bluuebunny/crossref_metadata_2025 huggingface dataset:
Occurrence Of Viruses Infecting Watermelon, Other Cucurbits, and Weeds in the Parts of Southern United States
Authors: Ali Akhtar , Abdalla Osama , Bruton Benny , Fish Wayne , Sikora Edward , Zhang Shouan , Taylor Merritt
Published: August 2012

Field surveys were conducted to determine the distribution and frequency of viruses infecting watermelon and other cucurbits in the southern US in 2010 and 2011. Leaf samples were collected from 715 symptomatic plants from 10 states and were tested by dot-immunobinding assays or reverse transcriptionpolymerase chain reaction for 17 viruses that included Alfalfa mosaic virus (AMV), Bean pod mottle virus (BPMV), Cucurbit aphid born yellows virus (CABYV), Cucurbit yellow stunting disorder virus (CYSDV), Cucumber green mottle mosaic virus (CGMMV), Cucumber mosaic virus (CMV), Melon necrotic spot virus (MNSV), Papaya ringspot virus-W (PRSV-W), Squash leaf curl virus (SLCuV), Soybean mosaic virus (SMV), Squash mosaic virus (SqMV), Squash vein yellowing virus (SqVYV), Tobacco ringspot virus (TRSV), Watermelon mosaic virus (WMV), Watermelon silver mottle virus (WSMoV), Zucchini yellow mosaic virus (ZYMV), and Zucchini green mottle mosaic virus (ZGMMV). Thirteen out of 17 viruses were detected in this study. The distribution of detected viruses varied with the highest average frequency for WMV (30.6%), followed by PRSV-W (24.7%), ZYMV (13.9%), TRSV (5.7%), SqMV (3.5%), and MNSV (2.6%). The percent frequency of the remaining viruses was less than 2%. Seven viruses (AMV, BPMV, CMV, SqMV, TRSV, PRSV-W, and ZYMV) were also detected either from nearby agricultural crops or weeds species. Mixed infections were also recorded for some viruses with potyviruses being the most common. There is limited information on frequency and distribution of viruses that occur on watermelon and other cucurbits. These results indicate that potyviruses, particularly PRSV-W, WMV, and ZYMV, are frequently present in infected watermelon and other cucurbits in the southern US.

Accepted for publication 30 July 2012. Published 24 August 2012.
Spatial memory: are lizards really deficient?
Authors: LaDage L. D. , Roth T. C. , Cerjanic A. M. , Sinervo B. , Pravosudov V. V.
Published: August 2012

In many animals, behaviours such as territoriality, mate guarding, navigation and food acquisition rely heavily on spatial memory abilities; this has been demonstrated in diverse taxa, from invertebrates to mammals. However, spatial memory ability in squamate reptiles has been seen as possible, at best, or non-existent, at worst. Of the few previous studies testing for spatial memory in squamates, some have found no evidence of spatial memory while two studies have found evidence of spatial memory in snakes, but have been criticized based on methodological issues. We used the Barnes maze, a common paradigm to test spatial memory abilities in mammals, to test for spatial memory abilities in the side-blotched lizard (
Uta stansburiana
). We found the existence of spatial memory in this species using this spatial task. Thus, our study supports the existence of spatial memory in this squamate reptile species and seeks to parsimoniously align this species with the diverse taxa that demonstrate spatial memory ability.
The consequences of climate change at an avian influenza ‘hotspot’
Authors: Brown V. L. , Rohani Pejman
Published: August 2012

Avian influenza viruses (AIVs) pose significant danger to human health. A key step in managing this threat is understanding the maintenance of AIVs in wild birds, their natural reservoir. Ruddy turnstones (
Arenaria interpres
) are an atypical bird species in this regard, annually experiencing high AIV prevalence in only one location—Delaware Bay, USA, during their spring migration. While there, they congregate on beaches, attracted by the super-abundance of horseshoe crab eggs. A relationship between ruddy turnstone and horseshoe crab (
Limulus polyphemus
) population sizes has been established, with a declining horseshoe crab population linked to a corresponding drop in ruddy turnstone population sizes. The effect of this interaction on AIV prevalence in ruddy turnstones has also been addressed. Here, we employ a transmission model to investigate how the interaction between these two species is likely to be altered by climate change. We explore the consequences of this modified interaction on both ruddy turnstone population size and AIV prevalence and show that, if climate change leads to a large enough mismatch in species phenology, AIV prevalence in ruddy turnstones will increase even as their population size decreases.
Embodied linearity of speed control inDrosophila melanogaster
Authors: Medici V. , Fry S. N.
Published: August 2012

Fruitflies regulate flight speed by adjusting their body angle. To understand how low-level posture control serves an overall linear visual speed control strategy, we visually induced free-flight acceleration responses in a wind tunnel and measured the body kinematics using high-speed videography. Subsequently, we reverse engineered the transfer function mapping body pitch angle onto flight speed. A linear model is able to reproduce the behavioural data with good accuracy. Our results show that linearity in speed control is realized already at the level of body posture-mediated speed control and is therefore embodied at the level of the complex aerodynamic mechanisms of body and wings. Together with previous results, this study reveals the existence of a linear hierarchical control strategy, which can provide relevant control principles for biomimetic implementations, such as autonomous flying micro air vehicles.
Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification
Authors: Ballester Pedro J. , Mangold Martina , Howard Nigel I. , Robinson Richard L. Marchese , Abell Chris , Blumberger Jochen , Mitchell John B. O.
Published: August 2012

