bluuebunny/crossref_metadata_2025 huggingface dataset:
Activation of the ERK signal transduction pathway by Epstein–Barr virus immediate-early protein Rta
Authors: Lee Yu-Hsiu , Chiu Ya-Fang , Wang Wen-Hung , Chang Li-Kwan , Liu Shih-Tung
Published: September 2008

BRCA1-associated protein 2 (BRAP2) is known to interact with the kinase suppressor of Ras 1 (KSR1), inhibiting the ERK signal transduction cascade. This study found that an Epstein–Barr virus (EBV) immediate-early protein, Rta, is a binding partner of BRAP2 in yeast and confirmed the bindingin vitroby a glutathioneS-transferase pull-down assay andin vivoby co-immunoprecipitation in 293(maxi-EBV) cells. Binding studies also showed that Rta and KSR1 interacted with the C-terminal 202 aa region in BRAP2. Additionally, Rta appeared to prevent the binding of KSR1 to BRAP2, activating the ERK signal transduction pathway and the transcription of an EBV immediate-early gene,BZLF1. Activation of the ERK signal transduction pathway by Rta may be critical for the maintenance of the lytic state of EBV.
Exploring the potential of group II introns to inactivate human immunodeficiency virus type 1
Authors: Nazari Reza , Joshi Sadhna
Published: September 2008

This study examined whether insertion of a mobile group II intron into infectious human immunodeficiency virus type 1 (HIV-1) provirus DNA could inhibit virus replication. Introns targeted against two sites within the integrase-coding region were used. The intron-inserted HIV-1 provirus DNA clones were isolated and tested for virus replication. Similar amounts of HIV-1 RNA, Gag protein and progeny virus were produced from HIV-1 provirus DNA and intron-inserted HIV-1 provirus DNA. However, when the progeny virus was tested for its infectivity, although the group II intron-inserted HIV-1 RNA was packaged and reverse-transcribed, the dsDNA failed to integrate, as expected in the absence of a functional integrase, and virus replication was aborted. These results demonstrate that group II introns can confer ‘complete’ inhibition of HIV-1 replication at the intended step and should be further exploited for HIV-1 gene therapy and other targeted genetic repairs.
Association of dengue virus NS1 protein with lipid rafts
Authors: Noisakran Sansanee , Dechtawewat Thanyaporn , Avirutnan Panisadee , Kinoshita Taroh , Siripanyaphinyo Uamporn , Puttikhunt Chunya , Kasinrerk Watchara , Malasit Prida , Sittisombut Nopporn
Published: September 2008

During the replication of dengue virus, a viral non-structural glycoprotein, NS1, associates with the membrane on the cell surface and in the RNA replication complex. NS1 lacks a transmembrane domain, and the mechanism by which it associates with the membrane remains unclear. This study aimed to investigate whether membrane-bound NS1 is present in lipid rafts in dengue virus-infected cells. Double immunofluorescence staining of infected HEK-293T cells revealed that NS1 localized with raft-associated molecules, ganglioside GM1 and CD55, on the cell surface. In a flotation gradient centrifugation assay, a small proportion of NS1 in Triton X-100 cell lysate consistently co-fractionated with raft markers. Association of NS1 with lipid rafts was detected for all four dengue serotypes, as well as for Japanese encephalitis virus. Analysis of recombinant NS1 forms showed that glycosylated NS1 dimers stably expressed in HEK-293T cells without an additional C-terminal sequence, or with a heterologous transmembrane domain, failed to associate with lipid rafts. In contrast, glycosylphosphatidylinositol-linked recombinant NS1 exhibited a predilection for lipid rafts. These results indicate an association of a minor subpopulation of NS1 with lipid rafts during dengue virus infection and suggest that modification of NS1, possibly lipidation, is required for raft association.
Medea SUMOylation restricts the signaling range of the Dpp morphogen in the Drosophila embryo
Authors: Miles Wayne O. , Jaffray Ellis , Campbell Susan G. , Takeda Shugaku , Bayston Laura J. , Basu Sanjay P. , Li Mingfa , Raftery Laurel A. , Ashe Mark P. , Hay Ronald T. , Ashe Hilary L.
Published: September 2008

Morphogens are secreted signaling molecules that form concentration gradients and control cell fate in developing tissues. During development, it is essential that morphogen range is strictly regulated in order for correct cell type specification to occur. One of the best characterized morphogens is Drosophila Decapentaplegic (Dpp), a BMP signaling molecule that patterns the dorsal ectoderm of the embryo by activating the Mad and Medea (Med) transcription factors. We demonstrate that there is a spatial and temporal expansion of the expression patterns of Dpp target genes in SUMO pathway mutant embryos. We identify Med as the primary SUMOylation target in the Dpp pathway, and show that failure to SUMOylate Med leads to the increased Dpp signaling range observed in the SUMO pathway mutant embryos. Med is SUMO modified in the nucleus, and we provide evidence that SUMOylation triggers Med nuclear export. Hence, Med SUMOylation provides a mechanism by which nuclei can continue to monitor the presence of extracellular Dpp signal to activate target gene expression for an appropriate duration. Overall, our results identify an unusual strategy for regulating morphogen range that, rather than impacting on the morphogen itself, targets an intracellular transducer.
Proline 54 trans‐cis isomerization is responsible for the kinetic partitioning at the last‐step photocycle of photoactive yellow protein
Authors: Lee Byoung‐Chul , Hoff Wouter D.
Published: September 2008

