bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating adult sex ratios in nature
Authors: Ancona Sergio , Dénes Francisco V. , Krüger Oliver , Székely Tamás , Beissinger Steven R. 
Published: August 2017

Adult sex ratio (ASR, the proportion of males in the adult population) is a central concept in population and evolutionary biology, and is also emerging as a major factor influencing mate choice, pair bonding and parental cooperation in both human and non-human societies. However, estimating ASR is fraught with difficulties stemming from the effects of spatial and temporal variation in the numbers of males and females, and detection/capture probabilities that differ between the sexes. Here, we critically evaluate methods for estimating ASR in wild animal populations, reviewing how recent statistical advances can be applied to handle some of these challenges. We review methods that directly account for detection differences between the sexes using counts of unmarked individuals (observed, trapped or killed) and counts of marked individuals using mark–recapture models. We review a third class of methods that do not directly sample the number of males and females, but instead estimate the sex ratio indirectly using relationships that emerge from demographic measures, such as survival, age structure, reproduction and assumed dynamics. We recommend that detection-based methods be used for estimating ASR in most situations, and point out that studies are needed that compare different ASR estimation methods and control for sex differences in dispersal.This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Persistent effect of sex ratios on relationship quality and life satisfaction
Authors: Grosjean Pauline , Brooks Robert C. 
Published: August 2017

Convict transportation to Australia imposed heavily male-biased sex ratios in some areas, altering the convict-era mating market and generating long-running cultural effects that persist to the present day. We test whether convict-era sex ratios have altered marital and overall life satisfaction today, through their persistent effects on gender norms and household bargaining. We find that both women and men are happier, and the happiness gap within married couples is smaller in areas where convict-era sex ratios were heavily male-biased than in areas where sex ratios were historically more even. We discuss our results in light of household bargaining theory, evolutionary sexual conflict theory and the well-documented relationship between conservative attitudes and self-reported happiness.
This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
The potential pitfalls of studying adult sex ratios at aggregate levels in humans
Authors: Pollet Thomas V. , Stoevenbelt Andrea H. , Kuppens Toon 
Published: August 2017

Human adult sex ratios have been studied extensively across the biological and social sciences. While several studies have examined adult sex ratio effects in a multilevel perspective, many studies have focused on effects at an aggregated level only. In this paper, we review some key issues relating to such analyses. We address not only nation-level analyses, but also aggregation at lower levels, to investigate whether these issues extend to lower levels of aggregation. We illustrate these issues with novel databases covering a broad range of variables. Specifically, we discuss distributional issues with aggregated measures of adult sex ratio, significance testing, and statistical non-independence when using aggregate data. Firstly, we show that there are severe distributional issues with national adult sex ratio, such as extreme cases. Secondly, we demonstrate that many ‘meaningless’ variables are significantly correlated with adult sex ratio (e.g. the max. elevation level correlates with sex ratio at US state level). Finally, we re-examine associations between adult sex ratios and teenage fertility and find no robust evidence for an association at the aggregate level. Our review highlights the potential issues of using aggregate data on adult sex ratios to test hypotheses from an evolutionary perspective in humans.This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Evolution of male strategies with sex-ratio–dependent pay-offs: connecting pair bonds with grandmothering
Authors: Loo Sara L. , Hawkes Kristen , Kim Peter S. 
Published: August 2017

Men's provisioning of mates and offspring has been central to ideas about human evolution because paternal provisioning is absent in our closest evolutionary cousins, the great apes, and is widely assumed to result in pair bonding, which distinguishes us from them. Yet mathematical modelling has shown that paternal care does not readily spread in populations where competition for multiple mates is the common male strategy. Here we add to models that point to the mating sex ratio as an explanation for pairing as pay-offs to mate guarding rise with a male-biased sex ratio. This is of interest for human evolution because our grandmothering life history shifts the mating sex ratio from female- to male-biased. Using a difference equation model, we explore the relative pay-offs for three competing male strategies (dependant care, multiple mating, mate guarding) in response to changing adult sex ratios. When fertile females are abundant, multiple mating prevails. As they become scarce, mate guarding triumphs. The threshold for this shift depends on guarding efficiency. Combined with mating sex ratios of hunter–gatherer and chimpanzee populations, these results strengthen the hypothesis that the evolution of our grandmothering life history propelled the shift to pair bonding in the human lineage.
This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Automated collection of pathogen-specific diagnostic data for real-time syndromic epidemiological studies
Authors: Meyers Lindsay , Ginocchio Christine C. , Faucett Aimie N. , Nolte Frederick S. , Gesteland Per H. , Leber Amy , Janowiak Diane , Donovan Virginia , Dien Bard Jennifer , Spitzer Silvia , Stellrecht Kathleen A. , Salimnia Hossein , Selvarangan Rangaraj , Juretschko Stefan , Daly Judy A. , Wallentine Jeremy C. , Lindsey Kristy , Moore Franklin , Reed Sharon L. , Aguero-Rosenfeld Maria , Fey Paul D. , Storch Gregory A. , Melnick Steve J. , Robinson Christine C. , Meredith Jennifer F. , Cook Camille V. , Nelson Robert K. , Jones Jay D. , Scarpino Samuel V. , Althouse Benjamin M. , Ririe Kirk M. , Malin Bradley A. , Poritz Mark A. 
Published: August 2017

