bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of protein binding surfaces using surface triplet propensities
Authors: Mehio Wissam , Kemp Graham J.L. , Taylor Paul , Walkinshaw Malcolm D.
Published: September 2010

Motivation: The ability to reliably predict protein–protein and protein–ligand interactions is important for identifying druggable binding sites and for understanding how proteins communicate. Most currently available algorithms identify cavities on the protein surface as potential ligand recognition sites. The method described here does not explicitly look for cavities but uses small surface patches consisting of triplets of adjacent surface atomic groups that can be touched simultaneously by a probe sphere representing a solvent molecule. A total of 455 different types of triplets can be identified. A training set of 309 protein–ligand protein X-ray structures has been used to generate interface propensities for the triplets, which can be used to predict their involvement in ligand–binding interactions.

Results: The success rate for locating protein–ligand binding sites on protein surfaces using this new surface triplet propensities (STP) algorithm is 88% which compares well with currently available grid-based and energy-based approaches. Q-SiteFinder's dataset (Laurie and Jackson, 2005. Bioinformatics, 21, 1908–1916) was used to show the favorable performance of STP. An analysis of the different triplet types showed that higher ligand binding propensity is related to more polarizable surfaces. The interaction statistics between triplet atoms on the protein surface and ligand atoms have been used to estimate statistical free energies of interaction. The ΔGstat for halogen atoms interacting with hydrophobic triplets is −0.6 kcal/mol and an estimate of the maximal ΔGstat for a ligand atom interacting with a triplet in a binding pocket is −1.45 kcal/mol.

Availability: Freely available online at http://opus.bch.ed.ac.uk/stp. Website implemented in Php, with all major browsers supported.

Contact:  m.walkinshaw@ed.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
The mRNA landscape at yeast translation initiation sites
Authors: Robbins-Pianka A. , Rice M. D. , Weir M. P.
Published: September 2010

Summary: Although translation initiation has been well studied, many questions remain in elucidating its mechanisms. An ongoing challenge is to understand how ribosomes choose a translation initiation site (TIS). To gain new insights, we analyzed large sets of TISs with the aim of identifying common characteristics that are potentially of functional importance. Nucleotide sequence context has previously been demonstrated to play an important role in the ribosome's selection of a TIS, and mRNA secondary structure is also emerging as a contributing factor.

Here, we analyze mRNA secondary structure using the folding predictions of the RNAfold algorithm. We present a method for analyzing these results using a rank-ordering approach to assess the overall degree of predicted secondary structure in a given region of mRNA. In addition, we used a modified version of the algorithm that makes use of only a subset of the standard version's output to incorporate base-pairing polarity constraints suggested by the ribosome scanning process. These methods were employed to study the TISs of 1735 genes in Saccharomyces cerevisiae.

Trends in base composition and base-pairing probabilities suggest that efficient translation initiation and high protein expression are aided by reduced secondary structure upstream and downstream of the TIS. However, the downstream reduction is not observed for sets of TISs with nucleotide sequence contexts unfavorable for translation initiation, consistent with previous suggestions that secondary structure downstream of the ribosome can facilitate TIS recognition.

Contact:  mweir@wesleyan.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A combined Gadget/FLR model for management strategy evaluations of the Barents Sea fisheries
Authors: Howell Daniel , Bogstad Bjarte
Published: September 2010

Howell, D., and Bogstad, B. 2010. A combined Gadget/FLR model for management strategy evaluations of the Barents Sea fisheries. – ICES Journal of Marine Science, 67: 1998–2004. A biologically sensible age–length structured multispecies Gadget model (incorporating minke whales, cod, herring, and capelin) for the Barents Sea—acting as the operating model—has been linked to Fisheries Library in R—acting as the management procedure—to perform management strategy evaluations. Assessments may be run using either XSA, survey-based methods, or by taking modelled stock numbers directly. Total allowable catches are based on the assessment and harvest control rules (HCRs). The tool can be used for assessing a wide variety of sources of uncertainties within the assessment process. Model structure and linkages are described and a fit to the historical data is presented. A base case of future dynamic (non-steady state) stock trends, based on the existing HCRs, is compared with alternative management and environmental scenarios. The relative differences for each scenario in terms of stock size and catches highlight a number of uncertainties within the biological and fisheries system. The results indicate that the current management rules are robust to the range of scenarios examined so far.
Integrating vessel monitoring systems (VMS) data with daily catch data from logbooks to explore the spatial distribution of catch and effort at high resolution
Authors: Gerritsen Hans , Lordan Colm
Published: September 2010

