On Probability Distributions for Trees: Representations, Inference and Learning

We study probability distributions over free algebras of trees. Probability distributions can be seen as particular (formal power) tree series [Berstel et al 82, Esik et al 03], i.e. mappings from trees to a semiring K . A widely studied class of tree series is the class of rational (or recognizable) tree series which can be defined either in an algebraic way or by means of multiplicity tree automata. We argue that the algebraic representation is very convenient to model probability distributions over a free algebra of trees. First, as in the string case, the algebraic representation allows to design learning algorithms for the whole class of probability distributions defined by rational tree series. Note that learning algorithms for rational tree series correspond to learning algorithms for weighted tree automata where both the structure and the weights are learned. Second, the algebraic representation can be easily extended to deal with unranked trees (like XML trees where a symbol may have an unbounded number of children). Both properties are particularly relevant for applications: nondeterministic automata are required for the inference problem to be relevant (recall that Hidden Markov Models are equivalent to nondeterministic string automata); nowadays applications for Web Information Extraction, Web Services and document processing consider unranked trees

Ultrastructure of calcareous dinophytes (Thoracosphaeraceae, Peridiniales) with a focus on vacuolar crystal-like particles.

Biomineralization in calcareous dinophytes (Thoracosphaeracaea, Peridiniales) takes place in coccoid cells and is presently poorly understood. Vacuolar crystal-like particles as well as collection sites within the prospective calcareous shell may play a crucial role during this process at the ultrastructural level. Using transmission electron microscopy, we investigated the ultrastructure of coccoid cells at an early developmental stage in fourteen calcareous dinophyte strains (corresponding to at least ten species of Calciodinellum, Calcigonellum, Leonella, Pernambugia, Scrippsiella, and Thoracosphaera). The shell of the coccoid cells consisted either of one (Leonella, Thoracosphaera) or two matrices (Scrippsiella and its relatives) of unknown element composition, whereas calcite is deposited in the only or the outer layer, respectively. We observed crystal-like particles in cytoplasmic vacuoles in cells of nine of the strains investigated and assume that they are widespread among calcareous dinophytes. However, similar structures are also found outside the Thoracosphaeraceae, and we postulate an evolutionarily old physiological pathway (possibly involved in detoxification) that later was specialized for calcification. We aim to contribute to a deeper knowledge of the biomineralization process in calcareous dinophytes

Effects of hypoxia on benthic macrofauna and bioturbation in the Estuary and Gulf of St. Lawrence, Canada

The bottom water in the 4300 m deep Lower St. Lawrence Estuary (LSLE) is persistently hypoxic in contrast to the normoxic bottom waters in the Gulf of St. Lawrence (GSL). We photographed the seabed at 11 stations in the Estuary and Gulf of St. Lawrence (EGSL) during the summers 2006 and 2007 and analysed the images to identify bioturbation traces (lebensspuren) and benthic macrofauna. The objective was to identify the environmental variables that influence the density and diversity of benthic macrofauna and bioturbation traces, and the differences that exist among regions with high, medium and low oxygen levels in the bottom water. The bottom water oxygen concentration is the variable that best explains the densities of total-traces as well as surface-traces. However, the density of these traces was higher in hypoxic regions than in well-oxygenated regions. The higher density of traces in the hypoxic region of the LSLE is mainly due to the activities of the surface deposit feeder Ophiura sp., which occurs in large numbers in this region. Possible explanations explored are stress behaviour of the organisms in response to hypoxia and different benthic macrofauna community structures between the hypoxic regions of the LSLE and the normoxic regions of the GSL. In the former, surface deposit feeders and low-oxygen tolerant species dominate over suspension feeders and low-oxygen intolerant species

Nederlandse klanken in Parijs anno 1600. Een Nederlandstalig liedfragment op een façon-de-veniseglas gevonden onder de Cour Napoléon van het Louvre

Tijdens de archeologische opgravingen onder de Cour Napoléon van het Louvre in de periode 1984-1985, werden er zoals te verwachten in het hartje van een grootstad als Parijs heel wat vondsten gedaan die een boeiend licht werpen op de 2000-jarige geschiedenis van de Franse hoofdstad. Verrassend voor een groot publiek was ook dat op de plaats van het prestigieuze Louvre met zijn indrukwekkende voorhof de resten van een hele stadswijk zijn gevonden. Uit de duizenden glasscherven, het merendeel fragmenten van laatmiddeleeuws en 16de-18de-eeuws drinkgerei, zijn meer dan 10.000 glazen gereconstrueerd. Tussen al deze glazen is er echter één buitenbeentje, een coupe die typologisch afwijkt van de andere glasvondsten maar die ook qua kleur en vooral decoratie in het oog springt door de versiering en de inscriptie in diamantlijngravure. Het is dit glas dat in deze bijdrage onderzocht werd. De ontdekking van deze cuppa bleek een interessante vondst. Het was verrassend in hartje Parijs een façon-de-veniseglas met Nederlands opschrift in diamant- of lijngravure aan te treffen. Het bleek dat de graveur dit opschrift ontleend heeft aan een Nederlands lied uit de tweede helft van de 16de eeuw. Uit de diverse verwijzingen naar zowel het lied als het refrein voor wijsaanduidingen en het voorkomen op dit glas, blijkt het lied in het laatste kwart van de 16de en in het begin van de 17de eeuw een zekere populariteit gekend te hebben. De toeschrijving van het glas zelf aan een glasmanufactuur is op dit moment nog niet te bepalen, maar diverse karakteristieken wijzen duidelijk in de richting van een Nederlands productiecentrum