AbstractHealth-care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are pathogen-specific. We describe a system, FilmArray®Trend, for rapid disease reporting that is syndrome-based but pathogen-specific. Results from a multiplex molecular diagnostic test are sent directly to a cloud database.www.syndromictrends.compresents these data in near real-time. Trend preserves patient privacy by removing or obfuscating patient identifiers. We summarize the respiratory pathogen results, for 20 organisms from 344,000 patient samples acquired as standard of care testing over the last four years from 20 clinical laboratories in the United States. The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks and adenovirus and bacterial pathogens show constant detection over the year. Interestingly, the rate of pathogen co-detections, on average 7.7%, matches predictions based on the relative abundance of organisms present.
Inferring proteome dynamics during yeast cell cycle using gene expression data
Authors: Kuchta Krzysztof , Towpik Joanna , Biernacka Anna , Kutner Jan , Kudlicki Andrzej , Ginalski Krzysztof , Rowicka Maga 
Published: August 2017

AbstractProtein levels are most relevant physiologically, but measuring them genome-wide remains a challenge. In contrast, mRNA levels are much easier and less expensive to measure globally. Therefore, RNA levels are typically used to infer the corresponding protein levels. The steady-state condition (assumption that protein levels remain constant) is typically used to calculate protein abundances, as it is mathematically very convenient, even though it is often clear that it is not satisfied for proteins of interest. Here, we propose a simple, yet very effective, method to estimate genome wide protein abundances, which does not require the assumption that protein levels remain constant, and thus allows us to also predict proteome dynamics. Instead, we assume that the system returns to the baseline at the end of experiments; such an assumption is satisfied in many time-course experiments and in all periodic conditions (e.g. cell cycle). The approach only requires availability of gene expression and protein half-life data. As proof-of-concept, we calculated the predicted proteome dynamics for the budding yeast proteome during the cell cycle, which can be conveniently browsed online. The approach was validated experimentally by verifying that the predicted protein concentration changes were consistent with measurements for all proteins tested. Additionally, if proteomic data are also available, our approach can be used to predict how half-lives change in response to posttranslational regulation. We illustrated this application of our method withde novoprediction of changes in the degradation rate of Clb2 in response to post-translational modifications. The predicted changes were consistent with earlier observations in the literature.
Population and conservation genomics of the world's rarest hyena species, the brown hyena (Parahyena brunnea)
Authors: Westbury Michael , Hartmann Stefanie , Barlow Axel , Wiesel Ingrid , Leo Viyanna , Welch Rebecca , Parker Daniel M , Sicks Florian , Ludwig Arne , Dalén Love , Hofreiter Michael 
Published: August 2017

AbstractWith an estimated population size of less than 10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) has been listed as ‘near threatened’ by the IUCN. Despite this rank, studies involving DNA analyses of the brown hyena are limited. Little consideration has been focussed towards population structure within the brown hyena, which could provide valuable insights about its evolutionary history and aid in conservation efforts of the species. Here we report both mitochondrial and nuclear genomes of wild-caught brown hyena individuals from across southern Africa. Mitochondrial DNA shows little to no phylogeographic structure, whereas low-coverage nuclear genomes reveal several potential sub-populations. Moreover, we find that brown hyenas harbour the lowest genetic diversity for a species on both the mitochondrial and nuclear level when compared to a number of mammalian species for which such information is currently available. Our data also reveal that at least on the nuclear DNA level, this low diversity could be the result of a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. Moreover, our findings also show that the correlation between genetic diversity and the perceived risk of extinction is not particularly strong, since many species with higher genetic diversity than the brown hyena are considered to be at greater risk of extinction. Taken together, our results have important implications for the conservation status and conservation approaches of the brown hyena.
Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships
Authors: Prasanna Arun N. , Gerber Daniel , Teeratas Kijpornyongpan , Aime M. Catherina , Doyle Vinson , Nagy Laszlo G. 
Published: August 2017

