bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compensation for inundation‐induced embryonic diapause in a freshwater turtle: achieving predictability in the face of environmental stochasticity
Authors: FORDHAM D. , GEORGES A. , COREY B. 
Published: July 2006

Summary

We investigated the influence of duration of inundation‐induced diapause, incubation temperature and clutch of origin on incubation duration and survivorship of eggs of the Snake‐Necked Turtle, Chelodina rugosa, from the wet–dry tropics of northern Australia.
Eggs of C. rugosa survive at least 25 weeks’ inundation, almost 6 months, with a clear optimal inundation duration of 6 weeks. Eggs not held under water suffered the same mortality as eggs inundated for 25 weeks. Underwater nesting is not a facultative capacity but, rather, inundation is essential for optimal survivorship of embryos.
Inundation duration had a profound effect on incubation period, reducing it by up to 9 weeks over what would be expected for a given temperature. Eggs inundated for up to 7 weeks complete incubation faster than had they been laid at the same time in dry ground.
There was remarkable variability in incubation period remaining after correcting for the effect of incubation temperature, inundation duration and clutch.
We interpret these traits as adaptations that match the timing and duration of the period available for nesting to the timing and duration of the period available for successful hatching, emergence from the nest and hatchling survival. Our interpretation is placed in the context of considerable environmental stochasticity in the factors driving these variables.
Rapid detection of fungal endophytes in grasses for large‐scale studies
Authors: KOH S. , VICARI M. , BALL J. P. , RAKOCEVIC T. , ZAHEER S. , HIK D. S. , BAZELY D. R. 
Published: July 2006

Summary

Standard visual screening methods for determining the qualitative and quantitative presence of fungal endophytes are too time‐consuming for large‐scale ecological studies.
We investigated whether commercially available immunoblot kits, using monoclonal antibody techniques and designed for rapid‐screening of the presence of Neotyphodium endophytes in fresh samples of the pasture grasses Festuca arundinacea and Lolium perenne, could be used for Neotyphodium detection using other grasses and preserved samples. We also determined whether immunoblot kits could provide quantitative information about the amount of Neotyphodium in the grass.
The kits accurately detected endophyte presence in F. rubra, F. ovina, F. pratensis and F. altaica, in both preserved samples (dried and fixed), including 12‐year‐old stored, dried samples of F. rubra.
Endophytes were detected in 7‐day‐old seedlings of Lolium perenne, 3 days (30%) earlier than previously recognized.
The intensity of the coloured tissue prints on scanned immunoblot cards was significantly positively correlated with hyphal density, demonstrating a previously unrecognized accurate quantitative application.
These findings greatly reduce logistical barriers to large‐scale field research into the broader ecological significance of Neotyphodium in temperate and arctic grasses in non‐agricultural ecosystems (particularly in remote areas) and suggest potential for estimating historical infection rates using stored and herbarium specimens.
The percentage of gutta‐percha‐filled area in simulated curved canals when filled using Endo Twinn, a new heat device source
Authors: Pagavino G. , Giachetti L. , Nieri M. , Giuliani V. , Russo D. Scaminaci 
Published: July 2006

AbstractAim  To compare the percentage of gutta‐percha‐filled area (PGP) in simulated root canals when varying the penetration depth and function of the pluggers (heat versus heat plus vibration) using Endo Twinn.Methodology  Sixty‐four resin blocks with simulated 34–35° curved canals were randomly divided into two groups in order to obtain two canal shapes: group A with 0.8 taper and group B with 0.4 taper. The apical portion of each canal was prepared to a size 20 K‐file. The canals were filled with gutta‐percha in combination with a root canal sealer. In each group 16 canals were filled using the Endo Twinn heat function and 16 canals by means of both the heat and the vibration function. All samples were sectioned horizontally at three levels (1.25, 2.5 and 4.0 mm from the working length) and the PGP was measured. Data were analysed using anova test.Results  At the 1.25 mm level PGP was significantly greater using the vibration function (P = 0.0329) and in 0.8 taper canals (P < 0.0001). At the 2.5 mm level the PGP was greater in the canals with 0.8 taper compared with a 0.4 taper with or without vibration (vibration, P = 0.0056; interaction taper‐vibration, P = 0.0020). In 0.4 taper canals the PGP was greater when the vibration function was activated. At the 4 mm level in 0.8 taper canals there was no significant difference in PGP with or without the vibration (P = 0.6742).Conclusions  0.8 taper canals had significantly greater PGP than 0.4 taper canals. At the 1.25 mm level there was significantly greater PGP when the vibration function was activated.
An ex vivo comparison of three different gutta‐percha cones when compacted at different temperatures: rheological considerations in relation to the filling of lateral canals
Authors: Venturi M. , Di Lenarda R. , Breschi L. 
Published: July 2006

