authors: Olsen Jørn , Saracci Rodolfo
Published: September 2009

This chapter demonstrates the important role played by the World Health Organisation (WHO), International Agency for Research on Cancer (IARC), and the EU in fostering education, training, and cooperation in epidemiology in Europe. The possibilities for improving the health of the population in Europe have not and are not being exploited in an optimal way. Unfortunately, the concentration on wealth creation and the illusory glamour of developing new technologies, for example molecular biology, permeates international bodies as much as it does national governments.
The development of epidemiology: Spain
Authors: Bolúmar Francisco
Published: September 2009

This chapter traces the development of epidemiology in Spain, with special emphasis on the period from the mid-1970s to the present. After a brief historical introduction, it presents the major factors which influenced the author's to start in epidemiology and the options available at that time for training. This is followed by a description of the major obstacles encountered in the practice of epidemiology, including the restricted availability and use of data sources. The chapter highlights the relationship with and the influence of epidemiology on some public health policies. Finally, it discusses the future perspectives for epidemiology in Spain.
Factor graphs and graph ensembles
Authors: Mézard Marc , Montanari Andrea
Published: September 2009

Probabilistic systems involving a large number of simple variables with mutual dependencies appear recurrently in several fields of science. It is often the case that such dependencies can be factorized in a non-trivial way, and distinct variables interact only ‘locally’. This important structural property plays a crucial role. It is described here in a graphical language — the one of factor graphs. Ensembles of probability distributions naturally map to ensemble of random graphs, or hypergraphs. Several basic properties of these ensembles are discussed, from the appearance of a giant component to the motifs appearing in their local structure. The graph description is a necessary background for the understanding of message passing algorithms.
The assignment problem
Authors: Mézard Marc , Montanari Andrea
Published: September 2009

This chapter discusses the use of message passing techniques in a combinatorial optimization problem assignment. Given N ‘agents’ and N ‘jobs’, and the cost matrix E(i,j) for having job i executed by agent j, the problem is to find the lowest cost assignment of jobs to agents. On the algorithmic side, the Min-Sum variant of Belief Propagation is shown to converge to an optimal solution in polynomial time. On the probabilistic side, the large N limit of random instances, when the costs E(i,j) are independent uniformly random variables, is studied analytically. The cost of the optimal assignment is first computed heuristically within the replica symmetric cavity method, giving the celebrated zeta(2) result. This study is confirmed by a rigorous combinatorial argument which provides a proof of the Parisi and Coppersmith–Sorkin conjectures.
An ongoing story
Authors: Mézard Marc , Montanari Andrea
Published: September 2009

The emerging field that has been described in this book is remarkably coherent, but it also opens up a number of challenges. This chapter provides a synthetic description of such challenges, as well as a survey of recent progress. The ambition is to set an agenda for this new research field. Three research directions are emphasized. Firstly, achieving a better qualitative understanding of 1RSB glass phase. What is a pure state decomposition? What is the relation between emergence of long range correlations and clustering of the probability measure? Secondly, developing methods for the full-RSB phase. Where does such a phase emerge in sparse graphical models? Does the cavity method have a compact formulation? Thirdly, understanding algorithmic implications. There is large evidence that phase transitions affect the performances of algorithms. However, a crisp and general formulation is still missing.
A life course approach to cancer epidemiology
Authors: Kuh Diana , Ben-Shlomo Yoav
Published: September 2009

Epidemiologic studies have evaluated a limited number of cancer sites for risk factors over the life course. This chapter examines in utero and perinatal factors, and attempts to link these factors and motivating biology to subsequent time periods to incorporate a life course perspective. Breast, testicular, and prostate cancers are considered in detail due to the large volume of literature on these cancers.
Should we intervene to improve childhood circumstances?
Authors: Kuh Diana , Ben-Shlomo Yoav
Published: September 2009

