A unifying framework for seed sensitivity and its application to subset seeds

We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of target alignments, an associated probability distribution, and a seed model -- that are specified by distinct finite automata. The approach is then applied to a new concept of subset seeds for which we propose an efficient automaton construction. Experimental results confirm that sensitive subset seeds can be efficiently designed using our approach, and can then be used in similarity search producing better results than ordinary spaced seeds

Combinatorics and Algorithmics of Strings

Edited in cooperation with Robert MercaşStrings (aka sequences or words) form the most basic and natural data structure. They occur whenever information is electronically transmitted (as bit streams), when natural language text is spoken or written down (as words over, for example, the Latin alphabet), in the process of heredity transmission in living cells (through DNA sequences) or the protein synthesis (as sequence of amino acids), and in many more different contexts. Given this universal form of representing information, the need to process strings is apparent and is actually a core purpose of computer use. Algorithms to efficiently search through, analyze, (de-)compress, match, encode and decode strings are therefore of chief interest. Combinatorial problems about strings lie at the core of such algorithmic questions. Many such combinatorial problems are common in the string processing efforts in the different fields of application.http://drops.dagstuhl.de/opus/volltexte/2014/4552

The dynamic nature of Cu sites in Cu-SSZ-13 and the origin of the seagull NOx conversion profile during NH3-SCR

Cu-Zeolites with chabazite structure show a peculiar dual-maxima NO conversion profile, also known as a seagull profile, during the selective catalytic reduction by ammonia. In order to understand the origin of this behavior, systematic catalytic tests and operando spectroscopy were applied to derive structure–performance relationships for Cu-SSZ-13 catalysts with low and high Cu loading. Operando X-ray absorption, X-ray emission and in situ electron paramagnetic resonance spectroscopy measurements, including novel photon-in/photon-out techniques, demonstrated the interconversion of isolated Cu sites and dimeric bis(μ-oxo) Cu species, the former occurring via formation of ammonia Cu2+/Cu+ complexes and the latter in an oxidizing gas mixture. The formation of dimeric Cu+–O2–Cu+ species by involving Cu sites in close vicinity was linked to the high activity at low temperatures of the highly loaded Cu-SSZ-13 sample. In contrast, the isolated Cu sites present at very low Cu loadings are strongly poisoned by adsorbed NH3. The activity decrease around 350 °C that gives rise to the seagull shaped NO conversion profile could be attributed to a more localized structure of mono(μ-oxo)dicopper complexes. Above this temperature, which corresponds to partial NH3 desorption from Cu sites, the isolated Cu sites migrate to form additional dimeric entities thus recovering the SCR activity

The dynamic nature of Cu sites in Cu-SSZ-13 and the origin of the seagull NOx conversion profile during NH₃-SCR

Cu-Zeolites with chabazite structure show a peculiar dual-maxima NO conversion profile, also known as a seagull profile, during the selective catalytic reduction by ammonia. In order to understand the origin of this behavior, systematic catalytic tests and operando spectroscopy were applied to derive structure–performance relationships for Cu-SSZ-13 catalysts with low and high Cu loading. Operando X-ray absorption, X-ray emission and in situ electron paramagnetic resonance spectroscopy measurements, including novel photon-in/photon-out techniques, demonstrated the interconversion of isolated Cu sites and dimeric bis(μ-oxo) Cu species, the former occurring via formation of ammonia Cu2+/Cu+ complexes and the latter in an oxidizing gas mixture. The formation of dimeric Cu+–O2–Cu+ species by involving Cu sites in close vicinity was linked to the high activity at low temperatures of the highly loaded Cu-SSZ-13 sample. In contrast, the isolated Cu sites present at very low Cu loadings are strongly poisoned by adsorbed NH3. The activity decrease around 350 °C that gives rise to the seagull shaped NO conversion profile could be attributed to a more localized structure of mono(μ-oxo)dicopper complexes. Above this temperature, which corresponds to partial NH3 desorption from Cu sites, the isolated Cu sites migrate to form additional dimeric entities thus recovering the SCR activity

A suffix tree or not a suffix tree?

In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question ”Is τ a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as τ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol. This corresponds to considering the more general definition of implicit or extended suffix trees. Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online. Deciding if τ is a suffix tree is not an easy task, because, with no restrictions on the final symbol, we cannot guess the length of a string that realizes τ from the number of leaves. And without an upper bound on the length of such a string, it is not even clear how to solve the problem by an exhaustive search. In this paper, we prove that τ is a suffix tree if and only if it is realized by a string S of length n−1, and we give a linear-time algorithm for inferring S when the first letter on each edge is known. This generalizes the work of I et al. [Discrete Appl. Math. 163, 2014]

The impact of the programs of medical rehabilitation on the growth and development of adolescents with the pathology of the urinary system

Physical development (PD) of the child and the teenager is one of the main criteria for health (6). However, the interpretation of the only indicators of physical development and level of harmony does not give an opportunity to judge the themed processes of increase does not reflect the integral characteristics of the flow of development of an individual (1,5). One of the integral characteristics of the growth and development of the patient is the diagnosis of somatic body type (2), used in pediatric and adolescent practice for several decades. To complement the data on the rate of development to the use of diagnostic tempo of biological maturation, teenagers have the diagnosis of secondary sexual characteristics of the runway (2). Diagnosis of somatic body types and biological maturity of children and adolescents have long been required components assessment of the state of health (MOH Order MP of the Russian Federation № 292 «On improvement of medical-sports services of the Russian Federation» dated 19.07.1996; Order of Ministry of health of the Russian Federation №337 «on measures for further development and improvement of sports medicine and physical therapy» from 20.08.2001; Order of Ministry of health of the Russian Federation №1346 Order of minors medical examination» of 21.12.2012).Физическое развитие (ФР) ребенка и подростка является одним из основных критериев здоровья (6). Однако трактовка только показателей физического развития и уровня гармоничности не дает возможность судить о темповых процессах прироста показателей, не полностью отражает интегральную характеристику течения развития индивидуума (1,5). Одной из интегральных характеристик роста и развития пациента является диагностика соматического типа телосложения (2), используемая в педиатрической и подростковой практике несколько десятилетий. Для дополнения данных о темпе развития используют диагностику темпа биологического созревания, у подростков - по диагностике вторичных половых признаков ВПП (2). Диагностика соматических типов телосложения и биологической зрелости детей и подростков уже давно являются обязательными компонентами оценки состояния здоровья (Приказ М3 МП РФ № 292 «О совершенствовании врачебно-физкультурной службы РФ» от 19.07.1996; Приказ М3 РФ №337 «О мерах по дальнейшему развитию и совершенствованию спортивной медицины и лечебной физкультуры» от 20.08.2001; Приказ М3 РФ №1346 «Порядок прохождения несовершеннолетними медицинских осмотров» от 21.12.2012)

Optimal neighborhood indexing for protein similarity search

Background: Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet.\ud \ud Results: The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum.\ud \ud Conclusions: We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction

Rapid Ring-Opening Metathesis Polymerization of Monomers Obtained from Biomass-Derived Furfuryl Amines and Maleic Anhydride

Well-controlled and extremely rapid ring-opening metathesis polymerization of unusual oxanorbornene lactam esters by Grubbs third-generation catalyst is used to prepare a range of bio-based homo- and copolymers. Bio-derived oxanorbornene lactam monomers were prepared at room temperature from maleic anhydride and secondary furfuryl amines by using a 100 % atom economical, tandem Diels–Alder lactamization reaction, followed by esterification. Several of the resulting homo- and copolymers show good control over polymer molecular weight and have narrow molecular weight distributions