Ontogeny of the spheno‐occipital synchondrosis in a modern Queensland,Australian population using computed tomography

Due to disparity regarding the age at which skeletal maturation of the spheno‐occipital synchondrosis occurs in forensic and biological literature, this study provides recalibrated multislice computed tomography (MSCT) age standards for the Australian (Queensland) population, using a Bayesian statistical approach. The sample comprises retrospective cranial/cervical MSCT scans obtained from 448 males and 416 females aged birth to 20 years from the Skeletal Biology and Forensic Anthropology Research Osteological Database. Fusion status of the synchondrosis was scored using a modified six‐stage scoring tier on an MSCT platform, with negligible observer error (κ = 0.911 ± 0.04, intraclass correlation coefficient = 0.994). Bayesian transition analysis indicates that females are most likely to transition to complete fusion at 13.1 years and males at 15.6 years. Posterior densities were derived for each morphological stage, with complete fusion of the synchondrosis attained in all Queensland males over 16.3 years of age and females aged 13.8 years and older. The results demonstrate significant sexual dimorphism in synchondrosis fusion and are suggestive of intrapopulation variation between major geographic regions in Australia. This study contributes to the growing repository of contemporary anthropological standards calibrated for the Queensland milieu to improve the efficacy of the coronial process for medicolegal death investigation. As a stand‐alone age indicator, the basicranial synchondrosis may be consulted as an exclusion criterion when determining the age of majority that constitutes 17 years in Queensland forensic practice. Am J Phys Anthropol 157:42–57, 2015. © 2014 Wiley Periodicals, Inc.     

Age-at-death estimation in an Italian historical sample: A test of the Suchey-Brooks and transition analysis methods

A growing body of research is demonstrating increased accuracy in aging from a relatively new method, transition analysis. Although transition analysis was developed for paleodemographic research, a majority of subsequent studies have been in the forensic arena, with very little work in bioarchaeological contexts. Using the Suchey‐Brooks pubic symphysis phases, scored on a target sample of historic Italians from the island of Sardinia, we compare accuracy of aging between transition analysis combined with a Bayesian approach and the standard Suchey‐Brooks age ranges. Because of the difficulty in identifying a reasonable informative prior for bioarchaeological samples, we also compared results of both an informative prior and a uniform prior for age estimation. Published ages‐of‐transition for the Terry Collection and Balkan genocide victims were used in conjunction with parameters generated from Gompertz hazard models derived from the priors. The ages‐of‐transition and hazard parameters were utilized to calculate the highest posterior density regions, otherwise known as “coverages” or age ranges, for each Suchey‐Brooks phase. Each prior, along with the parameters, were input into cumulative binomial tests. The results indicate that the Bayesian approach outperformed the Suchey‐Brooks technique alone. The Terry Collection surpassed the Balkans as a reasonable sample from which to derive transition analysis parameters. This discrepancy between populations is due to different within phase age‐at‐death distributions that reflect differences in aging between the populations. These results indicate bioarchaeologists should strive to apply a Bayesian analysis when aging historic and archaeological populations by employing an informative prior. Am J Phys Anthropol 149:259–265, 2012. © 2012 Wiley Periodicals, Inc.     

A revised method of age determination using the os pubis, with a review and tests of accuracy of other current methods of pubic symphyseal aging

All current standardized methods of age determination using the os pubis were tested by blind assessment of a skeletal sample with documented ages (from the Todd collection; N = 96). No demographic data (sex, age, race, age composition) were known to the assessors prior to completion of the test. Results showed the Todd method to be more reliable than more recent component techniques and that all systems tended to underage. Therefore, modifications were made of the Todd system to eliminate this and other deficiencies, and a second test using a new sample was conducted (N = 109). The age distribution determined by the revised Todd method did not significantly differ from the actual age distribution of the second sample. Error due to race was nonsignificant. Biological stages of pubic metamorphosis are described and possible evolutionary specializations of the hominid symphysis are discussed. Revised standards for age determination are presented.     

A precise and non-destructive method to calculate the surface area in living scleractinian corals using X-ray computed tomography and 3D modeling

