bluuebunny/crossref_metadata_2025 huggingface dataset:
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
Authors: Wolf Yuri I. , Novichkov Pavel S. , Karev Georgy P. , Koonin Eugene V. , Lipman David J.
Published: April 2009

The evolutionary rates of protein-coding genes in an organism span, approximately, 3 orders of magnitude and show a universal, approximately log-normal distribution in a broad variety of species from prokaryotes to mammals. This universal distribution implies a steady-state process, with identical distributions of evolutionary rates among genes that are gained and genes that are lost. A mathematical model of such process is developed under the single assumption of the constancy of the distributions of the propensities for gene loss (PGL). This model predicts that genes of different ages, that is, genes with homologs detectable at different phylogenetic depths, substantially differ in those variables that correlate with PGL. We computationally partition protein-coding genes from humans, flies, and
Aspergillus
fungus into age classes, and show that genes of different ages retain the universal log-normal distribution of evolutionary rates, with a shift toward higher rates in “younger” classes but also with a substantial overlap. The only exception involves human primate-specific genes that show a heavy tail of rapidly evolving genes, probably owing to gene annotation artifacts. As predicted, the gene age classes differ in characteristics correlated with PGL. Compared with “young” genes (e.g., mammal-specific human ones), “old” genes (e.g., eukaryote-specific), on average, are longer, are expressed at a higher level, possess a higher intron density, evolve slower on the short time scale, and are subject to stronger purifying selection. Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation.
Co-selection phenomena across New Englishes
Authors: Nesselhauf Nadja
Published: April 2009

Similarities of the phraseology of institutionalized second language varieties and foreign learner varieties have gone almost completely unnoticed so far. In this paper, different types of co-selection phenomena are examined across ESL and EFL varieties on the basis of the ICE-corpora of Kenyan, Indian, Singaporean, and Jamaican English and of ICLE, the International Corpus of Learner English. Among the features investigated are the use of competing collocations such as play a role and play a part, the noun complementation of collocations (HAVE + INTENTION + of -ing vs. to + infinitive), and non-L1 (or “new”) prepositional verbs such as comprise of, demand for or emphasize on. The exploration shows that many co-selection phenomena do indeed recur not only across individual institutionalized L2 varieties but also across the two variety types. Certain kinds of language-internal irregularities in the phraseology of Standard English are shown to be a major reason for the observed parallels
Collostructional nativisation in New Englishes
Authors: Mukherjee Joybrato , Gries Stefan Th.
Published: April 2009

The present paper investigates the strength of verb-construction associations across various New Englishes on the basis of comparable corpora. In contrast to previous studies into verb complementation in New Englishes, we start off from three basic constructions in English — the intransitive, the monotransitive and the ditransitive construction — and analyse the co-occurrences of the three constructions and a wide range of verbs. The present study is based on the Hong Kong, the Indian, and the Singapore components of the International Corpus of English (ICE) because the three varieties represent markedly different stages in the process of the evolution of New Englishes with British English as the historical input variety. Our quantitative analysis includes multiple distinctive collexeme analyses for the different varieties. The results show, inter alia, that, firstly, processes of structural nativisation of New Englishes can also be observed at the level of verb-construction associations, which can be subsumed under the notion of “collostructional nativisation”, and that, secondly, there are identifiable intervarietal differences between British English and New Englishes as well as between individual New Englishes. In general, there is a correlation between the evolutionary stage of a New English variety and its collostructional nativisation: The more advanced a New English variety is in the developmental cycle, the more dissimilar its collostructional preferences are to British English.
Pragmatic functions of reported speech with jako in the Old Russian Primary Chronicle
Authors: Perelmutter Renee
Published: April 2009

This article, in an attempt to add to the growing literature on Old Russian reported speech, considers the pragmatics of jako recitativum, i.e. direct discourse introduced by the particle jako ‘that, how’, a multifunctional conjunction with a variety of subordinating uses. Through a detailed pragmatic and quantitative analysis of corpus data, I show that in the Old Russian Primary Chronicle, jako recitativum contrasts two conflicting points of orientation, the narrator’s and the speaker’s. By using the construction with jako, the narrator expresses a negative and/or distancing attitude towards the content of the speaker’s utterance. The contrast between reported speech with jako and reported speech without jako is shown to be more significant than the contrast between direct and indirect discourse.
“Be steady then, my countrymen, be firm, united and determined”
Authors: Levorato Alessandra
Published: April 2009

This paper examines the linguistic resources adopted by pamphlet writers to express their stance and engage their readers during the so-called Irish paper war that preceded the 1800 Union between Great Britain and Ireland. The data (about 100,000 words) consists of 23 pamphlets divided, according to their position in the debate, into two sub-corpora of approximately the same number of words. My purpose in this paper is to investigate the communicative and rhetorical functionality of the linguistic features writers use to express their stance towards the union, with a view to determining how writers establish themselves as morally and intellectually authoritative in their texts. The analysis brings out the crucial role lexico-grammatical patterns play, but also demonstrates the need for a broader interactive perspective, in order to fully account for the dynamics of persuasive discourse.
Impact of a hypomorphic Artemis disease allele on lymphocyte development, DNA end processing, and genome stability
Authors: Huang Ying , Giblin William , Kubec Martina , Westfield Gerwin , St. Charles Jordan , Chadde Laurel , Kraftson Stephanie , Sekiguchi JoAnn
Published: April 2009