AbstractAim  To compare ex vivo the penetration of three brands of gutta‐percha cones, compacted under a constant force and heated to different temperatures, into artificial lateral canals.Methodology  Resin blocks with simulated main canals, each having two lateral canals (C at 6.5 and A at 13 mm from the surface of the resin block), were selected. A gutta‐percha cone, either Mynol MF, Hygenic MF or GT Tulsa 0.04 was compacted into each main canal for 5 s using a wire rod with a diameter of 0.7 mm soldered to the bottom of a metal cylinder, with a force of 2.7 kg at controlled temperatures of 37, 42, 47, 52, 60 °C. The penetration of each brand of gutta‐percha into 60 lateral canals (10 at each temperature) was measured using a stereomicroscope. Statistical analysis was performed using the anova, the Scheffè test and the t‐test.Results  None of the three brands of cones entered up to 0.1 mm within either lateral canal until a temperature of 47 °C was reached; at that temperature only Mynol cones (P ≤ 0.05) penetrated in four of 10 A‐level canals (mean 0.13 ± 0.19 mm) and in all 10 C‐level canals (mean 0.43 ± 0.12 mm).The A‐level lateral canals were penetrated at 52 °C by Mynol cones (mean 0.76 ± 0.34 mm) to a significantly greater distance (P ≤ 0.05) than Tulsa cones (mean 0.31 ± 0.12 mm) and Hygenic cones (mean 0.11 ± 0.08 mm). At 60 °C the Mynol cones (mean 1.93 ± 0.34 mm) penetrated significantly more (P ≤ 0.05) than the Tulsa cones (mean 0.86 ± 0.22 mm) and Hygenic cones (mean 0.67 ± 0.19 mm). The C‐level lateral canals were penetrated at 52 °C by Mynol cones (mean 0.91 ± 0.29 mm) to a significantly greater distance (P ≤ 0.05) than Tulsa cones (mean 0.47 ± 0.16 mm) and Hygenic cones (mean 0.46 ± 0.15 mm), whilst no significant difference was found at 60 °C.Conclusions  When heated and compacted, the three gutta‐percha cones penetrated the lateral canals to different degrees. They penetrated more than 0.43 mm into the lateral canals only at temperatures higher than 47 °C.
Confidence intervals in Cavalieri sampling
Authors: GARCÍA‐FIÑANA M. 
Published: July 2006

SummaryThe aim of this study is to derive a formula that allows the prediction, from a Cavalieri data sample, of an appropriate confidence interval for a parameter Q. Two different approaches are used to address the problem. The first approach is to investigate whether the asymptotic distribution of the Cavalieri estimator exists when the sampling period T tends to zero. In particular, the distribution of the standardized version of the Cavalieri estimator zT is analysed for a measurement function f whose smoothness constant is an integer number m. The analysis reveals that when the first noncontinuous derivative of f, f(m), exhibits a unique discontinuity, the asymptotic distribution of zT exists and it has a bounded support. An analytical expression of the distribution is derived for the cases m = 0 and 1. However, when f(m) has two or more discontinuities, the asymptotic distribution of zT does not exist and its support may be unbounded. In the second approach, a generalized version of the refined Euler Mac‐Laurin summation formula, valid for measurement functions with a fractional, rather than just an integer, smoothness constant, is applied to the Cavalieri estimator. As a result, a formula that predicts a lower and upper bound for the true parameter is derived for small T. This bound prediction formula is applied to Cavalieri data samples of human cerebral cortex. In particular, for sample sizes n = 8, 12 and 16, the true volume of cerebral cortex is bounded by relative distances 8%, 4% and 2% of the Cavalieri estimate, respectively.
New variance expressions for systematic sampling: the filtering approach
Authors: GUAL‐ARNAU XIMO , CRUZ‐ORIVE LUIS M. 
Published: July 2006