The surface area of corals represents a major reference parameter for the standardization of flux rates, for coral growth investigations, and for investigations of coral metabolism. The methods currently used to determine the surface area of corals are rather approximate approaches lacking accuracy, or are invasive and often destructive methods that are inapplicable for experiments involving living corals. This study introduces a novel precise and non-destructive technique to quantify surface area in living coral colonies by applying computed tomography (CT) and subsequent 3D reconstruction. Living coral colonies of different taxa were scanned by conventional medical CT either in air or in sea water. Resulting data volumes were processed by 3D modeling software providing realistic 3D coral skeleton surface reconstructions, thus enabling surface area measurements. Comparisons of CT datasets obtained from calibration bodies and coral colonies proved the accuracy of the surface area determination. Surface area quantifications derived from two different surface rendering techniques applied for scanning living coral colonies showed congruent results (mean deviation ranging from 1.32 to 2.03%). The validity of surface area measurement was verified by repeated measurements of the same coral colonies by three test persons. No significant differences between all test persons in all coral genera and in both surface rendering techniques were found (independent sample t-test: all n.s.). Data analysis of a single coral colony required approximately 15 to 30 min for a trained user using the isosurface technique regardless of the complexity and growth form of the latter, rendering the method presented in this study as a time-saving and accurate method to quantify surface areas in both living coral colonies and bare coral skeletons. Communicated by Biology Editor Dr Michael Lesser     

Assessment of temporal resolution of multi-detector row computed tomography in helical acquisition mode using the impulse method

The purpose of this study was to propose a method for assessing the temporal resolution (TR) of multi-detector row computed tomography (CT) (MDCT) in the helical acquisition mode using temporal impulse signals generated by a metal ball passing through the acquisition plane. An 11-mm diameter metal ball was shot along the central axis at approximately 5 m/s during a helical acquisition, and the temporal sensitivity profile (TSP) was measured from the streak image intensities in the reconstructed helical CT images. To assess the validity, we compared the measured and theoretical TSPs for the 4-channel modes of two MDCT systems. A 64-channel MDCT system was used to compare TSPs and image quality of a motion phantom for the pitch factors P of 0.6, 0.8, 1.0 and 1.2 with a rotation time R of 0.5 s, and for two R/P combinations of 0.5/1.2 and 0.33/0.8. Moreover, the temporal transfer functions (TFs) were calculated from the obtained TSPs. The measured and theoretical TSPs showed perfect agreement. The TSP narrowed with an increase in the pitch factor. The image sharpness of the 0.33/0.8 combination was inferior to that of the 0.5/1.2 combination, despite their almost identical full width at tenth maximum values. The temporal TFs quantitatively confirmed these differences. The TSP results demonstrated that the TR in the helical acquisition mode significantly depended on the pitch factor as well as the rotation time, and the pitch factor and reconstruction algorithm affected the TSP shape.     

Incorporating capture heterogeneity in the estimation of autoregressive coefficients of animal population dynamics using capture–recapture data

Population dynamic models combine density dependence and environmental effects. Ignoring sampling uncertainty might lead to biased estimation of the strength of density dependence. This is typically addressed using state‐space model approaches, which integrate sampling error and population process estimates. Such models seldom include an explicit link between the sampling procedures and the true abundance, which is common in capture–recapture settings. However, many of the models proposed to estimate abundance in the presence of capture heterogeneity lead to incomplete likelihood functions and cannot be straightforwardly included in state‐space models. We assessed the importance of estimating sampling error explicitly by taking an intermediate approach between ignoring uncertainty in abundance estimates and fully specified state‐space models for density‐dependence estimation based on autoregressive processes. First, we estimated individual capture probabilities based on a heterogeneity model for a closed population, using a conditional multinomial likelihood, followed by a Horvitz–Thompson estimate for abundance. Second, we estimated coefficients of autoregressive models for the log abundance. Inference was performed using the methodology of integrated nested Laplace approximation (INLA). We performed an extensive simulation study to compare our approach with estimates disregarding capture history information, and using R‐package VGAM, for different parameter specifications. The methods were then applied to a real data set of gray‐sided voles Myodes rufocanus from Northern Norway. We found that density‐dependence estimation was improved when explicitly modeling sampling error in scenarios with low process variances, in which differences in coverage reached up to 8% in estimating the coefficients of the autoregressive processes. In this case, the bias also increased assuming a Poisson distribution in the observational model. For high process variances, the differences between methods were small and it appeared less important to model heterogeneity.     

A test of the central–marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)

The central–marginal hypothesis (CMH) predicts that population size, genetic diversity and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core‐to‐edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core‐to‐edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean centre on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core‐to‐edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.     

Temporal resolution measurement of 128-slice dual source and 320-row area detector computed tomography scanners in helical acquisition mode using the impulse method

