End-to-end information extraction without token-level supervision

Most state-of-the-art information extraction approaches rely on token-level labels to find the areas of interest in text. Unfortunately, these labels are time-consuming and costly to create, and consequently, not available for many real-life IE tasks. To make matters worse, token-level labels are usually not the desired output, but just an intermediary step. End-to-end (E2E) models, which take raw text as input and produce the desired output directly, need not depend on token-level labels. We propose an E2E model based on pointer networks, which can be trained directly on pairs of raw input and output text. We evaluate our model on the ATIS data set, MIT restaurant corpus and the MIT movie corpus and compare to neural baselines that do use token-level labels. We achieve competitive results, within a few percentage points of the baselines, showing the feasibility of E2E information extraction without the need for token-level labels. This opens up new possibilities, as for many tasks currently addressed by human extractors, raw input and output data are available, but not token-level labels

Simulating tissue mechanics with Agent Based Models: concepts and perspectives

International audienceIn this paper we present an overview of agent based models that are used to simulate mechanical and physiological phenomena in cells and tissues, and we discuss underlying concepts, limitations and future perspectives of these models. As the interest in cell and tissue mechanics increase, agent based models are becoming more common the modeling community. We overview the physical aspects, complexity, shortcomings and capabilities of the major agent based model categories: lattice-based models (cellular automata, lattice gas cellular automata, cellular Potts models), off-lattice models (center based models, deformable cell models, vertex models), and hybrid discrete-continuum models. In this way, we hope to assist future researchers in choosing a model for the phenomenon they want to model and understand. The article also contains some novel results

Progress in human picornavirus research : New findings from the AIROPico consortium

Several research groups in Europe are active on different aspects of human picornavirus research. The AIROPico (Academia-Industry R&D Opportunities for Picornaviruses) consortium combined the disciplines of pathogenesis, diagnostics and therapy development in order to fill the gaps in our understanding of how picornaviruses cause human disease and how to combat them. AIROPico was the first EU consortium dedicated to human picornavirus research and development, and has largely accelerated and improved R&D on picornavirus biology, diagnostics and therapy. In this article, we present the progress on pathogenesis, diagnostics and treatment strategy developments for human picornaviruses resulting from the structured, translational research approach of the AIROPico consortium. We here summarize new insights in protection against infection by maternal or cross-protective antibodies, the visualisation of interactions between virus and neutralizing antibodies by cryoEM structural imaging, and the outcomes from a picornavirus-infected human 3D organoid. Progress in molecular detection and a fast typing assay for rhinovirus species are presented, as well as the identification of new compounds potentially interesting as therapeutic compounds.Peer reviewe

Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR.

Bacillus subtilis encodes redox-sensing MarR-type regulators of the OhrR and DUF24-families that sense organic hydroperoxides, diamide, quinones or aldehydes via thiol-based redox-switches. In this article, we characterize the novel redox-sensing MarR/DUF24-family regulator HypR (YybR) that is activated by disulphide stress caused by diamide and NaOCl in B. subtilis. HypR controls positively a flavin oxidoreductase HypO that confers protection against NaOCl stress. The conserved N-terminal Cys14 residue of HypR has a lower pK(a) of 6.36 and is essential for activation of hypO transcription by disulphide stress. HypR resembles a 2-Cys-type regulator that is activated by Cys14-Cys49' intersubunit disulphide formation. The crystal structures of reduced and oxidized HypR proteins were resolved revealing structural changes of HypR upon oxidation. In reduced HypR a hydrogen-bonding network stabilizes the reactive Cys14 thiolate that is 8-9 Å apart from Cys49'. HypR oxidation breaks these H-bonds, reorients the monomers and moves the major groove recognition α4 and α4' helices ∼4 Å towards each other. This is the first crystal structure of a redox-sensing MarR/DUF24 family protein in bacteria that is activated by NaOCl stress. Since hypochloric acid is released by activated macrophages, related HypR-like regulators could function to protect pathogens against the host immune defense

Synchronous micromechanically resonant programmable photonic circuits

Programmable photonic integrated circuits (PICs) are emerging as powerful tools for the precise manipulation of light, with applications in quantum information processing, optical range finding, and artificial intelligence. The leading architecture for programmable PICs is the mesh of Mach-Zehnder interferometers (MZIs) embedded with reconfigurable optical phase shifters. Low-power implementations of these PICs involve micromechanical structures driven capacitively or piezoelectrically but are limited in modulation bandwidth by mechanical resonances and high operating voltages. However, circuits designed to operate exclusively at these mechanical resonances would reduce the necessary driving voltage from resonantly enhanced modulation as well as maintaining high actuation speeds. Here we introduce a synchronous, micromechanically resonant design architecture for programmable PICs, which exploits micromechanical eigenmodes for modulation enhancement. This approach combines high-frequency mechanical resonances and optically broadband phase shifters to increase the modulation response on the order of the mechanical quality factor $Q_m$, thereby reducing the PIC's power consumption, voltage-loss product, and footprint. The architecture is useful for broadly applicable circuits such as optical phased arrays, $1$ x $N$, and $N$ x $N$ photonic switches. We report a proof-of-principle programmable 1 x 8 switch with piezoelectric phase shifters at specifically targeted mechanical eigenfrequencies, showing a full switching cycle of all eight channels spaced by approximately 11 ns and operating at >3x average modulation enhancement across all on-chip modulators. By further leveraging micromechanical devices with high $Q_m$, which can exceed 1 million, our design architecture should enable a new class of low-voltage and high-speed programmable PICs.Comment: 18 pages, 5 figures, 5 supplementary figure

