Virtual tissue alignment and cutting plane definition--a new method to obtain optimal longitudinal histological sections.

Histomorphometric evaluation of the buccal aspects of periodontal tissues in rodents requires reproducible alignment of maxillae and highly precise sections containing central sections of buccal roots; this is a cumbersome and technically sensitive process due to the small specimen size. The aim of the present report is to describe and analyze a method to transfer virtual sections of micro-computer tomographic (CT)-generated image stacks to the microtome for undecalcified histological processing and to describe the anatomy of the periodontium in rat molars. A total of 84 undecalcified sections of all buccal roots of seven untreated rats was analyzed. The accuracy of section coordinate transfer from virtual micro-CT slice to the histological slice, right-left side differences and the measurement error for linear and angular measurements on micro-CT and on histological micrographs were calculated using the Bland-Altman method, interclass correlation coefficient and the method of moments estimator. Also, manual alignment of the micro-CT-scanned rat maxilla was compared with multiplanar computer-reconstructed alignment. The supra alveolar rat anatomy is rather similar to human anatomy, whereas the alveolar bone is of compact type and the keratinized gingival epithelium bends apical to join the junctional epithelium. The high methodological standardization presented herein ensures retrieval of histological slices with excellent display of anatomical microstructures, in a reproducible manner, minimizes random errors, and thereby may contribute to the reduction of number of animals needed.

A new, fast and flexible radiative transfer method for Venus general circulation models

We present a new radiation scheme for the Oxford Planetary Unified Model System for Venus, suitable for the solar and thermal bands. This new and fast radiative parameterization uses a different approach in the two main radiative wavelength bands: solar radiation (0.1-5.5 mu m) and thermal radiation (1.7-260 mu m). The solar radiation calculation is based on the delta-Eddington approximation (two-stream-type) with an adding layer method. For the thermal radiation case, a code based on an absorptivity/emissivity formulation is used. The new radiative transfer formulation implemented is intended to be computationally light, to allow its incorporation in 3D global circulation models, but still allowing for the calculation of the effect of atmospheric conditions on radiative fluxes. This will allow us to investigate the dynamical-radiative-microphysical feedbacks. The model flexibility can be also used to explore the uncertainties in the Venus atmosphere such as the optical properties in the deep atmosphere or cloud amount. The results of radiative cooling and heating rates and the global-mean radiative-convective equilibrium temperature profiles for different atmospheric conditions are presented and discussed. This new scheme works in an atmospheric column and can be easily implemented in 3D Venus global circulation models. (C) 2014 Elsevier Ltd. All rights reserved.

Validity of an automatic measure protocol in distal femur for allograft selection from a three-dimensional virtual bone bank system

Osteoarticular allograft is one possible treatment in wide surgical resections with large defects. Performing best osteoarticular allograft selection is of great relevance for optimal exploitation of the bone databank, good surgery outcome and patient’s recovery. Current approaches are, however, very time consuming hindering these points in practice. We present a validation study of a software able to perform automatic bone measurements used to automatically assess the distal femur sizes across a databank. 170 distal femur surfaces were reconstructed from CT data and measured manually using a size measure protocol taking into account the transepicondyler distance (A), anterior-posterior distance in medial condyle (B) and anterior-posterior distance in lateral condyle (C). Intra- and inter-observer studies were conducted and regarded as ground truth measurements. Manual and automatic measures were compared. For the automatic measurements, the correlation coefficients between observer one and automatic method, were of 0.99 for A measure and 0.96 for B and C measures. The average time needed to perform the measurements was of 16 h for both manual measurements, and of 3 min for the automatic method. Results demonstrate the high reliability and, most importantly, high repeatability of the proposed approach, and considerable speed-up on the planning.

Computed tomography (CT) virtual autopsy and classical autopsy discrepancies: radiologist's error or a demonstration of post-mortem multi-detector computed tomography (MDCT) limitation?

Modern imaging technologies, such as computed tomography (CT) techniques, represent a great challenge in forensic pathology. The field of forensics has experienced a rapid increase in the use of these new techniques to support investigations on critical cases, as indicated by the implementation of CT scanning by different forensic institutions worldwide. Advances in CT imaging techniques over the past few decades have finally led some authors to propose that virtual autopsy, a radiological method applied to post-mortem analysis, is a reliable alternative to traditional autopsy, at least in certain cases. The authors investigate the occurrence and the causes of errors and mistakes in diagnostic imaging applied to virtual autopsy. A case of suicide by a gunshot wound was submitted to full-body CT scanning before autopsy. We compared the first examination of sectional images with the autopsy findings and found a preliminary misdiagnosis in detecting a peritoneal lesion by gunshot wound that was due to radiologist's error. Then we discuss a new emerging issue related to the risk of diagnostic failure in virtual autopsy due to radiologist's error that is similar to what occurs in clinical radiology practice.