One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from
Mycobacterium tuberculosis
and
Streptomyces coelicolor
), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated
K
i
ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated
in silico
screening tools is likely to bring to antibacterial hit identification.
Evolutionary medicine: its scope, interest and potential
Authors: Stearns Stephen C.
Published: August 2012

This review is aimed at readers seeking an introductory overview, teaching courses and interested in visionary ideas. It first describes the range of topics covered by evolutionary medicine, which include human genetic variation, mismatches to modernity, reproductive medicine, degenerative disease, host–pathogen interactions and insights from comparisons with other species. It then discusses priorities for translational research, basic research and health management. Its conclusions are that evolutionary thinking should not displace other approaches to medical science, such as molecular medicine and cell and developmental biology, but that evolutionary insights can combine with and complement established approaches to reduce suffering and save lives. Because we are on the cusp of so much new research and innovative insights, it is hard to estimate how much impact evolutionary thinking will have on medicine, but it is already clear that its potential is enormous.
Stable isotopes provide independent support for the use of mesowear variables for inferring diets in African antelopes
Authors: Louys Julien , Ditchfield Peter , Meloro Carlo , Elton Sarah , Bishop Laura C.
Published: August 2012

We examine the relationship between mesowear variables and carbon and nitrogen isotopes in 16 species of African antelope (Mammalia: Bovidae). We show significant differences in carbon and nitrogen isotope values between individuals exhibiting sharp versus round cusps, and high versus low occlusal relief. We show significant correlations between mesowear variables and both carbon and nitrogen isotopes. We find significant correlations between mesowear score and nitrogen, but not carbon isotopes. Finally, we find no significant correlations between hypsodonty index and either isotope examined. Our results provide strong support for the use of mesowear variables in palaeodietary reconstructions of antelopes. Our results further suggest that for the antelopes examined here, mesowear signals are a direct result of diet, while hyposodonty may be the result of phylogenetic legacy.
Development of lateralization of the magnetic compass in a migratory bird
Authors: Gehring Dennis , Wiltschko Wolfgang , Güntürkün Onur , Denzau Susanne , Wiltschko Roswitha
Published: August 2012

The magnetic compass of a migratory bird, the European robin (
Erithacus rubecula
), was shown to be lateralized in favour of the right eye/left brain hemisphere. However, this seems to be a property of the avian magnetic compass that is not present from the beginning, but develops only as the birds grow older. During first migration in autumn, juvenile robins can orient by their magnetic compass with their right as well as with their left eye. In the following spring, however, the magnetic compass is already lateralized, but this lateralization is still flexible: it could be removed by covering the right eye for 6 h. During the following autumn migration, the lateralization becomes more strongly fixed, with a 6 h occlusion of the right eye no longer having an effect. This change from a bilateral to a lateralized magnetic compass appears to be a maturation process, the first such case known so far in birds. Because both eyes mediate identical information about the geomagnetic field, brain asymmetry for the magnetic compass could increase efficiency by setting the other hemisphere free for other processes.
Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number
Authors: Sankaran Vijay G. , Ludwig Leif S. , Sicinska Ewa , Xu Jian , Bauer Daniel E. , Eng Jennifer C. , Patterson Heide Christine , Metcalf Ryan A. , Natkunam Yasodha , Orkin Stuart H. , Sicinski Piotr , Lander Eric S. , Lodish Harvey F.
Published: August 2012

Genome-wide association studies (GWASs) have identified a genetic variant of moderate effect size at 6p21.1 associated with erythrocyte traits in humans. We show that this variant affects an erythroid-specific enhancer of CCND3. A Ccnd3 knockout mouse phenocopies these erythroid phenotypes, with a dramatic increase in erythrocyte size and a concomitant decrease in erythrocyte number. By examining human and mouse primary erythroid cells, we demonstrate that the CCND3 gene product cyclin D3 regulates the number of cell divisions that erythroid precursors undergo during terminal differentiation, thereby controlling erythrocyte size and number. We illustrate how cell type-specific specialization can occur for general cell cycle components—a finding resulting from the biological follow-up of unbiased human genetic studies.
Arabidopsis ECERIFERUM2 Is a Component of the Fatty Acid Elongation Machinery Required for Fatty Acid Extension to Exceptional Lengths
Authors: Haslam Tegan M. , Mañas-Fernández Aurora , Zhao Lifang , Kunst Ljerka
Published: August 2012

