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Start Over Author "German Federal Ministry of Education and Research" Publisher elsevier bv
11 results on '"German Federal Ministry of Education and Research"'

1. Venous lactate improves the prediction of in-hospital adverse outcomes in normotensive pulmonary embolism

Author

Burkert Pieske, Karl Stangl, Charlotta F. Pagel, Matthias Ebner, Veli-Pekka Harjola, Carmen Sentler, Stavros Konstantinides, Gerd Hasenfuß, Mareike Lankeit, Markus H. Lerchbaumer, Héctor Bueno, Ministerio de Economía y Competitividad (España), Fundación ProCNIC, German Federal Ministry of Education and Research, HUS Emergency Medicine and Services, University of Helsinki, and Helsinki University Hospital Area

Subjects
medicine.medical_specialty, Adverse outcomes, Venous lactate, 030204 cardiovascular system & hematology, GUIDELINES, DIAGNOSIS, 03 medical and health sciences, THROMBOEMBOLISM, 0302 clinical medicine, Internal medicine, MANAGEMENT, Internal Medicine, medicine, Humans, In patient, Lactic Acid, Prospective Studies, 030212 general & internal medicine, Prospective cohort study, Risk stratification, RISK, Venipuncture, business.industry, Biomarker, ARTERIAL, Prognosis, medicine.disease, EUROPEAN-SOCIETY, Hospitals, 3. Good health, Peripheral, Pulmonary embolism, 3121 General medicine, internal medicine and other clinical medicine, Cardiology, Biomarker (medicine), Pulmonary Embolism, business, TASK-FORCE
Abstract

Arterial lactate is an established risk marker in patients with pulmonary embolism (PE). However, its clinical applicability is limited by the need of an arterial puncture. In contrast, venous lactate can easily be measured from blood samples obtained via routine peripheral venepuncture. We investigated the prognostic value of venous lactate with regard to in-hospital adverse outcomes and mortality in 419 consecutive PE patients enrolled in a single-center registry between 09/2008 and 09/2017. An optimised venous lactate cut-off value of 3.3 mmol/l predicted both, in-hospital adverse outcome (OR 11.0 [95% CI 4.6-26.3]) and all-cause mortality (OR 3.8 [95%CI 1.3-11.3]). The established cut-off value for arterial lactate (2.0 mmol/l) and the upper limit of normal for venous lactate (2.3 mmol/l) had lower prognostic value for adverse outcomes (OR 3.6 [95% CI 1.5-8.7] and 5.7 [95% CI 2.4-13.6], respectively) and did not predict mortality. If added to the 2019 European Society of Cardiology (ESC) algorithm, venous lactate

Published
2021

2. Short-term effects of macrophyte removal on aquatic biodiversity in rivers and lakes

Author

Benjamin Misteli, Alexandrine Pannard, Eirin Aasland, Sarah Faye Harpenslager, Samuel Motitsoe, Kirstine Thiemer, Stéphanie Llopis, Julie Coetzee, Sabine Hilt, Jan Köhler, Susanne C. Schneider, Christophe Piscart, Gabrielle Thiébaut, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Norwegian University of Life Sciences (NMBU), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Rhodes University, Grahamstown, This work is part of the MadMacs (Mass development of aquatic macrophytes – causes and consequences of macrophyte removal for ecosystem structure, function, and services) project in the framework of the collaborative international consortium of the 2017 call of the Water Challenges for a Changing World Joint Programme Initiative (Water JPI). The MadMacs project is supported by the French Agence Nationale de la Recherche (N° ANR-18-IC4W-0004–06), the Research Council of Norway (297202/E10), the German Federal Ministry of Education and Research (02WGR005), the South African Water Research Commission (K5/2951), and the Fundação Araucária in Brazil (N° 186/2019). Additional funding was provided by Krypsiv på Sørlandet, NIVA and NMBU., and ANR-18-IC4W-0004,MadMacs,Mass development of aquatic macrophytes – causes and consequences of macrophyte removal for ecosystem structure, function, and services(2018)

Subjects
Environmental Engineering, [SDE.IE]Environmental Sciences/Environmental Engineering, macroinvertebrates, Biodiversity, General Medicine, Plants, Management, Monitoring, Policy and Law, Zooplankton, Lakes, Rivers, Phytoplankton, Animals, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Aquatic plants, Waste Management and Disposal, management, BACI, Ecosystem
Abstract

