bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving distance sampling: accounting for covariates and non‐independency between sampled sites
Authors: Oedekoven Cornelia S. , Buckland Stephen T. , Mackenzie Monique L. , Evans Kristine O. , Burger Loren W. 
Published: March 2013

SummaryThere is currently much interest in replacing the design‐based component of conventional distance sampling methods by a modelling approach where animal densities are related to environmental covariates. These models allow identification of relationships between density and covariates. One of the uses of such models is to assess the effects of some intervention on numbers for species of conservation interest in designed distance sampling experiments.In this context, we use an integrated likelihood approach for modelling sample counts, adopting a Poisson model and allowing imperfect detectability on the sample plots. We use the method of Royle, Dawson & Bates (2004,Ecology,85, 1591), extended to model heterogeneity in detection probabilities using either multiple covariate distance sampling methods or stratification. Moreover, we include a random effect for site in the plot abundance model to accommodate correlation in repeat counts at a single site.These developments were motivated by a large‐scale experimental study to assess the effects of establishing conservation buffers along field margins on indigo buntings in severalUSstates. We analyse the data using an integrated likelihood and include model selection for both the Poisson rate of counts and detection probabilities. We assess model performance by comparing our results with those using a two‐stage approach (Bucklandet al. 2009,Journal of Agricultural, Biological, and Environmental Statistics,14, 432) which we extended by including a random effect for site in the plot abundance model.The two methods led to the same selected models and gave similar results for parameters, which revealed significant beneficial effects of buffers on indigo bunting densities. Densities on buffered fields were on average 35% higher than on unbuffered fields. Using a detection function stratified by state captured some of the heterogeneity in detection probabilities between the nine states included in the analyses.Synthesis and applications. We develop and compare two methods for analysing data from large‐scale distance sampling experiments with imbalanced repeat measures. By including a random site effect in the plot abundance model, we relax the assumption of independent sample counts which is generally made for distance sampling methods, and we allow inference to be drawn for the wider region that the sites represent.
Using Illumina next generation sequencing technologies to sequence multigene families in de novo species
Authors: Hughes Graham M. , Gang Li , Murphy William J. , Higgins Desmond G. , Teeling Emma C. 
Published: March 2013

AbstractThe advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene family, for species with and without a reference genome. We develop novel assembly methods to annotate and filter these data, which can be utilized for any gene family or any species. We find no significant difference between the ratio of genes within their respective gene families of our data compared with available genomic data. Using simulated data we explore the limitations of short‐read sequence data and our assembly in recovering this gene family. We highlight the benefits and shortcomings of these methods. Compared with data generated from traditional polymerase chain reaction, cloning and Sanger sequencing methodologies, sequence data generated using our pipeline increases yield and sequencing efficiency without reducing the number of unique genes amplified. A cloning step is not required, therefore shortening data generation time. The novel downstream methodologies and workflows described provide a tool to be utilized by many fields of biology, to access and analyze the vast quantities of data generated. By combining laboratory and in silico methods, we provide a means of extracting genomic information for multigene families without complete genome sequencing.
Suppression of B‐cell activation and IgE, IgA, IgG1 and IgG4 production by mammalian telomeric oligonucleotides
Authors: Sackesen C. , van de Veen W. , Akdis M. , Soyer O. , Zumkehr J. , Ruckert B. , Stanic B. , Kalaycı O. , Alkan S. S. , Gursel I. , Akdis C. A. 
Published: March 2013

