A Dynamic Model of mRNA Metabolism

RNA is one of the key components in the central dogma of biology. The protein-coding mRNAs are synthesised in the nucleus, processed to form the mature mRNA molecule, exported to the cytosol where they are translated into the functional protein, and eventually degraded. Gene expression can be regulated by adjusting, for example, mRNA synthesis or degradation rates. These mRNA metabolic rates are measured with RNA metabolic labelling experiments: Newly synthesised RNAs are tagged with modified nucleosides and can thereby be distinguished from pre-existing RNA transcripts. Yet, the analysis of metabolic labelling data is statistically challenging. The tagging of newly synthesised RNA transcripts is incomplete as only a fraction of the native nucleosides is replaced by the modified nucleoside. Also, to our knowledge, no currently available analysis tool provides a framework to investigate mRNA export. To address these challenges, I developed a dynamic model of mRNA metabolism. The model distinguishes between the nuclear and cytosolic compartment (two-compartment model) and thereby allows to analyse nuclear export in addition to cytosolic degradation. The data pre-processing steps are specifically tailored to metabolic labelling data and include the estimation of RNA labelling efficiencies in a time-dependent manner. We performed a metabolic labelling experiment on HeLa-S3 cells combined with cellular fractionation to measure nuclear and cytosolic RNA separately. We then applied my model to estimate nuclear and cytosolic RNA half lives. We find that nuclear half lives are much higher than cytosolic half lives, which leads to the conclusion that mRNA export is slower than mRNA degradation. Consequently, mRNA transcripts spend most of their lifetime in the nucleus and are more abundant in the nucleus than in the cytosol. We discover a group of outstanding genes, called ‘Supernova’ genes, which show an exceptionally fast mRNA export, arguing for a novel and distinct export mechanism

Radio-Frequency-Controlled Urea Dosing for NH3-SCR Catalysts : NH3 Storage Influence to Catalyst Performance under Transient Conditions

Current developments in exhaust gas aftertreatment led to a huge mistrust in diesel driven passenger cars due to their NOx emissions being too high. The selective catalytic reduction (SCR) with ammonia (NH3) as reducing agent is the only approach today with the capability to meet upcoming emission limits. Therefore, the radio-frequency-based (RF) catalyst state determination to monitor the NH3 loading on SCR catalysts has a huge potential in emission reduction. Recent work on this topic proved the basic capability of this technique under realistic conditions on an engine test bench. In these studies, an RF system calibration for the serial type SCR catalyst Cu-SSZ-13 was developed and different approaches for a temperature dependent NH3 storage were determined. This paper continues this work and uses a fully calibrated RF-SCR system under transient conditions to compare different directly measured and controlled NH3 storage levels, and NH3 target curves. It could be clearly demonstrated that the right NH3 target curve, together with a direct control on the desired level by the RF system, is able to operate the SCR system with the maximum possible NOx conversion efficiency and without NH3 slip

Radio-Frequency-Based NH₃-Selective Catalytic Reduction Catalyst Control : Studies on Temperature Dependency and Humidity Influences

The upcoming more stringent automotive emission legislations and current developments have promoted new technologies for more precise and reliable catalyst control. For this purpose, radio-frequency-based (RF) catalyst state determination offers the only approach for directly measuring the NH3 loading on selective catalytic reduction (SCR) catalysts and the state of other catalysts and filter systems. Recently, the ability of this technique to directly control the urea dosing on a current NH3 storing zeolite catalyst has been demonstrated on an engine dynamometer for the first time and this paper continues that work. Therefore, a well-known serial-type and zeolite-based SCR catalyst (Cu-SSZ-13) was investigated under deliberately chosen high space velocities. At first, the full functionality of the RF system with Cu-SSZ-13 as sample was tested successfully. By direct RF-based NH3 storage control, the influence of the storage degree on the catalyst performance, i.e., on NOx conversion and NH3 slip, was investigated in a temperature range between 250 and 400 °C. For each operation point, an ideal and a critical NH3 storage degree was found and analyzed in the whole temperature range. Based on the data of all experimental runs, temperature dependent calibration functions were developed as a basis for upcoming tests under transient conditions. Additionally, the influence of exhaust humidity was observed with special focus on cold start water and its effects to the RF signals

MO077AUTOMATIC SEGMENTATION OF ARTERIES, ARTERIOLES AND GLOMERULI IN NATIVE BIOPSIES WITH THROMBOTIC MICROANGIOPATHY AND OTHER VASCULAR DISEASES