Gerritsen, H., and Lordan, C. 2011. Integrating vessel monitoring systems (VMS) data with daily catch data from logbooks to explore the spatial distribution of catch and effort at high resolution. – ICES Journal of Marine Science, 68: 245–252. Vessel monitoring systems (VMS) automatically collect positional data from fishing vessels, and the data can be linked to catch data from logbooks to provide a census of spatially resolved catch-and-effort data. The most appropriate and practical method for integrating Irish VMS and logbook data is explored and validated. A simple speed rule is applied to identify VMS records that correspond to fishing activity. The VMS data are then integrated with the catch data from logbooks using date and vessel identifier. Several assumptions were investigated, and the resulting distribution maps of catch and effort appear to be unbiased. The method is illustrated with an example of a time-series of spatially explicit estimates of catch per unit effort. The proposed method is relatively simple and does not require specialist software or computationally intensive methods. It will be possible to generalize this approach to similar datasets that are available within the EU and many other regions. Analysis of integrated VMS and logbook data will allow fisheries data to be analysed on a considerably finer spatial scale than was possible previously, opening up a range of potential applications.
Analysis of the CYP1A1 mRNA Dose-Response in Human Keratinocytes Indicates that Relative Potencies of Dioxins, Furans, and PCBs Are Species and Congener Specific
Authors: Sutter Carrie H. , Bodreddigari Sridevi , Sutter Thomas R. , Carlson Erik A. , Silkworth Jay B.
Published: September 2010

Reports indicate that toxic equivalency factors (TEFs) based primarily on rodent data do not accurately predict in vitro human responsiveness to certain dioxin-like chemicals (DLCs). To investigate this in cells responsive to dioxins and relevant to chloracne, normal human epidermal keratinocytes were treated with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and several DLCs, each with a TEF value of 0.1, representing three classes of congeners. We estimated half maximal effective concentration (EC50)–based donor-specific relative potency (REP) values for cytochrome P450 1A1 (CYP1A1) messenger RNA (mRNA) induction for TCDD, 1,2,3,6,7,8-hexachlorodibenzo-p-dioxin (HxCDD), 2,3,7,8-tetrachlorodibenzofuran (TCDF), 1,2,3,6,7,8-hexachlorodibenzofuran (HxCDF), and 3,3′,4,4′,5-pentachlorobiphenyl (PCB 126). We also determined EC50-based population-level REP values (n = 4) for CYP1A1 mRNA induction for TCDD, HxCDF, and PCB 126. Furthermore, an alternative factor, the relative threshold factor (RTF) based on the low end (threshold) of the dose-response curve, was calculated. Our results demonstrated that HxCDF had a population-based REP value of 0.98, 9.8-fold higher than its assigned TEF value of 0.1. Conversely, PCB 126 had an REP value of 0.0027 and an RTF of 0.0022, 37-fold and 45-fold less than its assigned TEF of 0.1, respectively. The REP values for HxCDD and TCDF were 0.24 and 0.10, respectively, similar to their assigned value of 0.1. Therefore, although the DLCs tested in the current study all possessed the same assigned TEF value of 0.1, congener-specific differences in REPs and RTFs were observed for human keratinocytes. These congener-specific discrepancies are likely because of differences in interspecies factors that have yet to be defined.
Storage Stability of Flour‐Blasted Brown Rice
Authors: Guraya Harmeet S. , Patindol James A.
Published: September 2010

Brown rice was blasted with rice flour rather than sand in a sand blaster to make microperforations so that water could easily penetrate the brown rice endosperm and cook the rice in a shorter time. The flour‐blasted American Basmati brown rice, long‐grain brown rice, and parboiled long‐grain brown rice samples were stored in Ziploc storage bags under atmospheric conditions and in vacuum‐packed bags. They were periodically tested for over 10 months for changes in water absorption, free fatty acid (FFA), peroxide value (POV), viscosity changes of flour using the Rapid ViscoAnalyser (RVA), and texture of whole cooked kernel using a texture analyzer during cooking. Flour‐blasted brown rice absorbed less water but needed less cooking time than its counterpart that was not flour‐blasted. There was an increase in FFA, POV, peak viscosity (PV), final viscosity (FV), breakdown viscosity (BD), and setback viscosity (SB) during storage of flour‐blasted brown rice for 300 days, but no change was observed in texture (hardness, gumminess) and water absorption. The combined coefficient of correlation (including all types of rice) between FFA and FV is r = 0.86 and between FFA and SB is r = 0.90 at P < 0.0001.
Citrus Sudden Death Is Transmitted by Graft-Inoculation and Natural Transmission Is Prevented by Individual Insect-Proof Cages
Authors: Yamamoto Pedro T. , Bassanezi Renato B. , Wulff Nelson A. , Santos Mateus A. , Sanches André L. , Toloy Rodrigo S. , Gimenes-Fernandes Nelson , Ayres Antonio J. , Jesus Junior Waldir C. , Nagata Tatsuya , Tanaka Francisco A. O. , Kitajima Elliot W. , Bové Joseph M.
Published: September 2010

Citrus sudden death (CSD) transmission was studied by graft-inoculation and under natural conditions. Young sweet orange trees on Rangpur rootstock were used as indicator plants. They were examined regularly for one or two characteristic markers of CSD: (i) presence of a yellow-stained layer of thickened bark on the Rangpur rootstock, and (ii) infection with the CSD-associated marafivirus. Based on these two markers, transmission of CSD was obtained, not only when budwood for graft-inoculation was taken from symptomatic, sweet orange trees on Rangpur, but also when the budwood sources were asymptomatic sweet orange trees on Cleopatra mandarin, indicating that the latter trees are symptomless carriers of the CSD agent. For natural transmission, 80 young indicator plants were planted within a citrus plot severely affected by CSD. Individual insect-proof cages were built around 40 indicator plants, and the other 40 indicator plants remained uncaged. Only two of the 40 caged indicator plants were affected by CSD, whereas 17 uncaged indicator plants showed CSD symptoms and were infected with the marafivirus. An additional 12 uncaged indicator plants became severely affected with citrus variegated chlorosis and were removed. These results strongly suggest that under natural conditions, CSD is transmitted by an aerial vector, such as an insect, and that the cages protected the trees against infection by the vector.
A Bayesian Approach to Meta-Analysis of Plant Pathology Studies
Authors: Mila A. L. , Ngugi H. K.
Published: September 2010