International audience; Mass development of macrophytes is an increasing problem in many aquatic systems worldwide. Dense mats of macrophytes can negatively affect activities like boating, fishing, or hydropower production and one of the management measures often applied is mechanical removal. In this study, we analyzed the effect of mechanical macrophyte removal on phytoplankton, zooplankton, and macroinvertebrate (pelagic and benthic samples) assemblages. Our study covered five sites in four countries in Europe and Africa with highly variable characteristics. In all sites, dense mats of different macrophyte species (Juncus bulbosus in a river in Norway; a mix of native macrophytes in a German river, Elodea nuttallii in a lake in Germany, Ludwigia spp. in a French lake and Pontederia crassipes in a South African lake) are problematic and mechanical removal was applied. In every country, we repeated the same BACI (Before-After-Control-Impact) design, including "before", "one week after", and "six weeks after" sampling in a control and an impact section. Repeating the same experimental design at all sites allowed us to disentangle common effects across all sites from site-specific effects. For each taxonomic group, we analyzed three structural and three functional parameters, which we combined in a scoring system. Overall, the removal of macrophytes negatively affected biodiversity, in particular, of zooplankton and macroinvertebrate assemblages. In contrast, plant removal had positive effects on the phytoplankton assemblages. Effects were more pronounced one week after removal than six weeks after. Consequently, we suggest a stronger consideration of the effect of plant removal on biodiversity to arrive at more sustainable management practices in the future.

Published
2023

3. Nitrogen immobilization caused by chemical formation of black- and amide-N in soil

Author

Wei, Jing, Knicker, Heike, Zhou, Zheyan, Eckhardt, Kai-Uwe, Leinweber, Peter, Wissel, Holger, Yuan, Wenping, Brüggemann, Nicolas, Guangdong Province Key Laboratory for Climate Change and Natural Disaster Studies, German Federal Ministry of Education and Research, Southern Marine Science and Engineering Guangdong Laboratory, Chinese Scholarship Council, Knicker, Heike, and Brüggemann, Nicolas

Subjects
Amide, Soil organic matter, Make cities and human settlements inclusive, safe, resilient and sustainable, Chemical nitrogen immobilization, Nitrite, Black nitrogen, Soil Science, ddc:910
Abstract

11 páginas.- 7 figuras.- 4 tablas.- 46 referencias.- Supplementary data to this article can be found online at https://doi.org/10.1016/j.geoderma.2022.116274, Nitrogen (N) immobilization controls the N availability in soil, however, mechanisms involved in the chemical N fixation into soil organic N (SON) through reactions of reactive N compounds with soil organic matter (SOM) is not clear. Knowledge about the composition and stability of chemically produced SON is limited, which impedes understanding of the interplay of N and carbon (C) cycles at both the local and global scale. Here, we studied the chemical N immobilization of nitrite in soils from grassland, cropland, and forest with 15N labelling technique. And solid state 15N- and 13C NMR spectroscopies were applied to further explore the structure of chemically immobilized SON. We found that the chemical retention rate of nitrite did not differ significantly between land-uses, while the fulvic acid fraction was the SOM component most reactive to nitrite. In contrast to the common assumption that amides are mainly of biological origin and that black N compounds are formed from organic N compounds at high temperature during fires, our study revealed that amides and black N in the form of pyrroles were the main products of chemical reactions of nitrite with SOM. These findings indicate that chemical processes play a key role in biogeochemical N cycling, and provide new insight into the mechanisms of Csingle bondN interactions in soil, This study was supported by Guangdong Major Project of Basic and Applied Basic Research (2020B0301030004), Guangdong Province Key Laboratory for Climate Change and Natural Disaster Studies (Grant 2020B1212060025), the German Federal Ministry of Education and Research (BMBF) in the framework of the BonaRes INPLAMINT project (grant no. 031B0508A), by Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) (No. 311021009), and the Chinese Scholarship Council (scholarship no. 201406890023)

Published
2023

4. How invasive macrophytes affect macroinvertebrate assemblages and sampling efficiency: Results from a multinational survey

Author

Benjamin Misteli, Alexandrine Pannard, Frédéric Labat, Lorraine Kengne Fosso, Nompumelelo Catherine Baso, Sarah Faye Harpenslager, Samuel Nkopane Motitsoe, Gabrielle Thiebaut, Christophe Piscart, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Aquabio, Université de Yaoundé I, Rhodes University, Grahamstown, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), This study was funded by the French Agence National de Recherche (N° ANR-18-IC4W-0004-06), the South African Water Research Commision (K5/2951), the German Federal Ministry of Education and Research (033WU005), the Research Council of Norway (297202/E10), and the Fundação Araucária in Brazil (N° 186/2019) for funding of MadMacs (Mass development of aquatic macrophytes - causes and consequences of macrophyte removal for ecosystem structure, function, and services) in the framework of the collaborative international consortium of the 2017 call of the Water Challenges for a Changing World Joint Programme Initiative (Water JPI). Additional funding was provided by Aquabio (Saint-Germain-du-Puch, France)., and ANR-18-IC4W-0004,MadMacs,Mass development of aquatic macrophytes – causes and consequences of macrophyte removal for ecosystem structure, function, and services(2018)

