Estimation of peptide elongation times from ribosome profiling spectra.

Ribosome profiling spectra bear rich information on translation control and dynamics. Yet, due to technical biases in library generation, extracting quantitative measures of discrete translation events has remained elusive. Using maximum likelihood statistics and data set from Escherichia coli we develop a robust method for neutralizing technical biases (e.g. base specific RNase preferences in ribosome-protected mRNA fragments (RPF) generation), which allows for correct estimation of translation times at single codon resolution. Furthermore, we validated the method with available datasets from E. coli treated with antibiotic to inhibit isoleucyl-tRNA synthetase, and two datasets from Saccharomyces cerevisiae treated with two RNases with distinct cleavage signatures. We demonstrate that our approach accounts for RNase cleavage preferences and provides bias-corrected translation times estimates. Our approach provides a solution to the long-standing problem of extracting reliable information about peptide elongation times from highly noisy and technically biased ribosome profiling spectra.

Evaluation of an improved method of simulating lung nodules in chest tomosynthesis.

BACKGROUND: Simulated pathology is a valuable complement to clinical images in studies aiming at evaluating an imaging technique. In order for a study using simulated pathology to be valid, it is important that the simulated pathology in a realistic way reflect the characteristics of real pathology. PURPOSE: To perform a thorough evaluation of a nodule simulation method for chest tomosynthesis, comparing the detection rate and appearance of the artificial nodules with those of real nodules in an observer performance experiment. MATERIAL AND METHODS: A cohort consisting of 64 patients, 38 patients with a total of 129 identified pulmonary nodules and 26 patients without identified pulmonary nodules, was used in the study. Simulated nodules, matching the real clinically found pulmonary nodules by size, attenuation, and location, were created and randomly inserted into the tomosynthesis section images of the patients. Three thoracic radiologists and one radiology resident reviewed the images in an observer performance study divided into two parts. The first part included nodule detection and the second part included rating of the visual appearance of the nodules. The results were evaluated using a modified receiver-operating characteristic (ROC) analysis. RESULTS: The sensitivities for real and simulated nodules were comparable, as the area under the modified ROC curve (AUC) was close to 0.5 for all observers (range, 0.43-0.55). Even though the ratings of visual appearance for real and simulated nodules overlapped considerably, the statistical analysis revealed that the observers to were able to separate simulated nodules from real nodules (AUC values range 0.70-0.74). CONCLUSION: The simulation method can be used to create artificial lung nodules that have similar detectability as real nodules in chest tomosynthesis, although experienced thoracic radiologists may be able to distinguish them from real nodules.

Comparison of clinical and physical measures of image quality in chest and pelvis computed radiography at different tube voltages.

The aim of this work was to study the dependence of image quality in digital chest and pelvis radiography on tube voltage, and to explore correlations between clinical and physical measures of image quality. The effect on image quality of tube voltage in these two examinations was assessed using two methods. The first method relies on radiologists' observations of images of an anthropomorphic phantom, and the second method was based on computer modeling of the imaging system using an anthropomorphic voxel phantom. The tube voltage was varied within a broad range (50-150 kV), including those values typically used with screen-film radiography. The tube charge was altered so that the same effective dose was achieved for each projection. Two x-ray units were employed using a computed radiography (CR) image detector with standard tube filtration and antiscatter device. Clinical image quality was assessed by a group of radiologists using a visual grading analysis (VGA) technique based on the revised CEC image criteria. Physical image quality was derived from a Monte Carlo computer model in terms of the signal-to-noise ratio, SNR, of anatomical structures corresponding to the image criteria. Both the VGAS (visual grading analysis score) and SNR decrease with increasing tube voltage in both chest PA and pelvis AP examinations, indicating superior performance if lower tube voltages are employed. Hence, a positive correlation between clinical and physical measures of image quality was found. The pros and cons of using lower tube voltages with CR digital radiography than typically used in analog screen-film radiography are discussed, as well as the relevance of using VGAS and quantum-noise SNR as measures of image quality in pelvis and chest radiography.

Towards optimization in digital chest radiography using Monte Carlo modelling.