Artemis was initially discovered as the gene inactivated in human radiosensitive T−B− severe combined immunodeficiency, a syndrome characterized by the absence of B and T lymphocytes and cellular hypersensitivity to ionizing radiation. Hypomorphic Artemis alleles have also been identified in patients and are associated with combined immunodeficiencies of varying severity. We examine the molecular mechanisms underlying a syndrome of partial immunodeficiency caused by a hypomorphic Artemis allele using the mouse as a model system. This mutation, P70, leads to premature translation termination that deletes a large portion of a nonconserved C terminus. We find that homozygous Artemis-P70 mice exhibit reduced numbers of B and T lymphocytes, thereby recapitulating the patient phenotypes. The hypomorphic mutation results in impaired end processing during the lymphoid-specific DNA rearrangement known as V(D)J recombination, defective double-strand break repair, and increased chromosomal instability. Biochemical analyses reveal that the Artemis-P70 mutant protein interacts with the DNA-dependent protein kinase catalytic subunit and retains significant, albeit reduced, exo- and endonuclease activities but does not undergo phosphorylation. Together, our findings indicate that the Artemis C terminus has critical in vivo functions in ensuring efficient V(D)J rearrangements and maintaining genome integrity.
Control of T helper cell differentiation through cytokine receptor inclusion in the immunological synapse
Authors: Maldonado Roberto A. , Soriano Michelle A. , Perdomo L. Carolina , Sigrist Kirsten , Irvine Darrell J. , Decker Thomas , Glimcher Laurie H.
Published: April 2009

The antigen recognition interface formed by T helper precursors (Thps) and antigen-presenting cells (APCs), called the immunological synapse (IS), includes receptors and signaling molecules necessary for Thp activation and differentiation. We have recently shown that recruitment of the interferon-γ receptor (IFNGR) into the IS correlates with the capacity of Thps to differentiate into Th1 effector cells, an event regulated by signaling through the functionally opposing receptor to interleukin-4 (IL4R). Here, we show that, similar to IFN-γ ligation, TCR stimuli induce the translocation of signal transducer and activator of transcription 1 (STAT1) to IFNGR1-rich regions of the membrane. Unexpectedly, STAT1 is preferentially expressed, is constitutively serine (727) phosphorylated in Thp, and is recruited to the IS and the nucleus upon TCR signaling. IL4R engagement controls this process by interfering with both STAT1 recruitment and nuclear translocation. We also show that in cells with deficient Th1 or constitutive Th2 differentiation, the IL4R is recruited to the IS. This observation suggest that the IL4R is retained outside the IS, similar to the exclusion of IFNGR from the IS during IL4R signaling. This study provides new mechanistic cues for the regulation of lineage commitment by mutual immobilization of functionally antagonistic membrane receptors.
Brazilian Propolis Suppresses Angiogenesis by Inducing Apoptosis in Tube‐Forming Endothelial Cells through Inactivation of Survival Signal ERK1/2
Authors: Kunimasa Kazuhiro , Ahn Mok-Ryeon , Kobayashi Tomomi , Eguchi Ryoji , Kumazawa Shigenori , Fujimori Yoshihiro , Nakano Takashi , Nakayama Tsutomu , Kaji Kazuhiko , Ohta Toshiro
Published: April 2009

We recently reported that propolis suppresses tumor‐induced angiogenesis through tube formation inhibition and apoptosis induction in endothelial cells. However, molecular mechanisms underlying such angiogenesis suppression by propolis have not been fully elucidated. The aim of this study was to investigate the effects of ethanol extract of Brazilian propolis (EEBP) on two major survival signals, extracellular signal‐regulated kinase 1/2 (ERK1/2) and Akt, and to elucidate whether changes in these signals were actually involved in antiangiogenic effects of the propolis. Detection by western blotting revealed that EEBP suppressed phosphorylation of ERK1/2, but not that of Akt. Pharmacological inhibition by U0126 demonstrated that ERK1/2 inactivation alone was enough to inhibit tube formation and induce apoptosis. It was also shown that EEBP and U0126 similarly induced activation of caspase‐3 and cleavage of poly ADP‐ribose polymerase (PARP) and lamin A/C, all of which are molecular markers of apoptosis. These results indicate that inhibition of survival signal ERK1/2, and subsequent induction of apoptosis, is a critical mechanism of angiogenesis suppression by EEBP.
Temporal and size-related variation in the diet, consumption rate, and daily ration of mackerel tuna (Euthynnus affinis) in neritic waters of eastern Australia
Authors: Griffiths Shane P. , Kuhnert Petra M. , Fry Gary F. , Manson Fiona J.
Published: April 2009

