bluuebunny/crossref_metadata_2025 huggingface dataset:
Positive and negative alcohol‐related consequences: Associations with past drinking
Authors: Lee Christine M. , Maggs Jennifer L. , Neighbors Clayton , Patrick Megan E.
Published: March 2010

While recent attention suggests that positive and negative alcohol‐related expectancies are important determinants of alcohol use, less is known about what types of consequences young people report actually experiencing when drinking alcohol. The present study (N = 742, 54% women) examined positive (Fun/Social, Relaxation/Coping, Positive Image) and negative (Physical, Behavioral, Driving) consequences of alcohol use among individuals with prior drinking histories who completed surveys the summer before their first year at university. Fun/Social consequences were reported more frequently than any negative consequences. Alcohol consequences were associated with drinking behaviors. In particular, positive Fun/Social consequences and negative Physical and Driving‐related consequences were related to alcohol frequency, alcohol quantity, and frequency of heavy episodic drinking. Positive consequences were at least as strongly associated with drinking as were negative consequences. The possible role of Fun/Social consequences in the escalation and maintenance of high‐risk drinking is discussed.
Prologue: At the Symposium
Authors: Livingstone Niall , Nisbet Gideon
Published: March 2010

We are at a symposium in the house of Lysiteles of Athens in the last month of the 111th Olympiad, 328 BCE. The guest of honour is Charicles, a handsome and athletic young Athenian of good family, lately returned from abroad. Dinner has been lavish – the finest Copaic eels and the largest sea pike, Boeotian in their luxury – but this has now been cleared away. The slaves have distributed garlands of myrtle and roses, the pretty flute-girls have struck up their tune, and the symposiarch, master of festivities, has declared his rules for the mixing and drinking of the wine (old Chian, and chilled with snow). Next comes the question of entertainment. The company immediately rejects philosophy and gambling, but Ctesiphon's proposal is taken up with enthusiasm: they will play at riddles, each expressed in the form of a short and witty poem. These, then, are epigrams.
Introduction: Rock, Paper, Scissors
Authors: Livingstone Niall , Nisbet Gideon
Published: March 2010

Epigram: EPI-GRAMMA, a text written or incised upon something. ‘Inscription’ is one obvious translation of the root meaning, and epigram began with inscriptions: texts carved in stone to fix cultural memory. Epigram and epigraphy, the modern study of inscriptions, are two sides of the same linguistic coin. The classical Greek epigraphic habit manifested itself across many different contexts. Inscriptions broadcast the laws and decrees of the city-state, the polis, and secured the meaning of monuments and tombs against a forgetful future. Cut into trophies and statues, they celebrated victory in war and sport. Inscriptions were unavoidably costly in skilled labour, and competed for the attention of the passer-by with many others of their kind. Official decrees and honorific inscriptions were as long as their elaborate phrasing dictated, but for more personal messages these factors could combine to create a pressure to keep the text short and to the point. A small minority of these inscriptions were in verse.
I The Inscriptional Beginnings of Literary Epigram
Authors: Livingstone Niall , Nisbet Gideon
Published: March 2010

As was seen in the Introduction, the generic identity of epigram is governed by two senses of the Greek preposition epi: an epigram may be physically inscribed ‘on’ an object, or ‘on the subject of’ an object (or something else: a person, an event). This chapter is concerned with epigrams physically inscribed on a stone or other object. In spite of the fact that inscribed epigram comes first chronologically (beginning as early as the eighth century BCE), includes some of the most famous lines in Greek literature (such as those above), and numbers famous names such as Simonides among its exponents, it can sometimes be treated as the poor relation of literary epigram, which had its heyday in the Hellenistic period (see Chapter 2). There is a perception that epigram comes into its own once it has ‘escaped’, as it were, from its stone or other physical medium, and is thus at liberty to use its words to create a virtual object in the reader's mind (or not, as the poet chooses).
The Interplay between the State, the Market, and Culture in Shaping Civil Society: A Case Study of the People's Solidarity for Participatory Democracy in South Korea
Authors: Moon Seungsook
Published: March 2010

After the formal end of military rule in the late 1980s, a new type of voluntary association commonly called “citizens' organizations” emerged in Korean civil society. Pursuing progressive social change through legal and policy reforms, citizens' organizations became the voice of revived civil society in urban Korea and enjoyed public trust until the mid-2000s, when their influence began to wane. Using in-depth interviews and fieldwork data on the People's Solidarity for Participatory Democracy (PSPD), one of the most influential citizens' organizations, this paper examines how the specific social meanings of civil society informed the roles that the state and the market played in the rise and relative decline of the PSPD and how class and gender affected individual access to it. This focus on the interplay among culture, the state, and the market enables us to move beyond cultural relativism and liberal universalism concerning the theoretical and empirical debate on civil society.
Zinc and the immune system
Authors: Rink Lothar
Published: March 2010