A Monte Carlo based computer model of the x-ray imaging system was used to investigate how various image quality parameters of interest in chest PA radiography and the effective dose E vary with tube voltage (90-150 kV), additional copper filtration (0-0.5 mm), anti-scatter method (grid ratios 8-16 and air gap lengths 20-40 cm) and patient thickness (20-28 cm) in a computed radiography (CR) system. Calculated quantities were normalized to a fixed value of air kerma (5.0 microGy) at the automatic exposure control chambers. Soft-tissue nodules were positioned at different locations in the anatomy and calcifications in the apical region. The signal-to-noise ratio, SNR, of the nodules and the nodule contrast relative to the contrast of bone (C/C(B)) as well as relative to the dynamic range in the image (C(rel)) were used as image quality measures. In all anatomical regions, except in the densest regions in the thickest patients, the air gap technique provides higher SNR and contrast ratios than the grid technique and at a lower effective dose E. Choice of tube voltage depends on whether quantum noise (SNR) or the contrast ratios are most relevant for the diagnostic task. SNR increases with decreasing tube voltage while C/C(B) increases with increasing tube voltage.

A search for optimal x-ray spectra in iodine contrast media mammography.

The aim of this work was to search for the optimal x-ray tube voltage and anode-filter combination in digital iodine contrast media mammography. In the optimization, two entities were of interest: the average glandular dose, AGD, and the signal-to-noise ratio, SNR, for detection of diluted iodine contrast medium. The optimum is defined as the technique maximizing the figure of merit, SNR2/AGD. A Monte Carlo computer program was used which simulates the transport of photons from the x-ray tube through the compression plate, breast, breast support plate, anti-scatter grid and image detector. It computes the AGD and the SNR of an iodine detail inside the compressed breast. The breast thickness was varied between 2 and 8 cm with 10-90% glandularity. The tube voltage was varied between 20 and 55 kV for each anode material (Rh, Mo and W) in combination with either 25 microm Rh or 0.05-0.5 mm Cu added filtration. The x-ray spectra were calculated with MCNP4C (Monte Carlo N-Particle Transport Code System, version 4C). A CsI scintillator was used as the image detector. The results for Rh/0.3 mmCu, Mo/0.3 mmCu and W/0.3 mmCu were similar. For all breast thicknesses, a maximum in the figure of merit was found at approximately 45 kV for the Rh/Cu, Mo/Cu and W/Cu combinations. The corresponding results for the Rh/Rh combination gave a figure of merit that was typically lower and more slowly varying with tube voltage. For a 4 cm breast at 45 kV, the SNR2/AGD was 3.5 times higher for the Rh/0.3 mmCu combination compared with the Rh/Rh combination. The difference is even larger for thicker breasts. The SNR2/AGD increases slowly with increasing Cu-filter thickness. We conclude that tube voltages between 41 and 55 kV and added Cu-filtration will result in significant dose advantage in digital iodine contrast media mammography compared to using the Rh/Rh anode/filter combination at 25-32 kV.

The influence of patient thickness and imaging system on patient dose and physical image quality in digital chest imaging.

The aim of this work was to study the influence of patient thickness, tube voltage and image detector on patient dose, contrast and ideal observer signal-to-noise ratio (SNR(I)), for pathological details positioned at different regions in the image in posterior-anterior (PA) chest radiology. A Monte Carlo computational model was used to compute measures of physical image quality (contrast, SNR(I)) and patient effective dose, E. Two metastasis-like details positioned in the central right lung and right lung near the spine, respectively, were studied. The tube voltage was varied between 100 and 150 kV and the patient thickness between 20 and 28 cm. Both, a computed radiography (CR) system and a direct radiography (DR) system, were investigated. The DR system provides both lower doses and better image quality compared with the CR system. The SNR(I)2/E is approximately 2.9 times higher for the DR system compared with the CR system.

Distributions of scatter-to-primary and signal-to-noise ratios per pixel in digital chest imaging.

The aim of this work was to calculate distributions of scatter-to-primary ratios (epsilon(s)/epsilon(p)) and signal-to-noise ratios per pixel (SNRp) in chest images. Such distributions may provide useful information on how physical image quality (contrast, SNR) is distributed over the posterior/anterior (PA) chest image. A Monte Carlo computer program was used for the calculations, including a model of both the patient (voxel phantom) and the imaging system (X-ray tube, anti-scatter grid and image detector). The calculations were performed for three PA thicknesses 20, 24 and 28 cm. For a 24 cm patient, the epsilon(s)/epsilon(p) varies between 0.5 in the lung to 2.5 behind the spine and heart. The corresponding variation of the SNRp is a factor of 3, with the highest values in the lung. Increasing the patient thickness from 20 to 28 cm increases the epsilon(s)/epsilon(p) by a factor of 2.2 behind the spine and heart.

