Autocatalytic sets in a partitioned biochemical network

In previous work, RAF theory has been developed as a tool for making theoretical progress on the origin of life question, providing insight into the structure and occurrence of self-sustaining and collectively autocatalytic sets within catalytic polymer networks. We present here an extension in which there are two "independent" polymer sets, where catalysis occurs within and between the sets, but there are no reactions combining polymers from both sets. Such an extension reflects the interaction between nucleic acids and peptides observed in modern cells and proposed forms of early life.Comment: 28 pages, 8 figure

ParticleTracker: a gui based particle tracking software

Tracking the motion of objects in a video is an important part of the analysis in a diverse range of subject disciplines (Meijering, 2012; Rahman, 2019; Rose, 2020). It enables one to automate the extraction of quantitative information about size, shape, motion etc. A number of tracking softwares exist (Bradski, 2000; D. B. Allan, 2020; J. Tineveza, 2016) to help with this process but the code can be an entry barrier. Even for researchers with the necessary skills, developing the code and optimising the parameters requires a significant investment for each new project. Open source tools that can simplify and expedite this process, whilst remaining flexible and easy to extend by the end user, would help to make particle tracking accessible to a broader range of researchers

Simulation of greenhouse gases following land-use change to bioenergy crops using the ECOSSE model : a comparison between site measurements and model predictions

This work contributes to the ELUM (Ecosystem Land Use Modelling & Soil Carbon GHG Flux Trial) project, which was commissioned and funded by the Energy Technologies Institute (ETI). We acknowledge the E-OBS data set from the EU-FP6 project ENSEMBLES (http://ensembles-eu.metoffice.com) and the data providers in the ECA&D project (http://www.ecad.eu).Peer reviewedPublisher PD

Collective behavior of composite active particles

We describe simulations of active Brownian particles carried out to explore how dynamics and clustering are influenced by particle shape. Our particles are composed of four disks, held together by springs, whose relative size can be varied. These composite objects can be tuned smoothly from having a predominantly concave to a convex surface. We show that even two of these composite particles can exhibit collective motion which modifies the effective Peclet number. We then investigate how particle geometry can be used to explain the phase behavior of many such particles

Collective behavior of composite active particles

We describe simulations of active Brownian particles carried out to explore how dynamics and clustering are influenced by particle shape. Our particles are composed of four disks, held together by springs, whose relative size can be varied. These composite objects can be tuned smoothly from having a predominantly concave to a convex surface. We show that even two of these composite particles can exhibit collective motion which modifies the effective Peclet number. We then investigate how particle geometry can be used to explain the phase behavior of many such particles

Shear bands and the evolving microstructure in a drying colloidal film studied with scanning μ-SAXS

Shear localisation in thin bands is an important process involved in the plastic deformation of materials subject to stress. This process is often sensitive to the sample microstructure (amorphous / crystalline). Here we show using the scanning μ-SAXS technique, how these different microstructures influence the plastic deformations in a drying colloidal film. In crystalline samples, the presence of an ordering transition at the compaction front was directly identified through the development of a six-fold symmetry in the scattering pattern in 20wt% samples. It is shown that plastic deformations in individual groups of particles during the compaction process can be tracked and measured in real time. Higher concentration suspensions were found to result in amorphous structures. The transition between crystalline and amorphous microstructures with initial particle concentration was also found to correlate with the appearance of shear bands. Through 2D spatial mapping of the local film structure, the presence of shear bands in the films was directly related to the microscale spatial variations in strain magnitude and compression direction. Our measurements also showed that shear bands lead to a reduction in the local particle volume fraction ~ 1-2%, indicating significant dilatancy

Expressions 2011

https://openspace.dmacc.edu/expressions/1023/thumbnail.jp

Clinical expert guidelines for the management of cough in lung cancer: report of a UK task group on cough

