57 Works

Data from: Reward context determines risky choice in pigeons and humans

Elliot A. Ludvig, Christopher R. Madan, Jeffrey M. Pisklak & Marcia L. Spetch
Whereas humans are risk averse for monetary gains, other animals can be risk seeking for food rewards, especially when faced with variable delays or under significant deprivation. A key difference between these findings is that humans are often explicitly told about the risky options, whereas non-human animals must learn about them from their own experience. We tested pigeons (Columba livia) and humans in formally identical choice tasks where all outcomes were learned from experience. Both...

Data from: Quantifying crowd size with mobile phone and Twitter data

Federico Botta, Helen Susannah Moat & Tobias Preis
Being able to infer the number of people in a specific area is of extreme importance for the avoidance of crowd disasters and to facilitate emergency evacuations. Here, using a football stadium and an airport as case studies, we present evidence of a strong relationship between the number of people in restricted areas and activity recorded by mobile phone providers and the online service Twitter. Our findings suggest that data generated through our interactions with...

Data from: Barrier bednets target malaria vectors and expand the range of usable insecticides

Gregory P.D. Murray, Natalie Lissenden, Jeff Jones, Vitaly Voloshin, K. Hyacinthe Toé, Ellie Sherrard-Smith, Geraldine M. Foster, Thomas S. Churcher, Josephine E.A. Parker, Catherine E. Towers, Sagnon N’Falé, Wamdaogo M. Guelbeogo, Hilary Ranson, David Towers & Philip J. McCall
Transmission of Plasmodium falciparum malaria parasites occurs when nocturnal Anopheles mosquito vectors feed on human blood. In Africa, where malaria burden is greatest, bednets treated with pyrethroid insecticide were highly effective in preventing mosquito bites and reducing transmission, and essential to achieving unprecedented reductions in malaria until 2015. Since then, progress has stalled and with insecticidal bednets losing efficacy against pyrethroid-resistant Anopheles vectors, methods that restore performance are urgently needed to eliminate any risk of...

Data from: Discharge communication for chronic disease patients in three hospitals in India

Claire Humphries, Suganthi Jaganathan, Jeemon Panniyammakal, Sanjeev Singh, Prabhakaran Dorairaj, Malcolm Price, Paramjit Gill, Sheila Greenfield, Richard Lilford & Semira Manaseki-Holland
OBJECTIVES Poor discharge communication is associated with negative health outcomes in high-income countries. However, quality of discharge communication has received little attention in India and many other low and middle-income countries. Primary Objective To investigate verbal and documented discharge communication for chronic non-communicable disease (NCD) patients. Secondary objective To explore the relationship between quality of discharge communication and health outcomes. METHODS: Design Prospective study. Setting: Three public hospitals in Himachal Pradesh and Kerala states, India....

Subspecies variation of Daucus carota coastal (“gummifer”) morphotypes (Apiaceae) using genotyping-by-sequencing

Fernando Martínez-Flores, Manuel B. Crespo, Philipp W. Simon, Holly Ruess, Kathleen Reitsma, Emmanuel Geoffriau, Charlotte Allender, Najla Mezghani & David M. Spooner
The genus Daucus is widely distributed worldwide, but with a concentration of diversity in the Mediterranean Region. The D. carota complex presents the greatest taxonomic problems in the genus. We focus on a distinctive phenotypic group of coastal morphotypes of D. carota, strictly confined to the margins to within about 0.5 km of the Mediterranean Sea and the Atlantic Ocean, which we here refer to as coastal morphotypes or D. carota subsp. “gummifer” complex, the...

Plant circadian clock control of Medicago truncatula nodulation involving regulation of Nodule Cysteine-Rich genes

Miriam Gifford & Beatriz Lagunas
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset...

Data from: A new model for ancient DNA decay based on paleogenomic meta-analysis

Logan Kistler, Roselyn Ware, Oliver Smith, Matthew Collins & Robin G. Allaby
The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for...

Data from: Deep learning for bridge load capacity estimation in post-disaster and -conflict zones

Arya Pamuncak, Weisi Guo, Ahmed Soliman Khaled & Irwanda Laory
Many post-disaster and -conflict regions do not have sufficient data on their transportation infrastructure assets, hindering both mobility and reconstruction. In particular, as the number of aging and deteriorating bridges increase, it is necessary to quantify their load characteristics in order to inform maintenance and prevent failure. The load carrying capacity and the design load are considered as the main aspects of any civil structures. Human examination can be costly and slow when expertise is...

Data and scripts from: Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava

Marcelo F. Simon, J. Moises Mendoza F., Márcio Lacerda Lopes Martins, Sergei V. Drovetski, Natalia A. S. Przelomska, Hope Loiselle, Taciana B. Cavalcanti, Peter W. Inglis, Natalie G. Mueller, Robin G. Allaby, Fábio De Oliveira Freitas & Logan Kistler
The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only ~6Mya have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved. Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. We find that two recently described species from northeast...