Bayesian statistical methods are used for meta-analysis in many disciplines, including medicine, molecular biology, and engineering, but have not yet been applied for quantitative synthesis of plant pathology studies. In this paper, we illustrate the key concepts of Bayesian statistics and outline the differences between Bayesian and classical (frequentist) methods in the way parameters describing population attributes are considered. We then describe a Bayesian approach to meta-analysis and present a plant pathological example based on studies evaluating the efficacy of plant protection products that induce systemic acquired resistance for the management of fire blight of apple. In a simple random-effects model assuming a normal distribution of effect sizes and no prior information (i.e., a noninformative prior), the results of the Bayesian meta-analysis are similar to those obtained with classical methods. Implementing the same model with a Student's t distribution and a noninformative prior for the effect sizes, instead of a normal distribution, yields similar results for all but acibenzolar-S-methyl (Actigard) which was evaluated only in seven studies in this example. Whereas both the classical (P = 0.28) and the Bayesian analysis with a noninformative prior (95% credibility interval [CRI] for the log response ratio: –0.63 to 0.08) indicate a nonsignificant effect for Actigard, specifying a t distribution resulted in a significant, albeit variable, effect for this product (CRI: –0.73 to –0.10). These results confirm the sensitivity of the analytical outcome (i.e., the posterior distribution) to the choice of prior in Bayesian meta-analyses involving a limited number of studies. We review some pertinent literature on more advanced topics, including modeling of among-study heterogeneity, publication bias, analyses involving a limited number of studies, and methods for dealing with missing data, and show how these issues can be approached in a Bayesian framework. Bayesian meta-analysis can readily include information not easily incorporated in classical methods, and allow for a full evaluation of competing models. Given the power and flexibility of Bayesian methods, we expect them to become widely adopted for meta-analysis of plant pathology studies.
Effect of Meloidogyne incognita Inoculum Density and Application Rate of Paecilomyces lilacinus Strain 251 on Biocontrol Efficacy and Colonization of Egg Masses Analyzed by Real-Time Quantitative PCR
Authors: Kiewnick S. , Neumann S. , Sikora R. A. , Frey J. E.
Published: September 2010

The fungal biocontrol agent, Paecilomyces lilacinus strain 251 (PL251), was evaluated for its potential to control the root-knot nematode Meloidogyne incognita on tomato at varying application rates and inoculum densities. Conversely to previous studies, significant dose-response relationships could not be established. However, we demonstrated that a preplanting soil treatment with the lowest dose of commercially formulated PL251 (2 × 105 CFU/g soil) was already sufficient to reduce root galling by 45% and number of egg masses by 69% when averaged over inoculum densities of 100 to 1,600 eggs and infective juveniles per 100 cm3 of soil. To determine the role of colonization of M. incognita egg masses by PL251 for biocontrol efficacy, a real-time quantitative polymerase chain reaction (PCR) assay with a detection limit of 10 CFU/egg mass was used. Real-time PCR revealed a significant relationship between egg mass colonization by PL251 and the dose of product applied to soil but no correlation was found between fungal density and biocontrol efficacy or nematode inoculum level. These results demonstrate that rhizosphere competence is not the key mode of action for PL251 in controlling M. incognita on tomato.
Remarkably low mtDNA control‐region diversity and shallow population structure in Pacific cod Gadus macrocephalus
Authors: Liu M. , Lu Z. C. , Gao T. X. , Yanagimoto T. , Sakurai Y.
Published: September 2010

To investigate the genetic diversity and describe the population structure in Gadus macrocephalus, a 452 base pair (bp) fragment of the mitochondrial DNA control region was analysed in 259 individuals. The results showed remarkably low nucleotide diversity and a lack of genealogical structure. Small but significant genetic differentiations, however, were detected among north‐western Pacific populations, but no large‐scale regional differences were detected. These results indicate that populations of G. macrocephalus in the north‐western Pacific are genetically subdivided and represent evolutionary lineages that should be managed individually.
Oceans apart? Short‐term movements and behaviour of adult bull sharks Carcharhinus leucas in Atlantic and Pacific Oceans determined from pop‐off satellite archival tagging
Authors: Brunnschweiler J. M. , Queiroz N. , Sims D. W.
Published: September 2010

Adult bull sharks Carcharhinus leucas were monitored with electronic tags to investigate horizontal and vertical movements in the Atlantic and Pacific Oceans. In both locations, C. leucas showed some fidelity to specific coastal areas with only limited horizontal movements away from the tagging sites after tag attachment. Fish tagged in the Bahamas were detected mostly in the upper 20 m of the water column in water 25–26° C, whereas C. leucas tagged in Fiji spent most of their time below 20 m in water usually >26° C. The results highlight the importance of coastal inshore habitats for this species.
Non‐tuberculous mycobacterial infections of the skin: A retrospective study of 29 cases
Authors: LEE Woo J. , KANG Seong M. , SUNG Heungsup , WON Chong H. , CHANG Sung E. , LEE Mi W. , KIM Mi N. , CHOI Jee H. , MOON Kee C.
Published: September 2010

