bluuebunny/crossref_metadata_2025 huggingface dataset:
Would you Find Thirty online? Website use in a Western Australian physical activity campaign
Authors: Leavy J. E. , Rosenberg M. , Barnes R. , Bauman A. , Bull F. C.
Published: May 2013

Issue addressed

Mass media campaigns have used a range of traditional media (television, radio and print) to communicate health messages. In the past decade the Internet has added to these traditional methods with Web 2.0, smart phone technology and interactive media. ‘Find Thirty every day®’, a Western Australia population‐wide mass media campaign delivered over 2 years, used a combination of traditional mass media, a website, online resources and banner advertising. The aim of the present study is to describe the use of the Find Thirty every day® website during the campaign media activities of May 2008‐June 2010.

Methods

Cross‐sectional self‐reported survey data were collected from a random sample of adults using a computer‐assisted telephone interview over the period February‐March 2010. Objective online analytical measures of unique visits to the Find Thirty every day® website were collected between June 2008 and June 2010.

Results

Monthly visitors to the Find Thirty every day® website increased from 3193 in 2009 to 4374 in 2010. During the last two media waves (October 2009 and February 2010), site visits were 5388 and 5272 per month, respectively.

Conclusion

The impact of the Find Thirty every day® website was a positive outcome, considering the minimal online presence.

So what?

Health communication campaign planners should maximise the potential synergy of traditional mass media and new social media in future campaigns. Accordingly, a multidisciplinary approach that includes communication researchers, experts in information systems and a creative team experienced in online environments will need to be the way forward.
Geochemical conditions for the preservation of recent aragonite-rich sediments in Mediterranean karstic marine lakes (Mljet Island, Adriatic Sea, Croatia)
Authors: Lojen Sonja , Sondi Ivan , Juracic Mladen
Published: May 2013

Conditions for the preservation of recent aragonite-rich sediments during early diagenesis in two semi-enclosed Mediterranean karstic seawater lakes on the island of Mljet (Adriatic Sea) were examined. The concentrations and stable isotope compositions of carbonate and sedimentary organic matter, as well as the geochemical parameters in pore water were measured. It was found that the smaller lake (Malo Jezero) receives considerably more terrestrial detritus than the larger lake (Veliko Jezero). A decrease in carbonate δ13C values with depth indicated a rather intensive transfer of organically derived C into the carbonate pool by diagenetic recrystallisation, masking the changes in carbonate δ13C caused by increasing amounts of aragonite. Dissolution of calcite as a result of CO2 released from the decomposition of organic debris and the upward diffusive flux of dissolved inorganic carbon were together responsible for up to 24% of the dissolved inorganic carbon added to the pore water. This indicated locally occurring carbonate dissolution, irrespective of its saturation state in the bulk sediment. Despite the larger input of terrigenous material into Malo Jezero, the carbonate content in the sediment was much higher than in Veliko Jezero, indicating greater authigenic aragonite production. As magnesium calcite accounted for most of the carbonate dissolution, aragonite preservation in the sediment is favoured.
Introduction of routine polymerase chain reaction testing for Neisseria gonorrhoeae in a community laboratory
Authors: Upton Arlo , Wilson Janet , Bissessor Liselle
Published: May 2013

We introduced polymerase chain reaction (PCR) testing for Neisseria gonorrhoeae (NG) on the Cobas 4800 CT/NG assay for all samples received with a Chlamdyia trachomatis request in March 2012. From 1 March 2012 to 30 June 2012, all PCR-positive/culture-negative specimens had additional testing at another assay. A total of 40053 tests were performed. The estimated specificity and positive predictive value were 99.9% and 97.1%, respectively; thus routine additional testing is not required.
The relationship of post-fire white ash cover to surface fuel consumption
Authors: Hudak Andrew T. , Ottmar Roger D. , Vihnanek Robert E. , Brewer Nolan W. , Smith Alistair M. S. , Morgan Penelope
Published: May 2013

White ash results from the complete combustion of surface fuels, making it a logically simple retrospective indicator of surface fuel consumption. However, the strength of this relationship has been neither tested nor adequately demonstrated with field measurements. We measured surface fuel loads and cover fractions of white ash and four other surface materials (green vegetation, brown non-photosynthetic vegetation, black char and mineral soil) immediately before and after eight prescribed fires in four disparate fuelbed types: boreal forest floor, mixed conifer woody slash, mixed conifer understorey and longleaf pine understorey. We hypothesised that increased white ash cover should correlate significantly to surface fuel consumption. To test this hypothesis, we correlated field measures of surface fuel consumption with field measures of surface cover change. Across all four fuelbed types, we found increased white ash cover to be the only measure of surface cover change that correlated significantly to surface fuel consumption, supporting our hypothesis. We conclude that white ash load calculated from immediate post-fire measurements of white ash cover, depth and density may provide an even more accurate proxy for surface fuel consumption, and furthermore a more physically based indicator of fire severity that could be incorporated into rapid response, retrospective wildfire assessments.
Interaction of 14-3-3 proteins with the Estrogen Receptor Alpha F domain provides a drug target interface
Authors: De Vries-van Leeuwen Ingrid J. , da Costa Pereira Daniel , Flach Koen D. , Piersma Sander R. , Haase Christian , Bier David , Yalcin Zeliha , Michalides Rob , Feenstra K. Anton , Jiménez Connie R. , de Greef Tom F. A. , Brunsveld Luc , Ottmann Christian , Zwart Wilbert , de Boer Albertus H.
Published: May 2013