Photoactive yellow protein (PYP), a blue‐light photoreceptor for Ectothiorhodospira halophila, has provided a unique system for studying protein folding that is coupled with a photocycle. Upon receptor activation by blue light, PYP proceeds through a photocycle that includes a partially folded signaling state. The last‐step photocycle is a thermal recovery reaction from the signaling state to the native state. Bi‐exponential kinetics had been observed for the last‐step photocycle; however, the slow phase of the bi‐exponential kinetics has not been extensively studied. Here we analyzed both fast and slow phases of the last‐step photocycle in PYP. From the analysis of the denaturant dependence of the fast and slow phases, we found that the last‐step photocycle proceeds through parallel channels of the folding pathway. The burial of the solvent‐accessible area was responsible for the transition state of the fast phase, while structural rearrangement from the compact state to the native state was responsible for the transition state of the slow phase. The photocycle of PYP was linked to the thermodynamic cycle that includes both unfolding and refolding of the fast‐ and slow‐phase intermediates. In order to test the hypothesis of proline‐limited folding for the slow phase, we constructed two proline mutants: P54A and P68A. We found that only a single phase of the last‐step photocycle was observed in P54A. This suggests that there is a low energy barrier between trans to cis conformation in P54 in the light‐induced state of PYP, and the resulting cis conformation of P54 generates a slow‐phase kinetic trap during the photocycle‐coupled folding pathway of PYP.
Live colouration, morphology and habitat of Vanneaugobius dollfusi (Gobiidae) in the northern Adriatic Sea
Authors: Kovačić M
Published: September 2008

The rare deepwater gobiid fish Vanneaugobius dollfusi, hitherto described only from limited material identified in collections, was encountered and collected during scuba dives at depths of 30–45 m in the northern Adriatic Sea.
Effects of classical insect hormones on the expression profiles of a lipase gene from the cotton bollworm (Helicoverpa armigera)
Authors: Sui Yi‐Peng , Wang Jin‐Xing , Zhao Xiao‐Fan
Published: September 2008

A 967‐bp cDNA, encoding a 31 kDa lipase with an isoelectric point of 8.8, was cloned from Helicoverpa armigera. The gene was named Ha‐lipase. The Ha‐lipase transcript was present in the head‐thorax, midgut and fat body but not in integument and haemocytes from 5th instar larvae, with higher expression levels in feeding larvae than that in molting larvae. In the midgut, transcription of the gene during the 5th instar larval period was lower than during the 6th instar period. While in the fat body, lipase was not found at the 6th instar stage but only at the 5th instar stage. The expression of Ha‐lipase could be up‐regulated by methoprene and down‐regulated by methoxyfenozide (RH‐2485) and 20‐hydroxyecdysone (20E).
Gene structure and expression of nanos (nos) and oskar (osk) orthologues of the vector mosquito, Culex quinquefasciatus
Authors: Juhn J. , Marinotti O. , Calvo E. , James A. A.
Published: September 2008

The products of the maternal‐effect genes, nanos (nos) and oskar (osk), are important for the development of germ cells in insects. Furthermore, these genes have been proposed as candidates for donating functional DNA regulatory sequences for use in gene drive systems to control transmission of mosquito‐borne pathogens. The nos and osk genes of the cosmopolitan vector mosquito, Culex quinquefasciatus, encode proteins with domains common to orthologues found in other mosquitoes. Expression analyses support the conclusion that the role of these genes is conserved generally among members of the nematocera. Hybridization in situ analyses reveal differences in mRNA distribution in early embryos in comparison with the cyclorraphan, Drosophila melanogaster, highlighting a possible feature in the divergence of the clades each insect represents.
Seminal macrophages in ejaculates from men with couple infertility
Authors: Pelliccione Fiore , D’Angeli Anatolia , Cordeschi Giuliana , Mihalca Radu , Ciociola Francesco , Necozione Stefano , Francavilla Felice , Francavilla Sandro
Published: September 2008

Seminal macrophages are occasionally reported though their relevance in the evaluation of human ejaculate is unknown. Activated macrophages, engaging in sperm phagocytosis (spermiophages), might represent a marker of innate immunosystem activation. We investigated whether the presence of spermiophages in non‐leukocytospermic ejaculates from men complaining for couple infertility is associated with altered sperm features. Four hundred and thirty‐four ejaculates were retrospectively analysed after excluding samples with antisperm antibodies, or a leukocyte number ≥1 × 106/mL. Semen quality was compared in samples with or without spermiophages detected with transmission electron microscope. Presence of spermiophages, observed in 27% of ejaculates, was associated with a decreased number of sperm total count (p < 0.0001), of sperm forward motility (p = 0.048), and to an increased fraction of degenerating sperm (p = 0.0002) compared to ejaculates without spermiophages. A low number of total ejaculated sperm and an increased number of degenerating sperm independently predicted the presence of spermiophages (odds ratio 1.72; 95% confidence intervals 1.10 to 2.28 and odds ratio 1.85; 95% confidence intervals 1.19 to 2.88 respectively). Data demonstrate that activated macrophages, a marker of the innate immunosystem activation, are frequently observed in non‐leukocytospermic ejaculates of men suffering for couple infertility and this may be associated with altered sperm parameters. Ultrastructural analysis gives qualitative informations, hence sensitive quantitative tests should better define the association between semen activated macrophages and oligoasthenozoospermia and the possible relevance of this finding in the clinical evaluation of the male partner of couple infertility.
Effects of tumour necrosis factor alpha and interleukin‐6 on progesterone and calcium ionophore‐induced acrosome reaction
Authors: Lampiao F. , Du Plessis S. S.
Published: September 2008

