bluuebunny/crossref_metadata_2025 huggingface dataset:
Gorbachev’s unofficial arms-control advisers
Authors: von Hippel Frank
Published: August 2013

After President Ronald Reagan’s 1983 Star Wars speech, a puzzled group of Soviet scientists asked US colleagues opposed to ballistic-missile defense if they had changed their minds.
Quantum physics for everyone
Authors: Bobroff Julien
Published: August 2013

With the help of designers and unconventional demonstrations, a group of French condensed-matter physicists set out to engage people who never thought of themselves as interested in science.
Production Incentives from Static Decoupling: Land Use Exclusion Restrictions
Authors: Just David R. , Kropp Jaclyn D.
Published: August 2013

Many agricultural support payments are based on past production with restrictions on how land may currently be used. When support payments to field crops are analyzed in a static framework, they do not directly impact current production decisions. However, over time, as relative profits change, these payments affect current output. The payments may keep land in less profitable production of program crops through restrictions prohibiting potentially more profitable endeavors such as cultivating fruits and vegetables. These payments have the potential to lead to production and trade distortions similar in magnitude to the distortions associated with direct production subsidies.
TALENoffer: genome-wide TALEN off-target prediction
Authors: Grau Jan , Boch Jens , Posch Stefan
Published: August 2013

Summary: Transcription activator-like effector nucleases (TALENs) have become an accepted tool for targeted mutagenesis, but undesired off-targets remain an important issue. We present TALENoffer, a novel tool for the genome-wide prediction of TALEN off-targets. We show that TALENoffer successfully predicts known off-targets of engineered TALENs and yields a competitive runtime, scanning complete mammalian genomes within a few minutes.

Availability: TALENoffer is available as a command line program from http://www.jstacs.de/index.php/TALENoffer and as a Galaxy server at http://galaxy.informatik.uni-halle.de.

Contact:  grau@informatik.uni-halle.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A local-order regularization for geophysical inverse problems
Authors: Gheymasi H. Mohammadi , Gholami A.
Published: August 2013

Different types of regularization have been developed to obtain stable solutions to linear inverse problems. Among these, total variation (TV) is known as an edge preserver method, which leads to piecewise constant solutions and has received much attention for solving inverse problems arising in geophysical studies. However, the method shows staircase effects and is not suitable for the models including smooth regions. To overcome the staircase effect, we present a method, which employs a local-order difference operator in the regularization term. This method is performed in two steps: First, we apply a pre-processing step to find the edge locations in the regularized solution using a properly defined minmod limiter, where the edges are determined by a comparison of the solutions obtained using different order regularizations of the TV types. Then, we construct a local-order difference operator based on the information obtained from the pre-processing step about the edge locations, which is subsequently used as a regularization operator in the final sparsity-promoting regularization. Experimental results from the synthetic and real seismic traveltime tomography show that the proposed inversion method is able to retain the smooth regions of the regularized solution, while preserving sharp transitions presented in it.
The deluge
Authors: Johns Fleur
Published: August 2013

Glee and despair accompany the advent of ‘big data’—that is, the accumulation of vast digital datasets and enhanced capacities for their use. In light of new global development opportunities identified with this deluge, the article lays groundwork for a critical conversation about big data within public international law scholarship.
Large pre-inflationary thermal density perturbations
Authors: Lieu Richard , Kibble T. W. B.
Published: August 2013

In some versions of the theory of inflation, it is assumed that before inflation began the universe was in a Friedmann–Robertson–Walker stage, with the energy density dominated by massless particles. The origin of the nearly scale-invariant density perturbations is quantum fluctuations in the inflaton field. Here we point out that under those conditions there would necessarily also be large thermally induced density perturbations. It is asserted that inflation would smooth out any pre-existing perturbations. However, that argument relies on linear perturbation theory of the scalar modes, which would be rendered invalid because of the non-negligibility of the vector and tensor modes when the perturbation in the total density becomes large. Under those circumstances, the original proof that inflation would have the desired smoothing effect no longer applies, i.e. for the theory to be robust an alternative (and hitherto unavailable) demonstration of the smoothing that takes account of these non-linear terms is necessary.
The Chelyabinsk superbolide: a fragment of asteroid 2011 EO40?
Authors: de la Fuente Marcos C. , de la Fuente Marcos R.
Published: August 2013

Bright fireballs or bolides are caused by meteoroids entering the Earth's atmosphere at high speed. Some have a cometary origin, a few may have originated within the Venus–Earth–Mars region as a result of massive impacts in the remote past but a relevant fraction is likely the result of the break-up of asteroids. Disrupted asteroids produce clusters of fragments or asteroid families and meteoroid streams. Linking a bolide to a certain asteroid family may help to understand its origin and pre-impact dynamical evolution. On 2013 February 15, a superbolide was observed in the skies near Chelyabinsk, Russia. Such a meteor could be the result of the decay of an asteroid and here we explore this possibility applying a multistep approach. First, we use available data and Monte Carlo optimization (validated using 2008 TC3 as template) to obtain a robust solution for the pre-impact orbit of the Chelyabinsk impactor (a = 1.62 au, e = 0.53, i = 3 $_{.}^{\circ}$82, Ω = 326 $_{.}^{\circ}$41 and ω = 109 $_{.}^{\circ}$44). Then, we use this most probable orbit and numerical analysis to single out candidates for membership in, what we call, the Chelyabinsk asteroid family. Finally, we perform N-body simulations to either confirm or reject any dynamical connection between candidates and impactor. We find reliable statistical evidence on the existence of the Chelyabinsk cluster. It appears to include multiple small asteroids and two relatively large members: 2007 BD7 and 2011 EO40. The most probable parent body for the Chelyabinsk superbolide is 2011 EO40. The orbits of these objects are quite perturbed as they experience close encounters not only with the Earth–Moon system but also with Venus, Mars and Ceres. Under such conditions, the cluster cannot be older than about 20–40 kyr.
Detection of water absorption in the day side atmosphere of HD 189733 b using ground-based high-resolution spectroscopy at 3.2 μm
Authors: Birkby J. L. , de Kok R. J. , Brogi M. , de Mooij E. J. W. , Schwarz H. , Albrecht S. , Snellen I. A. G.
Published: August 2013