Background Cough is a common and distressing symptom in lung cancer patients. The clinical management of cough in lung cancer patients is suboptimal with limited high quality research evidence available. The aim of the present paper is to present a clinical guideline developed in the UK through scrutiny of the literature and expert opinion, in order to aid decision making in clinicians and highlight good practice. Methods Two systematic reviews, one focusing on the management of cough in respiratory illness and one Cochrane review specifically on cancer, were conducted. Also, data from reviews, phase II trials and case studies were synthesized. A panel of experts in the field was also convened in an expert consensus meeting to make sense of the data and make clinical propositions. Results A pyramid of cough management was developed, starting with the treatment of reversible causes of cough/specific pathology. Initial cough management should focus on peripherally acting and intermittent treatment; more resistant symptoms require the addition of (or replacement by) centrally acting and continuous treatment. The pyramid for the symptomatic management starts from the simpler and most practical regimens (demulcents, simple linctus) to weak opioids to morphine and methadone before considering less well-researched and experimental approaches. Conclusion The clinical guidelines presented aim to provide a sensible clinical approach to the management of cough in lung cancer. High quality research in this field is urgently required to provide more evidence-based recommendations

Unveiling the dynamic infrared sky with Gattini-IR

While optical and radio transient surveys have enjoyed a renaissance over the past decade, the dynamic infrared sky remains virtually unexplored. The infrared is a powerful tool for probing transient events in dusty regions that have high optical extinction, and for detecting the coolest of stars that are bright only at these wavelengths. The fundamental roadblocks in studying the infrared time-domain have been the overwhelmingly bright sky background (250 times brighter than optical) and the narrow field-of-view of infrared cameras (largest is 0.6 sq deg). To begin to address these challenges and open a new observational window in the infrared, we present Palomar Gattini-IR: a 25 sq degree, 300mm aperture, infrared telescope at Palomar Observatory that surveys the entire accessible sky (20,000 sq deg) to a depth of 16.4 AB mag (J band, 1.25μm) every night. Palomar Gattini-IR is wider in area than every existing infrared camera by more than a factor of 40 and is able to survey large areas of sky multiple times. We anticipate the potential for otherwise infeasible discoveries, including, for example, the elusive electromagnetic counterparts to gravitational wave detections. With dedicated hardware in hand, and a F/1.44 telescope available commercially and cost-effectively, Palomar Gattini-IR will be on-sky in early 2017 and will survey the entire accessible sky every night for two years. We present an overview of the pathfinder Palomar Gattini-IR project, including the ambitious goal of sub-pixel imaging and ramifications of this goal on the opto-mechanical design and data reduction software. Palomar Gattini-IR will pave the way for a dual hemisphere, infrared-optimized, ultra-wide field high cadence machine called Turbo Gattini-IR. To take advantage of the low sky background at 2.5 μm, two identical systems will be located at the polar sites of the South Pole, Antarctica and near Eureka on Ellesmere Island, Canada. Turbo Gattini-IR will survey 15,000 sq. degrees to a depth of 20AB, the same depth of the VISTA VHS survey, every 2 hours with a survey efficiency of 97%

Designing programs for eliminating canine rabies from islands: Bali, Indonesia as a case study

<p>Background: Canine rabies is one of the most important and feared zoonotic diseases in the world. In some regions rabies elimination is being successfully coordinated, whereas in others rabies is endemic and continues to spread to uninfected areas. As epidemics emerge, both accepted and contentious control methods are used, as questions remain over the most effective strategy to eliminate rabies. The Indonesian island of Bali was rabies-free until 2008 when an epidemic in domestic dogs began, resulting in the deaths of over 100 people. Here we analyze data from the epidemic and compare the effectiveness of control methods at eliminating rabies.</p> <p>Methodology/Principal Findings: Using data from Bali, we estimated the basic reproductive number, R0, of rabies in dogs, to be ~1·2, almost identical to that obtained in ten–fold less dense dog populations and suggesting rabies will not be effectively controlled by reducing dog density. We then developed a model to compare options for mass dog vaccination. Comprehensive high coverage was the single most important factor for achieving elimination, with omission of even small areas (<0.5% of the dog population) jeopardizing success. Parameterizing the model with data from the 2010 and 2011 vaccination campaigns, we show that a comprehensive high coverage campaign in 2012 would likely result in elimination, saving ~550 human lives and ~$15 million in prophylaxis costs over the next ten years.</p> <p>Conclusions/Significance: The elimination of rabies from Bali will not be achieved through achievable reductions in dog density. To ensure elimination, concerted high coverage, repeated, mass dog vaccination campaigns are necessary and the cooperation of all regions of the island is critical. Momentum is building towards development of a strategy for the global elimination of canine rabies, and this study offers valuable new insights about the dynamics and control of this disease, with immediate practical relevance.</p&gt