PurposeTo analyse the temporal resolution (TR) of modern computed tomography (CT) scanners using the impulse method, and assess the actual maximum TR at respective helical acquisition modes.MethodsTo assess the actual TR of helical acquisition modes of a 128-slice dual source CT (DSCT) scanner and a 320-row area detector CT (ADCT) scanner, we assessed the TRs of various acquisition combinations of a pitch factor (P) and gantry rotation time (R).ResultsThe TR of the helical acquisition modes for the 128-slice DSCT scanner continuously improved with a shorter gantry rotation time and greater pitch factor. However, for the 320-row ADCT scanner, the TR with a pitch factor of <1.0 was almost equal to the gantry rotation time, whereas with pitch factor of >1.0, it was approximately one half of the gantry rotation time. The maximum TR values of single- and dual-source helical acquisition modes for the 128-slice DSCT scanner were 0.138 (R/P = 0.285/1.5) and 0.074 s (R/P = 0.285/3.2), and the maximum TR values of the 64 × 0.5- and 160 × 0.5-mm detector configurations of the helical acquisition modes for the 320-row ADCT scanner were 0.120 (R/P = 0.275/1.375) and 0.195 s (R/P = 0.3/0.6), respectively.ConclusionBecause the TR of a CT scanner is not accurately depicted in the specifications of the individual scanner, appropriate acquisition conditions should be determined based on the actual TR measurement.     

Association of the SNP rs2623047 in the HSPG modification enzyme SULF1 with an Australian Caucasian Breast Cancer Cohort

Breast cancer is the second most common cancer worldwide and the most common cancer reported in women. This malignant tumour is characterised by a number of specific features including uncontrolled cell proliferation. It ranks fifth in the world as a cause of cancer death overall in developed countries and is the second most frequent cause of cancer death in women. Early diagnosis increases 5-year survival rates up to 95%. Heparan sulfate proteoglycans (HSPGs) are complex proteins composed of a core protein to which a number of highly sulfated side chains attach, ubiquitous to the cell surface and within the extracellular matrix. HSPG side chains are synthesised by a highly co-ordinated process resulting in distinct sulfation patterns, which determine specific interactions with cell-signalling partners including growth factors, their receptors, ligands and morphogens. The enzymes responsible for chain initiation, elongation and sulfation are critical for creating HS chain variability conferring biological functionality. This study investigated a single nucleotide polymorphism in SULF1, the enzyme responsible for the 6-O desulfation of heparan sulfate side chains. We investigated this SNP in an Australian Caucasian case–control breast cancer population and found a significant association between SULF1 and breast cancer at both the allelic and genotypic levels (allele, p = 0.016; genotype, p = 0.032). Our results suggest that the rs2623047 SNP in SULF1 may impact breast cancer susceptibility. Specifically, the T allele of rs2623047 in SULF1 is associated with an increased risk of developing breast cancer in our cohort. The identification of markers including SULF1 may improve detection of this disease at its earliest stages improving patient treatment and prognosis.     

Temporal–spatial distribution of an island‐based offshore population of common bottlenose dolphins (Tursiops truncatus) in the equatorial Atlantic

A little‐studied common bottlenose dolphin (Tursiops truncatus) population inhabits the offshore waters surrounding Saint Paul's Rocks, a Brazilian marine protected area in the equatorial Atlantic Ocean. Five field expeditions (May 2011–May 2013) were conducted to characterize the habitat use, population size, and site fidelity of this population. Three different survey methods were employed: line‐transect surveys, land‐based surveys, and photo‐identification surveys. A population size of 23 individuals (19–28, CI 95%), which were present on most sampling days (>90% of surveys), was estimated. The maximum resighting interval of photo‐identified animals was 9 yr and 3 mo for five distinct individuals, based on data from nonsystematic efforts that have been ongoing since 2004. The dolphins exhibited strong site fidelity, as the minimum convex polygon (MCP, 95%) method revealed that they restricted their movements to a 0.5 km² area across seasons and a 0.99 km² area across years (95% kernel). The dolphins preferred shallow waters close to the archipelago (<1.2 km from the islands), especially on the eastern and southeastern sides, where oceanographic models have revealed persistent upwelling that may result from underwater currents and where food may be more predictably available.     

Showcasing the application of synchrotron‐based X‐ray computed tomography in host–pathogen interactions: The role of wheat rachilla and rachis nodes in Type‐II resistance to Fusarium graminearum

Fusarium head blight, caused primarily by Fusarium graminearum (Fg), is one of the most devastating diseases of wheat. Host resistance in wheat is classified into five types (Type‐I to Type‐V), and a majority of moderately resistant genotypes carry Type‐II resistance (resistance to pathogen spread in the rachis) alleles, mainly from the Chinese cultivar Sumai 3. Histopathological studies in the past failed to identify the key tissue in the spike conferring resistance to pathogen spread, and most of the studies used destructive techniques, potentially damaging the tissue(s) under study. In the present study, nondestructive synchrotron‐based phase contrast X‐ray imaging and computed tomography techniques were used to confirm the part of the wheat spike conferring Type‐II resistance to Fg spread, thus showcasing the application of synchrotron‐based techniques to image host–pathogen interactions. Seven wheat genotypes of moderate resistance to Fusarium head blight were studied for changes in the void space volume fraction and grayscale/voxel intensity following Fg inoculation. Cell‐wall biopolymeric compounds were quantified using Fourier‐transform midinfrared spectroscopy for all genotype‐treatment combinations. The study revealed that the rachilla and rachis nodes together are structurally important in conferring Type‐II resistance. The structural reinforcement was not necessarily observed from lignin deposition but rather from an unknown mechanism.     