Primary aerial surfaces of land plants are coated by a lipidic cuticle, which forms a barrier against transpirational water loss and protects the plant from diverse stresses. Four enzymes of a fatty acid elongase complex are required for the synthesis of very-long-chain fatty acid (VLCFA) precursors of cuticular waxes. Fatty acid elongase substrate specificity is determined by a condensing enzyme that catalyzes the first reaction carried out by the complex. In Arabidopsis (Arabidopsis thaliana), characterized condensing enzymes involved in wax synthesis can only elongate VLCFAs up to 28 carbons (C28) in length, despite the predominance of C29 to C31 monomers in Arabidopsis stem wax. This suggests additional proteins are required for elongation beyond C28. The wax-deficient mutant eceriferum2 (cer2) lacks waxes longer than C28, implying that CER2, a putative BAHD acyltransferase, is required for C28 elongation. Here, we characterize the cer2 mutant and demonstrate that green fluorescent protein-tagged CER2 localizes to the endoplasmic reticulum, the site of VLCFA biosynthesis. We use site-directed mutagenesis to show that the classification of CER2 as a BAHD acyltransferase based on sequence homology does not fit with CER2 catalytic activity. Finally, we provide evidence for the function of CER2 in C28 elongation by an assay in yeast (Saccharomyces cerevisiae).
Carbon Deprivation-Driven Transcriptome Reprogramming in Detached Developmentally Arresting Arabidopsis Inflorescences
Authors: Trivellini Alice , Jibran Rubina , Watson Lyn M. , O’Donoghue Erin M. , Ferrante Antonio , Sullivan Kerry L. , Dijkwel Paul P. , Hunter Donald A.
Published: August 2012

Senescence is genetically controlled and activated in mature tissues during aging. However, immature plant tissues also display senescence-like symptoms when continuously exposed to adverse energy-depleting conditions. We used detached dark-held immature inflorescences of Arabidopsis (Arabidopsis thaliana) to understand the metabolic reprogramming occurring in immature tissues transitioning from rapid growth to precocious senescence. Macroscopic growth of the detached inflorescences rapidly ceased upon placement in water in the dark at 21°C. Inflorescences were completely degreened by 120 h of dark incubation and by 24 h had already lost 24% of their chlorophyll and 34% of their protein content. Comparative transcriptome profiling at 24 h revealed that inflorescence response at 24 h had a large carbon-deprivation component. Genes that positively regulate developmental senescence (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN92) and shade-avoidance syndrome (PHYTOCHROME INTERACTING FACTOR4 [PIF4] and PIF5) were up-regulated within 24 h. Mutations in these genes delayed degreening of the inflorescences. Their up-regulation was suppressed in dark-held inflorescences by glucose treatment, which promoted macroscopic growth and development and inhibited degreening of the inflorescences. Detached inflorescences held in the dark for 4 d were still able to reinitiate development to produce siliques upon being brought out to the light, indicating that the transcriptional reprogramming at 24 h was adaptive and reversible. Our results suggest that the response of detached immature tissues to dark storage involves interactions between carbohydrate status sensing and light deprivation signaling and that the dark-adaptive response of the tissues appears to utilize some of the same key regulators as developmental senescence.
The simple fool's guide to population genomics via RNA‐Seq: an introduction to high‐throughput sequencing data analysis
Authors: De Wit Pierre , Pespeni Melissa H. , Ladner Jason T. , Barshis Daniel J. , Seneca François , Jaris Hannah , Therkildsen Nina Overgaard , Morikawa Megan , Palumbi Stephen R.
Published: August 2012

High‐throughput sequencing technologies are currently revolutionizing the field of biology and medicine, yet bioinformatic challenges in analysing very large data sets have slowed the adoption of these technologies by the community of population biologists. We introduce the ‘Simple Fool's Guide to Population Genomics via RNA‐seq’ (SFG), a document intended to serve as an easy‐to‐follow protocol, walking a user through one example of high‐throughput sequencing data analysis of nonmodel organisms. It is by no means an exhaustive protocol, but rather serves as an introduction to the bioinformatic methods used in population genomics, enabling a user to gain familiarity with basic analysis steps. The SFG consists of two parts. This document summarizes the steps needed and lays out the basic themes for each and a simple approach to follow. The second document is the full SFG, publicly available at http://sfg.stanford.edu, that includes detailed protocols for data processing and analysis, along with a repository of custom‐made scripts and sample files. Steps included in the SFG range from tissue collection to de novo assembly, blast annotation, alignment, gene expression, functional enrichment, SNP detection, principal components and FST outlier analyses. Although the technical aspects of population genomics are changing very quickly, our hope is that this document will help population biologists with little to no background in high‐throughput sequencing and bioinformatics to more quickly adopt these new techniques.
Positive crosstalk between arginase‐II and S6K1 in vascular endothelial inflammation and aging
Authors: Yepuri Gautham , Velagapudi Srividya , Xiong Yuyan , Rajapakse Angana G. , Montani Jean‐Pierre , Ming Xiu‐Fen , Yang Zhihong
Published: August 2012