AbstractBackgroundThe fine balance of immunoglobulins (Ig) E, IgG1, IgG4 and IgA in healthy production is maintained by the interaction of B cells with adaptive and innate immune response. The regulation of toll‐like receptors (TLRs)‐driven innate and adaptive immune effector B‐cell response and the role of mammalian telomeric TTAGGG repeat elements represent an important research area.MethodsHuman PBMC and purified naive and memory B cells were stimulated with specific ligands for TLR2, TLR3, TLR4, TLR5, TLR7, TLR8 and TLR9 in the presence or absence of telomeric oligonucleotides. B‐cell proliferation, differentiation and antibody production were determined.ResultsTLR9 ligand directly activates naive and memory B cells, whereas TLR7 can stimulate them in the presence of plasmacytoid dendritic cells. Human B cells proliferate and turn into antibody‐secreting cells in response to TLR3, TLR7 and TLR9, but not to TLR2, TLR4, TLR5 and TLR8 ligands. Stimulation of B cells with intracellular TLR3, TLR7 and TLR9 induced an activation cascade leading to memory B‐cell generation and particularly IgG1, but also IgA, IgG4 and very low levels of IgE production. Mammalian telomeric oligodeoxynucleotide (ODN) significantly inhibited all features of TLR ligand‐induced events in B cells including B‐cell proliferation, IgE, IgG1, IgG4, IgA production, class switch recombination, plasma cell differentiation induced by TLR3, TLR7 and TLR9 ligands.ConclusionB cells require specific TLR stimulation, T‐cell and plasmacytoid dendritic cell help for distinct activation and Ig production profiles. Host‐derived telomeric ODN suppress B‐cell activation and antibody production demonstrating a natural mechanism for the control of overexuberant B‐cell activation, antibody production and generation of memory.
Meta‐analysis: serological markers and the risk of acute and chronic pouchitis
Authors: Singh S. , Sharma P. K. , Loftus E. V. , Pardi D. S. 
Published: March 2013

SummaryBackgroundSerological markers such as anti‐neutrophil cytoplasmic antibody (ANCA) and anti‐Saccharomyces cerevisiae antibody (ASCA) may be associated with pouchitis after ileal pouch‐anal anastomosis (IPAA).AimTo perform a systematic review with meta‐analysis of studies evaluating the association of ANCA and ASCA status with risk of acute and chronic pouchitis after IPAA.MethodsWe searched multiple databases (upto September 2012) for studies reporting ANCA and/or ASCA status along with risk of acute or chronic pouchitis after IPAA in adults with ulcerative colitis (UC). We abstracted odds ratio (OR) or raw data from the individual studies to calculate summary OR estimates with 95% CIs using random‐effects model.ResultsEight studies reporting 184 cases of acute pouchitis and six studies reporting 151 cases of chronic pouchitis were included. The odds of chronic pouchitis were 76% higher in ANCA‐positive patients than ANCA‐negative (six studies; OR: 1.76; 95% CI: 1.19–2.61; P < 0.01). ASCA‐positivity was not associated with the risk of chronic pouchitis (three studies; OR: 0.89; 95% CI: 0.49–1.59; P = 0.68). Neither ANCA (eight studies; OR: 1.54; 95% CI: 0.79–3.02; P = 0.21) nor ASCA‐positivity (two studies; OR: 1.28; 95% CI: 0.25–6.54; P = 0.77) were associated with the risk of acute pouchitis.ConclusionsThe risk of chronic pouchitis after IPAA is higher in ANCA‐positive patients, but the risk of acute pouchitis is unaffected by ANCA status. ASCA status was not associated with the risk of acute or chronic pouchitis. This information may be used to counsel UC patients regarding their risk of pouchitis after IPAA.
Temperature response of denitrification rate and greenhouse gas production in agricultural river marginal wetland soils
Authors: Bonnett S. A. F. , Blackwell M. S. A. , Leah R. , Cook V. , O'Connor M. , Maltby E. 
Published: March 2013