This chapter reviews epidemiological and developmental findings relevant to intervention that may improve childhood circumstances. It discusses the circumstances of contemporary childhood in an international context, the lifelong social disparities in health and wellbeing, and the likely biological and behavioural pathways that account for these disparities. It argues that despite major advances, there are reasons for continuing concern over the physical and social settings in which children are born and raised. The chapter provides evidence supporting a societal imperative to protect and nuture children of the world community.
HAART in HIV-infected children: one decade later
Authors: Dieudonne Arry , McIntyre James A. , Fregonese Federica , Giaquinto Carlo , Oleske James M.
Published: September 2009

This chapter provides an overview of paediatric HIV management in the population entering adulthood after a decade of highly active antiretroviral therapy (HAART). Topics discussed include prevention of mother-to-child transmission of HIV and the evolution of antiretroviral management.
US Cohorts review: The HIV Outpatient Study (HOPS) and the Multicenter AIDS Cohort Study (MACS)
Authors: Palella Frank J. , Moorman Anne C. , Brooks (HOPS) John T. , Phair John , Jacobson Lisa , Detels Roger , Margolick Joseph , Rinaldo (MACS) Charles
Published: September 2009

This chapter presents an overview of HIV Outpatient Study (HOPS) and Multicenter AIDS Cohort Study (MACS). HOPS is a prospective observational cohort study that was initiated in 1993 by the US Centers for Disease Control and Prevention (CDC), and is currently expected to continue collecting and analyzing longitudinal data on HIV-infected outpatients until mid-2011. It is the longest-running and only remaining US government-sponsored multi-site prospective cohort of a diverse spectrum of people living with HIV infection and receiving routine clinical care in the United States. MACS was funded in 1983 by the US National Institute of Allergy and Infectious Disease (NIAID), and recruitment of participants began in early 1984. The initial rationale for funding this epidemiological investigation was to collect specimens that could potentially be of use in identifying an infectious agent as the cause of AIDS and to delineate the natural history of pre-AIDS in men who have sex with men (MSM), the first epidemiologically identified group at high risk of developing the syndrome.
The French Hospital Database on HIV (FHDH) ANRS CO 4
Authors: Costagliola Dominique
Published: September 2009

This chapter begins with a description of the French Hospital Database on HIV (FHDH). The FHDH was created in 1992 in order to collect clinical information on HIV-infected patients managed in HIV/AIDS centres (CISIH). It is managed by the UMR S 720 (Clinical and Therapeutic Epidemiology of HIV Infection) team at the Institut National de la Santé et de la Recherche Médicale (INSERM). Data from the FHDH is used to describe HIV patients, the use of ART and its impact on clinical progression (CD4 counts and plasma HIV RNA), and morbidity in the last ten years.
Country review: Haiti
Authors: Koenig Serena , Carney Julia , Bendix Peter , Pape Jean William
Published: September 2009

This chapter begins with a description of the epidemiology of HIV/AIDS in Haiti. It then discusses HIV/AIDS prevention and treatment. It argues that despite ongoing political difficulties and limited resources, Haiti has launched one of the world's most effective responses to the HIV epidemic. International funding has played a contributing role in these programmatic successes, but more recent advances would not have been possible without the strong network of institutions that were firmly established and already providing prevention and treatment services for HIV/AIDS at the time that funding became available.
Single Spherical and Cylindrical Boundaries
Authors: Bordag M. , Klimchitskaya G. L. , Mohideen U. , Mostepanenko V. M.
Published: September 2009

This chapter presents important results obtained for the Casimir effect in the presence of spherical and cylindrical shells with various boundary conditions. It also includes the Casimir effect for a dielectric ball. The configuration of a spherical shell finds applications in the bag model of quantum chromodynamics. Mode summation for both interior and exterior regions is considered. Analytic continuation for obtaining the regularized vacuum energy, and the divergent contribution are analyzed. This allows for the renormalized vacuum energy for scalar, Electromagnetic, and spinor fields to be found. The case of nonzero temperature is considered on the basis of the general formalism presented in Chapter 5. The material in this chapter is focused on the technical methods necessary to calculate the Casimir effect in spherical and cylindrical geometry and on the analysis of the ultraviolet divergences.
The Casimir Interaction Between a Metal and a Dielectric
Authors: Bordag M. , Klimchitskaya G. L. , Mohideen U. , Mostepanenko V. M.
Published: September 2009

