bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying associations between amino acid changes and meta information in alignments
Authors: Spangenberg L. , Battke F. , Graña M. , Nieselt K. , Naya H.
Published: August 2011

Motivation: We present a method that identifies associations between amino acid changes in potentially significant sites in an alignment (taking into account several amino acid properties) with phenotypic data, through the phylogenetic mixed model. The latter accounts for the dependency of the observations (organisms). It is known from previous studies that the pathogenic aspect of many organisms may be associated with a single or just few changes in amino acids, which have a strong structural and/or functional impact on the protein. Discovering these sites is a big step toward understanding pathogenicity. Our method is able to discover such sites in proteins responsible for the pathogenic character of a group of bacteria.

Results: We use our method to predict potentially significant sites in the RpoS protein from a set of 209 bacteria. Several sites with significant differences in biological relevant regions were found.

Availability: Our tool is publicly available on the CRAN network at http://cran.r-project.org/

Contact:  naya@pasteur.edu.uy

Supplementary information:  Supplementary data are available at Bioinformatics online.
Digital Gene Expression Profiling of the Phytophthora sojae Transcriptome
Authors: Ye Wenwu , Wang Xiaoli , Tao Kai , Lu Yuping , Dai Tingting , Dong Suomeng , Dou Daolong , Gijzen Mark , Wang Yuanchao
Published: August 2011

The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at ten different developmental and infection stages based on a 3′-tag digital gene-expression protocol. More than 90 million clean sequence tags were generated and compared with the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A comparison of the whole-library genes' expression patterns suggested four groups: i) mycelia and zoosporangia, ii) zoospores and cysts, iii) germinating cysts, and iv) five infection site libraries (IF1.5 to IF24h). The libraries from the different groups showed major transitional shifts in gene expression. From the ten libraries, 722 gene expression–pattern clusters were obtained and the top 16 clusters, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and noncoding RNA metabolism. An evaluation of the average expression level of 30 pathogenesis-related gene families revealed that most were infection induced but with diverse expression patterns and levels. A web-based server named the Phytophthora Transcriptional Database has been established.
Characteristics of the Spread of Apple Proliferation by Its VectorCacopsylla picta
Authors: Jarausch Barbara , Schwind Nora , Fuchs Annette , Jarausch Wolfgang
Published: August 2011

The distribution and natural phytoplasma infection of Cacopsylla picta were investigated during a long-term field survey between 2002 and 2009 in commercial and abandoned apple proliferation-infected orchards throughout Germany, northern Switzerland, and eastern France. Comparable population dynamics were described for the different sites whereas considerable variations in the absolute population densities were observed among the years. Individual polymerase chain reaction (PCR) testing revealed, for each year, a rather stable natural infection rate with ‘Candidatus Phytoplasma mali’ of ≈10% for overwintered adults of C. picta. Both genders were equally highly infected although more females were caught. The overall male/female ratio was 1:1.5. No direct correlation was found between the infection status of the orchard and the infection rate of overwintered C. picta. No influence of agricultural practices was seen. However, a relationship between the incidence of the disease and the vector population density became evident on a regional scale. Successful transmission of ‘Ca. P. mali’ occurred each year with overwintered individuals as well as with new adults. The transmission efficiency varied among the years within 8 to 45% for overwintered adults and 2 to 20% for individuals of the new generation. The load of single C. picta with ‘Ca. P. mali’ was determined by quantitative real-time PCR. High phytoplasma titers were measured in overwintered adults already at their first appearance in the orchards after remigration from their overwintering hosts. Thus, the data indicate the transmission of the disease on a regional scale by remigrant adults of C. picta and at a local scale within the same season by emigrant adults which developed on infected plants.
Invasion Genetics of the Chestnut Blight Fungus Cryphonectria parasitica in Switzerland
Authors: Prospero S. , Rigling D.
Published: August 2011

Cryphonectria parasitica is the best-known example of an invasive forest pathogen in Europe. In southern Switzerland, chestnut blight was first reported in 1948 whereas, north of the Alps, it did not appear until the 1980s. Between 1995 and 2008, we sampled 640 C. parasitica isolates from nine populations south of the Alps and nine north of the Alps. Twelve historical isolates, collected between 1950 and 1972 in the south, were obtained from our collection. All 652 isolates were screened at 10 microsatellite loci to test for the existence of divergent genetic pools and to infer possible origins of haplotypes. In total, 52 haplotypes were identified. Structure software analysis indicated that 43 haplotypes (including all historical haplotypes) belonged to a main cluster, 6 haplotypes belonged to a different cluster, and 3 haplotypes had an intermediate allele pattern. All newly founded populations in northern Switzerland were initiated by one or just a few haplotypes from the main cluster, which probably came directly from the populations south of the Alps. Subsequently, genetic diversity increased through mutations, sexual reproduction, or new migrations. The highest increase in diversity was observed in populations where haplotypes from different genetic pools were encountered.
Selection on codon usage and base composition inDrosophila americana
Authors: de Procé Sophie Marion , Zeng Kai , Betancourt Andrea J. , Charlesworth Brian
Published: August 2011