Griffiths, S. P., Kuhnert, P. M., Fry, G. F., and Manson, F. J. 2009. Temporal and size-related variation in the diet, consumption rate, and daily ration of mackerel tuna (Euthynnus affinis) in neritic waters of eastern Australia. – ICES Journal of Marine Science, 66: 720–733. The diet, food consumption, and ration of mackerel tuna (Euthynnus affinis) were studied in Australian neritic waters. Overall, 43 prey taxa were identified from 271 stomachs. The diet was primarily pelagic clupeoids (78% by wet weight, WW; 71% by frequency of occurrence, FO) and demersal fish (19% WW; 32% FO). Multivariate regression tree analysis revealed that temporal differences, followed by fish size, explained most of the variation in the diet composition. Autumn diets differed from those in other seasons because tuna ate virtually only engraulids then. During other seasons, engraulids were still the dominant taxon in the diet, but fish also consumed a greater variety of other prey. Small tuna seemed to target small pelagic crustaceans and teleosts, and medium and large tuna to consume larger pelagic and demersal teleosts. Prey consumption increased with tuna size from 26.42 to 108.03 g d−1 for small and large tuna, respectively. Conversely, daily ration decreased with increasing tuna size from 4.10 to 1.95% body weight per day for medium and large tuna, respectively. Mackerel tuna consumed an estimated 25 036 t year−1 in the study region (170 990 km2). Diet studies are becoming increasingly important in informing ecosystem models, and this study confirmed the need for sampling regimes to capture temporal and size-related variation in diet composition, to maximize the utility of data for use in such models.
Modelling and simulations of the migration of pelagic fish
Authors: Barbaro Alethea , Einarsson Baldvin , Birnir Björn , Sigurðsson Sven , Valdimarsson Héðinn , Pálsson Ólafur Karvel , Sveinbjörnsson Sveinn , Sigurðsson Þorsteinn
Published: April 2009

Barbaro, A., Einarsson, B., Birnir, B., Sigurðsson, S., Valdimarsson, H., Pálsson, Ó. K., Sveinbjörnsson, S., and Sigurðsson, Þ. 2009. Modelling and simulations of the migration of pelagic fish. – ICES Journal of Marine Science, 66: 826–838. We applied an interacting particle model to the Icelandic capelin stock to reproduce the spawning migration route for three different years, successfully predicting the route for 2008. Using available temperature data and approximated currents, and without using artificial forcing terms or a homing instinct, our model was able to reproduce the observed migration routes from all 3 years. By a sensitivity analysis, we identified oceanic temperature and the balance between the influence of interaction among particles and the particles' response to temperature as the control parameters most significant in determining the migration route. One significant contribution of this paper is the inclusion of orders of magnitude more particles than similar models, which affects the global behaviour of the model by propagating information about surrounding temperature through the school more efficiently. To maintain the same dynamics between different simulations, we argue a linear relationship between the time-step, radii of interactions, and the spatial resolution, and we argue that these scale as N−1/2, where N is the number of particles.
The population genetic effects of ancestry and admixture in a subdivided cattle breed
Authors: Bray T. C. , Chikhi L. , Sheppy A. J. , Bruford M. W.
Published: April 2009

The genetic structure of the Dexter, a minority cattle breed with complex demographic history, was investigated using microsatellite markers and a range of statistical approaches designed to detect both admixture and genetic drift. Modern representatives of two putative ancestral populations, the Devon and Kerry, together with the different populations of the Dexter, which have experienced different demographic histories, were analysed. Breed units showed comparatively high levels of genetic variability (HE = 0.63–0.68); however, distinct genetic subgroups were detected within the Dexter, which could be attributed to known demographic events. Much lower diversity was identified in three small, isolated Dexter populations (HE = 0.52–0.55) and higher differentiation (FST > 0.13) was found. For one of these populations, where strong selection has taken place, we also found evidence of a demographic bottleneck. Three methods for quantifying breed admixture were applied and substantial method‐based variation in estimates for the genetic contribution of the two proposed ancestral populations for each subdivision of the Dexter was found. Results were consistent only in the case of a group consisting of selected Traditional Dexter animals, where the ancestor of the modern Kerry breed was also determined as the greater parental contributor to the Dexter. The inconsistency of estimation of admixture proportions between the methods highlights the potentially confounding role of genetic drift in shaping small population structure, and the consequences of accurately describing population histories from contemporary genetic data.
Detailed characterization of the porcine MC4R gene in relation to fatness and growth
Authors: Fan B. , Onteru S. K. , Plastow G. S. , Rothschild M. F.
Published: April 2009

In contrast to the human MC4R gene, where multiple variants have been described, several of which are associated with appetite and obesity, few MC4R variants have been reported in the pig. The most interesting polymorphism reported to date in the pig is p.Asp298Asn, which is significantly associated with variation in growth and fatness traits in most breeds and crosses. However, some reports have seemingly failed to confirm this association. The discrepancy of p.Asp298Asn associations in some pig populations suggested that further discovery of SNPs in MC4R would be useful. Utilizing the recently released pig genome sequence information, we obtained the whole MC4R genome sequence and detected five additional SNPs, a variable (CA)n repeat and a C indel in the ISU Berkshire × Yorkshire pig resource family. Linkage disequilibrium (LD) analysis revealed that the additional five SNPs were not in strong LD with p.Asp298Asn, but single marker association analysis indicated that they were significantly (P < 0.05) associated with fatness measures and very highly significantly (P < 0.0001) associated with average daily gain on test (ADGTEST). Three major haplotypes were identified and the subsequent association analyses suggested that the two non‐synonymous SNPs had different effects, e.g. p.Arg236His influenced back fat and growth on test while p.Asp298Asn was primarily associated with variation in growth rate in this population. An interaction effect between these two SNPs was found for ADGTEST, which may partly explain some of the previous discrepancies reported for MC4R in different pig populations. Examination of the p.Arg236His polymorphism in populations where the effect of p.Asp298Asn is limited is warranted.
PRNP haplotype distribution in Moroccan goats
Authors: Serrano C. , Hammouchi M. , Benomar A. , Lyahyai J. , Ranera B. , Acín C. , El Hamidi M. , Monzón M. , Badiola J. J. , Tligui N. , Zaragoza P. , Martín‐Burriel I.
Published: April 2009

