bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acquisition and maintenance of resistance to viruses in eukaryotic phytoplankton populations
Authors: Thomas Rozenn , Grimsley Nigel , Escande Marie‐line , Subirana Lucie , Derelle Evelyne , Moreau Hervé 
Published: March 2011

SummaryViruses are known to play a key role in the regulation of eukaryotic phytoplankton population densities; however, little is known about the mechanisms of how they interact with their hosts and how phytoplankton populations mediate their regulations. Viruses are obligate parasites that depend on host cell machinery for their dissemination in the environment (most of the time through host cell lysis that liberates many new particles). But viruses also depend on a reliable host population to carry on their replication before losing their viability. How do hosts cells survive when they coexist with their viruses? We show that clonal lines of three picoeukaryotic green algae (i.e. Bathycoccus sp., Micromonas sp., Ostreococcus tauri) reproducibly acquire resistance to their specific viruses following a round of infection. Our observations show that two mechanisms of resistance may operate in O. tauri. In the first resistant type, viruses can attach to their host cells but no new particles develop. In the second one, O. tauri acquires tolerance to its virus and releases these viruses consistently. These lines maintained their resistance over a 3‐year period, irrespective of whether or not they were re‐challenged with new viral inoculations. Co‐culturing resistant and susceptible lines revealed resistance to be associated with reduced host fitness in terms of growth rate.
Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing
Authors: Monchy Sébastien , Sanciu Giovanna , Jobard Marlène , Rasconi Serena , Gerphagnon Mélanie , Chabé Magali , Cian Amandine , Meloni Dionigia , Niquil Nathalie , Christaki Urania , Viscogliosi Eric , Sime‐Ngando Télesphore 
Published: March 2011

SummaryWater samples were collected along transects from the shore to the centre of two French lakes: the deep, volcanic, oligomesotrophic and low allochthonic‐impacted Lake Pavin, and the productive and higher allochthonic‐impacted Lake Aydat. The biodiversity was analysed using two approaches: the classical approach consisting of cloning/sequencing of the 18S, ITS1, 5.8S, ITS2 and partial 28S region using primers designed for fungus sequences, and the pyrosequencing of 18S rRNA hypervariable V2, V3 and V5 regions using two primer sets (one universal for eukaryotes and one for fungi). The classical approach yielded 146 (Lake Pavin) and 143 (Lake Aydat) sequences, corresponding to 46 and 63 operational taxonomic units (OTUs) respectively. Fungi represented half of the OTUs identified in Lake Pavin and 30% in Lake Aydat, and were dominated by sequences from Chytridiomycota found throughout Lake Pavin but mostly in the central pelagic zone of Lake Aydat. The pyrosequencing approach yielded 42 064 (Pavin) and 61 371 (Aydat) reads, of which 12–15% and 9–19% reads were assigned to fungi in Lakes Pavin and Aydat respectively. Chytridiomycota members were also dominant among these reads, with OTUs displaying up to > 33‐fold overrepresentation in the centre compared with the riparian areas of Lake Aydat. Besides fungi, both approaches revealed other major eukaryote groups, with the highest diversity in the central areas of lakes. One of the major findings of our study was that the two lakes displayed contrasting spatial distributions, homogenous for Lake Pavin and heterogeneous for Lake Aydat, which may be related to their peculiarities. This study represents the first unveiling of microbial eukaryote and fungus diversity assessed with two complementary molecular methods, and is considered a major milestone towards understanding the dynamics and ecology of fungi in freshwater lake ecosystems, which are directly link to the abundance and distribution of taxa.
Replication, lies and lesser‐known truths regarding experimental design in environmental microbiology
Authors: Lennon Jay T. 
Published: March 2011

SummaryA recent analysis revealed that most environmental microbiologists neglect replication in their science (Prosser, 2010). Of all peer‐reviewed papers published during 2009 in the field's leading journals, slightly more than 70% lacked replication when it came to analyzing microbial community data. The paucity of replication is viewed as an ‘endemic’ and ‘embarrassing’ problem that amounts to ‘bad science’, or worse yet, as the title suggests, lying (Prosser, 2010). Although replication is an important component of experimental design, it is possible to do good science without replication. There are various quantitative techniques – some old, some new – that, when used properly, will allow environmental microbiologists to make strong statistical conclusions from experimental and comparative data. Here, I provide examples where unreplicated data can be used to test hypotheses and yield novel information in a statistically robust manner.
Composition and dynamics of the gill microbiota of an invasive Indo‐Pacific oyster in the eastern Mediterranean Sea
Authors: Zurel Dror , Benayahu Yehuda , Or Amitai , Kovacs Amir , Gophna Uri 
Published: March 2011

