Fully automatic segmentation of AP pelvis X-rays via random forest regression with efficient feature selection and hierarchical sparse shape composition

In clinical practice, traditional X-ray radiography is widely used, and knowledge of landmarks and contours in anteroposterior (AP) pelvis X-rays is invaluable for computer aided diagnosis, hip surgery planning and image-guided interventions. This paper presents a fully automatic approach for landmark detection and shape segmentation of both pelvis and femur in conventional AP X-ray images. Our approach is based on the framework of landmark detection via Random Forest (RF) regression and shape regularization via hierarchical sparse shape composition. We propose a visual feature FL-HoG (Flexible- Level Histogram of Oriented Gradients) and a feature selection algorithm based on trace radio optimization to improve the robustness and the efficacy of RF-based landmark detection. The landmark detection result is then used in a hierarchical sparse shape composition framework for shape regularization. Finally, the extracted shape contour is fine-tuned by a post-processing step based on low level image features. The experimental results demonstrate that our feature selection algorithm reduces the feature dimension in a factor of 40 and improves both training and test efficiency. Further experiments conducted on 436 clinical AP pelvis X-rays show that our approach achieves an average point-to-curve error around 1.2 mm for femur and 1.9 mm for pelvis.

Performance of HBsAg point-of-care tests for detection of diagnostic escape-variants in clinical samples

BACKGROUND Hepatitis B viruses (HBV) harboring mutations in the a-determinant of the Hepatitis B surface antigen (HBsAg) are associated with reduced reactivity of HBsAg assays. OBJECTIVES To evaluate the sensitivity and specificity of three HBsAg point-of-care tests for the detection of HBsAg of viruses harboring HBsAg mutations. STUDY DESIGN A selection of 50 clinical plasma samples containing HBV with HBsAg mutations was used to evaluate the performance of three HBsAg point-of-care tests (Vikia(®), bioMérieux, Marcy-L'Étoile, France. Alere Determine HBsAg™, Iverness Biomedical Innovations, Köln, Germany. Quick Profile™, LumiQuick Diagnostics, California, USA) and compared to the ARCHITECT HBsAg Qualitative(®) assay (Abbott Laboratories, Sligo, Ireland). RESULTS The sensitivity of the point-of-care tests ranged from 98% to 100%. The only false-negative result occurred using the Quick Profile™ assay with a virus harboring a D144A mutation. CONCLUSIONS The evaluated point-of-care tests revealed an excellent sensitivity in detecting HBV samples harboring HBsAg mutations.

Feature-invariant image registration method for quantification of surgical outcomes in patients with craniosynostosis: a preliminary study

Craniosynostosis consists of a premature fusion of the sutures in an infant skull that restricts skull and brain growth. During the last decades, there has been a rapid increase of fundamentally diverse surgical treatment methods. At present, the surgical outcome has been assessed using global variables such as cephalic index, head circumference, and intracranial volume. However, these variables have failed in describing the local deformations and morphological changes that may have a role in the neurologic disorders observed in the patients. This report describes a rigid image registration-based method to evaluate outcomes of craniosynostosis surgical treatments, local quantification of head growth, and indirect intracranial volume change measurements. The developed semiautomatic analysis method was applied to computed tomography data sets of a 5-month-old boy with sagittal craniosynostosis who underwent expansion of the posterior skull with cranioplasty. Quantification of the local changes between pre- and postoperative images was quantified by mapping the minimum distance of individual points from the preoperative to the postoperative surface meshes, and indirect intracranial volume changes were estimated. The proposed methodology can provide the surgeon a tool for the quantitative evaluation of surgical procedures and detection of abnormalities of the infant skull and its development.

Detection of Chlamydia and complement factors in neovascular membranes of patients with age-related macular degeneration

PURPOSE To investigate whether Chlamydia pneumoniae and complement factors were present in surgically removed choroidal neovascular membranes (CNV) of patients with age-related macular degeneration (AMD). METHODS Paraffin sections of 26 CNV were stained for C. pneumoniae or the complement factors H (CFH) and C5, whereas macrophages were identified by positive CD68 staining. Clinical characteristics have been correlated to the immunohistochemical findings. RESULTS C. pneumoniae was found in 68% of the investigated membranes, and 88% of these membranes were also positive for CD68. Staining for CFH and C5 gave a positive reaction in 68 and 41% of the membranes, respectively. Patients with C5-positive membranes had significantly larger CNV mean area and were younger than patients with CFH-positive membranes at the operation time point. CONCLUSIONS Correlations between clinical symptoms and complement factor C5 could be shown. The results strengthen the hypothesis of an involvement of the complement system in AMD.