The incidence of infections caused by non‐tuberculous mycobacteria has increased in recent years, due to a rise in dermatological procedures and a greater prevalence of immunosuppression in the general population. This study investigated the clinical and microbiological findings of non‐tuberculous mycobacterial skin infections. The study population included 29 patients from whom non‐tuberculous mycobacteria were cultured after isolation from skin biopsy materials, cutaneous abscesses or exudates. Clinical, microbiological and epidemiological data were collected from each patient. Eight patients were immunocompromised while 21 were not. Precipitating factors such as acupuncture, filler injection, surgical procedures and other traumatic events preceded infection in 13 (including 11 normal hosts and two immunocompromised hosts) of the 29 patients. Multiple skin lesions were present in eight patients (including three normal hosts and five immunocompromised hosts). In eight patients (including four immunocompromised hosts), symptoms were accompanied by tenosynovitis, osteomyelitis and myositis. Mycobacterium abscessus was isolated from nine patients, Mycobacterium fortuitum was isolated from nine patients, Mycobacterium chelonae was isolated from six patients, Mycobacterium marinum was isolated from two patients, a Mycobacterium avium complex member was isolated from two patients, and Mycobacterium haemophilum was isolated from one patient. Ten of the 24 cases caused by rapidly growing organisms (i.e. M. chelonae, M. abscessus and M. fortuitum groups) were precipitated by skin injuries such as acupuncture, filler infection and other medical procedures. Increases in skin medical procedures, including both acupuncture and esthetic interventions, explain the increasing incidence of these organisms. Immunocompromised patients tended to develop multiple skin lesions and deep tissue infections.
Screening of marine algae for potential tyrosinase inhibitor: Those inhibitors reduced tyrosinase activity and melanin synthesis in zebrafish
Authors: CHA Seon‐Heui , KO Seok‐Chun , KIM Daekyung , JEON You‐Jin
Published: September 2010

In order to find new anti‐browning and whitening agents in this study, we investigated 43 indigenous marine algae for tyrosinase inhibitory activity. The extracts from Endarachne binghamiae, Schizymenia dubyi, Ecklonia cava (EC) and Sargassum silquastrum (SS) evidenced potent tyrosinase inhibitory activity similar to that of positive control, kojic acid. Among those marine algae, EC and SS are distributed abundantly on Jeju Island. Therefore, we selected those two species for further studies. Our results evidenced that both species reduced cellular melanin synthesis and tyrosinase activity. On the other hand, we utilized zebrafish as an alternative in vivo model. All the tested samples evidenced excellent inhibitory effects on the pigmentation of zebrafish, most likely due to their potential tyrosinase inhibitory activity. In simultaneous in vivo toxicity tests, no toxicity was observed in either algal species, on the other hand, toxicity was observed in positive controls. These results provided that EC and SS extract could be used as an ingredient for whiting cosmetics and that zebrafish is an alternative in vivo model.
Characterization of long-term mixed donor–donor chimerism after double cord blood transplantation
Authors: Gertow J , Berglund S , Okas M , Uzunel M , Berg L , Kärre K , Mattsson J , Uhlin M
Published: September 2010

Double cord blood transplantation (DCBT) with two matched or partially matched cord blood units has been implemented successfully to circumvent the limitations of graft cell dose associated with single CBT. After DCBT, sustained haematopoiesis is derived almost exclusively from only one of the donated units. None the less, we previously observed two of six evaluable DCBT patients still having mixed donor–donor chimerism at 28 and 45 months post-transplantation, respectively. In the present study we utilize flow cytometry techniques to perform the first thorough analysis of phenotype and functionality of cord blood units in patients with mixed donor–donor chimerism. Our results suggest that the two stable cord blood units are different phenotypically and functionally: one unit shows more naive T cells, lower T cell cytokine production and higher frequencies of natural killer cells, the other shows higher frequencies of well-differentiated and functional lymphocytes. Additionally, in comparison with control patients having a single prevailing cord blood unit, the patients with donor–donor chimerism exhibit less overall T cell cytokine production and a smaller fraction of memory T cells. Furthermore, our results indicate that human leucocyte antigen-C match of donor units may partly explain the development of a donor–donor mixed chimerism.
Beneficial effects of cathepsin inhibition to prevent chemotherapy-induced intestinal mucositis
Authors: Alamir I , Boukhettala N , Aziz M , Breuillé D , Déchelotte P , Coëffier M
Published: September 2010