Subjects
Sampling efficiency, Habitat heterogeneity, Shallow lakes, Methods, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Aquatic Science, Aquatic plants
Abstract

International audience; Macrophytes play an important role in the functioning and structuring of aquatic environments but rapid mass development of invasive macrophytes is causing global concerns. Macroinvertebrate richness and abundance are strongly influenced by macrophytes as macrophytes offer habitats and food resources, increase structural heterogeneity, and provide refuges. Meanwhile, the presence of macrophytes affects the efficiency of standard sampling methods for macroinvertebrates. These effects are not well studied but are leading to biased management decisions. To fill in this knowledge gap, we analysed macroinvertebrate communities from four lakes in four countries in Europe and Africa with mass development of invasive macrophytes. We compared macroinvertebrate communities in sediment samples from a plant-free part of the lake with those in sediment and sweep samples taken within macrophyte stands. We showed that taxa richness and density were higher in sediment samples beneath invasive macrophyte stands compared to plant-free habitats. Unique taxa were found in each sample type. Sampling efficiency of each sampling method varies greatly across lakes especially when replication is low. The taxonomic richness of macroinvertebrates within invasive macrophyte stands is often underestimated compared to open water sections with the same number of samples. To reach a high sampling coverage, a higher number of samples is necessary for sampling within invasive macrophytes. Our findings call for the development of a method that allows for comparable sampling within and outside of macrophyte stands. Such method will be the foundation for future research and management of aquatic systems.

Published
2022

5. Securing future decentralised industrial IoT infrastructures: Challenges and free open source solutions

Author

Sven Plaga, Stefan Tatschner, Hans D. Schotten, Thomas Newe, Norbert Wiedermann, Simon Duque Anton, German Federal Ministry of Education and Research, SFI, and Publica

Subjects
Computer Networks and Communications, Computer science, media_common.quotation_subject, Context (language use), Cloud computing, 02 engineering and technology, Decentralization, secure communications, 0202 electrical engineering, electronic engineering, information engineering, Resilience (network), Industrial Revolution, Implementation, media_common, business.industry, cyber security, decentralisation, Information technology, 020206 networking & telecommunications, Usability, Automation, Industrial Internet of Things, Risk analysis (engineering), Hardware and Architecture, smart environments, 020201 artificial intelligence & image processing, Smart environment, Psychological resilience, business, Software
Abstract

peer-reviewed The next industrial revolution is said to be paved by the use of novel Internet of Things (IoT) technology. One important aspect of the modern IoT infrastructures is decentralised communication, often called Peer-to-Peer (P2P). In the context of industrial communication, P2P contributes to resilience and improved stability for industrial components. Current industrial facilities, however, still rely on centralised networking schemes which are considered to be mandatory to comply with security standards. In order to succeed, introduced industrial P2P technology must maintain the current level of protection and also consider possible new threats. The presented work starts with a short analysis of well-established industrial communication infrastructures and how these could benefit from decentralised structures. Subsequently, previously undefined Information Technology (IT) security requirements are derived from the new cloud based decentralised industrial automation model architecture presented in this paper. To meet those requirements, state-of-the-art communication schemes and their open source implementations are presented and assessed for their usability in the context of industrial IoT. Finally, derived building blocks for industrial IoT P2P security are presented which are qualified to comply with the stated industrial IoT security requirements.