Zn is an essential trace element for all organisms. In human subjects body growth and development is strictly dependent on Zn. The nervous, reproductive and immune systems are particularly influenced by Zn deficiency, as well as by increased levels of Zn. The relationship between Zn and the immune system is complex, since there are four different types of influence associated with Zn. (1) The dietary intake and the resorption of Zn depends on the composition of the diet and also on age and disease status. (2) Zn is a cofactor in more than 300 enzymes influencing various organ functions having a secondary effect on the immune system. (3) Direct effects of Zn on the production, maturation and function of leucocytes. (4) Zn influences the function of immunostimulants used in the experimental systems. Here we summarize all four types of influence on the immune function. Nutritional aspects of Zn, the physiology of Zn, the influence of Zn on enzymes and cellular functions, direct effects of Zn on leucocytes at the cellular and molecular level, Zn-altered function of immunostimulants and the therapeutic use of Zn will be discussed in detail.
Moral Responsibility and Mental Illness: A Case Study
Authors: BROOME MATTHEW R. , BORTOLOTTI LISA , MAMELI MATTEO
Published: March 2010

Various authors have argued that progress in the neurocognitive and neuropsychiatric sciences might threaten the commonsense understanding of how the mind generates behavior, and, as a consequence, it might also threaten the commonsense ways of attributing moral responsibility, if not the very notion of moral responsibility. In the case of actions that result in undesirable outcomes (e.g., someone being harmed), the commonsense conception—which is reflected in sophisticated ways in the legal conception—tells us that there are circumstances in which the agent is entirely and fully responsible for the bad outcome (and deserves to be punished accordingly) and circumstances in which the agent is not at all responsible for the bad outcome (and thereby the agent does not deserve to be punished).
Does Public Health Have a Personality (and If So, Does It Matter If You Don't Like It)?
Authors: COGGON JOHN
Published: March 2010

“Dissecting Bioethics,” edited by Tuija Takala and Matti Häyry, welcomes contributions on the conceptual and theoretical dimensions of bioethics.

The section is dedicated to the idea that words defined by bioethicists and others should not be allowed to imprison people's actual concerns, emotions, and thoughts. Papers that expose the many meanings of a concept, describe the different readings of a moral doctrine, or provide an alternative angle to seemingly self-evident issues are therefore particularly appreciated.

The themes covered in the section so far include dignity, naturalness, public interest, community, disability, autonomy, parity of reasoning, symbolic appeals, and toleration.

All submitted papers are peer reviewed. To submit a paper or to discuss a suitable topic, contact Tuija Takala at tuija.takala@helsinki.fi.
The relationship between P-wave dispersion and diastolic functions in diabetic children
Authors: Köken Reşit , Demir Tevfik , Şen Tolga Altuğ , Kundak Ahmet Afşin , Öztekin Osman , Alpay Faruk
Published: March 2010

Objective

The aim of this study was to investigate the relations between the P-wave dispersion and diastolic functions in type 1 diabetic children.

Patients

A total of 33 diabetic patients without any cardiovascular disease, with a mean age of 12.3 plus or minus 4.2 years, and 29 healthy controls, with a mean age of 10.4 plus or minus 3.9 years were enrolled for this study. Left and right ventricular functions were assessed by using standard pulsed-wave Doppler echocardiography. P-wave dispersion was calculated by measuring minimum and maximum P-wave duration values on the surface electrocardiogram.

Results

For the diabetic patients, P-wave maximum duration and dispersion was found to be significantly increased compared with healthy controls. Likewise, mitral A velocity and A velocity time integral was significantly increased while the isovolumic contraction time was significantly higher in the diabetics. In tricuspid valve measurements, however, A velocity time integral was found to be significantly higher, whereas the deceleration time was significantly lower in the diabetics. No relation was found between the left ventricle diastolic functions and duration of diabetes, HbA1c levels and P-wave dispersion in the diabetic children. No correlation was found between the diastolic functions and P-wave minimum, maximum duration, and dispersion for all the participants.

Conclusion

In type-1 diabetic children, the diastolic functions of both the ventricles were observed to be affected negatively together. Diabetes might be causing the prolongation of P-wave dispersion, but there was no relationship between the diastolic functions and P-wave dispersion in the diabetic children.
THE INCIDENCE OF INFORMATIONAL CASCADES AND THE BEHAVIOR OF TRADE INTERARRIVAL TIMES DURING THE STOCK MARKET BUBBLE
Authors: Patterson Douglas M. , Sharma Vivek
Published: March 2010

This paper investigates the possible formation of informational cascades by traders in a random sample of 8,000 NYSE stock-days experiencing extreme price changes during 1998–2001. Our cascade measure is designed to detect informational cascades in high-frequency stock market prices. First, we find evidence of cascades on approximately 12% of the days when the NYSE experiences, on average, large price increases. This percentage increases to about 20% on days experiencing large price decreases, on average. Second, we find evidence that the interarrival times of trades in those stocks exhibiting significant informational cascades are generated by a nonlinear stochastic process. Third, the evidence supporting cascades is largely confined to smaller stocks and to stocks followed by fewer security analysts. Last, the occurrence of cascades appears to correlate with the incorporation of fundamental information into security prices.
Small, Focused Technical Conferences
Authors: Lyman Charles
Published: March 2010

