On Functionality of Visibly Pushdown Transducers

Visibly pushdown transducers form a subclass of pushdown transducers that (strictly) extends finite state transducers with a stack. Like visibly pushdown automata, the input symbols determine the stack operations. In this paper, we prove that functionality is decidable in PSpace for visibly pushdown transducers. The proof is done via a pumping argument: if a word with two outputs has a sufficiently large nesting depth, there exists a nested word with two outputs whose nesting depth is strictly smaller. The proof uses technics of word combinatorics. As a consequence of decidability of functionality, we also show that equivalence of functional visibly pushdown transducers is Exptime-Complete.Comment: 20 page

Reachability in Higher-Order-Counters

Higher-order counter automata (\HOCS) can be either seen as a restriction of higher-order pushdown automata (\HOPS) to a unary stack alphabet, or as an extension of counter automata to higher levels. We distinguish two principal kinds of \HOCS: those that can test whether the topmost counter value is zero and those which cannot. We show that control-state reachability for level $k$ \HOCS with $0$-test is complete for \mbox{$(k-2)$}-fold exponential space; leaving out the $0$-test leads to completeness for \mbox{$(k-2)$}-fold exponential time. Restricting \HOCS (without $0$-test) to level $2$, we prove that global (forward or backward) reachability analysis is \PTIME-complete. This enhances the known result for pushdown systems which are subsumed by level $2$ \HOCS without $0$-test. We transfer our results to the formal language setting. Assuming that \PTIME \subsetneq \PSPACE \subsetneq \mathbf{EXPTIME}, we apply proof ideas of Engelfriet and conclude that the hierarchies of languages of \HOPS and of \HOCS form strictly interleaving hierarchies. Interestingly, Engelfriet's constructions also allow to conclude immediately that the hierarchy of collapsible pushdown languages is strict level-by-level due to the existing complexity results for reachability on collapsible pushdown graphs. This answers an open question independently asked by Parys and by Kobayashi.Comment: Version with Full Proofs of a paper that appears at MFCS 201

A New Pipeline for the Normalization and Pooling of Metabolomics Data

Pooling metabolomics data across studies is often desirable to increase the statistical power of the analysis. However, this can raise methodological challenges as several preanalytical and analytical factors could introduce differences in measured concentrations and variability between datasets. Specifically, different studies may use variable sample types (e.g., serum versus plasma) collected, treated, and stored according to different protocols, and assayed in different laboratories using different instruments. To address these issues, a new pipeline was developed to normalize and pool metabolomics data through a set of sequential steps: (i) exclusions of the least informative observations and metabolites and removal of outliers; imputation of missing data; (ii) identification of the main sources of variability through principal component partial R-square (PC-PR2) analysis; (iii) application of linear mixed models to remove unwanted variability, including samples' originating study and batch, and preserve biological variations while accounting for potential differences in the residual variances across studies. This pipeline was applied to targeted metabolomics data acquired using Biocrates AbsoluteIDQ kits in eight case-control studies nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Comprehensive examination of metabolomics measurements indicated that the pipeline improved the comparability of data across the studies. Our pipeline can be adapted to normalize other molecular data, including biomarkers as well as proteomics data, and could be used for pooling molecular datasets, for example in international consortia, to limit biases introduced by inter-study variability. This versatility of the pipeline makes our work of potential interest to molecular epidemiologists

Transfusion-transmitted infections

Although the risk of transfusion-transmitted infections today is lower than ever, the supply of safe blood products remains subject to contamination with known and yet to be identified human pathogens. Only continuous improvement and implementation of donor selection, sensitive screening tests and effective inactivation procedures can ensure the elimination, or at least reduction, of the risk of acquiring transfusion transmitted infections. In addition, ongoing education and up-to-date information regarding infectious agents that are potentially transmitted via blood components is necessary to promote the reporting of adverse events, an important component of transfusion transmitted disease surveillance. Thus, the collaboration of all parties involved in transfusion medicine, including national haemovigilance systems, is crucial for protecting a secure blood product supply from known and emerging blood-borne pathogens

The life-course impact of smoking on hypertension, myocardial infarction and respiratory diseases

The Author(s) 2017. The objective of this study was to examine the impact of smoking on respiratory diseases, hypertension and myocardial infarction, with a particular focus from a life-course perspective. In this study, 28,577 males from a Chinese longitudinal survey were analysed. The effects of smoking on the risk of respiratory diseases, hypertension and myocardial infarction were assessed from a life-course perspective and a current view separately. No significant associations were found between smoking and the risk of incident respiratory diseases, hypertension and myocardial infarction in the group younger than 35. Among study participants aged between 36-55 and 56-80, smoking was positively associated with the risk of incident respiratory diseases, hypertension and myocardial infarction from the life-course perspective, and the risk increased with age. In contrast, the results from a current view showed inverse associations between smoking and the risk of the diseases mentioned above. Our findings highlight that it is essential to quantify the effects of smoking from a life-course perspective in future research and to suggest that smokers quit smoking as soon as possible, regardless of the temporary side effects of quitting