14,890 Works

Data from: An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor

Yasin F. Dagdas, Khaoula Belhaj, Abbas Maqbool, Angela Chaparro-Garcia, Pooja Pandey, Benjamin Petre, Nadra Tabassum, Neftaly Cruz-Mireles, Richard K. Hughes, Jan Sklenar, Joe Win, Frank Menke, Kim Findlay, Mark J. Banfield, Sophien Kamoun & Tolga O. Bozkurt
Plants use autophagy to safeguard against infectious diseases. However, how plant pathogens interfere with autophagy related processes is unknown. Here we show that PexRD54, an effector from the Irish potato famine pathogen Phytophthora infestans, binds host autophagy protein ATG8CL to stimulate autophagosome formation. PexRD54 depletes the autophagy cargo receptor Joka2 out of ATG8CL complexes and interferes with Joka2's positive effect on pathogen defense. Thus a plant pathogen effector has evolved to antagonize a host autophagy...

Data from: A large fraction of HLA class I ligands are proteasome-generated spliced peptides

Juliane Liepe, Fabio Marino, John Sidney, Anita Jeko, Daniel E. Bunting, Alessandro Sette, Peter M. Kloetzel, Michael P. H. Stumpf, Albert J. R. Heck & Michele Mishto
The proteasome generates the epitopes presented on human leukocyte antigen (HLA) class I molecules that elicit CD8+ T cell responses. Reports of proteasome-generated spliced epitopes exist, but they have been regarded as rare events. Here, however, we show that the proteasome-generated spliced peptide pool accounts for one-third of the entire HLA class I immunopeptidome in terms of diversity and one-fourth in terms of abundance. This pool also represents a unique set of antigens, possessing particular...

Data from: Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage

Roger B. J. Benson, Nicolás E. Campione, Matthew T. Carrano, Philip D. Mannion, Corwin Sullivan, Paul Upchurch & David C. Evans
Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation,...

Data from: Spatial and temporal escape from fungal parasitism in natural communities of anciently asexual bdelloid rotifers

Christopher G. Wilson & Paul W. Sherman
Sexual reproduction is costly, but it is nearly ubiquitous among plants and animals, whereas obligately asexual taxa are rare and almost always short-lived. The Red Queen hypothesis proposes that sex overcomes its costs by enabling organisms to keep pace with coevolving parasites and pathogens. If so, the few cases of stable long-term asexuality ought to be found in groups whose coevolutionary interactions with parasites are unusually weak. In theory, antagonistic coevolution will be attenuated if...

Data from: Poor infant and young child feeding practices and sources of caregivers’ feeding knowledge in rural Hebei Province, China: findings from a cross-sectional survey

Qiong Wu, Robert W. Scherpbier, Michelle Helena Van Velthoven, Li Chen, Wei Wang, Ye Li, Yanfeng Zhang & Josip Car
Objectives: To obtain a general overview of infant and young child feeding practices in one rural county in China and identify current delivery channels and challenges. Design: A cross-sectional study. Setting: A rural county, Zhao County, in Hebei Province, China. Participants: 10 clusters were first selected within each township (16 townships in total) with proportional to population size sampling. In each cluster, a name list was used to select 13 children aged 0–23 months. We...

Data from: Sex-biased immunity is driven by relative differences in reproductive investment

Crystal M. Vincent & Darryl T. Gwynne
Sex differences in immunity are often observed, with males generally having a weaker immune system than females. However, recent data in a sex-role-reversed species in which females compete to mate with males suggest that sexually competitive females have a weaker immune response. These findings support the hypothesis that sexual dimorphism in immunity has evolved in response to sex-specific fitness returns of investment in traits such as parental investment and longevity, but the scarcity of data...

Data from: Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

Amrita Srivathsan, John C. M. Sha, Alfried P. Vogler & Rudolf Meier
Fecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet, and parasite infestation of endangered species. Direct shotgun sequencing of fecal DNA could give information on these simultaneously, but this approach is largely untested. Here we use two fecal samples to characterize the diet of two Red-Shanked Doucs Langurs (Pygathrix nemaeus) that were fed a known combination of foliage, fruits, vegetables and cereals. Illumina HiSeq sequencing...

Data from: A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets

Tomochika Fujisawa, Amr Aswad & Timothy G. Barraclough
Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable...

Data from: Cough frequency during treatment associated with baseline cavitary volume and proximity to the airway in pulmonary TB

Alvaro Proaño, David P. Bui, José W. López, Nancy M. Vu, Marjory A. Bravard, Gwenyth O. Lee, Brian H. Tracey, Ziyue Xu, Germán Comina, Eduardo Ticona, Daniel J. Mollura, Jon S. Friedland, David A. J. Moore, Carlton A. Evans, Philip Caligiuri, Robert H. Gilman & Tuberculosis Working Group In Peru
Background: Cough frequency, and its duration, is a lab-free biomarker that can be used in low-resource settings and has been associated with transmission and treatment response. Radiological characteristics associated with increased cough frequency may be important in understanding transmission. The relationship between cough frequency and cavitary lung disease has never been studied. Methods: We analyzed 41 human immunodeficiency virus-negative adults with culture-confirmed, drug-susceptible pulmonary tuberculosis throughout treatment. Cough recordings were based on the Cayetano Cough...

