Fully Automatic Segmentation of Brain Tumor Images using Support Vector Machine Classiffication in Combination with Hierarchical Conditional Random Field Regularization

Delineating brain tumor boundaries from magnetic resonance images is an essential task for the analysis of brain cancer. We propose a fully automatic method for brain tissue segmentation, which combines Support Vector Machine classification using multispectral intensities and textures with subsequent hierarchical regularization based on Conditional Random Fields. The CRF regularization introduces spatial constraints to the powerful SVM classification, which assumes voxels to be independent from their neighbors. The approach first separates healthy and tumor tissue before both regions are subclassified into cerebrospinal fluid, white matter, gray matter and necrotic, active, edema region respectively in a novel hierarchical way. The hierarchical approach adds robustness and speed by allowing to apply different levels of regularization at different stages. The method is fast and tailored to standard clinical acquisition protocols. It was assessed on 10 multispectral patient datasets with results outperforming previous methods in terms of segmentation detail and computation times.

Magnetic field exposure and neurodegenerative diseases--recent epidemiological studies

OBJECTIVES: To analyse the results of recent studies not yet included in a 2003 report of the International Commission on Non-Ionizing Radiation Protection (ICNIRP) on occupational exposure to low-frequency electromagnetic fields as potential risk factor for neurodegenerative diseases. METHODS: A literature search was conducted in the online databases of PubMed, ISI Web of Knowledge, DIMDI and COCHRANE, as well as in specialised databases and journals. Eight studies published between January 2000 and July 2005 were included in the review. RESULTS: The findings of these studies contribute to the evidence of an association between occupational magnetic field exposure and the risk of dementia. Regarding amyotrophic lateral sclerosis, the recent results confirm earlier observations of an association with electric and electronic work and welding. Its relationship with magnetic field exposure remains unsolved. There are only few findings pointing towards an association between magnetic field exposure and Parkinson's disease. CONCLUSIONS: The epidemiological evidence for an association between occupational exposure to low-frequency electromagnetic fields and the risk of dementia has increased during the last five years. The impact of potential confounders should be evaluated in further studies.

Clinical field trial examining an implant with a sand-blasted, acid-etched surface

BACKGROUND: Conventionally, endosseous dental implants have required 3 to 6 months of uninterrupted healing based on observations for dental implants that were characterized by a relatively smooth machined surface. Many studies have since demonstrated that implants with a roughened surface resulted in greater bone apposition, earlier bone contact, and a stronger bond between the implant and the bone, suggesting that implants with roughened surfaces could be loaded earlier than 3 to 6 months. Formal clinical studies confirmed that implants with rough surfaces can have abutments placed and be loaded occlusally as early as 6 weeks postplacement. The purpose of this prospective, human clinical investigation was to evaluate a large number of implants with a specific rough surface (sand-blasted acid-etched [SLA]) placed in everyday practice under routine private-practice conditions. METHODS: A prospective, multicenter, human clinical observational study was initiated with the goal of recruiting a minimum of 500 patients and 800 implants. The implants were to be placed and restored in predominantly private-practice settings around the world. Ninety-two practitioners in 16 countries agreed to participate, and 86 followed the study design. Patients had to be in good health, have sufficient bone to encase the implant, and agree to return for recall appointments. Exclusion criteria included heavy smoking (>10 cigarettes a day) and bone augmentation procedures at the implant site. All implants were two-piece (an abutment was to be placed after 6 weeks of healing) and were characterized by the presence of a transmucosal polished collar. Each implant had an SLA surface. All implants were positioned using a non-submerged (single-stage) surgical technique. Survival and success rates were calculated by life-table analyses. RESULTS: A total of 706 patients were enrolled and 1,406 implants were placed. In the final analyses, 590 patients with 990 implants (70.4% of those enrolled) met all inclusion criteria, including placement of an abutment and provisional restoration within 63 days of surgical placement. The majority of implants were 10 and 12 mm long (78.7%) and were placed in type II and III bone (87%). Seventy-three percent of the implants were placed in the mandible, and 27% were placed in the maxilla. The cumulative survival rate was 99.56% at 3 years and 99.26% at 5 years. The overall success rate was 99.12% at 3 years and 97.38% after 5 years. CONCLUSIONS: Under private-practice conditions, implants with an SLA surface could be placed and restored predictably within 6 to 8 weeks. Data from this prospective, multicenter, human observational study reinforced the results of more formal clinical studies and demonstrated that implants with the SLA surface can be restored in patients in approximately half of the time of conventional healing periods.

