bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of tissue microarrays in oral epithelial dysplasia using a novel virtual-array technique
Authors: Nankivell Paul Christopher , Williams Hazel , Bartlett John M S , Mehanna Hisham 
Published: August 2012

BackgroundMalignant transformation risk in oral epithelial dysplasia (OED) is currently determined by histological assessment. The subjectivity of this approach has led to interest in identifying prognostic biomarkers. Tissue microarrays (TMA) can reduce the utilization of the finite resources of a pathological archive. However, the selectivity involved in TMA construction necessitates the need to ensure that individual cores are representative of the overall features of the donor specimen. We aimed to validate, for the first time, the use of the TMA technique in OED by using a novel virtual array technique.MethodsSections from 38 cases of OED were stained with H&E and 6 immunohistochemical (IHC) biomarkers. All were then digitally scanned. Virtual cores were generated by image capturing a 0.6mm2area of the IHC slide that corresponded to the same dysplastic area marked on the H&E slide. Two trained blinded observers scored both whole slides and virtual cores independently. The degree of reliability in scores between the individual raters and between virtual TMA cores and slides was assessed using both interclass correlation coefficient (ICCC) and weighted κ statistics.ResultsExcellent inter-observer reliability was demonstrated with all the immunohistochemical markers. ICCC ranged from 0.67−1.0 and κ scores >0.8. There was also a high reliability in the scores between whole slides and virtual TMAs, with ICCC of between 0.66 and 0.89 for the 6 markers.ConclusionsThis study validates the use of TMAs in OED using a variety of biomarkers. We also report a novel method for achieving this using a novel virtual-array technique.
Navigating non-positivity in neighbourhood studies: an analysis of collective efficacy and violence
Authors: Ahern Jennifer , Cerdá Magdalena , Lippman Sheri A , Tardiff Kenneth J , Vlahov David , Galea Sandro 
Published: August 2012

BackgroundIn multilevel studies, strong correlations of neighbourhood exposures with individual and neighbourhood confounders may generate problems with non-positivity (ie, inferences that are ‘off-support’). The authors used propensity restriction and matching to (1) assess the utility of propensity restriction to ensure analyses are ‘on-support’ and (2) examine the relation between collective efficacy and violence in a previously unstudied city.MethodsAssociations between neighbourhood collective efficacy and violent victimisation were estimated in data from New York City in 2005 (n=4000) using marginal models and propensity matching.ResultsIn marginal models adjusted for individual confounders and limited to observations ‘on-support’, under conditions of high collective efficacy, the estimated prevalence of violent victimisation was 3.5/100, while under conditions of low collective efficacy, it was 7.5/100, resulting in a difference of 4.0/100 (95% CI 2.6 to 5.8). In propensity-matched analysis, the comparable difference was 4.0/100 (95% CI 2.1 to 5.9). In analyses adjusted for individual and neighbourhood confounders and limited to observations ’on-support’, the difference in violent victimisation associated with collective efficacy was 3.1/100 (95% CI 1.2 to 5.2) in marginal models and 2.4/100 (95% CI 0.2 to 4.5) in propensity-matched analysis. Analyses without support restrictions produced surprisingly similar results.ConclusionsUnder conditions of high collective efficacy, there was about half the prevalence of violence compared with low collective efficacy. The results contribute to a growing body of evidence that suggests collective efficacy may shape violence, and illustrate how careful techniques can be used to disentangle exposures from highly correlated confounders without relying on model extrapolation.
Urban neighbourhood unemployment history and depressive symptoms over time among late middle age and older adults
Authors: Wight Richard G , Aneshensel Carol S , Barrett Christopher , Ko Michelle , Chodosh Joshua , Karlamangla Arun S 
Published: August 2012