Estrogen receptor alpha (ERα) is involved in numerous physiological and pathological processes, including breast cancer. Breast cancer therapy is therefore currently directed at inhibiting the transcriptional potency of ERα, either by blocking estrogen production through aromatase inhibitors or antiestrogens that compete for hormone binding. Due to resistance, new treatment modalities are needed and as ERα dimerization is essential for its activity, interference with receptor dimerization offers a new opportunity to exploit in drug design. Here we describe a unique mechanism of how ERα dimerization is negatively controlled by interaction with 14-3-3 proteins at the extreme C terminus of the receptor. Moreover, the small-molecule fusicoccin (FC) stabilizes this ERα/14-3-3 interaction. Cocrystallization of the trimeric ERα/14-3-3/FC complex provides the structural basis for this stabilization and shows the importance of phosphorylation of the penultimate Threonine (ERα-T
594
) for high-affinity interaction. We confirm that T
594
is a distinct ERα phosphorylation site in the breast cancer cell line MCF-7 using a phospho-T
594
–specific antibody and by mass spectrometry. In line with its ERα/14-3-3 interaction stabilizing effect, fusicoccin reduces the estradiol-stimulated ERα dimerization, inhibits ERα/chromatin interactions and downstream gene expression, resulting in decreased cell proliferation. Herewith, a unique functional phosphosite and an alternative regulation mechanism of ERα are provided, together with a small molecule that selectively targets this ERα/14-3-3 interface.
Coupled Ca
2+
/H
+
transport by cytoplasmic buffers regulates local Ca
2+
and H
+
ion signaling
Authors: Swietach Pawel , Youm Jae-Boum , Saegusa Noriko , Leem Chae-Hun , Spitzer Kenneth W. , Vaughan-Jones Richard D.
Published: May 2013

Significance

The concentration of Ca
2+
ions is kept low in cells by specialized ion-pumping proteins at the membrane. We show that in cardiac cells, cytoplasm also has an intrinsic ability to pump Ca
2+
. Histidyl dipeptides and ATP are diffusible cytoplasmic buffer molecules. By exchanging Ca
2+
for H
+
, they act like local “pumps,” producing uphill Ca
2+
movement within cytoplasm in response to H
+
ion gradients. Intracellular H
+
ions are generated locally by metabolism and competitively inhibit many Ca
2+
-activated biochemical processes. Recruiting Ca
2+
to acidic zones facilitates these processes. Cytoplasmic histidyl dipeptides and ATP thus act like a biological pump without a membrane.
A unified selection signal for attention and reward in primary visual cortex
Authors: Stănişor Liviu , van der Togt Chris , Pennartz Cyriel M. A. , Roelfsema Pieter R.
Published: May 2013

Stimuli associated with high rewards evoke stronger neuronal activity than stimuli associated with lower rewards in many brain regions. It is not well understood how these reward effects influence activity in sensory cortices that represent low-level stimulus features. Here, we investigated the effects of reward information in the primary visual cortex (area V1) of monkeys. We found that the reward value of a stimulus relative to the value of other stimuli is a good predictor of V1 activity. Relative value biases the competition between stimuli, just as has been shown for selective attention. The neuronal latency of this reward value effect in V1 was similar to the latency of attentional influences. Moreover, V1 neurons with a strong value effect also exhibited a strong attention effect, which implies that relative value and top–down attention engage overlapping, if not identical, neuronal selection mechanisms. Our findings demonstrate that the effects of reward value reach down to the earliest sensory processing levels of the cerebral cortex and imply that theories about the effects of reward coding and top–down attention on visual representations should be unified.
Prefrontal microcircuit underlies contextual learning after hippocampal loss
Authors: Zelikowsky Moriel , Bissiere Stephanie , Hast Timothy A. , Bennett Rebecca Z. , Abdipranoto Andrea , Vissel Bryce , Fanselow Michael S.
Published: May 2013

Specific brain circuits have been classically linked to dedicated functions. However, compensation following brain damage suggests that these circuits are capable of dynamic adaptation. Such compensation is exemplified by Pavlovian fear conditioning following damage to the dorsal hippocampus (DH). Although the DH normally underlies contextual fear and fear renewal after extinction, both can be learned in the absence of the DH, although the mechanisms and nature of this compensation are currently unknown. Here, we report that recruitment of alternate structures, specifically the infralimbic and prelimbic prefrontal cortices, is required for compensation following damage to the hippocampus. Disconnection of these cortices in DH-compromised animals and immediate early gene induction profiles for amygdala-projecting prefrontal cells revealed that communication and dynamic rebalancing within this prefrontal microcircuit is critical. Additionally, the infralimbic cortex normally plays a role in limiting generalization of contextual fear. These discoveries reveal that plasticity through recruitment of alternate circuits allows the brain to compensate following damage, offering promise for targeted treatment of memory disorders.
DNA barcoding for plant protection: applications and summary of available data for arthropod pests.
Authors: Frewin A. , Scott-Dupree C. , Hanner R.
Published: May 2013