The feature article in this issue is a prelude to the Microbeam Analysis Society (MAS) Topical Conference on electron backscatter diffraction (EBSD) to be held at the University of Wisconsin, May 24–26, 2010. The popularity of the EBSD technique is growing rapidly. This analytical method is capable of both identifying crystalline phases and determining the orientation of grains and second phases. Phase analysis by EBSD combined with elemental analysis by x-ray emission spectrometry provides the SEM with extraordinary analytical power. Maps of crystal grain orientations are widely used in metallurgical and geological research.
The Role of Intersectional Stereotypes on Evaluations of Gay and Lesbian Political Candidates
Authors: Doan Alesha E. , Haider-Markel Donald P.
Published: March 2010

Social scientists are increasingly taking a more complex theoretical approach to the role of stereotyping in the electorate's evaluation of political candidates. Within this literature, most studies investigate the impact of one stereotype on the public's evaluation of candidates from an underrepresented group. We build on and extend this literature by exploring what we term “intersectional stereotyping”: The role of stereotypes in shaping the electorate's evaluation of political candidates who share dual membership in stigmatized groups—women and sexual minorities. We empirically examine the impact of intersectional stereotyping in a unique 2003 survey of national adults. Our results indicate that gender, both of the respondent and the candidate, plays a key role in shaping attitudes toward gay and lesbian political candidates. These findings suggest that intersectional stereotyping plays a nuanced role in evaluations of candidates; in certain contexts gender stereotypes are more significant, and at other times stereotypes about sexual minorities appear to be driving evaluations of candidates.
Marriage and Bourgeois Respectability
Authors: Marso Lori Jo
Published: March 2010

Feminist critics of the institution of marriage point to its tendency to reproduce and solidify a gendered division of labor, norms of dependency and protection, and mandated monogamy. While I support the feminist call for a decoupling of state benefits, such as rights to health care and legal proxy, from the institution of marriage in light of discrimination against same-sex couples who are denied the right to marry, in this essay I draw attention to a separate but related issue. I focus here on what I consider one of the most troubling aspects of marriage for feminists, one highlighted by Simone de Beauvoir in her classic and still timely critique of marriage in The Second Sex (1952): the fact that marriage automatically confers bourgeois respectability on its participants. Even as we oppose antigay marriage legislation and recognize that marriage can protect vulnerable parties by guaranteeing health care, equity upon divorce, tax benefits, and so forth, feminists must continue to refuse the bourgeois respectability that is so deeply linked with the institution of marriage. Having the state accord legitimacy to some kinds of intimate relationships and consensual sex, but not others, goes against basic ideas of feminist freedom articulated most convincingly, I argue, by Beauvoir. While arguing this position, however, I will also ask whether only the relatively privileged are able to refuse the bourgeois respectability that marriage promises.
Kantian nonideal theory and nuclear proliferation
Authors: Doyle Thomas E.
Published: March 2010

Recent revelations of Iran’s hitherto undisclosed uranium enrichment programs have once again incited western fears that Tehran seeks nuclear weapons’ capability. Their fears seem motivated by more than the concern for compliance with the Nuclear Nonproliferation Treaty (NPT). Rather, they seem strongly connected to the western moral assumptions about what kind of government or people can be trusted with a nuclear arsenal. In this paper, I critically examine the western assumptions of the immorality of contemporary nuclear proliferation from an international ethical stance that otherwise might be expected to give it unequivocal support – the stance of Kantian nonideal theory. In contrast to the uses of Kant that were prominent during the Cold War, I advance and apply a sketch of a Kantian nonideal theory that specifies the conditions (althoughstrictconditions) under which nuclear proliferation for states like Iran is morally permissibleeven thoughthe NPT forbids it.
Enforcement and capacity building in international cooperation
Authors: Urpelainen Johannes
Published: March 2010

I examine enforcement and capacity building in international cooperation. In a game-theoretic model, a wealthy donor gives foreign aid in exchange for policy implementation by a poor recipient. The recipient has limited capacity to comply with international agreements, so the donor is not sure if cooperation failure is caused by willful disobedience or unintended error. I show that if perceived cooperation failure prompts reciprocal suspension of cooperation, the donor and recipient have a common preference for capacity building. But when the donor can request compensation for perceived cooperation failure, it only chooses to build capacity if cooperation is otherwise impossible. Consequently, the choice of enforcement mechanism shapes capacity building. This result lays a foundation for a genuine synthesis between the enforcement and managerialist schools of compliance. It generates falsifiable hypotheses and explains why reciprocal enforcement, which unfortunately inflicts collateral damage on the victim, is often considered legitimate.
Entropy theory for movement of moisture in soils
Authors: Singh Vijay P.
Published: March 2010