We report a 4.8σ detection of water absorption features in the day side spectrum of the hot Jupiter HD 189733 b. We used high-resolution (R ∼ 100 000) spectra taken at 3.2 μm with CRIRES on the VLT to trace the radial-velocity shift of the water features in the planet's day side atmosphere during 5 h of its 2.2 d orbit as it approached secondary eclipse. Despite considerable telluric contamination in this wavelength regime, we detect the signal within our uncertainties at the expected combination of systemic velocity ($V_{\rm sys}=-3^{+5}_{-6}$ km s−1) and planet orbital velocity ($K_{\rm p}=154^{+14}_{-10}$ km s−1), and determine a H2O line contrast ratio of (1.3 ± 0.2) × 10−3 with respect to the stellar continuum. We find no evidence of significant absorption or emission from other carbon-bearing molecules, such as methane, although we do note a marginal increase in the significance of our detection to 5.1σ with the inclusion of carbon dioxide in our template spectrum. This result demonstrates that ground-based, high-resolution spectroscopy is suited to finding not just simple molecules like CO, but also to more complex molecules like H2O even in highly telluric contaminated regions of the Earth's transmission spectrum. It is a powerful tool that can be used for conducting an immediate census of the carbon- and oxygen-bearing molecules in the atmospheres of giant planets, and will potentially allow the formation and migration history of these planets to be constrained by the measurement of their atmospheric C/O ratios.
Comptonization of photons near the photosphere of relativistic outflows
Authors: Aksenov A. G. , Ruffini R. , Vereshchagin G. V.
Published: August 2013

We consider the formation of photon spectrum at the photosphere of ultrarelativistically expanding outflow. We use the Fokker–Planck approximation to the Boltzmann equation, and obtain the generalized Kompaneets equation which takes into account anisotropic distribution of photons developed near the photosphere. This equation is solved numerically for relativistic steady wind and the observed spectrum is found in agreement with previous studies. We also study the photospheric emission for different temperature dependences on radius in such outflows. In particular, we found that for T ∝ r−2 the Band low-energy photon index of the observed spectrum is α ≃ −1, as typically observed in Gamma-Ray Bursts.
Algibacter wandonensis sp. nov., isolated from sediment around a brown algae (Undaria pinnatifida) reservoir
Authors: Yoon Jung-Hoon , Park Sooyeon
Published: August 2013

A Gram-stain-negative, non-flagellated, rod-shaped bacterial strain able to move by gliding, designated WS-MY22T, was isolated from sediment around a brown algae reservoir located on Wando in South Korea. It grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain WS-MY22Tclustered coherently with the type strains ofAlgibacter lectusandAlgibacter undariae. It exhibited sequence similarity of 99.4 and 98.9 % to the type strains ofA. lectusandA. undariae, respectively, and of 95.1–96.6 % to those of the other species of the genusAlgibacter. Strain WS-MY22Tcontained MK-6 as the predominant menaquinone and iso-C15 : 1G and iso-C17 : 03-OH as the major fatty acids. The major polar lipids of strain WS-MY22Twere phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain WS-MY22Twas 35.8 mol% and its DNA–DNA relatedness withA. lectusKCTC 12103TandA. undariaeWS-MY9Twas 31 and 19 %, respectively. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WS-MY22Tis separate from other species of the genusAlgibacter. On the basis of the data presented, strain WS-MY22Tis considered to represent a novel species of the genusAlgibacter, for which the nameAlgibacterwandonensissp. nov. is proposed. The type strain is WS-MY22T( = KCTC 32381T = CECT 8301T).
Kordia
aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia
Authors: Hameed Asif , Shahina Mariyam , Lin Shih-Yao , Cho Jang-Cheon , Lai Wei-An , Young Chiu-Chung
Published: August 2013

A Gram-staining-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming and gliding marine bacterium designated strain CC-AMZ-301T was isolated from coastal surface seawater near Taichung harbour, Taiwan. Strain CC-AMZ-301T predominantly synthesized zeaxanthin and thus formed yellow colonies on marine agar. The novel strain showed high pairwise 16S rRNA gene sequence similarity to

Kordia periserrulae

IMCC1412T (95.0 %),

K. algicida

KCTC 8814PT (94.4 %) and K. antarctica IMCC3317T (94.2 %), and formed a phylogenetic lineage tightly associated with species of the genus