Augmented activities of both arginase and S6K1 are involved in endothelial dysfunction in aging. This study was to investigate whether or not there is a crosstalk between arginase and S6K1 in endothelial inflammation and aging in senescent human umbilical vein endothelial cells and in aging mouse models. We show increased arginase‐II (Arg‐II) expression/activity in senescent endothelial cells. Silencing Arg‐II in senescent cells suppresses eNOS‐uncoupling, several senescence markers such as senescence‐associated‐β‐galactosidase activity, p53‐S15, p21, and expression of vascular adhesion molecule‐1 (VCAM1) and intercellular adhesion molecule‐1 (ICAM1). Conversely, overexpressing Arg‐II in nonsenescent cells promotes eNOS‐uncoupling, endothelial senescence, and enhances VCAM1/ICAM1 levels and monocyte adhesion, which are inhibited by co‐expressing superoxide dismutase‐1. Moreover, overexpressing S6K1 in nonsenescent cells increases, whereas silencing S6K1 in senescent cells decreases Arg‐II gene expression/activity through regulation of Arg‐II mRNA stability. Furthermore, S6K1 overexpression exerts the same effects as Arg‐II on endothelial senescence and inflammation responses, which are prevented by silencing Arg‐II, demonstrating a role of Arg‐II as the mediator of S6K1‐induced endothelial aging. Interestingly, mice that are deficient in Arg‐II gene (Arg‐II−/−) are not only protected from age‐associated increase in Arg‐II, VCAM1/ICAM1, aging markers, and eNOS‐uncoupling in the aortas but also reveal a decrease in S6K1 activity. Similarly, silencing Arg‐II in senescent cells decreases S6K1 activity, demonstrating that Arg‐II also stimulates S6K1 in aging. Our study reveals a novel mechanism of mutual positive regulation between S6K1 and Arg‐II in endothelial inflammation and aging. Targeting S6K1 and/or Arg‐II may decelerate vascular aging and age‐associated cardiovascular disease development.
Detection of infliximab levels and anti‐infliximab antibodies: a comparison of three different assays
Authors: Vande Casteele N. , Buurman D. J. , Sturkenboom M. G. G. , Kleibeuker J. H. , Vermeire S. , Rispens T. , van der Kleij D. , Gils A. , Dijkstra G.
Published: August 2012

Background

Formation of antibodies to infliximab (ATI) inversely correlates with functional drug levels and clinical outcome. Comparison of drug levels and anti‐drug antibody monitoring is hampered by lack of standardisation.

Aim

To determine the correlation between three different assays for measuring infliximab and ATI.

Methods

Serum samples and spiked controls (total 62) were evaluated in a blinded way in infliximab and ATI assays developed by Sanquin Amsterdam, Netherlands (A), Laboratory for Pharmaceutical Biology, KU Leuven, Belgium (B) and a commercially available kit from Biomedical Diagnostics (BMD), Paris, France (C) performed by the University Medical Center Groningen (UMCG), Netherlands.

Results

All infliximab assays showed a linear quantitative correlation (Pearson r = 0.91 for A vs. B, 0.83 for A vs. C and 0.73 for B vs. C). Assay C detected infliximab in 11 samples (18%) not detected by A and B, including samples containing only ATI. All ATI assays showed a good linear correlation (Pearson r = 0.95 for A vs. B, 0.99 for A vs. C and 0.97 for B vs. C). Assay A detected ATI in five samples with low ATI that were not detected by assays B and C. Assay B did not detect ATI in three patient samples with low ATI according to assays A and C.

Conclusions

There is a good correlation of infliximab and antibodies to infliximab measurements between these assays. Nevertheless, the Biomedical Diagnostics kit detected false positive infliximab levels in 18% of the samples.
Reactive gastropathy is associated with inflammatory conditions throughout the gastrointestinal tract
Authors: Maguilnik I. , Neumann W. L. , Sonnenberg A , Genta R. M.
Published: August 2012

Background

The epidemiology of reactive gastropathy and its relationship with other conditions of the gastrointestinal tract associated with NSAID use have not been evaluated.

Aims

To test the hypothesis that if reactive gastropathy shares common aetiological factors with these conditions, the analysis of a large cohort would unveil associations.

Methods

We queried a national pathology database for subjects with a diagnosis of reactive gastropathy; controls were patients with normal gastric biopsies. We also extracted diagnoses of H. pylori infection, intestinal metaplasia, duodenal lymphocytosis, duodenitis, ileitis, microscopic colitis and focal colitis.

Results

Of 504 011 patients with gastric biopsies, 69 101 had oesophageal, 166 134 duodenal, 13 010 ileal and 83 334 colonic biopsies. Reactive gastropathy was diagnosed in 15.6% of patients, H. pylori infection in 10.3% and normal gastric mucosa in 16.3%. Reactive gastropathy was evenly distributed across the US and increased from 2.0% in the first decade of life to >20% in octogenarians. Compared with controls, reactive gastropathy was significantly associated with Barrett's mucosa (OR 1.21 95% CI 1.16–129); duodenitis (OR 1.36; 95% CI 1.28–1.44); duodenal intraepithelial lymphocytosis (OR 1.25; 95% CI 1.13–1.39); active ileitis (OR 1.88; 95% CI 1.47–2.40); focal active colitis (OR 1.57; 95% CI 1.33–1.86); and collagenous colitis (OR 1.50; 95% CI 1.12–2.03).

Conclusions

Reactive gastropathy, a common histopathological feature of the stomach, shows an age‐dependent rise and is associated with changes of the digestive tract believed to be caused by NSAID use or duodenogastric reflux. However, a large fraction of reactive gastropathy remains unexplained; its frequent occurrence merits further efforts at elucidating its aetiology.
Expression of p16 alone does not differentiate between Spitz nevi and Spitzoid melanoma
Authors: Mason Ashley , Wititsuwannakul Jade , Klump Vincent R. , Lott Jason , Lazova Rossitza
Published: August 2012

Background

Spitz nevi and Spitzoid melanomas show overlapping histopathologic features, often making the diagnosis challenging. The p16 protein functions as a tumor suppressor and loss of its expression may be seen in some melanomas.