We have used a polymorphism dataset on introns and coding sequences of X-linked loci inDrosophila americanato estimate the strength of selection on codon usage and/or biased gene conversion (BGC), taking into account a recent population expansion detected by a maximum-likelihood method.Drosophila americanawas previously thought to have a stable demographic history, so that this evidence for a recent population expansion means that previous estimates of selection need revision. There was evidence for natural selection or BGC favouring GC over AT variants in introns, which is stronger for GC-rich than GC-poor introns. By comparing introns and coding sequences, we found evidence for selection on codon usage bias, which is much stronger than the forces acting on GC versus AT basepairs in introns.
To fear or to feed: the effects of turbidity on perception of risk by a marine fish
Authors: Leahy Susannah M. , McCormick Mark I. , Mitchell Matthew D. , Ferrari Maud C. O.
Published: August 2011

Coral reefs are currently experiencing a number of worsening anthropogenic stressors, with nearshore reefs suffering from increasing sedimentation because of growing human populations and development in coastal regions. In habitats where vision and olfaction serve as the primary sources of information, reduced visual input from suspended sediment may lead to significant alterations in prey fish behaviour. Here, we test whether prey compensate for reduced visual information by increasing their antipredator responses to chemically mediated risk cues in turbid conditions. Experiments with the spiny damselfish,Acanthochromis polyacanthus, found that baseline activity levels were reduced by 23 per cent in high turbidity conditions relative to low turbidity conditions. Furthermore, risk cues elicited strong antipredator responses at all turbidity levels; the strongest antipredator responses were observed in high turbidity conditions, with fish reducing their foraging by almost 40 per cent, as compared with 17 per cent for fish in clear conditions. This provides unambiguous evidence of sensory compensation in a predation context for a tropical marine fish, and suggests that prey fish may be able to behaviourally offset some of the fitness reductions resulting from anthropogenic sedimentation of their habitats.
James Croll, metaphysical geologist
Authors: Finnegan Diarmid A.
Published: August 2011

James Croll (1821–90) occupies a prominent position in the history of physical geology, and his pioneering work on the causes of long-term climate change has been widely discussed. During his life he benefited from the patronage of leading men of science; his participation in scientific debates was widely acknowledged, not least through his election as a Fellow of the Royal Society in 1876. For all that, the intellectual contribution that Croll himself considered to be of most significance—his articles and two books on metaphysics—has attracted very little attention. In addressing this neglect, it is argued here that Croll's interest in metaphysics, grounded in his commitment to a Calvinist form of Christianity, was central to his life and thought. Examining together Croll's geophysical and metaphysical writings offers a different and fruitful way of understanding his scientific career and points to the wider significance of metaphysics in late-Victorian scientific culture.
Pattern formation on the surface of a bubble driven by an acoustic field
Authors: Maksimov A. O. , Leighton T. G.
Published: August 2011

The final stable shape taken by a fluid–fluid interface when it experiences a growing instability can be important in determining features as diverse as weather patterns in the atmosphere and oceans, the growth of cell structures and viruses, and the dynamics of planets and stars. An example which is accessible to laboratory study is that of an air bubble driven by ultrasound when it becomes shape-unstable through a parametric instability. Above the critical driving pressure threshold for shape oscillations, which is minimal at the resonance of the breathing mode, regular patterns of surface waves are observed on the bubble wall. The existing theoretical models, which take account only of the interaction between the breathing and distortion modes, cannot explain the selection of the regular pattern on the bubble wall. This paper proposes an explanation which is based on the consideration of a three-wave resonant interaction between the distortion modes. Using a Hamiltonian approach to nonlinear bubble oscillation, corrections to the dynamical equations governing the evolution of the amplitudes of interacting surface modes have been derived. Steady-state solutions of these equations describe the formation of a regular structure. Our predictions are confirmed by images of patterns observed on the bubble wall.
Nonlinear time-series approaches in characterizing mood stability and mood instability in bipolar disorder
Authors: Bonsall M. B. , Wallace-Hadrill S. M. A. , Geddes J. R. , Goodwin G. M. , Holmes E. A.
Published: August 2011

Bipolar disorder is a psychiatric condition characterized by episodes of elevated mood interspersed with episodes of depression. While treatment developments and understanding the disruptive nature of this illness have focused on these episodes, it is also evident that some patients may have chronic week-to-week mood instability. This is also a major morbidity. The longitudinal pattern of this mood instability is poorly understood as it has, until recently, been difficult to quantify. We propose that understanding this mood variability is critical for the development of cognitive neuroscience-based treatments. In this study, we develop a time-series approach to capture mood variability in two groups of patients with bipolar disorder who appear on the basis of clinical judgement to show relatively stable or unstable illness courses. Using weekly mood scores based on a self-rated scale (quick inventory of depressive symptomatology—self-rated; QIDS-SR) from 23 patients over a 220-week period, we show that the observed mood variability is nonlinear and that the stable and unstable patient groups are described by different nonlinear time-series processes. We emphasize the necessity in combining both appropriate measures of the underlying deterministic processes (the QIDS-SR score) and noise (uncharacterized temporal variation) in understanding dynamical patterns of mood variability associated with bipolar disorder.
Understanding sex differences in the cost of terrestrial locomotion
Authors: Lees John J. , Nudds Robert L. , Folkow Lars P. , Stokkan Karl-Arne , Codd Jonathan R.
Published: August 2011

