On the representation error in data assimilation

Representation, representativity, representativeness error, forward interpolation error, forward model error, observation operator error, aggregation error and sampling error are all terms used to refer to components of observation error in the context of data assimilation. This paper is an attempt to consolidate the terminology that has been used in the earth sciences literature and was suggested at a European Space Agency workshop held in Reading in April 2014. We review the state-of-the-art, and through examples, motivate the terminology. In addition to a theoretical framework, examples from application areas of satellite data assimilation, ocean reanalysis and atmospheric chemistry data assimilation are provided. Diagnosing representation error statistics as well as their use in state-of-the-art data assimilation systems is discussed within a consistent framework

Linear Responses in Time-dependent Hartree-Fock-Bogoliubov Method with Gogny Interaction

A numerical method to integrate the time-dependent Hartree-Fock Bogoliubov (TDHFB) equations with Gogny interaction is proposed. The feasibility of the TDHFB code is illustrated by the conservation of the energy, particle numbers, and center-of-mass in the small amplitude vibrations of oxygen 20. The TDHFB code is applied to the isoscalar quadrupole and/or isovector dipole vibrations in the linear (small amplitude) region in oxygen isotopes (masses A = 18,20,22 and 24), titanium isotopes (A = 44,50,52 and 54), neon isotope (A = 26), and magnesium isotopes (A = 24 and 34). The isoscalar quadrupole and isovector dipole strength functions are calculated from the expectation values of the isoscalar quadrupole and isovector dipole moments.Comment: 10 pages, 13 figure

Retrievals of the main phytoplankton groups at Lake Constance using OLCI, DESIS, and evaluated with field observations

Phytoplankton play an important role in the aquatic biogeochemical cycling such as for the formation of organic matter by photosynthetic processes through the fixation of carbon dioxide, and assimilation of macro- and micronutrients depending on their metabolic needs. These processes are common to all phytoplankton, however some phytoplankton groups have specific needs and thus play different functional roles in the biogeochemical cycle, which are used to classify phytoplankton into different phytoplankton functional types (PFTs). Information on the phytoplankton groups can be obtained from satellite observations such as the Ocean and Land Colour Instrument (OLCI) onboard of ISS and Sentinel-3. PFTs global ocean abundance can be estimated based on the OC-PFT algorithm (Hirata et al. 2011 and related updates to it) which is based on the assumption that a marker pigment for a specific PFT varies in dependence to the chlorophyll-a concentration. In this study, OC-PFT retrieval has been developed and adapted for estimation of PFT from Lake Constance by using a large collection of in-situ HPLC data set measured since 2000 at the largest German inland water by the regional authority and further analysed to derive PFT using the diagnostic pigment analysis following Vidussi et al. (2001) with adapted coefficients for Lake Constance. The PFT retrieved from OLCI are validated using independent in situ data derived from HPLC pigment measurements from 4 field campaigns performed in 2019 and 2020 at Lake Constance. Concentrations for five phytoplankton groups (diatoms, dinoflagellates, cryptophytes, green algae, and prokaryotes) are retrieved for Lake Constance, being the dominants diatoms and cryptophytes and at lesser degree green algae. In addition, evaluation of synergistic PFT products are presented to enlarge the capabilities of PFT data in inland and coastal waters analytically retrieved from high spectral and high spatial data such as DESIS, EnMAP or PRISMA by synergistic use with OLCI OC-PFT data sets is discussed

Computer-assisted and fractal-based morphometric assessment of microvascularity in histological specimens of gliomas

