One of the first steps in building a spoken language understanding (SLU) module for dialogue systems is the extraction of flat concepts out of a given word sequence, usually provided by an automatic speech recognition (ASR) system. In this paper, six different modeling approaches are investigated to tackle the task of concept tagging. These methods include classical, well-known generative and discriminative methods like Finite State Transducers (FSTs), Statistical Machine Translation (SMT), Maximum Entropy Markov Models (MEMMs), or Support Vector Machines (SVMs) as well as techniques recently applied to natural language processing such as Conditional Random Fields (CRFs) or Dynamic Bayesian Networks (DBNs). Following a detailed description of the models, experimental and comparative results are presented on three corpora in different languages and with different complexity. The French MEDIA corpus has already been exploited during an evaluation campaign and so a direct comparison with existing benchmarks is possible. Recently collected Italian and Polish corpora are used to test the robustness and portability of the modeling approaches. For all tasks, manual transcriptions as well as ASR inputs are considered. Additionally to single systems, methods for system combination are investigated. The best performing model on all tasks is based on conditional random fields. On the MEDIA evaluation corpus, a concept error rate of 12.6% could be achieved. Here, additionally to attribute names, attribute values have been extracted using a combination of a rule-based and a statistical approach. Applying system combination using weighted ROVER with all six systems, the concept error rate (CER) drops to 12.0%.

Background/AimThe human intestinal microbiota plays an important role in modulation of mucosal immune responses. To study interactions between intestinal epithelial cells (IECs) and commensal bacteria, a functional metagenomic approach was developed. One interest of metagenomics is to provide access to genomes of uncultured microbes. We aimed at identifying bacterial genes involved in regulation of NF-κB signaling in IECs. A high throughput cell-based screening assay allowing rapid detection of NF-κB modulation in IECs was established using the reporter-gene strategy to screen metagenomic libraries issued from the human intestinal microbiota.MethodsA plasmid containing the secreted alkaline phosphatase (SEAP) gene under the control of NF-κB binding elements was stably transfected in HT-29 cells. The reporter clone HT-29/kb-seap-25 was selected and characterized. Then, a first screening of a metagenomic library from Crohn's disease patients was performed to identify NF-κB modulating clones. Furthermore, genes potentially involved in the effect of one stimulatory metagenomic clone were determined by sequence analysis associated to mutagenesis by transposition.ResultsThe two proinflammatory cytokines, TNF-α and IL-1β, were able to activate the reporter system, translating the activation of the NF-κB signaling pathway and NF-κB inhibitors, BAY 11-7082, caffeic acid phenethyl ester and MG132 were efficient. A screening of 2640 metagenomic clones led to the identification of 171 modulating clones. Among them, one stimulatory metagenomic clone, 52B7, was further characterized. Sequence analysis revealed that its metagenomic DNA insert might belong to a new Bacteroides strain and we identified 2 loci encoding an ABC transport system and a putative lipoprotein potentially involved in 52B7 effect on NF-κB.ConclusionsWe have established a robust high throughput screening assay for metagenomic libraries derived from the human intestinal microbiota to study bacteria-driven NF-κB regulation. This opens a strategic path toward the identification of bacterial strains and molecular patterns presenting a potential therapeutic interest.

BackgroundThe metagenomic analysis of gut microbiomes has emerged as a powerful strategy for the identification of biomass-degrading enzymes, which will be no doubt useful for the development of advanced biorefining processes. In the present study, we have performed a functional metagenomic analysis on comb and gut microbiomes associated with the fungus-growing termite, Pseudacanthotermes militaris.ResultsUsing whole termite abdomens and fungal-comb material respectively, two fosmid-based metagenomic libraries were created and screened for the presence of xylan-degrading enzymes. This revealed 101 positive clones, corresponding to an extremely high global hit rate of 0.49%. Many clones displayed either β-d-xylosidase (EC 3.2.1.37) or α-l-arabinofuranosidase (EC 3.2.1.55) activity, while others displayed the ability to degrade AZCL-xylan or AZCL-β-(1,3)-β-(1,4)-glucan. Using secondary screening it was possible to pinpoint clones of interest that were used to prepare fosmid DNA. Sequencing of fosmid DNA generated 1.46 Mbp of sequence data, and bioinformatics analysis revealed 63 sequences encoding putative carbohydrate-active enzymes, with many of these forming parts of sequence clusters, probably having carbohydrate degradation and metabolic functions. Taxonomic assignment of the different sequences revealed that Firmicutes and Bacteroidetes were predominant phyla in the gut sample, while microbial diversity in the comb sample resembled that of typical soil samples. Cloning and expression in E. coli of six enzyme candidates identified in the libraries provided access to individual enzyme activities, which all proved to be coherent with the primary and secondary functional screens.ConclusionsThis study shows that the gut microbiome of P. militaris possesses the potential to degrade biomass components, such as arabinoxylans and arabinans. Moreover, the data presented suggests that prokaryotic microorganisms present in the comb could also play a part in the degradation of biomass within the termite mound, although further investigation will be needed to clarify the complex synergies that might exist between the different microbiomes that constitute the termitosphere of fungus-growing termites. This study exemplifies the power of functional metagenomics for the discovery of biomass-active enzymes and has provided a collection of potentially interesting biocatalysts for further study.

We have developed a foolproof method to substitute a stretch of residues by alanines. After the introduction of aPstI site by IPCR, thus creating two alanine codons, additional codons are introduced at this site through the use of an 'alanine-stretch cartridge'. These cartridges comprise an antibiotic resistance gene flanked on both sides by alanine codons. Excision of the resistance gene byPvuII then yields the correct insertion of codons. The method is both highly reliable and flexible and should be of general use.

We investigated the cross-over effect of muscle fatigue and its time course on the non-exercising contralateral limb (NEL) after unilateral fatiguing contractions of the ipsilateral exercising limb (EL). For this purpose, 15 males performed two bouts of 100-second maximal isometric knee extensions with the exercising limb, and neuromuscular function of both the EL and NEL was assessed before (PRE), after a first fatiguing exercise (MID) and after a second fatiguing exercise (POST). Maximal voluntary isometric torque production declined in the EL after the first bout of exercise (−9.6%; p<0.001) while in the NEL, the decrease occurred after the second bout of exercise (−10.6%; p<0.001). At MID, torque decline of the EL was strictly associated to an alteration of the mechanical twitch properties evoked by neurostimulation of the femoral nerve (i.e., peak twitch torque, maximal rate of twitch development). According to these markers, we suggest that peripheral fatigue occurred. At POST, after the second bout of exercise, the voluntary activation level of the knee extensor muscles was altered from PRE (−9.1%; p<0.001), indicating an overall central failure in both the EL and NEL. These findings indicate that two bouts of unilateral fatiguing exercise were needed to induce a cross-over effect of muscle fatigue on the non-exercising contralateral limb. Differential adjustments of the motor pathway (peripheral fatigue vs. central fatigue) might contribute to the respective torque decline in the EL and the NEL. Given that our unilateral fatiguing exercise induced immediate maximal torque reduction in the EL and postponed the loss of torque production in the NEL, it is also concluded that the time course of muscle fatigue differed between limbs.