2,810 research outputs found
A Study of Archiving Strategies in Multi-Objective PSO for Molecular Docking
Molecular docking is a complex optimization problem aimed at predicting the position of a ligand molecule in the active site of a receptor with the lowest binding energy. This problem can be formulated as a bi-objective optimization problem by minimizing the binding energy and the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands. In this context, the SMPSO multi-objective swarm-intelligence algorithm has shown a remarkable performance. SMPSO is characterized by having an external archive used to store the non-dominated solutions and also as the basis of the leader selection strategy. In this paper, we analyze several SMPSO variants based on different archiving strategies in the scope of a benchmark of molecular docking instances. Our study reveals that the SMPSOhv, which uses an hypervolume contribution based archive, shows the overall best performance.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech
Aseptic meningitis in a patient taking etanercept for rheumatoid arthritis: a case report
Background \ud
We report a case of a 53 year old lady recently commenced on etanercept, an anti-TNF (tumour necrosis factor) therapy for rheumatoid arthritis presenting with \ud
confusion, pyrexia and an erythematous rash. \ud
\ud
Case presentation \ud
A lumbar puncture was highly suggestive of bacterial meningitis, but CSF cultures produced no growth, and polymerase chain reactions (PCR) for all previously reported bacterial, fungal and viral causes of meningitis were negative. \ud
\ud
Conclusions \ud
This case report describes aseptic meningitis as a previously unreported complication of etanercept therapy, and serves as a reminder of the rare but potentially lifethreatening risk of serious infections in patients taking anti-TNF therapy for a variety of conditions
Assessing Code Authorship: The Case of the Linux Kernel
Code authorship is a key information in large-scale open source systems.
Among others, it allows maintainers to assess division of work and identify key
collaborators. Interestingly, open-source communities lack guidelines on how to
manage authorship. This could be mitigated by setting to build an empirical
body of knowledge on how authorship-related measures evolve in successful
open-source communities. Towards that direction, we perform a case study on the
Linux kernel. Our results show that: (a) only a small portion of developers (26
%) makes significant contributions to the code base; (b) the distribution of
the number of files per author is highly skewed --- a small group of top
authors (3 %) is responsible for hundreds of files, while most authors (75 %)
are responsible for at most 11 files; (c) most authors (62 %) have a specialist
profile; (d) authors with a high number of co-authorship connections tend to
collaborate with others with less connections.Comment: Accepted at 13th International Conference on Open Source Systems
(OSS). 12 page
Exploring pig trade patterns to inform the design of risk-based disease surveillance and control strategies
An understanding of the patterns of animal contact networks provides essential information for the design of risk-based animal disease surveillance and control strategies. This study characterises pig movements throughout England and Wales between 2009 and 2013 with a view to characterising spatial and temporal patterns, network topology and trade communities. Data were extracted from the Animal and Plant Health Agency (APHA)’s RADAR (Rapid Analysis and Detection of Animal-related Risks) database, and analysed using descriptive and network approaches. A total of 61,937,855 pigs were moved through 872,493 movements of batches in England and Wales during the 5-year study period. Results show that the network exhibited scale-free and small-world topologies, indicating the potential for diseases to quickly spread within the pig industry. The findings also provide suggestions for how risk-based surveillance strategies could be optimised in the country by taking account of highly connected holdings, geographical regions and time periods with the greatest number of movements and pigs moved, as these are likely to be at higher risk for disease introduction. This study is also the first attempt to identify trade communities in the country, information which could be used to facilitate the pig trade and maintain disease-free status across the country in the event of an outbreak
Fashion, Cooperation, and Social Interactions
Fashion plays such a crucial rule in the evolution of culture and society
that it is regarded as a second nature to the human being. Also, its impact on
economy is quite nontrivial. On what is fashionable, interestingly, there are
two viewpoints that are both extremely widespread but almost opposite:
conformists think that what is popular is fashionable, while rebels believe
that being different is the essence. Fashion color is fashionable in the first
sense, and Lady Gaga in the second. We investigate a model where the population
consists of the afore-mentioned two groups of people that are located on social
networks (a spatial cellular automata network and small-world networks). This
model captures two fundamental kinds of social interactions (coordination and
anti-coordination) simultaneously, and also has its own interest to game
theory: it is a hybrid model of pure competition and pure cooperation. This is
true because when a conformist meets a rebel, they play the zero sum matching
pennies game, which is pure competition. When two conformists (rebels) meet,
they play the (anti-) coordination game, which is pure cooperation. Simulation
shows that simple social interactions greatly promote cooperation: in most
cases people can reach an extraordinarily high level of cooperation, through a
selfish, myopic, naive, and local interacting dynamic (the best response
dynamic). We find that degree of synchronization also plays a critical role,
but mostly on the negative side. Four indices, namely cooperation degree,
average satisfaction degree, equilibrium ratio and complete ratio, are defined
and applied to measure people's cooperation levels from various angles. Phase
transition, as well as emergence of many interesting geographic patterns in the
cellular automata network, is also observed.Comment: 21 pages, 12 figure
How Gaussian competition leads to lumpy or uniform species distributions
A central model in theoretical ecology considers the competition of a range
of species for a broad spectrum of resources. Recent studies have shown that
essentially two different outcomes are possible. Either the species surviving
competition are more or less uniformly distributed over the resource spectrum,
or their distribution is 'lumped' (or 'clumped'), consisting of clusters of
species with similar resource use that are separated by gaps in resource space.