Little is known regarding the physiological consequences of the behavioural and morphological differences that result from sexual selection in birds. Male and female Svalbard rock ptarmigans (Lagopus muta hyperborea) exhibit distinctive behavioural differences during the breeding season. In particular, males continuously compete for and defend territories in order to breed successfully, placing large demands on their locomotor system. Here, we demonstrate that male birds have improved locomotor performance compared with females, showing both a lower cost of locomotion (CoL) and a higher top speed. We propose that the observed sex differences in locomotor capability may be due to sexual selection for improved male performance. While the mechanisms underlying these energetic differences are unclear, future studies should be wary when pooling male and female data.
Multi-objective optimization shapes ecological variation
Authors: Kaitaniemi Pekka , Scheiner Annette , Klemola Tero , Ruohomäki Kai
Published: August 2011

Ecological systems contain a huge amount of quantitative variation between and within species and locations, which makes it difficult to obtain unambiguous verification of theoretical predictions. Ordinary experiments consider just a few explanatory factors and are prone to providing oversimplified answers because they ignore the complexity of the factors that underlie variation. We used multi-objective optimization (MO) for a mechanistic analysis of the potential ecological and evolutionary causes and consequences of variation in the life-history traits of a species of moth. Optimal life-history solutions were sought for environmental conditions where different life stages of the moth were subject to predation and other known fitness-reducing factors in a manner that was dependent on the duration of these life stages and on variable mortality rates. We found that multi-objective optimal solutions to these conditions that the moths regularly experience explained most of the life-history variation within this species. Our results demonstrate that variation can have a causal interpretation even for organisms under steady conditions. The results suggest that weather and species interactions can act as underlying causes of variation, and MO acts as a corresponding adaptive mechanism that maintains variation in the traits of organisms.
Parallel evolutionary trajectories underlie the origin of giant suspension-feeding whales and bony fishes
Authors: Friedman Matt
Published: August 2011

Giant suspension feeders such as mysticete whales, basking and whale sharks, and the extinct (indicated by ‘†’) †pachycormiform teleosts are conspicuous members of modern and fossil marine vertebrate faunas. Whether convergent anatomical features common to these clades arose along similar evolutionary pathways has remained unclear because of a lack of information surrounding the origins of all groups of large-bodied suspension feeders apart from baleen whales. New investigation reveals that the enigmatic ray-finned fish †
Ohmdenia
, from the Lower Jurassic (Toarcian, 183.0–175.6 Ma) Posidonia Shale
Lagerstätte
, represents the immediate sister group of edentulous †pachycormiforms, the longest lived radiation of large vertebrate suspension feeders. †
Ohmdenia
bisects the long morphological branch leading to suspension-feeding †pachycormiforms, providing information on the sequence of anatomical transformations preceding this major ecological shift that can be compared to changes associated with the origin of modern mysticetes. Similarities include initial modifications to jaw geometry associated with the reduction of dentition, followed by the loss of teeth. The evolution of largest body sizes within both radiations occurs only after the apparent onset of microphagy. Comparing the fit of contrasting evolutionary models to functionally relevant morphological measurements for whales and †pachycormiform fishes reveals strong support for a common adaptive peak shared by suspension-feeding members of both clades.
Metabolomics of a Single Vacuole Reveals Metabolic Dynamism in an Alga Chara australis
Authors: Oikawa Akira , Matsuda Fumio , Kikuyama Munehiro , Mimura Tetsuro , Saito Kazuki
Published: August 2011

Metabolomics is the most reliable analytical method for understanding metabolic diversity in single organelles derived from single cells. Although metabolites such as phosphate compounds are believed to be localized in different organelles in a highly specific manner, the process of metabolite compartmentalization in the cell is not thoroughly understood. The analysis of metabolites in single organelles has consequently presented a significant challenge. In this study, we used a metabolomic method to elucidate the localization and dynamics of 125 known metabolites isolated from the vacuole and cytoplasm of a single cell of the alga Chara australis. The amount of metabolites in the vacuole and the cytoplasm fluctuated asynchronously under various stress conditions, suggesting that metabolites are spatially regulated within the cell. Metabolite transport across the vacuolar membrane can be directly detected using the microinjection technique, which may reveal a previously unknown function of the vacuole.
Reducing the background from pressure vessels using a BRIM
Authors: Wilkinson Angus P. , Morelock Cody R. , Greve Benjamin K. , Jupe Andrew C. , Chapman Karena W. , Chupas Peter J. , Kurtz Charles
Published: August 2011

A collimator and beam-stop assembly that can be inserted inside a temperature-controlled pressure vessel, to reduce dramatically the parasitic Bragg scattering from the vessel, has been designed and evaluated. High-energy X-ray powder diffraction data, suitable for the Rietveld refinement of simple crystal structures, were collected using this background-reducing internal mask (BRIM). ZrW2O8was examined at up to 540 K and 124 MPa, using quite large pressure and temperature steps. No pressure dependence of the order–disorder transition temperature of this material was apparent. An orthorhombic to monoclinic phase transition (onset ∼83 MPa) was observed for Al2W3O12. Upon going through the transition, the bulk modulus of the material decreased from 41.8 to 20.8 GPa. Bulk moduli estimated for CaF2and α-Al2O3, from data collected at up to 280 MPa, were in good agreement with prior literature.
CrysPage: a program for displaying images of crystallization trials, rapid comparisons and analysis
Authors: Esser Lothar , Xia Di
Published: August 2011

