Generating large labeled data sets for laparoscopic image processing tasks using unpaired image-to-image translation

In the medical domain, the lack of large training data sets and benchmarks is often a limiting factor for training deep neural networks. In contrast to expensive manual labeling, computer simulations can generate large and fully labeled data sets with a minimum of manual effort. However, models that are trained on simulated data usually do not translate well to real scenarios. To bridge the domain gap between simulated and real laparoscopic images, we exploit recent advances in unpaired image-to-image translation. We extent an image-to-image translation method to generate a diverse multitude of realistically looking synthetic images based on images from a simple laparoscopy simulation. By incorporating means to ensure that the image content is preserved during the translation process, we ensure that the labels given for the simulated images remain valid for their realistically looking translations. This way, we are able to generate a large, fully labeled synthetic data set of laparoscopic images with realistic appearance. We show that this data set can be used to train models for the task of liver segmentation of laparoscopic images. We achieve average dice scores of up to 0.89 in some patients without manually labeling a single laparoscopic image and show that using our synthetic data to pre-train models can greatly improve their performance. The synthetic data set will be made publicly available, fully labeled with segmentation maps, depth maps, normal maps, and positions of tools and camera (http://opencas.dkfz.de/image2image).Comment: Accepted at MICCAI 201

Serum MMP7, MMP10 and MMP12 level as negative prognostic markers in colon cancer patients

Background: Matrixmetalloproteinases (MMPs) comprise a family of zinc-dependent endopeptidases which are involved in angiogenesis, tumor invasion and metastatic formation. Up to date, the prognostic relevance of MMPs in serum of patients with colon cancer remains unknown. Thus, we wanted to assess an expression pattern of MMPs in a homogenous cohort of colon cancer patients to assess their potential as prognostic biomarkers. Methods: Differences in the expression pattern of MMP7, MMP10 and MMP12 in 78 serum specimens of patients with an adenocarcinoma of the colon and serum specimens of a healthy control group were assessed using Luminex-100 technologies. Subsequently, we correlated these results with histopathological and clinical data of the patients. Results: Luminex based expression analysis revealed a significant overexpression of MMP7 and an overexpression of MMP10 and MMP12 in the sera of colon cancer patients compared to the healthy control group. Patients with vascular invasion showed a significantly higher MMP12 expression than V0-staged patients. Moreover overexpression of MMP7, MMP10 and MMP12 in colon cancer patients´ sera displayed a significantly impaired overall survival. Multivariate analysis revealed high MMP10 serum levels to be an independent adverse prognostic marker in colon cancer patients. Conclusions: Expression patterns of MMP7, MMP10 and MMP12 in colon cancer patients´ sera are different compared to serum specimens of healthy individuals. Furthermore, overexpression of MMP7, MMP10 and MMP12 in colon cancer patients´ sera correlates with a dismal prognosis and may help to stratify patients into different risk groups

Molecular understanding of the suppression of new-particle formation by isoprene

Nucleation of atmospheric vapours produces more than half of global cloud condensation nuclei and so has an important influence on climate. Recent studies show that monoterpene (C10H16) oxidation yields highly oxygenated products that can nucleate with or without sulfuric acid. Monoterpenes are emitted mainly by trees, frequently together with isoprene (C5H8), which has the highest global emission of all organic vapours. Previous studies have shown that isoprene suppresses new-particle formation from monoterpenes, but the cause of this suppression is under debate. Here, in experiments performed under atmospheric conditions in the CERN CLOUD chamber, we show that isoprene reduces the yield of highly oxygenated dimers with 19 or 20 carbon atoms - which drive particle nucleation and early growth - while increasing the production of dimers with 14 or 15 carbon atoms. The dimers (termed C-20 and C-15, respectively) are produced by termination reactions between pairs of peroxy radicals (RO2 center dot) arising from monoterpenes or isoprene. Compared with pure monoterpene conditions, isoprene reduces nucleation rates at 1.7 nm (depending on the isoprene = monoterpene ratio) and approximately halves particle growth rates between 1.3 and 3.2 nm. However, above 3.2 nm, C-15 dimers contribute to secondary organic aerosol, and the growth rates are unaffected by isoprene. We further show that increased hydroxyl radical (OH center dot) reduces particle formation in our chemical system rather than enhances it as previously proposed, since it increases isoprene-derived RO2 center dot radicals that reduce C-20 formation. RO2 center dot termination emerges as the critical step that determines the highly oxygenated organic molecule (HOM) distribution and the corresponding nucleation capability. Species that reduce the C-20 yield, such as NO, HO2 and as we show isoprene, can thus effectively reduce biogenic nucleation and early growth. Therefore the formation rate of organic aerosol in a particular region of the atmosphere under study will vary according to the precise ambient conditions.Peer reviewe

