Reply to No evidence for individual blood-brain barrier phenylalanine transport to influence clinical outcome in typical phenylketonuria patients

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On the Executability of Interactive Computation

The model of interactive Turing machines (ITMs) has been proposed to characterise which stream translations are interactively computable; the model of reactive Turing machines (RTMs) has been proposed to characterise which behaviours are reactively executable. In this article we provide a comparison of the two models. We show, on the one hand, that the behaviour exhibited by ITMs is reactively executable, and, on the other hand, that the stream translations naturally associated with RTMs are interactively computable. We conclude from these results that the theory of reactive executability subsumes the theory of interactive computability. Inspired by the existing model of ITMs with advice, which provides a model of evolving computation, we also consider RTMs with advice and we establish that a facility of advice considerably upgrades the behavioural expressiveness of RTMs: every countable transition system can be simulated by some RTM with advice up to a fine notion of behavioural equivalence.Comment: 15 pages, 0 figure

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

We introduce the \texttt{pyunicorn} (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. \texttt{pyunicorn} is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics or network surrogates. Additionally, \texttt{pyunicorn} provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis (RQA), recurrence networks, visibility graphs and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.Comment: 28 pages, 17 figure

Quark-Gluon Matter

A concise review of the experimental and phenomenological progress in high-energy heavy-ion physics over the past few years is presented. Emphasis is put on measurements at BNL-RHIC and CERN-SPS which provide information on fundamental properties of QCD matter at extreme values of temperature, density and low-x. The new opportunities accessible at the LHC, which may help clarify some of the current open issues, are also outlined.Comment: Minor changes to text. New refs. included. Updated figures with final dat

Bacteraemia among severely malnourished children infected and uninfected with the human immunodeficiency virus-1 in Kampala, Uganda

BACKGROUND: To establish the magnitude of bacteraemia in severely malnourished children, and describe the types of bacteria and antimicrobial sensitivity by HIV status. METHOD: Isolates were recovered from 76 blood specimens. Antibiotic susceptibility tests were performed using commercial antibiotic disks and demographic and clinical findings were recorded. RESULTS: Of the 450 children 63% were male; median age 17.0 months (inter quartile range, IQR 12–24) and 57% had oedema. 151 (36.7 %) of 411 tested HIV-positive; 76 (17.1%) of 445 blood specimens grew bacterial isolates; 58% were Gram negative – S. typhimurium (27.6%) and S. enteriditis (11.8%). Staph. aureus (26.3%) and Strep. pneumoniae (13.2%) were the main Gram positive organisms. There was no difference in the risk of bacteraemia by HIV status, age < 24 months, male sex, or oedema, except for oral thrush (OR 2.3 CI 1.0–5.1) and hypoalbuminaemia (OR 3.5 CI 1.0–12.1). Isolates from severely immuno-suppressed children (CD4% <15%) were more likely to grow Salmonella enteriditis (OR 5.4; CI 1.6 – 17.4). The isolates were susceptible (≥ 80%) to ciprofloxacin, ceftriaxone and gentamicin; with low susceptibility to chlorampenicol, ampicillin (< 50%) and co-trimoxazole (<25%). Suspicion of bacteraemia had 95.9% sensitivity and 99.2% specificity. Among bacteraemic children, mortality was higher (43.5% vs 20.5%) in the HIV-positive; OR 3.0 (95%CI 1.0, 8.6). CONCLUSION: Bacteraemia affects 1 in every 6 severely malnourished children and carries high mortality especially among the HIV-positive. Given the high level of resistance to common antibiotics, there is need for clinical trials to determine the best combinations of antibiotics for management of bacteraemia in severely malnourished children