One of the main secondary toxic side effects of anti-mitotic agents used to treat cancer patients is intestinal mucositis. Previous data showed that cathepsin D activity, contributing to the proteolytic lysosomal pathway, is up-regulated during intestinal mucositis in rats. At the same time, cathepsin inhibition limits intestinal damage in animal models of inflammatory bowel diseases. The aim of this study was to evaluate the effects of cathepsin inhibition on methotrexate-induced mucositis in rats. Male Sprague–Dawley rats received saline solution subcutaneously as the control group or 2·5 mg/kg of methotrexate for 3 days (D0–D2). From D0 to D3 methotrexate-treated rats also received intraperitoneal injections of pepstatin A, a specific inhibitor of cathepsin D or E64, an inhibitor of cathepsins B, H and L, or vehicle. Rats were euthanized at D4 and jejunal samples were collected. Body weight and food intake were partially preserved in rats receiving E64 compared with rats receiving vehicle or pepstatin A. Cathepsin D activity, used as a marker of lysosomal pathway, was reduced both in E64 and pepstatin-treated rats. However, villus atrophy and intestinal damage observed in methotrexate-treated rats were restored in rats receiving E64 but not in rats receiving pepstatin A. The intramucosal concentration of proinflammatory cytokines, interleukin-1β and cytokine-induced neutrophil chemoattractant (CINC)-2, was markedly increased in methotrexate-treated rats receiving vehicle or pepstatin A but not after E64 treatment. In conclusion, a large broad inhibition of cathepsins could represent a new potential target to limit the severity of chemotherapy-induced mucositis as opposed to the inhibition of cathepsin D alone.
Nurses’ risk assessment judgements: a confidence calibration study
Authors: Yang Huiqin , Thompson Carl
Published: September 2010

yang h. & thompson c. (2010) Nurses’ risk assessment judgements: a confidence calibration study. Journal of Advanced Nursing 66(12), 2751–2760.

Aim.  This paper is a report of a study of the relationship between nurses’ clinical experience and calibration of their self‐confidence and judgement accuracy for critical event risk assessment judgements.

Background.  Miscalibration (i.e. under‐confidence or over‐confidence of confidence levels) has an important impact on the quality of nursing care. Despite this, little is known about how nurses’ subjective confidence is calibrated with the accuracy of their judgments.

Methods.  A sample of 103 nursing students and 34 experienced nurses were exposed to 25 risk assessment vignettes. For each vignette they made dichotomous judgements of whether the patient in each scenario was at risk of a critical event, and assigned confidence ratings (0–100) to their judgement calls. The clinical vignettes and judgement criteria were generated from real patient cases. The methodology of confidence calibration was used to calculate calibration measures and generate calibration curves. Data were collected between March 2007 and January 2008.

Findings.  Experienced nurses were statistically significantly more confident than students but no more accurate. Whilst students tended towards under‐confidence, experienced nurses were over‐confident. Experienced nurses were no more calibrated than students. Experienced nurses were no better at discriminating between correct and incorrect judgements than students. These patterns were exacerbated when nurses and students were extremely over‐confident or extremely under‐confident.

Conclusion.  Nurses were systematically biased towards over/under‐confidence in their critical event risk assessment judgements. In particular, experienced nurses were no better calibrated than their student counterparts; with student under‐confidence countered by experienced nurses’ greater susceptibility to over‐confidence.
Implementing evidence‐based practice: effectiveness of a structured multifaceted mentorship programme
Authors: Wallen Gwenyth R. , Mitchell Sandra A. , Melnyk Bernadette , Fineout‐Overholt Ellen , Miller‐Davis Claiborne , Yates Janice , Hastings Clare
Published: September 2010

wallen g.r., mitchell s.a., melnyk b., fineout‐overholt e., miller‐davis c., yates j. & hastings c. (2010) Implementing evidence‐based practice: effectiveness of a structured multifaceted mentorship programme.Journal of Advanced Nursing 66(12), 2761–2771.

Aim. This paper is a report of the effectiveness of a structured multifaceted mentorship programme designed to implement evidence‐based practice in a clinical research intensive environment.

Background. Barriers to implementing evidence‐based practice are well‐documented in the literature. Evidence‐based practice is associated with higher quality care and better patient outcomes than care that is steeped in tradition. However, the integration of evidence‐based practice implementation into daily clinical practice remains inconsistent, and the chasm between research and bedside practice remains substantial.

Methods. This quasi‐experimental mixed methods study included three focused discussions with nursing leadership and shared governance staff as well as pre‐ (N = 159) and post‐intervention (N = 99) questionnaires administered between June 2006 and February 2007. Online questionnaires included measures of organizational readiness, evidence‐based practice beliefs, evidence‐based practice implementation, job satisfaction, group cohesion and intent to leave nursing and the current job.

Results. Participants in the evidence‐based practice mentorship programme had a larger increase in perceived organizational culture and readiness for evidence‐based practice and in evidence‐based practice belief scores than those who did not participate. Qualitative findings suggested that leadership support of a culture for evidence‐based practice and the dedication of resources for sustainability of the initiative needed to be a priority for engaging staff at all levels.

Conclusion. These findings corroborate other studies showing that nurses’ beliefs about evidence‐based practice are significantly correlated with evidence‐based practice implementation and that having a mentor leads to stronger beliefs and greater implementation by nurses as well as greater group cohesion, which is a potent predictor of nursing turnover rates.
Association of breathlessness with multiple symptoms in chronic obstructive pulmonary disease
Authors: Borge Christine Råheim , Wahl Astrid K. , Moum Torbjørn
Published: September 2010

borge c.r., wahl a.k. & moum t. (2010) Association of breathlessness with multiple symptoms in chronic obstructive pulmonary disease. Journal of Advanced Nursing 66(12), 2688–2700.