An entropy theory is formulated for one‐dimensional movement of moisture in unsaturated soils in the vertically downward direction. The theory is composed of five parts: (1) Tsallis entropy, (2) principle of maximum entropy, (3) specification of information on soil moisture in terms of constraints, (4) maximization of the Tsallis entropy, and (5) derivation of the probability distributions of soil moisture. The theory is applied to determine the soil moisture profile under three conditions: (1) the moisture is maximum at the soil surface and decreases downward to a minimum value at the bottom of the soil column (it may be near the water table); (2) the moisture is minimum at the soil surface and increases downward to a maximum value at the end of the soil column (this case is the opposite of case 1); and (3) the moisture at the soil surface is low and increases downward up to a distance and then decreases up to the bottom (this case combines case 2 and case 1). The entropy‐based soil moisture profiles are tested using experimental observations reported in the literature, and properties of these profiles are enumerated.
Sumoylation of eIF4E activates mRNA translation
Authors: Xu Xiang , Vatsyayan Jaya , Gao Chenxi , Bakkenist Christopher J , Hu Jing
Published: March 2010

Eukaryotic translation initiation factor 4E (eIF4E) is the cap‐binding protein that binds the 5′ cap structure of cellular messenger RNAs (mRNAs). Despite the obligatory role of eIF4E in cap‐dependent mRNA translation, how the translation activity of eIF4E is controlled remains largely undefined. Here, we report that mammalian eIF4E is regulated by SUMO1 (small ubiquitin‐related modifier 1) conjugation. eIF4E sumoylation promotes the formation of the active eIF4F translation initiation complex and induces the translation of a subset of proteins that are essential for cell proliferation and preventing apoptosis. Furthermore, disruption of eIF4E sumoylation inhibits eIF4E‐dependent protein translation and abrogates the oncogenic and antiapoptotic functions associated with eIF4E. These data indicate that sumoylation is a new fundamental regulatory mechanism of protein synthesis. Our findings suggest further that eIF4E sumoylation might be important in promoting human cancers.
Updated biotechnological approaches developed for 2,7′‐cyclolignan production1
Authors: Lautié Emmanuelle , Fliniaux Marc‐André , Villarreal Maria Luisa
Published: March 2010

2,7′‐Cyclolignans constitute a group of compounds regularly employed in clinical contexts due to their antiviral and anticancer properties as expressed in a number of already available designed drugs. Possibilities for other therapeutic developments are indicated. All commercial preparations actually originate from a single compound, podophyllotoxin, currently extracted from a few limited‐in‐abundance species of Podophyllum. This supply problem has stimulated considerable interest in the development of alternative strategies offering greater sustainable availability of the compound at affordable costs. Approaches such as plant breeding and micropropagation of the high‐producing Podophyllum species have been explored with the aim of establishing production of these compounds. Since 20 years of exploration of the total chemical synthesis of podophyllotoxin has not proved economically viable, extensive research has now been undertaken to find methods for stimulating the accumulation of 2,7′‐cyclolignans using tissue cultures. Both undifferentiated and differentiated cell cultures, mainly from Linum, Podophyllum, Juniperus, Callitris, Anthriscus and Forsynthia genera, have been reported. Although considerable progress has been made concerning the concentration and productivity of certain strains of Linum album, no economically viable production system has been established. Exploration and development of biosynthetical pathways leading to 2,7′‐cyclolignans may open paths for future metabolic engineering, such as the bioconversion of deoxypodophyllotoxin to epipodophyllotoxin employing a human hepatic enzyme heterologously expressed in Escherichia coli.
ESCRT & Co
Authors: Roxrud Ingrid , Stenmark Harald , Malerød Lene
Published: March 2010

Components of the ESCRT (endosomal sorting complex required for transport) machinery mediate endosomal sorting of ubiquitinated membrane proteins. They are key regulators of biological processes important for cell growth and survival, such as growth‐factor‐mediated signalling and cytokinesis. In addition, enveloped viruses, such as HIV‐1, hijack and utilize the ESCRTs for budding during virus release and infection. Obviously, the ESCRT‐facilitated pathways require tight regulation, which is partly mediated by a group of interacting proteins, for which our knowledge is growing. In this review we discuss the different ESCRT‐modulating proteins and how they influence ESCRT‐dependent processes, for example, by acting as positive or negative regulators or by providing temporal and spatial control. A number of the interactors influence the classical ESCRT‐mediated process of endosomal cargo sorting, for example, by modulating the interaction between ubiquitinated cargo and the ESCRTs. Certain accessory proteins have been implicated in regulating the activity or steady‐state expression levels of the ESCRT components, whereas other interactors control the cellular localization of the ESCRTs, for example, by inducing shuttling between cytosol and nucleus or endosomes. In conclusion, the discovery of novel interactors has and will extend our knowledge of the biological roles of ESCRTs.
Chinese Pidgin Russian
Authors: Shapiro Roman
Published: March 2010

The much-understudied Chinese Pidgin Russian (CPR) has existed at the Chinese–Russian border since at least the 18th century. Unlike many Western-based pidgins, it was formed in a territory where the lexifying language (Russian) was dominant. It also uses a typical inflecting language as its lexifier and an isolating language (Chinese) as its substrate. This paper considers the influence of both ‘parent’ languages at all CPR levels. The sources of CPR include: pidgin records and descriptions; ‘Russian’ textbooks compiled for the Chinese going to Russia; and works of literature depicting contacts between the Russians and indigenous peoples of Siberia, who often spoke a variety of CPR. Some of these sources are rarely accessible to Western linguists. The paper discusses all key aspects of CPR: history (both of the pidgin and its study), phonology (segmental inventory, stress, tone), morphology (verbs vs. non-verbs, final particles), syntax (syntactic roles, sentence and phrase word order, postpositions and prepositions, comparatives), and vocabulary (synonyms, loanwords, structural and semantic calques, ‘diminutive politeness’). The study provides new translations and etymologies for ‘difficult’ CPR words and sentences.
Vestiges of etymological gender in Malacca Creole Portuguese
Authors: Baxter Alan N.
Published: March 2010