Susceptibility/resistance to scrapie in sheep and goats is influenced by host prion protein gene (PRNP) genotype. In this study, we report the analysis of prion protein gene polymorphisms in 137 goats of two Moroccan populations: D’man and Chaouni. We found seven previously described amino acid polymorphisms at codons 37, 127, 137, 142, 154, 222 and 240, as well as three known silent mutations. In addition, we identified three new allelic variants: 101R and 139S in D’man goats and 145D in D’man and Chaouni individuals. The high frequency of the resistant allele 154H could offer genetic protection against the disease to the analysed animals. A total of 12 haplotypes and 28 genotypes were found, the distribution of which shows significant differences between both groups. Moreover, haplotype frequencies were compared with bibliographic data showing that the haplotype distribution of PRNP in Moroccan populations is genetically similar to Southern Italian and Greek goats.
Thymic stromal lymphopoietin, OX40‐ligand, and interleukin‐25 in allergic responses
Authors: Wang Y.‐H. , Liu Y.‐J.
Published: April 2009

Allergic diseases are often triggered by environmental allergens that induce dominant type 2 immune responses, characterized by the infiltrated T‐helper type 2 (TH2) lymphocytes, eosinophils, and elevated TH2 cytokines. In addition to TH2 type immune responses, epithelial stress and injury linked to tissue remodelling are often observed, suggesting that epithelial cells may play important role in regulating allergic responses. Dendritic cells (DCs), the professional antigen‐presenting cells with the capabilities of sampling allergens, are considered as the key player on instructing TH2 immune responses. Whether inflamed epithelium can regulate innate immunity, such as macrophages and DCs, which in turn instructs adaptive immunity has long been hypothesized. Studies of thymic stromal lymphopoietin (TSLP), an epithelial cells‐derived cytokine, that can strongly activate DCs, provide important evidences that the epithelial barrier can trigger allergic diseases by regulating immune responses. The finding that OX40/OX40Ligand (OX40L) interactions are the molecular trigger responsible for the induction and maintenance of TH2 responses by TSLP‐activated DCs provides a plausible molecular explanation for TSLP‐mediated allergy. Recent progresses in characterizing the pro‐inflammatory IL‐17 cytokine family have added an additional layer of complexity on the regulation of allergic inflammation. TSLP–DCs can induce a robust expansion of TH2 memory cells and strengthen functional attributes by up‐regulating their surface expression of IL‐17RB (IL‐25R), the receptor for cytokine IL‐17E (IL‐25), a distinct member of IL‐17 cytokine family. IL‐17E (also known as IL‐25) produced by epithelial cells, and other innate cells, such as eosinphils, basophils, and mast cells, are shown to regulate adaptive immunity by enhancing TH2 cytokine productions. These exciting findings expand our knowledge of the complex immunological cascades that result in allergic inflammation and may provide novel therapeutic approaches for the treatment of allergic diseases.
Association between total immunoglobulin E and antibody responses to naturally acquired Ascaris lumbricoides infection and polymorphisms of immune system-related LIG4, TNFSF13B and IRS2 genes
Authors: Acevedo N , Mercado D , Vergara C , Sánchez J , Kennedy M W , Jiménez S , Fernández A M , Gutiérrez M , Puerta L , Caraballo L
Published: April 2009

The 13q33–34 region harbours a susceptibility locus to Ascaris lumbricoides, although the underlying genes are unknown. Immunoglobulin (Ig)E and IgG confer protective immunity and here we sought to investigate in an endemic population whether LIG4, TNFSF13B and IRS2 genes influence IgE and IgG levels against Ascaris and the ABA-1 allergen as a putative resistance marker. Mite-allergic asthmatic patients were analysed for potential relationships between Ascaris predisposition and allergy. One thousand and sixty-four subjects from Cartagena, Colombia, were included. Single nucleotide polymorphisms (SNPs) were genotyped using TaqMan assays. Antibody levels were measured by enzyme-linked immunosorbent assay. Linear and logistic regressions were used to model effects of genotypes on antibody levels. The GG genotype of LIG4 (rs1805388) was associated with higher IgE levels to Ascaris compared with other genotypes. TNFSF13B (rs10508198) was associated positively with IgG levels against Ascaris extract and IgE levels against ABA-1. In asthmatics, IRS2 (rs2289046) was associated with high total IgE levels. Associations held up after correction by population stratification using a set of 52 ancestry markers, age, sex and disease status. There was no association with asthma or mite sensitization. In a tropical population, LIG4 and TNFSF13B polymorphisms are associated with specific IgE and IgG to Ascaris, supporting previous linkage studies implicating the 13q33 region. Our results suggest that genes protecting against parasite infections can be different to those predisposing to asthma and atopy.
Editor's choice: Disease dynamics in marine metapopulations: modelling infectious diseases on coral reefs
Authors: Sokolow Susanne H. , Foley Patrick , Foley Janet E. , Hastings Alan , Richardson Laurie L.
Published: April 2009

Coral reefs are experiencing devastating mortality due, in part, to emerging disease. Despite this growing problem, the long‐term consequences of infectious disease in marine ecosystems remain poorly understood, and the application of epidemiological models to marine disease systems represents a research priority for managing resources in the world's oceans.

