Reproducible Research in R: A Tutorial on How to Do the Same Thing More Than Once

Computational reproducibility is the ability to obtain identical results from the same data with the same computer code. It is a building block for transparent and cumulative science because it enables the originator and other researchers, on other computers and later in time, to reproduce and thus understand how results came about, while avoiding a variety of errors that may lead to erroneous reporting of statistical and computational results. In this tutorial, we demonstrate how the R package repro supports researchers in creating fully computationally reproducible research projects with tools from the software engineering community. Building upon this notion of fully automated reproducibility, we present several applications including the preregistration of research plans with code (Preregistration as Code, PAC). PAC eschews all ambiguity of traditional preregistration and offers several more advantages. Making technical advancements that serve reproducibility more widely accessible for researchers holds the potential to innovate the research process and to help it become more productive, credible, and reliable.Not Reviewe

Experimental tests of pseudo-complex General Relativity

Based on previous publications exploring pseudo-complex General Relativity (pc-GR) we present a selection of observable consequences of pc-GR and possible ways to experimentally access them. Whenever possible we compare the results to Einstein's GR and differences are worked out in detail. We propose experimental tests to check the predictions of pc-GR for the orbital frequency of test particles, the gravitational redshift effect and the last stable orbit. We will show that the orbital frequency of test particles at a given radius in pc-GR is in general lower compared to standard GR. Also the effect of frame dragging is modified (weakened) in pc-GR. Concerning the gravitational redshift of a radiation emitting object we find that it is also lower in pc-GR than in standard GR. Eventually the classical concept of a last stable orbit has to be modified in pc-GR.Comment: submitted for publication to the Monthly Notices of the Royal Astronomical Societ

How to Balance Individual and Collective Values After COVID-19?:Ethical Reflections on Crowd Management at Dutch Train Stations

This chapter explores the shift in the balance of individual versus collective values instigated by the COVID-19 pandemic. The incredible viral spread rate among the population and its relatively high fatality rate has initially resulted in an assertion of the primacy of collective values (such as collective safety, collective responsibility, conformism). In contrast, individual rights and values (such as the individual counterparts of autonomy, freedom, responsibility, and privacy) took a ‘back seat’ for the good of the collective. However, as the pandemic extended over the months, there emerged a pressure to reject the primacy of collective values and restore the importance of individual values. If we are to return to a healthy and prosperous living within a well-functioning society, this balance shift between collective and individual values will have to be re-negotiated and resolved to reach a societally acceptable balance position. We conduct this ethical exploration, first, by following the ethico-philosophical discussion on the balance between individual and collective values generally, as well as in times of crisis, with special focus on the COVID-19 crisis. Second, we explore this topic through the lens of recent changes to how particular technologies were and are used before and during the COVID-19 pandemic. More precisely, we identify and explore broad trends we see relevant to ethics – with a particular focus on crowd management and nudging and on the balance shift between individual and collective values. Finally, by exploring findings from a sociophysics case study dealing with crowd management of people before and during the pandemic, we argue that some sociophysical phenomena can be used as proxies for ethical principles. Here, distance is used as a conceptual proxy for individual and collective responsibility, having in mind COVID-19 distancing rules and recommendation. With all the above, we identify several broad trends that have been instigated by the pandemic that are relevant to ethics. These changes relate to future crowd management, nudging, and control; individual (per-person) tracking; insistence on the importance of collective values in times of crisis, and the rejection of this infringement upon individual rights. In this regard, we assert that such value changes are an opportunity to rethink and (re)set balance points between individual and collective rights for each particular society.</p

Transition from Jaynes-Cummings to Autler-Townes ladder in a quantum dot-microcavity system