Break detection of annual Swiss temperature series

[1] Instrumental temperature series are often affected by artificial breaks (“break points”) due to (e.g.,) changes in station location, land-use, or instrumentation. The Swiss climate observation network offers a high number and density of stations, many long and relatively complete daily to sub-daily temperature series, and well-documented station histories (i.e., metadata). However, for many climate observation networks outside of Switzerland, detailed station histories are missing, incomplete, or inaccessible. To correct these records, the use of reliable statistical break detection methods is necessary. Here, we apply three statistical break detection methods to high-quality Swiss temperature series and use the available metadata to assess the methods. Due to the complex terrain in Switzerland, we are able to assess these methods under specific local conditions such as the Foehn or crest situations. We find that the temperature series of all stations are affected by artificial breaks (average = 1 break point / 48 years) with discrepancies in the abilities of the methods to detect breaks. However, by combining the three statistical methods, almost all of the detected break points are confirmed by metadata. In most cases, these break points are ascribed to a combination of factors in the station history.

Detection of exon deletions within an entire gene (CFTR) by relative quantification on the LightCycler

BACKGROUND: Cystic fibrosis (CF) is associated with at least 1 pathogen point sequence variant on each CFTR allele. Some symptomatic patients, however, have only 1 detectable pathogen sequence variant and carry, on the other allele, a large deletion that is not detected by conventional screening methods. METHODS: For relative quantitative real-time PCR detection of large deletions in the CFTR gene, we designed DNA-specific primers for each exon of the gene and primers for a reference gene (beta2-microglobulin). For PCR we used a LightCycler system (Roche) and calculated the gene-dosage ratio of CFTR to beta2-microglobulin. We tested the method by screening all 27 exons in 3 healthy individuals and 2 patients with only 1 pathogen sequence variant. We then performed specific deletion screenings in 10 CF patients with known large deletions and a blinded analysis in which we screened 24 individuals for large deletions by testing 8 of 27 exons. RESULTS: None of the ratios for control samples were false positive (for deletions or duplications); moreover, for all samples from patients with known large deletions, the calculated ratios for deleted exons were close to 0.5. In addition, the results from the blinded analysis demonstrated that our method can also be used for the screening of single individuals. CONCLUSIONS: The LightCycler assay allows reliable and rapid screening for large deletions in the CFTR gene and detects the copy number of all 27 exons.

Should 3K zoom function be used for detection of pneumothorax in cesium iodide/amorphous silicon flat-panel detector radiographs presented on 1K-matrix soft copies?

The purpose of the study was to evaluate observer performance in the detection of pneumothorax with cesium iodide and amorphous silicon flat-panel detector radiography (CsI/a-Si FDR) presented as 1K and 3K soft-copy images. Forty patients with and 40 patients without pneumothorax diagnosed on previous and subsequent digital storage phosphor radiography (SPR, gold standard) had follow-up chest radiographs with CsI/a-Si FDR. Four observers confirmed or excluded the diagnosis of pneumothorax according to a five-point scale first on the 1K soft-copy image and then with help of 3K zoom function (1K monitor). Receiver operating characteristic (ROC) analysis was performed for each modality (1K and 3K). The area under the curve (AUC) values for each observer were 0.7815, 0.7779, 0.7946 and 0.7066 with 1K-matrix soft copies and 0.8123, 0.7997, 0.8078 and 0.7522 with 3K zoom. Overall detection of pneumothorax was better with 3K zoom. Differences between the two display methods were not statistically significant in 3 of 4 observers (p-values between 0.13 and 0.44; observer 4: p = 0.02). The detection of pneumothorax with 3K zoom is better than with 1K soft copy but not at a statistically significant level. Differences between both display methods may be subtle. Still, our results indicate that 3K zoom should be employed in clinical practice.

