Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Een experimentele studie betreffende het vergrotingsproces van rivierdijkbreuken (EXPERIMENTS ON ENLARGING PROCESS OF RIVER BANK BREACHES)

Vertaling van een origineel Japans rapport naar the Nederlands. Flood damage due to a bank breach increases with a river water inflow through it, which is enlarged by a hydraulic action of the inflow, while the influx rate is controlled by the geometry of the breach as weil as the stage and discharge of the river. For the purpose of predicrion on flooding inside the bank and mitigation of the damage, this process needs to be investigated to estimate the influx rate and to find out a efficient closure technique. We carried out fundamental experiments, and describe tbe enlarging process of modeled bank breaches as the results in detail, such as cbanges in geometrical characteristics, influx rates, water stages at tbe both sides of the bank models and their seepage states. These results were discussed on bydraulic properties at tbe breach, tbat is, flow resistanse, sediment transport, stage-discharge relationship between the water stage outside and the influx rate. lt is found out that the process has four enlarging phases, The first one is finished wben carving of initial failures, which are V·shaped grooves at the top of banks, reaches the outside slopes. During the second, scouring downward and widening of the breaches progress rapidly and increase in influx rate is very large. Gradual widening only continues at the third one and inflow increases a little. Finally, geometry and influx rate beoome rather constant in the fourth phase.KWP-collectio

Coherent spin-exchange via a quantum mediator

Coherent interactions at a distance provide a powerful tool for quantum simulation and computation. The most common approach to realize an effective long-distance coupling on-chip' is to use a quantum mediator, as has been demonstrated for superconducting qubits and trapped ions. For quantum dot arrays, which combine a high degree of tunability with extremely long coherence times, the experimental demonstration of the time evolution of coherent spin-spin coupling via an intermediary system remains an important outstanding goal. Here, we use a linear triple-quantum-dot array to demonstrate a coherent time evolution of two interacting distant spins via a quantum mediator. The two outer dots are occupied with a single electron spin each, and the spins experience a superexchange interaction through the empty middle dot, which acts as mediator. Using single-shot spin readout, we measure the coherent time evolution of the spin states on the outer dots and observe a characteristic dependence of the exchange frequency as a function of the detuning between the middle and outer dots. This approach may provide a new route for scaling up spin qubit circuits using quantum dots, and aid in the simulation of materials and molecules with non-nearest-neighbour couplings such as MnO (ref. 27), high-temperature superconductors and DNA. The same superexchange concept can also be applied in cold atom experiments.Accepted Author ManuscriptQCD/Vandersypen LabQuTec

ANAC 2017: Repeated Multilateral Negotiation League

The Automated Negotiating Agents Competition (ANAC) is annually organized competition to facilitate the research on automated negotiation. This paper presents the ANAC 2017 Repeated Multilateral Negotiation League. As human negotiators do, agents are supposed to learn from their previous negotiations and improve their negotiation skills over time. Especially, when they negotiate with the same opponent on the same domain, they can adopt their negotiation strategy according to their past experiences. They can adjust their acceptance threshold or bidding strategy accordingly. In ANAC 2017, participants aimed to develop such a negotiating agent. Accordingly, this paper describes the competition settings and results with a brief description of the winner negotiation strategies.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Interactive Intelligenc

ANAC 2018: Repeated Multilateral Negotiation League

This is an extension from a selected paper from JSAI2019. There are a number of research challenges in the field of Automated Negotiation. The Ninth International Automated Negotiating Agent Competition encourages participants to develop effective negotiating agents, which can negotiate with multiple opponents more than once. This paper discusses research challenges for such negotiations as well as presenting the competition set-up and results. The results show that winner agents mostly adopt hybrid bidding strategies that take their opponents’ preferences as well as their strategy into account.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Interactive Intelligenc

Quantum simulation of a Fermi-Hubbard model using a semiconductor quantum dot array