This chapter is devoted to the Casimir interaction between two parallel plates, one metallic and the other dielectric. It is shown that if the static permittivity of a dielectric plate is finite, the Lifshitz theory is thermodynamically consistent. In contrast, if the dc conductivity of the dielectric material is included in the model of the dielectric response, the Nernst theorem is violated. Experimentally, this opens up opportunities for the investigation of the role of the conductivity properties in the Casimir effect by keeping the metal plate fixed but considering dielectrics (semiconductors) with different conductivities. Such experiments have already been successfully performed and have yielded important new insights. Approximate analytical formulas for the Casimir energy density and pressure at zero temperature in the configuration of one metal and one dielectric plate are also presented.
Conclusions and Outlook
Authors: Bordag M. , Klimchitskaya G. L. , Mohideen U. , Mostepanenko V. M.
Published: September 2009

This chapter contains conclusions and some words about the outlook. The main conclusion is that at present there is already very good agreement between the theory, adapted for the case of real boundaries, and the measurements of the Casimir force. The generalization of this theory to the case of materials with spatial dispersion and a more fundamental approach to the Casimir effect at nonzero temperature are expected in the near future. The applications of the Casimir effect in both fundamental physics and nanotechnology appear very promising and may have an unexpected impact on basic scientific concepts and technological approaches.
Libertarian Theories of Intergenerational Justice
Authors: Steiner Hillel , Vallentyne Peter
Published: September 2009

This chapter discusses and assesses various libertarian positions on intergenerational justice. The implications of the following issues are examined: various provisos on appropriation (and thus versions of left- and right-libertarianism), whether rights protects choices or interests, generations being different sizes (and the issue of total vs. per capita shares of natural resources), overlapping vs. discrete generations, the duties of procreators to provide fair shares for their offspring, and gifts. A brief defense of a version of left-libertarianism is provided and it is suggested it provides no basis for a duty to conserve resources for future generations when (roughly) their per capita value of natural resources will be greater than the current per capita value (e.g., because of enhanced value from inherited technology).
Exploitation and Intergenerational Justice
Authors: Steiner Hillel , Vallentyne Peter
Published: September 2009

Injustice can take many forms of which exploitation is only one. This chapter explains and defends the basic idea of exploitation and its importance, and considers Marxian and non-Marxian variants. The notion of exploitation as a failure of fair reciprocity is explored and is then applied to intergenerational justice by looking at the possibility of a co-operative scheme that lasts over several generations.
A Transgenerational Difference Principle
Authors: Attas Daniel
Published: September 2009

Can Rawls's theory provide a framework for assessing obligations to future generations? Extending the veil of ignorance so that participants in the original position do not know to which generation they belong appears to fail in this endeavour. Earlier generations cannot improve their situation by ‘cooperating’ with later generations. Such circumstances, lacking mutuality, leave no room for an agreement or contract. Nevertheless, the original position can be reconstructed so as to model relations of mutuality between generations even if these are absent from the real world. This chapter assesses earlier attempts to do this and provides a rationale for viewing the just savings principle as a clause in the full formulation of the difference principle.
‘To Link or not to Link?’ The Problem of the Multinational Enterprise Group Business Structure
Authors: Mevorach Irit
Published: September 2009

Although enterprise groups are usually comprised of a bundle of separate legal entities, the traditional company law concepts of separate personality and limited liability might not match the economic reality of how groups operate. The question is therefore whether in dealing with group issues entity separateness should be kept for all purposes (adopting ‘entity law’) or whether in some circumstances ‘enterprise law’ should prevail, linking between the group members. This chapter overviews group problems as might arise in different areas of the law. It then considers the opposing views of entity and enterprise law proponents, appreciating the economic essence of legal separateness but also its limitations in the group context. It examines legal regimes' approaches to the group problem. It concludes by suggesting that the law should seek to balance between entity and enterprise law when proposing group solutions taking into account the objectives of the relevant area of the law and the type of group in hand.
Responsibility for Debts of MEG Members and Vulnerability of Intra-group Transactions
Authors: Mevorach Irit
Published: September 2009

