A functorial approach to regular homomorphisms

Classically, regular homomorphisms have been defined as a replacement for Abel--Jacobi maps for smooth varieties over an algebraically closed field. In this work, we interpret regular homomorphisms as morphisms from the functor of families of algebraically trivial cycles to abelian varieties and thereby define regular homomorphisms in the relative setting, e.g., families of schemes parameterized by a smooth variety over a given field. In that general setting, we establish the existence of an initial regular homomorphism, going by the name of algebraic representative, for codimension-2 cycles on a smooth proper scheme over the base. This extends a result of Murre for codimension-2 cycles on a smooth projective scheme over an algebraically closed field. In addition, we prove base change results for algebraic representatives as well as descent properties for algebraic representatives along separable field extensions. In the case where the base is a smooth variety over a subfield of the complex numbers we identify the algebraic representative for relative codimension-2 cycles with a subtorus of the intermediate Jacobian fibration which was constructed in previous work. At the heart of our descent arguments is a base change result along separable field extensions for Albanese torsors of separated, geometrically integral schemes of finite type over a field.Comment: 47 page

First Steps Towards RAT: A Protocol for Documenting Data Use in the Agent-Based Modeling Process

While there is a number of frameworks and protocols in Agent-Based Modeling (ABM) that support the documentation of different aspects of a simulation study, it is surprising to find only a small number dealing with the handling of data. Here we present the results of discussions we had on the topic at the Lorentz Center workshop on Integrating Qualitative and Quantitative Evidence using Social Simulation (8-12 April 2019, Leiden, the Netherlands). We believe that important distinctions to be considered in the context of data use documentation are the differences of data use in relation to modeling approaches (theory driven etc.) and data documentation needs at the different stages in the modeling process (conceptualization, specification, calibration, and validation). What we hope to achieve by presenting this paper at this conference, with the help of the community, is to move forward the development of a generally acceptable protocol for documenting data use in the ABM process

RAT-RS: a reporting standard for improving the documentation of data use in agent-based modelling

This article describes and justifies a reporting standard to improve data use documentation in Agent-Based Modelling. Following the development of reporting standards for models themselves, empirical modelling has now developed to the point where these standards need to take equally effective account of data use (which previously has tended to be an afterthought to model description). It is particularly important that a standard should allow the reporting of the different uses to which data may be put (specification, calibration and validation), but also that it should be compatible with the integration of different kinds of data (for example survey, ethnographic and experimental) sometimes known as mixed methods research. The article motivates the need for standards generally, and positions the distinctive contribution of the RAT-RS reporting standard. It describes how the standard was developed to ensure its usability, presents and explains it, and describes possibilities for future development

Comprehensive genomic profiles of small cell lung cancer

We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer

Insights into the accuracy of social scientists' forecasts of societal change

How well can social scientists predict societal change, and what processes underlie their predictions? To answer these questions, we ran two forecasting tournaments testing the accuracy of predictions of societal change in domains commonly studied in the social sciences: ideological preferences, political polarization, life satisfaction, sentiment on social media, and gender–career and racial bias. After we provided them with historical trend data on the relevant domain, social scientists submitted pre-registered monthly forecasts for a year (Tournament 1; N = 86 teams and 359 forecasts), with an opportunity to update forecasts on the basis of new data six months later (Tournament 2; N = 120 teams and 546 forecasts). Benchmarking forecasting accuracy revealed that social scientists’ forecasts were on average no more accurate than those of simple statistical models (historical means, random walks or linear regressions) or the aggregate forecasts of a sample from the general public (N = 802). However, scientists were more accurate if they had scientific expertise in a prediction domain, were interdisciplinary, used simpler models and based predictions on prior data

Theory development via replicated simulations and the added value of standards

Using the agent-based model of Miller et al. (2012), which depicts how different types of individuals’ memory affect the formation and performance of organizational routines, we show how a replicated simulation model can be used to develop theory. We also assess how standards, such as the ODD (Overview, Design concepts, and Details) protocol and DOE (design of experiments) principles, support the replication, evaluation, and further analysis of this model. Using the verified model, we conduct several simulation experiments as examples of different types of theory development. First, we show how previous theoretical insights can be generalized by investigating additional scenarios, such as mergers. Second, we show the potential of replicated simulation models for theory refinement, such as analyzing in-depth the relationship between memory functions and routine performance or routine adaptation