Abstract Background and Aims Thrombotic microangiopathies (TMAs) manifest themselves in arteries, arterioles and glomeruli. Nephropathologists need to differentiate TMAs from mimickers like hypertensive nephropathy and vasculitis which can be problematic due to interobserver disagreement and poorly defined diagnostic criteria over a wide spectrum of morphological changes with partial overlap. As a first step towards a machine learning analysis of TMAs, we developed a computer vision model for segmenting arteries, arterioles and glomeruli in TMA and mimickers. Method We manually segmented n=939 arteries, n=6,023 arterioles, n=4,507 glomeruli on whole slide images (WSIs) of 34 renal biopsies and their HE, PAS, trichrome and Jones sections (19 TMA, 11 hypertensive nephropathy, 4 vasculitis with preglomerular involvement). As a segmentation model we used DeepLab V3, pretrained on 61,734 segmented glomeruli from 768 WSIs. 58 randomly chosen WSIs served as the intrainstitutional holdout testing set after training of the model on the remaining slides. Automatic segmentation accuracies were reported as Cohen's kappa, intersection over union (IoU) and Matthews correlation coefficient (MCC) against the nephropathologist's segmentation as ground truth. Results Over all classes (artery, arteriole, glomerulus) Cohen's kappa was 0.86. IoU was 0.716 for artery, 0.491 for arteriole and 0.829 for glomerulus. MCC was 0.837 for artery, 0.664 for arteriole and 0.907 for glomerulus. Conclusion We achieved good automatic segmentation of arteries, arterioles and glomeruli, even with severe pathological distortion on routine histopathological slides. We will further improve this segmentation technology in order to enable the bulk analysis of these descisive tissue compartments in large clinicopathological repositories of native kidney biopsies with TMA using supervised and unsupervised machine learning algorithms

The price of tumor control

Ipilimumab, a cytotoxic T-lymphocyte antigen-4 (CTLA-4) blocking antibody, has been approved for the treatment of metastatic melanoma and induces adverse events (AE) in up to 64% of patients. Treatment algorithms for the management of common ipilimumab-induced AEs have lead to a reduction of morbidity, e.g. due to bowel perforations. However, the spectrum of less common AEs is expanding as ipilimumab is increasingly applied. Stringent recognition and management of AEs will reduce drug-induced morbidity and costs, and thus, positively impact the cost-benefit ratio of the drug. To facilitate timely identification and adequate management data on rare AEs were analyzed at 19 skin cancer centers. Patient files (n = 752) were screened for rare ipilimumab-associated AEs. A total of 120 AEs, some of which were life-threatening or even fatal, were reported and summarized by organ system describing the most instructive cases in detail. Previously unreported AEs like drug rash with eosinophilia and systemic symptoms (DRESS), granulomatous inflammation of the central nervous system, and aseptic meningitis, were documented. Obstacles included patientś delay in reporting symptoms and the differentiation of steroid-induced from ipilimumab-induced AEs under steroid treatment. Importantly, response rate was high in this patient population with tumor regression in 30.9% and a tumor control rate of 61.8% in stage IV melanoma patients despite the fact that some patients received only two of four recommended ipilimumab infusions. This suggests that ipilimumab-induced antitumor responses can have an early onset and that severe autoimmune reactions may reflect overtreatment. The wide spectrum of ipilimumab-induced AEs demands doctor and patient awareness to reduce morbidity and treatment costs and true ipilimumab success is dictated by both objective tumor responses and controlling severe side effects

The price of tumor control: an analysis of rare side effects of anti-CTLA-4 therapy in metastatic melanoma from the ipilimumab network

Background: Ipilimumab, a cytotoxic T-lymphocyte antigen-4 (CTLA-4) blocking antibody, has been approved for the treatment of metastatic melanoma and induces adverse events (AE) in up to 64% of patients. Treatment algorithms for the management of common ipilimumab-induced AEs have lead to a reduction of morbidity, e.g. due to bowel perforations. However, the spectrum of less common AEs is expanding as ipilimumab is increasingly applied. Stringent recognition and management of AEs will reduce drug-induced morbidity and costs, and thus, positively impact the cost-benefit ratio of the drug. To facilitate timely identification and adequate management data on rare AEs were analyzed at 19 skin cancer centers. Methods and Findings: Patient files (n = 752) were screened for rare ipilimumab-associated AEs. A total of 120 AEs, some of which were life-threatening or even fatal, were reported and summarized by organ system describing the most instructive cases in detail. Previously unreported AEs like drug rash with eosinophilia and systemic symptoms (DRESS), granulomatous inflammation of the central nervous system, and aseptic meningitis, were documented. Obstacles included patientś delay in reporting symptoms and the differentiation of steroid-induced from ipilimumab-induced AEs under steroid treatment. Importantly, response rate was high in this patient population with tumor regression in 30.9% and a tumor control rate of 61.8% in stage IV melanoma patients despite the fact that some patients received only two of four recommended ipilimumab infusions. This suggests that ipilimumab-induced antitumor responses can have an early onset and that severe autoimmune reactions may reflect overtreatment. Conclusion: The wide spectrum of ipilimumab-induced AEs demands doctor and patient awareness to reduce morbidity and treatment costs and true ipilimumab success is dictated by both objective tumor responses and controlling severe side effects