AbstractResolving deep divergences in the fungal tree of life remains a challenging task even for analyses of genome-scale phylogenetic datasets. Relationships between Basidiomycota subphyla, the rusts (Pucciniomycotina), smuts (Ustilaginomycotina) and mushroom forming fungi (Agaricomycotina) represent a particularly challenging situation that posed problems to both traditional multigene and genome-scale phylogenetic studies. Here, we address basal Basidiomycota relationships using three different phylogenomic datasets, concatenated and gene tree-based analyses and examine the contribution of several potential sources of uncertainty, including fast-evolving sites, putative long-branch taxa, model violation and missing data. We inferred conflicting results with different datasets and under different models. Fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and Astral analyses. The most conserved datasets grouped rusts with mushroom forming fungi, although this relationship proved labile, sensitive to model choice, different data subsets and missing data. Excluding putative long branch taxa, genes with the highest proportions of missing data and/or genes with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play too. Our analyses suggest that topologies uniting smuts with mushroom forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for rusts, smuts and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of the tree space that is difficult to access using both concatenation and gene tree based approaches. Thus, basal Basidiomycota relationships remain unresolved and might represent a phylogenetic problem that remains contentious even in the genomic era.
Functional consequences of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals
Authors: Coleman Jonathan R. I. , Bryois Julien , Gaspar Héléna A. , Jansen Philip R. , Savage Jeanne , Skene Nathan , Plomin Robert , Muñoz-Manchado Ana B. , Linnarsson Sten , Crawford Greg , Hjerling-Leffler Jens , Sullivan Patrick F. , Posthuma Danielle , Breen Gerome 
Published: August 2017

AbstractVariance in IQ is associated with a wide range of health outcomes, and 1% of the population are affected by intellectual disability. Despite a century of research, the fundamental neural underpinnings of intelligence remain unclear. We integrate results from genome-wide association studies (GWAS) of intelligence with brain tissue and single cell gene expression data to identify tissues and cell types associated with intelligence. GWAS data for IQ (N = 78,308) were meta-analyzed with an extreme-trait cohort of 1,247 individuals with mean IQ ∼170 and 8,185 controls. Genes associated with intelligence implicate pyramidal neurons of the somatosensory cortex and CA1 region of the hippocampus, and midbrain embryonic GABAergic neurons. Tissue-specific analyses find the most significant enrichment for frontal cortex brain expressed genes. These results suggest specific neuronal cell types and genes may be involved in intelligence and provide new hypotheses for neuroscience experiments using model systems.
A synthetic biology approach to probing nucleosome symmetry
Authors: Ichikawa Yuichi , Connelly Caitlin F. , Appleboim Alon , Miller Thomas C. , Jacobi Hadas , Abshiru Nebiyu A. , Chou Hsin-Jung , Chen Yuanyuan , Sharma Upasna , Zheng Yupeng , Thomas Paul M. , Chen Hsiuyi V. , Bajaj Vineeta , Müller Christoph W. , Kelleher Neil L. , Friedman Nir , Bolon Daniel N. , Rando Oliver J. , Kaufman Paul D. 
Published: August 2017

ABSTRACTThe repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.
Estimating Excitatory and Inhibitory Synaptic Conductances from Spike Trains using a Recursive Bayesian Approach
Authors: Lankarany Mila 
Published: August 2017