Which of these outcomes will occur crucially depends on the competition kernel,
which reflects the shape of the resource utilization pattern of the competing
species. Most models considered in the literature assume a Gaussian competition
kernel. This is unfortunate, since predictions based on such a Gaussian
assumption are not robust. In fact, Gaussian kernels are a border case
scenario, and slight deviations from this function can lead to either uniform
or lumped species distributions. Here we illustrate the non-robustness of the
Gaussian assumption by simulating different implementations of the standard
competition model with constant carrying capacity. In this scenario, lumped
species distributions can come about by secondary ecological or evolutionary
mechanisms or by details of the numerical implementation of the model. We
analyze the origin of this sensitivity and discuss it in the context of recent
applications of the model.Comment: 11 pages, 3 figures, revised versio
A child presenting with acute renal failure secondary to a high dose of indomethacin: a case report
<p>Abstract</p> <p>Introduction</p> <p>Acute renal failure caused by nonsteroidal anti-inflammatory drugs administered at therapeutic doses is generally mild, non-anuric and transitory. There are no publications on indomethacin toxicity secondary to high doses in children. The aim of this article is to describe acute renal failure secondary to a high dose of indomethacin in a child and to review an error in a supervised drug prescription and administration system.</p> <p>Case presentation</p> <p>Due to a medication error, a 20-day-old infant in the postoperative period of surgery for Fallot's tetralogy received a dose of 10 mg/kg of indomethacin, 50 to 100 times higher than the therapeutic dose. The child presented with acute, oligo-anuric renal failure requiring treatment with continuous venovenous renal replacement therapy, achieving complete recovery of renal function with no sequelae.</p> <p>Conclusion</p> <p>In order to reduce medication errors in critically ill children, it is necessary to develop a supervised drug prescription and administration system, with controls at various levels.</p
Multiple dynamical time-scales in networks with hierarchically nested modular organization
Many natural and engineered complex networks have intricate mesoscopic
organization, e.g., the clustering of the constituent nodes into several
communities or modules. Often, such modularity is manifested at several
different hierarchical levels, where the clusters defined at one level appear
as elementary entities at the next higher level. Using a simple model of a
hierarchical modular network, we show that such a topological structure gives
rise to characteristic time-scale separation between dynamics occurring at
different levels of the hierarchy. This generalizes our earlier result for
simple modular networks, where fast intra-modular and slow inter-modular
processes were clearly distinguished. Investigating the process of
synchronization of oscillators in a hierarchical modular network, we show the
existence of as many distinct time-scales as there are hierarchical levels in
the system. This suggests a possible functional role of such mesoscopic
organization principle in natural systems, viz., in the dynamical separation of
events occurring at different spatial scales.Comment: 10 pages, 4 figure
Ontology of core data mining entities
In this article, we present OntoDM-core, an ontology of core data mining
entities. OntoDM-core defines themost essential datamining entities in a three-layered
ontological structure comprising of a specification, an implementation and an application
layer. It provides a representational framework for the description of mining
structured data, and in addition provides taxonomies of datasets, data mining tasks,
generalizations, data mining algorithms and constraints, based on the type of data.
OntoDM-core is designed to support a wide range of applications/use cases, such as
semantic annotation of data mining algorithms, datasets and results; annotation of
QSAR studies in the context of drug discovery investigations; and disambiguation of
terms in text mining. The ontology has been thoroughly assessed following the practices
in ontology engineering, is fully interoperable with many domain resources and
is easy to extend
An effective all-atom potential for proteins
We describe and test an implicit solvent all-atom potential for simulations
of protein folding and aggregation. The potential is developed through studies
of structural and thermodynamic properties of 17 peptides with diverse
secondary structure. Results obtained using the final form of the potential are
presented for all these peptides. The same model, with unchanged parameters, is
furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta
protein and a three-helix-bundle protein, with very good results. The
computational efficiency of the potential makes it possible to investigate the
free-energy landscape of these 49--67-residue systems with high statistical
accuracy, using only modest computational resources by today's standards
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