AbstractSoils are predicted to exhibit significant feedback to global warming via the temperature response of greenhouse gas (GHG) production. However, the temperature response of hydromorphic wetland soils is complicated by confounding factors such as oxygen (O2), nitrate () and soil carbon (C). We examined the effect of a temperature gradient (2–25 °C) on denitrification rates and net nitrous oxide (N2O), methane (CH4) production and heterotrophic respiration in mineral (Eutric cambisol and Fluvisol) and organic (Histosol) soil types in a river marginal landscape of the Tamar catchment, Devon, UK, under non‐flooded and flooded with enriched conditions. It was hypothesized that the temperature response is dependent on interactions with ‐enriched flooding, and the physicochemical conditions of these soil types. Denitrification rate (mean, 746 ± 97.3 μg m−2 h−1), net N2O production (mean, 180 ± 26.6 μg m−2 h−1) and net CH4 production (mean, 1065 ± 183 μg m−2 h−1) were highest in the organic Histosol, with higher organic matter, ammonium and moisture, and lower concentrations. Heterotrophic respiration (mean, 127 ± 4.6 mg m−2 h−1) was not significantly different between soil types and dominated total GHG (CO2eq) production in all soil types. Generally, the temperature responses of denitrification rate and net N2O production were exponential, whilst net CH4 production was unresponsive, possibly due to substrate limitation, and heterotrophic respiration was exponential but limited in summer at higher temperatures. Flooding with increased denitrification rate, net N2O production and heterotrophic respiration, but a reduction in net CH4 production suggests inhibition of methanogenesis by or N2O produced from denitrification. Implications for management and policy are that warming and flood events may promote microbial interactions in soil between distinct microbial communities and increase denitrification of excess with N2O production contributing to no more than 50% of increases in total GHG production.
Oxidation of Fe(II) leads to increased C‐2 methylation of pentacyclic triterpenoids in the anoxygenic phototrophic bacterium Rhodopseudomonas palustris strain TIE‐1
Authors: Eickhoff M. , Birgel D. , Talbot H. M. , Peckmann J. , Kappler A. 
Published: March 2013

AbstractHopanoids are among the most widespread biomarkers of bacteria that are used as indicators for past and present bacterial activity. Our understanding of the production, function, and distribution of hopanoids in bacteria has improved greatly, partly due to genetic, culture‐independent studies. Culture‐based studies are important to determine hopanoid function and the environmental conditions under which these compounds are produced. This study compares the lipid inventory of Rhodopseudomonas palustris strain TIE‐1 under anoxic photoautotrophic conditions using either H2 or Fe(II) as electron donor. The high amount to which adenosylhopane is produced irrespective of the used electron donor suggests a specific function of this compound rather than its exclusive role as an intermediate in bacteriohopanepolyol biosynthesis. C‐2 methylated hopanoids and tetrahymanol account for as much as 59% of the respective C‐2 methylated/non‐methylated homologs during growth with Fe(II) as electron donor, as compared with 24% C‐2 methylation for growth with H2. This observation reveals that C‐2 methylated hopanoids have a specific function and are preferentially synthesized in response to elevated Fe(II) concentrations. The presence of C‐2 methylated pentacyclic triterpenoids has commonly been used as a biosignature for the interpretation of paleoenvironments. These new findings suggest that increased C‐2 methylation may indicate anoxic ferrous conditions, in addition to other environmental stressors that have been previously reported.
Effectiveness of a motivational–behavioural skills protocol for oral hygiene among patients with hyposalivation
Authors: López‐Jornet Pia , Fabio Camacho‐Alonso , Consuelo Rodríguez Agudo , Paz Andujar Mateos 
Published: March 2013

BackgroundThe main objective of this study was to assess the effectiveness of a motivational‐behavioural skills protocol for plaque control in patients with hyposalivation.Patients and methodsIn a randomised, evaluator‐blinded, controlled trial, 60 subjects with hyposalivation (12 men and 48 women) were randomly assigned to two groups: the control group received basic oral hygiene instruction, while for the study (intervention) group, oral hygiene instruction was based on cognitive behavioural principles and motivational interviewing (MI). Both groups were given oral hygiene instruction once every 15 days, with a total of four sessions over a 2‐month period: plaque extension and community periodontal index of treatment needs (CPITN), frequency and duration of brushing, frequency of interdental cleaning and scores based on scale of ‘self‐efficacy for brushing of the teeth’. Clinical characteristics were compared between the two groups.ResultsBoth control and intervention group patients showed significantly lower plaque indices, bleeding indices and an improvement in probe depth after the 2‐month study period. Interproximal brushing was significantly more frequent among the intervention group (p = 0.016).ConclusionIn patients with hyposalivation, the application of oral hygiene instruction based on cognitive principles and MI offers benefits for periodontal health. Longer‐term studies are needed to confirm these results.
Red blood cell morphology
Authors: Ford J. 
Published: March 2013

