Quantitative phosphoproteomics to unravel the cellular response to chemical stressors with different modes of action

Damage to cellular macromolecules and organelles by chemical exposure evokes activation of various stress response pathways. To what extent different chemical stressors activate common and stressor-specific pathways is largely unknown. Here, we used quantitative phosphoproteomics to compare the signaling events induced by four stressors with different modes of action: the DNA damaging agent: cisplatin (CDDP), the topoisomerase II inhibitor: etoposide (ETO), the pro-oxidant: diethyl maleate (DEM) and the immunosuppressant: cyclosporine A (CsA) administered at an equitoxic dose to mouse embryonic stem cells. We observed major differences between the stressors in the number and identity of responsive phosphosites and the amplitude of phosphorylation. Kinase motif and pathway analyses indicated that the DNA damage response (DDR) activation by CDDP occurs predominantly through the replication-stress-related Atr kinase, whereas ETO triggers the DDR through Atr as well as the DNA double-strand-break-associated Atm kinase. CsA shares with ETO activation of CK2 kinase. Congruent with their known modes of action, CsA-mediated signaling is related to down-regulation of pathways that control hematopoietic differentiation and immunity, whereas oxidative stress is the most prominent initiator of DEM-modulated stress signaling. This study shows that even at equitoxic doses, different stressors induce distinctive and complex phosphorylation signaling cascades.Toxicolog

STEPWISE Project: Sorption-Enhanced Water-Gas Shift Technology to Reduce Carbon Footprint in the Iron and Steel Industry

ndustrial processes contribute significantly to global carbon dioxide emissions, with iron and steel manufacturing alone responsible for 6% of the total figure. The STEPWISE project, funded through the European Horizon 2020 (H2020) Low Carbon Energy (LCE) programme under grant agreement number 640769, is looking at reducing CO 2 emissions in the iron and steel making industries. At the heart of this project is the ECN technology called sorption-enhanced water-gas shift (SEWGS), which is a solid sorption technology for CO 2 capture from fuel gases such as blast furnace gas (BFG). This technology combines water-gas shift (WGS) in the WGS section with CO 2 /H 2 separation steps in the SEWGS section. Scaling up of the SEWGS technology for CO 2 capture from BFG and demonstrating it in an industrially relevant environment are the key objectives of the STEPWISE project, which are achieved by international collaboration between the project partners towards design, construction and operation of a pilot plant at Swerea Mefos, Luleå, Sweden, next to the SSAB steel manufacturing site

Effect of Pretreatment Method on the Nanostructure and Performance of Supported Co Catalysts in Fischer−Tropsch Synthesis

ABSTRACT: Understanding precursor transformation to active catalysts is crucial to heterogeneous Fischer−Tropsch (FT) catalysis directed toward production of hydrocarbons for transportation fuels. Despite considerable literature on FT catalysis, the effect of pretreatment of supported cobalt catalysts on cobalt dispersion, dynamic atomic structure, and the activity of the catalysts is not well understood. Here we present systematic studies into the formation of active catalyst phases in supported Co catalyst precursors in FT catalysis using in situ environmental (scanning) transmission electron microscopy (E(S)TEM) with single-atom resolution under controlled reaction environments for in situ visualization, imaging, and analysis of reacting atomic species in real time, EXAFS, XAS, DRIFTS analyses, and catalytic activity measurements. We have synthesized and analyzed dried reduced (D) and dried calcined reduced (DC) Co real catalysts on reducible and nonreducible supports, such as SiO2, Al2O3, TiO2, and ZrO2. Comparisons of dynamic in situ atomic structural observations of reacting single atoms, atomic clusters, and nanoparticles of Co and DRIFTS, XAS, EXAFS, and catalytic activity data of the D and DC samples reveal in most cases better dispersion in the D samples, leading to a larger number of low-coordination Co0 sites and a higher number of active sites for CO adsorption. The experimental findings on the degree of reduction of D and 27 DC catalysts on reducible and nonreducible supports and correlations between hexagonal (hcp) Co sites and the activity of the catalysts generate structural insights into the catalyst dynamics, important to the development of efficient FT catalysts