Impact of UV-Induced Ozone and Low-Energy Ar+-Ion Cleaning on the Chemical Structure of Cu(In,Ga)(S,Se)2 Absorber Surfaces

Dry buffer layer deposition techniques for chalcopyrite (CIGSSe)-based thin-film solar cells lack the surface-cleaning characteristics of the commonly used CdS or Zn(O,S) wet-chemical bath deposition. A UV-induced ozone and/or a low-energy Ar+-ion treatment could provide dry CIGSSe surface cleaning steps. To study the impact of these treatments, the chemical surface structure of a CIGSSe absorber is investigated. For this purpose, a set of surface-sensitive spectroscopic methods, i.e., laboratory-based x-ray photoelectron spectroscopy and x-ray-excited Auger electron spectroscopy, is combined with synchrotron-based soft x-ray emission spectroscopy. After treatment times as short as 15 s, the UV-induced ozone treatment decreases the amount of carbon adsorbates at the CIGSSe surface significantly, while the oxygen content increases. This is accompanied by the oxidation of all absorber surface elements, i.e., indium, selenium, sulfur, and copper. Short (60 s) low-energy Ar+-ion treatments, in contrast, primarily remove oxygen from the surface. Longer treatment times also lead to a removal of carbon, while extremely long treatment times can also lead to additional (likely metallic) Cu phases at the absorber surface as well

Topical haemostatic agents for skin wounds: a systematic review

Background: Various agents and techniques have been introduced to limit intra-operative blood loss from skin lesions. No uniformity regarding the type of haemostasis exists and this is generally based on the surgeon's preference. To study the effectiveness of haemostatic agents, standardized wounds like donor site wounds after split skin grafting (SSG) appear particularly suitable. Thus, we performed a systematic review to assess the effectiveness of haemostatic agents in donor site wounds. Methods. We searched all randomized clinical trials (RCTs) on haemostasis after SSG in Medline, Embase and the Cochrane Library until January 2011. Two reviewers independently assessed trial relevance and quality and performed data analysis. Primary endpoint was effectiveness regarding haemostasis. Secondary endpoints were wound healing, adverse effects, and costs. Results: Nine relevant RCTs with a fair methodological quality were found, comparing epinephrine, thrombin, fibrin sealant, alginate dressings, saline, and mineral oil. Epinephrine achieved haemostasis significantly faster than thrombin (difference up to 2.5 minutes), saline or mineral oil (up to 6.5 minutes). Fibrin sealant also resulted in an up to 1 minute quicker haemostasis than thrombin and up to 3 minutes quicker than placebo, but was not directly challenged against epinephrine. Adverse effects appeared negligible. Due to lack of clinical homogeneity, meta-analysis was impossible. Conclusion: According to best available evidence, epinephrine and fibrin sealant appear superior to achieve haemostasis when substantial topical blood loss is anticipated, particularly in case of (larger) SSGs and burn debridement

Adaptive Radiation within Marine Anisakid Nematodes: A Zoogeographical Modeling of Cosmopolitan, Zoonotic Parasites

Parasites of the nematode genus Anisakis are associated with aquatic organisms. They can be found in a variety of marine hosts including whales, crustaceans, fish and cephalopods and are known to be the cause of the zoonotic disease anisakiasis, a painful inflammation of the gastro-intestinal tract caused by the accidental consumptions of infectious larvae raw or semi-raw fishery products. Since the demand on fish as dietary protein source and the export rates of seafood products in general is rapidly increasing worldwide, the knowledge about the distribution of potential foodborne human pathogens in seafood is of major significance for human health. Studies have provided evidence that a few Anisakis species can cause clinical symptoms in humans. The aim of our study was to interpolate the species range for every described Anisakis species on the basis of the existing occurrence data. We used sequence data of 373 Anisakis larvae from 30 different hosts worldwide and previously published molecular data (n = 584) from 53 field-specific publications to model the species range of Anisakis spp., using a interpolation method that combines aspects of the alpha hull interpolation algorithm as well as the conditional interpolation approach. The results of our approach strongly indicate the existence of species-specific distribution patterns of Anisakis spp. within different climate zones and oceans that are in principle congruent with those of their respective final hosts. Our results support preceding studies that propose anisakid nematodes as useful biological indicators for their final host distribution and abundance as they closely follow the trophic relationships among their successive hosts. The modeling might although be helpful for predicting the likelihood of infection in order to reduce the risk of anisakiasis cases in a given area