SummaryGill bacterial communities of Chama pacifica, an Indo‐Pacific invasive oyster to the eastern Mediterranean Sea, were compared with those of Chama savignyi, its northern Red Sea congeneric species. Summer and winter bacterial populations were characterized and compared using 16S rDNA clone libraries, and seasonal population dynamics were monitored by automated ribosomal intergenic spacer analysis (ARISA). Clone libraries revealed a specific clade of bacteria, closely related to marine endosymbionts from the Indo‐Pacific, found in both ecosystems, of which one taxon was conserved in oysters from both sites. This taxon was dominant in summer libraries and was weakly present in winter ones, where other members of this group were dominant. ARISA results revealed significant seasonal variation in bacterial populations of Mediterranean Sea oysters, as opposed to Red Sea ones that were stable throughout the year. We suggest that this conserved association between bacteria and oyster reflects either a symbiosis between the oyster host and some of its bacteria, a co‐invasion of both parties, or both.
Screening for prostate cancer: an updated Cochrane systematic review
Authors: Ilic Dragan , O’Connor Denise , Green Sally , Wilt Timothy J. 
Published: March 2011

OBJECTIVE• To determine whether screening for prostate cancer reduces prostate cancer‐specific mortality, impact on all‐cause mortality and patient health‐related quality of life.MATERIALS AND METHODS• An update to our 2006 Cochrane systematic review was performed by re‐running an updated search of several databases, including MEDLINE and the Cochrane CENTRAL Register of Controlled Trials.• Articles were included if they were a randomized controlled trial (RCT) examining screening vs no screening for prostate cancer. Data was collected and analysed according to the methods outlined in the Cochrane Handbook for Systematic Reviews of Interventions.RESULTS• Five RCTs with a total of 341 351 participants were included in this updated Cochrane systematic review. All involved PSA testing, although the interval and threshold for further evaluation varied across trials. The age of participants was 50–74 years, with durations of patient follow‐up of 7–15 years.• The methodological quality of three of the studies was assessed as posing a high risk of bias.• Meta‐analysis of the five included studies indicated no statistically significant difference in prostate cancer‐specific mortality between men randomized to screening and control [relative risk (RR) 0.95, 95% CI 0.85–1.07]. Sub‐group analyses indicated that prostate cancer‐specific mortality was not affected by age at which participants were screened. A pre‐planned analysis of a ‘core’ age group of men aged 55–69 years from the largest RCT (European Randomised Study of Screening for Prostate Cancer) reported a significant 20% relative reduction in prostate cancer‐specific mortality; (95% CI 0.65–0.98; absolute risk 0.71 per 1000 men). The number of men diagnosed with prostate cancer was significantly greater in men randomized to screening, compared with those randomized to control (RR 1.35, 95% CI 1.06–1.72).• Harms of screening included high rates of false‐positive results for the PSA test, over‐diagnosis and adverse events associated with transrectal ultrasonography guided biopsies such as infection, bleeding and pain.CONCLUSIONS• Prostate cancer screening did not significantly decrease all‐cause or prostate cancer‐specific mortality in a combined meta‐analysis of five RCTs.• Any benefits from prostate cancer screening may take >10 years to accrue; therefore, men who have a life expectancy of <10–15 years should be informed that screening for prostate cancer is not beneficial and has harms.
Outcomes of robot‐assisted radical prostatectomy in men with previous transurethral resection of prostate
Authors: Gupta Narmada P. , Singh Prabhjot , Nayyar Rishi 
Published: March 2011

