857 Works

Data from: No evidence of sibling cooperation in the absence of parental care in Nicrophorus vespilloides

Camille Magneville, Tom Ratz, Jon Richardson & Per T. Smiseth
Interactions among siblings fall on a continuum with competition and cooperation at opposite ends of the spectrum. Prior work on the burying beetle Nicrophorus vespilloides suggests that parental care shifts the balance between competition and cooperation by masking a density-dependent shift from cooperation to competition. However, these results should be interpreted with caution because they were based on correlational evidence for an association between larval density at dispersal and mean larval mass at dispersal. Here...

Data from: Antibodies and coinfection drive variation in nematode burdens in wild mice

Melanie Clerc, Godefroy Devevey, Andy Fenton & Amy B. Pedersen
Coinfections with parasitic helminths and microparasites are highly common in nature and can lead to complex within-host interactions between parasite species which can cause negative health outcomes for humans, and domestic and wild animals. Many of these negative health effects worsen with increasing parasite burdens. However, even though many studies have identified several key factors that determine worm burdens across various host systems, less is known about how the immune response interacts with these factors...

Data from: Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk

James E.N. Minchin, Catherine M. Scahill, Nicole Staudt, Elisabeth M. Busch-Nentwich & John F. Rawls
The regional distribution of adipose tissues is implicated in a wide range of diseases. For example, proportional increases in visceral adipose tissue increase the risk for insulin resistance, diabetes and cardiovascular disease. Zebrafish offer a tractable model system by which to obtain unbiased and quantitative phenotypic information on regional adiposity, and deep phenotyping can explore complex disease-related adiposity traits. To facilitate deep phenotyping of zebrafish adiposity traits, we used pairwise correlations between 67 adiposity traits...

Europarl-direct

Bruno Cartoni, Thomas Meyer & Philipp Koehn
These files provide statement pair extractions from the Europarl corpus of the same known source language directly translated to the target langages.

Data from: No evidence for sibling or parent-offspring coadaptation in a wild population of blue tits, despite high power.

Caroline Thomson, Jarrod D. Hadfield & Caroline E. Thomson
Parent and offspring behaviours are expected to act as both the agents and targets of selection. This may generate parent-offspring coadaptation in which parent and offspring behaviours become genetically correlated in a way that increases inclusive fitness. Cross-fostering has been used to study parent-offspring coadaptation, with the prediction that offspring raised by non-relatives, or parents raising non-relatives, should suffer fitness costs. Using long-term data from more than 400 partially crossed broods of blue tits (Cyanistes...

Data from: Species richness change across spatial scales

Jonathan M. Chase, Brian J. McGill, Patrick L. Thompson, Laura H. Antão, Amanda E. Bates, Shane A. Blowes, Maria Dornelas, Andrew Gonzalez, Anne E. Magurran, Sarah R. Supp, Marten Winter, Anne D. Bjorkmann, Helge Bruelheide, Jarrett E.K. Byrnes, Juliano Sarmento Cabral, Robin Ehali, Catalina Gomez, Hector M. Guzman, Forest Isbell, Isla H. Myers-Smith, Holly P. Jones, Jessica Hines, Mark Vellend, Conor Waldock & Mary O'Connor
Humans have elevated global extinction rates and thus lowered global-scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in...

Data from: Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms

Roberta Bergero, Jim Gardner, Beth Bader, Lengxob Yong & Deborah Charlesworth
It is often stated that polymorphisms for mutations affecting fitness of males and females in opposite directions [sexually antagonistic (SA) polymorphisms] are the main selective force for the evolution of recombination suppression between sex chromosomes. However, empirical evidence to discriminate between different hypotheses is difficult to obtain. We report genetic mapping results in laboratory-raised families of the guppy (Poecilia reticulata), a sexually dimorphic fish with SA polymorphisms for male coloration genes, mostly on the sex...

The early impact of paraquat ban on suicide in Taiwan

Shu-Sen Chang, Chien-Yu Lin, Ming-Been Lee, Lih-Jong Shen, David Gunnell & Michael Eddleston
Pesticide ingestion is a leading method for suicide worldwide. Paraquat is a highly lethal herbicide when ingested. We assessed the impact of the first-stage ban on the import and production of paraquat (from February 2018) on suicides by pesticide poisoning in Taiwan. Suicide data by method (pesticide vs. non-pesticide), pesticide (paraquat vs. non-paraquat), and area/sex/age were extracted from the national cause-of-death data files (2011–2019). Negative binomial regression was used to estimate changes in suicide rates...

