42 results on '"Hasso Plattner Institut"'
Search Results
2. Wachstumskern Potenzial - Verbundprojekt: DigiPolis, TP1: Forschung und Entwicklung von 3D-Annotations- und Fokus-&-Kontext-Visualisierungsverfahren für virtuelle 3D-Gebäudekomplexe : Schlussbericht ; Laufzeit des Vorhabens: 01.12.2009 - 30.11.2011
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Hasso-Plattner-Institut Für Softwaresystemtechnik
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Computer Science - Published
- 2011
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3. Climate-human interaction associated with southeast Australian megafauna extinction patterns
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Frédérik Saltré, Sean Ulm, Axel Timmermann, Matthew C. McDowell, Tobias Friedrich, Katharina J. Peters, Joël Chadoeuf, Corey J. A. Bradshaw, Flinders University [Adelaide, Australia], Biostatistique et Processus Spatiaux (BioSP), Institut National de la Recherche Agronomique (INRA), Institute for Cell and Molecular Biosciences, Newcastle University [Newcastle], University of Tasmania [Hobart, Australia] (UTAS), Hasso Plattner Institut, University of Hawaii, 2525 Correa Road, Honolulu, HI 96822, United States, Aging Research Center [Karolinska Institutet] (ARC ), Stockholm University-Karolinska Institutet [Stockholm], Global Ecology, College of Science and Engineering, Flinders University, and Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CE170100015) to S.U. and C.J.A.B. A.T. was supported by the Institute for Basic Science (IBS) under IBS-R028-D1.
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010506 paleontology ,Native Hawaiian or Other Pacific Islander ,010504 meteorology & atmospheric sciences ,Pleistocene ,Science ,[SDE.MCG]Environmental Sciences/Global Changes ,Climate Change ,Human Migration ,Biodiversity ,General Physics and Astronomy ,Climate change ,mégafaune ,Extinction, Biological ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,Megafauna ,Animals ,Humans ,Pleistocene megafauna ,lcsh:Science ,Macroecology ,Ecosystem ,0105 earth and related environmental sciences ,Changement climatique ,Spatial Analysis ,Multidisciplinary ,Extinction ,Ecology ,Australian megafauna ,Drinking Water ,Australia ,Palaeoecology ,Paleontology ,General Chemistry ,15. Life on land ,Archéologiques ,analyse chronologique ,Geography ,Archaeology ,13. Climate action ,Paleoecology ,paléontologique ,lcsh:Q - Abstract
The mechanisms leading to megafauna (>44 kg) extinctions in Late Pleistocene (126,000—12,000 years ago) Australia are highly contested because standard chronological analyses rely on scarce data of varying quality and ignore spatial complexity. Relevant archaeological and palaeontological records are most often also biased by differential preservation resulting in under-representated older events. Chronological analyses have attributed megafaunal extinctions to climate change, humans, or a combination of the two, but rarely consider spatial variation in extinction patterns, initial human appearance trajectories, and palaeoclimate change together. Here we develop a statistical approach to infer spatio-temporal trajectories of megafauna extirpations (local extinctions) and initial human appearance in south-eastern Australia. We identify a combined climate-human effect on regional extirpation patterns suggesting that small, mobile Aboriginal populations potentially needed access to drinkable water to survive arid ecosystems, but were simultaneously constrained by climate-dependent net landscape primary productivity. Thus, the co-drivers of megafauna extirpations were themselves constrained by the spatial distribution of climate-dependent water sources., Whether Australia’s Pleistocene megafauna extinctions were caused by climate change, humans, or both is debated. Here, the authors infer the spatio-temporal trajectories of regional extinctions and find that water availability mediates the relationship among climate, human migration and megafauna extinctions.
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- 2019
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4. Proceedings of the 15th ACM/SIGEVO Conference on Foundations of Genetic Algorithms
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Friedrich, Tobias, Doerr, Carola, Arnold, Dirk, Hasso Plattner Institut, Recherche Opérationnelle (RO), LIP6, Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Physikalisch-Technische Bundesanstalt [Braunschweig] (PTB)
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[INFO.INFO-NE]Computer Science [cs]/Neural and Evolutionary Computing [cs.NE] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
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- 2019
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5. Precession and atmospheric CO2 modulated variability of sea ice in the central Okhotsk Sea since 130,000 years ago
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Liang-Chi Wang, Stefan Schouten, Wei-Lung Wang, Sheng-Rong Song, Yu-Min Chou, Tien Hsi Fang, David A. Hodell, Patricia Cabedo-Sanz, Jyh Jaan Huang, Tsong Hua Ou, Simon T. Belt, Li Lo, Lukas Smik, Teh-Quei Lee, Sergey A Gorbarenko, Julie Lattaud, Kuo-Yen Wei, Liping Zhou, Christian Zeeden, Tobias Friedrich, Min-Te Chen, Yuan-Pin Chang, Axel Timmermann, Henry Elderfield, Chuan-Chou Shen, Biogeochemistry Research Centre (BGC), Plymouth University, Hasso Plattner Institut, Institut de Mécanique Céleste et de Calcul des Ephémérides (IMCCE), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Lille-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), University of Hawaii, 2525 Correa Road, Honolulu, HI 96822, United States, Department of Computer Science and Engineering [Shanghai] (CSE), Shanghai Jiao Tong University [Shanghai], High-Precision Mass Spectrometry and Environment Change Laboratory (HISPEC), National Taiwan University [Taiwan] (NTU), International Laboratory France-Taiwan CNRS-NSC ADEPT, Department of Marine Environmental Informatics, Institute of Earth Sciences [Tapei] (IES Sinica), Academia Sinica, Department of Earth Sciences [Cambridge, UK], University of Cambridge [UK] (CAM), Laboratoire Géosciences et Environnement Cergy (GEC), Fédération INSTITUT DES MATÉRIAUX DE CERGY-PONTOISE (I-MAT), Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine, and non-UU output of UU-AW members
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Marine isotope stage ,010504 meteorology & atmospheric sciences ,Orbital forcing ,sub-01 ,insolation ,010502 geochemistry & geophysics ,01 natural sciences ,precession cycle ,Geochemistry and Petrology ,greenhouse gases ,Sea ice ,Earth and Planetary Sciences (miscellaneous) ,14. Life underwater ,Glacial period ,Holocene ,ComputingMilieux_MISCELLANEOUS ,0105 earth and related environmental sciences ,Okhotsk Sea ,geography ,geography.geographical_feature_category ,Radiative forcing ,sea ice ,Sea surface temperature ,Oceanography ,Geophysics ,13. Climate action ,Space and Planetary Science ,Interglacial ,[PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph] ,Geology - Abstract
Recent reduction in high-latitude sea ice extent demonstrates that sea ice is highly sensitive to external and internal radiative forcings. In order to better understand sea ice system responses to external orbital forcing and internal oscillations on orbital timescales, here we reconstruct changes in sea ice extent and summer sea surface temperature (SSST) over the past 130,000 yrs in the central Okhotsk Sea. We applied novel organic geochemical proxies of sea ice (IP25), SSST (TEXL86 ) and open water marine productivity (a tri-unsaturated highly branched isoprenoid and biogenic opal) to marine sediment core MD01-2414 (53°11.77′N, 149°34.80′E, water depth 1123 m). To complement the proxy data, we also carried out transient Earth system model simulations and sensitivity tests to identify contributions of different climatic forcing factors. Our results show that the central Okhotsk Sea was ice-free during Marine Isotope Stage (MIS) 5e and the early-mid Holocene, but experienced variable sea ice cover during MIS 2–4, consistent with intervals of relatively high and low SSST, respectively. Our data also show that the sea ice extent was governed by precession-dominated insolation changes during intervals of atmospheric CO2 concentrations ranging from 190 to 260 ppm. However, the proxy record and the model simulation data show that the central Okhotsk Sea was near ice-free regardless of insolation forcing throughout the penultimate interglacial, and during the Holocene, when atmospheric CO2 was above ∼260 ppm. Past sea ice conditions in the central Okhotsk Sea were therefore strongly modulated by both orbital-driven insolation and CO2-induced radiative forcing during the past glacial/interglacial cycle.