Cost-effectiveness of point-of-care viral load monitoring of antiretroviral therapy in resource-limited settings: mathematical modelling study

BACKGROUND Monitoring of HIV viral load in patients on combination antiretroviral therapy (ART) is not generally available in resource-limited settings. We examined the cost-effectiveness of qualitative point-of-care viral load tests (POC-VL) in sub-Saharan Africa. DESIGN Mathematical model based on longitudinal data from the Gugulethu and Khayelitsha township ART programmes in Cape Town, South Africa. METHODS Cohorts of patients on ART monitored by POC-VL, CD4 cell count or clinically were simulated. Scenario A considered the more accurate detection of treatment failure with POC-VL only, and scenario B also considered the effect on HIV transmission. Scenario C further assumed that the risk of virologic failure is halved with POC-VL due to improved adherence. We estimated the change in costs per quality-adjusted life-year gained (incremental cost-effectiveness ratios, ICERs) of POC-VL compared with CD4 and clinical monitoring. RESULTS POC-VL tests with detection limits less than 1000 copies/ml increased costs due to unnecessary switches to second-line ART, without improving survival. Assuming POC-VL unit costs between US$5 and US$20 and detection limits between 1000 and 10,000 copies/ml, the ICER of POC-VL was US$4010-US$9230 compared with clinical and US$5960-US$25540 compared with CD4 cell count monitoring. In Scenario B, the corresponding ICERs were US$2450-US$5830 and US$2230-US$10380. In Scenario C, the ICER ranged between US$960 and US$2500 compared with clinical monitoring and between cost-saving and US$2460 compared with CD4 monitoring. CONCLUSION The cost-effectiveness of POC-VL for monitoring ART is improved by a higher detection limit, by taking the reduction in new HIV infections into account and assuming that failure of first-line ART is reduced due to targeted adherence counselling.

Combined Ultrasmall Superparamagnetic Particles of Iron Oxide–Enhanced and Diffusion-weighted Magnetic Resonance Imaging Facilitates Detection of Metastases in Normal-sized Pelvic Lymph Nodes of Patients with Bladder and Prostate Cancer

Background Conventional cross-sectional imaging with computed tomography and magnetic resonance imaging (MRI) has limited accuracy for lymph node (LN) staging in bladder and prostate cancer patients. Objective To prospectively assess the diagnostic accuracy of combined ultrasmall superparamagnetic particles of iron oxide (USPIO) MRI and diffusion-weighted (DW) MRI in staging of normal-sized pelvic LNs in bladder and/or prostate cancer patients. Design, setting, and participants Examinations with 3-Tesla MRI 24–36 h after administration of USPIO using conventional MRI sequences combined with DW-MRI (USPIO-DW-MRI) were performed in 75 patients with clinically localised bladder and/or prostate cancer staged previously as N0 by conventional cross-sectional imaging. Combined USPIO-DW-MRI findings were analysed by three independent readers and correlated with histopathologic LN findings after extended pelvic LN dissection (PLND) and resection of primary tumours. Outcome measurements and statistical analysis Sensitivity and specificity for LN status of combined USPIO-DW-MRI versus histopathologic findings were evaluated per patient (primary end point) and per pelvic side (secondary end point). Time required for combined USPIO-DW-MRI reading was assessed. Results and limitations At histopathologic analysis, 2993 LNs (median: 39 LNs; range: 17–68 LNs per patient) with 54 LN metastases (1.8%) were found in 20 of 75 (27%) patients. Per-patient sensitivity and specificity for detection of LN metastases by the three readers ranged from 65% to 75% and 93% to 96%, respectively; sensitivity and specificity per pelvic side ranged from 58% to 67% and 94% to 97%, respectively. Median reading time for the combined USPIO-DW-MRI images was 9 min (range: 3–26 min). A potential limitation is the absence of a node-to-node correlation of combined USPIO-DW-MRI and histopathologic analysis. Conclusions Combined USPIO-DW-MRI improves detection of metastases in normal-sized pelvic LNs of bladder and/or prostate cancer patients in a short reading time.