Aim.  This paper is a report of an exploration of relationships between demographic and clinical variables and the symptoms of breathlessness, depression, anxiety, fatigue, sleeping difficulties and pain for patients with chronic obstructive pulmonary disease.

Background.  Research into chronic obstructive pulmonary disease has focused on single symptoms and we lack knowledge about possible associations between several symptoms.

Methods.  A total of 154 patients with chronic obstructive pulmonary disease participated in a cross‐sectional study from June 2006 to December 2007 (response rate 40%). All underwent pulmonary lung function tests and completed questionnaires including demographic variables, the Brief Pain Inventory, Hospital Anxiety and Depression Scale, Lee Fatigue Scale, General Sleep Disturbance Scale and the Respiratory Quality of Life Questionnaire. Bivariate correlation and multiple regression analyses were performed.

Results.  Breathlessness was statistically significantly positively associated with the other symptoms, after controlling for demographic and clinical variables. Younger age was statistically significantly related to more breathlessness, anxiety and sleeping difficulties and lower levels of education was statistically significantly related to more breathlessness, depression and anxiety. In relation to clinical variables, smoking was statistically significantly related to more depression, whereas more co‐morbidity was statistically significantly related to more breathlessness and pain. Poorer lung function was statistically significantly related to more breathlessness. However, higher lung function was related to more sleeping difficulties.

Conclusion.  Breathlessness is associated with symptoms such as depression, anxiety, fatigue, sleeping difficulties and pain, suggesting the need for an expanded focus on symptoms in chronic obstructive pulmonary disease guidelines, health care and research.
Population genetics reveals origin and number of founders in a biological invasion
Authors: FICETOLA GENTILE FRANCESCO , BONIN AURELIE , MIAUD CLAUDE
Published: September 2010

Propagule pressure is considered the main determinant of success of biological invasions: when a large number of individuals are introduced into an area, the species is more likely to establish and become invasive. Nevertheless, precise data on propagule pressure exist only for a small sample of invasive species, usually voluntarily introduced. We studied the invasion of the American bullfrog,Rana catesbeiana,into Europe, a species that is considered a major cause of decline for native amphibians. For this major invader with scarce historical data, we used population genetics data (a partial sequence of the mitochondrial cytochromebgene) to infer the invasion history and to estimate the number of founders of non‐native populations. Based on differences between populations, at least six independent introductions from the native range occurred in Europe, followed by secondary translocations. Genetic diversity was strongly reduced in non‐native populations, indicating a very strong bottleneck during colonization. We used simulations to estimate the precise number of founders and found that most non‐native populations derive from less than six females. This capability of invasion from a very small number of propagules challenges usual management strategies; species with such ability should be identified at an early stage of introduction.
Skin diseases in the alpaca (Vicugna pacos): a literature review and retrospective analysis of 68 cases (Cornell University 1997–2006)
Authors: Scott Danny W. , Vogel Jeff W. , Fleis Rebekah I. , Miller William H. , Smith Mary C.
Published: September 2010

This retrospective study describes 68 alpacas with skin diseases investigated from 1997 through 2006 at Cornell University. During this time period, 40 of 715 (5.6%) alpacas presented to the university hospital had dermatological diseases. In addition, skin‐biopsy specimens accounted for 86 of 353 (24.4%) of alpaca biopsy specimens submitted to the diagnostic laboratory, and of these 86 specimens, follow‐up was available for 28 cases. The following diseases were most common: bacterial infections (22%); neoplasms, cysts and hamartomas (19%); presumed immunological disorders (12%); and ectoparasitisms (10%). Conditions described for the first time included intertrigo, collagen and hair follicle hamartomas, lymphoma, hybrid follicular cysts, melanocytoma, anagen defluxion, telogen defluxion, presumed insect‐bite hypersensitivity, ichthyosis, and possible hereditary bilateral aural haematomas and chondritis. The results of the retrospective study are compared and contrasted with the results of a literature review.
JC virus‐associated nephropathy in a renal transplant recipient and comparative analysis of previous cases
Authors: Kantarci G. , Eren Z. , Demirağ A. , Dogan I. , Çakalagaoglu F. , Yilmaz G.
Published: September 2010

G. Kantarci, Z. Eren, A. Demirağ, I. Dogan, F. Çakalagaoglu, G. Yilmaz. JC virus‐associated nephropathy in a renal transplant recipient and comparative analysis of previous cases. Transpl Infect Dis 2011: 13: 89–92. All rights reserved