Fractal analysis is widely applied to investigate the vascular system in physiological as well as pathological states. We propose and examine a computer-aided and fractal-based image analysis technique to quantify the microvascularity in histological specimens of WHO grade II and III gliomas. A computer-aided and fractal-based analysis was used to describe the microvessels and to quantify their geometrical complexity in histological specimens collected from 17 patients. The statistical analysis showed that the fractal-based indexes are the most discriminant parameters to describe the microvessels. The computer-aided quantitative analysis also showed that grade III gliomas are generally more vascularized than grade II gliomas. The fractal parameters are reliable quantitative indicators of the neoplastic microvasculature, making them potential surrogate biomarkers. The qualitative evaluation currently performed by the neuropathologist can be combined with the computer-assisted quantitative analysis of the microvascularity to improve the diagnosis and optimize the treatment of patients with brain cancer

Inhibition of Notch pathway arrests PTEN-deficient advanced prostate cancer by triggering p27-driven cellular senescence.

Activation of NOTCH signalling is associated with advanced prostate cancer and treatment resistance in prostate cancer patients. However, the mechanism that drives NOTCH activation in prostate cancer remains still elusive. Moreover, preclinical evidence of the therapeutic efficacy of NOTCH inhibitors in prostate cancer is lacking. Here, we provide evidence that PTEN loss in prostate tumours upregulates the expression of ADAM17, thereby activating NOTCH signalling. Using prostate conditional inactivation of both Pten and Notch1 along with preclinical trials carried out in Pten-null prostate conditional mouse models, we demonstrate that Pten-deficient prostate tumours are addicted to the NOTCH signalling. Importantly, we find that pharmacological inhibition of γ-secretase promotes growth arrest in both Pten-null and Pten/Trp53-null prostate tumours by triggering cellular senescence. Altogether, our findings describe a novel pro-tumorigenic network that links PTEN loss to ADAM17 and NOTCH signalling, thus providing the rational for the use of γ-secretase inhibitors in advanced prostate cancer patients

Obtaining Phytoplankton Diversity from Ocean Color: A Scientific Roadmap for Future Development

To improve our understanding of the role of phytoplankton for marine ecosystems and global biogeochemical cycles, information on the global distribution of major phytoplankton groups is essential. Although algorithms have been developed to assess phytoplankton diversity from space for over two decades, so far the application of these data sets has been limited. This scientific roadmap identifies user needs, summarizes the current state of the art, and pinpoints major gaps in long-term objectives to deliver space-derived phytoplankton diversity data that meets the user requirements. These major gaps in using ocean color to estimate phytoplankton community structure were identified as: (a) the mismatch between satellite, in situ and model data on phytoplankton composition, (b) the lack of quantitative uncertainty estimates provided with satellite data, (c) the spectral limitation of current sensors to enable the full exploitation of backscattered sunlight, and (d) the very limited applicability of satellite algorithms determining phytoplankton composition for regional, especially coastal or inland, waters. Recommendation for actions include but are not limited to: (i) an increased communication and round-robin exercises among and within the related expert groups, (ii) the launching of higher spectrally and spatially resolved sensors, (iii) the development of algorithms that exploit hyperspectral information, and of (iv) techniques to merge and synergistically use the various streams of continuous information on phytoplankton diversity from various satellite sensors' and in situ data to ensure long-term monitoring of phytoplankton composition

Phase I/II trial of doxorubicin and fixed dose-rate infusion gemcitabine in advanced soft tissue sarcomas: a GEIS study

The aim of the study was to determine the dose-limiting toxicity and maximum tolerated dose of a first-line combination of doxorubicin and gemcitabine in adult patients with advanced soft tissue sarcomas and to explore its activity and toxicity, and the presence of possible interactions between these agents. Patients with measurable disease were initially treated with doxorubicin 60 mg m−2 by i.v. bolus on day 1 followed by gemcitabine at 800 mg m−2 over 80 min on days 1 and 8, every 21 days. Concentrations of gemcitabine and 2′,2′-difluorodeoxyuridine in plasma, and gemcitabine triphosphate levels in peripheral blood mononuclear cells were determined during 8 h after the start of gemcitabine infusion. Myelosuppression and stomatitis were limiting toxicities, and the initial dose level was applied for the Phase II trial, where grade 3–4 granulocytopenia occurred in 70% of patients, grade 3 stomatitis in 46% and febrile neutropenia in 20%. Objective activity in 36 patients was 22% (95% CI: 9–35%), and a 50% remission rate was noted in leiomyosarcomas. Administration of doxorubicin preceding gemcitabine significantly reduced the synthesis of gemcitabine triphosphate. Clinical activity, similar to that of single-agent doxorubicin, and the toxicity encountered do not justify further studies with this schedule of administration