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- 2018
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6. Unknown solution length problems with no asymptotically optimal run time
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Carola Doerr, Timo Kötzing, Benjamin Doerr, Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Centre National de la Recherche Scientifique (CNRS), Recherche Opérationnelle (RO), Laboratoire d'Informatique de Paris 6 (LIP6), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Hasso Plattner Institut, and École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)
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Fitness function ,Matching (graph theory) ,Dimension (graph theory) ,[INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS] ,Evolutionary algorithm ,0102 computer and information sciences ,02 engineering and technology ,Function (mathematics) ,[INFO.INFO-NE]Computer Science [cs]/Neural and Evolutionary Computing [cs.NE] ,01 natural sciences ,Combinatorics ,Asymptotically optimal algorithm ,010201 computation theory & mathematics ,Log-log plot ,Position (vector) ,TheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITY ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,ComputingMilieux_MISCELLANEOUS ,Mathematics - Abstract
We revisit the problem of optimizing a fitness function of unknown dimension; that is, we face a function defined over bit-strings of large length N, but only n ≪ N of them have an influence on the fitness. Neither the position of these relevant bits nor their number is known. In previous work, variants of the (1 + 1) evolutionary algorithm (EA) have been developed that solve, for arbitrary s ∈ ℕ, such OneMax and LeadingOnes instances, simultaneously for all n ∈ ℕ, in expected time O(n(log(n))2 log log(n) ... log(s−1)(n)(log(s)(n))1+e) and O(n2 log(n) log log(n) ... log(s−1)(n)(log(s)(n))1+e), respectively; that is, in almost the same time as if n and the relevant bit positions were known.In this work, we prove the first, almost matching, lower bounds for this setting. For LeadingOnes, we show that, for every s ∈ ℕ, the (1 + 1) EA with any mutation operator treating zeros and ones equally has an expected run time of ω(n2 log(n) log log(n) ... log(s)(n)) when facing problem size n. Aiming at closing the small remaining gap, we realize that, quite surprisingly, there is no asymptotically best performance. For any algorithm solving, for all n, all instances of size n in expected time at most T(n), there is an algorithm doing the same in time T'(n) with T' = o(T). For OneMax we show results of similar flavor.
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- 2017
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7. Are We There Yet? Simple Language-Implementation Techniques for the 21st Century
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Tobias Pape, Stefan Marr, Wolfgang De Meuter, Analyses and Languages Constructs for Object-Oriented Application Evolution (RMOD), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Software Architecture Group (SAG), Hasso-Plattner-Institut, Software Languages Lab (SLL), Vrije Universiteit Brussel (VUB), and Software Languages Lab
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Domain-specific language ,Java ,Computer science ,virtual machines ,Computer programming ,Hasso-Plattner-Institut für Digital Engineering gGmbH ,computer.software_genre ,Domain (software engineering) ,RPython ,domain-specific languages ,programming languages ,Implementation ,computer.programming_language ,Truffle ,Compilers ,Computer Programming ,DSL ,Interpreter ,Interpreters ,Language Implementation ,Performance ,Programming Languages ,SOM ,Self-Optimizing ,Smalltalk ,Software Engineering ,Virtual Machines ,Software engineering ,[INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL] ,business.industry ,Programming language ,compilers ,language implementation ,computer programming ,High-level programming language ,Virtual machine ,Compiler ,business ,computer ,Software - Abstract
International audience; With the rise of domain-specific languages (DSLs), research in language implementation techniques regains importance. While DSLs can help to manage the domain's complexity, it is rarely affordable to build highly optimizing compilers or virtual machines, and thus, performance remains an issue. Ideally, one would implement a simple interpreter and still reach acceptable performance levels. RPython and Truffle are two approaches that promise to facilitate language implementation based on simple interpreters, while reaching performance of the same order of magnitude as highly optimizing virtual machines. In this case study, we compare the two approaches to identify commonalities, weaknesses, and areas for further research to improve their utility for language implementations.
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- 2014
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8. A Body-centric Design Space for Multi-surface Interaction
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Wagner, Julie, Nancel, Mathieu, Gustafson, Sean, Huot, Stéphane, Mackay, Wendy E., Situated interaction (IN-SITU), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Laboratoire Traitement et Communication de l'Information (LTCI), Télécom ParisTech-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), The Human Computer Interaction Lab, Hasso Plattner Institut, and ACM SIGCHI
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ACM: H.: Information Systems/H.5: INFORMATION INTERFACES AND PRESENTATION (e.g., HCI)/H.5.2: User Interfaces/H.5.2.13: Theory and methods ,[INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC] - Abstract
International audience; We introduce BodyScape, a body-centric design space that allows us to describe, classify and systematically compare multi-surface interaction techniques, both individually and in combination. BodyScape reflects the relationship between users and their environment, specifically how different body parts enhance or restrict movement within particular interaction techniques and can be used to analyze existing techniques or suggest new ones. We illustrate the use of BodyScape by comparing two free-hand techniques, on-body touch and mid-air pointing, first separately, then combined. We found that touching the torso is faster than touching the lower legs, since it affects the user's balance; and touching targets on the dominant arm is slower than targets on the torso because the user must compensate for the applied force.
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- 2013
9. Extended Abstracts of the 31st Annual CHI Conference on Human Factors in Computing Systems
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Patrick Baudisch, Michel Beaudouin-Lafon, Mackay, Wendy E., The Human Computer Interaction Lab, Hasso Plattner Institut, Situated interaction (IN-SITU), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), InSitu, and Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)
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[INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC] - Abstract
3318 pages; International audience; The CHI Papers and Notes program is continuing to grow along with many of our sister conferences. We are pleased that CHI is still the leading venue for research in human-computer interaction. CHI 2013 continued the use of subcommittees to manage the review process. Authors selected the subcommittee they believed was best qualified to review their work: For clarity, we retained the same committee identifiers as last year. Due to the continuing growth in submissions, we split several subcommittees into more manageable sizes. We are pleased with the subcommittee process: By dividing the work, each paper received much more careful discussion than would otherwise have been possible. This year we had 1963 total submissions, including 1347 papers and 617 notes, representing a 24% growth over last year. We accepted 392 submissions (20%): 316 papers and 76 notes. The CHI review process demands a tremendous amount of work from all areas of the human-computer interaction community. As co-chairs of the process, we are amazed at the ability of the community to organize itself to accomplish this task. We would like to thank the 2680 individual reviewers for their careful consideration of these papers. We also deeply appreciate the huge amount of time donated to this process by the 211-member program committee, who paid their own way to attend the face-to-face program committee meeting, an event larger than the average ACM conference. We are proud of the work of the CHI 2013 program committee and hope that you enjoy these papers and notes, which represent the best research in human-computer interaction.
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- 2013
10. Proceedings of the 31st Annual CHI Conference on Human Factors in Computing Systems
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Susanne Bødker, Stephen Brewster, Patrick Baudisch, Michel Beaudouin-Lafon, Mackay, Wendy E., Aarhus University [Aarhus], Glasgow Interactive Systems Group (GIST), University of Glasgow, The Human Computer Interaction Lab, Hasso Plattner Institut, Situated interaction (IN-SITU), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), InSitu, and Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)
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[INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC] - Abstract
3490 pages; International audience; The CHI Papers and Notes program is continuing to grow along with many of our sister conferences. We are pleased that CHI is still the leading venue for research in human-computer interaction. CHI 2013 continued the use of subcommittees to manage the review process. Authors selected the subcommittee they believed was best qualified to review their work: For clarity, we retained the same committee identifiers as last year. Due to the continuing growth in submissions, we split several subcommittees into more manageable sizes. We are pleased with the subcommittee process: By dividing the work, each paper received much more careful discussion than would otherwise have been possible. This year we had 1963 total submissions, including 1347 papers and 617 notes, representing a 24% growth over last year. We accepted 392 submissions (20%): 316 papers and 76 notes. The CHI review process demands a tremendous amount of work from all areas of the human-computer interaction community. As co-chairs of the process, we are amazed at the ability of the community to organize itself to accomplish this task. We would like to thank the 2680 individual reviewers for their careful consideration of these papers. We also deeply appreciate the huge amount of time donated to this process by the 211-member program committee, who paid their own way to attend the face-to-face program committee meeting, an event larger than the average ACM conference. We are proud of the work of the CHI 2013 program committee and hope that you enjoy these papers and notes, which represent the best research in human-computer interaction.
- Published
- 2013
11. CoExist: Preserving Immediate Access to Source Code and Run-time Information of Previous Development States
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Steinert, Bastian, Cassou, Damien, Hirschfeld, Robert, Software Architecture Group, Hasso-Plattner-Institut, Analyses and Languages Constructs for Object-Oriented Application Evolution (RMOD), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, and Institut National de Recherche en Informatique et en Automatique (Inria)
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change-oriented programming ,continuous versioning ,[INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL] ,evolution ,explore-first programming ,fine-grained changes ,Prototyping ,fault localization - Abstract
International audience; Programmers make many changes to the program to eventually find a good solution for a given task. Every little change and the respective development state can be of value in future development situations when, for example, promising ideas suddenly turn out inappropriate or the interplay of objects turns out more complex than initially expected before making changes. Programmers would benefit from tool sup-port that provides immediate access to source code and run-time of previous development states of interest. We present IDE extensions, implemented for Squeak/Smalltalk, to preserve, retrieve, and work with this information. With such tool support, programmers can work without worries be-cause they can rely on tools that help them with whatever their explorations will reveal. They no longer have to follow certain best practices only to avoid undesired consequences of changing code.