The research leading to these results has received funding from the German Research Foundation (DFG) via Projects No. Ka2318/4-1 and No. Re2974/3-1, the SFB 787 "Semiconductor Nanophotonics: Materials, Models, Devices", and from the European Research Council under the European Union's Seventh Framework ERC Grant Agreement No. 615613. A. C. gratefully acknowledges support from SFB 910: "Control of self-organizing nonlinear systems".We study experimentally and theoretically a coherently-driven strongly-coupled quantum dot-microcavity system. Our focus is on physics of the unexplored intermediate excitation regime where the resonant laser field dresses a strongly-coupled single exciton-photon (polariton) system resulting in a ladder of laser-dressed Jaynes-Cummings states. In that case both the coupling of the emitter to the confined light field of the microcavity and to the light field of the external laser are equally important, as proved by observation of injection pulling of the polariton branches by an external laser. This intermediate interaction regime is of particular interest since it connects the purely quantum mechanical Jaynes-Cummings ladder and the semi-classical Autler-Townes ladder. Exploring the driving strength-dependence of the mutually coupled system we establish the maximum in the resonance fluorescence signal to be a robust fingerprint of the intermediate regime and observe signatures indicating the laser-dressed Jaynes-Cummings ladder. In order to address the underlying physics we excite the coupled system via the matter component of fermionic nature undergoing saturation - in contrast to commonly used cavity-mediated excitation.PostprintPeer reviewe

Identification and tunable optical coherent control of transition-metal spins in silicon carbide

Color centers in wide-bandgap semiconductors are attractive systems for quantum technologies since they can combine long-coherent electronic spin and bright optical properties. Several suitable centers have been identified, most famously the nitrogen-vacancy defect in diamond. However, integration in communication technology is hindered by the fact that their optical transitions lie outside telecom wavelength bands. Several transition-metal impurities in silicon carbide do emit at and near telecom wavelengths, but knowledge about their spin and optical properties is incomplete. We present all-optical identification and coherent control of molybdenum-impurity spins in silicon carbide with transitions at near-infrared wavelengths. Our results identify spin $S=1/2$ for both the electronic ground and excited state, with highly anisotropic spin properties that we apply for implementing optical control of ground-state spin coherence. Our results show optical lifetimes of $\sim$60 ns and inhomogeneous spin dephasing times of $\sim$0.3 $\mu$s, establishing relevance for quantum spin-photon interfacing.Comment: Updated version with minor correction, full Supplementary Information include

Familial occurrence of cervical artery dissection - coincidence or sign of familial predisposition?

Background and Purpose: The etiology of spontaneous cervical artery dissection (CeAD) is poorly understood in most patients. Mild cervical trauma preceding the dissection event is a common finding, but many CeAD occur spontaneously. It is likely that genetic factors may increase the risk for CeAD. However, familial cases are excedingly rare. Familial clustering of CeAD may be accidental or associated with genetic or environmental risk factors shared between affected relatives. In this explorative study, we aim to show that specific risk factors for familial CeAD exist. Methods: Age of onset, sex, affected artery and number of recurrent CeAD were documented for familial patients and compared with published findings from patients with sporadic CeAD. Concordance of age, sex and dissected artery within the families was analyzed by correlation analysis and by analysis of variance or Kruskal-Wallis testing. Results: The study sample consisted of 9 new patients with a family history of CeAD enrolled in the Neurology Department of the University of Heidelberg or referred to Heidelberg from other centers. The study sample also included published findings from another 23 patients, in total 32 patients. The mean age of the patients with familial CeAD at their first dissections was 38.4 +/- 13.3 years. Twenty (62.5%) patients were female and 12 patients (37.5%) suffered multiple dissections. Four patients (12.5%) presented with recurrent dissections after >1 year. Patients with a familial history of CeAD were younger (p = 0.023) and presented more often with multiple dissections (p = 0.024) and recurrent dissections (p = 0.018). Age at the first event(correlation analysis p = 0.026; analysis of variance p = 0.029) and site of the dissection (correlation analysis p = 0.032; Kruskal-Wallis test p = 0.018) differed between the families, and there was no concordance of gender of affected family members (correlation analysis p = 0.500; Kruskal-Wallis test p = 0.211). Conclusions: The high prevalence of multiple dissection events and of long-term (>1 year) recurrent dissections in patients with a familial history of CeAD indicates that a specific predisposition for familial CeAD exists. Since age of onset and affected vessel differ between families, the risk profile for familial CeAD is heterogeneous. A large-scale (whole exome) sequencing analysis of 14 patients from 7 of the analyzed families is currently being performed in order to identify causative genetic variants

