37,847 Works

The InterMine Android app: Cross-organism genomic data in your pocket

Daria Komkova, Rachel Lyne, Julie Sullivan, Yo Yehudi & Thomas Micklem
InterMine is a data integration and analysis software system that has been used to create both inter-connected and stand-alone biological databases for the analysis of large and complex biological data sets. Together, the InterMine databases provide access to extensive data across multiple organisms. To provide more convenient access to these data from Android mobile devices, we have developed the InterMine app, an application that can be run on any Android mobile phone or tablet. The...

Sampling Configurational Energy Landscapes

Matthew Griffiths
The computational analysis of high dimensional surfaces is a fundamental problem across a wide range of scientific fields, for example in the study of models of clusters of atoms, glasses, self-assembling systems, and biomolecules; machine learning; physics; and other fields. This work presents a variety of novel methods developed to aid the computational study of the structures, dynamics, and thermodynamics of systems described by these surfaces, traditionally termed energy landscapes. When studying molecular systems, it...

The virtues of small grain size: Potential pathways to a distinguishing feature of Asian wheats

X Liu, Diane Lister, Z Zhao, RA Staff, PJ Jones, L Zhou, AK Pokharia, Cameron Petrie, A Pathak, H Lu, GM Matuzeviciute, Jennifer Bates, TK Pilgram & Martin Jones
Increase in grain/seed size recurrently features as a key element in the ‘domestication syndrome’ of plants (cf. Zohary and Hopf 2000; Fuller et al. 2014). In the context of its spread across Eurasia, however, the grain size of one of the world's major crop species underwent a substantial reduction. Between the fifth and second millennia BC, the grain length in a number of species of Triticum, collectively known as free-threshing wheat, decreased by around 30%....

Constraints on mediator-based dark matter and scalar dark energy models using root s= 13 TeV pp collision data collected by the ATLAS detector

M Aaboud, G Aad, B Abbott, DC Abbott, O Abdinov, A Abed Abud, DK Abhayasinghe, SH Abidi, OS AbouZeid, NL Abraham, H Abramowicz, H Abreu, Y Abulaiti, BS Acharya, S Adachi, L Adam, C Adam Bourdarios, L Adamczyk, L Adamek, J Adelman, M Adersberger, A Adiguzel, S Adorni, T Adye, AA Affolder … & ATLAS Collaboration

Measuring Aerosol Phase Changes and Hygroscopicity with a Microresonator Mass Sensor.

Arthur Zielinski, Peter Gallimore, Paul Griffiths, Roderic Jones, Ashwin Seshia & Markus Kalberer
The interaction between atmospheric aerosol particles and water vapor influences aerosol size, phase and composition, pa-rameters which critically influence their impacts in the atmosphere. Methods to accurately measure aerosol water uptake for a wide range of particle types are therefore merited. We present here a new method for characterizing aerosol hygroscopici-ty, an impaction stage containing a MicroElectroMechanical Systems (MEMS) microresonator. We find that deliquescence and efflorescence relative humidities (RHs) of sodium chloride and ammonium sulfate...

Strigolactone regulates shoot development through a core signalling pathway.

Thomas Bennett, Y Liang, Madeleine Seale, Sally Ward, D Müller & Henrietta Leyser
Strigolactones are a recently identified class of hormone that regulate multiple aspects of plant development. The DWARF14 (D14) α/β fold protein has been identified as a strigolactone receptor, which can act through the SCF^MAX2 ubiquitin ligase, but the universality of this mechanism is not clear. Multiple proteins have been suggested as targets for strigolactone signalling, including both direct proteolytic targets of SCF^MAX2, and downstream targets. However, the relevance and importance of these proteins to strigolactone...

The role of cryptotephra in refining the chronology of Late Pleistocene human evolution and cultural change in North Africa

RNE Barton, Christine Lane, PG Albert, D White, SN Collcutt, A Bouzouggar, P Ditchfield, Lucy Farr, A Oh, L Ottolini, VC Smith, P Van Peer & K Kindermann
© 2014.Sites in North Africa hold key information for dating the presence of Homo sapiens and the distribution of Middle Stone Age (MSA), Middle Palaeolithic (MP) and Later Stone Age (LSA) cultural activity in the Late Pleistocene. Here we present new and review recently published tephrochronological evidence for five cave sites in North Africa with long MSA/MP and LSA cultural sequences. Four tephra horizons have been identified at the Haua Fteah (Cyrenaica, Libya). They include...