Study Type – Therapy (case series)Level of Evidence 4OBJECTIVE• To critically analyze and compare surgical, oncological and functional outcomes of robot‐assisted radical prostatectomy (RARP) in patients with and without previous transurethral resection of prostate (TURP).PATIENTS AND METHODS• The study comprised 158 cases of RARP for clinically localized prostate cancer, including 26 cases that had undergone previous TURP (Group A).• Surgical, oncological and functional (short‐ and intermediate‐term) outcomes of Group A were compared with 132 cases without previous TURP (Group B).RESULTS• Post TURP patients were found to have significantly greater blood loss (494 vs 324 mL) and a need for bladder neck reconstruction (26.7% vs 9.7%) compared to the non‐TURP group.• Surgical time (189 vs 166 min), conversion rate, margin positivity rate and biochemical recurrence rate were also higher.• Incontinence rates were higher both at 6 (14% vs 11.8%) and 12 (25% vs 8%) months follow‐up.CONCLUSIONS• RARP is feasible but challenging after TURP. It entails a longer operating time, greater operative difficulty and compromised oncological or continence outcomes.• These cases should be handled by an experienced robotic surgeon with the appropriate expertise.
Partial Regulation in Vertically Differentiated Industries
Authors: BERGANTINO ANGELA S. , DE VILLEMEUR ETIENNE BILLETTE , VINELLA ANNALISA 
Published: March 2011

AbstractWe provide theoretical foundations for quality‐adjusted price‐cap regulation in industries where a regulated incumbent and an unregulated entrant offer vertically differentiated products competing in price and quality. We show that, whether or not the incumbent anticipates the reaction of the entrant, the optimal weights in the cap depend upon the market served by the entrant, despite the latter not being directly concerned by regulation. We further show that the cap is robust to small errors in the weights. Our findings point to the conclusion that, in partially regulated industries, regulators should use information about the whole sectors rather than on the sole regulated incumbents.
Democracy, Rule of Law, Corruption Incentives, and Growth
Authors: DE LA CROIX DAVID , DELAVALLADE CLARA 
Published: March 2011

AbstractWe bridge the gap between the standard theory of growth and the mostly static theory of corruption. Some public investment can be diverted from its purpose by corrupt individuals. Voters determine the level of public investment subject to an incentive constraint equalizing the returns from productive and corrupt activities. We concentrate on two exogenous institutional parameters: the “technology of corruption” is the ease with which rent‐seekers can capture a proportion of public spending. The “concentration of political power” is the extent to which rent‐seekers have more political influence than other people. One theoretical prediction is that the effects of the two institutional parameters on income growth and equilibrium corruption are different according to the constraints that are binding at equilibrium. In particular, the effect of judicial quality on growth should be stronger when political power is concentrated. We estimate a system of equations where both corruption and income growth are determined simultaneously and show that income growth is more affected by our proxies for legal and political institutions in countries where political rights and judicial institutions, respectively, are limited.
Capacity Investment with Dynamic Operation and Intertemporal Budget Balance
Authors: DANAU DANIEL 
Published: March 2011

AbstractWe characterize the optimal investment and production path in a project characterized by indivisible capacity and stochastic inverse demand curve. At first best (without budget requirements), the investment is made earlier the lower the price elasticity of demand, causing the trajectory of production to be below the trajectory of capacity. At second best (when the investor is required to break even), the investment delay is upward distorted, the distortion being larger the lower the price elasticity of demand. Moreover, in the particular case of constant elasticity demand, investment is delayed but production remains at its first‐best level.
A Risk‐Dominant Allocation: Maximizing Coalition Stability
Authors: McGINTY MATTHEW 
Published: March 2011

AbstractThis paper presents a rule to allocate a coalition’s worth for superadditive games with positive externalities. The allocation rule awards each member their outside payoff, plus an equal share of the surplus. The resulting allocation maximizes coalition stability. Stable coalitions are Strong Nash equilibria since no subset of members has an incentive to leave. Similarly, no subset of non‐members has an incentive to join a stable coalition if the game is concave in this region. The allocation is risk‐dominant. All stable coalitions are robust to the maximum probability of 50% that players’ deviate from their individual best‐responses. The paper compares the allocation to the Shapley value and the Nash bargaining solution, and illustrates why these traditional rules result in small coalitions when applied to issues such as international environmental agreements.
Regression for Compositional Data by using Distributions Defined on the Hypersphere
Authors: Scealy J. L. , Welsh A. H. 
Published: March 2011