Interacting fermions on a lattice can develop strong quantum correlations, which are the cause of the classical intractability of many exotic phases of matter. Current efforts are directed towards the control of artificial quantum systems that can be made to emulate the underlying Fermi-Hubbard models. Electrostatically confined conduction-band electrons define interacting quantum coherent spin and charge degrees of freedom that allow all-electrical initialization of low-entropy states and readily adhere to the Fermi-Hubbard Hamiltonian. Until now, however, the substantial electrostatic disorder of the solid state has meant that only a few attempts at emulating Fermi-Hubbard physics on solid-state platforms have been made. Here we show that for gate-defined quantum dots this disorder can be suppressed in a controlled manner. Using a semi-automated and scalable set of experimental tools, we homogeneously and independently set up the electron filling and nearest-neighbour tunnel coupling in a semiconductor quantum dot array so as to simulate a Fermi-Hubbard system. With this set-up, we realize a detailed characterization of the collective Coulomb blockade transition, which is the finite-size analogue of the interaction-driven Mott metal-to-insulator transition. As automation and device fabrication of semiconductor quantum dots continue to improve, the ideas presented here will enable the investigation of the physics of ever more complex many-body states using quantum dots.Accepted Author ManuscriptQCD/Vandersypen LabElectrical Engineering, Mathematics and Computer Scienc

The 13th International Automated Negotiating Agent Competition Challenges and Results

An international competition for negotiating agents has been organized for years to facilitate research in agent-based negotiation and to encourage the design of negotiating agents that can operate in various scenarios. The 13th International Automated Negotiating Agents Competition (ANAC 2022) was held in conjunction with IJCAI2022. In ANAC2022, we had two leagues: Automated Negotiation League (ANL) and Supply Chain Management League (SCML). For the ANL, the participants designed a negotiation agent that can learn from the previous bilateral negotiation sessions it was involved in. In contrast, the research challenge was to make the right decisions to maximize the overall profit in a supply chain environment, such as determining with whom and when to negotiate. This chapter describes the overview of ANL and SCML in ANAC2022, and reports the results of each league, respectively.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Interactive Intelligenc

Automated tuning of inter-dot tunnel coupling in double quantum dots

Semiconductor quantum dot arrays defined electrostatically in a 2D electron gas provide a scalable platform for quantum information processing and quantum simulations. For the operation of quantum dot arrays, appropriate voltages need to be applied to the gate electrodes that define the quantum dot potential landscape. Tuning the gate voltages has proven to be a time-consuming task, because of initial electrostatic disorder and capacitive cross-talk effects. Here, we report on the automated tuning of the inter-dot tunnel coupling in gate-defined semiconductor double quantum dots. The automation of the tuning of the inter-dot tunnel coupling is the next step forward in scalable and efficient control of larger quantum dot arrays. This work greatly reduces the effort of tuning semiconductor quantum dots for quantum information processing and quantum simulation.QuTechQCD/Vandersypen LabQN/Vandersypen La

Nonlinear and dot-dependent Zeeman splitting in GaAs/AlGaAs quantum dot arrays

We study the Zeeman splitting in lateral quantum dots that are defined in GaAs-AlGaAs heterostructures by means of split gates. We demonstrate a nonlinear dependence of the splitting on magnetic field and its substantial variations from dot to dot and from heterostructure to heterostructure. These phenomena are important in the context of information processing since the tunability and dot-dependence of the Zeeman splitting allow for a selective manipulation of spins. We show that spin-orbit effects related to the GaAs band structure quantitatively explain the observed magnitude of the nonlinear dependence of the Zeeman splitting. Furthermore, spin-orbit effects result in a dependence of the Zeeman splitting on predominantly the out-of-plane quantum dot confinement energy. We also show that the variations of the confinement energy due to charge disorder in the heterostructure may explain the dependence of Zeeman splitting on the dot position. This position may be varied by changing the gate voltages, which leads to an electrically tunable Zeeman splitting.QCD/Vandersypen LabQuTechQN/Nazarov Grou