@article{6821, abstract = {To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined.}, author = {Yourick, Miranda R. and Sandkam, Benjamin A. and Gammerdinger, William J and Escobar-Camacho, Daniel and Nandamuri, Sri Pratima and Clark, Frances E. and Joyce, Brendan and Conte, Matthew A. and Kocher, Thomas D. and Carleton, Karen L.}, issn = {1755-0998}, journal = {Molecular Ecology Resources}, number = {6}, pages = {1447--1460}, publisher = {Wiley}, title = {{Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses}}, doi = {10.1111/1755-0998.13062}, volume = {19}, year = {2019}, } @article{6788, abstract = {We consider the Nelson model with ultraviolet cutoff, which describes the interaction between non-relativistic particles and a positive or zero mass quantized scalar field. We take the non-relativistic particles to obey Fermi statistics and discuss the time evolution in a mean-field limit of many fermions. In this case, the limit is known to be also a semiclassical limit. We prove convergence in terms of reduced density matrices of the many-body state to a tensor product of a Slater determinant with semiclassical structure and a coherent state, which evolve according to a fermionic version of the Schrödinger–Klein–Gordon equations.}, author = {Leopold, Nikolai K and Petrat, Sören P}, issn = {1424-0661}, journal = {Annales Henri Poincare}, number = {10}, pages = {3471–3508}, publisher = {Springer Nature}, title = {{Mean-field dynamics for the Nelson model with fermions}}, doi = {10.1007/s00023-019-00828-w}, volume = {20}, year = {2019}, } @article{6795, abstract = {The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations.}, author = {Trubenova, Barbora and Hager, Reinmar}, issn = {20457758}, journal = {Ecology and Evolution}, number = {17}, pages = {9597--9608}, publisher = {Wiley}, title = {{Green beards in the light of indirect genetic effects}}, doi = {10.1002/ece3.5484}, volume = {9}, year = {2019}, } @article{6793, abstract = {The Regge symmetry is a set of remarkable relations between two tetrahedra whose edge lengths are related in a simple fashion. It was first discovered as a consequence of an asymptotic formula in mathematical physics. Here, we give a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic geometry.}, author = {Akopyan, Arseniy and Izmestiev, Ivan}, issn = {14692120}, journal = {Bulletin of the London Mathematical Society}, number = {5}, pages = {765--775}, publisher = {London Mathematical Society}, title = {{The Regge symmetry, confocal conics, and the Schläfli formula}}, doi = {10.1112/blms.12276}, volume = {51}, year = {2019}, } @misc{9786, author = {Ruess, Jakob and Pleska, Maros and Guet, Calin C and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Supporting text and results}}, doi = {10.1371/journal.pcbi.1007168.s001}, year = {2019}, }