Anna Wierzbicka, Semantic Decomposition, and the Meaning-Text Approach

The paper aims to demonstrate that the main contribution of Anna Wierzbicka to linguistics is the idea of semantic decomposition - that is, representing meaning in terms of structurally organized configurations of simpler meanings - and a huge amount of specific decompositions of lexical meanings from many languages. One of possible developments of this idea of Wierzbicka’s is the Meaning-Text linguistic approach, and in particular - the Meaning-Text model of natural language. To illustrate the importance and fruitfulness of semantic decomposition, two Meaning-Text mini-models are presented for English and Russian. Two semantically equivalent sentences of these languages are considered: (1) a. Eng. A honeymooner was fatally attacked by a shark. ~ b. Rus. Molodožën pogib v rezul´tate napadenija akuly vo vremja medovogo mesjaca lit. ‘Young.husband died as result of.attack of.shark during honey month’ The formal representations of these sentences at four levels-Meaning-Text style-are shown: semantic, deep-syntactic, surface-syntactic, and deep-morphological. Examples of formal rules relating the representations of two adjacent levels are presented

Mapping protein energy landscapes with amide hydrogen exchange and mass spectrometry: I. A generalized model for a two-state protein and comparison with experiment

Protein amide hydrogen exchange (HDX) is a convoluted process, whose kinetics is determined by both dynamics of the protein and the intrinsic exchange rate of labile hydrogen atoms fully exposed to solvent. Both processes are influenced by a variety of intrinsic and extrinsic factors. A mathematical formalism initially developed to rationalize exchange kinetics of individual amide hydrogen atoms is now often used to interpret global exchange kinetics (e.g., as measured in HDX MS experiments). One particularly important advantage of HDX MS is direct visualization of various protein states by observing distinct protein ion populations with different levels of isotope labeling under conditions favoring correlated exchange (the so-called EX1 exchange mechanism). However, mildly denaturing conditions often lead to a situation where the overall HDX kinetics cannot be clearly classified as either EX1 or EX2. The goal of this work is to develop a framework for a generalized exchange model that takes into account multiple processes leading to amide hydrogen exchange, and does not require that the exchange proceed strictly via EX1 or EX2 kinetics. To achieve this goal, we use a probabilistic approach that assigns a transition probability and a residual protection to each equilibrium state of the protein. When applied to a small protein chymotrypsin inhibitor 2, the algorithm allows complex HDX patterns observed experimentally to be modeled with remarkably good fidelity. On the basis of the model we are now in a position to begin to extract quantitative dynamic information from convoluted exchange kinetics