Code supporting "A new processing scheme for ultra-high resolution direct infusion mass spectrometry data"

Arthur Zielinski, Markus Kalberer, C Bortolini, C Giorio, SJ Fuller, I Kourtchev & Olalekan Popoola
Set of scripts used to process direct infusion mass spectrometry data as described in the associated paper. Scripts written and run using Wolfram Mathematica (confirmed with versions 10.2 to 11.1). Assumes raw data matches format produced by a LTQ Orbitrap Velos mass spectrometer and exported by the proprietary software (Xcalibur) to a comma-separated values (.csv) file. The .csv files are the expected input into the Mathematica scripts.

Prospective motion correction improves the sensitivity of fMRI pattern decoding.

Pei Huang, Johan Carlin, Arjen Alink, Nikolaus Kriegeskorte, Richard Henson & Marta M Correia
We evaluated the effectiveness of prospective motion correction (PMC) on a simple visual task when no deliberate subject motion was present. The PMC system utilizes an in-bore optical camera to track an external marker attached to the participant via a custom-moulded mouthpiece. The study was conducted at two resolutions (1.5mm vs 3mm) and under three conditions (PMC On and Mouthpiece On vs PMC Off and Mouthpiece On vs PMC Off and Mouthpiece Off). Multiple data...

A Mother's Joy at Her Child's Death: Conversion, Cognitive Dissonance, and Grief

Simon Goldhill
This article explores how a sophisticated woman, Minnie Benson, could have rejoiced when her beloved son died at school at age 18. Her joyous reaction—remarked on by all her family—is in stark contrast to that of her husband, Bishop Edward White Benson, who was devastated by the death and found it the most dismaying challenge to his deeply-felt faith. Her reaction is investigated in particular through her personal Evangelical conversion and her commitment to believing...

Semi-Interpenetrating Polymer Networks for Enhanced Supercapacitor Electrodes

Kara Fong, Tiesheng Wang, Hyunkyung Kim, Ramachandran Kumar & Stoyan Smoukov
Conducting polymers show great promise as supercapacitor materials due to their high theoretical specific capacitance, low cost, toughness, and flexibility. Poor ion mobility, however, can render active material more than a few tens of nanometers from the surface inaccessible for charge storage, limiting performance. Here, we use semi-interpenetrating networks (sIPNs) of a pseudocapacitive polymer in an ionically conductive polymer matrix to decrease ion diffusion length scales and make virtually all of the active material accessible...

Cytokinin Targets Auxin Transport to Promote Shoot Branching.

Tanya Waldie & Henrietta Leyser
Cytokinin promotes shoot branching by activating axillary buds, but its mechanism of action in this process is unclear. We have previously shown that a hextuple mutant lacking a clade of type-A Arabidopsis Response Regulators (ARRs) known to act in cytokinin signalling has reduced shoot branching compared to wild type. Since these proteins typically act as negative regulators of cytokinin signalling, this is an unexpected result. To explore this paradox more deeply, we characterised the effects...

Compositional Analysis of Adsorbed Organic Aerosol on a Microresonator Mass Sensor

Arthur Zielinski, Steven Campbell, Ashwin Seshia, Roderic Jones, Markus Kalberer & Chiara Giorio
Aerosol mass measurements are a key air pollution parameter that is regulated in most countries. Beyond mass measurements, the precise composition of the aerosol is essential in identifying sources and impacts on health and climate. The conventional method for simultaneously quantifying mass and composition is to collect aerosol onto filter or impactor samples followed by laboratory analysis. This approach requires long collection times – providing poor time resolution for mass measurements – and long sample...

Comprehensive modeling study of ozonolysis of oleic acid aerosol based on real-time, online measurements of aerosol composition

Peter Gallimore, Paul Griffiths, FD Pope, JP Reid & Markus Kalberer
The chemical composition of organic aerosols profoundly influences their atmospheric properties, but a detailed understanding of heterogeneous and in-particle reactivity is lacking. We present here a combined experimental and modeling study of the ozonolysis of oleic acid particles. An online mass spectrometry (MS) method, Extractive Electrospray Ionization (EESI), is used to follow the composition of the aerosol at a molecular level in real time; relative changes in the concentrations of both reactants and products are...

Buckwheat: a crop from outside the major Chinese domestication centres? A review of the archaeobotanical, palynological and genetic evidence

Harriet Hunt, X Shang & Martin Jones
The two cultivated species of buckwheat, Fagopyrum esculentum (common buckwheat) and F. tataricum (Tartary buckwheat) are Chinese domesticates whose origins are usually thought to lie in upland southwestern China, outside the major centres of agricultural origins associated with rice and millet. Synthesis of the macro- and microfossil evidence for buckwheat cultivation in China found just 26 records across all time periods, of which the majority are pollen finds. There are few or no identifying criteria...

