Segmentation of nerve bundles and ganglia in spine MRI using particle filters

14th International Conference, Toronto, Canada, September 18-22, 2011, Proceedings, Part IIIAutomatic segmentation of spinal nerve bundles that originate within the dural sac and exit the spinal canal is important for diagnosis and surgical planning. The variability in intensity, contrast, shape and direction of nerves seen in high resolution myelographic MR images makes segmentation a challenging task. In this paper, we present an automatic tracking method for nerve segmentation based on particle filters. We develop a novel approach to particle representation and dynamics, based on Bézier splines. Moreover, we introduce a robust image likelihood model that enables delineation of nerve bundles and ganglia from the surrounding anatomical structures. We demonstrate accurate and fast nerve tracking and compare it to expert manual segmentation.National Institutes of Health (U.S.) (NAMIC award U54-EB005149)National Science Foundation (U.S.) (CAREER grant 0642971

Room-Temperature Inter-Dot Coherent Dynamics in Multilayer Quantum Dot Materials

The full blossoming of quantum technologies requires the availability of easy-to-prepare materials where quantum coherences can be effectively initiated, controlled, and exploited, preferably at ambient conditions. Solid-state multilayers of colloidally grown quantum dots (QDs) are highly promising for this task because of the possibility of assembling networks of electronically coupled QDs through the modulation of sizes, inter-dot linkers, and distances. To usefully probe coherence in these materials, the dynamical characterization of their collective quantum mechanically coupled states is needed. Here, we explore by two-dimensional electronic spectroscopy the coherent dynamics of solid-state multilayers of electronically coupled colloidally grown CdSe QDs and complement it by detailed computations. The time evolution of a coherent superposition of states delocalized over more than one QD was captured at ambient conditions. We thus provide important evidence for inter-dot coherences in such solid-state materials, opening up new avenues for the effective application of these materials in quantum technologies

Synergistic Formation of Radicals by Irradiation with Both Vacuum Ultraviolet and Atomic Hydrogen: A Real-Time In Situ Electron Spin Resonance Study

We report on the surface modification of polytetrafluoroethylene (PTFE) as an example of soft- and bio-materials that occur under plasma discharge by kinetics analysis of radical formation using in situ real-time electron spin resonance (ESR) measurements. During irradiation with hydrogen plasma, simultaneous measurements of the gas-phase ESR signals of atomic hydrogen and the carbon dangling bond (C-DB) on PTFE were performed. Dynamic changes of the C-DB density were observed in real time, where the rate of density change was accelerated during initial irradiation and then became constant over time. It is noteworthy that C-DBs were formed synergistically by irradiation with both vacuum ultraviolet (VUV) and atomic hydrogen. The in situ real-time ESR technique is useful to elucidate synergistic roles during plasma surface modification.Comment: 14 pages, 4 figure

Primary skin fibroblasts as a model of Parkinson's disease

Parkinson's disease is the second most frequent neurodegenerative disorder. While most cases occur sporadic mutations in a growing number of genes including Parkin (PARK2) and PINK1 (PARK6) have been associated with the disease. Different animal models and cell models like patient skin fibroblasts and recombinant cell lines can be used as model systems for Parkinson's disease. Skin fibroblasts present a system with defined mutations and the cumulative cellular damage of the patients. PINK1 and Parkin genes show relevant expression levels in human fibroblasts and since both genes participate in stress response pathways, we believe fibroblasts advantageous in order to assess, e.g. the effect of stressors. Furthermore, since a bioenergetic deficit underlies early stage Parkinson's disease, while atrophy underlies later stages, the use of primary cells seems preferable over the use of tumor cell lines. The new option to use fibroblast-derived induced pluripotent stem cells redifferentiated into dopaminergic neurons is an additional benefit. However, the use of fibroblast has also some drawbacks. We have investigated PARK6 fibroblasts and they mirror closely the respiratory alterations, the expression profiles, the mitochondrial dynamics pathology and the vulnerability to proteasomal stress that has been documented in other model systems. Fibroblasts from patients with PARK2, PARK6, idiopathic Parkinson's disease, Alzheimer's disease, and spinocerebellar ataxia type 2 demonstrated a distinct and unique mRNA expression pattern of key genes in neurodegeneration. Thus, primary skin fibroblasts are a useful Parkinson's disease model, able to serve as a complement to animal mutants, transformed cell lines and patient tissues

