bluuebunny/crossref_metadata_2025 huggingface dataset:
14–19 education across Great Britain – convergence or divergence?
Authors: Gunning Dennis , Raffe David
Published: July 2011

This article reviews recent policies for 14–19 learning in Wales and Scotland, and discusses the extent to which these policies have diverged from England following parliamentary devolution in 1999. It distinguishes different types of divergence and suggests that many policy differences
have not been about major issues of educational philosophy or political principle but rather about different ways in which similar policy strands have been woven together in distinct agendas or programmes, and about associated differences in policy styles. Current policy differences do not
necessarily indicate divergence; significant policy differences already existed in 1999.
The fission yeast pleckstrin homology domain protein Spo7 is essential for initiation of forespore membrane assembly and spore morphogenesis
Authors: Nakamura-Kubo Michiko , Hirata Aiko , Shimoda Chikashi , Nakamura Taro
Published: July 2011

Sporulation in fission yeast represents a unique mode of cell division in which a new cell is formed within the cytoplasm of a mother cell. This event is accompanied by formation of the forespore membrane (FSM), which becomes the plasma membrane of spores. At prophase II, the spindle pole body (SPB) forms an outer plaque, from which formation of the FSM is initiated. Several components of the SPB play an indispensable role in SPB modification, and therefore in sporulation. In this paper, we report the identification of a novel SPB component, Spo7, which has a pleckstrin homology (PH) domain. We found that Spo7 was essential for initiation of FSM assembly, but not for SPB modification. Spo7 directly bound to Meu14, a component of the leading edge of the FSM, and was essential for proper localization of Meu14. The PH domain of Spo7 had affinity for phosphatidylinositol 3-phosphate (PI3P). spo7 mutants lacking the PH domain showed aberrant spore morphology, similar to that of meu14 and phosphatidylinositol 3-kinase (pik3) mutants. Our study suggests that Spo7 coordinates formation of the leading edge and initiation of FSM assembly, thereby accomplishing accurate formation of the FSM.
Membrane aberrancy and unfolded proteins activate the endoplasmic reticulum stress sensor Ire1 in different ways
Authors: Promlek Thanyarat , Ishiwata-Kimata Yuki , Shido Masahiro , Sakuramoto Mitsuru , Kohno Kenji , Kimata Yukio
Published: July 2011

Eukaryotic cells activate the unfolded-protein response (UPR) upon endoplasmic reticulum (ER) stress, where the stress is assumed to be the accumulation of unfolded proteins in the ER. Consistent with previous in vitro studies of the ER-luminal domain of the mutant UPR initiator Ire1, our study show its association with a model unfolded protein in yeast cells. An Ire1 luminal domain mutation that compromises Ire1's unfolded-protein–associating ability weakens its ability to respond to stress stimuli, likely resulting in the accumulation of unfolded proteins in the ER. In contrast, this mutant was activated like wild-type Ire1 by depletion of the membrane lipid component inositol or by deletion of genes involved in lipid homeostasis. Another Ire1 mutant lacking the authentic luminal domain was up-regulated by inositol depletion as strongly as wild-type Ire1. We therefore conclude that the cytosolic (or transmembrane) domain of Ire1 senses membrane aberrancy, while, as proposed previously, unfolded proteins accumulating in the ER interact with and activate Ire1.
Chaperone-mediated hierarchical control in targeting misfolded proteins to aggresomes
Authors: Zhang Xingqian , Qian Shu-Bing
Published: July 2011

Protein misfolding is a common event in living cells. Molecular chaperones not only assist protein folding; they also facilitate the degradation of misfolded polypeptides. When the intracellular degradative capacity is exceeded, juxtanuclear aggresomes are formed to sequester misfolded proteins. Despite the well-established role of chaperones in both protein folding and degradation, how chaperones regulate the aggregation process remains controversial. Here we investigate the molecular mechanisms underlying aggresome formation in mammalian cells. Analysis of the chaperone requirements for the fate of misfolded proteins reveals an unexpected role of heat shock protein 70 (Hsp70) in promoting aggresome formation. This proaggregation function of Hsp70 relies on the interaction with the cochaperone ubiquitin ligase carboxyl terminal of Hsp70/Hsp90 interacting protein (CHIP). Disrupting Hsp70–CHIP interaction prevents the aggresome formation, whereas a dominant-negative CHIP mutant sensitizes the aggregation of misfolded protein. This accelerated aggresome formation also relies on the stress-induced cochaperone Bcl2-associated athanogene 3. Our results indicate that a hierarchy of cochaperone interaction controls different aspects of the intracellular protein triage decision, extending the function of Hsp70 from folding and degradation to aggregation.
Simple high-throughput annotation pipeline (SHAP)
Authors: DeMaere Matthew Z. , Lauro Federico M. , Thomas Torsten , Yau Sheree , Cavicchioli Ricardo
Published: July 2011

Summary: SHAP (simple high-throughput annotation pipeline) is a lightweight and scalable sequence annotation pipeline capable of supporting research efforts that generate or utilize large volumes of DNA sequence data. The software provides Grid capable analysis, relational storage and Web-based full-text searching of annotation results. Implemented in Java, SHAP recognizes the limited resources of many smaller research groups.

Availability: Source code is freely available under GPLv3 at https://sourceforge.net/projects/shap.

