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Search Results: 1 - 10 of 3214 matches for " Neil Dalchau "
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Synthesizing and tuning chemical reaction networks with specified behaviours
Neil Dalchau,Niall Murphy,Rasmus Petersen,Boyan Yordanov
Computer Science , 2015, DOI: 10.1007/978-3-319-21999-8_2
Abstract: We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First, we identify candidate CRNs that have the possibility to produce correct computations for a given finite set of inputs. We then optimise the reaction rates of each CRN using a combination of stochastic search techniques applied to the chemical master equation, simultaneously improving the of correct behaviour and ruling out spurious solutions. In addition, we use techniques from continuous time Markov chain theory to study the expected termination time for each CRN. We illustrate our approach by identifying CRNs for majority decision-making and division computation, which includes the identification of both known and unknown networks.
A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization
Neil Dalchau ,Andrew Phillips ,Leonard D. Goldstein,Mark Howarth,Luca Cardelli,Stephen Emmott,Tim Elliott,Joern M. Werner
PLOS Computational Biology , 2011, DOI: 10.1371/journal.pcbi.1002144
Abstract: Major Histocompatibility Complex (MHC) class I molecules enable cytotoxic T lymphocytes to destroy virus-infected or cancerous cells, thereby preventing disease progression. MHC class I molecules provide a snapshot of the contents of a cell by binding to protein fragments arising from intracellular protein turnover and presenting these fragments at the cell surface. Competing fragments (peptides) are selected for cell-surface presentation on the basis of their ability to form a stable complex with MHC class I, by a process known as peptide optimization. A better understanding of the optimization process is important for our understanding of immunodominance, the predominance of some T lymphocyte specificities over others, which can determine the efficacy of an immune response, the danger of immune evasion, and the success of vaccination strategies. In this paper we present a dynamical systems model of peptide optimization by MHC class I. We incorporate the chaperone molecule tapasin, which has been shown to enhance peptide optimization to different extents for different MHC class I alleles. Using a combination of published and novel experimental data to parameterize the model, we arrive at a relation of peptide filtering, which quantifies peptide optimization as a function of peptide supply and peptide unbinding rates. From this relation, we find that tapasin enhances peptide unbinding to improve peptide optimization without significantly delaying the transit of MHC to the cell surface, and differences in peptide optimization across MHC class I alleles can be explained by allele-specific differences in peptide binding. Importantly, our filtering relation may be used to dynamically predict the cell surface abundance of any number of competing peptides by MHC class I alleles, providing a quantitative basis to investigate viral infection or disease at the cellular level. We exemplify this by simulating optimization of the distribution of peptides derived from Human Immunodeficiency Virus Gag-Pol polyprotein.
Ten Simple Rules for Effective Computational Research
James M. Osborne ,Miguel O. Bernabeu,Maria Bruna,Ben Calderhead,Jonathan Cooper,Neil Dalchau,Sara-Jane Dunn,Alexander G. Fletcher,Robin Freeman,Derek Groen,Bernhard Knapp,Greg J. McInerny,Gary R. Mirams,Joe Pitt-Francis,Biswa Sengupta,David W. Wright,Christian A. Yates,David J. Gavaghan,Stephen Emmott,Charlotte Deane
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003506
The Globalization-Deglobalization Policy Conundrum  [PDF]
Neil Dias Karunaratne
Modern Economy (ME) , 2012, DOI: 10.4236/me.2012.34048
Abstract: The dynamic process of economic globalization and deglobalization has been occurring in “waves” over the past 250 years. Diffusion models reveal how globalization policies occupy the policy-centre stage when the global economy is booming and is cast on the back-burner when the global economy nose-dives into a slump. According to the diffusion models, when the global economy is booming the nodes that establish crucial linkages in the economy exceed the social optimum generating negative externalities thereby eroding social welfare in such a context policy intervention is justified to reduce the linkages that facilitate the spread of negative shocks or contagion that reduce the capacity for risk- sharing. The globalization-deglobalization policy conundrum also resurfaces in relation to trade flows, cross-border capital mobility, current account sustainability and technology diffusion. The latter has exacerbate the “digital divide” that has accompanied the revolutionary changes in information and communication technology (ICT) revolution by overcoming the “tyranny of distance”. The recurrent global financial crises and speculative attacks on the currency peg have ignited the debate for reshaping the international financial architecture in order to reduce the vulnerability of the domestic economy to the disruptive effects of the global financial crises.
The Economic Value of Public Goods  [PDF]
Thaddeus Neil Cummins
Applied Mathematics (AM) , 2014, DOI: 10.4236/am.2014.518272
Abstract: This paper explores US entrepreneurial history and public budgets from President Eisenhower’s election in 1952 until the beginning of the Obama administration 2008. A mix of market forces, structural changes and a tendency toward unfettered capitalism [1] challenge diagnosis. This analysis examines these complexities with 216 business quarters of economic history. It also provides a mathematical model to characterize in broad strokes positive governance modeling for business. This work is important as economic growth ensures a nation’s ability to protect its citizens.
Royal Society Discussion Meeting: Utilising the Genome Sequence of Parasitic Protozoa
Neil Hall
Comparative and Functional Genomics , 2001, DOI: 10.1002/cfg.88
Abstract: Protozoan parasites cause some of the world’s most important diseases. Genome sequencing information is rapidly being acquired and combined with new developments in functional genome analysis to transform our understanding of parasites, and to enable new approaches to combating the diseases they cause.