Supplementary data, code, and information for ‘Discrepancies between the modeled and proxy-reconstructed response to volcanic forcing over the past millennium: Implications and possible mechanisms(Journal of Geophysical Research, Mann et al. 2013)

M.E. Mann, S. Rutherford, A. Schurer, Simon F.B. Tett & J.D. Fuentes
We show that a systematic discrepancy between model simulations and proxy reconstructions of hemispheric temperature changes over the past millennium appears to arise from a small number of radiatively large volcanic eruptions. Past work has shown that accounting for this mismatch alone appears to reconcile inconsistencies between the overall amplitude of simulated and proxy-reconstructed temperature changes. We provide empirical support for the previously posited hypothesis that this discrepancy may arise from threshold growth effects in...

Data from: The effect of uncertain bottom friction on estimates of tidal current power

Monika J. Kreitmair, Scott Draper, Alistair G.L. Borthwick & Ton S. Van Den Bremer
Uncertainty affects estimates of the power potential of tidal currents, resulting in large ranges in values reported for a given site, such as the Pentland Firth, UK. We examine the role of bottom friction, one of the most important sources of uncertainty. We do so by using perturbation methods to find the leading-order effect of bottom friction uncertainty in theoretical models by Garrett & Cummins (2005), Vennell (2010), and Garrett & Cummins (2013), which consider...

Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, &
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

Evolutionary mechanisms underpinning fitness response to multiple stressors in Daphnia

Maria Cuenca Cambronero, Jelena H. Pantel, Hollie Marshall, Tien T. T. Nguyen, Henar Tomero-Sanz & Luisa Orsine
Multiple stressors linked to anthropogenic activities can influence how organisms adapt and evolve. So far, a consensus on how multiple stressors drive adaptive trajectories in natural populations has not been reached. Some meta-analysis reports show predominance of additive effects of stressors on ecological endpoints (e.g. fecundity, mortality), whereas others show synergistic effects more frequently. Moreover, it is unclear what mechanisms of adaptation underpin responses to complex environments. Here, we use populations of the crustacean Daphnia...

A new prognostic risk model based on autophagy-related genes in kidney renal clear cell carcinoma

Guangzhen Wu, Yingkun Xu, Huayu Zhang, Zihao Ruan, Peizhi Zhang, Zicheng Wang, Han Gao, Xiangyu Che, Qinghua Xia & Feng Chen
This study aimed to explore the potential role of autophagy-related genes in kidney renal clear cell carcinoma (KIRC) and develop a new prognostic-related risk model. In our research, we used multiple bioinformatics methods to perform a pan-cancer analysis of the CNV, SNV, mRNA expression, and overall survival of autophagy-related genes, and displayed the results in the form of heat maps. We then performed cluster analysis and LASSO regression analysis on these autophagy-related genes in KIRC....

Data from: Environmental heterogeneity decreases reproductive success via effects on foraging behaviour

Alice Trevail, Jonathan Green, Jonathan Sharples, Jeff Polton, Peter Miller, Francis Daunt, Ellie Owen, Mark Bolton, Kendrew Colhoun, Stephen Newton, Gail Robertson & Samantha Patrick
Environmental heterogeneity shapes the uneven distribution of resources available to foragers, and is ubiquitous in nature. Optimal foraging theory predicts that an animal’s ability to exploit resource patches is key to foraging success. However, the potential fitness costs and benefits of foraging in a heterogeneous environment are difficult to measure empirically. Heterogeneity may provide higher quality foraging opportunities, or alternatively could increase the cost of resource acquisition because of reduced patch density or increased competition....

Feature: Being a researcher: The return of the native

Jenny Ozga

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

Jialiang Li, Yujiao Zhang, Markus Ruhsam, Richard Ian Milne, Yi Wang, Dayu Wu, Shiyu Jia, Tongzhou Tao & Kangshan Mao
The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus Thuja. Two separate clades...

Work and Family Lives Dataset

Sarah Cunningham-Burley, Lynn Jamieson & Jeni Harden
This project explores the ways in which working parents and their primary school-aged children negotiate their work and family lives over time, drawing on the changing experiences and perceptions of a varied sample of fourteen families over three waves of interviews (2007-2010). Set in a southern area of Scotland, the research investigated the impact of issues raised by working parenthood on the dynamics of everyday family life and practices. It provides insights into how parents...

Predictability of thermal fluctuations influences functional traits of a cosmopolitan marine diatom

Raissa Gill, Sinead Collins, Phoebe Argyle, Michaela Larsson, Robert Fleck & Martina Doblin
Evolutionary theory predicts that organismal plasticity should evolve in environments that fluctuate regularly. However, in environments that fluctuate less predictably, plasticity may be constrained because environmental cues become less reliable for expressing the optimum phenotype. Here we examine how the predictability of +5 °C temperature fluctuations impacts the phenotype of the marine diatom Thalassiosira pseudonana. Thermal regimes were informed by temperatures experienced by microbes in an ocean simulation, and featured regular or irregular temporal sequences...