SummaryCompositional data can be transformed to directional data by the square-root transformation and then modelled by using distributions defined on the hypersphere. One advantage of this approach is that zero components are catered for naturally in the models. The Kent distribution for directional data is a good candidate model because it has a sufficiently general covariance structure. We propose a new regression model which models the mean direction of the Kent distribution as a function of a vector of covariates. Our estimators can be regarded as asymptotic maximum likelihood estimators. We show that these estimators perform well and are suitable for typical compositional data sets, including those with some zero components.
Non-Parametric Bayesian Inference on Bivariate Extremes
Authors: Guillotte Simon , Perron François , Segers Johan 
Published: March 2011

SummaryThe tail of a bivariate distribution function in the domain of attraction of a bivariate extreme value distribution may be approximated by that of its extreme value attractor. The extreme value attractor has margins that belong to a three-parameter family and a dependence structure which is characterized by a probability measure on the unit interval with mean equal to 12, which is called the spectral measure. Inference is done in a Bayesian framework using a censored likelihood approach. A prior distribution is constructed on an infinite dimensional model for this measure, the model being at the same time dense and computationally manageable. A trans-dimensional Markov chain Monte Carlo algorithm is developed and convergence to the posterior distribution is established. In simulations, the Bayes estimator for the spectral measure is shown to compare favourably with frequentist non-parametric estimators. An application to a data set of Danish fire insurance claims is provided.
Usefulness of the script concordance test in dermatology
Authors: Bursztejn A.‐C. , Cuny J.‐F. , Adam J.‐L. , Sido L. , Schmutz J.‐L. , de Korwin J.‐D. , Latarche C. , Braun M. , Barbaud A. 
Published: March 2011

AbstractBackground  The script concordance test (SCT) measures clinical data interpretation in the context of uncertainty. To our knowledge, its feasibility has not yet been demonstrated in dermatology.Objectives  This study describes the feasibility, reliability and validity of the SCT for use in dermatology teaching to family medicine residents.Methods  We designed an SCT for dermatology teaching, adapted to the level of family medicine students. The family medicine residents attending a dermatology lecture course and a reference panel of dermatologists underwent the test. Software available on the SCT‐dedicated website was used to determine the scores. The Cronbach’s α was calculated. The scores were described by means, standard deviation, and minimum and maximum scores. Mann–Whitney tests were used to compare resident and reference panel scores.Results  The test contained 33 vignettes of four questions each. Cronbach’s α was 0.80. Mean scores were 75.6 for the reference panel and 65.0 for the residents (P = 0.0009).Conclusions  This study confirmed the SCT’s capacity to distinguish groups on the basis of experience. This study demonstrated the feasibility and reliability of the SCT in the field of dermatology.
Comparison of pegylated interferon α‐2b plus psoralen PUVA versus standard interferon α‐2a plus PUVA in patients with cutaneous T‐cell lymphoma
Authors: Hüsken A.C. , Tsianakas A. , Hensen P. , Nashan D. , Loquai C. , Beissert S. , Luger T.A. , Sunderkötter C. , Schiller M. 
Published: March 2011

AbstractObjective  The aim of this study was to evaluate the safety and efficacy profile of pegylated interferon α‐2b (PEG‐IFN α‐2b) in combination with photochemotherapy (PUVA) in the treatment of cutaneous T‐cell lymphoma (CTCL) in comparison with standard IFN α plus PUVA.Design  Retrospective cohort study over a period of 7 years.Patients and interventions  A total of 17 consecutive CTCL patients (stage IA–IV) were retrospectively analysed for toxicity and response rates associated with PEG‐IFN α‐2b (1.5 μg/kg weekly) plus PUVA (n = 9) or standard IFN α‐2a (9 MIU 3×/week) plus PUVA (n = 8).Main outcome measures  Differences of response rates (complete/partial remission), progression‐free survival, discontinuation of therapy, safety and toxicity profiles according to World Health Organization – Common Terminology Criteria of Adverse Events (WHO‐CTCAE).Results  Myelosuppression and liver toxicity occured more frequently during PEG‐IFN α‐2b plus PUVA treatment than during standard IFN α‐2a plus PUVA therapy [77.8 vs. 50% (odds ratio 1.477) and 77.8 vs. 50% (odds ratio 1.692), respectively]. By contrast, the occurence of constitutional side‐effects (mainly fatigue) [100 vs.77.8% (odds ratio 0.889)] and more adverse events leading to study discontinuation was considerably higher in the standard IFN α‐2a plus PUVA group. The overall response rate in the PEG‐IFN α‐2b plus PUVA group (89%) was significantly superior.Conclusions  In patients with cutaneous T‐cell lymphoma PEG‐IFN α‐2b plus PUVA might become a promising treatment alternative as its higher rate of myelosuppression and liver toxicity is outweighed by its lower percentage of constitutional side‐effects, and its significantly higher overall response. Due to the small number of participants at this retrospective study, a larger prospective study is essential to verify our results.
Comparison of the time and latitude trends of melanoma incidence in anorectal region and perianal skin with those of cutaneous malignant melanoma in Norway
Authors: Micu E. , Juzeniene A. , Moan J. 
Published: March 2011