For human spermatozoa to successfully fertilize the oocyte, they need to undergo a timely acrosome reaction (AR). Factors which disturb the AR may lead to fertilization failure. The objective of this study was to investigate the effects of two cytokines namely tumour necrosis factor alpha (TNF‐α) and interleukin‐6 (IL‐6) on the spontaneous, calcium ionophore‐induced and progesterone‐induced human sperm AR. Twenty‐two normal semen samples were treated with increasing concentrations of TNF‐α and IL‐6 after spermatozoa were isolated by a double wash swim‐up method. The AR was induced by calcium ionophore A23187 and progesterone. The AR was determined by using fluorescein isothiacyanate Pisum sativum agglutinin and observed under fluorescence microscope. Both TNF‐α and IL‐6 could decrease the spontaneous, ionophore and progesterone‐induced AR (p < 0.05) in a dose‐dependent manner. TNF‐α showed a more potent inhibiting effect than IL‐6 by inhibiting the AR at lower concentrations. This study has demonstrated that TNF‐α and IL‐6 play a role in inhibiting both the non‐physiological as well as physiologically elicited AR by calcium ionophore and progesterone respectively.
The effect of habitat management on home‐range size and survival of rural Norway rat populations
Authors: Lambert M. S. , Quy R. J. , Smith R. H. , Cowan D. P.
Published: September 2008

Norway rat Rattus norvegicus populations are usually controlled with toxic baits, but this approach is increasingly recognized as having negative welfare and environmental impacts. An integrated strategy that relies less on rodenticides is therefore required. Here we investigate the possibility of using a resource‐based approach to rat population management.

Structurally complex habitats provide rat populations with nest sites and opportunities to avoid predators; modifying habitats to reduce structural complexity might reduce their potential to support rat populations. As part of an integrated approach, this could be more sustainable than relying exclusively on lethal control. However, in order to target habitat management efforts most effectively with minimum impact on other species, an understanding of habitat utilization by Norway rats is required.

In this study, rat populations on farms in the north‐east of England were monitored by radio‐tracking and population counts before and after a single phase of habitat modification. Rats living near farm buildings utilized areas with high levels of cover; habitat modification reduced the survival rate and size of these rat populations. Rats living in field margins also preferred areas with high levels of cover, but they had significantly bigger home ranges than rats living near farm buildings and were largely unaffected by small‐scale habitat management.

Synthesis and applications. Our results indicate that habitat management near farm buildings has the potential to reduce the size of rat populations. As part of an integrated approach, this technique offers a way of reducing reliance on rodenticides. Habitat use by rats within the wider farm landscape suggests that land management practices have the potential to influence the size and distribution of rat populations; many game‐rearing practices and environmental policies designed to create habitats for ‘desirable’ farm wildlife, inadvertently create desirable habitats for rats.
Overexpression of an ADP‐ribose pyrophosphatase, AtNUDX2, confers enhanced tolerance to oxidative stress in Arabidopsis plants
Authors: Ogawa Takahisa , Ishikawa Kazuya , Harada Kazuo , Fukusaki Eiichiro , Yoshimura Kazuya , Shigeoka Shigeru
Published: September 2008

Mutant pqr‐216 from an Arabidopsis activation‐tagged line showed a phenotype of increased tolerance to oxidative stress after treatment with 3 μm paraquat (PQ). Based on the phenotype of transgenic plants overexpressing the genes flanking the T‐DNA insert, it was clear that enhanced expression of a Nudix (nucleoside diphosphates linked to some moiety X) hydrolase gene, AtNUDX2 (At5g47650), was responsible for the tolerance. It has been reported that the AtNUDX2 protein has pyrophosphatase activities towards both ADP‐ribose and NADH (Ogawa et al., 2005). Interestingly, the pyrophosphatase activity toward ADP‐ribose, but not NADH, was increased in pqr‐216 and Pro35S:AtNUDX2 plants compared with control plants. The amount of free ADP‐ribose was lower in the Pro35S:AtNUDX2 plants, while the level of NADH was similar to those in control plants under both normal conditions and oxidative stress. Depletion of NAD+ and ATP resulting from activation of poly(ADP‐ribosyl)ation under oxidative stress was observed in the control Arabidopsis plants. Such alterations in the levels of these molecules were significantly suppressed in the Pro35S:AtNUDX2 plants. The results indicate that overexpression of AtNUDX2, encoding ADP‐ribose pyrophosphatase, confers enhanced tolerance of oxidative stress on Arabidopsis plants, resulting from maintenance of NAD+ and ATP levels by nucleotide recycling from free ADP‐ribose molecules under stress conditions.
Exploring informed choice in the context of prenatal testing: findings from a qualitative study
Authors: Potter Beth K. , O’Reilly Natasha , Etchegary Holly , Howley Heather , Graham Ian D. , Walker Mark , Coyle Doug , Chorny Yelena , Cappelli Mario , Boland Isabelle , Wilson Brenda J.
Published: September 2008

Purpose  This study explored whether and how a sample of women made informed choices about prenatal testing for foetal anomalies; its aim was to provide insights for future health policy and service provision.

