bluuebunny/crossref_metadata_2025 huggingface dataset:
Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model
Authors: Zhang Chen , Wu Chunguo , Blanzieri Enrico , Zhou You , Wang Yan , Du Wei , Liang Yanchun
Published: August 2009

Motivation: Mislabeled samples often appear in gene expression profile because of the similarity of different sub-type of disease and the subjective misdiagnosis. The mislabeled samples deteriorate supervised learning procedures. The LOOE-sensitivity algorithm is an approach for mislabeled sample detection for microarray based on data perturbation. However, the failure of measuring the perturbing effect makes the LOOE-sensitivity algorithm a poor performance. The purpose of this article is to design a novel detection method for mislabeled samples of microarray, which could take advantage of the measuring effect of data perturbations.

Results: To measure the effect of data perturbation, we define an index named perturbing influence value (PIV), based on the support vector machine (SVM) regression model. The Column Algorithm (CAPIV), Row Algorithm (RAPIV) and progressive Row Algorithm (PRAPIV) based on the PIV value are proposed to detect the mislabeled samples. Experimental results obtained by using six artificial datasets and five microarray datasets demonstrate that all proposed methods in this article are superior to LOOE-sensitivity. Moreover, compared with the simple SVM and CL-stability, the PRAPIV algorithm shows an increase in precision and high recall.

Availability: The program and source code (in JAVA) are publicly available at http://ccst.jlu.edu.cn/CSBG/PIVS/index.htm

Contact:  blanzier@dit.unitn.it; ycliang@jlu.edu.cn
Depletion-corrected average catch: a simple formula for estimating sustainable yields in data-poor situations
Authors: MacCall Alec D.
Published: August 2009

MacCall, A. D. 2009. Depletion-corrected average catch: a simple formula for estimating sustainable yields in data-poor situations. – ICES Journal of Marine Science, 66: 2267–2271. The depletion-corrected average catch (DCAC) formula is an extension of the potential-yield formula, and it provides useful estimates of sustainable yield for data-poor fisheries on long-lived species. Over an extended period (e.g. a decade or more), the catch is divided into a sustainable yield component and an unsustainable “windfall” component associated with a one-time reduction in stock biomass. The size of the windfall is expressed as being equivalent to a number of years of sustainable production, in the form of a “windfall ratio”. The DCAC is calculated as the sum of catches divided by the sum of the number of years in the catch series and this windfall ratio. Input information includes the sum of catches and associated number of years, the relative reduction in biomass during that period, the natural mortality rate (M, which should be <0.2 year−1), and the assumed ratio of FMSY to M. These input values are expected to be approximate, and based on the estimates of their imprecision, the uncertainty can be integrated by Monte Carlo exploration of DCAC values.
Observing the Counterfactual? The Search for Political Experiments in Nature
Authors: Robinson Gregory , McNulty John E. , Krasno Jonathan S.
Published: August 2009

A search of recent political science literature and conference presentations shows substantial fascination with the concept of the natural experiment. However, there seems to be a wide array of definitions and applications employed in research that purports to analyze natural experiments. In this introductory essay to the special issue, we attempt to define natural experiments and discuss related issues of research design. In addition, we briefly explore the basic methodological issues around the appropriate analysis of natural experiments and give an overview of different techniques. The overarching theme of this essay and of this issue is to encourage applied researchers to look for natural experiments in their own work and to think more systematically about research design.
Integrated Management Strategies for Phytophthora sojae Combining Host Resistance and Seed Treatments
Authors: Dorrance A. E. , Robertson A. E. , Cianzo S. , Giesler L. J. , Grau C. R. , Draper M. A. , Tenuta A. U. , Anderson T. R.
Published: August 2009

Phytophthora sojae has re-emerged as a serious soybean pathogen in the past decade. This may be due in part to changes in resistance levels in current cultivars, adoption of P. sojae populations to deployed Rps genes, and highly favorable environments in the past decade. This multilocation study evaluated the effect of seed treatments on the incidence and severity of Phytophthora root and stem rot on soybeans with different combinations of Rps genes and levels of partial resistance. The efficacy of the seed treatments was highly variable across locations. Seed treatments (metalaxyl and mefenoxam) provided protection and increased yields across cultivars in locations where rain or irrigation occurred shortly after planting (Ohio, South Dakota, and Ontario). However, there were no significant differences in stand or yield consistently across cultivars in Iowa, Nebraska, Wisconsin, or Ohio, where heavy precipitation did not occur until later growth stages. The environment, levels of inoculum, and pathogen complex may have played a role in the different responses to the seed treatments and to the different combinations of Rps genes and levels of partial resistance to P. sojae in the cultivars. Fields that are poorly drained and have P. sojae populations with complex pathotypes may benefit the most from seed treatments. Individual fields where producers may see the greatest benefit to utilizing these integrated management strategies will need to be identified.
Identification and Frequency of Phytophthora Species Associated with Foliar Diseases in California Ornamental Nurseries
Authors: Yakabe L. E. , Blomquist C. L. , Thomas S. L. , MacDonald J. D.
Published: August 2009

