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Die moderne Biochemie ist eine Wissenschaft, die sich im Wandel befindet. Während die bisherige Forschung sehr stark experimentell geprägt ist, existiert eine theoretische Biologie, analog zur theoretischen Chemie, nur in Ansätzen. Trotzdem wandelt sich auch diese Wissenschaft hin zu einer stärkeren Einbindung theoretischer Ansätze. Der Grund hierfür liegt in der Betrachtung von zunehmend komplexeren Systemen. So beschäftigt man sich in der Systembiologie, einem Teilbereich der Biochemie, unter anderem mit der Aufklärung komplexer Reaktionsnetzwerke. Während Ausschnitte dieser Netzwerke weiterhin experimentell aufgeklärt und verstanden werden, lässt sich das zusammenhängende Bild zunehmend nur noch durch eine theoretisch geprägte Modellbildung fassen. Darüber hinaus zeigen neuere Forschungsergebnisse die Bedeutung der Tatsache, dass Moleküle, Zellen und Zellhaufen, also wichtige Forschungsubjekte der Biochmie, dreidimensionale Gebilde sind – eine Tatsache, die bei der Modellbildung berücksichtigt werden muss. Eine Antwort auf die genannten Herausforderungen ist der konzertierte Einsatz von Simulation und Visualisierung als Mittel des Erkenntnisgewinns. Damit ist die Informatik gefordert entsprechende dedizierte Werkzeuge zu entwickeln, die Simulation, Visualisierung und Interaktion im Kontext des von der Anwendungsdisziplin gesetzten räumlich-zeitlichen Problemkreises miteinander verbinden. In dieser Arbeit wird ein integriertes Konzept zu Simulation, Interaktivität und Visualisierung vorgelegt, das auf einer Anforderungsanalyse in Bezug auf Anforderungen an die Simulation und Anforderungen an die Interaktivität und Visualisierung basiert. Zur Lösung der aufgeworfenen Probleme wird ein „Baukastensystem“ auf Basis von Multi-Agenten-Systemen vorgeschlagen. Die Auswahl des geeigneten Simulationsverfahrens, z. B. die Auswahl eines stochastischen Verfahrens gegenüber einem deterministischen Verfahrens, wird so zur Auswahl eines Bausteins, wobei gezeigt wird, wie z. B. mit Hilfe von Regeln die Auswahl auch automatisiert werden kann. Ebenso wird gezeigt, wie man „Baussteine“ auch im räumlichen Sinne verstehen kann, als Dinge, die in einem dreidimensionalen Kontext einen bestimmten Raum einnehmen und die, in ihrer Gesamtheit betrachtet, den Beobachtungsraum der Simulation ausfüllen. Diese Bausteine finden sich entsprechend ebenfalls im Kontext der Interaktion wieder. Ein wichtiger Aspekt in diesem Baukastenkonzept ist die Frage der Kommunikationsstruktur und des Kommunikationsprotokolls, für den ein Vorschlag erarbeitet wird. Das entwickelte Gesamtkonzept besteht aus zwei Teilen: Einem Konzept für Ein- und Ausgabegeräte mit einer gemeinsamen Metapher, die die Geräte logisch in den Anwendungskontext einbettet und einem Simulations- und Visualisierungskonzept auf der Basis der Kopplung heterogener intelligenter Agenten in eine gemeinsame Simulationsumgebung. Hierfür wurde ein spezieller Dialekt einer Agentenkommunikationssprache entwickelt, der dabei insbesondere den Aspekt der dreidimensionalen Visualierung einer solchen Simulation berücksichtigt.
In dieser Arbeit werden Verfahren vorgestellt, mit dem sich hochaufgelöste wissenschaftliche Illustrationen in einem interaktiven Vorgang erstellen lassen. Die Basis dafür bildet die neu eingeführte GPU-basierte Illustrations-Pipeline, in der auf Grundlage eines 3D-Modells Bildebenen frei angelegt und miteinander kombiniert werden können. In einer Ebene wird ein bestimmter Aspekt der Illustration mit einer auswählbaren Technik gezeigt. Die Parameter der Technik sind interaktiv editierbar. Um Effizienz zu gewährleisten ist das gesamte Verfahren so konzipiert, dass es soweit wie möglich die Berechnungen auf der GPU durchführt. So ist es möglich, dass die Illustrationen mit interaktiven Frameraten gerendert werden.
Interactive Gorilla
(2010)
Beeindruckt von einer auf Annäherung reagierenden Dinosaurier-Animation des Brüsseler Naturkundemuseums, entstand die Idee einen noch komplexeren interaktiven Gorilla zu entwerfen. Der Gorilla soll dabei auf einer großen Leinwand dargestellt werden und die Besucher können mit diesem anhand ihrer Position interagieren, worauf er seine Tätigkeit und Gestik an diese anpasst.