Metapopulation models may provide a framework for modelling coral population dynamics at the regional scale, and we use this approach to investigate the effects of infectious disease. The model presented here incorporates a susceptible‐infected or ‘S‐I’ disease into a system of patchily distributed, dynamic coral hosts, and highlights some basic differences that set many marine disease systems apart from their terrestrial counterparts.

The model predicts several possible long‐term outcomes of disease introduction, and suggests that the consequences of disease may vary considerably among different pathogens and regions. Due to the long time‐scales for coral dynamics, epizootics are expected to be prolonged with recovery slow at the regional scale.

Our model results show how infectious disease can substantially alter host metapopulation dynamics, with some non‐linear relationships which are likely to affect the response of these systems to management and environmental change. For example, higher rates of coral colonization can have variable consequences for host population occupancy (i.e. coral cover) when infectious disease is considered, and chronic diseases with long‐lived pathogens pose the highest risks for regional coral extinction.

Synthesis and applications. We present a tractable epidemiological model within a metapopulation framework and compare the model output with empirical data for a white plague type II (WPII) outbreak among coral of the upper Florida Keys. We conclude that this model fits well with the spatial and temporal patterns of WPII over a decade. Despite terrestrial–marine differences, many patterns derived from our model are consistent with epidemiological principles. Thus, the careful application of these principles within the context of marine management may be a promising research frontier. Although we focus on coral disease, the methods and results may apply to other marine metapopulations.
Stable isotopes (δD) delineate the origins and migratory connectivity of harvested animals: the case of European woodpigeons
Authors: Hobson Keith A. , Lormée Hervé , Van Wilgenburg Steven L. , Wassenaar Leonard I. , Boutin Jean Marie
Published: April 2009

Quantifying connectivity between breeding, stopover, and wintering locations is critical to the management and conservation of migratory animals. Mark–recapture approaches to establishing connectivity are limited due to marking location bias and poor recovery. Alternatively, endogenous markers like stable isotopes can augment extrinsic markers and help to overcome their limitations.

We used a stable hydrogen isotope (δD) isoscape for Europe and δD analysis of feathers from harvested woodpigeons Columba palumbus in France, the Iberian Peninsula, and Corsica to estimate their natal origins.

We propagated error associated with the relationship between deuterium in feathers (δDf) and mean growing‐season precipitation (δDp) for woodpigeons in Europe. For every δDf value, we estimated a range of possible δDp values and used this to map the probability of origin.

We estimated that ~50% of the woodpigeon harvest in France was comprised of residents or from nearby countries to the east. About 30% of the take were medium‐distance migrants, and about 10% were long‐distance migrants from Scandinavia, northwest Russia and the Baltic. A greater proportion of the long‐distance migrants were taken in Spain. In Corsica, birds primarily originated from northern Italy to the Ukraine.

The proportion of northern migrants harvested decreased with latitude, suggesting a leapfrog migration pattern. Birds harvested at lower latitudes showed an inverse relationship between wing length and δDf, which suggested that longer‐distance migrants had longer wings.

Synthesis and applications. This is the first application of stable isotope methodology to quantify population structure and migratory connectivity for a European game species. In addition, we used statistical approaches accounting for potential geospatial assignment errors. Most of the French woodpigeons harvested are resident birds, which suggests that local management of the hunt in France may be most effective. However, southwestern France appeared to take a somewhat greater proportion of migrant woodpigeons, and thus, conservation and management of woodpigeons in France should recognize regional differences. Our approach provided a methodological template that can be applied to questions of migratory connectivity for numerous species of game and non‐game migrant birds.
Protocol‐based care: the standardisation of decision‐making?
Authors: Rycroft‐Malone Jo , Fontenla Marina , Seers Kate , Bick Debra
Published: April 2009

Aim.  To explore how protocol‐based care affects clinical decision‐making.

Background.  In the context of evidence‐based practice, protocol‐based care is a mechanism for facilitating the standardisation of care and streamlining decision‐making through rationalising the information with which to make judgements and ultimately decisions. However, whether protocol‐based care does, in the reality of practice, standardise decision‐making is unknown. This paper reports on a study that explored the impact of protocol‐based care on nurses’ decision‐making.

Design.  Theoretically informed by realistic evaluation and the promoting action on research implementation in health services framework, a case study design using ethnographic methods was used. Two sites were purposively sampled; a diabetic and endocrine unit and a cardiac medical unit.

Methods.  Within each site, data collection included observation, postobservation semi‐structured interviews with staff and patients, field notes, feedback sessions and document review. Data were inductively and thematically analysed.