Kordia

. The polar lipid profile of strain CC-AMZ-301T consisted of three unidentified lipids, three unidentified aminolipids and one unidentified phospholipid. The major fatty acids (>5 % of total) were iso-C17 : 0 3-OH, iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The DNA G+C content was 36.4 mol%. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The major polyamine was the triamine sym-homospermidine. Based on evidence from the present polyphasic study, strain CC-AMZ-301T is proposed to represent a novel species of the genus

Kordia

, for which the name

Kordia

aquimaris sp. nov. is proposed; the type strain is CC-AMZ-301T ( = JCM 18556T = BCRC 80464T). An emended description of the genus

Kordia

is also proposed.
An immunodominant HLA-A*1101-restricted CD8+ T-cell response targeting hepatitis B surface antigen in chronic hepatitis B patients
Authors: Chen Xiaoling , Wang Wenbo , Wang Shufeng , Meng Gang , Zhang Mengjun , Ni Bing , Wu Yuzhang , Wang Li
Published: August 2013

Hepatitis B virus (HBV) infection is a worldwide public health problem. HBV-specific CD8+CTLs are vital for viral clearance. Identification of immunodominant CTL epitopes from HBV-associated antigens is necessary for therapeutic vaccine development. We showed that the HLA-A*1101 allele is one of the most common alleles in both healthy individuals and chronic hepatitis B (CHB) patients in the Chongqing area, China. However, less than 10 % of epitopes of HBV-associated antigens have been identified in an HLA-A*1101 context. Here, we describe an immunodominant CD8+T-cell response targeting a hepatitis B surface antigen determinant (HBs295–304) restricted by HLA-A*1101 in both healthy individuals and CHB patients. Moreover, HBs295–304is more immunogenic for CTL induction than a known naturally HLA-A*1101-processed epitope from hepatitis B core antigen (HBc88–96). Therefore, the newly identified epitope, HBs295–304, will benefit the development of immunotherapeutic approaches for HBV infection.
Pharmacological disruption of hepatitis C NS5A protein intra- and intermolecular conformations
Authors: Bhattacharya Dipankar , Ansari Israrul H. , Hamatake Robert , Walker Jill , Kazmierski Wieslaw M. , Striker Rob
Published: August 2013

Non-structural 5A protein (NS5A) has emerged as an important pharmacological target for hepatitis C virus (HCV). However, little is known about the conformation of NS5A intracellularly or how NS5A inhibitors achieve the picomolar (pM) inhibition of virus replication. Here, we have presented two structurally related small molecules, one that potently inhibits HCV replication and selects for resistance in NS5A, and another that is inactive. Resistance to this antiviral was greater in genotype 1a than in genotype 1b replicons and mapped to domain 1 of NS5A. Using a novel cell-based assay that measures the intracellular proximity of fluorescent tags covalently attached to NS5A, we showed that only the active antiviral specifically disrupted the close proximity of inter- and intramolecular positions of NS5A. The active antiviral, termed compound 1, caused a repositioning of both the N and C termini of NS5A, including disruption of the close approximation of the N termini of two different NS5A molecules in a multimolecular complex. These data provide the first study of how antivirals that select resistance in domain 1 of NS5A alter the cellular conformation of NS5A. This class of antiviral disrupts the close proximity of the N termini of domain 1 in a NS5A complex but also alters the conformation of domain 3, and leads to large aggregates of NS5A. Current models predict that a multicomponent cocktail of antivirals is needed to treat HCV infection, so a mechanistic understanding of what each component does to the viral machinery will be important.
Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types
Authors: Chouhy Diego , Bolatti Elisa M. , Pérez Germán R. , Giri Adriana A.
Published: August 2013

More than 170 human papillomavirus (HPV) types have been completely sequenced, curated and divided into five genera: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. With the application of PCR methods, hundreds of putative novel HPV types have been identified as PCR amplicons in mucosa and skin. However, at present there are no studies reporting a systematic search of the currently known L1 amplicons and their phylogenetic relationships. This survey revealed the existence of at least 202 different putative HPV types that are pending for full-genome characterization: five alphapapillomaviruses, 37 betapapillomaviruses, 159 gammapapillomaviruses and one mupapillomavirus. All potential viruses of the genera Alphapapillomavirus and Betapapillomavirus were grouped in the defined species, while 59 putative gammapapillomaviruses types were segregated in 21 unidentified putative species. These data highlight the need for progress in the identification of additional taxa of the family Papillomaviridae in order to elucidate the diversity, evolution and medical implications of these viruses.
Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations
Authors: Ibrahim Daniel M. , Hansen Peter , Rödelsperger Christian , Stiege Asita C. , Doelken Sandra C. , Horn Denise , Jäger Marten , Janetzki Catrin , Krawitz Peter , Leschik Gundula , Wagner Florian , Scheuer Till , Schmidt-von Kegler Mareen , Seemann Petra , Timmermann Bernd , Robinson Peter N. , Mundlos Stefan , Hecht Jochen
Published: August 2013