Da keine Umsetzung, die durch gezielte Anpassungen das gewünschte Ergebnis liefern würde, vorhanden war, wurde das System im Rahmen dieser Arbeit angefertigt. Der Aufbau lässt sich dabei in drei große Module aufteilen, die auf den Ergebnissen des vorherigen Moduls arbeiten.
Zuerst wurde ein System entwickelt, mit dem es möglich ist die Besucher im Raum zu erfassen und festzustellen an welchen Positionen sie sich aufhalten. Diese Informationen werden von einer Verhaltenssimulation weiterverarbeitet. Diese ist durch einen endlichen Automaten realisiert, der auf einem Graphen operiert. Die Ergebnisse, die vom Erkennungssystem geliefert werden, sind dann dafür verantwortlich, dass sich das Verhalten entsprechend ändert. Zuletzt wird das aktuelle Verhalten des Gorillas mit Hilfe eines 3D-Modells und Animationen auf der Leinwand dargestellt.
Des weiteren sind im Rahmen dieser Arbeit zusätzliche Editoren entstanden um die Zustände des Graphen und die dadurch darzustellenden Animationen nachträglich anzupassen.
Background Although current molecular clock methods offer greater flexibility in modelling historical evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates. Results According to the most reliable model, as indicated by Bayes factor comparison, modern lacertids arose shortly after the K/T transition and entered Africa about 45 million years ago, with the majority of their African radiation occurring in the Eocene and Oligocene. Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic. Conclusions This study represents the first attempt to estimate evolutionary ages of a specific group of reptiles exhibiting uncertain phylogenetic relationships, molecular rate variation and a poor fossil record. Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints. The bioinformatics program used here, TreeTime, is publicly available, and we recommend its use for molecular dating of taxa faced with similar challenges.
Integer point sets minimizing average pairwise L1 distance: What is the optimal shape of a town?
(2010)
An n-town, n[is an element of]N , is a group of n buildings, each occupying a distinct position on a 2-dimensional integer grid. If we measure the distance between two buildings along the axis-parallel street grid, then an n-town has optimal shape if the sum of all pairwise Manhattan distances is minimized. This problem has been studied for cities, i.e., the limiting case of very large n. For cities, it is known that the optimal shape can be described by a differential equation, for which no closed-form solution is known. We show that optimal n-towns can be computed in O(n[superscript 7.5]) time. This is also practically useful, as it allows us to compute optimal solutions up to n=80.
Two-particle angular correlations were measured in pp collisions at s√=7 TeV for pions, kaons, protons, and lambdas, for all particle/anti-particle combinations in the pair. Data for mesons exhibit an expected peak dominated by effects associated with mini-jets and are well reproduced by general purpose Monte Carlo generators. However, for baryon-baryon and anti-baryon--anti-baryon pairs, where both particles have the same baryon number, a near-side anti-correlation structure is observed instead of a peak. This effect is interpreted in the context of baryon production mechanisms in the fragmentation process. It currently presents a challenge to Monte Carlo models and its origin remains an open question.
Two-particle angular correlations were measured in pp collisions at s√=7 TeV for pions, kaons, protons, and lambdas, for all particle/anti-particle combinations in the pair. Data for mesons exhibit an expected peak dominated by effects associated with mini-jets and are well reproduced by general purpose Monte Carlo generators. However, for baryon-baryon and anti-baryon--anti-baryon pairs, where both particles have the same baryon number, a near-side anti-correlation structure is observed instead of a peak. This effect is interpreted in the context of baryon production mechanisms in the fragmentation process. It currently presents a challenge to Monte Carlo models and its origin remains an open question.
Two-particle angular correlations were measured in pp collisions at s√=7 TeV. The analysis was carried out for pions, kaons, protons, and lambdas, for all particle/anti-particle combinations in the pair. Data for mesons exhibit an expected peak dominated by effects associated with mini-jets and are well reproduced by general purpose Monte Carlo generators. However, for baryon--baryon and anti-baryon--anti-baryon pairs, where both particles have the same baryon number, a near-side anti-correlation structure is observed instead of a peak. This effect is interpreted in the context of baryon production mechanisms in the fragmentation process. It currently presents a challenge to Monte Carlo models and its origin remains an open question.
The formulation of the Partial Information Decomposition (PID) framework by Williams and Beer in 2010 attracted a significant amount of attention to the problem of defining redundant (or shared), unique and synergistic (or complementary) components of mutual information that a set of source variables provides about a target. This attention resulted in a number of measures proposed to capture these concepts, theoretical investigations into such measures, and applications to empirical data (in particular to datasets from neuroscience). In this Special Issue on “Information Decomposition of Target Effects from Multi-Source Interactions” at Entropy, we have gathered current work on such information decomposition approaches from many of the leading research groups in the field. We begin our editorial by providing the reader with a review of previous information decomposition research, including an overview of the variety of measures proposed, how they have been interpreted and applied to empirical investigations. We then introduce the articles included in the special issue one by one, providing a similar categorisation of these articles into: i. proposals of new measures; ii. theoretical investigations into properties and interpretations of such approaches, and iii. applications of these measures in empirical studies. We finish by providing an outlook on the future of the field.
