Regularization of statistical inverse problems and the Bakushinskii veto

In the deterministic context Bakushinskii's theorem excludes the existence of purely data driven convergent regularization for ill-posed problems. We will prove in the present work that in the statistical setting we can either construct a counter example or develop an equivalent formulation depending on the considered class of probability distributions. Hence, Bakushinskii's theorem does not generalize to the statistical context, although this has often been assumed in the past. To arrive at this conclusion, we will deduce from the classic theory new concepts for a general study of statistical inverse problems and perform a systematic clarification of the key ideas of statistical regularization.Comment: 20 page

Digging into acceptor splice site prediction : an iterative feature selection approach

Feature selection techniques are often used to reduce data dimensionality, increase classification performance, and gain insight into the processes that generated the data. In this paper, we describe an iterative procedure of feature selection and feature construction steps, improving the classification of acceptor splice sites, an important subtask of gene prediction. We show that acceptor prediction can benefit from feature selection, and describe how feature selection techniques can be used to gain new insights in the classification of acceptor sites. This is illustrated by the identification of a new, biologically motivated feature: the AG-scanning feature. The results described in this paper contribute both to the domain of gene prediction, and to research in feature selection techniques, describing a new wrapper based feature weighting method that aids in knowledge discovery when dealing with complex datasets

Pause Point Spectra in DNA Constant-Force Unzipping

Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. A simple theoretical model of DNA constant-force unzipping is demonstrated to produce good agreement with the experimental pause point spectrum of lambda phage DNA. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 bp. The model only requires the sequence, temperature and a set of empirical base pair binding and stacking energy parameters, and the good agreement with experiment suggests that pause points are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the BacterioPhage PhiX174 genome. The algorithm for extracting the pause point spectrum might also be useful for studying related systems which exhibit pausing behavior such as molecular motors.Comment: 15 pages, 12 figure

Innovation et gouvernance territoriale : une analyse par les dispositifs

International audienceCette communication vise à présenter les outils méthodologiques d'analyse/évaluation de la gouvernance territoriale élaborés dans le cadre du projet de recherche PSDR Gouv.Innov sur les innovations organisationnelles relatives à la gouvernance territoriale. Il s'agit d'étudier les transformations introduites par les politiques de développement durable au niveau des dispositifs de gouvernance territoriale visant à favoriser une gestion intégrée des espaces ruraux. Dans un contexte de recomposition de l'action publique où les procédures d'aménagement sont plutôt normées par des représentations urbaines, l'accent est mis sur la question des modalités de représentation des activités rurales, pour lesquelles nous faisons l'hypothèse qu'elles sont sous représentées. Les premiers résultats méthodologiques permettent, dans une première partie, de proposer une définition générique et pragmatique de la gouvernance territoriale et de préciser la notion de dispositifs de gouvernance comme objet d'observation. A partir de cette définition une grille d'analyse permettant d'appréhender l'ensemble des dimensions en jeu dans les processus de gouvernance territoriale est élaborée. Dans la deuxième partie nous explorons l'intérêt de la notion de dispositif pour observer les processus de gouvernance et proposons une grille de collecte et de structuration des informations pour constituer des chroniques des dispositifs étudiés. / This paper seeks to present the methodological tools used in the analysis/evaluation of territorial governance developed during research undertaken within the framework of the PSDR Gouv-Innov project on organisational innovations with respect to territorial governance. It involves the study of the changes resulting from the emergence of sustainable development policies in territorial governance systems aiming to implement the integrated management of rural areas. In a context of changes in the way in which public action is implemented (for instance, public-private partnerships), where development procedures are usually standardised by urban representations, the emphasis is placed on the issue of the representation of rural activities, the hypothesis being that they are under-represented. The initial methodological results lead, in the first instance, to a proposition for a generic and pragmatic definition of territorial governance and a clarification of the notion of governance systems as objects of observation. This definition can be used as the basis of a framework to address all the analytical dimensions of the territorial governance process. In the second part, the authors explore the idea of system in order to observe governance processes and suggest a matrix for the collection and structuring of information in order to report on the studied systems

Aquaculture system diversity and sustainable development : fish farms and their representation

Initiatives for the sustainable development of aquaculture have so far focused on the production of codes of conduct, of best management practices, of standards etc., most of which have been developed by international organisations, the industrial sector and non governmental organisations. They were, to a large extent, produced using a "top down" process and inspired by models from intensive industrial shrimp and sea fish farming (mainly salmon). However, most of global aquaculture production comes from small-and medium-sized farms, essentially in Asia which contributes 92% of the total world aquaculture production volume. The objective of this article is to define the contours of systemic typologies that are able to express the sustainability conditions of aquaculture systems. The proposed approach builds on surveys of aquaculture systems which differ in terms of their biogeographical nature (temperate/tropical and north/south countries) or their farming techniques and their governance systems. This work is a prerequisite to any attempt at an individualised and comparative evaluation of specific aquaculture systems from either global or territorial viewpoints. In order to go beyond the cleavage of a typology based on the differentiation between developed and developing countries, three typologies were produced. These typologies allow for discriminatory variables to be identified such as for example the marketing methods or the pace of innovation: a structural typology, a functional typology and a systemic typology. Finally, the representations of aquaculture activity and of its sustainability that producers have of the 4 different types that emerge from the systemic typology were recorded and analyzed