CrysPageis a program to facilitate the rapid evaluation of high-throughput crystallization trials by experienced crystallographers. Emphasis is placed on a clear overview and the display of individual drops. Chemical space can be searched and selected drops can be displayed for detailed inspection, allowing the user to narrow down the range of trial conditions for further optimization.
Diagnosis and management of hymenoptera venom allergy: British Society for Allergy and Clinical Immunology (BSACI) guidelines
Authors: Krishna M. T. , Ewan P. W. , Diwakar L. , Durham S. R. , Frew A. J. , Leech S. C. , Nasser S. M.
Published: August 2011

This guidance for the management of patients with hymenoptera venom allergy has been prepared by the Standards of Care Committee (SOCC) of the British Society for Allergy and Clinical Immunology (BSACI). The guideline is based on evidence as well as on expert opinion and is for use by both adult physicians and pediatricians practising allergy. During the development of these guidelines, all BSACI members were included in the consultation process using a web‐based system. Their comments and suggestions were carefully considered by the SOCC. Where evidence was lacking, consensus was reached by the experts on the committee. Included in this guideline are epidemiology, risk factors, clinical features, diagnostic tests, natural history of hymenoptera venom allergy and guidance on undertaking venom immunotherapy (VIT). There are also separate sections on children, elevated baseline tryptase and mastocytosis and mechanisms underlying VIT. Finally, we have made recommendations for potential areas of future research.

Cite this as: M. T. Krishna, P. W. Ewan, L. Diwakar, S. R. Durham, A. J. Frew, S. C. Leech and S. M. Nasser, Clinical & Experimental Allergy, 2011 (41) 1201–1220.
Immunotherapy for allergic rhinitis
Authors: Walker S. M. , Durham S. R. , Till S. J. , Roberts G. , Corrigan C. J. , Leech S. C. , Krishna M. T. , Rajakulasingham R. K. , Williams A. , Chantrell J. , Dixon L. , Frew A. J. , Nasser S. M.
Published: August 2011

Allergic rhinitis (AR) affects more than 20% of the population in the United Kingdom and western Europe and represents a major cause of morbidity that includes interference with usual daily activities and impairment of sleep quality. This guidance prepared by the Standards of Care Committee (SOCC) of the British Society for Allergy and Clinical Immunology (BSACI) is for the management of AR in patients that have failed to achieve adequate relief of symptoms despite treatment with intranasal corticosteroids and/or antihistamines. The guideline is based on evidence and is for use by both adult physicians and paediatricians practising allergy. During the development of these guidelines, all BSACI members were included in the consultation process using a web‐based system. Their comments and suggestions were carefully considered by the SOCC. Where evidence was lacking, consensus was reached by the experts on the committee. Included in this guideline are indications and contraindications for immunotherapy, criteria for patient selection, the evidence for short‐ and long‐term efficacy of subcutaneous and sublingual immunotherapy, and discussion on safety and the different modes of immunotherapy including, pre‐seasonal and co‐seasonal treatments. There are sections on children, allergen standardization, vaccines used in the United Kingdom, oral allergy syndrome, cost effectiveness of immunotherapy and practical considerations of undertaking immunotherapy including recommendations on who should undertake immunotherapy and dosing schedules. Finally, there is discussion on potential biomarkers of response to immunotherapy, the use of component‐resolved diagnostics, novel approaches, alternative routes and potential areas for future research.

Cite this as: S. M. Walker, S. R. Durham, S. J. Till, G. Roberts, C. J. Corrigan, S. C. Leech, M. T. Krishna, R. K. Rajakulasingham, A. Williams, J. Chantrell, L. Dixon, A. J. Frew and S. M. Nasser, Clinical & Experimental Allergy, 2011 (41) 1177–1200.
Sublingual immunotherapy for allergic conjunctivitis: Cochrane systematic review and meta‐analysis
Authors: Calderon M. A. , Penagos M. , Sheikh A. , Canonica G. W. , Durham S. R.
Published: August 2011

Background. Allergic conjunctivitis (AC) is a common manifestation and represents an important co‐morbidity of allergic rhinitis (AR). Sublingual immunotherapy (SLIT) is an effective and safe treatment for nasal symptoms of AR; its effectiveness is however less well established for ocular symptoms.

Objectives. To evaluate the effectiveness of SLIT in reducing ocular symptoms, the need for ocular treatments and the threshold exposure for conjunctival immediate allergen sensitivity (CIAS).

Methods. We searched eight databases up to January 2010. We included only randomized controlled trials (RCT), double‐blind and placebo‐controlled evaluating the efficacy of SLIT in patients with symptoms of allergic rhinoconjunctivitis (ARC) or AC. Primary outcome measures were total ocular symptom scores, individual ocular symptoms scores (itchy eyes, eye redness, watery eyes, swelling eyes), eye drops use and CIAS. Meta‐analysis was undertaken using RevMan 5 software.