Abstract: We report JC virus (JCV)‐associated nephropathy in a renal allograft recipient and summarize the clinical and laboratory data of the 8 previous cases. A 28‐year‐old male renal allograft recipient received a preemptive transplant from his father. Six months later, a kidney biopsy was performed because of deterioration of allograft function. Biopsy revealed tubulointerstitial mononuclear infiltrates with normal glomeruli; on hematoxylin and eosin staining, basophilic nuclear inclusions were seen in the nucleus of tubular cells. Urinary cytology failed to demonstrate decoy cells, but polymerase chain reaction of a urinary sample was positive for JCV 3.15 × 1010 copies/mL. Additionally, polyomavirus (SV40) immunohistochemical staining was performed and was positive in the enlarged nuclei of tubular epithelial cells in the kidney biopsy sample. After the diagnosis of polyomavirus‐associated nephropathy (PVAN) was confirmed by kidney biopsy, immunosuppressive agents were reduced. Intravenous immunoglobulin was administered 5 times at a dose of 500 mg/kg every other 3 weeks. Two months after diagnosis, the serum creatinine became stable and urinary viral load of JCV was decreased. Because viruria was still present, tacrolimus was converted to sirolimus. Four months after immunosuppressive agent conversion from tacrolimus to sirolimus, the viruria had disappeared. Review of the literature and our case demonstrates that male gender, previous acute rejection episode, low incidence of JCV viremia, PVAN pattern B histology, and reducing immunosuppression are the diagnostic touchstones for PVAN due to JCV.
H1N1 infection in a cohort of hematopoietic stem cell transplant recipients: prompt antiviral therapy might be life saving
Authors: Suyani E. , Aki Z. , Güzel Ö. , Altindal Ş. , Şenol E. , Sucak G.
Published: September 2010

E. Suyani, Z. Aki, Ö. Güzel, Ş. Altindal, E. Şenol, G. Sucak. H1N1 infection in a cohort of hematopoietic stem cell transplant recipients: prompt antiviral therapy might be life saving. Transpl Infect Dis 2011: 13: 208–212. All rights reserved

Abstract: Influenza A H1N1 virus, causing a pandemic since spring 2009, has been an important cause of morbidity and mortality worldwide. Patients with hematological malignancies and hematopoietic stem cell transplant (HCT) recipients are in a high‐risk group and might require hospitalization more commonly because of H1N1 infection. Early demonstration of H1N1 influenza virus and commencing antiviral therapy promptly can be life saving particularly in immunosuppressed patients. We retrospectively reviewed the data of 10 HCT recipients who were diagnosed with influenza H1N1 infection at the Stem Cell Transplantation Unit of Gazi University Hospital in Turkey, from October through December 2009. All patients, except 1, were started empirically on oseltamivir on admission, after nasopharyngeal and oropharyngeal sampling for H1N1 virus. Four of the patients, 2 of whom developed pneumonia, required hospitalization. One of the patients with pneumonia died of respiratory failure caused by bacterial co‐infection. The course of the remaining patients was uneventful. In conclusion, HCT recipients infected with H1N1 during the influenza H1N1 pandemic did not necessarily have an adverse prognosis, particularly with prompt administration of the appropriate antiviral therapy.
Enantiomorphs differ in shape in opposite directions between populations
Authors: NAKADERA Y. , SUTCHARIT C. , UBUKATA T. , SEKI K. , UTSUNO H. , PANHA S. , ASAMI T.
Published: September 2010

AbstractDevelopment is left–right reversed between dextral and sinistral morphs of snails. In sympatry, they share the same gene pool, including polygenes for shell shape. Nevertheless, their shell shapes are not the mirror images of each other. This triggered a debate between hypotheses that argue either for a developmental constraint or for zygotic pleiotropic effects of the polarity gene. We found that dextrals can be wider or narrower than sinistrals depending on the population, contrary to the prediction of invariable deviation under a developmental constraint. If the pleiotropy is solely responsible instead, the mean shape of each morph should change, depending on the frequency of polarity genotype. Our simulations of this mean shape change under zygotic pleiotropy, however, show that the direction of interchiral difference remains the same regardless of genotype frequency. Our results suggest the presence of genetic variation among populations that changes the maternal or zygotic pleiotropic effect of the polarity gene.
Duplicate retention in signalling proteins and constraints from network dynamics
Authors: SOYER O. S. , CREEVEY C. J.
Published: September 2010

Duplications are a major driving force behind evolution. Most duplicates are believed to fix through genetic drift, but it is not clear whether this process affects all duplications equally or whether there are certain gene families that are expected to show neutral expansions under certain circumstances. Here, we analyse the neutrality of duplications in different functional classes of signalling proteins based on their effects on response dynamics. We find that duplications involving intermediary proteins in a signalling network are neutral more often than those involving receptors. Although the fraction of neutral duplications in all functional classes increase with decreasing population size and selective pressure on dynamics, this effect is most pronounced for receptors, indicating a possible expansion of receptors in species with small population size. In line with such an expectation, we found a statistically significant increase in the number of receptors as a fraction of genome size in eukaryotes compared with prokaryotes. Although not confirmative, these results indicate that neutral processes can be a significant factor in shaping signalling networks and affect proteins from different functional classes differently.
Collagen cross‐linking: a new treatment paradigm in corneal disease – a review
Authors: Snibson Grant R
Published: September 2010