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- 2012
12. Test Quality Feedback Improving Effectivity and Efficiency of Unit Testing
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Michael Perscheid, Robert Hirschfeld, Damien Cassou, Software Architecture Group, Hasso-Plattner-Institut, Analyses and Languages Constructs for Object-Oriented Application Evolution (RMOD), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, and Institut National de Recherche en Informatique et en Automatique (Inria)
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Test strategy ,[INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL] ,Computer science ,business.industry ,Test Quality Feedback ,Dynamic Analysis ,computer.software_genre ,Test harness ,Test script ,Unit Tests ,Test case ,System under test ,Regression testing ,Operating system ,Test suite ,Test Management Approach ,Software engineering ,business ,computer - Abstract
International audience; Writing unit tests for a software system enhances the confidence that a system works as expected. Since time pressure often prevents a complete testing of all application details developers need to know which new tests the system requires. Developers also need to know which existing tests take the most time and slow down the whole development process. Missing feedback about less tested functionality and reasons for long running test cases make it, however, harder to create a test suite that covers all important parts of a software system in a minimum of time. As a result a software system may be inadequately tested and developers may test less frequently. Our approach provides test quality feedback to guide developers in identifying missing tests and correcting low-quality tests. We provide developers with a tool that analyzes test suites with respect to their effectivity (e.g., missing tests) and efficiency (e.g., time and memory consumption). We implement our approach, named PathMap, as an extended test runner within the Squeak Smalltalk IDE and demonstrate its benefits by improving the test quality of representative software systems.
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- 2012
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13. Using the DiaSpec design language and compiler to develop robotics systems
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Cassou, Damien, Stinckwich, Serge, Koch, Pierrick, Software Architecture Group, Hasso Plattner Institut (HPI), University of Potsdam = Universität Potsdam, Equipe MAD - Laboratoire GREYC - UMR6072, Groupe de Recherche en Informatique, Image et Instrumentation de Caen (GREYC), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), University of Potsdam, Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
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design language ,software architecture ,robotics ,Software Engineering (cs.SE) ,FOS: Computer and information sciences ,Computer Science - Robotics ,Computer Science - Software Engineering ,programming framework ,generative programming ,[INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO] ,[INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE] ,Robotics (cs.RO) - Abstract
A Sense/Compute/Control (SCC) application is one that interacts with the physical environment. Such applications are pervasive in domains such as building automation, assisted living, and autonomic computing. Developing an SCC application is complex because: (1) the implementation must address both the interaction with the environment and the application logic; (2) any evolution in the environment must be reflected in the implementation of the application; (3) correctness is essential, as effects on the physical environment can have irreversible consequences. The SCC architectural pattern and the DiaSpec domain-specific design language propose a framework to guide the design of such applications. From a design description in DiaSpec, the DiaSpec compiler is capable of generating a programming framework that guides the developer in implementing the design and that provides runtime support. In this paper, we report on an experiment using DiaSpec (both the design language and compiler) to develop a standard robotics application. We discuss the benefits and problems of using DiaSpec in a robotics setting and present some changes that would make DiaSpec a better framework in this setting., Comment: DSLRob'11: Domain-Specific Languages and models for ROBotic systems (2011)
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- 2011
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14. Hypergraph-Based Modeling of Ad-Hoc Business Processes
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Polyvyanyy, Artem, Weske, Mathias, Hasso Plattner Institut, Ardagna, Danilo, Mecella, Massimo, and Yang, Jian
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080500 DISTRIBUTED COMPUTING ,Business process modeling ,Process modeling ,Process (engineering) ,Artifact-centric business process model ,Business process ,Computer science ,Distributed computing ,02 engineering and technology ,dissemin ,Process graph ,business process modeling, hypergraph-structured process, ad-hoc process, process formalism, execution semantics ,Business Process Model and Notation ,Business process discovery ,Hypergraph-structured process ,020204 information systems ,0202 electrical engineering, electronic engineering, information engineering ,[INFO]Computer Science [cs] ,020201 artificial intelligence & image processing ,Process formalism ,Execution semantics ,080600 INFORMATION SYSTEMS ,Ad-hoc process - Abstract
International audience; Process models are usually depicted as directed graphs, with nodes representing activities and directed edges control flow. While structured processes with pre-defined control flow have been studied in detail, flexible processes including ad-hoc activities need further investigation. This paper presents flexible process graph, a novel approach to model processes in the context of dynamic environment and adaptive process participants’ behavior. The approach allows defining execution constraints, which are more restrictive than traditional ad-hoc processes and less restrictive than traditional control flow, thereby balancing structured control flow with unstructured ad-hoc activities. Flexible process graph focuses on what can be done to perform a process. Process participants’ routing decisions are based on the current process state. As a formal grounding, the approach uses hypergraphs, where each edge can associate any number of nodes. Hypergraphs are used to define execution semantics of processes formally. We provide a process scenario to motivate and illustrate the approach.
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- 2009
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15. TapTap and MagStick: Improving One-Handed Target Acquisition on Small Touch-screens
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Stéphane Huot, Anne Roudaut, Eric Lecolinet, The Human Computer Interaction Lab, Hasso Plattner Institut, Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Situated interaction (IN-SITU), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire Traitement et Communication de l'Information (LTCI), and Télécom ParisTech-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Computer science ,Word error rate ,02 engineering and technology ,Thumb ,ACM: H.: Information Systems/H.5: INFORMATION INTERFACES AND PRESENTATION (e.g., HCI)/H.5.2: User Interfaces/H.5.2.7: Interaction styles (e.g., commands, menus, forms, direct manipulation) ,ACM: H.: Information Systems/H.5: INFORMATION INTERFACES AND PRESENTATION (e.g., HCI)/H.5.2: User Interfaces/H.5.2.6: Input devices and strategies (e.g., mouse, touchscreen) ,0202 electrical engineering, electronic engineering, information engineering ,medicine ,0501 psychology and cognitive sciences ,Computer vision ,[INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC] ,Controlled experiment ,Visual occlusion ,050107 human factors ,Selection (genetic algorithm) ,ACM: H.: Information Systems/H.5: INFORMATION INTERFACES AND PRESENTATION (e.g., HCI)/H.5.2: User Interfaces/H.5.2.10: Screen design (e.g., text, graphics, color) ,business.industry ,05 social sciences ,020207 software engineering ,Direct touch ,Target acquisition ,medicine.anatomical_structure ,ACM: D.: Software/D.2: SOFTWARE ENGINEERING/D.2.2: Design Tools and Techniques/D.2.2.12: User interfaces ,Artificial intelligence ,business ,Mobile device - Abstract
International audience; We present the design and evaluation of TapTap and MagStick, two thumb interaction techniques for target acquisition on mobile devices with small touch-screens. These two techniques address all the issues raised by the selection of targets with the thumb on small tactile screens: screen accessibility, visual occlusion and accuracy. A controlled experiment shows that TapTap and MagStick allow the selection of targets in all areas of the screen in a fast and accurate way. They were found to be faster than four previous techniques except Direct Touch which, although faster, is too error prone. They also provided the best error rate of all tested techniques. Finally the paper also provides a comprehensive study of various techniques for thumb based touch-screen target selection.
- Published
- 2008
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16. Type Feedback for Bytecode Interpreters
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Haupt, Michael, Hirschfeld, Robert, Denker, Marcus, Software Architecture Group (SAG), Hasso-Plattner-Institut, Software Architecture Group, Software Composition Group [Bern] (SCG), Universität Bern [Bern], and Lse, Lse
- Subjects
510 Mathematics ,TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES ,[INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL] ,020204 information systems ,0202 electrical engineering, electronic engineering, information engineering ,020207 software engineering ,02 engineering and technology ,Software_PROGRAMMINGLANGUAGES ,000 Computer science, knowledge & systems ,[INFO.INFO-PL] Computer Science [cs]/Programming Languages [cs.PL] - Abstract
International audience; This position paper proposes the exploitation of type feedback mechanisms, or more precisely, polymorphic inline caches, for purely interpreting implementations of object-oriented programming languages. Using Squeak's virtual machine as an example, polymorphic inline caches are discussed as an alternative to global caching. An implementation proposal for polymorphic inline caches in the Squeak virtual machine is presented, and possible future applications for online optimization are outlined.
- Published
- 2007
17. Association between plausible genetic factors and weight loss from GLP1-RA and bariatric surgery: a multi-ancestry study in 10 960 individuals from 9 biobanks.