Over the last decade, DNA barcoding - the use of short, standardized DNA sequences for species identification - has emerged as an important tool to study biodiversity. However, given the challenge and importance of accurately identifying plant pests, we argue for the use of DNA barcoding as a tool to aid in phytosanitary regulation and integrated pest management. Additionally, the rigorous data quality standard of DNA barcoding complements both regulatory and management tasks. In this review, we describe the current and potential applications of DNA barcoding for plant pest management, with a particular focus on terrestrial arthropods, as well as introduce and discuss some analytical methodologies and tools used for DNA barcoding research. Furthermore, we summarize the currently available DNA barcode data for a composite global pest list of 1044 plant pests, compiled from six international pest lists.
Longitudinal Variation in the Ohio River Fish Community
Authors: Seegert Greg , Vondruska Joe , Perry Elgin , Dixon Doug
Published: May 2013

The Ohio River fish community was sampled three times (June, August, and October) in 2005 by electrofishing near 17 power plants encompassing nearly the entire length of the Ohio River (river kilometer 82–1,527). Six 500-m zones were electrofished at each plant. Using a generalized additive model, we examined this data set of 306 electrofishing samples to determine how the abundance of 31 taxa varied over the length of the river. We also looked for trends in several measures of community health (catch rate, species richness, index of biotic integrity, and modified index of well-being). Of the 31 taxa examined, all but three showed longitudinal differences over the course of the river. Based on the patterns for the 31 taxa and 5 community measures, we assigned each taxon or measure to one of seven classes. The largest class included 10 taxa that declined steadily in abundance from upriver to downriver. All community measures followed a similar pattern except that each measure increased near the downstream-most plant. Conversely, only two taxa (Striped Bass Morone saxatilis and River Carpsucker Carpiodes carpio) showed the opposite trend (i.e., increasing in a downstream direction). Some taxa were restricted to the upper or lower end of the river or to certain reaches along the river. Species that were restricted to the upper river were primarily stream fishes (certain minnows Notropis spp. and several darters Etheostoma spp.). Conversely, fish species that were restricted to the lower river were primarily large-river fishes as well as species that were typical of the Mississippi River fauna. Site-specific differences in water temperature, Secchi depth, specific conductance, and dissolved oxygen were generally unimportant in explaining the observed patterns. Substrate type (percent cobble/boulder and percent silt) occasionally was important. The observed longitudinal trends appeared to be primarily in response to natural temperature and habitat differences between the upper and lower sections of the Ohio River.

Received March 16, 2012; accepted March 10, 2013
A fairy tale dictator: children's letters to the Duce
Authors: Bernasconi Paola
Published: May 2013

One of the aspects of the formation of consensus under the Fascist state concerns the construction of the Fascist ‘man’. This article takes up this notion and explores it in relation to children. The first part deal with the legislative process according to which Fascist rituals and myths were introduced into the school curriculum. The second part examines the letters that were sent to the Duce by children during the period of the regime. The majority of letters appear to have been dictated by elementary school teachers according to precise directives, but nonetheless there is some evidence of the spontaneous manifestation of the feelings of infants. The most significant aspect concerns the transfiguration of the Duce himself into a figure of fable in ways that could not but impact on the imagination of those who were born and raised between the 1920s and later 1930s.
Playing the dictator: re-enactments of Mussolini in film and television
Authors: Gundle Stephen
Published: May 2013

This article explores the portrayal of Mussolini in film and television drama. It considers the contexts in which films and mini-series were made from the 1970s and the problems faced in bringing the Duce to the screen, mostly in dramas that stressed the final phase of his rule. Despite efforts to ensure authenticity in the reconstruction of locations, events and people, there was a notable emphasis on the private and personal dimensions of the dictator's life, a sphere in which screenplays had to indulge in invention in keeping with the practices of all ‘biopics’. The resulting ‘screen Mussolini’ is more human and potentially more sympathetic than the Mussolini of historiography. In a situation in which the legacies of Fascism and anti-fascism are still debated, this media construction has been controversial. The article assesses, using textual analysis, the meanings of the different representational solutions deployed in the films and considers some of the issues involved in playing Mussolini.
‘Il nostro Duce’:Mussolini's visit to Trieste in 1938 and the workings of the cult of the Duce1
Authors: Baxa Paul
Published: May 2013

On September 18, 1938, Benito Mussolini disembarked in the port city of Trieste to begin a seven-day visit of theTre Venezie. The tour was in keeping with Mussolini's policy ofandare verso il popolowhich involved periodic visits to Italy's regions. It was also an opportunity to impose the cult of the Duce on a frontier region which had, since the 1920s, been the site of harsh anti-Slav policies designed to Italianize the Venezia-Giulia region. This article examines the workings of the cult in Trieste where the regime was anxious to demonstrate that it was present in a city that had felt neglected by Rome. Often viewed as a top-down enterprise, this article will explore how the cult of the Duce relied significantly on local dynamics and spaces.
Forest-dependent communities' livelihood in decentralized forest governance policy epoch: case study from West Shoa zone, Ethiopia
Authors: Mohammed Abrar Juhar , Inoue Makoto
Published: May 2013