A new method to monitor visual field defects caused by photoreceptor degeneration by quantitative optical coherence tomography

PURPOSE: To correlate the dimension of the visual field (VF) tested by Goldman kinetic perimetry with the extent of visibility of the highly reflective layer between inner and outer segments of photoreceptors (IOS) seen in optical coherence tomography (OCT) images in patients with retinitis pigmentosa (RP). METHODS: In a retrospectively designed cross-sectional study, 18 eyes of 18 patients with RP were examined with OCT and Goldmann perimetry using test target I4e and compared with 18 eyes of 18 control subjects. A-scans of raw scan data of Stratus OCT images (Carl Zeiss Meditec, AG, Oberkochen, Germany) were quantitatively analyzed for the presence of the signal generated by the highly reflective layer between the IOS in OCT images. Starting in the fovea, the distance to which this signal was detectable was measured. Visual fields were analyzed by measuring the distance from the center point to isopter I4e. OCT and visual field data were analyzed in a clockwise fashion every 30 degrees , and corresponding measures were correlated. RESULTS: In corresponding alignments, the distance from the center point to isopter I4e and the distance to which the highly reflective signal from the IOS can be detected correlate significantly (r = 0.75, P < 0.0001). The greater the distance in VF, the greater the distance measured in OCT. CONCLUSIONS: The authors hypothesize that the retinal structure from which the highly reflective layer between the IOS emanates is of critical importance for visual and photoreceptor function. Further research is warranted to determine whether this may be useful as an objective marker of progression of retinal degeneration in patients with RP.

Recovery of visual field and acuity after removal of epiretinal and inner limiting membranes

BACKGROUND: Visual acuity serves as only a rough gauge of macular function. The aim therefore was to ascertain whether central an assessment of the central visual field afforded a closer insight into visual function after removal of epiretinal membranes and Infracyanine-Green- or Trypan-Blue-assisted peeling of the inner limiting membrane. Patients and methods: Fourty-three patients undergoing pars-plana vitrectomy for the removal of epimacular membranes and dye-assisted peeling of the inner limiting membrane using either Infracyanine Green (n = 29; group 1) or Trypan Blue (n = 14; group 2) were monitored prospectively for 12 months. Preoperatively, and 1, 6 and 12 months postoperatively, distance and reading visual acuities were evaluated; the central visual field was assessed by automated static perimetry. RESULTS: Twelve months after surgery, distance and reading visual acuities had improved in both groups, but to a significant degree only in Trypan-Blue-treated eyes. The difference between the two groups was not significant. Likewise at this juncture, the mean size of the visual-field defect remained unchanged in Trypan-Blue-treated eyes (preoperative: 4.3 (SD 2.1) dB; 12 months: 4.0 (2.1) dB (p = 0.15)), but had increased in Infracyanine-Green-treated ones (from 5.3 (3.7) dB to 8.0 (5.2) dB (p = 0.027)). CONCLUSION: Unlike visual acuity, the central visual field had deteriorated in Infracyanine-Green-treated eyes but not in Trypan-Blue-treated eyes 12 months after surgery. Hence, as a predictor of functional outcome, testing of the central visual field may be a more sensitive gauge than visual acuity. Furthermore, Infracyanine Green may have a chronic and potentially clinically relevant effect on the macula which is not reflected in the visual acuity.