This paper is concerned with the nature of etymological gender inflection in Malacca Creole Portuguese and its place in the diachrony of the language. The discussion considers pairs of items with etymological gender inflection and human referents. Speaker intuitions of the word-pair vitality are assessed by word recognition and judgments of the acceptability of test words in specific syntactic contexts. The items surveyed are initially contemplated as a type of derivational morphology. Subsequently, the question is posed as to whether this etymological gender morphology could have a contextual dimension, and it is observed that some limited traces thereof may be found. The incorporation and retention of etymological gender inflection is attributed to second language input to the creole, involving early second language lexical and phrasal development, influenced by a combination of communication pragmatics, salience, and potential Indian substrate features. It is suggested that such input could be both an early diachronic occurrence or could have arisen through an ongoing diglossia involving a wider lectal grid that may have existed until the 19th century.
Bazaar Malay topics
Authors: Bao Zhiming , Aye Khin Khin
Published: March 2010

Bazaar Malay is a Malay-lexified pidgin with a Chinese substratum spoken in the marketplace of Singapore (and elsewhere in Southeast Asia). Although it is no longer a lingua franca in Singapore today, it is nevertheless still spoken by older Singaporeans. Like Chinese and Malay, Bazaar Malay is a topic-prominent language. We document three types of the Bazaar Malay topic construction and show that they are identical to the topic structures found in Chinese. The degree of convergence in the topic construction between Chinese and Bazaar Malay, and between Chinese and Singapore English, supports the systemic view of substratum transfer.
Duality Theory for Variable Costs in Joint Production
Authors: LaFrance Jeffrey T. , Pope Rulon D.
Published: March 2010

Duality methods for incomplete systems of consumer demand equations are adapted to the dual structure of variable cost functions in joint production. This allows identification of necessary and sufficient restrictions on technology and cost so that conditional factor demands can be written as functions of input prices, fixed inputs, and cost. These are observable when variable inputs are chosen and committed to production, hence the identified restrictions allow ex ante conditional demands to be studied using observable data. This class of production technologies is consistent with all von Neumann–Morgenstern utility functions when ex post production and/or output prices are uncertain.
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
Authors: Johannes Frank , Wardenaar René , Colomé-Tatché Maria , Mousson Florence , de Graaf Petra , Mokry Michal , Guryev Victor , Timmers H.Th. Marc , Cuppen Edwin , Jansen Ritsert C.
Published: March 2010

Motivation: ChIP-chip and ChIP-seq technologies provide genome-wide measurements of various types of chromatin marks at an unprecedented resolution. With ChIP samples collected from different tissue types and/or individuals, we can now begin to characterize stochastic or systematic changes in epigenetic patterns during development (intra-individual) or at the population level (inter-individual). This requires statistical methods that permit a simultaneous comparison of multiple ChIP samples on a global as well as locus-specific scale. Current analytical approaches are mainly geared toward single sample investigations, and therefore have limited applicability in this comparative setting. This shortcoming presents a bottleneck in biological interpretations of multiple sample data.

Results: To address this limitation, we introduce a parametric classification approach for the simultaneous analysis of two (or more) ChIP samples. We consider several competing models that reflect alternative biological assumptions about the global distribution of the data. Inferences about locus-specific and genome-wide chromatin differences are reached through the estimation of multivariate mixtures. Parameter estimates are obtained using an incremental version of the Expectation–Maximization algorithm (IEM). We demonstrate efficient scalability and application to three very diverse ChIP-chip and ChIP-seq experiments. The proposed approach is evaluated against several published ChIP-chip and ChIP-seq software packages. We recommend its use as a first-pass algorithm to identify candidate regions in the epigenome, possibly followed by some type of second-pass algorithm to fine-tune detected peaks in accordance with biological or technological criteria.

Availability: R source code is available at http://gbic.biol.rug.nl/supplementary/2009/ChromatinProfiles/

Access to Chip-seq data: GEO repository GSE17937

Contact:  f.johannes@rug.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integrative mixture of experts to combine clinical factors and gene markers
Authors: Lê Cao Kim-Anh , Meugnier Emmanuelle , McLachlan Geoffrey J.
Published: March 2010

Motivation: Microarrays are being increasingly used in cancer research to better characterize and classify tumors by selecting marker genes. However, as very few of these genes have been validated as predictive biomarkers so far, it is mostly conventional clinical and pathological factors that are being used as prognostic indicators of clinical course. Combining clinical data with gene expression data may add valuable information, but it is a challenging task due to their categorical versus continuous characteristics. We have further developed the mixture of experts (ME) methodology, a promising approach to tackle complex non-linear problems. Several variants are proposed in integrative ME as well as the inclusion of various gene selection methods to select a hybrid signature.