This study analyzed the livelihoods of households located in and around forests in Ethiopia, and investigated the impacts of two major forest policies of the country, delegation and devolution. The results showed that forest-related livelihoods are an important mechanism to cope with drought and concomitant food shortages. The forest is also an important source of income, especially for the relatively resource-poor community and for the poor and very poor households in the community. The delegation policy has frustrated this role of the forest in local people's livelihoods while devolution yielded mixed results, with some forest-related benefits declining while others showed increase.
Theoretical Equivalence and the Semantic View of Theories
Authors: Glymour Clark
Published: May 2013

Halvorson argues through a series of examples and a general result due to Myers that the “semantic view” of theories has no available account of formal theoretical equivalence. De Bouvere provides criteria overlooked in Halvorson’s paper that are immune to his counterexamples and to the theorem he cites. Those criteria accord with a modest version of the semantic view that rejects some of Van Fraassen’s apparent claims while retaining the core of Patrick Suppes’s proposal. I do not endorse any version of the semantic view of theories.
Tate (co)homology via pinched complexes
Authors: Christensen Lars , Jorgensen David
Published: May 2013

For complexes of modules we study two new constructions which we call the pinched tensor product and the pinched Hom. They provide new methods for computing Tate homology

T
o
r

^

\operatorname {\widehat {Tor}}

and Tate cohomology

E
x
t

^

\operatorname {\widehat {Ext}}

, which lead to conceptual proofs of balancedness of Tate (co)homology for modules over associative rings. Another application we consider is in local algebra. Under conditions of the vanishing of Tate (co)homology, the pinched tensor product of two minimal complete resolutions yields a minimal complete resolution.
The WASH complex, an endosomal Arp2/3 activator, interacts with the Hermansky–Pudlak syndrome complex BLOC-1 and its cargo phosphatidylinositol-4-kinase type IIα
Authors: Ryder P. V. , Vistein R. , Gokhale A. , Seaman M. N. , Puthenveedu M. A. , Faundez V.
Published: May 2013

Vesicle biogenesis machinery components such as coat proteins can interact with the actin cytoskeleton for cargo sorting into multiple pathways. It is unknown, however, whether these interactions are a general requirement for the diverse endosome traffic routes. In this study, we identify actin cytoskeleton regulators as previously unrecognized interactors of complexes associated with the Hermansky–Pudlak syndrome. Two complexes mutated in the Hermansky–Pudlak syndrome, adaptor protein complex-3 and biogenesis of lysosome-related organelles complex-1 (BLOC-1), interact with and are regulated by the lipid kinase phosphatidylinositol-4-kinase type IIα (PI4KIIα). We therefore hypothesized that PI4KIIα interacts with novel regulators of these complexes. To test this hypothesis, we immunoaffinity purified PI4KIIα from isotope-labeled cell lysates to quantitatively identify interactors. Strikingly, PI4KIIα isolation preferentially coenriched proteins that regulate the actin cytoskeleton, including guanine exchange factors for Rho family GTPases such as RhoGEF1 and several subunits of the WASH complex. We biochemically confirmed several of these PI4KIIα interactions. Of importance, BLOC-1 complex, WASH complex, RhoGEF1, or PI4KIIα depletions altered the content and/or subcellular distribution of the BLOC-1–sensitive cargoes PI4KIIα, ATP7A, and VAMP7. We conclude that the Hermansky–Pudlak syndrome complex BLOC-1 and its cargo PI4KIIα interact with regulators of the actin cytoskeleton.
Instantaneous inactivation of cofilin reveals its function of F-actin disassembly in lamellipodia
Authors: Vitriol Eric A. , Wise Ariel L. , Berginski Mathew E. , Bamburg James R. , Zheng James Q.
Published: May 2013

Cofilin is a key regulator of the actin cytoskeleton. It can sever actin filaments, accelerate filament disassembly, act as a nucleation factor, recruit or antagonize other actin regulators, and control the pool of polymerization-competent actin monomers. In cells these actions have complex functional outputs. The timing and localization of cofilin activity are carefully regulated, and thus global, long-term perturbations may not be sufficient to probe its precise function. To better understand cofilin's spatiotemporal action in cells, we implemented chromophore-assisted laser inactivation (CALI) to instantly and specifically inactivate it. In addition to globally inhibiting actin turnover, CALI of cofilin generated several profound effects on the lamellipodia, including an increase of F-actin, a rearward expansion of the actin network, and a reduction in retrograde flow speed. These results support the hypothesis that the principal role of cofilin in lamellipodia at steady state is to break down F-actin, control filament turnover, and regulate the rate of retrograde flow.
Mice overexpressing CD97 in intestinal epithelial cells provide a unique model for mammalian postnatal intestinal cylindrical growth
Authors: Aust Gabriela , Kerner Christiane , Gonsior Susann , Sittig Doreen , Schneider Hartmut , Buske Peter , Scholz Markus , Dietrich Norman , Oldenburg Sindy , Karpus Olga N. , Galle Jörg , Amasheh Salah , Hamann Jörg
Published: May 2013