Methods  We conducted semi‐structured interviews with 38 mothers in Ottawa, Ontario, all of whom had been offered prenatal tests in at least one pregnancy. Using the Multi‐dimensional Measure of Informed Choice as a general guide to analysis, we explored themes relevant to informed choice, including values and knowledge, and interactions with health professionals.

Results  Many, but not all, participants seemed to have made informed decisions about prenatal testing. Values and knowledge were interrelated and important components of informed choice, but the way they were discussed differed from the way they have been presented in scientific literature. In particular, ‘values’ related to expressions of women’s moral views or ideas about ‘how life should be lived’ and ‘knowledge’ related to the ways in which women prioritized and interpreted factual information, through their own and others’ experiences and in ‘thinking through’ the personal implications of testing. While some women described non‐directive discussions with health professionals, others perceived testing as routine or felt pressured to accept it.

Conclusions  Our findings suggest a need for maternity care providers to be vigilant in promoting active decision making about prenatal testing, particularly around the consideration of personal implications. Further development of measures of informed choice may be necessary to fully evaluate decision support tools and to determine whether prenatal testing programmes are meeting their objectives.
Phenotypic analysis of circulating dendritic cells during the second half of human gestation
Authors: Holloway Judith A. , Thornton Catherine A. , Diaper Norma D. , Howe David T. , Warner John O.
Published: September 2008

Dendritic cells (DCs) have been characterized as having an immature phenotype in infants when compared with adults; but it is unclear whether the phenotype or function of these populations changes during human intrauterine development. Three‐colour flow cytometry was used to phenotype fetal/neonatal circulating DCs during the second half (>20‐wk gestation) of pregnancy, (n = 34) and adults (n = 9). DCs were identified from peripheral blood mononuclear cells (PBMCs) or cord blood mononuclear cells (CBMCs) as staining brightly for HLA‐DR but negative for T cell, B cell, monocyte, and NK cell lineage markers. The surface molecule of interest was detected in a third colour. During gestation CD34, a marker of immaturity was significantly higher, and CD4, a differentiation marker, was significantly lower than adult levels. The percentage of CD11c+ cells did not differ significantly at any age, although a trend to reduced intensity of expression at earlier stages of gestation was observed. Significantly fewer DCs expressed the IgG receptors CD32 and CD64 at all gestations. The percentage of HLA‐DR+/lin‐ cells expressing CD40 was lowest at 20–23 wks and was always significantly lower on DCs from cord blood vs. adult blood. Similarly, the percentage of CD86+ and CD54+ DCs was significantly lower than adults throughout gestation. Thus, immaturity of cord blood DCs is likely to arise as a consequence of decreased ability to take up antigen (at least via IgG‐mediated mechanisms) and reduced provision of co‐stimulation.
Food allergy: Is strict avoidance the only answer?
Authors: Allen C. W. , Campbell D. E. , Kemp A. S.
Published: September 2008

It is an immunological paradigm that avoidance of food allergen may reduce the risk or prevent immunological reactions and conversely that a greater exposure increases the magnitude of the immune response. Consequently, food allergen avoidance has been recommended to reduce the risk of sensitization in infants and to prevent clinical reactions in children with positive skin prick tests (SPT). In the latter setting, it is hoped that avoidance may either promote or at least not retard the development of tolerance. Animal studies, however, have demonstrated that tolerance to food allergens may be induced by either large (high zone tolerance) or small (low zone tolerance) doses, whereas doses in between may actually stimulate immune responses. In this review, we discuss whether strict allergen avoidance is always the most appropriate strategy for preventing or managing IgE‐mediated food allergy.
Prenatal Differentiation of Bovine Oviductal Epithelium: An Electron Microscopic Study
Authors: Kenngott R. A.‐M. , Neumüller C. , Sinowatz F.
Published: September 2008

In this study, we investigated the ultrastructural changes during the prenatal differentiation of oviductal epithelium in 16 bovine embryos and fetuses from CRL of 18.0 cm to a CRL of 94.0 cm. Ciliated and secretory cells of bovine uterine tube, a derivative of the Müllerian duct, differentiate to distinct development stages in the prenatal period. The typical cellular pattern, which is generally characteristic for the adult bovine oviduct, is also obtained during fetal life. In the early stages (CRL 18.0/20.4 cm), the bovine oviductal epithelium appears mostly undifferentiated. The epithelial cells show only a few mitochondria, some cisternae of rough endoplasmic reticulum (rER) and a small Golgi‐complex. Most of the cytoplasm is filled with a large amount of glycogen, which decreases during later development. Interspersed between the undifferentiated epithelial cells, a few cells undergoing ciliogenesis can be observed. Ciliogenesis increased significantly during the later prenatal developmental stages. At a CRL of 55.0 cm, ciliated cells appear fully differentiated with mature cells covering their luminal surface. Formation of cilia usually use the acentriolar pathway. Fibrous granules occurred initially in association with the Golgi‐apparatus and r(ER) in the supranuclear cytoplasm. Fibrous granules later fuse with deuterosomes and give rise to procentrioles, which are translocated to the luminal plasma membrane. There they become arranged in a line just beneath the apical cell membrane and further differentiate to basal bodies from which the formation of cilia and striated rootlets take place. Clear signs of differentiation of secretory cells were first seen in our material in fetuses with a CRL of 51.0 cm and 64.0 cm. These cells contain a well developed rER and Golgi‐apparatus with dilated cisterns. In the supranuclear cytoplasm, the number of secretory granules continuously increases during later development and the cells adapt to the morphology of mature secretory cells at the CRL 94.0 cm.
Morphometric Study of the Tricuspid Valve in Dogs
Authors: Alves J. R. , Wafae N. , Beu C. C. , Tuzuki L. C. , Ruiz C. R. , Wafae G. C.
Published: September 2008

