ABCtoolbox: a versatile toolkit for approximate Bayesian computations

Background The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. Results Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. Conclusion ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.

How reliable are Hounsfield-unit measurements in forensic radiology?

OBJECTIVE: To assess the reliability of computed tomography (CT) numbers, also known as Hounsfield-units (HU) in the differentiation and identification of forensically relevant materials and to provide instructions to improve the reproducibility of HU measurements in daily forensic practice. MATERIALS AND METHODS: We scanned a phantom containing non-organic materials (glass, rocks and metals) on three different CT scanners with standardized parameters. The t-test was used to assess the influence of the scanner, the size and shape of different types of regions-of-interest (ROI), the composition and shape of the object, and the reader performance on HU measurements. Intra-class correlation coefficient was used to assess intra- and inter-reader reliability. RESULTS: HU values did not change significantly as a function of ROI-shape or -size (p>0.05). Intra-reader reliability reached ICC values >0.929 (p<0.001). Inter-reader reliability was also excellent with an ICC of 0.994 (p<0.001). Four of seven objects yielded significantly different CT numbers at different levels within the object (p<0.05). In 6/7 objects the HU changed significantly from CT scanner to CT scanner (p<0.05). CONCLUSION: Reproducible CT number measurements can be achieved through correct ROI-placement and repeat measurements within the object of interest. However, HU may differ from CT-scanner to CT-scanner. In order to obtain comparable CT numbers we suggest that a dedicated Forensic Reference Phantom be developed.

Radiologic identification of disaster victims: a simple and reliable method using CT of the paranasal sinuses

To assess the reliability of radiologic identification using visual comparison of ante and post mortem paranasal sinus computed tomography (CT).

Deglaciation records of 17O-excess in East Antarctica: reliable reconstruction of oceanic relative humidity from coastal sites

We measured δ17O and δ18O in two Antarctic ice cores at EPICA Dome C (EDC) and TALDICE (TD), respectively and computed 17O-excess with respect to VSMOW. The comparison of our 17O-excess data with the previous record obtained at Vostok (Landais et al., 2008) revealed differences up to 35 ppm in 17O-excess mean level and evolution for the three sites. Our data showed that the large increase depicted at Vostok (20 ppm) during the last deglaciation, is a regional and not a general pattern in the temporal distribution of 17O-excess in East Antarctica. The EDC data display an increase of 13 ppm, whereas the TD data show no significant variation from the Last Glacial Maximum (LGM) to the Early Holocene (EH). Lagrangian moisture source diagnostic revealed very different source regions for Vostok and EDC compared to TD. These findings combined with the results of a sensitivity analysis, using a Rayleigh-type isotopic model, suggest that relative humidity (RH) at the oceanic source region (OSR) are a determining factor for the spatial differences of 17O-excess in East Antarctica. However, 17O-excess in remote sites of continental Antarctica (e.g. Vostok) may be highly sensitive to local effects. Hence, we consider 17O-excess in coastal East Antarctic ice cores (TD) to be more reliable as a proxy for RH at the OSR.

Are endodontically treated incisors reliable abutments for zirconia-based fixed partial dentures in the esthetic zone?

This ex vivo pilot study tested the influence of defect extension and quartz-fiber post placement (QFP) on the ex vivo survival rate and fracture resistance of root-treated upper central incisors served as abutments for zirconia 2-unit cantilever fixed partial dentures (2U-FPDs) exposed to 10 years of simulated clinical function.

How reliable is Ki-67 immunohistochemistry in grade 2 breast carcinomas? A QA study of the Swiss Working Group of Breast- and Gynecopathologists