Postnatal enlargement of the mammalian intestine comprises cylindrical and luminal growth, associated with crypt fission and crypt/villus hyperplasia, respectively, which subsequently predominate before and after weaning. The bipartite adhesion G protein–coupled receptor CD97 shows an expression gradient along the crypt–villus axis in the normal human intestine. We here report that transgenic mice overexpressing CD97 in intestinal epithelial cells develop an upper megaintestine. Intestinal enlargement involves an increase in length and diameter but does not affect microscopic morphology, as typical for cylindrical growth. The megaintestine is acquired after birth and before weaning, independent of the genotype of the mother, excluding altered availability of milk constituents as driving factor. CD97 overexpression does not regulate intestinal growth factors, stem cell markers, and Wnt signaling, which contribute to epithelial differentiation and renewal, nor does it affect suckling-to-weaning transition. Consistent with augmented cylindrical growth, suckling but not adult transgenic mice show enlarged crypts and thus more crypt fissions caused by a transient increase of the crypt transit-amplifying zone. Intestinal enlargement by CD97 requires its seven-span transmembrane/cytoplasmic C-terminal fragment but not the N-terminal fragment binding partner CD55. In summary, ectopic expression of CD97 in intestinal epithelial cells provides a unique model for intestinal cylindrical growth occurring in breast-fed infants.
A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number
Authors: Woodcock Dan J. , Vance Keith W. , Komorowski Michał , Koentges Georgy , Finkenstädt Bärbel , Rand David A.
Published: May 2013

Motivation:  cis-regulatory DNA sequence elements, such as enhancers and silencers, function to control the spatial and temporal expression of their target genes. Although the overall levels of gene expression in large cell populations seem to be precisely controlled, transcription of individual genes in single cells is extremely variable in real time. It is, therefore, important to understand how these cis-regulatory elements function to dynamically control transcription at single-cell resolution. Recently, statistical methods have been proposed to back calculate the rates involved in mRNA transcription using parameter estimation of a mathematical model of transcription and translation. However, a major complication in these approaches is that some of the parameters, particularly those corresponding to the gene copy number and transcription rate, cannot be distinguished; therefore, these methods cannot be used when the copy number is unknown.

Results: Here, we develop a hierarchical Bayesian model to estimate biokinetic parameters from live cell enhancer–promoter reporter measurements performed on a population of single cells. This allows us to investigate transcriptional dynamics when the copy number is variable across the population. We validate our method using synthetic data and then apply it to quantify the function of two known developmental enhancers in real time and in single cells.

Availability: Supporting information is submitted with the article.

Contact:  d.j.woodcock@warwick.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Relation between sequence and structure in membrane proteins
Authors: Olivella Mireia , Gonzalez Angel , Pardo Leonardo , Deupi Xavier
Published: May 2013

Motivation: Integral polytopic membrane proteins contain only two types of folds in their transmembrane domains: α-helix bundles and β-barrels. The increasing number of available crystal structures of these proteins permits an initial estimation of how sequence variability affects the structure conservation in their transmembrane domains. We, thus, aim to determine the pairwise sequence identity necessary to maintain the transmembrane molecular architectures compatible with the hydrophobic nature of the lipid bilayer.

Results: Root-mean-square deviation (rmsd) and sequence identity were calculated from the structural alignments of pairs of homologous polytopic membrane proteins sharing the same fold. Analysis of these data reveals that transmembrane segment pairs with sequence identity in the so-called ‘twilight zone’ (20–35%) display high-structural similarity (rmsd < 1.5 Å). Moreover, a large group of β-barrel pairs with low-sequence identity (<20%) still maintain a close structural similarity (rmsd < 2.5 Å). Thus, we conclude that fold preservation in transmembrane regions requires less sequence conservation than for globular proteins. These findings have direct implications in homology modeling of evolutionary-related membrane proteins.

Contact:  Mireia.Olivella@uvic.cat or Xavier.Deupi@psi.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification of hidden relationships from the coupling of Hydrophobic Cluster Analysis and Domain Architecture information
Authors: Faure Guilhem , Callebaut Isabelle
Published: May 2013

Motivation: Describing domain architecture is a critical step in the functional characterization of proteins. However, some orphan domains do not match any profile stored in dedicated domain databases and are thereby difficult to analyze.

Results: We present here an original novel approach, called TREMOLO-HCA, for the analysis of orphan domain sequences and inspired from our experience in the use of Hydrophobic Cluster Analysis (HCA). Hidden relationships between protein sequences can be more easily identified from the PSI-BLAST results, using information on domain architecture, HCA plots and the conservation degree of amino acids that may participate in the protein core. This can lead to reveal remote relationships with known families of domains, as illustrated here with the identification of a hidden Tudor tandem in the human BAHCC1 protein and a hidden ET domain in the Saccharomyces cerevisiae Taf14p and human AF9 proteins. The results obtained in such a way are consistent with those provided by HHPRED, based on pairwise comparisons of HHMs. Our approach can, however, be applied even in absence of domain profiles or known 3D structures for the identification of novel families of domains. It can also be used in a reverse way for refining domain profiles, by starting from known protein domain families and identifying highly divergent members, hitherto considered as orphan.

Availability: We provide a possible integration of this approach in an open TREMOLO-HCA package, which is fully implemented in python v2.7 and is available on request. Instructions are available at http://www.impmc.upmc.fr/∼callebau/tremolohca.html.