One of the main things that we as humans do in our lifetime is the recognition and/or classification of all kind of visual objects. It is known that about fifty percentage of the neocortex is responsible for visual processing. This fact tells us that object recognition (OR) is a complex task in our and in the animal brain, but we do it in a fraction of a second.
The main question is: How does the brain exactly do it? Does the brain use some feature extraction algorithm for OR tasks? The hierarchical structure of the visual cortex and studies on a part of the visual cortex called V1 tell us that our brain uses feature extraction for OR tasks by Gabor filters. We also use our previous knowledge in object recognition to detect and recognize the objects which we never saw before. Also, as we grow up we learn new objects faster than before.
These facts imply that the visual cortex of human and other animals uses some common (universal) features at least in the first stages to distinguish between different objects. In this context, we might ask: Do universal features in images exist, such that by using them we are able to efficiently recognize any unknown object? Is it necessary to extract new special features for any new object? How about using existing features from other tasks for this? Is it possible to efficiently use extracted feature of a specific task for other tasks? Are there some general features in natural and non-natural images which can also be used for specific object recognition? For example, can we use extracted features of natural images also for handwritten digit classification?
In this context, our work proposes a new information-based approach and tries to give some answers to the questions above. As a result, in our case we found that we could indeed extract unique features which are valid in all three different kinds of tasks. They give classification results that are about as good as the results reported by the corresponding literature for the specialized systems, or even better ones.
Another problem of the OR task is the recognition of objects, independently of any perception changes. We as humans or also animals can recognize objects in spite of many deformations (e.g. changes in illumination, rotation in any direction or angles, distortion and scaling up or down) in a fraction of a second. When observing an object which we never saw, we can imagine the rotated or scaled up objectin our mind. Here, also the question arises: How does the brain solve this problem? To do this, does the brain learn some mapping algorithm (transformation), independent of the objects or their features?
There are many approaches to model the mapping task. One of the most versatile ones is the idea of dynamically changing mappings, the dynamic link mapping (DLM). Although the dynamic link mapping systems show interesting results, the DLM system has the problem of a high computational complexity. In addition, because it uses the least mean squared error as risk function, the performance for classification is also not optimal. For random values where outliers are present, this system may not work well because outliers influence the mean squared error classification much more than probability-based systems. Therefore, we would like to complete the DLM system by a modified approach.
In our contribution, we will introduce a new system which employs the information criteria (i.e. probabilities) to overcome the outlier problem of the DLM systems and has a smaller computational complexity. The new information based selforganised system can solve the problem of invariant object recognition, especially in the task of rotation in depth, and does not have the disadvantage of current DLM systems and has a smaller computational complexity.
Recent lattice QCD results, comparing to a hadron resonance gas model, have shown the need for hundreds of particles in hadronic models. These extra particles influence both the equation of state and hadronic interactions within hadron transport models. Here, we introduce the PDG21+ particle list, which contains the most up-to-date database of particles and their properties. We then convert all particles decays into 2 body decays so that they are compatible with SMASH in order to produce a more consistent description of a heavy-ion collision.
Im Zeitraum 1. 11. 1993 bis 30. 3. 1997 wurden 1149 allgemeinchirurgische Intensivpatienten prospektiv erfaßt, von denen 114 die Kriterien des septischen Schocks erfüllten. Die Letalität der Patienten mit einem septischen Schock betrug 47,3%. Nach Training eines neuronalen Netzes mit 91 (von insgesamt n = 114) Patienten ergab die Testung bei den verbleibenden 23 Patienten bei der Berücksichtigung von Parameterveränderungen vom 1. auf den 2. Tag des septischen Schocks folgendes Ergebnis: Alle 10 verstorbenen Patienten wurden korrekt als nicht überlebend vorhergesagt, von den 13 Überlebenden wurden 12 korrekt als überlebend vorhergesagt (Sensitivität 100%; Spezifität 92,3%).
We introduce the relationship between incremental cryptography and memory checkers. We present an incremental message authentication scheme based on the XOR MACs which supports insertion, deletion and other single block operations. Our scheme takes only a constant number of pseudorandom function evaluations for each update step and produces smaller authentication codes than the tree scheme presented in [BGG95]. Furthermore, it is secure against message substitution attacks, where the adversary is allowed to tamper messages before update steps, making it applicable to virus protection. From this scheme we derive memory checkers for data structures based on lists. Conversely, we use a lower bound for memory checkers to show that so-called message substitution detecting schemes produce signatures or authentication codes with size proportional to the message length.