Numerous ornamental nurseries in 32 California counties were surveyed for leaf spots as part of the California Department of Food and Agriculture mandated surveys targeting Phytophthora ramorum. Tissue collected during the 2005 and 2006 surveys was initially screened by a Phytophthora-specific enzyme-linked immunosorbent assay. All positives samples were further tested using polymerase chain reaction to determine if P. ramorum was present. P. ramorum was detected in 1% of the total number of samples taken during the surveys. A total of 377 isolates were identified as species of Phytophthora other than P. ramorum, and their identity was determined by internal transcriber spacer (ITS) sequences. Subsets of the putative ITS-species were further verified using accepted morphological characters. Thirteen species of Phytophthora were found: P. cactorum, P. cambivora, P. citricola, P. citrophthora, P. cryptogea, P. foliorum, P. gonapodyides, P. hibernalis, P. nemorosa, P. ‘Pgchlamydo’, P. pseudosyringae, P. syringae, and P. tropicalis. P. syringae and P. citricola made up 55% of the total number of isolates. Species thought to be strictly forest pathogens, P. nemorosa and P. pseudosyringae, each made up less than 4% of the isolates. To test pathogenicity of acquired isolates, subsets of different species of Phytophthora were inoculated onto leaves of selected host plant genera. Of the 66 pathogen–host genera combinations tested, 44 resulted in lesion formation. Disease symptoms appeared as dark, water-soaked lesions with irregular margins and were similar among Phytophthora species.
Development of a Method for Detection of the Biocontrol Agent Penicillium oxalicum Strain 212 by Combining PCR and a Selective Medium
Authors: Larena I. , Melgarejo P.
Published: August 2009

The registration of biological control agents requires the development of monitoring systems to detect and quantify the agent in the environment. Penicillium oxalicum strain 212 (PO212) is being developed for the control of tomato pathogens. In this study, we demonstrated that PO212 was more effective for controlling Fusarium oxysporum f. sp. lycopersici in tomato plants than 13 other P. oxalicum strains. A new semiselective medium was developed as a preliminary screen for P. oxalicum from soil. This semiselective medium was a modified Fusarium selective medium that contained 0.006 g of nystatin per liter. The growth of P. oxalicum strain 212 was not inhibited on this medium, but it did inhibit the growth of 11 fungal species. Specific identification of the biocontrol strain and its quantification were achieved using a polymerase chain reaction with a strain-specific pair of primers (POITS1F/POITS2R1) and dilution plating. This primer set differentiated the biocontrol strain from 13 other strains of P. oxalicum. There were differences in the nucleotide sequences of the internal transcribed spacer (ITS) regions of the ribosomal DNA of 25 strains of P. oxalicum and those of PO212. Based on the differences in the nucleotide sequences of the ITS regions in rDNA of PO212 and other P. oxalicum strains, a relationship between the nucleotide sequences in the ITS region and biocontrol efficacy is postulated.
Foliar Fungicides to Control Wheat Stem Rust, Race TTKS (Ug99), in Kenya
Authors: Wanyera R. , Macharia J. K. , Kilonzo S. M. , Kamundia J. W.
Published: August 2009

The emergence of a new virulent race of stem rust (Puccinia graminis f. sp. tritici) of wheat (Triticum aestivum), TTKS (Ug99), calls for urgent measures to contain the disease, which is a serious threat to wheat production in Kenya. Nine commercial fungicides were evaluated for control of stem rust in the field in three locations in 2005 and 2006. Ten treatments, including untreated control, were applied on field plots in a randomized complete block design with four replications. Assessment of stem rust severity was done at growth stage (GS) 55 (heading), GS 65 (flowering), and GS 75 (late milk) and expressed in terms of mean rust severity and area under the disease progress curve (AUDPC). In general, fungicide treatment significantly (P ≤ 0.05) reduced rust severity, AUDPC, and losses in grain yield and 1,000-kernel weight for cv. Duma compared with the untreated control. Stem rust was severe in both years across all sites, resulting in significantly less grain yield in the control treatment. The 1,000-kernel weight was significantly less at two locations in 2006. Fungicides azoxystrobin at 200 g/liter + cyproconazole at 80 g/liter (AmistarXtra 280 SC), tebuconazole (Folicur 250 EC), tebuconazole + tridimenol (Silvacur 375 EC), and tebuconazole (Orius 25 EW) were more effective in reducing stem rust across the sites. Fungicides trifloxystrobin + propiconazole (Stratego 250 EC), hexaconazole (Cotaf 5 EC), epoxiconazole + carbendazim (Swing 250 EC), cyproconazole at 80 g/liter + propiconazole at 250 g/liter (Artea 330EC), and epoxiconazole at 125 g/liter + carbendazim at 125 g/liter (Soprano C 250 EC) were inconsistent in the reduction of the disease. The results suggest that fungicides can be used effectively in reducing stem rust severity and increasing yield of susceptible wheat cultivars in stem-rust-prone areas.
Variability of Fusarium Crown Rot Tolerances Among Cultivars of Spring and Winter Wheat
Authors: Smiley Richard W. , Yan Hui
Published: August 2009