Results. From 811 abstracts that were screened, 109 studies were reviewed in their full text version. Forty two trials including 3958 participants (n=2011 SLIT and n=1947 placebo) had data suitable for inclusion in the meta‐analysis. SLIT induced a significant reduction on both total ocular symptom scores (SMD: −0.41; 95%CI: −0.53 to −0.28; I2: 59%) and individual ocular symptoms scores [red (−0.33; −0.45 to −0.22), itchy (−0.31; −0.42 to −0.20) and watery eyes (−0.23; −0.34 to −0.11)] compared with placebo. Participants in the SLIT group showed an increase in the threshold dose for the CIAS (SMD: 0.35; 0.00–0.69). No significant reduction was observed on eye drops use (SMD: −0.10; −0.22 to 0.03).

Conclusions and Clinical Relevance. SLIT is effective in reducing total and individual ocular symptom scores in subjects with ARC or conjunctivitis. No significant reduction was observed in ocular eye drops use.

Cite this as: M. A. Calderon, M. Penagos, A. Sheikh, G. W. Canonica and S. R. Durham, Clinical & Experimental Allergy, 2011 (41) 1263–1272.
Are serum TSH levels associated with oxidized low‐density lipoprotein? Results from the Study of Health in Pomerania
Authors: Ittermann Till , Baumeister Sebastian E. , Völzke Henry , Wasner Christina , Schminke Ulf , Wallaschofski Henri , Nauck Matthias , Lüdemann Jan
Published: August 2011

Objective  Oxidized LDL (oxLDL) is involved in the pathogenesis of atherosclerosis. Thus, it is important to investigate putative risk factors for increased oxLDL. Evidence suggests that, compared to euthyroid individuals, LDL‐cholesterol (LDL‐C) levels are lower in individuals with overt hyperthyroidism. Whereas oxidization of LDL‐C into oxLDL is increased in overt hyper‐ and hypothyroidism, it has not been investigated whether subclinical thyroid dysfunction impacts on oxLDL levels in general. We have analysed the association between serum thyrotrophin (TSH) levels and oxLDL in a population‐based study.

Design, Patients and Measurements  Of the 4308 individuals enrolled in the Study of Health in Pomerania, data from 3519 individuals were analysed (680 missing the oxLDL variable). oxLDL was measured by the oxLDL competitive ELISA on a BEP 2000. Multivariable linear regression models were performed to assess the association between serum TSH and oxLDL levels.

Results  TSH was positively associated with oxLDL in a curvilinear fashion with increasing serum TSH levels. Subgroup analyses revealed a significant association only in the group of individuals >60 years. Additionally, serum TSH levels were not associated with the ratio of oxLDL to LDL (β = −0·04; 95% CI = −0·08, 0·01; P = 0·084).

Conclusions  We demonstrate an association between serum TSH and oxLDL levels especially in the range of subclinical thyroid disease. Our study suggests that serum TSH levels affect LDL‐C production or clearance rather than the LDL‐C oxidation processes.
Out‐of‐office and central blood pressure for risk stratification: a cross‐sectional study in patients treated for hypertension
Authors: Schultz Martin G. , Gilroy Deborah , Wright Leah , Bishop Warrick L. J. , Abhayaratna Walter P. , Stowasser Michael , Sharman James E.
Published: August 2011

Eur J Clin Invest 2012; 42 (4): 393–401

Background  Central blood pressure (BP) predicts mortality independent of office brachial BP. Whether central BP may be useful to differentiate BP control requires examination and was the first aim of this study. Secondly, we sought to determine the variability in central BP among patients from different categories of BP control [controlled hypertension (CH), masked hypertension (MH), white coat (WCHT) and uncontrolled hypertension (UH)].

Materials and methods  We assessed patients with uncomplicated hypertension using measurement of central BP (SphygmoCor 8.1), brachial BP and 24‐h ambulatory BP monitoring. BP control was defined according to guidelines using office BP and 24‐h BP.

Results  Of the 201 patients (63 ± 8 years, 51% men), 67 (33%) were classified as CH; 59 (29%) with MH; 31 (15%) with WCHT; and 44 (22%) with UH. There were no differences in central BP parameters (augmentation pressure, augmentation index, pulse pressure) between patients with CH and MH or between patients with WCHT and UH (P > 0·05 for all). However, there was significant overlap in central systolic BP between BP control categories. For example, 27% of patients with normal brachial systolic BP had central systolic BP above age‐ and gender‐specific normal values, including patients from three classifications of BP control (CH: n = 27; MH: n = 22; and WCHT: n = 4).

