Semantic segmentation of non-linear multimodal images for disease grading of inflammatory bowel disease: A segnet-based application

Non-linear multimodal imaging, the combination of coherent anti-stokes Raman scattering (CARS), two-photon excited fluorescence (TPEF) and second harmonic generation (SHG), has shown its potential to assist the diagnosis of different inflammatory bowel diseases (IBDs). This label-free imaging technique can support the ‘gold-standard’ techniques such as colonoscopy and histopathology to ensure an IBD diagnosis in clinical environment. Moreover, non-linear multimodal imaging can measure biomolecular changes in different tissue regions such as crypt and mucosa region, which serve as a predictive marker for IBD severity. To achieve a real-time assessment of IBD severity, an automatic segmentation of the crypt and mucosa regions is needed. In this paper, we semantically segment the crypt and mucosa region using a deep neural network. We utilized the SegNet architecture (Badrinarayanan et al., 2015) and compared its results with a classical machine learning approach. Our trained SegNet mod el achieved an overall F1 score of 0.75. This model outperformed the classical machine learning approach for the segmentation of the crypt and mucosa region in our study

Computational tissue staining of non-linear multimodal imaging using supervised and unsupervised deep learning

Hematoxylin and Eosin (H&E) staining is the 'gold-standard' method in histopathology. However, standard H&E staining of high-quality tissue sections requires long sample preparation times including sample embedding, which restricts its application for 'real-time' disease diagnosis. Due to this reason, a label-free alternative technique like non-linear multimodal (NLM) imaging, which is the combination of three non-linear optical modalities including coherent anti-Stokes Raman scattering, two-photon excitation fluorescence and second-harmonic generation, is proposed in this work. To correlate the information of the NLM images with H&E images, this work proposes computational staining of NLM images using deep learning models in a supervised and an unsupervised approach. In the supervised and the unsupervised approach, conditional generative adversarial networks (CGANs) and cycle conditional generative adversarial networks (cycle CGANs) are used, respectively. Both CGAN and cycle CGAN models generate pseudo H&E images, which are quantitatively analyzed based on mean squared error, structure similarity index and color shading similarity index. The mean of the three metrics calculated for the computationally generated H&E images indicate significant performance. Thus, utilizing CGAN and cycle CGAN models for computational staining is beneficial for diagnostic applications without performing a laboratory-based staining procedure. To the author's best knowledge, it is the first time that NLM images are computationally stained to H&E images using GANs in an unsupervised manner

Water for dairy cattle

The Oklahoma Cooperative Extension Service periodically issues revisions to its publications. The most current edition is made available. For access to an earlier edition, if available for this title, please contact the Oklahoma State University Library Archives by email at [email protected] or by phone at 405-744-6311

An overview of atmospheric deposition chemistry over the Alps: present status and long-term trends

Several research programs monitoring atmospheric deposition have been launched in the Alpine countries in the last few decades. This paper uses data from previous and ongoing projects to: (i) investigate geographical variability in wet deposition chemistry over the Alps; (ii) assess temporal trends of the major chemical variables in response to changes in the atmospheric emission of pollutants; (iii) discuss the potential relationship between the status of atmospheric deposition and its effects on forest ecosystems in the alpine and subalpine area, focusing particularly on nitrogen input. We also present results of studies performed at a local level on specific topics such as long-term changes in lead deposition and the role of occult deposition in total nitrogen input. The analysis performed here highlights the marked geographical variability of atmospheric deposition in the Alpine region. Apart from some evidence of geographically limited effects, due to local sources, no obvious gradients were identified in the major ion deposition. The highest ionic loads were recorded in areas in the foothills of the Alps, such as the pre-alpine area in North-Western Italy and the area of Canton Ticino, Switzerland. Trend analysis shows a widespread decrease in the acidity of precipitation in the last 15–20 years as a consequence of the reduced emission of S compounds. On the other hand, nitrate concentrations in rain have not changed so much, and ammonium has decreased significantly only at the Austrian sampling sites. The deposition of N is still well above the estimated critical loads of nutrient N at some forest sites in the alpine and subalpine areas, thus confirming the critical situation of both terrestrial and aquatic ecosystems regarding N inputs. Existing data highlights the importance of continuously monitoring atmospheric deposition chemistry in the Alpine area, taking account of acidifying elements, nutrients and other pollutants such as heavy metals and organic compounds. There is also a need for unifying sampling and analytical methods in order to obtain comparable data from the different regions of the Alps

Geostrategies of the European neighbourhood policy

The debate about the European Neighbourhood Policy (ENP) has, in essence, been about borders and bordering. Such departures could contribute — and often do so — to a rather fixed geopolitical vision of what the EU is about and how it aims to run and to organize the broader European space. However, this article aims to retain space for viewing the ENP as a developmental and somewhat fluid process. A conceptual framework, based on outlining three geopolitical models and a series of different geopolitical strategies employed by the EU in regard to its borders, is hence employed in order to be able to tell a more dynamic story regarding the developing nature of the ENP and the EU's evolving nature more generally. The complexity traced informs us that various geostrategies may be held at the same time at the external border. Moreover, the dominance of one geostrategy may be replaced by another or a different combination of them with regard to the same neighbourhood. It is, more generally, argued that if anything it is precisely this dynamism that should be championed as a valuable resource, avoiding the tendency to close off options through the reification of particular visions of the nature of the EU and its borders

Intestinal epithelial barrier integrity investigated by label-free techniques in ulcerative colitis patients

The intestinal epithelial barrier, among other compartments such as the mucosal immune system, contributes to the maintenance of intestinal homeostasis. Therefore, any disturbance within the epithelial layer could lead to intestinal permeability and promote mucosal inflammation. Considering that disintegration of the intestinal epithelial barrier is a key element in the etiology of ulcerative colitis, further assessment of barrier integrity could contribute to a better understanding of the role of epithelial barrier defects in ulcerative colitis (UC), one major form of chronic inflammatory bowel disease. Herein, we employ fast, non-destructive, and label-free non-linear methods, namely coherent anti-Stokes Raman scattering (CARS), second harmonic generation (SHG), two-photon excited fluorescence (TPEF), and two-photon fluorescence lifetime imaging (2P-FLIM), to assess the morpho-chemical contributions leading to the dysfunction of the epithelial barrier. For the first time, the formation of epithelial barrier gaps was directly visualized, without sophisticated data analysis procedures, by the 3D analysis of the colonic mucosa from severely inflamed UC patients. The results were compared with histopathological and immunofluorescence images and validated using transmission electron microscopy (TEM) to indicate structural alterations of the apical junction complex as the underlying cause for the formation of the epithelial barrier gaps. Our findings suggest the potential advantage of non-linear multimodal imaging is to give precise, detailed, and direct visualization of the epithelial barrier in the gastrointestinal tract, which can be combined with a fiber probe for future endomicroscopy measurements during real-time in vivo imaging

Managing milk composition: Normal sources of variation

The Oklahoma Cooperative Extension Service periodically issues revisions to its publications. The most current edition is made available. For access to an earlier edition, if available for this title, please contact the Oklahoma State University Library Archives by email at [email protected] or by phone at 405-744-6311

Managing milk composition: Maximizing rumen function

The Oklahoma Cooperative Extension Service periodically issues revisions to its publications. The most current edition is made available. For access to an earlier edition, if available for this title, please contact the Oklahoma State University Library Archives by email at [email protected] or by phone at 405-744-6311