Published
2019

6. Progress in DMAPS developments and first tests of the Monopix2 chips in 150 nm LFoundry and 180 nm TowerJazz technology

Author

J. Dingfelder, M. Barbero, P. Barrillon, I. Berdalovic, C. Bespin, P. Breugnon, I. Caicedo, R. Cardella, Y. Degerli, L. Flores Sanz de Acedo, F. Guilloux, A. Habib, T. Hirono, T. Hemperek, F. Hügging, H. Krüger, T. Kugathasan, K. Moustakas, P. Pangaud, H. Pernegger, F. Piro, D.-L. Pohl, P. Riedler, A. Rozanov, P. Rymaszewski, P. Schwemling, W. Snoeys, T. Wang, N. Wermes, S. Zhang, Physikalisches Institut [Bonn], Rheinische Friedrich-Wilhelms-Universität Bonn, Centre de Physique des Particules de Marseille (CPPM), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), European Organization for Nuclear Research (CERN), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Deutsche Forschungsgemeinschaft DFG (grant WE 976/4-1), German Federal Ministry of Education and Research BMBF (grant 05H15PDCA9), Test Beam Facility, European Project: 675587,H2020,H2020-MSCA-ITN-2015,STREAM(2016), and European Project: 654168,H2020,H2020-INFRAIA-2014-2015,AIDA-2020(2015)

Subjects
Radiation hardness, Nuclear and High Energy Physics, DMAPS, Monolithic pixel, Pixel detector, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], CMOS sensor, Instrumentation
Abstract

VERTEX 2021 - 30th International Workshop on Vertex Detectors. September 27th–30th, 2021, Online from Oxford University, UK; International audience; Depleted Monolithic Active Pixel Sensors (DMAPS) are monolithic pixel detectors with high-resistivity substrates designed for use in high-rate and high-radiation environments. They are produced in commercial CMOS processes, resulting in relatively low production costs and short turnaround times, and offer a low material budget. LF-Monopix1 and TJ-Monopix1 are large DMAPS prototypes produced in 150 nm LFoundry and 180 nm TowerJazz technology, respectively, that follow two different design concepts regarding the charge collection electrode. Prototypes of both development lines have been extensively tested and characterized over the last years. The second-generation Monopix prototypes, Monopix2, were recently produced. They were designed to address the shortcomings of their predecessors, in particular related to radiation hardness and cross talk, and further improve upon their performance. The latest measurements with LF-Monopix1 and TJ-Monopix1 concerning hit efficiency, depletion, and radiation hardness as well as the initial test results of the new Monopix2 prototypes are presented

Published
2022

7. Evaluating the precision of eight spatial sampling schemes in estimating regional means of simulated yield for two crops

Author

Elisabet Lewan, Eckart Priesack, Edmar Teixeira, Davide Cammarano, Balázs Grosz, Julie Constantin, Elsa Coucheney, Senthold Asseng, Jagadeesh Yeluripati, Pier Paolo Roggero, Giacomo Trombi, Henrik Eckersten, Stefan Siebert, Specka Xenia, Reimund P. Rötter, Frank Ewert, Thomas Gaiser, Marco Bindi, Marco Moriondo, Matthias Kuhnert, Luca Doro, Christian Klein, Fulu Tao, Gang Zhao, Helene Raynal, Ralf Kiese, Kurt Christian Kersebaum, Claas Nendel, Belay T. Kassie, Christian Biernath, Holger Hoffmann, Edwin Haas, Florian Heinlein, Daniel Wallach, Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, The James Hutton Institute, Departement of Soil and Environment, Swedish University of Agricultural Sciences (SLU), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institute of landscape systems analysis, INSTITUTE OF BIOLOGICAL AND ENVIRONMENTAL SCIENCES, University of Aberdeen, Environmental Impacts Group, Natural resources institute Finland, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Systems Modelling Team (Sustainable Production Group), Plant & Food Research, Johann Heinrich von Thünen Institut, Università degli Studi di Sassari, Dipartimento di Agraria, University of Sassari, Karlsruhe Institute of Technology (KIT), University of Agricultural Sciences (UAS), Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Consiglio Nazionale delle Ricerche (CNR), Department of Agri-Food Production and Environmental Sciences, University delgi Studi di Firenze, Institute of Biochemical Plant Pathology (BIOP), German Research Center for Environmental Health - Helmholtz Center München (GmbH), German Federal Ministry of Food and Agriculture (BMEL) through the Federal Office for Agriculture and Food (BLE) [2851ERA01J], Joint Programme Initiative FACCE, MACSUR Knowledge Hub, German Federal Ministry of Education and Research (BMBF) through the SPACES project 'Living Landscapes Limpopo', WASCAL (West African Science Service Center on Climate Change and Adapted Land Use) project, NOAA RISA grant, FACCE MACSUR project by the Finnish Ministry of Agriculture and Forestry (MMM), Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning [220-2007-1218], strategic funding 'Soil-Water-Landscape' from the faculty of Natural Resources and Agricultural Sciences (Swedish University of Agricultural Sciences), ACCAF INRA meta-program, and Università degli Studi di Sassari = University of Sassari [Sassari] (UNISS)