BackgroundLittle is known about how a neighbourhood's unemployment history may set the stage for depressive symptomatology. This study examines the effects of urban neighbourhood unemployment history on current depressive symptoms and subsequent symptom trajectories among residentially stable late middle age and older adults. Contingent effects between neighbourhood unemployment and individual-level employment status (ie, cross-level interactions) are also assessed.MethodsIndividual-level survey data are from four waves (2000, 2002, 2004 and 2006) of the original cohort of the nationally representative US Health and Retirement Study. Neighbourhoods are operationalised with US Census tracts for which historical average proportion unemployed between 1990 and 2000 and change in proportion unemployed between 1990 and 2000 are used to characterise the neighbourhood's unemployment history. Hierarchical linear regressions estimate three-level (time, individual and neighbourhood) growth models.ResultsSymptoms in 2000 are highest among those residing in neighbourhoods characterised by high historical average unemployment beginning in 1990 and increasing unemployment between 1990 and 2000, net of a wide range of socio-demographic controls including individual-level employment status. These neighbourhood unemployment effects are not contingent upon individual-level employment status in 2000. 6-year trajectories of depressive symptoms decrease over time on average but are not significantly influenced by the neighbourhood's unemployment history.ConclusionsGiven the current US recession, future studies that do not consider historical employment conditions may underestimate the mental health impact of urban neighbourhood context. The findings suggest that exposure to neighbourhood unemployment earlier in life may be consequential to mental health later in life.
Healing of saccular aneurysms following platinum coil embolization: lack of improved efficacy with vitamin C supplementation
Authors: Dai Daying , Yong-Hong Ding , Rezek Issa , Lewis Debra A , Kallmes David F , Kadirvel Ramanathan 
Published: August 2012

Background and purposeTo test the hypothesis that systemic administration of vitamin C, through its action of stimulating collagen synthesis and crosslinking, would decrease the recurrence and improve the occlusion of experimental aneurysms treated with platinum coils.MethodsExperimental aneurysms were created in female rabbits and were embolized with platinum coils (>30% packing density). The animals were divided into three groups: group 1 (n=6) rabbits served as controls, group 2 (n=5) rabbits were fed with a vitamin C supplemented feed and group 3 (n=8) rabbits were medicated with vitamin C pills. Digital subtraction angiography was used to evaluate stability after embolization. Subjects were euthanized at 12 weeks after coil implantation, and serum vitamin C levels were then measured. Histological samples were examined with a grading system (range 0–12) based on the neck and dome features. Masson Trichrome staining was used to evaluate collagen deposition. Parametric data were analyzed with one way analysis of variance and non-parametric data were examined using a Kruskal–Wallis test.ResultsThere were no significant differences between groups in mean aneurysm size. Mean serum vitamin C concentration was significantly higher in group 3 and group 2 compared with group 1, while vitamin C levels between group 2 and group 3 were statistically comparable. Coil compaction was noted in one of six subjects in group 1 and in three of eight subjects in group 3. All of the remaining aneurysms in the test and control groups showed stable occlusion. There were no significant differences in histological scores or collagen deposition among groups.ConclusionsVitamin C supplementation following platinum coil embolization does not demonstrate improvement of long term occlusion rates of aneurysms.
HIV and STI control in El Salvador: results from an integrated behavioural survey among men who have sex with men
Authors: Creswell Jacob , Guardado Maria Elena , Lee Janet , Nieto Ana Isabel , Kim Andrea A , Monterroso Edgar , Paz-Bailey Gabriela 
Published: August 2012