AbstractInference of excitatory and inhibitory synaptic conductances (SCs) from the spike trains is poorly addressed in the literature due to the complexity of the problem. As recent technological advancements make recording spikes from multiple (neighbor) neurons of a behaving animal (in some rare cases from humans) possible, this paper tackles the problem of estimating SCs solely from the recorded spike trains. Given an ensemble of spikes corresponding to population of neighbor neurons, we aim to infer the average excitatory and inhibitory SCs underlying the shared neural activity. In this paper, we extended our previously established Kalman filtering (KF)–based algorithm to incorporate the voltage-to-spike nonlinearity (mapping from membrane potential to spike rate). Having estimated the instantaneous spike rate using optimal linear filtering (Gaussian kernel), our proposed algorithm uses KF followed by expectation maximization (EM) algorithm in a recursive fashion to infer the average SCs. As the dynamics of SCs and membrane potential is included in our model, the proposed algorithm, unlike other related works, considers different sources of stochasticity, i.e., the variabilities of SCs, membrane potential, and spikes. Moreover, it is worth mentioning that our algorithm is blind to the external stimulus, and it performs only based on observed spikes. We validate the accuracy and practicality of our technique through simulation studies where leaky integrate and fire (LIF) model is used to generate spikes. We show that the estimated SCs can precisely track the original ones. Moreover, we show that the performance of our algorithm can be further improved given enough number of trials (spikes). As a rule of thumb, 50 trials of neurons with the average firing rate of 5 Hz can guarantee the accuracy of our proposed algorithm.
A Prototype for Modular Cell Engineering
Authors: Wilbanks Brandon , Layton Donovan S. , Garcia Sergio , Trinh Cong T. 
Published: August 2017

ABSTRACTWhen aiming to produce a target chemical at high yield, titer, and productivity, various combinations of genetic parts available to build the target pathway can generate a large number of strains for characterization. This engineering approach will become increasingly laborious and expensive when seeking to develop desirable strains for optimal production of a large space of biochemicals due to extensive screening. Our recent theoretical development of modular cell (MODCELL) design principles can offer a promising solution for rapid generation of optimal strains by coupling a modular cell and exchangeable production modules in a plug-and-play fashion. In this study, we experimentally validated some designed properties of MODCELL by demonstrating: i) a modular (chassis) cell is required to couple with a production module, a heterologous ethanol pathway, as a testbed, ii) degree of coupling between the modular cell and production modules can be modulated to enhance growth and product synthesis, iii) a modular cell can be used as a host to select an optimal pyruvate decarboxylase (PDC) of the ethanol production module and to help identify a hypothetical PDC protein, and iv) adaptive laboratory evolution based on growth selection of the modular cell can enhance growth and product synthesis rates. We envision that the MODCELL design provides a powerful prototype for modular cell engineering to rapidly create optimal strains for synthesis of a large space of biochemicals.
Rap1 acts via multiple mechanisms to position Canoe/Afadin and adherens junctions and mediate apical-basal polarity establishment
Authors: Bonello Teresa T. , Perez-Vale Kia Z. , Sumigray Kaelyn D. , Peifer Mark 
Published: August 2017

AbstractEpithelial apical-basal polarity drives assembly and function of most animal tissues. Polarity initiation requires cell-cell adherens junction assembly at the apical-basolateral boundary. The mechanisms underlying this remain key issues. Drosophila embryos provide a superb model, as 6000 polarized cells assemble simultaneously. Current data place the actin-junctional linker Canoe (mammalian Afadin’s homolog) at the top of the polarity hierarchy, where it directs Bazooka/Par3 and adherens junctions positioning. Here we define mechanisms regulating Canoe localization/function. Spatial organization of Canoe is multifaceted, involving membrane-localization, recruitment to nascent junctions and macromolecular assembly into cables at tricellular junctions. Our data suggest apical activation of the small GTPase Rap1 regulates all three events, but support multiple modes of regulation. The Rap1GEF Dizzy/PDZ-GEF is critical for Canoe tricellular junction enrichment but not apical retention. Canoe’s Rap1-interacting RA-domains mediate adherens junction and tricellular junction recruitment but are dispensable for membrane-localization. Our data also support a role for Canoe-multimerization. These multifactorial inputs all shape Canoe localization, correct Bazooka/Par3 and adherens junction positioning, and thus apical-basal polarity. We integrate existing data into a new polarity establishment model.Abbreviations usedα-cat, alpha-catenin; β-cat, beta-catenin; AJ, adherens junction; Arm, Armadillo; Baz, Bazooka; CA, constitutively active; Cno, Canoe; DE-cad,DrosophilaE-cadherin; Dzy, Dizzy; GAP, GTPase activating protein; GDP, guanosine diphosphate; GEF, guanine nucleotide exchange factor; GFP, green fluorescent protein; GTP, guanosine triphosphate; IF, immunofluorescence; MIP, maximum intensity projection; RA, Ras-associated; RFP, red fluorescent protein; SAJ, spot adherens junction; shRNA, short hairpin RNA; TCJ, tricellular junction; WT, wildtype