Lymphotoxin β receptor signaling promotes tertiary lymphoid organogenesis in the aorta adventitia of aged ApoE−/− mice

Atherosclerosis involves a macrophage-rich inflammation in the aortic intima. It is increasingly recognized that this intimal inflammation is paralleled over time by a distinct inflammatory reaction in adjacent adventitia. Though cross talk between the coordinated inflammatory foci in the intima and the adventitia seems implicit, the mechanism(s) underlying their communication is unclear. Here, using detailed imaging analysis, microarray analyses, laser-capture microdissection, adoptive lymphocyte transfers, and functional blocking studies, we undertook to identify this mechanism. We show that in aged apoE−/− mice, medial smooth muscle cells (SMCs) beneath intimal plaques in abdominal aortae become activated through lymphotoxin β receptor (LTβR) to express the lymphorganogenic chemokines CXCL13 and CCL21. These signals in turn trigger the development of elaborate bona fide adventitial aortic tertiary lymphoid organs (ATLOs) containing functional conduit meshworks, germinal centers within B cell follicles, clusters of plasma cells, high endothelial venules (HEVs) in T cell areas, and a high proportion of T regulatory cells. Treatment of apoE−/− mice with LTβR-Ig to interrupt LTβR signaling in SMCs strongly reduced HEV abundance, CXCL13, and CCL21 expression, and disrupted the structure and maintenance of ATLOs. Thus, the LTβR pathway has a major role in shaping the immunological characteristics and overall integrity of the arterial wall

Individual attentional selection capacities are reflected in interhemispheric connectivity of the parietal cortex

Modelling psychophysical data using the Theory of Visual Attention (TVA) allows for a quantification of attentional sub-processes, such as the resolution of competition amongst multiple stimuli by top-down control signals for target selection (TVA-parameter alpha). This fMRI study investigated the neural correlates of alpha by comparing activity differences and changes of effective connectivity between conditions where a target was accompanied by a distractor or by a second target. Twenty-five participants performed a partial report task inside the MRI scanner. The left angular gyrus (ANG), medial frontal, and posterior cingulate cortex showed higher activity when a target was accompanied by a distractor as opposed to a second target. The reverse contrast yielded activation of a bilateral fronto-parietal network, the anterior insula, anterior cingulate cortex, and left inferior occipital gyrus. A psychophysiological interaction analysis revealed that the connectivity between left ANG and the left and right supramarginal gyrus (SMG), left anterior insula, and right putamen was enhanced in the target-distractor condition in participants with worse attentional top-down control. Dynamic causal modelling suggested that the connection from left ANG to right SMG during distractor presence was modulated by alpha. Our data show that interindividual differences in attentional processing are reflected in changes of effective connectivity without significant differences in activation strength of network nodes. (C) 2016 Elsevier Inc. All rights reserved

Modulation of top-down control of visual attention by cathodal tDCS over right IPS.

The right intraparietal sulcus (rIPS) is a key region for the endogenous control of selective visual attention in the human brain. Previous studies suggest that the rIPS is especially involved in top-down control and spatial distribution of attention across both visual hemifields. We further explored these attentional functions using transcranial direct current stimulation (tDCS) of the rIPS to modulate behavioral performance in a partial report task. Performance was analyzed according to the theory of visual attention (TVA) (Bundesen, 1990), which provides a computational framework to investigate different parameters of visuo-attentional processing such as top-down control, attentional weighting, capacity of visual short term memory, and processing speed. We investigated the effects of different tDCS current strengths (1 mA and 2 mA) in two experiments: 1 mA tDCS (anodal, cathodal, sham) did not affect any of the TVA parameters, but cathodal 2 mA stimulation significantly enhanced top-down control as evidenced by a reduction of the alpha parameter of TVA, regardless of hemifield. This differential impact on the top-down control component of attentional processing suggests that the horizontal rIPS is mainly involved in attentional selection as none of the spatial or resource variables of TVA were altered. Furthermore, the data add evidence to previous work highlighting (1) the importance of using appropriate current strength in stimulation protocols, and (2) that the often reported inhibitory effect of cathodal stimulation in e. g., motor tasks might not extend to cognitive paradigms