Subjects
Environmental Engineering, 010504 meteorology & atmospheric sciences, Simple random sampling, [SDV]Life Sciences [q-bio], Stratified random sampling, 01 natural sciences, [SHS]Humanities and Social Sciences, Environment variable, Ecosystem model, Statistics, [INFO]Computer Science [cs], Crop model, [MATH]Mathematics [math], 0105 earth and related environmental sciences, Mathematics, 2. Zero hunger, Ecological Modeling, Crop yield, fungi, food and beverages, Sampling (statistics), Model comparison, 04 agricultural and veterinary sciences, 15. Life on land, Simple random sample, Stratified sampling, Sample size determination, [SDE]Environmental Sciences, Soil water, Up-scaling, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Clustering, Crop Model, Model Comparison, Precision Gain, Simple Random Sampling, Stratified Random Sampling, Precision gain, Software
Abstract

We compared the precision of simple random sampling (SimRS) and seven types of stratified random sampling (StrRS) schemes in estimating regional mean of water-limited yields for two crops (winter wheat and silage maize) that were simulated by fourteen crop models. We found that the precision gains of StrRS varied considerably across stratification methods and crop models. Precision gains for compact geographical stratification were positive, stable and consistent across crop models. Stratification with soil water holding capacity had very high precision gains for twelve models, but resulted in negative gains for two models. Increasing the sample size monotonously decreased the sampling errors for all the sampling schemes. We conclude that compact geographical stratification can modestly but consistently improve the precision in estimating regional mean yields. Using the most influential environmental variable for stratification can notably improve the sampling precision, especially when the sensitivity behavior of a crop model is known. We compare eight sampling schemes for estimating regional mean crop yield.Precision of eight schemes is compared across fourteen crop models.Compact geographical stratification can always improve the precision.Stratification with soil had very high gains of precision for twelve crop models.Our findings can improve the precision of site-based regional crop modeling.

Published
2016

8. Shape-aware surface reconstruction from sparse 3D point-clouds

Author

Dennis Jentsch, Alexander Tack, Frank Hertel, Hans Lamecker, Johan Thunberg, Jorge Goncalves, Luis Salamanca, Peter Gemmar, Florian Bernard, Stefan Zachow, Mendes Silva Goncalves, Jorge [0000-0002-5228-6165], Apollo - University of Cambridge Repository, Fonds National de la Recherche - FnR [sponsor], German federal ministry of education and research (BMBF) [sponsor], and Einstein Center for Mathematics (ECMath), Berlin [sponsor]

Subjects
FOS: Computer and information sciences, Computer Vision and Pattern Recognition (cs.CV), Point cloud, Computer Science - Computer Vision and Pattern Recognition, Normal Distribution, 02 engineering and technology, 030218 nuclear medicine & medical imaging, 0302 clinical medicine, Statistics - Machine Learning, Point distribution model, Active shape model, 0202 electrical engineering, electronic engineering, information engineering, Femur, Mathematics, Radiological and Ultrasound Technology, Statistical shape model, Brain, Sciences informatiques [C05] [Ingénierie, informatique & technologie], Computer Graphics and Computer-Aided Design, Data point, Gaussian mixture model, Liver, Computer Vision and Pattern Recognition, Surface reconstruction, Algorithms, Sparse shape reconstruction, Machine Learning (stat.ML), Health Informatics, Expected conditional maximisation, 03 medical and health sciences, statistical shape model, Imaging, Three-Dimensional, Maximum a posteriori estimation, Humans, Radiology, Nuclear Medicine and imaging, Sparse matrix, Computer science [C05] [Engineering, computing & technology], Hip, Models, Statistical, Tibia, business.industry, point distribution model, 020207 software engineering, Pattern recognition, Mixture model, expected conditional maximisation, Artificial intelligence, sparse shape reconstruction, business
Abstract

The reconstruction of an object's shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process of aligning intra-operative navigation and preoperative planning data. In such scenarios, one usually has to deal with sparse data, which significantly aggravates the problem of reconstruction. However, medical applications often provide contextual information about the 3D point data that allow to incorporate prior knowledge about the shape that is to be reconstructed. To this end, we propose the use of a statistical shape model (SSM) as a prior for surface reconstruction. The SSM is represented by a point distribution model (PDM), which is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we formulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given points are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are "oriented" according to the surface normals at the PDM points, a surface-based fitting is accomplished. Estimating the parameters of the GMM in a maximum a posteriori manner yields the reconstruction of the surface from the given data points. We compare our method to the extensively used Iterative Closest Points method on several different anatomical datasets/SSMs (brain, femur, tibia, hip, liver) and demonstrate superior accuracy and robustness on sparse data.