Gene regulation by transcription factors (TFs) determines developmental programs and cell identity. Consequently, mutations in TFs can lead to dramatic phenotypes in humans by disrupting gene regulation. To date, the molecular mechanisms that actually cause these phenotypes have been difficult to address experimentally. ChIP-seq, which couples chromatin immunoprecipitation with high-throughput sequencing, allows TF function to be investigated on a genome-wide scale, enabling new approaches for the investigation of gene regulation. Here, we present the application of ChIP-seq to explore the effect of missense mutations in TFs on their genome-wide binding profile. Using a retroviral expression system in chicken mesenchymal stem cells, we elucidated the mechanism underlying a novel missense mutation in HOXD13 (Q317K) associated with a complex hand and foot malformation phenotype. The mutated glutamine (Q) is conserved in most homeodomains, a notable exception being bicoid-type homeodomains that have lysine (K) at this position. Our results show that the mutation results in a shift in the binding profile of the mutant toward a bicoid/PITX1 motif. Gene expression analysis and functional assays using in vivo overexpression studies confirm that the mutation results in a partial conversion of HOXD13 into a TF with bicoid/PITX1 properties. A similar shift was not observed with another mutation, Q317R, which is associated with brachysyndactyly, suggesting that the bicoid/PITX1-shift observed for Q317K might be related to the severe clinical phenotype. The methodology described can be used to investigate a wide spectrum of TFs and mutations that have not previously been amenable to ChIP-seq experiments.
Integration of Biosynthesis and Long-Distance Transport Establish Organ-Specific Glucosinolate Profiles in VegetativeArabidopsis
Authors: Andersen Tonni Grube , Nour-Eldin Hussam Hassan , Fuller Victoria Louise , Olsen Carl Erik , Burow Meike , Halkier Barbara Ann
Published: August 2013

Although it is essential for plant survival to synthesize and transport defense compounds, little is known about the coordination of these processes. Here, we investigate the above- and belowground source-sink relationship of the defense compounds glucosinolates in vegetative Arabidopsis thaliana. In vivo feeding experiments demonstrate that the glucosinolate transporters1 and 2 (GTR1 and GTR2), which are essential for accumulation of glucosinolates in seeds, are likely to also be involved in bidirectional distribution of glucosinolates between the roots and rosettes, indicating phloem and xylem as their transport pathways. Grafting of wild-type, biosynthetic, and transport mutants show that both the rosette and roots are able to synthesize aliphatic and indole glucosinolates. While rosettes constitute the major source and storage site for short-chained aliphatic glucosinolates, long-chained aliphatic glucosinolates are synthesized both in roots and rosettes with roots as the major storage site. Our grafting experiments thus indicate that in vegetative Arabidopsis, GTR1 and GTR2 are involved in bidirectional long-distance transport of aliphatic but not indole glucosinolates. Our data further suggest that the distinct rosette and root glucosinolate profiles in Arabidopsis are shaped by long-distance transport and spatially separated biosynthesis, suggesting that integration of these processes is critical for plant fitness in complex natural environments.
Cytochrome b5 Reductase Encoded byCBR1Is Essential for a Functional Male Gametophyte inArabidopsis
Authors: Wayne Laura L. , Wallis James G. , Kumar Rajesh , Markham Jennifer E. , Browse John
Published: August 2013

In all eukaryotes, NADH:cytochrome b5 reductase provides electrons, via cytochrome b5, for a range of biochemical reactions in cellular metabolism, including for fatty acid desaturation in the endoplasmic reticulum. Studies in mammals, yeast, and in vitro plant systems have shown that cytochrome b5 can, at least in some circumstances, also accept electrons from NADPH:cytochrome P450 reductase, potentially allowing for redundancy in reductase function. Here, we report characterization of three T-DNA insertional mutants of the gene encoding cytochrome b5 reductase in Arabidopsis thaliana, CBR1. The progeny of plants heterozygous for the cbr1-2 allele segregated 6% homozygous mutants, while cbr1-3 and cbr1-4 heterozygotes segregated 1:1 heterozygous:wild type, indicating a gametophyte defect. Homozygous cbr1-2 seeds were deformed and required Suc for successful germination and seedling establishment. Vegetative growth of cbr1-2 plants was relatively normal, and they produced abundant flowers, but very few seeds. The pollen produced in cbr1-2 anthers was viable, but when germinated on cbr1-2 or wild-type stigmas, most of the resulting pollen tubes did not extend into the transmitting tract, resulting in a very low frequency of fertilization. These results indicate that cytochrome b5 reductase is not essential during vegetative growth but is required for correct pollen function and seed maturation.
Pragmatic language difficulties in children with hyperactivity and attention problems: an integrated review
Authors: Green Benita C. , Johnson Katherine A. , Bretherton Lesley
Published: August 2013

Background

Diagnostic criteria for attention deficit hyperactivity disorder (ADHD) suggest a range of difficulties in the pragmatic aspects of language, including excessive talking and interrupting others. Such difficulties have been periodically reported over several decades in studies on the language abilities of children with features of ADHD, yet a comprehensive review of the literature has been lacking.

Aims

This review aims to integrate evidence from several lines of research from 1979 to the present on pragmatic language difficulties in children with ADHD or symptoms of ADHD.

Methods & Procedures

A comprehensive search of empirical literature on pragmatic language in children with ADHD or symptoms of ADHD was conducted using PsycINFO and PubMed databases and through following up relevant references cited in articles. Literature was reviewed with respect to the nature and extent of pragmatic language difficulties in ADHD.