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German J, Cordioli M, Tozzo V, Urbut S, Arumäe K, Smit RAJ, Lee J, Li JH, Janucik A, Ding Y, Akinkuolie A, Heyne H, Eoli A, Saad C, Al-Sarraj Y, Abdel-Latif R, Barry A, Wang Z, Natarajan P, Ripatti S, Philippakis A, Szczerbinski L, Pasaniuc B, Mbarek H, Loos RJF, Vainik U, and Ganna A
- Abstract
Obesity is a significant public health concern. GLP-1 receptor agonists (GLP1-RA), predominantly in use as a type 2 diabetes treatment, are a promising pharmacological approach for weight loss, while bariatric surgery (BS) remains a durable, but invasive, intervention. Despite observed heterogeneity in weight loss effects, the genetic effects on weight loss from GLP1-RA and BS have not been extensively explored in large sample sizes, and most studies have focused on differences in race and ethnicity, rather than genetic ancestry. We studied whether genetic factors, previously shown to affect body weight, impact weight loss due to GLP1-RA therapy or BS in 10,960 individuals from 9 multi-ancestry biobank studies in 6 countries. The average weight change between 6 and 12 months from therapy initiation was -3.93% for GLP1-RA users, with marginal differences across genetic ancestries. For BS patients the weight change between 6 and 48 months from the operation was -21.17%. There were no significant associations between weight loss due to GLP1-RA and polygenic scores for BMI or type 2 diabetes or specific missense variants in the GLP1R, PCSK1 and APOE genes, after multiple-testing correction. However, a higher polygenic score for BMI was significantly linked to lower weight loss after BS (+0.7% for 1 standard deviation change in the polygenic score, P = 1.24×10
-4 ). In contrast, higher weight at baseline was associated with greater weight loss. Our findings suggest that existing polygenic scores related to weight and type 2 diabetes and missense variants in the drug target gene do not have a large impact on GLP1-RA effectiveness. Our results also confirm the effectiveness of these treatments across all major continental ancestry groups considered.- Published
- 2024
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18. [Digital medicine in neurological research-Between hype and evidence].
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Masanneck L, Pawlitzki MG, and Meuth SG
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- Humans, Telemedicine
- Abstract
Background: The rapid advancement of digital medicine and health technologies in neurology offers both significant potential and challenges. This article outlines fundamental aspects of digital medicine related to neurological research and highlights application examples of digital technologies in neurological research., Aim: To provide a comprehensive overview of current digital developments in neurology and their impact on neurological research., Material and Methods: In this narrative review articles from various sources and references related to digital medicine and health technologies in neurology were compiled and analyzed., Results and Discussion: The data presented indicate that digital health technologies and digital therapeutics have the potential to decisively shape neurological care and research; however, it is emphasized that a critical evaluation and evidence-based approach to these technologies are essential to determine their actual value in neurology., (© 2023. The Author(s), under exclusive licence to Springer Medizin Verlag GmbH, ein Teil von Springer Nature.)
- Published
- 2024
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19. Beyond the 510(k): The regulation of novel moderate-risk medical devices, intellectual property considerations, and innovation incentives in the FDA's De Novo pathway.
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Aboy M, Crespo C, and Stern A
- Abstract
Moderate-risk medical devices constitute 99% of those that have been regulated by the U.S. Food and Drug Administration (FDA) since it gained authority to regulate medical technology nearly five decades ago. This article presents an analysis of the interaction between the 510(k) process -the historically dominant path to market for most medical devices- and the De Novo pathway, a more recent alternative that targets more novel devices, including those involving new technologies, diagnostics, hardware, and software. The De Novo pathway holds significant potential for innovators seeking to define new categories of medical devices, as it represents a less burdensome approach than would have otherwise been needed historically. Moreover, it supports the FDA in its effort to modernize the long-established 510(k) pathway by promoting the availability of up-to-date device "predicates" upon which subsequent device applications can be based, reflecting positive spillovers that are likely to encourage manufacturers to adopt current state-of-the-art technologies and modern standards of safety and effectiveness. We analyze the of characteristics all the De Novo classification requests to date, including the submission type, trends, FDA review times, and device types. After characterizing how the De Novo process has been used over time, we discuss its unique challenges and opportunities with respect to medical device software and AI-enabled devices, including considerations for intellectual property, innovation, and competition economics., (© 2024. The Author(s).)
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- 2024
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20. Moving cholera vaccines ahead of the epidemic curve.
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Memish ZA, Blumberg L, Al-Maani AS, Baru R, Dube E, Gao GF, Jernigan DB, Leo YS, Peiris JSM, Masud JHB, McVernon J, Nonvignon J, Ogunsola FT, Reese H, Safdar RM, Ungchusak K, Wieler LH, and Heymann D
- Subjects
- Humans, Cholera Vaccines, Cholera epidemiology, Cholera prevention & control, Vibrio cholerae, Epidemics prevention & control
- Abstract
Competing Interests: LB declares an appointment at the non-profit organisation Right to Care. All authors are members of the Strategic and Technical Advisory Group on Infectious Hazards with Pandemic and Epidemic Potential (STAG-IH) that provides independent advice to WHO. We declare no competing interests.
- Published
- 2024
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21. Epilepsies of presumed genetic etiology show enrichment of rare variants that occur in the general population.
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Bundalian L, Su YY, Chen S, Velluva A, Kirstein AS, Garten A, Biskup S, Battke F, Lal D, Heyne HO, Platzer K, Lin CC, Lemke JR, and Le Duc D
- Subjects
- Humans, Phenotype, Alleles, Brain, Gene Frequency genetics, Epilepsy, Generalized genetics
- Abstract
Previous studies suggested that severe epilepsies, e.g., developmental and epileptic encephalopathies (DEEs), are mainly caused by ultra-rare de novo genetic variants. For milder disease, rare genetic variants could contribute to the phenotype. To determine the importance of rare variants for different epilepsy types, we analyzed a whole-exome sequencing cohort of 9,170 epilepsy-affected individuals and 8,436 control individuals. Here, we separately analyzed three different groups of epilepsies: severe DEEs, genetic generalized epilepsy (GGE), and non-acquired focal epilepsy (NAFE). We required qualifying rare variants (QRVs) to occur in control individuals with an allele count ≥ 1 and a minor allele frequency ≤ 1:1,000, to be predicted as deleterious (CADD ≥ 20), and to have an odds ratio in individuals with epilepsy ≥ 2. We identified genes enriched with QRVs primarily in NAFE (n = 72), followed by GGE (n = 32) and DEE (n = 21). This suggests that rare variants may play a more important role for causality of NAFE than for DEE. Moreover, we found that genes harboring QRVs, e.g., HSGP2, FLNA, or TNC, encode proteins that are involved in structuring the brain extracellular matrix. The present study confirms an involvement of rare variants for NAFE that occur also in the general population, while in DEE and GGE, the contribution of such variants appears more limited., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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22. [Application areas of artificial intelligence in the context of One Health with a focus on antimicrobial resistance].
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Irrgang C, Eckmanns T, V Kleist M, Antão EM, Ladewig K, Wieler LH, and Körber N
- Subjects
- Animals, Humans, Artificial Intelligence, Drug Resistance, Bacterial, Germany, Anti-Bacterial Agents pharmacology, One Health
- Abstract
Societal health is facing a number of new challenges, largely driven by ongoing climate change, demographic ageing, and globalization. The One Health approach links human, animal, and environmental sectors with the goal of achieving a holistic understanding of health in general. To implement this approach, diverse and heterogeneous data streams and types must be combined and analyzed. To this end, artificial intelligence (AI) techniques offer new opportunities for cross-sectoral assessment of current and future health threats. Using the example of antimicrobial resistance as a global threat in the One Health context, we demonstrate potential applications and challenges of AI techniques.This article provides an overview of different applications of AI techniques in the context of One Health and highlights their challenges. Using the spread of antimicrobial resistance (AMR), an increasing global threat, as an example, existing and future AI-based approaches to AMR containment and prevention are described. These range from novel drug development and personalized therapy, to targeted monitoring of antibiotic use in livestock and agriculture, to comprehensive environmental surveillance., (© 2023. The Author(s).)
- Published
- 2023
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23. Programming techniques for improving rule readability for rule-based information extraction natural language processing pipelines of unstructured and semi-structured medical texts.
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Ladas N, Borchert F, Franz S, Rehberg A, Strauch N, Sommer KK, Marschollek M, and Gietzelt M
- Subjects
- Humans, Comprehension, Algorithms, Information Storage and Retrieval, Electronic Health Records, Natural Language Processing
- Abstract
Background: Extraction of medical terms and their corresponding values from semi-structured and unstructured texts of medical reports can be a time-consuming and error-prone process. Methods of natural language processing (NLP) can help define an extraction pipeline for accomplishing a structured format transformation strategy., Objectives: In this paper, we build an NLP pipeline to extract values of the classification of malignant tumors (TNM) from unstructured and semi-structured pathology reports and import them further to a structured data source for a clinical study. Our research interest is not focused on standard performance metrics like precision, recall, and F-measure on the test and validation data. We discuss how with the help of software programming techniques the readability of rule-based (RB) information extraction (IE) pipelines can be improved, and therefore minimize the time to correct or update the rules, and efficiently import them to another programming language., Methods: The extract rules were manually programmed with training data of TNM classification and tested in two separate pipelines based on design specifications from domain experts and data curators. Firstly we implemented each rule directly in one line for each extraction item. Secondly, we reprogrammed them in a readable fashion through decomposition and intention-revealing names for the variable declaration. To measure the impact of both methods we measure the time for the fine-tuning and programming of the extractions through test data of semi-structured and unstructured texts., Results: We analyze the benefits of improving through readability of the writing of rules, through parallel programming with regular expressions (REGEX), and the Apache Uima Ruta language (AURL). The time for correcting the readable rules in AURL and REGEX was significantly reduced. Complicated rules in REGEX are decomposed and intention-revealing declarations were reprogrammed in AURL in 5 min., Conclusion: We discuss the importance of factor readability and how can it be improved when programming RB text IE pipelines. Independent of the features of the programming language and the tools applied, a readable coding strategy can be proven beneficial for future maintenance and offer an interpretable solution for understanding the extraction and for transferring the rules to other domains and NLP pipelines.