The Influence of Macroscopic Pedestrian Structures on Train Boarding Efficiency

A deeper understanding of pedestrian dynamics is essential to improve crowd flows in public spaces such as train stations. It is essential to understand both the physical and the psychological processes present in this context. However, current research on train boarding behavior is limited in scope and mainly focuses on how group level variables such as number of boarders/deboarders influence train boarding efficiency. Viewing pedestrian dynamics through a psychological lens is important for a detailed understanding of the train boarding context and to recognize target areas for improving crowd flows. At Dutch train stations, boarders follow a social norm of waiting at the train door until deboarding is complete. Although people generally adhere to this norm, the way it is executed may not be optimal for deboarding efficiency. We investigate how waiting boarders form a deboarding channel (a corridor where deboarders exit the train) which is a macroscopic structure formed by pedestrians, and how this channel in turn influences the efficiency of deboarding. Analyzing a dataset with 3278 boarding events at Utrecht Centraal Station in the Netherlands from 2017 - 2020 (a subset of a trajectory dataset that captures 100,000 trajectories per day), we found that higher numbers of boarders and a higher ratio of boarders to deboarders, reduced the width of the deboarding channel, and a lower width was associated with lower deboarding efficiency. These results shift the focus from group level variables to identifying macroscopic structures that are formed when pedestrians interact within a social system and provide specific target areas where nudges/behavioral interventions could be implemented

Doubled lattice Chern–Simons–Yang–Mills theories with discrete gauge group

We construct doubled lattice Chern–Simons–Yang–Mills theories with discrete gauge group G in the Hamiltonian formulation. Here, these theories are considered on a square spatial lattice and the fundamental degrees of freedom are defined on pairs of links from the direct lattice and its dual, respectively. This provides a natural lattice construction for topologically-massive gauge theories, which are invariant under parity and time-reversal symmetry. After defining the building blocks of the doubled theories, paying special attention to the realization of gauge transformations on quantum states, we examine the dynamics in the group space of a single cross, which is spanned by a single link and its dual. The dynamics is governed by the single-cross electric Hamiltonian and admits a simple quantum mechanical analogy to the problem of a charged particle moving on a discrete space affected by an abstract electromagnetic potential. Such a particle might accumulate a phase shift equivalent to an Aharonov–Bohm phase, which is manifested in the doubled theory in terms of a nontrivial ground-state degeneracy on a single cross. We discuss several examples of these doubled theories with different gauge groups including the cyclic group Z(k)⊂U(1), the symmetric group S3⊂O(2), the binary dihedral (or quaternion) group View the MathML source, and the finite group Δ(27)⊂SU(3). In each case the spectrum of the single-cross electric Hamiltonian is determined exactly. We examine the nature of the low-lying excited states in the full Hilbert space, and emphasize the role of the center symmetry for the confinement of charges. Whether the investigated doubled models admit a non-Abelian topological state which allows for fault-tolerant quantum computation will be addressed in a future publication

Affine Toda field theories related to Coxeter groups of non-crystallographic type

We propose affine Toda field theories related to the non-crystallographic Coxeter groups H_2, H_3 and H_4. The classical mass spectrum, the classical three-point couplings and the one-loop corrections to the mass renormalisation are determined. The construction is carried out by means of a reduction procedure from crystallographic to non-crystallographic Coxeter groups. The embedding structure explains for various affine Toda field theories that their particles can be organised in pairs, such that their relative masses differ by the golden ratio.Comment: 28 pages LaTe