Contact:  matt.demaere@unsw.edu.au; r.cavicchioli@unsw.edu.au
CalcTav—integration of a spreadsheet and Taverna workbench
Authors: Sroka Jacek , Krupa Łukasz , Kierzek Andrzej M. , Tyszkiewicz Jerzy
Published: July 2011

Motivation:  Taverna workbench is an environment for construction, visualization and execution of bioinformatic workflows that integrates specialized tools available on the Internet. It already supports major bioinformatics services and is constantly gaining popularity. However, its user interface requires considerable effort to learn, and sometimes requires programming or scripting experience from its users. We have integrated Taverna with OpenOffice Calc, making the functions of the scientific workflow system available in the spreadsheet. In CalcTav, one can define workflows using the spreadsheet interface and analyze the results using the spreadsheet toolset.

Results: Technically, CalcTav is a plugin for OpenOffice Calc, which provides the functionality of Taverna available in the form of spreadsheet functions. Even basic familiarity with spreadsheets already suffices to define and use spreadsheet workflows with Taverna services. The data processed by the Taverna components is automatically transferred to and from spreadsheet cells, so all the visualization and data analysis tools of OpenOffice Calc are available to the workflow creator within one, consistent user interface.

Availability:  CalcTav is available under GPLv2 from http://code.google.com/p/calctav/

Contact:  sroka@mimuw.edu.pl
Identification of novel phosphorylation modification sites in human proteins that originated after the human–chimpanzee divergence
Authors: Kim Dong Seon , Hahn Yoonsoo
Published: July 2011

Motivation: Phosphorylation modifications of specific protein residues are involved in a wide range of biological processes such as modulation of intracellular signal networks. Here, we present the development and application of a bioinformatics procedure for systematic identification of human-specific phosphorylation sites in proteins that may have occurred after the human–chimpanzee divergence.

Results: We collected annotated human phosphorylation sites and compared each site to orthologous mammalian proteins across taxa including chimpanzee, orangutan, rhesus macaque, marmoset, mouse, dog, cow, elephant, opossum and platypus. We identified 37 human-specific gains of annotated phosphorylation sites in 35 proteins: 22 serines, 12 threonines and 3 tyrosines. The novel phosphorylation sites are situated in highly conserved segments of the protein. Proteins with novel phosphorylation sites are involved in crucial biological processes such as cell division (AURKB, CASC5, MKI67 and PDCD4) and chromatin remodeling (HIRA, HIRIP3, HIST1H1T, NAP1L4 and LRWD1). Modified phosphorylatable residues produce novel target sites for protein kinases such as cyclin-dependent kinases and casein kinases, possibly resulting in rewiring and fine-tuning of phosphorylation regulatory networks. The potential human-specific phosphorylation sites identified in this study are useful as candidates for functional analysis to identify novel phenotypes in humans.

Contact:  hahny@cau.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Human-like external function of the foot, and fully upright gait, confirmed in the 3.66 million year old Laetoli hominin footprints by topographic statistics, experimental footprint-formation and computer simulation
Authors: Crompton Robin H. , Pataky Todd C. , Savage Russell , D'Août Kristiaan , Bennett Matthew R. , Day Michael H. , Bates Karl , Morse Sarita , Sellers William I.
Published: July 2011

It is commonly held that the major functional features of the human foot (e.g. a functional longitudinal medial arch, lateral to medial force transfer and hallucal (big-toe) push-off) appear only in the last 2 Myr, but functional interpretations of footbones and footprints of early human ancestors (hominins) prior to 2 million years ago (Mya) remain contradictory. Pixel-wise topographical statistical analysis of Laetoli footprint morphology, compared with results from experimental studies of footprint formation; foot-pressure measurements in bipedalism of humans and non-human great apes; and computer simulation techniques, indicate that most of these functional features were already present, albeit less strongly expressed than in ourselves, in the maker of the Laetoli G-1 footprint trail, 3.66 Mya. This finding provides strong support to those previous studies which have interpreted the G-1 prints as generally modern in aspect.
The natural history of early hepatitis C virus evolution; lessons from a global outbreak in human immunodeficiency virus-1-infected individuals
Authors: Thomson Emma C. , Smith Jennifer A. , Klenerman Paul
Published: July 2011

New insights into the early viral evolution and cellular immune response during acute hepatitis C virus (HCV) infection are being gained following a global outbreak in human immunodeficiency virus-1 (HIV)-positive men who have sex with men. Cross-sectional and longitudinal sequence analysis at both the population and individual level have facilitated tracking of the HCV epidemic across the world and enabled the development of tests of viral diversity in individual patients in order to predict spontaneous clearance of HCV and response to treatment. Immunological studies in HIV-positive cohorts have highlighted the role of the CD4+T-cell response in the control of early HCV infection and will increase the opportunity for the identification of protective epitopes that could be used in future vaccine development.
Bell pepper endornavirus: molecular and biological properties, and occurrence in the genus Capsicum
Authors: Okada Ryo , Kiyota Eri , Sabanadzovic Sead , Moriyama Hiromitsu , Fukuhara Toshiyuki , Saha Prasenjit , Roossinck Marilyn J. , Severin Ake , Valverde Rodrigo A.
Published: July 2011