ObjectiveThis cross-sectional study investigates HIV, other sexually transmitted infections (STI), and risk behaviours among men who have sex with men (MSM) in two cities in El Salvador.MethodsRespondent-driven sampling (RDS) was used to recruit MSM in the cities of San Salvador and San Miguel, El Salvador. Participants responded to questions about HIV risk behaviours; and blood, urine and anal swabs were collected. Blood samples were tested for herpes simplex type 2, syphilis and HIV infection. Urine and anal samples were tested by polymerase chain reaction (PCR) forChlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, and Mycoplasma genitalium. HIV-positive samples were tested with the BED capture enzyme immunoassay to distinguish recent from longstanding HIV infection. We estimated population-adjusted prevalence of behavioural variables, STI and HIV, and identified risk factors for HIV.ResultsThe final sample included 596 and 195 MSM in San Salvador and San Miguel, respectively. Consistent condom use was low across all partner types as was recent HIV testing. RDS-adjusted HIV prevalence was 10.8% (95% CI 7.4% to 14.7%) in San Salvador, and 8.8% (95% CI 4.2% to 14.5%) in San Miguel. The proportion of recent testing among HIV-positive samples was 20%. Prevalence of any bacterial STI by PRC testing was 12.7% (95% CI 8.2% to 17.5%) in San Salvador, and 9.6% (95% CI 4.9% to 15.4%) in San Miguel.ConclusionsWe found a high prevalence of HIV, high levels of recent infection, and low condom usage. In El Salvador, targeted interventions towards MSM are needed to promote condom use, as well as to diagnose, treat and prevent HIV and other STIs.
Effects of collection time and after-ripening on chemical constituents and germinability of Scotch thistle (Onopordum acanthium) cypselas
Authors: Qaderi Mirwais M. , Cavers Paul B. , Hamill Allan S. , Bernards Mark A. 
Published: August 2012

Earlier studies have shown that seed germinability decreases with the physiological age of plants during seed development, but the effects of plant physiological age on the chemical constituents of fresh and after-ripened seeds and the relationship between chemicals and germination of such seeds have not been investigated fully. We studied this phenomenon in Scotch thistle ( Onopordum acanthium L.) cypselas. Mature cypselas were collected twice (early and late) from the same mother plants, which were grown under the temperature regime of 25/10 °C (14 h light, 10 h dark) in a walk-in growth chamber in 2000 and 2001. Cypselas were used fresh and after 4 months of dry storage at room temperature (∼25 °C, ∼37% relative humidity). Germination percentage, coefficient of germination rate, moisture content, wax load, lignin content, and phenolic compounds were determined for cypselas from all treatments. Germination percentages were higher for early-matured than for late-matured cypselas, and higher for after-ripened cypselas than for fresh ones. Late-matured fresh cypselas had greater moisture content than the early-matured fresh cypselas. After-ripening decreased cypsela moisture content and wax load. Plant physiological age and after-ripening did not affect lignin content. Overall, after-ripened cypselas had more phenolic compounds than fresh cypselas. Plant physiological age and after-ripening affect the chemical constituents of O. acanthium cypselas and their germination patterns.
Alternate host ranges of Cronartium flaccidum and Cronartium ribicola in northern Europe
Authors: Kaitera Juha , Hiltunen Ritva , Samils Berit 
Published: August 2012

Attached and detached leaves of 60 potential host species were inoculated in the greenhouse and laboratory with aeciospores of Cronartium ribicola J.C. Fisch. from six Finnish locations and of Cronartium flaccidum (Alb. & Schw.) Wint. from 20 locations in Finland and Sweden in 2011. Candidate hosts represented 16 plant families: Solanaceae, Verbenaceae, Asclepiadaceae, Grossulariaceae, Paeoniaceae, Balsaminaceae, Gentianaceae, Scrophulariaceae, Loasaceae, Tropaeolaceae, Acanthaceae, Myricaceae, Phrymaceae, Plantaginaceae, Orobanchaceae, and Apocynaceae. Inoculations of C. flaccidum produced uredinia after 2 weeks and (or) telia after 4 weeks of incubation on 25 hosts. Inoculation trials identified several new hosts for C. flaccidum in Fennoscandia, namely Impatiens balsamina, Swertia fedtschenkoana, Loasa tricolor, Myrica gale, Verbena canadensis, Saxifraga spp., Paeonia obovata, and Veronica daurica. Myricaceae and Saxifragaceae represent new host families for these rusts. Cronartium ribicola formed uredinia or telia on 10 species: Ribes spp. (7 species/cultivars), Pedicularis palustris subsp. palustris, Bartsia alpina, and Loasa triphylla. Results suggest wider alternate host ranges for both C. flaccidum and C. ribicola than previously recognized. Spores were virulent regardless of their source location, suggesting a lack of host-specificity among Fennoscandian populations of Cronartium.
Allometries of coarse tree, stem, and crown measures in Douglas-fir are altered by Armillaria root disease
Authors: Cruickshank M.G. , Filipescu C.N. 
Published: August 2012