Integration of electrical neuroimaging with other functional imaging methods

Integrating evidence from different imaging modalities is important to overcome specific limitations of any given imaging method, such as insensitivity of the EEG to unsynchronized neural events, or the lack of fMRI sensitivity to events of low metabolic demand. Processes that are visible in one modality may be related in a nontrivial way to other processes visible in another modality and insight may only be obtained by integrating both methods through a common analysis. For example, brain activity at rest seems to be at least partly determined by an interaction of cortical rhythms (visible to EEG but not to fMRI) with sub-cortical activity (visible to fMRI, but usually not to EEG without averaging). A combination of EEG and fMRI data during rest may thus be more informative than the sum of two separate analyses in both modalities. Integration is also an important source of converging evidence about specific aspects and general principles of neural functions and their dysfunctions in certain pathologies. This is because not only electrical, but also energetic, biochemical, hemodynamic and metabolic processes characterize neural states and functions, and because brain structure provides crucial constraints upon neural functions. Focusing on multimodal integration of functional data should not distract from the privileged status of the electric field as the primary direct, noninvasive real-time measure of neural transmission. The preceding chapters illustrate how electrical neuroimaging has turned scalp EEG into an imaging modality which directly captures the full temporal dynamics of neural activity in the brain.

Scalp field maps and their characterization

The present chapter gives a comprehensive introduction into the display and quantitative characterization of scalp field data. After introducing the construction of scalp field maps, different interpolation methods, the effect of the recording reference and the computation of spatial derivatives are discussed. The arguments raised in this first part have important implications for resolving a potential ambiguity in the interpretation of differences of scalp field data. In the second part of the chapter different approaches for comparing scalp field data are described. All of these comparisons can be interpreted in terms of differences of intracerebral sources either in strength, or in location and orientation in a nonambiguous way. In the present chapter we only refer to scalp field potentials, but mapping also can be used to display other features, such as power or statistical values. However, the rules for comparing and interpreting scalp field potentials might not apply to such data. Generic form of scalp field data Electroencephalogram (EEG) and event-related potential (ERP) recordings consist of one value for each sample in time and for each electrode. The recorded EEG and ERP data thus represent a two-dimensional array, with one dimension corresponding to the variable “time” and the other dimension corresponding to the variable “space” or electrode. Table 2.1 shows ERP measurements over a brief time period. The ERP data (averaged over a group of healthy subjects) were recorded with 19 electrodes during a visual paradigm. The parietal midline Pz electrode has been used as the reference electrode.

Reliability of intraoperative high-resolution 2D ultrasound as an alternative to high-field strength MR imaging for tumor resection control: a prospective comparative study

OBJECT: Ultrasound may be a reliable but simpler alternative to intraoperative MR imaging (iMR imaging) for tumor resection control. However, its reliability in the detection of tumor remnants has not been definitely proven. The aim of the study was to compare high-field iMR imaging (1.5 T) and high-resolution 2D ultrasound in terms of tumor resection control. METHODS: A prospective comparative study of 26 consecutive patients was performed. The following parameters were compared: the existence of tumor remnants after presumed radical removal and the quality of the images. Tumor remnants were categorized as: detectable with both imaging modalities or visible only with 1 modality. RESULTS: Tumor remnants were detected in 21 cases (80.8%) with iMR imaging. All large remnants were demonstrated with both modalities, and their image quality was good. Two-dimensional ultrasound was not as effective in detecting remnants<1 cm. Two remnants detected with iMR imaging were missed by ultrasound. In 2 cases suspicious signals visible only on ultrasound images were misinterpreted as remnants but turned out to be a blood clot and peritumoral parenchyma. The average time for acquisition of an ultrasound image was 2 minutes, whereas that for an iMR image was approximately 10 minutes. Neither modality resulted in any procedure-related complications or morbidity. CONCLUSIONS: Intraoperative MR imaging is more precise in detecting small tumor remnants than 2D ultrasound. Nevertheless, the latter may be used as a less expensive and less time-consuming alternative that provides almost real-time feedback information. Its accuracy is highest in case of more confined, deeply located remnants. In cases of more superficially located remnants, its role is more limited.