Bell peppers (Capsicum annuum) harbour a large dsRNA virus. The linear genome (14.7 kbp) of two isolates from Japanese and USA bell pepper cultivars were completely sequenced and compared. They shared extensive sequence identity and contained a single, long ORF encoding a 4815 aa protein. This polyprotein contained conserved motifs of putative viral methyltransferase (MTR), helicase 1 (Hel-1), UDP-glycosyltransferase and RNA-dependent RNA polymerase. This unique arrangement of conserved domains has not been reported in any of the known endornaviruses. Hence this virus, for which the name Bell pepper endornavirus (BPEV) is proposed, is a distinct species in the genus Endornavirus (family Endornaviridae). The BPEV-encoded polyprotein contains a cysteine-rich region between the MTR and Hel-1 domains, with conserved CXCC motifs shared among several endornaviruses, suggesting an additional functional domain. In agreement with general endornavirus features, BPEV contains a nick in the positive-strand RNA molecule. The virus was detected in all bell pepper cultivars tested and transmitted through seed but not by graft inoculations. Analysis of dsRNA patterns and RT-PCR using degenerate primers revealed putative variants of BPEV, or closely related species, infecting other C. annuum genotypes and three other Capsicum species (C. baccatum, C. chinense and C. frutescens).
The remarkable evolutionary history of endornaviruses
Authors: Roossinck Marilyn J. , Sabanadzovic Sead , Okada Ryo , Valverde Rodrigo A.
Published: July 2011

The family Endornaviridae contains several members from diverse hosts, including plants, fungi and oomycetes. They are found as large dsRNA elements with a nick in the coding strand. All members encode a conserved RNA-dependent RNA polymerase, but no other domain that is conserved among all members. Based on the conserved domain database comparison the various domains have different origins, indicating a highly modular evolutionary history. In some cases, domains with similar putative functions are found that are derived from different protein families, indicating convergent evolution for a required function.
From humans to rats and back again: Bridging the divide between human and animal studies of recognition memory with receiver operating characteristics
Authors: Koen Joshua D. , Yonelinas Andrew P.
Published: July 2011

Receiver operating characteristics (ROCs) have been used extensively to study the processes underlying human recognition memory, and this method has recently been applied in studies of rats. However, the extent to which the results from human and animal studies converge is neither entirely clear, nor is it known how the different methods used to obtain ROCs in different species impact the results. A recent study used a response bias ROC manipulation with rats and demonstrated that speeding memory responses reduced the contribution of recollection, not familiarity. The current study confirms this finding in humans using a comparable response bias method. Moreover, a comparison of the response bias methods commonly used in animal studies and the confidence rating method typically employed in human studies produced similar ROC functions. The present results suggest that the analysis of recognition memory ROCs provides a fruitful method to bridge the human and animal memory literatures.
Phylogenetic relationships among superfamilies of Hymenoptera
Authors: Sharkey Michael J. , Carpenter James M. , Vilhelmsen Lars , Heraty John , Liljeblad Johan , Dowling Ashley P.G. , Schulmeister Susanne , Murray Debra , Deans Andrew R. , Ronquist Fredrik , Krogmann Lars , Wheeler Ward C.
Published: July 2011

The first comprehensive analysis of higher‐level phylogeny of the order Hymenoptera is presented. The analysis includes representatives of all extant superfamilies, scored for 392 morphological characters, and sequence data for four loci (18S, 28S, COI and EF‐1α). Including three outgroup taxa, 111 terminals were analyzed. Relationships within symphytans (sawflies) and Apocrita are mostly resolved. Well supported relationships include: Xyeloidea is monophyletic, Cephoidea is the sister group of Siricoidea + [Xiphydrioidea + (Orussoidea + Apocrita)]; Anaxyelidae is included in the Siricoidea, and together they are the sister group of Xiphydrioidea + (Orussoidea + Apocrita); Orussoidea is the sister group of Apocrita, Apocrita is monophyletic; Evanioidea is monophyletic; Aculeata is the sister group of Evanioidea; Proctotrupomorpha is monophyletic; Ichneumonoidea is the sister group of Proctotrupomorpha; Platygastroidea is sister group to Cynipoidea, and together they are sister group to the remaining Proctotrupomorpha; Proctotrupoidea s. str. is monophyletic; Mymarommatoidea is the sister group of Chalcidoidea; Mymarommatoidea + Chalcidoidea + Diaprioidea is monophyletic. Weakly supported relationships include: Stephanoidea is the sister group of the remaining Apocrita; Diaprioidea is monophyletic; Ceraphronoidea is the sister group of Megalyroidea, which together form the sister group of [Trigonaloidea (Aculeata + Evanioidea)]. Aside from paraphyly of Vespoidea within Aculeata, all currently recognized superfamilies are supported as monophyletic. The diapriid subfamily Ismarinae is raised to family status, Ismaridae stat. nov.

© The Will Henning Society 2011.
Bioimaging analysis of nuclear factor‐κB activity in Philadelphia chromosome‐positive acute lymphoblastic leukemia cells reveals its synergistic upregulation by tumor necrosis factor‐α‐stimulated changes to the microenvironment
Authors: Tsai Hui‐Jen , Kobayashi Seiichiro , Izawa Kiyoko , Ishida Takaomi , Watanabe Toshiki , Umezawa Kazuo , Lin Sheng‐Fung , Tojo Arinobu
Published: July 2011