Sudden Death after Chest Pain: Feasibility of Virtual Autopsy with Postmortem CT Angiography and Biopsy

Purpose:To determine the potential of minimally invasive postmortem computed tomographic (CT) angiography combined with image-guided tissue biopsy of the myocardium and lungs in decedents who were thought to have died of acute chest disease and to compare this method with conventional autopsy as the reference standard.Materials and Methods:The responsible justice department and ethics committee approved this study. Twenty corpses (four female corpses and 16 male corpses; age range, 15-80 years), all of whom were reported to have had antemortem acute chest pain, were imaged with postmortem whole-body CT angiography and underwent standardized image-guided biopsy. The standard included three biopsies of the myocardium and a single biopsy of bilateral central lung tissue. Additional biopsies of pulmonary clots for differentiation of pulmonary embolism and postmortem organized thrombus were performed after initial analysis of the cross-sectional images. Subsequent traditional autopsy with sampling of histologic specimens was performed in all cases. Thereafter, conventional histologic and autopsy reports were compared with postmortem CT angiography and CT-guided biopsy findings. A Cohen k coefficient analysis was performed to explore the effect of the clustered nature of the data.Results:In 19 of the 20 cadavers, findings at postmortem CT angiography in combination with CT-guided biopsy validated the cause of death found at traditional autopsy. In one cadaver, early myocardial infarction of the papillary muscles had been missed. The Cohen κ coefficient was 0.94. There were four instances of pulmonary embolism, three aortic dissections (Stanford type A), three myocardial infarctions, three instances of fresh coronary thrombosis, three cases of obstructive coronary artery disease, one ruptured ulcer of the ascending aorta, one ruptured aneurysm of the right subclavian artery, one case of myocarditis, and one pulmonary malignancy with pulmonary artery erosion. In seven of 20 cadavers, CT-guided biopsy provided additional histopathologic information that substantiated the final diagnosis of the cause of death.Conclusion:Postmortem CT angiography combined with image-guided biopsy, because of their minimally invasive nature, have a potential role in the detection of the cause of death after acute chest pain.© RSNA, 2012.

Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray

Classical antibody-based serotyping of Escherichia coli is an important method in diagnostic microbiology for epidemiological purposes, as well as for a rough virulence assessment. However, serotyping is so tedious that its use is restricted to a few reference laboratories. To improve this situation we developed and validated a genetic approach for serotyping based on the microarray technology. The genes encoding the O-antigen flippase (wzx) and the O-antigen polymerase (wzy) were selected as target sequences for the O antigen, whereas fliC and related genes, which code for the flagellar monomer, were chosen as representatives for the H phenotype. Starting with a detailed bioinformatic analysis and oligonucleotide design, an ArrayTube-based assay was established: a fast and robust DNA extraction method was coupled with a site-specific, linear multiplex labeling procedure and hybridization analysis of the biotinylated amplicons. The microarray contained oligonucleotide DNA probes, each in duplicate, representing 24 of the epidemiologically most relevant of the over 180 known O antigens (O antigens 4, 6 to 9, 15, 26, 52, 53, 55, 79, 86, 91, 101, 103, 104, 111, 113, 114, 121, 128, 145, 157, and 172) as well as 47 of the 53 different H antigens (H antigens 1 to 12, 14 to 16, 18 to 21, 23 to 34, 37 to 43, 45, 46, 48, 49, 51 to 54, and 56). Evaluation of the microarray with a set of defined strains representing all O and H serotypes covered revealed that it has a high sensitivity and a high specificity. All of the conventionally typed 24 O groups and all of the 47 H serotypes were correctly identified. Moreover, strains which were nonmotile or nontypeable by previous serotyping assays yielded unequivocal results with the novel ArrayTube assay, which proved to be a valuable alternative to classical serotyping, allowing processing of single colonies within a single working day.