Additive Manufacturing of Biomechanically Tailored Meshes for Compliant Wearable and Implantable Devices

Sebastian Pattinson, Meghan Huber, Sanha Kim, Jongwoo Lee, Sarah Grunsfeld, Ricardo Roberts, Gregory Dreifus, Christoph Meier, Liu Lei, Neville Hogan & John Hart
Additive manufacturing (AM) of medical devices such as orthopedic implants and hearing aids is highly attractive because of AM’s potential to match the complex form and mechanics of individual human bodies. Externally worn and implantable tissue-support devices, such as ankle or knee braces, and hernia repair mesh, offer a new opportunity for AM to mimic tissue-like mechanics and improve both patient outcomes and comfort. Here, it is demonstrated how explicit programming of the toolpath in...

Research data supporting "Cartilage-like electrostatic stiffening of responsive cryogel scaffolds

Giovanni Offeddu, Ioanna Mela, P Jeggle, Robert Henderson, SK Smoukov & Michelle Oyen
The following data files are provided: Summary of results: numerical values used to plot each figure in the manuscript, as well as values used to calculate each parameter when applicable. Raw macroindentation and microindentation data: the load vs. time curves obtained by spherical indentation on a universal testing machine and on an AFM. Confocal data: contains representative confocal datasets, presented as .lsm files, for each physical cryogel sample in the neutral and activated states. READ...

Currency regimes and the carry trade

O Accominotti, J Cen, Alan Chambers & IW Marsh
This study exploits a new long-run data set of daily bid and offered exchange rates in spot and forward markets from 1919 to the present to analyze carry returns in fixed and floating currency regimes. We first find that outsized carry returns occur exclusively in the floating regime, being zero in the fixed regime. Second, we show that fixed-to-floating regime shifts are associated with negative returns to a carry strategy implemented only on floating currencies,...

From Secure Messaging to Secure Collaboration

Martin Kleppmann, Stephan Alexander Kollmann, Diana-Alexandra Vasile & Alastair Beresford
© 2018, Springer Nature Switzerland AG. We examine the security of collaboration systems, where several users access and contribute to some shared resource, document, or database. To protect such systems against malicious servers, we can build upon existing secure messaging protocols that provide end-to-end security. However, if we want to ensure the consistency of the shared data in the presence of malicious users, we require features that are not available in existing messaging protocols. We...

Genetic evidence for a western Chinese origin of broomcorn millet (Panicum miliaceum).

Harriet Hunt, Anna Rudzinski, Hongen Jiang, Ruiyun Wang, Mark G Thomas & Martin Jones
Broomcorn millet (Panicum miliaceum) is a key domesticated cereal that has been associated with the north China centre of agricultural origins. Early archaeobotanical evidence for this crop has generated two major debates: First, its contested presence in pre-7000 cal BP sites in eastern Europe has admitted the possibility of a western origin. Second, its occurrence in the 7th and 8th millennia cal BP in diverse regions of northern China is consistent with several possible origin...

A new processing scheme for ultra-high resolution direct infusion mass spectrometry data

Arthur Zielinski, Ivan Kourtchev, Claudio Bortolini, Stephen J Fuller, Chiara Giorio, Olalekan Popoola, Sara Bogialli, Andrea Tapparo, Roderic Jones & Markus Kalberer
High resolution, high accuracy mass spectrometry is widely used to characterise environmental or biological samples with highly complex composition enabling the identification of chemical composition of often unknown compounds. Despite instrumental advancements, the accurate molecular assignment of compounds acquired in high resolution mass spectra remains time consuming and requires automated algorithms, especially for samples covering a wide mass range and large numbers of compounds. A new processing scheme is introduced implementing filtering methods based on...

An ill wind? Terrorist attacks and CEO compensation

Y Dai, Raghavendra Rau, A Stouraitis & W Tan
Using multiple measures of attack proximity, we show that CEOs employed at firms located near terrorist attacks earn an average pay increase of 12% after the attack relative to CEOs at firms located far from attacks. CEOs at terrorist attack-proximate firms prefer cash-based compensation increases (e.g., salary and bonus) over equity-based compensation (e.g., options and stocks granted). The effect is causal and it is larger when the bargaining power of the CEO is high. Other...

Fine-mapping inflammatory bowel disease loci to single-variant resolution.

Hailiang Huang, Ming Fang, Luke Jostins, Maša Umićević Mirkov, Gabrielle Boucher, Carl A Anderson, Vibeke Andersen, Isabelle Cleynen, Adrian Cortes, François Crins, Mauro D'Amato, Valérie Deffontaine, Julia Dmitrieva, Elisa Docampo, Mahmoud Elansary, Kyle Kai-How Farh, Andre Franke, Ann-Stephan Gori, Philippe Goyette, Jonas Halfvarson, Talin Haritunians, Jo Knight, Ian C Lawrance, Charlie W Lees, Edouard Louis … & Jeffrey C Barrett

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