Dominance style of female white‐faced capuchins

Dominance style, the level of tolerance displayed by dominant individuals toward subordinate ones, is exhibited along a continuum from despotic to relaxed. It is a useful concept to describe the nature of dominance relationships in macaque species and it bridges among multiple features of dominance hierarchies, aggression, kinship and conflict resolution. Capuchins share many behavioral similarities with Old World monkeys and like macaques, may exhibit a suite of covarying characteristics related to dominance. Here, we provide an assessment of dominance style by examining measures of aggression and kin bias in 22 adult female white‐faced capuchin monkeys (Cebus capucinus) in three social groups at Santa Rosa Sector, Costa Rica. We found that bidirectionality of aggression was low (mean = 6.9% ± SE 1.6). However, there were few significant correlations between kin relatedness and social behavior (approaching, grooming, proximity, and co‐feeding), even though the intensity of kin bias in grooming was moderate and higher in the larger group. We conclude that patterns of aggression and kin‐biased behavior in our study animals are dissimilar to the patterns of covariation observed in macaque species. While unidirectional aggression suggests a despotic dominance style, the moderate expression of kin bias suggests an intermediate to relaxed classification when compared with results from an analysis of 19 macaque species. Additional studies of capuchin species and behaviors associated with dominance style (i.e., conciliatory tendencies) would help to create a comparative framework for the genus Cebus, and allow for more detailed cross‐species comparison of dominance relationships across all primates. Am J Phys Anthropol 150:591–601, 2013. © 2013 Wiley Periodicals, Inc.     

Social encounter networks: characterizing Great Britain

A major goal of infectious disease epidemiology is to understand and predict the spread of infections within human populations, with the intention of better informing decisions regarding control and intervention. However, the development of fully mechanistic models of transmission requires a quantitative understanding of social interactions and collective properties of social networks. We performed a cross-sectional study of the social contacts on given days for more than 5000 respondents in England, Scotland and Wales, through postal and online survey methods. The survey was designed to elicit detailed and previously unreported measures of the immediate social network of participants relevant to infection spread. Here, we describe individual-level contact patterns, focusing on the range of heterogeneity observed and discuss the correlations between contact patterns and other socio-demographic factors. We find that the distribution of the number of contacts approximates a power-law distribution, but postulate that total contact time (which has a shorter-tailed distribution) is more epidemiologically relevant. We observe that children, public-sector and healthcare workers have the highest number of total contact hours and are therefore most likely to catch and transmit infectious disease. Our study also quantifies the transitive connections made between an individual''s contacts (or clustering); this is a key structural characteristic of social networks with important implications for disease transmission and control efficacy. Respondents'' networks exhibit high levels of clustering, which varies across social settings and increases with duration, frequency of contact and distance from home. Finally, we discuss the implications of these findings for the transmission and control of pathogens spread through close contact.     

Band reporting rates of waterfowl: does individual heterogeneity bias estimated survival rates?

In capture–recapture studies, the estimation accuracy of demographic parameters is essential to the efficacy of management of hunted animal populations. Dead recovery models based upon the reporting of rings or bands are often used for estimating survival of waterfowl and other harvested species. However, distance from the ringing site or condition of the bird may introduce substantial individual heterogeneity in the conditional band reporting rates (r), which could cause bias in estimated survival rates (S) or suggest nonexistent individual heterogeneity in S. To explore these hypotheses, we ran two sets of simulations (n = 1000) in MARK using Seber''s dead recovery model, allowing time variation on both S and r. This included a series of heterogeneity models, allowing substantial variation on logit(r), and control models with no heterogeneity. We conducted simulations using two different values of S: S = 0.60, which would be typical of dabbling ducks such as mallards (Anas platyrhynchos), and S = 0.80, which would be more typical of sea ducks or geese. We chose a mean reporting rate on the logit scale of −1.9459 with SD = 1.5 for the heterogeneity models (producing a back-transformed mean of 0.196 with SD = 0.196, median = 0.125) and a constant reporting rate for the control models of 0.196. Within these sets of simulations, estimation models where σ_S = 0 and σ_S > 0 (σ_S is SD of individual survival rates on the logit scale) were incorporated to investigate whether real heterogeneity in r would induce apparent individual heterogeneity in S. Models where σ_S = 0 were selected approximately 91% of the time over models where σ_S > 0. Simulation results showed < 0.05% relative bias in estimating survival rates except for models estimating σ_S > 0 when true S = 0.8, where relative bias was a modest 0.5%. These results indicate that considerable variation in reporting rates does not cause major bias in estimated survival rates of waterfowl, further highlighting the robust nature of dead recovery models that are being used for the management of harvested species.     