To gain an insight into the microenvironmental regulation of nuclear factor (NF)‐κB activity in the progression of leukemia, we established a bioluminescent imaging model of Philadelphia chromosome‐positive acute lymphoblastic leukemia (Ph+ALL) cells transduced with a NF‐κB/luciferase (Luc) reporter and cocultured with murine stromal cells and cytokines. Stromal cells alone did not augment Luc activity, taken as an index of NF‐κB, but Luc activity was synergistically upregulated by the combination of stromal cells and tumor necrosis factor (TNF)‐α. Dehydroxymethylepoxyquinomicin (DHMEQ), a specific inhibitor of NF‐κB DNA binding, rapidly induced the apoptosis of Ph+ALL cells, indicating that NF‐κB is necessary for the growth and survival of these cells. However, the DHMEQ‐induced suppression of NF‐κB activity and the apoptosis of leukemia cells were attenuated by the presence of stromal cells and TNF‐α. In NOD‐SCID mice transplanted with NF‐κB/Luc reporter‐containing Ph+ALL cell lines and monitored periodically during the progression of the leukemia, murine TNF‐α was significantly expressed in lesions in which the leukemia cells emitted a significant NF‐κB signal. These results support the notion that TNF‐α also triggers microenvironmental upregulation of NF‐κB activity in vivo. Collectively, the results indicated that TNF‐α‐stimulated microenvironment may contribute to the survival and progression of Ph+ALL cells through the synergistic upregulation of NF‐κB activity. (Cancer Sci 2011; 102: 2014–2021)
Ketamine use: a review
Authors: Morgan Celia J. A. , Curran H. Valerie ,   the Independent Scientific Committee on Drugs (ISCD)
Published: July 2011

Aims  Ketamine remains an important medicine in both specialist anaesthesia and aspects of pain management. At the same time, its use as a recreational drug has spread in many parts of the world during the past few years. There are now increasing concerns about the harmful physical and psychological consequences of repeated misuse of this drug. The aim of this review was to survey and integrate the research literature on physical, psychological and social harms of both acute and chronic ketamine use.

Method  The literature on ketamine was systematically searched and findings were classified into the matrix of Nutt et al.'s (2007) rational scale for assessing the harms of psychoactive substances.

Results  A major physical harm is ketamine induced ulcerative cystitis which, although its aetiology is unclear, seems particularly associated with chronic, frequent use of the drug. Frequent, daily use is also associated with neurocognitive impairment and, most robustly, deficits in working and episodic memory. Recent studies suggest certain neurological abnormalities which may underpin these cognitive effects. Many frequent users are concerned about addiction and report trying but failing to stop using ketamine.

Conclusions  The implications of these findings are drawn out for treatment of ketamine‐induced ulcerative cystitis in which interventions from urologists and from addiction specialists should be coordinated. Neurocognitive impairment in frequent users can impact negatively upon achievement in education and at work, and also compound addiction problems. Prevention and harm minimization campaigns are needed to alert young people to these harmful and potentially chronic effects of ketamine.
Plasma concentration of pigment epithelium‐derived factor is closely associated with blood pressure and predicts incident hypertension in Chinese: a 10‐year prospective study
Authors: Chen Cheng , Tso Annette W. K. , Cheung Bernard M. Y. , Law Lawrence S. C. , Ong K. L. , Wat Nelson M. S. , Janus Edward D. , Xu Aimin , Lam Karen S. L.
Published: July 2011

Objectives  Pigment epithelium‐derived factor (PEDF) is secreted from the adipose tissue. It circulates at high concentrations, and was reported to play a causal role in obesity‐induced insulin resistance and metabolic dysfunctions in mice. Previous cross‐sectional studies also demonstrated plasma PEDF concentration correlated positively with systolic blood pressure (BP) and pulse pressure, and inversely with small artery elasticity. Here we investigated the relationship of plasma PEDF concentration with BP and incident hypertension in a 10‐year prospective study.

Methods  Baseline plasma PEDF concentrations were measured by ELISA in 520 Chinese subjects, aged 51 ± 12 years, followed up long‐term from the population‐based Hong Kong Cardiovascular Risk Factor Prevalence Study. The association between plasma PEDF concentration and BP was investigated in both cross‐sectional and prospective studies, using multiple linear regression and path analyses. Cox proportional hazards analysis was used to determine whether baseline PEDF concentration was independently related to the subsequent development of hypertension over 10 years.

Results  Baseline plasma concentrations of PEDF were higher in men (P < 0·001), and were directly related to systolic BP at 2 and 5 years, and to diastolic BP at 2 years, after adjustment for covariates. Of the 386 normotensive subjects at baseline, high baseline PEDF concentration was predictive of incident hypertension, independent of the effects of age, sex, baseline BP and obesity parameters (hazard ratio: 1·135; 95% CI: 1·039–1·241; P = 0·005).

Conclusion  Our data suggest that plasma PEDF concentration is significantly associated with BP, and incident hypertension. PEDF may be involved in the pathogenesis of hypertension in humans.
Assessment of serum visfatin levels in girls with anorexia nervosa
Authors: Ziora Katarzyna , Oświęcimska Joanna , Świętochowska Elżbieta , Ziora Dariusz , Stojewska Małgorzata , Suwała Andrzej , Ostrowska Zofia , Gorczyca Piotr , Klimacka‐Nawrot Ewa , Lukas Witold , Błońska‐Fajfrowska Barbara
Published: July 2011

Objective  Visfatin (VISF) is a recently described peptide regulating the process of adipocyte differentiation. Only one pilot study of VISF expression in the fat tissue and its circulating concentrations in a small group of patients with anorexia nervosa (AN) have been published, yet.