Conclusion  Office central BP alone cannot delineate categories of BP control. However, given the high degree of variability in central BP among patients from different categories of BP control, measurement of central BP may result in significant reclassification of risk related to BP.
Neuroendocrinology of Parental Response to Baby‐Cry
Authors: Swain J. E. , Kim P. , Ho S. S.
Published: August 2011

This overview attempts to synthesise current understandings of the neuroendocrine basis of parenting. The parent–infant bond is central to the human condition, contributes to risks for mood and anxiety disorders, and provides the potential for resiliency and protection against the development of psychopathology. Animal models of parenting provide compelling evidence that biological mechanisms may be studied in humans. This has led to brain imaging and endocrine system studies of human parents using baby stimuli and concerted psychological and behavioural measures. Certain brain circuits and related hormonal systems, including subcortical regions for motivation (striatum, amygdala, hypothalamus and hippocampus) and cortical regions for social cognition (anterior cingulate, insula, medial frontal and orbitofrontal cortices), appear to be involved. These brain circuits work with a range of endocrine systems to manage stress and motivate appropriate parental caring behaviour with a flexibility appropriate to the environment. Work in this field promises to link evolving models of parental brain performance with resilience, risk and treatment toward mother–infant mental health.
Experience‐dependent induction of hypnagogic images during daytime naps: a combined behavioural and EEG study
Authors: KUSSE CAROLINE , SHAFFII‐LE BOURDIEC ANAHITA , SCHROUFF JESSICA , MATARAZZO LUCA , MAQUET PIERRE
Published: August 2011

This study characterizes hypnagogic hallucinations reported during a polygraphically recorded 90‐min daytime nap following or preceding practice of the computer game Tetris. In the experimental group (N = 16), participants played Tetris in the morning for 2 h during three consecutive days, while in a first control group (N = 13, controlling the effect of experience) participants did not play any game, and in a second control group (N = 14, controlling the effect of anticipation) participants played Tetris after the nap. During afternoon naps, participants were repetitively awakened 15, 45, 75, 120 or 180 s after the onset of S1, and were asked to report their mental content. Reports content was scored by three judges (inter‐rater reliability 85%). In the experimental group, 48 out of 485 (10%) sleep‐onset reports were Tetris‐related. They mostly consisted of images and sounds with very little emotional content. They exactly reproduced Tetris elements or mixed them with other mnemonic components. By contrast, in the first control group, only one report out of 107 was scored as Tetris‐related (1%), and in the second control group only three reports out of 112 were scored as Tetris‐related (3%; between‐groups comparison; P = 0.006). Hypnagogic hallucinations were more consistently induced by experience than by anticipation (P = 0.039), and they were predominantly observed during the transition of wakefulness to sleep. The observed attributes of experience‐related hypnagogic hallucinations are consistent with the particular organization of regional brain activity at sleep onset, characterized by high activity in sensory cortices and in the default‐mode network.
Severe fatigue in narcolepsy with cataplexy
Authors: DROOGLEEVER FORTUYN HAL A. , FRONCZEK ROLF , SMITSHOEK MIRJAN , OVEREEM SEBASTIAAN , LAPPENSCHAAR MARTIJN , KALKMAN JOKE , RENIER WILLY , BUITELAAR JAN , LAMMERS GERT JAN , BLEIJENBERG GIJS
Published: August 2011

Excessive daytime sleepiness (EDS) is the core symptom of narcolepsy. However, there have been indications that fatigue – which should be separated from EDS – is also a frequent complaint. We determined the prevalence of severe fatigue in a group of narcolepsy patients and its relation with excessive daytime sleepiness, psychological distress, functional impairment and quality of life. We included 80 patients fulfilling the International Classification of Sleep Disorders (ICSD)‐2 diagnostic criteria of narcolepsy with cataplexy. Fatigue was measured using the Checklist Individual Strength (CIS). In addition psychological distress, including symptoms of depression, functional impairment and quality of life, were assessed. Comparisons were made between patients with (CIS‐fatigue score ≥ 35) and without severe experienced fatigue. Fifty patients (62.5%) reported severe fatigue. There were no sex or age differences between patients with and without severe fatigue. Both fatigued and non‐fatigued patients had the same amount of daytime sleepiness (Epworth Sleepiness Score 14.3 ± 4.2 versus 13.1 ± 4.4, P = 0.22), confirming the separation between sleepiness and fatigue. Interestingly, fatigued patients more often used stimulant medication (64% versus 40%, P = 0.02). Severe fatigue was associated with a significantly increased functional impairment, increased depressive symptoms and a lowered general quality of life. In conclusion, a majority of patients with narcolepsy suffer from severe fatigue, which can be distinguished from daytime sleepiness, and results in severe functional impairment.
Multi‐stage exhumation of the NE Tarim Precambrian bedrock, NW China: constraints from apatite fission track thermochronology in the Kuluketage area
Authors: Zhang Zhiyong , Zhu Wenbin , Shu Liangshu , Wan Jinglin , Yang Wei , Zheng Bihai , Su Jinbao
Published: August 2011

Terra Nova, 23, 324–332, 2011

Fourteen samples of Precambrian bedrocks from the Kuluketage area, located in the north‐eastern Tarim Craton, yield apatite fission track ages ranging from 166 to 82 Ma. These ages are far younger than their Precambrian age of stratigraphy or metamorphism, indicating that the samples experienced total annealing before Mesozoic exhumation. The samples were subdivided into three groups based on locations and ages. Multi‐stage Mesozoic exhumation is linked to collisions of the Qiangtang, Lhasa and Kohistan terranes with the South Eurasian continental margin. The three cooling phases are also shown by stratigraphy and seismology. Considering modelling results with different constraint boxes, seismic profiles and the stratigraphic sequences of surrounding sedimentary basins, faint Cenozoic reheating and recooling were likely to take place in the Kuluketage area by northwards propagating deformation from India–Eurasia collision and continued convergence.
Functional HAK/KUP/KT‐like potassium transporter encoded by chlorella viruses
Authors: Greiner Timo , Ramos José , Alvarez Maria C. , Gurnon James R. , Kang Ming , Van Etten James L. , Moroni Anna , Thiel Gerhard
Published: August 2011