How distorted food prices discourage a healthy diet

Thijs Van Rens, Roberto Pancrazi & Marija Vukotic
Public policy making for the prevention of diet-related disease is impeded by a lack of evidence on whether poor diets are a matter of personal responsibility or a choice set narrowed by environmental conditions. An important element of the environment are market imperfections in food retail that distort prices. We use a rich dataset on quantities and prices of food purchases in the US and a structural model of dietary choices to examine variation in...

Calponin-Homology Domain mediated bending of membrane associated actin filaments

Saravanan Palani, Mohan Balasubramanian & Darius Vasco Köster
This dataset contains data from experiments described in 'Palani S, Ghosh S, Ivorra-Molla E, Clarke S, Suchenko A, Balasubramanian MK, Köster DV. 2021. Calponin-homology domain mediated bending of membrane associated actin filaments. Elife 10. doi:10.7554/eLife.61078'. This dataset consists of fluorescence microscopy images obtained by total internal reflection fluorescence (TIRF) microscopy. Using an in vitro approach, we studied the effect of the IQGAP protein fragment Rng2(1-189) on the geometry of actin filaments when tethered to supported...

Data from: Comparative and population mitogenomic analyses of Madagascar’s extinct, giant ‘subfossil’ lemurs

Logan Kistler, Aakrosh Ratan, Laurie R. Godfrey, Brooke E. Crowley, Cris E. Hughes, Runhua Lei, Yinqui Cui, Mindy L. Wood, Kathleen M. Muldoon, Haingoson Andriamialison, John J. McGraw, Lynn P. Tomsho, Stephan C. Schuster, Webb Miller, Edward E. Louis, Anne D. Yoder, Ripan S. Malhi, George H. Perry & Yinqiu Cui
Humans first arrived on Madagascar only a few thousand years ago. Subsequent habitat destruction and hunting activities have had significant impacts on the island's biodiversity, including the extinction of megafauna. For example, we know of 17 recently extinct ‘subfossil’ lemur species, all of which were substantially larger (body mass ∼11–160 kg) than any living population of the ∼100 extant lemur species (largest body mass ∼6.8 kg). We used ancient DNA and genomic methods to study...

Data from: Fractal measures of spatial pattern as a heuristic for return rate in vegetative systems

Michael A. Irvine, Emma L. Jackson, Emma J. Kenyon, Kevan J. Cook, Matthew J. Keeling & James C. Bull
Measurement of population persistence is a long-standing problem in ecology; in particular, whether it is possible to gain insights into persistence without long time-series. Fractal measurements of spatial patterns, such as the Korcak exponent or boundary dimension, have been proposed as indicators of the persistence of underlying dynamics. Here we explore under what conditions a predictive relationship between fractal measures and persistence exists. We combine theoretical arguments with an aerial snapshot and time series from...

Data from: Functional morphology and efficiency of the antenna cleaner in Camponotus rufifemur ants

Alexander Hackmann, Henry Delacave, Adam Robinson, David Labonte & Walter Federle
Contamination of body surfaces can negatively affect many physiological functions. Insects have evolved different adaptations for removing contamination, including surfaces that allow passive self-cleaning and structures for active cleaning. Here, we study the function of the antenna cleaner in Camponotus rufifemur ants, a clamp-like structure consisting of a notch on the basitarsus facing a spur on the tibia, both bearing cuticular ‘combs’ and ‘brushes’. The ants clamp one antenna tightly between notch and spur, pull...

Data from: DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities

Shashank Keshavmurthy, Sung-Yin Yang, Ada Alamaru, Yao-Yang Chuang, Michel Pichon, David Obura, Silvia Fontana, Stephane De Palmas, Fabrizio Stefani, Francesca Benzoni, Angus MacDonald, Annika M. E. Noreen, Chienshun Chen, Carden C. Wallace, Ruby M. Pillay, Vianney Denis, Affendi Yang Amri, James D. Reimer, Takuma Mezaki, Charles Sheppard, Yossi Loya, Avidor Abelson, Mohammed S. Mohammed, Andrew C. Baker, Pargol G. Mostafavi … & Chaolun A. Chen
Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar- Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four...

Data from: Long-term and trans-generational effects of neonatal experience on sheep behaviour

Michael Mendl, Corinna Clark, Joanna Murrell, Mia Fernyhough & Treasa O'Rourke
Early life experiences can have profound long-term, and sometimes trans-generational, effects on individual phenotypes. However, there is a relative paucity of knowledge about effects on pain sensitivity, even though these may impact on an individual's health and welfare, particularly in farm animals exposed to painful husbandry procedures. Here, we tested in sheep whether neonatal painful and non-painful challenges can alter pain sensitivity in adult life, and also in the next generation. Ewes exposed to tail-docking...