Outcomes & Results

Thirty studies met the review inclusion criteria, including recent questionnaire studies, observational studies of children's communication patterns, and studies of higher‐level language comprehension and production. The studies indicate a consistent profile of pragmatic language impairments in children with features of ADHD, particularly in the areas of excessive talking, poor conversational turn‐taking, and lack of coherence and organization in elicited speech.

Conclusions & Implications

Pragmatic language difficulties are common in children with features of ADHD. These difficulties are consistent with deficits in executive function that are thought to characterize ADHD, thus providing some support for the theory that executive function contributes to pragmatic language competency. As yet there is very little empirical evidence of specific relationships between particular aspects of pragmatic language and particular domains of executive function. Given the importance of pragmatic language competency for children's social and academic functioning, pragmatic language abilities should be considered during clinical assessment for ADHD and targeted for intervention.
SNP development from RNA‐seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?
Authors: Schunter C. , Garza J. C. , Macpherson E. , Pascual M.
Published: August 2013

Single nucleotide polymorphisms (SNPs) are rapidly becoming the marker of choice in population genetics due to a variety of advantages relative to other markers, including higher genomic density, data quality, reproducibility and genotyping efficiency, as well as ease of portability between laboratories. Advances in sequencing technology and methodologies to reduce genomic representation have made the isolation of SNPs feasible for nonmodel organisms. RNA‐seq is one such technique for the discovery of SNPs and development of markers for large‐scale genotyping. Here, we report the development of 192 validated SNP markers for parentage analysis in Tripterygion delaisi (the black‐faced blenny), a small rocky‐shore fish from the Mediterranean Sea. RNA‐seq data for 15 individual samples were used for SNP discovery by applying a series of selection criteria. Genotypes were then collected from 1599 individuals from the same population with the resulting loci. Differences in heterozygosity and allele frequencies were found between the two data sets. Heterozygosity was lower, on average, in the population sample, and the mean difference between the frequencies of particular alleles in the two data sets was 0.135 ± 0.100. We used bootstrap resampling of the sequence data to predict appropriate sample sizes for SNP discovery. As cDNA library production is time‐consuming and expensive, we suggest that using seven individuals for RNA sequencing reduces the probability of discarding highly informative SNP loci, due to lack of observed polymorphism, whereas use of more than 12 samples does not considerably improve prediction of true allele frequencies.
Rapid Bayesian inference of heritability in animal models without convergence problems
Authors: Ahlinder Jon , Sillanpää Mikko J.
Published: August 2013

The rapid advancement in genome sequencing techniques allows the dissection of complex traits of non‐model organisms of importance in evolutionary biology, conservation genetics, breeding and medicine. This advancement requires new statistical analysis tools that can handle large amount of sequencing data efficiently.

We propose an analytic Bayesian implementation of the mixed linear model which allows rapid and robust inferences of heritability. The two main features of the method are (i) breeding values and residual variance component are analytically integrated out of the model and (ii) the parameter space of the variance ratio parameter is discretized so that a Gibbs sampling distribution can be utilized. We propose further two separate methods to infer breeding values that acknowledge uncertainty of the learned heritability. The benefit of the method compared to a standard Markov Chain Monte Carlo (MCMC) method is visualized on public data sets: two simulated data sets and one Wheat (Triticum aestivum L.) pedigree.

Results show that while the accuracy of inferred heritability obtained by the proposed and standard methods are almost identical, the computational performance is very encouraging: up to hundred fold speed up and the possibility to make parallel implementation is particularly appealing here, which may further speed up computations.

The method allows analysis using a non‐invertible relationship matrix so that ad hoc manipulation is avoided which can be important as our results imply. We completely avoid convergence and mixing problems here: this is a well‐known problem of MCMC simulation, which sometimes can severely reduce the inferential power. Bayes factors for model comparisons can be conveniently calculated as a by‐product of the inference procedure. The source code will be available for download at http://www.rni.helsinki.fi/~mjs.
Precipitation of the warmest quarter and temperature of the warmest month are key to understanding the effect of climate change on plant species diversity in Southern African savannah
Authors: Gwitira Isaiah , Murwira Amon , Shekede Munyaradzi Davis , Masocha Mhosisi , Chapano Christopher
Published: August 2013

In this study, we test for the key bioclimatic variables that significantly explain the current distribution of plant species richness in a southern African ecosystem as a preamble to predicting plant species richness under a changed climate. We used 54,000 records of georeferenced plant species data to calculate species richness and spatially interpolated climate data to derive nineteen bioclimatic variables. Next, we determined the key bioclimatic variables explaining variation in species richness across Zimbabwe using regression analysis. Our results show that two bioclimatic variables, that is, precipitation of the warmest quarter (R2 = 0.92, P < 0.001) and temperature of the warmest month (R2 = 0.67, P < 0.001) significantly explain variation in plant species richness. In addition, results of bioclimatic modelling using future climate change projections show a reduction in the current bio‐climatically suitable area that supports high plant species richness. However, in high‐altitude areas, plant richness is less sensitive to climate change while low‐altitude areas show high sensitivity. Our results have important implications to biodiversity conservation in areas sensitive to climate change; for example, high‐altitude areas are likely to continue being biodiversity hotspots, as such future conservation efforts should be concentrated in these areas.
Association of maternal anti‐HLA class II antibodies with protection from allergy in offspring
Authors: Jones M. , Jeal H. , Harris J. M. , Smith J. D. , Rose M. L. , Taylor A. N. , Cullinan P.
Published: August 2013

Background

Recent studies have suggested that the birth order effect in allergy may be established during the prenatal period and that the protective effect may originate in the mother. HLA class II disparity between mother and foetus has been associated with significantly increased Th1 production. In this study, we investigated whether production of HLA antibodies 4 years after pregnancy with index child is associated with allergic outcomes in offspring at 8 years.