Chlorella viruses are a source of interesting membrane transport proteins. Here we examine a putative K+ transporter encoded by virus FR483 and related chlorella viruses. The protein shares sequence and structural features with HAK/KUP/KT‐like K+ transporters from plants, bacteria and fungi. Yeast complementation assays and Rb+ uptake experiments show that the viral protein, termed HAKCV (high‐affinity K+ transporter of chlorella virus), is functional, with transport characteristics that are similar to those of known K+ transporters. Expression studies revealed that the protein is expressed as an early gene during viral replication, and proteomics data indicate that it is not packaged in the virion. The function of HAKCV is unclear, but the data refute the hypothesis that the transporter acts as a substitute for viral‐encoded K+ channels during virus infection.
PPIase activities and interaction partners of FK506‐binding proteins in the wheat thylakoid
Authors: Gollan Peter J , Ziemann Mark , Bhave Mrinal
Published: August 2011

FK506‐binding proteins (FKBPs) and cyclophilins, collectively called immunophilins, conserve peptidyl‐prolyl cis/trans isomerase (PPIase) active sites, although many lack PPIase activity. The chloroplast thylakoid contains a large proportion of the plant immunophilin family, but their functions within this compartment are unclear. Some lumenal immunophilins are important for assembly of photosynthetic complexes, implicating them in the maintenance and turnover of the photosynthetic apparatus during acclimation processes. In this investigation into the functions of three FKBPs localized to the thylakoid of Triticum aestivum (wheat), we present the first evidence of PPIase activity in the thylakoid of a cereal plant, and also show that PPIase activity is not conserved in all lumenal FKBPs. Using yeast two‐hybrid analysis we found that the PPIase‐active FKBP13 interacts with the globular domain of the wheat Rieske protein, with potential impact on photosynthetic electron transfer. Specific interaction partners for PPIase‐deficient FKBP16‐1 and FKBP16‐3 link these isoforms to photosystem assembly.
Pleural fluid nucleic acid testing enhances pneumococcal surveillance in children
Authors: STRACHAN ROXANNE. E. , CORNELIUS ANITA , GILBERT GWENDOLYN. L. , GULLIVER TANYA , MARTIN ANDREW , MCDONALD TIM , NIXON GILLIAN , ROSEBY ROB , RANGANATHAN SARATH , SELVADURAI HIRAN , SMITH GREG , SOTO‐MARTINEZ MANUEL , SURESH SADASIVAM , TEOH LAUREL , THAPA KIRAN , WAINWRIGHT CLAIRE E. , JAFFÉ ADAM
Published: August 2011

Background and objective:  National surveillance of invasive pneumococcal disease (IPD) includes serotyping Streptococcus pneumoniae (SP) isolates from sterile site cultures. PCR is more sensitive and can identify more SP serotypes (STs) in culture‐negative samples. The aim of this study was to determine whether enhanced surveillance of childhood empyema, using PCR, provides additional serotype information compared with conventional surveillance.

Methods:  Pleural fluid (PF) from children with empyema were cultured and tested by PCR to identify SP, targeting the autolysin gene (lytA). Multiplex PCR‐based reverse line blot assay was used to identify SP STs. Corresponding IPD surveillance and serotype data were obtained from the National Notifiable Diseases Surveillance System (NNDSS).

Results:  Eighty‐nine children with empyema, aged ≤16 years, were recruited between April 2008 and March 2009, inclusive. SP was isolated from 5/84 (5.9%) PF cultures and by PCR in 43/79 (54.4%) PF samples. Serotypes were unidentifiable in 15 samples. The frequency of six serotypes (or serotype pairs) identified in 28 samples, including one with two serotypes, were: ST1, n = 4/29 (13.8%); ST3, n = 9/29 (31.0%); ST19A, n = 12/29 (41.4%); ST7F/7A, n = 1/29 (3.4%); ST9V/9A, n = 1/29 (3.4%); ST22F/22A, n = 2/29 (6.9%). Over the same period, 361 IPD patients, aged 16 years or less, were notified to NNDSS. Among 331 serotypeable NNDSS isolates (71.5% from blood), the frequencies of ST1 and 3 were significantly lower than in PF samples: ST1, n = 8/331 (2.4%; P < 0.05); ST3, n = 13/331 (3.9%; P < 0.0001).

Conclusions:  The use of PCR to identify and serotype SP in culture‐negative specimens provides additive information.
Increasing antibiotic resistance in Streptococcus pneumoniae colonizing children attending day‐care centres in Singapore
Authors: VASOO SHAWN , SINGH KAMALJIT , HSU LI YANG , CHIEW YOKE FONG , CHOW CAROL , LIN RAYMOND T.P. , TAMBYAH PAUL A.
Published: August 2011

Background and objective:  Streptococcus pneumoniae is an important cause of morbidity and mortality in both the paediatric and adult population. This study aimed to define pneumococcal colonization rates, and antibiotic resistance patterns across two periods a decade apart, and also assess the serotypes of colonizing strains in children in the era of early pneumococcal conjugate vaccine uptake in Singapore.