SummaryWe present a collection of variance models for estimators obtained by geometric systematic sampling with test points, quadrats, and n‐boxes in general, on a bounded domain in n‐dimensional Euclidean space ℝn, n = 1, 2, ... , and for systematic rays and sectors on the circle. The approach adopted − termed the filtering approach − is new and different from the current transitive approach. This report is only preliminary, however, because it includes only variance models in terms of the covariogram of the measurement function. The estimation step is in preparation.
Using biased image analysis for improving unbiased stereological number estimation – a pilot simulation study of the smooth fractionator
Authors: GARDI J. E. , NYENGAARD J. R. , GUNDERSEN H. J. G. 
Published: July 2006

SummaryThe smooth fractionator was introduced in 2002. The combination of a smoothing protocol with a computer‐aided stereology tool provides better precision and a lighter workload. This study uses simulation to compare fractionator sampling based on the smooth design, the commonly used systematic uniformly random sampling design and the ordinary simple random sampling design. The smooth protocol is performed using biased information from crude (but fully automatic) image analysis of the fields of view. The different design paradigms are compared using simulation in three different cell distributions with reference to sample size, noise and counting frame position. Regardless of clustering, sample size or noise, the fractionator based on a smooth design is more efficient than the fractionator based on a systematic uniform random design, which is more efficient than a fractionator based on simple random design. The fractionator based on a smooth design is up to four times more efficient than a simple random design.
A new fractionator principle with varying sampling fractions: exemplified by estimation of synapse number using electron microscopy
Authors: WITGEN B. M. , GRADY M. S. , NYENGAARD J. R. , GUNDERSEN H. J. G. 
Published: July 2006

SummaryThe quantification of ultrastructure has been permanently improved by the application of new stereological principles. Both precision and efficiency have been enhanced. Here we report for the first time a fractionator method that can be applied at the electron microscopy level. This new design incorporates a varying sampling fraction paradigm. The method allows for systematic random sampling from blocks of variable slab thickness, thereby eliminating the need for exhaustive serial sectioning through an entire containing space. This novel approach acknowledges the inaccuracy inherent in estimating the total object number using section sampling fractions based on the average thickness of sections of variable thicknesses. As an alternative, this approach estimates the correct particle section sampling probability based on an estimator of the Horvitz–Thompson type, resulting in a theoretically more satisfying and accurate estimate of the expected number of particles for the defined containing space.
Prediction of the variance of stereological volume estimates from systematic sections using computer‐intensive methods
Authors: MATTFELDT TORSTEN 
Published: July 2006

AbstractThe Cavalieri method is an unbiased estimator of the total volume of a body from its transectional areas on systematic sections. The coefficient of error (CE) of the Cavalieri estimator was predicted by a computer‐intensive method. The method is based on polynomial regression of area values on section number and simulation of systematic sectioning. The measurement function is modelled as a quadratic polynomial, with an error term superimposed. The relative influence of the trend and the error component is estimated by techniques of analysis of variance. This predictor was compared with two established short‐cut estimators of the CE based on transitive theory. First, all predictors were applied to data sets from six deterministic models with analytically known CE. For these models, the CE was best predicted by the older short‐cut estimator and by the computer‐intensive approach, if the measurement function had finite jumps. The best prediction was provided by the newer short‐cut estimator when the measurement function was continuous. The predictors were also applied to published empirical datasets. The first data set consisted of 10 series of areas of systematically sectioned rat hearts with 10–13 items, the second data set consisted of 13 series of systematically sampled transectional areas of various biological structures with 38–90 items. On the whole, similar mean values for the predicted CE were obtained with the older short‐cut estimator and the computer‐intensive method. These ranged in the same order of magnitude as resampling estimates of the CE from the empirical data sets, which were used as a cross‐check. The mean values according to the newer short‐cut CE estimator ranged distinctly lower than the resampling estimates. However, for individual data sets, it happened that the closest prediction as compared to the cross‐check value could be provided by any of the three methods. This finding is discussed in terms of the statistical variability of the resampling estimate itself.
A note on the stereological implications of irregular spacing of sections
Authors: BADDELEY A. , DORPH‐PETERSEN K.A. , VEDEL JENSEN E.B. 
Published: July 2006