Contact:  isabelle.callebaut@impmc.upmc.fr

Supplementary information:  Supplementary Data are available at Bioinformatics online.
The Exopolysaccharide of Xylella fastidiosa Is Essential for Biofilm Formation, Plant Virulence, and Vector Transmission
Authors: Killiny N. , Martinez R. Hernandez , Dumenyo C. Korsi , Cooksey D. A. , Almeida R. P. P.
Published: May 2013

Exopolysaccharides (EPS) synthesized by plant-pathogenic bacteria are generally essential for virulence. The role of EPS produced by the vector-transmitted bacterium Xylella fastidiosa was investigated by knocking out two genes implicated in the EPS biosynthesis, gumD and gumH. Mutant strains were affected in growth characteristics in vitro, including adhesion to surfaces and biofilm formation. In addition, different assays were used to demonstrate that the mutant strains produced significantly less EPS compared with the wild type. Furthermore, gas chromatography–mass spectrometry showed that both mutant strains did not produce oligosaccharides. Biologically, the mutants were deficient in movement within plants, resulting in an avirulent phenotype. Additionally, mutant strains were affected in transmission by insects: they were very poorly transmitted by and retained within vectors. The gene expression profile indicated upregulation of genes implicated in cell-to-cell signaling and adhesins while downregulation in genes was required for within-plant movement in EPS-deficient strains. These results suggest an essential role for EPS in X. fastidiosa interactions with both plants and insects.
Evidence for Multiple Introductions and Clonality in Spanish Populations ofFusarium circinatum
Authors: Berbegal M. , Pérez-Sierra A. , Armengol J. , Grünwald N. J.
Published: May 2013

Fusarium circinatum is thought to have been moved around the world with pine planting stock consisting, most probably, of infected seed. In this effort, we investigate the genetic structure of F. circinatum in Spain and globally. In total, 223 isolates were studied from five regions in northern Spain and eight countries. Eight microsatellite markers revealed 66 multilocus genotypes (MLGs). Minimum spanning network analysis of MLGs by region within Spain as well as globally, discriminant analysis of principal components, and analysis of molecular variance revealed that Spanish populations are significantly differentiated and structured into two distinct groups, each one including one of the dominant genotypes observed. This result suggests that two independent introductions occurred into Spain that subsequently underwent clonal divergence and admixture. This result is further supported by the linkage disequilibrium and clonality observed for F. circinatum populations in northern Spain. The maintenance of differentiation between the clusters could result from the lack of or rare sexual reproduction in Spain. Possible introduction pathways from other countries and subsequent routes of dispersion of F. circinatum in Spain are discussed.
Transmissible gastroenteritis virus infection induces cell apoptosis via activation of p53 signalling
Authors: Huang Yong , Ding Li , Li Zhaocai , Dai Meiling , Zhao Xiaomin , Li Wei , Du Qian , Xu Xingang , Tong Dewen
Published: May 2013

Transmissible gastroenteritis virus (TGEV) infection induced apoptosis in several cell lines in vitro. Our previous studies demonstrated that TGEV could activate FasL- and mitochondria-mediated pathways to induce apoptosis in PK-15 cells. In this study, we investigated the regulation of p53 and p38 mitogen-activated protein kinases (MAPK) signalling pathways in the interaction of TGEV with host cells. We observed that TGEV infection decreased p300/CBP, downregulated MDM2 and promoted p53 phosphorylation at serines 15, 20 and 46, resulting in accumulation and activation of p53 in PK-15 cells. TGEV infection induced the transient activation of p38 MAPK in the early phase of inoculation and constant activation in the later phase of infection. However, UV-irradiated TGEV did not promote the activation of p53 and p38 MAPK in the later phase, whereas it only triggered the transient activation of p38 MAPK in the early phase. Blocking of p53 activation significantly inhibited the occurrence of apoptosis through suppressing the TGEV-induced FasL expression, Bcl-2 reduction, Bax and cytochrome c redistribution, while inhibition of p38 activity moderately blocked apoptosis induction and partly attenuated the accumulation and activation of p53. However, inhibition of p38 and p53 activity had no significant effects on viral gene transcription at 12 and 24 h post-infection. Taken together, these results demonstrated that TGEV infection promoted the activation of p38 MAPK and p53 signalling, and p53 signalling might play a dominant role in the regulation of cell apoptosis. These findings provide new insights into the function of p53 and p38 MAPK in the interaction of TGEV with host cells.
Human papillomavirus type 16 viral load measurement as a predictor of infection clearance
Authors: Trevisan Andrea , Schlecht Nicolas F. , Ramanakumar Agnihotram V. , Villa Luisa L. , Franco Eduardo L. ,   the Ludwig-McGill Study Group
Published: May 2013