SummaryThe foundation of laboratory hematologic diagnosis is the complete blood count and review of the peripheral smear. In patients with anemia, the peripheral smear permits interpretation of diagnostically significant red blood cell (RBC) findings. These include assessment of RBC shape, size, color, inclusions, and arrangement. Abnormalities of RBC shape and other RBC features can provide key information in establishing a differential diagnosis. In patients with microcytic anemia, RBC morphology can increase or decrease the diagnostic likelihood of thalassemia. In normocytic anemias, morphology can assist in differentiating among blood loss, marrow failure, and hemolysis—and in hemolysis, RBC findings can suggest specific etiologies. In macrocytic anemias, RBC morphology can help guide the diagnostic considerations to either megaloblastic or nonmegaloblastic causes. Like all laboratory tests, RBC morphologies must be interpreted with caution, particularly in infants and children. When used properly, RBC morphology can be a key tool for laboratory hematology professionals to recommend appropriate clinical and laboratory follow‐up and to select the best tests for definitive diagnosis.
Sirolimus ameliorates inflammatory responses by switching the regulatory T/T helper type 17 profile in murine colitis
Authors: Yin Hui , Li Xiangyong , Zhang Bobin , Liu Tao , Yuan Baohong , Ni Qian , Hu Shilian , Gu Hongbiao 
Published: March 2013

SummaryInflammatory bowel disease is characterized by dysregulated immune responses in inflamed intestine, with dominance of interleukin‐17 (IL‐17) ‐producing cells and deficiency of regulatory T (Treg) cells. The aim of this study was to investigate the effect and mechanisms of sirolimus, an inhibitor of the mammalian target of rapamycin, on immune responses in a murine model of Crohn's disease. Murine colitis was induced by intrarectal administration of 2,4,6‐trinitrobenzene sulphonic acid at day 0. Mice were then treated intraperitoneally with sirolimus daily for 3 days. The gross and histological appearances of the colon and the numbers, phenotype and cytokine production of lymphocytes were compared with these characteristics in a control group. Sirolimus treatment significantly decreased all macroscopic, microscopic and histopathological parameters of colitis that were analysed. The therapeutic effects of sirolimus were associated with a down‐regulation of pro‐inflammatory cytokines tumour necrosis factor‐α, IL‐6 and IL‐17A. Intriguingly, sirolimus administration resulted in a prominent up‐regulation of the regulatory cytokine transforming growth factor‐β. Supporting the hypothesis that sirolimus directly affects the functional activity of CD4+ CD25+ Treg cells, we observed a remarkable enhancement of FoxP3 expression in colon tissues and isolated CD4+ T cells of sirolimus‐treated mice. Simultaneously, sirolimus treatment led to a significant reduction in the number of CD4+ IL‐17A+ T cells in the mesenteric lymph node cells as well as IL‐17A production in mesenteric lymph node cells. Therefore, sirolimus may offer a promising new therapeutic strategy for the treatment of inflammatory bowel disease.
RADIOGRAPHIC FEATURES OF PRIMARY AND CONCOMITANT FLEXOR ENTHESOPATHY IN THE CANINE ELBOW
Authors: de Bakker Evelien , Saunders Jimmy H. , van Bree Henri , Gielen Ingrid , Van Ryssen Bernadette 
Published: March 2013

