Foreign molecules in biomembranes : Molecular effects on intact stratum corneum and model lipid systems

This thesis mainly explores how the molecular mobility of lipid and protein components in the outermost layer of the skin, the stratum corneum (SC), varies with different conditions and upon adding foreign compounds. These studies require methods that makes it possible to detect and characterize the minor amount of fluid components in the highly ordered solid SC sample with resolved molecular information. 13C polarization transfer solid-state nuclear magnetic resonance (PT ssNMR) is well suited for this task, and was employed as the main method through this thesis. The aims of this thesis were achieved by studies on well-controlled systems of intact SC, extracted corneocyte, and model lipid systems, and by combining PT ssNMR with different complementary biophysical techniques.A general conclusion from the presented studies of different foreign compounds is that apolar compounds mainly affect SC lipids, while more polar compounds affect both SC lipid and protein components. The effects strongly depend on the identity of the additive, and on the hydration conditions, and they vary with concentrations and temperatures. One interesting finding is the essential role of water in the mobility of keratin filaments. Apart from the effects on SC components, one can also simultaneously characterize the molecular mobility of the additves that are incorporated in the complex SC matrix by using PT ssNMR.We also demonstrate a clear correlation between the molecular mobility in SC lipids and proteins and the skin permeability upon additives, which forwards the understanding of the skin macroscopic barrier function at a molecular level. The findings of this research can be applied in topical formulations for, e.g., drug delivery and skin care products

A Robust Transformation-Based Learning Approach Using Ripple Down Rules for Part-of-Speech Tagging

In this paper, we propose a new approach to construct a system of transformation rules for the Part-of-Speech (POS) tagging task. Our approach is based on an incremental knowledge acquisition method where rules are stored in an exception structure and new rules are only added to correct the errors of existing rules; thus allowing systematic control of the interaction between the rules. Experimental results on 13 languages show that our approach is fast in terms of training time and tagging speed. Furthermore, our approach obtains very competitive accuracy in comparison to state-of-the-art POS and morphological taggers.Comment: Version 1: 13 pages. Version 2: Submitted to AI Communications - the European Journal on Artificial Intelligence. Version 3: Resubmitted after major revisions. Version 4: Resubmitted after minor revisions. Version 5: to appear in AI Communications (accepted for publication on 3/12/2015

Ripple Down Rules for Question Answering

Recent years have witnessed a new trend of building ontology-based question answering systems. These systems use semantic web information to produce more precise answers to users' queries. However, these systems are mostly designed for English. In this paper, we introduce an ontology-based question answering system named KbQAS which, to the best of our knowledge, is the first one made for Vietnamese. KbQAS employs our question analysis approach that systematically constructs a knowledge base of grammar rules to convert each input question into an intermediate representation element. KbQAS then takes the intermediate representation element with respect to a target ontology and applies concept-matching techniques to return an answer. On a wide range of Vietnamese questions, experimental results show that the performance of KbQAS is promising with accuracies of 84.1% and 82.4% for analyzing input questions and retrieving output answers, respectively. Furthermore, our question analysis approach can easily be applied to new domains and new languages, thus saving time and human effort.Comment: V1: 21 pages, 7 figures, 10 tables. V2: 8 figures, 10 tables; shorten section 2; change sections 4.3 and 5.1.2. V3: Accepted for publication in the Semantic Web journal. V4 (Author's manuscript): camera ready version, available from the Semantic Web journal at http://www.semantic-web-journal.ne

Sentiment classification on polarity reviews: an empirical study using rating-based features

We present a new feature type named rating-based feature and evaluate the contribution of this feature to the task of document-level sentiment analysis. We achieve state-of-the-art results on two publicly available standard polarity movie datasets: on the dataset consisting of 2000 reviews produced by Pang and Lee (2004) we obtain an accuracy of 91.6% while it is 89.87% evaluated on the dataset of 50000 reviews created by Maas et al. (2011). We also get a performance at 93.24% on our own dataset consisting of 233600 movie reviews, and we aim to share this dataset for further research in sentiment polarity analysis task

The oxidized phospholipid PazePC modulates interactions between Bax and mitochondrial membranes

AbstractActivation of the pro-apoptotic protein Bax under intracellular oxidative stress is closely related to its association with the mitochondrial outer membrane (MOM) system, ultimately resulting in cell death. The precise mechanism by which this activation and the subsequent structural changes in the protein occur is currently unknown. In addition to triggering the onset of apoptosis, oxidative stress generates oxidized lipids whose impact on mitochondrial membrane integrity and the activity of membrane-associated Bax is unclear. We therefore devised a model system that mimics oxidative stress conditions by incorporating oxidized phospholipids (OxPls) into mitochondria-like liposomes, and studied the OxPls' impact on Bax-membrane interactions. Differential scanning calorimetry (DSC) was used to study membrane organization and protein stability, while conformational changes in the protein upon contact with lipid vesicles were monitored using far-UV circular dichroism (CD) spectroscopy. The thermograms for liposomes containing the OxPl 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC) differed dramatically from those for unmodified liposomes. Moreover, Bax exhibited enhanced thermal stability in the presence of the modified liposomes, indicating that it interacted strongly with PazePC-containing membranes. The presence of PazePC also increased the α-helical character of Bax compared to the protein alone or with PazePC-free vesicles, at 10°C, 20°C, and 37°C. Presumably, the presence of PazePC-like OxPls a) increases the population of membrane-associated Bax and b) facilitates the protein's insertion into the membrane by distorting the bilayer's organization, as seen by solid-state high-resolution 1H and 31P magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy

Influence of polar co-solutes and salt on the hydration of lipid membranes

The influence of the co-solutes TMAO, urea, and NaCl on the hydration repulsion between lipid membranes is investigated in a combined experimental/simulation approach. Pressure–hydration curves obtained via sorption experiments reveal that the repulsion significantly increases when the membranes are loaded with co-solutes, most strongly for TMAO. As a result, the co-solutes retain additional water molecules and therefore provide membranes with a fluid and more physiological environment. The experimental data are quantitatively reproduced in complementary solvent-explicit atomistic molecular dynamics simulations, which yield the chemical potential of water. Simulation analysis reveals that the additional repulsion arises from the osmotic pressure generated by the co-solutes, an effect which is maximal for TMAO, due to its unfavorable interactions with the lipid headgroup layer and its extraordinarily high osmotic coefficient

Controlling water evaporation through self-assembly

Water evaporation concerns all land-living organisms, as ambient air is dryer than their corresponding equilibrium humidity. Contrarily to plants, mammals are covered with a skin that not only hinders evaporation but also maintains its rate at a nearly constant value, independently of air humidity. Here, we show that simple amphiphiles/water systems reproduce this behavior, which suggests a common underlying mechanism originating from responding self-assembly structures. The composition and structure gradients arising from the evaporation process were characterized using optical microscopy, infrared microscopy, and small-angle X-ray scattering. We observed a thin and dry outer phase that responds to changes in air humidity by increasing its thickness as the air becomes dryer, which decreases its permeability to water, thus counterbalancing the increase in the evaporation driving force. This thin and dry outer phase therefore shields the systems from humidity variations. Such a feedback loop achieves a homeostatic regulation of water evaporation