Methods:  Two cross‐sectional prevalence surveys were carried out in 1997 and 2007–2008 on children attending day‐care centres across Singapore. Nasopharyngeal swabs were obtained and cultured for S. pneumoniae, and antibiotic susceptibility testing was performed. Serotyping was also done in the 2007–2008 survey.

Results:  Three hundred and ninety‐five children participated in the first survey in 1997, and 418 in the 2007–2008 survey. Pneumococcal colonization rates were 25.8 and 14.1%, respectively. There was a marked increase in antimicrobial non‐susceptibility (penicillin 27.4% vs 69.5%; erythromycin 33.4% vs 78%; clindamycin 24.5% vs 45.8%, tetracycline 48% vs 67.8%), and multi‐drug resistance (defined as non‐susceptibility to three or more classes of antibiotics) increased from 33.3 to 74.6%. In the 2007–2008 survey, serotypes 6B (16.9%), 23F (11.9%) and 19F (10.2%) were most commonly observed. The projected coverage of the 7 and 13‐valent conjugate pneumococcal vaccine for colonizing serotypes were 61.9 and 67%, respectively.

Conclusions:  S. pneumoniae antibiotic resistance has risen dramatically over the last 10 years in Singapore. Wider conjugate vaccine uptake and improved antibiotic stewardship should be made priorities. Surveillance of sentinel sites like day‐care centres provides important data with respect to shifts in pneumococcal ecology.
Phenotypes of patients with mild to moderate obstructive sleep apnoea as confirmed by cluster analysis
Authors: JOOSTEN SIMON A. , HAMZA KAIS , SANDS SCOTT , TURTON ANTHONY , BERGER PHILIP , HAMILTON GARUN
Published: August 2011

Background and objective:  Patients with OSA manifest different patterns of disease. However, this heterogeneity is more evident in patients with mild‐moderate OSA than in those with severe disease and a high total AHI. We hypothesized that mild‐moderate OSA can be categorized into discreet disease phenotypes, and the aim of this study was to comprehensively describe the pattern of OSA phenotypes through the use of cluster analysis techniques.

Methods:  The data for 1184 consecutive patients, collected over 24 months, was analysed. Patients with a total AHI of 5–30/h were categorized according to the sleep stage and position in which they were predominantly affected. This categorization was compared with one in which patients were grouped using a K‐means clustering technique with log linear modelling and cross‐tabulation.

Results:  Patients with mild‐moderate OSA can be categorized according to polysomnographic parameters. This clinical categorization was validated by comparison with a categorization in which patients were grouped by unsupervised K‐means cluster analysis. The clinical groups identified were: (i) rapid eye movement (REM) predominant OSA, 44.6%; (ii) non‐REM predominant OSA, 18.9%; (iii) supine predominant OSA, 61.9%; and (iv) intermittent OSA, 12.4%. Patients categorized as having both REM and supine predominant OSA showed characteristics of both the REM predominant and supine predominant OSA groups.

Conclusions:  Patients with mild‐moderate OSA show different polysomnographic phenotypes. This approach to categorization more appropriately reflects disease heterogeneity and the likely multiple pathophysiological processes involved in OSA.
Commanding insights in a survey of psychiatrists' and registered nurses' levels of mental health literacy in a Chinese general hospital
Authors: Adler‐Collins Je Kan
Published: August 2011

ADLER‐COLLINS J.K. (2011) Commentary: commanding insights in a survey of psychiatrists' and registered nurses' levels of mental health literacy in a Chinese general hospital. International Nursing Review58, 370–371
Self‐management programme for cancer patients: a literature review
Authors: Gao W.J. , Yuan C.R.
Published: August 2011

GAO W.J. & YUAN C.R. (2011) Self‐management programme for cancer patients: a literature review. International Nursing Review58, 288–295

Background:  With increased cancer survivorship, cancer, in its chronic form, self‐management among cancer patients has become an international research focus. Self‐management programmes are used to guide the self‐care process. Over the past 10 years, six self‐management programmes for cancer patients (Taking CHARGE, Expert Patients Programme, Living with Cancer Education Program, Focus Program, PRO‐SELF Program and Oncologist‐referred exercise self‐management programme) were used in a variety of self‐management studies for cancer patients.

Aim:  The aims of this paper are to describe, compare and critique these six self‐management programmes that are commonly used to guide self‐management for cancer patients, and propose directions for new self‐management programme development among cancer patients.

Methods:  Medline, Pubmed and Embase, Springer, Elsevier, EBSCO and ProQuest were searched for literatures on self‐management programmes for cancer patients from 2000 to November 2010. Search terms such as ‘self‐management’ or ‘self‐care’ or ‘patient education’ or ‘self‐management’ or ‘self‐care’ or ‘self‐efficacy’, ‘intervention’ or ‘program*’‘cancer’ or ‘carcinoma’ or ‘neoplasms’ were used.

Results:  Comparison and critique of these programmes revealed important limitations of cancer self‐management programmes including lack of the facilitators' training process, failure to assess the cultural differences and failure to cover all of the outcome measures.

Conclusion:  Researchers and clinicians need to build more individualized and dynamic self‐management programmes that parallel advances in clinical research and practice for cancer patients.