Viral load measurements may predict whether human papillomavirus (HPV) type 16 infections may become persistent and eventually lead to cervical lesions. Today, multiple PCR methods exist to estimate viral load. We tested three protocols to investigate viral load as a predictor of HPV clearance. We measured viral load in 418 HPV16-positive cervical smears from 224 women participating in the Ludwig–McGill Cohort Study by low-stringency PCR (LS-PCR) using consensus L1 primers targeting over 40 known HPV types, and quantitative real-time PCR (qRT-PCR) targeting the HPV16 E6 and L1 genes. HPV16 clearance was determined by MY09/11 and PGMY PCR testing on repeated smears collected over 5 years. Correlation between viral load measurements by qRT-PCR (E6 versus L1) was excellent (Spearman’s rank correlation, ρ = 0.88), but decreased for L1 qRT-PCR versus LS-PCR (ρ = 0.61). Viral load by LS-PCR was higher for HPV16 and related types independently of other concurrent HPV infections. Median duration of infection was longer for smears with high copy number by all three PCR protocols (log rankP<0.05). Viral load is inversely related to HPV16 clearance independently of concurrent HPV infections and PCR protocol.
The respiratory syncytial virus nucleoprotein–RNA complex forms a left-handed helical nucleocapsid
Authors: Bakker Saskia E. , Duquerroy Stéphane , Galloux Marie , Loney Colin , Conner Edward , Eléouët Jean-François , Rey Félix A. , Bhella David
Published: May 2013

Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC helix would be right-handed, as the N–N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a left-handed helix. We further show that the contacts in the ring can be distorted to maintain key N–N-protein interactions in a left-handed helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.
NR2A- and NR2B-containing NMDA receptors in the prelimbic medial prefrontal cortex differentially mediate trace, delay, and contextual fear conditioning
Authors: Gilmartin Marieke R. , Kwapis Janine L. , Helmstetter Fred J.
Published: May 2013

Activation of N-methyl-D-aspartate receptors (NMDAR) in the prelimbic medial prefrontal cortex (PL mPFC) is necessary for the acquisition of both trace and contextual fear memories, but it is not known how specific NR2 subunits support each association. The NR2B subunit confers unique properties to the NMDAR and may differentially regulate these two fear memories. Here we show that NR2A-containing NMDARs mediate trace, delay, and contextual fear memories, but NR2B-containing NMDARs are required only for trace conditioning, consistent with a role for PL mPFC in working memory.
Alkyl levulinates as `green chemistry' precursors: butane-1,4-diyl bis(4-oxopentanoate) and hexane-1,6-diyl bis(4-oxopentanoate)
Authors: Gainsford Graeme J. , Hinkley Simon
Published: May 2013

Levulinic acid derivatives are potential `green chemistry' renewably sourced molecules with utility in industrial coatings applications. Suitable single crystals of the centrosymmetric title compounds, C14H22O6and C16H26O6, respectively, were obtained with difficulty. The data for the latter hexane-1,6-diyl compound were extracted from the major fragment of a three-component twinned crystal. Both compounds crystallize in similar-sized unit cells with identical symmetry, utilizing the same weak nonconventional attractive C—H...O(ketone) hydrogen bondsvia C(4) andC(5) motifs, which expand toR22(30) ring andC22(14) chain motifs. Their different packing orientations in similar-sized unit cells suggest that crystal growth involving packing mixes could lead to intergrowths or twins.
Three salts from the reactions of cysteamine and cystamine withL-(+)-tartaric acid
Authors: Benylles Amina , Cairns Donald , Cox Philip J. , Kay Graeme
Published: May 2013

Reaction between cysteamine (systematic name: 2-aminoethanethiol, C2H7NS) and L-(+)-tartaric acid [systematic name: (2R,3R)-2,3-dihydroxybutanedioic acid, C4H6O6] results in a mixture of cysteamine tartrate(1−) monohydrate, C2H8NS+·C4H5O6−·H2O, (I), and cystamine bis[tartrate(1−)] dihydrate, C4H14N2S22+·2C4H5O6−·2H2O, (III). Cystamine [systematic name: 2,2′-dithiobis(ethylamine), C4H12N2S2], reacts with L-(+)-tartaric acid to produce a mixture of cystamine tartrate(2−), C4H14N2S22+·C4H4O62−, (II), and (III). In each crystal structure, the anions are linked by O—H...O hydrogen bonds that run parallel to theaaxis. In addition, hydrogen bonding involving protonated amino groups in all three salts, and water molecules in (I) and (III), leads to extensive three-dimensional hydrogen-bonding networks. All three salts crystallize in the orthorhombic space groupP212121.
Di-μ2-chlorido-dichloridobis(dimethylformamide)tetrakis[μ3-1-(2-oxidobenzoyl)-2-(2-oxo-2-phenylethanethioyl)hydrazine-1,2-diido]octacopper(II) dimethylformamide disolvate
Authors: Liu Jian-Jun , Liao Jian-Zhen , Li Zuo-Yin , Wang Yao , Huang Chang-Cang
Published: May 2013

The title compound, [Cu8(C15H10N3O3S)4Cl4(C3H7NO)2]·2C3H7NO, consisting of eight CuIIcations, four trianionic 1-(2-oxidobenzoyl)-2-(2-oxo-2-phenylethanethioyl)hydrazine-1,2-diide ligands, four chloride ligands and two coordinated and two solvent dimethylformamide molecules, crystallizes with the octanuclear molecule located on an inversion centre. The two halves of the molecule are connected by two bridging Cl atoms. This is the first example of an octanuclear complex based on a thiosemicarbazone-derived ligand.
Intercultural therapy and the limitations of a cultural competency framework: about cultural differences, universalities and the unresolvable tensions between them
Authors: Rober Peter , De Haene Lucia
Published: May 2013

Working with a family from a cultural background other than one's own is considered to be challenging for the therapist. Influenced by social constructionism, the family therapy field highlights the importance of contingency and cultural differences and therapists are encouraged to develop their cultural competency in order to deal with these differences. In this article, starting from contemporary critiques of notions of Western societies' cultural diversity, we address the way in which the cultural competency framework, by highlighting the importance of cultural differences and the therapist's culture‐specific knowledge, may underestimate the importance of the social dimensions of the issues involved. Furthermore, highlighting cultural differences may obscure the shared humanity present in a transcultural encounter. In this article, as an alternative to the cultural competency framework, we propose a view of intercultural family therapy in which the unresolvable dialectical tension between differences and universalities is central.