SummaryStereological methods for serial sections traditionally assume that the sections are exactly equally spaced. In reality, the spacing and thickness of sections can be quite irregular. This may affect the validity and accuracy of stereological techniques, especially the Cavalieri estimator of volume. We present a new formula for the accuracy of the Cavalieri estimator that includes the effect of random variability in section spacing. A modest amount of variability in section spacing can cause a substantial increase in estimator variance.
Precision of stereological planar area predictors
Authors: KIÊU KIÊN , MORA MARIANNE 
Published: July 2006

SummaryTotal planar area can be estimated based on sampling by a lattice of figures (e.g. point patterns, line segments, quadrats). General formulae are provided for the approximation of mean squared errors. The approximation formulae are products of the boundary length and of a parameter that depends only on the sampling scheme. An R package is provided by the authors for the numerical computation of the mean squared error formulae. The speed of convergence of the mean squared error approximation is assessed on the basis of several simulations. Several sampling schemes are compared in view of the approximated mean squared errors.
On error prediction in circular systematic sampling
Authors: JÓNSDÓTTIR K. Ý. , HOFFMANN L. M. , HOBOLTH A. , VEDEL JENSEN E. B. 
Published: July 2006

SummaryAn extended covariogram model is discussed for estimating the precision of circular systematic sampling. The extension is motivated by recent developments in shape analysis of featureless planar objects. Preliminary simulation results indicate that it is important to consider the extended covariogram model.
Optimized HREM imaging of objects supported by amorphous substrates using spherical aberration adjustment
Authors: ALLSOP NICHOLAS A. , DOBSON PETER J. , HUTCHISON JOHN L. 
Published: July 2006

SummaryHigh Resolution Electron Microscopy (HREM) is often used to characterize objects supported by amorphous substrates, usually amorphous carbon. HREM is currently undergoing step change in performance due to aberration correctors. This paper examines the aberration corrected imaging of objects supported by amorphous substrates. In particular, we show that a substantial increase in the ratio of the object contrast to the substrate contrast can be achieved by utilizing the strong variation of phase contrast with height, which is present when the spherical aberration has been adjusted to a small value. This variation is examined using the familiar Weak Phase Object Approximation model from which it is determined that the contrast ratio achieves a maximum at a small nonzero value of the spherical aberration. This result is confirmed by multislice modelling which allows for deviations from the Weak Phase Object Approximation and delocalization effects. One important practical result of this study is the need to place the object of interest on the correct side of the amorphous carbon substrate.
Hard X‐ray microscopy with Zernike phase contrast
Authors: YOUN HWA SHIK , JUNG SUK‐WON 
Published: July 2006

SummaryZernike phase contrast has been added to a full‐field X‐ray microscope with Fresnel zone plates that was in operation at 6.95 keV. The spatial resolution has also been improved by increasing the magnification of the microscope objective looking at the CsI(Tl) scintillation crystal. Cu no. 2000 meshes and a zone plate have been imaged to see the contrast as well as the spatial resolution. A Halo effect coming from the Zernike phase contrast was clearly visible on the images of meshes.
Angular distribution of polarized photon‐pairs in a scattering medium with a Zeeman laser scanning confocal microscope
Authors: CHANG H. F. , CHOU C. , YAU H. F. , CHAN Y. H. , YIH J. N. , WU J. S. 
Published: July 2006