Design and patients  Cross‐sectional assessment of VISF serum concentrations in 195 girls aged 11–18·9 years with AN (n = 87), eating disorders not otherwise specified (NOS; n = 17), simple obesity (OB; n = 30), and healthy controls (H; n = 61).

Measurements  Blood samples were collected during the fasting state between 7:00 am–8:30 am. VISF serum concentrations were determined using enzyme immunoassay. Comparisons of VISF levels between groups were performed.

Results  Mean serum VISF concentrations in girls with AN and NOS were significantly lower than those in the H and OB groups. Serum VISF concentrations were higher in the OB than in the H groups. When were calculated per body mass index (BMI), VISF concentrations were significantly lower in the AN, NOS, and OB groups than in healthy controls. Among participants with a normal BMI, serum VISF concentrations correlated positively with BMI (r = 0·27; P < 0·05). In the OB group, a significant, negative correlation between BMI and VISF levels (r = −0·38; P = 0·04) was observed.

Conclusions  Compared with healthy girls, serum VISF concentrations are decreased in girls with AN. Conversely, obese girls have elevated VISF levels. When calculated per BMI (VISF/BMI), the results in AN and OB groups were lower than in healthy participants.
Rapid rescreening of cervical smears as a quality control method
Authors: CROSS P. A.
Published: July 2011

Rapid rescreening of cervical smears as a quality control method

The use of a rapid rescreening method as part of an internal quality control programme is reported. During a 12‐month period 33 976 smears were reviewed (90.9% of total workload). Two‐hundred and nineteen reports were altered, with 23 dyskaryotic smears identified, a false‐negative rate of 0.07%, a false‐negative dyskaryotic rate of 1.7%. Smears reported as dyskaryotic were also subjected to the rapid screening method (with 86.8% correctly identified) as well as using the method to assess smears before the usual primary screen (with 67.2% of dyskaryotic smears correctly identified). Rapid rescreening as a quality control method is effective, and although it has limitations, should replace 10% proportional rescreening as the preferred daily quality control method of choice.

La relecture rapide des frottis cervico‐utérins comme méthode de contrôle de qualité

Ce travail décrit l'utilisation de la méthode de relecture rapide dans le cadre d'un programme de contrôle de qualité interne. Pendant une période de 12 mois, 33 976 frottis ont été revus (90,9% du recrutement). Deux cent dix neuf comptes‐rendus ont été modifiés dont 23 concernant des frottis avec dyscaryoses, ce qui donne un taux de faux négatifs de 0,07% et un taux de faux négatifs pour les dyscaryoses de 1,7%. La méthode rapide a été appliquée à la relecture des frottis initialement classés comme dyscaryotiques (86,8% ont été correctement identifiés) ainsi qu'a la lecture de frottis avant le screening primaire (avec 67,2% de frottis dyscaryotiques correctement identifiés). La méthode de relecture rapide utilisée comme méthode de contrôle de qualité est efficace et, malgré ses limitations, elle devrait remplacer la relecture de 10% comme méthode de contrôle de qualité de routine.

Rasches Nachscreenen als Methode der Qualitätskontrolle

Während 12 Monaten wurden 33.976 Abstriche durch rasches Nachscreenen überprüft (90,9% aller Abstriche). 219 Befunde wurden abgeädert darunter 23 neue Dyskariosen, Dies entspricht einer Rate falsch negativer von 0,07% und falsch negativer Dyskariosen von 1,7%. Sämtliche Dyskariosen wurden ebenfalls überprüft mit einer Ausbeute von 86,8%, während die Methode als Vorlauf vor dem normalen Screening 67,2% erfasste. Trotz ihrer Einschränkungen ist die Methode wirkungsvoll und sollte die übliche Überprüfung von 10% der negativen Abstriche ersetzen.
An agronomic assessment of greenhouse gas emissions from major cereal crops
Authors: Linquist Bruce , van Groenigen Kees Jan , Adviento‐Borbe Maria Arlene , Pittelkow Cameron , van Kessel Chris
Published: July 2011

Agricultural greenhouse gas (GHG) emissions contribute approximately 12% to total global anthropogenic GHG emissions. Cereals (rice, wheat, and maize) are the largest source of human calories, and it is estimated that world cereal production must increase by 1.3% annually to 2025 to meet growing demand. Sustainable intensification of cereal production systems will require maintaining high yields while reducing environmental costs. We conducted a meta‐analysis (57 published studies consisting of 62 study sites and 328 observations) to test the hypothesis that the global warming potential (GWP) of CH4 and N2O emissions from rice, wheat, and maize, when expressed per ton of grain (yield‐scaled GWP), is similar, and that the lowest value for each cereal is achieved at near optimal yields. Results show that the GWP of CH4 and N2O emissions from rice (3757 kg CO2 eq ha−1 season−1) was higher than wheat (662 kg CO2 eq ha−1 season−1) and maize (1399 kg CO2 eq ha−1 season−1). The yield‐scaled GWP of rice was about four times higher (657 kg CO2 eq Mg−1) than wheat (166 kg CO2 eq Mg−1) and maize (185 kg CO2 eq Mg−1). Across cereals, the lowest yield‐scaled GWP values were achieved at 92% of maximal yield and were about twice as high for rice (279 kg CO2 eq Mg−1) than wheat (102 kg CO2 eq Mg−1) or maize (140 kg CO2 eq Mg−1), suggesting greater mitigation opportunities for rice systems. In rice, wheat and maize, 0.68%, 1.21%, and 1.06% of N applied was emitted as N2O, respectively. In rice systems, there was no correlation between CH4 emissions and N rate. In addition, when evaluating issues related to food security and environmental sustainability, other factors including cultural significance, the provisioning of ecosystem services, and human health and well‐being must also be considered.
Elevated CO2 affects photosynthetic responses in canopy pine and subcanopy deciduous trees over 10 years: a synthesis from Duke FACE
Authors: Ellsworth David S. , Thomas Richard , Crous Kristine Y. , Palmroth Sari , Ward Eric , Maier Chris , DeLucia Evan , Oren Ram
Published: July 2011