Results: We show on three cancer studies that prediction accuracy can be improved when combining both types of variables. Furthermore, the selected genes were found to be of high relevance and can be considered as potential biomarkers for the prognostic selection of cancer therapy.

Availability: Integrative ME is implemented in the R package integrativeME (http://cran.r-project.org/).

Contact:  k.lecao@uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
TiSGeD: a database for tissue-specific genes
Authors: Xiao Sheng-Jian , Zhang Chi , Zou Quan , Ji Zhi-Liang
Published: March 2010

Summary: The tissue-specific genes are a group of genes whose function and expression are preferred in one or several tissues/cell types. Identification of these genes helps better understanding of tissue–gene relationship, etiology and discovery of novel tissue-specific drug targets. In this study, a statistical method is introduced to detect tissue-specific genes from more than 123 125 gene expression profiles over 107 human tissues, 67 mouse tissues and 30 rat tissues. As a result, a novel subject-specialized repository, namely the tissue-specific genes database (TiSGeD), is developed to represent the analyzed results. Auxiliary information of tissue-specific genes was also collected from biomedical literatures.

Availability:  http://bioinf.xmu.edu.cn/databases/TiSGeD/index.html

Contact:  appo@bioinf.xmu.edu.cn; zhiliang.ji@gmail.com
Central venous pressure at emergency room presentation predicts cardiac rehospitalization in patients with decompensated heart failure
Authors: Uthoff Heiko , Thalhammer Christoph , Potocki Mihael , Reichlin Tobias , Noveanu Markus , Aschwanden Markus , Staub Daniel , Arenja Nisha , Socrates Thenral , Twerenbold Raphael , Mutschmann‐Sanchez Sarah , Heinisch Corinna , Jaeger Kurt A. , Mebazaa Alexandre , Mueller Christian
Published: March 2010

Aims

To investigate the relationship between central venous pressure (CVP) at presentation to the emergency room (ER) and the risk of cardiac rehospitalization and mortality in patients with decompensated heart failure (DHF).

Methods and results

Central venous pressure was determined non‐invasively using high‐resolution compression sonography at presentation in 100 patients with DHF. Cardiac hospitalizations and cardiac and all‐cause mortality were assessed as a function of continuous CVP levels and predefined CVP categories (low <6 cm H2O, intermediate 6–23 cm H2O, and high >23 cm H2O). Endpoints were adjudicated blinded to CVP. At presentation, mean age was 78 ± 11 years, 60% of patients were male, mean B‐type natriuretic peptide level was 1904 ± 1592 pg/mL, and mean CVP was 13.7 ± 7.0 cm H2O (range 0–33). During follow‐up (median 12 months), 25 cardiac rehospitalizations, 26 cardiac deaths, and 7 non‐cardiac deaths occurred. Univariate and stepwise multivariate Cox regression analysis revealed an independent relationship between CVP and cardiac rehospitalization (HR 1.09, 95% CI 1.01–1.18, P = 0.034). Kaplan–Meier analyses confirmed a stepwise increase in cardiac rehospitalization for low‐to‐high CVP (log‐rank test P = 0.015). No association between CVP and (cardiac) mortality was detectable.

Conclusion

Central venous pressure at ER presentation in patients with DHF is an independent predictor of cardiac rehospitalization but not of cardiac and all‐cause mortality.
Molecular epidemiology of vancomycin-resistant Enterococcus faecium strains isolated from haematological malignancy patients in a research hospital in Turkey
Authors: Kirdar S. , Sener A. G. , Arslan U. , Yurtsever S. G.
Published: March 2010

Infections and outbreaks of vancomycin-resistant enterococci (VRE) still appear to be rare in Turkey. In the present study, VRE strains isolated during an outbreak in a haematology unit of a training and research hospital in Turkey were typed and their antimicrobial-resistance patterns were characterized by molecular methods. Twelve vancomycin-resistantEnterococcus faeciumstrains isolated from patients with haematological malignancies were investigated by PCR for the presence of genes encoding resistance to vancomycin, tetracycline, chloramphenicol, gentamicin and erythromycin. Their clonal relationship was evaluated by PFGE and multilocus sequence typing. All strains were resistant to vancomycin and erythromycin, and had thevanAandermBgenes, respectively. PFGE was used to determine the presence of two pulsotypes and determine their subtypes. Pulsotype A belonged to sequence type (ST) 17 and pulsotype B belonged to ST 78. All strains with thevanAgene were not the same clone, indicating multiple acquisitions of resistant isolates, even over such a short time period.
Emergence and genetic diversity of El Tor Vibrio cholerae O1 that possess classical biotype ctxB among travel-associated cases of cholera in Japan
Authors: Morita Masatomo , Ohnishi Makoto , Arakawa Eiji , Yamamoto Shouji , Nair G. Balakrish , Matsushita Shigeru , Yokoyama Keiko , Kai Akemi , Seto Kazuko , Watanabe Haruo , Izumiya Hidemasa
Published: March 2010