An anatomical study of the tricuspid valve was performed in the hearts of 45 dogs using a method of dissection which preserves the integrity of the valve. Morphometrical criteria such as the width of the cusp base and larger depth of cusp and morphological criteria such as the number of tendinous cords, the perimeter of the fibrous ring and the properties of the papillary muscle were adopted for the characterization of a cusp. The tricuspid valve was not consistent with three cusps, but it was observed to present 2, 4 or 5 cusps in 68% of the cases.
Cold Stress Injury during the Pod‐Filling Phase in Chickpea (Cicer arietinum L.): Effects on Quantitative and Qualitative Components of Seeds
Authors: Kaur G. , Kumar S. , Nayyar H. , Upadhyaya H. D.
Published: September 2008

Chilling stress (<10 °C) is detrimental for chickpea, especially at the reproductive phase and leads to abortion of flowers, pods and impaired seed filling, causing severe reduction in yield. The information on the effects of low temperature during different pod‐filling stages on quality and quantity of developing seeds is lacking in chickpea and hence this study. In this study, chickpea plants growing under warm conditions of the glasshouse were subjected to cold conditions of the field at the two stages, (a) early pod‐filling and (b) late pod‐filling, and subsequently analysed for stress injury in terms of electrolyte leakage (EL), 2,3,5‐triphenyl tetrazolium chloride reduction, relative leaf water content and total chlorophyll content in the leaves of control and cold‐stressed plants. Cold stress caused elevation of EL but reduced all the other parameters. Sucrose content decreased significantly in the leaves of cold‐stressed plants. The differences between the effects of stress at two stages on the total plant dry weight were small and insignificant. The seed growth rate, seed fill duration, seed number, and average seed weight and size decreased greatly in the plants cold‐stressed at the late pod‐filling stage than those stressed at the early pod‐filling stage. Greater reduction was observed in starch, proteins, soluble sugars, fat, crude fibre and storage protein fractions in the seeds of the plants cold‐stressed at the late pod‐filling stage. This coincided with a larger decrease in sucrose content, the activities of sucrose synthase, invertase and starch synthase observed at this stage. The germination and growth potential were, however, inhibited to a greater extent in seeds of plants stressed at the early pod‐filling stage.
The (dis)appearance of the dying patient in generalist hospital and care home nurses' talk about the patient
Authors: Schou Kirsten , Alvsvåg Herdis , Blåka Gunnhild , Gjengedal Eva
Published: September 2008

Abstract  This article explores interview data from a study of 50 Norwegian generalist nurses' focus group accounts of caring for dying patients in the hospital and care home. An eclectic discourse analytic approach was applied to nurses' accounts of the patient and three discursive contexts of reference to the patient were identified: the ‘taken as read’ patient, the patient paired with particular characteristics and the patient as psychologically present. Talk about the patient falls mainly into the first two contexts, which position the patient in relation to three closely related discursive processes: individualization, anonymization and objectification. The third context presents the patient as a person with a particular identity. The analysis is discussed in a broader philosophical and sociological context in which we return to some of the theoretical work on death and dying of the 1990s and the topic of sequestration. We suggest that nurses' talk about the patient can be heard to participate in a continuing sequestration of the dying patient in healthcare institutions focused on ‘result‐oriented’ care.
Testing in Semiparametric Models with Interaction, with Applications to Gene–Environment Interactions
Authors: Maity Arnab , Carroll Raymond J. , Mammen Enno , Chatterjee Nilanjan
Published: September 2008

Motivated from the problem of testing for genetic effects on complex traits in the presence of gene–environment interaction, we develop score tests in general semiparametric regression problems that involves Tukey style 1 degree-of-freedom form of interaction between parametrically and non-parametrically modelled covariates. We find that the score test in this type of model, as recently developed by Chatterjee and co-workers in the fully parametric setting, is biased and requires undersmoothing to be valid in the presence of non-parametric components. Moreover, in the presence of repeated outcomes, the asymptotic distribution of the score test depends on the estimation of functions which are defined as solutions of integral equations, making implementation difficult and computationally taxing. We develop profiled score statistics which are unbiased and asymptotically efficient and can be performed by using standard bandwidth selection methods. In addition, to overcome the difficulty of solving functional equations, we give easy interpretations of the target functions, which in turn allow us to develop estimation procedures that can be easily implemented by using standard computational methods. We present simulation studies to evaluate type I error and power of the method proposed compared with a naive test that does not consider interaction. Finally, we illustrate our methodology by analysing data from a case–control study of colorectal adenoma that was designed to investigate the association between colorectal adenoma and the candidate gene NAT2 in relation to smoking history.
Multiscale Methods for Data on Graphs and Irregular Multidimensional Situations
Authors: Jansen Maarten , Nason Guy P. , Silverman B. W.
Published: September 2008