Non-Gaussianity from Particle Production during Inflation
Neil Barnaby
Advances in Astronomy , 2010, DOI: 10.1155/2010/156180
Abstract: In a variety of models the motion of the inflaton may trigger the production of some non-inflaton particles during inflation, for example via parametric resonance or a phase transition. Such models have attracted interest recently for a variety of reasons, including the possibility of slowing the motion of the inflaton on a steep potential. In this review we show that interactions between the produced particles and the inflaton condensate can lead to a qualitatively new mechanism for generating cosmological fluctuations from inflation. We illustrate this effect using a simple prototype model 2(?0)22 for the interaction between the inflaton, , and iso-inflaton, . Such interactions are quite natural in a variety of inflation models from supersymmetry and string theory. Using both lattice field theory and analytical calculations, we study the production of particles and their subsequent rescatterings off the condensate (), which generates bremsstrahlung radiation of light inflaton fluctuations . This mechanism leads to observable features in the primordial power spectrum. We derive observational constraints on such features and discuss their implications for popular models of inflation. Inflationary particle production also leads to a very novel kind of nongaussian signature which may be observable in future missions.
Exercise Training for Heart Failure Patients with and without Systolic Dysfunction: An Evidence-Based Analysis of How Patients Benefit
Neil Smart
Cardiology Research and Practice , 2011, DOI: 10.4061/2011/837238
Abstract: Significant benefits can be derived by heart failure patients from exercise training. This paper provides an evidence-based assessment of expected clinical benefits of exercise training for heart failure patients. Meta-analyses and randomized, controlled trials of exercise training in heart failure patients were reviewed from a search of PubMed, Cochrane Controlled Trial Registry (CCTR), CINAHL, and EMBASE. Exercise training improves functional capacity, quality of life, hospitalization, and systolic and diastolic function in heart failure patients. Heart failure patients with preserved systolic function (HFnEF) participating in exercise training studies are more likely to be women and are 5–7 years older than their systolic heart failure (CHF) counterparts. All patients exhibit low functional capacities, although in HFnEF patients this may be age related, therefore subtle differences in exercise prescriptions are required. Published works report that exercise training is beneficial for heart failure patients with and without systolic dysfunction.
Hydroxyethylstarch 200/0.5 - the horse has bolted
Neil Soni
Critical Care , 2012, DOI: 10.1186/cc11155
Abstract: The paradox that using higher molecular weight starches to prevent organ failure might actually cause it has been an anxiety. The authors of a recent paper in Critical Care are to be congratulated for trying to nail the issue of whether hydroxyethylstarch (HES) 200/0.5 is associated with renal failure [1]. Colloids such as Dextran 40 have been similarly implicated but the culprit, this time, is allegedly the hyperoncotic higher molecular weight HES 200/0.5 [2]. In 1993 the possibility of renal effects was raised [3]. The evidence included the presence of the same osmotic nephrosis lesions that were seen with Dextran 40 and functional changes. These renal lesions are found with various colloids, not just HES, and their relevance to renal impairment is loose association rather than cause. They are lysozomes and it is suggested that while they might be a marker of early injury, they are not usually involved with functional effects and usually resolve without sequelae [4]. Perhaps not such a refined end point. Not so with either interstitial cell proliferation, which was not measured in the study by Simon and colleagues [1], nor necrosis, which was [5]. Both HES and gelatins had 'increased' acute tubular necrosis (ATN) but only HES 200/0.5 rates mention. As both haemorrhagic and septic shock can cause ATN, response to shock in animals is variable and actual histological ATN in humans is probably low, it would be wise to be cautious in attributing these histological changes to the fluid.The functional changes were first described when HES 220/0.6 given to renal donors was associated with impaired renal function in the subsequent recipients, although this was contentious [6,7]. In septic shock, HES 200/0.5 was also associated with apparent renal impairment but these are complex populations despite the simple collective title and so any findings are in the context of both relatively small and heterogenous populations and are considered by some to be inconclusive [8,9].Ther
Prevention for those who have freedom of choice – or among the choice-disabled: confronting equity in the AIDS epidemic
Neil Andersson
AIDS Research and Therapy , 2006, DOI: 10.1186/1742-6405-3-23
Abstract: AIDS prevention in southern Africa serves those who can choose their HIV risks. Promoting abstinence [1], male or female condom use [2,3], microbicides [4] or reduced concurrency [5,6] all presume that beneficiaries will be choice-enabled. Male circumcision [7], quintessentially for choice-enabled males, does not address prevention for those who are coerced to have sex, female or male.Victims of sexual abuse make up a big part of the southern Africa population. One in every ten – males and females – is sexually abused every year and one in every three has suffered sexual abuse by the age of 18 years [8]. With the exception of post-exposure prophylaxis for reported rape, no preventive strategy addresses these, the choice disabled, who might like to benefit from prevention but who are unable to do so because they do not have the power to make and to act on prevention decisions.If the shortage of prevention approaches for the choice disabled is an equity oversight, it is a singularly dangerous one. The physical risk of HIV infection to victims is increased by lack of lubrication and trauma [9,10]. Champion reported an STI rate of 47% among sexual violence victims compared with 30% in the rest of the population from which they were drawn [11]. HIV prevalence rates are much higher among young women than men: 16% compared with 5% in one South African study [12]. In another, intimate partner violence and high levels of male control in a woman's current relationship were significantly associated with HIV infection [13]. In fact dozens of studies have found HIV risk factors associated with sexual coercion and that HIV-infected people experience more sexual coercion than those who are HIV-negative [14]. But these are nearly all cross sectional studies, making it impossible to conclude that sexual violence causes HIV infection.Even so, however one looks at it, victims of sexual violence are a reservoir for infection that is not reached by existing prevention initiatives.The wo
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