Leaf responses to elevated atmospheric CO2 concentration (Ca) are central to models of forest CO2 exchange with the atmosphere and constrain the magnitude of the future carbon sink. Estimating the magnitude of primary productivity enhancement of forests in elevated Ca requires an understanding of how photosynthesis is regulated by diffusional and biochemical components and up‐scaled to entire canopies. To test the sensitivity of leaf photosynthesis and stomatal conductance to elevated Ca in time and space, we compiled a comprehensive dataset measured over 10 years for a temperate pine forest of Pinus taeda, but also including deciduous species, primarily Liquidambar styraciflua. We combined over one thousand controlled‐response curves of photosynthesis as a function of environmental drivers (light, air Ca and temperature) measured at canopy heights up to 20 m over 11 years (1996–2006) to generate parameterizations for leaf‐scale models for the Duke free‐air CO2 enrichment (FACE) experiment. The enhancement of leaf net photosynthesis (Anet) in P. taeda by elevated Ca of +200 μmol mol−1 was 67% for current‐year needles in the upper crown in summer conditions over 10 years. Photosynthetic enhancement of P. taeda at the leaf‐scale increased by two‐fold from the driest to wettest growing seasons. Current‐year pine foliage Anet was sensitive to temporal variation, whereas previous‐year foliage Anet was less responsive and overall showed less enhancement (+30%). Photosynthetic downregulation in overwintering upper canopy pine needles was small at average leaf N (Narea), but statistically significant. In contrast, co‐dominant and subcanopy L. styraciflua trees showed Anet enhancement of 62% and no Anet–Narea adjustments. Various understory deciduous tree species showed an average Anet enhancement of 42%. Differences in photosynthetic responses between overwintering pine needles and subcanopy deciduous leaves suggest that increased Ca has the potential to enhance the mixed‐species composition of planted pine stands and, by extension, naturally regenerating pine‐dominated stands.
Spatial autocorrelation patterns of stream invertebrates: exogenous and endogenous factors
Authors: Bonada Núria , Dolédec Sylvain , Statzner Bernhard
Published: July 2011

Aim  To investigate spatial autocorrelation of taxonomic stream invertebrate groups (richness and composition) at a large geographical scale and to analyse the importance of exogenous and endogenous factors.

Location  The Mediterranean Basin.

Methods  For exogenous factors, we used large‐scale factors related to climate, geology and river zonation; for endogenous factors, we used the dispersal mode of each taxonomic group. After describing and analysing spatial patterns of genus richness and genus composition of stream invertebrate groups in the Mediterranean Basin, we computed Moran’s I before and after accounting for the exogenous factors and related it to the endogenous factors.

Results  In relation to genus richness, most of the taxonomic groups did not show significant spatial autocorrelation, suggesting that no main large‐scale exogenous or endogenous factors were important and that local‐scale factors were probably controlling taxonomic richness. In contrast, for genus composition, all taxonomic groups except Odonata had significant spatial autocorrelation before accounting for the environment. After accounting for the environment, most taxonomic groups still had a significant spatial autocorrelation, but it decreased with their increasing dispersal ability (from Crustacea to Coleoptera). Thus, spatial taxonomic composition of groups with the strongest dispersal potential is mainly related to exogenous factors, whereas that of groups with weaker dispersal potential is related to a combination of exogenous and endogenous factors.

Main conclusions  Our results illustrate the importance of dispersal as an endogenous factor causing spatial autocorrelation and suggest that ignoring endogenous factors can lead to misunderstandings when explaining large‐scale community patterns.
Adapted cardiac rehabilitation programme to improve uptake in patients of Moroccan and Turkish origin in The Netherlands: a qualitative study
Authors: Sloots Maurits , Bartels Edien AC , Angenot Edmond LD , Geertzen Jan HB , Dekker Joost
Published: July 2011

Aim.  To explore the treatment experiences in patients of Moroccan and Turkish origin and their rehabilitation therapists regarding an adapted outpatient cardiac rehabilitation programme.

Background.  Non‐native patients who participated in a cardiac rehabilitation programme at a Dutch rehabilitation centre had more difficulties to achieve the treatment aims than native Dutch patients. Therefore, an adapted programme for non‐native patients, lacking proficiency in Dutch, has been instigated. The programme contains six adapted treatment modules and additional strategies: adapted education regarding (1) the heart and the vascular system and (2) the use of healthy food, with use the of (audio) visual educational materials, (3) adapted physical exercise module with explicit involvement of the patients’ relatives, (4) standard use of professional interpreters, (5) increase in the number and length of consultations and (6) individual treatment instead of a group programme.

Design.  Qualitative study.

Method.  Semi‐structured, face‐to‐face interviews were conducted with eight patients of Moroccan and Turkish origin and five native Dutch rehabilitation therapists. By comparison, three native Dutch patients were interviewed regarding the regular programme.