Prediction of human drug-induced liver injury (DILI) in relation to oral doses and blood concentrations

Drug-induced liver injury (DILI) cannot be accurately predicted by animal models. In addition, currently available in vitro methods do not allow for the estimation of hepatotoxic doses or the determination of an acceptable daily intake (ADI). To overcome this limitation, an in vitro/in silico method was established that predicts the risk of human DILI in relation to oral doses and blood concentrations. This method can be used to estimate DILI risk if the maximal blood concentration (Cmax) of the test compound is known. Moreover, an ADI can be estimated even for compounds without information on blood concentrations. To systematically optimize the in vitro system, two novel test performance metrics were introduced, the toxicity separation index (TSI) which quantifies how well a test differentiates between hepatotoxic and non-hepatotoxic compounds, and the toxicity estimation index (TEI) which measures how well hepatotoxic blood concentrations in vivo can be estimated. In vitro test performance was optimized for a training set of 28 compounds, based on TSI and TEI, demonstrating that (1) concentrations where cytotoxicity first becomes evident in vitro (EC10) yielded better metrics than higher toxicity thresholds (EC50); (2) compound incubation for 48 h was better than 24 h, with no further improvement of TSI after 7 days incubation; (3) metrics were moderately improved by adding gene expression to the test battery; (4) evaluation of pharmacokinetic parameters demonstrated that total blood compound concentrations and the 95%-population-based percentile of Cmax were best suited to estimate human toxicity. With a support vector machine-based classifier, using EC10 and Cmax as variables, the cross-validated sensitivity, specificity and accuracy for hepatotoxicity prediction were 100, 88 and 93%, respectively. Concentrations in the culture medium allowed extrapolation to blood concentrations in vivo that are associated with a specific probability of hepatotoxicity and the corresponding oral doses were obtained by reverse modeling. Application of this in vitro/in silico method to the rat hepatotoxicant pulegone resulted in an ADI that was similar to values previously established based on animal experiments. In conclusion, the proposed method links oral doses and blood concentrations of test compounds to the probability of hepatotoxicity

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Doping liquid argon with xenon in ProtoDUNE Single-Phase: effects on scintillation light

Doping of liquid argon TPCs (LArTPCs) with a small concentration of xenon is a technique for light-shifting and facilitates the detection of the liquid argon scintillation light. In this paper, we present the results of the first doping test ever performed in a kiloton-scale LArTPC. From February to May 2020, we carried out this special run in the single-phase DUNE Far Detector prototype (ProtoDUNE-SP) at CERN, featuring 720 t of total liquid argon mass with 410 t of fiducial mass. A 5.4 ppm nitrogen contamination was present during the xenon doping campaign. The goal of the run was to measure the light and charge response of the detector to the addition of xenon, up to a concentration of 18.8 ppm. The main purpose was to test the possibility for reduction of non- uniformities in light collection, caused by deployment of photon detectors only within the anode planes. Light collection was analysed as a function of the xenon concentration, by using the pre-existing photon detection system (PDS) of ProtoDUNE-SP and an additional smaller set-up installed specifically for this run. In this paper we first summarize our current understanding of the argon-xenon energy transfer process and the impact of the presence of nitrogen in argon with and without xenon dopant. We then describe the key elements of ProtoDUNE-SP and the injection method deployed. Two dedicated photon detectors were able to collect the light produced by xenon and the total light. The ratio of these components was measured to be about 0.65 as 18.8 ppm of xenon were injected. We performed studies of the collection efficiency as a function of the distance between tracks and light detectors, demonstrating enhanced uniformity of response for the anode-mounted PDS. We also show that xenon doping can substantially recover light losses due to contamination of the liquid argon by nitrogen