Data from: Pathogeography: leveraging the biogeography of human infectious diseases for global health management

Kris A. Murray, Jesús Olivero, Benjamin Roche, Sonia Tiedt & Jean-François Guégan
Biogeography is an implicit and fundamental component of almost every dimension of modern biology, from natural selection and speciation to invasive species and biodiversity management. However, biogeography has rarely been integrated into human or veterinary medicine nor routinely leveraged for global health management. Here we review the theory and application of biogeography to the research and management of human infectious diseases, an integration we refer to as ‘pathogeography’. Pathogeography represents a promising framework for understanding...

Data from: Pesticide exposure affects flight dynamics and reduces flight endurance in bumblebees

Daniel Kenna, Hazel Cooley, Ilaria Pretelli, Ana Ramos Rodrigues, Steve D. Gill & Richard J. Gill
The emergence of agricultural land use change creates a number of challenges that insect pollinators, such as eusocial bees, must overcome. Resultant fragmentation and loss of suitable foraging habitats, combined with pesticide exposure, may increase demands on foraging, specifically the ability to collect or reach sufficient resources under such stress. Understanding effects that pesticides have on flight performance is therefore vital if we are to assess colony success in these changing landscapes. Neonicotinoids are one...

Data from: A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan

Imran Rahman, Jeffrey Thompson, Derek Briggs, David Siveter, Derek Siveter & Mark Sutton
Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, Sollasina cthulhu, from the Silurian Herefordshire Lagerstätte, UK. S. cthulhu belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical-optical...

Data from: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study

Lina Cai, Eleanor Wheeler, Nicola D. Kerrison, Jian'an Luan, Panos Deloukas, Paul W. Franks, Pilar Amiano, Eva Ardanaz, Catalina Bonet, Guy Fagherazzi, Leif C. Groop, Rudolf Kaaks, José María Huerta, Giovanna Masala, Peter M. Nilsson, Kim Overvad, Valeria Pala, Salvatore Panico, Miguel Rodriguez-Barranco, Olov Rolandsson, Carlotta Sacerdote, Matthias B. Schulze, Annemieke M.W. Spijkeman, Anne Tjonneland, Rosario Tumino … & Nicholas J. Wareham
Type 2 diabetes (T2D) is a global public health challenge. Whilst the advent of genome-wide association studies has identified >400 genetic variants associated with T2D, our understanding of its biological mechanisms and translational insights is still limited. The EPIC-InterAct project, centred in 8 countries in the European Prospective Investigations into Cancer and Nutrition study, is one of the largest prospective studies of T2D. Established as a nested case-cohort study to investigate the interplay between genetic...

Predicting the impact of patient and private provider behaviour on diagnostic delay for pulmonary tuberculosis patients in India: A simulation modelling approach

Sarang Deo, Simrita Singh, Neha Jha, Nimalan Arinaminpathy & Puneet Dewan
Background TB incidence in India continues to be high due, in large part, to long delays experienced by patients before successful diagnosis and treatment initiation, especially in the private sector. This diagnostic delay is driven by patients’ inclination to switch between different type of providers and providers’ inclination to delay ordering of accurate diagnostic tests relevant to TB. Our objective is to quantify the impact of changes in these behavioural characteristics of providers and patients...

Data from: Quantifying team cooperation through intrinsic multi-scale measures: respiratory and cardiac synchronisation in choir singers and surgical teams

Apit Hemakom, Katarzyna Powezka, Valentin Goverdovsky, Usman Jaffer & Danilo P. Mandic
A highly localised data-association measure, termed intrinsic synchrosqueezing transform (ISC), is proposed for the analysis of coupled nonlinear and nonstationary multivariate signals. This is achieved based on a combination of noise-assisted multivariate empirical mode decomposition (NA-MEMD) and short-time Fourier transform (STFT)-based univariate and multivariate synchrosqueezing transforms (FSST and F-MSST). It is shown that the ISC outperforms six other combinations of algorithms in estimating degrees of synchrony in synthetic linear and nonlinear bivariate signals. Its advantage...

Data from: Bird and bat species' global vulnerability to collision mortality at wind farms revealed through a trait-based assessment

Chris B. Thaxter, Graeme M. Buchanan, Carr Jamie, Stuart H.M. Butchart, Tim Newbold, Rhys E. Green, Joseph A. Tobias, Wendy B. Foden, Sue O'Brien & James W. Pearce-Higgins
Mitigation of anthropogenic climate change involves deployments of renewable energy worldwide, including wind farms, which can pose a significant collision risk to volant animals. Most studies into the collision risk between species and wind turbines, however, have taken place in industrialized countries. Potential effects for many locations and species therefore remain unclear. To redress this gap, we conducted a systematic literature review of recorded collisions between birds and bats and wind turbines within developed countries....