Confidence interval of intrinsic optimum temperature estimated using thermodynamic SSI model

The intrinsic optimum temperature for the development of ectotherms is one of the most important factors not only for their physiological processes but also for ecological and evolutional processes. The Sharpe–Schoolfield–Ikemoto (SSI) model succeeded in defining the temperature that can thermodynamically meet the condition that at a particular temperature the probability of an active enzyme reaching its maximum activity is realized. Previously, an algorithm was developed by Ikemoto (Tropical malaria does not mean hot environments. Journal of Medical Entomology, 45, 963–969) to estimate model parameters, but that program was computationally very time consuming. Now, investigators can use the SSI model more easily because a full automatic computer program was designed by Shi et al. (A modified program for estimating the parameters of the SSI model. Environmental Entomology, 40, 462–469). However, the statistical significance of the point estimate of the intrinsic optimum temperature for each ectotherm has not yet been determined. Here, we provided a new method for calculating the confidence interval of the estimated intrinsic optimum temperature by modifying the approximate bootstrap confidence intervals method. For this purpose, it was necessary to develop a new program for a faster estimation of the parameters in the SSI model, which we have also done.     

Single‐nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula

Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single‐nucleotide polymorphism (SNP) markers in M. truncatula through large‐scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.     

Lifestyle factors and prostate-specific antigen (PSA) testing in UK Biobank: Implications for epidemiological research

BackgroundThe central role of prostate-specific antigen (PSA) testing in the diagnosis of prostate cancer leads to the possibility that observational studies that report associations between risk factors and prostate cancer could be affected by detection bias. This study aims to investigate whether reported risk factors for prostate cancer are associated with PSA testing in a large middle-aged population-based cohort in the UK.MethodsThe cross-sectional association between a wide range of sociodemographic, lifestyle, dietary and health characteristics with PSA testing was examined in 212,039 men aged 40–69 years in UK Biobank.ResultsA total of 62,022 (29%) men reported they had ever had a PSA test. A wide range of factors was associated with a higher likelihood of PSA testing including age, height, education level, family history of prostate cancer, black ethnic origin, not being in paid/self-employment, living with a wife or partner, having had a vasectomy, being diagnosed with cancer or hypertension and having a high dietary intake of cereal, cooked and salad/raw vegetables, fresh fruit and tea. Conversely, socioeconomic deprivation, Asian ethnic origin, current smoking, low alcohol intake, high body-mass index, high coffee consumption and being diagnosed with diabetes, heart disease or stroke were associated with a lower likelihood of PSA testing.ConclusionsA variety of sociodemographic, lifestyle and health-related characteristics are associated with PSA testing, suggesting that observed associations of some of these traits with risk for prostate cancer in epidemiological studies may be, at least partially, due to detection bias.     

RNA approaches the B‐form in stacked single strand dinucleotide contexts

Duplex RNA adopts an A‐form structure, while duplex DNA interconverts between the A‐ and B‐forms depending on the environment. The C2′‐endo sugar pucker seen in B‐form DNA can occur infrequently in ribose sugars as well, but RNA is not understood to assume B‐form conformations. Through analysis of over 45,000 stacked single strand dinucleotide (SSD) crystal structure conformations, this study demonstrates that RNA is capable of adopting a wide conformational range between the canonical A‐ and B‐forms at the localized SSD level, including many B‐form‐like conformations. It does so through C2′‐endo ribose conformations in one or both nucleotides, and B‐form‐like neighboring base stacking patterns. As chemical reactions on nucleic acids involve localized changes in chemical bonds, the understanding of how enzymes distinguish between DNA and RNA nucleotides is altered by the energetic accessibility of these rare B‐form‐like RNA SSD conformations. The existence of these conformations also has direct implications in parametrization of molecular mechanics energy functions used extensively to model nucleic acid behavior., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 65–82, 2016