SummaryA novel confocal microscope designed for use with turbid media is proposed. We use a Zeeman laser as the light source. Based on the properties of two‐frequency polarized photon‐pairs and the common‐path feature of polarized photon‐pairs with heterodyne detection employed in the proposed confocal microscope, three gatings (spatial filtering gating, polarization gating and spatial coherence gating) are thus simultaneously incorporated in the microscope. Experimental results for the angular distribution of polarized photon‐pairs in a scattering medium indicate that polarization gating and spatial coherence gating preclude the detection of multiply scattered photons, whereas the pinhole selects the least scattered photon‐pairs. Thus, better performance for axial resolution than can be obtained with a conventional confocal microscope is demonstrated experimentally. In addition, the proposed microscope is able to either look deeper into a turbid medium or work with a denser medium; furthermore, the axial resolution is improved.
Characterization of intact subcellular bodies in whole bacteria by cryo‐electron tomography and spectroscopic imaging
Authors: COMOLLI L. R. , KUNDMANN M. , DOWNING K. H. 
Published: July 2006

SummaryWe illustrate the combined use of cryo‐electron tomography and spectroscopic difference imaging in the study of subcellular structure and subcellular bodies in whole bacteria. We limited our goal and focus to bodies with a distinct elemental composition that was in a sufficiently high concentration to provide the necessary signal‐to‐noise level at the relatively large sample thicknesses of the intact cell. This combination proved very powerful, as demonstrated by the identification of a phosphorus‐rich body in Caulobacter crescentus. We also confirmed the presence of a body rich in carbon, demonstrated that these two types of bodies are readily recognized and distinguished from each other, and provided, for the first time to our knowledge, structural information about them in their intact state. In addition, we also showed the presence of a similar type of phosphorus‐rich body in Deinococcus grandis, a member of a completely unrelated bacteria genus. Cryo‐electron microscopy and tomography allowed the study of the biogenesis and morphology of these bodies at resolutions better than 10 nm, whereas spectroscopic difference imaging provided a direct identification of their chemical composition.
Scleroderma in South Australia: further epidemiological observations supporting a stochastic explanation
Authors: Roberts‐Thomson P. J. , Walker J. G. , Lu T. Y.‐T. , Esterman A. , Hakendorf P. , Smith M. D. , Ahern M. J. 
Published: July 2006

AbstractBackground: The aim of this study was to determine the incidence, prevalence, survival and selective demographic characteristics of scleroderma occurring in South Australia over the 10‐year period 1993–2002.Methods: Analysis of the database of the South Australian Scleroderma Register: a population‐based register established in 1993. Patients with scleroderma resident in South Australia (n = 353 at 2002) were ascertained from multiple sources and clinical and demographic data were obtained from mailed questionnaire and from review of computerized hospital databases, case notes or referring letters. Time–space cluster analysis was carried out according to the Knox method. Control data were obtained from the Australian Bureau of Statistics census.Results: The mean prevalence was 21.4 per 105 (95% confidence interval 20.2–22.6) and the mean cumulative incidence of 1.5 per 105 (95% confidence interval 1.32–1.73) with no significant change in incidence over the study period (P = 0.13). Cumulative survival improved over the study period, with patients with diffuse disease having significantly reduced survival (as compared with limited disease, P < 0.001). The proportion with diffuse disease (∼22%) remained steady. There was a small but significant predisposition in patients with a continental European birthplace (P < 0.001). A family history of scleroderma was noted in 1.6% with λ1 (familial risk) of 14.3 (95% confidence interval 5.9–34.5). However, a family history of systemic autoimmunity (especially rheumatoid arthritis) was more common (6%). No socioeconomic stratification, temporal clustering nor spatio‐temporal clustering was observed either at time of initial symptom or at 10 years before disease onset.Conclusion: Scleroderma occurs relatively infrequently in South Australia with no significant change in incidence observed over the 10‐year study period. However, cumulative survival has improved. Identified risk factors include family history of scleroderma (risk ∼14‐fold), female sex (risk ∼5‐fold) and European birthplace (risk ∼2.5‐fold); however, the majority of the disease variance appears unexplained. A stochastic explanation based on genetic instability is favoured to explain this paradox.