Generalized Multivariate Extreme Value Models for Explicit Route Choice Sets

This paper analyses a class of route choice models with closed-form probability expressions, namely, Generalized Multivariate Extreme Value (GMEV) models. A large group of these models emerge from different utility formulas that combine systematic utility and random error terms. Twelve models are captured in a single discrete choice framework. The additive utility formula leads to the known logit family, being multinomial, path-size, paired combinatorial and link-nested. For the multiplicative formulation only the multinomial and path-size weibit models have been identified; this study also identifies the paired combinatorial and link-nested variations, and generalizes the path-size variant. Furthermore, a new traveller's decision rule based on the multiplicative utility formula with a reference route is presented. Here the traveller chooses exclusively based on the differences between routes. This leads to four new GMEV models. We assess the models qualitatively based on a generic structure of route utility with random foreseen travel times, for which we empirically identify that the variance of utility should be different from thus far assumed for multinomial probit and logit-kernel models. The expected travellers' behaviour and model-behaviour under simple network changes are analysed. Furthermore, all models are estimated and validated on an illustrative network example with long distance and short distance origin-destination pairs. The new multiplicative models based on differences outperform the additive models in both tests

Anarchy, Groups, and Conflict: An Experiment on the Emergence of Protective Associations

In this paper, we investigate the implications of the philosophical considerations presented in Nozick’s Anarchy, State, and Utopia, by examining group formation in a laboratory setting where subjects engage in both cooperative and conflictual interactions. We endow participants with a commodity used to generate earnings, plunder others, or protect against plunder. In our primary treatment, we allow participants to form groups to pool their resources. We conduct a baseline comparison treatment that does not allow group formation. We find that allowing subjects to organize themselves into groups does not lead to more cooperation and may in fact exacerbate tendencies for conflict.Nozickian protective associations, Conflict, Anarchy, Experimental economics

A new robust diagnostic polymerase chain reaction for determining the mating status of female Anopheles gambiae mosquitoes.

The principal malaria vector in Africa, Anopheles gambiae, contains two pairs of autosomes and one pair of sex chromosomes. The Y chromosome is only associated with males and other Y chromosome-specific DNA sequences, which are transferred to women during mating. A reliable tool to determine the mating status of dried wild An. gambiae females is currently lacking. DNA was extracted from dried virgin and mated females and used to test whether Y chromosome-specific polymerase chain reaction (PCR) markers can be successfully amplified and used as a predictor of mating. Here we report a new PCR-based method to determine the mating status among successfully inseminated and virgin wild An. gambiae females, using three male-specific primers. This dissection-free method has the potential to facilitate studies of both population demographics and gene flow from dried mosquito samples routinely collected in epidemiologic monitoring and aid existing and new malaria-vector control approaches

Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome

Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio- generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of nextgeneration sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBiogenerated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome sanalyses to facilitate functional studies into an organism’s biology