Methods

Anti‐HLA class I and II antibodies were measured in maternal serum (n = 284) and levels correlated to numbers of pregnancies and birth order, and allergic outcomes in offspring at 8 years of age.

Results

Maternal anti‐HLA class I and II antibodies were significantly higher when birth order, and the number of pregnancies were larger. Anti‐HLA class II, but not class I antibodies were associated with significantly less atopy and seasonal rhinitis in the offspring at age 8 years. Mothers with nonatopic (but not atopic) offspring had a significant increase in anti‐HLA class I and II antibodies with birth order.

Conclusion

This study suggests that the ‘birth order’ effect in children may be due to parity‐related changes in the maternal immune response to foetal antigens. We have observed for the first time an association between maternal anti‐HLA class II antibodies and protection from allergy in the offspring. Further work is required to determine immunologically how HLA disparity between mother and father can protect against allergy.
Diagnosis of immediate hypersensitivity reactions to radiocontrast media
Authors: Salas M. , Gomez F. , Fernandez T. D. , Doña I. , Aranda A. , Ariza A. , Blanca‐López N. , Mayorga C. , Blanca M. , Torres M. J.
Published: August 2013

Background

No consensus exists on the diagnostic approach for immediate hypersensitivity reactions (IHR) to radiocontrast media (RCM). We analyzed the diagnostic value of a skin test (ST), drug provocation test (DPT) and basophil activation test (BAT) in patients with symptoms compatible with IHR to RCM.

Methods

Ninety patients with symptoms suggestive of IHR to RCM were evaluated. ST with a panel of RCM was performed, and if negative, DPT was carried out with the culprit RCM. If ST or DPT were positive, tolerance was assessed with an alternative RCM and BAT was carried out with the same panel used for ST.

Results

Eight (8.9%) cases were confirmed as having IHR, 5 (62.5%) by ST and 3 (37.5%) by DPT. Five from those confirmed as IHR (62.5%) had a positive BAT.

Conclusions

Hypersensitivity to RCM was confirmed in 9%, by ST or DPT. BAT proved a valuable method for diagnosis.
Increased risk of developing dementia in patients with bipolar disorder: a nested matched case–control study
Authors: Wu Kuan‐Yi , Chang Chia‐Ming , Liang Hsin‐Yi , Wu Chi‐Shin , Chia‐Hsuan Wu Erin , Chen Chia‐Hsiang , Chau Yeuk‐Lun , Tsai Hui‐Ju
Published: August 2013

Objective

The association between bipolar disorder and subsequent dementia risk is not well established. The objective of this study was to investigate whether patients with bipolar disorder were at an increased risk for developing dementia.

Methods

A conditional logistic regression model was performed using data from the National Health Insurance Research Database, a nationwide dataset in Taiwan. The study sample included 9,304 patients with incident dementia first diagnosed between 2000 and 2009, and 55,500 gender‐, age‐, and index date‐matched subjects without dementia. Cerebrovascular disease, diabetes, hypertension, head injury, chronic pulmonary disease, alcohol‐related disorders, substance use disorders, and health system utilization were treated as covariates in the analyses.

Results

After controlling for the covariates, bipolar disorder was significantly associated with an increased risk of subsequent dementia [adjusted odds ratio (aOR) = 4.32, 95% confidence interval (CI): 3.21–5.82]. An increased risk of developing dementia was observed in males and females alike (aOR = 4.01, 95% CI: 2.53–6.35 in males; aOR = 4.55, 95% CI: 3.07–6.73 in females). Moreover, a significantly increased risk was observed in subjects diagnosed with dementia before the age of 65 years (aOR = 3.77, 95% CI: 1.78–8.01).

Conclusions

Findings from this study suggest a positive association between the presence of a lifetime history of bipolar disorder and an increased risk of developing dementia. Furthermore, our results also suggest that subjects with bipolar disorder tend to develop dementia in middle age. Going forward, it will be of importance to confirm our findings in different populations.
An investigation into the public health roles of community learning disability nurses
Authors: Mafuba Kay , Gates Bob
Published: August 2013

Accessible summary

People with learning disabilities find it difficult to get their health checked and to get information about their health.

Community learning disability nurses play an important role in supporting people with learning disabilities to stay healthy.

Community learning disability nurses support people with learning disabilities to get their health checked and to get information about their health.

International studies have shown poor uptake of public health initiatives by people with learning disabilities. In addition, studies have shown that people with learning disabilities experience poor access to public health services. The contribution of community learning disability nurses in meeting the public health needs of people with learning disabilities has evolved differently across the UK resulting in conflicting understanding of this role. This paper reports on a study that explored and explained the contribution of community learning disability nurses in the implementation of public health policies for people with learning disabilities. The study demonstrates that community learning disability nurses are involved in health surveillance, health promotion, health facilitation, health prevention and protection, health education, and healthcare delivery.
Measuring and decomposing oral health inequalities in an UK population
Authors: Shen Jing , Wildman John , Steele Jimmy
Published: August 2013

Objectives

With health inequalities high on the policy agenda, this study measures oral health inequalities in the UK.