SNP Discovery and Linkage Map Construction in Cultivated Tomato

Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/

Phase I clinical trial with IL-2-transfected xenogeneic cells administered in subcutaneous metastatic tumours: clinical and immunological findings

Various studies have emphasized an immunodepression state observed at the tumour site. To reverse this defect and based upon animal studies, we initiated a phase I clinical trial of gene therapy in which various doses of xenogeneic monkey fibroblasts (Vero cells) genetically engineered to produce human IL-2 were administered intratumorally in 8 patients with metastatic solid tumours. No severe adverse effect was observed in the 8 patients analysed during this clinical trial even in the highest dose (5 ¥ 107 cells) group. This absence of toxicity seems to be associated with rapid elimination of Vero-IL-2 cells from the organism. Indeed, exogenous IL-2 mRNA could no longer be detected in the peripheral whole blood 48 hours after Vero-IL-2 cell administration. In addition, we did not find any expression of exogenous IL-2 mRNA in post-therapeutic lesions removed 29 days after the start of therapy. A major finding of this trial concerns the two histological responses of two treated subcutaneous nodules not associated with an apparent clinical response. The relationship between local treatment and tumour regression was supported by replacement of tumour cells by inflammatory cells in regressing lesions and marked induction of T and natural killer cell derived cytokines (IL-2, IL-4, IFNg …) in post-therapeutic lesions analysed 28 days after the start of Vero-IL-2 administration. Gene therapy using xenogeneic cells as vehicle may therefore present certain advantages over other vectors, such as its complete absence of toxicity. Furthermore, the in vivo biological effect of immunostimulatory genes, i.e IL-2-, may be potentiated by the xenogeneic rejection reaction. © 2000 Cancer Research Campaign http://www.bjcancer.co

Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century

We report genome-wide data for 33 Ashkenazi Jews (AJ), dated to the 14th century, following a salvageexcavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are geneticallysimilar to modern AJ and have substantial Southern European ancestry, but they show more variabilityin Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried the samenearly-AJ-specific mitochondrial haplogroup and eight carried pathogenic variants known to affect AJtoday. These observations, together with high levels of runs of homozygosity, suggest that the Erfurtcommunity had already experienced the major reduction in size that affected modern AJ. However, theErfurt bottleneck was more severe, implying substructure in medieval AJ. Together, our results suggestthat the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14th centuryand highlight late medieval genetic heterogeneity no longer present in modern AJ

When Is a Principal Charged With an Agent’s Knowledge?

Question: Detecting species presence in vegetation and making visual assessment of abundances involve a certain amount of skill, and therefore subjectivity. We evaluated the magnitude of the error in data, and its consequences for evaluating temporal trends. Location: Swedish forest vegetation. Methods: Vegetation data were collected independently by two observers in 342 permanent 100-m2 plots in mature boreal forests. Each plot was visited by one observer from a group of 36 and one of two quality assessment observers. The cover class of 29 taxa was recorded, and presence/absence for an additional 50. Results: Overall, one third of each occurrence was missed by one of the two observers, but with large differences among species. There were more missed occurrences at low abundances. Species occurring at low abundance when present tended to be frequently overlooked. Variance component analyses indicated that cover data on 5 of 17 species had a significant observer bias. Observer-explained variance was < 10% in 15 of 17 species. Conclusion: The substantial number of missed occurrences suggests poor power in detecting changes based on presence/absence data. The magnitude of observer bias in cover estimates was relatively small, compared with random error, and therefore potentially analytically tractable. Data in this monitoring system could be improved by a more structured working model during field work.Original publication: Milberg, P., Bergstedt, J., Fridman, J., Odell, G & Westerberg, L., Systematic and random variation in vegetation monitoring data, 2008, Journal of Vegetation Science, (19), 633-644. http://dx.doi.org/10.3170/2008-8-18423. Copyright: Opulus Press, http://www.opuluspress.se/index.ph