Efficient Learning of Quadratic Variance Function Directed Acyclic Graphs via Topological Layers

Wei Zhou, Xin He, Wei Zhong & Junhui Wang
Directed acyclic graph (DAG) models are widely used to represent casual relationships among random variables in many application domains. This article studies a special class of non-Gaussian DAG models, where the conditional variance of each node given its parents is a quadratic function of its conditional mean. Such a class of non-Gaussian DAG models are fairly flexible and admit many popular distributions as special cases, including Poisson, Binomial, Geometric, Exponential, and Gamma. To facilitate learning,...

Global biogeography of warning colouration in the butterfly Danaus chrysippus

Wanzhen Liu, David A. S. Smith, Gayatri Raina, Rowan Stanforth, Ivy Ng’Iru, Piera Ireri, Dino J. Martins, Ian J. Gordon & Simon H. Martin
Warning colouration provides a textbook example of natural selection, but the frequent observation of polymorphism in aposematic species presents an evolutionary puzzle. We investigated biogeography and polymorphism of warning patterns in the widespread butterfly Danaus chrysippus using records from citizen science (n=5467), museums (n=8864), and fieldwork (n=2586). We find that polymorphism in three traits controlled by known mendelian loci is extensive. Broad allele frequency clines, hundreds of km wide, suggest a balance between long-range dispersal...

The symmetry spectrum in a hybridising, tropical group of rhododendrons

Valerie L. Soza, Ricardo Kriebel, Elizabeth Ramage, Benjamin Hall & Alex Twyford
Many diverse plant clades possess bilaterally symmetrical flowers and specialized pollination syndromes suggesting these traits may promote diversification. We examine the evolution of diverse floral morphologies and the association with diversification history in a species-rich tropical radiation of Rhododendron. We used restriction-site associated DNA sequencing on 114 taxa from Rhododendron sect. Schistanthe to reconstruct phylogenetic relationships, infer colonization of Southeast Asia and examine hybridization. We then captured and quantified floral variation using geometric morphometric analyses...

Memory markers in the continuum of the Alzheimer’s clinical syndrome

Mario A. Parra, Clara Calia, Vivek Pattan & Sergio Della Sala
Abstract Background The individual and complementary value of the Visual Short-Term Memory Binding Test (VSTMBT) and the Free and Cued Selective Reminding Test (FCSRT) as markers to trace the AD continuum was investigated. It was hypothesised that the VSTMBT would be an early indicator while the FCSRT would inform on imminent progression. Methods Healthy older adults (n=70) and patients with mild cognitive impairment (MCI) (n=80) were recruited and followed up between 2012 and 2017. Participants...

Memory markers in the continuum of the Alzheimer’s clinical syndrome

Mario A. Parra, Clara Calia, Vivek Pattan & Sergio Della Sala
Abstract Background The individual and complementary value of the Visual Short-Term Memory Binding Test (VSTMBT) and the Free and Cued Selective Reminding Test (FCSRT) as markers to trace the AD continuum was investigated. It was hypothesised that the VSTMBT would be an early indicator while the FCSRT would inform on imminent progression. Methods Healthy older adults (n=70) and patients with mild cognitive impairment (MCI) (n=80) were recruited and followed up between 2012 and 2017. Participants...

Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis

Stephen J. Clark, Ricard Argelaguet, Tim Lohoff, Felix Krueger, Deborah Drage, Berthold Göttgens, John C. Marioni, Jennifer Nichols & Wolf Reik
Abstract Background Perturbation of DNA methyltransferases (DNMTs) and of the active DNA demethylation pathway via ten-eleven translocation (TET) methylcytosine dioxygenases results in severe developmental defects and embryonic lethality. Dynamic control of DNA methylation is therefore vital for embryogenesis, yet the underlying mechanisms remain poorly understood. Results Here we report a single-cell transcriptomic atlas from Dnmt and Tet mutant mouse embryos during early organogenesis. We show that both the maintenance and de novo methyltransferase enzymes are...

Additional file 2 of Memory markers in the continuum of the Alzheimer’s clinical syndrome

Mario A. Parra, Clara Calia, Vivek Pattan & Sergio Della Sala
Additional file 2: Supplementary Figure 1. Example trial of the Perceptual Binding Task used for screening purposes (A) and both conditions of the VSTMB task (B). See text in the manuscript (Method) for a full description of these tasks.

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