This chapter focuses on the issue of group opportunism and examines the desirability of imposing various remedies in the course of insolvency within MEGs which could combat such behaviour and enhance fairness in distribution. It starts by examining the particular consideration that should be taken in regard to intra-group transactions in the vicinity of insolvency. It suggests that it should be possible to reverse intra-group transactions where these were detrimental to the affiliate in hand; yet such reversal of transactions should be avoided where in terms of economic realities the affiliate was not injured by the transaction. The chapter also considers the need for creditor protection from mismanagement by group members when insolvency is anticipated considering measures such as lifting the veil, wrongful trading, subordination and contribution orders, and their application in the international insolvency case.
Recognition and response to microbial infection in Drosophila
Authors: Broderick Nichole A. , Welchman David P. , Lemaitre Bruno
Published: September 2009

This chapter discusses the mechanisms whereby Drosophila recognize foreign microbes, the signalling systems that regulate adapted responses against them, and the effector mechanisms used to control them. It first focuses on the so-called systemic antimicrobial response. The second section of the chapter looks at local immune response, particularly gut epithelial immunity. The final section of the chapter discusses current research themes exploring the integration of local and systemic immunity, as well as their integration in host physiology.
Population genetics of insect immune responses
Authors: Juneja Punita , Lazzaro Brian P.
Published: September 2009

This chapter examines the evolutionary genetics of immune defence, interpreting molecular evolutionary patterns in light of protein function to draw insight into how the immune response adapts to pathogen pressures. Topics discussed include evolutionary patterns in the antimicrobial immune response and the evolutionary patterns in the antiviral immune response.
Partial Intentionalism
Authors: Livingston Paisley
Published: September 2009

This chapter defends a partial intentionalist approach that is distinct from the strongest forms of actualist intentionalism as well as the kind of conditionalist intentionalism advocated by some of the advocates of philosophically motivated interpretations of art, such as Thomas Wartenberg. The chapter argues that partial intentionalism is not vulnerable to the objections leveled against other versions of intentionalism. One of those objections hinges on the fallibility of intentions and of the art-making actions related to them. This chapter responds to this problem by discussing the conditions under which intentions are successfully realized in the work. Different approaches to this question are surveyed with reference to the work of H. P. Grice and his followers. The chapter defends a proposal involving a ‘meshing’ or congruence relation between intentions and features of the audio-visual display. The application of this type of success condition is illustrated in a discussion of the determination of the fictional content of Carl Theodor Dreyer's 1943 film, Day of Wrath.
Malebranche and the Cognitive Model of Causation
Authors: Ott Walter
Published: September 2009

Drawing on Descartes's “little souls” argument, Malebranche claims that attributing causal powers to bodies is in effect a category mistake. According to the cognitive model of causation Malebranche develops, only minds can have the kind of directedness causal powers require. This is not a rejection of the scholastic notion of power so much as a transformation of that notion in light of ontological mechanism. This chapter argues that many of Malebranche's most important arguments, including the famous “no necessary connection” argument, come into focus only when we have a firm grasp of Malebranche's intentionality requirement.
Causation and Explanation
Authors: Ott Walter
Published: September 2009

These two analyses of law, while consistent, allow us to explain Malebranche's complex attitude toward the connection between causation and explanation. Taken as summaries of God's volitions, laws cannot serve as explanations, since all bodily events have one and the same cause, namely, God. Taken, however, as conditionals, which themselves are made true in virtue of God's volitional activity, such laws can serve as explanations (though they can for that reason no longer be genuine causes).
Necessity
Authors: Ott Walter
Published: September 2009

Among Hume's most famous arguments, we find his own version of Malebranche's “no necessary connection” argument: roughly, if x had the power to produce y, it should be impossible to conceive of x without y. But since it is always possible to do this, there cannot be any real (mind‐independent) causal connections. This chapter shows how the argument comes into focus only when seen as an episode in the larger argument from nonsense. Although the conception of causation as logical necessitation, which forms the target of Hume's argument, has its source in the scholastics, it lives on in the cognitive and geometrical models. The chapter shows just how Hume's argument applies to these models and points toward Hume's own subjective account of necessity as the felt determination of the mind to form one perception on the basis of another.
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information
Authors: Bartoli Lisa , Fariselli Piero , Krogh Anders , Casadio Rita
Published: September 2009

Motivation:The widespread coiled-coil structural motif in proteins is known to mediate a variety of biological interactions. Recognizing a coiled-coil containing sequence and locating its coiled-coil domains are key steps towards the determination of the protein structure and function. Different tools are available for predicting coiled-coil domains in protein sequences, including those based on position-specific score matrices and machine learning methods.