Crown rot caused by Fusarium pseudograminearum reduces the yield of wheat (Triticum aestivum) in Oregon. Observations of crown rot symptoms in traditional breeding and yield testing nurseries have not been useful for describing tolerance ratings of wheat cultivars. Yield data from inoculated experiments were therefore evaluated to determine if differences in cultivar response could be identified. A comparison of yields in inoculated and noninoculated plots was made for one group of spring wheat entries and four groups of winter wheat entries. Significant differences among spring wheat entries were identified and were validated against standards for tolerance and intolerance to F. pseudograminearum in Australia. Locally adapted and Australian standards exhibited a comparable range of yield reduction due to inoculation. Spring wheat tolerance reactions can be accurately described using as few as 24 yield comparisons. However, this screening method will not be practical for winter wheat due to stronger effects of year and location on the phenotypic tolerance response, requiring about 95 yield comparisons to accurately define the crown rot phenotype of a winter wheat cultivar.
Neutrons for biologists: a beginner's guide, or why you should consider using neutrons
Authors: Lakey Jeremy H.
Published: August 2009

From the structures of isolated protein complexes to the molecular dynamics of whole cells, neutron methods can achieve a resolution in complex systems that is inaccessible to other techniques. Biology is fortunate in that it is rich in water and hydrogen, and this allows us to exploit the differential sensitivity of neutrons to this element and its major isotope, deuterium. Furthermore, neutrons exhibit wave properties that allow us to use them in similar ways to light, X-rays and electrons. This review aims to explain the basics of biological neutron science to encourage its greater use in solving difficult problems in the life sciences.
Interfacial assembly of proteins and peptides: recent examples studied by neutron reflection
Authors: Zhao XiuBo , Pan Fang , Lu Jian R.
Published: August 2009

Through reviewing a number of recent neutron reflection studies of interfacial adsorption of peptides and proteins, this paper aims to demonstrate the significance of this technique in studying interfacial biomolecular processes by illustrating the typical structural details that can be derived. The review will start with the introduction of relevant theoretical background, followed by an outline of representative biomolecular systems that have recently been studied to indicate the technical strengths of neutron reflection.
Low-frequency pulsed electromagnetic field exposure can alter neuroprocessing in humans
Authors: Robertson John A. , Théberge Jean , Weller Julie , Drost Dick J. , Prato Frank S. , Thomas Alex W.
Published: August 2009

Extremely low-frequency magnetic fields (from DC to 300 Hz) have been shown to affect pain sensitivity in snails, rodents and humans. Here, a functional magnetic resonance imaging study demonstrates how the neuromodulation effect of these magnetic fields influences the processing of acute thermal pain in normal volunteers. Significant interactions were found between pre- and post-exposure activation between the sham and exposed groups for the ipsilateral (right) insula, anterior cingulate and bilateral hippocampus/caudate areas. These results show, for the first time, that the neuromodulation induced by exposure to low-intensity low-frequency magnetic fields can be observed in humans using functional brain imaging and that the detection mechanism for these effects may be different from those used by animals for orientation and navigation. Magnetoreception may be more common than presently thought.
Filter-feeding bivalves can remove avian influenza viruses from water and reduce infectivity
Authors: Faust Christina , Stallknecht David , Swayne David , Brown Justin
Published: August 2009

Avian influenza (AI) viruses are believed to be transmitted within wild aquatic bird populations through an indirect faecal–oral route involving contaminated water. This study examined the influence of filter-feeding bivalves,
Corbicula fluminea
, on the infectivity of AI virus in water. Clams were placed into individual flasks with distilled water inoculated 1:100 with a low pathogenic (LP) AI virus (A/Mallard/MN/190/99 (H3N8)). Viral titres in water with clams were significantly lower at 24 and 48 h post-inoculation compared to LPAI-infected water without clams. To determine whether clams affected the infectivity of AI viruses, 18 wood ducks (
Aix sponsa
) were divided into test groups and inoculated with a variety of treatments of clam supernatants, whole clams and water exposed to a high pathogenic (HP) AI (A/whooper swan/Mongolia/244/05 (H5N1)). None of the wood ducks inoculated with HPAI-infected water that was filtered by clams or that was inoculated with or fed tissue from these clams exhibited morbidity or mortality. All wood ducks exposed to either HPAI-infected water without clams or the original viral inoculum died. These results indicate that filter-feeding bivalves can remove and reduce the infectivity of AI viruses in water and demonstrate the need to examine biotic environmental factors that can influence AI virus transmission.
Density-dependent impact of the human malaria parasite
Plasmodium falciparum
gametocyte sex ratio on mosquito infection rates
Authors: Mitri C. , Thiery I. , Bourgouin C. , Paul R. E. L.
Published: August 2009

Malaria parasites produce male and female life cycle stages (gametocytes) that must fertilize to achieve successful colonization of the mosquito. Gametocyte sex ratios have been shown to be under strong selection pressure both as an adaptive response to a worsening blood environment for transmission and according to the number of co-infecting clones in the vertebrate. Evidence for an impact of sex ratio on the transmission success of
Plasmodium falciparum
has, however, been more controversial. Theoretical models of fertilization predict that increasingly male sex ratios will be favoured at low gametocyte densities to ensure fertilization. Here, we analyse
in vitro
transmission studies of
P. falciparum
to
Anopheles gambiae
mosquitoes and test this prediction. We find that there is a discernible effect of sex ratio on transmission but which is dependent upon the gametocyte density. While increasingly male sex ratios do give higher transmission success at low gametocyte densities, they reduce success at higher densities. This therefore provides empirical confirmation that sex ratio has an immediate impact on transmission success and that it is density-dependent. Identifying the signals used by the parasite to alter its sex ratio is essential to determine the success of transmission-blocking vaccines that aim to impede the fertilization process.
Protection of
Salmonella
by ampicillin-resistant
Escherichia coli
in the presence of otherwise lethal drug concentrations
Authors: Perlin Michael H. , Clark Denise R. , McKenzie Courtney , Patel Himati , Jackson Nikki , Kormanik Cecile , Powell Cayse , Bajorek Alexander , Myers David A. , Dugatkin Lee A. , Atlas Ronald M.
Published: August 2009

Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or ‘public goods’ traits
within species
. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of
multi-species communities
, particularly those that affect human health. We examined whether β-lactamase-producing
Escherichia coli
could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both β-lactamase-secreting
E. coli
and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of
Salmonella enterica
serovar Typhimurium, including both laboratory and clinical isolates. The
Salmonella
survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer.
Salmonella
survival did not even require direct physical contact with the resistant
E. coli
. The observed phenomenon appears to involve increased release of β-lactamase from the
E. coli
when present with
S. enterica
. Significantly, these findings imply that resistant
E. coli
, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other
E. coli
. Thus,
Salmonella
can gain protection against antibiotics from
E. coli
without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant
E. coli
can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
Lift production in the hovering hummingbird
Authors: Warrick Douglas R. , Tobalske Bret W. , Powers Donald R.
Published: August 2009

Aerodynamic theory and empirical observations of animals flying at similar Reynolds numbers (Re) predict that airflow over hummingbird wings will be dominated by a stable, attached leading edge vortex (LEV). In insects exhibiting similar kinematics, when the translational movement of the wing ceases (as at the end of the downstroke), the LEV is shed and lift production decreases until the energy of the LEV is re-captured in the subsequent half-cycle translation. We here show that while the hummingbird wing is strongly influenced by similar sharp-leading-edge aerodynamics, leading edge vorticity is inconsistent, varying from 0.7 to 26 per cent (mean 16%) of total lift production, is always generated within 3 mm of the dorsal surface of the wing, showing no retrograde (trailing to leading edge) flow, and does not increase from proximal to distal wing as would be expected with a conical vortex (class III LEV) described for hawkmoths. Further, the bound circulation is not shed as a vortex at the end of translation, but instead remains attached and persists after translation has ceased, augmented by the rotation (pronation, supination) of the wing that occurs between the wing-translation half-cycles. The result is a near-continuous lift production through wing turn-around, previously unknown in vertebrates, able to contribute to weight support as well as stability and control during hovering. Selection for a planform suited to creating this unique flow and nearly-uninterrupted lift production throughout the wingbeat cycle may help explain the relatively narrow hummingbird wing.
Modulation of the Poly(ADP-ribosyl)ation Reaction via the Arabidopsis ADP-Ribose/NADH Pyrophosphohydrolase, AtNUDX7, Is Involved in the Response to Oxidative Stress
Authors: Ishikawa Kazuya , Ogawa Takahisa , Hirosue Eisuke , Nakayama Yasumune , Harada Kazuo , Fukusaki Eiichiro , Yoshimura Kazuya , Shigeoka Shigeru
Published: August 2009

Here, we assessed modulation of the poly(ADP-ribosyl)ation (PAR) reaction by an Arabidopsis (Arabidopsis thaliana) ADP-ribose (Rib)/NADH pyrophosphohydrolase, AtNUDX7 (for Arabidopsis Nudix hydrolase 7), in AtNUDX7-overexpressed (Pro35S:AtNUDX7) or AtNUDX7-disrupted (KO-nudx7) plants under normal conditions and oxidative stress caused by paraquat treatment. Levels of NADH and ADP-Rib were decreased in the Pro35S:AtNUDX7 plants but increased in the KO-nudx7 plants under normal conditions and oxidative stress compared with the control plants, indicating that AtNUDX7 hydrolyzes both ADP-Rib and NADH as physiological substrates. The Pro35S:AtNUDX7 and KO-nudx7 plants showed increased and decreased tolerance, respectively, to oxidative stress compared with the control plants. Levels of poly(ADP-Rib) in the Pro35S:AtNUDX7 and KO-nudx7 plants were markedly higher and lower, respectively, than those in the control plants. Depletion of NAD+ and ATP resulting from the activation of the PAR reaction under oxidative stress was completely suppressed in the Pro35S:AtNUDX7 plants. Accumulation of NAD+ and ATP was observed in the KO-nudx7- and 3-aminobenzamide-treated plants, in which the PAR reaction was suppressed. The expression levels of DNA repair factors, AtXRCC1 and AtXRCC2 (for x-ray repair cross-complementing factors 1 and 2), paralleled that of AtNUDX7 under both normal conditions and oxidative stress, although an inverse correlation was observed between the levels of AtXRCC3, AtRAD51 (for Escherichia coli RecA homolog), AtDMC1 (for disrupted meiotic cDNA), and AtMND1 (for meiotic nuclear divisions) and AtNUDX7. These findings suggest that AtNUDX7 controls the balance between NADH and NAD+ by NADH turnover under normal conditions. Under oxidative stress, AtNUDX7 serves to maintain NAD+ levels by supplying ATP via nucleotide recycling from free ADP-Rib molecules and thus regulates the defense mechanisms against oxidative DNA damage via modulation of the PAR reaction.
A Bayesian model for estimating the effects of drug use when drug use may be under‐reported
Authors: McMillan Garnett P. , Bedrick Edward , C'deBaca Janet
Published: August 2009

Aims  We present a statistical model for evaluating the effects of substance use when substance use might be under‐reported. The model is a special case of the Bayesian formulation of the ‘classical’ measurement error model, requiring that the analyst quantify prior beliefs about rates of under‐reporting and the true prevalence of substance use in the study population.