- Published
- 2023
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24. Genetic susceptibility to diabetic kidney disease is linked to promoter variants of XOR.
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Wang Q, Qi H, Wu Y, Yu L, Bouchareb R, Li S, Lassén E, Casalena G, Stadler K, Ebefors K, Yi Z, Shi S, Salem F, Gordon R, Lu L, Williams RW, Duffield J, Zhang W, Itan Y, Böttinger E, and Daehn I
- Subjects
- Humans, Male, Mice, Animals, Xanthine Dehydrogenase genetics, Xanthine Dehydrogenase metabolism, Genetic Predisposition to Disease, Mice, Inbred DBA, Mice, Inbred C57BL, Diabetic Nephropathies genetics, Diabetes Mellitus
- Abstract
The lifetime risk of kidney disease in people with diabetes is 10-30%, implicating genetic predisposition in the cause of diabetic kidney disease (DKD). Here we identify an expression quantitative trait loci (QTLs) in the cis-acting regulatory region of the xanthine dehydrogenase, or xanthine oxidoreductase (Xor), a binding site for C/EBPβ, to be associated with diabetes-induced podocyte loss in DKD in male mice. We examine mouse inbred strains that are susceptible (DBA/2J) and resistant (C57BL/6J) to DKD, as well as a panel of recombinant inbred BXD mice, to map QTLs. We also uncover promoter XOR orthologue variants in humans associated with high risk of DKD. We introduced the risk variant into the 5'-regulatory region of XOR in DKD-resistant mice, which resulted in increased Xor activity associated with podocyte depletion, albuminuria, oxidative stress and damage restricted to the glomerular endothelium, which increase further with type 1 diabetes, high-fat diet and ageing. Therefore, differential regulation of Xor contributes to phenotypic consequences with diabetes and ageing., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)
- Published
- 2023
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25. The role of rare genetic variants enrichment in epilepsies of presumed genetic etiology.
- Author
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Bundalian L, Su YY, Chen S, Velluva A, Kirstein AS, Garten A, Biskup S, Battke F, Lal D, Heyne HO, Platzer K, Lin CC, Lemke JR, and Le Duc D
- Abstract
Previous studies suggested that severe epilepsies e.g., developmental and epileptic encephalopathies (DEE) are mainly caused by ultra-rare de novo genetic variants. For milder phenotypes, rare genetic variants could contribute to the phenotype. To determine the importance of rare variants for different epilepsy types, we analyzed a whole-exome sequencing cohort of 9,170 epilepsy-affected individuals and 8,436 controls. Here, we separately analyzed three different groups of epilepsies : severe DEEs, genetic generalized epilepsy (GGE), and non-acquired focal epilepsy (NAFE). We required qualifying rare variants (QRVs) to occur in controls at a minor allele frequency ≤ 1:1,000, to be predicted as deleterious (CADD≥20), and to have an odds ratio in epilepsy cases ≥2. We identified genes enriched with QRVs in DEE (n=21), NAFE (n=72), and GGE (n=32) - the number of enriched genes are found greatest in NAFE and least in DEE. This suggests that rare variants may play a more important role for causality of NAFE than in DEE. Moreover, we found that QRV-carrying genes e.g., HSGP2 , FLNA or TNC are involved in structuring the brain extracellular matrix. The present study confirms an involvement of rare variants for NAFE, while in DEE and GGE, the contribution of such variants appears more limited., Competing Interests: 11.Conflict of Interest The authors declare no competing interests.
- Published
- 2023
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26. Myositis in Germany: epidemiological insights over 15 years from 2005 to 2019.
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Pawlitzki M, Acar L, Masanneck L, Willison A, Regner-Nelke L, Nelke C, L'hoest H, Marschall U, Schmidt J, Meuth SG, and Ruck T
- Abstract
Background: The medical care of patients with myositis is a great challenge in clinical practice. This is due to the rarity of these disease, the complexity of diagnosis and management as well as the lack of systematic analyses., Objectives: Therefore, the aim of this project was to obtain an overview of the current care of myositis patients in Germany and to evaluate epidemiological trends in recent years., Methods: In collaboration with BARMER Insurance, retrospective analysis of outpatient and inpatient data from an average of approximately 8.7 million insured patients between January 2005 and December 2019 was performed using ICD-10 codes for myositis for identification of relevant data. In addition, a comparative analysis was performed between myositis patients and an age-matched comparison group from other populations insured by BARMER., Results: 45,800 BARMER-insured individuals received a diagnosis of myositis during the observation period, with a relatively stable prevalence throughout. With regard to comorbidities, a significantly higher rate of cardiovascular disease as well as neoplasm was observed compared to the control group within the BARMER-insured population. In addition, myositis patients suffer more frequently from psychiatric disorders, such as depression and somatoform disorders. However, the ICD-10 catalogue only includes the specific coding of "dermatomyositis" and "polymyositis" and thus does not allow for a sufficient analysis of all idiopathic inflammatory myopathies subtypes., Conclusion: The current data provide a comprehensive epidemiological analysis of myositis in Germany, highlighting the multimorbidity of myositis patients. This underlines the need for multidisciplinary management. However, the ICD-10 codes currently still in use do not allow for specific analysis of the subtypes of myositis. The upcoming ICD-11 coding may improve future analyses in this regard., (© 2022. The Author(s).)
- Published
- 2022
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27. AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics.
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Lund JB, Lindberg EL, Maatz H, Pottbaecker F, Hübner N, and Lippert C
- Abstract
With the current surge of spatial transcriptomics (ST) studies, researchers are exploring the deep interactive cell-play directly in tissues, in situ. However, with the current technologies, measurements consist of mRNA transcript profiles of mixed origin. Recently, applications have been proposed to tackle the deconvolution process, to gain knowledge about which cell types (SC) are found within. This is usually done by incorporating metrics from single-cell (SC) RNA, from similar tissues. Yet, most existing tools are cumbersome, and we found them hard to integrate and properly utilize. Therefore, we present AntiSplodge , a simple feed-forward neural-network-based pipeline designed to effective deconvolute ST profiles by utilizing synthetic ST profiles derived from real-life SC datasets. AntiSplodge is designed to be easy, fast and intuitive while still being lightweight. To demonstrate AntiSplodge , we deconvolute the human heart and verify correctness across time points. We further deconvolute the mouse brain, where spot patterns correctly follow that of the underlying tissue. In particular, for the hippocampus from where the cells originate. Furthermore, AntiSplodge demonstrates top of the line performance when compared to current state-of-the-art tools. Software availability: https://github.com/HealthML/AntiSplodge/., (© The Author(s) 2022. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)
- Published
- 2022
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28. A Systematic Review of Diagnostic Accuracy and Clinical Applications of Wearable Movement Sensors for Knee Joint Rehabilitation.
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Prill R, Walter M, Królikowska A, and Becker R
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- Humans, Knee Joint, Reproducibility of Results, Movement, Wearable Electronic Devices
- Abstract
In clinical practice, only a few reliable measurement instruments are available for monitoring knee joint rehabilitation. Advances to replace motion capturing with sensor data measurement have been made in the last years. Thus, a systematic review of the literature was performed, focusing on the implementation, diagnostic accuracy, and facilitators and barriers of integrating wearable sensor technology in clinical practices based on a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. For critical appraisal, the COSMIN Risk of Bias tool for reliability and measurement of error was used. PUBMED, Prospero, Cochrane database, and EMBASE were searched for eligible studies. Six studies reporting reliability aspects in using wearable sensor technology at any point after knee surgery in humans were included. All studies reported excellent results with high reliability coefficients, high limits of agreement, or a few detectable errors. They used different or partly inappropriate methods for estimating reliability or missed reporting essential information. Therefore, a moderate risk of bias must be considered. Further quality criterion studies in clinical settings are needed to synthesize the evidence for providing transparent recommendations for the clinical use of wearable movement sensors in knee joint rehabilitation.
- Published
- 2021
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29. Predicting the SARS-CoV-2 effective reproduction number using bulk contact data from mobile phones.
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Rüdiger S, Konigorski S, Rakowski A, Edelman JA, Zernick D, Thieme A, and Lippert C
- Subjects
- COVID-19 epidemiology, Germany epidemiology, Humans, COVID-19 transmission, COVID-19 virology, Cell Phone, Contact Tracing, SARS-CoV-2 physiology
- Abstract
Over the last months, cases of SARS-CoV-2 surged repeatedly in many countries but could often be controlled with nonpharmaceutical interventions including social distancing. We analyzed deidentified Global Positioning System (GPS) tracking data from 1.15 to 1.4 million cell phones in Germany per day between March and November 2020 to identify encounters between individuals and statistically evaluate contact behavior. Using graph sampling theory, we estimated the contact index (CX), a metric for number and heterogeneity of contacts. We found that CX, and not the total number of contacts, is an accurate predictor for the effective reproduction number R derived from case numbers. A high correlation between CX and R recorded more than 2 wk later allows assessment of social behavior well before changes in case numbers become detectable. By construction, the CX quantifies the role of superspreading and permits assigning risks to specific contact behavior. We provide a critical CX value beyond which R is expected to rise above 1 and propose to use that value to leverage the social-distancing interventions for the coming months., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)
- Published
- 2021
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30. The trans-ancestral genomic architecture of glycemic traits.