We used allometric relationships to quantify Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) stem and crown adaptation to Armillaria root disease (caused by Armillaria ostoyae (Romagn.) Herink). At four sites, we measured height, diameter, height to live crown, crown width and length, sapwood area at base of live crown, and infection duration for healthy and infected Douglas-fir trees. Diseased trees were on average smaller than healthy trees for all measured variables, but there were also proportional changes between tree parts suggesting allocation shifts to disease. Infected trees were shorter in relation to stem diameter compared with healthy trees by 4% on average. Crown diameter was positively related to stem diameter (0.24 m·cm–1) but not to disease or competition. Diseased tree crown lengths were on average 0.5 m shorter for a given crown diameter than healthy trees—akin to response to light competition except this also occurred in the upper canopy. Prolonged infection reduced crown length probably through shedding of lower branches and by reducing stem apical growth, possibly related to changed hydraulic architecture or light requirements. Crown surface area was related to stem sapwood area (0.81 m2·cm–2) but unaffected by disease or competition. We discuss how shifting allocation could reveal important implications for life strategies involving whole tree adaptations to disease and tree to tree interactions, and for wood quality and forest inventory.
Testing the interaction between inter-sexual competition and phosphorus availability in a dioecious grass
Authors: Rogers Sally R. , Eppley Sarah M. 
Published: August 2012

Spatial segregation of the sexes (SSS) occurs in many dioecious plants, usually along an environmental gradient. However, little data is available on how male and female plants of species with SSS respond to environmental conditions along these gradients. We examined whether male and female plants of Distichlis spicata (L.) Greene, a dioecious grass species that exhibits extreme SSS along a phosphorus gradient, differed in their responses to phosphorus and competition treatments in the greenhouse. We found little evidence that phosphorus plays a role in SSS in D. spicata. However, supporting earlier work, we found that plants subject to inter-sexual competition were significantly more likely to have high root/shoot ratios than plants subject to intra-sexual competition, suggesting that competition is an important driver of SSS in this species.
The estimation and robustness of FMSY and alternative fishing mortality reference points associated with high long-term yield
Authors: Horbowy Jan , Luzeńczyk Anna 
Published: August 2012

Equations for equilibrium yield and biomass are presented and used to derive FMSY and alternative reference points (ARPs). ARPs are analogues of the traditional points based on yield-per-recruit (YPR) or spawning stock-per-recruit (SPR) (F0.1, F40%, F50%), but refer to the equilibrium total yield or biomass. The method combines YPR and SPR analysis with stock–recruitment relationships. The sensitivity of FMSY and ARPs to the range of available stock–recruitment data, recruitment variance, various steepness levels in the stock–recruitment models, assessment variance, and bias are tested. The analysis showed that in most cases, F40%B and F50%B, defined by the equilibrium biomass (B), were the most robust relative to the different sources of uncertainty. However, in the case of the misspecification of the stock–recruitment relationship, FMSY showed superior performance. F40%B for the Beverton and Holt stock–recruitment model and F50%B for the Ricker recruitment model can be recommended as conservative fishing mortalities associated with high long-term yield. For the considered steepness, they produced yield up to 5%–10% lower than yield at FMSY.
Latitudinal and seasonal effects on growth of the Australian eastern king prawn (Melicertus plebejus)
Authors: Lloyd-Jones Luke R. , Wang You-Gan , Courtney Anthony J. , Prosser Andrew J. , Montgomery Steven S. 
Published: August 2012