Published
2017
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9. Complexity of and algorithms for the manipulation of Borda, Nanson's and Baldwin's voting rules

Author

Lirong Xia, George Katsirelos, Toby Walsh, Nina Narodytska, Jessica Davies, University of Toronto, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), National Information and Communication Technology Australia, Partenaires INRAE, University of New South Wales [Sydney] (UNSW), Rensselaer Polytechnic Institute (RPI), and French ANR UNLOC project ANR 08-BLAN-0289-01. Australian Department of Broadband, Communications and the Digital Economy, the Australian Research Council, and the Asian Office of Aerospace Research and Development (AOARD-104123). German Federal Ministry for Education and Research through the Alexander von Humboldt Foundation. RPI startup fund, NSF Grant #1136996 to the Computing Research Association for the CIFellows Project. NSF CAREER0953756 and IIS-0812113.

Subjects
Linguistics and Language, Voting methods, Nanson's voting rule, Computational complexity theory, media_common.quotation_subject, Social choice, Condorcet method, Language and Linguistics, Cardinal voting systems, Artificial Intelligence, Voting, Bullet voting, Manipulation, [INFO]Computer Science [cs], [MATH]Mathematics [math], Mathematics, media_common, Anti-plurality voting, Heuristic, business.industry, Baldwin's voting rule, 16. Peace & justice, Borda voting, Artificial intelligence, business, Social choice theory, Algorithm
Abstract

International audience; We investigate manipulation of the Borda voting rule, as well as two elimination style voting rules, Nanson's and Baldwin's voting rules, which are based on Borda voting. We argue that these rules have a number of desirable computational properties. For unweighted Borda voting, we prove that it is NP-hard for a coalition of two manipulators to compute a manipulation. This resolves a long-standing open problem in the computational complexity of manipulating common voting rules. We prove that manipulation of Baldwin's and Nanson's rules is computationally more difficult than manipulation of Borda, as it is NP-hard for a single manipulator to compute a manipulation. In addition, for Baldwin's and Nanson's rules with weighted votes, we prove that it is NP-hard for a coalition of manipulators to compute a manipulation with a small number of candidates. Because of these NP-hardness results, we compute manipulations using heuristic algorithms that attempt to minimise the number of manipulators. We propose several new heuristic methods. Experiments show that these methods significantly outperform the previously best known heuristic method for the Borda rule. Our results suggest that, whilst computing a manipulation of the Borda rule is NP-hard, computational complexity may provide only a weak barrier against manipulation in practice. In contrast to the Borda rule, our experiments with Baldwin's and Nanson's rules demonstrate that both of them are often more difficult to manipulate in practice. These results suggest that elimination style voting rules deserve further study.

Published
2014

10. Community-Driven Data Analysis Training for Biology

Author

Dannon Baker, Aisanjiang Wubuli, Anthony Bretaudeau, Saskia Hiltemann, John Chilton, Bérénice Batut, Vivek Bhardwaj, Thomas Manke, Loraine Brillet-Guéguen, Mallory A. Freeberg, Olivia Doppelt-Azeroual, Fabien Mareuil, Gildas Le Corguillé, Nicola Soranzo, Fidel Ramírez, Joachim Wolff, Clemens Blank, Rolf Backofen, Anton Nekrutenko, Pavankumar Videm, Youri Hoogstrate, Dave Clements, Dilmurat Yusuf, Delphine Larivière, Markus Wolfien, Anika Erxleben, Simon Gladman, Devon Ryan, James Taylor, Florian Christoph Sigloch, Björn Grüning, Hans-Rudolf Hotz, Torsten Houwaart, Pratik D. Jagtap, Martin Čech, Andrea Bagnacani, Bioinformatics Group [Freiburg], Department of Computer Science [Freiburg], Albert-Ludwigs-Universität Freiburg-Albert-Ludwigs-Universität Freiburg, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Department of Systems Biology and Bioinformatics, University of Rostock, Johns Hopkins University (JHU), Department of Biology [Fribourg], University of Freiburg [Freiburg], Plateforme bioinformatique GenOuest [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Pennsylvania State University (Penn State), Penn State System, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Melbourne Bioinformatics [Australia], University of Melbourne, Friedrich Miescher Institute for Biomedical Research (FMI), Novartis Research Foundation, University of Minnesota Medical School, University of Minnesota System, Max Planck Institute of Immunobiology and Epigenetics (MPI-IE), Max-Planck-Gesellschaft, Earlham Institute [Norwich], Leibniz Institute for Farm Animal Biology (FBN), This project was supported by Collaborative Research Centre 992 Medical Epigenetics (DFG grant SFB 992/1 2012), German Federal Ministry of Education and Research (BMBF grant 031 A538A RBC [de.NBI]), NIH grants U41 HG006620 and R01 AI134384-01, as well as NSF grant 1661497., The authors are grateful to the Freiburg Galaxy and Core Galaxy teams as, without these resources, this work would not be possible. Adoption of Galaxy Tours has been accelerated with the introduction of Galaxy Tour Builder (https://zenodo.org/record/830481) by William Durand (https://tailordev.fr)., Galaxy Training Network, Pathology, Urology, Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Histology, data analysis, Space (commercial competition), Training (civil), Article, Pathology and Forensic Medicine, Education, Distance, 03 medical and health sciences, proteomics, 0302 clinical medicine, Software, ComputingMilieux_COMPUTERSANDEDUCATION, genomics, Feature (machine learning), Humans, Curriculum, Web browser, training, business.industry, 4. Education, Computational Biology, Cell Biology, Data science, Research Personnel, 030104 developmental biology, Key (cryptography), Data analysis, next-generation sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, 030217 neurology & neurosurgery
Abstract