Design  Prospective study.

Setting  A diversion program for youths on probation for drug‐related crimes.

Participants  A total of 257 youths at risk for re‐incarceration.

Measurements  The effects of true cocaine use on recidivism risks while accounting for possible under‐reporting.

Findings  The proposed model showed a 60% lower mean time to re‐incarceration among actual cocaine users. This effect size is about 75% larger than that estimated in the analysis that relies only on self‐reported cocaine use. Sensitivity analysis comparing different prior beliefs about prevalence of cocaine use and rates of under‐reporting universally indicate larger effects than the analysis that assumes that everyone tells the truth about their drug use.

Conclusion  The proposed Bayesian model allows one to estimate the effect of actual drug use on study outcome measures.
Startle cue–reactivity differentiates between light and heavy smokers
Authors: Rehme Anne K. , Frommann Ingo , Peters Sandra , Block Verena , Bludau Julia , Quednow Boris B. , Maier Wolfgang , Schütz Christian , Wagner Michael
Published: August 2009

Aims  It was assumed that the startle amplitude in smokers is reduced while viewing pictures of smoking, suggesting that smoking cues are appetitive. The goal of the present study was to investigate (i) whether smoking scenes induce appetitive cue effects in smokers, and (ii) whether smoking intensity is related to cue–reactivity.

Design  Smokers and non‐smokers participated in a single session.

Participants  A total of 62 individuals participated: 36 smokers and 26 non‐smokers.

Measurements  Participants took part in an acoustic affective startle experiment using standardized pleasant, neutral and unpleasant scenes from the International Affective Picture System (IAPS), as well as pictures of smoking. The effect of smoking cues was assessed by comparing neutral and smoking scenes (termed cue‐related startle suppression, CSS).

Findings  While there was no overall difference between smokers and non‐smokers regarding the CSS, light smokers showed significantly increased cue–reactivity towards smoking‐related cues, as compared with heavy smokers and non‐smokers. In addition, light smokers also displayed stronger appetitive responses towards positive stimuli.

Conclusions  These data support recent theories which discriminate between habit‐based and incentive‐based drug abuse. This distinction may have consequences for the assessment and treatment of drug‐addicted subjects. Furthermore, incentive‐based light smoking seems to have general effects on the reward system.
First positive reactions to cannabis constitute a priority risk factor for cannabis dependence
Authors: Le Strat Yann , Ramoz Nicolas , Horwood John , Falissard Bruno , Hassler Christine , Romo Lucia , Choquet Marie , Fergusson David , Gorwood Philip
Published: August 2009

Aim  To assess the association between first reactions to cannabis and the risk of cannabis dependence.

Design  A cross‐sectional population‐based assessment in 2007.

Setting  A campus in a French region (Champagne‐Ardennes).

Participants  A total of 1472 participants aged 18–21 years who reported at least one life‐time cannabis consumption, of 3056 students who were screened initially [the Susceptibility Addiction Gene Environment (SAGE) study].

Measurements  Positive and negative effects of first cannabis consumptions, present cannabis dependence and related risk factors were assessed through questionnaires.

Findings  The effects of first cannabis consumptions were associated dose‐dependently with cannabis dependence at age 18–21 years, both according to the transversal approach of the SAGE study and to the prospective cohort of the Christchurch Health and Development Study (CHDS) assessed at the age of 25 years. Participants of the SAGE study who reported five positive effects of their first cannabis consumption had odds of life‐time cannabis dependence that were 28.7 (95% confidence interval: 14.6–56.5) higher than those who reported no positive effects. This association remains significant after controlling for potentially confounding factors, including individual and familial variables.

Conclusions  This study suggests an association between positive reactions to first cannabis uses and risk of life‐time cannabis dependence, this variable having a central role among, and through, other risk factors.
Population pharmacokinetic analysis of varenicline in adult smokers
Authors: Ravva Patanjali , Gastonguay Marc R. , Tensfeldt Thomas G. , Faessel Hélène M.
Published: August 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT?

• Several clinical pharmacology studies have characterized the pharmacokinetics of varenicline in young adult and elderly smokers and subjects with impaired renal function.

• Varenicline pharmacokinetics is linear over the recommended dose range.

• Varenicline total clearance is linearly related to its renal clearance.

• Both are progressively reduced as renal function declines, which results in a progressive increase in varenicline systemic exposure and prolonged half‐life.

WHAT THIS STUDY ADDS?

• This work provides an integrated model‐based analysis of varenicline pharmacokinetics across multiple studies in the target patient population.

• The model describes the impact of patient‐specific covariates, such as renal function, and provides a rationale for dose adjustment.

• The resulting model also provides a means to predict individual‐specific drug exposures to clinical responses in subsequent analyses.