Primary flexor enthesopathy is a recently recognized elbow disorder and should be considered in the differential diagnosis of elbow lameness. For treatment planning purposes, it is important to make a distinction between primary and concomitant forms of the disease. The purpose of this prospective study was to compare radiographic findings for dogs with primary flexor enthesopathy (n = 17), concomitant flexor enthesopathy (n = 24), elbow dysplasia (n = 13), and normal dogs (n = 7). All dogs underwent a complete radiographic examination and each radiographic image was evaluated for the presence or absence of following characteristics: irregular medial humeral epicondyle, spur and calcified body. Additionally, the presence or absence of other elbow disorders (medial coronoid process disease, osteochondritis dissecans, ununited anconeal process, incongruity, subtrochlear sclerosis, and osteoarthritis) was recorded. Radiographic characteristics of flexor enthesopathy were found in 86% of painful joints in the primary flexor enthesopathy group and in 100% of painful joints in the concomitant flexor enthesopathy group. Radiographic characteristics of flexor enthesopathy were not found in sound elbow and elbow dysplasia groups. Frequencies and details of individual radiographic characteristics did not differ between primary and concomitant flexor enthesopathy groups. Findings support the use of radiography as a first screening method for detection of flexor enthesopathy, but not as a technique for distinguishing primary vs. concomitant forms.
The impact of seasonal flooding on agriculture: the spring 2012 floods in Somerset, England
Authors: Morris J. , Brewin P. 
Published: March 2013

AbstractExceptional rainfall in spring 2012 caused widespread flooding and damage to agricultural grasslands in Somerset in south western England, much of them farmed under agri‐environment agreements. The seasonal timing of the flood and its relatively long duration (in excess of 4 weeks in some areas) led to a serious loss of grazing and winter feed in 2012. A survey of farmers, combined with the development of a framework to estimate the impact of seasonal flooding, identified the effects on farm businesses and the ways that farmers coped. Impacts on agri‐environment outcomes were valued at the cost of funding stewardship schemes. The methods and estimates can help inform strategies to deal with changes in flood risk in areas of agricultural and environmental interest, whether induced by changes in catchment land use or climate.
Sarcoidosis and Sjögren's syndrome: clinical and salivary evaluation
Authors: Mansour Mohammed J. , He Cixin , Al‐Farra Sharif T. , Khuder Sadik A. , Wright John M. , Kessler Harvey P. , Hinton Robert J. , Al‐Hashimi Ibtisam 
Published: March 2013

BackgroundSarcoidosis and Sjögren's syndrome are two different diseases; however, when affecting the salivary glands, both diseases exhibit similar clinical signs and symptoms, which often complicates the diagnosis. The purpose of this study was to investigate the possibility of using salivary electrophoresis to differentiate between the two diseases.MethodsSaliva was collected from patients with sarcoidosis and patients with Sjögren's syndrome. Salivary flow rate, total protein, and electrophoretic profiles were examined.ResultsMean salivary flow rate was 0.41 ± 0.07 ml/min/gland vs. 0.43 ± 0.07 ml/min/gland; total salivary protein was 130.0 ± 29.2 mg% vs. 104.0 ± 8.8 mg% for sarcoidosis vs. Sjögren's syndrome, respectively. No differences were observed in salivary flow rate, total salivary protein, or electrophoretic profile between patients with sarcoidosis and patients with Sjögren's syndrome (P = 0.768, 0.718, and 1.000, respectively).ConclusionsSalivary protein electrophoresis does not appear to be useful to differentiate between sarcoidosis and Sjögren's syndrome.
A Markov‐Based Road Maintenance Optimization Model Considering User Costs
Authors: Gao Hui , Zhang Xueqing 
Published: March 2013

AbstractUser costs of different maintenance actions need to be assessed in road maintenance as well as the maintenance costs. The vehicle operating cost (VOC) and the travel delay cost are two major components of the user costs associated with road maintenance actions. This article simplifies the general calculation models of these two user cost components and develops a multiobjective Markov‐based model to minimize both maintenance cost and user cost subject to a number of constraints including the average annual budget limit and the performance requirement. The road deterioration process is modeled as a discrete‐time Markov process, the states of road performance are defined in terms of the road roughness, and the state transition probabilities are estimated considering the effects of deterioration and maintenance actions. An example is provided to illustrate the use of the proposed road maintenance optimization model. The results show that the optimal road maintenance plan obtained from the model is practical to implement and is cost‐effective compared with the periodical road maintenance plan. The results also indicate that the maintenance cost and the user cost are competitive. When maintenance works are carried out more frequently, the life‐cycle maintenance costs will increase while the life‐cycle user costs will decrease. This is because the VOC contributes the most amount of the user cost and its change has a contrary trend to the change of the maintenance cost over time.