[Field validation of a real-time PCR test for the detection of Mycoplasma hyopneumoniae in nasal swabs of live pigs]

Enzootic pneumonia (EP) of pigs, caused by Mycoplasma hyopneumoniae has been a notifiable disease in Switzerland since May 2003. The diagnosis of EP has been based on multiple methods, including clinical, bacteriological and epidemiological findings as well as pathological examination of lungs (mosaic diagnosis). With the recent development of a real-time PCR (rtPCR) assay with 2 target sequences a new detection method for M. hyopneumoniae became available. This assay was tested for its applicability to nasal swab material from live animals. Pigs from 74 herds (average 10 pigs per herd) were tested. Using the mosaic diagnosis, 22 herds were classified as EP positive and 52 as EP negative. From the 730 collected swab samples we were able to demonstrate that the rtPCR test was 100% specific. In cases of cough the sensitivity on herd level of the rtPCR is 100%. On single animal level and in herds without cough the sensitivity was lower. In such cases, only a positive result would be proof for an infection with M. hyopneumoniae. Our study shows that the rtPCR on nasal swabs from live pigs allows a fast and accurate diagnosis in cases of suspected EP.

Genotyping of Francisella tularensis strains by pulsed-field gel electrophoresis, amplified fragment length polymorphism fingerprinting, and 16S rRNA gene sequencing

We evaluated three molecular methods for identification of Francisella strains: pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP) analysis, and 16S rRNA gene sequencing. The analysis was performed with 54 Francisella tularensis subsp. holarctica, 5 F. tularensis subsp. tularensis, 2 F. tularensis subsp. novicida, and 1 F. philomiragia strains. On the basis of the combination of results obtained by PFGE with the restriction enzymes XhoI and BamHI, PFGE revealed seven pulsotypes, which allowed us to discriminate the strains to the subspecies level and which even allowed us to discriminate among some isolates of F. tularensis subsp. holarctica. The AFLP analysis technique produced some degree of discrimination among F. tularensis subsp. holarctica strains (one primary cluster with three major subclusters and minor variations within subclusters) when EcoRI-C and MseI-A, EcoRI-T and MseI-T, EcoRI-A and MseI-C, and EcoRI-0 and MseI-CA were used as primers. The degree of similarity among the strains was about 94%. The percent similarities of the AFLP profiles of this subspecies compared to those of F. tularensis subsp. tularensis, F. tularensis subsp. novicida, and F. philomiragia were less than 90%, about 72%, and less than 24%, respectively, thus permitting easy differentiation of this subspecies. 16S rRNA gene sequencing revealed 100% similarity for all F. tularensis subsp. holarctica isolates compared in this study. These results suggest that although limited genetic heterogeneity among F. tularensis subsp. holarctica isolates was observed, PFGE and AFLP analysis appear to be promising tools for the diagnosis of infections caused by different subspecies of F. tularensis and suitable techniques for the differentiation of individual strains.

Overview of data assimilation methods

We present the data assimilation approach, which provides a framework for combining observations and model simulations of the climate system, and has led to a new field of applications for paleoclimatology. The three subsequent articles explore specific applications in more detail.