Methods

We evaluated 18 Spitz nevi and 19 Spitzoid melanomas from the Yale Spitzoid Neoplasm Repository for p16 expression. A staining intensity score (SIS) was calculated by multiplying a score for the percentage of stained cells (0–3) by a score for staining intensity (0–3).

Results

Staining with p16 was positive in 15/18 (83%) Spitz nevi and 15/19 (79%) Spitzoid melanomas (p = 0.73). Both Spitz nevi and Spitzoid melanomas had a similar SISs, 4.9 and 3.8, respectively (p = 0.057). All 19 patients with Spitzoid melanomas had poor outcome with either death (6 patients) or metastases (13 patients) at a median (3 years) and mean (5.4 years) follow up. In contrast, all 18 patients with Spitz nevi had a benign course with no adverse events at a median (4 years) and mean (4 years) follow up.

Conclusions

We found no significant difference in p16 staining in Spitz nevi and Spitzoid melanomas. We conclude that p16 does not appear to be a useful immunohistochemical marker in distinguishing between Spitz nevi and Spitzoid melanomas.
Incidence of dieback disease following fungal inoculations of sexually and asexually propagated shisham (Dalbergia sissoo)
Authors: Ahmad By I. , Khan R. A. , Siddiqui M. T.
Published: August 2012

Shisham (Dalbergia sissoo) is an important multipurpose tree with great economic importance, but this tree has been devastated by dieback disease. Seedlings and asexually propagated (cuttings) plants were artificially inoculated with four fungi (Fusarium solani, Botryodiplodia theobromae, Curvularia lunata and Ganoderma lucidum) to evaluate the potential role of these fungi in shisham dieback disease. Results at 2 years revealed that highest disease was caused by inoculation of F. solani (31.39%), followed by B. theobromae (19.042%) and C. lunata (12.22%), but no dieback disease was caused by G. lucidum. During both years, seedlings exhibited greater susceptibility to disease (17.24%) compared to cuttings (7.83%). In particular, F. solani caused more disease in seedlings (46.18%) compared to cuttings (16.61%). With the F. solani inoculations, maximum disease rate was observed at 8 weeks post‐inoculation both in seedlings (77%) and in cuttings (31%), but the maximum disease increase was observed at 4–5 weeks post‐inoculation. Analysis of variance showed significant differences among the different fungi and also between seedlings and cuttings. F. solani can be considered as a major fungal pathogen contributing to dieback disease of shisham, and asexual propagation can reduce the severity of dieback.
Scale‐dependent longitudinal patterns in mussel communities
Authors: ATKINSON CARLA L. , JULIAN JASON P. , VAUGHN CARYN C.
Published: August 2012

1. Species richness and assemblage patterns of organisms are dictated by numerous factors, probably operating at multiple scales. Freshwater mussels (Unionidae) are an endangered, speciose faunal group, making them an interesting model system to study the influence of landscape features on organisms. In addition, landscape features that influence species distributions and the scale at which the factors have the greatest impact are important issues that need to be answered to conserve freshwater mussels.

2. In this study, we quantified freshwater mussel communities at 16 sites along three mid‐sized rivers in the south‐central United States. We addressed the following questions: (i) Are there predictable longitudinal changes in mussel community composition? (ii) What landscape variables best explain shifts in community composition? and (iii) At what scale do landscape variables best predict mussel community composition?

3. After controlling for the influence of longitudinal position along the stream, we compared mussel distributions to a suite of hypothesised explanatory landscape variables across multiple scales – catchment scale (entire drainage area), buffer scale (100‐m riparian buffer of the entire catchment) and reach scale (100‐m riparian buffer extending 1 km upstream from the sampling site).

4. We found a significant and consistent longitudinal shift in dominant mussel species across all three rivers, with community composition strongly related to distance from the headwaters, which is highly correlated with stream size. After accounting for stream size, variables at the buffer scale were the best predictors of mussel community composition. After accounting for catchment position, mean channel slope was the best explanatory variable of community composition and appeared in all top candidate models at the catchment and buffer scales. Coverage of wetland and urban area were also correlated with community composition at the catchment and buffer scales.

5. Our results suggest that landscape‐scale habitat factors influence mussel community composition. Landscape features at the buffer scale performed best at determining community composition after accounting for position in the catchment; thus, further protection of riparian buffers will help to conserve mussel communities.
A Frequent Toll‐Like Receptor 1 Gene Polymorphism Affects NK‐ and T‐cell IFN‐γ Production and is Associated with Helicobacter pylori‐induced Gastric Disease
Authors: Yang Chin‐An , Scheibenbogen Carmen , Bauer Sandra , Kleinle Christoph , Wex Thomas , Bornschein Jan , Malfertheiner Peter , Hellmig Stephan , Schumann Ralf R. , Hamann Lutz
Published: August 2012

Background

Helicobacter pylori infects approximately 50% of the world population. Among the infected individuals, only 10–20% develop peptic ulcers and <3% progress to gastric cancer (GC). Th1‐predominant immune responses have been suggested to underlie H. pylori‐induced gastric diseases. However, the reason for a strong inter‐individual variation of susceptibility and course of the disease is currently far from being understood. It has been shown that H. pylori stimulates the host's Toll‐like receptor (TLR) 2/1 complex. Furthermore, the single nucleotide polymorphism (SNP) I602S of TLR1 alters the inflammatory cytokine response of monocytes. Therefore, we hypothesized an association of this TLR1 SNP with H. pylori‐mediated gastric pathologies.