The growth of the Australian eastern king prawn ( Melicertus plebejus ) is understood in greater detail by quantifying the latitudinal effect. The latitudinal effect is the change in the species’ growth rate during migration. Mark–recapture data (N = 1635, latitude 22.21°S–34.00°S) presents northerly movement of the eastern king prawn, with New South Wales prawns showing substantial average movement of 140 km (standard deviation: 176 km) north. A generalized von Bertalanffy growth model framework is used to incorporate the latitudinal effect together with the canonical seasonal effect. Applying this method to eastern king prawn mark–recapture data guarantees consistent estimates for the latitudinal and seasonal effects. For M. plebejus, it was found that growth rate peaks on 25 and 29 January for males and females, respectively; is at a minimum on 27 and 31 July, respectively; and that the shape parameter, k (per year), changes by –0.0236 and –0.0556 every 1 degree of latitude south increase for males and females, respectively.
Small-scale dispersal and population structure in stream-living brown trout (Salmo trutta) inferred by mark–recapture, pedigree reconstruction, and population genetics
Authors: Vøllestad Leif Asbjørn , Serbezov Dimitar , Bass Arthur , Bernatchez Louis , Olsen Esben Moland , Taugbøl Annette 
Published: August 2012

Many animals move among habitats, and even small-scale dispersal of individuals between habitat patches may have strong implications for population dynamics and structure. Here, we use long-term mark–recapture data combined with extensive genotyping and parentage assignment to investigate the importance of small-scale location change of resident brown trout ( Salmo trutta ) in a small stream (1500 m). During the first summer, juvenile fish dispersed downstream (mean displacement 200 m), with smaller juveniles dispersing longer distances. Downstream movement was also predominant during the first winter, but older fish moved little. This limited dispersal resulted in a significant isolation-by-distance structure for ages 1 and 2, but not for older age groups or for the mature fish. Individual pairwise relatedness coefficients decreased with waterway distance for mature fish during the 2002 and 2003 spawning seasons, but only weakly. Overall, between-site genetic differentiation was stronger for the younger age classes, and the signal decayed with age, indicating that the genetic structure observed in the stream is mainly driven by spatial aggregation of close relatives.
Allopatric distribution of generalist parasites: interplay between postglacial dispersal and host species
Authors: Cyr Frédéric , Peres-Neto Pedro , Angers Bernard 
Published: August 2012

Dispersal of freshwater mussels occurs when the larvae parasitize fishes. In northeastern North America, distributions of floater mussels ( Pyganodon spp.) are allopatric and arranged in an east–west pattern that corresponds poorly with the biogeographic patterns of the regional fish fauna. This study aims at determining whether associations with distinct fish species can explain the distribution of floaters. Here, we devised a framework based on a series of novel distributional null models to elucidate dispersal of species that are dependent on host species. The distributional patterns of floaters were tested by controlling for associations with fishes, while host–parasite associations were assessed with null models based on co-occurrence patterns. The disjoint distribution of the giant floater ( Pyganodon grandis ) and the eastern floater ( Pyganodon cataracta ) could not be explained by their association with distinct host fish and is likely the result of associations with distinct host populations rather than distinct species. In contrast, the distribution of the Newfoundland floater ( Pyganodon fragilis ) could be explained by its association with euryhaline fishes. Such associations may have also promoted differentiation with its sister taxa, the eastern floater. This study demonstrated the effects of positive biological associations on distributional patterns and the utility of a null model framework to uncover them.
Spawning biomass reference points for exploited marine fishes, incorporating taxonomic and body size information
Authors: Thorson James T. , Cope Jason M. , Branch Trevor A. , Jensen Olaf P. 
Published: August 2012

Surplus production represents the processes that affect sustainable fishery harvest and is central to the ecology and management of marine fishes. Taxonomy and life history influence the ratio of spawning biomass at maximum sustainable yield to average unfished spawning biomass (SBMSY/SB0), and estimating this ratio for individual stocks is notoriously difficult. We use a database of published landings data and stock assessment biomass estimates and determine that process errors predominate in this data set by fitting a state–space model to data from each stock individually. We then fit multispecies process-error models while treating SBMSY/SB0as a random effect that varies by taxonomic order and maximum length. The estimated SBMSY/SB0 = 0.40 for all 147 stocks is intermediate between the values assumed by the Fox and the Schaefer models, although Clupeiformes and Perciformes have lower and Gadiformes and Scorpaeniformes have higher SBMSY/SB0values. Model selection supports the hypothesis that large-bodied fishes for a given taxonomic order have relatively higher SBMSY/SB0. Results can be used to define reference points for data-poor fisheries or as input in emerging assessment methods.