Results.  The results indicate that the patients’ disease symptoms reduced and that patients adopted lifestyle changes. Therapists experienced that the number and length of the consultations, the structural use of interpreters and (audio) visual educational materials contributed to the achievement of the treatment aims.

Conclusion.  An adapted cardiac rehabilitation programme with separate modules and additional strategies for non‐native patients appears to lead to satisfied patients who adopted lifestyle changes.

Relevance to clinical practice.  The findings of this study are important as the study highlights the practical actions that may be taken by physicians and healthworkers to adjust rehabilitation treatment to the needs of patients of non‐native origin.
Challenges faced by nurses in managing pain in a critical care setting
Authors: Subramanian Pathmawathi , Allcock Nick , James Veronica , Lathlean Judith
Published: July 2011

Aim.  To explore nurses’ challenges in managing pain among ill patients in critical care.

Background.  Pain can lead to many adverse medical consequences and providing pain relief is central to caring for ill patients. Effective pain management is vital since studies show patients admitted to critical care units still suffer from significant levels of acute pain. The effective delivery of care in clinical areas remains a challenge for nurses involved with care which is dynamic and constantly changing in critically ill.

Design.  Qualitative prospective exploratory design.

Methods.  This study employed semi structured interviews with nurses, using critical incident technique. Twenty‐one nurses were selected from critical care settings from a large acute teaching health care trust in the UK. A critical incident interview guide was constructed from the literature and used to elicit responses.

Results.  Framework analysis showed that nurses perceived four main challenges in managing pain namely lack of clinical guidelines, lack of structured pain assessment tool, limited autonomy in decision making and the patient’s condition itself.

Conclusions.  Nurses’ decision making and pain management can influence the quality of care given to critically ill patients. It is important to overcome the clinical problems that are faced when dealing with pain experience.

Relevance to clinical practice.  There is a need for nursing education on pain management. Providing up to date and practical strategies may help to reduce nurses’ challenges in managing pain among critically ill patients. Broader autonomy and effective decision making can be seen as beneficial for the nurses besides having a clearer and structured pain management guidelines.
Stage of adoption for preventive behaviour against passive smoking among pregnant women and women with young children in Taiwan
Authors: Huang Chiu‐Mieh , Guo Jong‐Long , Wu Hsein‐Lin , Chien Li‐Yin
Published: July 2011

Aims.  This study assessed the applicability of the transtheoretical model to prevent exposure to passive smoking among pregnant women and women with young children in Taiwan. We examined whether women in different stages of change had different knowledge, processes of change, decisional balance and self‐efficacy.

Background.  Although previous studies have found a positive association between the presence of children and a mother’s readiness to prevent exposure to passive smoking, a few studies have systematically examined the mothers’ stage of adoption for preventive behaviour against passive smoking.

Methods.  A cross‐sectional survey based on self‐reported data was conducted in 2005–2006. A total of 315 women was recruited from perinatal and paediatric clinics at four hospitals. The transtheoretical model measures included knowledge, stages of change, processes of change, decisional balance and self‐efficacy towards passive smoking.

Results.  Of the 315 women in the study, 17·1% were at the precontemplation stage, 7·9% were at the contemplation/preparation stage and 74·9% were at the action/maintenance stage. Women at the action/maintenance stage scored the highest in knowledge, process of change, pros of decisional balance and self‐efficacy, followed by the women at the contemplation/preparation stage and the women at the precontemplation stage.

Conclusions.  This study supported the applicability of the transtheoretical model theory for adoption of preventive behaviour against passive smoking among pregnant women and women with young children.

Relevance to clinical practice.  Nurses could educate pregnant women and women with young children to adopt preventive behaviours against passive smoking using stage‐matched intervention strategies, targeting the transtheoretical model constructs, to promote behavioural change.
Pathogenesis, investigation and dietary and medical management of gastroparesis
Authors: Keld R. , Kinsey L. , Athwal V. , Lal S.
Published: July 2011

Delayed gastric emptying (gastroparesis) is associated with significant morbidity and, occasionally, mortality; clinicians therefore need a high index of suspicion to avoid missing the diagnosis. This review discusses the aetiology, diagnostic criteria and investigations pertinent to gastroparesis, and also critically reviews the evidence for nutritional and medical management strategies. Dietary manipulation plays a key role in management, and simple adjustment to meal routines and diets can lead to an improvement in symptoms, whereas alternative feeding routes play an important role in more severe cases. The role of pharmaceutical intervention is less clear; prokinetics and antiemetics are often prescribed; however, evidence for their efficacy is lacking, whereas gastric electric stimulation has an evolving role in the management of patients with symptoms refractory to medical therapies. The optimal treatment of gastroparesis would be to resolve symptoms and normalise gastric emptying times, and this may be achieved with future treatments that target the underlying pathology. For most patients with mild to moderate disease, dietary intervention plays a central role in the management of gastroparesis.
Recovery: what mental health nurses and service users say about the concept of recovery
Authors: ASTON V. , COFFEY M.
Published: July 2011

Accessible summary

This qualitative study investigated the subjective experiences of recovery in mental health with service users and mental health nurses.

Data from two focus groups were analysed and found differing perceptions of how mental health services are delivered and the barriers that are seen to hinder the implementation of a recovery philosophy.

The main findings of the study are that recovery is a difficult‐to‐define concept and remains a challenge for both this group of service users and nurses.