Estimation of sex and age of "virtual skeletons"--a feasibility study

This article presents a feasibility study with the objective of investigating the potential of multi-detector computed tomography (MDCT) to estimate the bone age and sex of deceased persons. To obtain virtual skeletons, the bodies of 22 deceased persons with known age at death were scanned by MDCT using a special protocol that consisted of high-resolution imaging of the skull, shoulder girdle (including the upper half of the humeri), the symphysis pubis and the upper halves of the femora. Bone and soft-tissue reconstructions were performed in two and three dimensions. The resulting data were investigated by three anthropologists with different professional experience. Sex was determined by investigating three-dimensional models of the skull and pelvis. As a basic orientation for the age estimation, the complex method according to Nemeskéri and co-workers was applied. The final estimation was effected using additional parameters like the state of dentition, degeneration of the spine, etc., which where chosen individually by the three observers according to their experience. The results of the study show that the estimation of sex and age is possible by the use of MDCT. Virtual skeletons present an ideal collection for anthropological studies, because they are obtained in a non-invasive way and can be investigated ad infinitum.

A new optical detection method to assess the erosion inhibition by in vitro salivary pellicle layer

OBJECTIVES Application of the recently developed optical method based on the monitoring of the specular reflection intensity to study the protective potential of the salivary pellicle layer against early enamel erosion. METHODS The erosion progression was compared between two treatment groups: enamel samples coated by the 15 h-in vitro-formed salivary pellicle layer (group P, n=90) and the non-coated enamel surfaces (control group C, n=90). Different severity of the erosive impact was modelled by the enamel incubation in 1% citric acid (pH=3.6) for 2, 4, 8, 10 or 15 min. Erosion quantification was performed by the optical method as well as by the microhardness and calcium release analyses. RESULTS Optical assessment of the erosion progression showed erosion inhibition by the in vitro salivary pellicle in short term acidic treatments (≤ 4 min) which was also confirmed by microhardness measurements proving significantly less (p<0.05) enamel softening in the group P at 2 and 4 min of erosion compared to the group C. SEM images demonstrated less etched enamel interfaces in the group P at short erosion durations as well. CONCLUSIONS Monitoring of the specular reflection intensity can be successfully applied to quantify early erosion progression in comparative studies. In vitro salivary pellicle (2h) provides erosion inhibition but only in short term acidic exposures. CLINICAL SIGNIFICANCE The proposed optical technique is a promising tool for the fast and non-invasive erosion quantification in clinical studies.

Radiographic and safety details of vertebral body stenting: results from a multicenter chart review

BACKGROUND Up to one third of BKP treated cases shows no appreciable height restoration due to loss of both restored height and kyphotic realignment after balloon deflation. This shortcoming has called for an improved method that maintains the height and realignment reached by the fully inflated balloon until stabilization of the vertebral body by PMMA-based cementation. Restoration of the physiological vertebral body height for pain relief and for preventing further fractures of adjacent and distant vertebral bodies must be the main aim for such a method. A new vertebral body stenting system (VBS) stabilizes the vertebral body after balloon deflation until cementation. The radiographic and safety results of the first 100 cases where VBS was applied are presented. METHODS During the planning phase of an ongoing international multicenter RCT, radiographic, procedural and followup details were retrospectively transcribed from charts and xrays for developing and testing the case report forms. Radiographs were centrally assessed at the institution of the first/senior author. RESULTS 100 patients (62 with osteoporosis) with a total of 103 fractured vertebral bodies were treated with the VBS system. 49 were females with a mean age of 73.2 years; males were 66.7 years old. The mean preoperative anterior-middle-posterior heights were 20.3-17.6-28.0 mm, respectively. The mean local kyphotic angle was 13.1[degree sign]. The mean preoperative Beck Index (anterior edge height/posterior edge height) was 0.73, the mean alternative Beck Index (middle height/posterior edge height) was 0.63. The mean postoperative heights were restored to 24.5-24.6-30.4 mm, respectively. The mean local kyphotic angle was reduced to 8.9[degree sign]. The mean postoperative Beck Index was 0.81, the mean alternative one was 0.82. The overall extrusion rate was 29.1%, the symptomatic one was 1%. In the osteoporosis subgroup there were 23.8% extrusions. Within the three months followup interval there were 9% of adjacent and 4% of remote new fractures, all in the osteoporotic group. CONCLUSIONS VBS showed its strengths especially in realignment of crush and biconcave fractures. Given that fracture mobility is present, the realignment potential is sound and increases with the severity of preoperative vertebral body deformation.

Development and Validation of a Fast and Homogeneous Cell-Based Fluorescence Screening Assay for Divalent Metal Transporter 1 (DMT1/SLC11A2) Using the FLIPR Tetra.