Probabilistic approach to cloud and snow detection on Advanced Very High Resolution Radiometer (AVHRR) imagery

Derivation of probability estimates complementary to geophysical data sets has gained special attention over the last years. Information about a confidence level of provided physical quantities is required to construct an error budget of higher-level products and to correctly interpret final results of a particular analysis. Regarding the generation of products based on satellite data a common input consists of a cloud mask which allows discrimination between surface and cloud signals. Further the surface information is divided between snow and snow-free components. At any step of this discrimination process a misclassification in a cloud/snow mask propagates to higher-level products and may alter their usability. Within this scope a novel probabilistic cloud mask (PCM) algorithm suited for the 1 km × 1 km Advanced Very High Resolution Radiometer (AVHRR) data is proposed which provides three types of probability estimates between: cloudy/clear-sky, cloudy/snow and clear-sky/snow conditions. As opposed to the majority of available techniques which are usually based on the decision-tree approach in the PCM algorithm all spectral, angular and ancillary information is used in a single step to retrieve probability estimates from the precomputed look-up tables (LUTs). Moreover, the issue of derivation of a single threshold value for a spectral test was overcome by the concept of multidimensional information space which is divided into small bins by an extensive set of intervals. The discrimination between snow and ice clouds and detection of broken, thin clouds was enhanced by means of the invariant coordinate system (ICS) transformation. The study area covers a wide range of environmental conditions spanning from Iceland through central Europe to northern parts of Africa which exhibit diverse difficulties for cloud/snow masking algorithms. The retrieved PCM cloud classification was compared to the Polar Platform System (PPS) version 2012 and Moderate Resolution Imaging Spectroradiometer (MODIS) collection 6 cloud masks, SYNOP (surface synoptic observations) weather reports, Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) vertical feature mask version 3 and to MODIS collection 5 snow mask. The outcomes of conducted analyses proved fine detection skills of the PCM method with results comparable to or better than the reference PPS algorithm.

Procedure for short-lived particle detection in the OPERA experiment and its application to charm decays

The OPERA experiment, designed to perform the first observation of νμ→ντ oscillations in appearance mode through the detection of the τ leptons produced in ντ charged current interactions, has collected data from 2008 to 2012. In the present paper, the procedure developed to detect τ particle decays, occurring over distances of the order of 1 mm from the neutrino interaction point, is described in detail. The results of its application to the search for charmed hadrons are then presented as a validation of the methods for ντ appearance detection.

COSIMA calibration for the detection and characterization of the cometary solid organic matter

On the orbiter of the Rosetta spacecraft, the Cometary Secondary Ion Mass Analyser (COSIMA) will provide new in situ insights about the chemical composition of cometary grains all along 67P/Churyumov–Gerasimenko (67P/CG) journey until the end of December 2015 nominally. The aim of this paper is to present the pre-calibration which has already been performed as well as the different methods which have been developed in order to facilitate the interpretation of the COSIMA mass spectra and more especially of their organic content. The first step was to establish a mass spectra library in positive and negative ion mode of targeted molecules and to determine the specific features of each compound and chemical family analyzed. As the exact nature of the refractory cometary organic matter is nowadays unknown, this library is obviously not exhaustive. Therefore this library has also been the starting point for the research of indicators, which enable to highlight the presence of compounds containing specific atom or structure. These indicators correspond to the intensity ratio of specific peaks in the mass spectrum. They have allowed us to identify sample containing nitrogen atom, aliphatic chains or those containing polyaromatic hydrocarbons. From these indicators, a preliminary calibration line, from which the N/C ratio could be derived, has also been established. The research of specific mass difference could also be helpful to identify peaks related to quasi-molecular ions in an unknown mass spectrum. The Bayesian Positive Source Separation (BPSS) technique will also be very helpful for data analysis. This work is the starting point for the analysis of the cometary refractory organic matter. Nevertheless, calibration work will continue in order to reach the best possible interpretation of the COSIMA observations.

Detection of low energy antimatter with emulsions

Emulsion detectors feature a very high position resolution and consequently represent an ideal device when particle detection is required at the micrometric scale. This is the case of quantum interferometry studies with antimatter, where micrometric fringes have to be measured. In this framework, we designed and realized a new emulsion based detector characterized by a gel enriched in terms of silver bromide crystal contents poured on a glass plate. We tested the sensitivity of such a detector to low energy positrons in the range 10–20 keV . The obtained results prove that nuclear emulsions are highly efficient at detecting positrons at these energies. This achievement paves the way to perform matter-wave interferometry with positrons using this technology.