Inclusive, prompt and non-prompt J/ψ production at midrapidity in p−Pb collisions at √sNN = 5.02 TeV
(2021)
A measurement of inclusive, prompt, and non-prompt J/ψ production in p−Pb collisions at a nucleon--nucleon centre-of-mass energy sNN−−−√=5.02 TeV is presented. The J/ψ mesons are reconstructed in the dielectron decay channel at midrapidity down to a transverse momentum pT=0. The inclusive J/ψ nuclear modification factor RpPb is calculated by comparing the results in p−Pb collisions to a measured proton−proton reference at the same centre-of-mass energy. Non-prompt J/ψ mesons, which originate from the decay of beauty hadrons, are separated from promptly produced J/ψ on a statistical basis for pT larger than 1.0 GeV/c. These results are based on the data sample collected by the ALICE detector during the 2016 LHC p−Pb run, corresponding to an integrated luminosity Lint=292±11μb−1, which is six times larger than the previous publications. The total uncertainty on the pT-integrated inclusive J/ψ and non-prompt J/ψ cross section are reduced by a factor 1.7 and 2.2, respectively. The measured cross sections and RpPb are compared with theoretical models that include various combinations of cold nuclear matter effects. From the non-prompt J/ψ production cross section, the bb¯¯¯ production cross section at midrapidity, dσbb¯¯¯/dy, and the total cross section extrapolated over full phase space, σbb¯¯¯, are derived.
Inclusive, prompt and non-prompt J/ψ production at midrapidity in p−Pb collisions at √sNN = 5.02 TeV
(2022)
A measurement of inclusive, prompt, and non-prompt J/ψ production in p−Pb collisions at a nucleon−nucleon centre-of-mass energy sNN−−−√=5.02 TeV is presented. The inclusive J/ψ mesons are reconstructed in the dielectron decay channel at midrapidity down to a transverse momentum pT=0. The inclusive J/ψ nuclear modification factor RpPb is calculated by comparing the new results in p−Pb collisions to a recently measured proton−proton reference at the same centre-of-mass energy. Non-prompt J/ψ mesons, which originate from the decay of beauty hadrons, are separated from promptly produced J/ψ on a statistical basis for pT larger than 1.0 GeV/c. These results are based on the data sample collected by the ALICE detector during the 2016 LHC p−Pb run, corresponding to an integrated luminosity Lint=292±11μb−1, which is six times larger than the previous publications. The total uncertainty on the pT-integrated inclusive J/ψ and non-prompt J/ψ cross section are reduced by a factor 1.7 and 2.2, respectively. The measured cross sections and RpPb are compared with theoretical models that include various combinations of cold nuclear matter effects. From the non-prompt J/ψ production cross section, the bb¯¯¯ production cross section at midrapidity, dσbb¯¯¯/dy, and the total cross section extrapolated over full phase space, σbb¯¯¯, are derived.
The transverse momentum (pT) dependence of the nuclear modification factor RAA and the centrality dependence of the average transverse momentum ⟨pT⟩ for inclusive J/ψ have been measured with ALICE for Pb-Pb collisions at sNN−−−√ = 2.76 TeV in the e+e− decay channel at mid-rapidity (|y|<0.8). The ⟨pT⟩ is significantly smaller than the one observed for pp collisions at the same centre-of-mass energy. Consistently, an increase of RAA is observed towards low pT. These observations might be indicative of a sizable contribution of charm quark coalescence to the J/ψ production. Additionally, the fraction of non-prompt J/ψ from beauty hadron decays, fB, has been determined in the region 1.5<pT<10 GeV/c in three centrality intervals. No significant centrality dependence of fB is observed. Finally, the RAA of non-prompt J/ψ is discussed and compared with model predictions. The nuclear modification in the region 4.5<pT<10 GeV/c is found to be stronger than predicted by most models.
The transverse momentum (pT) dependence of the nuclear modification factor RAA and the centrality dependence of the average transverse momentum ⟨pT⟩ for inclusive J/ψ have been measured with ALICE for Pb-Pb collisions at sNN−−−√ = 2.76 TeV in the e+e− decay channel at mid-rapidity (|y|<0.8). The ⟨pT⟩ is significantly smaller than the one observed for pp collisions at the same centre-of-mass energy. Consistently, an increase of RAA is observed towards low pT. These observations might be indicative of a sizable contribution of charm quark coalescence to the J/ψ production. Additionally, the fraction of non-prompt J/ψ from beauty hadron decays, fB, has been determined in the region 1.5<pT<10 GeV/c in three centrality intervals. No significant centrality dependence of fB is observed. Finally, the RAA of non-prompt J/ψ is discussed and compared with model predictions. The nuclear modification in the region 4.5<pT<10 GeV/c is found to be stronger than predicted by most models.