Divalent metal ion transporter 1 (DMT1) is a proton-coupled Fe(2+) transporter that is essential for iron uptake in enterocytes and for transferrin-associated endosomal iron transport in many other cell types. DMT1 dysfunction is associated with several diseases such as iron overload disorders and neurodegenerative diseases. The main objective of the present work is to develop and validate a fluorescence-based screening assay for DMT1 modulators. We found that Fe(2+) or Cd(2+) influx could be reliably monitored in calcium 5-loaded DMT1-expressing HEK293 cells using the FLIPR Tetra fluorescence microplate reader. DMT1-mediated metal transport shows saturation kinetics depending on the extracellular substrate concentration, with a K0.5 value of 1.4 µM and 3.5 µM for Fe(2+) and Cd(2+), respectively. In addition, Cd(2+) was used as a substrate for DMT1, and we find a Ki value of 2.1 µM for a compound (2-(3-carbamimidoylsulfanylmethyl-benzyl)-isothiourea) belonging to the benzylisothioureas family, which has been identified as a DMT1 inhibitor. The optimized screening method using this compound as a reference demonstrated a Z' factor of 0.51. In summary, we developed and validated a sensitive and reproducible cell-based fluorescence assay suitable for the identification of compounds that specifically modulate DMT1 transport activity.

Fourier transform infrared spectroscopy, a new method for rapid determination of total organic and inorganic carbon and biogenic silica concentration in lake sediments

Abstract We demonstrate the use of Fourier transform infrared spectroscopy (FTIRS) to make quantitative measures of total organic carbon (TOC), total inorganic carbon (TIC) and biogenic silica (BSi) concentrations in sediment. FTIRS is a fast and costeffective technique and only small sediment samples are needed (0.01 g). Statistically significant models were developed using sediment samples from northern Sweden and were applied to sediment records from Sweden, northeast Siberia and Macedonia. The correlation between FTIRS-inferred values and amounts of biogeochemical constituents assessed conventionally varied between r = 0.84–0.99 for TOC, r = 0.85– 0.99 for TIC, and r = 0.68–0.94 for BSi. Because FTIR spectra contain information on a large number of both inorganic and organic components, there is great potential for FTIRS to become an important tool in paleolimnology.

A hybrid method for large-scale short-term scheduling of make-and-pack production processes

Due to the ongoing trend towards increased product variety, fast-moving consumer goods such as food and beverages, pharmaceuticals, and chemicals are typically manufactured through so-called make-and-pack processes. These processes consist of a make stage, a pack stage, and intermediate storage facilities that decouple these two stages. In operations scheduling, complex technological constraints must be considered, e.g., non-identical parallel processing units, sequence-dependent changeovers, batch splitting, no-wait restrictions, material transfer times, minimum storage times, and finite storage capacity. The short-term scheduling problem is to compute a production schedule such that a given demand for products is fulfilled, all technological constraints are met, and the production makespan is minimised. A production schedule typically comprises 500–1500 operations. Due to the problem size and complexity of the technological constraints, the performance of known mixed-integer linear programming (MILP) formulations and heuristic approaches is often insufficient. We present a hybrid method consisting of three phases. First, the set of operations is divided into several subsets. Second, these subsets are iteratively scheduled using a generic and flexible MILP formulation. Third, a novel critical path-based improvement procedure is applied to the resulting schedule. We develop several strategies for the integration of the MILP model into this heuristic framework. Using these strategies, high-quality feasible solutions to large-scale instances can be obtained within reasonable CPU times using standard optimisation software. We have applied the proposed hybrid method to a set of industrial problem instances and found that the method outperforms state-of-the-art methods.

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

Background Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Results Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. Conclusions 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch webcite and should provide useful assistance to drug discovery projects.

Fast Prediction of Femoral Biomechanics Using Supervised Machine Learning and Statistical Shape Modeling

Finite element (FE) analysis is an important computational tool in biomechanics. However, its adoption into clinical practice has been hampered by its computational complexity and required high technical competences for clinicians. In this paper we propose a supervised learning approach to predict the outcome of the FE analysis. We demonstrate our approach on clinical CT and X-ray femur images for FE predictions ( FEP), with features extracted, respectively, from a statistical shape model and from 2D-based morphometric and density information. Using leave-one-out experiments and sensitivity analysis, comprising a database of 89 clinical cases, our method is capable of predicting the distribution of stress values for a walking loading condition with an average correlation coefficient of 0.984 and 0.976, for CT and X-ray images, respectively. These findings suggest that supervised learning approaches have the potential to leverage the clinical integration of mechanical simulations for the treatment of musculoskeletal conditions.

A fast protocol for purification of translating mRNAs

We present a protocol that enables easy extraction of translating mRNAs by purification of tagged ribosomes and associated mRNAs. By studying three different examples of stress influenced genes, we demonstrate the effectiveness and compare our rapid method to an older protocol (Halbeisen et al., 2009).