- Author
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Chen J, Spracklen CN, Marenne G, Varshney A, Corbin LJ, Luan J, Willems SM, Wu Y, Zhang X, Horikoshi M, Boutin TS, Mägi R, Waage J, Li-Gao R, Chan KHK, Yao J, Anasanti MD, Chu AY, Claringbould A, Heikkinen J, Hong J, Hottenga JJ, Huo S, Kaakinen MA, Louie T, März W, Moreno-Macias H, Ndungu A, Nelson SC, Nolte IM, North KE, Raulerson CK, Ray D, Rohde R, Rybin D, Schurmann C, Sim X, Southam L, Stewart ID, Wang CA, Wang Y, Wu P, Zhang W, Ahluwalia TS, Appel EVR, Bielak LF, Brody JA, Burtt NP, Cabrera CP, Cade BE, Chai JF, Chai X, Chang LC, Chen CH, Chen BH, Chitrala KN, Chiu YF, de Haan HG, Delgado GE, Demirkan A, Duan Q, Engmann J, Fatumo SA, Gayán J, Giulianini F, Gong JH, Gustafsson S, Hai Y, Hartwig FP, He J, Heianza Y, Huang T, Huerta-Chagoya A, Hwang MY, Jensen RA, Kawaguchi T, Kentistou KA, Kim YJ, Kleber ME, Kooner IK, Lai S, Lange LA, Langefeld CD, Lauzon M, Li M, Ligthart S, Liu J, Loh M, Long J, Lyssenko V, Mangino M, Marzi C, Montasser ME, Nag A, Nakatochi M, Noce D, Noordam R, Pistis G, Preuss M, Raffield L, Rasmussen-Torvik LJ, Rich SS, Robertson NR, Rueedi R, Ryan K, Sanna S, Saxena R, Schraut KE, Sennblad B, Setoh K, Smith AV, Sparsø T, Strawbridge RJ, Takeuchi F, Tan J, Trompet S, van den Akker E, van der Most PJ, Verweij N, Vogel M, Wang H, Wang C, Wang N, Warren HR, Wen W, Wilsgaard T, Wong A, Wood AR, Xie T, Zafarmand MH, Zhao JH, Zhao W, Amin N, Arzumanyan Z, Astrup A, Bakker SJL, Baldassarre D, Beekman M, Bergman RN, Bertoni A, Blüher M, Bonnycastle LL, Bornstein SR, Bowden DW, Cai Q, Campbell A, Campbell H, Chang YC, de Geus EJC, Dehghan A, Du S, Eiriksdottir G, Farmaki AE, Frånberg M, Fuchsberger C, Gao Y, Gjesing AP, Goel A, Han S, Hartman CA, Herder C, Hicks AA, Hsieh CH, Hsueh WA, Ichihara S, Igase M, Ikram MA, Johnson WC, Jørgensen ME, Joshi PK, Kalyani RR, Kandeel FR, Katsuya T, Khor CC, Kiess W, Kolcic I, Kuulasmaa T, Kuusisto J, Läll K, Lam K, Lawlor DA, Lee NR, Lemaitre RN, Li H, Lin SY, Lindström J, Linneberg A, Liu J, Lorenzo C, Matsubara T, Matsuda F, Mingrone G, Mooijaart S, Moon S, Nabika T, Nadkarni GN, Nadler JL, Nelis M, Neville MJ, Norris JM, Ohyagi Y, Peters A, Peyser PA, Polasek O, Qi Q, Raven D, Reilly DF, Reiner A, Rivideneira F, Roll K, Rudan I, Sabanayagam C, Sandow K, Sattar N, Schürmann A, Shi J, Stringham HM, Taylor KD, Teslovich TM, Thuesen B, Timmers PRHJ, Tremoli E, Tsai MY, Uitterlinden A, van Dam RM, van Heemst D, van Hylckama Vlieg A, van Vliet-Ostaptchouk JV, Vangipurapu J, Vestergaard H, Wang T, Willems van Dijk K, Zemunik T, Abecasis GR, Adair LS, Aguilar-Salinas CA, Alarcón-Riquelme ME, An P, Aviles-Santa L, Becker DM, Beilin LJ, Bergmann S, Bisgaard H, Black C, Boehnke M, Boerwinkle E, Böhm BO, Bønnelykke K, Boomsma DI, Bottinger EP, Buchanan TA, Canouil M, Caulfield MJ, Chambers JC, Chasman DI, Chen YI, Cheng CY, Collins FS, Correa A, Cucca F, de Silva HJ, Dedoussis G, Elmståhl S, Evans MK, Ferrannini E, Ferrucci L, Florez JC, Franks PW, Frayling TM, Froguel P, Gigante B, Goodarzi MO, Gordon-Larsen P, Grallert H, Grarup N, Grimsgaard S, Groop L, Gudnason V, Guo X, Hamsten A, Hansen T, Hayward C, Heckbert SR, Horta BL, Huang W, Ingelsson E, James PS, Jarvelin MR, Jonas JB, Jukema JW, Kaleebu P, Kaplan R, Kardia SLR, Kato N, Keinanen-Kiukaanniemi SM, Kim BJ, Kivimaki M, Koistinen HA, Kooner JS, Körner A, Kovacs P, Kuh D, Kumari M, Kutalik Z, Laakso M, Lakka TA, Launer LJ, Leander K, Li H, Lin X, Lind L, Lindgren C, Liu S, Loos RJF, Magnusson PKE, Mahajan A, Metspalu A, Mook-Kanamori DO, Mori TA, Munroe PB, Njølstad I, O'Connell JR, Oldehinkel AJ, Ong KK, Padmanabhan S, Palmer CNA, Palmer ND, Pedersen O, Pennell CE, Porteous DJ, Pramstaller PP, Province MA, Psaty BM, Qi L, Raffel LJ, Rauramaa R, Redline S, Ridker PM, Rosendaal FR, Saaristo TE, Sandhu M, Saramies J, Schneiderman N, Schwarz P, Scott LJ, Selvin E, Sever P, Shu XO, Slagboom PE, Small KS, Smith BH, Snieder H, Sofer T, Sørensen TIA, Spector TD, Stanton A, Steves CJ, Stumvoll M, Sun L, Tabara Y, Tai ES, Timpson NJ, Tönjes A, Tuomilehto J, Tusie T, Uusitupa M, van der Harst P, van Duijn C, Vitart V, Vollenweider P, Vrijkotte TGM, Wagenknecht LE, Walker M, Wang YX, Wareham NJ, Watanabe RM, Watkins H, Wei WB, Wickremasinghe AR, Willemsen G, Wilson JF, Wong TY, Wu JY, Xiang AH, Yanek LR, Yengo L, Yokota M, Zeggini E, Zheng W, Zonderman AB, Rotter JI, Gloyn AL, McCarthy MI, Dupuis J, Meigs JB, Scott RA, Prokopenko I, Leong A, Liu CT, Parker SCJ, Mohlke KL, Langenberg C, Wheeler E, Morris AP, and Barroso I
- Subjects
- Alleles, Epigenesis, Genetic, Gene Expression Profiling, Genome, Human, Genome-Wide Association Study, Glycated Hemoglobin metabolism, Humans, Multifactorial Inheritance genetics, Physical Chromosome Mapping, Quantitative Trait Loci genetics, Blood Glucose genetics, Quantitative Trait, Heritable, White People genetics
- Abstract
Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10
-8 ), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.- Published
- 2021
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31. Monitoring of Sitting Postures With Sensor Networks in Controlled and Free-living Environments: Systematic Review.
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Kappattanavar AM, Steckhan N, Sachs JP, Freitas da Cruz H, Böttinger E, and Arnrich B
- Abstract
Background: A majority of employees in the industrial world spend most of their working time in a seated position. Monitoring sitting postures can provide insights into the underlying causes of occupational discomforts such as low back pain., Objective: This study focuses on the technologies and algorithms used to classify sitting postures on a chair with respect to spine and limb movements, using sensors and wearables such as inertial measurement units, pressure or piezoresistive sensors, accelerometers or gyroscopes, combined with machine learning approaches., Methods: A total of three electronic literature databases were surveyed to identify studies classifying sitting postures in adults. Quality appraisal was performed to extract critical details and assess biases in the shortlisted papers., Results: A total of 14 papers were shortlisted from 952 papers obtained after a systematic search. The majority of the studies used pressure sensors to measure sitting postures, whereas neural networks were the most frequently used approaches for classification tasks in this context. Only 2 studies were performed in a free-living environment. Most studies presented ethical and methodological shortcomings. Moreover, the findings indicate that the strategic placement of sensors can lead to better performance and lower costs., Conclusions: The included studies differed in various aspects of design and analysis. The majority of studies were rated as medium quality according to our assessment. Our study suggests that future work for posture classification can benefit from using inertial measurement unit sensors, since they make it possible to differentiate among spine movements and similar postures, considering transitional movements between postures, and using three-dimensional cameras to annotate the data for ground truth. Finally, comparing such studies is challenging, as there are no standard definitions of sitting postures that could be used for classification. In addition, this study identifies five basic sitting postures along with different combinations of limb and spine movements to help guide future research efforts., (©Arpita Mallikarjuna Kappattanavar, Nico Steckhan, Jan Philipp Sachs, Harry Freitas da Cruz, Erwin Böttinger, Bert Arnrich. Originally published in JMIR Biomedical Engineering (http://biomedeng.jmir.org), 08.03.2021.)