Lunar intrusive domes: Morphometric analysis and laccolith modelling

Wöhler C, Lena R. Lunar intrusive domes: Morphometric analysis and laccolith modelling. ICARUS. 2009;204(2):381-398.This study examines a set of lunar domes with very low flank slopes which differ in several respects from the frequently occurring lunar effusive domes. Some of these domes are exceptionally large, and most of them are associated with faults or linear rilles of presumably tensional origin. Accordingly, they might be interpreted as surface manifestations of laccolithic intrusions formed by flexure-induced vertical uplift of the lunar crust (or, alternatively, as low effusive edifices due to lava mantling of highland terrain, or kipukas, or structural features). All of them are situated near the borders of mare regions or in regions characterised by extensive effusive volcanic activity. Clementine multispectral UVVIS imagery indicates that they do not preferentially occur in specific types of mare basalt. Our determination of their morphometric properties, involving a combined photoclinometry and shape from shading technique applied to telescopic CCD images acquired at oblique illumination, reveals large dome diameters between 10 and more than 30 km, flank slopes below 0.9 degrees, and volumes ranging from 0.5 to 50 km(3). We establish three morphometric classes. The first class, In1, comprises large domes with diameters above 25 kin and flank slopes of 0.2 degrees-0.6 degrees, class In2 is made up by smaller and slightly steeper domes with diameters of 1015 kin and flank slopes between 0.4 degrees and 0.9 degrees, and domes of class In3 have diameters of 13-20 km and flank slopes below 0.3 degrees. While the morphometric properties of several candidate intrusive domes overlap with those of some classes of effusive domes, we show that a possible distinction criterion are the characteristic elongated Outlines of the candidate intrusive domes. We examine how they differ from typical effusive domes of classes 5 and 6 defined by Head and Gifford [Head, J.W., Gifford, A., 1980. Lunar mare domes: classification and modes of origin. Moon Planets 22, 235-257], and show that they are likely no highland kipukas due to the absence of spectral contrast to their surrounding. These considerations serve as a motivation for an analysis of the candidate intrusive domes in terms of the laccolith model by Kerr and Pollard [Kerr, A.D., Pollard, D.D., 1998. Toward more realistic formulations for the analysis of laccoliths. J. Struct. Geol. 20(12), 1783-1793], to estimate the geophysical parameters, especially the intrusion depth and the magma pressure, which would result from the observed morphometric properties. Accordingly, domes of class In1 are characterised by intrusion depths of 2.3-3.5 km and magma pressures between 18 and 29 MPa. For the smaller and steeper domes of class In2 the magma intruded to shallow depths between 0.4 and 1.0 km while the inferred magma pressures range from 3 to 8 MPa. Class In3 domes are similar to those of class In1 with intrusion depths of 1.8-2.7 km and magma pressures of 15-23 MPa. As an extraordinary feature, we describe in some detail the concentric crater Archytas G associated with the intrusive dome At1 and discuss possible modes of origin. In comparison to the candidate intrusive domes, terrestrial laccoliths tend to be smaller, but it remains unclear if this observation is merely a selection effect due to the limited resolution of our telescopic CCD images. An elongated outline is common to many terrestrial laccoliths and the putative lunar laccoliths, while the thickness values measured for terrestrial laccoliths are typically higher than those inferred for lunar laccoliths, but the typical intrusion depths are comparable. C) 2009 Elsevier Inc. All rights reserved