Results: In this article, we introduce a hidden Markov model (CCHMM_PROF) that exploits the information contained in multiple sequence alignments (profiles) to predict coiled-coil regions. The new method discriminates coiled-coil sequences with an accuracy of 97% and achieves a true positive rate of 79% with only 1% of false positives. Furthermore, when predicting the location of coiled-coil segments in protein sequences, the method reaches an accuracy of 80% at the residue level and a best per-segment and per-protein efficiency of 81% and 80%, respectively. The results indicate that CCHMM_PROF outperforms all the existing tools and can be adopted for large-scale genome annotation.

Availability: The dataset is available at http://www.biocomp.unibo.it/∼lisa/coiled-coils. The predictor is freely available at http://gpcr.biocomp.unibo.it/cgi/predictors/cchmmprof/pred_cchmmprof.cgi.

Contact:  piero@biocomp.unibo.it
Inhibitory Effects of Ethyl Acetate Extract of Andrographis paniculata on NF‐κB Trans‐Activation Activity and LPS‐Induced Acute Inflammation in Mice
Authors: Chao Wen-Wan , Kuo Yueh-Hsiung , Hsieh Shie-Liang , Lin Bi-Fong
Published: September 2009

This study was to investigate anti‐inflammatory effect of Andrographis paniculata (Burm. f.) Nees (Acanthaceae) (AP). The effects of ethyl acetate (EtOAc) extract from AP on the level of inflammatory mediators were examined first using nuclear factor kappa B (NF‐κB) driven luciferase assay. The results showed that AP significantly inhibited NF‐κB luciferase activity and tumor necrosis factor α (TNF‐α), interleukin 6 (IL‐6), macrophage inflammatory protein‐2 (MIP‐2) and nitric oxide (NO) secretions from lipopolysaccharide (LPS)/interferon‐γ stimulated Raw264.7 cells. To further evaluate the anti‐inflammatory effects of AP in vivo, BALB/c mice were tube‐fed with 0.78 (AP1), 1.56 (AP2), 3.12 (AP3) and 6.25 (AP4) mg kg−1 body weight (BW)/day in soybean oil, while the control and PDTC (pyrrolidine dithiocarbamate, an anti‐inflammatory agent) groups were tube‐fed with soybean oil only. After 1 week of tube‐feeding, the PDTC group was injected with 50 mg kg−1 BW PDTC and 1 h later, all of the mice were injected with 15 mg kg−1 BW LPS. The results showed that the AP1, AP2, AP3 and PDTC groups, but not AP4, had significantly higher survival rate than the control group. Thus, the control, AP1, AP2, AP3 and PDTC groups were repeated for in vivo parameters. The results showed that the AP and PDTC groups had significantly lower TNF‐α, IL‐12p40, MIP‐2 or NO in serum or peritoneal macrophages and infiltration of inflammatory cells into the lung of mice. The AP1 group also had significantly lower MIP‐2 mRNA expression in brain. This study suggests that AP can inhibit the production of inflammatory mediators and alleviate acute hazards at its optimal dosages.
Claude Elwood Shannon 30 April 1916 — 24 February 2001
Authors: James Ioan
Published: September 2009

According to an anonymous obituary in The Times newspaper on 12 March 2001, Claude Shannon was

[a] playful genius who invented the bit, separated the medium from the message, and laid the foundations for all digital communications. … [He] single-handedly laid down the general rules of modern information theory, creating the mathematical foundations for a technical revolution. Without his clarity of thought and sustained ability to work his way through intractable problems, such advances as e-mail and the World Wide Web would not have been possible.

the great breakthroughs in understanding which heralded the convergence of computing and communications. To colleagues in the corridors at the Massachusetts Institute of Technology who used to warn each other about the unsteady advance of Shannon on his unicycle, it may have seemed improbable that he could remain serious for long enough to do any important work. Yet the unicycle was characteristic of his quirky thought processes, and became the topsy-turvy symbol of unorthodox progress towards unexpected theoretical insights.