- Published
- 2021
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32. The Collaborative Research Center FONDA.
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Leser U, Hilbrich M, Draxl C, Eisert P, Grunske L, Hostert P, Kainmüller D, Kao O, Kehr B, Kehrer T, Koch C, Markl V, Meyerhenke H, Rabl T, Reinefeld A, Reinert K, Ritter K, Scheuermann B, Schintke F, Schweikardt N, and Weidlich M
- Abstract
Today's scientific data analysis very often requires complex Data Analysis Workflows (DAWs) executed over distributed computational infrastructures, e.g., clusters. Much research effort is devoted to the tuning and performance optimization of specific workflows for specific clusters. However, an arguably even more important problem for accelerating research is the reduction of development, adaptation, and maintenance times of DAWs. We describe the design and setup of the Collaborative Research Center (CRC) 1404 "FONDA -- Foundations of Workflows for Large-Scale Scientific Data Analysis", in which roughly 50 researchers jointly investigate new technologies, algorithms, and models to increase the portability, adaptability, and dependability of DAWs executed over distributed infrastructures. We describe the motivation behind our project, explain its underlying core concepts, introduce FONDA's internal structure, and sketch our vision for the future of workflow-based scientific data analysis. We also describe some lessons learned during the "making of" a CRC in Computer Science with strong interdisciplinary components, with the aim to foster similar endeavors., (© Gesellschaft für Informatik e.V. and Springer-Verlag GmbH Germany, part of Springer Nature 2021.)
- Published
- 2021
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33. EWASex: an efficient R-package to predict sex in epigenome-wide association studies.
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Lund JB, Li W, Mohammadnejad A, Li S, Baumbach J, and Tan Q
- Abstract
Summary: Epigenome-Wide Association Study (EWAS) has become a powerful approach to identify epigenetic variations associated with diseases or health traits. Sex is an important variable to include in EWAS to ensure unbiased data processing and statistical analysis. We introduce the R-package EWASex, which allows for fast and highly accurate sex-estimation using DNA methylation data on a small set of CpG sites located on the X-chromosome under stable X-chromosome inactivation in females., Results: We demonstrate that EWASex outperforms the current state of the art tools by using different EWAS datasets. With EWASex, we offer an efficient way to predict and to verify sex that can be easily implemented in any EWAS using blood samples or even other tissue types. It comes with pre-trained weights to work without prior sex labels and without requiring access to RAW data, which is a necessity for all currently available methods., Availability and Implementation: The EWASex R-package along with tutorials, documentation and source code are available at https://github.com/Silver-Hawk/EWASex., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2020
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34. Time to reality check the promises of machine learning-powered precision medicine.
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Wilkinson J, Arnold KF, Murray EJ, van Smeden M, Carr K, Sippy R, de Kamps M, Beam A, Konigorski S, Lippert C, Gilthorpe MS, and Tennant PWG
- Subjects
- Humans, Delivery of Health Care methods, Machine Learning, Precision Medicine methods
- Abstract
Machine learning methods, combined with large electronic health databases, could enable a personalised approach to medicine through improved diagnosis and prediction of individual responses to therapies. If successful, this strategy would represent a revolution in clinical research and practice. However, although the vision of individually tailored medicine is alluring, there is a need to distinguish genuine potential from hype. We argue that the goal of personalised medical care faces serious challenges, many of which cannot be addressed through algorithmic complexity, and call for collaboration between traditional methodologists and experts in medical machine learning to avoid extensive research waste., (Copyright © 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2020
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35. Mobile phone ownership and willingness to receive mHealth services among patients with diabetes mellitus in South-West, Nigeria.
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Olamoyegun MA, Raimi TH, Ala OA, and Fadare JO
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- Adult, Aged, Cross-Sectional Studies, Delivery of Health Care economics, Delivery of Health Care methods, Educational Status, Female, Humans, Male, Middle Aged, Nigeria, Patient Acceptance of Health Care statistics & numerical data, Surveys and Questionnaires, Telemedicine economics, Text Messaging, Cell Phone statistics & numerical data, Diabetes Mellitus therapy, Ownership statistics & numerical data, Telemedicine methods
- Abstract
Introduction: mobile phone technology is increasingly used to overcome traditional barriers to limiting access to diabetes care. This study evaluated mobile phone ownership and willingness to receive and pay for mobile phone-based diabetic services among people with diabetes in South-West, Nigeria., Methods: two hundred and fifty nine patients with diabetes were consecutively recruited from three tertiary health institutions in South-West, Nigeria. Questionnaire was used to evaluate mobile phone ownership, willingness to receive and pay for mobile phone-based diabetic health care services via voice call and text messaging., Results: 97.3% owned a mobile phone, with 38.9% and 61.1% owning smartphone and basic phone respectively. Males were significantly more willing to receive mobile-phone-based health services than females (81.1% vs 68.1%, p=0.025), likewise married compared to unmarried [77.4% vs 57.1%, p=0.036]. Voice calls (41.3%) and text messages (32.4%), were the most preferred modes of receiving diabetes-related health education with social media (3.1%) and email (1.5%) least. Almost three-quarter of participants (72.6%) who owned mobile phone, were willing to receive mobile phone-based diabetes health services. The educational status of patients (adjusted OR [AOR]: 1.7{95% CI: 1.6 to 2.1}), glucometers possession (AOR: 2.0 [95% CI: 1.9 to 2.1) and type of mobile phone owned (AOR: 2.9 [95% CI: 2.8 to 5.0]) were significantly associated with the willingness to receive mobile phone-based diabetic services., Conclusion: the majority of study participants owned mobile phones and would be willing to receive and pay for diabetes-related healthcare delivery services provided the cost is minimal and affordable., Competing Interests: The authors declare no competing interests., (Copyright: Michael Adeyemi Olamoyegun et al.)
- Published
- 2020
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36. The Polygenic and Monogenic Basis of Blood Traits and Diseases.
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Vuckovic D, Bao EL, Akbari P, Lareau CA, Mousas A, Jiang T, Chen MH, Raffield LM, Tardaguila M, Huffman JE, Ritchie SC, Megy K, Ponstingl H, Penkett CJ, Albers PK, Wigdor EM, Sakaue S, Moscati A, Manansala R, Lo KS, Qian H, Akiyama M, Bartz TM, Ben-Shlomo Y, Beswick A, Bork-Jensen J, Bottinger EP, Brody JA, van Rooij FJA, Chitrala KN, Wilson PWF, Choquet H, Danesh J, Di Angelantonio E, Dimou N, Ding J, Elliott P, Esko T, Evans MK, Felix SB, Floyd JS, Broer L, Grarup N, Guo MH, Guo Q, Greinacher A, Haessler J, Hansen T, Howson JMM, Huang W, Jorgenson E, Kacprowski T, Kähönen M, Kamatani Y, Kanai M, Karthikeyan S, Koskeridis F, Lange LA, Lehtimäki T, Linneberg A, Liu Y, Lyytikäinen LP, Manichaikul A, Matsuda K, Mohlke KL, Mononen N, Murakami Y, Nadkarni GN, Nikus K, Pankratz N, Pedersen O, Preuss M, Psaty BM, Raitakari OT, Rich SS, Rodriguez BAT, Rosen JD, Rotter JI, Schubert P, Spracklen CN, Surendran P, Tang H, Tardif JC, Ghanbari M, Völker U, Völzke H, Watkins NA, Weiss S, Cai N, Kundu K, Watt SB, Walter K, Zonderman AB, Cho K, Li Y, Loos RJF, Knight JC, Georges M, Stegle O, Evangelou E, Okada Y, Roberts DJ, Inouye M, Johnson AD, Auer PL, Astle WJ, Reiner AP, Butterworth AS, Ouwehand WH, Lettre G, Sankaran VG, and Soranzo N
- Subjects
- Female, Gene Regulatory Networks genetics, Genome-Wide Association Study methods, Hematopoiesis genetics, Humans, Male, Phenotype, Polymorphism, Single Nucleotide genetics, Genetic Predisposition to Disease genetics, Multifactorial Inheritance genetics
- Abstract
Blood cells play essential roles in human health, underpinning physiological processes such as immunity, oxygen transport, and clotting, which when perturbed cause a significant global health burden. Here we integrate data from UK Biobank and a large-scale international collaborative effort, including data for 563,085 European ancestry participants, and discover 5,106 new genetic variants independently associated with 29 blood cell phenotypes covering a range of variation impacting hematopoiesis. We holistically characterize the genetic architecture of hematopoiesis, assess the relevance of the omnigenic model to blood cell phenotypes, delineate relevant hematopoietic cell states influenced by regulatory genetic variants and gene networks, identify novel splice-altering variants mediating the associations, and assess the polygenic prediction potential for blood traits and clinical disorders at the interface of complex and Mendelian genetics. These results show the power of large-scale blood cell trait GWAS to interrogate clinically meaningful variants across a wide allelic spectrum of human variation., Competing Interests: Declaration of Interests Adam Butterworth has received grants (outside of this work) from AstraZeneca, Biogen, BioMarin, Bioverativ, Merck, Novartis, and Sanofi; James Floyd has consulted for Shionogi; Qi Guo is a full-time employee of BenevolentAI; Joanna Howson is a full-time employee of Novo Nordisk. Parsa Akbari is a full-time employee of Regeneron Pharmaceuticals., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
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37. Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations.