AIMS

To characterize the population pharmacokinetics of varenicline and identify factors leading to its exposure variability in adult smokers.

METHODS

Data were pooled from nine clinical studies consisting of 1878 subjects. Models were developed to describe concentration–time profiles across individuals. Covariates were assessed using a full model approach; parameters and bootstrap 95% confidence intervals (CI) were estimated using nonlinear mixed effects modelling.

RESULTS

A two‐compartment model with first‐order absorption and elimination best described varenicline pharmacokinetics. The final population parameter estimates (95% CI) were: CL/F, 10.4 l h−1 (10.2, 10.6); V2/F, 337 l (309, 364); V3/F, 78.1 l (61.9, 98.9); Q/F, 2.08 l h−1 (1.39, 3.79); Ka, 1.69 h−1 (1.27, 2.00); and Alag, 0.43 h (0.37, 0.46). Random interindividual variances were estimated for Ka[70% coefficient of variation (CV)], CL/F (25% CV), and V2/F (50% CV) using a block covariance matrix. Fixed effect parameters were precisely estimated [most with % relative standard error < 10 and all with % relative standard error < 25], and a visual predictive check indicated adequate model performance. CL/F decreased from 10.4 l h−1 for a typical subject with normal renal function (CLcr = 100 ml min−1) to 4.4 l h−1 for a typical subject with severe renal impairment (CLcr = 20 ml min−1), which corresponds to a 2.4‐fold increase in daily steady‐state exposure. Bodyweight was the primary predictor of variability in volume of distribution. After accounting for renal function, there was no apparent effect of age, gender or race on varenicline pharmacokinetics.

CONCLUSIONS

Renal function is the clinically important factor leading to interindividual variability in varenicline exposure. A dose reduction to 1 mg day−1, which is half the recommended dose, is indicated for subjects with severe renal impairment.
Reduced incidence and severity of experimental autoimmune arthritis in mice expressing catalytically inactive A disintegrin and metalloproteinase 8 (ADAM8)
Authors: Zack M D , Melton M A , Stock J L , Storer C E , Barve R A , Minnerly J C , Weiss D J , Stejskal J A , Tortorella M D , Turk J R , Shevlin K M , Malfait A-M
Published: August 2009

A disintegrin and metalloproteinase 8 (ADAM8), a catalytically active member of the ADAMs family of enzymes, is expressed primarily on immune cells and thus probably involved in inflammatory responses. ADAM8 is also produced by chondrocytes, and recombinant ADAM8 can induce cartilage catabolism. We therefore decided to test the role of ADAM8 in autoimmune inflammatory arthritis using transgenic mice expressing catalytically inactive ADAM8. Transgenic DBA/1J mice expressing an inactivating point mutation in the ADAM8 gene to change Glu330 to Gln330 (ADAM8EQ) were generated to evaluate the proteolytic function of ADAM8 in an lipopolysaccharide-synchronized collagen-induced arthritis (LPS-CIA) model of autoimmune arthritis. The systemic inflammatory reaction to LPS was also evaluated in these mice. Expression profiling of paw joints from wild-type mice revealed that ADAM8 mRNA levels increased at the onset of clinical arthritis and correlated well with cellular macrophage markers. When subjected to LPS-CIA, ADAM8EQ mice demonstrated decreased incidence and severity of clinical arthritis compared to wild-type mice. Histological examination of paw joints from ADAM8EQ mice confirmed marked attenuation of synovial inflammation, cartilage degradation and bone resorption when compared to wild-type mice. However, transgenic mice and wild-type mice responded similarly to LPS-induced systemic inflammation with regard to mortality, organ weights, neutrophil sequestration and serum cytokine/chemokine production. We conclude that ADAM8 proteolytic activity plays a key role in the development of experimental arthritis and may thus be an attractive target for the treatment of arthritic disorders while minimizing risk of immunocompromise.
Influence of harvest date of primary growth on microbial flora of grass herbages and haylage, and on fermentation and aerobic stability of haylage conserved in laboratory silos
Authors: Müller C. E.
Published: August 2009

The influence of harvest date of the primary growth of grass herbages on the microbial flora of herbage pre‐conservation and haylage post‐conservation was studied along with fermentation variables and aerobic stability of haylage. The primary growths of two grass swards, one intensely (Int) and one extensively (Ext) managed, were cut at three different harvest dates (May, June, August) and ensiled in laboratory silos for 120 d. Later harvest dates resulted in increased counts of yeast, mould and enterobacteria in the pre‐conserved herbage (P < 0·001). Counts of lactic acid bacteria (LAB) (P < 0·001) and number of mould species (P < 0·001) were highest in the pre‐conserved herbage harvested in August. Later harvest dates resulted in higher yeast (P < 0·001) and LAB (P < 0·001) counts in the haylage while counts of enterobacteria decreased (P < 0·001). Clostridial spore counts were unaffected by harvest date both in herbage and haylage. The haylage harvested in August had the lowest pH and the lowest concentration of ethanol but the concentration of lactic acid was in general low. Aerobic stability was longer (P < 0·01) for haylage from herbage harvested in August compared with haylage from herbage harvested in May and June. Sward type had less influence than harvest date on microbial variables in herbage and haylage and on fermentation variables of haylage, and did not influence the aerobic stability of haylage.
Effect of three forages and two forage allowances offered to pregnant dry dairy cows in winter on periparturient performance and milk yield in early lactation
Authors: Keogh B. , French P. , McGrath T. , Storey T. , Mulligan F. J.
Published: August 2009