The ability to make astonishing leaps beyond the intellects of his colleagues (all the more remarkable at MIT, the forcing house of technological theory) had to be acknowledged as genius, and Claude Shannon was recognised as a giant throughout the industry.
Sequential Monte Carlo methods for diffusion processes
Authors: Jasra Ajay , Doucet Arnaud
Published: September 2009

In this paper, we show how to use sequential Monte Carlo methods to compute expectations of functionals of diffusions at a given time and the gradients of these quantities w.r.t. the initial condition of the process. In some cases, via the exact simulation of the diffusion, there is no time discretization error, otherwise the methods use Euler discretization. We illustrate our approach on both high- and low-dimensional problems from optimal control and establish that our approach substantially outperforms standard Monte Carlo methods typically adopted in the literature. The methods developed here are appropriate for solving a certain class of partial differential equations as well as for option pricing and hedging.
Detection of Aspergillus DNA by a nested PCR assay is able to improve the diagnosis of invasive aspergillosis in paediatric patients
Authors: Hummel Margit , Spiess Birgit , Roder Julia , von Komorowski Gregor , Dürken Matthias , Kentouche Karim , Laws Hans J. , Mörz Handan , Hehlmann Ruediger , Buchheidt Dieter
Published: September 2009

Fungal infections are a leading cause of morbidity and mortality in severely immunocompromised patients and have been increasing in incidence in recent years. Invasive aspergillosis (IA) is the most common filamentous fungal infection and is, in adults as well as in children, difficult to diagnose. Several PCR assays to detectAspergillusDNA have been established, but so far, studies on molecular tools for the diagnosis of IA in children are few. We evaluated the results of a nested PCR assay to detectAspergillusDNA in clinical samples from paediatric and adolescent patients with suspected IA. Blood and non-blood samples from immunocompromised paediatric and adolescent patients with suspected invasive fungal infection were sent for processingAspergillusPCR to our laboratory. PCR results from consecutive patients from three university children's hospitals investigated between November 2000 and January 2007 were evaluated. Fungal infections were classified according to the EORTC classification on the grounds of clinical findings, microbiology and radio-imaging results. Two hundred and ninety-one samples from 71 patients were investigated for the presence ofAspergillusDNA by our previously described nested PCR assay. Two, 3 and 34 patients had proven, probable and possible IA, respectively. Sensitivity (calculated from proven and probable patients,n=5) and specificity (calculated from patients without IA,n=32) rates of the PCR assay were 80 and 81 %, respectively. Our nested PCR assay was able to detectAspergillusDNA in blood, cerebrospinal fluid and bronchoalveolar lavage samples from paediatric and adolescent patients with IA with high sensitivity and specificity rates.
Vertebral osteomyelitis and discitis due to Gardnerella vaginalis
Authors: Graham Simon , Howes Claire , Dunsmuir Robert , Sandoe Jonathan
Published: September 2009

Gardnerella vaginalisis a facultative anaerobic Gram-variable pleomorphic rod that forms part of the normal vaginal flora. It is most commonly associated with infection of the genital tract in women, but recognition of extravaginalG. vaginalisinfection is becoming more frequent. We describe an unusual case ofG. vaginalisvertebral osteomyelitis and discitis in a 38-year-old woman with no apparent predisposing factors.
Contribution of OmpK36 to carbapenem susceptibility in KPC-producing Klebsiella pneumoniae
Authors: Landman David , Bratu Simona , Quale John
Published: September 2009