For regularly spaced one-dimensional data, wavelet shrinkage has proven to be a compelling method for non-parametric function estimation. We create three new multiscale methods that provide wavelet-like transforms both for data arising on graphs and for irregularly spaced spatial data in more than one dimension. The concept of scale still exists within these transforms, but as a continuous quantity rather than dyadic levels. Further, we adapt recent empirical Bayesian shrinkage techniques to enable us to perform multiscale shrinkage for function estimation both on graphs and for irregular spatial data. We demonstrate that our methods perform very well when compared with several other methods for spatial regression for both real and simulated data. Although we concentrate on multiscale shrinkage (regression) we present our new ‘wavelet transforms’ as generic tools intended to be the basis of methods that might benefit from a multiscale representation of data either on graphs or for irregular spatial data.
PROBABILITY AND UNCERTAINTY: THE LEGACY OF GEORGESCU‐ROEGEN
Authors: Fontini Fulvio
Published: September 2008

In this paper we consider Georgescu‐Roegen's approach to uncertainty, showing that his characterization of expectations cannot be reduced to any probabilistic decision‐making model. Drawing upon Georgescu‐Roegen's lesson a lexicographical utility function is proposed and analysed in the mark of his own peculiar scientific methodology. It is demonstrated that such a formulation can be useful in solving the usual failure of the expected utility model, such as the Ellsberg paradoxes. The epistemic limits of our re‐construction are considered.
On Critical Values of Tests against a Change in Persistence*
Authors: Hassler Uwe , Scheithauer Jan
Published: September 2008

Kim, Belaire‐Franch and Amador [Journal of Econometrics (2002) Vol. 109, pp. 389–392] and Busetti and Taylor [Journal of Econometrics (2004) Vol. 123, pp. 33–66] present different percentiles for the same mean score test statistic. We find that the difference by a factor 0.6 is due to systematically different sample analogues. Furthermore, we clarify which sample versions of the mean‐exponential test statistic should be correctly used with which set of critical values. At the same time, we correct some of the limiting distributions found in the literature.
A national review of assessment and monitoring of HIV‐infected patients
Authors: Lomax N , Curtis H , Johnson M ,   on behalf of the British HIV Association (BHIVA) and BHIVA Clinical Audit Subcommittee
Published: September 2008

Objectives

The British HIV Association (BHIVA) audit subcommittee aimed to survey UK clinic policy and practice regarding baseline assessment and immunization of newly diagnosed HIV‐positive patients, and frequency of follow‐up and testing in established patients in the UK.

Methods

UK centres providing HIV care were requested to complete an online survey between October 2006 and March 2007.

Results

111 centres participated in the survey. 89.2% of centres routinely performed baseline HIV resistance testing. 99% of centres had a policy of routine screening for hepatitis B. Only 91% of centres were routinely offering a sexual health screen at diagnosis. Frequency of routine follow‐up for patients not requiring antiretroviral therapy (ART) and stable on ART varied between three and six months.

Discussion

This review showed variations in practice regarding the post diagnosis assessment and routine monitoring of HIV patients. It is of concern that not all centres perform baseline HIV resistance testing. It has also been noted that hepatitis B vaccination is not being offered to non‐immune patients at diagnosis. Less frequent follw‐up of stable patients (both on and off ART) should allow resources to be focussed on those with specific clinical needs.
Truth as a ‘Living Bond’: A Dialectical Response to Recent Rhetorical Theology
Authors: KLASSEN JUSTIN D.
Published: September 2008

Abstract:  In recent years, the Radical Orthodoxy movement (especially John Milbank) has developed an influential theological response to the putative nihilism inherent in modern philosophical tendencies to construe the relation between finite and infinite realities as utterly disjunctive and thus incapable of mediation. This response, which generally implies the championing of a ‘participatory’ ontology, has been very hostile to Protestant or ‘dialectical’ theology, whose insistence upon an ‘indirect’ rather than a ‘rhetorical’ form of truth is taken to implicate such theology in the nihilism of a ‘univocal’ ontology. In this article I offer another reading of the dialectical, via Søren Kierkegaard and René Girard, according to which its anti‐objectivism is due not to the inheritance of modern epistemological dilemmas but to a quite biblical existential rigor. I argue, contrary to Milbank, that this rigor is not finally gnostic, but instead that it alone can preserve the form of truth as a living, spiritual form.
PKU in Minas Gerais State, Brazil: Mutation Analysis
Authors: Santos L. L. , Castro‐Magalhães M. , Fonseca C.G. , Starling A. L. P. , Januário J. N. , Aguiar M. J. B. , Carvalho M. R. S.
Published: September 2008