The nuclear energy density functional formalism

The present document focuses on the theoretical foundations of the nuclear energy density functional (EDF) method. As such, it does not aim at reviewing the status of the field, at covering all possible ramifications of the approach or at presenting recent achievements and applications. The objective is to provide a modern account of the nuclear EDF formalism that is at variance with traditional presentations that rely, at one point or another, on a {\it Hamiltonian-based} picture. The latter is not general enough to encompass what the nuclear EDF method represents as of today. Specifically, the traditional Hamiltonian-based picture does not allow one to grasp the difficulties associated with the fact that currently available parametrizations of the energy kernel $E[g',g]$ at play in the method do not derive from a genuine Hamilton operator, would the latter be effective. The method is formulated from the outset through the most general multi-reference, i.e. beyond mean-field, implementation such that the single-reference, i.e. "mean-field", derives as a particular case. As such, a key point of the presentation provided here is to demonstrate that the multi-reference EDF method can indeed be formulated in a {\it mathematically} meaningful fashion even if $E[g',g]$ does {\it not} derive from a genuine Hamilton operator. In particular, the restoration of symmetries can be entirely formulated without making {\it any} reference to a projected state, i.e. within a genuine EDF framework. However, and as is illustrated in the present document, a mathematically meaningful formulation does not guarantee that the formalism is sound from a {\it physical} standpoint. The price at which the latter can be enforced as well in the future is eventually alluded to.Comment: 64 pages, 8 figures, submitted to Euroschool Lecture Notes in Physics Vol.IV, Christoph Scheidenberger and Marek Pfutzner editor

Re-education of Tumor-Associated Macrophages by CXCR2 Blockade Drives Senescence and Tumor Inhibition in Advanced Prostate Cancer

Tumor-associated macrophages (TAMs) represent a major component of the tumor microenvironment supporting tumorigenesis. TAMs re-education has been proposed as a strategy to promote tumor inhibition. However, whether this approach may work in prostate cancer is unknown. Here we find that Pten-null prostate tumors are strongly infiltrated by TAMs expressing C-X-C chemokine receptor type 2 (CXCR2), and activation of this receptor through CXCL2 polarizes macrophages toward an anti-inflammatory phenotype. Notably, pharmacological blockade of CXCR2 receptor by a selective antagonist promoted the re-education of TAMs toward a pro-inflammatory phenotype. Strikingly, CXCR2 knockout monocytes infused in Ptenpc−/−; Trp53pc−/− mice differentiated in tumor necrosis factor alpha (TNF-α)-releasing pro-inflammatory macrophages, leading to senescence and tumor inhibition. Mechanistically, PTEN-deficient tumor cells are vulnerable to TNF-α-induced senescence, because of an increase of TNFR1. Our results identify TAMs as targets in prostate cancer and describe a therapeutic strategy based on CXCR2 blockade to harness anti-tumorigenic potential of macrophages against this disease. © 2019 The Author(s) Di Mitri et al. show that CXCR2 blockade in prostate cancer triggers TAMs re-education, leading to tumor inhibition. CXCR2-KO monocytes infused in Ptenpc−/−; Trp53pc−/− tumor-bearing mice differentiate into TNFα-releasing pro-inflammatory macrophages that induce senescence in tumor cells. PTEN-null tumors display higher sensitivity to TNF-α-induced senescence because of TNFR1 upregulation