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Chen MH, Raffield LM, Mousas A, Sakaue S, Huffman JE, Moscati A, Trivedi B, Jiang T, Akbari P, Vuckovic D, Bao EL, Zhong X, Manansala R, Laplante V, Chen M, Lo KS, Qian H, Lareau CA, Beaudoin M, Hunt KA, Akiyama M, Bartz TM, Ben-Shlomo Y, Beswick A, Bork-Jensen J, Bottinger EP, Brody JA, van Rooij FJA, Chitrala K, Cho K, Choquet H, Correa A, Danesh J, Di Angelantonio E, Dimou N, Ding J, Elliott P, Esko T, Evans MK, Floyd JS, Broer L, Grarup N, Guo MH, Greinacher A, Haessler J, Hansen T, Howson JMM, Huang QQ, Huang W, Jorgenson E, Kacprowski T, Kähönen M, Kamatani Y, Kanai M, Karthikeyan S, Koskeridis F, Lange LA, Lehtimäki T, Lerch MM, Linneberg A, Liu Y, Lyytikäinen LP, Manichaikul A, Martin HC, Matsuda K, Mohlke KL, Mononen N, Murakami Y, Nadkarni GN, Nauck M, Nikus K, Ouwehand WH, Pankratz N, Pedersen O, Preuss M, Psaty BM, Raitakari OT, Roberts DJ, Rich SS, Rodriguez BAT, Rosen JD, Rotter JI, Schubert P, Spracklen CN, Surendran P, Tang H, Tardif JC, Trembath RC, Ghanbari M, Völker U, Völzke H, Watkins NA, Zonderman AB, Wilson PWF, Li Y, Butterworth AS, Gauchat JF, Chiang CWK, Li B, Loos RJF, Astle WJ, Evangelou E, van Heel DA, Sankaran VG, Okada Y, Soranzo N, Johnson AD, Reiner AP, Auer PL, and Lettre G
- Subjects
- Genetics, Genome-Wide Association Study methods, HEK293 Cells, Humans, Interleukin-7 genetics, Phenotype, Asian People genetics, Mutation, Missense genetics, Polymorphism, Single Nucleotide genetics, White People genetics
- Abstract
Most loci identified by GWASs have been found in populations of European ancestry (EUR). In trans-ethnic meta-analyses for 15 hematological traits in 746,667 participants, including 184,535 non-EUR individuals, we identified 5,552 trait-variant associations at p < 5 × 10
-9 , including 71 novel associations not found in EUR populations. We also identified 28 additional novel variants in ancestry-specific, non-EUR meta-analyses, including an IL7 missense variant in South Asians associated with lymphocyte count in vivo and IL-7 secretion levels in vitro. Fine-mapping prioritized variants annotated as functional and generated 95% credible sets that were 30% smaller when using the trans-ethnic as opposed to the EUR-only results. We explored the clinical significance and predictive value of trans-ethnic variants in multiple populations and compared genetic architecture and the effect of natural selection on these blood phenotypes between populations. Altogether, our results for hematological traits highlight the value of a more global representation of populations in genetic studies., Competing Interests: Declaration of Interests Competing financial interests are declared in Table S1F., (Copyright © 2020 Elsevier Inc. All rights reserved.)- Published
- 2020
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38. [Latent Tuberculosis Infection (LTBI) among Medical Personnel after Foreign Assignments].
- Author
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Meier I, Schablon A, Nienhaus A, and Konigorski S
- Subjects
- Cross-Sectional Studies, Germany epidemiology, Humans, Interferon-gamma Release Tests, Latent Tuberculosis epidemiology, Prevalence, Risk Factors, Health Personnel statistics & numerical data, Latent Tuberculosis diagnosis
- Abstract
Introduction: Every year, medical personnel are sent abroad via relief organisations in order to provide humanitarian aid. The areas they are sent to are often countries with a high incidence of tuberculosis. The prevalence of latent tuberculosis infections (LTBI) and associated risk factors among returnees in Germany have not yet been systematically investigated., Methods: In a cross-sectional study (N = 95), medical personnel in Germany who had completed at least one foreign assignment were tested for LTBI with the Interferon-Gamma Release Assay in order to examine the LTBI prevalence among them. Relevant risk factors were assessed using a questionnaire. Statistical evaluation was carried out using cross-tables and multiple logistic regression., Results: The LTBI prevalence in our sample was 12.63 %, 95 %CI (7.70 %; 23.89 %). The odds of LTBI increased with age (OR = 1.06, 95 %CI [1.01; 1.12], p-value = 0.021, per one life-year) and length of stay abroad (OR = 1.11, 95 %CI [1.03; 1.21], p-value = 0.009, per month)., Discussion: The study showed a higher LTBI prevalence among returnees after assignments abroad than among medical personnel in Germany after TB contact who had been investigated in previous studies. In order to be able to detect LTBI infections acquired abroad, routine testing before and after an assignment abroad seems to be necessary., Competing Interests: Die Autorinnen/Autoren geben an, dass kein Interessenkonflikt besteht., (© Georg Thieme Verlag KG Stuttgart · New York.)
- Published
- 2020
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39. Editorial for the Special Issue on Theory of Evolutionary Algorithms 2014.
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Oliveto PS and Sutton AM
- Subjects
- Computational Biology, Humans, Algorithms, Biological Evolution
- Published
- 2015
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40. Question answering for biology.
- Author
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Neves M and Leser U
- Subjects
- Animals, Biology trends, Humans, Internet trends, Biology methods, Databases, Factual trends, Natural Language Processing, User-Computer Interface
- Abstract
Biologists often pose queries to search engines and biological databases to obtain answers related to ongoing experiments. This is known to be a time consuming, and sometimes frustrating, task in which more than one query is posed and many databases are consulted to come to possible answers for a single fact. Question answering comes as an alternative to this process by allowing queries to be posed as questions, by integrating various resources of different nature and by returning an exact answer to the user. We have surveyed the current solutions on question answering for Biology, present an overview on the methods which are usually employed and give insights on how to boost performance of systems in this domain., (Copyright © 2014 Elsevier Inc. All rights reserved.)
- Published
- 2015
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41. An analysis on the entity annotations in biological corpora.
- Author
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Neves M
- Abstract
Collection of documents annotated with semantic entities and relationships are crucial resources to support development and evaluation of text mining solutions for the biomedical domain. Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain. Annotations for entity types were classified into six semantic groups and an overview on the semantic entities which can be found in each corpus is shown. Results show that while some semantic entities, such as genes, proteins and chemicals are consistently annotated in many collections, corpora available for diseases, variations and mutations are still few, in spite of their importance in the biological domain.
- Published
- 2014
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42. State of the "art": a taxonomy of artistic stylization techniques for images and video.
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Kyprianidis JE, Collomosse J, Wang T, and Isenberg T
- Subjects
- Computer Graphics trends, Creativity, Forecasting, Imaging, Three-Dimensional methods, Paintings trends, User-Computer Interface, Video Recording trends
- Abstract
This paper surveys the field of nonphotorealistic rendering (NPR), focusing on techniques for transforming 2D input (images and video) into artistically stylized renderings. We first present a taxonomy of the 2D NPR algorithms developed over the past two decades, structured according to the design characteristics and behavior of each technique. We then describe a chronology of development from the semiautomatic paint systems of the early nineties, through to the automated painterly rendering systems of the late nineties driven by image gradient analysis. Two complementary trends in the NPR literature are then addressed, with reference to our taxonomy. First, the fusion of higher level computer vision and NPR, illustrating the trends toward scene analysis to drive artistic abstraction and diversity of style. Second, the evolution of local processing approaches toward edge-aware filtering for real-time stylization of images and video. The survey then concludes with a discussion of open challenges for 2D NPR identified in recent NPR symposia, including topics such as user and aesthetic evaluation.
- Published
- 2013
- Full Text
- View/download PDF
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