Methods

We compare an objective clinical measure of oral health (number of natural teeth) with a self‐reported measure of the impact of oral health (the Oral Health Impact Profile, OHIP) to establish whether the type of measure affects the scale of inequality measured. Gini coefficients and Concentration Indices (CIs) are calculated with subsequent decompositions using data from the 1998 UK Adult Dental Health Survey. Because the information on OHIP is only available on dentate individuals, analyses on the number of natural teeth are conducted for two samples – the entire sample and the sample with dentate individuals only, the latter to allow direct comparison with OHIP.

Results

We find considerable overall pure oral health inequalities (number of teeth: Gini = 0.68 (including edentate), Gini = 0.40 (excluding edentate); OHIP: Gini = 0.33) and income‐related inequalities for both measures (number of teeth: CI = 0.35 (including edentate), CI = 0.15 (excluding edentate); OHIP: CI = 0.03), and the CI is generally higher for the number of teeth than for OHIP. There are differences across age groups, with CI increasing with age for the number of teeth (excluding edentate: 16–30 years: CI = 0.01, 65 + years: CI = 0.11; including edentate: 16–30 years: CI = 0.01, 65 + years: CI = 0.19). However, inequalities for OHIP were highest in the youngest age group (CI = 0.05). Number of teeth reflects the accumulation of damage over a lifetime, while OHIP records more immediate concerns.

Conclusions

There are considerable pure oral health inequalities and income‐related oral health inequalities in the UK. Using sophisticated methods to measure oral health inequality, we have been able to compare inequality in oral health with inequality in general health. The results provide a benchmark for future comparisons but also indicate that the type of health measure may be of considerable significance in how we think about and measure oral health inequalities.
Women with high early pregnancy urinary iodine levels have an increased risk of hyperthyroid newborns: the population‐based Generation R Study
Authors: Medici Marco , Ghassabian Akhgar , Visser Willy , de Muinck Keizer‐Schrama Sabine M. P. F. , Jaddoe Vincent W. V. , Visser W. Edward , Hooijkaas Herbert , Hofman Albert , Steegers Eric A. P. , Bongers‐Schokking Jacoba J. , Ross H. Alec , Tiemeier Henning , Visser Theo J. , de Rijke Yolanda B. , Peeters Robin P.
Published: August 2013

Objective

Iodine deficiency during pregnancy results in thyroid dysfunction and has been associated with adverse obstetric and foetal effects, leading to worldwide salt iodization programmes.

As nowadays 69% of the world's population lives in iodine‐sufficient regions, we investigated the effects of variation in iodine status on maternal and foetal thyroid (dys)function in an iodine‐sufficient population.

Design, Participants and Measurements

Urinary iodine, serum TSH, free T4 (FT4) and TPO‐antibody levels were determined in early pregnancy (13·3 (1·9) week; mean (SD)) in 1098 women from the population‐based Generation R Study. Newborn cord serum TSH and FT4 levels were determined at birth.

Results

The median urinary iodine level was 222·5 μg/l, indicating an iodine‐sufficient population. 30·8% and 11·5% had urinary iodine levels <150 and >500 μg/l, respectively.

When comparing mothers with urinary iodine levels <150 vs ≥150 μg/l, and >500 vs ≤500 μg/l, there were no differences in the risk of maternal increased or decreased TSH, hypothyroxinaemia or hyperthyroidism. Mothers with urinary iodine levels >500 μg/l had a higher risk of a newborn with decreased cord TSH levels (5·6 ± 1·4 (mean ± SE) vs 2·1 ± 0·5%, P = 0·04), as well as a higher risk of a hyperthyroid newborn (3·1 ± 0·9 vs 0·6 ± 0·3%, P = 0·02). These mothers had newborns with higher cord FT4 levels (21·7 ± 0·3 vs 21·0 ± 0·1 pm, P = 0·04).

Maternal urinary iodine levels <150 μg/l were not associated with newborn thyroid dysfunction.

Conclusions

In an iodine‐sufficient population, higher maternal urinary iodine levels are associated with an increased risk of a hyperthyroid newborn.
Non‐Oriented MLS Gradient Fields
Authors: Chen Jiazhou , Guennebaud Gaël , Barla Pascal , Granier Xavier
Published: August 2013

We introduce a new approach for defining continuous non‐oriented gradient fields from discrete inputs, a fundamental stage for a variety of computer graphics applications such as surface or curve reconstruction, and image stylization. Our approach builds on a moving least square formalism that computes higher‐order local approximations of non‐oriented input gradients. In particular, we show that our novel isotropic linear approximation outperforms its lower‐order alternative: surface or image structures are much better preserved, and instabilities are significantly reduced. Thanks to its ease of implementation (on both CPU and GPU) and small performance overhead, we believe our approach will find a widespread use in graphics applications, as demonstrated by the variety of our results.
Systematic review of methods to predict and detect anastomotic leakage in colorectal surgery
Authors: Hirst N. A. , Tiernan J. P. , Millner P. A. , Jayne D. G.
Published: August 2013

Aim

Anastomotic leakage is a serious complication of gastrointestinal surgery resulting in increased morbidity and mortality, poor function and predisposing to cancer recurrence. Earlier diagnosis and intervention can minimize systemic complications but is hindered by current diagnostic methods that are non‐specific and often uninformative. The purpose of this paper is to review current developments in the field and to identify strategies for early detection and treatment of anastomotic leakage.