Isolates of Klebsiella pneumoniae harbouring the carbapenemase KPC may have carbapenem MICs that remain in the susceptible range, and may therefore go unrecognized. To understand the mechanisms contributing to the variability in carbapenem MICs, 20 clinical isolates, all belonging to either of two clonal groups of KPC-possessing K. pneumoniae endemic to New York City, were examined. Expression of genes encoding KPC, the porins OmpK35 and OmpK36, and the efflux pump AcrAB was examined by real-time RT-PCR. Outer-membrane profiles of selected KPC-producing isolates were examined by SDS-PAGE, and proteins were identified by matrix-assisted laser desorption/ionization mass spectrometry. The identification of SHV and TEM β-lactamases and the genomic sequences of ompK35 and ompK36 were determined by PCR and DNA sequencing, respectively. For one clonal group, carbapenem MICs increased with decreasing expression of ompK36. A second clonal group also had carbapenem MICs that correlated with ompK36 expression. However, all of the isolates in this latter group continued to produce OmpK36, suggesting that porin configuration may affect entry of carbapenems. For isolates that had the greatest expression of ompK36, carbapenem MICs tended to be lower when determined by the broth microdilution technique, and scattered colonies were seen around the Etest zones of inhibition. All of the KPC-producing isolates were highly resistant to ertapenem, regardless of ompK36 expression. In conclusion, isolates of KPC-possessing K. pneumoniae that express ompK36 tend to have lower MICs to carbapenems and therefore may be more difficult to detect by clinical laboratories. Regardless of ompK36 expression, all of the KPC producers were consistently resistant to ertapenem.
Arabidopsis LON2 Is Necessary for Peroxisomal Function and Sustained Matrix Protein Import
Authors: Lingard Matthew J. , Bartel Bonnie
Published: September 2009

Relatively little is known about the small subset of peroxisomal proteins with predicted protease activity. Here, we report that the peroxisomal LON2 (At5g47040) protease facilitates matrix protein import into Arabidopsis (Arabidopsis thaliana) peroxisomes. We identified T-DNA insertion alleles disrupted in five of the nine confirmed or predicted peroxisomal proteases and found only two—lon2 and deg15, a mutant defective in the previously described PTS2-processing protease (DEG15/At1g28320)—with phenotypes suggestive of peroxisome metabolism defects. Both lon2 and deg15 mutants were mildly resistant to the inhibitory effects of indole-3-butyric acid (IBA) on root elongation, but only lon2 mutants were resistant to the stimulatory effects of IBA on lateral root production or displayed Suc dependence during seedling growth. lon2 mutants displayed defects in removing the type 2 peroxisome targeting signal (PTS2) from peroxisomal malate dehydrogenase and reduced accumulation of 3-ketoacyl-CoA thiolase, another PTS2-containing protein; both defects were not apparent upon germination but appeared in 5- to 8-d-old seedlings. In lon2 cotyledon cells, matrix proteins were localized to peroxisomes in 4-d-old seedlings but mislocalized to the cytosol in 8-d-old seedlings. Moreover, a PTS2-GFP reporter sorted to peroxisomes in lon2 root tip cells but was largely cytosolic in more mature root cells. Our results indicate that LON2 is needed for sustained matrix protein import into peroxisomes. The delayed onset of matrix protein sorting defects may account for the relatively weak Suc dependence following germination, moderate IBA-resistant primary root elongation, and severe defects in IBA-induced lateral root formation observed in lon2 mutants.
Unique Features of Plant Cleavage and Polyadenylation Specificity Factor Revealed by Proteomic Studies
Authors: Zhao Hongwei , Xing Denghui , Li Qingshun Quinn
Published: September 2009