Adjuvant chemotherapy decisions in breast cancer are increasingly based on the pathologist's assessment of tumor proliferation. The Swiss Working Group of Gyneco- and Breast Pathologists has surveyed inter- and intraobserver consistency of Ki-67-based proliferative fraction in breast carcinomas. Methods Five pathologists evaluated MIB-1-labeling index (LI) in ten breast carcinomas (G1, G2, G3) by counting and eyeballing. In the same way, 15 pathologists all over Switzerland then assessed MIB-1-LI on three G2 carcinomas, in self-selected or pre-defined areas of the tumors, comparing centrally immunostained slides with slides immunostained in the different laboratoires. To study intra-observer variability, the same tumors were re-examined 4 months later. Results The Kappa values for the first series of ten carcinomas of various degrees of differentiation showed good to very good agreement for MIB-1-LI (Kappa 0.56–0.72). However, we found very high inter-observer variabilities (Kappa 0.04–0.14) in the read-outs of the G2 carcinomas. It was not possible to explain the inconsistencies exclusively by any of the following factors: (i) pathologists' divergent definitions of what counts as a positive nucleus (ii) the mode of assessment (counting vs. eyeballing), (iii) immunostaining technique, and (iv) the selection of the tumor area in which to count. Despite intensive confrontation of all participating pathologists with the problem, inter-observer agreement did not improve when the same slides were re-examined 4 months later (Kappa 0.01–0.04) and intra-observer agreement was likewise poor (Kappa 0.00–0.35). Conclusion Assessment of mid-range Ki-67-LI suffers from high inter- and intra-observer variability. Oncologists should be aware of this caveat when using Ki-67-LI as a basis for treatment decisions in moderately differentiated breast carcinomas.

How reliable and safe is full-body low-dose radiography (LODOX Statscan) in detecting foreign bodies ingested by adults?

OBJECTIVE: Foreign body ingestion is common and potentially lethal. This study evaluates the use of low-dose Statscans (LODOX) in emergency departments. DESIGN: This comparative cross-sectional study retrospectively assessed 28 289 digital chest x-rays and 2301 LODOX scans performed between 2006 and 2010 at a tertiary emergency centre. The radiographic appearance, image quality and location of ingested foreign bodies were evaluated in standard digital chest and LODOX radiography. The mean irradiation (μSv) and cumulative mean radiation dose per patient with the ingested foreign body were calculated according to literature-based data, together with the sensitivity and specificity for each modality. RESULTS: A total of 62 foreign bodies were detected in 39 patients, of whom 19 were investigated with LODOX and 20 with conventional digital chest radiography. Thirty-three foreign bodies were located in the two upper abdominal quadrants, 21 in the lower quadrants-which are not visible on conventional digital chest radiography-seven in the oesophagus and one in the bronchial system. The sensitivity and specificity of digital chest radiography were 44.4% and 94.1%, respectively, and for the LODOX Statscan 90% and 100%, respectively. The calculated mean radiation dose for LODOX investigations was 184 μS, compared with 524 μS for digital chest radiography. CONCLUSIONS: LODOX Statscan is superior to digital chest radiography in the diagnostic work-up of ingested foreign bodies because it makes it possible to enlarge the field of view to the entire body, has higher sensitivity and specificity, and reduces the radiation dose by 65%.

Microsurgery and liver research: Lumbricus terrestris, a reliable animal model for training?

Experiments using animal models are the most common way to learn microsurgery. This expertise is necessary for liver research, microsurgical reconstruction of the esophagus by free jejunum or reconstruction of the hepatic artery during reimplantation from living donors. The goal of this prospective study is to assess the reliability of an invertebrate model for microsurgical training.

Deglaciation records of 17O-excess in East Antarctica: reliable reconstruction of oceanic normalized relative humidity from coastal sites

We measured δ17O and δ18O in two Antarctic ice cores at EPICA Dome C (EDC) and TALDICE (TD), respectively, and computed 17O-excess with respect to VSMOW. The comparison of our 17O-excess data with the previous record obtained at Vostok (Landais et al., 2008a) revealed differences up to 35 ppm in 17O-excess mean level and evolution for the three sites. Our data show that the large increase depicted at Vostok (20 ppm) during the last deglaciation is a regional and not a general pattern in the temporal distribution of 17O-excess in East Antarctica. The EDC data display an increase of 12 ppm, whereas the TD data show no significant variation from the Last Glacial Maximum (LGM) to the Early Holocene (EH). A Lagrangian moisture source diagnostic revealed very different source regions for Vostok and EDC compared to TD. These findings combined with the results of a sensitivity analysis, using a Rayleigh-type isotopic model, suggest that normalized relative humidity (RHn) at the oceanic source region (OSR) is a determining factor for the spatial differences of 17O-excess in East Antarctica. However, 17O-excess in remote sites of continental Antarctica (e.g. Vostok) may be highly sensitive to local effects. Hence, we consider 17O-excess in coastal East Antarctic ice cores (TD) to be more reliable as a proxy for RHn at the OSR.