Sixty multiparous, Holstein–Friesian pregnant dry dairy cows were allocated to three forage treatments (n = 20; fodder beet, kale or grass silage) at two feeding allowances (n = 30; high and low) for 70 (s.e. of mean, 16) d before parturition. Cows offered the high feeding allowance were offered 9 kg of dry matter (DM) of kale or fodder beet grazed in situ plus 5 kg DM of baled grass silage daily or clamp grass silage ad libitum offered indoors. Cows offered the low feeding allowance were offered 6 kg DM of kale or fodder beet grazed in situ plus 3·5 kg DM baled grass silage daily, or 9·5 kg DM of clamp grass silage daily offered indoors. After calving, all cows received a daily allowance of 14 kg DM perennial ryegrass herbage at pasture plus 4 kg concentrate cow−1 for the first 35 d of lactation. Cows offered grass silage had a greater increase in body condition score pre‐partum compared to those offered kale or fodder beet. Cows offered fodder beet pre‐partum had a greater milk solid and solids‐corrected milk yield in the first 35 d of lactation than those offered kale and grass silage pre‐partum. Offering fodder beet and kale pre‐partum increased plasma non‐esterified fatty acid concentrations pre‐partum relative to offering grass silage. Offering kale pre‐partum resulted in higher insulin‐like growth factor‐1 concentration post‐partum but lower plasma copper concentration pre‐partum and at calving than kale or grass silage. Offering the higher forage allowance pre‐partum resulted in a higher plasma calcium concentration at calving and higher plasma non‐esterified fatty acid concentration post‐partum.
Toothache referred from auriculotemporal neuralgia: case report
Authors: Murayama R. A. , Stuginski‐Barbosa J. , Moraes N. P. , Speciali J. G.
Published: August 2009

Aim  To present a 52‐year‐old male patient who complained of intense pain of short duration in the region of the left external ear and in the ipsilateral maxillary second molar that was relieved by blockade of the auriculotemporal nerve in the infratemporal fossa.

Summary  Extra‐ and intraoral physical examination revealed a trigger point that reproduced the symptoms upon finger pressure in the ipsilateral auriculotemporal nerve and in the outer auricular pavilion. The patient’s medical history was unremarkable. The maxillary left second molar tooth was not responsive to pulp sensitivity testing and there was no pain upon percussion or palpation of the buccal sulcus. Periapical radiographs revealed a satisfactory root filling in the maxillary left second molar. On the basis of the clinical signs and symptoms, the auriculotemporal was blocked with 0.5 mL 2% lidocaine and 0.5 mL of a suspension containing dexamethasone acetate (8 mg mL−1) and dexamethasone disodium sulfate (2 mg mL−1), with full remission of pain 6 months later. The diagnosis was auriculotemporal neuralgia.

Key learning point

Auriculotemporal neuralgia should be considered as a possible cause of nonodontogenic toothache and thus included in the differential diagnoses.

The blockade of the auriculotemporal nerve in the infratemporal fossa is diagnostic and therapeutic. It can be achieved with a solution of lidocaine and dexamethasone.
Diversity and frequency of yeasts from the dorsum of the tongue and necrotic root canals associated with primary apical periodontitis
Authors: Miranda T. T. , Vianna C. R. , Rodrigues L. , Monteiro A. S. , Rosa C. A. , Corrêa A.
Published: August 2009

Aims  To determine the frequency and diversity of yeasts from the dorsum of the tongue and necrotic root canals with teeth associated with primary apical periodontitis.

Methodology  Detailed medical and dental histories of 168 patients were recorded. The samples were collected from the dorsum of tongue and from 168 teeth with root canals contained necrotic pulps. Yeasts were isolated on Sabouraud agar with 100 mg L−1 chloramphenicol, purified and characterized by standard methods. Identification was confirmed by EI1 PCR fingerprint technique. Yeast isolates of uncertain identity or with a different genetic fingerprint profile from the reference strains were identified by sequencing the D1/D2 variable domains of the large subunit rDNA.

Results  Yeasts were isolated from 22.6% of teeth sampled and from 45.8% of tongue samples. Candida albicans was the most frequently isolated species at both investigated sites but other species were also found. Saccharomyces cerevisiae and Kluyveromyces lactis were recovered from the tongue.

Conclusions  Although the detection of yeasts in the root canal does not imply an involvement in the disease process, the study suggests a frequency of Candida spp. in primary endodontic infections that deserves further clarification.
Supportive counselling programme for nursing students experiencing academic failure: randomized controlled trial
Authors: Peyrovi Hamid , Parvizy Soroor , Haghani Hamid
Published: August 2009

Title.  Supportive counselling programme for nursing students experiencing academic failure: randomized controlled trial.

Aim.  This paper is a report of a study examining the effects of a supportive counselling programme on the academic performance of Iranian nursing students experiencing academic failure.

Background.  In order to using limited educational resources effectively, nursing students experiencing academic failure should be immediately identified in order that appropriate intervention can take place.