Validated method for the therapeutic drug monitoring of flunitrazepam in human serum using liquid chromatography–atmospheric pressure chemical ionization tandem mass spectrometry with an ion trap detector

An HPLC–MS–MS method for the quantitative analysis of flunitrazepam in human serum was established. The method features a very simple liquid–liquid extraction, the use of a standard 4-mm HPLC column, isocratic elution using a buffer-free solvent, short retention times in connection with good peak resolution and the sensitivity and selectivity of an ion trap MS–MS detector. The procedure enables unambiguous identification of analytes by their product ion spectra, as well as sensitive quantitation (limit of quantitation for flunitrazepam=0.5 ng/ml). This feature was used for the confirmation of HPLC–UV results for nitrazepam.     

Cold‐adapted species in a warming world – an explorative study on the impact of high winter temperatures on a continental butterfly

Increasing evidence suggests that global warming significantly alters the range and phenology of plants and animals. Whereas thermophilous species usually benefit from rising temperatures, the living conditions of taxa adapted to cooler or continental climates are deteriorating. The woodland ringlet butterfly, Erebia medusa Fabricius (Lepidoptera: Nymphalidae) is one of the continental species that are supposed to be adversely affected by climate change, especially by rising winter temperatures. Here, we conduct an explorative study on the effects of low, moderate, and high winter temperatures on the pre‐adult and adult stages of E. medusa in a laboratory experiment. Compared to the two other temperature regimes, the warm winter treatment led to an earlier termination of diapause and higher larval weights at the end of the winter, but significantly lower survival rates. The after‐effects of the warm treatment included lower weight of the pupae and adult females, shorter forewings of adult males, and earlier emergence of both adult males and females. In natural environments, which are characterized by a much greater thermal variability and a much higher frequency of soil freeze‐thaw events compared to our experiment, the effects of rising winter temperatures might be stronger than in this study. Thus, we conclude that warmer winters pose a non‐negligible long‐term threat to E. medusa.     

Replication of an association of variation in the FOXO3A gene with human longevity using both case–control and longitudinal data

Genetic variation in FOXO3A has previously been associated with human longevity. Studies published so far have been case–control studies and hence vulnerable to bias introduced by cohort effects. In this study we extended the previous findings in the cohorts of oldest old Danes (the Danish 1905 cohort, N = 1089) and middle‐aged Danes (N = 736), applying a longitudinal study design as well as the case–control study design. Fifteen SNPs were chosen in order to cover the known common variation in FOXO3A. Comparing SNP frequencies in the oldest old with middle‐aged individuals, we found association (after correction for multiple testing) of eight SNPs; 4 (rs13217795, rs2764264, rs479744, and rs9400239) previously reported to be associated with longevity and four novel SNPs (rs12206094, rs13220810, rs7762395, and rs9486902 (corrected P‐values 0.001–0.044). Moreover, we found association of the haplotypes TAC and CAC of rs9486902, rs10499051, and rs12206094 (corrected P‐values: 0.01–0.03) with longevity. Finally, we here present data applying a longitudinal study design; when using follow‐up survival data on the oldest old in a longitudinal analysis, we found no SNPs to remain significant after the correction for multiple testing (Bonferroni correction). Hence, our results support and extent the proposed role of FOXO3A as a candidate longevity gene for survival from younger ages to old age, yet not during old age.     

Gas chromatographic method using nitrogen–phosphorus detection for the measurement of tramadol and its O-desmethyl metabolite in plasma and brain tissue of mice and rats

A method that allows the measurement of plasma and brain levels of the centrally-acting analgesic tramadol and its major metabolite (O-desmethyl tramadol) in mice and rats was developed using gas chromatography equipped with nitrogen–phosphorus detection (GC–NPD). Plasma samples were extracted with methyl tert.-butyl ether (MTBE) and were injected directly into the GC system. Brain tissue homogenates were precipitated with methanol, the resulting supernatant was dried then acidified with hydrochloric acid. The aqueous solution was washed with MTBE twice, alkalinized, and extracted with MTBE. The MTBE layer was dried, reconstituted and injected into the GC system. The GC assay used a DB-1 capillary column with an oven temperature ramp (135 to 179°C at 4°C/min). Dextromethorphan was used as the internal standard. The calibration curves for tramadol and O-desmethyl tramadol in plasma and brain tissue were linear in the range of 10 to 10 000 ng/ml (plasma) and ng/g (brain). Assay accuracy and precision of back calculated standards were within ±15%.