Vibrio cholerae O1 are classified into two biotypes, classical and El Tor, each encoding a biotype-specific cholera toxin. However, El Tor strains have recently emerged with a classical cholera-toxin genotype (El Tor variant). We characterized El Tor strains of V. cholerae O1 from travel-associated cases of cholera in Japan isolated from 1991 to 2006 by cholera toxin B subunit gene (ctxB) typing and by molecular epidemiological methods. ctxB in the biotype El Tor shifted from the El Tor-specific type to the classical-specific type around 1993, and this type fully dominated the later half of the 1990s. Based on the results of PFGE and multilocus variable-number tandem repeat analysis, strains of the classical biotype remained diverse from those of El Tor biotype. The El Tor biotype strains formed multiple minor clusters and intermingled with each other irrespective of their origins and toxin types. El Tor variant strains are widespread in Asian countries and show significant genetic diversity, indicating that their spread is a result of multiclonal expansion rather than spread from a single clone.
Characterization of the haem-uptake system of the equine pathogen Streptococcus equi subsp. equi
Authors: Meehan Mary , Burke Fiona M. , Macken Susan , Owen Peter
Published: March 2010

Streptococcus equipossesses a haem-uptake system homologous to that ofStreptococcus pyogenesandStreptococcus zooepidemicus.The system consists of two ligand-binding proteins (Shr and Shp) and proteins (HtsA–C) with homology to an ABC transporter. The haem-uptake system ofS. equidiffers from that ofS. pyogenesandS. zooepidemicusin that Shr is truncated by two-thirds. This study focused on the SeShr, SeShp and SeHtsA proteins ofS. equi. Analysis of shr,shpandshphtsAknockout mutants showed that all three proteins were expressedin vitroand that expression was upregulated under conditions of iron limitation. SeShr possesses no membrane-/cell wall-spanning sequences and was shown to be secreted. Both SeShp and SeHtsA were confirmed to be envelope-associated. Recombinant SeShp and SeHtsA proteins have been previously shown to bind haem and SeHtsA could capture haem from SeShp. This report extends these studies and shows that both SeShp and SeHtsA can sequester haem from haemoglobin but not from haemoglobin–haptoglobin complexes. Like full-length Shr, SeShr possesses haemoglobin and haemoglobin–haptoglobin binding ability but unlike full-length Shr, it lacks haem- or fibronectin-binding capabilities. Analysis of SeShr truncates showed that residues within and upstream of the near transporter (NEAT) domain are required for this ligand binding. Structural predictions suggest that truncation of NEAT1 in SeShr accounts for its impaired ability to bind haem. Haem and haemoglobin restored to almost normal the impaired growth rates of wild-typeS. equicultured under iron-limiting conditions. However, no difference in the growth rates of wild-type and mutants could be detected under thein vitrogrowth conditions tested.
Characterization and inactivation of the membrane-bound polyol dehydrogenase in Gluconobacter oxydans DSM 7145 reveals a role in meso-erythritol oxidation
Authors: Voss Jörn , Ehrenreich Armin , Liebl Wolfgang
Published: March 2010

The growth ofGluconobacter oxydansDSM 7145 onmeso-erythritol is characterized by two stages: in the first stage,meso-erythritol is oxidized almost stoichiometrically tol-erythrulose according to the Bertrand–Hudson rule. The second phase is distinguished from the first phase by a global metabolic change from membrane-boundmeso-erythritol oxidation tol-erythrulose assimilation with concomitant accumulation of acetic acid. The membrane-associated erythritol-oxidizing enzyme was found to be encoded by a gene homologous tosldAknown from other species of acetic acid bacteria. Disruption of this gene in the genome ofG. oxydansDSM 7145 revealed that the membrane-bound polyol dehydrogenase not only oxidizesmeso-erythritol but also has a broader substrate spectrum which includes C3–C6 polyols andd-gluconate and supports growth on these substrates. Cultivation ofG. oxydansDSM 7145 on different substrates indicated that expression of the polyol dehydrogenase was not regulated, implying that the production of biomass ofG. oxydansto be used as whole-cell biocatalysts in the biotechnological conversion ofmeso-erythritol tol-erythrulose, which is used as a tanning agent in the cosmetics industry, can be conveniently carried out with glucose as the growth substrate.
A tale of CIN—the Cannabis Infringement Notice scheme in Western Australia
Authors: Lenton Simon , Allsop Steve
Published: March 2010

Aims To describe the development and enactment of the Western Australian (WA) Cannabis Infringement Notice scheme and reflect on the lessons for researchers and policy‐makers interested in the translation of policy research to policy practice.

Methods An insiders' description of the background research, knowledge transfer strategies and political and legislative processes leading to the enactment and implementation of the WA Cannabis Control Act 2003. Lenton and Allsop were involved centrally in the process as policy‐researcher and policy‐bureaucrat.

Results In March 2004, Western Australia became the fourth Australian jurisdiction to adopt a ‘prohibition with civil penalties’ scheme for possession and cultivation of small amounts of cannabis. We reflect upon: the role of research evidence in the policy process; windows for policy change; disseminating findings when apparently no one is listening; the risks and benefits of the researcher as advocate; the differences between working on the inside and outside of government; and the importance of relationships, trust and track record.