Method.  Data were collected over a 12‐month period in 2006–2007, with 42 Bachelor of Science nursing students who displayed poor academic performance. They were randomly allocated to receive either supportive or ordinary counselling. The mean grades in basic theoretical courses, special courses, and also the combination of both basic and special courses was compared between the two groups.

Findings.  Over the study period, there were improvements in the mean grades of special courses and also in both basic and special courses of male students in the experimental group, compared with those of male students in the control group (0·27 against −1·43, P = 0·014; and 1·87 against −0·40, P = 0·009; respectively).

Conclusion.  A supportive counselling programme can improve the academic performance of male nursing students. Replication of the current study with larger samples and longer duration is recommended.
Bodily change following faecal stoma formation: qualitative interpretive synthesis
Authors: Thorpe Gabrielle , McArthur Margaret , Richardson Barbara
Published: August 2009

Title.  Bodily change following faecal stoma formation: qualitative interpretive synthesis.

Aim.  This paper is a report of a literature review conducted to answer the question ‘How has the experience of bodily change following stoma formation been explored and interpreted through existing qualitative research?’.

Background.  A faecal stoma alters the function, appearance and sensation of the body. Quantitative research highlights the importance of bodily change following stoma formation but is limited in being able to explore what this experience means to ostomists. Qualitative research can identify ways in which ostomists experience their changed body but a conceptual framework of their experience drawn from qualitative findings which can inform patient‐centred care has not yet been identified.

Method.  The Amed, ASSIA, CINAHL, Embase, Medline and Psycinfo databases were searched from inception to April 2009 using predefined inclusion criteria. Of 144 papers identified, 11 were selected for review. An interpretive review methodology for qualitative research synthesis was employed.

Findings.  Three broad themes of bodily experience following stoma formation were identified: loss of embodied wholeness, awareness of a disrupted lived body and disrupted bodily confidence. These highlight the impact of the experience of living with a stoma on the embodied self and the ostomist’s embodiment within their lifeworld.

Conclusion. A loss of embodied wholeness which underpins the experience of stoma formation can be represented through awareness of the disrupted lived body and impact on the lifeworld. Findings suggest the need for further research to identify a comprehensive conceptualization of bodily change, which can more closely match healthcare service to individual patient need.
Habitat‐specific differences in adult survival rates and its links to parental workload and on‐nest predation
Authors: Low Matthew , Arlt Debora , Eggers Sönke , Pärt Tomas
Published: August 2009

1. Adult survival rates strongly affect population growth, but few studies have quantified if and why adult survival differs between breeding habitats. We investigated potential causes of habitat‐specific adult survival rates for male and female northern wheatears (Oenanthe oenanthe L.) breeding in Swedish farmland.

2. We used multistate mark–recapture models based on 1263 breeding records between 1993 and 2007 to estimate survival rates based on habitat‐type (SHORT vs. TALL ground vegetation) and breeding‐success state parameters. We also used breeding‐season observations from 2002 to 2007 and an experimental manipulation of ground vegetation height to identify factors influencing adult mortality.

3. Females had lower annual survival than males (0·42 ± 0·02 vs. 0·50 ± 0·02); this difference largely resulted from low female survival in TALL habitats because of higher nest‐predation risk and the large proportion of adult females being killed on the nest (>20%) during nest predation events.

4. Among successful breeders, both sexes displayed similar survival rates, but survival was lower for breeders in TALL as compared to SHORT habitats (0·43 ± 0·03 vs. 0·51 ± 0·02). Experimental manipulation of ground vegetation height, controlling for individual and territory quality (n = 132), suggested the cost of rearing young to be higher in TALL habitats (survival of successful breeders in TALL vs. SHORT; 0·43 ± 0·11 vs. 0·57 ± 0·05).

5. Detailed observations of food provisioning behaviour during chick rearing revealed a habitat‐related difference in parental workload corresponding to the observed habitat differences in adult survival for successful breeders. Adults breeding in TALL habitats were forced to forage further from the nest relative to SHORT‐habitat breeders (mean ± SE; 69 ± 10 vs. 21 ± 2 m), which increased the estimated daily workload for adults in TALL vs. SHORT habitats by c. 20%.

6. On‐nest predation and parental workload during chick rearing combine to largely explain habitat‐specific adult survival rates. The results have implications for our understanding of adult sex ratios, causes of source–sink demography and habitat‐specific growth rates. Furthermore, it suggests SHORT field margins and other residual habitat elements to be important for the conservation of farmland passerines breeding in cropland plains.
Sex‐specific fitness correlates of dispersal in a house sparrow metapopulation
Authors: Pärn Henrik , Jensen Henrik , Ringsby Thor H. , Sæther Bernt‐Erik
Published: August 2009

1. Dispersal affects many important ecological and evolutionary processes. Still, little is known about the fitness of dispersing individuals.

2. Here, we use data from a long‐term study of a house sparrowPasser domesticusmetapopulation to compare lifetime reproductive success (LRS) of resident and immigrant individuals, all with known origin.

3. Lifetime production of recruits by immigrant males was much lower than for resident males, because of shorter life span and lower annual mating success. In contrast, lifetime production of recruits did not differ significantly between immigrant and resident females.

4. Over their lifetime, dispersers contributed fewer recruits to the local population than residents. This shows that immigrant house sparrows have different, sex specific, demographic effects on the population dynamics than residents.