Abstract

The last 2 years has seen a marked increase in the prominence of corneal collagen cross‐linking as a treatment strategy for progressive keratoconus. This interest has arisen from a body of laboratory evidence documenting the biomechanical and cellular changes induced by cross‐linking. The findings of this research provide a plausible rationale for its use in keratoconus to retard the progression of this common disease. The rapidly growing number of clinical reports suggests, not only a consistent stabilizing effect of cross‐linking, but that a variable improvement in corneal shape and visual function may also occur in some patients. However, the marked variation in the clinical course of keratoconus, together with the challenges of accurately evaluating refractive error, visual acuity and even corneal shape in this condition, demands further evidence from randomized controlled clinical trials. The aim of this review is to summarize the theoretical basis and risks of corneal collagen cross‐linking, along with the available evidence for its use in keratoconus and other corneal disease states.
Early change detection in humans as revealed by auditory brainstem and middle‐latency evoked potentials
Authors: Slabu Lavinia , Escera Carles , Grimm Sabine , Costa‐Faidella Jordi
Published: September 2010

The ability to detect unexpected novel stimuli is crucial for survival, as it might urge a prompt adaptive response. Human auditory novelty detection has been associated to the mismatch negativity long‐latency auditory‐evoked potential, peaking at 100–200 ms. Yet, recent animal studies showing novelty responses at a very short latency (about 20–30 ms) in individual neurons already at the level of the midbrain and thalamus suggest that novelty detection might be a basic principle of the functional organization of the auditory system, expanding from lower levels in the brainstem along the auditory pathway up to higher‐order areas of the cerebral cortex. To test this suggestion, we here measured auditory brainstem and middle latency response (MLR) to frequency novel stimuli embedded in an oddball sequence. To oversee refractoriness confounds a ‘control block’ was used. The results showed that occasional changes in auditory frequency information were detected as early as 30 ms (Pa waveform of the MLR) after stimulus onset. The control block precluded these effects as resulting merely from refractoriness, altogether supporting the notion of ‘true’ early auditory change detection in humans, matching the latency range of auditory novelty responses described in individual neurons of subhuman species. Our results suggest that auditory change detection of frequency information is a multistage process that occurs at the primary auditory cortex and is transmitted to the higher levels of the auditory pathway.
Comparing organic farming and land sparing: optimizing yield and butterfly populations at a landscape scale
Authors: Hodgson Jenny A. , Kunin William E. , Thomas Chris D. , Benton Tim G. , Gabriel Doreen
Published: September 2010

Ecology Letters (2010) 13: 1358–1367

Organic farming aims to be wildlife‐friendly, but it may not benefit wildlife overall if much greater areas are needed to produce a given quantity of food. We measured the density and species richness of butterflies on organic farms, conventional farms and grassland nature reserves in 16 landscapes. Organic farms supported a higher density of butterflies than conventional farms, but a lower density than reserves. Using our data, we predict the optimal land‐use strategy to maintain yield whilst maximizing butterfly abundance under different scenarios. Farming conventionally and sparing land as nature reserves is better for butterflies when the organic yield per hectare falls below 87% of conventional yield. However, if the spared land is simply extra field margins, organic farming is optimal whenever organic yields are over 35% of conventional yields. The optimal balance of land sparing and wildlife‐friendly farming to maintain production and biodiversity will differ between landscapes.
Ability of cystatin C to detect acute changes in glomerular filtration rate provoked by hyperglycaemia in uncomplicated Type 1 diabetes
Authors: Cherney D. Z. I. , Sochett E. B. , Dekker M. G. , Perkins B. A.
Published: September 2010

Diabet. Med. 27, 1358–1365 (2010)

Aims  Systematic study of hyperfiltration in diabetic nephropathy has been hindered by the lack of a simple glomerular filtration rate (GFR) measure that is accurate in this range of renal function. Serum cystatin C (GFRCYSTATIN C) reflects long‐term trends in GFR in normal or elevated ranges. To test whether it can reflect acute changes, we examined the impact of clamped hyperglycaemia on GFRCYSTATIN C and GFRINULIN in subjects with Type 1 diabetes.

Methods  GFRINULIN and GFRCYSTATIN C were measured in 32 normotensive, normoalbuminuric subjects during clamped euglycaemia and hyperglycaemia. For comparison, GFRMDRD was estimated according to the four‐variable equation.

Results  During clamped euglycaemia, agreement between GFRCYSTATIN C and GFRINULIN was excellent, with mean bias +1.9 (90% distribution −29 to +31) ml min−1 1.73 m−2, while GFRMDRD had mean bias +11.4 (−45 to +51) ml min−1 1.73 m−2. With exposure to clamped hyperglycaemia, the mean increase in GFRCYSTATIN C (+17.5 ± 13.5 ml min−1 1.73 m−2) reflected that observed with GFRINULIN (+15.3 ± 28.1 ml min−1 1.73 m−2, P = 0.74), while GFRMDRD demonstrated a mean decline of −4.4 ± 33.6 ml min−1 1.73 m−2 (P = 0.01). In all 24 subjects in whom GFRINULIN increased in response to hyperglycaemia, GFRCYSTATIN C reflected a concordant change (sensitivity, 100%) while GFRMDRD increased in 10/24 (sensitivity, 42%). In the eight remaining subjects, specificity was 25 and 75% for GFRCYSTATIN C and GFRMDRD, respectively.

Conclusion  GFRCYSTATIN C reflects normal and elevated renal function better than GFRMDRD even under the acute influences of hyperglycaemia, suggesting a role for cystatin C in clinical practice and research for the study of early renal function changes in Type 1 diabetes.