This study presents a thematic analysis of focus group talk to examine what recovery in mental health means to service users and nurses. Data were collected from two focus groups, one group of service users and one group of nurses. The service user group (n= 6) were adults with previous or recent experience of inpatient mental health services. The nursing group were registered nurses (n= 5) of various grades and experience currently working in inpatient mental health services in one region of the UK. Thematic analysis using Krueger and Casey's framework led to four themes being developed. These were ‘understandings of recovery’, ‘semantics’, ‘therapeutics’ and ‘a journey’. While the recovery concept was not new to either group, understandings of recovery were vague and contradictory.
Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems
Authors: ST. ONGE KATE R. , KÄLLMAN THOMAS , SLOTTE TANJA , LASCOUX MARTIN , PALMÉ ANNA E.
Published: July 2011

Both mating system and population history can have large impacts on genetic diversity and population structure. Here, we use multilocus sequence data to investigate how these factors impact two closely related Brassicaceae species: the selfing Capsella rubella and the outcrossing C. grandiflora. To do this, we have sequenced 16 loci in approximately 70 individuals from 7 populations of each species. Patterns of population structure differ strongly between the two species. In C. grandiflora, we observe an isolation‐by‐distance pattern and identify three clearly delineated genetic groups. In C. rubella, where we estimate the selfing rate to be 0.90–0.94, the pattern is less clear with some sampling populations forming separate genetic clusters while others are highly mixed. The two species also have divergent histories. Our analysis gives support for a bottleneck approximately 73 kya (20–139 kya) in C. rubella, which most likely represents speciation from C. grandiflora. In C. grandiflora, there is moderate support for the standard neutral model in 2 of 3 genetic clusters, while the third cluster and the total data set show evidence of expansion. It is clear that mating system has an impact on these two species, for example affecting the level of genetic variation and the genetic structure. However, our results also clearly show that a combination of past and present processes, some of which are not affected by mating system, is needed to explain the differences between C. rubella and C. grandiflora.
Glutamate utilization promotes meningococcal survival in vivo through avoidance of the neutrophil oxidative burst
Authors: Talà Adelfia , Monaco Caterina , Nagorska Krzysztofa , Exley Rachel M. , Corbett Anne , Zychlinsky Arturo , Alifano Pietro , Tang Christoph M.
Published: July 2011

Polymorphonuclear neutrophil leucocytes (PMNs) are a critical part of innate immune defence against bacterial pathogens, and only a limited subset of microbes can escape killing by these phagocytic cells. Here we show that Neisseria meningitidis, a leading cause of septicaemia and meningitis, can avoid killing by PMNs and this is dependent on the ability of the bacterium to acquire l‐glutamate through its GltT uptake system. We demonstrate that the uptake of available l‐glutamate promotes N. meningitidis evasion of PMN reactive oxygen species produced by the oxidative burst. In the meningococcus, l‐glutamate is converted to glutathione, a key molecule for maintaining intracellular redox potential, which protects the bacterium from reactive oxygen species such as hydrogen peroxide. We show that this mechanism contributes to the ability of N. meningitidis to cause bacteraemia, a critical step in the disease process during infections caused by this important human pathogen.
Maternal injuries during the periconceptional period and the risk of birth defects, National Birth Defects Prevention Study, 1997–2005
Authors: Tinker Sarah C. , Reefhuis Jennita , Dellinger Ann M. , Jamieson Denise J. ,   the National Birth Defects Prevention Study
Published: July 2011

Tinker SC, Reefhuis J, Dellinger AM, Jamieson DJ, the National Birth Defects Prevention Study. Maternal injuries during the periconceptional period and the risk of birth defects, National Birth Defects Prevention Study, 1997–2005. Paediatric and Perinatal Epidemiology 2011; 25: 487–496.

Maternal injuries during pregnancy are common (∼7% prevalence). However, few studies have examined the association between maternal injuries and birth defects. The National Birth Defects Prevention Study is a population‐based case–control study of birth defects in 10 US states. Cases were ascertained through surveillance; controls were randomly selected from infants delivered without major birth defects in the study regions. Mothers completed a telephone interview on exposures before and during pregnancy, including injuries. We assessed associations between periconceptional (month before until the end of the third month of pregnancy) maternal injuries and birth defects. We used logistic regression to estimate adjusted odds ratios (AORs) and 95% confidence intervals (CI). Periconceptional injuries were associated with interrupted aortic arch type B [AOR = 5.2, 95% CI 1.2, 23.2]; atrioventricular septal defect [AOR = 2.2, 95% CI 1.1, 4.4]; pulmonary atresia [AOR = 3.2, 95% CI 1.6, 6.4]; tricuspid atresia [AOR = 2.8, 95% CI 1.2, 6.7]; hypoplastic left heart syndrome [AOR = 2.0, 95% CI 1.1, 3.4]; anorectal atresia/stenosis [AOR = 1.7, 95% CI 1.0, 2.7]; longitudinal limb deficiency [AOR = 2.1, 95% CI 1.1, 3.9]; and gastroschisis [AOR = 1.8, 95% CI 1.2, 2.8]. Associations with longitudinal limb deficiency, gastroschisis and hypoplastic left heart syndrome were stronger for intentional injuries. Our results suggest maternal injury during the periconceptional period, particularly those inflicted intentionally, may be associated with select birth defects. This analysis was hypothesis‐generating, with many associations tested. Further research is warranted.