Materials and Methods

Subjects with different TLR1 genotypes were analyzed for their IFN‐γ response of NK‐ and T‐cells. We further genotyped 548 patients with gastric diseases for this SNP and compared patients with gastritis with those having ulcer, and patients with high‐risk gastritis versus patients with GC.

Results

Homozygous 602S allele carriers exhibited impaired in vitro IFN‐γ responses to the TLR2/1 agonist Pam3CSK4. The TLR1 I602S SNP is significantly associated with GC (p = .002) and gastric ulcer (p = .051). Odds ratios showed significantly reduced risk regarding GC and peptic ulcer for the homozygous mutated genotype. The odds ratios were 0.4 (95% CI, 0.22–0.72) and 0.588 (95% CI, 0.35–1.00), respectively.

Conclusion

In conclusion, our results suggest that the nonfunctional TLR1 602S/S genotype is associated with a reduced risk of H. pylori‐induced gastric diseases, probably via diminished Th1 responses.
PAX8 and PAX5 are differentially expressed in B‐cell and T‐cell lymphomas
Authors: Morgan Elizabeth A , Pozdnyakova Olga , Nascimento Alessandra F , Hirsch Michelle S
Published: August 2012

Aims:  The purpose of this study was to evaluate the expression patterns of B‐cell specific activator protein (BSAP)/PAX5 and PAX8 in a wide variety of B‐cell and T‐cell neoplasms.

Methods and results:  A wide range of B‐cell and T‐cell neoplasms were subjected to immunohistochemical staining with antibodies against BSAP/PAX5 and PAX8 (polyclonal, pPAX8; monoclonal, mPAX8). Ten non‐neoplastic lymph node specimens were examined with the same panel. All of the tested neoplastic and non‐neoplastic B‐cells reacted with the BSAP/PAX5 and pPAX8 antibodies, but did not show reactivity with the mPAX8 antibody. All tested T‐cell neoplasms were negative using the BSAP/PAX5, pPAX8 and mPAX8 antibodies.

Conclusions:  This is the first study to show the absence of reactivity to an mPAX8 antibody in an expanded panel of B‐cell lymphomas as well as in a variety of T‐cell neoplasms. In contrast to the mPAX8 antibody, the pPAX8 antibody shows nuclear positivity in non‐neoplastic B cells and mature B‐cell neoplasms; however, this expression is probably a result of cross‐reactivity with PAX5. Given that many laboratories use the pPAX8 antibody, a clear understanding of the differential staining patterns is necessary. The differential diagnosis of a B‐cell lymphoma should be entertained when a pPAX8‐positive, epithelial marker‐negative neoplasm of uncertain primary origin is encountered.
Using physiology and behaviour to understand the responses of fish early life stages to toxicants
Authors: Sloman K. A. , McNeil P. L.
Published: August 2012

The use of early life stages of fishes (embryos and larvae) in toxicity testing has been in existence for a long time, generally utilizing endpoints such as morphological defects and mortality. Behavioural endpoints, however, may represent a more insightful evaluation of the ecological effects of toxicants. Indeed, recent years have seen a considerable increase in the use of behavioural measurements in early life stages reflecting a substantial rise in zebrafishDanio rerioearly life‐stage toxicity testing and the development of automated behavioural monitoring systems. Current behavioural endpoints identified for early life stages in response to toxicant exposure include spontaneous activity, predator avoidance, capture of live food, shoaling ability and interaction with other individuals. Less frequently used endpoints include measurement of anxiogenic behaviours and cognitive ability, both of which are suggested here as future indicators of toxicant disruption. For many simple behavioural endpoints, there is still a need to link behavioural effects with ecological relevance; currently, only a limited number of studies have addressed this issue. Understanding the physiological mechanisms that underlie toxicant effects on behaviour so early in life has received far less attention, perhaps because physiological measurements can be difficult to carry out on individuals of this size. The most commonly established physiological links with behavioural disruption in early life stages are similar to those seen in juveniles and adults including sensory deprivation (olfaction, lateral line and vision), altered neurogenesis and neurotransmitter concentrations. This review highlights the importance of understanding the integrated behavioural and physiological response of early life stages to toxicants and identifies knowledge gaps which present exciting areas for future research.
Predictors of abstinence among smokers recruited actively to quitline support
Authors: Tzelepis Flora , Paul Christine L. , Walsh Raoul A. , Wiggers John , Duncan Sarah L. , Knight Jenny
Published: August 2012

Aims

Active recruitment of smokers increases the reach of quitlines; however, some quitlines restrict proactive telephone counselling (i.e. counsellor‐initiated calls) to smokers ready to quit within 30 days. Identifying characteristics associated with successful quitting by actively recruited smokers could help to distinguish those most likely to benefit from proactive telephone counselling. This study assessed the baseline characteristics of actively recruited smokers associated with prolonged abstinence at 4, 7 and 13 months and the proportion achieving prolonged abstinence that would miss out on proactive telephone counselling if such support was offered only to smokers intending to quit within 30 days at baseline.

Design

Secondary analysis of a randomized controlled trial in which the baseline characteristics associated with prolonged abstinence were examined.