Results.  Decisions made by nurses in both sites were varied according to many different and interacting factors. While several standardised care approaches were available for use, in reality, a variety of information sources informed decision‐making. The primary approach to knowledge exchange and acquisition was person‐to‐person; decision‐making was a social activity. Rarely were standardised care approaches obviously referred to; nurses described following a mental flowchart, not necessarily linked to a particular guideline or protocol. When standardised care approaches were used, it was reported that they were used flexibly and particularised.

Conclusions.  While the logic of protocol‐based care is algorithmic, in the reality of clinical practice, other sources of information supported nurses’ decision‐making process. This has significant implications for the political goal of standardisation.

Relevance to clinical practice.  The successful implementation and judicious use of tools such as protocols and guidelines will likely be dependant on approaches that facilitate the development of nurses’ decision‐making processes in parallel to paying attention to the influence of context.
Bacillus anthracis HssRS signalling to HrtAB regulates haem resistance during infection
Authors: Stauff Devin L. , Skaar Eric P.
Published: April 2009

Bacillus anthracis proliferates to high levels within vertebrate tissues during the pathogenesis of anthrax. This growth is facilitated by the acquisition of nutrient iron from host haem. However, haem acquisition can lead to the accumulation of toxic amounts of haem within B. anthracis. Here, we show that B. anthracis resists haem toxicity by sensing haem through the HssRS two‐component system, which regulates expression of the haem‐detoxifying transporter HrtAB. In addition, we demonstrate that B. anthracis exhibits elevated HssRS function compared with its evolutionary relative Staphylococcus aureus. Elevated haem sensing is likely required by B. anthracis due to the significant haem sensitivity exhibited by members of the genus Bacilli. We also demonstrate that B. anthracis depends on conserved residues within the previously uncharacterized sensing domain of the histidine kinase HssS for HssS function. Finally, we show that the haem‐ and HssRS‐regulated hrtAB promoter is activated in a murine model of anthrax. These results demonstrate the evolutionary conservation of haem sensing among multiple Gram‐positive bacteria and begin to provide a mechanistic explanation for the haem resistance of B. anthracis. Further, these data suggest that haem stress is experienced by bacterial pathogens during infection.
Inducer responses of BenM, a LysR‐type transcriptional regulator from Acinetobacter baylyi ADP1
Authors: Craven Sarah H. , Ezezika Obidimma C. , Haddad Sandra , Hall Ruth A. , Momany Cory , Neidle Ellen L.
Published: April 2009

BenM and CatM control transcription of a complex regulon for aromatic compound degradation. These Acinetobacter baylyi paralogues belong to the largest family of prokaryotic transcriptional regulators, the LysR‐type proteins. Whereas BenM activates transcription synergistically in response to two effectors, benzoate and cis,cis‐muconate, CatM responds only to cis,cis‐muconate. Here, site‐directed mutagenesis was used to determine the physiological significance of an unexpected benzoate‐binding pocket in BenM discovered during structural studies. Residues in BenM were changed to match those of CatM in this hydrophobic pocket. Two BenM residues, R160 and Y293, were found to mediate the response to benzoate. Additionally, alteration of these residues caused benzoate to inhibit activation by cis,cis‐muconate, positioned in a separate primary effector‐binding site of BenM. The location of the primary site, in an interdomain cleft, is conserved in diverse LysR‐type regulators. To improve understanding of this important family, additional regulatory mutants were analysed. The atomic‐level structures were characterized of the effector‐binding domains of variants that do not require inducers for activation, CatM(R156H) and BenM(R156H,T157S). These structures clearly resemble those of the wild‐type proteins in their activated muconate‐bound complexes. Amino acid replacements that enable activation without effectors reside at protein interfaces that may impact transcription through effects on oligomerization.
Calcineurin inhibitor minimization in pediatric liver allograft recipients
Authors: Dell‐Olio Dominic , Kelly Deirdre A.
Published: April 2009

Abstract:  The use of CNI in pediatric LTx has dramatically improved the outcome for children with end‐stage liver disease by significantly reducing the rate of acute and chronic rejection. Long‐term concerns about CNI‐induced nephrotoxicity and other adverse effects remain an issue, particularly as the emphasis moves from short‐term survival to long‐term quality of life. This review summarizes lessons learnt from pediatric and adult solid organ transplantation in minimizing CNI use in immunosuppression protocols in children following LTx. There are three models for CNI minimization: dose reduction, withdrawal or avoidance, supplemented by the use of IL‐2 receptor blocking antibodies in the peri‐transplant period, and early transition to alternate drugs such as MMF or SRL. Prospective studies evaluating reduction or withdrawal protocols in adult and pediatric LTx indicate that rejection rates are comparable with traditional CNI‐based immunosuppression and that two and five yr patient and graft survival are similar, with recovery in renal function. There are few studies evaluating complete avoidance of CNI, apart from that in renal transplantation, although the benefits of long‐term reduction in cardiovascular, metabolic, and possibly neoplastic side effects may justify this approach. It is not clear yet how CNI minimization will affect the development of tolerance but experimental and preliminary clinical studies indicate that CNI and steroid avoidance or minimization in the peri‐operative period may favor the development of long‐term graft tolerance. In summary, CNI minimization may be safe and effective in the short term but large‐scale pediatric randomized studies are required to evaluate the long‐term efficacy of these regimes in the development of chronic rejection, PTLD, and graft tolerance.
Temperature‐dependent developmental model of Neoseiulus californicus (McGregor) (Acari, Phytoseiidae)
Authors: Kim T. , Ahn J. , Lee J.‐H.
Published: April 2009

