104 research outputs found
Molecular strain typing of M. tuberculosis isolates from a suspected outbreak involving a faulty bronchoscope
Mycobacterium tuberculosis lineage: a naming of the parts
There have been many reports of groups of related Mycobacterium tuberculosis strains described variously as lineages, families or clades. There is no objective definition of these groupings making it impossible to define relationships between those groups with biological advantages. Here we describe two groups of related strains obtained from an epidemiological study in Tanzania which we define as the Kilimanjaro and Meru lineages on the basis of IS6110 restriction fragment length polymorphism (RFLP), polymorphic GC rich sequence (PGRS) RFLP and mycobacterial interspersed repeat unit (MIRU) typing. We investigated the concordance between each of the typing techniques and the dispersal of the typing profiles from a core pattern. The Meru lineage is more dispersed than the Kilimanjaro lineage and we speculate that the Meru lineage is older.
We suggest that this approach provides an objective definition that proves robust in this epidemiological study. Such a framework will permit associations between a lineage and clinical or bacterial phenomenon to be tested objectively. This definition will also enable new putative lineages to be objectively tested
Uloga Ivana Merza u liturgijskoj obnovi
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189757.pdf (Publisher’s version ) (Open Access
Neural networks impedance control of robots interacting with environments
In this paper, neural networks impedance control is proposed for robot-environment interaction. Iterative learning control is developed to make the robot dynamics follow a given target impedance model. To cope with the problem of unknown robot dynamics, neural networks are employed such that neither the robot structure nor the physical parameters are required for the control design. The stability and performance of the resulted closed-loop system are discussed through rigorous analysis and extensive remarks. The validity and feasibility of the proposed method are verified through simulation studies
Molecular strain typing of M. tuberculosis isolates from a suspected outbreak involving a faulty bronchoscope
<i>Pseudomonas aeruginosa</i> intensive care unit outbreak:winnowing of transmissions with molecular and genomic typing
Bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award [grant 097831/Z/11/Z]. BJP, KO, MP, MTGH, GP and SHG are funded by the Chief Scientist Office through the Scottish Infection Research Network, a part of the SHAIPI consortium grant reference number SIRN/10.Background: Pseudomonas aeruginosa healthcare outbreaks can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical to base decisions on. Aim: We explore the usefulness of whole genome sequencing (WGS) in the investigation of a Pseudomonas aeruginosa outbreak describing how it compares with pulsed-field gel electrophoresis (PFGE) and variable number tandem repeat (VNTR) analysis. Methods: Six patient isolates and six environmental samples from an Intensive Care Unit (ICU) positive for P. aeruginosa over two years underwent VNTR, PFGE and WGS. Findings: VNTR and PFGE were required to fully determine the potential source of infection and rule out others. WGS results unambiguously distinguished linked isolates giving greater assurance of the transmission route between wash hand basin (WHB) water and two patients supporting control measures employed. Conclusion: WGS provided detailed information without need for further typing. When allied to epidemiological information it can be used to understand outbreak situations rapidly and with certainty. Implementation of WGS in real-time would be a major advance in day-to-day practice. It could become a standard of care as it becomes more widespread due to its reproducibility and reduction in costs.Publisher PDFPeer reviewe
Ab initio atomistic thermodynamics and statistical mechanics of surface properties and functions
Previous and present "academic" research aiming at atomic scale understanding
is mainly concerned with the study of individual molecular processes possibly
underlying materials science applications. Appealing properties of an
individual process are then frequently discussed in terms of their direct
importance for the envisioned material function, or reciprocally, the function
of materials is somehow believed to be understandable by essentially one
prominent elementary process only. What is often overlooked in this approach is
that in macroscopic systems of technological relevance typically a large number
of distinct atomic scale processes take place. Which of them are decisive for
observable system properties and functions is then not only determined by the
detailed individual properties of each process alone, but in many, if not most
cases also the interplay of all processes, i.e. how they act together, plays a
crucial role. For a "predictive materials science modeling with microscopic
understanding", a description that treats the statistical interplay of a large
number of microscopically well-described elementary processes must therefore be
applied. Modern electronic structure theory methods such as DFT have become a
standard tool for the accurate description of individual molecular processes.
Here, we discuss the present status of emerging methodologies which attempt to
achieve a (hopefully seamless) match of DFT with concepts from statistical
mechanics or thermodynamics, in order to also address the interplay of the
various molecular processes. The new quality of, and the novel insights that
can be gained by, such techniques is illustrated by how they allow the
description of crystal surfaces in contact with realistic gas-phase
environments.Comment: 24 pages including 17 figures, related publications can be found at
http://www.fhi-berlin.mpg.de/th/paper.htm
Model Revision from Temporal Logic Properties in Computational Systems Biology
International audienceSystems biologists build models of bio-molecular processes from knowledge acquired both at the gene and protein levels, and at the phenotype level through experiments done in wildlife and mutated organisms. In this chapter, we present qualitative and quantitative logic learning tools, and illustrate how they can be useful to the modeler. We focus on biochemical reaction models written in the Systems Biology Markup Language SBML, and interpreted in the Biochemical Abstract Machine BIOCHAM. We first present a model revision algorithm for inferring reaction rules from biological properties expressed in temporal logic. Then we discuss the representations of kinetic models with ordinary differential equations (ODEs) and with stochastic logic programs (SLPs), and describe a parameter search algorithm for finding parameter values satisfying quantitative temporal properties. These methods are illustrated by a simple model of the cell cycle control, and by an application to the modelling of the conditions of synchronization in period of the cell cycle by the circadian cycle
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