Setting

New South Wales (NSW) community, Australia.

Participants

A total of 1562 smokers recruited at random from the electronic NSW telephone directory.

Measurements

Baseline socio‐demographic and smoking‐related characteristics associated with prolonged abstinence at 4, 7 and 13 months post‐recruitment.

Findings

Waiting more than an hour to smoke after waking and intention to quit within 30 days at baseline predicted five of the six prolonged abstinence measures. If proactive telephone counselling was restricted to smokers who at baseline intended to quit within 30 days, 53.8–65.9% of experimental group participants who achieved prolonged abstinence would miss out on telephone support.

Conclusions

Less addicted and more motivated smokers who are actively recruited to quitline support are more likely to achieve abstinence. Most actively recruited smokers reported no intention to quit within the next 30 days, but such smokers still achieved long‐term abstinence.
A meta‐analysis of the accuracy and precision of the ultrasonic cardiac output monitor (USCOM)
Authors: Chong S. W. , Peyton P. J.
Published: August 2012

The ultrasonic cardiac output monitor is a non‐invasive, continuous‐wave Doppler monitor that can be used to measure cardiac output. Its accuracy and precision in peri‐operative and critical care has been assessed with varied results. We conducted a meta‐analysis to calculate a pooled mean bias, precision and percentage error for this device. Six studies were suitable for inclusion into a pooled parametric analysis consisting of 320 measurements. The mean weighted bias was −0.39 l.min−1(95% CI −0.25 to −0.53 l.min−1), precision 1.27 l.min−1and percentage error 42.7% (95% CI 38.5−46.9%). The ultrasonic cardiac output monitor achieved similar agreement with bolus thermodilution to that of other minimally invasive methods of peri‐operative cardiac output monitoring, and may have a useful role in cardiac output monitoring.
Descriptive and factor analysis of the Developmental Coordination Disorder Questionnaire (DCDQ‘07) in a population‐based sample of children with and without Developmental Coordination Disorder
Authors: Rivard L. , Missiuna C. , McCauley D. , Cairney J.
Published: August 2012

Background

The Developmental Coordination Disorder Questionnaire (DCDQ‘07) discriminates children with Developmental Coordination Disorder (DCD) from their peers. Studies employing the DCDQ have typically used clinical samples. To further validate the DCDQ'07, this study: (1) described its distributions in a population‐based sample, and a sample of children with DCD; (2) explored sex and age differences at important cut‐points; and (3) examined its factor structure.

Methods

This secondary analysis of data collected from 23 schools (n = 3151) included a sample of 3070 children (1526 boys, 1544 girls) and a sample of 122 children (73 boys, 49 girls) who met DCD diagnostic criteria. DCDQ‘07 distributions were described by age and sex. Chi‐square analyses were conducted using three clinically important percentile ranges; a factor analysis explored the construct validity of DCDQ scores.

Results

Parents of 3070 children (97.4%) completed the questionnaire independently. Significant sex differences were noted in both samples. Significant differences in proportions by sex, and DCDQ means by age were found in the population sample. A three‐factor solution was found, accounting for 70.3% of the variance.

Conclusions

This is one of the largest studies using the DCDQ'07 with a non‐clinical sample. The three‐factor solution, including item loading, was consistent with previous research. When using DCDQ cut‐offs it is important to consider sex and age.
Why do Romanian junior high school students start to smoke?
Authors: Lotrean L. M. , Mesters I. , de Vries H.
Published: August 2012

Background

Adolescence is a crucial period in the development of smoking behaviour. To develop efficient prevention programmes for teenagers, it is essential to understand why adolescents start to smoke. The objective of this study was to assess the predictors of smoking onset among Romanian junior high school students aged 13–14.

Methods

The data were obtained from a two‐wave, 9‐month longitudinal study carried out among 504 junior high school non‐smokers from Cluj‐Napoca, Romania. Questionnaires assessed smoking behaviour, attitudes, social influence, self‐efficacy and intention regarding smoking (motivational variables), as well as different sociodemographic features.

Results

The results from the logistic regression analysis revealed that baseline lower self‐efficacy in refraining from smoking in several social situations, baseline pressures from peers to smoke and baseline intentions to smoke significantly increased the risk of non‐smokers to become smokers at follow‐up 9 months later.

Conclusions

These findings underline that reinforcing social self‐efficacy to refuse smoking, resisting peer pressures and maintaining negative intentions regarding smoking are essential ingredients for smoking prevention programmes among Romanian junior high school students.
The European Principles of Haemophilia Care: a pilot investigation of adherence to the principles in Europe
Authors: Fischer K. , Hermans C. ,   European Haemophilia Therapy Standardisation Board (EHTSB)
Published: August 2012