The DUNE far detector vertical drift technology. Technical design report

DUNE is an international experiment dedicated to addressing some of the questions at the forefront of particle physics and astrophysics, including the mystifying preponderance of matter over antimatter in the early universe. The dual-site experiment will employ an intense neutrino beam focused on a near and a far detector as it aims to determine the neutrino mass hierarchy and to make high-precision measurements of the PMNS matrix parameters, including the CP-violating phase. It will also stand ready to observe supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector implements liquid argon time-projection chamber (LArTPC) technology, and combines the many tens-of-kiloton fiducial mass necessary for rare event searches with the sub-centimeter spatial resolution required to image those events with high precision. The addition of a photon detection system enhances physics capabilities for all DUNE physics drivers and opens prospects for further physics explorations. Given its size, the far detector will be implemented as a set of modules, with LArTPC designs that differ from one another as newer technologies arise. In the vertical drift LArTPC design, a horizontal cathode bisects the detector, creating two stacked drift volumes in which ionization charges drift towards anodes at either the top or bottom. The anodes are composed of perforated PCB layers with conductive strips, enabling reconstruction in 3D. Light-trap-style photon detection modules are placed both on the cryostat's side walls and on the central cathode where they are optically powered. This Technical Design Report describes in detail the technical implementations of each subsystem of this LArTPC that, together with the other far detector modules and the near detector, will enable DUNE to achieve its physics goals

Performance of a modular ton-scale pixel-readout liquid argon time projection chamber

The Module-0 Demonstrator is a single-phase 600 kg liquid argon time projection chamber operated as a prototype for the DUNE liquid argon near detector. Based on the ArgonCube design concept, Module-0 features a novel 80k-channel pixelated charge readout and advanced high-coverage photon detection system. In this paper, we present an analysis of an eight-day data set consisting of 25 million cosmic ray events collected in the spring of 2021. We use this sample to demonstrate the imaging performance of the charge and light readout systems as well as the signal correlations between the two. We also report argon purity and detector uniformity measurements and provide comparisons to detector simulations

Substituting Chromium in Iron-Based Catalysts for the High-Temperature Water-Gas Shift Reaction

A set of doped iron oxides (chromium, aluminium, gallium, indium, manganese, zinc, niobium) were prepared by a one-step co-precipitation/calcination approach, evaluated for their WGS activity under industrially relevant conditions, and characterized in detail. The WGS activity after ageing the doped catalyst for 4 days at 25 bar follows the order chromium ≈ aluminium > gallium > indium > manganese > zinc > niobium for copper co-doped catalysts. The activated catalysts predominantly consist of magnetite, irrespective of the dopant. Mössbauer spectra of aged catalysts showed that aluminium and zinc occupy both tetrahedral and octahedral sites of magnetite, while chromium, gallium, indium, manganese, and niobium preferentially substitute octahedral iron. The incorporation of trivalent metal ions of similar size to octahedral Fe3+ (i.e., chromium, aluminium, gallium) increases the CO conversion relative to a non-doped catalyst, irrespective of incorporation in tetrahedral or octahedral sites. The substitution of Fe2+ with Mn2+ results in an increased Fe3+/Fe2+ ratio. Incorporation of Zn2+ in tetrahedral sites (replacing Fe3+ ions) leads to a complex structure where the charge balance is compensated from the octahedral sites. Separate dopant metal oxide phases were observed in indium- and niobium-doped catalysts. XPS shows that copper is present as a separate phase in activated copper co-doped catalysts. Aluminium is identified as the most promising promoter for substituting chromium in commercial high-temperature WGS catalysts on the basis of their similar high CO conversion, although incorporation of these dopants into the magnetite structure differed substantially

To Promote the Progress: Why Do States Create New Intellectual Property Rights? ACES Working Papers, August 2012

The question I seek to answer is not about explaining support or resistance to the globalization or harmonization of IP rights. Rather, I am interested in new IP rights: what happened to cause a certain intangible to change from something that was not considered intellectual property to something that was considered intellectual property? Explaining the globalization or harmonization of already-existing IP rights is an important task, but fundamentally different than explaining why some things became intellectual property in the first place