Method

A systematic literature search was performed using theMEDLINE, Embase, PubMed and Cochrane Library databases. Search terms included ‘anastomosis’ and ‘leak’ and ‘diagnosis’ or ‘detection’ and ‘gastrointestinal’ or ‘colorectal’. Papers concentrating on the diagnosis of gastrointestinal anastomotic leak were identified and further searches were performed by cross‐referencing.

Results

Computerized tomographyCTscanning and water‐soluble contrast studies are the current preferred techniques for diagnosing anastomotic leakage but suffer from variable sensitivity and specificity, have logistical constraints and may delay timely intervention. Intra‐operative endoscopy and imaging may offer certain advantages, but the ability to predict anastomotic leakage is unproven. Newer techniques involve measurement of biomarkers for anastomotic leakage and have the potential advantage of providing cheap real‐time monitoring for postoperative complications.

Conclusion

Current diagnostic tests often fail to diagnose anastomotic leak at an early stage that enables timely intervention and minimizes serious morbidity and mortality. Emerging technologies, based on detection of local biomarkers, have achieved proof of concept status but require further evaluation to determine whether they translate into improved patient outcomes. Further research is needed to address this important, yet relatively unrecognized, area of unmet clinical need.
Mucocutaneous disorders in renal transplant recipients receiving sirolimus‐based immunosuppressive therapy: a prospective, case–control study
Authors: Özcan Deren , Seçkin Deniz , Ada Simin , Haberal Mehmet
Published: August 2013

Background

Sirolimus (SRL) has some dermatologic complications including acneiform eruptions, edema, aphthous ulceration, and onychopathy. However, controlled studies reporting the prevalence and clinical characteristics of mucocutaneous disorders are scarce.

Objective

To investigate the prevalence and clinical spectrum of mucocutaneous disorders in renal transplant recipients (RTRs) receiving SRL and to compare the findings with those in RTRs not receiving SRL.

Methods

Fifty RTRs (35 men, 15 women; mean age, 34.6 ± 11.6 yr) receiving SRL, 50 RTRs (36 men, 14 women; mean age, 34.4 ± 11.3 yr) not on SRL were screened for mucocutaneous disorders.

Results

In RTRs receiving SRL, skin infection (78%) was the most common dermatologic disorder followed by facial hyperpigmentation (50%) and acneiform eruption (46%). Herpes simplex virus infections (14%) and seborrheic dermatitis (38%) were significantly more common in RTRs on SRL (p < 0.05); the frequencies of edema, aphthous ulceration, acne, and longitudinal nail ridging were similar in both groups (p > 0.05).

Limitations

This study had a small sample size. The investigator was not blinded to immunosuppressive treatment protocols.

Conclusion

Renal transplant recipients receiving SRL are more likely to develop seborrheic dermatitis and herpes simplex virus infections than those not taking SRL. Whereas, they are not more prone to edema, aphthous ulceration, acne, or longitudinal nail ridging.
The potential role of transient receptor potential type A1 as a mechanoreceptor in human periodontal ligament cells
Authors: Tsutsumi Takashi , Kajiya Hiroshi , Fukawa Teruhisa , Sasaki Mina , Nemoto Tetsuomi , Tsuzuki Takashi , Takahashi Yutaka , Fujii Shinsuke , Maeda Hidefumi , Okabe Koji
Published: August 2013

Transient receptor potential type A1 (TRPA1) is reported to be a Ca2+‐permeable channel and is activated by cold temperatures and mechanical stimuli in the hair cells and in dorsal root ganglion. Using a DNA microarray, we found that TRPA1 was significantly up‐regulated in human periodontal ligament (hPDL) cells 2 d after intermittent mechanical stimulation (iMS) loading compared with unloaded cells. Although hPDL cells are known to respond to mechanical stimulation induced by occlusal force, little is known about the expression and functional role of TRPA1 in these cells. Therefore, we investigated the effects of iMS on TRPA1 expression and its signaling pathway in hPDL cells. Intermittent mechanical stimulation loading up‐regulated TRPA1 expression in hPDL cells in a time‐dependent manner, but had no effect on other mechanoreceptors. Furthermore, iMS significantly increased the phosphorylation of mitogen‐activated protein kinases (MAPKs), especially extracellular signal‐regulated kinase 1/2 (ERK1/2) and p38, and the expression of C‐C chemokine ligand 2 (CCL2). Transient receptor potential type A1 agonists also increased MAPK phosphorylation and the intracellular Ca2+ concentration. By contrast, inhibition or silencing of TRPA1 partially suppressed iMS‐induced MAPK phosphorylation. In summary, iMS during occlusion activates TRPA1 and MAPK signaling in periodontal ligament tissues, suggesting that TRPA1 regulates the mechanosensitivity of occlusal force via activation of MAPKs in hPDL cells.