In 2008 the 10 Principles of Haemophilia Care were outlined to provide a benchmark for haemophilia treatment. The EHTSB performed a survey to establish to what extent the Principles of Haemophilia Care were being applied throughout Europe. In total, 21 centres from 14 countries (France, UK, Germany, Switzerland, Sweden, Norway, the Netherlands, Belgium, Poland, Portugal, Slovakia, Spain, Greece and Italy), were surveyed. A central organization of haemophilia care (principle 1) was present in 79%, and a central patient registry in 57% (principle 2). National haemophilia care decision‐making was performed by clinicians, ministries and patient organizations (principle 4). All had designated comprehensive care centres (CCC – principle 3), responsible the majority of severe patients, but in 36% some patients were treated outside CCC/haemophilia treatment centres (HTC)s. Clotting factor concentrates were available everywhere, without dosing restraints (principle 5), including recombinant products in 86% of countries. Prophylactic treatment was available for all children but not for all adults (principle 7). Immune tolerance was available in all countries (principle 9). Home treatment was supported and taught by all centres (principle 6). At centre level, 86% had 24‐h laboratory facilities and all participated in education and research (principle 10). An experienced haematologist was available at all centres, a paediatrician in 47%, and prompt out of hours review was available in all (principle 8). The Principles of Haemophilia Care were generally applied throughout Europe. Some aspects of centralization, national organization of care, use of registries, formal paediatric care and prophylaxis for adults may be improved.
Off‐host aggregation in the non‐fed, female brown dog tick, Rhipicephalus sanguineus (Latreille), is induced by tick excreta and enhanced by low relative humidity
Authors: YODER J. A. , JAJACK A. J. , HEDGES B. Z. , BENOIT J. B.
Published: August 2012

We report that Rhipicephalus sanguineus (Ixodida: Ixodidae) faeces and its main component, guanine, act as assembly pheromones in short‐range Petri plate bioassays. Arrestment activity in response to guanine was lower than that in response to natural excreta, indicating the presence of other active ingredients in natural excreta. The selective removal of appendages was used to establish the important roles played by the palps and the front pair of legs in the detection of the pheromone. Reaction to chemically pure guanine at varying concentrations occurred without a dose response; thus only the presence of guanine, not a critical amount, is required to induce assembly. Higher speed and intensity of clustering occurred at 33% relative humidity (RH). We conclude that female adults of R. sanguineus are more prone to assemble under dry conditions that match the arid microhabitats preferred by this species and that this tendency allows this tick to reside in human dwellings and dog kennels that maintain standards of comfort at 30–50% RH. Cleaning or removing tick excreta‐covered surfaces on which ticks aggregate from within and around human dwellings may prove useful as a means of interfering with the establishment of off‐host clusters of R. sanguineus.
Spontaneous and transient defence against bacteriophage by phase‐variable glucosylation of O‐antigen in Salmonella enterica serovar Typhimurium
Authors: Kim Minsik , Ryu Sangryeol
Published: August 2012

As natural killers of bacteria, bacteriophages have forced bacteria to develop a variety of defence mechanisms. The alteration of host receptors is one of the most common bacterial defence strategies against phage infection, which completely blocks phage attachment but comes at a potential fitness cost to the bacteria. Here, we report the cost‐free, transient emergence of phage resistance in Salmonella enterica subspecies enterica serovar Typhimurium through a phase‐variable modification of the O‐antigen. Phage SPC35 typically requires BtuB as a host receptor but also uses the Salmonella O12‐antigen as an adsorption‐assisting apparatus for the successful infection of S. Typhimurium. The α‐1,4‐glucosylation of galactose residues in the O12‐antigen by phase variably expressed O‐antigen glucosylating genes, designated the LT
2
gtrABC1 cluster, blocks the adsorption‐assisting function of the O12‐antigen. Consequently, it confers transient SPC35 resistance to Salmonella without any mutations to the btuB gene. This temporal switch‐off of phage adsorption through phase‐variable antigenic modification may be widespread among Gram‐negative bacteria‐phage systems.
Maternal Use of Cystitis Medication and Childhood Epilepsy in a Danish Population‐based Cohort
Authors: Miller Jessica E. , Pedersen Lars Henning , Sun Yuelian , Olsen Jørn
Published: August 2012

Background:  Maternal infections during pregnancy have been associated with an increased risk for neurological outcomes in the child, including epilepsy. We examined cystitis antibiotics commonly used during pregnancy, as a marker of cystitis, and the risk of childhood epilepsy in a population‐based cohort in Denmark.

Methods:  We examined all liveborn singletons born in Denmark between January 1996 and September 2004, identified from the Danish National Birth Registry. Epilepsy diagnoses were obtained from the Danish National Hospital Register and maternal antibiotic use from the National Register of Medicinal Product Statistics. Cystitis antibiotics consisted of pivmecillinam, sulphamethizole and nitrofurantoin. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated with Cox proportional hazard regression models.

Results:  The study followed 447 629 singletons for up to 9.9 years and identified 2848 children diagnosed with epilepsy. We found slightly increased risks of epilepsy in children whose mothers had redeemed prescriptions during pregnancy for pivmecillinam HR = 1.2 [95% CI 1.0, 1.4], sulphamethizole HR = 1.2 [95% CI 1.1, 1.4] or nitrofurantoin HR = 1.1 [95% CI 0.8, 1.5], compared with those unexposed. Among mothers with multiple redeemed prescriptions during pregnancy, adjusted HR were for pivmecillinam HR = 1.3 [95% CI 1.1, 1.5], sulphamethizole HR = 1.3 [95% CI 1.1, 1.5] and nitrofurantoin HR = 1.3 [95% CI 1.0, 1.8].

Conclusions:  Similar magnitudes of associations between chemically different drugs, used almost exclusively to treat cystitis, may suggest an impact of maternal infection on the fetal brain. However, direct drug effects or confounding factors are also possible explanations.