Ecosystem emergence : an investigation of the emergence processes of six digital service ecosystems

Llewellyn Thomas
This thesis investigates processes of ecosystem emergence. Ecosystem research has thus far focused on understanding the structure and dynamics of already existing ecosystems. However much less attention has been devoted to the emergence of ecosystems. I first theoretically develop an institutional approach to ecosystems, arguing that the ecosystem is an organisational field which has value co-creation as its recognised area of institutional life. Synthesising the theories of dominant design, social movements, and institutional entrepreneurship, I...

A magnetic resonance imaging (MRI) investigation into the effects of ageing on the functional and structural connectivity of the brain

Emer Hughes
Ageing in the absence of disease is associated with reduced cognitive function. Cognitive function depends on the integrated operation of large-scale distributed brain networks. In this thesis I use structural and functional magnetic resonance imaging to test the hypothesis that age related cognitive decline arises from disruption to the integrated operation of large-scale networks, and the disrupted operation of these networks is associated with structural disconnection to white matter tracts. There are five studies presented...

A search for supersymmetry using the alphaT variable with the CMS detector and the impact of experimental searches for supersymmetry on supersymmetric parameter space

Samuel Rogerson
A search for supersymmetry in final states with jets and missing transverse energy is performed in pp collisions at a centre-of-mass energy of sqrt(s)=7TeV. The data sample corresponds to 4.98fb^-1 collected by the CMS experiment at the LHC in 2011. A dimensionless kinematic variable is used as the main discriminant between genuine and misreconstructed signal events. The search is performed in a signal region binned according to the scalar sum of the transverse energy of...

Uniform Linear Poly(ethylenimine) via Poly(oxazoline)s - Synthesis, Mechanism of Toxicity and the Role of the Free Polymer during Transfection

Bryn Monnery
Linear poly(ethylenimine) is the current “gold standard” gene transfection agent. It is synthesised via the cationic ring opening polymerisation of 2-ethyl-2-oxazoline followed by the acid catalysed hydrolysis to the hydrochloride salt. However the synthesis of the parent polymer produces a broad distribution of molecular weights. Ideally the polymer should have a narrow molecular weight distribution - it should be “uniform”. By exploring the possible side reactions it is possible to minimise them and optimise the...

Quadtree Structured Approximation Algorithms

Adam Scholefield
The success of many image restoration algorithms is often due to their ability to sparsely describe the original signal. Many sparse promoting transforms exist, including wavelets, the so called ‘lets’ family of transforms and more recent non-local learned transforms. The first part of this thesis reviews sparse approximation theory, particularly in relation to 2-D piecewise polynomial signals. We also show the connection between this theory and current state of the art algorithms that cover the...

Development and application of atomistic force fields for ionic materials

Joanne Sarsam
In the field of molecular dynamics (MD), the time evolution of a set of interacting atoms is determined by integrating their equations of motion using Newton’s Second Law. By using efficient potentials that capture the essential physics of a material, the properties of systems containing tens of thousands of atoms can be accurately modelled. This thesis describes three substantial developments in the science and simulation of ionic materials. In the opening chapters, we provide an...

Synthetic approaches to improving perylene diimide-based organic electronics

Stuart John Oram
This thesis deals with the family of small molecules known as perylene diimides, their synthesis, properties, and use in organic electronics. In particular it is focussed on the use of perylene diimides as small molecular organic semiconductors in organic photovoltaics and organic field-effect transistors. Here is reported the synthesis, characterisation, properties and device testing of a range of new perylene diimide materials, designed to have properties amenable to use as acceptors in organic photovoltaics. Also...

Charge separation, triplets and photochemical stability in polymer / fullerene solar cells

Ying Soon
Charge generation and stability are key issues that have great impact upon the commercial viability of organic solar cells. In this thesis, a range of donor polymers, mainly of donor-acceptor class, were employed. Various materials characterisation, photophysical and photostability studies were performed on neat polymer films and polymer/fullerene blend films with the aim of establishing relationships between material structure and device function/stability. Transient absorption spectroscopy (TAS) was employed for the photophysical studies on neat films....

Investigating inhomogeneous FM at SC/FM interfaces using point-contact Andreev spectroscopy

Irham Tri Muharram Usman
The unconventional long range (m=1) spin triplet proximity effect is theorised to be created at a Superconductor/Ferromagnet (SC/FM) interface that is magnetically inhomogeneous and provides the conditions for spin mixing. Many experimental and theoretical works have identified the existence of the m=1 spin triplet state using Josephson junctions to show how the critical current does not diminish significantly in a thick FM layer, (thickness being relative to the decay length of a Cooper pair in...

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