Anomalous zipping dynamics and forced polymer translocation

We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high temperature equilibrium configuration to a low temperature state, so that the two strands zip up by closing up a "Y"-fork. In unzipping, the polymers are brought from a low temperature double stranded configuration to high temperatures, so that the two strands separate. Simulations show that the unzipping time, $\tau_u$, scales as a function of the polymer length as $\tau_u \sim L$, while the zipping is characterized by anomalous dynamics $\tau_z \sim L^\alpha$ with $\alpha = 1.37(2)$. This exponent is in good agreement with simulation results and theoretical predictions for the scaling of the translocation time of a forced polymer passing through a narrow pore. We find that the exponent $\alpha$ is robust against variations of parameters and temperature, whereas the scaling of $\tau_z$ as a function of the driving force shows the existence of two different regimes: the weak forcing ($\tau_z \sim 1/F$) and strong forcing ($\tau_z$ independent of $F$) regimes. The crossover region is possibly characterized by a non-trivial scaling in $F$, matching the prediction of recent theories of polymer translocation. Although the geometrical setup is different, zipping and translocation share thus the same type of anomalous dynamics. Systems where this dynamics could be experimentally investigated are DNA (or RNA) hairpins: our results imply an anomalous dynamics for the hairpins closing times, but not for the opening times.Comment: 15 pages, 9 figure

Long-term outcomes of liver transplant patients with human immunodeficiency virus infection and end-stage-liver-disease: single center experience

<p>Abstract</p> <p>Objective</p> <p>Orthotopic-liver-transplantation (OLT) in patients with Human-Immunodeficiency-Virus infection (HIV) and end-stage-liver-disease (ESDL) is rarely reported. The purpose of this study is to describe our institutional experience on OLT for HIV positive patients.</p> <p>Material and methods</p> <p>This is a retrospective study of all HIV-infected patients who underwent OLT at the University Hospital of Essen, from January 1996 to December 2009. Age, sex, HIV transmission-way, CDC-stage, etiology of ESDL, concomitant liver disease, last CD4cell count and HIV-viral load prior to OLT were collected and analysed. Standard calcineurin-inhibitors-based immunosuppression was applied. All patients received anti-fungal and anti-pneumocystis carinii pneumonia prophylaxis post-OLT.</p> <p>Results</p> <p>Eight transplanted HIV-infected patients with a median age of 46 years (range 35-61 years) were included. OLT indications were HCV (n = 5), HBV (n = 2), HCV/HBV/HDV-related cirrhosis (n = 1) and acute liver-failure (n = 1). At OLT, CD4 cell-counts ranged from 113-621 cells/μl, and HIV viral-loads from < 50-175,000 copies/ml. Seven of eight patients were exposed to HAART before OLT. Patients were followed-up between 1-145 months. Five died 1, 3, 10, 31 and 34 months after OLT due to sepsis and graftfailure respectively. Graft-failure causes were recurrent hepatic-artery thrombosis, HCV-associated hepatitis, and chemotherapy-induced liver damage due to Hodgkin-disease. One survivor is relisted for OLT due to recurrent chronic HCV-disease but non-progredient HIV-infection 145 months post-OLT. Two other survivors show stable liver function and non-progredient HIV-disease under HAART 21 and 58 months post-OLT.</p> <p>Conclusions</p> <p>OLT in HIV-infected patients and ESLD is an acceptable therapeutic option in selected patients. Long-term survival can be achieved without HIV disease-progression under antiretroviral therapy and management of the viral hepatitis co-infection.</p

Duration learning for analysis of nanopore ionic current blockades

<p>Abstract</p> <p>Background</p> <p>Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties, with potential implications for DNA sequencing. The alpha-Hemolysin transmembrane channel interacts with a translocating molecule in a nontrivial way, frequently evidenced by a complex ionic flow blockade pattern. Typically, recorded current blockade signals have several levels of blockade, with various durations, all obeying a fixed statistical profile for a given molecule. Hidden Markov Model (HMM) based duration learning experiments on artificial two-level Gaussian blockade signals helped us to identify proper modeling framework. We then apply our framework to the real multi-level DNA hairpin blockade signal.</p> <p>Results</p> <p>The identified upper level blockade state is observed with durations that are geometrically distributed (consistent with an a physical decay process for remaining in any given state). We show that mixture of convolution chains of geometrically distributed states is better for presenting multimodal long-tailed duration phenomena. Based on learned HMM profiles we are able to classify 9 base-pair DNA hairpins with accuracy up to 99.5% on signals from same-day experiments.</p> <p>Conclusion</p> <p>We have demonstrated several implementations for <it>de novo </it>estimation of duration distribution probability density function with HMM framework and applied our model topology to the real data. The proposed design could be handy in molecular analysis based on nanopore current blockade signal.</p