This work was undertaken in order to ascertain the PKU mutational spectrum in Minas Gerais, Brazil, the relative frequency of the mutations in the State and the origin of these mutations by haplotype determination. Minas Gerais is a trihybrid population formed by miscegenation from Europeans, Africans and Amerindians. All 13 exons of the PAH gene from 78 PKU patients were analyzed, including splicing sites and the promoter region. We identified 30 different mutations and 98% of the PAH alleles were established. A new mutation (Q267X) was identified as well. The most common mutations found were V388M (21.2), R261Q (16.0%), IVS10‐11G>A (15.3%), I65T (5.8%), IVS2+5G>C (5.8%), R252W (5.1%), IVS2+5G>A (4.5%), P281L (3.8%) and L348V (3.2%). These nine mutations correspond to 80% of the PKU alleles in the state. Haplotypes were determined to characterize the origin of the PAH alleles. The majority of the mutations found, with respective haplotypes, are frequent in the Iberian Peninsula. However, there were some mutations that are rare in Europe and four previously unreported mutation‐haplotype associations. I65T and Q267X were found in association with haplotype 38 and may be African in origin or the result of miscegenation in the Brazilian population.
An update on the taxonomy and geographic distribution of the cryptic species Mastomys kollmannspergeri (Muridae, Murinae) using combined cytogenetic and molecular data
Authors: Dobigny G. , Lecompte E. , Tatard C. , Gauthier P. , Bâ K. , Denys C. , Duplantier J. M. , Granjon L.
Published: September 2008

Multi‐mammate rats (Muridae, Murinae, Mastomys spp.) are Sub‐Saharan pest rodents, the systematics of which has long remained confused due to poor morphologic differentiation. Cytotaxonomy and DNA sequencing have provided excellent diagnostic markers for species identification, thus improving the assessment of taxonomic diversity within the genus. In West and Central Africa, three species have been unambiguously identified and are now well documented: Mastomys erythroleucus, Mastomys natalensis and Mastomys huberti. However, recent studies suggest the existence of two other taxa on the basis of morphology, DNA sequencing (Mastomys verheyeni, from Nigeria and Northern Cameroon) or karyotypes (Mastomys cf. kollmannspergeri, from Northern Niger and Chad). In order to clarify the systematic status of the latter taxa, we collected all the available cytotaxonomic as well as cytochrome b sequencing data to which were added results obtained from recently trapped specimens in Northern Cameroon. Our combined molecular and cytogenetic analyses unambiguously confirm the presence of another Mastomys species inhabiting various habitats in Niger, Nigeria, Cameroon, Chad and Sudan. This taxon is clearly differentiated from M. erythroleucus, M. huberti and M. natalensis. Furthermore, the inclusion in our analysis of two M. verheyeni paratypes as well as individuals trapped in close vicinity to the type locality of M. kollmannspergeri supports the assignation of all specimens to M. kollmanspergeri, thus making M. verheyeni its junior synonym. Our study once again highlights the reliability of DNA‐ and karyotype‐based methods to accurately assess specific diversity in African rodents, particularly in the Mastomys genus, which shelters several species of agricultural and epidemiological importance.
Properties of cholesterol‐reduced Camembert cheese made by crosslinked β‐cyclodextrin
Authors: KIM SOO‐YUN , BAE HYUN‐YOUNG , KIM HYE‐YOUNG , AHN JOUNGJWA , KWAK HAE‐SOO
Published: September 2008

The present study was designed to examine the physicochemical and sensory properties in cholesterol‐reduced Camembert cheese made by crosslinked β‐cyclodextrin (β‐CD). The composition of cholesterol‐reduced Camembert cheese was similar to the control and the cholesterol reduction reached 90.6%. No difference was found in the total amount of short‐chain free fatty acids between the cholesterol‐reduced cheese and the control at every ripening period. The release of butyric and capric acid mostly contributed to the increase of total amount of short‐chain free fatty acids in both groups. The cholesterol‐reduced cheese produced similar amounts of individual free amino acids to the control in all periods. The scores of all rheological characteristics except for springiness were continuously increased up to 2 weeks’ ripening and decreased thereafter. Mouldy characteristics in both appearance and flavour were increased dramatically through the ripening period in both cholesterol‐reduced and the control cheeses. Based on these results, no significant difference was found in most physicochemical and sensory properties between cholesterol‐reduced Camembert cheese and the control. Therefore, we may find it possible to develop cholesterol‐reduced Camembert cheese using crosslinked β‐cyclodextrin.
Moulting strategies of a long‐distance migratory seabird, the Mediterranean Cory's ShearwaterCalonectris diomedea diomedea
Authors: RAMOS RAÜL , MILITÃO TERESA , GONZÁLEZ‐SOLÍS JACOB , RUIZ XAVIER
Published: September 2008

Seabird moult is poorly understood because most species undergo moult at sea during the non‐breeding season. We scored moult of wings, tail and body feathers on 102 Mediterranean Cory's ShearwatersCalonectris diomedea diomedeaaccidentally caught by longliners throughout the year. Primary renewal was found to be simple and descendant from the most proximal (P1) to the most distal (P10) feather. Secondaries showed a more complex moulting pattern, with three different asynchronous foci: the first starting on the innermost secondaries (S21), the second on the middle secondaries (S5) and the latest on the outermost secondaries (S1). Rectrix moult started at a later stage and was simple and descendant from the most proximal feather (R1) expanding distally. Although a few body feathers can be moulted from prelaying to hatching, moult of ventral and dorsal feathers clearly intensified during chick rearing. Different moulting sequences and uncoupled phenology between primary and secondary renewal suggest that flight efficiency is a strong constraint factor in the evolution of moulting strategies. Moreover, moult of Cory's Shearwaters was synchronous between wings and largely asynchronous between tail halves, with no more than one rectrix moulted at once. This result is probably related to the differential sensitivity of wings and the tail on flight performance, ultimately derived from different aerodynamic functions. Finally, Cory's Shearwater females renewed feathers earlier and faster than males, which may be related to the lower chick attendance of females.
Intraspecific Chromosome Number Variation: a Neglected Threat to the Conservation of Rare Plants
Authors: SEVERNS PAUL M. , LISTON AARON
Published: September 2008