Nodule detection in digital chest radiography: effect of nodule location.

Most detection studies in chest radiography treat the entire chest image as a single background or divided into the two regions parenchyma and mediastinum. However, the different parts of the lung show great variations in attenuation and structure, leading to different amounts of quantum noise and scattered radiation as well as different complexity. Detailed data on the difference in detectability in the different regions are of importance. The purpose of this study was to quantify the difference in detectability between different regions of a chest image. The chest X ray was divided into six different regions, where each region was considered to be uniform in terms of detectability. Thirty clinical chest images were collected and divided into the different regions. Simulated designer nodules with a full-width-at-fifth-maximum of 10 mm but with varying contrast were added to the images. An equal number of images lacking pathology were included and a receiver operating characteristic (ROC) study was conducted with five observers. Results show that the image contrast needed to obtain a constant value of A(z) (area under an ROC curve) differs by more than a factor of four between different regions.

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation.

Transcription factors mediate gene regulation by site-specific binding to chromosomal operators. It is commonly assumed that the level of repression is determined solely by the equilibrium binding of a repressor to its operator. However, this assumption has not been possible to test in living cells. Here we have developed a single-molecule chase assay to measure how long an individual transcription factor molecule remains bound at a specific chromosomal operator site. We find that the lac repressor dimer stays bound on average 5 min at the native lac operator in Escherichia coli and that a stronger operator results in a slower dissociation rate but a similar association rate. Our findings do not support the simple equilibrium model. The discrepancy with this model can, for example, be accounted for by considering that transcription initiation drives the system out of equilibrium. Such effects need to be considered when predicting gene activity from transcription factor binding strengths.

Simulation of lung nodules in chest tomosynthesis.

The aim of the present work was to develop an adequate method for simulating lung nodules in clinical chest tomosynthesis images. Based on the visual appearance of real nodules, artificial, three-dimensional nodules with irregular shape and surface structure were created using an approach of combining spheres of different sizes and central points. The nodules were virtually positioned at the desired locations inside the patient and by using the known geometry of the tomosynthesis acquisition, the radiation emitted from the focal spot, passing through the nodule and reaching the detector could be simulated. The created nodules were thereby projected into raw-data tomosynthesis projection images before reconstruction of the tomosynthesis section images. The focal spot size, signal spread in the detector, scattered radiation, patient motion and existing anatomy at the location of the nodule were taken into account in the simulations. It was found that the blurring caused by the modulation transfer function and the patient motion overshadows the effects of a finite focal spot and aliasing and also obscures the surface structure of the nodules, which provides an opportunity to simplify the simulations and decrease the simulation times. Also, the limited in-depth resolution of the reconstructed tomosynthesis section images reduces the necessity to take details of the anatomical structures at the location of the inserted nodule into account.

A Monte Carlo-based model for simulation of digital chest tomosynthesis.

The aim of this work was to calculate synthetic digital chest tomosynthesis projections using a computer simulation model based on the Monte Carlo method. An anthropomorphic chest phantom was scanned in a computed tomography scanner, segmented and included in the computer model to allow for simulation of realistic high-resolution X-ray images. The input parameters to the model were adapted to correspond to the VolumeRAD chest tomosynthesis system from GE Healthcare. Sixty tomosynthesis projections were calculated with projection angles ranging from +15 to -15 degrees. The images from primary photons were calculated using an analytical model of the anti-scatter grid and a pre-calculated detector response function. The contributions from scattered photons were calculated using an in-house Monte Carlo-based model employing a number of variance reduction techniques such as the collision density estimator. Tomographic section images were reconstructed by transferring the simulated projections into the VolumeRAD system. The reconstruction was performed for three types of images using: (i) noise-free primary projections, (ii) primary projections including contributions from scattered photons and (iii) projections as in (ii) with added correlated noise. The simulated section images were compared with corresponding section images from projections taken with the real, anthropomorphic phantom from which the digital voxel phantom was originally created. The present article describes a work in progress aiming towards developing a model intended for optimisation of chest tomosynthesis, allowing for simulation of both existing and future chest tomosynthesis systems.