Data from: Resilience or robustness: identifying topological vulnerabilities in rail networks

Alessio Pagani, Guillem Mosquera, Aseel Alturki, Samuel Johnson, Stephen Jarvis, Alan Wilson, Weisi Guo & Liz Varga
Many critical infrastructure systems have network structure and are under stress. Despite their national importance, the complexity of large-scale transport networks means we do not fully understand their vulnerabilities to cascade failures. The research in this paper examines the interdependent rail networks in Greater London and surrounding commuter area. We focus on the morning commuter hours, where the system is under the most demand stress. There is increasing evidence that the topological shape of the...

Data from: Spatially coordinated dynamic gene transcription in living pituitary tissue

Karen Featherstone, Kirsty Hey, Hiroshi Momiji, Anne V. McNamara, Amanda L. Patist, Joanna Woodburn, David G. Spiller, Helen C. Christian, Alan S. McNeilly, John J. Mullins, Barbel F. Finkenstadt, David A. Rand, Michael R. H. White & Julian R. E. Davis
Transcription at individual genes in single cells is often pulsatile and stochastic. A key question emerges regarding how this behaviour contributes to tissue phenotype, but it has been a challenge to quantitatively analyse this in living cells over time, as opposed to studying snap-shots of gene expression state. We have used imaging of reporter gene expression to track transcription in living pituitary tissue. We integrated live-cell imaging data with statistical modelling for quantitative real-time estimation...

Thesis code: Stochastic modelling and projection of age-specific fertility rates

Joanne Ellison
This dataset contains R code and Stan files to perform analyses in Chapters 2, 3 and 4 of the PhD thesis entitled 'Stochastic modelling and projection of age-specific fertility rates' awarded by the University of Southampton in 2021. See the readme file for further information.

Statistical analysis code for output from a model used to simulate foot-and-mouth disease dynamics in the United Kingdom

Rachel Seibel, Amanda Meadows, Jean Contina, Christopher Mundt & Michael Tildesley
Epidemics can sometimes be managed through reductions of host density, such as social distancing for human diseases, reducing plant density through cultural and genetic means, and host culling for epizootics. These approaches allow for a certain density of hosts to remain within a targeted area. By contrast, total ring depopulation is often used as a management strategy for emerging infectious diseases in livestock. In this study, we explore the trade-offs of a density-based culling strategy...

Data from: Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane

Julien Venail, Paolo Da Silva Santos, Joao Manechini, Leonardo Alves, Maximiliano Scarpari, Thais Falcao, Elisson Romanel, Michael Brito, Renato Vicentini, Luciana Pinto & Stephen Jackson
Sugarcane (Saccharum spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes, two MOTHER OF FT AND TFL (MFT)-like genes, and four...

Data for: Feedback between coevolution and epidemiology can help or hinder the maintenance of genetic variation in host-parasite models

Ailene MacPherson, Matthew Keeling & Sarah Otto
Antagonistic coevolution has long been suggested to help maintain host genetic variation. While, ecological and epidemiological feedbacks are known to have important consequences on coevolutionary allele frequency dynamics, their effects on the maintenance of genetic variation remains poorly understood.Here, we extend our previous work on the maintenance of genetic variation in a classic matching-alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to...

Blood pressure and dementia

Ruth Peters, Jane Warwick, Kaarin J. Anstey & Craig S. Anderson
High blood pressure (BP) has been associated with an increased risk of cerebrovascular disease, stroke, and Alzheimer disease pathology. Epidemiologic studies are consistent in showing that high BP, particularly in midlife, is a risk factor for the development of dementia in late life. However, supporting randomized evidence of the inference that BP-lowering therapy can prevent dementia has been slow in coming over the last 30 years. The most recent randomized trial, the Systolic Blood Pressure...

Data from: Global network centrality of university rankings

Weisi Guo, Marco Del Vecchio & Ganna Pogrebna
Universities and higher education institutions form an integral part of the national infrastructure and prestige. As academic research benefits increasingly from international exchange and cooperation, many universities have increased investment in improving and enabling their global connectivity. Yet, the relationship of university performance and its global physical connectedness has not been explored in detail. We conduct the first large-scale data-driven analysis into whether there is a correlation between university relative ranking performance and its global...

Data from: Multi-proxy evidence highlights a complex evolutionary legacy of maize in South America

Logan Kistler, S. Yoshi Maezumi, Jonas Gregorio De Souza, Natalia A. S. Przelomska, Flaviane Malaquias Costa, Oliver Smith, Hope Loiselle, Jazmín Ramos-Madrigal, Nathan Wales, Eduardo Rivail Ribeiro, Ryan R. Morrison, Claudia Grimaldo, Andre P. Prous, Bernardo Arriaza, M. Thomas P. Gilbert, Fabio De Oliveira Freitas & Robin G. Allaby
Domesticated maize evolved from wild teosinte under human influences in Mexico beginning around 9,000 BP, traversed Central America by ~7,500 BP, and spread into South America by ~6,500 BP. Landrace and archaeological maize genomes from South America suggest that the ancestral population to South American maize was brought out of the domestication center in Mexico and became isolated from the wild teosinte gene pool before traits of domesticated maize were fixed. Deeply structured lineages then...

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