La version finale de l'article a été déposée sur PMC. The final version of this article has been deposed on PMC; The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.

Published
2018

11. Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels

Author

Karin R. Engelhardt, Bernhard Fleckenstein, Ekrem Unal, C. I. Edvard Smith, Dietmar Pfeifer, Mohamed-Ridha Barbouche, Meriem Ben-Ali, Hans J. Stauss, Mohamed Bejaoui, Mirzokhid Rakhmanov, Lamia Borchani, Monia Khemiri, Stuart M. Haslam, Zineb Jouhadi, Khadija Khadir, Imen Ben-Mustapha, Bodo Grimbacher, Karin E. Lundin, A. Charlotta Asplund, Manfred Fliegauf, Uwe Kölsch, Gang Wu, A. Sassi, Sandra Lazaroski, Turkan Patiroglu, Magdalena Dziadzio, Anne Dell, Mats Nilsson, Sellama Nadifi, Khairunnadiya Prayitno, Mehmet Akif Ozdemir, Fethi Mellouli, Andrea Maul-Pavicic, Manuela O. Gustafsson, Helene Kraus, Hermann Eibel, Lotte Moens, Hatice Eke Gungor, Thilo Jakob, Elin Falk-Sörqvist, Alejandro A. Schäffer, Sandra Schaffer, Rebecca Meier, Leila Ben-Khemis, Philipp Henneke, Laboratoire d'Immunopathologie, Vaccinologie et Génétique Moléculaire (LVGM), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg, Freiburg, Germany, Department of Life Sciences, Imperial College London, London, United Kingdom, Pediatrics Department, Bone Marrow Transplantation Center, Tunis,Tunisia, Pediatrics Department, Bone Marrow Transplantation Center, Tunis, Tunisia, Department of Pediatrics, Division of Pediatric Hematology and Oncology, Faculty of Medicine, Erciyes University, Kayseri, Turkey, Department of Pediatrics, Division of Pediatric Immunology, Faculty of Medicine, Erciyes University, Kayseri, Turkey, Department of Pediatric Infectious Diseases, CHU IBN ROCHD, Hassan II University, Casablanca, Morocco, Laboratoire des Venins et Biomolécules Thérapeutiques - Laboratory of Venoms and Therapeutic Biomolecules (LR11IPT08), Department of Medicine I, Specialties: Hematology, Oncology, and Stem-Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany, Pediatrics Department A, Children's Hospital of Tunis, Tunis, Tunisia, Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden, Karolinska Institutet [Stockholm]-Karolinska University Hospital [Stockholm], Royal Free Hospital, Institute of Immunity & Transplantation, University College London, London, United Kingdom, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden, Institute of Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany, Division of Immunology, Labor Berlin and Institute of Medical Immunology, Charité, Campus Virchow Klinikum, Berlin, Germany, Department of Genetics, Hassan II University, Casablanca, Morocco, Pediatrics Department, Bone Marrow Transplantation Center, Tunis, Tunisia., National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Md, National Institutes of Health [Bethesda] (NIH), and Supported by the German Federal Ministry of Education and Research (BMBF 01 EO 0803). The research was supported in part by the Intramural Research Program of the National Library of Medicine–National Institutes of Health. Parts of the study were supported by the Tunisian Ministry for Higher Education and Research, the Swedish Medical Research Council, the Swedish Cancer Society and the Stockholm County Council (research grant ALF), and the European Community’s 6th and 7th Framework Programs FP7/2007-2013 under grant agreement Health-F5-2008-223292 (Euro-Gene-Scan). This work was also supported by the Biotechnology and Biological Sciences Research Council (BBF0083091 and BB/ K016164/1 to A.D. and S.M.H).