The developmental time and survival of immature stages of Neoseiulus californicus were studied at nine constant temperatures (12, 16, 24, 24, 28 32, 36, 38 and 40°C), 60–70% RH, and a photoperiod of 16 : 8 (L : D) h. The total mortality of immature N. californicus was lowest at 24°C (4.5%) and highest at 38°C (15.2%). The total developmental time decreased with increasing temperature between 12°C (18.38 days) and 32°C (2.98 days), and increased beyond 32°C. The relationship between the developmental rate and temperature was fitted by five nonlinear developmental rate models (Logan 6, Lactin 1, 2 and Briere 1, 2). The nonlinear shape of temperature development was best described by the Lactin 1 model (r2 = 0.98). The developmental variation of each stage was well described by the three‐parameter Weibull distribution model (r2 = 0.91–0.93). The temperature‐dependent developmental models of N. californicus developed in this study could be used to determine optimal temperature conditions for its mass rearing, to predict its seasonal population dynamics in fruit tree orchards or greenhouse crops, or to develop a population dynamics model of N. californicus.
Tobacco smoke exposure in hospitalised Aboriginal children in Central Australia
Authors: Hudson Lee , White Andrew , Roseby Rob
Published: April 2009

Aim:  Child exposure to tobacco smoke is detrimental to health. Australian Aboriginal people have a higher rate of cigarette smoking compared with the national average. Thus, we aim to measure the proportion of children admitted to Alice Springs Hospital who are exposed to tobacco smoke at home, to correlate this with prevalence of regular cough and gauge smokers' interest in quitting.

Method:  A questionnaire was administered verbally to carers of children admitted to Alice Springs Hospital, November 2006 to January 2007. Main outcome measures were presence of a smoker at home and presence of a regular cough. We measured the interest of carers and speculated interest of other smokers in quitting. Eighty‐two questionnaires were completed (60% of children admitted during the study period). Eighty‐nine per cent of children were Aboriginal.

Results:  As so few non‐Aboriginal children were included in the study, their results were not included in analysis. Sixty‐four per cent of children lived with at least one smoker. Seventy per cent of children exposed to smoke at home lived with more than one smoker. Point prevalence of reported regular cough was 33%. Forty‐three per cent of children who lived with at least one smoker had regular cough compared with 13% in those who did not (P= 0.035). The rate ratio for regular cough when living with a smoker versus when not living with a smoker was 2.77 (95% confidence interval: 1.06–7.23). Forty‐two per cent of the smokers expressed interest in quitting.

Conclusion:  It is concerning that the majority of hospitalised children were exposed to tobacco smoke at home, while fewer than half of smokers were interested in quitting.
Milk curd obstruction in premature infants receiving fortified expressed breast milk
Authors: Wagener Silke , Cartwright David , Bourke Christopher
Published: April 2009

Aim:  Milk curd obstruction is one of the less common causes of neonatal bowel obstruction. It has been described in premature infants who received high caloric formula feeds. We report presentation, management and outcome of premature neonates who developed milk curd obstruction while being fed fortified expressed breast milk.

Methods:  A retrospective case note review of babies who were treated for milk curd obstruction in Royal Children's Hospital and Mater Children's Hospital in Brisbane between 2001 and 2007 was performed.

Results:  Nine preterm neonates developed milk curd obstruction (mean gestational age 27 weeks). All babies received ortified expressed breast milk. Symptoms presented were those of bowel obstruction in the majority of cases. Laparotomy was required in eight babies, one had a pre‐existing ileostomy that was washed out. Two babies died shortly after surgery, while two followed several months later.

Conclusion:  The diagnosis of milk curd obstruction should be considered in all premature babies with signs of bowel obstruction who are fed expressed breast milk with caloric fortification.
New electrophysiological mapping combined with MRI in parkinsonian’s subthalamic region
Authors: Coste J. , Ouchchane L. , Sarry L. , Derost P. , Durif F. , Gabrillargues J. , Hemm S. , Lemaire J. J.
Published: April 2009

The subthalamic nucleus (STN) is the main target for deep brain stimulation in Parkinson’s disease. We analysed the relationships between magnetic resonance imaging (MRI) anatomy and spontaneous neuronal activity to confirm the potential of microelectrode recordings to assist in determining the optimal surgical target. Ten bilateral surgeries were performed after 1.5‐T (T2‐weighted) anatomical MRI identification of the STN, zona incerta (ZI), Forel’s field H2 (H2) and substantia nigra (SN). Spontaneous neuronal activity was recorded simultaneously along the distal 10 mm on a central track (optimally covering the STN) and a 2‐mm anterior track. We calculated off‐line mean firing rate and burst frequency on 248 neurons clustered according to anatomical structure. Subjective visual analysis of signal was also realized on‐line, during surgery, to classify patterns of activity. Mean firing rate and burst frequency increased from H2–ZI to SN. The mean firing rate was higher in SN only using paired comparison (SN vs. its neighbours). The burst frequency was lower in H2 than in SN; using comparison with neighbours, it was lower in H2 and ZI. An irregular high activity (type 2C) was more often detected in STN and SN than in H2 and ZI. Anatomical boundaries and unitary recordings appear to be linked, supporting the ability of MRI to provide a detailed anatomy. Electrophysiological mapping combined with MRI is a useful tool for precise targeting in the subthalamic region.
TRPA1‐mediated responses in trigeminal sensory neurons: interaction between TRPA1 and TRPV1
Authors: Salas Margaux M. , Hargreaves Kenneth M. , Akopian Armen N.
Published: April 2009