Cleavage and polyadenylation of precursor mRNA is an essential process for mRNA maturation. Among the 15 to 20 protein factors required for this process, a subgroup of proteins is needed for both cleavage and polyadenylation in plants and animals. This subgroup of proteins is known as the cleavage and polyadenylation specificity factor (CPSF). To explore the in vivo structural features of plant CPSF, we used tandem affinity purification methods to isolate the interacting protein complexes for each component of the CPSF subunits using Arabidopsis (Arabidopsis thaliana ecotype Landsberg erecta) suspension culture cells. The proteins in these complexes were identified by mass spectrometry and western immunoblots. By compiling the in vivo interaction data from tandem affinity purification tagging as well as other available yeast two-hybrid data, we propose an in vivo plant CPSF model in which the Arabidopsis CPSF possesses AtCPSF30, AtCPSF73-I, AtCPSF73-II, AtCPSF100, AtCPSF160, AtFY, and AtFIPS5. Among them, AtCPSF100 serves as a core with which all other factors, except AtFIPS5, are associated. These results show that plant CPSF possesses distinct features, such as AtCPSF73-II and AtFY, while sharing other ortholog components with its yeast and mammalian counterparts. Interestingly, these two unique plant CPSF components have been associated with embryo development and flowering time controls, both of which involve plant-specific biological processes.
The Metabolic Role of the Legume Endosperm: A Noninvasive Imaging Study
Authors: Melkus Gerd , Rolletschek Hardy , Radchuk Ruslana , Fuchs Johannes , Rutten Twan , Wobus Ulrich , Altmann Thomas , Jakob Peter , Borisjuk Ljudmilla
Published: September 2009

Although essential for normal seed development in the legumes, the metabolic role of the endosperm remains uncertain. We designed noninvasive nuclear magnetic resonance tools for the in vivo study of key metabolites in the transient liquid endosperm of intact pea (Pisum sativum) seeds. The steady-state levels of sucrose, glutamine, and alanine could be monitored and their distribution within the embryo sac visualized. Seed structure was digitalized as a three-dimensional model, providing volume information for distinct seed organs. The nuclear magnetic resonance method, combined with laser microdissection, isotope labeling, in situ hybridization, and electron microscopy, was used to contrast the wild-type endosperm with that of a mutant in which embryo growth is retarded. Expression of sequences encoding amino acid and sucrose transporters was up-regulated earlier in the endosperm than in the embryo, and this activity led to the accumulation of soluble metabolites in the endosperm vacuole. The endosperm provides a temporary source of nutrition, permits space for embryo growth, and acts as a buffer between the maternal organism and its offspring. The concentration of sucrose in the endosperm vacuole is developmentally controlled, while the total amount accumulated depends on the growth of the embryo. The endosperm concentration of glutamine is a limiting factor for protein storage. The properties of the endosperm ensure that the young embryo develops within a homeostatic environment, necessary to sustain embryogenesis. We argue for a degree of metabolite-mediated control exerted by the endosperm on the growth of, and assimilate storage by, the embryo.
A Small GTPase of the Rab Family Is Required for Root Hair Formation and Preinfection Stages of the Common Bean–RhizobiumSymbiotic Association
Authors: Blanco Flavio Antonio , Peltzer Meschini Eitel , Zanetti María Eugenia , Aguilar O. Mario
Published: September 2009

Legume plants are able to establish a symbiotic relationship with soil bacteria from the genus Rhizobium, leading to the formation of nitrogen-fixing root nodules. Successful nodulation requires both the formation of infection threads (ITs) in the root epidermis and the activation of cell division in the cortex to form the nodule primordium. This study describes the characterization of RabA2, a common bean (Phaseolus vulgaris) cDNA previously isolated as differentially expressed in root hairs infected with Rhizobium etli, which encodes a protein highly similar to small GTPases of the RabA2 subfamily. This gene is expressed in roots, particularly in root hairs, where the protein was found to be associated with vesicles that move along the cell. The role of this gene during nodulation has been studied in common bean transgenic roots using a reverse genetic approach. Examination of root morphology in RabA2 RNA interference (RNAi) plants revealed that the number and length of the root hairs were severely reduced in these plants. Upon inoculation with R. etli, nodulation was completely impaired and no induction of early nodulation genes (ENODs), such as ERN1, ENOD40, and Hap5, was detected in silenced hairy roots. Moreover, RabA2 RNAi plants failed to induce root hair deformation and to initiate ITs, indicating that morphological changes that precede bacterial infection are compromised in these plants. We propose that RabA2 acts in polar growth of root hairs and is required for reorientation of the root hair growth axis during bacterial infection.