Conclusions There was a window of opportunity and change was influenced by research that was communicated by a reliable and trusted source. Those who want to conduct research that informs policy need to understand the policy process more clearly, look for and help create emerging windows that occur in the problem and political spheres, and make partnerships with key stakeholders in the policy arena. The flipside of the process is that, when governments change, policy born in windows of opportunity can be a casualty.
Pharmacodynamic and efficacy studies of the novel proteasome inhibitor NPI‐0052 (marizomib) in a human plasmacytoma xenograft murine model
Authors: Singh Ajita V. , Palladino Michael A. , Lloyd George Kenneth , Potts Barbara C. , Chauhan Dharminder , Anderson Kenneth C.
Published: March 2010

Our previous study showed that the novel proteasome inhibitor NPI‐0052 induces apoptosis in multiple myeloma (MM) cells resistant to conventional and bortezomib (Velcade™, Takeda, Boston, MA, USA) therapies. In vivo studies using human MM‐xenografts demonstrated that NPI‐0052 is well tolerated, prolongs survival, and reduces tumour recurrence. These preclinical studies provided the basis for an ongoing phase‐1 clinical trial of NPI‐0052 in relapsed/refractory MM patients. Here we performed pharmacodynamic (PD) studies of NPI‐0052 using human MM xenograft murine model. Our results showed that NPI‐0052: (i) rapidly left the vascular compartment in an active form after intravenous (i.v.) administration, (ii) inhibited 20S proteasome chymotrypsin‐like (CT‐L, β5), trypsin‐like (T‐L, β2), and caspase‐like (C‐L, β1) activities in extra‐vascular tumours, packed whole blood (PWB), lung, liver, spleen, and kidney, but not brain and (iii) triggered a more sustained (>24 h) proteasome inhibition in tumours and PWB than in other organs (<24 h). Tissue distribution analysis of radiolabeled compound (3H‐NPI‐0052) in mice demonstrated that NPI‐0052 left the vascular space and entered organs as the parent compound. Importantly, treatment of MM.1S‐bearing mice with NPI‐0052 showed reduced tumour growth without significant toxicity, which was associated with prolonged inhibition of proteasome activity in tumours and PWB but not normal tissues.
Gillnet fishing drives lake‐migrating brown trout to near extinction in the Lake Päijänne region, Finland
Authors: SYRJÄNEN J. , VALKEAJÄRVI P.
Published: March 2010

Abstract Wild stocks of brown trout,Salmo truttaL., collapsed in Finnish inland waters during the 20th Century because dams prevented upstream migration, and low water quality and stream dredging weakened reproduction. The demise in migratory stocks was coupled with overfishing, mainly by gillnetting on lakes. Consequently, the migratory spawning stocks have diminished to negligible levels. The remaining stocks exhibit restricted immigration and emigration, are supplemented by continuous stocking, and their natural genetic diversity is affected by human activities. In recent years, various recovery actions have been implemented including stream channel restorations, fish passage facilities constructed and stocking of eggs and smolts. Gillnetting has also been regulated by banning certain mesh sizes, and catch‐and‐release of wild trout is spreading amongst sport fishers. However, these measures seem to be inadequate and almost no recovery of migratory populations has been reported. The problem of by‐catch in intensive gillnetting continues to threaten stocks and creates disputes between stakeholders.
The psychosocial effect of Tai Chi on nursing home residents
Authors: Lee Linda YK , Lee Diana TF , Woo Jean
Published: March 2010

Aim. To determine the psychosocial effect of Tai Chi on nursing home residents.

Background. Moving into a nursing home usually imposes a certain degree of psychosocial challenge to older people. However, there is limited evidence suggesting a promising intervention that can promote the psychosocial health for this group. Although previous studies suggest that Tai Chi has the potential to enhance psychosocial well‐being, existing evidence is deemed scarce and thus imposes a limitation on drawing out conclusions on this matter.

Design. Non‐equivalent pretest–posttest control group design.

Methods. A convenience sample of 139 residents from six nursing homes in Hong Kong was recruited for this study. The experimental group (n = 66) participated in a 26‐week Tai Chi programme, while the control group (n = 73) continued its normal daily activities. The outcome measures included state self‐esteem, the physical and mental component of health‐related quality of life, social support network and social support satisfaction. Resident satisfaction was identified as a covariate because it demonstrated significant correlation with the outcome variables and, likewise, showed significant difference between the two study groups at baseline. Doubly multivariate analysis of covariance was performed to examine the effect of the intervention.

Results. Results indicate significant Group × Time interactions, with the experimental group experiencing significant improvement in the composite outcome of state self‐esteem, the physical component of health‐related quality of life and the mental component of health‐related quality of life across the 26‐week study period [F(6, 131) = 2·61,p = 0·02)]. No significant changes were detected regarding the effect of the Tai Chi programme on social support.

Conclusion. Tai Chi practice is beneficial for nursing home residents.

Relevance to clinical practice. Tai Chi has unique characteristics that are particularly suitable in the practice of health exercise for nursing home residents. The inclusion of Tai Chi in residential care practice for older people is recommended.