The transient receptor potential (TRP)A1 channel is involved in the transduction of inflammation‐induced noxious stimuli from the periphery. Previous studies have characterized the properties of TRPA1 in heterologous expression systems. However, there is little information on the properties of TRPA1‐mediated currents in sensory neurons. A capsaicin‐sensitive subset of rat and mouse trigeminal ganglion sensory neurons was activated with TRPA1‐specific agonists, mustard oil and the cannabinoid WIN55,212. Mustard oil‐ and WIN55,212‐gated currents exhibited marked variability in their kinetics of activation and acute desensitization. TRPA1‐mediated responses in neurons also possess a characteristic voltage dependency with profound outward rectification that is influenced by extracellular Ca2+ and the type and concentration of TRPA1‐specific agonists. Examination of TRPA1‐mediated responses in TRPA1‐containing cells indicated that the features of neuronal TRPA1 are not duplicated in cells expressing only TRPA1 and, instead, can be restored only when TRPA1 and TRPV1 channels are coexpressed. In summary, our results suggest that TRPA1‐mediated responses in sensory neurons have distinct characteristics that can be accounted for by the coexpression of the TRPV1 and TRPA1 channels.
Reconstructing Christian Ethics: Exploring Constructivist Practices for Teaching Christian Ethics in the Masters of Divinity Curriculum
Authors: Danaher William
Published: April 2009

This article reflects on an effort to incorporate constructivist pedagogies (learner‐centered, inquiry‐guided, problem‐based models of teaching) into an introductory class on Christian Ethics in an M.Div. curriculum. Although some students preferred more traditional pedagogies, the majority found that constructivist pedagogies better accommodated different life experiences, diverse learning styles, and other features of the M.Div. curriculum. Further, a qualitative assessment of one student exercise indicates that constructivist pedagogies have benefits over traditional pedagogies. Specifically, students' work on a learning‐group research project displayed creativity, depth, and breadth not found in individual research papers. Nonetheless, lukewarm student feedback also demonstrated the need to consider wider factors when attempting such innovations.
Understanding Predictors of Low Physical Activity in Adults with Intellectual Disabilities
Authors: Finlayson Janet , Jackson Alison , Cooper Sally‐Ann , Morrison Jillian , Melville Craig , Smiley Elita , Allan Linda , Mantry Dipali
Published: April 2009

Background  Lack of regular physical activity is globally one of the most significant risks to health. The main aims of this study were to describe the types and levels of regular physical activity undertaken by adults with intellectual disabilities, and to investigate the factors predicting low activity.

Materials and Methods  Interviews were conducted with a community‐based sample of adults with intellectual disabilities (n = 433) at two time points. Data hypothesized to be predictive of low levels of activity were collected at time 1. Descriptive data were collected on the frequency and intensity, and actual level of participation in activities at time 2.

Results  Only 150 (34.6%) adults with intellectual disabilities undertook any regular activity of at least moderate intensity. This was of shorter duration, compared with the general population. Older age, having immobility, epilepsy, no daytime opportunities, living in congregate care and faecal incontinence were independently predictive of low levels of activity.

Conclusions  These results are a step towards informing the development of interventions to promote the health of adults with intellectual disabilities through increased physical activity.
Breaking Out of a Distinct Social Space: Reflections on Supporting Community Participation for People with Severe and Profound Intellectual Disability
Authors: Clement Tim , Bigby Christine
Published: April 2009

Background  Typically people with intellectual disability have small, highly restricted social networks characterized by interactions with other people with intellectual disabilities, family members, and paid workers. The goal of ‘inclusion’ has been central to policies that have shaped services over the past 30 years. It is an ill defined concept with disagreement about its meaning, the problems it seeks to overcome and how it should be realized.

Method  Ethnographic and action research methods were used to support and collect data on the implementation of a programme, known as the Community Inclusion Framework, in a group home for five adults with severe intellectual disabilities in Victoria, Australia.

Results and Conclusions  A pattern of service delivery based on community presence rather than participation evolved and endured over 16 months. The findings show that most staff attached a different meaning to inclusion from that proposed in the Community Inclusion Framework, disagreed with the proposed meaning or felt these residents were too different for it to be meaningful. This suggests that priority will only be accorded to activities that lead to inclusion if staff are convinced of the veracity of this and given strong and consistent direction and support.
The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices isolate 494 and implications for the phylogenetic placement of Glomus
Authors: Lee Jaikoo , Young J. Peter W.
Published: April 2009

DOI: 10.1111/j.1469-8137.2009.02885.xCommentary p 3