Subjects
Male, Candidate gene, Glycosylation, Allergy, Genetic Linkage, [SDV]Life Sciences [q-bio], T-Lymphocytes, medicine.disease_cause, chemistry.chemical_compound, MESH: Child, 2.1 Biological and endogenous factors, Immunology and Allergy, Aetiology, Child, MESH: Immunity, Genetics, Mutation, MESH: Immunoglobulin E, Homozygote, MESH: Glycosylation, Disease gene identification, MESH: Amino Acid Substitution, MESH: Infant, Phenotype, 3. Good health, Hyper-IgE syndrome, Genetic Diseases, signal transducer and activator of transcription 3, [SDV.IMM]Life Sciences [q-bio]/Immunology, Chromosomes, Human, Pair 6, Female, Pair 6, Dock8, MESH: Tunisia, MESH: Phosphoglucomutase, Job Syndrome, MESH: Homozygote, Human, Adult, MESH: Genetic Diseases, Inborn, Staphylococcus aureus, Tunisia, MESH: Chromosomes, Human, Pair 6, Immunology, Mutation, Missense, MESH: Genetic Linkage, Biology, phosphoglucomutase 3, Article, Chromosomes, Rare Diseases, Clinical Research, Genetic linkage, MESH: Cell Proliferation, medicine, Humans, Cell Proliferation, MESH: Mutation, Missense, MESH: Humans, MESH: Job Syndrome, Genetic Diseases, Inborn, Immunity, Infant, MESH: Adult, Immunoglobulin E, medicine.disease, Molecular biology, MESH: Male, MESH: T-Lymphocytes, Inborn, Emerging Infectious Diseases, Phosphoglucomutase, Amino Acid Substitution, chemistry, Missense, dedicator of cytokinesis 8, MESH: Female, Congenital disorder of glycosylation
Abstract

International audience; BACKGROUND: Recurrent bacterial and fungal infections, eczema, and increased serum IgE levels characterize patients with the hyper-IgE syndrome (HIES). Known genetic causes for HIES are mutations in signal transducer and activator of transcription 3 (STAT3) and dedicator of cytokinesis 8 (DOCK8), which are involved in signal transduction pathways. However, glycosylation defects have not been described in patients with HIES. One crucial enzyme in the glycosylation pathway is phosphoglucomutase 3 (PGM3), which catalyzes a key step in the synthesis of uridine diphosphate N-acetylglucosamine, which is required for the biosynthesis of N-glycans. OBJECTIVE: We sought to elucidate the genetic cause in patients with HIES who do not carry mutations in STAT3 or DOCK8. METHODS: After establishing a linkage interval by means of SNPchip genotyping and homozygosity mapping in 2 families with HIES from Tunisia, mutational analysis was performed with selector-based, high-throughput sequencing. Protein expression was analyzed by means of Western blotting, and glycosylation was profiled by using mass spectrometry. RESULTS: Mutational analysis of candidate genes in an 11.9-Mb linkage region on chromosome 6 shared by 2 multiplex families identified 2 homozygous mutations in PGM3 that segregated with disease status and followed recessive inheritance. The mutations predict amino acid changes in PGM3 (p.Glu340del and p.Leu83Ser). A third homozygous mutation (p.Asp502Tyr) and the p.Leu83Ser variant were identified in 2 other affected families, respectively. These hypomorphic mutations have an effect on the biosynthetic reactions involving uridine diphosphate N-acetylglucosamine. Glycomic analysis revealed an aberrant glycosylation pattern in leukocytes demonstrated by a reduced level of tri-antennary and tetra-antennary N-glycans. T-cell proliferation and differentiation were impaired in patients. Most patients had developmental delay, and many had psychomotor retardation. CONCLUSION: Impairment of PGM3 function leads to a novel primary (inborn) error of development and immunity because biallelic hypomorphic mutations are associated with impaired glycosylation and a hyper-IgE-like phenotype.

Published
2014

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