AbstractBackground  Melanoma incidence is increasing in many parts of the world. The main environmental risk factor is exposure to solar radiation. However, melanomas may arise also on non‐sun‐exposed areas (uveal and mucosal melanomas) and little is known about a possible relationship between sun exposure and melanoma on such locations.Objectives  We have compared the time and latitude trends of melanoma incidence in the anorectal region and perianal skin (non‐sun‐exposed sites) with those of cutaneous malignant melanoma (CMM) (sun‐exposed skin) to gain more information about the relationship between sun exposure and melanoma on such sites.Methods  We analysed epidemiological data from the Cancer Registry of Norway for melanomas of the anorectal mucosa, perianal skin and overall CMM for the time period 1966–2007.Results  We found that melanoma incidence on these shielded sites tends to decrease or remain constant over a period during which the CMM rates increase. This is true both in the North and in the South regions of Norway. Comparison of latitudinal trends of the incidence rates of CMM and melanoma on these shielded sites shows that there is no latitude gradient for melanoma of the anorectal mucosa and perianal skin, whereas there is a strong one for CMM.Conclusions  The time and latitudinal trends are likely to support the assumption that melanomas on these shielded sites are not generated by ultraviolet radiation. Possible causes and significances of these trends are discussed.
Regulation of cyclooxygenase‐2 and cytosolic phospholipase A2 gene expression by lipopolysaccharide through the RNA‐binding protein HuR: involvement of NADPH oxidase, reactive oxygen species and mitogen‐activated protein kinases
Authors: Lin Wei‐Ning , Lin Chih‐Chung , Cheng Hsin‐Yi , Yang Chuen‐Mao 
Published: March 2011

BACKGROUND AND PURPOSE Lipopolysaccharide (LPS)‐induced expression of cyclooxygenase‐2 (COX‐2) and cytosolic phospholipase A2 (cPLA2) has been implicated in several respiratory diseases. HuR is known to enhance the expression of genes by binding to 3′‐untranslated region (3′‐UTR) of mRNA and stabilizing mRNA. However, the exact mechanisms by which HuR affects the stability of mRNA and modulates LPS‐induced COX‐2 and cPLA2 expression in human tracheal smooth muscle cells (HTSMCs) are not known.EXPERIMENTAL APPROACH The expression of prostaglandin E2 (PGE2) was measured by ELISA, and pro‐inflammatory proteins were determined by use of a promoter assay, PCR or Western blot analysis. Overexpression of siRNAs to knock down the target components was used to manipulate the expression of HuR. Release of reactive oxygen species (ROS) was detected by fluorescence dye. The activation of signalling components was assessed by comparing phosphorylation levels, localization of protein kinases or coimmunoprecipitation assay.KEY RESULTS LPS induced COX‐2 and cPLA2 expression via post‐translational regulation of mRNA stabilization, which were attenuated by transfection with HuR siRNA in HTSMCs. In addition, LPS‐stimulated NADPH oxidase activation and ROS generation were attenuated by the NADPH oxidase inhibitors diphenyleneiodonium chloride (DPI) and apocynin (APO). Generation of ROS induced phosphorylation of p42/p44 mitogen‐activated protein kinase (MAPK), p38 MAPK and JNK1/2, which was attenuated by DPI and APO and the ROS scavenger N‐acetylcysteine.CONCLUSIONS AND IMPLICATIONS These results suggested that in HTSMCs, LPS‐induced COX‐2 and cPLA2 expression is mediated through NADPH oxidase/ROS‐dependent MAPKs associated with HuR accumulation in the cytoplasm. Activated MAPKs may regulate the nucleocytoplasmic shuttling of HuR, and thus induce the cytoplasmic accumulation of HuR.