Influence of Chironomus riparius (Diptera, Chironomidae) and Tubifex tubifex (Annelida, Oligochaeta) on oxygen uptake by sediments. Consequences of uranium contamination

The diffusive oxygen uptake (DOU) of sediments inhabited by Chironomus riparius and Tubifex tubifex was investigated using a planar oxygen optode device, and complemented by measurements of bioturbation activity. Additional experiments were performed within contaminated sediments to assess the impact of uranium on these processes. After 72 h, the two invertebrate species significantly increased the DOU of sediments (13–14%), and no temporal variation occurred afterwards. Within contaminated sediments, it was already 24% higher before the introduction of the organisms, suggesting that uranium modified the sediment biogeochemistry. Although the two species firstly reacted by avoidance of contaminated sediment, they finally colonized it. Their bioturbation activity was reduced but, for T. tubifex, it remained sufficient to induce a release of uranium to the water column and an increase of the DOU (53%). These results highlight the necessity of further investigations to take into account the interactions between bioturbation, microbial metabolism and pollutants

301. Efficient Delivery of Nuclear and Cytoplasmic Proteins Fused to HIV-1 Gag Polypeptide By Means of Virus-Like Particles

The expression of the retroviral polypeptide Gag can induce the formation of virus-like particles (VLP). Upon expression, the polypeptide is targeted to the cell membrane and incorporated in the VLP during membrane budding. Chimeric proteins consisting of Gag polypeptide fused to different proteins were engineered and the VLP produced were used as vehicles for protein delivery. One major advantage of this approach is the low mutation risk due to the absence of DNA transfer and genomic integration. In this study, the C-Terminus of Gag from HIV-1 was fused to the green fluorescent protein (GFP), a chimeric transactivator (cTA) and a reprogamming factor (KLF4). VLP were produced by transfection using a stable cell line (293SF-pacLV) that expresses VSVg and Gag-pol. Analysis of the supernatants from producing cells by western blot confirmed the presence of Gag-GFP, -cTA and -KLF4. Confocal microscopy showed that the vast majority of the cells (> 90%) treated with VLP-GFP/polybrene complexes was successfully transduced. The cells also displayed a GFP signal almost exclusively localized inside the cytoplasm. Additional VSVg expression during the production facilitated the endosomal escape of VLP-GFP in transduced cells. The insertion of a nuclear localisation signal (NLS) shifted the localization of the GFP to the cell nucleus demonstrating that a nuclear protein could be successfully delivered by VLP. The experiment was thus repeated using two transcription factors. Lentiviral vectors were used to make two stable pools of HEK293 cells each containing a specific GFP reporter cassette. The GFP gene was regulated either by the CR5 promoter (specifically activated by the cTA) or by a minimal promoter fused to KLF4 transcription response elements (TRE). Transduction of the CR5-GFP pool with VLP-cTA/polybrene complexes showed a powerful activation of the reporter (365-fold compared to the negative control) as measured by flow cell cytometry two days post-transduction. Surprisingly, no activation was observed in the TRE-GFP pool three days after transduction by VLP-KLF4/polybrene complexes. Evidence obtained by transfection suggested that the Gag fusion inhibits KLF4 activity. To augment activity, the activation domain of VP16 was fused to KLF4. Transfection of a plasmid encoding Gag-VP16KLF4 strongly activated the reporter by a factor of 126-fold (6-fold higher than wild type KLF4). The ability of VLP produced with Gag-VP16KLF4 to activate transcription is currently under investigation. In summary, VLP based on HIV-1 Gag can deliver nuclear and cytoplasmic proteins directly into cells with a low mutation risk. Therefore, our platform for VLP production could be useful for several applications including cell reprogramming and genome editing oriented toward cell therapies of diseases like Duchenne muscular dystrophy

Series, Weighted Automata, Probabilistic Automata and Probability Distributions for Unranked Trees.

We study tree series and weighted tree automata over unranked trees. The message is that recognizable tree series for unranked trees can be defined and studied from recognizable tree series for binary representations of unranked trees. For this we prove results of Denis et al (2007) as follows. We extend hedge automata -- a class of tree automata for unranked trees -- to weighted hedge automata. We define weighted stepwise automata as weighted tree automata for binary representations of unranked trees. We show that recognizable tree series can be equivalently defined by weighted hedge automata or weighted stepwise automata. Then we consider real-valued tree series and weighted tree automata over the field of real numbers. We show that the result also holds for probabilistic automata -- weighted automata with normalisation conditions for rules. We also define convergent tree series and show that convergence properties for recognizable tree series are preserved via binary encoding. From Etessami and Yannakakis (2009), we present decidability results on probabilistic tree automata and algorithms for computing sums of convergent series. Last we show that streaming algorithms for unranked trees can be seen as slight transformations of algorithms on the binary representations