Abstract: The effectiveness of rare plant conservation will increase when life history, demographic, and genetic data are considered simultaneously. Inbreeding depression is a widely recognized genetic concern in rare plant conservation, and the mixing of genetically diverse populations in restoration efforts is a common remedy. Nevertheless, if populations with unrecognized intraspecific chromosome variation are crossed, progeny fitness losses will range from partial to complete sterility, and reintroductions and population augmentation of rare plants may fail. To assess the current state of cytological knowledge of threatened and endangered plants in the continental United States, we searched available resources for chromosome counts. We also reviewed recovery plans to discern whether recovery criteria potentially place listed species at risk by requiring reintroductions or population augmentation in the absence of cytological information. Over half the plants lacked a chromosome count, and when a taxon did have a count it generally originated from a sampling intensity too limited to detect intraspecific chromosome variation. Despite limited past cytological sampling, we found 11 plants with documented intraspecific cytological variation, while 8 others were ambiguous for intraspecific chromosome variation. Nevertheless, only one recovery plan addressed the chromosome differences. Inadequate within‐species cytological characterization, incomplete sampling among listed taxa, and the prevalence of interspecific and intraspecific chromosome variation in listed genera, suggests that other rare plants are likely to have intraspecific chromosome variation. Nearly 90% of all recovery plans called for reintroductions or population augmentation as part of recovery criteria despite the dearth of cytological knowledge. We recommend screening rare plants for intraspecific chromosome variation before reintroductions or population augmentation projects are undertaken to safeguard against inadvertent mixtures of incompatible cytotypes.
Rapid Evolution in the Wild: Changes in Body Size, Life‐History Traits, and Behavior in Hunted Populations of the Japanese Mamushi Snake
Authors: SASAKI KIYOSHI , FOX STANLEY F. , DUVALL DAVID
Published: September 2008

Abstract:  Rapid evolution caused by human exploitation of wildlife is not usually addressed in studies of the impacts of such exploitation despite its direct relevance to population persistence. Japanese mamushi (Gloydius blomhoffii), an endemic venomous snake of the Japanese archipelago, has been heavily hunted by humans, and many populations appear to be declining or are already extirpated. We compared local populations that have been hunted regularly with populations that have not been hunted. Mamushi in hunted populations were smaller, had fewer vertebrae, produced more and smaller offspring, had increased reproductive effort among smaller females, and in nature fled at greater distances from an approaching human and were less defensive than mamushi in unhunted populations, as predicted from life‐history theory. Heritability estimates for body size, number of vertebrae, and antipredator behavior were statistically significant, and neonates from hunted sites showed the same distribution of altered characters (compared with those from unhunted sites) as adults. Thus, distribution of the divergent trait between hunted and unhunted sites appeared in part to be genetically based, which suggests rapid evolution to human predation pressures. Trait distributions in hunted populations probably deviate from naturally (as opposed to anthropogenically) selected optima and, therefore, may have long‐term negative repercussions on population persistence. Because rapid evolution affects a suite of parameters that characterize exploited populations, accurate understanding of the impacts of exploitation and effective resource management and conservation can only be achieved if evolutionary consequences are considered explicitly.
Effectiveness of Vegetation Surrogates for Parasitoid Wasps in Reserve Selection
Authors: FRASER SALLY E. M. , BERESFORD ALISON E. , PETERS JENNIFER , REDHEAD JOHN W. , WELCH ALASTAIR J. , MAYHEW PETER J. , DYTHAM CALVIN
Published: September 2008

Abstract:  Selecting suitable nature reserves is a continuing challenge in conservation, particularly for target groups that are time‐consuming to survey, species rich, and extinction prone. One such group is the parasitoid Hymenoptera, which have been excluded from conservation planning. If basic characteristics of habitats or vegetation could be used as reliable surrogates of specific target taxa, this would greatly facilitate appropriate reserve selection. We identified a range of potential habitat indicators of the species richness of pimpline parasitoid communities (Hymenoptera: Ichneumonidae: Pimplinae, Diacritinae, Poemeniinae) and tested their efficiency at capturing the observed diversity in a group of small woodlands in the agricultural landscape of the Vale of York (United Kingdom). Eight of the 18 vegetation‐based reserve‐selection strategies were significantly better at parasitoid species inclusion than random selection of areas. The best strategy maximized richness of tree species over the entire reserve network through complementarity. This strategy omitted only 2–3 species more (out of 38 captured in the landscape as a whole) than selections derived from the parasitoid survey data. In general, strategies worked equally well at capturing species richness and rarity. Our results suggest that vegetation data as a surrogate for species richness could prove an informative tool in parasitoid conservation, but further work is needed to test how broadly applicable these indicators may be.