Standard methods for Nosema research

Methods are described for working with Nosema apis and Nosema ceranae in the field and in the laboratory. For fieldwork, different sampling methods are described to determine colony level infections at a given point in time, but also for following the temporal infection dynamics. Suggestions are made for how to standardise field trials for evaluating treatments and disease impact. The laboratory methods described include different means for determining colony level and individual bee infection levels and methods for species determination, including light microscopy, electron microscopy, and molecular methods (PCR). Suggestions are made for how to standardise cage trials, and different inoculation methods for infecting bees are described, including control methods for spore viability. A cell culture system for in vitro rearing of Nosema spp. is described. Finally, how to conduct different types of experiments are described, including infectious dose, dose effects, course of infection and longevity tests

Long-term diffusion experiment at Mont Terri: first results from field and laboratory data

The diffusion of radionuclides is an important safety aspect for nuclear waste disposal in argillaceous host rocks. A long-term diffusion experiment, termed DI-A, is being carried out at the Mont Terri Rock Laboratory in the Opalinus Clay formation. The aim of this experiment is the understanding of the migration and sorption behaviour of cationic and anionic species in consolidated clays. This study reports on the experimental layout and the first results obtained from the DI-A experiment, which include the investigation of HTO, Na-22(+), Cs+, and I- migration during a period of 1 year by analysing these tracers in the water circulating in the borehole. In addition, results obtained from through-diffusion experiments on small-sized samples with HTO, I-, and Cl-36(-) are presented. The decrease of tracer concentrations in the borehole is fastest for Cs+, followed by Na-22(+), HTO, and finally I-. The chemical composition of the artificial pore water in the borehole shows very little variation with time, thus indicating almost no chemical disturbance around the borehole. Through-diffusion experiments in the laboratory that were performed parallel to the bedding plane with two different methods yielded effective diffusion coefficients for HTO of 4-5 X 10(-11) m(2) s(-1) and significantly lower ones for anions Cl- and I- (0.7-1.6 X 10(-11) m(2) s(-1)). The results indicate the importance of anion exclusion effects arising from the negatively charged clay surfaces. Furthermore, they demonstrate the anisotropic diffusion properties of the clay formation with significantly increased diffusion rates parallel to bedding relative to the perpendicular direction. The tracer data of the in situ experiment were successfully described with 2D diffusion models using diffusion and sorption parameters obtained from the above mentioned and other laboratory studies. The modelling results indicate that HTO and I- diffused with no retardation. The retardation of Na+ and Cs+ could be described by empirical sorption expressions from previously derived batch sorption (Cs+) or diffusion (Na+) experiments. Overall, the obtained results demonstrate the feasibility of the technical concept to study the diffusion of nonsorbing and sorbing tracers in consolidated clays. (C) 2004 Elsevier B.V. All rights reserved.

Feasibility of post mortem cardiac proton density weighted fast field echo imaging in two cases of sudden death

OBJECTIVE The aim of this work is to investigate and compare cardiac proton density (PD) weighted fast field echo (FFE) post-mortem magnetic resonance (PMMR) imaging with standard cardiac PMMR imaging (T1-weighted and T2-weighted turbo spin-echo (TSE)), postmortem CT (PMCT) as well as autopsy. MATERIALS AND METHODS Two human cadavers sequentially underwent cardiac PMCT and PMMR imaging (PD-weighted FFE, T1-weighted and T2-weighted TSE) and autopsy. The cardiac PMMR images were compared to each other as well as to PMCT and autopsy findings. RESULTS For the first case, cardiac PMMR exhibited a focal region of low signal in PD-weighted FFE and T2-weighted TSE images, surrounded by a signal intense rim in the T2-weighted images. T1-weighted TSE and PMCT did not appear to identify any focal abnormality. Macroscopic inspection identified a blood clot; histology confirmed this to be a thrombus with an adhering myocardial infarction. In the second case, a myocardial rupture with heart tamponade was identified in all PMMR images, located at the anterior wall of the left ventricle; PMCT excluded additional ruptures. In PD-weighted FFE and T2-weighted TSE images, it occurred hypo-intense, while resulting in small clustered hyper-intense spots in T1-weighted TSE. Autopsy confirmed the PMMR and PMCT findings. CONCLUSIONS Presented initial results have shown PD-weighted FFE to be a valuable imaging sequence in addition to traditional T2-weighted TSE imaging for blood clots and myocardial haemorrhage with clearer contrast between affected and healthy myocardium.