Practitioner points

The article addresses the challenge of working with families from diverse cultural backgrounds.

The traditional framework of cultural competence is critically reviewed.

Family therapists should not only be open for cultural differences, but also for universalities and especially for the never‐ending tension between differences and universalities.
Fracturing Hegemony: Regionalism and State Rescaling in South Korea, 1961–71
Authors: Gimm Dong‐Wan
Published: May 2013

This study is informed by the theorizing prompted by recent work on state rescaling. I aim to examine the interaction between the top‐down and bottom‐up rescaling processes that took place in the South Korean developmental state during the late 1960s and early 1970s. I focus on a regionalism that both built a regional scale and influenced the hegemonic crisis of the ruling regime. Specifically, the study illustrates the features of state space that were shaped during the developmental era and the factors that allow state space to be stable and coherent. By dealing with these questions, I provide a possible interpretation of why and how regionalism was a crucial factor in the hegemonic crisis of the 1960s and generated a rescaling of state space. What makes this study significant is not merely the fact that this space is located in East Asia. It could also, more generally, open up an alternative perspective on state rescaling during the early stages of state‐led industrialization.
Implementation of the INTERGROWTH‐21st Project in Kenya
Authors: Carvalho M , Vinayak S , Ochieng R , Choksey V , Musee N , Stones W , Knight HE , Cheikh Ismail L ,   for the International Fetal and Newborn Growth Consortium for the 21 Century (INTERGROWTH‐21)
Published: May 2013

Please cite this paper as: Carvalho M, Vinayak S, Ochieng R, Choksey V, Musee N, Stones W, Knight H, Cheikh Ismail L, for the International Fetal and Newborn Growth Consortium for the 21st Century (INTERGROWTH‐21st). Implementation of the INTERGROWTH‐21st Project in Kenya. BJOG 2013; 120 (Suppl. 2): 105–110.

The African site in the INTERGROWTH‐21st Project was Parklands, a wealthy suburb of Nairobi, Kenya, with a largely middle‐to‐high socio‐economic status population. There are three hospitals with obstetric units in Parklands, with approximately 4300 births per year. The Newborn Cross‐Sectional Study (NCSS) sample was drawn from all three hospitals, covering 100% of births in this target population. The Fetal Growth Longitudinal Study (FGLS) sample was recruited from antenatal clinics serving these hospitals, using the eligibility criteria in the INTERGROWTH‐21st protocol. Special activities to raise awareness of the study included securing media coverage and distributing leaflets in antenatal clinic waiting rooms. FGLS required women to be recruited in the first trimester; therefore, a major challenge at this study site was the high background frequency of first antenatal consultations in the second trimester. The problem was overcome by the study awareness campaign, as a result of which more women started attending antenatal care earlier in pregnancy.
Evaluation of clinical hypothyroidism risk due to irradiation of thyroid and pituitary glands in radiotherapy of nasopharyngeal cancer patients
Authors: Lin Zhixiong , Wang Xiaoyan , Xie Wenjia , Yang Zhining , Che Kaijun , Wu Vincent WC
Published: May 2013

Introduction

Radiation‐induced thyroid dysfunction after radiotherapy for nasopharyngeal cancer (NPC) has been reported. This study investigated the radiation effects of the thyroid and pituitary glands on thyroid function after radiotherapy for NPC.

Methods

Sixty‐five NPC patients treated with radiotherapy were recruited. Baseline thyroid hormone levels comprising free triiodothyronine (fT3), free thyroxine (fT4) and thyroid‐stimulating hormone (TSH) were taken before treatment and at 3, 6, 12 and 18 months. A seven‐beam intensity‐modulated radiotherapy plan was generated for each patient. Thyroid and pituitary gland dose volume histograms were generated, dividing the patients into four groups: high (>50 Gy) thyroid and pituitary doses (HTHP group); high thyroid and low pituitary doses (HTLP group); low thyroid and high pituitary doses; and low thyroid and pituitary doses. Incidence of hypothyroidism was analysed.

Results

Twenty‐two (34%) and 17 patients (26%) received high mean thyroid and pituitary doses, respectively. At 18 months, 23.1% of patients manifested various types of hypothyroidism. The HTHP group showed the highest incidence (83.3%) of hypothyroidism, followed by the HTLP group (50%).

Conclusions

NPC patients with high thyroid and pituitary gland doses carried the highest risk of abnormal thyroid physiology. The dose to the thyroid was more influential than the pituitary dose at 18 months after radiotherapy, and therefore more attention should be given to the thyroid gland in radiotherapy planning.